Direct measurement of the kinetic energy shift between the molecular and atomic M4.5N4.5N4.5 Auger spectra of iodine

The M4.5N4.5N4.5 Auger electron spectrum of iodine has been measured from molecular and atomic iodine vapours. The energy shift of 3.25 = 0.10 eV between molecular and atomic Auger spectra has been determined using a least-squares fitting procedure to spectra containing both molecular and atomic contributions. Different initial and final state splittings for atomic and molecular spectra, as well as the extra-atomic relaxation energy, are discussed.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu
Contributors: Rantala, T., Väyrynen, J., Kumpula, R., Aksela, S.
Number of pages: 3
Pages: 384-386
Publication date: 1 Oct 1979
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 66
Issue number: 2
ISSN (Print): 0009-2614
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Spectroscopy, Condensed Matter Physics, Atomic and Molecular Physics, and Optics, Surfaces and Interfaces
Source: Scopus
Source ID: 49249145180

Research output: Contribution to journalArticleScientificpeer-review

Anomalous Auger-electron spectra of metallic calcium

A1 Kα-excited L2, 3 MM and L2, 3 MV Auger-electron spectra of Ca have been measured in ultrahigh vacuum from a metallic sample evaporated onto an Ag substrate. An interpretation of the spectra is made by applying a line-fitting procedure. The lineshape and the solid-state-free-atom kinetic-energy shift are also studied. The extrinsic loss structure in the L2, 3 MM Auger-electron emission is found to be similar to that in 2p photoelectron emission. Spin-density-functional (SDF) calculations for the singularity index describing the intrinsic lineshape give a value of ∼ 0.35 for both processes. Thus the experimental 2p 3 2 photoelectron line broadened from 1.2 to ∼ 5 eV FWHM has been used as a standard line in the line fitting of the L2, 3MM transitions. The term splitting of the L2, 3 M2, 3 M2, 3 transition is larger than in the corresponding free-atom spectrum. This result is also supported by the SDF calculations. The L2, 3 M2, 3 V spectrum is anomalously sharp, probably both because of the structure of the local density of states at the site of the core-ionized atom and because of differences in the transition probabilities into the different parts of the band. The experimental solid-state shift is 20.3 eV for the L2, 3 M2,3 M2, 3:1 D transition, and the binding-energy shifts are 8.3 and 6.1 eV for the 2p and 3p levels, respectively. The SDF shifts for the above transitions are 19.9 (configurational average), 9.4 and 8.0 eV, consecutively, in agreement with the experimental values. The calculations also show a localized d-type (atomic-like) structure for the screening of the initial- and final-state core hole (s). This is the origin of the large values of both the singularity index and the solid-state shift.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Physics, University of Oulu, University of Turku
Contributors: Väyrynen, J., Rantala, T. T., Minni, E., Suoninen, E.
Number of pages: 13
Pages: 293-305
Publication date: 1983
Peer-reviewed: Yes

Publication information

Journal: Journal of Electron Spectroscopy and Related Phenomena
Volume: 31
Issue number: 3
ISSN (Print): 0368-2048
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Spectroscopy, Atomic and Molecular Physics, and Optics, Surfaces and Interfaces
Source: Scopus
Source ID: 0342803978

Research output: Contribution to journalArticleScientificpeer-review

A finite cluster approach to the electron-hole pair damping of the adsorbate vibration: CO adsorbed on Cu(100)

A finite cluster method is applied to describe the energy transfer from the adsorbate vibrations to the electron-hole pair excitations. For CO stretch vibration on Cu(100) surface a value of 0.5 meV is found for the consequent damping (corresponding to the lifetime of 1.3·10-12- s) in an agreement with a recently measured vibrational line width. The mechanism behind the electron-hole pair excitations is found to be charge oscillations between the molecular 2π{black star} resonance and the substrate, caused by the molecular vibration. Cluster size effects have been found to be negligible.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chalmers University of Technology, University of California, Santa Barbara
Contributors: Rantala, T. T., Rosén, A., Hellsing, B.
Number of pages: 9
Pages: 173-181
Publication date: 1986
Peer-reviewed: Yes

Publication information

Journal: Journal of Electron Spectroscopy and Related Phenomena
Volume: 39
Issue number: C
ISSN (Print): 0368-2048
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Spectroscopy, Atomic and Molecular Physics, and Optics, Surfaces and Interfaces
Source: Scopus
Source ID: 0001168090

Research output: Contribution to journalArticleScientificpeer-review

A Finite Cluster Approach to the Electron-Hole Pair Damping of the Adsorbate Vibration: CO Adsorbed on Cu(100)

Abstract: A finite cluster method is applied to describe the energy transfer from the adsorbate vibrations to the electron-hole pair excitations. For CO stretch vibration on Cu(100) surface a value of 0.5 meV is found for the consequent damping (corresponding to the lifetime of 1.3·10 -12 s) in an agreement with a recently measured vibrational line width. The mechanism behind the electron-hole pair excitations is found to be charge oscillations between the molecular 2π * resonance and the substrate, caused by the molecular vibration. Cluster size effects have been found to be negligible.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chalmers University of Technology, University of California, Santa Barbara
Contributors: Rantala, T. T., Rosén, A., Hellsing, B.
Number of pages: 9
Pages: 173-181
Publication date: 1986
Peer-reviewed: Yes

Publication information

Journal: Studies in Surface Science and Catalysis
Volume: 26
Issue number: C
ISSN (Print): 0167-2991
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Catalysis, Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 77956976821

Research output: Contribution to journalArticleScientificpeer-review

Potential energy curves for diatomic molecules calculated with numerical basis functions

A computational scheme for molecules is presented for the evaluation of total enregy properties such as potential energy curves and vibrational frequencies. The calculations are performed within the local density approximation utilizing the LCAO MO scheme with numerical basis functions, and multipole expansion of the molecular charge density is used to obtain the molecular potential. The total energy expression is written in terms of matrix elements already used for solving one-electron equations, and hence any evaluation of explicit integrals over charge density is avoided. The accuracy of the method and the effect of basis set incompleteness are studied for the CO and N2 molecules and compared with fully numerical (basis-free) results.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chalmers University of Technology
Contributors: Rantala, T. T., Wästberg, B., Rosén, A.
Number of pages: 8
Pages: 261-268
Publication date: 15 Nov 1986
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics
Volume: 109
Issue number: 2-3
ISSN (Print): 0301-0104
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Spectroscopy, Atomic and Molecular Physics, and Optics
Source: Scopus
Source ID: 2842530832

Research output: Contribution to journalArticleScientificpeer-review

Numerical simulation of temperature distributions in layered structures during laser processing

A numerical simulation approach for the evaluation of temperature distribution in layer structured substrates during laser processing is introduced. The explicit finite-difference solution of the heat equation is used and the full non-linearity of the heat diffusion is taken into account by temperature dependent substrate parameters. The heat equations for layered structures are solved using both rectangular and cylindrical coordinate systems. The method is applied to CW Ar+ laser-induced temperature distributions in some commonly used layer structures in microelectronics, such as silicon on sapphire (SOS) and SiO2 coated silicon. Results are compared with experiments.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, Microelectronics and Materials Physics Laboratories
Contributors: Levoska, J., Rantala, T. T., Lenkkeri, J.
Number of pages: 11
Pages: 12-22
Publication date: 1989
Peer-reviewed: Yes

Publication information

Journal: Applied Surface Science
Volume: 36
Issue number: 1-4
ISSN (Print): 0169-4332
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Condensed Matter Physics
Source: Scopus
Source ID: 0024301353

Research output: Contribution to journalArticleScientificpeer-review

Sorption and retention of ethylene glycol monoethyl ether (EGME) on silicas

Sorption of ethylene glycol monoethyl ether (EGME) was studied gravimetrically and correlated with the results of retention experiments where samples wetted with EGME were evacuated. If a sorption measurement is done conventionally by increasing the vapor pressure slowly by small steps, molecules are packed smoothly along the surface, and a fairly flat isotherm is obtained. If the sample is directly exposed to a high vapor pressure or the normal sorption mode is disturbed by directly reducing the pressure, more EGME is sorbed. Then some of the molecules may be fixed only at their hydroxy ends. The evacuation curves are best interpreted in a semilogarithmic form, by which the value of the monolayer capacity can be estimated. EGME can be used for surface area measurements of silicas, but with porous samples areas that are too large are probably obtained. When EGME is packed smoothly on standard silica TK 800, one molecule occupies an area of 0.44 nm2, computed by the BET equation with three parameters, or 1 mg of EGME covers 3.0 m2.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Rakennetekniikka, Tampere University of Technology, University of Tampere
Contributors: Kellomäki, A., Kuula-Väisänen, P., Nieminen, P.
Number of pages: 6
Pages: 373-378
Publication date: 1989
Peer-reviewed: Yes

Publication information

Journal: Journal of Colloid and Interface Science
Volume: 129
Issue number: 2
ISSN (Print): 0021-9797
Original language: English
ASJC Scopus subject areas: Colloid and Surface Chemistry, Physical and Theoretical Chemistry, Surfaces and Interfaces
Source: Scopus
Source ID: 45149145866

Research output: Contribution to journalArticleScientificpeer-review

Morphological and structural changes in laser CVD of silicon: comparison of theoretical temperature calculations with experimental results

The paper considers to what extent theoretical calculation of the laser induced temperature profile in a substrate can be used to predict the morphology and structure of silicon tracks deposited by pyrolytic LCVD. The micron scale tracks are deposited from silane using a focussed argon ion laser onto a substrate consisting of 1000 Å SiO2 upon a 300 μm thick, 100 mm diameter, [100] silicon wafer. The influence of various experimental parameters such as scan speed, laser power, gas pressure and gas composition on the temperature profile and on the deposited silicon track is investigated. Temperature profiles and their time evolution are simulated by numerically solving the heat diffusion equation using a finite difference approach. The track deposition is simulated using experimental temperature and pressure dependent growth rates. Gaussian shaped low laser power track profiles are well reproduced but the volcano like structures of high power deposition are not explained by the present model alone. The calculations are found to explain, at least qualitatively, the observed relationships between various experimental parameters.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Herriot-Watt University, Microelectronics and Materials Physics Laboratories, University of Oulu
Contributors: Milne, D., Wilson, J. I. B., Rantala, T. T., Lenkkeri, J.
Number of pages: 6
Pages: 81-86
Publication date: 2 Dec 1989
Peer-reviewed: Yes

Publication information

Journal: Applied Surface Science
Volume: 43
Issue number: 1-4
ISSN (Print): 0169-4332
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Condensed Matter Physics
Source: Scopus
Source ID: 0024900802

Research output: Contribution to journalArticleScientificpeer-review

Electronic and structural properties of Si10 cluster

Possible structures for Si10 cluster are considered using a tight-binding model and drawing on significant work done in the past. It is shown that the tight-binding parametrization, fitted to the bulk, is also valid for smaller systems. This model is found to essentially reproduce other published results, but requires much less effort than ab initio techniques-thus, allowing the study of a wide variety of structures and their ions. However, unlike classical force-field calculations, it yields information about the electronic structure of clusters. A new geometric structure for Si10 is found, which is not only of lowest energy, but which also matches the experimental photoelectron band gap and explains the experimental reactivity data. Because of the Jahn-Teller effect, the photoelectron spectrum is very sensitive to geometry. Also, ionization of the cluster alters the geometry slightly.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Departments of Chemistry, and Physics and Astronomy, 239 Fronczak Hall, State University of New York, College at Fredonia
Contributors: Rantala, T. T., Jelski, D. A., George, T. F.
Number of pages: 12
Pages: 189-200
Publication date: Jun 1990
Peer-reviewed: Yes

Publication information

Journal: Journal of Cluster Science
Volume: 1
Issue number: 2
ISSN (Print): 1040-7278
Original language: English
ASJC Scopus subject areas: Inorganic Chemistry
Keywords: Silicon clusters, tight-binding model
Source: Scopus
Source ID: 21544431551

Research output: Contribution to journalArticleScientificpeer-review

Rate equation simulation of the height of Schottky barriers at the surface of oxidic semiconductors

Rate equation simulatin is used in the present computational approach in order to study the role of different adsorbed oxygen ions (O2 - and O-) in controlling the height of the Schottky barrier at the surface of SnO2, a key material in the field of semiconductor gas sensors. Computations are based on the adsorption/desorption model and consider the electron transfer between different oxygen species on the surface and the bulk conduction band. Different values have been tested for both the frequency factors and the activation energies of the rate constants in order to consider the relative population between the O- and O2 - ions on the surface at different temperatures, the dependence of the height of the surface Schottky barrier on temperature and oxygen partial pressure, and also the response and recovery times of the barrier heights as a consequence of rapid temperature changes. Comparisons of calculated barrier heights with some empirical values are also given at different temperatures and oxygen partial pressures.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu
Contributors: Rantala, T. S., Lantto, V., Rantala, T. T.
Number of pages: 4
Pages: 234-237
Publication date: 1993
Peer-reviewed: Yes

Publication information

Journal: Sensors and Actuators B: Chemical
Volume: 13
Issue number: 1-3
ISSN (Print): 0925-4005
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Electrochemistry, Electrical and Electronic Engineering
Source: Scopus
Source ID: 0027590715

Research output: Contribution to journalArticleScientificpeer-review

Melting of copper clusters

Melting of icosahedral and Wulff polyhedral copper clusters are studied using molecular dynamics and effective medium theory. Icosahedral closed shell copper clusters are most stable up to a cluster size of ∼ 2500 atoms and their melting temperature is highest for small clusters, accordingly. Wulff polyhedra are most stable for larger clusters and, consequently, their melting temperature is highest for large clusters. The melting temperature decreases with decreasing cluster size and is proportional to the average coordination number of atoms. The whole icosahedral cluster melts simultaneously and can possibly be superheated. Icosahedral clusters with partially filled shells melt at lower temperatures than closed shell icosahedra, but no surface premelting is observed. (111) surface layers of large Wulff polyhedra are also solid up to the cluster melting temperatures, but (100) facets premelt at a lower temperature than the whole cluster.

General information

Publication status: Published
MoE publication type: Not Eligible
Organisations: Jyväskylän yliopisto
Contributors: Valkealahti, S., Manninen, M.
Number of pages: 12
Pages: 123-134
Publication date: 1 Jan 1993
Peer-reviewed: Yes

Publication information

Journal: Computational Materials Science
Volume: 1
Issue number: 2
ISSN (Print): 0927-0256
Original language: English
ASJC Scopus subject areas: Computer Science(all), Chemistry(all), Materials Science(all), Mechanics of Materials, Physics and Astronomy(all), Computational Mathematics
Source: Scopus
Source ID: 0027553804

Research output: Contribution to journalArticleScientificpeer-review

A cluster approach for the SnO2 (110) face

Some results are given from a cluster approach for the electronic structure of the SnO2 (110) face together with some oxygen vacancies and 'adsorbates'. Computations are based on ab initio methods, the local-density approximation and atomic orbitals as a basis set. Solutions were calculated self-consistently, but also using a composition of atomic potentials (for some smaller clusters). The atomic-orbital nature (origin) of the cluster levels was traced by projection onto the atomic bases set. The results here refer to a basic cluster [SnO213 with 17 surface atoms moedelling the SnO2 (110) face and the other 22 atoms in the next five suface layers. The effect of oxyggen 'adsrobates' and oxygen vacancies in the few uppermost subsurface layers on the electronic structure was considered. In particular, the focus was on the levels related to oxygen vacancies and originating from Sn 5s orbitals, which are well-known donor levels in the deep bulk, making SnO2 an n-type semiconductor. The results support some other theoretical and experimental predictions that oxygen vacancies behave as neutral defects at or near SnO2 surfaces.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Microelectronics Laboratory, University of Oulu
Contributors: Rantala, T. S., Lantto, V., Rantala, T. T.
Number of pages: 4
Pages: 716-719
Publication date: 1994
Peer-reviewed: Yes

Publication information

Journal: Sensors and Actuators B: Chemical
Volume: 19
Issue number: 1-3
ISSN (Print): 0925-4005
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Electrochemistry, Electrical and Electronic Engineering
Source: Scopus
Source ID: 0028407824

Research output: Contribution to journalArticleScientificpeer-review

Si10 and photoabsorption spectra of mid-sized silicon clusters

The photoabsorption spectra of various isomers of Si10, Si9, Si11 and other silicon clusters are calculated using a tight-binding method. Remarkable similarities between the calculated results and the experimental spectra for mid-sized clusters are noted. It is suggested that the mid-sized clusters are composed of aggregates of smaller clusters.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, College at Fredonia, Washington State University Pullman
Contributors: Rantala, T. T., Jelski, D. A., George, T. F.
Number of pages: 6
Pages: 215-220
Publication date: 13 Jan 1995
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 232
Issue number: 3
ISSN (Print): 0009-2614
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 4243879058

Research output: Contribution to journalArticleScientificpeer-review

Synthesis of chlorinated 5-hydroxy 4-methyl-2(5H)-furanones and mucochloric acid

An improved procedure for the synthesis of chlorinated 5-hydroxy-4-methyl-2(5H)-furanones is described. By this method also carbon-labelled (13C and 14C at C-3) hydroxyfuranones, including mucochioric acid, can be prepared. Each step of the method was examined in an effort to optimize both the yield and the purity of the compounds.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Abo Akademi University
Contributors: Franzén, R., Kronberg, L.
Number of pages: 4
Pages: 3905-3908
Publication date: 29 May 1995
Peer-reviewed: Yes

Publication information

Journal: Tetrahedron Letters
Volume: 36
Issue number: 22
ISSN (Print): 0040-4039
Original language: English
ASJC Scopus subject areas: Biochemistry, Organic Chemistry, Drug Discovery
Source: Scopus
Source ID: 0029012567

Research output: Contribution to journalArticleScientificpeer-review

Effects of two double bonds on the hydrocarbon interior of a phospholipid bilayer

A phospholipid bilayer was modelled by duplicating a monolayer system of 36 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) molecules ( 16:0 18:2) plus 1368 water molecules and simulated using molecular dynamics. The analyses revealed distinct characteristics in the membrane structure due to polyunsaturation. The orientational behaviour of the fatty acid chains in the PLPC bilayer was found to be seemingly different from that in monounsaturated or in saturated phospholipid bilayers. The specific attributes responsible for the observed behaviour of the saturated and polyunsaturated chains are discussed and their relative importance assessed.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, Hammersmith Hospital, Department of Physical Sciences
Contributors: Hyvönen, M., Ala-Korpela, M., Vaara, J., Rantala, T. T., Jokisaari, J.
Number of pages: 7
Pages: 300-306
Publication date: 24 Nov 1995
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 246
Issue number: 3
ISSN (Print): 0009-2614
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 4243491046

Research output: Contribution to journalArticleScientificpeer-review

Mutational spectra of Salmonella typhimurium revertants induced by chlorohydroxyfuranones, byproducts of chlorine disinfection of drinking water

The base substitution specificities of 3-chloro-4-(dichloromethyl)-5- hydroxy-2(5H)-furanone (MX), 3-chloro-4-(chloromethyl)-5-hydroxy-2(SH)- furanone (CMCF), 3,4-dichloro-5-hydroxy-2(5H)-furanone (MCA), and chloromalonaldehyde (CMA), a putative breakdown product of MCA, were examined in the hisG46 gene and in the hisG428 gene of Salmonella typhimurium using allele specific oligonucleotide hybridization. Although the compounds are structurally closely related, they induced substantially different mutation spectra: MCA and CMA caused primarily GC → AT transitions in the hisG46 allele (target sequence CCC), in particular, at the second position of the codon in strain TA100. In TA100 the mutation spectrum of MCA was similar to that of CMA. The mutational specificity of MCA can be explained as a consequence of misincorporation opposite to cyclic ethene adducts identical to those formed by the carcinogen vinyl chloride. The spectra induced by MX and CMCF in TA100 were almost identical but distinctively different from the spectra of MCA and CMA. Both compounds induced primarily GC → TA transversions, in particular, at the second position of the codon, and to a lesser extent in the first position of the codon. An identical site bias is induced by carcinogens such as polycyclic aromatic hydrocarbons and heterocyclic amines as a consequence of formation of (noncyclic) guanosine adducts. In hisG428 (target sequence TAA) MX induced again primarily GC → TA transversions in Tyr tRNA genes (supC/M) and, to a lesser extent, intragenic AT → TA transversions (TAA → AAA). The possible involvement of guanosine and adenosine adducts in the mutational specificity of MX is addressed.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Der Technischen Universitat Wien Fakultät für Elektrotechnik und Informationstechnik, Tumor Biology/Cancer Research Inst., University of Vienna, Abo Akademi University
Contributors: Knasmuller, S., Zöhrer, E., Kronberg, L., Kundi, M., Franzen, R., Schulte-Hermann, R.
Number of pages: 8
Pages: 374-381
Publication date: 1996
Peer-reviewed: Yes

Publication information

Journal: Chemical Research in Toxicology
Volume: 9
Issue number: 2
ISSN (Print): 0893-228X
Original language: English
ASJC Scopus subject areas: Drug Discovery, Organic Chemistry, Chemistry(all), Toxicology, Health, Toxicology and Mutagenesis
Source: Scopus
Source ID: 0029882809

Research output: Contribution to journalArticleScientificpeer-review

Surface relaxation of the (1010) face of wurtzite CdS

Atomic geometry and electronic density of states of the wurtzite CdS (1010) cleavage surface have been calculated. Calculations were carried out with two different self-consistent ab initio LDA methods leading to similar results. Surface relaxation is found to be strong: cations relax towards bulk and anions outwards from the surface. This is in accordance with experimental observations and other published calculations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Physical Sciences, University of Oulu
Contributors: Rantala, T. T., Rantala, T. S., Lantto, V., Vaara, J.
Number of pages: 6
Pages: 77-82
Publication date: 15 May 1996
Peer-reviewed: Yes

Publication information

Journal: Surcface Science
Volume: 352-354
ISSN (Print): 0039-6028
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Condensed Matter Physics, Surfaces and Interfaces
Keywords: Cadmium sulphide, Density-functional calculation, Semiconducting surfaces, Single crystal surfaces, Surface electronic phenomena, Surface relaxation and reconstruction
Source: Scopus
Source ID: 0030147848

Research output: Contribution to journalArticleScientificpeer-review

Melting and evaporation of argon clusters

Molecular dynamics simulation with a Nosé-Hoover thermostat was used to study melting and evaporation of free icosahedral argon clusters containing 13 to 1415 atoms. Clusters of 147 atoms or less were found to melt at temperatures clearly below the bulk melting temperature in agreement with previous results. Clusters containing 309 atoms or more were observed to desorb atoms at temperatures where the core of the cluster is solid. As a consequence of this a reliable determination of their melting temperatures using molecular dynamics was found to be complicated.

General information

Publication status: Published
MoE publication type: Not Eligible
Organisations: Jyväskylän yliopisto
Contributors: Rytkönen, A., Valkealahti, S., Manninen, M.
Number of pages: 5
Pages: 1888-1892
Publication date: 1 Feb 1997
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Physics
Volume: 106
Issue number: 5
ISSN (Print): 0021-9606
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 0001441087

Research output: Contribution to journalArticleScientificpeer-review

Start-up and Operation of Laboratory-Scale Thermophilic Upflow Anaerobic Sludge Blanket Reactors Treating Vegetable Processing Wastewaters

Thermophilic anaerobic treatment of hot vegetable processing wastewaters was studied in laboratory-scale UASB reactors at 55°C. The high-strength wastewater streams, deriving from steam peeling and blanching of carrot, potato and swede were used. The reactors were inoculated with mesophilic granular sludge. Stable thermophilic methanogenesis with about 60% COD removal was reached within 28 days. During the 134 day study period the loading rate was increased up to 24 kg COD m-3 day-1. High treatment efficiency of more than 90% COD removal and concomitant methane production of 7.3 m3 CH4 m-3 day-1 were achieved. The anaerobic process performance was not affected by the changes in the wastewater due to the different processed vegetables. The results demonstrated the feasibility of thermophilic anaerobic treatment of vegetable processing wastewaters in UASB reactors.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Science and Environmental Engineering, Tampere University of Technology, University of Jyväskylä, Jyväskylän yliopisto, Aalto University
Contributors: Lepistö, S. S., Rintala, J. A.
Number of pages: 9
Pages: 331-339
Publication date: Mar 1997
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Technology and Biotechnology
Volume: 68
Issue number: 3
ISSN (Print): 0268-2575
Original language: English
ASJC Scopus subject areas: Biotechnology, Chemical Engineering(all), Bioengineering, Chemistry(all)
Keywords: Anaerobic treatment, Food industry, Granular sludge, Start-up, Thermophilic, Vegetable processing wastewater

Bibliographical note

Contribution: organisation=bio,FACT1=1

Source: researchoutputwizard
Source ID: 30520

Research output: Contribution to journalArticleScientificpeer-review

Inequivalence of single CHa and CHb methylene bonds in the interior of a diunsaturated lipid bilayer from a molecular dynamics simulation

Orientational order parameters for individual CHa and CHb bonds are local measures for the alignment of the bonds in a membrane interior. Experimental values exist for some lipid systems but no results are available from molecular dynamics (MD) simulations, although they are increasingly used to study biomembranes. We present such detailed analysis of a one nanosecond MD simulation for a PLPC (16:0/18:2Δ9.12) bilayer. The results show marked inequivalence for the CHa and CHb bonds of the methylene segments in the beginning and in the double bond region of the diunsaturated sn-2 chain. They also suggest slight inequivalences in the saturated chain.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Ita-Suomen yliopisto, University of Oulu, Department of Physical Sciences
Contributors: Hyvönen, M., Ala-Korpela, M., Vaara, J., Rantala, T. T., Jokisaari, J.
Number of pages: 6
Pages: 55-60
Publication date: 4 Apr 1997
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 268
Issue number: 1-2
ISSN (Print): 0009-2614
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Spectroscopy, Atomic and Molecular Physics, and Optics
Source: Scopus
Source ID: 0031552317

Research output: Contribution to journalArticleScientificpeer-review

Calculation of the molecular ordering parameters of (±)-3-butyn-2-ol dissolved in an organic solution of poly(γ-benzyl-L-glutamate)

The proton and natural abundance carbon-13 NMR spectra of (±)-3-butyn-2-ol enriched in the S enantiomer (ee = 72%) and oriented in the chiral nematic liquid crystalline phase of [poly(γ-benzyl-L-glutamate)/ deuterochloroform] have been obtained and analyzed. The residual 1H-1H and 1H-13C dipolar couplings were corrected for the effects of molecular harmonic vibrational motions and used to determine the ra structure and the five independent order parameters, Sαβ, for each enantiomer. It is shown that the data is consistent with the two enantiomers having an identical rα, structure, but the order matrices differ in both the magnitudes of their elements and the orientation of their principal axes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Université de Paris-Sud, University of Southampton, United Kingdom, Dept. of Physical Sciences Linnanmaa, University of Oulu
Contributors: Lesot, P., Merlet, D., Courtieu, J., Emsley, J. W., Rantala, T. T., Jokisaari, J.
Number of pages: 6
Pages: 5719-5724
Publication date: 31 Jul 1997
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 101
Issue number: 31
ISSN (Print): 1089-5639
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 0031175387

Research output: Contribution to journalArticleScientificpeer-review

Investigation of the adducts formed by reaction of butenedioic acids with adenosine

Several genotoxic butenedioic acids present in chlorine-disinfected drinking water were allowed to react with adenosine, guanosine, and cytidine in aqueous solution. HPLC analyses, with detection at 254 and 310 nm, showed that clearly detectable products were formed only in the reactions with adenosine. The major products from the reactions between either 2-chloro-3- methyl-2-butenedioic acid (ox-MCF) or 2-chloro-3-(chloromethyl)-2- butenedioic acid (ox-CMCF) and adenosine were the same. This substance was isolated by C18 column chromatography and characterized by UV absorbance, 1H and 13C NMR spectroscopy, and mass spectrometry. It was identified as 3-(β-D-ribofuranosyl)-7-carboxy-7-formyl-8-[9'-(β-D-ribofuranosyl)-N 6- adenosinyl]-1,N 6-ethanoadenosine (cfεA,A). The yields of cfεA,A in reactions performed at pH 7.4 and 37 °C were 0.7% and 0.3% with ox-MCF and ox-CMCF, respectively.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Natl. Inst. for Environ. Studies
Contributors: Franzén, R., Morita, M., Tanabe, K., Takagi, H., Shibata, Y.
Number of pages: 6
Pages: 1186-1191
Publication date: Oct 1997
Peer-reviewed: Yes

Publication information

Journal: Chemical Research in Toxicology
Volume: 10
Issue number: 10
ISSN (Print): 0893-228X
Original language: English
ASJC Scopus subject areas: Drug Discovery, Organic Chemistry, Chemistry(all), Toxicology, Health, Toxicology and Mutagenesis
Source: Scopus
Source ID: 0030778905

Research output: Contribution to journalArticleScientificpeer-review

Computational approaches to the chemical sensitivity of semiconducting tin dioxide

Some computational approaches to the chemical sensitivity of semiconducting tin dioxide are presented. Chemical sensitivity is often observed using conductance measurement. Therefore, the potential energy barriers in grain contacts between adjacent grains of a polycrystalline semiconductor are the key parameters for transducing the chemical surface sensitivity into the conductance response. The rate equation model describes the electronic exchange between the adsorbed oxygen species and the bulk conduction band of a semiconductor. It predicts the type of the major negative oxygen ion (O2- or O-) at the surface as a function of temperature in agreement with experimental findings. The grain geometry has only a small effect on the potential energy barrier at the surface of finite grains. Even a small neck contact between grains, in the case of mobile donors, decreases strongly the potential energy barrier between grains compared to that in the case of an open grain contact. Results from Monte Carlo simulations with random barrier networks reveal that the current-voltage characteristic of a polycrystalline semiconductor is non-linear at higher voltages and the non-linearity of the network increases with increasing width of the barrier distributions. Electronic-structure calculations with clusters give qualitative information on the role of oxygen vacancies in different atomic planes in SnO2 and its unrelaxed and unreconstructed (110) surface.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, Department of Physical Sciences, Chalmers University of Technology, State University of New York
Contributors: Rantala, T., Lantto, V., Rantala, T.
Number of pages: 6
Pages: 59-64
Publication date: 1 Jan 1998
Peer-reviewed: Yes

Publication information

Journal: Sensors and Actuators B: Chemical
Volume: 47
Issue number: 1-3
ISSN (Print): 0925-4005
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Electrochemistry, Electrical and Electronic Engineering
Keywords: Electronic structure, Grain contact, Mobile donor, Surface energy barrier
Source: Scopus
Source ID: 0032041202

Research output: Contribution to journalArticleScientificpeer-review

Effect of nitro groups and alkyl chain length on the negative ion tandem mass spectra of alkyl 3-hydroxy-5-(4'-nitrophenoxy) and alkyl 3-hydroxy-5-(2', 4'-dinitrophenoxy) benzoates

Tandem mass spectrometric behaviour was studied for a small combinatorial library of alkyl 3-hydroxy-5(4'-nitrophenoxy) benzoates (A1-A5) and alkyl 3-hydroxy-5-(2', 4'-dinitrophenoxy) benzoates (B1-B5). The spectra were recorded by negative ion electrospray low-energy collision induced dissociation (CID) tandem mass spectrometry. The product ion spectra of [M - H]- of the benzoates A1-A5 are similar, as are those of benzoates B1-B5. However, the spectra of the B series compounds differ significantly from those of the A series owing to the second electron-withdrawing nitro substituent in the B compounds. In addition, the length of the alkyl chain has an effect on the fragmentation. However, both series of compounds exhibit an abundant nitrophenoxy ion formed by the loss of 3-hydroxybenzoate. This is at m/z 138 in A1-A5 and at m/z 183 in B1-B5. A precursor ion scan of the nitrophenoxy ion provides a rapid method to identify the synthesised compounds in this type of combinatorial mixture.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Division of Pharmaceutical Chemistry, University of Helsinki, Department of Pharmacy
Contributors: Kangas, H., Franzén, R., Tois, J., Taskinen, J., Kostiainen, R.
Number of pages: 5
Pages: 1680-1684
Publication date: 1999
Peer-reviewed: Yes

Publication information

Journal: Rapid Communications in Mass Spectrometry
Volume: 13
Issue number: 16
ISSN (Print): 0951-4198
Ratings: 
  • Scopus rating (1999): SJR 1.379 SNIP 1.096
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Spectroscopy
Source: Scopus
Source ID: 0032814434

Research output: Contribution to journalArticleScientificpeer-review

Surface relaxation of the (110) face of rutile SnO2

Surface relaxation of the stoichiometric and reduced SnO2 (110) surfaces is studied with first-principles calculations. Calculations are carried out with two different self-consistent ab initio LDA methods, which lead to similar results. The most prominent feature in the relaxation is that the surface layer oxygens of the reduced surface move outwards about 0.4Å with respect to the surface tin atoms. The stoichiometric (oxidized) surface is stabilized by the "bridging" oxygen atoms, and therefore, relaxes less. The valence band density-of-states is similar at both surfaces, except that removing bridging oxygens leaves behind electrons that occupy gap states formed at the reduced tin atoms.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Physical Sciences, University of Oulu
Contributors: Rantala, T. T., Rantala, T. S., Lantto, V.
Number of pages: 7
Pages: 103-109
Publication date: 11 Jan 1999
Peer-reviewed: Yes

Publication information

Journal: Surcface Science
Volume: 420
Issue number: 1
ISSN (Print): 0039-6028
Ratings: 
  • Scopus rating (1999): SJR 1.752 SNIP 0.974
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Condensed Matter Physics, Surfaces and Interfaces
Keywords: Density functional calculations, Semiconducting surfaces, Single crystal surfaces, Surface relaxation and reconstruction, Tin oxides
Source: Scopus
Source ID: 0032784368

Research output: Contribution to journalArticleScientificpeer-review

Experimental and theoretical study of the spin-spin coupling tensors in methylsilane

The experimental and theoretical 13C-29Si spin-spin coupling tensors, 1JCsi, are reported for methylsilane, 13CH3 29SiH3. The experiments are performed by applying the liquid crystal NMR (LC NMR) method. The data obtained by dissolving CH3SiH3 in nematic phases of two LC's is analyzed by taking into account harmonic and anharmonic vibrations, internal rotation, and solvent-induced anisotropic deformation of the molecule. The necessary parameters describing the relaxation of the molecular geometry during the internal rotation, as well as the harmonic force field, are produced theoretically with semiempirical (AM1 and PM3) and ab initio (MP2) calculations. A quantum mechanical approach has been taken to treat the effects arising from internal rotation. All the J tensors are determined theoretically by ab initio MCSCF linear response calculations. The theoretical and experimental J coupling anisotropies, Δ1JCsi = -59.3 Hz and -89 ± 10 Hz, respectively, are in fair mutual agreement. These results indicate that the indirect contribution has to be taken into account when experimental 1DCsi exp couplings are to be applied to the determination of molecular geometry and orientation. The theoretically determined J tensors are found to be qualitatively similar to what was found in our previous calculations for ethane, which suggests that the indirect contributions can be partially corrected for by transferring the corresponding J tensors from a model molecule to another.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, Oulu Polytechnic, Raahe Institute of Computer Engineering, Max-Planck-Institut für Festkörperforschung
Contributors: Kaski, J., Lantto, P., Rantala, T. T., Schroderus, J., Vaara, J., Jokisaari, J.
Number of pages: 9
Pages: 9669-9677
Publication date: 2 Dec 1999
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 103
Issue number: 48
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (1999): SJR 1.443 SNIP 1.592
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 0001687009

Research output: Contribution to journalArticleScientificpeer-review

The Suzuki, the Heck, and the Stille reaction - Three versatile methods, for the introduction of new C-C bonds on solid support

Metal-catalyzed coupling reactions are very efficient and reliable methods for the introduction of new carbon-carbon bonds onto molecules attached to a solid support. This review summarizes recent advances in utilizing the three most used methods, the Suzuki reaction, the Heck reaction, and the Stille reaction, in the field of solid phase organic synthesis resulting in small organic molecule libraries.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Helsinki
Contributors: Franzén, R.
Number of pages: 6
Pages: 957-962
Publication date: 2000
Peer-reviewed: Yes

Publication information

Journal: Canadian Journal of Chemistry - Revue Canadienne de Chimie
Volume: 78
Issue number: 7
ISSN (Print): 0008-4042
Ratings: 
  • Scopus rating (2000): SJR 0.628 SNIP 0.672
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Keywords: Carbon-carbon bonds, Combinatorial chemistry, Drug discovery, Metal-catalyzed coupling reactions, Solid phase synthesis
Source: Scopus
Source ID: 0033843143

Research output: Contribution to journalArticleScientificpeer-review

Utilization of Grignard reagents in solid-phase synthesis: A review of the literature

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: University of Helsinki
Contributors: Franzén, R. G.
Number of pages: 7
Pages: 685-691
Publication date: 28 Jan 2000
Peer-reviewed: Yes

Publication information

Journal: Tetrahedron
Volume: 56
Issue number: 5
ISSN (Print): 0040-4020
Ratings: 
  • Scopus rating (2000): SJR 1.536 SNIP 1.113
Original language: English
ASJC Scopus subject areas: Biochemistry, Organic Chemistry, Drug Discovery
Source: Scopus
Source ID: 0034723167

Research output: Contribution to journalReview ArticleScientificpeer-review

Preparation of 5-substituted 2-carboxyindoles on solid support

The preparation of 5-substituted 2-carboxyindoles on solid support is reported. In the approach, the indole moiety is synthesized in solution phase, followed by nitro-group reduction, reductive amination and alkylation on solid support. The method provides a simple and convenient route for the preparation of 5-substituted 2-carboxyindoles with high purity and good yield. (C) 2000 Elsevier Science Ltd.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Div. Pharmaceutical Chem., Dept. P., University of Helsinki, Helsinki University
Contributors: Tois, J., Franzén, R., Aitio, O., Huikko, K., Taskinen, J.
Number of pages: 4
Pages: 2443-2446
Publication date: 1 Apr 2000
Peer-reviewed: Yes

Publication information

Journal: Tetrahedron Letters
Volume: 41
Issue number: 14
ISSN (Print): 0040-4039
Ratings: 
  • Scopus rating (2000): SJR 1.626 SNIP 0.962
Original language: English
ASJC Scopus subject areas: Biochemistry, Organic Chemistry, Drug Discovery
Source: Scopus
Source ID: 0034175579

Research output: Contribution to journalArticleScientificpeer-review

Recent advances in the preparation of heterocycles on solid support: A review of the literature

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: University of Helsinki
Contributors: Franzén, R. G.
Number of pages: 20
Pages: 195-214
Publication date: May 2000
Peer-reviewed: Yes

Publication information

Journal: Journal of Combinatorial Chemistry
Volume: 2
Issue number: 3
ISSN (Print): 1520-4766
Original language: English
ASJC Scopus subject areas: Chemistry(all), Organic Chemistry, Discrete Mathematics and Combinatorics, Drug Discovery
Source: Scopus
Source ID: 0041037814

Research output: Contribution to journalReview ArticleScientificpeer-review

Computational studies for the interpretation of gas response of SnO2(110) surface

Tin dioxide is a widely used material in gas sensing applications. This is partly due to its stable surface structure and high sensitivity to many gases. The interaction of different gas components with an oxide surface may lead to changes in the lattice oxygen content at the surface in addition to changes in the amount of adsorbed species. The electronic and atomic structures of the surface change with the changes in the lattice oxygen content. This leads to surface relaxation and changes in the surface dipole layer of the ionic surface in addition to changes in the Schottky barrier which is a result of the charge accumulation onto the surface from the bulk of the semiconducting oxide. Changes in both the dipole layer and the Schottky barrier change the work function of the semiconductor and may reflect in its electrical conductivity. Here we have used first-principles calculations based on LDA-SCF to study changes in the electronic and atomic structures of the SnO2(110) surface as a result of oxygen exchange between the lattice and the ambient gas. The transducer function relating the changes at the surface to the changes in the conductivity of a ceramic microstructure is also described by an example.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Oulu, Department of Physical Sciences
Contributors: Rantala, T. S., Rantala, T. T., Lantto, V.
Number of pages: 4
Pages: 375-378
Publication date: 30 Jun 2000
Peer-reviewed: Yes

Publication information

Journal: Sensors and Actuators B: Chemical
Volume: 65
Issue number: 1
ISSN (Print): 0925-4005
Ratings: 
  • Scopus rating (2000): SJR 0.952 SNIP 1.337
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Electrochemistry, Electrical and Electronic Engineering
Source: Scopus
Source ID: 0034733267

Research output: Contribution to journalArticleScientificpeer-review

Solid-phase bromination and Suzuki coupling of 2-carboxyindoles

As part of an ongoing lead discovery project we have developed a convenient method for the modification and substitution of indole moieties at the 3-position. Selective bromination of three different 2-carboxyindoles was followed by Suzuki cross-coupling with aryl and heteroaryl boronic acids on a Merrifield resin solid-phase. After column chromatography, yields of the 3- substituted indoles ranged from 42-98%.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Helsinki, Department of Pharmacy
Contributors: Tois, J., Franzén, R., Aitio, O., Laakso, I., Huuskonen, J., Taskinen, J.
Number of pages: 4
Pages: 521-524
Publication date: 2001
Peer-reviewed: Yes

Publication information

Journal: Combinatorial Chemistry and High Throughput Screening
Volume: 4
Issue number: 6
ISSN (Print): 1386-2073
Ratings: 
  • Scopus rating (2001): SJR 0.78 SNIP 0.872
Original language: English
ASJC Scopus subject areas: Clinical Biochemistry, Chemistry (miscellaneous), Pharmacology
Source: Scopus
Source ID: 0034861953

Research output: Contribution to journalArticleScientificpeer-review

Vilsmeier formylation of 2-carboxyindoles and preparation of O-benzylhydroxyureas on solid phase

The Vilsmeier formylation has been introduced for the solid-phase functionalization of five different 2-carboxyindoles. The aldehyde functionality has been utilized in the preparation of O-benzylhydroxyureas.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Helsinki University, Department of Pharmacy, Division of Pharmaceutical Chemistry, Division of Pharmacognosy, Viikki Drug Discov. Technol. Center, University of Tokyo
Contributors: Tois, J., Franzèn, R., Aitio, O., Laakso, I., Kylänlahti, I.
Number of pages: 4
Pages: 542-545
Publication date: Nov 2001
Peer-reviewed: Yes

Publication information

Journal: Journal of Combinatorial Chemistry
Volume: 3
Issue number: 6
ISSN (Print): 1520-4766
Original language: English
ASJC Scopus subject areas: Chemistry(all), Organic Chemistry, Discrete Mathematics and Combinatorics, Drug Discovery
Source: Scopus
Source ID: 0035514539

Research output: Contribution to journalArticleScientificpeer-review

Control of matrix interferences by the multiple linear regression model in the determination of arsenic, antimony and tin in lead pellets by inductively coupled plasma atomic emission spectrometry

A multiple linear regression technique was used to evaluate the matrix interferences in the determination of hydride-forming elements in lead shotgun pellets by inductively coupled plasma atomic emission spectrometry. The determination of arsenic, antimony, and tin in SRM C2416 (Bullet Lead) by ICP-AES failed to obtain the certified concentrations at the 95% level of confidence using the t-test. However, it proved possible, by using the multiple linear regression technique, to correct the concentrations of all three elements to a statistically acceptable level. This method of correction is based on the multiple regression line obtained from the analysis of 19 synthetic mixtures of matrix elements (arsenic, antimony, bismuth, copper, silver, and tin) in five levels of concentrations. The direct determination of bismuth, copper and silver in SRM C2416 was performed with high accuracy and precision (RSD < 2.2%) as was the determination of arsenic, antimony, and tin after the correction. Total element recovery varied from 95.6% to 101.8% in the SRM sample analyzed.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Jyväskylä
Contributors: Väisänen, A., Suontamo, R., Rintala, J.
Number of pages: 3
Pages: 274-276
Publication date: 2002
Peer-reviewed: Yes

Publication information

Journal: Journal of Analytical Atomic Spectrometry
Volume: 17
Issue number: 3
ISSN (Print): 0267-9477
Ratings: 
  • Scopus rating (2002): SJR 1.978 SNIP 1.28
Original language: English
ASJC Scopus subject areas: Spectroscopy
Source: Scopus
Source ID: 0036009258

Research output: Contribution to journalArticleScientificpeer-review

Ultrasound-assisted extraction in the determination of arsenic, cadmium, copper, lead, and silver in contaminated soil samples by inductively coupled plasma atomic emission spectrometry

An extraction method was developed for the determination of toxic elements in contaminated soil samples by inductively coupled plasma atomic emission spectrometry (ICP-AES). The determination of arsenic, cadmium, lead, and silver in ultrasound-assisted extracts of SRM 2710 and SRM 2711 by ICP-AES was carried out with high accuracy and precision (RSD<3.7%). The certified concentrations of the SRMs were obtained for arsenic, cadmium, lead, and silver by using an ultrasound-assisted extraction method with a digestion solution of (1+1)-diluted aqua regia. The determination of copper in SRMs by the ultrasound-assisted extraction method and analysis by ICP-AES failed to obtain the certified concentrations at the 95% level of confidence using (±2 s) as confidence limits of the mean. However, the same results were observed with the use of the microwave digestion method and reflux, which is the ISO 11466 standard method. The analysis of the SRMs showed that the ultrasound-assisted extraction method is highly comparable with the other methods used for such purposes. The major advantages of the ultrasound-assisted extraction method compared to the microwave and reflux methods are the high treatment rate (50 samples simultaneously in nine minutes) and low reagent usage, the main benefit of which are the low chloride and nitrate concentrations in the extracts.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Jyväskylän yliopisto, University of Jyväskylä
Contributors: Väisänen, A., Suontamo, R., Silvonen, J., Rintala, J.
Number of pages: 5
Pages: 93-97
Publication date: 2002
Peer-reviewed: Yes

Publication information

Journal: Analytical and Bioanalytical Chemistry
Volume: 373
Issue number: 1-2
ISSN (Print): 1618-2642
Ratings: 
  • Scopus rating (2002): SJR 0.72 SNIP 0.771
Original language: English
ASJC Scopus subject areas: Clinical Biochemistry, Analytical Chemistry
Keywords: Contaminated soil, Elemental analyses, ICP-AES, Toxic metals, Ultrasound-assisted extraction
Source: Scopus
Source ID: 0036012773

Research output: Contribution to journalArticleScientificpeer-review

Statistical modeling of water vapor transmission rates for extrusion-coated papers

The testing of water vapor transmission rates (WVTR) for extrusion-coated papers can be a time-consuming task for laboratories. This study introduces a prediction model that provides an effective and helpful option to laboratory measurements. In practice, the WVTR of an extrusion-coated paper is affected by three main factors: coating weight (or squared mass) of the polymer concerned, the temperature and moisture content of the immediate surroundings. The prediction model determines mathematical connections between the WVTR and these variables covering the detected region of experimental WVTR results with a continuous estimation. By using mixing ratio as a variable of humidity, the model was found to provide accurate estimation across the field of experiments. As a result of this study, a practical computer program, which predicts the WVTR of a multilayer extrusion-coated paper as a function of user-defined temperature and relative humidity values and the layer structure of the coating, was developed. APPLICATION STATEMENT: This work shows how WVTR of a multilayer extrusion-coated paper can be estimated with the help of a statistical prediction model.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Energy and Process Engineering, Department of Materials Science
Contributors: Lahtinen, K., Kuusipalo, J.
Publication date: 2008

Host publication information

Title of host publication: TAPPI 2008 PLACE Conference: Innovations in Flexible Consumer Packaging
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all), Mechanical Engineering, Media Technology, Materials Science(all)
Source: Scopus
Source ID: 77950684840

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Batch dark fermentative hydrogen production from grass silage: The effect of inoculum, pH, temperature and VS ratio

The potential for fermentative hydrogen (H2) production from grass silage was evaluated in laboratory batch assays. First, two different inocula (from a dairy farm digester and digested sewage sludge) were studied with and without prior heat treatment and pH adjustment. Only the inoculum from the dairy farm digester produced H2 from grass silage. Without heat treatment, methane (CH4) was mainly produced, but heat treatment efficiently inhibited CH4 production. pH adjustment to 6 further increased H2 production. The effects of initial pH (4, 5 and 6), temperature (35, 55 and 70 {ring operator} C) and the substrate to inoculum volatile solids (VS) ratio (henceforth VS ratio) (1:1; 1.5:1 and 2:1) on H2 production from grass silage were evaluated with heat-treated dairy farm digester sludge as inoculum. Optimal pH was found to be between 5 and 6, while at pH 4 no H2 was formed. The highest H2 yield was achieved at 70 {ring operator} C. H2 production also increased when the VS ratio was increased. However, the overall energy value of H2 compared to that of CH4 production remained low.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Jyväskylän yliopisto, University of Jyväskylä
Contributors: Pakarinen, O., Lehtomäki, A., Rintala, J.
Number of pages: 8
Pages: 594-601
Publication date: Jan 2008
Peer-reviewed: Yes

Publication information

Journal: International Journal of Hydrogen Energy
Volume: 33
Issue number: 2
ISSN (Print): 0360-3199
Ratings: 
  • Scopus rating (2008): SJR 1.389 SNIP 2.1
Original language: English
ASJC Scopus subject areas: Electrochemistry, Fuel Technology, Renewable Energy, Sustainability and the Environment
Keywords: Fermentative hydrogen production, Grass silage, Heat treatment, pH, Temperature, VS ratio
Source: Scopus
Source ID: 39049172869

Research output: Contribution to journalArticleScientificpeer-review

The structural information content of chemical networks

We present an information-theoretic method to measure the structural information content of networks and apply it to chemical graphs. As a result, we find that our entropy measure is more general than classical information indices known in mathematical and computational chemistry. Further, we demonstrate that our measure reflects the essence of molecular branching meaningfully by determining the structural information content of some chemical graphs numerically.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: TU Vienna, Department of Biostatistics, Visiting Graduate Student in Department of Urban Design and Planning, University of Washington, Seattle, USA 1.1.2012-15.6.2012 (12.9.2011 alkaen)
Contributors: Dehmer, M., Emmert-Streib, F.
Number of pages: 4
Pages: 155-158
Publication date: Mar 2008
Peer-reviewed: Yes

Publication information

Journal: Zeitschrift fur Naturforschung Section A: A Journal of Physical Sciences
Volume: 63
Issue number: 3-4
ISSN (Print): 0932-0784
Ratings: 
  • Scopus rating (2008): SJR 0.318 SNIP 0.78
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Keywords: Chemical graph theory, Graph entropy, Information theory, Structural information content
Source: Scopus
Source ID: 46649096825

Research output: Contribution to journalArticleScientificpeer-review

Structural information content of networks: Graph entropy based on local vertex functionals

In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: TU Vienna, Department of Biostatistics, Visiting Graduate Student in Department of Urban Design and Planning, University of Washington, Seattle, USA 1.1.2012-15.6.2012 (12.9.2011 alkaen), Department of Genome Sciences
Contributors: Dehmer, M., Emmert-Streib, F.
Number of pages: 8
Pages: 131-138
Publication date: Apr 2008
Peer-reviewed: Yes

Publication information

Journal: Computational Biology and Chemistry
Volume: 32
Issue number: 2
ISSN (Print): 1476-9271
Ratings: 
  • Scopus rating (2008): SJR 0.795 SNIP 0.687
Original language: English
ASJC Scopus subject areas: Biochemistry, Structural Biology, Analytical Chemistry, Physical and Theoretical Chemistry
Keywords: Chemical graph theory, Gene networks, Graph entropy, Information theory, Structural information content
Source: Scopus
Source ID: 40049085450

Research output: Contribution to journalArticleScientificpeer-review

The effects of corona and flame treatment: Part 2. PE-HD and PP coated papers

The most important function of a packaging material is to shield the product inside the package. Extrusion coated papers and paperboards are generally used in various consumer packages like food, medical and cosmetic packages. Extrusion coatings give a barrier against water, water vapour, aroma, grease, oxygen, etc. In addition to barrier properties, heat sealability and printability are important properties in packaging applications. From the point of view of printing, the dense and impervious structure of extrusion coatings is challenging: printing inks and toners do not penetrate into the coatings. The durability of the printed image is significant, because the image must withstand various converting operations when the package is constructed. The most common method for obtaining good ink or toner adhesion is to oxidise the surface. Surface treatments are used to change the chemical composition, increase surface energy, modify surface morphology and topography, or remove contaminants and weak boundary layers. Two widely used methods are corona discharge treatment and flame treatment. These processes generally cause physical and chemical changes in a thin surface layer without affecting the bulk properties. Treatments will increase surface energy and also provide polar molecular groups necessary for good bonds between ink/toner and polymer molecules. In addition to printability, surface treatments also affect the sealing properties, i.e. initial heat sealing temperature, initial hot tack temperature, sealing window and seal strength of extrusion coatings. Both the sealability of packaging material and the tightness of the seal are critical points in the manufacturing process of packages and of the final package. The printability must be obtained without losing the sealability properties. In the first part of this research (TAPPI European PLACE 2007), surface energy, printability and sealability of low density polyethylene (PE-LD) coated paperboard after flame and corona treatments were studied. In this second part of the study, the research is extended to other polyolefins, i.e. high-density polyethylene (PE-HD) and polypropylene (PP). The surface chemistry is evaluated with contact angle measurements and X-ray photoelectron spectroscopy (XPS) measurements. Scanning electron microscopy (SEM) and optical profilometry are used to study the topographical and morphological changes on the surfaces. Furthermore, the heat sealing and hot tack properties, and water vapour barrier properties of the extrusion coatings are evaluated. The aim of this study is also to evaluate the printability of the extrusion coatings and to map out the role of surface modification in print quality formation. This study has concentrated on digital printing, particularly on the dry toner-based electrophotographic printing process. Flame treatment decreases the contact angle of water on PE-LD, PE-HD and PP coated papers more than corona treatment, but the lowest contact angle is obtained when the treatments are used simultaneously (i.e. co-effect of the treatments). Flame treatment deteriorates the sealability properties of PE-LD coated paper, whereas corona treatment improves sealability for example by decreasing the minimum heat sealing temperature. The sealability properties of PE-HD and PP coated papers are improved not only by corona treatment, but also by flame treatment. Flame treatment significantly improves the water vapour barrier of PEs. Where printability is concerned, it can be noticed that all the treatments improve rub-off resistance with PEs. With PE-LD flame is the most effective, and with PE-HD corona. With PP, the co-treatment gives the best result. Morphological changes in micro- and nano- scale were most observed on the flame treated PE-LD surface, whereas the electret phenomenon was observed on PE-LD, PE-HD and PP surfaces only after corona treatment.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Paper Converting and Packaging Technology, Stora Enso
Contributors: Lahti, J., Tuominen, M., Penttinen, T., Räsänen, J. P., Kuusipalo, J.
Number of pages: 37
Pages: 278-314
Publication date: 2009

Host publication information

Title of host publication: TAPPI Press - 12th European PLACE Conference 2009
Volume: 1
ISBN (Print): 9781615679850
ASJC Scopus subject areas: Media Technology, Chemical Engineering(all), Chemistry(all), Mechanical Engineering, Materials Science(all)
Source: Scopus
Source ID: 77952354412

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On entropy-based molecular descriptors: Statistical analysis of real and synthetic chemical structures

This paper presents an analysis of entropy-based molecular descriptors. Specifically, we use real chemical structures, as well as synthetic isomeric structures, and investigate properties of and among descriptors with respect to the used data set by a statistical analysis. Our numerical results provide evidence that synthetic chemical structures are notably different to real chemical structures and, hence, should not be used to investigate molecular descriptors. Instead, an analysis based on real chemical structures is favorable. Further, we find strong hints that molecular descriptors can be partitioned into distinct classes capturing complementary information.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: TU Vienna, Technical University Darmstadt, Computational Biology and Machine Learning, School of Medicine
Contributors: Dehmer, M., Varmuza, K., Borgert, S., Emmert-Streib, F.
Number of pages: 9
Pages: 1655-1663
Publication date: 27 Jul 2009
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Information and Modeling
Volume: 49
Issue number: 7
ISSN (Print): 1549-9596
Ratings: 
  • Scopus rating (2009): SJR 1.039 SNIP 1.219
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all), Computer Science Applications, Library and Information Sciences
Source: Scopus
Source ID: 68149167631

Research output: Contribution to journalArticleScientificpeer-review

Efficient production of NV colour centres in nanodiamonds using high-energy electron irradiation

Nanodiamond powders with an average size of 50 nm have been irradiated using high-energy electron beam. After annealing and chemical treatment, nanodiamond colloidal solutions were obtained and deposited on silica coverslips by spin-coating. The fluorescence of nanodiamonds was studied by confocal microscopy together with atomic force microscopy. We evaluated the proportion of luminescent nanodiamonds as a function of the irradiation duration and showed that large quantities, exceeding hundreds of mg, of luminescent nanodiamonds can be produced within 1 h of electron irradiation.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Laboratoire de Physique Quantique et Moléculaire
Contributors: Dantelle, G., Slablab, A., Rondin, L., Lainé, F., Carrel, F., Bergonzo, P., Perruchas, S., Gacoin, T., Treussart, F., Roch, J. F.
Number of pages: 4
Pages: 1655-1658
Publication date: Sep 2010
Peer-reviewed: Yes

Publication information

Journal: Journal of Luminescence
Volume: 130
Issue number: 9
ISSN (Print): 0022-2313
Ratings: 
  • Scopus rating (2010): SJR 0.909 SNIP 1.103
Original language: English
ASJC Scopus subject areas: Atomic and Molecular Physics, and Optics, Condensed Matter Physics, Chemistry(all), Biochemistry, Biophysics
Keywords: Diamond, Luminescence, NV centre
Source: Scopus
Source ID: 77955274026

Research output: Contribution to journalArticleScientificpeer-review

An electro-optically tunable Bragg reflector based on liquid crystals

In this paper we report the analysis of a distributed feedback guided-wave reflector in liquid crystals and we describe the main properties of the device. The device is based on a comb-shaped interdigitated electrodes and a liquid crystal slab. The device shows a wide tuning range exceeding 100 nm covering C and L bands for wavelength division multiplexing.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Sapienza University, University “Roma Tre”, Dipartimento di Ingegneria dell'Informazione, Elettronica e Telecomunicazioni
Contributors: Gilardi, G., Asquini, R., D'Alessandro, A., Assanto, G.
Number of pages: 7
Pages: 62-68
Publication date: 2011
Peer-reviewed: Yes

Publication information

Journal: Molecular Crystals and Liquid Crystals
Volume: 549
ISSN (Print): 1542-1406
Ratings: 
  • Scopus rating (2011): CiteScore 0.53 SJR 0.288 SNIP 0.473
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Materials Science(all)
Keywords: electro-optic effect, liquid crystals, Optical waveguides
Source: Scopus
Source ID: 80053362957

Research output: Contribution to journalArticleScientificpeer-review

Effect of pre-treatments on barrier properties of layers applied by atomic layer deposition onto polymer-coated substrates

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Department of Materials Science, Engineering materials science and solutions (EMASS), VTT Technical Research Centre of Finland
Contributors: Vähä-Nissi, M., Hirvikorpi, T., Sievänen, J., Salo, E., Harlin, A., Johansson, P., Kuusipalo, J.
Number of pages: 1
Pages: 447
Publication date: 2011

Host publication information

Title of host publication: 13th European PLACE Conference 2011
Volume: 1
ISBN (Print): 9781618394392
ASJC Scopus subject areas: Media Technology, Chemical Engineering(all), Chemistry(all), Mechanical Engineering, Materials Science(all)
Source: Scopus
Source ID: 84859608155

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Enrichment polymer layers for detection of volatile vapors by ATR FT-IR

Fourier Transformed Infrared Spectroscopy (FT-IR) is an effective analytical method for the identification of organic compounds be they man made or naturally produced. There is, however, a limitation to what a normal FT-IR can detect if an analyte is in vapor phase or in low concentration. To this end, we have applied enrichment polymer layer systems (EPLS) to an attenuated total reflection (ATR) crystal waveguide to enhance detection capability for the method. These EPLS are comprised of polymers with different functionality along the backbone and provide unique interaction capabilities that can attract volatile chemicals and concentrate them in the evanescence wave region. The thickness of the polymer layers is kept on 30-50nm level. The EPLS were characterized by atomic force microscopy, ellipsometry and FT-IR. The overall goal of this work is to construct a "universal" sensor platform capable of detecting a wide range of volatile organic chemicals via infrared spectroscopy.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Massachusetts Institute of Technology, School of Materials Science and Engineering/COMSET, Clemson University, Department of Materials Science and Engineering, University of Delaware
Contributors: Giammarco, J. M., Zdyrko, B., Hu, J., Agarwal, A., Kimerling, L., Carlie, N., Petit, L., Richardson, K., Luzinov, I.
Publication date: 2011
Peer-reviewed: Yes

Publication information

Journal: ACS National Meeting Book of Abstracts
ISSN (Print): 0065-7727
Original language: English
ASJC Scopus subject areas: Chemistry(all), Chemical Engineering(all)
Source: Scopus
Source ID: 80051876637

Research output: Contribution to journalArticleScientificpeer-review

Interactions of molecular ions with model phospholipid membranes

The affinities of a series of biologically relevant ions for a hydrated phospholipid membrane were investigated using molecular dynamics simulation. Interactions of molecular ions, such as guanidinium, tetramethylammonium, and thiocyanate with the bilayer were computationally characterized for the first time. Simulations reveal strong ion specificity. On one hand, ions like guanidinium and thiocyanate adsorb relatively strongly to the headgroup region of the membrane. On the other hand, potassium or chloride interact very weakly with the phospholipids and merely act as neutralizing counterions. Calculations also show that these ions affect differently biophysical properties of the membrane, such as lipid diffusion, headgroup hydration and tilt angle.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Academy of Sciences of Czech Republic, J. Heyrovský Institute of Physical Chemistry
Contributors: Petrov, M., Cwiklik, L., Jungwirth, P.
Number of pages: 17
Pages: 695-711
Publication date: 2011
Peer-reviewed: Yes

Publication information

Journal: Collection of Czechoslovak Chemical Communications
Volume: 76
Issue number: 6
ISSN (Print): 0010-0765
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Keywords: Biophysics, Molecular dynamics, Phospholipids
Source: Scopus
Source ID: 79958070440

Research output: Contribution to journalArticleScientificpeer-review

Nanoparticle deposition on packaging materials by the liquid flame spray

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Department of Physics, Research area: Aerosol Physics, Department of Software Systems, Engineering materials science and solutions (EMASS), Paper Converting and Packaging Technology, Aerosol Physics Laboratory, Abo Akad Univ, Abo Akademi University, Dept Phys, Center for Functional Materials at Biological Interfaces (FUNMAT)
Contributors: Teisala, H., Tuominen, M., Aromaa, M., Mäkelä, J. M., Stepien, M., Saarinen, J. J., Toivakka, M., Kuusipalo, J.
Number of pages: 2
Publication date: 2011

Host publication information

Title of host publication: 13th European PLACE Conference 2011
Volume: 1
ISBN (Print): 9781618394392
ASJC Scopus subject areas: Media Technology, Chemical Engineering(all), Chemistry(all), Mechanical Engineering, Materials Science(all)
Source: Scopus
Source ID: 84859599609

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Quantifying structural complexity of graphs: Information measures in mathematical chemistry

In this chapter, we give a conceptional view about information measures for graphs which can be used to quantify their structural complexity. We focus on treating such measures in the context of mathematical chemistry but we want to mention that those are also applicable for arbitrary complex networks. Besides reviewing the most known information indices often used in chemical graph theory, we propose an information functional that is based on degree-degree associations in a graph. This leads us to a parametric graph entropy measure to quantify the structural information content of a graph. A brief numerical example shows how the measure can be calculated explicitly.

General information

Publication status: Published
MoE publication type: A3 Part of a book or another research book
Organisations: Research Community on Data-to-Decision (D2D), Institute for Bioinformatics and Translational Research, Computational Biology and Machine Learning Lab., Faculty of Medicine, Health and Life Sciences, Queen's University, Belfast, Northern Ireland, Tomsk Polytechnic University, TU Vienna
Contributors: Dehmer, M., Emmert-Streib, F., Tsoy, Y. R., Varmuza, K.
Number of pages: 19
Pages: 479-497
Publication date: 2011

Host publication information

Title of host publication: Quantum Frontiers of Atoms and Molecules
Publisher: Nova Science Publishers, Inc.
Editor: Putz, M. V.
ISBN (Print): 9781616681586
ASJC Scopus subject areas: Chemistry(all)
Source: Scopus
Source ID: 84895219944

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Site-specific polarizabilities as predictors of favorable adsorption sites on Nan clusters

The adsorption of water and ammonia molecules to Nan (n = 7, 18, and 25) clusters was studied using density functional theory calculations. Calculated adsorption energies are small (

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Central Michigan University, Argonne National Laboratory
Contributors: Ma, L., Jackson, K. A., Jellinek, J.
Number of pages: 6
Pages: 80-85
Publication date: 8 Feb 2011
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 503
Issue number: 1-3
ISSN (Print): 0009-2614
Ratings: 
  • Scopus rating (2011): CiteScore 2.38 SJR 1.159 SNIP 1.004
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 79751533497

Research output: Contribution to journalArticleScientificpeer-review

Ionization of purine tautomers in nucleobases, nucleosides, and nucleotides: From the gas phase to the aqueous environment

We have simulated ionization of purine nucleic acid components in the gas phase and in a water environment. The vertical and adiabatic ionization processes were calculated at the PMP2/aug-cc-pVDZ level with the TDDFT method applied to obtain ionization from the deeper lying orbitals. The water environment was modeled via microsolvation approach and using a nonequilibrium polarizable continuum model. We have characterized a set of guanine tautomers and investigated nucleosides and nucleotides in different conformations. The results for guanine, i.e., the nucleic acid base with the lowest vertical ionization potential, were also compared to those for the other purine base, adenine. The main findings of our study are the following: (i) Guanine remains clearly the base with the lowest ionization energy even upon aqueous solvation. (ii) Water solvent has a strong effect on the ionization energetics of guanine and adenine and their derivatives; the vertical ionization potential (VIP) is lowered by about 1 eV for guanine while it is ∼1.5 eV higher in the nucleotides, overall resulting in similar VIPs for GMP-, guanosine and guanine in water. (iii) Water efficiently screens the electrostatic interactions between nucleic acid components. Consequently, ionization in water always originates from the base unit of the nucleic acid and all the information about conformational state is lost in the ionization energetics. (iv) The energy splitting between ionization of the two least bound electrons increases upon solvation. (v) Tautomerism does not contribute to the width of the photoelectron spectra in water. (vi) The effect of specific short-range interactions with individual solvent molecules is negligible for purine bases, compared to the long-range dielectric effects of the aqueous medium.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Department of Physical Chemistry, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, University of Southern California
Contributors: Pluhařová, E., Jungwirth, P., Bradforth, S. E., Slavíček, P.
Number of pages: 12
Pages: 1294-1305
Publication date: 10 Feb 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 115
Issue number: 5
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2011): CiteScore 3.62 SJR 1.801 SNIP 1.223
Original language: English
ASJC Scopus subject areas: Surfaces, Coatings and Films, Physical and Theoretical Chemistry, Materials Chemistry
Source: Scopus
Source ID: 79952844542

Research output: Contribution to journalArticleScientificpeer-review

Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer

We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces β-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal β-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Calcutta
Contributors: Manna, M., Mukhopadhyay, C.
Number of pages: 10
Pages: 3713-3722
Publication date: 5 Apr 2011
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 27
Issue number: 7
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2011): CiteScore 4.42 SJR 2.051 SNIP 1.341
Original language: English
ASJC Scopus subject areas: Electrochemistry, Condensed Matter Physics, Surfaces and Interfaces, Materials Science(all), Spectroscopy
Source: Scopus
Source ID: 79953236597

Research output: Contribution to journalArticleScientificpeer-review

Energetic origin of proton affinity to the air/water interface

Recent experimental and theoretical studies showed the preference of the hydronium ion for the vapor/water interface. To investigate the mechanism responsible for the surface propensity of this ion, we performed a series of novel quantum chemical simulations combined with the theory of solutions. The solvation free energy of the H3O+ solute placed at the interface was obtained as -97.9 kcal/mol, being more stable by 3.6 kcal/mol than that of the solute embedded in the bulk. Further, we decomposed the solvation free energies into contributions from the water molecules residing in the oxygen and the hydrogen sides of the solute to clarify the origin of the surface preference. When the solute was displaced from the bulk to the interface, it was shown that the free energy contribution from the oxygen side is destabilized by ∼10 kcal/mol because of a reduction of the number of surrounding solvent water molecules. It was observed, however, that the free energy contribution due to the hydrogen side of the solute is unexpectedly stabilizing and surpasses the destabilization in the opposite side. We found that the stabilization in the hydrogen side originates from the solute-solvent interaction in the medium range beyond the nearest neighbor. It was also revealed that the free energy contribution due to the solute's electronic polarization amounts to about the half of the total free energy change associated with the solute displacement from the bulk to the interface.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Tohoku University, Osaka University, Kyoto Women's University, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Japan Science and Technology Agency
Contributors: Takahashi, H., Maruyama, K., Karino, Y., Morita, A., Nakano, M., Jungwirth, P., Matubayasi, N.
Number of pages: 7
Pages: 4745-4751
Publication date: 28 Apr 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 115
Issue number: 16
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2011): CiteScore 3.62 SJR 1.801 SNIP 1.223
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 79955461660

Research output: Contribution to journalArticleScientificpeer-review

Detection of DNA hybridisation in a diluted serum matrix by surface plasmon resonance and film bulk acoustic resonators

Nanomolar quantities of single-stranded DNA products ∼ 100 nucleotides long can be detected in diluted 1% serum by surface plasmon resonance (SPR) and film bulk acoustic resonators (FBARs). We have used a novel FBAR sensor in parallel with SPR and obtained promising results with both the acoustic and the optical device. Oligonucleotides and a repellent lipoamide, Lipa-DEA, were allowed to assemble on the sensor chip surfaces for only 15 min by dispensing. Lipa-DEA surrounds the analyte-binding probes on the surface and effectively reduces the non-specific binding of bovine serum albumin and non-complementary strands. In a highly diluted serum matrix, the non-specific binding is, however, a hindrance, and the background response must be reduced. Nanomolar concentrations of short complementary oligos could be detected in buffer, whereas the response was too low to be measured in serum. DNA strands that are approximately 100 base pairs long at concentrations as low as 1-nM could be detected both in buffer and in 1% serum by both SPR and the FBAR resonator.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), VTT Technical Research Centre of Finland, HCI e 486.1, Siemens AG
Contributors: Auer, S., Nirschl, M., Schreiter, M., Vikholm-Lundin, I.
Number of pages: 10
Pages: 1387-1396
Publication date: May 2011
Peer-reviewed: Yes

Publication information

Journal: Analytical and Bioanalytical Chemistry
Volume: 400
Issue number: 5
ISSN (Print): 1618-2642
Ratings: 
  • Scopus rating (2011): CiteScore 3.47 SJR 1.37 SNIP 1.27
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Biochemistry
Keywords: DNA hybridisation detection, DNA sensor, Film bulk acoustic resonator, Self-assembled monolayer, Serum, Surface plasmon resonance
Source: Scopus
Source ID: 79955562374

Research output: Contribution to journalArticleScientificpeer-review

Preparation of zinc oxide free, transparent rubber nanocomposites using a layered double hydroxide filler

A layered double hydroxide (LDH) mineral filler particle has been designed and employed in rubber vulcanization to prepare a more environmentally friendly rubber composite. The LDH delivers zinc ions in the vulcanization process as accelerators, stearate anions as activators and simultaneously the mineral sheets act as a nanofiller to reinforce the rubber matrix whilst totally replacing the separate zinc oxide (ZnO) and stearic acid conventionally used in the formulation of rubber. This method leads to a significant reduction (nearly 10 times) of the zinc level and yields excellent transparent properties in the final rubber product. The morphological characterization, rheometric curing behaviour, mechanical properties and uniaxial multi-hysteresis behaviours of the resultant rubber/LDH nanocomposite are studied in this paper.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Durham University
Contributors: Das, A., Wang, D. Y., Leuteritz, A., Subramaniam, K., Greenwell, H. C., Wagenknecht, U., Heinrich, G.
Number of pages: 7
Pages: 7194-7200
Publication date: 28 May 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Materials Chemistry
Volume: 21
Issue number: 20
ISSN (Print): 0959-9428
Ratings: 
  • Scopus rating (2011): SJR 2.614 SNIP 1.539
Original language: English
ASJC Scopus subject areas: Chemistry(all), Materials Chemistry
Source: Scopus
Source ID: 79955619174

Research output: Contribution to journalArticleScientificpeer-review

Behavior of the eigen form of hydronium at the air/water interface

Surface affinity of hydronium was explored using umbrella sampling molecular dynamics simulations with a refined polarizable potential. The polarizable interaction potential of H3O+ was reparametrized against accurate ab initio calculations for geometries including a water molecule approaching the Eigen cation from its oxygen side. Although there is no true hydrogenbonding with H3O+ acting as an acceptor, respecting in the force field the very shallow ab initio minimum corresponding to this interaction leads to a decrease in surface propensity of hydronium compared to previous results. Qualitatively, the mild surface affinity and strong surface orientation of hydronium is, nevertheless, robustly predicted by various computational approaches, as well as by spectroscopic experiments.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, J. Heyrovský Institute of Physical Chemistry
Contributors: Jagoda-Cwiklik, B., Cwiklik, L., Jungwirth, P.
Number of pages: 6
Pages: 5881-5886
Publication date: 16 Jun 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 115
Issue number: 23
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2011): CiteScore 2.87 SJR 1.422 SNIP 1.131
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 79959934455

Research output: Contribution to journalArticleScientificpeer-review

Behavior of β-amyloid 1-16 at the air-water interface at varying ph by nonlinear spectroscopy and molecular dynamics simulations

The adsorption and aggregation of β-amyloid (1-16) fragment at the air-water interface was investigated by the combination of second harmonic generation (SHG) spectroscopy, Brewster angle microscopy (BAM), and molecular dynamics simulations (MD). The Gibbs free energy of surface adsorption was measured to be -10.3 kcal/mol for bulk pHs of 7.4 and 3, but no adsorption was observed for pH 10-11. The 1-16 fragment is believed not to be involved in fibril formation of the β-amyloid protein, but it exhibits interesting behavior at the air-water interface, as manifested in two time scales for the observed SHG response. The shorter time scale (minutes) reflects the surface adsorption, and the longer time scale (hours) reflects rearrangement and aggregation of the peptide at the air-water interface. Both of these processes are also evidenced by BAM measurements.MDsimulations confirm the pH dependence of surface behavior of the β-amyloid, with largest surface affinity found at pH = 7. It also follows from the simulations that phenylalanine is the most surface exposed residue, followed by tyrosine and histidine in their neutral form.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), American University, Crop and Soil Sciences, Cornell Univ., Midwest Research Institute - Kansas City, Berkeley, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Miller, A. E., Petersen, P. B., Hollars, C. W., Saykally, R. J., Heyda, J., Jungwirth, P.
Number of pages: 8
Pages: 5873-5880
Publication date: 16 Jun 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 115
Issue number: 23
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2011): CiteScore 2.87 SJR 1.422 SNIP 1.131
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 79959981055

Research output: Contribution to journalArticleScientificpeer-review

Steric and electronic effects in the host-guest hydrogen bonding in clathrate hydrates

Clathrate hydrates with polar guest molecules (dimethyl ether, ethylene oxide, trimethylene oxide, tetrahydrofuran, and tetrahydropyran) were studied by means of the density functional theory. A model of a large cage of structure-I clathrate was employed. Optimal configurations of encaged guests were investigated with a focus on the host-guest hydrogen bond formation. Weak hydrogen bonds were found to be formed by each guest, while for THP a strong hydrogen bond and formation of L-defect was also observed. This is in accord with previous computational and experimental studies. Steric factors were shown to play a key role for the strength of the hydrogen bond formed. Interestingly, the host-guest binding is influenced not only by the size of a guest molecule but also by its shape. This work demonstrates that both electronic and steric properties of a polar guest should be considered for a full description of clathrate systems.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), K. Gumiński Department of Theoretical Chemistry, Uniwersytet Jagiellonski w Krakowie, J. Heyrovský Institute of Physical Chemistry, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Kulig, W., Kubisiak, P., Cwiklik, L.
Number of pages: 6
Pages: 6149-6154
Publication date: 16 Jun 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 115
Issue number: 23
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2011): CiteScore 2.87 SJR 1.422 SNIP 1.131
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 79959539436

Research output: Contribution to journalArticleScientificpeer-review

Internal structure, hygroscopic and reactive properties of mixed sodium methanesulfonate-sodium chloride particles

Internal structures, hygroscopic properties and heterogeneous reactivity of mixed CH3SO3Na/NaCl particles were investigated using a combination of computer modeling and experimental approaches. Surfactant properties of CH3SO3- ions and their surface accumulation in wet, deliquesced particles were assessed using molecular dynamics (MD) simulations and surface tension measurements. Internal structures of dry CH3SO3Na/NaCl particles were investigated using scanning electron microscopy (SEM) assisted with X-ray microanalysis mapping, and time-of-flight secondary ion mass spectrometry (TOF-SIMS). The combination of these techniques shows that dry CH3SO3Na/NaCl particles are composed of a NaCl core surrounded by a CH3SO3Na shell. Hygroscopic growth, deliquescence and efflorescence phase transitions of mixed CH3SO3Na/NaCl particles were determined and compared to those of pure NaCl particles. These results indicate that particles undergo a two step deliquescence transition: first at ∼69% relative humidity (RH) the CH3SO3Na shell takes up water, and then at ∼75% RH the NaCl core deliquesces. Reactive uptake coefficients for the particle-HNO3 heterogeneous reaction were determined at different CH3SO3Na/NaCl mixing ratios and RH. The net reaction probability decreased notably with increasing CH3SO3Na and at lower RH.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Colorado at Denver, Kyushu University, Colorado State University, University of Southern California, Pacific Northwest National Laboratory, Defence Science and Technology Laboratory, Lawrence Berkeley National Laboratory, Department of Aerospace and Mechanical Engineering, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Liu, Y., Minofar, B., Desyaterik, Y., Dames, E., Zhu, Z., Cain, J. P., Hopkins, R. J., Gilles, M. K., Wang, H., Jungwirth, P., Laskin, A.
Number of pages: 12
Pages: 11846-11857
Publication date: 7 Jul 2011
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 13
Issue number: 25
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2011): CiteScore 3.6 SJR 1.707 SNIP 1.184
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 79960772846

Research output: Contribution to journalArticleScientificpeer-review

Defined-size DNA triple crossover construct for molecular electronics: Modification, positioning and conductance properties

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Jyväskylän yliopisto, Adult Stem Cells, School of Management (JKK)
Contributors: Linko, V., Leppiniemi, J., Paasonen, S. T., Hytönen, V. P., Jussi Toppari, J.
Publication date: 8 Jul 2011
Peer-reviewed: Yes

Publication information

Journal: Nanotechnology
Volume: 22
Issue number: 27
Article number: 275610
ISSN (Print): 0957-4484
Ratings: 
  • Scopus rating (2011): CiteScore 3.86 SJR 1.899 SNIP 1.471
Original language: English
ASJC Scopus subject areas: Bioengineering, Chemistry(all), Electrical and Electronic Engineering, Mechanical Engineering, Mechanics of Materials, Materials Science(all)
Source: Scopus
Source ID: 79957825438

Research output: Contribution to journalArticleScientificpeer-review

Urea and guanidinium induced denaturation of a Trp-cage miniprotein

Using a combination of experimental techniques (circular dichroism, differential scanning calorimetry, and NMR) and molecular dynamics simulations, we performed an extensive study of denaturation of the Trp-cage miniprotein by urea and guanidinium. The experiments, despite their different sensitivities to various aspects of the denaturation process, consistently point to simple, two-state unfolding process. Microsecond molecular dynamics simulations with a femtosecond time resolution allow us to unravel the detailed molecular mechanism of Trp-cage unfolding. The process starts with a destabilizing proline shift in the hydrophobic core of the miniprotein, followed by a gradual destruction of the hydrophobic loop and the α-helix. Despite differences in interactions of urea vs guanidinium with various peptide moieties, the overall destabilizing action of these two denaturants on Trp-cage is very similar.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, University of Leeds
Contributors: Heyda, J., Kožíšek, M., Bednárova, L., Thompson, G., Konvalinka, J., Vondrášek, J., Jungwirth, P.
Number of pages: 15
Pages: 8910-8924
Publication date: 21 Jul 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 115
Issue number: 28
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2011): CiteScore 3.62 SJR 1.801 SNIP 1.223
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 79960344032

Research output: Contribution to journalArticleScientificpeer-review

Machine learning: How it can help nanocomputing

We examine possibilities for making advances in nanocomputing by bringing in ideas from the field of machine learning. The potential from combining machine learning with nanocomputing seems to be underutilized. We review three complementary approaches. Firstly, machine learning can be used in the different phases of developing complicated nanocomputing devices: in modeling, designing, constructing, and programming the devices. Secondly, machine learning methods implemented by nanocomputing hardware can be a competitive solution especially for specialized application areas like sensory information processing; working towards such implementations advances nanocomputing by guiding development of the nanocomponents and architectures required for such applications. Thirdly, nanotechnology enabled quantum computing can significantly increase our capacity to solve NP-complete optimization problems; although this increase is not specific to machine learning, several such problems occur in machine learning and artificial intelligence, hence solving such problems is a useful goal that partly motivates development of quantum computing. The main value of this paper is to provide new ideas for researchers working on nanocomputing, nanoarchitectures, development and design of nanoprocessors and other nanocomponents, or nanomanufacturing.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Research Community on Data-to-Decision (D2D), Nokia, Aalto University
Contributors: Uusitalo, M. A., Peltonen, J., Ryhänen, T.
Number of pages: 17
Pages: 1347-1363
Publication date: Aug 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Computational and Theoretical Nanoscience
Volume: 8
Issue number: 8
ISSN (Print): 1546-1955
Ratings: 
  • Scopus rating (2011): CiteScore 0.86 SJR 0.398 SNIP 0.477
Original language: English
ASJC Scopus subject areas: Chemistry(all), Materials Science(all), Condensed Matter Physics, Computational Mathematics, Electrical and Electronic Engineering
Keywords: Machine Learning, Nanoarchitectures, Nanocomputing, Nanotechnology, Neural Networks, Quantum Computing
Source: Scopus
Source ID: 84856844597

Research output: Contribution to journalReview ArticleScientificpeer-review

From a localized H3O radical to a delocalized H 3O+⋯e- solvent-separated pair by sequential hydration

The impact of microhydration on the electronic structure and reactivity of the H3O moiety is investigated by ab initio calculations. In the gas phase, H3O is a radical with spin density localized on its hydrogen end, which is only kinetically stable and readily decomposes into a water molecule and a hydrogen atom. When solvated by a single water molecule, H 3O preserves to a large extent its radical character, however, two water molecules are already capable to shift most of the spin density to the solvent. With three solvating water molecules this shift is practically completed and the system is best described as a solvent-separated pair of a hydronium cation and a hydrated electron. The electronic structure of this system and its proton transfer reactivity leading to formation of a hydrogen atom already resemble those of a proton-electron pair in bulk water.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Uhlig, F., Marsalek, O., Jungwirth, P.
Number of pages: 7
Pages: 14003-14009
Publication date: 21 Aug 2011
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 13
Issue number: 31
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2011): CiteScore 3.6 SJR 1.707 SNIP 1.184
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 79960952162

Research output: Contribution to journalArticleScientificpeer-review

Towards universal enrichment nanocoating for IR-ATR waveguides

Polymer multilayered nanocoating capable of concentrating various chemical substances at IR-ATR waveguide surfaces is described. The coating affinity to an analyte played a pivotal role in sensitivity enhancement of the IR-ATR measurements, since the unmodified waveguide did not show any analyte detection.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Clemson University, School of Materials Science and Engineering/COMSET, University of Delaware, Massachusetts Institute of Technology
Contributors: Giammarco, J., Zdyrko, B., Petit, L., Musgraves, J. D., Hu, J., Agarwal, A., Kimerling, L., Richardson, K., Luzinov, I.
Number of pages: 3
Pages: 9104-9106
Publication date: 28 Aug 2011
Peer-reviewed: Yes

Publication information

Journal: Chemical Communications
Volume: 47
Issue number: 32
ISSN (Print): 1359-7345
Ratings: 
  • Scopus rating (2011): CiteScore 5.96 SJR 2.889 SNIP 1.326
Original language: English
ASJC Scopus subject areas: Catalysis, Electronic, Optical and Magnetic Materials, Ceramics and Composites, Chemistry(all), Surfaces, Coatings and Films, Metals and Alloys, Materials Chemistry
Source: Scopus
Source ID: 79961012632

Research output: Contribution to journalArticleScientificpeer-review

Tube-like natural halloysite/fluoroelastomer nanocomposites with simultaneous enhanced mechanical, dynamic mechanical and thermal properties

A novel kind of fluoroelastomer nanocomposites based on tube-like halloysite clay mineral were successfully prepared using a bis-phenol curing system, which resulted in prominent improvements in mechanical and dynamic mechanical properties and in the elevation as high as 30 K of the thermal decomposition temperature. Wide-angle X-ray scattering and transmission electron microscopy techniques were employed to assess the morphology developed in the nanocomposites, while stress strain diagrams were used to evaluate the mechanical properties. These nanocomposites were further characterized by moving die rheometer, dynamic mechanical properties and thermo-gravimetric analysis. Structure-properties relationship and the improvement of the mechanical, dynamic mechanical and thermal properties of fluoroelastomers are reported in the present study. Increasing amount of the filler reduced the curing efficiency of the bis-phenol curing system, which was evident from the rheometric and physical properties of the resulting composites. A sort of filler-filler interaction was perceived during the strain sweep analysis of the composites. The polymer-filler interaction was reflected in the improved mechanical and thermal properties which were the consequence of proper dispersion of the nanotubes in the polymer matrix; whereas the intercalation of macromolecular chains into the nanotubes was not reflected in the X-ray diffraction analysis.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Vodafone Department of Mobile Communications Systems
Contributors: Rooj, S., Das, A., Heinrich, G.
Number of pages: 10
Pages: 1746-1755
Publication date: Sep 2011
Peer-reviewed: Yes

Publication information

Journal: European Polymer Jounal
Volume: 47
Issue number: 9
ISSN (Print): 0014-3057
Ratings: 
  • Scopus rating (2011): CiteScore 3.03 SJR 1.109 SNIP 1.822
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Polymers and Plastics, Organic Chemistry
Keywords: Curing chemistry, Fluoroelastomers, Halloysite nanotube, Nanocomposites, Thermal stability
Source: Scopus
Source ID: 80052038140

Research output: Contribution to journalArticleScientificpeer-review

Quantitative glycoproteomic analysis of optimal cutting temperature-embedded frozen tissues identifying glycoproteins associated with aggressive prostate cancer

Prostate cancer is the most common malignancy in men in the United States, and one in seven men with prostate cancer dies of the disease. A major issue of prostate diagnosis is that there is no good method to reliably distinguish aggressive prostate cancer from nonaggressive prostate cancer. This leads to significant unnecessary suffering among prostate cancer patients and massive unnecessary health care expenditures. In this study, we aim to identify glycoproteins associated with aggressive prostate cancer using optimal cutting temperature (OCT)-embedded frozen tissues obtained from patients with known clinical outcome. To eliminate the interference of mass spectrometric analysis by the compounds in OCT and identify extracellular proteins that are likely to serve as biomarkers in body fluids, we employed glycoproteomic analysis using solid-phase extraction of glycopeptides, which allowed the immobilization of glycopeptides to solid support and removal of OCT from sample proteins before releasing the glycopeptides from the solid support for mass spectrometry analysis. Tumor tissues were cryostat microdissected from four cases of aggressive and four cases of nonaggressive prostate tumors, and glycopeptides were isolated and labeled with iTRAQ reagents before the samples were analyzed with LTQ Orbitrap Velos. From the aggressive prostate cancer tissues, we identified the overexpression of three glycoproteins involved in an extracellular matrix remodeling and further examined two glycoproteins, cathepsin L and periostin, using Western blot and immunohistochemistry analyses. This is the first proteomic study to identify proteins potentially associated with aggressive prostate cancer using OCT-embedded frozen tissues. Further study of these proteins will be needed to understand the roles of extracellular matrix proteins in cancer progression and their potential clinical utility in improving diagnosis of aggressive prostate cancer.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), Johns Hopkins University
Contributors: Tian, Y., Bova, G. S., Zhang, H.
Number of pages: 7
Pages: 7013-7019
Publication date: 15 Sep 2011
Peer-reviewed: Yes

Publication information

Journal: Analytical Chemistry
Volume: 83
Issue number: 18
ISSN (Print): 0003-2700
Ratings: 
  • Scopus rating (2011): CiteScore 5.86 SJR 2.616 SNIP 1.658
Original language: English
ASJC Scopus subject areas: Analytical Chemistry
Source: Scopus
Source ID: 80052805542

Research output: Contribution to journalArticleScientificpeer-review

Versatile bio-ink for covalent immobilization of chimeric avidin on sol-gel substrates

A bio-ink for covalent deposition of thermostable, high affinity biotin-binding chimeric avidin onto sol-gel substrates was developed. The bio-ink was prepared from heterobifunctional crosslinker 6-maleimidohexanoic acid N-hydroxysuccinimide which was first reacted either with 3-aminopropyltriethoxysilane or 3-aminopropyldimethylethoxysilane to form silane linkers 6-maleimide- N-(3-(triethoxysilyl)propyl)hexanamide or -(ethoxydimethylsilyl)propyl)-hexanamide. C-terminal cysteine genetically engineered to chimeric avidin was reacted with the maleimide group of silane linker in methanol/PBS solution to form a suspension, which was printed on sol-gel modified PMMA film. Different concentrations of chimeric avidin and ratios between silane linkers were tested to find the best properties for the bio-ink to enable gravure or inkjet printing. Bio-ink prepared from 3-aminopropyltriethoxysilane was found to provide the highest amount of active immobilized chimeric avidin. The developed bio-ink was shown to be valuable for automated fabrication of avidin-functionalized polymer films.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Univ of Oulu, VTT Technical Research Centre of Finland, Tampere University Hospital
Contributors: Heikkinen, J. J., Kivimäki, L., Määttä, J. A. E., Mäkelä, I., Hakalahti, L., Takkinen, K., Kulomaa, M. S., Hytönen, V. P., Hormi, O. E. O.
Number of pages: 6
Pages: 409-414
Publication date: 15 Oct 2011
Peer-reviewed: Yes

Publication information

Journal: Colloids and Surfaces B: Biointerfaces
Volume: 87
Issue number: 2
ISSN (Print): 0927-7765
Ratings: 
  • Scopus rating (2011): CiteScore 3.49 SJR 1.051 SNIP 1.27
Original language: English
ASJC Scopus subject areas: Biotechnology, Colloid and Surface Chemistry, Physical and Theoretical Chemistry, Surfaces and Interfaces
Keywords: Avidin-biotin technology, Biomolecule immobilization, Biosensing, Chimeric avidin, Maleimide, Printing, Sol-gel
Source: Scopus
Source ID: 79960384544

Research output: Contribution to journalArticleScientificpeer-review

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Division of Organic Chemistry and Biochemistry, Bijenička Cesta 54
Contributors: Vazdar, M., Vymětal, J., Heyda, J., Vondrášek, J., Jungwirth, P.
Number of pages: 9
Pages: 11193-11201
Publication date: 20 Oct 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 115
Issue number: 41
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2011): CiteScore 2.87 SJR 1.422 SNIP 1.131
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 80054686180

Research output: Contribution to journalArticleScientificpeer-review

Efficient surface structuring and photoalignment of supramolecular polymer-azobenzene complexes through rational chromophore design

Rational selection of the para-substituent of azobenzene chromophores in supramolecular polymeric complexes is exploited to control the chromophore-chromophore intermolecular interactions occurring in the material system. This allows optimizing the material system for either efficient surface-relief formation or for high and stable photoalignment. The surface-relief gratings can be subsequently coated with amorphous TiO 2 using atomic layer deposition, resulting in high-quality and high-index organic-inorganic gratings with vastly improved thermal stability compared to all-polymeric gratings.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Frontier Photonics, Department of Applied Physics, Aalto University, Tokyo Institute of Technology
Contributors: Vapaavuori, J., Valtavirta, V., Alasaarela, T., Mamiya, J. I., Priimagi, A., Shishido, A., Kaivola, M.
Number of pages: 5
Pages: 15437-15441
Publication date: 21 Oct 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Materials Chemistry
Volume: 21
Issue number: 39
ISSN (Print): 0959-9428
Ratings: 
  • Scopus rating (2011): SJR 2.614 SNIP 1.539
Original language: English
ASJC Scopus subject areas: Materials Chemistry, Chemistry(all)
Source: Scopus
Source ID: 80053301644

Research output: Contribution to journalArticleScientificpeer-review

The effect of lipid oxidation on the water permeability of phospholipids bilayers

The effect of lipid oxidation on water permeability of phosphatidylcholine membranes was investigated by means of both scattering stopped flow experiments and atomistic molecular dynamics simulations. Formation of water pores followed by a significant enhancement of water permeability was observed. The molecules of oxidized phospholipids facilitate pore formation and subsequently stabilize water in the membrane interior. A wide range of oxidation ratios, from 15 to 100 mol%, was considered. The degree of oxidation was found to strongly influence the time needed for the opening of a pore. In simulations, the oxidation ratio of 75 mol% was found to be a threshold for spontaneous pore formation in the tens of nanosecond timescale, whereas 15 mol% of oxidation led to significant water permeation in the timescale of seconds. Once a pore was formed, the water permeability was found to be virtually independent of the oxidation ratio. This journal is

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Wrocław University of Technology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, J. Heyrovský Institute of Physical Chemistry
Contributors: Lis, M., Wizert, A., Przybylo, M., Langner, M., Swiatek, J., Jungwirth, P., Cwiklik, L.
Number of pages: 9
Pages: 17555-17563
Publication date: 21 Oct 2011
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 13
Issue number: 39
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2011): CiteScore 3.6 SJR 1.707 SNIP 1.184
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 80053535630

Research output: Contribution to journalArticleScientificpeer-review

Orientational dependence of the affinity of guanidinium ions to the water surface

The behavior of guanidinium chloride at the surface of aqueous solutions is investigated using classical molecular dynamics (MD) simulations. It is found that the population of guanidinium ions oriented parallel to the interface is greater in the surface region than in bulk. The opposite is true for ions in other orientations. Overall, guanidinium chloride is depleted in the surface region, in agreement with the fact that the addition of guanidinium chloride increases the surface tension of water. The orientational dependence of the surface affinity of the guanidinium cation is related to its anisotropic hydration. To bring the ion to the surface in the parallel orientation does not require hydrogen bonds to be broken, in contrast to other orientations. The surface enrichment of parallel-oriented guanidinium indicates that its solvation is more favorable near the surface than in bulk solution for this orientation. The dependence of the bulk and surface properties of guanidinium on the force field parameters is also investigated. Despite significant quantitative differences between the force fields, the surface behavior is qualitatively robust. The implications for the orientations of the guanidinium groups of arginine side chains on protein surfaces are also outlined.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Division of Organic Chemistry and Biochemistry, Bijenička Cesta 54, Lund University, Crop and Soil Sciences, Cornell Univ.
Contributors: Wernersson, E., Heyda, J., Vazdar, M., Lund, M., Mason, P. E., Jungwirth, P.
Number of pages: 6
Pages: 12521-12526
Publication date: 3 Nov 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 115
Issue number: 43
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2011): CiteScore 3.62 SJR 1.801 SNIP 1.223
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 80054988916

Research output: Contribution to journalArticleScientificpeer-review

Detection and verification of glycosylation patterns of glycoproteins from clinical specimens using lectin microarrays and lectin-based immunosorbent assays

Aberrant glycosylation is a fundamental characteristic of progression of diseases such as cancer. Therefore, characterization of glycosylation patterns of proteins from disease tissues may identify changes specific to the disease development and improve diagnostic performance. Thus, analysis strategies with sufficient sensitivity for evaluation of glycosylation patterns in clinical specimens are needed. Here, we describe an analytical strategy for detection and verification of glycosylation patterns. It is based on a two-phase platform including a pattern discovery phase to identify the glycosylation changes using high-density lectin microarrays and a verification phase by developing lectin-based immunosorbent assays using the identified lectins. We evaluated the analytical performance of the platform using the glycoprotein standard and found that the lectin microarray could detect specific bindings of glycoprotein to lectins at the nanogram level and the lectin-based immunosorbent assay could be used for verification of protein glycosylation. We then applied the approach to the analysis of glycosylation patterns of two glycoproteins, which are highly expressed in prostate cancer in our prior studies, prostate specific antigen (PSA) and membrane metallo-endopeptidase (MME), from aggressive (AC) and nonaggressive prostate cancer (NAC) tissues. The observed differences in glycosylation patterns of PSA and MME may represent a significant clinical importance and could be used to develop multiplex assays for diagnosis of aggressive prostate cancer.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Prostate cancer research center (PCRC), Institute of Biophysics Chinese Academy of Sciences, Shanghai Jiaotong University, Johns Hopkins University, Visiting Graduate Student in Department of Urban Design and Planning, University of Washington, Seattle, USA 1.1.2012-15.6.2012 (12.9.2011 alkaen)
Contributors: Li, Y., Tao, S. C., Bova, G. S., Liu, A. Y., Chan, D. W., Zhu, H., Zhang, H.
Number of pages: 8
Pages: 8509-8516
Publication date: 15 Nov 2011
Peer-reviewed: Yes

Publication information

Journal: Analytical Chemistry
Volume: 83
Issue number: 22
ISSN (Print): 0003-2700
Ratings: 
  • Scopus rating (2011): CiteScore 5.86 SJR 2.616 SNIP 1.658
Original language: English
ASJC Scopus subject areas: Analytical Chemistry
Source: Scopus
Source ID: 81255146498

Research output: Contribution to journalArticleScientificpeer-review

Arrhenius analysis of anisotropic surface self-diffusion on the prismatic facet of ice

We present an Arrhenius analysis of self-diffusion on the prismatic surface of ice calculated from molecular dynamics simulations. The six-site water model of Nada and van der Eerden was used in combination with a structure-based criterion for determining the number of liquid-like molecules in the quasi-liquid layer. Simulated temperatures range from 230 K-287 K, the latter being just below the melting temperature of the model, 289 K. Calculated surface diffusion coefficients agree with available experimental data to within quoted precision. Our results indicate a positive Arrhenius curvature, implying a change in the mechanism of self-diffusion from low to high temperature, with a concomitant increase in energy of activation from 29.1 kJ mol -1 at low temperature to 53.8 kJ mol -1 close to the melting point. In addition, we find that the surface self-diffusion is anisotropic at lower temperatures, transitioning to isotropic in the temperature range of 240-250 K. We also present a framework for self-diffusion in the quasi-liquid layer on ice that aims to explain these observations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, University of Puget Sound
Contributors: Gladich, I., Pfalzgraff, W., Maršálek, O., Jungwirth, P., Roeselová, M., Neshyba, S.
Number of pages: 10
Pages: 19960-19969
Publication date: 28 Nov 2011
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 13
Issue number: 44
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2011): CiteScore 3.6 SJR 1.707 SNIP 1.184
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 80455123676

Research output: Contribution to journalArticleScientificpeer-review

Effect of ionic liquid on dielectric, mechanical and dynamic mechanical properties of multi-walled carbon nanotubes/polychloroprene rubber composites

This paper focuses on the influence of ionic liquid on carbon nanotube based elastomeric composites. Multi-walled carbon nanotubes (MWCNTs) are modified using an ionic liquid at room temperature, 1-butyl 3-methyl imidazolium bis (trifluoromethylsulphonyl) imide (BMI) and modified MWCNTs exhibit physical (cation-π/π-π) interaction with BMI. The polychloroprene rubber (CR) composites are prepared using unmodified and BMI modified MWCNTs. The presence of BMI not only increases the alternating current (AC) electrical conductivity and polarisability of the composites but also improves the state of dispersion of the tubes as observed from dielectric spectroscopy and transmission electron microscopy respectively. In addition to the hydrodynamic reinforcement, the formation of improved filler-filler networks is reflected in the dynamic storage modulus (E′) for modified MWCNTs/CR composites in amplitude sweep measurement upon increasing the proportion of BMI. Hardness and mechanical properties are also studied for the composites as a function of BMI.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Deutsches Institut für Kautschuktechnologie e.V., Vodafone Department of Mobile Communications Systems
Contributors: Subramaniam, K., Das, A., Steinhauser, D., Klüppel, M., Heinrich, G.
Number of pages: 10
Pages: 2234-2243
Publication date: Dec 2011
Peer-reviewed: Yes

Publication information

Journal: European Polymer Jounal
Volume: 47
Issue number: 12
ISSN (Print): 0014-3057
Ratings: 
  • Scopus rating (2011): CiteScore 3.03 SJR 1.109 SNIP 1.822
Original language: English
ASJC Scopus subject areas: Polymers and Plastics, Physics and Astronomy(all), Organic Chemistry
Keywords: Carbon nanotubes, Electrical conductivity, Ionic liquids, Polychloroprene rubber
Source: Scopus
Source ID: 81155135001

Research output: Contribution to journalArticleScientificpeer-review

Cholesterol driven alteration of the conformation and dynamics of phospholamban in model membranes

The effects of cholesterol on various membrane proteins are of long-standing interest in membrane biophysics. Here we present systematic molecular dynamics simulations (totaling 1.4 μs) of integral protein phospholamban incorporated in POPC/cholesterol bilayers (containing 0, 11.11, 22.03, 33.33, and 50 mol% of cholesterol). Phospholamban is a key regulator of cardiac contractility and has recently emerged as a potential drug target. In agreement with experiments, our results show that in a cholesterol-free pure POPC bilayer, phospholamban exhibits broad conformational distribution, ranging from the closed T-state to the extended R-state, crucial for its functionality. Increasing cholesterol concentration progressively stabilizes the bent conformers of phospholamban over open structures, and favors extensive interactions of its amphipathic N-terminal helix with the bilayer surface. The interaction energies between the N-terminal helix of PLB and different POPC/cholesterol bilayers quantitatively confirm its stronger interaction with a higher cholesterol-containing membrane. Simulation with 50 mol% of cholesterol further supports the above conclusions, where phospholamban undergoes rapid conformational transition from extended to closed form, which remains stable for the rest of the simulation time and exhibits the strongest interaction with the membrane. Cholesterol participates in hydrogen-bonding and π-stacking interactions with polar and/or aromatic residues and favors membrane association of phospholamban. We observed cholesterol-enrichment in the neighborhood of phospholamban. Moreover, as a modulator of membrane biophysical properties, cholesterol modifies the hydrophobic matching and trans-membrane tilting of phospholamban and also hinders its 2D-lateral mobility. Altogether, our results highlight atomistic details of protein-lipid interplay and provide new insights into the possible effects of cholesterol on conformational dynamics of phospholamban in membrane bilayers.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Calcutta
Contributors: Manna, M., Mukhopadhyay, C.
Number of pages: 11
Pages: 20188-20198
Publication date: 7 Dec 2011
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 13
Issue number: 45
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2011): CiteScore 3.6 SJR 1.707 SNIP 1.184
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 81255129160

Research output: Contribution to journalArticleScientificpeer-review

The Discovery of Compounds That Stimulate the Activity of Kallikrein-Related Peptidase3 (KLK3)

Kallikrein-related peptidase3 (KLK3), also known as prostate-specific antigen (PSA), is the most useful biomarker for prostate cancer (PCa). KLK3 is suggested to play a role in regulating cancer growth through anti-angiogenic activity invivo and invitro. This feature, together with its specificity for prostate tissue, makes KLK3 an intriguing target for the design of new therapies for PCa. 3D pharmacophores for KLK3-stimulating compounds were generated based on peptides that bind specifically to KLK3 and increase its enzymatic activity. As a result of pharmacophore-based virtual screening, four small, drug-like compounds with affinity for KLK3 were discovered and validated by capillary differential scanning calorimetry. One of the compounds also stimulated the activity of KLK3, and is therefore the first published small molecule with such an activity. Target specificity: Successful 3D pharmacophore-based virtual screening resulted in the first small, drug-like molecule that stimulates the activity of kallikrein-related peptidase3 (KLK3, PSA). The compound discovered can be applied to the design of novel KLK3-stimulating compounds with the potential to inhibit tumor angiogenesis and progression of prostate cancer.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Ita-Suomen yliopisto, Helsinki University Central Hospital, Tampere University Hospital, Kobenhavns Universitet, European ScreeningPort GmbH
Contributors: Härkönen, H. H., Mattsson, J. M., Määttä, J. A. E., Stenman, U. H., Koistinen, H., Matero, S., Windshügel, B., Poso, A., Lahtela-Kakkonen, M.
Number of pages: 9
Pages: 2170-2178
Publication date: 9 Dec 2011
Peer-reviewed: Yes

Publication information

Journal: CHEMMEDCHEM
Volume: 6
Issue number: 12
ISSN (Print): 1860-7179
Ratings: 
  • Scopus rating (2011): CiteScore 3.24 SJR 1.267 SNIP 0.933
Original language: English
ASJC Scopus subject areas: Molecular Medicine, Pharmacology, Toxicology and Pharmaceutics(all), Organic Chemistry
Keywords: Angiogenesis, Kallikrein, Molecular modeling, Peptides, Virtual screening
Source: Scopus
Source ID: 82955165662

Research output: Contribution to journalArticleScientificpeer-review

Chasing charge localization and chemical reactivity following photoionization in liquid water

The ultrafast dynamics of the cationic hole formed in bulk liquid water following ionization is investigated by ab initio molecular dynamics simulations and an experimentally accessible signature is suggested that might be tracked by femtosecond pump-probe spectroscopy. This is one of the fastest fundamental processes occurring in radiation-induced chemistry in aqueous systems and biological tissue. However, unlike the excess electron formed in the same process, the nature and time evolution of the cationic hole has been hitherto little studied. Simulations show that an initially partially delocalized cationic hole localizes within ∼30 fs after which proton transfer to a neighboring water molecule proceeds practically immediately, leading to the formation of the OH radical and the hydronium cation in a reaction which can be formally written as H 2O + H 2O → OH H 3O. The exact amount of initial spin delocalization is, however, somewhat method dependent, being realistically described by approximate density functional theory methods corrected for the self-interaction error. Localization, and then the evolving separation of spin and charge, changes the electronic structure of the radical center. This is manifested in the spectrum of electronic excitations which is calculated for the ensemble of ab initio molecular dynamics trajectories using a quantum mechanics/molecular mechanics (QMMM) formalism applying the equation of motion coupled-clusters method to the radical core. A clear spectroscopic signature is predicted by the theoretical model: as the hole transforms into a hydroxyl radical, a transient electronic absorption in the visible shifts to the blue, growing toward the near ultraviolet. Experimental evidence for this primary radiation-induced process is sought using femtosecond photoionization of liquid water excited with two photons at 11 eV. Transient absorption measurements carried out with ∼40 fs time resolution and broadband spectral probing across the near-UV and visible are presented and direct comparisons with the theoretical simulations are made. Within the sensitivity and time resolution of the current measurement, a matching spectral signature is not detected. This result is used to place an upper limit on the absorption strength andor lifetime of the localized H 2O + (aq) species.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, University of Kansas Lawrence, University of Wisconsin-Madison, HCI e 486.1, University of Southern California
Contributors: Marsalek, O., Elles, C. G., Pieniazek, P. A., Pluhaov, E., Vandevondele, J., Bradforth, S. E., Jungwirth, P.
Publication date: 14 Dec 2011
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Physics
Volume: 135
Issue number: 22
Article number: 224510
ISSN (Print): 0021-9606
Ratings: 
  • Scopus rating (2011): CiteScore 3.07 SJR 1.845 SNIP 1.231
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry, Medicine(all)
Source: Scopus
Source ID: 83755182728

Research output: Contribution to journalArticleScientificpeer-review

Modification of olivomycin A at the side chain of the aglycon yields the derivative with perspective antitumor characteristics

A novel way of chemical modification of the antibiotic olivomycin A (1) at the side chain of the aglycon moiety was developed. Interaction of olivomycin A with the sodium periodate produced the key acid derivative olivomycin SA (2) in 86% yield. This acid was used in the reactions with different amines in the presence of benzotriazol-1-yl-oxy-trispyrrolidino-phosphonium hexafluorophosphate (PyBOP) or diphenylphosphoryl azide (DPPA) to give corresponding amides. Whereas olivomycin SA was two orders of magnitude less cytotoxic than the parent antibiotic, the amides of 2 demonstrated a higher cytotoxicity. In particular, N,N-dimethylaminoethylamide of olivomycin SA showed a pronounced antitumor effect against transplanted experimental lymphoma and melanoma and a remarkably high binding constant to double stranded DNA. The therapeutic effects of this derivative were achievable at tolerable concentrations, suggesting that modifications of the aglycon's side chain, namely, its shortening to methoxyacetic residue and blocking of free carboxyl group, are straightforward for the design of therapeutically applicable derivatives of olivomycin A.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Frontier Photonics, Russian Academy of Medical Sciences, N.N. Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, Emanuel’ Institute of Biochemical Physics, Russian Academy of Sciences
Contributors: Tevyashova, A. N., Shtil, A. A., Olsufyeva, E. N., Luzikov, Y. N., Reznikova, M. I., Dezhenkova, L. G., Isakova, E. B., Bukhman, V. M., Durandin, N. A., Vinogradov, A. M., Kuzmin, V. A., Preobrazhenskaya, M. N.
Number of pages: 7
Pages: 7387-7393
Publication date: 15 Dec 2011
Peer-reviewed: Yes

Publication information

Journal: BIOORGANIC AND MEDICINAL CHEMISTRY
Volume: 19
Issue number: 24
ISSN (Print): 0968-0896
Ratings: 
  • Scopus rating (2011): CiteScore 3.09 SJR 1.137 SNIP 1.254
Original language: English
ASJC Scopus subject areas: Biochemistry, Molecular Medicine, Molecular Biology, Pharmaceutical Science, Drug Discovery, Clinical Biochemistry, Organic Chemistry
Keywords: Antibiotics, Antitumor activity, Aureolic acid, Chemical modifications, Drug-DNA complexes, Olivomycin A, Olivomycin SA
Source: Scopus
Source ID: 82255193979

Research output: Contribution to journalReview ArticleScientificpeer-review

Conductive layers on surface modified natural fibre based substrates for printed functionality

Formation of conductive surfaces by flexographical printing has been studied using an IGT test printer with PEDOT-PSS and Ag conductive inks on coated papers. Printability of multilayer coated paper and TiO2 nanoparticle coating generated by the liquid flame spray process are compared to commercial plastic film used in printed electronics applications. The wettability of TiO2 nanoparticle coating can be altered between superhydrophobic and superhydrophilic states by ultraviolet light. It is observed that superhydrophobicity induced by TiO2 nanoparticles results in poorer ink setting and hence lower conductivities with water-based PEDOT:PSS ink. Therefore, we observe conductivity only after several successive prints. On contrary, we observe several orders of magnitude better conductivities when using a silver ink in flexography. It is believed that sustainable natural fibre based substrates will find more applications in printed electronics application in the future.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Department of Physics, Engineering materials science and solutions (EMASS), Abo Akad Univ, Abo Akademi University, Dept Phys, Paper Converting and Packaging Technology, Aerosol Physics Laboratory, Hokkai-Gakuen University
Contributors: Valtakari, D., Bollström, R., Tuominen, M., Teisala, H., Aromaa, M., Toivakka, M., Kuusipalo, J., Mäkelä, J. M., Uozumi, J., Saarinen, J. J.
Publication date: 2012

Host publication information

Title of host publication: AIChE 2012 - 2012 AIChE Annual Meeting, Conference Proceedings
ISBN (Print): 9780816910731
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all)
Source: Scopus
Source ID: 84871794294

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Layered Double Hydroxides (LDH): A multifunctional versatile system for nanocomposites

Layered Double Hydroxides gained tremendous research efforts in the last years as a filler for polymer nanocomposites similar to montmorillonite in order to increase barrier properties, improve mechanical properties and reduce flammability. Due to its broad variety in composition and possibility to organically modify the layers LDH might be used in very different applications. This summary intends to show possibilities of integration of additional functionalities apart from the benefits of LDH as platelet decomposing like the classical flame retardant magnesium hydroxide, by selecting a specific metal combination, by fine tuning structural features and by selecting an organic modification with a functionality thus providing a true added value to filler for nanocomposite applications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V.
Contributors: Leuteritz, A., Kutlu, B., Meinl, J., Wang, D., Das, A., Wagenknecht, U., Heinrich, G.
Number of pages: 7
Pages: 107-113
Publication date: 2012
Peer-reviewed: Yes

Publication information

Journal: Molecular Crystals and Liquid Crystals
Volume: 556
ISSN (Print): 1542-1406
Ratings: 
  • Scopus rating (2012): CiteScore 0.44 SJR 0.246 SNIP 0.379
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Materials Science(all)
Keywords: Conductivity, Flame retardancy, Layered double hydroxide, Photostability, Vulcanization
Source: Scopus
Source ID: 84861542986

Research output: Contribution to journalArticleScientificpeer-review

Location of the Azobenzene moieties within the cross-linked liquid-crystalline polymers can dictate the direction of photoinduced bending

We present a simple way to control the photoinduced bending direction of azobenzene-containing cross-linked liquidcrystalline polymers. By changing the location of the photoactive azobenzene moieties from cross-links to side-chains, the bending direction of the sample is reversed under identical irradiation conditions. In addition to providing a versatile route toward directionality control of the photoinduced macroscopic motions, this observation highlights the complicated nature of the photomechanical response of azobenzene-containing cross-linked liquidcrystalline polymers, showing that the photomobile behavior can be determined by seemingly small details on the materials design.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Aalto University, Tokyo Institute of Technology, University of Hyogo, Kobe, Tohoku University, Chuo University
Contributors: Priimagi, A., Shimamura, A., Kondo, M., Hiraoka, T., Kubo, S., Mamiya, J. I., Kinoshita, M., Ikeda, T., Shishido, A.
Number of pages: 4
Pages: 96-99
Publication date: 2012
Peer-reviewed: Yes

Publication information

Journal: ACS Macro Letters
Volume: 1
Issue number: 1
ISSN (Print): 2161-1653
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Inorganic Chemistry
Source: Scopus
Source ID: 84861898337

Research output: Contribution to journalArticleScientificpeer-review

Structure, dynamics, and reactivity of hydrated electrons by Ab initio molecular dynamics

Understanding the properties of hydrated electrons, which were first observed using pulse radiolysis of water in 1962, is crucial because they are key species in many radiation chemistry processes. Although time-resolved spectroscopic studies and molecular simulations have shown that an electron in water (prepared, for example, by water photoionization) relaxes quickly to a localized, cavity-like structure ∼2.5 Å in radius, this picture has recently been questioned. In another experimental approach, negatively charged water clusters of increasing size were studied with photoelectron and IR spectroscopies. Although small water clusters can bind an excess electron, their character is very different from bulk hydrated species. As data on electron binding in liquid water have become directly accessible experimentally, the cluster-to-bulk extrapolations have become a topic of lively debate. Quantum electronic structure calculations addressing experimental measurables have, until recently, been largely limited to small clusters; extended systems were approached mainly with pseudopotential calculations combining a classical description of water with a quantum mechanical treatment of the excess electron.In this Account, we discuss our investigations of electrons solvated in water by means of ab initio molecular dynamics simulations. This approach, applied to a model system of a negatively charged cluster of 32 water molecules, allows us to characterize structural, dynamical, and reactive aspects of the hydrated electron using all of the system's valence electrons. We show that under ambient conditions, the electron localizes into a cavity close to the surface of the liquid cluster. This cavity is, however, more flexible and accessible to water molecules than an analogous area around negatively charged ions.The dynamical process of electron attachment to a neutral water cluster is strongly temperature dependent. Under ambient conditions, the electron relaxes in the liquid cluster and becomes indistinguishable from an equilibrated, solvated electron on a picosecond time scale. In contrast, for solid, cryogenic systems, the electron only partially localizes outside of the cluster, being trapped in a metastable, weakly bound "cushion-like" state. Strongly bound states under cryogenic conditions could only be prepared by cooling equilibrated, liquid, negatively charged clusters. These calculations allow us to rationalize how different isomers of electrons in cryogenic clusters can be observed experimentally. Our results also bring into question the direct extrapolation of properties of cryogenic, negatively charged water clusters to those of electrons in the bulk liquid.Ab initio molecular dynamics represents a unique computational tool for investigating the reactivity of the solvated electron in water. As a prototype, the electron-proton reaction was followed in the 32-water cluster. In accord with experiment, the molecular mechanism is a proton transfer process that is not diffusion limited, but rather controlled by a proton-induced deformation of the excess electron's solvent shell. We demonstrate the necessary ingredients of a successful density functional methodology for the hydrated electron that avoids potential pitfalls, such as self-interaction error, insufficient basis set, or lack of dispersion interactions. We also benchmark the density functional theory methods and outline the path to faithful ab initio simulations of dynamics and reactivity of electrons solvated in extended aqueous systems.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, University of Zurich, Center for Biomolecules
Contributors: Marsalek, O., Uhlig, F., Vandevondele, J., Jungwirth, P.
Number of pages: 10
Pages: 23-32
Publication date: 17 Jan 2012
Peer-reviewed: Yes

Publication information

Journal: Accounts of Chemical Research
Volume: 45
Issue number: 1
ISSN (Print): 0001-4842
Ratings: 
  • Scopus rating (2012): CiteScore 21.17 SJR 12.299 SNIP 5.413
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Source: Scopus
Source ID: 84855914692

Research output: Contribution to journalArticleScientificpeer-review

Surface-relief gratings and stable birefringence inscribed using light of broad spectral range in supramolecular polymer-bisazobenzene complexes

We report on phenol-pyridine hydrogen-bonded supramolecular polymer-azobenzene complexes made from a newly designed polar bisazobenzene chromophore. Because of the substitution with a polar nitro group, the chromophore possesses an extremely broad absorption band, spanning from near-UV up to 650 nm. Moreover, the inclusion of two methoxy groups to the central benzene ring prevents excessive chromophore-chromophore intermolecular interactions and provides advantageous size-related properties. Together, these features of the prepared photoresponsive polymer materials enable efficient inscription of (i) photoinduced birefringence with outstanding stability at various chromophore concentrations and (ii) surface-relief grating formation over a wide range of writing wavelengths from 405 to 633 nm. The photoresponsive behavior is compared to that of Disperse Yellow 7-based supramolecular complexes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Department of Applied Physics, Aalto University, Tokyo Institute of Technology, University of Bristol
Contributors: Koskela, J. E., Vapaavuori, J., Hautala, J., Priimagi, A., Faul, C. F. J., Kaivola, M., Ras, R. H. A.
Number of pages: 8
Pages: 2363-2370
Publication date: 26 Jan 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry C
Volume: 116
Issue number: 3
ISSN (Print): 1932-7447
Ratings: 
  • Scopus rating (2012): CiteScore 4.98 SJR 2.529 SNIP 1.461
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Energy(all)
Source: Scopus
Source ID: 84856360260

Research output: Contribution to journalArticleScientificpeer-review

Glycerol mediated synthesis of 5-substituted 1H-tetrazole under catalyst free conditions

We have developed simple, cost effective and environmentally benign protocol for the synthesis of 5-substituted 1H-tetrazoles via [2,3] cycloaddition reaction from organic nitriles and sodium azide in glycerol under catalyst free condition. The corresponding 5-substituted 1H-tetrazoles were obtained with good to excellent yields (68-95%).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: North Maharashtra University, N Maharashtra Univ, North Maharashtra University, Dept Organ Chem
Contributors: Nandre, K. P., Salunke, J. K., Nandre, J. P., Patil, V. S., Borse, A. U., Bhosale, S. V.
Number of pages: 4
Pages: 161-164
Publication date: Feb 2012
Peer-reviewed: Yes

Publication information

Journal: Chinese Chemical Letters
Volume: 23
Issue number: 2
ISSN (Print): 1001-8417
Ratings: 
  • Scopus rating (2012): CiteScore 1.21 SJR 0.419 SNIP 0.759
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Keywords: 5-Substituted 1H-tetrazole, [3+2] Cycloaddition, Catalyst free, Glycerol, Nitriles

Bibliographical note

EXT="Salunke, Jagadish"

Source: Scopus
Source ID: 84855928133

Research output: Contribution to journalArticleScientificpeer-review

A novel thermotropic elastomer based on highly-filled LDH-SSB composites

Elastomeric composites are prepared based on solution styrene butadiene elastomer and zinc-aluminium layered double hydroxides (LDH), using a conventional sulphur cure system. Up to 100 parts per hundred rubber of LDH are incorporated into the elastomer matrix. The composites exhibit an interesting phenomenon of thermoreversible transparency, i.e. the transparent sample becomes opaque at warm condition and restores the transparency at room temperature. The transparency is found to be increased as the amount of LDH was increased. The addition of LDH gradually improved the mechanical, dynamic mechanical performance and thermal stability of the base elastomer. These developped elastomers could be utilised as smart materials in different applications

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Vodafone Department of Mobile Communications Systems
Contributors: Das, A., George, J. J., Kutlu, B., Leuteritz, A., Wang, D. Y., Rooj, S., Jurk, R., Rajeshbabu, R., Stöckelhuber, K. W., Galiatsatos, V., Heinrich, G.
Number of pages: 6
Pages: 337-342
Publication date: 27 Feb 2012
Peer-reviewed: Yes

Publication information

Journal: Macromolecular Rapid Communications
Volume: 33
Issue number: 4
ISSN (Print): 1022-1336
Ratings: 
  • Scopus rating (2012): CiteScore 4.7 SJR 2.096 SNIP 1.251
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics
Source: Scopus
Source ID: 84863149624

Research output: Contribution to journalArticleScientificpeer-review

Excited-state polarizability in crystalline sexithiophene: Charge-transfer and vibronic effects

A model of vibronic coupling in a manifold of coupled Frenkel and charge transfer states is applied to evaluate the electric-field-induced shifts of lowest vibronic levels deriving from the lower Davydov component of the Frenkel exciton in sexithiophene. With respect to the isolated-molecule value, vibronic terms combined with the mixing between Frenkel and CT configurations amplify the field-induced shift by the factor of seven for the 0-0 line and by further 60% for the vibronic replica in the main progression-forming mode. Confirmation is found in the existing experimental literature.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Groningen, K. Gumiński Department of Theoretical Chemistry, Uniwersytet Jagiellonski w Krakowie
Contributors: Stradomska, A., Kulig, W., Slawik, M., Petelenz, P.
Number of pages: 4
Pages: 27-30
Publication date: 9 Mar 2012
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 529
ISSN (Print): 0009-2614
Ratings: 
  • Scopus rating (2012): CiteScore 2.2 SJR 1.104 SNIP 0.901
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 84857532168

Research output: Contribution to journalArticleScientificpeer-review

Highly exfoliated natural rubber/Clay composites by "propping-open procedure": The influence of fatty-acid chain length on exfoliation

A high degree of exfoliation of MMT in NR is achieved by using the so-called "propping-open approach" in which a stepwise expansion of the interlayer spacing of MMT takes place. The nanostructure is characterized by WAXD and TEM which indicate different extents of clay dispersion depending on the fatty-acid chain length. Curing kinetics of different nanocomposites is studied and interestingly low activation energies of the vulcanization process are observed in the case of NR/EMMT nanocomposites. The incorporation of EMMT dramatically affects composite properties whereas DMA indicates significant reduction of tan δ peak height and the tensile strength approximately doubles from 14 to 30 MPa with only 5 phr EMMT.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Vodafone Department of Mobile Communications Systems
Contributors: Rooj, S., Das, A., Stöckelhuber, K. W., Reuter, U., Heinrich, G.
Number of pages: 15
Pages: 369-383
Publication date: Apr 2012
Peer-reviewed: Yes

Publication information

Journal: Macromolecular Materials and Engineering
Volume: 297
Issue number: 4
ISSN (Print): 1438-7492
Ratings: 
  • Scopus rating (2012): CiteScore 2.34 SJR 0.963 SNIP 1.187
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Organic Chemistry, Polymers and Plastics, Materials Chemistry
Keywords: curing kinetics, exfoliation, Mooney-Rivlin equation, nanocomposites, propping-open approach
Source: Scopus
Source ID: 84859811037

Research output: Contribution to journalArticleScientificpeer-review

Structural characteristics and flammability of fire retarding EPDM/layered double hydroxide (LDH) nanocomposites

A high performance elastomeric flame retardant nanocomposite was prepared which was based on maleic anhydride grafted ethylene-propylene-diene terpolymer (mEPDM), a one-step synthesised organo-layered double hydroxide (LDH), and an intumescent flame retardant (FR) comprised of pentaerythritol (PER), ammonium polyphosphate (APP) and methyl cyanoacetate (MCA). The morphology, fire behavior and mechanical properties of the flame-retarded mEPDM/LDH nanocomposite have been studied in detail. Wide angle X-ray scattering (WAXS), small angle X-ray scattering (SAXS) and TEM observation confirmed an exfoliated structure of LDH in a particular composite containing 2 phr (parts per hundred) LDH and 38 phr FR. As an effective flame retardant synergistic agent, MgAl-LDH shows a significant decrease in the heat release rate (HRR), low mass loss (ML) and low fire growth rate (FIGRA) of the nanocomposite. The flame retardant mechanism has been proposed, which is mainly due to the condensed phase flame retardant mechanism to form reinforced char layers during combustion, leading to the low volatiles produced. Moreover, as far as the mechanical properties of the vulcanizates are concerned, in all cases of flame retardant mEPDM and flame retarded mEPDM/LDH nanocomposites, they exhibit superior values compared to the gum compound.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., Vodafone Department of Mobile Communications Systems
Contributors: Wang, D. Y., Das, A., Leuteritz, A., Mahaling, R. N., Jehnichen, D., Wagenknecht, U., Heinrich, G.
Number of pages: 7
Pages: 3927-3933
Publication date: 21 Apr 2012
Peer-reviewed: Yes

Publication information

Journal: RSC Advances
Volume: 2
Issue number: 9
ISSN (Print): 2046-2069
Ratings: 
  • Scopus rating (2012): CiteScore 2.4 SJR 0.872 SNIP 0.619
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all)
Source: Scopus
Source ID: 84863098130

Research output: Contribution to journalArticleScientificpeer-review

Elemental and mixed actinide dioxides: An ab initio study

We present a systematic study of the electronic, geometric, and magnetic properties of the actinide dioxides, UO 2, PuO 2, AmO 2, U 0.5Pu 0.5O 2, U 0.5Am 0.5O 2 and Pu 0.5Am 0.5O 2. For UO 2, PuO 2 and AmO 2, both density functional and hybrid density functional theory (DFT and HDFT) have been used. The fractions of exact HartreeFock (HF) exchange chosen were 25% and 40% for the hybrid density functional. For U 0.5Pu 0.5O 2, U 0.5Am 0.5O 2 and Pu 0.5Am 0.5O 2, only HDFT with 40% exact HF exchange was used. Each compound has been studied at the nonmagnetic, ferromagnetic and anti-ferromagnetic configurations, with and without spinorbit coupling (SOC). The lattice parameters, magnetic structures, bulk moduli, band gaps and density of states have been computed and compared to available experimental data and other theoretical results. Pure DFT fails to provide a satisfactory qualitative description of the electronic and magnetic structures of the actinide dioxides. On the other hand, HDFT performs very well in the prediction and description of the properties of the actinide dioxides. Our total energy calculations clearly indicate that the ground-state structures are anti-ferromagnetic for all actinide dioxides considered here. The lattice constants and the band gaps expand with an increase of HF exchange in HDFT. The influence of SOC is found to be significant.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Texas at Arlington, Pacific Northwest National Laboratory
Contributors: Ma, L., Atta-Fynn, R., Ray, A. K.
Number of pages: 19
Pages: 611-629
Publication date: Jun 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Theoretical and Computational Chemistry
Volume: 11
Issue number: 3
ISSN (Print): 0219-6336
Ratings: 
  • Scopus rating (2012): CiteScore 0.69 SJR 0.315 SNIP 0.304
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Computational Theory and Mathematics, Computer Science Applications
Keywords: Actinide dioxides, hybrid density functional theory, mixed actinide oxides
Source: Scopus
Source ID: 84862874223

Research output: Contribution to journalArticleScientificpeer-review

Behavior of 4-hydroxynonenal in phospholipid membranes

Under conditions of oxidative stress, 4-hydroxy-2-nonenal (4-HNE) is commonly present in vivo. This highly reactive and cytotoxic compound is generated by oxidation of lipids in membranes and can be easily transferred from a membrane to both cytosol and the extracellular space. Employing time-dependent fluorescence shift (TDFS) method and molecular dynamics simulations, we found that 4-HNE is stabilized in the carbonyl region of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. 4-HNE is thus able to react with cell membrane proteins and lipids. Stabilization in the membrane is, however, moderate and a transfer of 4-HNE to either extra- or intracellular space occurs on a microsecond time scale. These molecular-level details of 4-HNE behavior in the lipid membrane rationalize the experimentally observed reactivity of 4-HNE with proteins inside and outside the cell. Furthermore, these results support the view that 4-HNE may play an active role in cell signaling pathways.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, V.v.i.
Contributors: Vazdar, M., Jurkiewicz, P., Hof, M., Jungwirth, P., Cwiklik, L.
Number of pages: 5
Pages: 6411-6415
Publication date: 7 Jun 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 116
Issue number: 22
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2012): CiteScore 3.66 SJR 1.943 SNIP 1.243
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84861861948

Research output: Contribution to journalArticleScientificpeer-review

Halogen bonding versus hydrogen bonding in driving self-assembly and performance of light-responsive supramolecular polymers

Halogen bonding is arguably the least exploited among the many non-covalent interactions used in dictating molecular self-assembly. However, its directionality renders it unique compared to ubiquitous hydrogen bonding. Here, the role of this directionality in controlling the performance of light-responsive supramolecular polymers is highlighted. In particular, it is shown that light-induced surface patterning, a unique phenomenon occurring in azobenzene-containing polymers, is more efficient in halogen-bonded polymer-azobenzene complexes than in the analogous hydrogen-bonded complexes. A systematic study is performed on a series of azo dyes containing different halogen or hydrogen bonding donor moieties, complexed to poly(4-vinylpyridine) backbone. Through single-atom substitution of the bond-donor, control of both the strength and the nature of the noncovalent interaction between the azobenzene units and the polymer backbone is achieved. Importantly, such substitution does not significantly alter the electronic properties of the azobenzene units, hence providing us with unique tools in studying the structure-performance relationships in the light-induced surface deformation process. The results represent the first demonstration of light-responsive halogen-bonded polymer systems and also highlight the remarkable potential of halogen bonding in fundamental studies of photoresponsive azobenzene-containing polymers.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Tokyo Institute of Technology, Politecnico di Milano, Università degli Studi di Milano, Aalto University, VTT Technical Research Centre of Finland
Contributors: Priimagi, A., Cavallo, G., Forni, A., Gorynsztejn-Leben, M., Kaivola, M., Metrangolo, P., Milani, R., Shishido, A., Pilati, T., Resnati, G., Terraneo, G.
Number of pages: 8
Pages: 2572-2579
Publication date: 20 Jun 2012
Peer-reviewed: Yes

Publication information

Journal: Advanced Functional Materials
Volume: 22
Issue number: 12
ISSN (Print): 1616-301X
Ratings: 
  • Scopus rating (2012): CiteScore 10.41 SJR 5.689 SNIP 2.614
Original language: English
ASJC Scopus subject areas: Electronic, Optical and Magnetic Materials, Biomaterials, Condensed Matter Physics, Electrochemistry
Keywords: halogen bonding, optically active materials, self-assembly, supramolecular polymers, surface relief gratings
Source: Scopus
Source ID: 84862000539

Research output: Contribution to journalArticleScientificpeer-review

Molecular mechanisms of ion-specific effects on proteins

The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG) 120, were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN - and I - interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl - binds far more weakly to the amide nitrogen/α-carbon binding site, while SO 4 2- is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na + counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Texas A and M University, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Rembert, K. B., Paterová, J., Heyda, J., Hilty, C., Jungwirth, P., Cremer, P. S.
Number of pages: 8
Pages: 10039-10046
Publication date: 20 Jun 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of the American Chemical Society
Volume: 134
Issue number: 24
ISSN (Print): 0002-7863
Ratings: 
  • Scopus rating (2012): CiteScore 10.37 SJR 6.211 SNIP 2.374
Original language: English
ASJC Scopus subject areas: Chemistry(all), Catalysis, Biochemistry, Colloid and Surface Chemistry
Source: Scopus
Source ID: 84862532625

Research output: Contribution to journalArticleScientificpeer-review

Accurate description of aqueous carbonate ions: An effective polarization model verified by neutron scattering

The carbonate ion plays a central role in the biochemical formation of the shells of aquatic life, which is an important path for carbon dioxide sequestration. Given the vital role of carbonate in this and other contexts, it is imperative to develop accurate models for such a high charge density ion. As a divalent ion, carbonate has a strong polarizing effect on surrounding water molecules. This raises the question whether it is possible to describe accurately such systems without including polarization. It has recently been suggested the lack of electronic polarization in nonpolarizable water models can be effectively compensated by introducing an electronic dielectric continuum, which is with respect to the forces between atoms equivalent to rescaling the ionic charges. Given how widely nonpolarizable models are used to model electrolyte solutions, establishing the experimental validity of this suggestion is imperative. Here, we examine a stringent test for such models: a comparison of the difference of the neutron scattering structure factors of K 2CO3 vs KNO3 solutions and that predicted by molecular dynamics simulations for various models of the same systems. We compare standard nonpolarizable simulations in SPC/E water to analogous simulations with effective ion charges, as well as simulations in explicitly polarizable POL3 water (which, however, has only about half the experimental polarizability). It is found that the simulation with rescaled charges is in a very good agreement with the experimental data, which is significantly better than for the nonpolarizable simulation and even better than for the explicitly polarizable POL3 model.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Mason, P. E., Wernersson, E., Jungwirth, P.
Number of pages: 9
Pages: 8145-8153
Publication date: 19 Jul 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 116
Issue number: 28
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2012): CiteScore 3.66 SJR 1.943 SNIP 1.243
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84863696122

Research output: Contribution to journalArticleScientificpeer-review

Nematicons in azobenzene liquid crystals

We review our comprehensive investigation of light self-localization phenomena in planarly configured azobenzene liquid crystals. Cis-trans isomerization of azobenzene molecules and related changes in the order parameter of the liquid crystals support a high nonlinear response and the formation of optical spatial solitons at microwatt excitations. We describe bright soliton angular steering, deflection, interleaving and merging, as well as dark solitons.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Beam Engineering for Advanced Measurements Co, Nonlinear Optics and OptoElectronics Lab
Contributors: Serak, S. V., Tabiryan, N. V., Assanto, G.
Number of pages: 12
Pages: 202-213
Publication date: 19 Jul 2012
Peer-reviewed: Yes

Publication information

Journal: Molecular Crystals and Liquid Crystals
Volume: 559
ISSN (Print): 1542-1406
Ratings: 
  • Scopus rating (2012): CiteScore 0.44 SJR 0.246 SNIP 0.379
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Materials Science(all)
Keywords: Cis-trans isomerization, laser, liquid crystals, solitons
Source: Scopus
Source ID: 84861494448

Research output: Contribution to journalArticleScientificpeer-review

Impact of biodiesel application at various blending ratios on passenger cars of different fueling technologies

The effect of biodiesel on emissions of diesel passenger cars is a combination of the fuel properties, the blending ratio, and the vehicle technology. In this study, saturated and unsaturated biodiesel fuels were tested neat (B100) and in 30% blend with fossil diesel (B30) on two Euro 3 diesel passenger cars of different engine technologies, namely common rail and unit injector. The measured dataset is enlarged by introducing B10 results from an earlier study [15] in order to produce generalized conclusions over a wider range of blends. None of these vehicles was equipped with a particle filter and different conclusions might be reached for filter-equipped vehicles. The results indicate that the influence of biodiesel on pollutant emissions primarily depends on the blending ratio and secondly on the level of unsaturation and engine technology. Tailpipe CO 2, NO x and PM emissions with biodiesel varied from -1% to +3%, -1% to 14%, and -18% to -35%, respectively, compared to fossil diesel. The difference over fossil diesel generally increased with an increasing blending ratio. CO and HC emissions increased over the fossil diesel but remained at low levels and did not threaten the compliance of the vehicles with their respective emission limits. Use of biodiesel on the common rail vehicle led to a smaller NO x increase and a higher PM reduction than in the unit-injector case. The unsaturated fuel generally led to higher NO x emissions from both engine technologies. However, the maximum blending ratio of saturated biodiesel is limited to around B30 due to cold-flow limitations. Hence, the saturated vs. unsaturated species ratio should be carefully designed in market fuels in order to optimize environmental and operational benefits. Overall, it appears that blends up to 10% v/v may be introduced with limited urban air quality implications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Urban circular bioeconomy (UrCirBio), Aristotle University of Thessaloniki, Laboratory of Applied Thermodynamics, European Commission-JRC
Contributors: Kousoulidou, M., Ntziachristos, L., Fontaras, G., Martini, G., Dilara, P., Samaras, Z.
Number of pages: 7
Pages: 88-94
Publication date: Aug 2012
Peer-reviewed: Yes

Publication information

Journal: Fuel
Volume: 98
ISSN (Print): 0016-2361
Ratings: 
  • Scopus rating (2012): CiteScore 3.99 SJR 1.813 SNIP 2.387
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Fuel Technology, Energy Engineering and Power Technology, Organic Chemistry
Keywords: Biodiesel, Fuel injection technology, Unsaturation level, Vehicle emissions
Source: Scopus
Source ID: 84861986728

Research output: Contribution to journalArticleScientificpeer-review

Solvation and ion-pairing properties of the aqueous sulfate anion: Explicit versus effective electronic polarization

We assessed the relative merits of two approaches for including polarization effects in classical force fields for the sulfate anion. One of the approaches is the explicit shell model for atomic polarization and the other is an implicit dielectric continuum representation of the electronic polarization, wherein the polarizability density is spatially uniform. Both the solvation and ion association properties of sulfate were considered. We carried out an ab initio molecular dynamics simulation for a single sulfate anion in aqueous solution to obtain a benchmark for the solvation structure. For the ion-pairing properties, the models were compared to experimental thermodynamic data through Kirkwood-Buff theory, which relates the integrals of the pair correlation functions to measurable properties. While deficiencies were found for both of the approaches, the continuum polarization model was not systematically worse than the shell model. The shell model was found to give a more structured solution than the continuum polarization model, both with respect to solvation and ion pairing.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Paul Scherrer Institut, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Lund University
Contributors: Pegado, L., Marsalek, O., Jungwirth, P., Wernersson, E.
Number of pages: 10
Pages: 10248-10257
Publication date: 7 Aug 2012
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 14
Issue number: 29
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2012): CiteScore 3.67 SJR 1.921 SNIP 1.164
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 84863652661

Research output: Contribution to journalArticleScientificpeer-review

Effect of sol-gel derived in situ silica on the morphology and mechanical behavior of natural rubber and acrylonitrile butadiene rubber blends

Silica particles were generated and grown in situ by sol-gel method into rubber blends comprised of natural rubber (NR) and acrylonitrile butadiene rubber (NBR) at various blend ratios. Silica formed into rubber matrix was amorphous in nature. Amount of in situ silica increased with increase in natural rubber proportion in the blends during the sol-gel process. Morphology studies showed that the generated in situ silica were nanoparticles of different shapes and sizes mostly grown into the NR phase of the blends. In situ silica filled NR/NBR blend composites showed improvement in the mechanical and dynamic mechanical behaviors in comparison to those of the unfilled and externally filled NR/ NBR blend composites. For the NR/NBR blend at 40/60 composition, in particular, the improvement was appreciable where size and dispersion of the silica particles into the rubber matrix were found to be more uniform. Dynamic mechanical analysis revealed a strong rubber-in situ silica interaction as indicated by a positive shift of the glass transition temperature of both the rubber phases in the blends.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Visvesvaraya National Institute of Technology, Leibniz-Institut für Polymerforschung Dresden E.V.
Contributors: Kapgate, B. P., Das, C., Das, A., Basu, D., Reuter, U., Heinrich, G.
Number of pages: 9
Pages: 501-509
Publication date: Sep 2012
Peer-reviewed: Yes

Publication information

Journal: JOURNAL OF SOL-GEL SCIENCE AND TECHNOLOGY
Volume: 63
Issue number: 3
ISSN (Print): 0928-0707
Ratings: 
  • Scopus rating (2012): CiteScore 1.82 SJR 0.732 SNIP 1.122
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Biomaterials, Ceramics and Composites, Electronic, Optical and Magnetic Materials, Materials Chemistry
Keywords: In situ silica, Reinforcement, Rubber blend, Rubber-filler interaction, Sol-gel
Source: Scopus
Source ID: 84875426374

Research output: Contribution to journalArticleScientificpeer-review

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecules structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular linear response model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Northeastern University, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Bardhan, J. P., Jungwirth, P., Makowski, L.
Publication date: 28 Sep 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Physics
Volume: 137
Issue number: 12
Article number: 124101
ISSN (Print): 0021-9606
Ratings: 
  • Scopus rating (2012): CiteScore 2.86 SJR 1.832 SNIP 1.16
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84867017908

Research output: Contribution to journalArticleScientificpeer-review

Biomimetic surface modification of polycarbonateurethane film via phosphorylcholine-graft for resisting platelet adhesion

Phosphorylcholine groups were covalently introduced onto a polycarbonateurethane (PCU) surface in order to create a biomimetic structure on the polymer surfaces. After introducing primary amine groups onto the polymer surface by 1,6-hexanediamine, phosphorylcholine groups were covalently linked onto the surface by the reductive amination between the amino group and the aldehyde group of phosphorylcholine glyceraldehyde (PCGA). The results of water contact angle test, X-ray photoelectron spectroscopy (XPS), and X-ray fluorescence spectrometer (XRF) analysis of the modified films indicated that PCGA had already been covalently linked to the PCU surface. The topographies and surface roughnesses were both imaged and measured by atomic force microscopy (AFM). Scanning electron microscopy (SEM) observation of the PCU films after treatment with platelet-rich plasma demonstrated that platelets had rarely adhered to the surface of the PCGA-grafted PCU films but had mainly adhered to the surface of the blank PCU films. The platelet adhesion result indicated that the PC modified PCU films could resist platelet adhesion after grafting with PCGA, and that these PCGA-grafted PCU materials, potentially, might be applied as blood-contacting materials.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Tianjin University, School of Chemical Engineering and Technology
Contributors: Gao, W., Feng, Y., Lu, J., Khan, M., Guo, J.
Number of pages: 7
Pages: 1063-1069
Publication date: Oct 2012
Peer-reviewed: Yes

Publication information

Journal: Macromolecular Research
Volume: 20
Issue number: 10
ISSN (Print): 1598-5032
Ratings: 
  • Scopus rating (2012): CiteScore 1.44 SJR 0.569 SNIP 0.801
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Chemical Engineering(all)
Keywords: Biomimetic, Phosphorylcholine glyceraldehydes, Platelet adhesion, Polycarbonateurethane, Surface modification
Source: Scopus
Source ID: 84867230066

Research output: Contribution to journalArticleScientificpeer-review

Kinetics of filler wetting and dispersion in carbon nanotube/rubber composites

The effects of the surface modification of multi-walled carbon nanotubes (MWCNTs) by an ionic liquid, 1-butyl 3-methyl imidazolium bis(trifluoromethyl- sulphonyl)imide (BMI) on the kinetics of filler wetting and dispersion as well as resulting electrical conductivity of polychloroprene (CR) composites were studied. Two different MWCNTs were used, Baytubes and Nanocyl, which differ in their structure, purity and compatibility to CR and BMI. The results showed that BMI can significantly improve the macrodispersion of Baytubes, and increases the electrical conductivity of the uncured BMI-Baytube/CR composites up to five orders of magnitude. In contrast, the use of BMI slows the dispersion process and the development of conductivity of BMI-Nanocyl/CR composites. Our wetting concept was further developed for the quantification of the bound polymer on the CNT surface. We found that the bonded BMI on the CNT surface is replaced by the CR molecules during mixing as a result of the concentration compensation effect. The de- and re-agglomeration processes of CNTs taking place during the subsequent curing process can increase or decrease the electrical conductivity significantly. The extent of the conductivity changes is strongly determined by the composition of the bound polymer and the curing technique used.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Martin-Luther-University Halle-Wittenberg, University of Technology - National University, Leibniz-Institut für Polymerforschung Dresden E.V., Vodafone Department of Mobile Communications Systems, Nepal Polymer Institute (NPI)
Contributors: Le, H. H., Hoang, X. T., Das, A., Gohs, U., Stoeckelhuber, K. W., Boldt, R., Heinrich, G., Adhikari, R., Radusch, H. J.
Number of pages: 14
Pages: 4543-4556
Publication date: Oct 2012
Peer-reviewed: Yes

Publication information

Journal: Carbon
Volume: 50
Issue number: 12
ISSN (Print): 0008-6223
Ratings: 
  • Scopus rating (2012): CiteScore 5.95 SJR 2.518 SNIP 2.118
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Source: Scopus
Source ID: 84863715656

Research output: Contribution to journalArticleScientificpeer-review

Fabrication of ssDNA/oligo(ethylene glycol) monolayers and complex nanostructures by an irradiation-promoted exchange reaction

Creative design: An approach to preparing mixed monolayers of thiolated single-stranded DNA (ssDNA) and oligo(ethylene glycol)s (OEG-AT) in a broad range of compositions as well as ssDNA/OEG-AT patterns of any required shape (see top figure) has been shown. A combination of this approach with surface-initiated enzymatic polymerization allows complex 3D DNA nanostructures to be sculpted with high spatial precision (bottom).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Universitat Heidelberg, Duke University
Contributors: Khan, M. N., Tjong, V., Chilkoti, A., Zharnikov, M.
Number of pages: 4
Pages: 10303-10306
Publication date: 8 Oct 2012
Peer-reviewed: Yes

Publication information

Journal: Angewandte Chemie (International Edition)
Volume: 51
Issue number: 41
ISSN (Print): 1433-7851
Ratings: 
  • Scopus rating (2012): CiteScore 10.55 SJR 6.407 SNIP 2.329
Original language: English
ASJC Scopus subject areas: Chemistry(all), Catalysis
Keywords: chemical lithography, DNA structures, monolayers, nanostructures, polymer brushes
Source: Scopus
Source ID: 84867091572

Research output: Contribution to journalArticleScientificpeer-review

Azobenzene photomechanics: Prospects and potential applications

The change in shape inducible in some photo-reversible molecules using light can effect powerful changes to a variety of properties of a host material. This class of reversible light-switchable molecules includes molecules that photodimerize, such as coumarins and anthracenes; those that allow intra-molecular photo-induced bond formation, such as fulgides, spiro-pyrans, and diarylethenes; and those that exhibit photo-isomerization, such as stilbenes, crowded alkenes, and azobenzenes. The most ubiquitous natural molecule for reversible shape change, however, and perhaps the inspiration for all artificial bio-mimics, is the rhodopsin/retinal protein system that enables vision, and this is the quintessential reversible photo-switch for performance and robustness. Here, the small retinal molecule embedded in a cage of rhodopsin helices isomerizes from a cis geometry to a trans geometry around a C=C double bond with the absorption of just a single photon. The modest shape change of just a few angstroms is quickly amplified and sets off a cascade of larger shape and chemical changes, eventually culminating in an electrical signal to the brain of a vision event, the energy of the input photon amplified many thousands of times in the process. Complicated biochemical pathways then revert the trans isomer back to cis, and set the system back up for another cascade upon subsequent absorption. The reversibility is complete, and many subsequent cycles are possible. The reversion mechanism back to the initial cis state is complex and enzymatic, hence direct application of the retinal/rhodopsin photo-switch to engineering systems is difficult. Perhaps the best artificial mimic of this strong photo-switching effect however in terms of reversibility, speed, and simplicity of incorporation, is azobenzene. Trans and cis states can be switched in microseconds with low-power light, reversibility of 10 5 and 10 6 cycles is routine before chemical fatigue, and a wide variety of molecular architectures is available to the synthetic materials chemist, permitting facile anchoring and compatibility, as well as chemical and physical amplification of the simple geometric change. This review article focuses on photo-mechanical effect taking place in various material systems incorporating azobenzene. The photo-mechanical effect can be defined as reversible change in shape by absorption of light, which results in a significant macroscopic mechanical deformation, and reversible mechanical actuation, of the host material. Thus, we exclude simple thermal expansion effects, reversible but non-mechanical photo-switching or photo-chemistry, as well as the wide range of optical and electro-optical switching effects for which good reviews exist elsewhere. Azobenzene-based material systems are also of great interest for light energy harvesting applications across much of the solar spectrum, yet this emerging field is still in an early enough stage of research output as to not yet warrant review, but we hope that some of the ideas put forward here toward promising future directions of research, will help guide the field.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, McGill University, Brookhaven National Laboratory, Tokyo Institute of Technology, Aalto University
Contributors: Mahimwalla, Z., Yager, K. G., Mamiya, J. I., Shishido, A., Priimagi, A., Barrett, C. J.
Number of pages: 40
Pages: 967-1006
Publication date: Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Polymer Bulletin
Volume: 69
Issue number: 8
ISSN (Print): 0170-0839
Ratings: 
  • Scopus rating (2012): CiteScore 1.49 SJR 0.559 SNIP 1.027
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Polymers and Plastics, Materials Chemistry
Keywords: Azobenzene, Light harvesting, Liquid crystals, Photochemistry, Photomechanics, Thin films
Source: Scopus
Source ID: 84868637316

Research output: Contribution to journalArticleScientificpeer-review

Influence of ionic liquids on the dielectric relaxation behavior of CNT based elastomer nanocomposites

The influence of an imidazolium type ionic liquid (IL) on the relaxation behavior of carbon-nanotube (CNT) based polychloroprene nanocomposites prepared by melt mixing has been investigated by broadband dielectric spectroscopy. It is demonstrated that the presence of the ionic liquid modifies the relaxation behavior of the pure rubber matrix and leads to a significant increase of the conductivity for the CNT/rubber composites. For the unfilled rubber, a distinct glass transition of the IL is observed for high concentrations demonstrating that the IL forms a separate phase. The increased conductivity of the CNT-filled rubber composites is related to a physical coupling between CNTs and rubber matrix mediated by IL leading to a better dispersion of the CNTs.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Deutsches Institut für Kautschuktechnologie e.V., Leibniz-Institut für Polymerforschung Dresden E.V., Technische Universität Dresden, Vodafone Department of Mobile Communications Systems
Contributors: Steinhauser, D., Subramaniam, K., Das, A., Heinrich, G., Klüppel, M.
Number of pages: 10
Pages: 927-936
Publication date: Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Express Polymer Letters
Volume: 6
Issue number: 11
ISSN (Print): 1788-618X
Ratings: 
  • Scopus rating (2012): CiteScore 2.1 SJR 0.915 SNIP 1.597
Original language: English
ASJC Scopus subject areas: Polymers and Plastics, Materials Chemistry, Chemical Engineering(all), Organic Chemistry, Physical and Theoretical Chemistry
Keywords: Dielectric spectroscopy, Ionic liquid, Nanocomposites, Relaxation dynamics, Rubber
Source: Scopus
Source ID: 84866131281

Research output: Contribution to journalArticleScientificpeer-review

Superquenching of SYBRGreen dye fluorescence in complex with DNA by gold nanoparticles

The influence of gold nanoparticles (diameter of about 2.5 nm) on the complex between the SYBRGreen dye and double-stranded DNA in solutions has been investigated by fluorescence spectroscopy. Strong quenching of dye fluorescence by nanosized gold particles ("superquenching"), characterized by a high Stern-Volmer constant of KSV = 3.3 × 107 L/mol, has been found. The superquenching effect in the test system is explained in terms of contribution of several processes: electron transfer, formation of aggregates of gold nanoparticles involving dye dications, and enhancement of intersystem crossing by a heavy atom (gold atoms of nanoparticles).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Russian Academy of Sciences, Emanuel Institute of Biochemical Physics
Contributors: Lisitsyna, E. S., Lygo, O. N., Durandin, N. A., Dement'eva, O. V., Rudoi, V. M., Kuzmin, V. A.
Number of pages: 5
Pages: 363-367
Publication date: Nov 2012
Peer-reviewed: Yes

Publication information

Journal: HIGH ENERGY CHEMISTRY
Volume: 46
Issue number: 6
ISSN (Print): 0018-1439
Ratings: 
  • Scopus rating (2012): CiteScore 0.46 SJR 0.296 SNIP 0.443
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84870905943

Research output: Contribution to journalArticleScientificpeer-review

Transforming anion instability into stability: Contrasting photoionization of three protonation forms of the phosphate ion upon moving into water

We use photoelectron emission spectroscopy with vacuum microjet technique and quantum chemistry calculations to investigate electronic structure and stability of aqueous phosphate anions. On the basis of the measured photoelectron spectra of sodium phosphates at different pH, we report the lowest vertical ionization energies of monobasic (9.5 eV), dibasic (8.9 eV), and tribasic (8.4 eV) anions. Electron binding energies were in tandem modeled with ab initio methods, using a mixed dielectric solvation model together with up to 64 explicitly solvating water molecules. We demonstrate that two solvation layers of explicit water molecules are needed to obtain converged values of vertical ionization energies (VIEs) within this mixed solvation model, leading to very good agreement with experiment. We also show that the highly charged PO4 3- anion, which is electronically unstable in the gas phase, gains the electronic stability with about 16 water molecules, while only 2-3 water molecules are sufficient to stabilize the doubly charged phosphate anion. We also investigate the effect of ion pairing on the vertical ionization energy. In contrast to protonation (leading to a formation of covalent O-H bond), sodiation (leading to an anion···Na+ ion pair) has only a weak effect on the electron binding energy.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Department of Physical Chemistry, University of Southern California, Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, J. Heyrovský Institute of Physical Chemistry
Contributors: Pluhařová, E., Ončák, M., Seidel, R., Schroeder, C., Schroeder, W., Winter, B., Bradforth, S. E., Jungwirth, P., Slavíček, P.
Number of pages: 11
Pages: 13254-13264
Publication date: 8 Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 116
Issue number: 44
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2012): CiteScore 3.66 SJR 1.943 SNIP 1.243
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84868554130

Research output: Contribution to journalArticleScientificpeer-review

Search for global minimum geometries of medium sized Cd nTe n clusters (n = 15, 16, 20, 24 and 28)

Following our recent work which revealed the lowest-energy structures of Cd nTe n (n = 1-14) clusters follow the hollow cage and the endohedral cage structural growth patterns, we extend the search for the most stable structures to some larger clusters, i.e., Cd nTe n (n = 15, 16, 20, 24 and 28). Within the size range studied, the endohedral cages are more stable than the hollow cages. The endohedral atoms increase as the cluster size increases. The computed dipole moments and polarizabilities show a clear dependence on the cluster geometry and symmetry. The hollow cage isomers possess smaller dipole moments and larger polarizabilities than the endohedral ones.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Northwest University China, National Laboratory of Solid State Microstructures, Nanjing University, Institute of Photonics and Photo-technology
Contributors: Ma, L., Wang, J., Wang, G.
Number of pages: 5
Pages: 73-77
Publication date: 12 Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Chemical Physics Letters
Volume: 552
ISSN (Print): 0009-2614
Ratings: 
  • Scopus rating (2012): CiteScore 2.2 SJR 1.104 SNIP 0.901
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84868208985

Research output: Contribution to journalArticleScientificpeer-review

Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations

The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Freie Universität Berlin
Contributors: Pluhaová, E., Marsalek, O., Schmidt, B., Jungwirth, P.
Publication date: 14 Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Physics
Volume: 137
Issue number: 18
Article number: 185101
ISSN (Print): 0021-9606
Ratings: 
  • Scopus rating (2012): CiteScore 2.86 SJR 1.832 SNIP 1.16
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry, Medicine(all)
Source: Scopus
Source ID: 84876463177

Research output: Contribution to journalArticleScientificpeer-review

Semiclassical hybrid approach to condensed phase molecular dynamics: Application to the I2Kr17 cluster

We study the vibrational decoherence dynamics of an iodine molecule in a finite krypton cluster comprising the first solvation shell. A normal mode analysis allows us to successively increase the complexity of the description. For the ground state dynamics, comparison with experimental matrix results shows that already four degrees of freedom are sufficient to capture the main decoherence mechanism. For electronically excited iodine, we model the vibrational dynamics of initial Schrödinger cat-like states by the semiclassical hybrid dynamics [ Grossmann, F.J. Chem. Phys. 2006, 125, 014111 ] and full quantum calculations, where available. Good agreement of the results is found for a reduced model with three degrees of freedom. We find non-Gaussian distortions of the bath density matrix, which is a necessary condition, if Schrödinger catlike states in the bath are to be identified. However, in contrast to the experiment [ Segale, D.; et al. J. Chem. Phys. 2005, 122, 111104 ], we observe only incoherent superpositions of bath vibrational states.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Vodafone Department of Mobile Communications Systems, Freie Universität Berlin, Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Buchholz, M., Goletz, C. M., Grossmann, F., Schmidt, B., Heyda, J., Jungwirth, P.
Number of pages: 12
Pages: 11199-11210
Publication date: 26 Nov 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 116
Issue number: 46
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2012): CiteScore 2.78 SJR 1.513 SNIP 1.119
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84870038667

Research output: Contribution to journalArticleScientificpeer-review

New reports on anti-bacterial and anti-candidal activities of fatty acid methyl esters (FAME) obtained from Scenedesmus bijugatus var. bicellularis biomass

The present study evaluates the efficiency of fatty acid methyl esters (FAMEs) obtained from microalgal (Scenedesmus bijugatus var bicellularis) biomass as an antimicrobial agent against Staphylococcus aureus, Escherichia coli and Candida albicans. The FAME profiles were determined through Gas Chromatography (GC) with a Flame Ionization detector (FID). The FAMEs showed inhibitory activity against all three microorganisms and thereby exhibited both anti-bacterial and anti-candidal activity. GC-FID analysis reveals about 30 different FAMEs. Out of these, various pharmacologically active FAMEs like stearic acid methyl ester (C18:0) (0.6% w/w), oleic acid methyl ester (C18:1) (1% w/w), linoleic acid methyl ester (C18:2) (1.40% w/w), linolenic acid methyl ester (C18:3) (6.26%), eicosapentanoic acid methyl ester (C20:5) (1.13% w/w), erucic acid methyl ester (C22:1) (1.03% w/w) and docosahexenoic acid methyl ester (C22:6) (2.27% w/w) were detected, which accounted for the bioactivity. These results clearly indicate that the FAMEs of S. bijugatus var. bicellularis have strong antimicrobial properties and could thus be used as an effective source against microbial diseases.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Urban circular bioeconomy (UrCirBio), Bharathidasan University, King Saud University College of Science
Contributors: Mubarakali, D., Praveenkumar, R., Shenbagavalli, T., Mari Nivetha, T., Parveez Ahamed, A., Al-Dhabi, N. A., Thajuddin, N.
Number of pages: 5
Pages: 11552-11556
Publication date: 28 Nov 2012
Peer-reviewed: Yes

Publication information

Journal: RSC Advances
Volume: 2
Issue number: 30
ISSN (Print): 2046-2069
Ratings: 
  • Scopus rating (2012): CiteScore 2.4 SJR 0.872 SNIP 0.619
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all)
Source: Scopus
Source ID: 84868128339

Research output: Contribution to journalArticleScientificpeer-review

Improving the effect of a nanoscale barrier coating on BOPP film properties by surface pretreatments

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Engineering materials science and solutions (EMASS), Lappeenranta University of Technology, Paper Converting and Packaging Technology
Contributors: Lahtinen, K., Lahti, J., Johansson, P., Seppänen, T., Cameron, D. C.
Number of pages: 25
Pages: 469-493
Publication date: 2013

Host publication information

Title of host publication: 14th European PLACE Conference 2013
Volume: 1
Publisher: TAPPI Press
ISBN (Electronic): 9781510815568
ASJC Scopus subject areas: Media Technology, Chemical Engineering(all), Chemistry(all), Mechanical Engineering, Materials Science(all)
Source: Scopus
Source ID: 84962833172

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone

T-cell protein tyrosine phosphatase (TCPTP) is a ubiquitously expressed non-receptor protein tyrosine phosphatase. It is involved in the negative regulation of many cellular signaling pathways. Thus, activation of TCPTP could have important therapeutic applications in diseases such as cancer and inflammation. We have previously shown that the α-cytoplasmic tail of integrin α1β1 directly binds and activates TCPTP. In addition, we have identified in a large-scale high-throughput screen six small molecules that activate TCPTP. These small molecule activators include mitoxantrone and spermidine. In this study, we have investigated the molecular mechanism behind agonist-induced TCPTP activation. By combining several molecular modeling and biochemical techniques, we demonstrate that α1-peptide and mitoxantrone activate TCPTP via direct binding to the catalytic domain, whereas spermidine does not interact with the catalytic domain of TCPTP in vitro. Furthermore, we have identified a hydrophobic groove surrounded by negatively charged residues on the surface of TCPTP as a putative binding site for the α1-peptide and mitoxantrone. Importantly, these data have allowed us to identify a new molecule that binds to TCPTP, but interestingly cannot activate its phosphatase activity. Accordingly, we describe here mechanism of TCPTP activation by mitoxantrone, the cytoplasmic tail of α1-integrin, and a mitoxantrone-like molecule at the atomic level. These data provide invaluable insight into the development of novel TCPTP activators, and may facilitate the rational discovery of small-molecule cancer therapeutics.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Jyväskylän yliopisto, Turku Centre for Biotechnology, Turun Yliopisto/Turun Biomateriaalikeskus, School of Management (JKK)
Contributors: Ylilauri, M., Mattila, E., Nurminen, E. M., Käpylä, J., Niinivehmas, S. P., Määttä, J. A., Pentikäinen, U., Ivaska, J., Pentikäinen, O. T.
Number of pages: 10
Pages: 1988-1997
Publication date: 2013
Peer-reviewed: Yes

Publication information

Journal: Biochimica et biophysica acta: proteins and proteomics
Volume: 1834
Issue number: 10
ISSN (Print): 1570-9639
Ratings: 
  • Scopus rating (2013): CiteScore 3.71 SJR 1.854 SNIP 1.152
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Biophysics, Biochemistry, Molecular Biology
Keywords: Differential scanning fluorimetry, Integrin, Isothermal titration calorimetry, Mitoxantrone, Molecular dynamics simulation, T-cell protein tyrosine phosphatase
Source: Scopus
Source ID: 84884495216

Research output: Contribution to journalArticleScientificpeer-review

A 'clusters-in-liquid' method for calculating infrared spectra identifies the proton-transfer mode in acidic aqueous solutions

In liquid water the transfer of an excess proton between two water molecules occurs through the Zundel cation, H 2 O···H + ···OH 2. The proton-transfer mode is the asymmetric stretch of the central O···H + ···O moiety, but there is no consensus on its identification in the infrared spectra of acidic aqueous solutions. Also, in experiments with protonated gas-phase water clusters, its position shifts with cluster size, which makes its relationship with solution spectra unclear. Here we introduce a 'clusters-in-liquid' approach for calculating the infrared spectrum from any set of charges, even single protons. We apply this procedure to multistate empirical valence-bond trajectories of protonated liquid water and to ab initio molecular dynamics of the protonated water dimer and hexamer in the gas phase. The calculated proton-transfer mode is manifested in both systems as a peak near 1,740% cm -1, in quantitative agreement with a band of similar frequency in the experimental infrared spectrum of protonated water clusters.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Tallinn Technical University, Institute of Chemistry, Hebrew University of Jerusalem
Contributors: Kulig, W., Agmon, N.
Number of pages: 7
Pages: 29-35
Publication date: Jan 2013
Peer-reviewed: Yes

Publication information

Journal: Nature Chemistry
Volume: 5
Issue number: 1
ISSN (Print): 1755-4330
Ratings: 
  • Scopus rating (2013): CiteScore 12.35 SJR 8.691 SNIP 3.666
Original language: English
ASJC Scopus subject areas: Chemistry(all), Chemical Engineering(all)
Source: Scopus
Source ID: 84871565081

Research output: Contribution to journalArticleScientificpeer-review

A potential nonthrombogenic small-diameter vascular scaffold with polyurethane/poly(ethylene glycol) hybrid materials by electrospinning technique

A small-diameter vascular graft (inner diameter 4 mm) was fabricated from polyurethane (PU) and poly(ethylene glycol) (PEG) solutions by electrospinning technology. The fiber diameter decreased from 1023±185 nm to 394±106 nm with increasing weight ratio of PEG in electrospinning solutions. The PU/PEG scaffolds showed randomly nanofibrous morphology and well-interconnected porous structure. The hydrophilicity of these scaffolds was improved significantly with increasing weight ratio of PEG. The mechanical properties of electrospun PU/PEG scaffolds were obviously different from that of pure PU scaffold, which was caused by plasticizing or hardening effect imparted by PEG composition. Under hydrated state, the PU/PEG scaffolds demonstrated low mechanical performance due to the hydrophilic property of materials. Compared with dry PU/PEG scaffolds with the same weight ratio of PEG, the tensile strength and elastic modulus of hydrated PU/PEG scaffolds decreased significantly, while the elongation at break increased. The results demonstrated that the electrospun PU/PEG hybrid tubular scaffolds are potential candidates for artificial blood vessels.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Tianjin University, School of Chemical Engineering and Technology
Contributors: Wang, H., Feng, Y., Zhao, H., Fang, Z., Khan, M., Guo, J.
Number of pages: 5
Pages: 1578-1582
Publication date: Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Journal Nanoscience and Nanotechnology
Volume: 13
Issue number: 2
ISSN (Print): 1533-4880
Ratings: 
  • Scopus rating (2013): CiteScore 1.26 SJR 0.339 SNIP 0.545
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Chemistry(all), Materials Science(all), Bioengineering, Biomedical Engineering
Keywords: Electrospinning, Nanofiber, Poly(ethylene glycol), Polyurethane, Vascular scaffold
Source: Scopus
Source ID: 84876246258

Research output: Contribution to journalArticleScientificpeer-review

Density functional theory study of FePdn (n = 2-14) clusters and interactions with small molecules

First-principles calculations have been conducted to investigate the properties of FePdn (n = 2-14) clusters. In the lowest energy structures of FePdn clusters, the Fe atom gradually moves from the convex to the surface, and then to the interior site with the number of Pd atoms increasing from 2 to 14. The magnetic moments of Pdn clusters have been enhanced by the doping of Fe impurity. Furthermore, the adsorption of small molecules, including NH3, H2O, CO, H2, and O2, on the higher stability of FePdn (n = 5, 7, 10, and 12) clusters were studied. The lowest energy adsorption structures are obtained for each molecule. On the whole, the adsorption energies vary as the order of Ea(H2O) <Ea(H2) <E a(NH3) <Ea(O2) <E a(CO). NH3, CO and H2 molecules prefer to adsorb on the FePd10 cluster with the highest adsorption energy, while H2O and O2 are more like to adsorb on the FePd 5. The magnetic moments of FePdn clusters are reduced with the adsorption of molecules.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Northwest University China, National Laboratory of Solid State Microstructures, Nanjing University, Institute of Photonics and Photo-technology
Contributors: Ma, L., Wang, J., Hao, Y., Wang, G.
Number of pages: 8
Pages: 166-173
Publication date: Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Computational Materials Science
Volume: 68
ISSN (Print): 0927-0256
Ratings: 
  • Scopus rating (2013): CiteScore 2.15 SJR 0.951 SNIP 1.306
Original language: English
ASJC Scopus subject areas: Computer Science(all), Chemistry(all), Materials Science(all), Mechanics of Materials, Physics and Astronomy(all), Computational Mathematics
Keywords: Cluster, Density functional theory, Small molecule adsorption
Source: Scopus
Source ID: 84869874680

Research output: Contribution to journalArticleScientificpeer-review

Growth behavior and magnetic properties of spherical uranium oxide nanoclusters

The growth behavior and magnetic properties of spherical uranium oxide nanoclusters have been investigated using the generalized gradient approximation (GGA) to density functional theory (DFT). The geometries of UnO m clusters remain the Oh symmetry after DFT relaxation. The largest binding energy corresponds to the cluster with the smallest deviation from the bulk (UO2) ratio. The electronic structures and magnetic properties of these nanoclusters are presented. We find the chemical bonding between the U and O atoms has a significant ionic character. The reduction of magnetism in the inner positions can be understood by the charge transfer and the hybridization between U atoms and the neighboring O atoms.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Texas at Arlington
Contributors: Ma, L., Ray, A. K.
Number of pages: 7
Pages: 334-340
Publication date: Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Computational and Theoretical Nanoscience
Volume: 10
Issue number: 2
ISSN (Print): 1546-1955
Ratings: 
  • Scopus rating (2013): CiteScore 0.96 SJR 0.384 SNIP 0.593
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Electrical and Electronic Engineering, Materials Science(all), Computational Mathematics, Chemistry(all)
Keywords: Growth behavior, Magnetism, Nanoclusters, Uranium oxide
Source: Scopus
Source ID: 84876525693

Research output: Contribution to journalArticleScientificpeer-review

Networking of ionic liquid modified CNTs in SSBR

Carbon nanotubes (CNTs) were modified using an ionic liquid (IL) and were admixed with a non-polar solution styrene butadiene rubber (SSBR). A local re-agglomeration of ionic liquid modified CNTs (m-CNTs) was found to occur in the SSBR composites, which was confirmed from transmission electron micrographs, as IL cannot couple CNTs and elastomer in order to maintain the disentangled state of the tubes. The conducting networks were established as a consequence of agglomerate-tube percolation and the maximum electrical conductivity of the investigated samples was found to be ∼0.01 S/cm. The reinforcing effect of m-CNTs was not profound in the composites due to the plasticizing nature of IL in non-polar SSBR.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Vodafone Department of Mobile Communications Systems, Leibniz-Institut für Polymerforschung Dresden E.V.
Contributors: Subramaniam, K., Das, A., Simon, F., Heinrich, G.
Number of pages: 8
Pages: 345-352
Publication date: Feb 2013
Peer-reviewed: Yes

Publication information

Journal: European Polymer Jounal
Volume: 49
Issue number: 2
ISSN (Print): 0014-3057
Ratings: 
  • Scopus rating (2013): CiteScore 3.43 SJR 1.087 SNIP 1.66
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Organic Chemistry, Polymers and Plastics
Keywords: Carbon nanotubes, Electrical properties, Ionic liquids, Mechanical properties, Nanocomposites
Source: Scopus
Source ID: 84873192692

Research output: Contribution to journalArticleScientificpeer-review

Chemically tailored dielectric-to-metal transition for the design of metamaterials from nanoimprinted colloidal nanocrystals

We demonstrate optical metamaterial design using colloidal gold nanocrystal building blocks. In the solid state, chemically exchanging the nanocrystals' surface-capping molecules provides a tailorable dielectric-to-metal transition exhibiting a 1010 range in DC conductivity and dielectric permittivity ranging from everywhere positive to everywhere negative throughout the visible-to-near-IR. Direct, wide-area nanoimprinting of subwavelength superstructures at room temperature, on plastic and glass substrates, affords plasmonic resonances ranging from 660 to 1070 nm, in agreement with numerical simulations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Pennsylvania, Department of Electrical and Systems Engineering
Contributors: Fafarman, A. T., Hong, S. H., Caglayan, H., Ye, X., Diroll, B. T., Paik, T., Engheta, N., Murray, C. B., Kagan, C. R.
Number of pages: 8
Pages: 350-357
Publication date: 13 Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Nano Letters
Volume: 13
Issue number: 2
ISSN (Print): 1530-6984
Ratings: 
  • Scopus rating (2013): CiteScore 14.23 SJR 9.081 SNIP 3.355
Original language: English
ASJC Scopus subject areas: Bioengineering, Chemistry(all), Materials Science(all), Condensed Matter Physics, Mechanical Engineering
Keywords: ammonium thiocyanate, dielectric function, gold nanoparticles, ligand exchange, Plasmonics, soft lithography

Bibliographical note

EXT="Caglayan, Humeyra"

Source: Scopus
Source ID: 84873680258

Research output: Contribution to journalArticleScientificpeer-review

Aqueous guanidinium-carbonate interactions by molecular dynamics and neutron scattering: Relevance to ion-protein interactions

Guanidinium carbonate was used in this study as a simple proxy for the biologically relevant arginine-carbonate interactions in water. Molecular dynamics (MD) simulations of guanidinium carbonate were performed with nonpolarizible water using two implementations of the ion force fields. In the first, the ions had full charges, while in the second, the ions had reduced charges in order to effectively account for electronic polarization effects of water. The results from the simulations were then compared to data from previous neutron scattering experiments. It was found that there were significant discrepancies between the full charge force field MD simulations and the experimental results due to excessive ion pairing and clustering in the former. In contrast, reducing the ionic charges yields a more regular solution with a simulated structure, which fits well the experimental data.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Division of Organic Chemistry and Biochemistry, Bijenička Cesta 54
Contributors: Vazdar, M., Jungwirth, P., Mason, P. E.
Number of pages: 5
Pages: 1844-1848
Publication date: 14 Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 6
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Surfaces, Coatings and Films, Physical and Theoretical Chemistry, Materials Chemistry
Source: Scopus
Source ID: 84873899176

Research output: Contribution to journalArticleScientificpeer-review

Fabrication of a sub-10 nm silicon nanowire based ethanol sensor using block copolymer lithography

This paper details the fabrication of ultrathin silicon nanowires (SiNWs) on a silicon-on-insulator (SOI) substrate as an electrode for the electro-oxidation and sensing of ethanol. The nanowire surfaces were prepared by a block copolymer (BCP) nanolithographic technique using low molecular weight symmetric poly(styrene)-block-poly(methyl methacrylate) (PS-b-PMMA) to create a nanopattern which was transferred to the substrate using plasma etching. The BCP orientation was controlled using a hydroxyl-terminated random polymer brush of poly(styrene)-random-poly(methyl methacrylate) (HO-PS-r-PMMA). TEM cross-sections of the resultant SiNWs indicate an anisotropic etch process with nanowires of sub-10 nm feature size. The SiNWs obtained by etching show high crystallinity and there is no evidence of defect inclusion or amorphous region production as a result of the pattern transfer process. The high density of SiNWs at the substrate surface allowed the fabrication of a sensor for cyclic voltammetric detection of ethanol. The sensor shows better sensitivity to ethanol and a faster response time compared to widely used polymer nanocomposite based sensors.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Materials Chemistry and Analysis Group, University College Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Tyndall National Institute at National University of Ireland, Cork, Collinstown Industrial Estate
Contributors: Rasappa, S., Borah, D., Faulkner, C. C., Lutz, T., Shaw, M. T., Holmes, J. D., Morris, M. A.
Publication date: 15 Feb 2013
Peer-reviewed: Yes

Publication information

Journal: Nanotechnology
Volume: 24
Issue number: 6
Article number: 065503
ISSN (Print): 0957-4484
Ratings: 
  • Scopus rating (2013): CiteScore 2.74 SJR 1.602 SNIP 1.27
Original language: English
ASJC Scopus subject areas: Bioengineering, Chemistry(all), Electrical and Electronic Engineering, Mechanical Engineering, Mechanics of Materials, Materials Science(all)
Source: Scopus
Source ID: 84872971946

Research output: Contribution to journalArticleScientificpeer-review

Optical vortex generation in nematic liquid crystal light valves

A nematic liquid crystal light valve (LCLV) is made by using a photosensitive material as one of the cell-confining walls. The liquid crystals (LCs) are homeotropically aligned and with a negative anisotropy; therefore, they naturally produce topological defects when they reorient under the application of an electric field. In our work, we show that by sending circularly polarized light beams onto the photosensitive wall of the light valve, it is possible to locally induce the reorientation and to generate vortex-like defects that remain, each stable and trapped at the chosen location. We demonstrate the ability of the system to create optical vortices with opposite topological charge that, consistently with angular momentum conservation, both derive from the same defect created in the LC texture.The efficiency of the spin-to-orbital angular momentum conversion is measured as a function of the system control parameters, namely the low-frequency electric field applied to the light valve and the intensity of the optical beam inducing the matter defect.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, CNRS, NooEL (Nonlinear Optics and OptoElectronics Laboratory), University “Roma Tre”
Contributors: Barboza, R., Bortolozzo, U., Assanto, G., Residori, S.
Number of pages: 7
Pages: 24-30
Publication date: 1 Mar 2013
Peer-reviewed: Yes

Publication information

Journal: Molecular Crystals and Liquid Crystals
Volume: 572
Issue number: 1
ISSN (Print): 1542-1406
Ratings: 
  • Scopus rating (2013): CiteScore 0.52 SJR 0.279 SNIP 0.38
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics, Materials Science(all)
Keywords: Liquid crystal light valves, optical vortices, spin-to-orbital angular momentum conversion, topological defects
Source: Scopus
Source ID: 84876183883

Research output: Contribution to journalArticleScientificpeer-review

Molecularly functionalized silicon substrates for orientation control of the microphase separation of PS-b-PMMA and PS-b-PDMS block copolymer systems

The use of block copolymer (BCP) thin films to generate nanostructured surfaces for device and other applications requires precise control of interfacial energies to achieve the desired domain orientation. Usually, the surface chemistry is engineered through the use of homo- or random copolymer brushes grown or attached to the surface. Herein, we demonstrate a facile, rapid, and tunable approach to surface functionalization using a molecular approach based on ethylene glycol attachment to the surface. The effectiveness of the molecular approach is demonstrated for the microphase separation of PS-b-PMMA and PS-b-PDMS BCPs in thin films and the development of nanoscale features at the substrate.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Tyndall National Institute at National University of Ireland, Cork, Selcuk University, Materials Chemistry and Analysis Group, University College Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Collinstown Industrial Estate
Contributors: Borah, D., Ozmen, M., Rasappa, S., Shaw, M. T., Holmes, J. D., Morris, M. A.
Number of pages: 12
Pages: 2809-2820
Publication date: 5 Mar 2013
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 29
Issue number: 9
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2013): CiteScore 4.55 SJR 1.896 SNIP 1.333
Original language: English
ASJC Scopus subject areas: Electrochemistry, Condensed Matter Physics, Surfaces and Interfaces, Materials Science(all), Spectroscopy
Source: Scopus
Source ID: 84874584704

Research output: Contribution to journalArticleScientificpeer-review

Site-specific analysis of dipole polarizabilities of heterogeneous systems: Iron-doped Sin (n = 1-14) clusters

Following the recent work of decomposing the total dipole moment and polarizability of a homogeneous system into site-specific contributions, we extend the study to the heterogeneous systems of iron-doped Sin (n = 1-14) clusters by introducing a weighting function. The structure-/shape- and size-specific aspects of the dipole moments and polarizabilities of Si nFe (n = 1-14) clusters are analyzed and compared with pure silicon clusters. It is shown that the polarizabilities associated with the individual constituent atoms vary considerably with the structure/shape of the cluster and the location of the atom or site within a given structure. For atoms at peripheral sites, the polarizabilities are substantially larger than atoms at the interior sites, and the more peripheral an atom is, the larger is its polarizability. The polarizability of the Fe atom in SinFe clusters decreases as the cluster size increases. This is related to the position of Fe atom in SinFe clusters and indicates significant screening of the interior of the cluster by its surface. The correlation between the anisotropy of the total polarizability and the anisotropy of the cluster shape is also analyzed. Comparing with pure Sin clusters, the polarizabilities of Si atoms are increased after Fe atom doping. The structures are more compact for SinFe than the same sizes of Sin+1 clusters and the polarizabilities of SinFe are smaller than Sin+1 for the sizes of n = 7-14.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Northwest University China, National Laboratory of Solid State Microstructures, Nanjing University, Institute of Photonics and Photo-technology
Contributors: Ma, L., Wang, J., Wang, G.
Publication date: 7 Mar 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Physics
Volume: 138
Issue number: 9
Article number: 094304
ISSN (Print): 0021-9606
Ratings: 
  • Scopus rating (2013): CiteScore 2.95 SJR 1.559 SNIP 1.182
Original language: English
ASJC Scopus subject areas: Physics and Astronomy(all), Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84874852980

Research output: Contribution to journalArticleScientificpeer-review

Biomimetic zinc chlorin-poly(4-vinylpyridine) assemblies: Doping level dependent emission-absorption regimes

To develop biomimetic dye-polymers for photonics, two different types of Zn chlorin-poly(4-vinylpyridine) (P4VP) assemblies were prepared by varying Zn pyro-pheophorbide a methylester (ZnPPME) and Zn 31-OH-pyro- pheophorbide a methylester (Zn-31-OH-PPME) doping levels. 1H NMR spectroscopy and diffusion ordered NMR spectroscopy (DOSY) studies revealed that a coordinative interaction between Zn chlorin and P4VP was predominant in solution (d5-nitrobenzene). Small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) characterization of bulk samples of polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) doped with variable amounts of Zn chlorin showed that the pigment doping transformed the native cylindrical block copolymer nanostructures to lamellar morphologies. The result indicates that the pyridine moiety-Zn chlorin coordination is stronger than the aggregation tendency between the pigment molecules even in the solid state. UV-Vis absorption spectroscopy studies of a Zn chlorin-P4VP thin film showed characteristic monomeric chlorin spectra, while steady-state fluorescence spectroscopy displayed quenching of fluorescence and time-resolved studies indicated shortening of fluorescence lifetimes with an increasing chlorin doping level. Notably, time-resolved fluorescence spectroscopy revealed that the lifetime decay changed from monoexponential to biexponential above 0.5 wt% (ca. 0.001 equiv.) loadings. The Förster analysis implies that excitonic chlorin-chlorin interactions are observed in the thin films when the distance between the pigment molecules is approximately 50 Å. The Zn chlorin-P4VP solid films emit strongly up to 1 wt% (ca. 0.002 equiv.) doping level above which the chlorin-chlorin interactions start to linearly dominate with an increase of doping level, while with 10 wt% (ca. 0.02 equiv.) loading less than 10% of fluorescence remains. Doping levels up to 300 wt% (0.5 equiv.) can be used in absorbing materials without the formation of chlorin aggregates. These defined optical response regions pave the way for photonic materials based on biopigment assemblies.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Aalto University, University of Helsinki, Department of Applied Physics
Contributors: Pale, V., Nikkonen, T., Vapaavuori, J., Kostiainen, M., Kavakka, J., Selin, J., Tittonen, I., Helaja, J.
Number of pages: 8
Pages: 2166-2173
Publication date: 21 Mar 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Materials Chemistry C
Volume: 1
Issue number: 11
ISSN (Print): 2050-7534
Original language: English
ASJC Scopus subject areas: Chemistry(all), Materials Chemistry
Source: Scopus
Source ID: 84875847322

Research output: Contribution to journalArticleScientificpeer-review

Understanding the reinforcing behavior of expanded clay particles in natural rubber compounds

We report the unusual mechanical percolation behavior of expanded clay nanoparticles in a natural rubber (NR) matrix. This phenomenon is discussed in terms of fractal dimensions of the nanoparticle cluster. Highly exfoliated structures of nanoparticles in NR are obtained by a process we call the 'propping-open approach'. The impact of filler dispersion and rubber-filler interactions on the viscoelastic behavior of NR-clay nanocomposites is systematically investigated. We observe non-linear viscoelastic behavior (Payne effect) at very low nanoparticle concentrations which we attribute to the formation of a network-like structure of the exfoliated clay particles. We rely on the Kraus and Maier-Göritz models to interpret such nonlinear viscoelastic behavior. We find that the chain mobility of the NR is greatly reduced based on the viscoelastic master curves. The value of the mechanical percolation threshold (φp) and the fractal nature of nanoparticle clusters are determined through an analysis of the experimental data based on a theory put forward by Huber and Vilgis. The nature of rubber-filler interactions is further understood from swelling experiments utilizing the Kraus and Cunneen-Russell equations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Vodafone Department of Mobile Communications Systems, Leibniz-Institut für Polymerforschung Dresden E.V.
Contributors: Rooj, S., Das, A., Stöckelhuber, K. W., Wang, D. Y., Galiatsatos, V., Heinrich, G.
Number of pages: 11
Pages: 3798-3808
Publication date: 14 Apr 2013
Peer-reviewed: Yes

Publication information

Journal: Soft Matter
Volume: 9
Issue number: 14
ISSN (Print): 1744-683X
Ratings: 
  • Scopus rating (2013): CiteScore 4.2 SJR 1.748 SNIP 1.193
Original language: English
ASJC Scopus subject areas: Chemistry(all), Condensed Matter Physics
Source: Scopus
Source ID: 84875027182

Research output: Contribution to journalArticleScientificpeer-review

Nanoindentation study of light-induced softening of supramolecular and covalently functionalized azo polymers

Nanoindentation studies on thin films of the widely used azo polymer pDR1A and a supramolecular polymer-azobenzene complex p4VP(DY7)0.5 demonstrate significant light-induced softening upon visible-light irradiation due to trans-cis-trans photoisomerization of the azobenzene units. More specifically, the strain-rate sensitivities of pDR1A and p4VP(DY7)0.5 upon 532 nm irradiation increase by 80% and 120%, respectively. These results imply a photosoftening contribution to the mechanisms of light-induced surface patterning of azo polymers and the photomechanical effect. The finding that under the experimental conditions used photosoftening is more significant in the supramolecular complex than in the covalently functionalized polymer highlights the potential of noncovalent functionalization strategies in designing materials with efficient photomechanical response, and nanoindentation provides a powerful technique to quantify the connection between the photoinduced changes in mechanical properties and photoinduced macroscopic movement of azo polymer films.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Department of Applied Physics, Aalto University, McGill University
Contributors: Vapaavuori, J., Mahimwalla, Z., Chromik, R. R., Kaivola, M., Priimagi, A., Barrett, C. J.
Number of pages: 5
Pages: 2806-2810
Publication date: 28 Apr 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Materials Chemistry C
Volume: 1
Issue number: 16
ISSN (Print): 2050-7534
Original language: English
ASJC Scopus subject areas: Chemistry(all), Materials Chemistry
Source: Scopus
Source ID: 84879524974

Research output: Contribution to journalArticleScientificpeer-review

Immobilized bioactive agents onto polyurethane surface with heparin and phosphorylcholine group

Heparin (HEP) and phosphorylcholine groups (PC) were grafted onto the polyurethane (PU) surface in order to improve biocompatibility and anticoagulant activity. After the surface grafting sites of PU were amplified with the primary amine groups of polyethylenimine (PEI), heparin was covalently linked onto the surface by the reaction between the amino group and the carboxyl group. PC groups were covalently immobilized on the PU-PEI surface through the reaction between the amino group and the aldehyde group of phosphorylcholine glyceraldehyde (PCGA). The surface density of primary amine groups was determined by a ninhydrin assay. The amino group density reached a maximum of 0.88 μmol/cm2 upon incorporation of 10 wt% PEI. The amount of heparin covalently immobilized on the PU-PEI surface was determined by the toluidine blue method. The grafting chemistry resulted in the comparatively dense immobilization of HEP (2.6 μg/cm2) and PC to the PU-PEI surfaces. The HEP and PC modified surfaces were characterized by water uptake (PU 0.15 mg/cm2, PU-PEI 3.54 mg/cm2, PU-HEP 2.04 mg/cm2, PU-PC 2.38 mg/cm2), water contact angle (PU 95.3, PU-PEI 34.0, PU-HEP 39.5, PU-PC 37.2), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and scanning electron microscope (SEM). The results demonstrated that the PUPEI surface was successfully grafted with HEP and PC. The hydrophilicity and hemocompatibility of these grafted surfaces were significantly improved. These results suggested that the PU-HEP and PU-PC composite films are promising candidates for blood contacting tissue engineering.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Tianjin University, Shihezi University, School of Chemical Engineering and Technology, Tianjin Chest Hospital
Contributors: Tan, M., Feng, Y., Wang, H., Zhang, L., Khan, M., Guo, J., Chen, Q., Liu, J.
Number of pages: 9
Pages: 541-549
Publication date: May 2013
Peer-reviewed: Yes

Publication information

Journal: Macromolecular Research
Volume: 21
Issue number: 5
ISSN (Print): 1598-5032
Ratings: 
  • Scopus rating (2013): CiteScore 1.66 SJR 0.553 SNIP 0.769
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Chemical Engineering(all)
Keywords: hemocompatibility, heparin, phosphorylcholine group, polyethylenimine, polyurethane
Source: Scopus
Source ID: 84877763417

Research output: Contribution to journalArticleScientificpeer-review

Screening pretreatment methods to enhance thermophilic anaerobic digestion of pulp and paper mill wastewater treatment secondary sludge

The effect of hydrothermal (150°C for 10min and 70°C for 40min), enzymatic (Accelerase 1500, 0.07g/g volatile solids (VS)), ultrasound (45kHz for 30min) and chemical pretreatments (HNO3 at pH3 and NaOH at pH12) alone or in combination on the chemical composition and methane yield of the pulp and paper mill secondary sludge was studied in batch assays at 55°C. In total, 12 different pretreatment combinations were compared. Chemical analyses showed that all pretreatments except for HNO3 and ultrasound pretreatments improved the organic matter solubilization. Among the studied pretreatments, hydrothermal (150°C, 10min) pretreatment alone or in combination with enzymatic and/or ultrasound pretreatment had the highest impact on sludge solubilization and methane yield. The increase in methane yield was 31% (from 108ml/g VSoriginal to 141ml/gVSoriginal). In addition, enzymatic pretreatment also improved the methane yields but only when combined with hydrothermal pretreatment at 150°C or ultrasound+hydrothermal pretreatment at 150°C. On the other hand, ultrasound pretreatment did not improve the methane yields while acid and alkaline pretreatments resulted in lower methane yields than control. Improved hydrolysis and higher methane production rates noticed in assays subjected to hydrothermal pretreatment alone or in combination with enzymes and/or ultrasound could make these treatments more attractive in reducing the retention times required during full-scale anaerobic digestion of pulp and paper mill wastewater sludges. © 2013 Elsevier B.V.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Tampere University of Technology, Department of Chemistry and Bioengineering, Urban circular bioeconomy (UrCirBio), Jyväskylän yliopisto, University of Jyväskylä
Contributors: Bayr, S., Kaparaju, P., Rintala, J.
Number of pages: 8
Pages: 479-486
Publication date: 1 May 2013
Peer-reviewed: Yes

Publication information

Journal: Chemical Engineering Journal
Volume: 223
ISSN (Print): 1385-8947
Ratings: 
  • Scopus rating (2013): CiteScore 4.59 SJR 1.597 SNIP 1.902
Original language: English
ASJC Scopus subject areas: Chemical Engineering(all), Chemistry(all), Industrial and Manufacturing Engineering, Environmental Chemistry
Keywords: Anaerobic digestion, Methane yield, Pretreatment, Pulp and paper mill, Secondary sludge

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2013-11-29<br/>Publisher name: Elsevier BV

Source: researchoutputwizard
Source ID: 1974

Research output: Contribution to journalArticleScientificpeer-review

Depth profiling of PLGA copolymer in a novel biomedical bilayer using confocal raman spectroscopy

Confocal Raman spectroscopy was undertaken to identify separate layers of PLGA and gentamicin sulfate (GS) coatings on a titanium alloy substrate for a novel drug-delivery system. Additionally, it was found that it was possible to measure the layer thickness and uniformity of the PLGA accurately by detecting intensity and wavelength changes in the vibrational bands of the copolymer bonds. Further analysis of the materials was done using FIB, SEM/EDX, and profilometry; these techniques were used to confirm the findings of the Raman data. It was determined that the substrate was extremely rough and therefore the coating was not uniform in thickness but the materials were uniformly dispersed. Most importantly, two distinct GS and PLGA layers were present.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, University College Cork, DePuy Ireland, Trinity College Dublin, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN)
Contributors: McManamon, C., Delaney, P., Kavanagh, C., Wang, J. J., Rasappa, S., Morris, M. A.
Number of pages: 6
Pages: 5905-5910
Publication date: 14 May 2013
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 29
Issue number: 19
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2013): CiteScore 4.55 SJR 1.896 SNIP 1.333
Original language: English
ASJC Scopus subject areas: Electrochemistry, Condensed Matter Physics, Surfaces and Interfaces, Materials Science(all), Spectroscopy
Source: Scopus
Source ID: 84877784340

Research output: Contribution to journalArticleScientificpeer-review

Surface properties and interaction forces of biopolymer-doped conductive polypyrrole surfaces by atomic force microscopy

Surface properties and electrical charges are critical factors elucidating cell interactions on biomaterial surfaces. The surface potential distribution and the nanoscopic and microscopic surface elasticity of organic polypyrrole-hyaluronic acid (PPy-HA) were studied by atomic force microscopy (AFM) in a fluid environment in order to explain the observed enhancement in the attachment of human adipose stem cells on positively charged PPy-HA films. The electrostatic force between the AFM tip and a charged PPy-HA surface, the tip-sample adhesion force, and elastic moduli were estimated from the AFM force curves, and the data were fitted to electrostatic double-layer and elastic contact models. The surface potential of the charged and dried PPy-HA films was assessed with Kelvin probe force microscopy (KPFM), and the KPFM data were correlated to the fluid AFM data. The surface charge distribution and elasticity were both found to correlate well with the nodular morphology of PPy-HA and to be sensitive to the electrochemical charging conditions. Furthermore, a significant change in the adhesion was detected when the surface was electrochemically charged positive. The results highlight the potential of positively charged PPy-HA as a coating material to enhance the stem cell response in tissue-engineering scaffolds.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), VTT Technical Research Centre of Finland, University of Wollongong
Contributors: Pelto, J. M., Haimi, S. P., Siljander, A. S., Miettinen, S. S., Tappura, K. M., Higgins, M. J., Wallace, G. G.
Number of pages: 10
Pages: 6099-6108
Publication date: 21 May 2013
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 29
Issue number: 20
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2013): CiteScore 4.55 SJR 1.896 SNIP 1.333
Original language: English
ASJC Scopus subject areas: Materials Science(all), Condensed Matter Physics, Surfaces and Interfaces, Spectroscopy, Electrochemistry
Source: Scopus
Source ID: 84878234949

Research output: Contribution to journalArticleScientificpeer-review

Cation-specific effects on enzymatic catalysis driven by interactions at the tunnel mouth

Cationic specificity which follows the Hofmeister series has been established for the catalytic efficiency of haloalkane dehalogenase LinB by a combination of molecular dynamics simulations and enzyme kinetic experiments. Simulations provided a detailed molecular picture of cation interactions with negatively charged residues on the protein surface, particularly at the tunnel mouth leading to the enzyme active site. On the basis of the binding affinities, cations were ordered as Na+ > K+ > Rb+ > Cs+. In agreement with this result, a steady-state kinetic analysis disclosed that the smaller alkali cations influence formation and productivity of enzyme-substrate complexes more efficiently than the larger ones. A subsequent systematic investigation of two LinB mutants with engineered charge in the cation-binding site revealed that the observed cation affinities are enhanced by increasing the number of negatively charged residues at the tunnel mouth, and vice versa, reduced by decreasing this number. However, the cation-specific effects are overwhelmed by strong electrostatic interactions in the former case. Interestingly, the substrate inhibition of the mutant LinB L177D in the presence of chloride salts was 7 times lower than that of LinB wild type in glycine buffer. Our work provides new insight into the mechanisms of specific cation effects on enzyme activity and suggests a potential strategy for suppression of substrate inhibition by the combination of protein and medium engineering.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), International Clinical Research Center, St. Anne's University Hospital Brno, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment, Masaryk University
Contributors: Štěpánková, V., Paterová, J., Damborský, J., Jungwirth, P., Chaloupková, R., Heyda, J.
Number of pages: 9
Pages: 6394-6402
Publication date: 30 May 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 21
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84878363659

Research output: Contribution to journalArticleScientificpeer-review

Cell toxicity and oxidative potential of engine exhaust particles: Impact of using particulate filter or biodiesel fuel blend

The link between emissions of vehicular particulate matter (PM) and adverse health effects is well established. However, the influence of new emission control technologies and fuel types on both PM emissions and health effects has been less well investigated. We examined the health impact of PM emissions from two vehicles equipped with or without a diesel particulate filter (DPF). Both vehicles were powered either with diesel (B0) or a 50% v/v biodiesel blend (B50). The DPF effectively decreased PM mass emissions (∼85%), whereas the fuel B50 without DPF lead to less reduction (∼50%). The hazard of PM per unit distance driven was decreased for the DPF-equipped vehicle as indicated by a reduced cytotoxicity, oxidative, and pro-inflammatory potential. This was not evident and even led to an increase when the hazard was expressed on a per unit of mass basis. In general, the PM oxidative potential was similar or reduced for the B50 compared to the B0 powered vehicle. However, the use of B50 resulted in increased cytotoxicity and IL-6 release in BEAS-2B cells irrespective of the expression metric. This study shows that PM mass reduction achieved by the use of B50 will not necessarily decrease the hazard of engine emissions, while the application of a DPF has a beneficial effect on both PM mass emission and PM hazard.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Urban circular bioeconomy (UrCirBio), National Institute for Public Health and the Environment, Norwegian Institute of Public Health, Aristotle University of Thessaloniki, Laboratory of Applied Thermodynamics, Utrecht University
Contributors: Gerlofs-Nijland, M. E., Totlandsdal, A. I., Tzamkiozis, T., Leseman, D. L. A. C., Samaras, Z., Låg, M., Schwarze, P., Ntziachristos, L., Cassee, F. R.
Number of pages: 8
Pages: 5931-5938
Publication date: 4 Jun 2013
Peer-reviewed: Yes

Publication information

Journal: Environmental Science and Technology
Volume: 47
Issue number: 11
ISSN (Print): 0013-936X
Ratings: 
  • Scopus rating (2013): CiteScore 5.52 SJR 2.952 SNIP 2.094
Original language: English
ASJC Scopus subject areas: Chemistry(all), Environmental Chemistry
Source: Scopus
Source ID: 84878655379

Research output: Contribution to journalArticleScientificpeer-review

Shape-dependent plasmonic response and directed self-assembly in a new semiconductor building block, indium-doped cadmium oxide (ICO)

The influence of particle shape on plasmonic response and local electric field strength is well-documented in metallic nanoparticles. Morphologies such as rods, plates, and octahedra are readily synthesized and exhibit drastically different extinction spectra than spherical particles. Despite this fact, the influence of composition and shape on the optical properties of plasmonic semiconductor nanocrystals, in which free electrons result from heavy doping, has not been well-studied. Here, we report the first observation of plasmonic resonance in indium-doped cadmium oxide (ICO) nanocrystals, which exhibit the highest quality factors reported for semiconductor nanocrystals. Furthermore, we are able to independently control the shape and free electron concentration in ICO nanocrystals, allowing for the influence of shape on the optical response of a plasmonic semiconductor to be conclusively demonstrated. The highly uniform particles may be self-assembled into ordered single component and binary nanocrystal superlattices, and in thin films, exhibit negative permittivity in the near infrared (NIR) region, validating their use as a new class of tunable low-loss plasmonic building blocks for 3-D optical metamaterials.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: University of Pennsylvania, Purdue University, Department of Electrical and Systems Engineering
Contributors: Gordon, T. R., Paik, T., Klein, D. R., Naik, G. V., Caglayan, H., Boltasseva, A., Murray, C. B.
Number of pages: 7
Pages: 2857-2863
Publication date: 12 Jun 2013
Peer-reviewed: Yes

Publication information

Journal: Nano Letters
Volume: 13
Issue number: 6
ISSN (Print): 1530-6984
Ratings: 
  • Scopus rating (2013): CiteScore 14.23 SJR 9.081 SNIP 3.355
Original language: English
ASJC Scopus subject areas: Bioengineering, Chemistry(all), Materials Science(all), Condensed Matter Physics, Mechanical Engineering
Keywords: indium-doped cadmium oxide, metamaterials, nanocrystal superlattices, Plasmonics, shape effects, transparent conducting oxide

Bibliographical note

EXT="Caglayan, Humeyra"

Source: Scopus
Source ID: 84879097164

Research output: Contribution to journalArticleScientificpeer-review

Development and characterization of poly(ε-caprolactone) hollow fiber membranes for vascular tissue engineering

The fabrication of tissue-engineered scaffolds for small-caliber blood vessels still remains a challenge. In the present work, we prepared poly(ε-caprolactone) (PCL) hollow fiber (HF) membranes, suitable for small-diameter blood vessel regeneration, by a phase separation spinning technique. The difficulty of processing PCL, a highly elastic material prone to suffer die swelling by extrusion, was overcome by tailoring the dope solution temperature and extrusion flow rate during the spinning procedure. The influence of the composition of the coagulation bath (water, ethanol, isopropanol) on the HF membrane physico-chemical properties (morphology, transport and mechanical properties) and cell attachment and proliferation was studied. The HF membranes fabricated using ethanol as coagulation bath had the most uniform morphology, good mechanical and transport properties and showed human adipose stem cell attachment and proliferation. Therefore, these fibers are promising scaffolds for small-caliber blood vessel regeneration.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Cantabria, University of Twente
Contributors: Diban, N., Haimi, S., Bolhuis-Versteeg, L., Teixeira, S., Miettinen, S., Poot, A., Grijpma, D., Stamatialis, D.
Number of pages: 9
Pages: 29-37
Publication date: 1 Jul 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Membrane Science
Volume: 438
ISSN (Print): 0376-7388
Ratings: 
  • Scopus rating (2013): CiteScore 5.38 SJR 2.451 SNIP 1.98
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Science(all), Biochemistry, Filtration and Separation
Keywords: Adipose stem cell, Hollow fiber, Phase-inversion, Poly(ε-caprolactone), Vascular regeneration
Source: Scopus
Source ID: 84876440642

Research output: Contribution to journalArticleScientificpeer-review

Photoswitchable hydrogel surface topographies by polymerisation-induced diffusion

Herein, we describe the preparation of patterned photoresponsive hydrogels by using a facile method. This polymer-network hydrogel coating consists of N-isopropylacrylamide (NIPAAM), cross-linking agent tripropylene glycol diacrylate (TPGDA), and a new photochromic spiropyran monoacrylate. In a pre-study, a linear NIPAAM copolymer (without TPGDA) that contained the spiropyran dye was synthesised, which showed relatively fast photoswitching behaviour. Subsequently, the photopolymerisation of a similar monomer mixture that included TPGDA afforded freestanding hydrogel polymer networks. The light-induced isomerisation of protonated merocyanine into neutral spiropyran under slightly acidic conditions resulted in macroscopic changes in the hydrophilicity of the entire polymer film, that is, shrinkage of the hydrogel. The degree of shrinkage could be controlled by changing the chemical composition of the acrylate mixture. After these pre-studies, a hydrogel film with spatially modulated cross-link density was fabricated through polymerisation-induced diffusion, by using a patterned photomask. The resulting smooth patterned hydrogel coating swelled in slightly acidic media and the swelling was higher in the regions with lower cross-linking densities, thus yielding a corrugated surface. Upon exposure to visible light, the surface topography flattened again, thus showing that a hydrogel coating could be created, the topography of which could be controlled by light irradiation.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Laboratory of Functional Organic Materials and Devices, Eindhoven University of Technology
Contributors: Stumpel, J. E., Liu, D., Broer, D. J., Schenning, A. P. H. J.
Number of pages: 6
Pages: 10922-10927
Publication date: 2 Jul 2013
Peer-reviewed: Yes

Publication information

Journal: Chemistry: A European Journal
Volume: 19
Issue number: 33
ISSN (Print): 0947-6539
Ratings: 
  • Scopus rating (2013): CiteScore 5.68 SJR 2.643 SNIP 1.239
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Keywords: hydrogels, photoresponsive materials, polymerization, spiropyran compounds, surface chemistry

Bibliographical note

EXT="Stumpel, Jelle"

Source: Scopus
Source ID: 84881229562

Research output: Contribution to journalArticleScientificpeer-review

Reversal of the hofmeister series: Specific ion effects on peptides

Ion-specific effects on salting-in and salting-out of proteins, protein denaturation, as well as enzymatic activity are typically rationalized in terms of the Hofmeister series. Here, we demonstrate by means of NMR spectroscopy and molecular dynamics simulations that the traditional explanation of the Hofmeister ordering of ions in terms of their bulk hydration properties is inadequate. Using triglycine as a model system, we show that the Hofmeister series for anions changes from a direct to a reversed series upon uncapping the N-terminus. Weakly hydrated anions, such as iodide and thiocyanate, interact with the peptide bond, while strongly hydrated anions like sulfate are repelled from it. In contrast, reversed order in interactions of anions is observed at the positively charged, uncapped N-terminus, and by analogy, this should also be the case at side chains of positively charged amino acids. These results demonstrate that the specific chemical and physical properties of peptides and proteins play a fundamental role in ion-specific effects. The present study thus provides a molecular rationalization of Hofmeister ordering for the anions. It also provides a route for tuning these interactions by titration or mutation of basic amino acid residues on the protein surface.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Pennsylvania State University, Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Texas A and M University
Contributors: Paterová, J., Rembert, K. B., Heyda, J., Kurra, Y., Okur, H. I., Liu, W. R., Hilty, C., Cremer, P. S., Jungwirth, P.
Number of pages: 9
Pages: 8150-8158
Publication date: 11 Jul 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 27
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84880155215

Research output: Contribution to journalArticleScientificpeer-review

Tuning PDMS brush chemistry by UV-O3 exposure for PS-b-PDMS microphase separation and directed self-assembly

The directed self-assembly (DSA) of block copolymer (BCP) thin films could enable a scalable, bottom-up alternative to photolithography for the generation of substrate features. The PS-b-PDMS (polystyrene-b-polydimethylsiloxane) system is attractive as it can be extended toward very small feature sizes as well as having two blocks that can be readily differentiated during pattern transfer. However, PS-b-PDMS offers a considerable challenge because of the chemical differences in the blocks which lead to poor surface-wetting, poor pattern orientation control, and structural instabilities. These challenges can be mitigated by careful definition of the interface chemistry between the substrate and the BCP. Here, we report controlled pattern formation in cylinder forming PS-b-PDMS system by use of a carefully controlled PDMS brush. Control of the brush was achieved using exposure to UV-O3 for varying time. It is demonstrated that this treatment enhances surface wetting and coverage of the BCP. The modified brushes also enable DSA of the BCP on topographically patterned substrates. UV-O3 exposure was also used to reveal the BCP structure and provide an in situ "hard mask" for pattern transfer to the substrate.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Tyndall National Institute at National University of Ireland, Cork, Materials Chemistry and Analysis Group, University College Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin
Contributors: Borah, D., Rasappa, S., Senthamaraikannan, R., Holmes, J. D., Morris, M. A.
Number of pages: 10
Pages: 8959-8968
Publication date: 16 Jul 2013
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 29
Issue number: 28
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2013): CiteScore 4.55 SJR 1.896 SNIP 1.333
Original language: English
ASJC Scopus subject areas: Electrochemistry, Condensed Matter Physics, Surfaces and Interfaces, Materials Science(all), Spectroscopy
Source: Scopus
Source ID: 84880308592

Research output: Contribution to journalArticleScientificpeer-review

Irradiation promoted exchange reaction with disulfide substituents

Exchange reaction between the primary self-assembled monolayer (SAM) on gold and potential molecular substituents capable of forming a SAM on the same substrate can be promoted by electron irradiation. Here we demonstrate that such a promoted reaction can be performed not only with thiols but with disulfides as substituents as well. This extends significantly the assortments of the suitable compounds, resulting in a broader variety of mixed SAMs and chemical patterns which can be fabricated by this technique. The kinetics of the promoted exchange reaction was studied in detail. The feasibility and practical usefulness of the approach were demonstrated by the experiments with a disulfide substituent bearing a tail group which can serve as an initiator for surface-initiated polymerization. A variety of complex polymer brush patterns was prepared using several representative polymers, relevant for biomedical research and applications, as test systems.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Universitat Heidelberg
Contributors: Khan, M. N., Zharnikov, M.
Number of pages: 10
Pages: 14534-14543
Publication date: 18 Jul 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry C
Volume: 117
Issue number: 28
ISSN (Print): 1932-7447
Ratings: 
  • Scopus rating (2013): CiteScore 5.14 SJR 2.143 SNIP 1.432
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Energy(all)
Source: Scopus
Source ID: 84880559790

Research output: Contribution to journalArticleScientificpeer-review

Mechanisms of acceleration and retardation of water dynamics by ions

There are fundamental and not yet fully resolved questions concerning the impact of solutes, ions in particular, on the structure and dynamics of water, which can be formulated as follows: Are the effects of ions local or long-ranged? Is the action of cations and anions on water cooperative or not? Here, we investigate how the reorientation and hydrogen-bond dynamics of water are affected by ions in dilute and concentrated aqueous salt solutions. By combining simulations and analytic modeling, we first show that ions have a short-ranged influence on the reorientation of individual water molecules and that depending on their interaction strength with water, they may accelerate or slow down water dynamics. A simple additive picture combining the effects of the cations and anions is found to provide a good description in dilute solutions. In concentrated solutions, we show that the average water reorientation time ceases to scale linearly with salt concentration due to overlapping hydration shells and structural rearrangements which reduce the translational displacements induced by hydrogen-bond switches and increase the solution viscosity. This effect is not ion-specific and explains why all concentrated salt solutions slow down water dynamics. Our picture, which is demonstrated to be robust vis-a-vis a change in the force-field, reconciles the seemingly contradictory experimental results obtained by ultrafast infrared and NMR spectroscopies, and suggests that there are no long-ranged cooperative ion effects on the dynamics of individual water molecules in dilute solutions.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Columbia University in the City of New York, Lund University, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, UMR ENS-CNRS-UPMC 8640
Contributors: Stirnemann, G., Wernersson, E., Jungwirth, P., Laage, D.
Number of pages: 8
Pages: 11824-11831
Publication date: 14 Aug 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of the American Chemical Society
Volume: 135
Issue number: 32
ISSN (Print): 0002-7863
Ratings: 
  • Scopus rating (2013): CiteScore 11.38 SJR 5.993 SNIP 2.446
Original language: English
ASJC Scopus subject areas: Chemistry(all), Catalysis, Biochemistry, Colloid and Surface Chemistry
Source: Scopus
Source ID: 84882270662

Research output: Contribution to journalArticleScientificpeer-review

Spectroscopic study of a DNA brush synthesized in situ by surface initiated enzymatic polymerization

We used a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the chemical integrity, purity, and possible internal alignment of single-strand (ss) adenine deoxynucleotide (poly(A)) DNA brushes. The brushes were synthesized by surface-initiated enzymatic polymerization (SIEP) on a 25-mer of adenine self-assembled monolayer (SAM) on gold (A25-SH), wherein the terminal 3′-OH of the A25-SH serve as the initiation sites for SIEP of poly(A). XPS and NEXAFS spectra of poly(A) brushes were found to be almost identical to those of A25-SH initiator, with no unambiguous traces of contamination. Apart from the well-defined chemical integrity and contamination-free character, the brushes were found to have a high degree of orientational order, with an upright orientation of individual strands, despite their large thickness up to ∼55 nm, that corresponds to a chain length of at least several hundred nucleotides for individual ssDNA molecules. The orientational order exhibited by these poly(A) DNA brushes, mediated presumably by base stacking, was found to be independent of the brush thickness as long as the packing density was high enough. The well-defined character and orientational ordering of the ssDNA brushes make them a potentially promising system for different applications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Universitat Heidelberg, Duke University
Contributors: Khan, M. N., Tjong, V., Chilkoti, A., Zharnikov, M.
Number of pages: 10
Pages: 9929-9938
Publication date: 29 Aug 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 34
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84883395998

Research output: Contribution to journalArticleScientificpeer-review

Zinc coordination spheres in protein structures

Zinc metalloproteins are one of the most abundant and structurally diverse proteins in nature. In these proteins, the Zn(II) ion possesses a multifunctional role as it stabilizes the fold of small zinc fingers, catalyzes essential reactions in enzymes of all six classes, or assists in the formation of biological oligomers. Previously, a number of database surveys have been conducted on zinc proteins to gain broader insights into their rich coordination chemistry. However, many of these surveys suffer from severe flaws and misinterpretations or are otherwise limited. To provide a more comprehensive, up-to-date picture on zinc coordination environments in proteins, zinc containing protein structures deposited in the Protein Data Bank (PDB) were analyzed in detail. A statistical analysis in terms of zinc coordinating amino acids, metal-to-ligand bond lengths, coordination number, and structural classification was performed, revealing coordination spheres from classical tetrahedral cysteine/histidine binding sites to more complex binuclear sites with carboxylated lysine residues. According to the results, coordination spheres of hundreds of crystal structures in the PDB could be misinterpreted due to symmetry-related molecules or missing electron densities for ligands. The analysis also revealed increasing average metal-to-ligand bond length as a function of crystallographic resolution, which should be taken into account when interrogating metal ion binding sites. Moreover, one-third of the zinc ions present in crystal structures are artifacts, merely aiding crystal formation and packing with no biological significance. Our analysis provides solid evidence that a minimal stable zinc coordination sphere is made up by four ligands and adopts a tetrahedral coordination geometry.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Ita-Suomen yliopisto, School of Management (JKK)
Contributors: Laitaoja, M., Valjakka, J., Jänis, J.
Number of pages: 9
Pages: 10983-10991
Publication date: 7 Oct 2013
Peer-reviewed: Yes

Publication information

Journal: Inorganic Chemistry
Volume: 52
Issue number: 19
ISSN (Print): 0020-1669
Ratings: 
  • Scopus rating (2013): CiteScore 4.9 SJR 1.821 SNIP 1.368
Original language: English
ASJC Scopus subject areas: Inorganic Chemistry, Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84885131955

Research output: Contribution to journalArticleScientificpeer-review

Importance of the ion-pair interactions in the OPEP coarse-grained force field: Parametrization and validation

We have derived new effective interactions that improve the description of ion pairs in the Optimized Potential for Efficient protein structure Prediction (OPEP) coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all-atom simulations by targeting the radial distribution function of the distance between the center of mass of the side chains. The new potentials have stabilities, and number of ion pairs. Our modeling, by refining the packing of the charged amino acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions. (Figure Presented)

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Université Paris Diderot, Laboratoire de Biochimie Théorique, Institut Universitaire de France
Contributors: Sterpone, F., Nguyen, P. H., Kalimeri, M., Derreumaux, P.
Number of pages: 11
Pages: 4574-4584
Publication date: 8 Oct 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Theory and Computation
Volume: 9
Issue number: 10
ISSN (Print): 1549-9618
Ratings: 
  • Scopus rating (2013): CiteScore 5.41 SJR 2.437 SNIP 1.558
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Computer Science Applications

Bibliographical note

EXT="Kalimeri, Maria"

Source: Scopus
Source ID: 84891948959

Research output: Contribution to journalArticleScientificpeer-review

Reversible biofunctionalization of surfaces with a switchable mutant of avidin

Label-free biosensors detect binding of prey molecules (″ analytes″) to immobile bait molecules on the sensing surface. Numerous methods are available for immobilization of bait molecules. A convenient option is binding of biotinylated bait molecules to streptavidin-functionalized surfaces, or to biotinylated surfaces via biotin-avidin-biotin bridges. The goal of this study was to find a rapid method for reversible immobilization of biotinylated bait molecules on biotinylated sensor chips. The task was to establish a biotin-avidin-biotin bridge which was easily cleaved when desired, yet perfectly stable under a wide range of measurement conditions. The problem was solved with the avidin mutant M96H which contains extra histidine residues at the subunit-subunit interfaces. This mutant was bound to a mixed self-assembled monolayer (SAM) containing biotin residues on 20% of the oligo(ethylene glycol)-terminated SAM components. Various biotinylated bait molecules were bound on top of the immobilized avidin mutant. The biotin-avidin-biotin bridge was stable at pH ≥3, and it was insensitive to sodium dodecyl sulfate (SDS) at neutral pH. Only the combination of citric acid (2.5%, pH 2) and SDS (0.25%) caused instantaneous cleavage of the biotin-avidin-biotin bridge. As a consequence, the biotinylated bait molecules could be immobilized and removed as often as desired, the only limit being the time span for reproducible chip function when kept in buffer (2-3 weeks at 25 C). As expected, the high isolectric pH (pI) of the avidin mutant caused nonspecific adsorption of proteins. This problem was solved by acetylation of avidin (to pI <5), or by optimization of SAM formation and passivation with biotin-BSA and BSA.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Johannes Kepler University, Fimlab Laboratories Ltd, University of Salzburg, University of Basel, University of South Bohemia, Goethe-University Frankfurt
Contributors: Pollheimer, P., Taskinen, B., Scherfler, A., Gusenkov, S., Creus, M., Wiesauer, P., Zauner, D., Schöfberger, W., Schwarzinger, C., Ebner, A., Tampé, R., Stutz, H., Hytönen, V. P., Gruber, H. J.
Number of pages: 13
Pages: 1656-1668
Publication date: 16 Oct 2013
Peer-reviewed: Yes

Publication information

Journal: Bioconjugate Chemistry
Volume: 24
Issue number: 10
ISSN (Print): 1043-1802
Ratings: 
  • Scopus rating (2013): CiteScore 5.12 SJR 2.02 SNIP 1.201
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Organic Chemistry, Pharmaceutical Science, Biomedical Engineering, Pharmacology
Source: Scopus
Source ID: 84886070072

Research output: Contribution to journalArticleScientificpeer-review

Porphyrin adsorbed on the (1010) surface of the wurtzite structure of ZnO-conformation induced effects on the electron transfer characteristics

Electron transfer at the adsorbate-surface interface is crucial in many applications but the steps taking place prior to and during the electron transfer are not always thoroughly understood. In this work a model system of 4-(porphyrin-5-yl)benzoic acid adsorbed as a corresponding benzoate on the ZnO wurtzite (1010) surface is studied using density functional theory (DFT) and time-dependent DFT. Emphasis is on the initial photoexcitation of porphyrin and on the strength of coupling between the porphyrin LUMO or LUMO + 1 and the ZnO conduction band that plays a role in the electron transfer. Firstly, ZnO wurtzite bulk is optimized to minimum energy geometry and the properties of the isolated ZnO (1010) surface model and the porphyrin model are discussed to gain insight into the combined system. Secondly, various orientations of the model porphyrin on the ZnO surface are studied: the porphyrin model standing perpendicularly to the surface and gradually brought close to the surface by tilting the linker in a few steps. The porphyrin model approaches the surface either sideways with hydrogen atoms of the porphyrin ring coming down first or twisted in a ca. 45° angle, giving rise to π-interactions of the porphyrin ring with ZnO. Because porphyrins are closely packed and near the surface, emerging van der Waals (vdW) interactions are examined using Grimme's D2 method. While the orientation affects the initial excitation of porphyrin only slightly, the coupling between the LUMO and LUMO + 1 of porphyrin and the conduction band of ZnO increases considerably if porphyrin is close to the surface, especially if the π-electrons are interacting with the surface. Based on the results of coupling studies, not only the distance between porphyrin and the ZnO surface but also the orientation of porphyrin can greatly affect the electron transfer. © 2013 the Owner Societies.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research group: Supramolecular photochemistry, Department of Chemistry and Bioengineering, Tampere University of Technology, Department of Physics, Department of Physics, Research area: Computational Physics, Research group: Electronic Structure Theory, Computational Science X (CompX), Frontier Photonics
Contributors: Niskanen, M., Kuisma, M., Cramariuc, O., Golovanov, V., Hukka, T. I., Tkachenko, N., Rantala, T. T.
Number of pages: 11
Pages: 17408-17418
Publication date: 28 Oct 2013
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 15
Issue number: 40
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2013): CiteScore 4.05 SJR 1.72 SNIP 1.196
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)

Bibliographical note

poistettu tuplat r=2454 ja r=3218<br/>Contribution: organisation=keb,FACT1=0.5<br/>Contribution: organisation=fys,FACT2=0.5<br/>Portfolio EDEND: 2013-10-29<br/>Publisher name: R S C Publications

Source: researchoutputwizard
Source ID: 2999

Research output: Contribution to journalArticleScientificpeer-review

Embedded cluster models for reactivity of the hydrated electron

Our computational study presents embedded cluster models of the hydrated electron focusing on its reactivity with the hydrated proton and the nitrous oxide molecule leading to formation of a hydrogen atom in the former case and a nitrogen molecule plus hydroxyl radical and hydroxide anion in the latter case. We show using ab initio calculations combined with the nudged elastic band method for determining minimum energy paths that carefully chosen cluster models with no more than six water molecules embedded in a polarizable continuum are able to capture the essential features of the reactive processes of the hydrated electron.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Uhlig, F., Jungwirth, P.
Number of pages: 11
Pages: 1583-1593
Publication date: Nov 2013
Peer-reviewed: Yes

Publication information

Journal: ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY AND CHEMICAL PHYSICS
Volume: 227
Issue number: 11
ISSN (Print): 0942-9352
Ratings: 
  • Scopus rating (2013): CiteScore 1.13 SJR 0.463 SNIP 0.603
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Keywords: Clusters, Hydrated Electron, Hydronium, Nitrous Oxide, Reactivity
Source: Scopus
Source ID: 84888629620

Research output: Contribution to journalArticleScientificpeer-review

Soft-graphoepitaxy using nanoimprinted polyhedral oligomeric silsesquioxane substrates for the directed self-Assembly of PS-b-PDMS

We report here the fabrication of periodic sub-25 nm diameter size cylinder structures using block copolymer (BCP) directed self-Assembly on nanoimprinted topographically patterned substrates. Tailored polyhedral oligomeric silsesquioxanes (POSSs) films were spin coated onto silicon substrates and were patterned by nanoimprint lithography to produce topographies commensurable with the BCP domain spacing. The chemistry of the POSS was tuned to control the alignment and orientation of the BCP films. The substrates were used to direct the microphase separation (following toluene solvent annealing) of a hexagonal structure forming polystyrene-block-polydimethylsiloxane (PS-b-PDMS) having a domain spacing of 42.6 nm and PDMS cylinder widths of 23.7 nm. On more hydrophilic POSS substrates the cylinders were obtained parallel to the substrate plane and aligned with the topography. In contrast, in more hydrophobic POSS patterns, the cylinders align perpendicular to the substrate plane. The use of these methods for the nanofabrication of vias, nanofluidic devices or interconnect structures of sub-25 nm feature size is discussed.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Nanophotonics, Frontier Photonics, Trinity College Dublin, Edifici CM3, University College Cork, Tyndall National Institute at National University of Ireland, Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Profactor GmbH, CNRS/UJF-Grenoble1/CEA LTM, Catalan Institute for Research and Advanced Studies (ICREA)
Contributors: Borah, D., Simao, C. D., Senthamaraikannan, R., Rasappa, S., Francone, A., Lorret, O., Salaun, M., Kosmala, B., Kehagias, N., Zelsmann, M., Sotomayor-Torres, C. M., Morris, M. A.
Number of pages: 10
Pages: 3512-3521
Publication date: Nov 2013
Peer-reviewed: Yes

Publication information

Journal: European Polymer Jounal
Volume: 49
Issue number: 11
ISSN (Print): 0014-3057
Ratings: 
  • Scopus rating (2013): CiteScore 3.43 SJR 1.087 SNIP 1.66
Original language: English
ASJC Scopus subject areas: Polymers and Plastics, Physics and Astronomy(all), Organic Chemistry
Keywords: Block copolymer-Polyhedral oligomeric silsesquioxanes, Directed self-Assembly, Graphoepitaxy, Nanoimprint lithography, Surface chemistry
Source: Scopus
Source ID: 84885020807

Research output: Contribution to journalArticleScientificpeer-review

How conformational flexibility stabilizes the hyperthermophilic elongation factor G-domain

Proteins from thermophilic organisms are stable and functional well above ambient temperature. Understanding the molecular mechanism underlying such a resistance is of crucial interest for many technological applications. For some time, thermal stability has been assumed to correlate with high mechanical rigidity of the protein matrix. In this work we address this common belief by carefully studying a pair of homologous G-domain proteins, with their melting temperatures differing by 40 K. To probe the thermal-stability content of the two proteins we use extensive simulations covering the microsecond time range and employ several different indicators to assess the salient features of the conformational landscape and the role of internal fluctuations at ambient condition. At the atomistic level, while the magnitude of fluctuations is comparable, the distribution of flexible and rigid stretches of amino-acids is more regular in the thermophilic protein causing a cage-like correlation of amplitudes along the sequence. This caging effect is suggested to favor stability at high T by confining the mechanical excitations. Moreover, it is found that the thermophilic protein, when folded, visits a higher number of conformational substates than the mesophilic homologue. The entropy associated with the occupation of the different substates and the thermal resilience of the protein intrinsic compressibility provide a qualitative insight on the thermal stability of the thermophilic protein as compared to its mesophilic homologue. Our findings potentially open the route to new strategies in the design of thermostable proteins.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Laboratoire de Biochimie Théorique, Université Paris Diderot, Centro S3
Contributors: Kalimeri, M., Rahaman, O., Melchionna, S., Sterpone, F.
Number of pages: 11
Pages: 13775-13785
Publication date: 7 Nov 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 44
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films

Bibliographical note

EXT="Kalimeri, Maria"

Source: Scopus
Source ID: 84887752230

Research output: Contribution to journalArticleScientificpeer-review

The Halogen Bond in the Design of Functional Supramolecular Materials: Recent Advances

Halogen bonding is an emerging noncovalent interaction for constructing supramolecular assemblies. Though similar to the more familiar hydrogen bonding, four primary differences between these two interactions make halogen bonding a unique tool for molecular recognition and the design of functional materials. First, halogen bonds tend to be much more directional than (single) hydrogen bonds. Second, the interaction strength scales with the polarizability of the bond-donor atom, a feature that researchers can tune through single-atom mutation. In addition, halogen bonds are hydrophobic whereas hydrogen bonds are hydrophilic. Lastly, the size of the bond-donor atom (halogen) is significantly larger than hydrogen. As a result, halogen bonding provides supramolecular chemists with design tools that cannot be easily met with other types of noncovalent interactions and opens up unprecedented possibilities in the design of smart functional materials.This Account highlights the recent advances in the design of halogen-bond-based functional materials. Each of the unique features of halogen bonding, directionality, tunable interaction strength, hydrophobicity, and large donor atom size, makes a difference. Taking advantage of the hydrophobicity, researchers have designed small-size ion transporters. The large halogen atom size provided a platform for constructing all-organic light-emitting crystals that efficiently generate triplet electrons and have a high phosphorescence quantum yield. The tunable interaction strengths provide tools for understanding light-induced macroscopic motions in photoresponsive azobenzene-containing polymers, and the directionality renders halogen bonding useful in the design on functional supramolecular liquid crystals and gel-phase materials. Although halogen bond based functional materials design is still in its infancy, we foresee a bright future for this field. We expect that materials designed based on halogen bonding could lead to applications in biomimetics, optics/photonics, functional surfaces, and photoswitchable supramolecules.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Aalto University, Politecnico di Milano, VTT Technical Research Centre of Finland
Contributors: Priimagi, A., Cavallo, G., Metrangolo, P., Resnati, G.
Number of pages: 10
Pages: 2686-2695
Publication date: 19 Nov 2013
Peer-reviewed: Yes

Publication information

Journal: Accounts of Chemical Research
Volume: 46
Issue number: 11
ISSN (Print): 0001-4842
Ratings: 
  • Scopus rating (2013): CiteScore 21.67 SJR 10.742 SNIP 4.856
Original language: English
ASJC Scopus subject areas: Chemistry(all)
Source: Scopus
Source ID: 84888619396

Research output: Contribution to journalArticleScientificpeer-review

Ion pairing in aqueous lithium salt solutions with monovalent and divalent counter-anions

Molecular dynamics simulations of concentrated aqueous solutions of LiCl and Li2SO4 were conducted in order to provide molecular insight into recent neutron scattering data. The structures predicted from the molecular dynamics simulations using standard nonpolarizable force fields provided a very poor fit to the experiment; therefore, refinement was needed. The electronic polarizability of the medium was effectively accounted for by implementing the electronic continuum correction, which practically means rescaling the ionic charges. Consistent with previous studies, we found that this approach in each case provided a significantly improved fit to the experimental data, which was further enhanced by slightly adjusting the radius of the lithium ion. The polarization effect was particularly pronounced in the Li2SO4 solution where the ions in the nonpolarizable simulations tended to cluster unphysically. With the above alterations, the employed force field displayed an excellent fit to the neutron scattering data and provided a useful interpretative framework for the experimental measurements. At the same time, the present study underlines the importance of solvent polarization effects in hydration of ions with high charge density.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Pluhařová, E., Mason, P. E., Jungwirth, P.
Number of pages: 8
Pages: 11766-11773
Publication date: 21 Nov 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry A
Volume: 117
Issue number: 46
ISSN (Print): 1089-5639
Ratings: 
  • Scopus rating (2013): CiteScore 2.84 SJR 1.205 SNIP 1.1
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry
Source: Scopus
Source ID: 84879340380

Research output: Contribution to journalArticleScientificpeer-review

Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations

Release of halide ions is an essential step of the catalytic cycle of haloalkane dehalogenases. Here we describe experimentally and computationally the process of release of a halide anion from the buried active site of the haloalkane dehalogenase LinB. Using stopped-flow fluorescence analysis and umbrella sampling free energy calculations, we show that the anion binding is ion-specific and follows the ordering I- > Br- > Cl-. We also address the issue of the protonation state of the catalytic His272 residue and its effect on the process of halide release. While deprotonation of His272 increases binding of anions in the access tunnel, we show that the anionic ordering does not change with the switch of the protonation state. We also demonstrate that a sodium cation could relatively easily enter the active site, provided the His272 residue is singly protonated, and replace thus the missing proton. In contrast, Na+ is strongly repelled from the active site containing the doubly protonated His272 residue. Our study contributes toward understanding of the reaction mechanism of haloalkane dehalogenase enzyme family. Determination of the protonation state of the catalytic histidine throughout the catalytic cycle remains a challenge for future studies.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Masaryk University
Contributors: Hladilkova, J., Prokop, Z., Chaloupkova, R., Damborsky, J., Jungwirth, P.
Number of pages: 7
Pages: 14329-14335
Publication date: 21 Nov 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 117
Issue number: 46
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2013): CiteScore 3.53 SJR 1.504 SNIP 1.194
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84888618153

Research output: Contribution to journalArticleScientificpeer-review

Fabrication of ssDNA/Oligo(ethylene glycol) monolayers and patterns by exchange reaction promoted by ultraviolet light irradiation

Using a representative test system, we present here a versatile approach to prepare mixed monolayers of thiolated single-stranded DNA (ssDNA) and oligo(ethylene glycol) substituted alkanethiols (OEG-AT) in a broad range of compositions as well as ssDNA/OEG-AT patterns of desired shape imbedded into a biorepulsive background. The procedure involves two steps. First, a primary, well-defined OEG-AT monolayer on a solid support is exposed to UV light in either homogeneous or lithographic fashion. Second, the exchange reaction between the damaged OEG-AT species in the film and ssDNA substituents in solution occurs, resulting in formation of ssDNA/OEG-AT monolayer or pattern. The above procedure relies on commercially available compounds and does not require vacuum, which simplifies its application in research and industrial laboratories. The composition of the mixed films or ssDNA/OEG-AT spots (lithography) can be precisely adjusted by UV dose in an almost entire composition range. It was demonstrated that the procedure can be performed with UV light of different wavelengths (254 or 365 nm), which opens new possibilities for lithography. Using advanced spectroscopic tools, it was shown that ssDNA molecules imbedded into the OEG-AT matrix maintain their identity and intact character as well as exhibit predominant upright orientation typical of one-component films of thiolated ssDNA. The OEG-AT constituents of the mixed monolayers were found to be intact as well, with all UV damaged OEG-AT species being exchanged for ssDNA. Finally, a representative ssDNA/OEG-AT pattern was fabricated.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Universitat Heidelberg
Contributors: Khan, M. N., Zharnikov, M.
Number of pages: 11
Pages: 24883-24893
Publication date: 27 Nov 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry C
Volume: 117
Issue number: 47
ISSN (Print): 1932-7447
Ratings: 
  • Scopus rating (2013): CiteScore 5.14 SJR 2.143 SNIP 1.432
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Energy(all)
Source: Scopus
Source ID: 84889582340

Research output: Contribution to journalArticleScientificpeer-review

Effect of surface morphology of poly(ïμ-caprolactone) scaffolds on adipose stem cell adhesion and proliferation

Summary The effect of the surface morphology of flat poly(Ïμ- caprolactone) (PCL) scaffolds on human adipose stem cell (hASC) adherence and proliferation was studied. During fabrication of the scaffolds by phase inversion, the employment of different non-solvents (water (W), ethanol (EtOH) or isopropanol (IPA)) led to distinct surface morphologies. It was found that PCL scaffolds fabricated using IPA as a non-solvent had a higher roughness and porosity compared to the other groups. Moreover, during culturing of hASCs under static conditions, best cell attachment, spreading and growth were observed on the PCL scaffold. Our results show the potential of PCL scaffolds prepared using IPA as a non-solvent for especially soft tissue engineering applications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Twente, University of Groningen
Contributors: Diban, N., Haimi, S. P., Bolhuis-Versteeg, L., Teixeira, S., Miettinen, S., Poot, A. A., Grijpma, D. W., Stamatialis, D.
Number of pages: 7
Pages: 126-132
Publication date: Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Macromolecular symposia
Volume: 334
Issue number: 1
ISSN (Print): 1022-1360
Ratings: 
  • Scopus rating (2013): CiteScore 0.71 SJR 0.326 SNIP 0.388
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Condensed Matter Physics
Keywords: morphology, phase inversion, poly(Ïμ-caprolactone), roughness, scaffold porosity
Source: Scopus
Source ID: 84890745371

Research output: Contribution to journalArticleScientificpeer-review

Human adipose stem cells in chondrogenic differentiation medium without growth factors differentiate towards annulus fibrosus phenotype in vitro

Summary Intervertebral disc degeneration is the main cause of chronic back pain. Disc degeneration mainly leads to tearing of annulus fibrosus (AF), which is with current methods difficult to restore and impossible to regenerate. Stem cell technology offers a potential technique to repair the ruptured AF by enabling new matrix synthesis at the defect site. Previous studies have shown that human adipose stem cells (hASCs) are able to differentiate towards AF phenotype when treated with suitable growth factors. There are concerns about the use of growth factors in clinical applications because of their short half-lives, high costs and low effectiveness. The main aim of this research project was to regenerate AF tissue in vitro using hASCs and serum free chondrogenic medium without supplementation of growth factors. Differentiation of hASCs was induced by using the micromass culture technique. Human annulus fibrosus cell (hAFCs) cultured in commercial AF growth medium were used as positive control. Assessment of AF phenotype of hASCs and hAFCs was done at 14 and 21 days of culture. Quantification of sulphated glycosaminoglycan (GAG) content showed that hASCs cultured in chondrogenic medium expressed similar levels of sulphated GAGs as hAFCs. qRT-PCR confirmed the similarity of the differentiated hASCs with AF phenotype. Several markers for AF phenotype (aggrecan, collagen type I and glypican-3) were expressed in both hAFCs and differentiated hASCs. This is the first study that demonstrated that hASCs can be differentiated towards AF phenotype using serum free chondrogenic medium without growth factors. In a next step, scaffolds manufactured from biodegradable polymers will be used in combination with ASCs to find an optimal construct to repair AF defects.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Twente, University of Groningen
Contributors: Gebraad, A. W. H., Miettinen, S., Grijpma, D. W., Haimi, S. P.
Number of pages: 8
Pages: 49-56
Publication date: Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Macromolecular symposia
Volume: 334
Issue number: 1
ISSN (Print): 1022-1360
Ratings: 
  • Scopus rating (2013): CiteScore 0.71 SJR 0.326 SNIP 0.388
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Condensed Matter Physics
Keywords: adipose stem cells, annulus fibrosus, intervertebral disc, tissue engineering
Source: Scopus
Source ID: 84890722713

Research output: Contribution to journalArticleScientificpeer-review

Proliferation and differentiation of adipose stem cells towards smooth muscle cells on poly(trimethylene carbonate) membranes

Summary Multipotent human adipose stem cells (hASCs) are an abundant and potential source of cells for vascular tissue engineering when combined with a suitable biomaterial scaffold. Poly(trimethylene carbonate) (PTMC) has been shown to be a useful biodegradable material for tissue engineered vascular grafts due to its flexibility, excellent biocompatibility and enzymatic degradation by surface erosion in vivo. The purpose of the current study was to evaluate the proliferation and differentiation of hASCs towards smooth muscle cells (SMCs) on gamma-crosslinked and photo-crosslinked PTMC membranes. PTMC macromers were functionalized with methacrylate end groups and crosslinked by UV initiated radical polymerization. High molecular weight linear PTMC was crosslinked by gamma irradiation. Cell viability, cell numbers and SMC differentiation of hASCs were evaluated on the differently crosslinked PTMC films at 7 and 14 days (d). On the photo-crosslinked membranes, homogenous monolayers of hASC were detected by live/dead assay. Consistently, cells on the photo-crosslinked membranes had significantly higher cell numbers compared to cells on the gamma-crosslinked membranes after 14 d of culture. SMC specific genes were expressed on both membranes at 14 d. Photo-crosslinked membranes showed higher expression of SMC specific proteins at 14 d compared to gamma-crosslinked membranes. These results suggest that especially the photo-crosslinked PTMC membranes are suitable for vascular tissue engineering applications when combined with hASCs.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Aachen University of Applied Sciences, University of Groningen
Contributors: German, S. J., Behbahani, M., Miettinen, S., Grijpma, D. W., Haimi, S. P.
Number of pages: 10
Pages: 133-142
Publication date: Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Macromolecular symposia
Volume: 334
Issue number: 1
ISSN (Print): 1022-1360
Ratings: 
  • Scopus rating (2013): CiteScore 0.71 SJR 0.326 SNIP 0.388
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Polymers and Plastics, Organic Chemistry, Materials Chemistry
Keywords: adipose stem cell differentiation, poly (trimethylene carbonate), smooth muscle cells, tissue engineering
Source: Scopus
Source ID: 84890729494

Research output: Contribution to journalArticleScientificpeer-review

Location of dispersing agent in rubber nanocomposites during mixing process

In the present work, the development of morphology and selective wetting of nanoclay and carbon nanotubes (CNTs) in rubber nanocomposites were characterized qualitatively by means of the optical microscopy, TEM and AFM and quantitatively by means of the wetting concept. Carboxylated hydrogenated nitrile butadiene rubber (XHNBR), ionic liquid and ethanol were used as dispersing agent and they show very good effect on the macro- and microdispersion of nanofillers in different rubbers. It was found that the selective wetting of filler surface by the dispersing agent and rubber matrix is controlled by thermodynamic and kinetic factors. A model basing on surface energy data of polymer components (rubber and dispersing agent) and filler was introduced in order to determine the thermodynamic equilibrium state of filler wetting, which is found to be simultaneously determined by the filler-polymer affinity and the rubber/dispersing agent mass ratio. During the mixing process a replacement process of bound polymer components takes place on the filler surface until the predicted state is reached.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Leibniz-Institut für Polymerforschung Dresden E.V., University of Applied Sciences Merseburg, Martin-Luther-University Halle-Wittenberg, Vodafone Department of Mobile Communications Systems, Polymer Service Merseburg
Contributors: Le, H. H., Oßwald, K., Wießner, S., Das, A., Stöckelhuber, K. W., Boldt, R., Gupta, G., Heinrich, G., Radusch, H. J.
Number of pages: 13
Pages: 7009-7021
Publication date: 13 Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Polymer
Volume: 54
Issue number: 26
ISSN (Print): 0032-3861
Ratings: 
  • Scopus rating (2013): CiteScore 4.07 SJR 1.414 SNIP 1.635
Original language: English
ASJC Scopus subject areas: Polymers and Plastics, Organic Chemistry
Keywords: Carbon nanotubes, Dispersing agent, Localization
Source: Scopus
Source ID: 84889099442

Research output: Contribution to journalArticleScientificpeer-review

Analysis of free, mono- and diacetylated polyamines from human urine by LC-MS/MS

Polyamines are promising biochemical markers of cancer and many other pathophysiological conditions, and thus their concentrations in biological fluids are a matter of interest. However, since the concentrations of these compounds are low, their quantitation is typically based on methods requiring laborious sample preparation. Here we developed and validated an LC-MS/MS method to analyze simultaneously free (DAP, PUT, CAD, SPD, SPM) monoacetylated (AcPUT, AcCAD, N1AcSPD, N8AcSPD, N1AcSPM) and diacetylated (DiAcPUT, DiAcCAD, DiAcSPD, DiAcSPM) polyamines from human urine without the need for derivatization. Deuterium labeled polyamines were the internal standards for each analyte. Diluted urine samples spiked with internal standards were filtered through a strong anion exchange resin prior to LC-MS/MS analysis. The chromatographic separation of 14 polyamines was achieved in 12min on C18 column with 0.1% HFBA (v/v) as the ion-pairing agent and a water-acetonitrile gradient. Ionization was performed with positive electrospray ionization (ESI) and detection was with a triple quadrupole mass spectrometer with selected reaction monitoring. Calibration curves ranged from up to 5 to 10,000nM. The accuracy and precision of the method were determined using urine based quality control samples, and matrix effects were examined by using standard addition methods. This novel method is suitable for elucidating differences in urinary polyamine excretion in cancer patients and healthy humans.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Ita-Suomen yliopisto, Tampere University Hospital, Karolinska University Hospital, School of Management (JKK)
Contributors: Häkkinen, M. R., Roine, A., Auriola, S., Tuokko, A., Veskimäe, E., Keinänen, T. A., Lehtimäki, T., Oksala, N., Vepsäläinen, J.
Number of pages: 9
Pages: 81-89
Publication date: 15 Dec 2013
Peer-reviewed: Yes

Publication information

Journal: JOURNAL OF CHROMATOGRAPHY B: ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
Volume: 941
ISSN (Print): 1570-0232
Ratings: 
  • Scopus rating (2013): CiteScore 2.78 SJR 1.061 SNIP 1.278
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Biochemistry, Clinical Biochemistry, Cell Biology
Keywords: Cancer diagnostic markers, Liquid chromatography-tandem mass spectrometry, N-acetylated, Polyamines, Prostate cancer, Urine
Source: Scopus
Source ID: 84887097655

Research output: Contribution to journalArticleScientificpeer-review

Self-assembly of polystyrene-block-poly(4-vinylpyridine) block copolymer on molecularly functionalized silicon substrates: Fabrication of inorganic nanostructured etchmask for lithographic use

Block copolymers (BCPs) are seen as a possible cost effective complementary technique to traditional lithography currently used in the semiconductor industry. This unconventional approach has received increased attention in recent years as a process capable of facilitating the ever decreasing device size demanded. Control over microdomain orientation and enhancing long range order are key aspects for the utility of BCPs for future lithographic purposes. This paper provides an efficient route for the fabrication of highly ordered nanostructures suitable for such application. We investigate the significant effect of surface treatment regarding the self-assembly process of polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) by employing an ethylene glycol layer, producing well defined perpendicular P4VP cylinders with long range order over large surface areas. Nanopores are generated through surface reconstruction using a preferential solvent, which allows for the incorporation of an inorganic moiety. Treatment of this pattern with UV/Ozone leads to formation of well-ordered iron oxide nanodots with a pitch of ∼26 nm. Furthermore, high aspect ratio silicon nanopillars result following pattern transfer (using Ar/O2).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Tyndall National Institute at National University of Ireland, Cork, Trinity College Dublin, University College Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN)
Contributors: Cummins, C., Borah, D., Rasappa, S., Chaudhari, A., Ghoshal, T., O'Driscoll, B. M. D., Carolan, P., Petkov, N., Holmes, J. D., Morris, M. A.
Number of pages: 11
Pages: 7941-7951
Publication date: 21 Dec 2013
Peer-reviewed: Yes

Publication information

Journal: Journal of Materials Chemistry C
Volume: 1
Issue number: 47
ISSN (Print): 2050-7534
Original language: English
ASJC Scopus subject areas: Chemistry(all), Materials Chemistry
Source: Scopus
Source ID: 84887902210

Research output: Contribution to journalArticleScientificpeer-review

A full-potential linearized augmented plane wave study of the interaction of CO2 with α-Pu (020) surface nanolayers

Adsorption of CO2 on α-Pu (020) surface nanolayers is investigated using GGA-DFT and the suite of software DMOL3 and WIEN2k. Completely dissociated configurations (C+O+O) exhibit the strongest binding with the surface (7.94 eV), followed by partially dissociated (CO+O) and molecular CO2 configurations (5.18 and 1.90 eV, respectively). For initial vertically upright orientations, final configuration of the CO 2 molecule does not change after optimization. For initial flat lying orientations, the final states correspond to bent geometry with a bond angle of ∼130°. For CO+O coadsorptions, the stable configurations correspond to CO dipole moment orientations of 105°-167° with respect to the normal surface.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Texas at Arlington
Contributors: Wang, J., Ray, A. K.
Number of pages: 8
Pages: 1710-1717
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Computational and Theoretical Nanoscience
Volume: 11
Issue number: 7
ISSN (Print): 1546-1955
Ratings: 
  • Scopus rating (2014): CiteScore 1.17 SJR 0.326 SNIP 0.778
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Electrical and Electronic Engineering, Materials Science(all), Computational Mathematics, Chemistry(all)
Keywords: Adsorption, Alpha-Plutonium, Carbon Dioxide, Density Functional Theory, Nanolayers
Source: Scopus
Source ID: 84898458971

Research output: Contribution to journalArticleScientificpeer-review

A microscopic view of the mechanisms of active transport across the cellular membrane

Membrane transporters are molecular machines that couple active transport of their specific substrates to various sources of cellular energy through a set of highly coordinated protein conformational changes. The alternating-access mechanism of transport in these proteins, which ensures that the substrate is only accessible from one side of the membrane at any given time, relies on complex and global protein conformational changes that are also closely coupled to molecular events such as substrate binding and translocation. In this review, we describe the application of advanced molecular modeling and simulation technologies to a number of membrane transport proteins studied in our laboratory. The goal is to demonstrate the power of the methods in describing functionally relevant molecular events ranging from more localized events such as substrate binding and gating motions to large, global protein conformational changes governing the transition of the protein between major functional states.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Department of Biochemistry, Univ Illinois, University of Illinois System, University of Illinois Urbana-Champaign, Frederick Seitz Mat Res Lab, Dept Mat Sci & Engn
Contributors: Enkavi, G., Li, J., Wen, P., Thangapandian, S., Moradi, M., Jiang, T., Han, W., Tajkhorshid, E.
Number of pages: 49
Pages: 77-125
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Annual Reports in Computational Chemistry
Volume: 10
ISSN (Print): 1574-1400
Ratings: 
  • Scopus rating (2014): CiteScore 1.25 SJR 0.74 SNIP 0.985
Original language: English
ASJC Scopus subject areas: Chemistry(all), Computational Mathematics
Keywords: Conformational changes, Membrane transporters, Molecular dynamics, Nonequilibrium simulation, Primary transporters, Secondary transporters, Substrate binding
Source: Scopus
Source ID: 84919386963

Research output: Contribution to journalArticleScientificpeer-review

Direct observation of the collapse of the delocalized excess electron in water

It is generally assumed that the hydrated electron occupies a quasi-spherical cavity surrounded by only a few water molecules in its equilibrated state. However, in the very moment of its generation, before water has had time to respond to the extra charge, it is expected to be significantly larger in size. According to a particle-in-a-box picture, the frequency of its absorption spectrum is a sensitive measure of the initial size of the electronic wavefunction. Here, using transient terahertz spectroscopy, we show that the excess electron initially absorbs in the far-infrared at a frequency for which accompanying ab initio molecular dynamics simulations estimate an initial delocalization length of ≈40 Å. The electron subsequently shrinks due to solvation and thereby leaves the terahertz observation window very quickly, within ≈200 fs.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), University of Zurich, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Savolainen, J., Uhlig, F., Ahmed, S., Hamm, P., Jungwirth, P.
Number of pages: 5
Pages: 697-701
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Nature Chemistry
Volume: 6
Issue number: 8
ISSN (Print): 1755-4330
Ratings: 
  • Scopus rating (2014): CiteScore 13.67 SJR 10.562 SNIP 4.441
Original language: English
ASJC Scopus subject areas: Chemistry(all), Chemical Engineering(all)
Source: Scopus
Source ID: 84904805160

Research output: Contribution to journalArticleScientificpeer-review

Effect of non-rubber components of NR on the carbon nanotube (CNT) localization in SBR/NR blends

Carbon nanotubes (CNTs) are mixed into SBR/NR and SBR/IR blends using a wet mixing process. The phase specific localization of CNTs in rubber blends is predicted theoretically using surface energy data of blend components and determined experimentally by means of the wetting concept. Almost all CNTs are found to be localized in the SBR matrix of SBR/IR blends due to the better affinity of CNTs to SBR than to IR. In contrast, a high CNT loading localized in the NR phase of SBR/NR blends results from the presence of phospholipids in NR. Electrical and mechanical properties of the rubber blends depend strongly on CNT localization. A lower CNT loading in SBR matrix of SBR/NR blends imparts a better wet grip and lower rolling resistance to tire tread compounds.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), Martin-Luther-University Halle-Wittenberg, Styron Deutschland GmbH, Fraunhofer IWM, Leibniz-Institut für Polymerforschung Dresden E.V., Dau Mot University, Tribhuvan University, Vodafone Department of Mobile Communications Systems
Contributors: Le, H. H., Parsekar, M., Ilisch, S., Henning, S., Das, A., Stöckelhuber, K. W., Beiner, M., Ho, C. A., Adhikari, R., Wießner, S., Heinrich, G., Radusch, H. J.
Number of pages: 14
Pages: 569-582
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Macromolecular Materials and Engineering
Volume: 299
Issue number: 5
ISSN (Print): 1438-7492
Ratings: 
  • Scopus rating (2014): CiteScore 2.81 SJR 1.009 SNIP 1.294
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Materials Chemistry, Polymers and Plastics, Chemical Engineering(all)
Keywords: carbon nanotubes, filler localization, nanocomposites, rubber blends
Source: Scopus
Source ID: 84899990693

Research output: Contribution to journalArticleScientificpeer-review

Fabrication of 3-D nanodimensioned electric double layer capacitor structures using block copolymer templates

The need for materials for high energy storage has led to very significant research in supercapacitor systems. These can exhibit electrical double layer phenomena and capacitances up to hundreds of F/g. Here, we demonstrate a new supercapacitor fabrication methodology based around the microphase separation of PS-b-PMMA which has been used to prepare copper nanoelectrodes of dimension ~13 nm. These structures provide excellent capacitive performance with a maximum specific capacitance of ~836 F/g for a current density of 8.06 A/g at a discharge current as high as 75 mA. The excellent performance is due to a high surface area: volume ratio. We suggest that this highly novel, easily fabricated structure might have a number of important applications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Materials Chemistry and Analysis Group, University College Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Tyndall National Institute at National University of Ireland, Cork
Contributors: Rasappa, S., Borah, D., Senthamaraikannan, R., Faulkner, C. C., Holmes, J. D., Morris, M. A.
Number of pages: 7
Pages: 5221-5227
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Journal Nanoscience and Nanotechnology
Volume: 14
Issue number: 7
ISSN (Print): 1533-4880
Ratings: 
  • Scopus rating (2014): CiteScore 1.36 SJR 0.327 SNIP 0.515
Original language: English
ASJC Scopus subject areas: Bioengineering, Chemistry(all), Biomedical Engineering, Materials Science(all), Condensed Matter Physics
Keywords: 3-D Nanostructure, Block Copolymer, Capacitance, Copper Nanowires, PS-b-PMMA, Supercapacitor
Source: Scopus
Source ID: 84903822885

Research output: Contribution to journalArticleScientificpeer-review

Improving the effect of nanoscale barrier coating on BOPP film properties: Influence of substrate contamination, web handling and pretreatments

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Research group: Paper Converting and Packaging, Engineering materials science and solutions (EMASS), Lappeenranta University of Technology, ASTRaL, Miktech Oy, Masaryk Univ, Masaryk University Brno, R&D Ctr Low Cost Plasma & Nanotechnol Surface Mod
Contributors: Lahti, J., Johansson, P., Lahtinen, K., Cameron, D. C., Seppänen, T.
Number of pages: 23
Pages: 1039-1061
Publication date: 2014

Host publication information

Title of host publication: TAPPI PLACE Conference 2014
Volume: 2
Publisher: TAPPI Press
ISBN (Print): 9781510801271
ASJC Scopus subject areas: Materials Science(all), Chemistry(all), Mechanical Engineering, Media Technology, Chemical Engineering(all)
Source: Scopus
Source ID: 84939521131

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Kinetics of bioconjugate nanoparticle label binding in a sandwich-type immunoassay

Nanoparticle labels have enhanced the performance of diagnostic, screening, and other measurement applications and hold further promise for more sensitive, precise, and costeffective assay technologies. Nevertheless, a clear view of the biomolecular interactions on the molecular level is missing. Controlling the ratio of molecular recognition over undesired nonspecific adhesion is the key to improve biosensing with nanoparticles. To improve this ratio with an aim to disallow nonspecific binding, a more detailed perspective into the kinetic differences between the cases is needed. We present the application of two novel methods to determine complex binding kinetics of bioconjugate nanoparticles, interferometry, and force spectroscopy. Force spectroscopy is an atomic force microscopy technique and optical interferometry is a direct method to monitor reaction kinetics in second-hour timescale, both having steadily increasing importance in nanomedicine. The combination is perfectly suited for this purpose, due to the high sensitivity to detect binding events and the ability to investigate biological samples under physiological conditions. We have attached a single biofunctionalized nanoparticle to the outer tip apex and studied the binding behavior of the nanoparticle in a sandwich-type immunoassay using dynamic force spectroscopy in millisecond timescale. Utilization of the two novel methods allowed characterization of binding kinetics in a time range spanning from 50 ms to 4 h. These experiments allowed detection and demonstration of differences between specific and nonspecific binding. Most importantly, nonspecific binding of a nanoparticle was reduced at contact times below 100 ms with the solid-phase surface.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Turun Yliopisto/Turun Biomateriaalikeskus, Johannes Kepler University, Agilent Technologies Osterrreich GmbH, Fimlab Laboratories Ltd, Center for Advanced Bioanalysis
Contributors: Näreoja, T., Ebner, A., Gruber, H. J., Taskinen, B., Kienberger, F., Hänninen, P. E., Hytönen, V. P., Hinterdorfer, P., Härmä, H.
Number of pages: 11
Pages: 493-503
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Analytical and Bioanalytical Chemistry
Volume: 406
Issue number: 2
ISSN (Print): 1618-2642
Ratings: 
  • Scopus rating (2014): CiteScore 3.26 SJR 1.126 SNIP 1.212
Original language: English
ASJC Scopus subject areas: Analytical Chemistry, Biochemistry
Keywords: Biofunctionalized nanoparticle labels, Biolayer interferometry, Force spectroscopy, Nonspecific binding, Sandwich-type immunoassay
Source: Scopus
Source ID: 84899084023

Research output: Contribution to journalArticleScientificpeer-review

Magnetic origin of the chemical balance in alloyed Fe-Cr stainless steels: First-principles and Ising model study

Iron-chromium is the base material for most of the stainless steel grades. Recently, new insights into the origins of fundamental physical and chemical characteristics of Fe-Cr based alloys have been achieved. Some of the new results are quite unexpected and call for further investigations. The present study focuses on the magnetic contribution in the atomic driving forces related to the chemical composition in Fe-Cr when alloyed with Al, Ti, V, Mn, Co, Ni, and Mo. Using the ab initio exact muffin-tin orbitals method combined with an Ising-type spin model, we demonstrate that the magnetic moment of the solute atoms with the induced changes in the magnetic moments of the host atoms form the main factor in determining the mixing energy and chemical potentials of low-Cr Fe-Cr based alloys. The results obtained in the present work are related to the designing and tuning of the microstructure and corrosion protection of low-Cr steels.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Turun Yliopisto/Turun Biomateriaalikeskus, Department of Physics and Astronomy, University of Turku, Abo Akad Univ, Abo Akademi University, Dept Phys, Uppsala University, Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences
Contributors: Airiskallio, E., Nurmi, E., Väyrynen, I. J., Kokko, K., Ropo, M., Punkkinen, M. P. J., Johansson, B., Vitos, L.
Number of pages: 6
Pages: 135-140
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Computational Materials Science
Volume: 92
ISSN (Print): 0927-0256
Ratings: 
  • Scopus rating (2014): CiteScore 2.47 SJR 1.098 SNIP 1.612
Original language: English
ASJC Scopus subject areas: Computer Science(all), Chemistry(all), Materials Science(all), Mechanics of Materials, Physics and Astronomy(all), Computational Mathematics
Keywords: Al, Chemical potential, Co, Corrosion protection, Cr, Fe, First principles calculation, Ising model, Magnetic moment, Mixing energy, Mn, Mo, Ni, Stainless steel, Ti, V
Source: Scopus
Source ID: 84902660256

Research output: Contribution to journalArticleScientificpeer-review

Molekuly a ionty v pohybu: Počítačové simulace biochemických a biofyzikálních procesů

The review presents research activities aimed at better understanding of the effects of salt ions on biological processes (protein salting out/in, protein denaturation, enzymatic activity, processes in biological membranes, and radiation damage to DNA) using molecular simulations in close contact with the experiment.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Jungwirth, P.
Number of pages: 7
Pages: 278-284
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Chemicke Listy
Volume: 108
Issue number: 4
ISSN (Print): 0009-2770
Ratings: 
  • Scopus rating (2014): CiteScore 0.33 SJR 0.198 SNIP 0.504
Original language: Undefined/Unknown
ASJC Scopus subject areas: Chemistry(all)
Source: Scopus
Source ID: 84899732053

Research output: Contribution to journalArticleScientificpeer-review

Novel derivatives of bacteriochlorophyll a: Complex formation with albumin and the mechanism of tumor cell photodamage

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Emanuel’ Institute of Biochemical Physics, Russian Academy of Sciences, M.V. Lomonosov Moscow State University of Fine Chemical Technologies, Georgian Technical University, St. Petersburg State Polytechnical University, N.N. Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences
Contributors: Akimova, A. V., Grin, M. A., Golovina, G. V., Kokrashvili, T. A., Vinogradov, A. M., Mironov, A. F., Rychkov, G. N., Shtil, A. A., Kuzmin, V. A., Durandin, N. A.
Number of pages: 4
Pages: 17-20
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: DOKLADY BIOCHEMISTRY AND BIOPHYSICS
Volume: 454
Issue number: 1
ISSN (Print): 1607-6729
Ratings: 
  • Scopus rating (2014): CiteScore 0.38 SJR 0.208 SNIP 0.312
Original language: English
ASJC Scopus subject areas: Biophysics, Chemistry(all), Medicine(all), Biochemistry
Source: Scopus
Source ID: 84896349301

Research output: Contribution to journalArticleScientificpeer-review

pH-dependent deformations of the energy landscape of avidin-like proteins investigated by single molecule force spectroscopy

Avidin and avidin-like proteins are widely used in numerous techniques since the avidin-biotin interaction is known to be very robust and reliable. Within this study, we investigated this bond at the molecular level under harsh conditions ranging from very low to very high pH values. We compared avidin with streptavidin and a recently developed avidin-based mutant, chimeric avidin. To gain insights of the energy landscape of these interactions we used a single molecule approach and performed the Single Molecule Force Spectroscopy atomic force microscopy technique. There, the ligand (biotin) is covalently coupled to a sharp AFM tip via a distensible hetero-bi-functional crosslinker, whereas the receptor of interest is immobilized on the probe surface. Receptor-ligand complexes are formed and ruptured by repeatedly approaching and withdrawing the tip from the surface. Varying both pulling velocity and pH value, we could determine changes of the energy landscape of the complexes. Our results clearly demonstrate that avidin, streptavidin and chimeric avidin are stable over a wide pH range although we could identify differences at the outer pH range. Taking this into account, they can be used in a broad range of applications, like surface sensors at extreme pH values.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Johannes Kepler University, Center for Advanced Bioanalysis, Fimlab Laboratories Ltd
Contributors: Köhler, M., Karner, A., Leitner, M., Hytönen, V. P., Kulomaa, M., Hinterdorfer, P., Ebner, A.
Number of pages: 16
Pages: 12531-12546
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Molecules
Volume: 19
Issue number: 8
ISSN (Print): 1420-3049
Ratings: 
  • Scopus rating (2014): CiteScore 2.62 SJR 0.738 SNIP 1.307
Original language: English
ASJC Scopus subject areas: Organic Chemistry, Medicine(all)
Keywords: Avidin mutant, Avidin-biotin, Biophysics, Force spectroscopy, Molecular recognition, PH dependence, Single molecules
Source: Scopus
Source ID: 84906691065

Research output: Contribution to journalReview ArticleScientificpeer-review

Study of the kinetics and mechanism of rapid self-assembly in block copolymer thin films during solvo-microwave annealing

Microwave annealing is an emerging technique for achieving ordered patterns of block copolymer films on substrates. Little is understood about the mechanisms of microphase separation during the microwave annealing process and how it promotes the microphase separation of the blocks. Here, we use controlled power microwave irradiation in the presence of tetrahydrofuran (THF) solvent, to achieve lateral microphase separation in high-χ lamellar-forming poly(styrene-b-lactic acid) PS-b-PLA. A highly ordered line pattern was formed within seconds on silicon, germanium and silicon on insulator (SOI) substrates. In-situ temperature measurement of the silicon substrate coupled to condition changes during "solvomicrowave" annealing allowed understanding of the processes to be attained. Our results suggest that the substrate has little effect on the ordering process and is essentially microwave transparent but rather, it is direct heating of the polar THF molecules that causes microphase separation. It is postulated that the rapid interaction of THF with microwaves and the resultant temperature increase to 55 °C within seconds causes an increase of the vapor pressure of the solvent from 19.8 to 70 kPa. This enriched vapor environment increases the plasticity of both PS and PLA chains and leads to the fast self-assembly kinetics. Comparing the patterns formed on silicon, germanium and silicon on insulator (SOI) and also an in situ temperature measurement of silicon in the oven confirms the significance of the solvent over the role of substrate heating during "solvo-microwave" annealing. Besides the short annealing time which has technological importance, the coherence length is on a micron scale and dewetting is not observed after annealing. The etched pattern (PLA was removed by an Ar/O2 reactive ion etch) was transferred to the underlying silicon substrate fabricating sub-20 nm silicon nanowires over large areas demonstrating that the morphology is consistent both across and through the film.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Trinity College Dublin, Tyndall National Institute at National University of Ireland, Cork, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Department of Micro and Nanotechnology, Danmarks Tekniske Universitet, DTU Informatik, Universitat Autònoma de Barcelona, Catalan Institute for Research and Advanced Studies (ICREA)
Contributors: Mokarian-Tabari, P., Cummins, C., Rasappa, S., Simao, C., Torres, C. M. S., Holmes, J. D., Morris, M. A.
Number of pages: 12
Pages: 10728-10739
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Langmuir
Volume: 30
Issue number: 35
ISSN (Print): 0743-7463
Ratings: 
  • Scopus rating (2014): CiteScore 4.59 SJR 1.81 SNIP 1.363
Original language: English
ASJC Scopus subject areas: Medicine(all), Materials Science(all), Condensed Matter Physics, Surfaces and Interfaces, Spectroscopy, Electrochemistry
Source: Scopus
Source ID: 84925424888

Research output: Contribution to journalArticleScientificpeer-review

Natural thermal adaptation increases heat shock protein levels and decreases oxidative stress

Heat shock proteins (HSPs), originally identified as heat-inducible gene products, are a family of highly conserved proteins that respond to a wide variety of stress including oxidative stress. Although both acute and chronic oxidative stress have been well demonstrated to induce HSP responses, little evidence is available whether increased HSP levels provide enhanced protection against oxidative stress under elevated yet sublethal temperatures. We studied relationships between oxidative stress and HSPs in a physiological model by using Garra rufa (doctor fish), a fish species naturally acclimatized to different thermal conditions. We compared fish naturally living in a hot spring with relatively high water temperature (34.4±0.6. °C) to those living in normal river water temperature (25.4±4.7. °C), and found that levels of all the studied HSPs (HSP70, HSP60, HSP90, HSC70 and GRP75) were higher in fish living in elevated water temperature compared with normal river water temperature. In contrast, indicators of oxidative stress, including protein carbonyls and lipid hydroperoxides, were decreased in fish living in the elevated temperature, indicating that HSP levels are inversely associated with oxidative stress. The present results provide evidence that physiologically increased HSP levels provide protection against oxidative stress and enhance cytoprotection.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Tampere, Medical School, University of Hacettepe, University of Düzce, Ita-Suomen yliopisto, University Central Hospital Kuopio
Contributors: Oksala, N. K. J., Ekmekçi, F. G., Özsoy, E., Kirankaya, Ş., Kokkola, T., Emecen, G., Lappalainen, J., Kaarniranta, K., Atalay, M.
Number of pages: 4
Pages: 25-28
Publication date: 1 Jan 2014
Peer-reviewed: Yes

Publication information

Journal: REDOX BIOLOGY
Volume: 3
ISSN (Print): 2213-2317
Ratings: 
  • Scopus rating (2014): CiteScore 5.13 SJR 1.584 SNIP 1.24
Original language: English
ASJC Scopus subject areas: Biochemistry, Organic Chemistry
Keywords: Garra rufa, Oxidation, Regulation, Stress, Thermal
Source: Scopus
Source ID: 84912102339

Research output: Contribution to journalArticleScientificpeer-review

Both zundel and eigen isomers contribute to the IR spectrum of the gas-phase H9O4 + cluster

The "Eigen cation", H3O+(H 2O)3, is the most prevalent protonated water structure in the liquid phase and the most stable gas-phase isomer of the H +(H2O)4 cluster. Nevertheless, its 50 K argon predissociation vibrational spectrum contains unexplainable low frequency peak(s). We have simulated the IR spectra of 10 gas-phase H+(H 2O)4 isomers, that include zero to three argon ligands, using dipole autocorrelation functions from ab initio molecular dynamics with the CP2K software. We have also tested the effect of elevated temperature and dispersion correction. The Eigen isomers describe well the high frequency portion of the spectrum but do not agree with experiment below 2000 cm -1. Most notably, they completely lack the "proton transfer bands" observed at 1050 and 1750 cm-1, which characterize Zundel-type (H5O2+) isomers. In contrast, linear isomers with a Zundel core, although not the lowest in energy, show very good agreement with experiment, particularly at low frequencies. Peak assignments made with partial velocity autocorrelation functions verify that the 1750 cm-1 band does not originate with the Eigen isomer but is rather due to coupled proton transfer/water bend in the Zundel isomer.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Tallinn Technical University, Institute of Chemistry, Hebrew University of Jerusalem
Contributors: Kulig, W., Agmon, N.
Number of pages: 9
Pages: 278-286
Publication date: 9 Jan 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 118
Issue number: 1
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2014): CiteScore 3.28 SJR 1.449 SNIP 1.13
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84892594412

Research output: Contribution to journalArticleScientificpeer-review

Azopolymer-based micro- and nanopatterning for photonic applications

Azopolymers comprise a unique materials platform, in which the photoisomerization reaction of azobenzene molecules can induce substantial material motions at molecular, mesoscopic, and even macroscopic length scales. In particular, amorphous azopolymer films can form stable surface relief patterns upon exposure to interfering light. This allows obtaining large-area periodic micro- and nanostructures in a remarkably simple way. Herein, recent progress in the development of azopolymer-based surface-patterning techniques for photonic applications is reviewed. Starting with a thin azopolymer layer, one can create a variety of photonic elements, such as diffraction gratings, microlens arrays, plasmonic sensors, antireflection coatings, and nanostructured light-polarization converters, either by using the azopolymer surface patterns themselves as optical elements or by utilizing them to microstructure or nanostructure other materials. Both of these domains are covered, with the aim of triggering further research in this fascinating field of science and technology that is far from being harnessed. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 163-182 The aim of this review is to cover the existing research and trigger future research on the development of azopolymer-based micro- and nanopatterning techniques for applications in photonics. These techniques exploit a remarkably simple inscription of large-area surface relief gratings on azopolymer films. Starting with such an azopolymer pattern, one can create a variety of photonic elements, including diffraction gratings, distributed Bragg reflectors, microlens arrays, plasmonic sensors, antireflection coatings, and nanostructured converters of light polarization.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Aalto University
Contributors: Priimagi, A., Shevchenko, A.
Number of pages: 20
Pages: 163-182
Publication date: 1 Feb 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Polymer Science. Part B, Polymer Physics
Volume: 52
Issue number: 3
ISSN (Print): 0887-6266
Ratings: 
  • Scopus rating (2014): CiteScore 3.91 SJR 1.503 SNIP 1.412
Original language: English
ASJC Scopus subject areas: Condensed Matter Physics, Physical and Theoretical Chemistry, Polymers and Plastics, Materials Chemistry
Keywords: azo polymers, isomer/isomerization, lithography, nanotechnology, periodic arrays, photonics; surface-relief grating
Source: Scopus
Source ID: 84890653328

Research output: Contribution to journalArticleScientificpeer-review

Fabrication of ssDNA/oligo(ethylene glycol) monolayers by promoted exchange reaction with thiol and disulfide substituents

Biorepulsive oligo(ethylene glycol)-substituted alkanethiolate (OEG-AT) monolayers on gold can serve as primary templates for promoted (by electron irradiation) exchange reaction with thiolated ssDNA species, resulting in the formation of mixed OEG-AT/ssDNA monolayers of desired composition. Here we test the ability of alternative, disulfide precursors to serve as substituents in such a reaction. Two representative molecules, based on adenine-based homo-oligonucleotide (25-mer), were used, viz., asymmetric disulfide with a short second chain (A25SSOH) and symmetric disulfide (A25SSA25). The results were compared to the reference system of thiolated ssDNA (A25SH). Both disulfide precursors were found to be suitable for the reaction, further extending the types of commercially available compounds which can be used for this approach. A25SSOH exhibited quite high efficiency, similar to A25SH, while the efficiency of A25SSA25 was noticeably lower, especially at low irradiation doses (2). Also, the single component, A25SSA25-based ssDNA monolayer, was of lower quality as compared to the films prepared from the A25SH and A25SSOH precursors. The above observations were explained by the bulky character and conformational flexibility of A25SSA25, which hinder the proper assembly and efficient exchange reaction.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Universitat Heidelberg
Contributors: Khan, M. N., Zharnikov, M.
Number of pages: 9
Pages: 3093-3101
Publication date: 13 Feb 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry C
Volume: 118
Issue number: 6
ISSN (Print): 1932-7447
Ratings: 
  • Scopus rating (2014): CiteScore 5.08 SJR 2.032 SNIP 1.435
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Energy(all)
Source: Scopus
Source ID: 84894037828

Research output: Contribution to journalArticleScientificpeer-review

Deciphering the infrared spectrum of the protonated water pentamer and the hybrid Eigen-Zundel cation

Traditionally, infrared band assignment for the protonated water clusters, such as H+(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H+(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Hebrew University of Jerusalem
Contributors: Kulig, W., Agmon, N.
Number of pages: 9
Pages: 4933-4941
Publication date: 14 Mar 2014
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 16
Issue number: 10
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2014): CiteScore 4.29 SJR 1.771 SNIP 1.231
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 84894129482

Research output: Contribution to journalArticleScientificpeer-review

Protein conformation as a regulator of cell-matrix adhesion

The dynamic regulation of cell-matrix adhesion is essential for tissue homeostasis and architecture, and thus numerous pathologies are linked to altered cell-extracellular matrix (ECM) interaction and ECM scaffold. The molecular machinery involved in cell-matrix adhesion is complex and involves both sensory and matrix-remodelling functions. In this review, we focus on how protein conformation controls the organization and dynamics of cell-matrix adhesion. The conformational changes in various adhesion machinery components are described, including examples from ECM as well as cytoplasmic proteins. The discussed mechanisms involved in the regulation of protein conformation include mechanical stress, post-translational modifications and allosteric ligand-binding. We emphasize the potential role of intrinsically disordered protein regions in these processes and discuss the role of protein networks and co-operative protein interactions in the formation and consolidation of cell-matrix adhesion and extracellular scaffolds.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Fimlab Laboratories Ltd, University of Geneva
Contributors: Hytönen, V. P., Wehrle-Haller, B.
Number of pages: 16
Pages: 6342-6357
Publication date: 14 Apr 2014
Peer-reviewed: Yes

Publication information

Journal: Physical Chemistry Chemical Physics
Volume: 16
Issue number: 14
ISSN (Print): 1463-9076
Ratings: 
  • Scopus rating (2014): CiteScore 4.29 SJR 1.771 SNIP 1.231
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Physics and Astronomy(all)
Source: Scopus
Source ID: 84896364401

Research output: Contribution to journalArticleScientificpeer-review

Microphase mechanism of "superquenching" of luminescent probes in aqueous solutions of DNA and some other polyelectrolytes

A new approach in terms of microphase model of aqueous solutions of polyelectrolytes is proposed for explanation of a very strong quenching of luminescent probes ("superquenching") in these solutions. This phenomenon is used in literature for creation of extremely sensitive chemical and biosensors and was attributed predominantly to efficient energy or electron transfer. Microphase approach considers this phenomenon in terms of local concentrations of both the luminescent compound and of the quencher in microphase, formed by DNA and other polyelectrolytes, which can be several (4-10) orders of magnitude greater than their apparent concentrations in solution. Large local concentrations of the light absorbing centers in the microphase also provide conditions for aggregation of these centers and efficient energy transfer, which provides a significant increase in quenching constants (∼102-105). Microphase approach provides good quantitative description of all the features of the superquenching, new possibilities for analysis and control of kinetics of DNA reactions, and for improvement of the sensitivity of luminescent sensors. It reveals nonspecific localization of the luminescent centers and of Aun nanoparticles in different positions of DNA molecules that hinders from the simultaneous use of optical methods and electron or tunneling microscopy for the combined study of the structure of DNA.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Moscow State University, Emanuel’ Institute of Biochemical Physics, Russian Academy of Sciences
Contributors: Kuzmin, M. G., Soboleva, I. V., Durandin, N. A., Lisitsyna, E. S., Kuzmin, V. A.
Number of pages: 8
Pages: 4245-4252
Publication date: 17 Apr 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 118
Issue number: 15
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2014): CiteScore 3.28 SJR 1.449 SNIP 1.13
Original language: English
ASJC Scopus subject areas: Surfaces, Coatings and Films, Physical and Theoretical Chemistry, Materials Chemistry
Source: Scopus
Source ID: 84899003075

Research output: Contribution to journalArticleScientificpeer-review

Light-fuelled transport of large dendrimers and proteins

This work presents a facile water-based supramolecular approach for light-induced surface patterning. The method is based upon azobenzene- functionalized high-molecular weight triazine dendrimers up to generation 9, demonstrating that even very large globular supramolecular complexes can be made to move in response to light. We also demonstrate light-fuelled macroscopic movements in native biomolecules, showing that complexes of apoferritin protein and azobenzene can effectively form light-induced surface patterns. Fundamentally, the results establish that thin films comprising both flexible and rigid globular particles of large diameter can be moved with light, whereas the presented material concepts offer new possibilities for the yet marginally explored biological applications of azobenzene surface patterning.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, COMP Centre of Excellence, Department of Applied Physics, Aalto University, Aalto University, Texas Christian University
Contributors: Koskela, J. E., Liljeström, V., Lim, J., Simanek, E. E., Ras, R. H. A., Priimagi, A., Kostiainen, M. A.
Number of pages: 4
Pages: 6850-6853
Publication date: 14 May 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of the American Chemical Society
Volume: 136
Issue number: 19
ISSN (Print): 0002-7863
Ratings: 
  • Scopus rating (2014): CiteScore 11.92 SJR 6.294 SNIP 2.573
Original language: English
ASJC Scopus subject areas: Chemistry(all), Catalysis, Biochemistry, Colloid and Surface Chemistry, Medicine(all)
Source: Scopus
Source ID: 84900818359

Research output: Contribution to journalArticleScientificpeer-review

Bioprocessing of enhanced cellulase production from a mutant of Trichoderma asperellum RCK2011 and its application in hydrolysis of cellulose

A mutant strain of Trichoderma asperellum RCK2011 was developed through UV-irradiation for enhanced cellulase production and lower catabolite repression. The production of FPase, CMCase and β-glucosidase was optimized under solid state fermentation; up to 20 mM of glucose did not inhibit cellulase production. The mutant strain T. asperellum SR1-7 produced FPase (2.2 IU/gds), CMCase (13.2 IU/gds), and β-glucosidase (9.2 IU/gds) under optimized conditions, which is, 1.4, 1.3, 1.5-fold higher than the wild type. The wild as well as mutant strain produced the cellulases at pH range, 4.0-10.0. Saccharification of pretreated corn cob, wheat straw, and sugarcane bagasse by cellulase from mutant strain SR1-7 resulted in release of reducing sugar at the rate of 530.0 mg/g, 290.0 mg/g, and 335.0 mg/g of substrate, respectively; this is 1.6-fold higher than the wild type strain. © 2014 Published by Elsevier Ltd.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Tampere University of Technology, Urban circular bioeconomy (UrCirBio), Department of Microbiology, University of Delhi South Campus, Lignocellulose Biotechnology Laboratory
Contributors: Raghuwanshi, S., Deswal, D., Karp, M., Kuhad, R. C.
Number of pages: 7
Pages: 183-189
Publication date: 15 May 2014
Peer-reviewed: Yes

Publication information

Journal: Fuel
Volume: 124
ISSN (Print): 0016-2361
Ratings: 
  • Scopus rating (2014): CiteScore 4.14 SJR 1.634 SNIP 2.281
Original language: English
ASJC Scopus subject areas: Fuel Technology, Energy Engineering and Power Technology, Chemical Engineering(all), Organic Chemistry
Keywords: Alkaline cellulase, Catabolite repression, Saccharification, Solid state fermentation

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2014-03-15

Source: researchoutputwizard
Source ID: 1327

Research output: Contribution to journalArticleScientificpeer-review

Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics

Neutron scattering experiments were performed on 6 m LiCl solutions in order to obtain the solvation structure around the chloride ion. Molecular dynamics simulations on systems mirroring the concentrated electrolyte conditions of the experiment were carried out with a variety of chloride force-fields. In each case the simulations were run with both full ionic charges and employing the electronic continuum correction (implemented through charge scaling) to account effectively for electronic polarisation. The experimental data were then used to assess the successes and shortcomings of the investigated force-fields. We found that due to the very good signal-to-noise ratio in the experimental data, they provide a very narrow window for the position of the first hydration shell of the chloride ion. This allowed us to establish the importance of effectively accounting for electronic polarisation, as well as adjusting the ionic size, for obtaining a force-field which compares quantitatively to the experimental data. The present results emphasise the utility of performing neutron diffraction with isotopic substitution as a powerful tool in gaining insight and examining the validity of force-fields in concentrated electrolyte solutions.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Institut Laue-Langevin
Contributors: Pluhařová, E., Fischer, H. E., Mason, P. E., Jungwirth, P.
Number of pages: 11
Pages: 1230-1240
Publication date: 19 May 2014
Peer-reviewed: Yes

Publication information

Journal: Molecular Physics
Volume: 112
Issue number: 9-10
ISSN (Print): 0026-8976
Ratings: 
  • Scopus rating (2014): CiteScore 1.48 SJR 0.693 SNIP 0.642
Original language: English
ASJC Scopus subject areas: Biophysics, Molecular Biology, Condensed Matter Physics, Physical and Theoretical Chemistry
Keywords: Chloride, Lithium, Molecular dynamics, Neutron scattering, Solution
Source: Scopus
Source ID: 84901191483

Research output: Contribution to journalArticleScientificpeer-review

Carbon nanotubes-filled thermoplastic polyurethane-urea and carboxylated acrylonitrile butadiene rubber blend nanocomposites

This article reports the preparation and characterization of multiwalled carbon nanotubes (MWCNTs)-filled thermoplastic polyurethane-urea (TPUU) and carboxylated acrylonitrile butadiene rubber (XNBR) blend nanocomposites. The dispersion of the MWCNTs was carried out using a laboratory two roll mill. Three different loadings, that is, 1, 3, and 5 wt % of the MWCNTs were used. The electron microscopy image analysis proves that the MWCNTs are evenly dispersed along the shear flow direction. Through incorporation of the nanotubes in the blend, the tensile modulus was increased from 9.90 ± 0.5 to 45.30 ± 0.3 MPa, and the tensile strength at break was increased from 25.4 ± 2.5 to 33.0 ± 1.5 MPa. The wide angle X-ray scattering result showed that the TPUU:XNBR blends were arranged in layered structures. These structures are formed through chemical reactions of -NH group from urethane and urea with the carboxylic group on XNBR. Furthermore, even at a very low loading, the high degree of nanotubes dispersion results in a significant increase in the electrical percolation threshold. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40341.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Engineering materials science and solutions (EMASS), COMSATS Institute of Information Technology Lahore, Leibniz-Institut für Polymerforschung Dresden E.V., Institut für Polymerwerkstoffe, Vodafone Department of Mobile Communications Systems
Contributors: Mahmood, N., Khan, A. U., Stöckelhuber, K. W., Das, A., Jehnichen, D., Heinrich, G.
Publication date: 5 Jun 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Applied Polymer Science
Volume: 131
Issue number: 11
ISSN (Print): 0021-8995
Ratings: 
  • Scopus rating (2014): CiteScore 1.76 SJR 0.664 SNIP 0.98
Original language: English
ASJC Scopus subject areas: Materials Chemistry, Polymers and Plastics, Surfaces, Coatings and Films, Chemistry(all)
Keywords: blends, elastomers, graphene and fullerenes, nanotubes, polyurethanes, rubber
Source: Scopus
Source ID: 84897664169

Research output: Contribution to journalArticleScientificpeer-review

Surface behavior of hydrated guanidinium and ammonium ions: A comparative study by photoelectron spectroscopy and molecular dynamics

Through the combination of surface sensitive photoelectron spectroscopy and molecular dynamics simulation, the relative surface propensities of guanidinium and ammonium ions in aqueous solution are characterized. The fact that the N 1s binding energies differ between these two species was exploited to monitor their relative surface concentration through their respective photoemission intensities. Aqueous solutions of ammonium and guanidinium chloride, and mixtures of these salts, have been studied in a wide concentration range, and it is found that the guanidinium ion has a greater propensity to reside at the aqueous surface than the ammonium ion. A large portion of the relative excess of guanidinium ions in the surface region of the mixed solutions can be explained by replacement of ammonium ions by guanidinium ions in the surface region in combination with a strong salting-out effect of guanidinium by ammonium ions at increased concentrations. This interpretation is supported by molecular dynamics simulations, which reproduce the experimental trends very well. The simulations suggest that the relatively higher surface propensity of guanidinium compared with ammonium ions is due to the ease of dehydration of the faces of the almost planar guanidinium ion, which allows it to approach the water-vapor interface oriented parallel to it.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Swedish University of Agricultural Sciences, Lund University, Uppsala University, FOM-Institute AMOLF, Science Park 102, Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Contributors: Werner, J., Wernersson, E., Ekholm, V., Ottosson, N., Öhrwall, G., Heyda, J., Persson, I., Söderström, J., Jungwirth, P., Björneholm, O.
Number of pages: 9
Pages: 7119-7127
Publication date: 26 Jun 2014
Peer-reviewed: Yes

Publication information

Journal: Journal of Physical Chemistry Part B
Volume: 118
Issue number: 25
ISSN (Print): 1520-6106
Ratings: 
  • Scopus rating (2014): CiteScore 3.28 SJR 1.449 SNIP 1.13
Original language: English
ASJC Scopus subject areas: Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Materials Chemistry
Source: Scopus
Source ID: 84903466740

Research output: Contribution to journalArticleScientificpeer-review

Accurate description of calcium solvation in concentrated aqueous solutions

Calcium is one of the biologically most important ions; however, its accurate description by classical molecular dynamics simulations is complicated by strong electrostatic and polarization interactions with surroundings due to its divalent nature. Here, we explore the recently suggested approach for effectively accounting for polarization effects via ionic charge rescaling and develop a new and accurate parametrization of the calcium dication. Comparison to neutron scattering and viscosity measurements demonstrates that our model allows for an accurate description of concentrated aqueous calcium chloride solutions. The present model should find broad use in efficient and accurate modeling of calcium in aqueous environments, such as those encountered in biological and technological applications.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic