The M_4.5N_4.5N_4.5 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.

A1 Kα-excited L_{2, 3} MM and L_{2, 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 L_{2, 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 L_{2, 3}MM transitions. The term splitting of the L_{2, 3} M_{2, 3} M_{2, 3} transition is larger than in the corresponding free-atom spectrum. This result is also supported by the SDF calculations. The L_{2, 3} M_{2, 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 L_{2, 3} M_2,3 M_{2, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Orientational order parameters for individual CH_a and CH_b 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 (16:0/18:2^Δ9.12) bilayer. The results show marked inequivalence for the CH_a and CH_b 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.

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 r_a structure and the five independent order parameters, S_αβ, for each enantiomer. It is shown that the data is consistent with the two enantiomers having an identical r_α, structure, but the order matrices differ in both the magnitudes of their elements and the orientation of their principal axes.

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.

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.

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.

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.

The experimental and theoretical ¹³C-²⁹Si spin-spin coupling tensors, ¹J_Csi, 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, Δ¹J_Csi = -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 ¹D_Csi ^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.

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.

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.

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.

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%.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.