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Aqueous cation-amide binding: Free energies and IR spectral signatures by ab initio molecular dynamics

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Aqueous cation-amide binding : Free energies and IR spectral signatures by ab initio molecular dynamics. / Pluhařová, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel.

In: Journal of Physical Chemistry Letters, Vol. 5, No. 13, 03.07.2014, p. 2235-2240.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Pluhařová, E, Baer, MD, Mundy, CJ, Schmidt, B & Jungwirth, P 2014, 'Aqueous cation-amide binding: Free energies and IR spectral signatures by ab initio molecular dynamics', Journal of Physical Chemistry Letters, vol. 5, no. 13, pp. 2235-2240. https://doi.org/10.1021/jz500976m

APA

Pluhařová, E., Baer, M. D., Mundy, C. J., Schmidt, B., & Jungwirth, P. (2014). Aqueous cation-amide binding: Free energies and IR spectral signatures by ab initio molecular dynamics. Journal of Physical Chemistry Letters, 5(13), 2235-2240. https://doi.org/10.1021/jz500976m

Vancouver

Pluhařová E, Baer MD, Mundy CJ, Schmidt B, Jungwirth P. Aqueous cation-amide binding: Free energies and IR spectral signatures by ab initio molecular dynamics. Journal of Physical Chemistry Letters. 2014 Jul 3;5(13):2235-2240. https://doi.org/10.1021/jz500976m

Author

Pluhařová, Eva ; Baer, Marcel D. ; Mundy, Christopher J. ; Schmidt, Burkhard ; Jungwirth, Pavel. / Aqueous cation-amide binding : Free energies and IR spectral signatures by ab initio molecular dynamics. In: Journal of Physical Chemistry Letters. 2014 ; Vol. 5, No. 13. pp. 2235-2240.

Bibtex - Download

@article{ca292a085b114377a01b0dbea2154ed6,
title = "Aqueous cation-amide binding: Free energies and IR spectral signatures by ab initio molecular dynamics",
abstract = "Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (IR) shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Because sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water.",
keywords = "calcium, N -methylacetamide, peptide bond, sodium, umbrella sampling",
author = "Eva Pluhařov{\'a} and Baer, {Marcel D.} and Mundy, {Christopher J.} and Burkhard Schmidt and Pavel Jungwirth",
year = "2014",
month = "7",
day = "3",
doi = "10.1021/jz500976m",
language = "English",
volume = "5",
pages = "2235--2240",
journal = "Journal of Physical Chemistry Letters",
issn = "1948-7185",
publisher = "American Chemical Society",
number = "13",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Aqueous cation-amide binding

T2 - Free energies and IR spectral signatures by ab initio molecular dynamics

AU - Pluhařová, Eva

AU - Baer, Marcel D.

AU - Mundy, Christopher J.

AU - Schmidt, Burkhard

AU - Jungwirth, Pavel

PY - 2014/7/3

Y1 - 2014/7/3

N2 - Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (IR) shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Because sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water.

AB - Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (IR) shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Because sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water.

KW - calcium

KW - N -methylacetamide

KW - peptide bond

KW - sodium

KW - umbrella sampling

UR - http://www.scopus.com/inward/record.url?scp=84903848758&partnerID=8YFLogxK

U2 - 10.1021/jz500976m

DO - 10.1021/jz500976m

M3 - Article

VL - 5

SP - 2235

EP - 2240

JO - Journal of Physical Chemistry Letters

JF - Journal of Physical Chemistry Letters

SN - 1948-7185

IS - 13

ER -