Literature DB >> 15268273

Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra.

Kijeong Kwac1, Hochan Lee, Minhaeng Cho.   

Abstract

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.

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Year:  2004        PMID: 15268273     DOI: 10.1063/1.1633549

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  16 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

2.  Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules.

Authors:  Matthias M Waegele; Robert M Culik; Feng Gai
Journal:  J Phys Chem Lett       Date:  2011-09-23       Impact factor: 6.475

3.  Quantum corrections in vibrational and electronic condensed phase spectroscopy: line shapes and echoes.

Authors:  C P Lawrence; J L Skinner
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-22       Impact factor: 11.205

4.  Comparison of linear and 2D IR spectra in the presence of fast exchange.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2006-05-04       Impact factor: 2.991

5.  Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins.

Authors:  Thomas la Cour Jansen; Jasper Knoester
Journal:  Biophys J       Date:  2007-11-02       Impact factor: 4.033

6.  Nonlinear response of vibrational excitons: simulating the two-dimensional infrared spectrum of liquid water.

Authors:  A Paarmann; T Hayashi; S Mukamel; R J D Miller
Journal:  J Chem Phys       Date:  2009-05-28       Impact factor: 3.488

7.  2D IR provides evidence for mobile water molecules in beta-amyloid fibrils.

Authors:  Yung Sam Kim; Liu Liu; Paul H Axelsen; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-08       Impact factor: 11.205

8.  Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy.

Authors:  Kevin C Jones; Chunte Sam Peng; Andrei Tokmakoff
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-04       Impact factor: 11.205

Review 9.  Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles.

Authors:  Y-S Lin; J M Shorb; P Mukherjee; M T Zanni; J L Skinner
Journal:  J Phys Chem B       Date:  2009-01-22       Impact factor: 2.991

10.  Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  J Phys Chem B       Date:  2009-06-18       Impact factor: 2.991

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