Literature DB >> 16852342

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions.

M F DeCamp1, L DeFlores, J M McCracken, A Tokmakoff, K Kwac, M Cho.   

Abstract

The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

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Year:  2005        PMID: 16852342     DOI: 10.1021/jp050257p

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  51 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.  Chemical exchange 2D IR of hydrogen-bond making and breaking.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-22       Impact factor: 11.205

4.  Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra.

Authors:  Ziad Ganim; Andrei Tokmakoff
Journal:  Biophys J       Date:  2006-07-14       Impact factor: 4.033

5.  Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study.

Authors:  Phuong H Nguyen; Roman D Gorbunov; Gerhard Stock
Journal:  Biophys J       Date:  2006-05-26       Impact factor: 4.033

6.  The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study.

Authors:  Chi-Jui Feng; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2017-08-28       Impact factor: 3.488

Review 7.  How to turn your pump-probe instrument into a multidimensional spectrometer: 2D IR and Vis spectroscopies via pulse shaping.

Authors:  Sang-Hee Shim; Martin T Zanni
Journal:  Phys Chem Chem Phys       Date:  2008-12-10       Impact factor: 3.676

8.  Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy.

Authors:  Kyungwon Kwak; Daniel E Rosenfeld; Jean K Chung; Michael D Fayer
Journal:  J Phys Chem B       Date:  2008-10-15       Impact factor: 2.991

9.  A peptide's perspective of water dynamics.

Authors:  Ayanjeet Ghosh; Robin M Hochstrasser
Journal:  Chem Phys       Date:  2011-08-11       Impact factor: 2.348

10.  A strongly absorbing class of non-natural labels for probing protein electrostatics and solvation with FTIR and 2D IR spectroscopies.

Authors:  Ann Marie Woys; Sudipta S Mukherjee; David R Skoff; Sean D Moran; Martin T Zanni
Journal:  J Phys Chem B       Date:  2013-04-15       Impact factor: 2.991

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