Literature DB >> 16460180

A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy.

Thomas la Cour Jansen1, Jasper Knoester.   

Abstract

A method for modeling infrared solvent shifts using the electrostatic field generated by the solvent is presented. The method is applied to the amide I vibration of N-methyl acetamide. Using ab initio calculations the fundamental frequency, anharmonicity, and the transition dipoles between the three lowest vibrational states are parametrized in terms of the electrostatic field. The generated map, which takes into account the electric field and its gradients at four molecular positions, is tested in a number of common solvents. Agreement of solvent shift and linewidths with experimental Fourier transform infrared (FTIR) data is found to within seven and four wave numbers, respectively, for polar solvents. This shows that in these solvents electrostatic contributions dominate solvation effects and the map is transferable between these types of solvents. The effect of motional narrowing arising from the fast solvent fluctuations is found to be substantial for the FTIR spectra. Also the two-dimensional infrared (2DIR) spectra, simulated using the constructed map, reproduce experimental results very well. The effect of anharmonicity fluctuations on the 2DIR spectra was found to be negligible.

Entities:  

Year:  2006        PMID: 16460180     DOI: 10.1063/1.2148409

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


  46 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.  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

4.  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

5.  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

6.  Two Dimensional Electronic Correlation Spectroscopy of the npi* and pipi* Protein Backbone Transitions: A Simulation Study.

Authors:  Zhenyu Li; Darius Abramavicius; Wei Zhuang; Shaul Mukamel
Journal:  Chem Phys       Date:  2007-11-15       Impact factor: 2.348

7.  Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Abeta40.

Authors:  Yung Sam Kim; Liu Liu; Paul H Axelsen; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-22       Impact factor: 11.205

8.  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

9.  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 10.  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

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