Literature DB >> 16833288

Electrostatic DFT map for the complete vibrational amide band of NMA.

Tomoyuki Hayashi1, Wei Zhuang, Shaul Mukamel.   

Abstract

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

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Year:  2005        PMID: 16833288     DOI: 10.1021/jp052324l

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  42 in total

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

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Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

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

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Journal:  Biophys J       Date:  2006-07-14       Impact factor: 4.033

3.  Two-dimensional spectroscopy at infrared and optical frequencies.

Authors:  Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-30       Impact factor: 11.205

4.  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

5.  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

6.  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

7.  Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges.

Authors:  Daniel Healion; Haitao Wang; Shaul Mukamel
Journal:  J Chem Phys       Date:  2011-03-28       Impact factor: 3.488

8.  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 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.  Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy.

Authors:  Zaizhi Lai; Nicholas K Preketes; Shaul Mukamel; Jin Wang
Journal:  J Phys Chem B       Date:  2013-04-05       Impact factor: 2.991

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