Literature DB >> 18754632

Dependence of amide vibrations on hydrogen bonding.

Nataliya S Myshakina1, Zeeshan Ahmed, Sanford A Asher.   

Abstract

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.

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Year:  2008        PMID: 18754632      PMCID: PMC2633779          DOI: 10.1021/jp8057355

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


  7 in total

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2.  The partial charge of the nitrogen atom in peptide bonds.

Authors:  E J Milner-White
Journal:  Protein Sci       Date:  1997-11       Impact factor: 6.725

3.  Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water.

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Journal:  J Phys Chem B       Date:  2005-04-28       Impact factor: 2.991

4.  The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR.

Authors:  Scott T R Walsh; Richard P Cheng; Wayne W Wright; Darwin O V Alonso; Valerie Daggett; Jane M Vanderkooi; William F DeGrado
Journal:  Protein Sci       Date:  2003-03       Impact factor: 6.725

5.  Polyproline II structure in a sequence of seven alanine residues.

Authors:  Zhengshuang Shi; C Anders Olson; George D Rose; Robert L Baldwin; Neville R Kallenbach
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-28       Impact factor: 11.205

6.  Peptide secondary structure folding reaction coordinate: correlation between uv raman amide III frequency, Psi Ramachandran angle, and hydrogen bonding.

Authors:  Aleksandr V Mikhonin; Sergei V Bykov; Nataliya S Myshakina; Sanford A Asher
Journal:  J Phys Chem B       Date:  2006-02-02       Impact factor: 2.991

Review 7.  Polyproline II structure in proteins: identification by chiroptical spectroscopies, stability, and functions.

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  7 in total
  33 in total

1.  UV resonance Raman investigation of the aqueous solvation dependence of primary amide vibrations.

Authors:  David Punihaole; Ryan S Jakubek; Elizabeth M Dahlburg; Zhenmin Hong; Nataliya S Myshakina; Steven Geib; Sanford A Asher
Journal:  J Phys Chem B       Date:  2015-02-27       Impact factor: 2.991

2.  UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide.

Authors:  Ryan S Jakubek; Stephen E White; Sanford A Asher
Journal:  J Phys Chem B       Date:  2019-02-19       Impact factor: 2.991

3.  UV resonance Raman spectroscopy monitors polyglutamine backbone and side chain hydrogen bonding and fibrillization.

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4.  Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

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Journal:  J Phys Chem B       Date:  2015-09-30       Impact factor: 2.991

5.  Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study.

Authors:  Xiuchan Xiao; Ying Tan; Lijuan Zhu; Yanzhi Guo; Zhining Wen; Menglong Li; Xuemei Pu; Anmin Tian
Journal:  J Mol Model       Date:  2011-07-15       Impact factor: 1.810

6.  A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

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7.  UV resonance Raman investigation of the conformations and lowest energy allowed electronic excited states of tri- and tetraalanine: charge transfer transitions.

Authors:  Bhavya Sharma; Sanford A Asher
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

8.  Impact of ion binding on poly-L-lysine (un)folding energy landscape and kinetics.

Authors:  Kan Xiong; Sanford A Asher
Journal:  J Phys Chem B       Date:  2012-06-06       Impact factor: 2.991

9.  Photophysical and Electrochemical Studies of 4-Dicyanomethylene 2,6-Dimethyl-4H-Pyran (DDP) Dye with Amides in Water.

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Journal:  J Fluoresc       Date:  2018-10-01       Impact factor: 2.217

10.  Dependence of the AmII'p proline Raman band on peptide conformation.

Authors:  Zeeshan Ahmed; Nataliya S Myshakina; Sanford A Asher
Journal:  J Phys Chem B       Date:  2009-08-13       Impact factor: 2.991

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