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Issue 40, 2009
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Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

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Abstract

A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute–solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency–time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.

Graphical abstract: Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

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Publication details

The article was received on 26 May 2009, accepted on 14 Jul 2009 and first published on 05 Aug 2009


Article type: Paper
DOI: 10.1039/B910269H
Citation: Phys. Chem. Chem. Phys., 2009,11, 9149-9159
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    Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

    K. Cai, C. Han and J. Wang, Phys. Chem. Chem. Phys., 2009, 11, 9149
    DOI: 10.1039/B910269H

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