Paper Citing NAMD - Abstract
Cai, Kaicong; Su, Tingting; Lin, Shen; Zheng, Renhui
Molecular mechanics force field-based general map for the solvation effect on amide I probe of peptide in different micro-environments
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 117:548-556, JAN 3 2014
A general electrostatic potential map based on molecular mechanics force field for modeling the amide I frequency is presented. This map is applied to N-methylacetamide (NMA) and designed to be transferable in different micro-environments. The electrostatic potentials from solvent and peptide side chain are projected on the amide unit of NMA to induce the frequency shift of amide I mode. It is shown that the predicted amide I frequency reproduces the experimental data satisfactorily, especially when NMA in polar solvents. The amide I frequency shift is largely determined by the solvents in aqueous solution while it is dominated by the local structure of peptide in other solvent environments. The map parameters are further applied on NMA-MeOH system and the obtained IR spectra show doublet peak profile with negligible deviation from the experimental data, suggesting the usefulness of this general map for providing information about vibrational parameters of amide motions of peptide in different environments. (C) 2013 Elsevier B.V. All rights reserved.
