Paper Citing NAMD - Abstract
Cai, Kaicong; Du, Fenfen; Zheng, Xuan; Liu, Jia; Zheng, Renhui; Zhao, Juan; Wang, Jianping
General Applicable Frequency Map for the Amide-I Mode in beta-Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1069-1079, FEB 18 2016
In this work, a general applicable amide-I vibrational frequency map (GA map) for beta-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for beta-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in beta-polypeptides.
