Paper Citing NAMD - Abstract
Maekawa, Hiroaki; Ge, Nien-Hui
Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1434-1446, JAN 28 2010
We have carried out a comparative Study of five ab initio electrostatic frequency maps and a semiempirical model for the amide-I and -II modes. Unrestrained molecular dynamics Simulation of a 3(10)-helical peptide, Z-Aib-L-Leu-(Aib)(2)-Gly-OtBu, in CDCl(3) is performed using the AMBER ff99SB force field, and the linear and two-dimensional infrared (2D IR) spectra are simulated oil the basis of a vibrational exciton Hamiltonian model. A new electrostatic potential-based amide-I and -II frequency map for N-methylacetamide is developed in this study. This map and other maps developed by different research groups are applied to calculate the local mode frequencies of the amide linkages ill the hexapeptide. The simulated amide-I line shape from all models agrees well with the previous experimental results on the same system, except for ail overall frequency shift. In contrast, the Simulated amide-II bands are more sensitive to the frequency maps. Essential features obtained in the electrostatic models are captured by the semiempirical model that takes into account only the intramolecular hydrogen bonding effects and solvent shifts. Detailed comparisons between the models are also drawn through analysis of the local mode frequency shifts. Among all of the maps tested in this study, the new four-site potential map performs quite well in Simulating the amide-II bands. It properly predicts the effects of hydrogen bonding oil the amide-I and -II frequencies and reasonably simulates the isotope-dependent amide-I/II cross peaks upon (13)C=(18)O/(15)N substitutions.
