Paper Citing NAMD - Abstract
Wang, Jianping; Cai, Kaicong; Ma, Xiaoyan
Ultrafast Structural Dynamics of Biomolecules Examined by Multiple-Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony
CHEMPHYSCHEM, 10:2242-2250, SEP 9 2009
Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L-alpha-glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal-mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by cross peaks in the femtosecond broadband two-dimensional infrared (2D IR) spectra, which are simulated using time-domain third-order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.
