Paper Citing NAMD - Abstract
Cai, Kaicong; Wang, Jianping
Multiple Anharmonic Vibrational Probes of Sugar Structure and Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1681-1692, FEB 12 2009
Quantum mechanical computations and molecular dynamics simulations are carried out for the simplest sugar glycolaldehyde to gain insight into the underlying force fields that determine the vibrational spectroscopic parameters relevant to structure and dynamics. The harmonic and anharmonic vibrational frequencies of the 3N - 6 modes and their diagonal and off-diagonal anharmonicities are evaluated using the hybrid B3LYP functional in comparison with other high-level theories. Very good performance of B3LYP/6-31+G** is found in predicting the anharmonic frequencies by statistical analysis and by comparison to gas-phase experiments. Full cubic and semidiagonal quartic anharmonic force constants, the origin of the anharmonicities, the isotope dependence of the anharmonicities, and the polarizable continuum solvent effect on the anharmonicities are examined, in particular, for the C=O, C-H, and O-H stretching modes. Site-dependent dynamical interactions between glycolaldehyde and water molecules in the hydration shells are examined by molecular dynamics simulations employing a set of molecular mechanical force fields developed on the basis of quantum mechanical computations. The statistical distributions and correlations of the fundamental transition frequencies and transition dipoles are obtained through instantaneous normal-mode analysis. The simultaneous assessment of multiple parameters of multiple vibrational probes shall prove useful in understanding the characteristics of sugar structure and dynamics expressed in two-dimensional infrared correlation spectra.
