Paper Citing NAMD - Abstract
Xu, Xuefei; Zheng, Jingjing; Truhlar, Donald G.
Ultraviolet Absorption Spectrum of Malonaldehyde in Water Is Dominated by Solvent-Stabilized Conformations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:8026-8029, JUL 1 2015
Free energy calculations for eight enol isomers of malonaldehyde (MA) and simulation of the ultraviolet (UV) absorption spectrum in both the gas phase and water (pH = 3, where the molecule exists in neutral undeprotonated form) show that in water the two s-trans nonchelated enol conformers of MA become thermodynamically more stable than the internally hydrogen-bonded (chelated enol) conformer (CE). The pure CE conformer in water has a slightly red-shifted UV spectrum with respect to that in the gas phase, but the blue-shifted spectrum observed in water at pH 3 is dominated by solvent-stabilized conformations that have negligible populations in the gas phase. Density functional calculations with the solvation model based on density (SMD) and an ensemble-averaged vertical excitation model explain the experimental observations in detail.
