Paper Citing NAMD - Abstract
Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 015101, JAN 7 2015
Molecular dynamics simulations of the single-stranded DNA oligomer (5'-CGCGAAT TCGCG-3') in aqueous solution have been carried out at different temperatures between 160 K and 300 K. The effects of temperature on the low-frequency vibrational spectrum and local structural arrangements of water molecules hydrating the DNA strand have been explored in detail. The low-frequency density of states distributions reveal that increasingly trapped transverse water motions play a dominant role in controlling the band corresponding to O center dot center dot center dot O center dot center dot center dot O bending or transverse oscillations of hydration water at supercooled temperatures. In addition, presence of a broad band around 260 (+/- 20) cm(-1) under supercooled conditions indicates transformation from high density liquid-like structuring of hydration water at higher temperatures to that of a low density liquid at lower temperatures. It is found that long-range correlations between the supercooled hydration water molecules arise due to such local structural transition around the DNA oligomer. (C) 2015 AIP Publishing LLC.
