Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA

Kaushik Chakraborty; Sanjoy Bandyopadhyay

doi:10.1063/1.4904896

Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA

J Chem Phys. 2015 Jan 7;142(1):015101. doi: 10.1063/1.4904896.

Authors

Kaushik Chakraborty¹, Sanjoy Bandyopadhyay¹

Affiliation

¹ Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.

PMID: 25573583
DOI: 10.1063/1.4904896

Abstract

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⋯O⋯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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA, Single-Stranded / chemistry*
Molecular Dynamics Simulation*
Molecular Structure
Spectrum Analysis
Temperature*
Vibration*
Water / chemistry*

Substances

DNA, Single-Stranded
Water