Hydration of nucleic acid bases: A Car-Parrinello molecular dynamics approach

Al'Ona Furmanchuk, Olexandr Isayev, Oleg V. Shishkin, Leonid Gorb, Jerzy Leszczynski*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment has been performed with use of Car-Parrinello molecular dynamics. Detailed analysis of average number, lifetimes and mobility of water molecules, orientation and 3D organization of hydrogen bond network in the first hydration shell of adenine, guanine, cytosine and thymine has been carried out. Effect of hydration by bulk water environment has been compared with the data from polyhydrated complexes of NABs. During bulk water hydration the presence of mixed Hw⋯N/Hw⋯π type of bonding is detected for imino nitrogen atoms. The formation of three hydrogen bonds to carbonyl groups reflects the significance of polarizing effects of aqueous environments. Hydration of hydrophobic sites revealed the presence of extremely weak bonding. Hydration of C6-H6 site of thymine is standing significantly apart from the hydration of other hydrophobic sites. An average coordination numbers of adenine, guanine, cytosine and thymine in bulk water environment are 6.87, 8.52, 6.12 and 6.42 water molecules, correspondingly. The lifetime of water molecules in the first hydration shell varies from 1 to 3 ps. Some differences in hydration studied by CPMD (bulk water) and quantum chemical (less than 20 water molecules) methods indicate a significant effect of the second hydration shell on structure and properties of the first hydration shell for the considered compounds.

Original languageEnglish (US)
Pages (from-to)3363-3375
Number of pages13
JournalPhysical Chemistry Chemical Physics
Volume12
Issue number14
DOIs
StatePublished - Apr 2 2010

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Fingerprint Dive into the research topics of 'Hydration of nucleic acid bases: A Car-Parrinello molecular dynamics approach'. Together they form a unique fingerprint.

Cite this