Intermolecular interactions in microhydrated ribonucleoside and deoxyribonucleoside: A computational study

Venkataramanan Natarajan Sathiyamoorthy, Ambigapathy Suvitha, Royoji Sahara, Yoshiyuki Kawazoe

Research output: Contribution to journalArticlepeer-review

Abstract

The nature of interactions between the ribonucleoside and deoxyribonucleoside with water molecule was examined employing the dispersion corrected density functional theory and wave functional analysis. In the nucleosides, the water binds with the 5′–OH hydrogen and N3 nitrogen or N7-H group. In the deoxynucleosides, the water binds through 3′–OH and N3 nitrogen or carbonyl oxygen. The interaction energy, binding energy, hydration entropy and enthalpy do not show any appreciable change for the nucleoside-water complexes, emulating the experimental findings. Electrostatic potential analysis shows that the most positive region is observed near the 5′–OH hydrogen atom of the ribose unit in nucleosides. In deoxynucleosides, the 3′–OH hydrogen has Vs,max values equivalent to 5′–OH hydrogen atom. Hence, the water binds with the 3′–OH hydrogen and the nucleobase. QTAIM analysis shows the presence of medium-strength hydrogen bonds between water and nucleoside. In deoxynucleoside-water complexes, in addition to the 3′–OH hydrogen bonding with water, the nearby 2′C[sbnd]H in ribose unit bonds with oxygen in the water molecule. QTAIM and EDA analysis show the intermolecular bonds are noncovalent and electrostatic dominant. The 2D RDG plot shows, additional spikes due to the interaction of 2′C hydrogen with water oxygen. The 3D spatial diagram shows the existence of several green patches in the deoxynucleoside-water complexes, associated with the weak van der Waal's interactions which make them more stable.

Original languageEnglish
Article number113422
JournalComputational and Theoretical Chemistry
Volume1204
DOIs
Publication statusPublished - 2021 Oct
Externally publishedYes

Keywords

  • AIM
  • DFT
  • Electrostatic potentials
  • Non-covalent interactions

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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