Homodimers of Cytosine and 1-MethylCytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents

  • Guvanchmyrat Paytakov
  • Leonid Gorb
  • Andriy Stepanyugin
  • Svitlana Samiylenko
  • Dmytro Hovorun
  • Jerzy Leszczynski
Original Paper

Abstract

Dimers of cytosine and its N1-methylated counterpart were investigated in gas-phase and in various solvents including chloroform, dimethylsulfoxide, and water. The studies were performed at DFT/M06-2X/6-31+G(d,p) level of theory. Relative stabilities of tautomers of cytosine solvated explicitly by a small number of solvent molecules were evaluated. Further solvation effect calculations for homodimers were carried out with conductor-like polarizable continuum model (CPCM). H-NMR shifts and IR frequencies for optimized structures were calculated and compared with available experimental data.

Keywords

Chloroform CPCM Cytosine dimer DFT DMSO H-NMR Hydrogen bonding IR frequency 1-methylcytosine dimer M06-2X π-π stacking Water 

Supplementary material

894_2014_2115_MOESM1_ESM.doc (36 kb)
Table S1(DOC 35 kb)
894_2014_2115_Fig2_ESM.jpg (673 kb)
Fig. S1

Starting geometries of cytosine and 1-methylcytosine monomers and dimers with labeled* atoms. * This labeling will be used to identify atoms and bond distances throughout this work. (JPEG 673 kb)

894_2014_2115_Fig3_ESM.jpg (289 kb)
Fig. S2

Geometry and H-NMR shifts for cytosine dimer in chloroform calculated at M06-2X/6-31+G(d,p). (JPEG 288 kb)

894_2014_2115_MOESM2_ESM.doc (316 kb)
Fig. S3(DOC 315 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Guvanchmyrat Paytakov
    • 1
  • Leonid Gorb
    • 2
  • Andriy Stepanyugin
    • 2
  • Svitlana Samiylenko
    • 2
  • Dmytro Hovorun
    • 2
  • Jerzy Leszczynski
    • 1
  1. 1.Interdisciplinary Center for Nanotoxicity, Department of Chemistry and BiochemistryJackson State UniversityJacksonUSA
  2. 2.Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Key State Laboratory in Molecular and Cell BiologyKyivUkraine

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