In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm-1. However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D2O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the 18O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.
Bibliographical noteFunding Information:
This work was supported by the CRIP grant from Korea Science and Engineering Foundation (KOSEF), MOST. One of the authers (C.L.) thanks Dr. S. Hahn for helpful discussions and providing the computer program for numerically calculating 2D photon echo spectra.
ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry