Calculation and analysis of vibrational spectra of adenine–thymine, guanine–cytosine, and adenine–uracil complementary pairs in the condensed state

Abstract

We have calculated the frequencies of the normal vibrations of the complementary nucleic acid base pairs adenine-thymine, guanine-cytosine, adenine-uracil, corresponding to the Watson-Crick structure, and the adenine-uracil pair, corresponding to the Hoogsteen structure, in condensed states and we interpret the spectra. We determine the contributions of hydrogen bonds to the vibrational modes of the complementary pairs. We have analyzed the nature of the relative displacements of the nucleic acid bases as integral molecular units along the hydrogen bonds. We show the role of hydrogen bonds in tautomeric interconversions of complementary nucleic acid base pairs.Introduction. The hydrogen bond joining nucleic acid base pairs into an integral unit plays a number of roles that allow the DNA to fulfill its main purpose: storing and replicating genetic information. A large number of theoretical and experimental papers are available that examine various aspects of the hydrogen bond in DNA, such as the role of the hydrogen bond in formation of the spatial structure and in tautomeric interconversions, the effect of hydrogen bonds on the physicochemical properties and stability of hydrogen-bonded pairs, etc. [1][2][3][4][5][6][7]. One of the most perfect tools for studying the properties of the hydrogen bond is vibrational spectroscopy. The effect of a hydrogen bond on the vibrational spectrum can be determined by comparing the spectra of the isolated molecule and the molecule in the liquid or solid phase, or the spectra of the isolated molecule and the spectra of isolated dimers or an isolated complex of the molecule, for example with water. In all these cases the position of the bands in the IR spectra and their intensity change, which is the major carrier of information about the effect of a hydrogen bond on the change in structure and properties of the molecule.For nucleic acid base pairs, an analogous study has been carried out in the following directions: the change in the IR and Raman spectra of the complementary pairs has been studied in different phase states and different temperature intervals; the spectra of isolated nucleic acid bases have been compared with the spectra of the complementary pairs; the spectra of the pairs adenine-thymine, guanine-cytosine have been compared with the spectra of the corresponding nucleotides and nucleosides [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22]. Usually study of the experimental spectra is accompanied by nonempirical calculations of the normal vibrations and their interpretations. As shown by analysis of the vibrational spectra, in the range 200-1800 cm -1 major changes are observed in the spectra of complementary pairs compared with the

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