Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes

The vibrational spectra of the nucleic acid bases adenine, thymine, guanine, and cytosine are calculated in the frame of density functional theory Ž . DFT . In particular we use the Kohn]Sham scheme with gradient corrections for exchange and correlation to determine normal modes, frequencies, and intensities. The DFT results are found to be in good agreement with the experiment. Our computations provide assignments for IR, Raman, and neutron inelastic scattering spectroscopies; yield characteristic vibrational fingerprints of each compound for its identification in larger systems; and show general vibrational trends of nucleic acids. The Kohn]Sham scheme is further applied to obtain the spectra of the Watson]Crick pairs adenine-thymine and guaninecytosine. A large number of monomeric vibrations are recognized in dimers; characteristic vibrations of pairs, which are mainly attributed to hydrogen bridges, are quantified according to changes in normal modes and frequency shifts. Binding and zero-point vibrational energies are analyzed to establish the stability of the complexes and discuss the quality of the energetic calculations. Q 1999 John Wiley & Sons, Inc. J Comput Chem 20: 511]530, 1999