Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG_n: dC _n and dA_n: dT_n double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG₅C ₅ and dA₅T₅ double helices in D₂O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP/6-31G* calculations for the nine basis modes. The simulated 2D IR spectra of dG_n: dC_n double helix in D ₂O solution are directly compared with closely related experimental results. The 2D IR spectra of dG_n: dC_n and dA _n: dT_n are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.