Molecular structures of G, C, A, and T bases, their derivatives, and Watson-Crick base pairs. In the case of guanine (adenine), when the substituted group at the N(9) atom is H, methyl, deoxyribose, or monophosphase deoxyribose, they are denoted as G (A), 9mG (9mA), dG (dA), and dGmP (dAmP), respectively. For the cytosine (thymine) analog, we consider C (T), 1mC (1mT), dC (dT), and dCmp (dTmP) in the present work.
Eight basis modes and their eigenvectors. The red arrows indicate the directions of vibrational transition dipoles.
IR absorption spectra of four bases, their derivatives, and Watson-Crick BP’s. Vibrational frequencies and dipole strengths were directly obtained from the DFT calculations. Each absorption line shape was assumed to be Lorentzian with vibrational dephasing constant of .
Stepwise description of the Hessian matrix reconstruction method and its application to GC base pair system.
Local mode frequencies and coupling constants obtained by using the Hessian matrix reconstruction method with its application to the GC and AT base pairs are plotted with respect to the intermolecular distance , which is the hydrogen bond length HB2.
IR absorption spectra of GC and AT base pairs are shown in this figure. The intermolecular distance varies from and from for the 9mG-1mC and 9mA-1mT base pairs, respectively.
Vibrational motions of eight normal modes in the 9mG-1mC and 9mA-1mT base pairs.
Potential energy distribution of local vibrational modes in the six normal modes of GC and AT base pairs.
Three degrees of freedom involving translation (stretch), propeller twist, and buckle motions of the two base molecules.
Basis mode frequencies and coupling constants of GC and AT base pairs are plotted with respect to the propeller twist angle .
Basis mode frequencies and coupling constants of GC and AT base pairs are plotted with respect to the buckle angle .
Geometry-optimized double- and triple-layer structures of GC and AT stacks, and with and 3.
Numerically simulated IR absorption spectra (solid curves) of multilayer and complexes (for ). The dashed curves are the IR absorption spectra directly obtained by using the dipole strengths and vibrational frequencies from the DFT calculations.
Comparisons between theoretical calculations and experiments for the carbonyl stretching and bending (scissoring) mode frequencies (in ).
Hydrogen bond lengths and angles obtained from the present calculations for GC and AT base pairs are compared with other previous works. The three (two) hydrogen bonds in a GC (AT) base pair are denoted as HB1, HB2, and HB3 (see Fig. 1).
Vibrational coupling constants (in ) obtained by using the Hessian matrix reconstruction method.
Basis mode frequencies of and for undeuterated bases (in ).
Vibrational coupling constants for double-, triple-, and quadruple-layer GC and double- and triple-layer AT base pairs (in ).
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