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Vibrational dynamics of DNA. I. Vibrational basis modes and couplings
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10.1063/1.2213257
/content/aip/journal/jcp/125/11/10.1063/1.2213257
http://aip.metastore.ingenta.com/content/aip/journal/jcp/125/11/10.1063/1.2213257

Figures

Image of FIG. 1.
FIG. 1.

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.

Image of FIG. 2.
FIG. 2.

Eight basis modes and their eigenvectors. The red arrows indicate the directions of vibrational transition dipoles.

Image of FIG. 3.
FIG. 3.

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 .

Image of FIG. 4.
FIG. 4.

Stepwise description of the Hessian matrix reconstruction method and its application to GC base pair system.

Image of FIG. 5.
FIG. 5.

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.

Image of FIG. 6.
FIG. 6.

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.

Image of FIG. 7.
FIG. 7.

Vibrational motions of eight normal modes in the 9mG-1mC and 9mA-1mT base pairs.

Image of FIG. 8.
FIG. 8.

Potential energy distribution of local vibrational modes in the six normal modes of GC and AT base pairs.

Image of FIG. 9.
FIG. 9.

Three degrees of freedom involving translation (stretch), propeller twist, and buckle motions of the two base molecules.

Image of FIG. 10.
FIG. 10.

Basis mode frequencies and coupling constants of GC and AT base pairs are plotted with respect to the propeller twist angle .

Image of FIG. 11.
FIG. 11.

Basis mode frequencies and coupling constants of GC and AT base pairs are plotted with respect to the buckle angle .

Image of FIG. 12.
FIG. 12.

Geometry-optimized double- and triple-layer structures of GC and AT stacks, and with and 3.

Image of FIG. 13.
FIG. 13.

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.

Tables

Generic image for table
Table I.

Comparisons between theoretical calculations and experiments for the carbonyl stretching and bending (scissoring) mode frequencies (in ).

Generic image for table
Table II.

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).

Generic image for table
Table III.

Vibrational coupling constants (in ) obtained by using the Hessian matrix reconstruction method.

Generic image for table
Table IV.

Basis mode frequencies of and for undeuterated bases (in ).

Generic image for table
Table V.

Vibrational coupling constants for double-, triple-, and quadruple-layer GC and double- and triple-layer AT base pairs (in ).

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/content/aip/journal/jcp/125/11/10.1063/1.2213257
2006-09-20
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Vibrational dynamics of DNA. I. Vibrational basis modes and couplings
http://aip.metastore.ingenta.com/content/aip/journal/jcp/125/11/10.1063/1.2213257
10.1063/1.2213257
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