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Rezac J.,Czech Institute of Organic Chemistry And Biochemistry | Rezac J.,Center for Biomolecules and Complex Molecular Systems | Hobza P.,Czech Institute of Organic Chemistry And Biochemistry | Hobza P.,Center for Biomolecules and Complex Molecular Systems | Harris S.A.,University of Leeds
Biophysical Journal | Year: 2010

We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular- mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5′ ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed. © 2010 by the Biophysical Society. Source


Spirko V.,Czech Institute of Organic Chemistry And Biochemistry | Spirko V.,Center for Biomolecules and Complex Molecular Systems | Rubes M.,Czech Institute of Organic Chemistry And Biochemistry | Rubes M.,Center for Biomolecules and Complex Molecular Systems | And 2 more authors.
Journal of Chemical Physics | Year: 2010

The interaction potential confining the stretching and translational motions of a molecular hydrogen physisorbed on the graphene surface has been calculated by means of the DFT/CC approach. Using a simple adiabatic separation of the stretching and translational motions, a set of effective stretching potentials is generated by performing a "finite box" integrating over the translational degrees of freedom. The resulting potentials, forming energetically narrow bands, are used to evaluate the corresponding average stretching energies, which are in turn compared to their experimental counterparts. The mass-dependent "translational" corrections of the purely stretching potential significantly improve the theory versus experiment agreement, thus evidencing their importance in the physisorption processes. Although not fully quantitative, the DFT/CC stretching potentials seem to exhibit physically correct shapes, as their morphing by only a few parameters allows for a quantitative fitting of the observed vibrational energies in terms of the effective (mass-dependent) interaction potentials. © 2010 American Institute of Physics. Source

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