Paper Citing NAMD - Abstract
Etienne, Thibaud; Gattuso, Hugo; Monari, Antonio; Assfeld, Xavier
QM/MM modeling of Harmane cation fluorescence spectrum in water solution and interacting with DNA
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:367-372, JUL 15 2014
We report the calculation of the emission spectrum of an organic fluorophore, the Harmane cation, in water solution and in interaction with DNA. The spectra have been calculated at time-dependent density functional theory level, and different descriptions of the environment have been taken into account. In particular the difference between linear-response and state-specific equilibrium polarizable continuum allows taking into account the effects of solvent reorganization. Conversely the explicit description of the solvent via hybrid quantum mechanics/molecular mechanics methods coupled with molecular dynamics will allow a description of the dynamic effects that can induce significant shifts on the absorption and emission maxima. Finally the interaction of Harmane cation with DNA is also reported, two stable interaction modes may be recognized and their emission spectrum is therefore calculated. (C) 2014 Elsevier B.V. All rights reserved.
