Paper Citing NAMD - Abstract
Etienne, Thibaud; Very, Thibaut; Perpete, Eric A.; Monari, Antonio; Assfeld, Xavier
A QM/MM Study of the Absorption Spectrum of Harmane in Water Solution and Interacting with DNA: The Crucial Role of Dynamic Effects
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4973-4980, MAY 2 2013
We present a time dependent density functional theory computation of the absorption spectra of one beta-carboline system: the harmane molecule in its neutral and cationic forms. The spectra are computed in aqueous solution. The interaction of cationic harmane with DNA is also studied. In particular, the use of hybrid quantum mechanics/molecular mechanics methods is discussed, together with its coupling to a molecular dynamics strategy to take into account dynamic effects of the environment and the vibrational degrees of freedom of the chromophore. Different levels of treatment of the environment are addressed starting from purely mechanical embedding to electrostatic and polarizable embedding. We show that a static description of the spectrum based on equilibrium geometry only is unable to give a correct agreement with experimental results, and dynamic effects need to be taken into account The presence of two stable noncovalent interaction modes between harmane and DNA is also presented, as well as the associated absorption spectrum of harmane cation.
