Paper Citing NAMD - Abstract
Ghane, Tahereh; Brancolini, Giorgia; Varsano, Daniele; Di Felice, Rosa
Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10693-10702, SEP 6 2012
We present a combined investigation of the dynamics and optics of triplex DNA, based on classical molecular dynamics and time-dependent density functional theory. Our approach is devised to include the effects of conformational fluctuations on the electronic structure and optical excitations of the system. We find that the structural flexibility has a strong role in the determination of the optical signals. Our results allow us to unravel the peculiar fingerprints of Watson-Crick and Hoogsteen H-bonding in the optical absorption spectra. We find a specific optical absorption feature that is due to the simultaneous presence of the two H-bonding patterns in C(+)GC triplets. While this peculiar triplet signal is wiped out in some structures that are representative of the finite-temperature dynamics, it can be recovered in an average view, so that it is a pristine result of this work.
