Paper Citing NAMD - Abstract
McCullagh, Martin; Hariharan, Mahesh; Lewis, Frederick D.; Markovitsi, Dimitra; Douki, Thierry; Schatz, George C.
Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5215-5221, APR 22 2010
The paper presents quantum yield results for the [2+2] and 6-4 photodimerization of TT steps in several DNA structures, including hairpins where the context dependence of the photodimerization yield is determined, and it develops a theoretical model that correctly describes the trends in dimerization yield with DNA structure. The DNA conjugates considered include dT(20), dA(20)dT(20), and three alkane-linked hairpins that contain a single TT step. The theoretical modeling of the [2+2] process is based on CASSCF electronic structure calculations for ethylene + ethylene, which show that photoexcitation of low-lying excited states leads to potential surfaces that correlate without significant barriers to a conical intersection with the ground state surface at geometries close to the dimer structure. The primary constraint on dimerization is the distance d between the two double bonds, and it is found that d < 3.52 angstrom leads to quantum yield trends that match the observed trends within a factor of 3. Constraints on the dihedral angle between the two double bonds are not as important, and although it is possible to generate better dimerization yield predictions for some structures by including these constraints, the best overall picture is obtained with no constraint. For 6-4 dimerization, a distance g < 2.87 angstrom and no constraint on dihedral angle provide an accurate description of the yield.
