Paper Citing NAMD - Abstract
Haverkort, Frank; Stradomska, Anna; Knoester, Jasper
First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8877-8890, JUL 24 2014
Using first-principles simulations, we investigated the initial steps of the self-aggregation of the dye pseudoisocyanine (PLC) in water. First, we performed molecular dynamics (MD) simulations of the self-aggregation process, in which pile-of-coins oligomers ranging from dimers to stacks of about 20 molecules formed. The oligomer structures were found to be very flexible, with the dimers entering a weakly coupled state and then returning to a stable pi-pi stacked conformation on a nanosecond time scale. The structural information from the MD simulations was combined with quantum chemical calculations to generate a time-dependent Frenkel exciton Hamiltonian for monomers, dimers, and trimers, which included vibronic coupling. This Hamiltonian, in turn, was used to calculate the absorption spectra for these systems. The simulated dimer spectrum compared well to experiment, validating the face-to-face stacked dimer arrangement found in our MD simulations. Comparison of the simulated trimer spectrum to experiment suggested that oligomers larger than the dimer cannot be abundant at the onset of J-aggregation. Finally, the conformation of the PLC J-aggregate was investigated by testing the stability of several possible conformations in our MD simulations; none of the tested structures was found to be stable.
