Using molecular dynamics and quantum mechanics calculations to model fluorescence observables.

ABSTRACT: We provide a critical examination of two different methods for generating a donor-acceptor electronic coupling trajectory from a molecular dynamics (MD) trajectory and three methods for sampling that coupling trajectory, allowing the modeling of experimental observables directly from the MD simulation. In the first coupling method we perform a single quantum-mechanical (QM) calculation to characterize the excited state behavior, specifically the transition dipole moment, of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on ea

SUBMITTER: Speelman AL 

PROVIDER: S-EPMC3087818 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature