Thermal site energy fluctuations in photosystem I: New insights from MD/QM/MM calculations

We calculated the site energies of all 96 chlorophylls in a fully atomistic, trimeric and membrane-embedded model of cyanobacterial photosystem I (PDB Code: 1JB0). The resulting data set accounts for 

thermal fluctuations within the entire photosystem by sampling 40 conformational snapshots from molecular dynamics trajectories.

the electrostatic effects of the natural environment on the chlorophyll excitation by means of QM/MM calculations.

the multireference nature of chlorophyll excitations by using the high-level DFT/MRCI method in the QM region.

Analysis of the data set reveals thermal fluctuations which prevent the formation of a single prominent energy funnel in the antenna complex. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers.

v1.1.0

Added more snapshots for reaction center chlorophylls, results from statistical analysis and excitonic couplings in the point dipole approximation.

v1.0.0

Site energies, site energy shifts and absorption spectra of each chlorophyll in each snapshot, computed with and without environmental point charges. Structures and newly derived or modified force field parameters are also provided.

For a detailed overview of each file, please refer to the README.