Paper Citing NAMD - Abstract
Walch, Stephen P.; Komadina, Jason D.; Prinz, Fritz B.
A Computational Comparison of Electron Transfer from Reduced Ferredoxin to Flavin Adenine Dinucleotide and a Gold Electrode
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7298-7307, MAY 21 2009
We have carried out calculations of the electronic structure of ferredoxin and of the electronic coupling matrix element H(if) for electron transfer from reduced ferredoxin to flavin adenine dinucleotide (FAD) and to cluster models of the Au111 surface and a Au111 surface with a mercaptopyridene self-assembled monolayer (SAM). We conclude, based on H(if)(2), that a gold electrode is similar to 14 times less efficient as an electron acceptor than FAD and that the mercaptopyridine SAM enhances electron transfer. The magnitude of H(if) is large enough for these systems that the weak coupling limit approximations may no longer be valid. However, the barrier to electron transfer in the strong coupling limit is computed to be small due to minimal geometry change between oxidized and reduced ferredoxin. MD simulations of the interaction of ferredoxin and protonated pyridine within a water solvation box indicate that the protonated pyridine does strongly orient the ferredoxin, favoring electron transfer as compared to a bare gold surface, where we speculate the orientation of the ferredoxin may be more random.
