Progress and challenges in simulating and understanding electron transfer in proteins

Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

“…We introduce the ability of the electronic density of the heme in cytochrome c to redistribute in response to a thermal fluctuation of the bath. This goal is shared by essentially all QM/MM algorithms which all start by defining the quantum center, i.e., a part of the system which can be treated on the quantum-mechanical (QM) level53040424344. The choice of the level of QM calculations is dictated by the physics of the problem and, to a large degree, by the time-scale required to capture the essential collective modes of the thermal bath contributing to the activation barrier45.…”

Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase

“…Conceptual DFT calculations and topological analysis of electron density, which have been applied to P450 and other enzymes [ 174 , 175 ], could provide unprecedented insight into the chemical properties of NOSox active site during oxidation [ [176] , [177] , [178] ]. Use of QM/MM and DFTB-QM/MM metadynamics might also be considered for studying electron transfer from the reductase to the oxygenase domain and identifying the key players involved in this process [ [179] , [180] , [181] ]. Overall, there is a wide range of possibilities for the study of NOS molecular mechanisms with molecular modeling and simulations, opening perspectives that could lead to important breakthroughs on this topic.…”

Ultrafast photoinduced energy and charge transfer

“…This expression applies provided nuclear motion is treated classically, a reasonable approximation in the high temperature limit, and if the electronic coupling between the ET states is weak, typically below a few tens of cm À1 . 48 Goldsmith et al (DOI: 10.1039/c8fd00240a) present in this issue a nice discussion of Marcus theory applied to the case of photoinduced proton-coupled-electrontransfer.…”