Electron transfer and other reactions in proteins – towards an understanding of the effects of quantum decoherence

We have embarked on a multistage research program on the multiscale theory, simulation, computation and understanding of electron transfer and other reactions in complex bio-systemsi.     Our entry into the fieldi was our recent tunneling pathway analysis on molecular dynamics simulations of the methylamine dehydrogenase (MADH)—amicyanin (Am) redox pair. We found that the most frequently occurring molecular configurations afford superior electronic coupling, via a hydrogen-bonded “water bridge” between donor and acceptor. Surface residues are crucial to the recognition and dynamic docking of the proteins as well as the organisation of the aqueous environment at the active site, increasing the lifetime of the water bridge. Mutant complexes fail to achieve the same bridge stability. A second contributionii reports our first attempts to understand the effects of quantum decoherence on the rates of chemical reactions. Multiple-state reaction rates can be estimated within semi-classical approaches provided the hopping probability between the quantum states is taken into account. This probability is intimately related to the transition from the fully quantum to the semi-classical description, but this issue is not adequately handled with kinetic models commonly in use that so far have treated this transition only in a perturbative manner. Quantum nuclear effects like decoherence and dephasing are not present in the rate constant expressions. Retaining the intuitive semi-classical picture, we included these effects through the introduction of a phenomenological quantum decoherence function. In addition to the electronic coupling term, a characteristic decoherence time τdec now also appears as a key parameter of the rate constant. The introduction of this new dimension may imply profound changes to our understanding of chemical reactivity. The new formula has been tested by means of Density Functional Theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct and for an electron-transfer model involving a Li donor and a Li+ acceptor, separated by up to five peptide units. We are now setting up to re-examine the MADH- Am with this new method, hence avoiding the empiricism of the pathway model.