In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton poten...

The mixed quantum/classical molecular dynamics with quantum transitions ~MDQT! method is extended to treat the donor–acceptor vibrational motion as well as the hydrogen motion quantum mechanically for proton transfer reactions. The quantum treatment of both the hydrogen and the donor–acceptor motions requires the calculation of two-dimensional vibrational wave functions. The MDQT surface hoppin...

Histidine is a very common metal ligand in metalloenzymes. Besides being an efficient Lewis base, its electronic properties are essential to shape the metal ability to catalyze the reaction. Here we show that histidine's properties can be tuned, in turn, by an easy proton transfer to a nearby glutamate. We study this situation in Human Carbonic Anhydrase II (HCA II) in which one of the three hi...

The nucleotide sequence of the structural gene for benzyl alcohol dehydrogenase encoded by TOL plasmid pWWO of Pseudomonas putida has been determined. Benzyl alcohol dehydrogenase is a member of the long-chain zinc alcohol dehydrogenase family and, like other alcohol dehydrogenases of this family, contains two zinc atoms per subunit. Benzyl alcohol dehydrogenase, while sharing 31% identical res...

Histidine is a very common metal ligand in metalloenzymes. Besides being an efficient Lewis base, its electronic properties are essential to shape the metal ability to catalyze the reaction. Here we show that histidine’s properties can be tuned, in turn, by an easy proton transfer to a nearby glutamate. We study this situation in Human Carbonic Anhydrase II (HCA II) in which one of the three hi...

We have computed the free energy profiles of the deprotonation reactions of lumiflavin in the semiquinone and fully reduced oxidation states using constrained DFT-based molecular dynamics simulations. In the semiquinone state, the N5 nitrogen atom and the N1 nitrogen atom can become protonated. We find, in agreement with experiment, that the N5 site is the predominant proton acceptor in the sem...

The dynamic nature of hydrogen bonds in phenolic polymers, where the hydrogen bond donor/acceptor reorientation can occur in a single site, presents lower barriers for proton transport.

A comparison of hydride, hydrogen atom, and proton-coupled electron transfer reactions is presented. Herein, hydride and hydrogen atom transfer refer to reactions in which the electrons and protons transfer between the same donor and acceptor, while proton-coupled electron transfer (PCET) refers to reactions in which the electrons and protons transfer between different centers. Within these def...

According to current estimates, the photosynthetic water oxidase functions with a quite restricted driving force. This emphasizes the importance of the catalytic mechanisms in this enzyme. The general problem of coupling electron and proton transfer is discussed from this viewpoint and it is argued that 'weak coupling' is preferable to 'strong coupling'. Weak coupling can be achieved by facilit...