The large interest in long-range proton transfer in biomolecules is triggered by its importance for many biochemical processes such as biological energy transduction and drug detoxification. Since long-range proton transfer occurs on a microsecond time scale, simulating this process on a molecular level is still a challenging task and not possible with standard simulation methods. In general, t...

Bacteriorhodopsin, a light activated protein that creates a proton gradient in halobacteria, has long served as a simple model of proton pumps. Within bacteriorhodopsin, several key sites undergo protonation changes during the photocycle, moving protons from the higher pH cytoplasm to the lower pH extracellular side. The mechanism underlying the long-range proton translocation between the centr...

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. ...

A detailed theoretical investigation of the charge transport mechanism in poly(4-vinyl-imidazole) (P4VI), the parent polymer of a series of N-heterocyclic-based membranes used as an electrolyte in proton exchange membrane fuel cells, is presented. In particular, Density Functional Theory (DFT) results obtained for small model systems (protonated imidazole dimers and trimers) suggest that the co...

a new proton transfer compound, formulated as (hamp-6-pic)(hpyzd) ∙h2o (1), has been synthesized from the reaction of pyrazine-2,3-dicarboxylic acid (h2pyzd)  and 2-amino-6-methyl pyridine (amp-6-pic), in 1:1 molar ratio. extensive o−h×××o, n−h×××n and o−h×××o hydrogen bonds involving (hamp-6-pic)+ cation, (hpyzd)- anion and co-crystal water molecule٫ static electronic٫ and π…π stacking interac...

This article presents the methodology we have developed for the simulation of hydrogen transfer reactions, including multiple proton transfer and proton-coupled electron transfer reactions. The central method discussed is molecular dynamics with quantum transitions (MDQT), which is a mixed quantum/classical surface hopping method that incorporates nonadiabatic transitions between the proton vib...

We have performed ab initio molecular dynamics simulations to study the nature of the synchronous double proton transfer in formic acid dimer. In order to understand the evolution of the bonding during the double proton transfer, we have used the electron localization function and the molecular orbital isosurfaces. During the dynamics of the double proton transfer in formic acid dimer the two f...

Proton transfer plays an important role in the optical properties of green fluorescent protein (GFP). While much is known about excited-state proton transfer reactions (ESPT) in GFP occurring on ultrafast time scales, comparatively little is understood about the factors governing the rates and pathways of ground-state proton transfer. We have utilized a specific isotopic labeling strategy in co...

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...

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 sys tem as a function of proton donor proton acceptor distance as well as nonbonding parameters By classical molecular dynamics we evaluate a swarm of proton po ten...