title: "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis.
abstract: Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.
authors.affiliation: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA.
authors.forename: Demian
authors.initials: D
authors.lastname: Riccardi
authors.forename: Peter
authors.initials: P
authors.lastname: König
authors.forename: Xavier
authors.initials: X
authors.lastname: Prat-Resina
authors.forename: Haibo
authors.initials: H
authors.lastname: Yu
authors.forename: Marcus
authors.initials: M
authors.lastname: Elstner
authors.forename: Thomas
authors.initials: T
authors.lastname: Frauenheim
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
mesh_terms: D019342:Acetic Acid / Q000737:chemistry; D001665:Binding Sites; D024402:Carbonic Anhydrase II / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D003198:Computer Simulation; D006639:Histidine / Q000235:genetics / Q000378:metabolism; D007093:Imidazoles / Q000737:chemistry; D008745:Methylation; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009154:Mutation / Q000235:genetics; D010100:Oxygen / Q000737:chemistry; D011522:Protons; D012996:Solutions; D055672:Static Electricity
chemical_list: D007093:Imidazoles; D011522:Protons; D012996:Solutions; D006639:Histidine; C029899:imidazole; D024402:Carbonic Anhydrase II; D019342:Acetic Acid; D010100:Oxygen