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The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t(-3/2) asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Bond-order analysis is introduced to facilitate the study of cooperative many-molecule effects on proton mobility in liquid water, as simulated using the multistate empirical valence-bond methodology. We calculate the temperature dependence for proton mobility and the total effective bond orders in the first two solvation shells surrounding the H5O2+ proton-transferring complex. We find that proton-hopping between adjacent water molecules proceeds via this intermediate, but couples to hydrogen-bond dynamics in larger water clusters than previously anticipated. A two-color classification of these hydrogen bonds leads to an extended mechanism for proton mobility.© 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Protonatedwater clusters that are hydrogen-bonded to a neutralbenzene molecule are a reductionist model for protons at hydrophobicsurfaces, which are of fundamental importance in biological energytransduction processes. Of particular interest is the protonated waterdimer (“Zundel ion”) on benzene, whose gas-phase messengerIR spectrum has been previously interpreted in terms of an asymmetricbinding of the protonated water dimer to the benzene ring througha single water molecule. This “standing Eigen” isomerhas a hydronium core. We have found an alternative “crouchingZundel” isomer, which attaches to the benzene ring symmetricallyvia both of its water molecules. When Ar-tagged, it has an IR spectrumin much better agreement with experiment than the standing Eigen isomer,particularly at the lower frequencies. These conclusions are basedon static harmonic (and anharmonic) normal-mode analysis using densityfunctional theory with various (dispersion corrected) functionalsand particularly on dynamic anharmonic spectra obtained from the dipoleautocorrelation functions from classical ab initio molecular dynamicswith the BLYP, PBE, and B3LYP functionals. Possible implications toprotons on water/organic-phase interfaces are discussed. [ABSTRACT FROM AUTHOR]

We analyse the distributions of donor and acceptor HBs in liquid water and their relation to deviations from tetrahedral symmetry. Their joint, unconditional and conditional distributions are calculated at several temperatures from classical molecular dynamics trajectories for two water models. Surprisingly, the distribution of acceptor HBs terminating at the water lone-pairs is wider than the donor distribution emanating from its hydrogen atoms. This correlates with a higher probability of forming over-coordinated oxygen (OCO) atoms as compared with bifurcated hydrogen bonds (BHBs). Such bonds are possibly formed by HB exchange reactions competing with HB cleavage and formation. The latter obey the binomial distribution, whereas OCOs and BHBs deviate from it considerably. The conditional HB probabilities indicate that acceptor and donor HBs are correlated, so that forming a HB of one type increases the probability of the other, particularly for polarizable water. Conditional distributions exhibit a common intersection suggestive of two types of water structures: high coordination (tetrahedral) and low coordination (polygons). The temperature effect shows that the enthalpy required to cleave a HB in the AMOEBA polarizable model is 9.4 kJ mol-1, close to the experimental value of 10.5 kJ mol-1. As a result, the fraction of HBs decreases with T near room temperature with a slope closer to experiment than older simulations. [ABSTRACT FROM AUTHOR]

"Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.9 Å). It allows the identification of some pivotal hydrogen atoms pertinent to uncertainties concerning the protonation state of the chromophore. Applying a computer algorithm for mapping proton wires in proteins reveals the previously observed "active site wire" connecting Glu222 with the surface carboxylate Glu5. In addition, it is now possible to identify what appears to be a proton-collecting apparatus of GFP. It consists of a negative surface patch containing carboxylates, threonines, and water molecules, connected by a HB network to Glu5. Furthermore, we detect exit points via Asn146 and His148 to a hydrophobic surface region. The more extensive HB network of the present structure, as compared with earlier GFP structures, is not accidental. A systematic investigation of over 100 mutants shows a clear correlation between the observed water content of GFP X-ray structures and their resolution. With increasing water content, the proton wires become progressively larger. These findings corroborate the scenario in which the photodissociated proton from wild-type GFP can leak outside, whereafter another proton is recruited via the proton-collecting apparatus reported herein. [ABSTRACT FROM AUTHOR]