Proton Transport In Water Research Articles

A Multistate Empirical Valence Bond Description of Protonatable Amino Acids

The multistate empirical valence bond (MS-EVB) model, which was developed for molecular dynamics simulations of proton transport in water and biomolecular systems, is extended for the modeling of protonatable amino acid residues in aqueous environments, specifically histidine and glutamic acid. The parameters of the MS-EVB force field are first determined to reproduce the geometries and energetics of the gas phase amino acid-water clusters. These parameters are then optimized to reproduce experimental pK(a) values. The free energy profiles for acid ionization and the corresponding pK(a) values are calculated by MS-EVB molecular dynamics simulations utilizing the umbrella sampling technique, with the center of excess charge coordinate chosen as the dissociation reaction coordinate. A general procedure for fitting the MS-EVB parameters is formulated, which allows for the parametrization of other amino acid residues with protonatable groups and the subsequent use of the MS-EVB approach for molecular dynamics simulations of proton transfer processes in proteins involving protonation/deprotonation of the protonatable amino acid groups.

A polarizable multistate empirical valence bond model for proton transport in aqueous solution

A multistate empirical valence bond model for proton transport in water, which explicitly includes solvent polarization, is presented. Polarization is included for each valence-bond state via induced point dipoles, and the model is parametrized to be used with an effective path integral derived potential surface, so as to include quantum effects of the transferring proton. The new model is shown to reproduce ab initio geometries and energetics for small protonated clusters. It is also shown that the new model gives a diffusion constant for the excess proton in water, which is in good agreement with experiment, and that the qualitative features of ab initio path integral simulations [D. Marx, M. E. Tuckerman, J. Hutter, and M. Parrinello, Nature (London) 397, 601 (1999)] are well reproduced.

Kinetics of Proton Transport in Water

AbstractFor Abstract see ChemInform Abstract in Full Text.

Theoretical study of role of H 2O molecule on initial stage of reduction of O 2 molecule in active site of cytochrome c oxidase

Mechanism of formation of [Fe–O–O–H, Cu B] from [Fe–O–O, Cu B] in active site of cytochrome c oxidase was theoretically investigated. It was found that the H 2O molecule is hydrogen-bonded to both Tyr244 and His290, and is a key molecule to produce Fe–O–O–H. This H 2O molecule plays a role as a carrier of a proton toward Fe–O–O to yield [Fe–O–O–H, Cu B]. Cu B atom is formally changed from cuprous state to cupric state through transportation of a proton by the H 2O molecule. A new reaction mechanism, which we call ‘water-proton transport’ (WPT) mechanism, is proposed for the initial stage of reduction of the O 2 molecule.

Kinetics of Proton Transport in Water

The excess proton mobility in water has attracted scientific attention for more than a century. Detailed theoretical concepts and models are also presently in strong focus in efforts toward understanding this ubiquitous phenomenon. In the present report, we discuss a theoretical framework for rationalizing the excess proton mobility, based on computer simulations, theory of proton transfer (PT) in condensed media, and analysis of classical proton conductivity experiments over broad temperature ranges. The mechanistic options involved are (i) classical hydrodynamic motion of the hydronium ion (H3O+), (ii) proton transfer from hydronium to a neighboring water molecule, and (iii) structural diffusion of the Zundel complex (H5O2+), the processes all controlled by orientational fluctuations or hydrogen bond breaking in neighboring hydration shells. Spontaneous conversion of excess proton states between Zundel and hydrated hydronium states and between hydrated and bare hydronium states are the crucial parts of the scheme. A comparison between experimental data and molecular dynamics (MD) simulations shows that prototropic structural diffusion is determined by comparable contributions of the Zundel and hydrated hydronium states. The temperature dependent mobility is, moreover, determined not only by activation free energies of the three different acts of charge transfer, but also by labile equilibria between the different PT clusters. The proton conduction mechanisms of the three clusters are brought into the framework of quantum mechanical PT theory in condensed media. Both the nature of the elementary act and the reaction coordinates are, however, different for the two types of PT clusters. The corresponding rate constants are calculated and compared with MD simulations. Within the framework of PT theory we can also identify the nature of the kinetic deuterium isotope effect in the strongly interacting proton donor and acceptor groups in the clusters. The views and models introduced may carry over to PT in more composite, heterogeneous, and confined environments such as in polymer electrolyte membrane systems.

A comparative study of proton migration in water and deuteron transport in heavy water by means of mixed quantum/classical molecular dynamics simulation

Deuteron transfer in heavy water is investigated by means of mixed quantum/classical molecular dynamics simulation and compared to proton transport in water, which was treated in a previous study [D. Zahn, J. Brickmann, Isr. J. Chem. 39 (1999) 483]. Therein the migration of a positive charge is treated as a two-step process; (i) the displacement of a H 3O +/D 3O + ion, followed by (ii) proton/deuteron transfer to an adjacent (heavy) water molecule. The water molecules as well as the H 3O +/D 3O + ions are treated classically. The proton/deuteron transfer between two neighbor molecules is treated on the basis of a quantum degree of freedom. It is shown that our model allows a numerically very effective simulation of proton/deuteron transfer processes in aqueous solution.

The Mechanism of Hydrated Proton Transport in Water

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Mechanism of Hydrated Proton Transport in WaterTyler J. F. Day, Udo W. Schmitt, and Gregory A. VothView Author Information Department of Chemistry and Henry Eyring Center for Theoretical Chemistry 315 South 1400 East, RM 2020, University of Utah Salt Lake City, Utah 84112-0850 Cite this: J. Am. Chem. Soc. 2000, 122, 48, 12027–12028Publication Date (Web):November 14, 2000Publication History Received12 July 2000Revised16 October 2000Published online14 November 2000Published inissue 1 December 2000https://doi.org/10.1021/ja002506nCopyright © 2000 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1618Altmetric-Citations154LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (27 KB) Get e-AlertsSUBJECTS:Hydrogen,Molecules,Noncovalent interactions,Oxygen,Reaction mechanisms Get e-Alerts

The computer simulation of proton transport in water

The dynamics and energetics of an excess proton in bulk phase water are examined computationally with a special emphasis on a quantum-dynamical treatment of the nuclear motion. The potential model used, the recently developed multistate empirical valence bond (MS-EVB) approach [U. W. Schmitt and G. A. Voth, J. Phys. Chem. B 102, 5547 (1998)], is also further refined and described in more detail. The MS-EVB model takes into account the interaction of an exchange charge distribution of the charge-transfer complex with the polar solvent, which qualitatively changes the nature of the solvated complex. Classical and quantum molecular dynamics simulations of the excess proton in bulk phase water reveal that quantization of the nuclear degrees of freedom results in an increased stabilization of the solvated H5O2+ (Zundel) cation relative to the H9O4+ (Eigen) cation, though the latter is still more stable, and that a species intermediate between the two also exists. The quantum proton transport rate, which is evaluated by the centroid molecular dynamics approach, is found to be on the order of two times faster compared to a purely classical treatment of the system and in good agreement with the experimental value. Calculation of the hydrogen-bonding lifetime beyond the first solvation shell of the excess proton reveals a similar quantum enhancement factor compared to the classical regime.

Multistate Empirical Valence Bond Model for Proton Transport in Water

A multistate empirical valence bond (MS-EVB) model for describing proton transport in aqueous systems is presented. In this approach the electrostatic interaction of the solvent water molecules with an exchange charge distribution is explicitly included in the off-diagonal elements of the EVB Hamiltonian. The MS-EVB model is parametrized to reproduce geometrical and energetic quantities of selected H3O+·(H2O)N clusters. The obtained geometries, formation energies, and energy barriers are in excellent agreement with results from high-level ab initio calculations. It is furthermore applied in a classical molecular dynamics simulation of condensed-phase water with an excess proton in order to estimate the proton-transfer rate.

Molecular dynamics simulation of the proton transport in water

AbstractThe proton transport in water is treated within a mixed molecular dynamic (MD) and Monte Carlo (MC) scheme. Therein the migration of a positive charge is treated as a two step process; (i) as a displacement of a hydronium ion and (ii) as a proton transfer between a hydronium ion and an adjacent water molecule. Both, the hydronium ion and the water molecules are treated as rigid molecules. It is found that the determining step for the proton transport rate is the dissociation rate of H5O2+ complexes. In these complexes the O‐O distance is only 2.4–2.5 Å while the corresponding distance for two water molecules in solution is 2.83 Å. In the H5O2+ complex the proton does no longer belong to a single water molecule, but is delocalized between the two oxygen atoms. This situation is modelled by an exchange of the water and the hydronium every time step with a probability p = 1/2.

Proton transport in water modeled by a quantum chemical dielectric cavity model

Proton transport in water modeled by a quantum chemical dielectric cavity model

Unusual proton transfer patterns in crystalline ammonia hemihydrate (2NH3⋅H2O)

The crystalline hemihydrate of ammonia (2NH3⋅H2O) resembles water–ice in having an H-bonded network structure. However, the H bonds are all hetero in nature with the result that the hemihydrate offers a marked contrast to ice in its proton transport properties. At low temperatures ice is characterized by a very few highly mobile ion defects with the mobility believed to depend on H3O+ tunneling involving O—H—O linkages. By contrast, the hemihydrate is presumed to have an abundance of ion-pair defects (NH+4, OH−) which, the present study suggests, are lacking in mobility. As a result proton transport in water–ice at 140 K is comparatively very rapid. The ability to matrix-isolate D2O intact in crystalline ice by a codeposition at T≊125 K, was basic to the 140 K water–ice proton-transport study. Similarly, all compositions of the hemihydrate embodied in the formula xNH3⋅(2−x)ND3⋅yH2O⋅(1−y) D2O are now accessible by codeposition methods, and thermally induced proton exchange has been monitored for a number of such crystalline samples. Though little, if any, exchange occurs for the pure hemihydrate at T≊140 K, proton transfer within the ammonia subsystem can be induced by either ammonia or water doping of the hemihydrate. Since ion defects are abundant in the pure hemihydrate, the role of the dopant molecules is considered to be the mobilization of the NH+4 ion defects rather than a modification of the ion-defect concentrations, the normal dopant role in ice proton transfer. Despite the induced proton transfer within the ammonia subsystem, the water subsystem invariably remained blocked to proton transfer such that, despite reaction times of several hours at 135 K, much less than 5% of the water molecules normally experienced isotopic exchange.

The proton pump at work: Part I. The basic concept of excess proton/defect proton translocation

The Nagle-Morowitz proton pump, which is based on proton transport in water and ice, is shown to be inapplicable to weakly H-bonded proton transport systems. It is demonstrated that in weakly or non H-bonded systems protons can migrate either as excess protons H♭ using a high-lying proton conduction band or as defect protons H′ using intermediate energy levels. As H′ the protons act as positive charge carriers endowed with a very high mobility. As H′ they act as negative charge carriers. The H′ transport mechanism involves thermally activated proton tunneling. Owing to the very large mobility differences between H • and H′, > 10 6, very high potentials can be self-generated in any situation which creates a concentration gradient. Proton conductivity data on inorganic model compounds are presented. Applying these results to proton transport across biomembranes, transmembrane potentials U m , acidification Δ pH and transient phenomena can be explained as result of H • and H′ translocation.

470—The proton pump at work: Part I. The basic concept of excess proton/defect proton translocation

The Nagle-Morowitz proton pump, which is based on proton transport in water and ice, is shown to be inapplicable to weakly H-bonded proton transport systems. It is demonstrated that in weakly or non H-bonded systems protons can migrate either as excess protons H using a high-lying proton conduction band or as defect protons H′ using intermediate energy levels. As H• the protons act as positive charge carriers endowed with a very high mobility. As H′ they act as negative charge carriers. The H′ transport mechanism involves thermally activated proton tunneling. Owing to the very large mobility differences between H• and H′, > 10 6, very high potentials can be self-generated in any situation which creates a concentration gradient. Proton conductivity data on inorganic model compounds are presented. Applying these results to proton transport across biomembranes, transmembrane potentials U m , acidification Δ pH and transient phenomena can be explained as result of H• and H′ translocation.