Proton Transfer Events Research Articles

Enantioselective protonation of α-hetero carboxylic acid-derived ketene disilyl acetals under chiral ionic Brønsted acid catalysis.

Highly enantioselective protonation of α-halo and alkoxy carboxylic acid-derived ketene disilyl acetals is achieved by using P-spiro chiral diaminodioxaphosphonium barfate as a Brønsted acid catalyst, where the enantiofacial discrimination by the catalyst mainly stems from the recognition of the electronic difference between two substituents on the ketene disilyl acetal.

Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency

Photochemical water splitting is a promising avenue to sustainable, clean energy and fuel production. Gallium nitride (GaN) and its solid solutions are excellent photocatalytic materials; however, the efficiency of the process is low on pure GaN, and cocatalysts are required to increase the yields. We present the first time-domain theoretical study of the initial steps of photocatalytic water splitting on a GaN surface. Our state-of-the-art simulation technique, combining nonadiabatic molecular dynamics and time-dependent density functional theory, allows us to characterize the mechanisms and time scales of the evolution of the photogenerated positive charge (hole) and the subsequent proton transfer at the GaN/water interface. The calculations show that the hole loses its excess energy within 100 fs and localizes primarily on the nitrogen atoms of the GaN surface, initiating a sequence of proton-transfer events from the surface N-H group to the nearby OH groups and bulk water molecules. Water splitting requires hole localization on oxygen rather than nitrogen, necessitating nonadiabatic transitions uphill in energy on pure GaN. Such transitions happen rarely, resulting in low yields of the photocatalytic water splitting observed experimentally. We conclude that efficient cocatalysts should favor localization of the photogenerated hole on oxygen-containing species at the semiconductor/water interface.

Organic Synthesis in the Interstellar Medium by Low-Energy Carbon Irradiation

We present a first principles molecular dynamics (FPMD) study of the interaction of low-energy neutral carbon projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon atom at an initial energy of 11 and 1.7 eV with 30-molecule clusters have been investigated. Simulations indicate that the formation of hydroxymethylene, an intermediate in formaldehyde production, dominates at the higher energy. The reaction proceeds by fragmenting a water molecule, binding the carbon to the OH radical, and saturating the C valence with a hydrogen atom that can arise from the originally dissociated water molecule, or through a chain of proton transfer events. We identified several possible pathways for the formation of HCOH. When the initial collision occurs at the periphery of the cluster, we observe the formation of CO and the evaporation of water molecules. At the lower energy water fragmentation is not favorable, thus leading to the formation of weakly bound carbon-water complexes.

A polarizable reactive force field for water to enable molecular dynamics simulations of proton transport

A new polarizable water model is developed for molecular dynamics (MD) simulations of the proton transport process. The interatomic potential model has three important submodels corresponding to electrostatic interactions, making and breaking of covalent bonds, and treatment of electron exchange and correlation through a van der Waals potential. A polarizable diffuse charge density function was used to describe Coulombic interactions between atoms. Most of the model parameters were obtained from ab initio data for a lone water molecule. Molecules respond realistically to their electrochemical environment by the use of coupled fluctuating charge and fluctuating dipole dynamics, which controlled the charge density. The main purpose of the work is to develop a general model and framework for future studies, though some validation work was performed here. We applied the model to a MD simulation study of bulk properties of liquid water at room temperature and model gave good agreement with thermodynamic and transport properties at the same conditions. The model was then applied to a preliminary study of proton transfer, in which multiple proton transfer events were observed, though the rate of proton transfer was under-predicted by a factor of 5.

Ground-state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa

The reversible photoswitching between the 'on' and 'off' states of the fluorescent protein Dronpa involves photoisomerization as well as protein side-chain rearrangements, but the process of interconversion remains poorly characterized. Here we use time-resolved infrared measurements to monitor the sequence of these structural changes, but also of proton transfer events, which are crucial to the development of spectroscopic contrast. Light-induced deprotonation of the chromophore phenolic oxygen in the off state is a thermal ground-state process, which follows ultrafast (9 ps) trans-cis photoisomerization, and so does not involve excited-state proton transfer. Steady-state infrared difference measurements exclude protonation of the imidazolinone nitrogen in both the on and off states. Pump-probe infrared measurements of the on state reveal a weakening of the hydrogen bonding between Arg66 and the chromophore C=O, which could be central to initiating structural rearrangement of Arg66 and His193 coinciding with the low quantum yield cis-trans photoisomerization.

Homogeneous water oxidation catalysts containing a single metal site

The recent recognition that a single metal site is capable of mediating the multiple electron and proton transfer events associated with water oxidation represents a pivotal discovery for the field. This finding has led to a remarkable expansion of known synthetic water oxidation catalysts, and has provided the means to gain unprecedented insight into the reaction steps involved with O-O bond formation. This perspective reflects on the key studies that have advanced our understanding of water oxidation catalysis while summarizing molecular features that are integral to negotiating this complicated reaction pathway with the goal of helping identify new frontiers of discovery for the field.

6,6′-Dihydroxy terpyridine: a proton-responsive bifunctional ligand and its application in catalytic transfer hydrogenation of ketones

The ligand 6,6'-dihydroxy terpyridine (dhtp) is presented as a bifunctional ligand capable of directing proton transfer events with metal-coordinated substrates. Solid-state analysis of a Ru(II)-dhtp complex reveals directed hydrogen-bonding interactions of the hydroxyl groups of dhtp with a Ru-bound chloride ligand. The utility of dhtp was demonstrated by chemoselective transfer hydrogenation of ketones.

Excess protons in mesoscopic water-acetone nanoclusters

We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ~ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain.

Prediction of Absolute Hydroxyl pKa Values for 3-Hydroxypyridin-4-ones.

pKa values have been calculated for a series of 3-hydroxypyridin-4-one (HPO) chelators in aqueous solution using coordination constrained ab initio molecular dynamics (AIMD) in combination with thermodynamic integration. This dynamics-based methodology in which the solvent is treated explicitly at the ab initio level has been compared with more commonly used simple, static, approaches. Comparison with experimental numbers has confirmed that the AIMD-based approach predicts the correct trend in the pKa values and produces the lowest average error (∼0.3 pKa units). The corresponding pKa predictions made via static quantum mechanical calculations overestimate the pKa values by 0.3-7 pKa units, with the extent of error dependent on the choice of thermodynamic cycle employed. The use of simple quantitative structure property relationship methods gives prediction errors of 0.3-1 pKa units, with some values overestimated and some underestimated. Beyond merely calculating pKa values, the AIMD simulations provide valuable additional insight into the atomistic details of the proton transfer mechanism and the solvation structure and dynamics at all stages of the reaction. For all HPOs studied, it is seen that proton transfer takes place along a chain of three H2O molecules, although direct hydrogen bonds are seen to form transiently. Analysis of the solvation structure before and after the proton transfer event using radial pair distribution functions and integrated number densities suggests that the trends in the pKa values correlate with the strength of the hydrogen bond and the average number of solvent molecules in the vicinity of the donor oxygen.

Ultrafast Conformational Dynamics of Pyranine during Excited State Proton Transfer in Aqueous Solution Revealed by Femtosecond Stimulated Raman Spectroscopy

Proton transfer reaction plays an essential role in a myriad of chemical and biological processes, and to reveal the choreography of the proton motion intra- and intermolecularly, a spectroscopic technique capable of capturing molecular structural snapshots on the intrinsic time scale of proton transfer motions is needed. The photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) serves as a paradigm case to dissect excited state proton transfer (ESPT) events in aqueous solution, triggered precisely by photoexcitation. We have used femtosecond stimulated Raman spectroscopy (FSRS) to yield novel insights into the ultrafast conformational dynamics of photoexcited HPTS in complex with water and acetate molecules. Marker bands attributed to the deprotonated form of HPTS (1139 cm(-1), ∼220 fs rise) appear earlier and faster than the monomer acetic acid peak (864 cm(-1), ∼530 fs rise), indicating that water molecules actively participate in the ESPT chain. Several key low-frequency modes at 106, 150, 195, and 321 cm(-1) have been identified to facilitate ESPT at different stages from 300 fs, 1 ps, to 6 ps and beyond, having distinctive dynamics contributing through hydrogen bonds with 0, 1, and more intervening water molecules. The time-resolved FSRS spectroscopy renders a direct approach to observe the reactive coupling between the vibrational degrees of freedom of photoexcited HPTS in action, therefore revealing the anharmonicity matrix both within HPTS and between HPTS and the neighboring acceptor molecules. The observed excited state conformational dynamics are along the ESPT multidimensional reaction coordinate and are responsible for the photoacidity of HPTS in aqueous solution.

Role of Environment for Catalysis of the DNA Repair Enzyme MutY

Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. Our findings suggest that the entire reaction is an energetically neutral process, in which the first step is rate determining, requiring protonation of adenine (N(7)) to initiate cleavage, and the second step is strongly exothermic, involving hydrolysis of an oxacarbenium ion intermediate. Although water molecules are catalytically active in both steps, the first step requires an entirely different level of solvent organization compared to the second. Needed to secure protonation at N(7), a long-term solvation pattern is established which facilitates the involvement of three out of the five structured water molecules in the active site. This persistent arrangement coordinates the catalytically active water molecules into prime positions to assist the proton transfer: (i) a water molecule frequently bridges the catalytic residues and (ii) the bridging water molecule is assisted by 1-2 other 'supporting' water molecules. To maintain this configuration, MutY, surprisingly, uses hydrophobic residues in combination with hydrophilic residues to tune the microenvironment into a 'water trap'. Hydrophilic residues prolong solvent residence times by maintaining hydrogen-bonding networks, whereas the hydrophobic residues constrain the positioning of the catalytic water molecules that assist the proton-transfer event. In this way, the enzyme uses both entropic and enthalpic considerations to guide the water-assisted reaction.

First Observation of Ultrafast Intramolecular Proton Transfer Rate between Electronic Ground States in Solution

Despite the importance of ultrafast (time scale exceeding 10(-11) s) intramolecular proton transfer (PT) events between electronic ground states in solution, experimental determination of the rates of such reactions has not yet been accomplished because of the limitations of the utilized methods. The objective of this study was to evaluate the PT rates of intramolecular O···H···O hydrogen-bonded systems in solution through the (1)H spin-lattice relaxation times of the hydroxyl protons, induced by the (1)H-(17)O dipolar interactions (T(1dd)(OH)), taking into account the contribution of the OH reorientational motion to T(1dd)(OH). Solutions of the benzoic acid dimer (BA dimer), 1-benzoyl-6-hydroxy-6-phenylfulvene (Fulvene), and dibenzoylmethane (DBM) were chosen as test systems. For Fulvene in CCl(4), the PT time, τ(PT), was deduced to be 7 × 10(-11) s. In the case of the BA dimer in CCl(4), the τ(PT) value was considerably greater than the OH reorientational correlation time, τ(R(OH)) = 4.3 × 10(-11) s. In contrast, the experimental results for DBM in CCl(4) indicated that the proton is located about midway between the two oxygen atoms, that is, the PT potential energy surface is a single well or a double well with a PT barrier near or below the zero-point energy.

Combining a Dissociative Water Model with a Hybrid QM/MM Approach-A Simulation Strategy for the Study of Proton Transfer Reactions in Solution.

An implementation strategy for a dissociative water potential in hybrid QM/MM simulations is outlined. As the knowledge of the time-dependent topology is crucial for the assignment of solvent molecules to the QM or MM subregion, proton transfer events and the associated change of the molecular composition have to be monitored as the simulation is progressing. A simple and effective update criterion is proposed, which was found to be an efficient tool to identify sustained proton transfer reactions. The resulting topology data enable the application of the dissociative solvent model in QM/MM simulations and serve as a reference for the analysis of time-dependent properties such as the proton hopping rate and the diffusion coefficient. For the latter, an interpolation scheme is proposed linking subsequent proton transfer events into a single diffusive entity. Suitable settings of key parameters for the topology update and the interpolation scheme have been determined by analyzing MD trajectories of an excess proton in water and 1 M HCl. The resulting values for the proton hopping rate and the diffusion coefficient are well within the range estimated by EVB models and CPMD approaches. An investigation of the hydrolytic conversion of As(III) to [As(OH)2](+) serves as an exemplary application of the dissociative model in a QM/MM simulation study.

Natural polarizability and flexibility via explicit valency: The case of water

As the dominant physiological solvent, water drives the folding of biological macromolecules, influences conformational changes, determines the ionization states of surface groups, actively participates in catalytic events, and provides "wires" for long-range proton transfer. Elucidation of all these roles calls for atomistic simulations. However, currently available methods do not lend themselves to efficient simulation of proton transfer events, or even polarizability and flexibility. Here, we report that an explicit account of valency can provide a unified description for the polarizability, flexibility, and dissociability of water in one intuitive and efficient setting. We call this approach LEWIS, after the chemical theory that inspires the use of valence electron pairs. In this paper, we provide details of the method, the choice of the training set, and predictions for the neat ambient liquid, with emphasis on structure, dynamics, and polarization. LEWIS water provides a good description of bulk properties, and dipolar and quadrupolar responses.

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N–terminal amine.

Potential of mean force of water–proton bath and molecular dynamic simulation of proteins at constant pH

An advanced implicit solvent model of water-proton bath for protein simulations at constant pH is presented. The implicit water-proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water-proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom-atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water-proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH-dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water-proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH-dependent ionization-conformation coupling, and proton transfer events.

Differences in the catalytic mechanisms of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures

Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An alternative hypothesis, however, is that complementary thermophilic–mesophilic enzyme pairs simply operate through different evolutionary-optimized catalytic mechanisms. In this communication, we present evidence that while the steps of the catalytic mechanisms for mesophilic and thermophilic indole-3-glycerol phosphate synthase (IGPS) enzymes are fundamentally similar, the identity of the rate-determining step changes as a function of temperature. Our findings indicate that while product release is rate-determining at 25°C for thermophilic IGPS, near its adaptive temperature (75°C), a proton transfer event, involving a general acid, becomes rate-determining. The rate-determining steps for thermophilic and mesophilic IGPS enzymes are also different at their respective, adaptive temperatures with the mesophilic IGPS-catalyzed reaction being rate-limited before irreversible CO2 release, and the thermophilic IGPS-catalyzed reaction being rate limited afterwards.

Reaction of OH and NO at Low Temperatures in the Presence of Water: the Role of Clusters

Abstract There has been a lot of speculation about the role of water in gas phase reactions involving neutrals, radicals and ions. The reaction of NO and OH has attracted a lot of attention in the past due to its relevance for ozone chemistry in the atmosphere. In the present contribution we report low temperature measurements of the recombination of OH and NO at low temperatures in Laval nozzle expansions between 300 K and 60 K. We find an increase of the bimolecular rate constant in the presence of water of up to 40%. This effect has been attributed to water molecules acting either as an efficient collider releasing energy from the intermediate (in collisions) or – which is more likely for the present experimental conditions – as a cluster partner of the reaction intermediate HONO that also dissipates energy via cluster dissociation, which can in turn both stabilize the reaction intermediate, decrease back reaction to OH and NO, and enh ance finally the overall reaction to the products. The supersaturation of water vapor in the cold Laval nozzle expansion strongly favors the formation of clusters in the nozzle throat; their exact concentration is, however, difficult to estimate due to non-equilibrium conditions. The possible role of clusters in the recombination of OH and NO is investigated using ab initio molecular dynamics calculations. Beyond the reaction intermediate HONO and intramolecular proton transfer events also transient HOON was observed in the theoretical study.

Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations

Proton transfer and dissociation processes following excitation of the OH or NH stretching modes of the proton-bound complex GlyLysH(+) are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are sampled to correspond to the v=1 excited state of the OH or NH stretching modes. Five different conformers of the complex are studied as initial structures. The main findings are (1) Photoinduced proton transfer is on the picosecond time scale. (2) Proton transfer is much faster than the processes of dissociation. (3) Proton transfer involves different sites. Most trajectories show sequences of two proton transfer events. (4) The proton transfer events show high selectivity with regard to the initially excited vibration and the initial structure. (5) Photodissociation of the complex occurs on a typical time scale of 100 ps. (6) Conformational transitions are found to be often faster than proton transfer. These results have implications for the mass spectrometry of complexes, for dynamics of proton wires, and for proton migration in proteins.

A first principles theoretical study of the hydration structure and dynamics of an excess proton in water clusters of varying size and temperature

We present a theoretical study of the structure and dynamics of protonated water clusters by means of quantum chemical calculations and ab initio molecular dynamics simulations. We have considered the clusters H +(H 2O) n for four different sizes corresponding to n = 5, 9, 17 and 21. We have first looked at the solvation states of the excess proton in several lower energy structures of these clusters with a special interest in finding its surface versus interior states and its hydrogen bonding environment. Subsequently, we have investigated the finite temperature behavior of these clusters through ab initio simulations. We have looked at vibrational spectral features with special emphasis given to the spectral features of free OH (deuterated) modes and their dependence on donor–acceptor hydrogen bonding states of the water molecules. We have also investigated the mechanism and kinetics of proton transfer events in these clusters by using a population correlation function approach.