Multiple Proton Transfer Research Articles

The Role of Amino Acid Composition in the Charge Inversion of Deprotonated Peptides via Gas-Phase Ion/Ion Reactions

Ion/ion charge inversion via multiple proton transfer reactions occurs via a long-lived intermediate. The intermediate can be observed if its lifetime is long relative to mechanisms for removal of excess energy (i.e., emission and collisional stabilization). The likelihood for formation of a stabilized intermediate is a function of characteristics of the reagent and analyte ions. This work is focused on the role acidic and basic sites of a deprotonated peptide play in the formation of a stabilized intermediate upon charge inversion with multiply protonated polypropyleniminediaminobutane dendrimers. A group of model peptides based on leucine enkephalin was used, which included YGGFL, YGGFLF, YGGFLK, YGGFLR and YGGFLH as well as methyl esterified and acetylated versions. Results showed that peptides containing basic amino acid residues charge inverted primarily by proton transfer from the DAB dendrimer to the peptide, whereas peptides without basic amino acids charge inverted primarily by complex formation with the DAB dendrimer. The modified versions of the peptides highlighted the importance of the presence of the C-terminus as well as the basicity of the peptide in the observation of a stabilized intermediate. These results provide new insights into the nature of the interactions that occur in the charge inversion of polypeptide anions via ion/ion reactions.

Theoretical study of the mechanism behind the para-selective nitration of toluene in zeolite H-Beta

Periodic density functional theory calculations were performed to investigate the origin of the favourable para-selective nitration of toluene exhibited by zeolite H-beta with acetyl nitrate nitration agent. Energy calculations were performed for each of the 32 crystallographically unique Brønsted acid sites of a beta polymorph B zeolite unit cell with multiple Brønsted acid sites of comparable stability. However, one particular aluminum T-site with three favourable Brønsted site oxygens embedded in a straight 12-T channel wall provides multiple favourable proton transfer sites. Transition state searches around this aluminum site were performed to determine the barrier to reaction for both para and ortho nitration of toluene. A three-step process was assumed for the nitration of toluene with two organic intermediates: the π- and σ-complexes. The rate limiting step is the proton transfer from the σ-complex to a zeolite Brønsted site. The barrier for this step in ortho nitration is shown to be nearly 2.5 times that in para nitration. This discrepancy appears to be due to steric constraints imposed by the curvature of the large 12-T pore channels of beta and the toluene methyl group in the ortho approach that are not present in the para approach.

The Role of Free Energy Change in Coupled Electron−Proton Transfer

The kinetics of oxidation of tyrosine by the series of metal complex oxidants, M(bpy)33+ (M = Os, Fe, Ru), in the presence of added bases (acetate, succinate monoanion, histidine, phosphate, and tris), were investigated in 0.5 M buffer with 0.8 M NaCl at 25 °C by utilizing a catalytic cyclic voltammetry technique. As reported in an earlier study, oxidation occurs by a series of pathwayselectron transfer followed by proton transfer (ET−PT), proton transfer followed by electron transfer (PT−ET), and concerted electron−proton transfer (EPT). The latter two occur within H-bonded association complex between tyrosine and the added base. Kinetic isolation was used to focus on the EPT pathway, in which multiple site-electron proton transfer (MS-EPT) occurs with electron transfer to the oxidant and proton transfer to the base. Measured rate constants varied from kEPT = 5.0 × 103 to 9.8 × 107 M-1 s-1. Systematic variations in RT ln kEPT with ΔG°‘ were observed with RT lnkEPT increasing with −ΔG°‘ with a slope of ∼0.6 regardless of whether ΔG°‘ was varied either by varying E°‘ for the oxidant or the strength of the base. Over the ∼0.7 eV variation in ΔG°‘ for the complete data set the variation with ΔG°‘ is consistent with the importance of quantum effects arising from the O−H transfer mode with possible appearance of a novel “quantum beat” effect at ∼3000 cm-1.

Multiple Proton-Transfer Reactions in DNA Base Pairs by Coordination of Pt Complex

The possibility of multiple proton-transfer reactions in DNA base pairs because of coordination of cisplatin is theoretically elucidated by density functional theory (DFT) and by quantum mechanics/molecular mechanics (QM/MM) methods with an ONIOM method. From the energetics of two base pairs with the cisplatin, it is theoretically confirmed that the Pt complex is likely to bind in the order cis-(CG)-Pt-(GC), cis-(CG)-Pt-(AT), cis-(TA)-Pt-(AT), where G, C, A, and T are guanine, cytosine, adenine, and thymine, respectively, and the Pt atom bonds to the N7 site of G and A. This result supports the experimental evidence, where the structure cis-A-Pt-A is seldom observed at room temperature. The single proton-transfer reaction occurs in one of the two GC pairs. No simultaneous single proton-transfer reaction can occur in both base pairs. Two different single proton-transferred structures (cis-(CG*)(d)-Pt-(GC)(p) and cis-(CG)(d)-Pt-(G*C)(p), where the asterisk means a proton donor of G) are as stable as the original structures (CG)(d)-Pt-(GC)(p). The same tendency was observed with cis-(CG*)-Pt-(AT). In contrast to cisplatin, multiple single proton-transfer reactions occur in the system consisting of two base pairs with transplatin. The optimized structure agrees with the experimental data for Pt-G coordination except for the hydrogen-bonding length.

Kinetic Isotope Effects in Multiple Proton Transfer

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer Process in the Green Fluorescent Protein: Classical Molecular Dynamics and Multiconfigurational Electronic Structure Calculations

The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S0, the photoactive 1pi pi* state, and the charge-transfer 1pi sigma* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.

Quantum Mechanical Studies for Proton Transfer in HOCl + HCl and H2O + ClONO2on Water Clusters

We have performed high-level quantum mechanical calculation for multiple proton transfer in HOCl + HCl and H 2 O + ClONO 2 on water clusters, which can be used as a model of the reactions on ice surface in stratospheric clouds. Multiple proton transfer on ice surface plays crucial role in these reactions. The structures of the clusters with 0-3 water molecules and the transition state structures for the multiple proton transfer have been calculated. The energies and barrier heights of the proton transfer were calculated at various levels of theory including multi-coefficient correlated quantum mechanical methods (MCCM) that have recently been developed. The transition state structures and the predicted reaction mechanism depend very much on the level of theory. In particular, the HF level can not correctly predict the TS structure and barrier heights, so the electron correlation should be considered appropriately.

Theoretical study of intermolecular proton transfer reaction in isolated 5-hydroxyisoxazole–water complexes

A systematic investigation in isolated 5-hydroxyisoxazole–water complexes (5-HIO · (H 2O) n n = 1–3) is performed at the DFT level, employing B3LYP/6-31G(d, p) basis set. Single-point energy calculations are also performed at the MP2 level using B3LYP/6-31G(d, p) optimized geometries and the 6-311++G(d, p) basis set. The computational results show that the keto tautomer K 2 is the most stable isomer in the gas phase, and the tautomer K 1 to be the next most stable tautomer. Hydrogen bonding between HIO and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process of 3WE cis ↔ 3WK 1 and 2WE trans ↔ 2WK 2 is found to be more efficient in two tautomerization, and the barrier heights are 7.03 and 14.15 kcal/mol at B3LYP/6-31G(d, p) level, respectively. However, the proton transfer reaction between E cis and K 1 cannot happen without solvent-assisted.

Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase

L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.

DFT explorations of tautomerism of 2-mercaptoimidazole in aqueous solution

A systematic investigation of the proton transfer in the tautomerization of 2-mercaptoimidazole was undertaken. Calculations in aqueous solution were performed using the combined supramolecular/continuum and the direct continuum models, respectively. Complexes containing one and two water molecules around the hydrophilic site of 2-mercaptoimidazole were used for the combined supramolecular/continuum calculation. DFT results predict that the barrier height for non-water-assisted intramolecular proton transfer is very high (175.8 kJ/mol). Hydrogen bonding between 2-mercaptoimidazole and the water molecule(s) will dramatically lower the barrier by the concerted multiple proton transfer mechanism. The proton transfer process through a eight-member ring formed by 2-mercaptoimidazole and two water molecules is found to be more efficient one and the calculated barrier height is reduced to ca. 72 kJ/mol.

Reagent Anions for Charge Inversion of Polypeptide/Protein Cations in the Gas Phase

Various reagent anions capable of converting polypeptide cations to anions via ion/ion reactions have been investigated. The major charge inversion reaction channels include multiple proton transfer and adduct formation. Dianions composed of sulfonate groups as the negative charge carriers show essentially exclusive adduct formation in converting protonated peptides and proteins to anions. Dianions composed of carboxylate groups, on the other hand, show far more charge inversion via multiple proton transfer, with the degree of adduct formation dependent upon both the size of the polypeptide and the spacings between carboxylate groups in the dianion. More highly charged carboxylate-containing anions, such as those derived from carboxylate-terminated polyamidoamine half-generation dendrimers show charge inversion to give anion charges as high in magnitude as -4, with the degree of adduct formation being inversely related to dendrimer generation. All observations can be interpreted on the basis of charge inversion taking place via a long-lived chemical complex. The lifetime of this complex is related to the strengths and numbers of the interactions of the reactants in the complex. Calculations with model systems are fully consistent with sulfonate groups giving rise to more stable complexes. The kinetic stability of the complex can also be affected by the presence of electrostatic repulsion if it is multiply charged. In general, this situation destabilizes the complex and reduces the likelihood for observation of adducts. The findings highlight the characteristics of multiply charged anions that play roles in determining the nature of charge inversion products associated with protonated peptides and proteins.

Intermediates and Transition States in Thiamin Diphosphate-Dependent Decarboxylases. A Kinetic and NMR Study on Wild-Type Indolepyruvate Decarboxylase and Variants Using Indolepyruvate, Benzoylformate, and Pyruvate as Substrates

The thiamin diphosphate (ThDP)-dependent enzyme indolepyruvate decarboxylase (IPDC) is involved in the biosynthetic pathway of the phytohormone 3-indoleacetic acid and catalyzes the nonoxidative decarboxylation of 3-indolepyruvate to 3-indoleacetaldehyde and carbon dioxide. The steady-state distribution of covalent ThDP intermediates of IPDC reacting with 3-indolepyruvate and the alternative substrates benzoylformate and pyruvate has been analyzed by (1)H NMR spectroscopy. For the first time, we are able to isolate and directly assign covalent intermediates of ThDP with aromatic substrates. The intermediate analysis of IPDC variants is used to infer the involvement of active site side chains and functional groups of the cofactor in distinct catalytic steps during turnover of the different substrates. As a result, three residues (glutamate 468, aspartate 29, and histidine 115) positioned perpendicular to the thiazolium moiety of ThDP are involved in binding of all substrates and decarboxylation of the respective tetrahedral ThDP-substrate adducts. Most likely, interactions of these side chains with the substrate-derived carboxylate account for an optimal orientation of the substrate and/or intermediate in the course of carbon-carbon ligation and decarboxylation supporting the suggested least-motion, maximum overlap mechanism. The active site residue glutamine 383, which is located at the opposite site of the thiazolium nucleus as the "carboxylate pocket" (formed by the Glu-Asp-His triad), is central to the substrate specificity of IPDC, probably through orbital alignment. The Glu51-cofactor proton shuttle is, conjointly with the Glu-Asp-His triad, involved in multiple proton transfer steps, including ylide generation, substrate binding, and product release. Studies with para-substituted benzoylformate substrates demonstrate that the electronic properties of the substrate affect the stabilization or destabilization of the carbanion intermediate or carbanion-like transition state and in that way alter the rate dependence on decarboxylation. In conclusion, general mechanistic principles of catalysis of ThDP-dependent enzymes are discussed.

Prototropic tautomerism of imidazolone in aqueous solution: a density functional approach using the combined discrete/self-consistent reaction field (SCRF) models

A systematic investigation of the proton transfer in the keto-amino/enol tautomerization of imidazolone was undertaken. Calculations in aqueous solution were performed using both combined discrete/self-consistent reaction field (SCRF) and SCRF methods. Complexes containing one to three water molecules around the hydrophilic site of imidazolone were used for the combined discrete/SCRF calculations. The DFT results predict that the barrier height for non-water-assisted intramolecular proton transfer is very high (214.8 kJmol(-1)). Hydrogen bonding between imidazolone and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process through a eight-member ring formed by imidazolone and two water molecules is found to be more efficient and the calculated barrier height is ca. 61 kJmol(-1).

Role of the Retinal Hydrogen Bond Network in Rhodopsin Schiff Base Stability and Hydrolysis

Little is known about the molecular mechanism of Schiff base hydrolysis in rhodopsin. We report here our investigation into this process focusing on the role of amino acids involved in a hydrogen bond network around the retinal Schiff base. We find conservative mutations in this network (T94I, E113Q, S186A, E181Q, Y192F, and Y268F) increase the activation energy (E(a)) and abolish the concave Arrhenius plot normally seen for Schiff base hydrolysis in dark state rhodopsin. Interestingly, two mutants (T94I and E113Q) show dramatically faster rates of Schiff base hydrolysis in dark state rhodopsin, yet slower hydrolysis rates in the active MII form. We find deuterium affects the hydrolysis process in wild-type rhodopsin, exhibiting a specific isotope effect of approximately 2.5, and proton inventory studies indicate that multiple proton transfer events occur during the process of Schiff base hydrolysis for both dark state and MII forms. Taken together, our study demonstrates the importance of the retinal hydrogen bond network both in maintaining Schiff base integrity in dark state rhodopsin, as well as in catalyzing the hydrolysis and release of retinal from the MII form. Finally, we note that the dramatic alteration of Schiff base stability caused by mutation T94I may play a causative role in congenital night blindness as has been suggested by the Oprian and Garriga laboratories.

Dynamic NMR study of the mechanisms of double, triple, and quadruple proton and deuteron transfer in cyclic hydrogen bonded solids of pyrazole derivatives.

Using dynamic solid state (15)N CPMAS NMR spectroscopy (CP = cross polarization, MAS = magic angle spinning), the kinetics of the degenerate intermolecular double and quadruple proton and deuteron transfers in the cyclic dimer of (15)N labeled polycrystalline 3,5-diphenyl-4-bromopyrazole (DPBrP) and in the cyclic tetramer of (15)N labeled polycrystalline 3,5-diphenylpyrazole (DPP) have been studied in a wide temperature range at different deuterium fractions in the mobile proton sites. Rate constants were measured on a millisecond time scale by line shape analysis of the doubly (15)N labeled compounds, and by magnetization transfer experiments on a second timescale of the singly (15)N labeled compounds in order to minimize the effects of proton-driven (15)N spin diffusion. For DPBrP the multiple kinetic HH/HD/DD isotope effects could be directly obtained. By contrast, four rate constants k(1) to k(4) were obtained for DPP at different deuterium fractions. Whereas k(1) corresponds to the rate constant k(HHHH) of the HHHH isotopolog, an appropriate kinetic reaction model was needed for the kinetic assignment of the other rate constants. Using the model described by Limbach, H. H.; Klein, O.; Lopez Del Amo, J. M.; Elguero, J. Z. Phys. Chem. 2004,218, 17, a concerted quadruple proton-transfer mechanism as well as a stepwise consecutive single transfer mechanism could be excluded. By contrast, using the kinetic assignment k(2) approximately k(3) approximately k(HHHD) approximately k(HDHD) and k(3) approximately k(HDDD) approximately k(DDDD), the results could be explained in terms of a two-step process involving a zwitterionic intermediate. In this mechanism, each reaction step involves the concerted transfer of two hydrons, giving rise to primary kinetic HH/HD/DD isotope effects, whereas the nontransferred hydrons only contribute small secondary effects, which are not resolved experimentally. By contrast, the multiple kinetic isotope effects of the double proton transfer in DPBrP and of the triple proton proton transfer in cyclic pyrazole trimers studied previously indicate concerted transfer processes. Thus, between n = 3 and 4 a switch of the reaction mechanism takes place. This switch is rationalized in terms of hydrogen bond compression effects associated with the multiple proton transfers. The Arrhenius curves of all processes are nonlinear and indicate tunneling processes at low temperatures. In a preliminary analysis, they are modeled in terms of the Bell-Limbach tunneling model.

Determination of a Unique Solution to Parallel Proton Transfer Reactions Using the Genetic Algorithm

Kinetic analysis of the dynamics as measured in multiequilibria systems is readily attained by curve-fitting methodologies, a treatment that can accurately retrace the shape of the measured signal. Still, these reconstructions are not related to the detailed mechanism of the process. In this study we subjected multiple proton transfer reactions to rigorous kinetic analysis, which consists of solving a set of coupled-nonlinear differential rate equations. The manual analysis of such systems can be biased by the operator; thus the analysis calls for impartial corroboration. What is more, there is no assurance that such a complex system has a unique solution. In this study, we used the Genetic Algorithm to investigate whether the solution of the system will converge into a single global minimum in the multidimensional parameter space. The experimental system consisted of proton transfer between four proton-binding sites with seven independent adjustable parameters. The results of the search indicate that the solution is unique and all adjustable parameters converge into a single minimum in the multidimensional parameter space, thus corroborating the accuracy of the manual analysis.

Solvent-mediated tautomerization of purine: single to quadruple proton transfer

We present calculations for the structures and the tautomerization reaction of purine and purine – (H 2O) n ( n=1–3) clusters. We find two pathways (via the carbene and the sp 3-type intermediate) for the 9 ↔ 7 tautomerization of bare purine. The barrier heights for the 9 → 3 and 9 → 7 tautomerization of bare purine are calculated to be large (60–70 kcal/mol). Hydrogen bonding with the water molecule(s), however, dramatically lowers the 9 → 3 barrier by the concerted multiple proton transfer mechanism, favoring the formation of the conformer 3(H)- relative to the 7(H)-purine in the microsolvated environment, in contrast to the gas phase or the aqueous solution.

Solvent effects on glycine II. Water-assisted tautomerization.

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.

Kinetic Hydrogen/Deuterium Isotope Effects in Multiple Proton Transfer Reactions

Abstract In this paper, a description of multiple kinetic isotope effects (MKIE) of degenerate double, triple and quadruple proton transfer reactions in terms of formal kinetics is developped. Both single and multiple barrier processes are considered, corresponding to so-called “concerted” and “stepwise” reaction pathways. Each step is characterized by a rate constant and the transfer of a given H isotopes or ensemble of H isotopes. The MKIE are expanded in terms of kinetic H/D isotope effects P contributed by single sites in which a proton is transferred in the rate limiting steps. By combination with a modified Bell tunneling model the formalism developed can be used in order to take into account tunneling effects of both concerted and stepwise multiple proton transfers at low temperatures.

Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II.

The rate constant of the reaction catalyzed by the enzyme carbonic anhydrase II, which removes carbon dioxide from body fluids, is calculated for a model of the active site. The rate-determining step is proton transfer from a zinc-bound water molecule to a histidine residue via a bridge of two or more water molecules. The structure of the active site is known from X-ray studies except for the number and location of the water molecules. Model calculations are reported for a system of 58 atoms including a four-coordinated zinc ion connected to a methylimidazole molecule by a chain of two waters, constrained to reproduce the size of the active site. The structure and vibrational force field are calculated by an approximate density functional treatment of the proton-transfer step at the Self-Consistent-Charge Density Functional Tight Binding (SCC-DFTB) level. A single transition state is found indicating concerted triple proton transfer. Direct-dynamics calculations for proton and deuteron transfer and combinations thereof, based on the Approximate Instanton Method and on Variational Transition State Theory with Tunneling Corrections, are in fair agreement and yield rates that are considerably higher and kinetic isotope effects (KIEs) that are somewhat higher than experiment. Classical rate constants obtained from Transition State Theory are smaller than the quantum values but the corresponding KIEs are five times larger. For multiple proton transfer along water bridges classical KIEs are shown to be generally larger than quantum KIEs, which invalidates the standard method to distinguish tunneling and over-barrier transfer. In the present case, a three-way comparison of classical and quantum results with the observed data is necessary to conclude that proton transfer along the bridge proceeds by tunneling. The results suggest that the two-water bridge is present in low concentrations but makes a substantial contribution to proton transport because of its high efficiency. Bridging structures containing more water molecules may have lower energies but are expected to be less efficient. The observed exponential dependence of the KIEs on the deuterium concentration in H(2)O/D(2)O mixtures implies concerted transfer and thus rules out substantial contributions from structures that lead to stepwise transfer via solvated hydronium ions, which presumably dominate proton transfer in less efficient carbonic anhydrase isozymes.