Curve Crossing Formulation for Proton Transfer Reactions in Solution

The Possible Role of Proton-Coupled Electron Transfer (PCET) in Water Oxidation by Photosystem II

All higher life forms use oxygen and respiration as their primary energy source. The oxygen comes from water by solar-energy conversion in photosynthetic membranes. In green plants, light absorption in photosystem II (PSII) drives electron-transfer activation of the oxygen-evolving complex (OEC). The mechanism of water oxidation by the OEC has long been a subject of great interest to biologists and chemists. With the availability of new molecular-level protein structures from X-ray crystallography and EXAFS, as well as the accumulated results from numerous experiments and theoretical studies, it is possible to suggest how water may be oxidized at the OEC. An integrated sequence of light-driven reactions that exploit coupled electron-proton transfer (EPT) could be the key to water oxidation. When these reactions are combined with long-range proton transfer (by sequential local proton transfers), it may be possible to view the OEC as an intricate structure that is "wired for protons".

Temperature Dependence of Excited State Proton Transfer in Ice

We have studied the excited-state proton-transfer rate of four photoacids in ice as a function of temperature. For all four photoacids, we have found a non Arrhenius behavior of the proton-transfer rate constant, k(PT). d(ln k(PT))/d(1/T) decreases as the temperature decreases. The average slope of ln(k(PT))versus 1/T depends on the photoacid strength (pK*). The stronger the photoacid is, the smaller the slope. For the strongest photoacid 2-naphthol-6,8-disulfonate (2N68DS) the largest slope is 35 kJ/mol at about 270 K, and the smallest measured slope is about 8 kJ/mol at about 215 K. We propose that the temperature dependence of k(PT) in ice at the temperature range 270 > T > 200 K can be explained as arising from contributions of two proton-transfer mechanisms over the barrier and tunneling under the barrier. At very low temperatures T < 200 K, the slope of ln(k(PT)) versus 1/T increases again. At about 170 K, the proton-transfer rate is much slower than the radiative rate, and the deprotonated form of the photoacid cannot be detected in the steady-state emission spectrum. At lower temperatures, T < 200 K, the rate further decreases because of a limitation on the reaction caused by the restrictions on the H2O hydrogen reorientations.

Enzymatic catalysis and transfers in solution. I. Theory and computations, a unified view

The transfer of hydride, proton, or H atom between substrate and cofactor in enzymes has been extensively studied for many systems, both experimentally and computationally. A simple equation for the reaction rate, an analog of an equation obtained earlier for electron transfer rates, is obtained, but now containing an approximate analytic expression for the bond rupture-bond forming feature of these H transfers. A "symmetrization," of the potential energy surfaces is again introduced [R. A. Marcus, J. Chem. Phys. 43, 679 (1965); J. Phys. Chem. 72, 891 (1968)], together with Gaussian fluctuations of the remaining coordinates of the enzyme and solution needed for reaching the transition state. Combining the two expressions for the changes in the difference of the two bond lengths of the substrate-cofactor subsystem and in the fluctuation coordinates of the protein leading to the transition state, an expression is obtained for the free energy barrier. To this end a two-dimensional reaction space (m,n) is used that contains the relative coordinates of the H in the reactants, the heavy atoms to which it is bonded, and the protein/solution reorganization coordinate, all leading to the transition state. The resulting expression may serve to characterize in terms of specific parameters (two "reorganization" terms, thermodynamics, and work terms), experimental and computational data for different enzymes, and different cofactor-substrate systems. A related characterization was used for electron transfers. To isolate these factors from nuclear tunneling, when the H-tunneling effect is large, use of deuterium and tritium transfers is of course helpful, although tunneling has frequently and understandably dominated the discussions. A functional form is suggested for the dependence of the deuterium kinetic isotope effect (KIE) on DeltaG degrees and a different form for the 13C KIE. Pressure effects on deuterium and 13C KIEs are also discussed. Although formulated for a one-step transfer of a light particle in an enzyme, the results would also apply to single-step transfers of other atoms and groups in enzymes and in solution.

Summarizing lecture: factors influencing enzymatic H-transfers, analysis of nuclear tunnelling isotope effects and thermodynamic versus specific effects

In the articles in this Discussion, a wide variety of topics are treated, including reorganization energy, initially introduced for electron transfers ('environmentally assisted tunnelling'), nuclear tunnelling, H/D and 12C/13C kinetic isotope effects (KIEs), the effect of changes of distal and nearby amino acid residues using site-directed mutagenesis, and dynamics versus statistical effects. A coordinate-free form of semi-classical theory is used to examine topics on data such as tunnelling versus 'over-the-barrier' paths and temperature and pressure effects on KIEs. The multidimensional semi-classical theory includes classically allowed and classically forbidden transitions. More generally, we address the question of relating kinetic to thermodynamic factors, as in the electron transfer field, so learning about specific versus thermodynamic effects in enzyme catalysis and KIEs.

The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase

Residues M42 and G121 of Escherichia coli dihydrofolate reductase (ecDHFR) are on opposite sides of the catalytic centre (15 and 19 A away from it, respectively). Theoretical studies have suggested that these distal residues might be part of a dynamics network coupled to the reaction catalysed at the active site. The ecDHFR mutant G121V has been extensively studied and appeared to have a significant effect on rate, but only a mild effect on the nature of H-transfer. The present work examines the effect of M42W on the physical nature of the catalysed hydride transfer step. Intrinsic kinetic isotope effects (KIEs), their temperature dependence and activation parameters were studied. The findings presented here are in accordance with the environmentally coupled hydrogen tunnelling. In contrast to the wild-type (WT), fluctuations of the donor-acceptor distance were required, leading to a significant temperature dependence of KIEs and deflated intercepts. A comparison of M42W and G121V to the WT enzyme revealed that the reduced rates, the inflated primary KIEs and their temperature dependences resulted from an imperfect potential surface pre-arrangement relative to the WT enzyme. Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry.

Protein motions during catalysis by dihydrofolate reductases

Dihydrofolate reductase (DHFR) maintains the intracellular pool of tetrahydrofolate through catalysis of hydrogen transfer from reduced nicotinamide adenine dinucleotide to 7,8-dihydrofolate. We report results for pre-steady-state kinetic studies of the temperature dependence of the rates and the hydrogen/deuterium-kinetic isotope effects for the reactions catalysed by the enzymes from the mesophilic Escherichia coli and the hyperthermophilic Thermatoga maritima. We propose an evolutionary pattern in which catalysis progressed from a relatively rigid active site structure in the ancient thermophilic DHFR to a more flexible and kinetically more efficient structure in E. coli that actively promotes hydrogen transfer at physiological pH by modulating the tunnelling distance. The E. coli enzyme appeared relatively robust, in that kinetically severely compromised mutants still actively propagated the reaction. The reduced hydrogen transfer rates of the extensively studied Gly121Val mutant of DHFR from E. coli were most likely due to sterically unfavourable long-range effects from the introduction of the bulky isopropyl group.

Further Evidence of an Inverted Region in Proton Transfer within the Benzophenone/Substituted Aniline Contact Radical Ion Pairs; Importance of Vibrational Reorganization Energy

The dynamics of proton transfer within the triplet contact radical ion pair of a variety of substituted benzophenones with N,N-diethylaniline, N,N-dimethyl-p-toluinide, and N,N-diallylaniline are examined in solvents of varying polarity. The correlation of the rate constants with driving force reveal both a normal region and an inverted region providing support for the nonadiabatic nature of proton transfer within these systems. The reorganization of both the solvent and the molecular framework are central in governing the overall reaction dynamics.

Coupling of protein motions and hydrogen transfer during catalysis by Escherichia coli dihydrofolate reductase

The enzyme DHFR (dihydrofolate reductase) catalyses hydride transfer from NADPH to, and protonation of, dihydrofolate. The physical basis of the hydride transfer step catalysed by DHFR from Escherichia coli has been studied through the measurement of the temperature dependence of the reaction rates and the kinetic isotope effects. Single turnover experiments at pH 7.0 revealed a strong dependence of the reaction rates on temperature. The observed relatively large difference in the activation energies for hydrogen and deuterium transfer led to a temperature dependence of the primary kinetic isotope effects from 3.0+/-0.2 at 5 degrees C to 2.2+/-0.2 at 40 degrees C and an inverse ratio of the pre-exponential factors of 0.108+/-0.04. These results are consistent with theoretical models for hydrogen transfer that include contributions from quantum mechanical tunnelling coupled with protein motions that actively modulate the tunnelling distance. Previous work had suggested a coupling of a remote residue,Gly121, with the kinetic events at the active site. However, pre-steady-state experiments at pH 7.0 with the mutant G121V-DHFR, in which Gly121 was replaced with valine, revealed that the chemical mechanism of DHFR catalysis was robust to this replacement. The reduced catalytic efficiency of G121V-DHFR was mainly a consequence of the significantly reduced pre-exponential factors, indicating the requirement for significant molecular reorganization during G121V-DHFR catalysis. In contrast, steady-state measurements at pH 9.5, where hydride transfer is rate limiting, revealed temperature-independent kinetic isotope effects between 15 and 35 degrees C and a ratio of the pre-exponential factors above the semi-classical limit, suggesting a rigid active site configuration from which hydrogen tunnelling occurs. The mechanism by which hydrogen tunnelling in DHFR is coupled with the environment appears therefore to be sensitive to pH.

A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: An analysis of tunneling and thermal activation

We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.

Effects of a distal mutation on active site chemistry

Previous studies of Escherichia coli dihydrofolate reductase (ecDHFR) have demonstrated that residue G121, which is 19 A from the catalytic center, is involved in catalysis, and long distance dynamical motions were implied. Specifically, the ecDHFR mutant G121V has been extensively studied by various experimental and theoretical tools, and the mutation's effect on kinetic, structural, and dynamical features of the enzyme has been explored. This work examined the effect of this mutation on the physical nature of the catalyzed hydride transfer step by means of intrinsic kinetic isotope effects (KIEs), their temperature dependence, and activation parameters as described previously for wild type ecDHFR [Sikorski, R. S., et al. (2004) J. Am. Chem. Soc. 126, 4778-4779]. The temperature dependence of initial velocities was used to estimate activation parameters. Isotope effects on the preexponential Arrhenius factors, and the activation energy, could be rationalized by an environmentally coupled hydrogen tunneling model, similar to the one used for the wild-type enzyme. Yet, in contrast to that in the wild type, fluctuations of the donor-acceptor distance were now required. Secondary (2 degrees ) KIEs were also measured for both H- and D-transfer, and as in the case of the wild-type enzyme, no coupled motion was detected. Despite these similarities, the reduced rates, the slightly inflated primary (1 degrees ) KIEs, and their temperature dependence, together with relatively deflated 2 degrees KIEs, indicate that the potential surface prearrangement was not as ideal as for the wild-type enzyme. These findings support theoretical studies suggesting that the G121V mutation led to a different conformational ensemble of reactive states and less effective rearrangement of the potential surface but has an only weak effect on H-tunneling.

Models for proton-coupled electron transfer in photosystem II

The coupling of proton and electron transfers is a key part of the chemistry of photosynthesis. The oxidative side of photosystem II (PS II) in particular seems to involve a number of proton-coupled electron transfer (PCET) steps in the S-state transitions. This mini-review presents an overview of recent studies of PCET model systems in the authors' laboratory. PCET is defined as a chemical reaction involving concerted transfer of one electron and one proton. These are thus distinguished from stepwise pathways involving initial electron transfer (ET) or initial proton transfer (PT). Hydrogen atom transfer (HAT) reactions are one class of PCET, in which H(+) and e (-) are transferred from one reagent to another: AH + B --> A + BH, roughly along the same path. Rate constants for many HAT reactions are found to be well predicted by the thermochemistry of hydrogen transfer and by Marcus Theory. This includes organic HAT reactions and reactions of iron-tris(alpha-diimine) and manganese-(mu-oxo) complexes. In PS II, HAT has been proposed as the mechanism by which the tyrosine Z radical (Y(Z)*) oxidizes the manganese cluster (the oxygen evolving complex, OEC). Another class of PCET reactions involves transfer of H(+) and e (-) in different directions, for instance when the proton and electron acceptors are different reagents, as in AH-B + C(+) --> A-HB(+) + C. The oxidation of Y(Z) by the chlorophyll P680 + has been suggested to occur by this mechanism. Models for this process - the oxidation of phenols with a pendent base - are described. The oxidation of the OEC by Y(Z)* could also occur by this second class of PCET reactions, involving an Mn-O-H fragment of the OEC. Initial attempts to model such a process using ruthenium-aquo complexes are described.

Photoreduction of 4,4‘-Bipyridine by Amines in Acetonitrile−Water Mixtures: Influence of H-Bonding on the Ion-Pair Structure and Dynamics

The photoreduction of 4,4'-bipyridine (44BPY) by diazabicyclo[2.2.2]octane and triethylamine (TEA) is investigated by using picosecond transient absorption and time-resolved resonance Raman spectroscopy in various acetonitrile-water mixtures. The results are interpreted on the basis of a preferential solvation effect resulting from the presence of a specific interaction between 44BPY and water by hydrogen bonding. Below 10% water, the free 44BPY species is dominant and leads upon photoreduction to a contact ion pair that undergoes efficient intrapair proton transfer if TEA is the amine donor. Above 10% water, most of the 44BPY population is H-bonded and leads upon photoreduction to a hydrated ion pair in which the intrapair proton transfer is inhibited. Instead, the 44BPY(-*) species is protonated by water through the hydrogen bond with a rate constant that increases by more than 3 orders of magnitude on going from 10% to 100% water. The dependence of this rate constant on the solvent mixture composition suggests that the reaction of intracomplex proton transfer is controlled by the hydration of the residual OH(-) species by three molecules of water, leading to a trihydrated HO(-)(H(2)O)(3) species.

Spectral Signatures of Hydrated Proton Vibrations in Water Clusters

The ease with which the pH of water is measured obscures the fact that there is presently no clear molecular description for the hydrated proton. The mid-infrared spectrum of bulk aqueous acid, for example, is too diffuse to establish the roles of the putative Eigen (H3O+) and Zundel (H5O2+) ion cores. To expose the local environment of the excess charge, we report how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules. Signature bands indicating embedded Eigen or Zundel limiting forms are observed in all of the spectra with the exception of the three- and five-membered clusters. These unique species display bands appearing at intermediate energies, reflecting asymmetric solvation of the core ion. Taken together, the data reveal the pronounced spectral impact of subtle changes in the hydration environment.

Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study

The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.

Exploring excited-state hydrogen atom transfer along an ammonia wire cluster: Competitive reaction paths and vibrational mode selectivity

The excited-state hydrogen-atom transfer (ESHAT) reaction of the 7-hydroxyquinoline(NH(3))(3) cluster involves a crossing from the initially excited (1)pipi(*) to a (1)pisigma(*) state. The nonadiabatic coupling between these states induces homolytic dissociation of the O-H bond and H-atom transfer to the closest NH(3) molecule, forming a biradical structure denoted HT1, followed by two more Grotthus-type translocation steps along the ammonia wire. We investigate this reaction at the configuration interaction singles level, using a basis set with diffuse orbitals. Intrinsic reaction coordinate calculations of the enol-->HT1 step predict that the H-atom transfer is preceded and followed by extensive twisting and bending of the ammonia wire, as well as large O-H...NH(3) hydrogen bond contraction and expansion. The calculations also predict an excited-state proton transfer path involving synchronous proton motions; however, it lies 20-25 kcal/mol above the ESHAT path. Higher singlet and triplet potential curves are calculated along the ESHAT reaction coordinate: Two singlet-triplet curve crossings occur within the HT1 product well and intersystem crossing to these T(n) states branches the reaction back to the enol reactant side, decreasing the ESHAT yield. In fact, a product yield of approximately 40% 7-ketoquinoline.(NH(3))(3) is experimentally observed. The vibrational mode selectivity of the enol-->HT1 reaction step [C. Manca, C. Tanner, S. Coussan, A. Bach, and S. Leutwyler, J. Chem. Phys. 121, 2578 (2004)] is shown to be due to the large sensitivity of the diffuse pisigma(*) state to vibrational displacements along the intermolecular coordinates.

Effect of Pressure on the Proton Transfer Rate from a Photoacid to a Solvent. 4. Photoacids in Methanol

The pressure dependence of the excited-state proton dissociation rate constant of four photoacids, 2-naphthol-6,8-disulfonate (2N68DS), 10-hydroxycamptothecin (10-CPT), 5-cyano-2-naphthol (5CN2), and 5,8-dicyano-2-naphthol (DCN2), are studied in methanol. The results are compared with the results of the pressure dependence study we recently conducted for several photoacids in water, ethanol, and propanol. The pressure dependence is explained using an approximate stepwise two-coordinate proton transfer model. The increase in rate, as a function of pressure, manifests a strong dependence of proton tunneling on the distance which decreases with an increase of pressure between the two oxygen atoms involved in the process. The decrease in the proton transfer rate with increasing pressure reflects the dependence of the reaction on the solvent relaxation rate. We found that, for the relatively weak photoacids 2N68DS, 10-CPT, and 5CN2, the proton transfer rate constant increases by a factor of about 5-8 at a pressure of about 1.5 GPa. For a strong photoacid like DCN2, the rate increase was only by a factor of 2.

Origin of Activation Barriers in the Dimerization of Neutral Radicals: A “Nonperfect Synchronization” Effect?

Dimerizations of delocalized neutral radicals may be endowed with quite significant activation barriers. The origin of these barriers is discussed in terms of a model that emphasizes the role of localization of the unpaired radical upon bond formation. Several examples are given in which the model is compared with the results of quantum chemical calculations including the coupling of allyl radicals and of benzyl radicals at various possible carbon sites. The dimerization behavior of radicals in the NADH family is also examined. The connection between the reasons that underlay the existence of the activation barrier and the principle of "nonperfect synchronization" is discussed. The dimerization of conjugated radicals indeed offers a precious example that can be used to decipher the reasons behind these behaviors, being devoid of the ambiguities arising from the simultaneous involvement of ionic and covalent states, significant solvent reorganization, and the contribution of extensive proton tunneling, in the mostly discussed case of proton transfer at carbon.

Proton Transfer in Nanoconfined Polar Solvents. 1. Free Energies and Solute Position

The reaction free energy curves for a model phenol-amine proton-transfer system in a confined CH3Cl solvent have been calculated by Monte Carlo simulations. The free energy curves, as a function of a collective solvent coordinate, have been obtained for several fixed reaction complex radial positions (based on the center-of-mass). A smooth, hydrophobic spherical cavity was used to confine the solvent, and radii of 10 and 15 A have been considered. Quantum effects associated with the transferring proton have been included by adding the proton zero-point energy to the classical free energy. The results indicate the reaction complex position can be an important component of the reaction coordinate for proton-transfer reactions in nanoconfined solvents.

Elementary Steps in Excited-State Proton Transfer

The absorption of a photon by a hydroxy-aromatic photoacid triggers a cascade of events contributing to the overall phenomenon of intermolecular excited-state proton transfer. The fundamental steps involved were studied over the last 20 years using a combination of theoretical and experimental techniques. They are surveyed in this sequel in sequential order, from fast to slow. The excitation triggers an intramolecular charge transfer to the ring system, which is more prominent for the anionic base than the acid. The charge redistribution, in turn, triggers changes in hydrogen-bond strengths that set the stage for the proton-transfer step itself. This step is strongly influenced by the solvent, resulting in unusual dependence of the dissociation rate coefficient on water content, temperature, and isotopic substitution. The photolyzed proton can diffuse in the aqueous solution in a mechanism that involves collective changes in hydrogen-bonding. On longer times, it may recombine adiabatically with the excited base or quench it. The theory for these diffusion-influenced geminate reactions has been developed, showing nice agreement with experiment. Finally, the effect of inert salts, bases, and acids on these reactions is analyzed.

Why Are Proton Transfers at Carbon Slow? Self-Exchange Reactions

When the quantum character of proton transfer is taken into account, the intrinsic slowness of self-exchange proton transfer at carbon appears as a result of its nonadiabatic character as opposed to the adiabatic character of proton transfer at oxygen and nitrogen. This difference is caused by the lesser polarity of C-H bonds as compared to that of O-H and N-H bonds. Besides solvent and heavy-atom intramolecular reorganizations, the kinetics of the reaction are consequently governed at the level of a pre-exponential term by proton tunneling through the barrier. These contrasting behaviors are illustrated by an analysis of the CH(3)H + (-)CH(3), H(2)O + OH(-), and (+)NH(4) + NH(3) self-exchange reactions. The effect of electron-withdrawing substituents and the case of cation radicals are discussed within the same framework taking the O(2)NCH(2)H + CH(2)=NO(2)(-) and (+.)H(2)NCH(2)H + (.)CH(2)NH(2) as examples. Illustrated by the CH(2)=CH-CH(2)H + (-)CH(2)-CH=CH(2) couple, it is shown that the "imbalanced character of the transition state" is related to heavy-atom intramolecular reorganization. Combination of these various effects is finally analyzed, taking the O(2)N-CH(2)=CH-CH(2)H + CH(2)=CH-CH=NO(2)(-) and (+.)H(2)N-CH(2)=CH-CH(2)H + (.)CH(2)-CH=CH(2)-NH(2) couples as examples.

Proton-coupled electron transfer: a reaction chemist's view

Proton-coupled electron transfer (PCET) reactions involve the concerted transfer of an electron and a proton. Such reactions play an important role in many areas of chemistry and biology. Concerted PCET is thermochemically more favorable than the first step in competing consecutive processes involving stepwise electron transfer (ET) and proton transfer (PT), often by >=1 eV. PCET reactions of the form X-H + Y X + H-Y can be termed hydrogen atom transfer (HAT). Another PCET class involves outersphere electron transfer concerted with deprotonation by another reagent, Y+ + XH-B Y + X-HB+. Many PCET/HAT rate constants are predicted well by the Marcus cross relation. The cross-relation calculation uses rate constants for self-exchange reactions to provide information on intrinsic barriers. Intrinsic barriers for PCET can be comparable to or larger than those for ET. These properties are discussed in light of recent theoretical treatments of PCET.

Hydrogen tunneling in quinoproteins

It is now widely accepted that substrate C-H bond breakage by quinoprotein enzymes occurs by quantum mechanical tunneling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (i.e., including zero-point energy but with no tunneling correction) has been driven over recent years by experimental studies of the temperature dependence of kinetic isotope effects for these reactions in the TTQ-dependent enzymes methylamine dehydrogenase and aromatic amine dehydrogenase, which produced observations also inconsistent with the simple Bell correction model of tunneling. However, these data-specifically, the strong temperature dependence of reaction rates and the variable temperature dependence of kinetic isotope effects-are consistent with other tunneling models (denoted full tunneling models) in which protein and/or substrate fluctuations generate a configuration compatible with tunneling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate quantum states and, when necessary, motion required to increase the probability of tunneling in these states. Furthermore, tunneling mechanisms in quinoproteins are supported by computational studies employing variational transition state theory with multidimensional tunneling corrections; these studies are also discussed in this review. Potential pitfalls in analyzing the temperature dependence of kinetic isotope effects as probes of tunneling are also discussed with reference to PQQ-dependent methanol dehydrogenase.

Evidence for environmentally coupled hydrogen tunneling during dihydrofolate reductase catalysis

Hydride transfer during catalysis by dihydrofolate reductase from Thermotoga maritima has been studied by stopped flow spectroscopy. The reduction of dihydrofolate by NADPH showed a biphasic temperature dependence of the deuterium kinetic isotope effect. At temperatures above 25 degrees C the KIE was temperature independent, while the reaction rates were strongly temperature dependent. Below 25 degrees C the KIE becomes dependent on temperature, and the ratio of the preexponential factors is inverse, suggesting a greater role for active dynamics that modulate the tunneling distance.

H atom transfer along an ammonia chain: Tunneling and mode selectivity in 7-hydroxyquinoline⋅(NH[sub 3])[sub 3]

Excitation of the 7-hydroxyquinoline(NH(3))(3) [7HQ(NH(3))(3)] cluster to the S(1) (1)pi pi(*) state results in an O-H-->NH(3) hydrogen atom transfer (HAT) reaction. In order to investigate the entrance channel, the vibronic S(1)<-->S(0) spectra of the 7HQ.(NH(3))(3) and the d(2)-7DQ.(ND(3))(3) clusters have been studied by resonant two-photon ionization, UV-UV depletion and fluorescence techniques, and by ab initio calculations for the ground and excited states. For both isotopomers, the low-frequency part of the S(1)<--S(0) spectra is dominated by ammonia-wire deformation and stretching vibrations. Excitation of overtones or combinations of these modes above a threshold of 200-250 cm(-1) for 7HQ.(NH(3))(3) accelerates the HAT reaction by an order of magnitude or more. The d(2)-7DQ.(ND(3))(3) cluster exhibits a more gradual threshold from 300 to 650 cm(-1). For both isotopomers, intermolecular vibrational states above the threshold exhibit faster HAT rates than the intramolecular vibrations. The reactivity, isotope effects, and mode selectivity are interpreted in terms of H atom tunneling through a barrier along the O-H-->NH(3) coordinate. The barrier results from a conical intersection of the optically excited (1)pi pi(*) state with an optically dark (1)pi sigma(*) state. Excitation of the ammonia-wire stretching modes decreases both the quinoline-O-H...NH(3) distance and the energetic separation between the (1)pi pi(*) and (1)pi sigma(*) states, thereby increasing the H atom tunneling rate. The intramolecular vibrations change the H bond distance and modulate the (1)pi pi(*)<-->(1)pi sigma(*) interaction to a much smaller extent.

Two-electron transfer reactions in proteins: bridge-mediated and proton-assisted processes

Nonadiabatic two-electron transfer (TET) reactions through donor-bridge-acceptor (DBA) systems is investigated within the approximation of fast vibrational relaxation. For TET reactions in which the population of bridging states remains small (less than 10(-2)) it is demonstrated that a multiexponential transition process reduces to three-state kinetics. The transfer starts at the state with two excess electrons at the D center (D(2-)BA), goes through the intermediate (transient) state with one electron at the D center and one at the A center (D-BA-), and ends up with the two electrons at the A center (DBA2-). Furthermore, if the population of the intermediate state becomes also small the two-exponential kinetics can be transformed with high accuracy to single-exponential D-A TET kinetics. The related overall transfer rate contains contributions from stepwise and from concerted TET. The latter process is determined by a specific two-electron superexchange coupling incorporating the bridging states (D-B-A and DB-A-) as well as the intermediate state (D-BA-). As an example, the reduction of micothione reductase by nicotinamide adenine dinucleotide phosphate is analyzed. Existing experimental data can be explained if one assumes that the proton-assisted reduction of the enzyme is realized by the concerted TET mechanism.

Phenomenological and molecular models of biological proton transfers

In this paper, the main models describing the transfer of a proton in a molecular system are presented. Models valid when the intersite coupling is weak (non-adiabatic and electronically adiabatic regimes) and strong (adiabatic regime) are described. We distinguish molecular models in which the rate constant is obtained by considering explicitly various degrees of freedom of the system and simpler, phenomenological models built to account for the kinetic isotope effect. The relations between the various models are discussed. Their application to specific systems is illustrated by several studies reported in the literature, with a special emphasis on biological systems.

H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase

The mechanism of flavin reduction in morphinone reductase (MR) and pentaerythritol tetranitrate (PETN) reductase, and flavin oxidation in MR, has been studied by stopped-flow and steady-state kinetic methods. The temperature dependence of the primary kinetic isotope effect for flavin reduction in MR and PETN reductase by nicotinamide coenzyme indicates that quantum mechanical tunneling plays a major role in hydride transfer. In PETN reductase, the kinetic isotope effect (KIE) is essentially independent of temperature in the experimentally accessible range, contrasting with strongly temperature-dependent reaction rates, consistent with a tunneling mechanism from the vibrational ground state of the reactive C-H/D bond. In MR, both the reaction rates and the KIE are dependent on temperature, and analysis using the Eyring equation suggests that hydride transfer has a major tunneling component, which, unlike PETN reductase, is gated by thermally induced vibrations in the protein. The oxidative half-reaction of MR is fully rate-limiting in steady-state turnover with the substrate 2-cyclohexenone and NADH at saturating concentrations. The KIE for hydride transfer from reduced flavin to the alpha/beta unsaturated bond of 2-cyclohexenone is independent of temperature, contrasting with strongly temperature-dependent reaction rates, again consistent with ground-state tunneling. A large solvent isotope effect (SIE) accompanies the oxidative half-reaction, which is also independent of temperature in the experimentally accessible range. Double isotope effects indicate that hydride transfer from the flavin N5 atom to 2-cyclohexenone, and the protonation of 2-cyclohexenone, are concerted and both the temperature-independent KIE and SIE suggest that this reaction also proceeds by ground-state quantum tunneling. Our results demonstrate the importance of quantum tunneling in the reduction of flavins by nicotinamide coenzymes. This is the first observation of (i) three H-nuclei in an enzymic reaction being transferred by tunneling and (ii) the utilization of both passive and active dynamics within the same native enzyme.

A perspective on enzyme catalysis

The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.

Formation of split electron paramagnetic resonance signals in photosystem II suggests that tyrosine(Z) can be photooxidized at 5 K in the S0 and S1 states of the oxygen-evolving complex

The effect of illumination at 5 K of photosystem II in different S-states was investigated with EPR spectroscopy. Two split radical EPR signals around g approximately 2.0 were observed from samples given 0 and 3 flashes, respectively. The signal from the 0-flash sample was narrow, with a width of approximately 80 G, in which the low-field peak can be distinguished. This signal oscillated with the S(1) state in the sample. The signal from the 3-flash sample was broad, with a symmetric shape of approximately 160 G width from peak to trough. This signal varied with the concentration of the S(0) state in the sample. Both signals are assigned to arise from the donor side of PSII. Both signals relaxed fast, were formed within 10 ms after a flash, and decayed with half-times at 5 K of 3-4 min. The signal in the S(0) state closely resembles split radical signals, originating from magnetic interaction between Y(Z)(*) and the S(2) state, that were first observed in Ca(2+)-depleted photosystem II samples. Therefore, we assign this signal to Y(Z)(*) in magnetic interaction with the S(0) state, Y(Z)(*)S(0). The other signal is assigned to the magnetic interaction between Y(Z)(*) and the S(1) state, Y(Z)(*)S(1). An important implication is that Y(Z) can be oxidized at 5 K in the S(0) and S(1) states. Oxidation of Y(Z) involves deprotonation of the tyrosine. This is restricted at 5 K, and we therefore suggest that the phenolic proton of Y(Z) is involved in a low-barrier hydrogen bond. This is an unusually short hydrogen bond in which proton movement at very low temperatures can occur.