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.     

Hydrogen/deuterium isotope effects on the excited-state proton transfer kinetics of 3-hydroxyflavone

The static and transient fluorescence spectroscopy of 3-hydroxyflavone, 3HF, has been investigated as a function of deuteration of the 3-hydroxy group and the solvent. Small H/D isotope effects are observed for at least two of the simple rate constants for the excited-state dynamics. The isotope effects are not significantly temperature dependent. The results suggest that the proton transfer process is not a simple barrier crossing reaction.     

Kinetic isotope effects for the C-H activation step in phase-transfer halogenations of alkanes

Within the scope of phase-transfer halogenations (Br and I) of alkanes, significant H/D kinetic isotope effects (KIE = 4-5) indicate that hydrogen abstraction is rate limiting. The excellent agreement of computed and experimentally determined H/D KIE as well as trapping experiments support the involvement of trihalomethyl radicals in the activation step.     

Pyridine as proton acceptor in the concerted proton electron transfer oxidation of phenol

Taking pyridine as a prototypal example of biologically important nitrogen bases involved in proton-coupled electron transfers, it is shown with the example of the photochemically triggered oxidation of phenol by Ru(III)(bpy)(3) that this proton acceptor partakes in a concerted pathway whose kinetic characteristics can be extracted from the overall kinetic response. The treatment of these data, implemented by the results of a parallel study carried out in heavy water, allowed the determination of the intrinsic kinetic characteristics of this proton acceptor. Comparison of the reorganization energies and of the pre-exponential factors previously derived for hydrogen phosphate and water (in water) as proton acceptors suggests that, in the case of pyridine, the proton charge is delocalized over a primary shell of water molecules firmly bound to the pyridinium cation.     

Kinetic effects of increased proton transfer distance on proton-coupled oxidations of phenol-amines

To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh(2)NH(2) substituent (1). Spectroscopic, structural, thermochemical, and computational studies show that the two amino-phenols are very similar, except that the O···N distance (d(ON)) is >0.1 ? longer in 2 than in 1. The difference in d(ON) is 0.13 ± 0.03 ? from X-ray crystallography and 0.165 ? from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations (?)OAr-NH(3)(+) by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. 2 orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C(6)H(4)OMe)(3)(?+) (3a(+)) occurs at (1.4 ± 0.1) × 10(4) M(-1) s(-1), only a factor of 2 slower than the closely related reaction of 1 with N(C(6)H(4)OMe)(2)(C(6)H(4)Br)(?+) (3b(+)). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG° (2 + 3a(+)) = +0.078 V versus ΔG° (1 + 3b(+)) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Br?nsted α, Δ ln(k)/Δ ln(K(eq))). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the two phenols emphasizes the importance of the highly anharmonic O···H···N potential energy surface and the influence of proton vibrational excited states.     

Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional methods for the dianionic methanolysis of the native (unsubstituted) and thio-substituted ethylene phosphates.     

Insights into palladium-catalyzed cyanation of bromobenzene: additive effects on the rate-limiting step

Kinetic studies using reaction calorimetry were conducted under synthetically relevant conditions to study the effect of additives in the cyanation of bromobenzene catalyzed by palladium complexes. This work demonstrates that the addition of a catalytic amount of ZnBr(2) facilitates the reaction with an elimination of the induction period observed without additive. This study afforded a qualitative assessment of the effect of water on the rate-limiting step and the apparent reaction order in bromobenzene.     

Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis

Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts, with the alterations presumably arising from interactions with active-site functional groups. In particular, the phosphate monoester hydrolysis reaction catalyzed by Escherichia coli alkaline phosphatase (AP) has been the subject of intensive scrutiny. Recent linear free energy relationship (LFER) studies suggest that AP catalyzes phosphate monoester hydrolysis through a loose transition state, similar to that in solution. To gain further insight into the nature of the transition state and active-site interactions, we have determined kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester substrates. The LFER and KIE data together provide a consistent picture for the nature of the transition state for AP-catalyzed phosphate monoester hydrolysis and support previous models suggesting that the enzymatic transition state is similar to that in solution. Moreover, the KIE data provides unique information regarding specific interactions between the transition state and the active-site Zn2+ ions. These results provide strong support for a model in which electrostatic interactions between the bimetallo Zn2+ site and a nonbridging phosphate ester oxygen atom make a significant contribution to the large rate enhancement observed for AP-catalyzed phosphate monoester hydrolysis.     

咪唑N-烷基化相转移催化反应动力学研究

本文报道在冠醚和季铵盐等相转移催化剂存在下咪唑N-正丁基化反应的动力学研究结果。在一定的催化剂浓度下,反应速度与烷基卤的浓度呈一级反应动力学关系,同时与催化剂浓度亦呈一级反应比例关系在60±0.05℃,以四丁基溴化铵为催化剂,咪唑N-正丁基化反应速率常数κ=(1.90±0.02)×10~(-2),活化能E_a=11.7±0.5 kcal/mol,此外还研究了不同类型冠醚和季铵盐对反应的影响。反应机理可设想为:在相转移催化反应条件下,由催化剂中的阳离子R_4N_ 和亲核试剂Im-形成的离子对转移到有机相中与烷基卤发生反应,因此反应速率对烷基卤浓度变化极为敏感,也与催化剂在两相间的分配系数α值有关。一般以α值为1左右的季铵盐的催化效果最好,这可能是选择有效相转移催化剂的一个标志。     

Testing the three step excited state proton transfer model by the effect of an excess proton

In a previous work, we proposed an extended model for intermolecular excited-state proton transfer to the solvent. The model invoked an intermediate species, the contact ion-pair RO(-)...H(3)O(+), where a proton is strongly hydrogen bonded to the conjugated photabase RO(-). In this study we tested the extended model by measuring the transient absorption and emission of 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) in an aqueous solution in the presence of a large concentration of mineral acids. In a neutral pH solution, the pump-probe signal consists of three time components, <1, 4, and 100 ps. The 4 ps time component, with a relative amplitude of about 0.3, was attributed to the formation of the contact ion-pair and the long 100 ps component to the dissociation of the ion-pair to a free proton and RO(-). In the presence of acid, the recombination of an excess proton competes with the geminate recombination. At a high acid concentration, the recombination process alters the time-dependent concentrations of the reactant, product and intermediate contact ion-pair. We observed that when the acid concentration increases, the amplitude of both the long and intermediate time components decreases. At about 3 M of acid, both components almost disappear. Model calculations of the acid effect on the transient HPTS signal indeed showed that the amplitude of the intermediate time component decreases as the excess proton concentration increases.     

Entropic intermediates and hidden rate-limiting steps in seemingly concerted cycloadditions. Observation, prediction, and origin of an isotope effect on recrossing

An unusual intramolecular kinetic isotope effect (KIE) in the reaction of dichloroketene with cis-2-butene does not fit with a simple asynchronous cycloaddition transition state, but it can be predicted from trajectory studies on a bifurcating energy surface. The origin of the KIE is related to a high propensity for transition state recrossing in this system, with heavier masses recrossing less. The KIE can also be predicted by a statistical model that treats the cycloaddition as a stepwise mechanism, the rate-limiting second step being associated with an entropic barrier for formation of the second carbon-carbon bond. The relevance of this stepwise mechanism to other asynchronous but seemingly concerted cycloadditions is suggested by examination of organocatalytic Diels-Alder reactions.     

Dynamics of the concerted triple proton transfer in cyclic water trimer using the multiconfiguration molecular mechanics algorithm

Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.     

Kinetic isotope effects on the dissolution kinetics of solid salicylic acid in aqueous solution: evidence for solubilisation via a proton dissociation-recombination mechanism

Quantitative Atomic Force Microscopy measurements made on the dissolving surface of solid salicylic acid in H2O and D2O reveal a kinetic isotope effect (kH/kD = 2.3 +/- 0.6) on the dissolution rate consistent with a transition state in which the proton is dissociated from the dissolving molecule.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.     

Comparative effects of curcuminoids on endothelial heme oxygenase-1 expression: ortho-methoxy groups are essential to enhance heme oxygenase activity and protection

Recently, it has been reported that curcumin, which is known as a potent antioxidant, acts as a non- stressful and non-cytotoxic inducer of the cytoprotective heme oxygenase (HO)-1. In this study, naturally occurring curcuminoids, such as pure curcumin, demethoxycurcumin (DMC) and bis-demethoxycurcumin (BDMC), were compared for their potential ability to modulate HO-1 expression and cytoprotective activity in human endothelial cells. All three curcuminoids could induce HO-1 expression and HO activity with differential levels. The rank order of HO activity was curcumin, DMC and BDMC. In comparison with endothelial protection against H2O2-induced cellular injury, cytoprotective capacity was found to be highest with curcumin, followed by DMC and BDMC. Interestingly, cytoprotective effects afforded by curcuminoids were considerably associated with their abilities to enhance HO activity. Considering that the main difference among the three curcuminoids is the number of methoxy groups (none for BDMC, one for DMC, and two for curcumin), the presence of methoxy groups in the ortho position on the aromatic ring was suggested to be essential to enhance HO-1 expression and cytoprotection in human endothelial cells. Our results may be useful in designing more efficacious HO-1 inducers which could be considered as promising pharmacological agents in the development of therapeutic approaches for the prevention or treatment of endothelial diseases caused by oxidative damages.     

Is the McLafferty rearrangement of ketones concerted or stepwise? The application of kinetic isotope effects

Intramolecular ¹³C and ²H isotope effects have been measured for unimolecular losses of ethene (the McLafferty rearrangement) from metastable molecular ions of 2-ethyl-1-phenylbutanl-1-one, 3-ethylpentan-2-one and heptan-4-one. Primary and secondary deuterium isotope effects are observed at the γ-(terminal) and β-positions, respectively. Large primary ¹³C isotope effects occur at β-positions and for the y positions of γ-ethylpentan-2-one and heptan-4-one. The carbon isotope effects in the cases of the doubly isotopically labelled CH₃COCH(C₂H₅)(¹³CH₂CH₃) and CD₃COCD(C₂D₅)(¹³CD₂CD₃) are 1.17 (±0.01) and 1.04 (±0.01), respectively. All of these isotope effects are consistent with a stepwise mechanism in which more than one step is rate determining.