Kinetic study on the reaction of OH radical with dimethyl sulfide in the absence of oxygen.

A variational transition-state theory calculation for the reaction of OH radical with dimethyl sulfide (DMS) in the absence of oxygen is presented. The potential energy surface was previously studied and the effects of different levels of theory were analyzed. Here we propose a kinetic model for the atmospheric DMS oxidation in the absence of oxygen. For the first time, addition of OH to DMS and CH(3)SOH elimination channels are connected, and the equilibrium approximation in the high-pressure regime is applied to the DMS-OH adduct in the absence of oxygen. Both low- and high-pressure limits are considered to analyze the two different mechanisms of the H-abstraction channel, and two different kinetic approaches are applied to study them. The rate constants for the addition-elimination and H-abstraction routes are compared and the branching ratios are also studied. Tunneling contributions and kinetic isotope effects are analyzed. We conclude, in agreement with experimental observations, that in the absence of oxygen DMS oxidation takes place via H-abstraction with a branching ratio of 1.0 at atmospheric temperatures.     

The effect of inert salts on the structure of the transition state in the SN2 reaction between thiophenoxide ion and butyl chloride

The effect of inert salts on the structure of the transition state has been determined by measuring the secondary alpha deuterium and the chlorine leaving group kinetic isotope effects for the S(N)2 reaction between n-butyl chloride and thiophenoxide ion in both methanol and DMSO. The smaller secondary alpha deuterium isotope effects and very slightly larger chlorine isotope effects found in both solvents when the inert salt is present suggests that the S(N)2 transition state is tighter and more product-like, with a shorter S-C(alpha) and very a slightly longer C(alpha)-Cl bond when the added salt is present. The salt effect on the reaction in methanol where the reacting nucleophile is the solvent-separated ion-pair complex is much greater than the salt effect on the reaction in DMSO where the reacting nucleophile is the free ion. This greater change in transition-state structure found when the inert salt is present in methanol is consistent with the solvation rule for S(N)2 reactions. The greater change in the S-C(alpha) bond is predicted by the bond strength hypothesis. A rationale for the changes found in transition-state structure when the inert salt is present is suggested for both the free-ion and the ion-pair reactions.     

A theoretical investigation of alpha-carbon kinetic isotope effects and their relationship to the transition-state structure of S(N)2 reactions

[reaction: see text] The transition structures and alpha-carbon 12C/13C kinetic isotope effects for 22 S(N)2 reactions between methyl chloride and a wide variety of nucleophiles have been calculated using the B1LYP/aug-cc-pVDZ level of theory. Anionic, neutral, and radical anion nucleophiles were used to give a wide range of S(N)2 transition states so the relationship between the magnitude of the alpha-carbon kinetic isotope effect and transition-state structure could be determined. The results suggest that the alpha-carbon 12C/13C kinetic isotope effects for S(N)2 reactions will be large (near the experimental maximum) and that the curve relating the magnitude of the KIE to the percent transfer of the alpha-carbon from the nucleophile to the leaving group in the transition state has a broad maximum. This means very similar KIEs will be found for early, symmetric, and late transition states and that one cannot use the magnitude of these KIEs to estimate transition-state structure.     

Thermal and state-selected rate constant calculations for O(3p) + H2 → OH + H and isotopic analogs

We present a new parametrization (based on ab initio calculations) of the bending potentials for the two lowest potential energy surfaces of the reaction O(³P) + H₂, and we use it for rate constant calculations by variational transition-state theory with multidimensional semiclassical tunneling corrections. We present results for the temperature range 250–2400 K for both the rate constants and the intermolecular kinetic isotope effects for the reactions of O(³P) with D₂ and HD. In general, the calculated rate constants for the thermal reactions are in excellent agreement with available experiments. We also calculate the enhancement effect for exciting H₂ to the first excited vibrational state. The calculations also provide information on which aspects of the potential energy surfaces are important for determining the predicted rate constants.     

Dependence of transition state structure on substrate: the intrinsic C-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures

Ornithine decarboxylase is the first and the rate-controlling enzyme in polyamine biosynthesis; it decarboxylates l-ornithine to form the diamine putrescine. We present calculations performed using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiempirical Hamiltonian for the wild-type ornithine decarboxylase reaction with ornithine (the physiological substrate) and lysine (a "slow" substrate) and for mutant E274A with ornithine substrate. The dynamical method is variational transition state theory with quantized vibrations. We employ a single reaction coordinate equal to the carbon-carbon distance of the dissociating bond, and we find a large difference between the intrinsic kinetic isotope effect for the physiological substrate, which equals 1.04, and that for the slow substrate, which equals 1.06. This shows that, contrary to a commonly accepted assumption, kinetic isotope effects on slow substrates are not always good models of intrinsic kinetic isotope effects on physiological substrates. Furthermore, analysis of free-energy-based samples of transition state structures shows that the differences in kinetic isotope effects may be traced to different numbers of hydrogen bonds at the different transition states of the different reactions.     

Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase

The H/D primary kinetic isotope effect (KIE) for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) is calculated as a function of temperature employing ensemble-averaged variational transition-state theory with multidimensional tunneling. The calculated KIEs display only a small temperature dependence over the temperature range of 5 to 45 degrees C. We identify two key features that contribute to canceling most of the temperature dependence of the KIE that would be expected on the basis of simpler models. Related issues such as the isotope effects on Arrhenius preexponential factors, large differences between free energies of activation and Arrhenius activation energy, and fluctuations of effective barriers are also discussed.     

Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase

The temperature dependence of the primary kinetic isotope effect (KIE), combined temperature-pressure studies of the primary KIE, and studies of the alpha-secondary KIE previously led us to infer that hydride transfer from nicotinamide adenine dinucleotide to flavin mononucleotide in morphinone reductase proceeds via environmentally coupled hydride tunneling. We present here a computational analysis of this hydride transfer reaction using QM/MM molecular dynamics simulations and variational transition-state theory calculations. Our calculated primary and secondary KIEs are in good agreement with the corresponding experimental values. Although the experimentally observed KIE lies below the semiclassical limit, our calculations suggest that approximately 99% of the reaction proceeds via tunneling: this is the first "deep tunneling" reaction observed for hydride transfer. We also show that the dominant tunneling mechanism is controlled by the isotope at the primary rather than the secondary position: with protium in the primary position, large-curvature tunneling dominates, whereas with deuterium in this position, small-curvature tunneling dominates. Also, our study is consistent with tunneling being preceded by reorganization: in the reactant, the rings of the nicotinamide and isoalloxazine moieties are stacked roughly parallel to each other, and as the system moves toward a "tunneling-ready" configuration, the nicotinamide ring rotates to become almost perpendicular to the isoalloxazine ring.     

New analytical potential energy surface for the F(2P)+CH4 hydrogen abstraction reaction: kinetics and dynamics

A new potential energy surface for the gas-phase F(2P)+CH4 reaction and its deuterated analogues is reported, and its kinetics and dynamics are studied exhaustively. This semiempirical surface is completely symmetric with respect to the permutation of the four methane hydrogen atoms, and it is calibrated to reproduce the topology of the reaction and the experimental thermal rate constants. For the kinetics, the thermal rate constants were calculated using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 180-500 K. The theoretical results reproduce the experimental variation with temperature. The influence of the tunneling factor is negligible, due to the flattening of the surface in the entrance valley, and we found a direct dependence on temperature, and therefore positive and small activation energies, in agreement with experiment. Two sets of kinetic isotope effects were calculated, and they show good agreement with the sparse experimental data. The coupling between the reaction coordinate and the vibrational modes shows qualitatively that the FH stretching and the CH3 umbrella bending modes in the products appear vibrationally excited. The dynamics study was performed using quasi-classical trajectory calculations, including corrections to avoid zero-point energy leakage along the trajectories. First, we found that the FH(nu',j') rovibrational distributions agree with experiment. Second, the excitation function presents an oscillatory pattern, reminiscent of a reactive resonance. Third, the state specific scattering distributions present reasonable agreement with experiment, and as the FH(nu') vibrational state increases the scattering angle becomes more forward. These kinetics and dynamics results seem to indicate that a single, adiabatic potential energy surface is adequate to describe this reaction, and the reasonable agreement with experiment (always qualitative and sometimes quantitative) lends confidence to the new surface.     

A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase

Combined quantum mechanical/molecular mechanical simulations have been carried out to investigate the origin of the carbon acidity enhancement in the alanine racemization reaction catalyzed by alanine racemase (AlaR). The present study shows that the enhancement of carbon acidity of alpha-amino acids by the cofactor pyridoxal 5'-phosphate (PLP) with an unusual, unprotonated pyridine is mainly due to solvation effects, in contrast to the intrinsic electron-withdrawing stabilization by the pyridinium ion to form a quinonoid intermediate. Alanine racemase further lowers the alpha-proton acidity and provides an overall 14-17 kcal/mol transition-state stabilization. The second key finding of this study is that the mechanism of racemization of an alanine zwitterion in water is altered from an essentially concerted process to a stepwise reaction by formation of an external aldimine adduct with the PLP cofactor. Finally, we have used a centroid path integral method to determine the intrinsic kinetic isotope effects for the two proton abstraction reactions, which are somewhat greater than the experimental estimates.     

Mechanistic investigation of the enantioselective intramolecular stetter reaction: proton transfer is the first irreversible step

A study on the mechanism of the asymmetric intramolecular Stetter reaction is reported. This investigation includes the determination of the rate law, kinetic isotope effects, and competition experiments. The reaction was found to be first order in aldehyde and azolium catalyst or free carbene. A primary kinetic isotope effect was found for the proton of the aldehyde. Taken together with a series of competition experiments, these results suggest that proton transfer from the tetrahedral intermediate formed upon nucleophilic attack of the carbene onto the aldehyde is the first irreversible step.     

Isotope effects and the nature of selectivity in rhodium-catalyzed cyclopropanations

The mechanism of the dirhodium tetracarboxylate catalyzed cyclopropanation of alkenes with both unsubstituted diazoacetates and vinyl- and phenyldiazoacetates was studied by a combination of (13)C kinetic isotope effects and density functional theory calculations. The cyclopropanation of styrene with methyl phenyldiazoacetate catalyzed by Rh(2)(octanoate)(4) exhibits a substantial (13)C isotope effect (1.024) at the terminal olefinic carbon and a smaller isotope effect (1.003-1.004) at the internal olefinic carbon. This is consistent with a highly asynchronous cyclopropanation process. Very similar isotope effects were observed in a bisrhodium tetrakis[(S)-N-(dodecylbenzenesulfonyl)prolinate] (Rh(2)(S-DOSP)(4) catalyzed reaction, suggesting that the chiral catalyst engages in a very similar cyclopropanation transition-state geometry. Cyclopropanation with ethyl diazoacetate was concluded to involve an earlier transition state, based on a smaller terminal olefinic isotope effect (1.012-1.015). Density functional theory calculations (B3LYP) predict a reaction pathway involving complexation of the diazoesters to rhodium, loss of N(2) to afford a rhodium carbenoid, and an asynchronous but concerted cyclopropanation transition state. The isotope effects predicted for reaction of a phenyl-substituted rhodium carbenoid with styrene match within the error of the experimental values, supporting the accuracy of the theoretical calculations and the rhodium carbenoid mechanism. The accuracy of the calculations is additionally supported by excellent predictions of reaction barriers, stereoselectivity, and reactivity trends. The nature of alkene selectivity and diastereoselectivity effects in these reactions is discussed, and a new model for enantioselectivity in Rh(2)(S-DOSP)(4)-catalyzed cyclopropanations is presented.     

Thermochemistry and accurate quantum reaction rate calculations for H2/HD/D2 + CH3

Accurate quantum-mechanical results for thermodynamic data, cumulative reaction probabilities (for J = 0), thermal rate constants, and kinetic isotope effects for the three isotopic reactions H2 + CH3 --> CH4 + H, HD + CH3 --> CH4 + D, and D2 + CH3 --> CH(3)D + D are presented. The calculations are performed using flux correlation functions and the multiconfigurational time-dependent Hartree (MCTDH) method to propagate wave packets employing a Shephard interpolated potential energy surface based on high-level ab initio calculations. The calculated exothermicity for the H2 + CH3 --> CH4 + H reaction agrees to within 0.2 kcal/mol with experimentally deduced values. For the H2 + CH3 --> CH4 + H and D2 + CH3 --> CH(3)D + D reactions, experimental rate constants from several groups are available. In comparing to these, we typically find agreement to within a factor of 2 or better. The kinetic isotope effect for the rate of the H2 + CH3 --> CH4 + H reaction compared to those for the HD + CH3 --> CH4 + D and D2 + CH3 --> CH(3)D + D reactions agree with experimental results to within 25% for all data points. Transition state theory is found to predict the kinetic isotope effect accurately when the mass of the transferred atom is unchanged. On the other hand, if the mass of the transferred atom differs between the isotopic reactions, transition state theory fails in the low-temperature regime (T < 400 K), due to the neglect of the tunneling effect.     

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction.

We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.     

Experimental and theoretical multiple kinetic isotope effects for an SN2 reaction. An attempt to determine transition-state structure and the ability of theoretical methods to predict experimental kinetic isotope effects

The secondary alpha-deuterium, the secondary beta-deuterium, the chlorine leaving-group, the nucleophile secondary nitrogen, the nucleophile (12)C/(13)C carbon, and the (11)C/(14)C alpha-carbon kinetic isotope effects (KIEs) and activation parameters have been measured for the S(N)2 reaction between tetrabutylammonium cyanide and ethyl chloride in DMSO at 30 degrees C. Then, thirty-nine readily available different theoretical methods, both including and excluding solvent, were used to calculate the structure of the transition state, the activation energy, and the kinetic isotope effects for the reaction. A comparison of the experimental and theoretical results by using semiempirical, ab initio, and density functional theory methods has shown that the density functional methods are most successful in calculating the experimental isotope effects. With two exceptions, including solvent in the calculation does not improve the fit with the experimental KIEs. Finally, none of the transition states and force constants obtained from the theoretical methods was able to predict all six of the KIEs found by experiment. Moreover, none of the calculated transition structures, which are all early and loose, agree with the late (product-like) transition-state structure suggested by interpreting the experimental KIEs.     

Transition states for glucopyranose interconversion

Glucose is a central molecule in biology and chemistry, and the anomerization reaction has been studied for more than 150 years. Transition-state structure is the last impediment to an in-depth understanding of its solution chemistry. We have measured kinetic isotope effects on the rate constants for approach of alpha-glucopyranose to its equilibrium with beta-glucopyranose, and these were converted into unidirectional kinetic isotope effects using equilibrium isotope effects. Saturation transfer 13C NMR spectroscopy has yielded the relative free energies of the transition states for the ring-opening and ring-closing reactions, and both transition states contribute to the experimental kinetic isotope effects. Both transition states of the anomerization process have been modeled with high-level computational theory with constraints from the primary, secondary, and solvent kinetic isotope effects. We have found the transition states for anomerization, and we have also concluded that it is forbidden for the water molecule to form a hydrogen bond bridge to both OH1 and O5 of glucose simultaneously in either transition state.     

Absolute rate calculations. Proton transfers in solution

The reaction path of the intersecting-state model is used in transition-state theory with the semiclassical correction for tunneling (ISM/scTST) to calculate the rates of proton-transfer reactions from hydrogen-bond energies, reaction energies, electrophilicity indices, bond lengths, and vibration frequencies of the reactive bonds. ISM/scTST calculations do not involve adjustable parameters. The calculated proton-transfer rates are within 1 order of magnitude of the experimental ones at room temperature, and cover very diverse systems, such as deprotonations of nitroalkanes, ketones, HCN, carboxylic acids, and excited naphthols. The calculated temperature dependencies and kinetic isotope effects are also in good agreement with the experimental data. These calculations elucidate the roles of the reaction energy, electrophilicity, structural parameters, hydrogen bonds, tunneling, and solvent in the reactivity of acids and bases. The efficiency of the method makes it possible to run absolute rate calculations through the Internet.     

Potential energy surface for the F(2P(3/2),2P(1/2)) + CH4 hydrogen abstraction reaction. kinetics and dynamics study

A modified and recalibrated potential energy surface (PES) is reported for the gas-phase F(2P(3/2),2P(1/2)) + CH4 reaction and its deuterated analogue. This semiempirical surface is completely symmetric with respect to the permutation of the four methane hydrogen atoms and is calibrated with respect to the updated experimental and theoretical stationary point properties and experimental thermal rate constants. To take into account the two spin-orbit electronic states of the fluorine atom, two versions of the surface were constructed, the PES-SO and PES-NOSO surfaces, which differ in the choice of the zero reference level of the reactants. On both surfaces, the thermal rate constants were calculated using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 180-500 K. While the PES-SO surface overestimates the experimental rate constants, the PES-NOSO surface shows a better agreement, reproducing the experimental variation with temperature. The influence of the tunneling factor is negligible, due to the flattening of the surface in the entrance valley, and we found a direct dependence on temperature, and therefore positive and small activation energies, in agreement with experiment. The kinetic isotope effects calculated showed good agreement with the sparse experimental data at 283 and 298 K. Finally, on the PES-NOSO surface, other dynamical features, such as the coupling between the reaction coordinate and the vibrational modes, were analyzed. It was found qualitatively that the FH stretching and the CH3 umbrella bending modes in the products appear vibrationally excited. These kinetics and dynamics results seem to indicate that a single, adiabatic PES is adequate to describe this reaction.     

A new insight into using chlorine leaving group and nucleophile carbon kinetic isotope effects to determine substituent effects on the structure of SN2 transition states

Chlorine leaving group k(35)/k(37), nucleophile carbon k(11)/k(14), and secondary alpha-deuterium [(kH/kD)alpha] kinetic isotope effects (KIEs) have been measured for the SN2 reactions between para-substituted benzyl chlorides and tetrabutylammonium cyanide in tetrahydrofuran at 20 degrees C to determine whether these isotope effects can be used to determine the substituent effect on the structure of the transition state. The secondary alpha-deuterium KIEs indicate that the transition states for these reactions are unsymmetric. The theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion; i.e., they suggest that the transition states for these reactions are unsymmetric with a long NC-C(alpha) and reasonably short C(alpha)-Cl bonds. The chlorine isotope effects suggest that these KIEs can be used to determine the substituent effects on transition state structure with the KIE decreasing when a more electron-withdrawing para-substituent is present. This conclusion is supported by theoretical calculations. The nucleophile carbon k(11)/k(14) KIEs for these reactions, however, do not change significantly with substituent and, therefore, do not appear to be useful for determining how the NC-C(alpha) transition-state bond changes with substituent. The theoretical calculations indicate that the NC-C(alpha) bond also shortens as a more electron-withdrawing substituent is placed on the benzene ring of the substrate but that the changes in the NC-C(alpha) transition-state bond with substituent are very small and may not be measurable. The results also show that using leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is more complicated than previously thought. The implication of using both chlorine leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is discussed.