Alanine racemase free energy profiles from global analyses of progress curves

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.     

The kinetic method reveals secondary deuterium isotope effects on the proton affinity and gas-phase basicity of glycine and alanine methyl esters

The kinetic method for measuring proton affinities (PA) and gas-phase basicities (GB) was applied to the methyl esters of simple amino acids. The experiments show that the GB and PA values for deuterium labeled glycine methyl ester are indeed greater than that of the corresponding unlabelled glycine methyl ester. The PA of -Ala-OCD₃ is also slightly greater than that of the unlabeled alanine methyl ester. The secondary isotope effects originate, as shown by density functional theory, in differences in zero-point energies and thermal-energy corrections between H and D-bearing molecules.     

Large primary kinetic isotope effects in the abstraction of hydrogen from organic compounds by a fluorinated radical in water

Isotope effects have been measured for the abstraction of hydrogen from a series of organic substrates by the perfluoro radical, Na+ -O3SCF2CF2OCF2CF2*, in water. Both primary and secondary deuterium isotope effects were measured, with the primary isotope effects ranging in value from 4.5 for isopropanol to 19.6 for acetic acid. The values for the alpha- and beta-secondary deuterium isotope effects were 1.06 and 1.035, respectively. It was concluded that tunneling contributes significantly to the production of the observed, large primary kinetic isotope effects in these C-H abstraction reactions.     

Large concentration effects on the magnitude of secondary alpha-deuterium kinetic isotope effects

Because the secondary alpha-deuterium kinetic isotope effects in some S_N2 and E2 reactions are strongly concentration dependent, isotope effects measured at a single concentration could lead to erroneous conclusions about the mechanisms and transition state structures.     

Primary and secondary kinetic isotope effects in E2 elimination reactions

Primary and secondary deuterium kinetic isotope effects have been measured for elimination of LCl (L = H or D) from some substituted 1,2-diaryl-1-chloroethanes. Although changes in these effects are in agreement with theoretical predictions, the high values of (E_H-E_D)_β and the significantly low A_H/A_D may suggest that either proton tunnelling or an internal return mechanism is complicating this E2 elimination.     

Analysis of kinetic isotope effects for nonadiabatic reactions

Factors influencing the rates of quantum mechanical particle transfer reactions in many-body systems are discussed. The investigations are carried out on a simple model for a proton transfer reaction that captures generic features seen in more realistic models of condensed phase systems. The model involves a bistable quantum oscillator coupled to a one-dimensional double-well reaction coordinate, which is in turn coupled to a bath of harmonic oscillators. Reactive-flux correlation functions that involve quantum-classical Liouville dynamics for chemical species operators and quantum equilibrium sampling are used to estimate the reaction rates. Approximate analytical expressions for the quantum equilibrium structure are derived. Reaction rates are shown to be influenced significantly by both the quantum equilibrium structure and nonadiabatic dynamics. Nonadiabatic dynamical effects are found to play the major role in determining the magnitude of the kinetic isotope effect for the model transfer reaction.     

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change

We report here a theoretical study of the 13C kinetic isotope effect (KIE) and its temperature dependence for the reaction OH + CH4 --> H2O + CH3, the major sink of atmospheric methane in the troposphere. The KIE values at various atmospherically significant temperatures were determined by direct dynamics using variational transition state theory with multidimensional tunneling contributions (VTST/MT). The potential energy surfaces (PESs) were generated by hybrid density functional theory as well as by recently developed doubly hybrid density functional theory methods. Comparisons of our calculated KIEs with experimental data and theoretical values in the literature reveal the critical contributions due to multidimensional tunneling and torsion anharmonicity as well as the critical issue of the choice of internal rotational axis.     

The effect of conjugation on the magnitude of secondary alpha deuterium kinetic isotope effects

The unexpectedly small secondary alpha deuterium KIE in the 4-methoxybenzyl chloride-thiophenoxide ion reaction is attributed to the increased conjugation between the aryl group and the alpha carbon in the S_N2 transition state.     

Equivalent isothermal curves for kinetic analysis of non-stoichiometry

The author proposed a method for analyzing kinetics of non-stoichiometry by observing cyclic mass change behavior under cyclic temperature change. Because relationship between the mass and the mass change rate is independent on the previous thermal history of the specimen, we can get equivalent isothermal curves (synthesized isothermal curves) by extracting datum pairs of mass and mass change rate at a given temperature and many conversions, changing the frequencies. The equivalent isothermal curves are really the same as curves of conversion and rate of conversion observed isothermally, so that conventional methods for kinetic analysis can be similarly applied to the equivalent isothermal curves. When multiple elementary processes are proceeding, they can be separately observed by changing the frequency, so that, the method proposed in this short communication is useful and effective to elucidate kinetics of non-stoichiometry as well as reversible reactions.     

Quantum treatment of hydrogen nuclei in primary kinetic isotope effects in a thermal [1,5]-sigmatropic hydrogen (or deuterium) shift from (Z)-1,3-pentadiene

The geometric and kinetic isotope effects (GIE and KIE) for thermal [1,5]-sigmatropic H and D shifts of (Z)-1,3-pentadiene were studied by including the direct quantum effect of the migrating H or D nucleus in the multi-component molecular orbital-Hartree-Fock (MC_MO-HF) method. Based on the results, the C(1)-D bond lengths are 0.007 Angstrom shorter than the C1-H bond lengths in both the reactant (A) and the transition states (TS), whereas other bond lengths resemble those between H and D. The ratio of the rate constant (k(H)/k(D)) of the reaction for the thermal [1,5]-H and D shifts determined using the MC_MO-HF method (8.28) is closer to the experimental value (12.2) than that determined using either the conventional restricted Hartree-Fock (4.10) or restricted M?ller-Plesset second-order perturbation (3.79) methods.     

Mechanistic analysis of oxidative C-H cleavages using inter- and intramolecular kinetic isotope effects

A series of monodeuterated benzylic and allylic ethers were subjected to oxidative carbon-hydrogen bond cleavage to determine the impact of structural variation on intramolecular kinetic isotope effects in DDQ-mediated cyclization reactions. These values are compared to the corresponding intermolecular kinetic isotope effects that were accessed through subjecting mixtures of non-deuterated and dideuterated substrates to the reaction conditions. The results indicate that carbon-hydrogen bond cleavage is rate determining and that a radical cation is most likely a key intermediate in the reaction mechanism.     

A primary kinetic isotope effect for the O-H insertion of dimethoxycarbene

The primary kinetic isotope effect for the insertion of dimethoxycarbene into MeOH(D) is 3.3 ± 0.5.     

Secondary alpha-deuterium kinetic isotope effects: assumptions simplifying interpretations of mechanisms of solvolyses of secondary alkyl sulfonates

For solvolyses of 2-propyl and cyclopentyl sulfonates, logarithms of alpha-deuterium kinetic isotope effects (alpha-KIE) correlate linearly with logarithms of nucleophilic solvent assistance (NSA); correlations have the same slopes, but different intercepts, consistent with both solvent and structural effects on alpha-KIEs for heterolysis, further supported by recent theoretical and experimental data. It is argued that alpha- and beta-KIEs cannot yet distinguish between mechanisms proceeding via one or more transition states of similar energies. Structural, solvent, and isotope effects can be rationalized by heterolysis accompanied by NSA.     

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.     

Transition state structure and isotope effects in unimolecular hydrogen elimination from carbocations

1,1 unimolecular hydrogen eliminations from carbocations are currently interpreted in terms of a concerted mechanism in which two CH bonds are synchronously stretched. Here we show, through MNDO and RRKM computations, that the available experimental data are compatible with all the reaction mechanisms in which both the CH bonds are significantly distorted in the transition state, irrespective of the synchronous or non-synchronous character of the reaction.     

天然氘核磁共振测定一级和二级动力学氘同位素效应I. 内标的分子内与分子间竞争法

应用氘核磁共振,而不用特别氘代化合物同时测定一级和二级动力学氘同位素效应,其特点是采用外标,并同时考虑分子内和分子间竞争,用建立的方法测定甲苯、乙苯及异丙苯的一级、α-及β-二级效应值。