Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects

The dynamical behavior and the temperature dependence of the kinetic isotope effects (KIEs) are examined for the proton-coupled electron transfer reaction catalyzed by the enzyme soybean lipoxygenase. The calculations are based on a vibronically nonadiabatic formulation that includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. The rate constant is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling and on time correlation functions of the energy gap and the proton donor-acceptor mode, which can be calculated from classical molecular dynamics simulations of the entire system. The dynamical behavior of the probability flux correlation function is dominated by the equilibrium protein and solvent motions and is not significantly influenced by the proton donor-acceptor motion. The magnitude of the overall rate is strongly influenced by the proton donor-acceptor frequency, the vibronic coupling, and the protein/solvent reorganization energy. The calculations reproduce the experimentally observed magnitude and temperature dependence of the KIE for the soybean lipoxygenase reaction without fitting any parameters directly to the experimental kinetic data. The temperature dependence of the KIE is determined predominantly by the proton donor-acceptor frequency and the distance dependence of the vibronic couplings for hydrogen and deuterium. The ratio of the overlaps of the hydrogen and deuterium vibrational wavefunctions strongly impacts the magnitude of the KIE but does not significantly influence its temperature dependence. For this enzyme reaction, the large magnitude of the KIE arises mainly from the dominance of tunneling between the ground vibronic states and the relatively large ratio of the overlaps between the corresponding hydrogen and deuterium vibrational wavefunctions. The weak temperature dependence of the KIE is due in part to the dominance of the local component of the proton donor-acceptor motion.     

Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance

Soybean lipoxygenase-1 (SLO) catalyzes the oxidation of linoleic acid. The rate-limiting step in this transformation is the net abstraction of the pro-S hydrogen atom from the center of the 1,5-pentadienyl moiety in linoleic acid. The large deuterium kinetic isotope effect (KIE) for this step appears in the first order rate constant ((D)k(cat) = 81 ± 5 at T = 25 °C). Furthermore, the KIE and the rate for protium abstraction are weakly temperature dependent (E(A,D) - E(A,H) = 0.9 ± 0.2 kcal/mol and E(A,H) = 2.1 ± 0.2 kcal/mol, respectively). Mutations at a hydrophobic site about 13 ? from the active site Fe(III), Ile(553), induce a marked temperature dependence that varies roughly in accordance with the degree to which the residue is changed in bulk from the wild type Ile. While the temperature dependence for these mutants varies from the wild type enzyme, the magnitude of the KIE at 25 °C is on the same order of magnitude. A hydrogen tunneling model [Kuznetsov, A.M., Ulstrup, J. Can. J. Chem. 77 (1999) 1085-1096] is utilized to model the KIE temperature profiles for the wild type SLO and each Ile(553) mutant. Hydrogenic wavefunctions are modeled using harmonic oscillators and Morse oscillators in order to explore the effects of anharmonicity upon computed kinetic observables used to characterize this hydrogen transfer.     

Anomalously large kinetic isotope effect

Activated diffusion of water between macromolecules in swollen cellulose is accompanied by anomalously high kinetic isotope effects of oxygen. The separation factor of heavy-oxygen water (H₂ ¹⁸O /H₂ ¹⁶O) is thousands of permilles instead of tens of permilles according to modern Absolute Rate Theory. This anomalous separation under usual conditions is disguised by the opposing process of very fast equalization to equilibrium through water-filled cellulose pores. This process is quicker by approximately 3 orders of magnitude than diffusion through the cellulose body. As a consequence, this opposition-directed equalization virtually eliminates the results of isotope separation. To reveal this anomaly it is necessary to suppress equalization, which was the primary problem for both discovery of this anomaly and its investigation. The method of investigating the anomalous separation in cellulose was developed with suppression of this negative influence. Discussion of the theoretical nature of the anomalous kinetic isotope effect is presented. This theoretical study would probably permit the discovery and use for isotope separation of the anomalously high isotope effect for other chemical elements, in particular, for those heavier than oxygen.      

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.     

Quantum-mechanical calculations on the kinetic hydrogen isotope effect

Conclusions Study has been made of the relation between the magnitude of the kinetic isotope effect and the free energy of reaction, account being taken of the anharmonicity of proton vibrations and the possibility of adiabatic transitions between the vibrational levels. Calculated values are compared with the results of measurements on proton transfer between ethyl nitroacetate and various bases in aqueous solution.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2414–2418, November, 1979.     

Lack of kinetic hydrogen isotope effect in acetylene pyrolysis

Second order rate constants for C₂H₂ or C₂D₂ polymerizations into vinylacetylene and higher C_nH_n products have been measured in a static reactor by dynamic mass spectrometry between 770–980 K. They are nearly identical within experimental error (±50%). It is shown that these results are consistent with the participation of thermally equilibrated vinylidene H₂C ? C: as a reactive intermediate: (1) since this assumption only introduces a modest reverse equilibrium isotope effect (K_iH/K_iD ca. 0.48 in this range) into overall rate constants. At the same time they seem to discriminate in general against alternative mechanisms in which the required H-atom transfers take place in rate determining steps. Present evidence, in conjunction with an updated analysis of relevant issues such as experimental and theoretical vs. termochemical estimates of the heat of formation of H₂C?C:, the nature of the transition states of singlet vinylidene addition reactions and the likelihood of discrete biradical intermediates in C₂H₂ dimerization, seems to lend further support to the notion that acetylene behaves as a singlet carbene at high temperatures.     

Conversion and origin of normal and abnormal temperature dependences of kinetic isotope effect in hydride transfer reactions

The effects of substituents on the temperature dependences of kinetic isotope effect (KIE) for the reactions of the hydride transfer from the substituted 5-methyl-6-phenyl-5,6-dihydrophenanthridine (G-PDH) to thioxanthylium (TX(+)) in acetonitrile were examined, and the results show that the temperature dependences of KIE for the hydride transfer reactions can be converted by adjusting the nature of the substituents in the molecule of the hydride donor. In general, electron-withdrawing groups can make the KIE to have normal temperature dependence, but electron-donating groups can make the KIE to have abnormal temperature dependence. Thermodynamic analysis on the possible pathways of the hydride transfer from G-PDH to TX(+) in acetonitrile suggests that the transfers of the hydride anion in the reactions are all carried out by the concerted one-step mechanism whether the substituent is an electron-withdrawing group or an electron-donating group. But the examination of Hammett-type free energy analysis on the hydride transfer reactions supports that the concerted one-step hydride transfer is not due to an elementary chemical reaction. The experimental values of KIE at different temperatures for the hydride transfer reactions were modeled by using a kinetic equation formed according to a multistage mechanism of the hydride transfer including a returnable charge-transfer complex as the reaction intermediate; the real mechanism of the hydride transfer and the root that why the temperature dependences of KIE can be converted as the nature of the substituents are changed were discovered.     

Hydrogen atom vs electron transfer in catecholase-mimetic oxidations by superoxometal complexes. Deuterium kinetic isotope effects

Dioximato-cobalt(II), -iron(II) and -manganese(II) complexes (1)-(6), acting as functional catecholase and phenoxazinone synthase models, exhibit a deuterium kinetic isotope effect predicted by theory (k4H/k4D < or = 3) in the catalytic oxidative dehydrogenation of 3,5-di-tert-butylcatechol and 2-aminophenol by O2. KIEs in the range of (k4H/k4D approximately 1.79-3.51) are observed with (1) and (2) as catalysts, pointing to hydrogen atom transfer in the rate-determining step from the substrate hydroxy group to the metal-bound superoxo ligand. Less significant KIEs (1.06-1.20) are exhibited by catalysts systems (3)-(6), indicating that proton-coupled electron transfer is the preferred route in those cases.     

Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridyl complexes

A theoretical investigation of proton-coupled electron transfer in ruthenium polypyridyl complexes is presented. The three reactions studied are as follows: (1) the comproportionation reaction of [(bpy)(2)(py)Ru(IV)O](2+) and [(bpy)(2)(py)Ru(II)OH(2)](2+) to produce [(bpy)(2)(py)Ru(III)OH](2+); (2) the comproportionation reaction of [(tpy)(bpy)Ru(IV)O](2+) and [(tpy)(bpy)Ru(II)OH(2)](2+) to produce [(tpy)(bpy)Ru(III)OH](2+); and (3) the cross reaction of [(tpy)(bpy)Ru(III)OH](2+) and [(bpy)(2)(py)Ru(II)OH(2)](2+) to produce [(tpy)(bpy)Ru(II)OH(2)](2+) and [(bpy)(2)(py)Ru(III)OH](2+). This investigation is motivated by experimental measurements of rates and kinetic isotope effects for these systems (Binstead, R. A.; Meyer, T. J. J. Am. Chem. Soc. 1987, 109, 3287. Farrer, B. T.; Thorp, H. H. Inorg. Chem. 1999, 38, 2497.). These experiments indicate that the second reaction is nearly one order of magnitude faster than the first reaction, and the third reaction is in the intermediate regime. The experimentally measured kinetic isotope effects for these three reactions are 16.1, 11.4, and 5.8, respectively. The theoretical calculations elucidate the physical basis for the experimentally observed trends in rates and kinetic isotope effects, as well as for the unusually high magnitude of the kinetic isotope effects. In this empirical model, the proton donor-acceptor distance is predicted to be largest for the first reaction and smallest for the third reaction. This prediction is consistent with the degree of steric crowding near the oxygen proton acceptor for the three reactions. The second reaction is faster than the first reaction since a smaller proton donor-acceptor distance leads to a larger overlap between the reactant and product proton vibrational wave functions. The intermediate rate of the third reaction is determined by a balance among several competing factors. The observed trend in the kinetic isotope effects arises from the higher ratio of the hydrogen to deuterium vibrational wave function overlap for larger proton donor-acceptor distances. Thus, the kinetic isotope effect increases for larger proton donor-acceptor distances. The unusually high magnitude of the kinetic isotope effects is due in part to the close proximity of the proton transfer interface to the electron donor and acceptor. This proximity results in strong electrostatic interactions that lead to a relatively small overlap between the reactant and product vibrational wave functions.     

Theoretical study of kinetic hydrogen isotope effect in proton-transfer reactions between ethyl nitroacetate and bases

Conclusions The relation between the kinetic isotope effect and the value of the free energy of proton-transfer reactions between ethyl nitroacetate and bases was calculated. The shape of the obtained KIE curve is in good agreement with the experimental values at the determined values of the parameters.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 959–962, April, 1978.The author expresses his gratitude to M. M. Bernfel'd for assistance in the numerical calculations.     

Simulations of the temperature dependence of amide I vibration

For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular structure. To obtain insights into the origin and size of the temperature solvent effects on the amide I spectra, combined molecular dynamics and density functional simulations were performed with the model N-methylacetamide molecule (NMA). The computations well reproduced frequency and intensity changes previously observed in aqueous NMA solutions. An empirical correction of vacuum frequencies in single NMA molecule based on the electrostatic potential of the water molecules provided superior results to a direct density functional average obtained for a limited number of solute-solvent clusters. The results thus confirm that the all-atom quantum and molecular mechanics approach captures the overall influence of the temperature dependent solvent properties on the amide I spectra and can improve the accuracy and reliability of molecular structural studies.     

Theoretical studies on the hydrogen atom transfer reaction

The hydrogen atom transfer reaction between substituted methanes (substituents; H, F, CH₃, OH, and CN) and methyl radicals was studied by 4-31G (UHF) calculations using the MINDO/3 geometries. The transition state structures and energy barriers were determined, and variations of the transition state and of the reactivity due to the change of substituent were analyzed based on the potential energy surface characteristics. It was concluded that the reaction is of the S_H2 type with a backside attack, and transition state variations are controlled by the vector sum of the component parallel to (Hammond rule) and one perpendicular to the reaction coordinate (anti-Hammond rule). It was also concluded that the most important factor influencing the reactivity is bond dissociation energy effect directly related to the spin transfer of the radical species, and the polar effect need not be overemphasized.     

Magnetic resonance studies of hydrogen atom transfer

The experimental results obtained on four different types of Raman spectra: pure rotational lines, the I_VV and _VH components of the vibrational Q-branch and the vibrational rotational lines are presented for H₂, D₂, HF and N₂ dissolved at low concentration in inert solvents. The line broadening and motional narrowing due to the solvent interaction is discussed.     

The temperature dependence of the kinetic isotope effect in the reaction of F atoms with CH4 and CD4

The kinetic isotope effect k_F+CH4/k_F+CD4 has been determined by reacting F atoms with mixtures of CH₄ and CD₄, using a discharge-flow-mass spectrometric technique. Experiments were carried out at four temperatures in the temperature range 183–298 K. The Arrhenius expression corresponding to the results is k_F+CH4/k_F+CD4=(0.99±0.02)×exp[(100±5)/T]. The present results are compared with previous published experimental and theoretical results.     

The kinetic isotope effect in the photochlorination of methane

The kinetic isotope effect for the photochemically initiated chlorination of methane-d₂ has been determined. The value is k_H/k_D = 12·1 at 0°C., and the variation with temperature is given by k_H/k_D = 1·09 exp (1300/RT. The results are considered in terms of a semiempirical potential energy surface, and the general subject of the magnitudes of primary kinetic isotope effects is discussed.