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Transition State Theory (transition + state_theory)
Kinds of Transition State Theory Selected AbstractsComparative study of kinetics and reactivity indices of free radical polymerization reactions,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005K. Van Cauter Abstract Density functional theory calculations are used to determine the kinetics and reactivity indices of the first propagation steps of the polyethylene and poly(vinyl chloride) polymerization. Transition state theory is applied to evaluate the rate coefficient from the microscopically determined energies and partition functions. A comparison with the experimental Arrhenius plots validates the level of theory. The ability of reactivity indices to predict certain aspects of the studied propagation reactions is tested. Global softnesses of the reactants give an indication of the relative energy barriers of subsequent monomer additions. The correlation between energy and hardness profiles along the reaction path confirm the principle of maximum hardness. Local indices predict the regioselectivity of the attack of the growing radical to vinyl chloride. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Quantum Chemical Study on the Interactions of NO3 with RDX and Four Decomposition IntermediatesPROPELLANTS, EXPLOSIVES, PYROTECHNICS, Issue 4 2010Jidong Zhang Abstract Recently, NO3 (nitrate radical) was predicted to be formed during the decomposition of RDX. However, experimental studies of the gaseous products have never detected it. In order to verify the prediction, we studied the interactions of NO3 with RDX and four RDX decomposition intermediates (RDR, C3H5N5O4, OST, and TAZ) by using density functional theory (DFT). It is found that NO3 radical can be converted into NO2 during the process of interactions with the above-mentioned five molecules. In other words, NO3 radical can be consumed in these processes, which gives an explanation for the disappearance of NO3. Transition state theory (TST) calculations lead to the same results. The binding energies are calculated to estimate the strength of interactions. The energy of NO3 with RDR is the largest, which indicates this process is most likely to occur. Our calculation provides a support to the prediction of the formation of NO3. [source] Kinetic isotope effects for the H2 + C2H , C2H2 + H reaction based on the ab initio calculations and a global potential energy surfaceINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2010Liping Ju In the present paper, kinetic isotope effects of the title reaction are studied with canonical variational transition state theory on the modified Wang Bowman (MWB) potential energy surface (PES) (Chem Phys Lett 2005, 409, 249) and the ab initio calculations at the quadratic configuration interaction (QCISD (T, full))/aug-cc-pVTZ//QCISD (full)/cc-pVTZ level. The calculated rate constants for the isotopic variants of this title reaction on the MWB PES have good agreement with those of the present ab initio calculations over the temperature range of 20,5000 K for the forward reactions and 800,5000 K for the reverse reactions, respectively. In particular, the forward rate constants for the title reaction and its isotopically substituted reactions have negative temperature dependences at about 40 K. Rate expressions are presented for all the studied reactions. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 289,298, 2010 [source] Ab initio chemical kinetics for the NH2 + HNOx reactions, part II: Kinetics and mechanism for NH2 + HONOINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2009Shucheng Xu The kinetics and mechanism for the reaction of NH2 with HONO have been investigated by ab initio calculations with rate constant prediction. The potential energy surface of this reaction has been computed by single-point calculations at the CCSD(T)/6-311+G(3df, 2p) level based on geometries optimized at the CCSD/6-311++G(d, p) level. The reaction producing the primary products, NH3 + NO2, takes place via precomplexes, H2N,,,c -HONO or H2N,,,t -HONO with binding energies, 5.0 or 5.9 kcal/mol, respectively. The rate constants for the major reaction channels in the temperature range of 300,3000 K are predicted by variational transition state theory or Rice,Ramsperger,Kassel,Marcus theory depending on the mechanism involved. The total rate constant can be represented by ktotal = 1.69 × 10,20 × T2.34 exp(1612/T) cm3 molecule,1 s,1 at T = 300,650 K and 8.04 × 10,22 × T3.36 exp(2303/T) cm3 molecule,1 s,1 at T = 650,3000 K. The branching ratios of the major channels are predicted: k1 + k3 producing NH3 + NO2 accounts for 1.00,0.98 in the temperature range 300,3000 K and k2 producing OH + H2NNO accounts for 0.02 at T > 2500 K. The predicted rate constant for the reverse reaction, NH3 + NO2 , NH2 + HONO represented by 8.00 × 10,26 × T4.25 exp(,11,560/T) cm3 molecule,1 s,1, is in good agreement with the experimental data. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 678,688, 2009 [source] Direct dynamic study on the hydrogen abstraction reaction of H2CO with NCOINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 6 2009Hao Sun A direct ab initio dynamics method is used to investigate the hydrogen-abstraction reaction of H2CO with NCO. The potential energy surface information is obtained at the MP2/6-311G(d,p) level. More accurate single-point energy is refined at the G3(MP2)//MP2/6-311G(d,p) level. Furthermore, the rate constants of reaction H2CO + NCO are evaluated by using the canonical variational transition state theory with small-curvature tunneling contributions over a wide temperature range of 200,2000 K. The calculated reaction enthalpy and rate constants are in good agreement with the available experimental values. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 394,400, 2009 [source] Ab initio study of the OH + CH2O reaction: The effect of the OH··OCH2 complex on the H-abstraction kineticsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 5 2006Shucheng Xu Kinetics for the reaction of OH radical with CH2O has been studied by single-point calculations at the CCSD(T)/6-311+G(3df, 2p) level based on the geometries optimized at the B3LYP/6-311+G(3df, 2p) and CCSD/6-311++G(d,p) levels. The rate constant for the reaction has been computed in the temperature range 200,3000 K by variational transition state theory including the significant effect of the multiple reflections above the OH··OCH2 complex. The predicted results can be represented by the expressions k1 = 2.45 × 10 -21T2.98 exp (1750/T) cm3 mol,1 s,1 (200,400 K) and 3.22 × 10 -18T2.11 exp(849/T) cm3 mol,1 s,1 (400,3000 K) for the H-abstraction process and k2 = 1.05 × 10 -17T1.63 exp(,2156/T) cm3 mol,1 s,1 in the temperature range of 200,3000 K for the HO-addition process producing the OCH2OH radical. The predicted total rate constants (k1 + k2) can reproduce closely the recommended kinetic data for OH + CH2O over the entire range of temperature studied. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 322,326, 2006 [source] A shock tube study of the reaction NH2 + CH4 , NH3 + CH3 and comparison with transition state theoryINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 7 2003Soonho Song The rate coefficient for NH2 + CH4 , NH3 + CH3 (R1) has been measured in a shock tube in the temperature range 1591,2084 K using FM spectroscopy to monitor NH2 radicals. The measurements are combined with a calculation of the potential energy surface and canonical transition state theory with WKB tunneling to obtain an expression for k1 = 1.47 × 103T3.01e,5001/T(K) cm3 mol,1 s,1 that describes available data in the temperature range 300 ,2100 K. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 304,309, 2003 [source] Rate constants for H + CH4, CH3 + H2, and CH4 dissociation at high temperatureINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2001J. W. Sutherland The Laser Photolysis-Shock Tube technique coupled with H-atom atomic resonance absorption spectrometry has been used to study the reaction, H + CH4 , CH3 + H2, over the temperature range, 928,1697 K. Shock-tube studies on the reverse of this reaction, CH3 + H2 , H + CH4, using CH3I dissociation in the presence of H2 yielded H-atom formation rates and rate constants for the reverse process over the temperature range, 1269,1806 K. These results were transformed (using well-established equilibrium constants) to the forward direction. The combined results for H + CH4 can be represented by an experimental three parameter expression, k = 6.78 × 10,21 T3.156 exp(,4406 K/T) cm3 molecule,1 s,1 (348,1950 K) that was evaluated from the present work and seven previous studies. Using this evaluation, disagreements between previously reported values for the dissociation of CH4 could be reconciled. The thermal decomposition of CH4 was then studied in Kr bath gas. The dissociation results agreed with the earlier studies and were theoretically modeled with the Troe formalism. The energy transfer parameter necessary to explain both the present results and those of Kiefer and Kumaran (J Phys Chem 1993, 97, 414) is, ,,,E,all/cm,1 = 0.3323 T0.7. The low temperature data on the reverse reaction, H + CH3 (in He) from Brouard et al. (J Phys Chem 1989, 93, 4047) were also modeled with the Troe formalism. Lastly, the rate constant for H + CH4 was theoretically calculated using conventional transition state theory with Eckart tunneling corrections. The potential energy surface used was from Kraka et al. (J Chem Phys 1993, 99, 5306) and the derived T-dependence with this method agreed almost perfectly with the experimental evaluation. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 669,684, 2001 [source] Theoretical study of the reactions BF3 + BX, where X = H or NINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005Patrícia R. P. Barreto Abstract This work presents the rate constant for the gas-phase reaction BF3 + BX, where X = H or N, over the temperature range of 200,4,000 K. Conventional transition state theory (TST) is used to study these reactions. Geometries, frequencies, and the potential energy for reactant, products, and saddle point are obtained from accurate electronic structure calculations performed with the GAUSSIAN 98 program. The reaction rate for these reactions are determined using a simple code developed for this task. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Theoretical and kinetic study of the H + C2H5CN reactionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2010Jingyu Sun Abstract The reaction of H radical with C2H5CN has been studied using various quantum chemistry methods. The geometries were optimized at the B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2d,2p) levels. The single-point energies were calculated using G3 and BMC-CCSD methods based on B3LYP/6-311++G(2d,2p) geometries. Four mechanisms were investigated, namely, hydrogen abstraction, C-addition/elimination, N-addition/elimination and substitution. The kinetics of this reaction were studied using the transition state theory and multichannel Rice-Ramsperger-Kassel-Marcus methodologies over a wide temperature range of 200,3000 K. The calculated results indicate that C-addition/elimination channel is the most feasible over the whole temperature range. The deactivation of initial adduct C2H5CHN is dominant at lower temperature with bath gas H2 of 760 Torr; whereas C2H5+HCN is the dominant product at higher temperature. Our calculated rate constants are in good agreement with the available experimental data. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Ab initio direct dynamics studies on the reactions of chlorine atom with CH3,nFnCH2OH (n = 1,3)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2007Ying Wang Abstract The hydrogen abstraction reactions of Cl atom with a series of fluorinated alcohols, i.e., CH3,nFnCH2OH + Cl (n = 1,3) (R1,R3) have been studied systematically by ab initio direct dynamics method and the canonical variational transition state theory (CVT). The potential energy surface information is calculated at the MP2/6-311G(d,p) level. Energies along the minimum energy paths are improved by a series of single-point calculations at the higher modified GAUSSIAN-2 (G2M) level of theory. Theoretical analysis shows that three kinds of hydrogen atoms can be abstracted from the reactants CH2FCH2OH and CHF2CH2OH, and for CF3CH2OH, two possible pathways are found. The rate constants for each reaction channel are evaluated by CVT with the small-curvature tunneling correction (SCT) over a wide range of temperature from 200 to 2000 K. The calculated CVT/SCT rate constants are in good agreement with the available experimental values for the reactions CHF2CH2OH + Cl and CF3CH2OH + Cl. However, for the reaction CH2FCH2OH + Cl, there is negative temperature dependence below 500 K, which is different from the experimental fitted. It is shown that in the low temperature ranges, the three reactions all proceed predominantly via H-abstraction from the methylene positions, and with the increase of the temperature the H-abstraction channels from the fluorinated-methyl positions should be taken into account, while the H-abstraction channels from the hydroxyl groups are negligible over the whole temperature ranges. Also, the reactivity decreases substantially with fluorine substitution at the methyl position of alcohol. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Theoretical study on the Br + CH3SCH3 reactionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2007Hui Zhang Abstract The multiple-channel reactions Br + CH3SCH3 , products are investigated by direct dynamics method. The optimized geometries, frequencies, and minimum energy path are all obtained at the MP2/6-31+G(d,p) level, and energetic information is further refined by the G3(MP2) (single-point) theory. The rate constants for every reaction channels, Br + CH3SCH3 , CH3SCH2 + HBr (R1), Br + CH3SCH3 , CH3SBr + CH3 (R2), and Br + CH3SCH3 ,CH3S + CH3Br (R3), are calculated by canonical variational transition state theory with small-curvature tunneling correction over the temperature range 200,3000 K. The total rate constants are in good agreement with the available experimental data, and the two-parameter expression k(T) = 2.68 × 10,12 exp(,1235.24/T) cm3/(molecule s) over the temperature range 200,3000 K is given. Our calculations indicate that hydrogen abstraction channel is the major channel due to the smallest barrier height among three channels considered, and the other two channels to yield CH3SBr + CH3 and CH3S + CH3Br are minor channels over the whole temperature range. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Theoretical study and rate constant calculation for reaction of CF3CH2OH with OHJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2007Ying Wang Abstract The reaction mechanism of CF3CH2OH with OH is investigated theoretically and the rate constants are calculated by direct dynamics method. The potential energy surface (PES) information, which is necessary for dynamics calculation, is obtained at the B3LYP/6-311G (d, p) level. The single-point energy calculations are performed at the MC-QCISD level using the B3LYP geometries. Complexes, with the energies being less than corresponding reactants and products, are found at the entrance and exit channels for methylene-H-abstraction channel, while for the hydroxyl-H-abstraction channel only entrance complex is located. By means of isodesmic reactions, the enthalpies of the formation for the species CF3CH2OH, CF3CHOH, and CF3CH2O are estimated at the MC-QCISD//B3LYP/6-311G (d, p) level of theory. The rate constants for two kinds of H-abstraction channels are evaluated by canonical variational transition state theory with the small-curvature tunneling correction (CVT/SCT) over a wide range of temperature 200,2000 K. The calculated results are in good agreement with the experimental values in the temperature region 250,430 K. The present results indicate that the two channels are competitive. Below 289 K, hydroxyl-H-abstraction channel has more contribution to the total rate constants than methylene-H-abstraction channel, while above 289 K, methylene-H-abstraction channel becomes more important and then becomes the major reaction channel. © 2007 Wiley Periodicals, Inc. J Comput Chem 28: 802,810, 2007 [source] Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O , H2O + OHJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2003Tadafumi Uchimaru Abstract This article describes an ab initio investigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O , H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen-bonding complexes [HOHOH] and [H2OHO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOHOH] complex, while the OH radical acts as a hydrogen donor in the [H2OHO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS-APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as ,2.1 , ,2.3 and ,4.1 , ,4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2OHO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS-APNO energy evaluations. After fitting the CBS-APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1538,1548, 2003 [source] OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2001Annia Galano Abstract Density functional theory (B3LYP and BHandHLYP) and unrestricted second-order Mřller,Plesset (MP2) calculations have been performed using 3-21G, 6-31G(d,p), and 6-311 G(2d,2p) basis sets, to study the OH hydrogen abstraction reaction from alanine and glycine. The structures of the different stationary points are discussed. Ring-like structures are found for all the transition states. Reaction profiles are modeled including the formation of prereactive complexes, and very low or negative net energy barriers are obtained depending on the method and on the reacting site. ZPE and thermal corrections to the energy for all the species, and BSSE corrections for B3LYP activation energies are included. A complex mechanism involving the formation of a prereactive complex is proposed, and the rate coefficients for the overall reactions are calculated using classical transition state theory. The predicted values of the rate coefficients are 3.54×108 L,mol,1,s,1 for glycine and 1.38×109 L,mol,1,s,1 for alanine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1138,1153, 2001 [source] Obtaining thermochemical data by the extended kinetic methodJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2004Guy Bouchoux Abstract A microcanonical analysis of the extended kinetic method is performed using statistical rate calculations based on orbiting transition state theory. The model systems simulate polydentate bases M which exhibit losses of entropy upon protonation of up to 35 kJ mol,1 K,1. It is shown that the correlations using the natural logarithm of the ratio of rate constants vs the proton affinity of the reference bases, at several effective temperatures, lead to correct proton affinity and protonation entropy of the base M of interest. A systematic underestimate of the latter quantity (by 5,15%), mainly due to the use of a linear rather than a polynomial curve fitting procedure, is noted, however. When considering experimental data, more severe underestimates are observed for the protonation entropies of polydentate bases (by 50,90%). The origins of these considerable discrepancies are beyond the limits of the present modeling and remain to be determined. Copyright © 2004 John Wiley & Sons, Ltd. [source] A Determination of Hydration Mechanisms for Tricalcium Silicate Using a Kinetic Cellular Automaton ModelJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 7 2008Jeffrey W. Bullard Reaction mechanisms for the early stages of hydration of tricalcium silicate (Ca3SiO5) have not been agreed upon, although theories have appeared in the literature. In this paper, a mechanistic description is proposed that is consistent with a wide range of reported experimental observations, and which is supported quantitatively by simulations using HydratiCA, a new three-dimensional microstructure model of chemical kinetics. Rate processes are quantitatively modeled using probabilistic cellular automaton algorithms that are based on the principles of transition state theory. The model can test alternate assumptions about the reaction paths and rate-controlling steps, making it a kind of experimental tool for investigating kinetics and interpreting experimental observations. It is used here to show that hydration of Ca3SiO5 is most likely controlled by nucleation and growth of a compositionally variable calcium silicate hydrate solid, mediated at very early times by a transient, thermodynamically metastable solid that rapidly covers and sharply reduces the dissolution rate of Ca3SiO5. This proposed mechanism involves important elements of two leading theories of Ca3SiO5 hydration, neither of which alone has been able to capture the full range of experimental data when tested by the model. [source] Kinetics and thermodynamics of isothermal curing reaction of epoxy-4, 4,-diaminoazobenzene reinforced with nanosilica and nanoclay particlesPOLYMER COMPOSITES, Issue 8 2010M. Barghamadi The kinetics of the cure reaction for a system of bisphenol-A epoxy resin (DGEBA), with 4, 4,-diaminoazobenzene (DAAB), reinforced with nanosilica (NS), and nanoclay (NC) by means of isothermal technique of differential scanning calorimetry were studied. The Kamal autocatalytic-like kinetic model was used to estimate the reaction orders (m, n), rate constants (k1, k2), and also active energies (Ea) and pre-exponential factors (A) of the curing reaction. However, the existence of NS and NC with hydroxyl groups in the structure improves the cure reaction and influence the rate of reaction and therefore kinetics parameters. The Ea of cure reaction of DGEBA/DAAB system showed a decrease when nanoparticles were present and therefore the rate of the reaction was increased. Using the rate constants from the kinetic analysis and transition state theory, thermodynamic parameters such as enthalpy (,H#), entropy (,S#), and Gibbs free energy (,G#) changes were also calculated. The thermodynamic functions were shown to be very sensitive parameters for evaluation of the cure reaction. POLYM. COMPOS., 31:1442,1448, 2010. © 2009 Society of Plastics Engineers [source] Mechanically unfolding proteins: The effect of unfolding history and the supramolecular scaffoldPROTEIN SCIENCE, Issue 12 2002Rebecca C. Zinober Abstract The mechanical resistance of a folded domain in a polyprotein of five mutant I27 domains (C47S, C63S I27)5is shown to depend on the unfolding history of the protein. This observation can be understood on the basis of competition between two effects, that of the changing number of domains attempting to unfold, and the progressive increase in the compliance of the polyprotein as domains unfold. We present Monte Carlo simulations that show the effect and experimental data that verify these observations. The results are confirmed using an analytical model based on transition state theory. The model and simulations also predict that the mechanical resistance of a domain depends on the stiffness of the surrounding scaffold that holds the domain in vivo, and on the length of the unfolded domain. Together, these additional factors that influence the mechanical resistance of proteins have important consequences for our understanding of natural proteins that have evolved to withstand force. [source] Accessibility of simple gases in disordered carbons: theory and simulationASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 5 2009T. X. Nguyen Abstract We present a review of our recent studies on the accessibility of simple gases (Ar, N2, CH4 and CO2) in disordered microporous carbons using transition state theory (TST) and molecular simulation techniques. A realistic carbon model rather than the slit-pore approximation is utilised, providing more accurate understanding of complex adsorption equilibrium and dynamics behaviour at the molecular level in porous carbons, especially kinetic restriction of adsorbate molecules through highly constricted pore mouths of coals and molecular sieve carbons (MSC). This kinetic restriction leads to a molecular sieving effect which plays a vital role in gas separation using the MSCs. In particular, the realistic carbon model of a saccharose char used in a recent study was obtained by hybrid reverse Monte Carlo simulation. The time of adsorption or desorption of the single gas molecule between two neighbouring pores through a highly constricted window of the realistic saccharose char model was determined using TST. Finally, the validation of TST calculated results of adsorption and desorption times against experimental measurements as well as molecular dynamics simulation is also presented in this article. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine DehydrogenaseCHEMPHYSCHEM, Issue 12 2007Kara E. Ranaghan Abstract The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions,an area of great current interest,for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified,to either of the carboxylate oxygen atoms of the catalytic base (Asp428,),and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5±0.9 kcal,mol,1 for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal,mol,1. In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474,(MADH)/Thr172,(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471,(MADH)/Phe169,(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions. [source] Reaction Mechanism and Dynamic Investigations of Poly-channel Decomposition Reactions of o -Pyridyl RadicalCHINESE JOURNAL OF CHEMISTRY, Issue 8 2005Cheng Xue-Li Abstract Utilizing Gaussian94 program package, all species involved in decomposition reactions of o -pyridyl radical were optimized fully at B3LYP/6-311++G** level. Intrinsic reaction coordinate calculations were employed to confirm the connections of the transition states and products, and transition states were ascertained by the number of imaginary frequency (0 or 1). The reaction mechanism was elucidated by the vibrational mode analysis and electronic population analysis, and the reaction rate constants were calculated with transition state theory. [source] | |||||||||||||