首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 15 毫秒
1.
The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for computational quantum chemistry. We present a divide‐and‐conquer strategy that departs from the potential energy surfaces obtained by standard density functional theory with inclusion of dispersion. The energies of the reactant and transition structures are refined by wavefunction‐type calculations for the reaction site. Thermal effects and entropies are calculated from vibrational partition functions, and the anharmonic frequencies are calculated separately for each vibrational mode. This method is applied to a key reaction of an industrially relevant catalytic process, the methylation of small alkenes over zeolites. The calculated reaction rate constants (free energies), pre‐exponential factors (entropies), and enthalpy barriers show that our computational strategy yields results that agree with experiment within chemical accuracy limits (less than one order of magnitude).  相似文献   

2.
Many important bimolecular hydrogen-transfer processes that take place in the atmosphere proceed via a potential energy minimum (hydrogen-bonded complex) that precedes along the minimum energy path the unique saddle point of the reaction, the one corresponding to the hydrogen transfer. It is clear that the one-step low-pressure rate constant of such a reaction does not depend on the existence of any complex along the minimum energy path below the reactant if the reaction takes place by thermal activation over a transition state that lies quite above the reactants (for instance 10 kcal/mol). However, we have quantitatively shown in this article that the scenario notoriously changes if the reaction involves significant tunneling. In this work, we have theoretically calculated the rate constants and their temperature dependence for the reaction HO+HOH→HOH+OH by means of a canonical variational transition state theory and a canonical unified statistical theory (when necessary). Multidimensional tunneling effects have been included with a semiclassical transmission coefficient. Two kinds of modified potential energy surfaces (PESs), obtained from an original ab initio potential energy surface, previously calculated by us, have been used. The Eckart-modified PESs serve to model the hydrogen-abstraction profiles with no complexes along the path, while the Gaussian-modified PESs model the energy profiles with two complexes along the path symmetrically distributed at each side of the abstraction saddle point. Our results show that the existence of those complexes reduces the thickness of the classically forbidden region for energies below the adiabatic barrier, and then tunneling is promoted and the reaction is accelerated. The effect of the complex formation in several kinetic magnitudes, as the Arrhenius parameters and the kinetic isotope effect has also been analyzed. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1685–1692, 1999  相似文献   

3.
Daum KA  Atkinson DA  Ewing RG 《Talanta》2001,55(3):491-500
The efficiency of chloride reactant ion formation, when chlorinated hydrocarbon reagent chemicals were added to the ionization region of an ion mobility spectrometer, corresponded to the electron attachment rate constant of the chemical. The chemicals investigated here included chloromethane, dichlormethane, trichloromethane, tetrachloromethane and chlorobenzene, with tetrachloromethane producing the greatest amount of chloride reactant ions for the amount of chemical added. Reagent chemicals with smaller electron attachment rate constants required the addition of more chemical to reach functional reactant ion levels. The excess neutral reagent molecules clustered to the chloride reactant ions and reduced the effectiveness of abstracting a proton from 2,4,6-trinitrotoluene (TNT). The effect of clustering was different for each chemical. Tetrachloromethane, which had the least exothermic clustering reaction, had the most effective production of the (TNT-H)(-) product ion per mole of reagent chemical. Bromide and iodide ions were also investigated as potential reactant ions. Bromide was found to effectively produce the proton abstracted (TNT-H)(-) ion. Iodide, however, was not a strong enough base to form (TNT-H)(-) from TNT. There was no apparent transfer of an electron to TNT by chloride, bromide or iodide.  相似文献   

4.
Chalcone isomerase catalyzes the transformation of chalcone to naringerin as a part of flavonoid biosynthetic pathways. The global reaction takes place through a conformational change of the substrate followed by chemical reaction, being thus an excellent example to analyze current theories about enzyme catalysis. We here present a detailed theoretical study of the enzymatic action on the conformational pre-equilibria and on the chemical steps for two different substrates of this enzyme. Free-energy profiles are obtained in terms of potentials of mean force using hybrid quantum mechanics/molecular mechanics potentials. The role of the enzyme becomes clear when compared to the counterpart equilibria and reactions in aqueous solution. The enzyme does not only favor the chemical reaction lowering the corresponding activation free energy but also displaces the conformational equilibria of the substrates toward the reactive form. These results, which can be rationalized in terms of the electrostatic interactions established in the active site between the substrate and the environment, agree with a more general picture of enzyme catalysis. According to this, an active site designed to accommodate the transition state of the reaction would also have consequences on the reactant state, stabilizing those forms which are geometrically and/or electronically closer to the transition structure.  相似文献   

5.
The complex-forming CH + H2 --> CH2 + H reaction is studied employing a recently developed global potential energy function. The reaction probability in the total angular momentum J = 0 limit is estimated with a four-atom quantum wave packet method and compared with classical trajectory and statistical theory results. The formation of complexes from different reactant internal states is also determined with wave packet calculations. While there is no barrier to reaction along the minimum energy path, we find that there are angular constraints to complex formation. Trajectory-based estimates of the low-pressure rate constants are made and compared with experimental results. We find that zero-point energy violation in the trajectories is a particularly severe problem for this reaction.  相似文献   

6.
We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the "transition state" towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further "tailor" the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process.  相似文献   

7.
The hydration process for two Ru(II) representative half-sandwich complexes: Ru(arene)(pta)Cl(2) (from the RAPTA family) and [Ru(arene)(en)Cl](+) (further labeled as Ru_en) were compared with analogous reaction of cisplatin. In the study, quantum chemical methods were employed. All the complexes were optimized at the B3LYP/6-31G(d) level using Conductor Polarizable Continuum Model (CPCM) solvent continuum model and single-point (SP) energy calculations and determination of electronic properties were performed at the B3LYP∕6-311++G(2df,2pd)/CPCM level. It was found that the hydration model works fairly well for the replacement of the first chloride by water where an acceptable agreement for both Gibbs free energies and rate constants was obtained. However, in the second hydration step worse agreement of the experimental and calculated values was achieved. In agreement with experimental values, the rate constants for the first step can be ordered as RAPTA-B > Ru_en > cisplatin. The rate constants correlate well with binding energies (BEs) of the Pt∕Ru-Cl bond in the reactant complexes. Substitution reactions on Ru_en and cisplatin complexes proceed only via pseudoassociative (associative interchange) mechanism. On the other hand in the case of RAPTA there is also possible a competitive dissociation mechanism with metastable pentacoordinated intermediate. The first hydration step is slightly endothermic for all three complexes by 3-5 kcal∕mol. Estimated BEs confirm that the benzene ligand is relatively weakly bonded assuming the fact that it occupies three coordination positions of the Ru(II) cation.  相似文献   

8.
The oxidation of a series of para-substituted phenyl methyl sulfides was carried out with several oxo(salen)iron (salen = N,N'-bis(salicylidine)ethylenediaminato) complexes in acetonitrile. The oxo complex [O=Fe(IV)(salen)](*+), generated from an iron(III) [bond] salen complex and iodosylbenzene, effectively oxidizes the organic sulfides to the corresponding sulfoxides. The formation of [O [double bond] Fe(IV)(salen)](*+) as the active oxidant is supported by resonance Raman studies. The kinetic data indicate that the reaction is first-order in the oxidant and fractional-order with respect to sulfide. The observed saturation kinetics of the reaction and spectral data indicate that the substrate binds to the oxidant before the rate-controlling step. The rate constant (k) values for the product formation step determined using Michaelis-Menten kinetics correlate well with Hammett sigma constants, giving reaction constant (rho) values in the range of -0.65 to -1.54 for different oxo(salen)iron complexes. The log k values observed in the oxidation of each aryl methyl sulfide by substituted oxo(salen)iron complexes also correlate with Hammett sigma constants, giving positive rho values. The substituent effect, UV-vis absorption, and EPR spectral studies indicate oxygen atom transfer from the oxidant to the substrate in the rate-determining step.  相似文献   

9.
The kinetics of the oxidation of beta-Re(2)X(4)(cis-1,2-bis(diphenylphosphino)ethylene)(2) (X = Cl, Br) by the cobalt clathrochelate [Co(dimethylglyoximate)(3)(BF)(2)]BF(4) and the oxidation of Re(2)Br(4)(PMe(2)Ph)(4) by the cobalt clathrochelate [Co(1,2-cyclohexanedione dioximate)(3)(BBu)(2)]BF(4) have been studied by the stopped-flow method as a function of temperature (-85 to -19 degrees C), added Bu(4)NBF(4) (0-0.100 M), and reactant concentration in the low dielectric solvent methylene chloride. For each reaction, approximately 100 different conditions were studied. The observed rate constants were well fit by a mechanism involving separate paths for free ion and the ion-paired Co(III) oxidant. The analysis yielded values for DeltaH() and DeltaS() for each path of each reaction and consistent DeltaH degrees and DeltaS degrees values for the ion-pairing of the cationic reactant and the electrolyte. In addition, temperature-dependent electrochemical measurements in 0.10 M Bu(4)NBF(4) yielded DeltaH degrees and DeltaS degrees for the electron transfer process. This is the first measurement of the homogeneous electron transfer reactivity of the dirhenium complexes, and they showed the expected high reactivity. The most notable result is a very high inhibition (ca. 700-fold) by added salt of only the [Co(dmg)(3)(BF)(2)]BF(4) reactions. We attribute this to a change of rate-controlling step, for the ion-paired path, to one involving anion migration. This appears only to occur when the magnitude of ion-pairing free energy is significantly greater than the magnitude of the free energy change for the electron transfer process.  相似文献   

10.
Cations 2-methyl-5-nitroisoquinolinium (IQ+), tropylium (T+), and xanthylium (Xn+) were treated by an NAD(P)H model 1-(p-substituted phenyl)-1.4-dihydronicotinamide series (1) in buffered aqueous solution to give the corresponding reduced products by accepting hydride. Effects of the 4-substituents of 1 on the reaction rates were investigated. Hammett's linear free energy relationship analysis on the three reactions of 1 provides the reaction constants of -0.48, -2.2, and -1.4 with IQ+, T+, and Xn+ as the hydride acceptors, respectively. Comparison of the present reactions with the reaction examples whose mechanisms are well-known, such as the reaction of 1 with a one-electron oxidant Fe(CN)6(-3), shows that the active site of 1 in the oxidation with IQ+ is at the 4-position on the dihydropyridine ring but that the active site of 1 in the oxidations with T+ and Xn+ is at the 1-position, which is in agreement with the results from the Br?nsted-type linear analysis and the relation studies of the logarithm of the second-order rate constants with the oxidation potentials of the hydride donors. According to the dependence of the reaction mechanism on the active site of 1, a conclusion can be made that the reaction of 1 with IQ+ proceeds by direct one-step hydride transfer mechanism, but the reactions of 1 with T+ and Xn+ would take place via multistep hydride transfer mechanism initiated by one-electron transfer.  相似文献   

11.
A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient kappa(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient kappa(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.  相似文献   

12.
Several quantum mechanical (QM) and hybrid quantum/molecular mechanical (QM/MM) studies have been employed recently to analyze the nucleotidyl transfer reaction in DNA polymerase beta (pol beta). Our examination reveals strong dependence of the reported mechanism on the initial molecular model. Thus, we explore here several model systems by QM methods to investigate pol beta's possible pathway variations. Although our most favorable pathway involves a direct proton transfer from O3'(primer) to O2alpha(Palpha), we also discuss other initial proton-transfer steps--to an adjacent water, to triphosphate, or to aspartic units--and the stabilizing effect of crystallographic water molecules in the active site. Our favored reaction route has an energetically undemanding initial step of less than 1.0 kcal/mol (at the B3LYP/6-31G(d,p) level), and involves a slight rearrangement in the geometry of the active site. This is followed by two major steps: (1) direct proton transfer from O3'(primer) to O2alpha(Palpha) leading to the formation of a pentavalent, trigonal bipyramidal Palpha center, via an associative mechanism, at a cost of about 28 kcal/mol, and (2) breakage of the triphosphate unit (exothermic process, approximately 22 kcal/mol) that results in the full transfer of the nucleotide to the DNA and the formation of pyrophosphate. These energy values are expected to be lower in the physical system when full protein effects are incorporated. We also discuss variations from this dominant pathway, and their impact on the overall repair process. Our calculated barrier for the chemical reaction clearly indicates that chemistry is rate-limiting overall for correct nucleotide insertion in pol beta, in accord with other studies. Protonation studies on relevant intermediates suggest that, although protonation at a single aspartic residue may occur, the addition of a second proton to the system significantly disturbs the active site. We conclude that the active site rearrangement step necessary to attain a reaction-competent geometry is essential and closely related to the "pre-chemistry" avenue described recently as a key step in the overall kinetic cycle of DNA polymerases. Thus, our work emphasizes the many possible ways for DNA polymerase beta's chemical reaction to occur, determined by the active site environment and initial models.  相似文献   

13.
This study investigated the effects of temperature, humidity, and benzene concentration on the photocatalytic oxidation of benzene vapor over titanium dioxide. An annular packed-bed photocatalytic reactor was employed to determine the intrinsic oxidation rates for the photocatalysis of benzene. Degussa P-25 TiO2 was used as the photocatalyst and a 15 W near-UV lamp (350 nm) was used as the light source. The experiments were conducted at influent benzene concentrations of 250–450 ppmv, water vapor concentrations of 13,500–27,500 ppmv, and reaction temperatures ranging from 100 to 200 °C. Benzene oxidation rates increased with temperature below 160–180 °C, but decreased with temperature above 160–180 °C. Raising the reaction temperature increased the chemical reaction rates but reduced the reactant adsorption rate on TiO2 surfaces. The overall reaction rate increased with temperature, indicating that the reduction of reactant adsorption rate did not affect the overall reaction, and thus the chemical reaction was the rate-limiting step. As the chemical reaction rate gradually exceeds the reactant adsorption rate with temperature, the rate-limiting step was shifted from the chemical reaction to the reactant adsorption. Additionally, the competitive adsorption between benzene and water for the active sites on TiO2 resulted in the promotion and inhibition of reaction rate by humidity. This study developed a modified bimolecular Langmuir–Hinshelwood kinetic model to simulate the temperature and humidity related promotion and inhibition of the photocatalysis of benzene. The correlation developed here was used as a basis for determining the apparent activation energy of 0.76 kcal/mol and adsorption enthalpies of benzene and water of −20.1 and −13.7 kcal/mol.  相似文献   

14.
A vibrational coupling model to treat the solvation effects in chemical reaction rate calculations is proposed and applied to the intramolecular hydrogen transfer reaction CH3O· → ·CH2OH in the condensed phase. The effect of solvation is taken into account in two ways: (1) the solvent effect on the activation energy of the reaction is simulated by including 39 surrounding water molecules, represented by fractional charges at the assumed atomic positions, in the potential energy surface calculation; and (2) the vibrational couplings between the 10 nearest solvent molecules and the molecules constituting the reaction system are explicitly included in a vibrational frequency calculation. RRKM theory with Miller's tunneling correction included is employed to calculate the rate constants. The effect of solvation causes a significant change in the chemical reaction rate, mainly through a lowering of the activation energy. The vibrational coupling causes a slight increase of the rate constant in the tunneling region by perturbing the vibrational frequencies of the reactant and transition states, which appear in the rate-constant expression, but has little effect at higher temperatures.  相似文献   

15.
Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,  相似文献   

16.
The reaction of 2,4,6-tribromophenol with dibromomethane in an alkaline solution of KOH/dibromomethane two-phase medium, catalyzed by tetrabutylammonium bromide (TBAB or QBr), was carried out. Both mono-substituted as well as bi-substituted products were found to have formed during or after the reaction, when dibromomethane was used both as organic solvent as well as organic-phase reactant. The active catalyst tetrabutylammonium 2,4,6-tribromophenoxide (ArOQ) was identified during the reaction, from which the organic-phase reaction was inferred to be the rate controlling step. The mass transfer of both the catalysts viz. QBr and ArOQ between the two phases was found to be fast. A peculiar phenomenon was observed while investigating the effect of KOH on the reaction rate, viz. the reaction rate does not monotonously increase or decrease with increase in the amount of KOH. This phenomenon is attributed to the activity of ArOQ, the distribution of active catalyst (ArOQ) between the two phases and the hydration of active catalyst in the organic phase, both of which are affected by the amount of KOH. An effective method is proposed to determine the two intrinsic rate constants of the organic-phase reaction, based on the reaction carried out at high KOH concentration.  相似文献   

17.
基于非平衡溶剂化能的约束平衡方法和溶剂重组能的新表达式, 实现了电子转移反应溶剂重组能的数值解, 研究了二氯二氰基苯醌(DDQ)及其阴离子体系DDQ-之间的自交换电子转移反应. 考虑了DDQ与DDQ-分子以平行方式形成受体-给体络合物时的两种构型. 引入线性反应坐标, 计算了该反应在不同溶剂中的溶剂重组能. 基于两态变分模型得到了反应的电子耦合矩阵元. 根据电子转移动力学模型, 计算了该自交换电子转移反应的速率常数.  相似文献   

18.
We present a global full dimensional potential energy surface (PES) for the Cl + O(3)→ ClO + O(2) reaction, which is an elementary step in a catalytic cycle that leads to the destruction of ozone in the stratosphere. The PES is constructed by interpolation of quantum chemistry data using the method developed by Collins and co-workers. Ab initio data points (energy, gradients and Hessian matrix elements) have been calculated at the UQCISD/aug-cc-pVDZ (unrestricted quadratic configuration interaction with single and double excitations) level of theory. The ab initio calculations predict a markedly non-coplanar (dihedral angle of 80°) transition state for the reaction, located very early in the reactant valley and slightly below the energy of the reactants as long as the spin-orbit splitting is neglected. Quasiclassical trajectory (QCT) calculations have been carried out at several collision energies to investigate the reaction dynamics. The QCT excitation function shows no threshold, displays a minimum at a collision energy of 2.5 kcal mol(-1), and then increases monotonically at larger collision energies. This behaviour is consistent with a barrierless reaction dominated by an oxygen-abstraction mechanism. The calculated product vibrational distributions (strongly inverted for ClO) and rate constants are compared with experimental determinations. Differential cross sections (DCS) summed over all final states are found to be in fairly good agreement with those derived from crossed molecular beam experiments.  相似文献   

19.
This study shows that the chemical reactivities depend on the orbital energy gaps contributing to the reactions. In the process where a reaction only makes progress through charge transfer with the minimal structural transformation of the reactant, the orbital energy gap gradient (OEGG) between the electron‐donating and electron‐accepting orbitals is proven to be very low. Using this relation, a normalized reaction diagram is constructed by plotting the normalized orbital energy gap with respect to the normalized intrinsic reaction coordinate. Application of this reaction diagram to 43 fundamental reactions showed that the majority of the forward reactions provide small OEGGs in the initial stages, and therefore, the initial processes of the forward reactions are supposed to proceed only through charge transfer. Conversely, more than 60% of the backward reactions are found to give large OEGGs implying very slow reactions associated with considerable structural transformations. Focusing on the anti‐activation‐energy reactions, in which the forward reactions have higher barriers than those of the backward ones, most of these reactions are shown to give large OEGGs for the backward reactions. It is also found that the reactions providing large OEGGs in the forward directions inconsistent with the reaction rate constants are classified into SN2, symmetric, and methyl radical reactions. Interestingly, several large‐OEGG reactions are experimentally established to get around the optimum pathways. This indicates that the reactions can take significantly different pathways from the optimum ones provided no charge transfer proceeds spontaneously without the structural transformations of the reactants. © 2014 Wiley Periodicals, Inc.  相似文献   

20.
We report a detailed examination of the effect of the steric and electronic properties of the ancillary ligand and the alkene reactant on the rate of migratory insertion of unactivated alkenes into the palladium-nitrogen bond of isolated palladium amido complexes. A series of THF-bound and THF-free amidopalladium complexes ligated by cyclometalated benzylphosphine ligands possessing varied steric and electronic properties were synthesized. The THF-free complexes react with ethylene at -50 °C to form olefin-amido complexes that were observed directly and that undergo migratory insertion, followed by β-hydride elimination to generate enamine products. The effect of the steric properties of the ancillary ligand on the binding of the alkene and the rate of migratory insertion were evaluated individually. The relative binding affinity of ethylene vs THF is larger for the less sterically hindered complex than for the more hindered complex, but the less hindered complex undergoes the insertion of ethylene more slowly than does the more hindered complex. These two changes in relative equilibrium and rate constants cause the rates of reaction of ethylene with the two THF-ligated species having different steric properties to be similar to each other. Reactions of the complexes containing electronically varied ancillary ligands showed that the more electron-poor complexes underwent the migratory insertion step faster than the more electron-rich complexes. Reactions of a THF-ligated palladium-amide with substituted vinylarenes showed that electron-poor vinylarenes reacted with the amido complex slightly faster than electron-rich vinylarenes. Separation of the energetics of binding and insertion indicate that the complex of an electron-rich vinylarene is more stable in this system than the complex of a more electron-poor vinylarene but that the insertion step of the bound, electron-rich vinylarene is slower than the insertion step with the bound, electron-poor vinylarene.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号