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1.
Solvent effects on the rate of the Claisen rearrangement of chorismate to prephenate have been examined in water and methanol. The preequilibrium free-energy differences between diaxial and diequatorial conformers of chorismate, which had previously been implicated as the sole basis for the observed 100-fold rate increase in water over methanol, have been reframed using the near attack conformation (NAC) concept of Bruice and co-workers. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively. As a consequence, the conversion of non-NACs to NACs provides no free-energy contributions to the overall relative reaction rates in water versus methanol. Free-energy perturbation calculations yielded differences in free energies of activation for the two polar protic solvents and the gas phase. The rate enhancement in water over the gas phase arises from preferential hydration of the transition state (TS) relative to the reactants via increased hydrogen bonding and long-range electrostatic interactions, which accompany bringing the two negatively charged carboxylates into closer proximity. More specifically, there is an increase of 1.3 and 0.6 hydrogen bonds to the carboxylate groups and the ether oxygen, respectively, in going from the reactant to the TS in water. In methanol, the corresponding changes in hydrogen bonding with first shell solvent molecules are small; the rate enhancement arises primarily from the enhanced long-range interactions with solvent molecules. Thus, the reaction occurs faster in water than in methanol due to greater stabilization of the TS in water by specific interactions with first shell solvent molecules.  相似文献   

2.
Degenerate hydrogen atom exchange reactions have been studied using calculations, based on density functional theory (DFT), for (i) benzyl radical plus toluene, (ii) phenoxyl radical plus phenol, and (iii) methoxyl radical plus methanol. The first and third reactions occur via hydrogen atom transfer (HAT) mechanisms. The transition structure (TS) for benzyl/toluene hydrogen exchange has C(2)(h)() symmetry and corresponds to the approach of the 2p-pi orbital on the benzylic carbon of the radical to a benzylic hydrogen of toluene. In this TS, and in the similar C(2) TS for methoxyl/methanol hydrogen exchange, the SOMO has significant density in atomic orbitals that lie along the C-H vectors in the former reaction and nearly along the O-H vectors in the latter. In contrast, the SOMO at the phenoxyl/phenol TS is a pi symmetry orbital within each of the C(6)H(5)O units, involving 2p atomic orbitals on the oxygen atoms that are essentially orthogonal to the O.H.O vector. The transferring hydrogen in this reaction is a proton that is part of a typical hydrogen bond, involving a sigma lone pair on the oxygen of the phenoxyl radical and the O-H bond of phenol. Because the proton is transferred between oxygen sigma orbitals, and the electron is transferred between oxygen pi orbitals, this reaction should be described as a proton-coupled electron transfer (PCET). The PCET mechanism requires the formation of a hydrogen bond, and so is not available for benzyl/toluene exchange. The preference for phenoxyl/phenol to occur by PCET while methoxyl/methanol exchange occurs by HAT is traced to the greater pi donating ability of phenyl over methyl. This results in greater electron density on the oxygens in the PCET transition structure for phenoxyl/phenol, as compared to the PCET hilltop for methoxyl/methanol, and the greater electron density on the oxygens selectively stabilizes the phenoxyl/phenol TS by providing a larger binding energy of the transferring proton.  相似文献   

3.
In this paper, the reactions of HNCO or CH3NCO with methanol have been studied using the ab initio MO method. The geometries of the reactants and products have been optimized by the energy gradient method. The calculated results are in accordance with experiment. Using Powell's method, by the minimization of the Euclidean norm σ of the gradient, the structures of the transition state (TS ) for the two reactions were obtained. The structures have been further confirmed as TS by finding that there is one and only one negative eigenvalue for their force constant matrix. The imaginary vibration mode corresponding to the TS was also discussed. The calculated activation barriers of these two reactions are 96.02 and 95.13 kJ/mol, respectively. It can be concluded that the alcoholysis reaction of isocyanate is a nucleophilic addition reaction with methanol as an electronic donor and isocyanate as an acceptor and that the hydroxyl hydrogen of CH3OH plays an important role in the reaction.  相似文献   

4.
To directly compare the reactivity of positively charged carbon-centered aromatic σ-radicals toward methanol in solution and in the gas phase, the 2-, 3-, and 4-dehydropyridinium cations (distonic isomers of the pyridine radical cation) were generated by ultraviolet photolysis of the corresponding iodo precursors in a mixture of water and methanol at varying pH. The reaction mixtures were analyzed by using liquid chromatography/mass spectrometry. Hydrogen atom abstraction was the only reaction observed for the 3- and 4-dehydropyridinium cations (and pyridines) in solution. This also was the major reaction observed earlier in the gas phase. Depending on the pH, the hydrogen atom can be abstracted from different molecules (i.e., methanol or water) and from different sites (in methanol) by the 3- and 4-dehydropyridinium cations/pyridines in solution. In the pH range 1-4, the methyl group of methanol is the main hydrogen atom donor site for both 3- and 4-dehydropyridinium cations (just like in the gas phase). At higher pH, the hydroxyl groups of water and methanol also act as hydrogen atom donors. This finding is rationalized by a greater abundance of the unprotonated radicals that preferentially abstract hydrogen atoms from the polar hydroxyl groups. The percentage yield of hydrogen atom abstraction by these radicals was found to increase with lowering the pH in the pH range 1.0-3.2. This pH effect is rationalized by polar effects: the lower the pH, the greater the fraction of protonated (more polar) radicals in the solution. This finding is consistent with previous results obtained in the gas phase and suggests that gas-phase studies can be used to predict solution reactivity, but only as long as the same reactive species is studied in both experiments. This was found not to be the case for the 2-iodopyridinium cation. Photolysis of this precursor in solution resulted in the formation of two major addition products, 2-hydroxy- and 2-methoxypyridinium cations, in addition to the hydrogen atom abstraction product. These addition products were not observed in the earlier gas-phase studies on 2-dehydropyridinium cation. Their observation in solution is explained by the formation of another reactive intermediate, the 2-pyridylcation, upon photolysis of 2-iodopyridinium cation (and 2-iodopyridine). The same intermediate was observed in the gas phase but it was removed before examining the reactions of the desired radical, 2-dehydropyridinium cation (which cannot be done in solution).  相似文献   

5.
The photochemical reactions in methanol of the vinylic halides 1-4, halostyrenes with a methyl or a trifluoromethyl substituent at the alpha- or beta-position, have been investigated quantitatively. Next to E/Z isomerization, the reactions are formation of vinyl radicals, leading to reductive dehalogenation products, and formation of vinyl cations, leading to elimination, nucleophilic substitution, and rearrangement products. The vinyl cations are parts of tight ion pairs with halide as the counterion. The elimination products are the result of beta-proton loss from the primarily generated alpha-CH(3) and alpha-CF(3) vinyl cations, or from the alpha-CH(3) vinyl cation formed from the beta-CH(3) vinyl cation via a 1,2-phenyl shift. The beta-CF(3) vinyl cation reacts with methanol yielding nucleophilic substitution products, no migration of the phenyl ring producing the alpha-CF(3) vinyl cation occurs. The alpha-CF(3) vinyl cation, which is the most destabilized vinyl cation generated thus far, gives a 1,2-fluorine shift in competition with proton loss. The experimentally derived order of stabilization of the vinyl cations photogenerated in this study, alpha-CF(3) < beta-CF(3) < beta-CH(3) < alpha-CH(3), is corroborated by quantum chemical calculations, provided the effect of solvent is taken into account.  相似文献   

6.
The Golgi glycosyltransferase, N-acetylglucosaminyltransferase I (GnT-I), catalyzes the transfer of a GlcNAc residue from the donor UDP-GlcNAc to the C2-hydroxyl group of a mannose residue in the trimannosyl core of the Man5GlcNAc2-Asn-X oligosaccharide. The catalytic mechanism of GnT-I was investigated using a hybrid quantum mechanical/molecular mechanical (QM/MM) method with a QM part containing 88 atoms treated with density functional theory (DFT) at the BP/TZP level. The remaining parts of a GnT-I complex, altogether 5633 atoms, were modeled using the AMBER molecular force field. A theoretical model of a Michaelis complex was built using the X-ray structure of GnT-I in complex with the donor having geometrical features consistent with kinetic studies. The QM(DFT)/MM model identified a concerted SN2-type of transition state with D291 as the catalytic base for the reaction in the enzyme active site. The TS model features nearly simultaneous nucleophilic addition and dissociation steps accompanied by the transfer of the nucleophile proton Hb2 to the catalytic base D291. The structure of the TS model is characterized by the Ob2-C1 and C1-O1 bond distances of 1.912 and 2.542 A, respectively. The activation energy for the proposed reaction mechanism was estimated to be approximately 19 kcal mol-1. The calculated alpha-deuterium kinetic isotope effect of 1.060 is consistent with the proposed reaction mechanism. Theoretical results also identified interactions between the Hb6 and beta-phosphate oxygen of the UDP and a low-barrier hydrogen bond between the nucleophile and the catalytic base D291. It is proposed that these interactions contribute to a stabilization of TS. This modeling study provided detailed insight into the mechanism of the GlcNAc transfer catalyzed by GnT-I, which is the first step in the conversion of high mannose oligosaccharides to complex and hybrid N-glycan structures.  相似文献   

7.
A significant contemporary question in enzymology involves the role of protein dynamics and hydrogen tunneling in enhancing enzyme catalyzed reactions. Here, we report a correlation between the donor-acceptor distance (DAD) distribution and intrinsic kinetic isotope effects (KIEs) for the dihydrofolate reductase (DHFR) catalyzed reaction. This study compares the nature of the hydride-transfer step for a series of active-site mutants, where the size of a side chain that modulates the DAD (I14 in E. coli DHFR) is systematically reduced (I14V, I14A, and I14G). The contributions of the DAD and its dynamics to the hydride-transfer step were examined by the temperature dependence of intrinsic KIEs, hydride-transfer rates, activation parameters, and classical molecular dynamics (MD) simulations. Results are interpreted within the framework of the Marcus-like model where the increase in the temperature dependence of KIEs arises as a direct consequence of the deviation of the DAD from its distribution in the wild type enzyme. Classical MD simulations suggest new populations with larger average DADs, as well as broader distributions, and a reduction in the population of the reactive conformers correlated with the decrease in the size of the hydrophobic residue. The more flexible active site in the mutants required more substantial thermally activated motions for effective H-tunneling, consistent with the hypothesis that the role of the hydrophobic side chain of I14 is to restrict the distribution and dynamics of the DAD and thus assist the hydride-transfer. These studies establish relationships between the distribution of DADs, the hydride-transfer rates, and the DAD's rearrangement toward tunneling-ready states. This structure-function correlation shall assist in the interpretation of the temperature dependence of KIEs caused by mutants far from the active site in this and other enzymes, and may apply generally to C-H→C transfer reactions.  相似文献   

8.
The oxidation of methanol to formaldehyde on silica supported vanadium oxide is studied by density functional theory. For isolated vanadium oxide species silsesquioxane-type models are adopted. The first step is dissociative adsorption of methanol yielding CH3O(O=)V(O-)2 surface complexes. This makes the O=V(OCH3)3 molecule a suited model system. The rate-limiting oxidation step involves hydrogen transfer from the methoxy group to the vanadyl oxygen atom. The transition state is biradicaloid and needs to be treated by the broken-symmetry approach. The activation energies for O=V(OCH3)3 and the silsesquioxane surface model are 147 and 154 kJ/mol. In addition, the (O=V(OCH3)3)(2) dimer (a model for polymeric vanadium oxide species) and the O=V(OCH3)3(*+) radical cation are studied. For the latter the barrier is only 80 kJ/mol, indicating a strong effect of the charge on the energy profile of the reaction and questioning the significance of gas-phase cluster studies for understanding the activity of supported oxide catalysts.  相似文献   

9.
刘朋军  潘秀梅  赵岷  孙昊  苏忠民  王荣顺 《化学学报》2002,60(11):1941-1945
用量子化学密度泛函理论的B3LYP方法,在6-31+G~*水平上按BERNY能量梯度解 析全参数优化了HNCO与CX(X=F,Cl,Br)反应势能面上各驻点的几何构型,通过 振动频率分析确认了中间体和过渡态,内禀反应坐标(IRC)对反应物、中间体、 过渡态和产物的相关性予以证实,对各驻点进行了零点能校正(ZPE)在此基础上 计算了反应能垒。研究结果表明,与HNCO和其它小分子自由基反应不同,HNCO与 CX自由基反应首先发生分子间H原子迁移,随后N与CX的C(1)原子相互靠近成键并 生成较稳定的中间体,再发生N-C(2)键的断裂,完成N向C(1)上的迁移并进一 步解离为产物。反应按反应物→TS1→IM→TS2→产物通道进行。反应为放热反应。  相似文献   

10.
Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH? and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxyacetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.  相似文献   

11.
12.
In an attempt to assess the potential role of the hydroxyl radical in the atmospheric degradation of sulfuric acid, the hydrogen transfer between H2SO4 and HO* in the gas phase has been investigated by means of DFT and quantum-mechanical electronic-structure calculations, as well as classical transition state theory computations. The first step of the H2SO4 + HO* reaction is the barrierless formation of a prereactive hydrogen-bonded complex (Cr1) lying 8.1 kcal mol(-1) below the sum of the (298 K) enthalpies of the reactants. After forming Cr1, a single hydrogen transfer from H2SO4 to HO* and a degenerate double hydrogen-exchange between H2SO4 and HO* may occur. The single hydrogen transfer, yielding HSO4* and H2O, can take place through three different transition structures, the two lowest energy ones (TS1 and TS2) corresponding to a proton-coupled electron-transfer mechanism, whereas the higher energy one (TS3) is associated with a hydrogen atom transfer mechanism. The double hydrogen-exchange, affording products identical to reactants, takes place through a transition structure (TS4) involving a double proton-transfer mechanism and is predicted to be the dominant pathway. A rate constant of 1.50 x 10(-14) cm(3) molecule(-1) s(-1) at 298 K is obtained for the overall reaction H2SO4 + HO*. The single hydrogen transfer through TS1, TS2, and TS3 contributes to the overall rate constant at 298 K with a 43.4%. It is concluded that the single hydrogen transfer from H2SO4 to HO* yielding HSO4* and H2O might well be a significant sink for gaseous sulfuric acid in the atmosphere.  相似文献   

13.
Quantitative analysis of the transition state (TS) structures for the reactions between 5-Cl- or 5-SiMe3-2-adamantyl cations and methanol revealed that the magnitude of antiperiplanar hyperconjugative stabilization involving the incipient bond (the AP effect) decrease at TS, strongly suggesting that the AP effect contributes to `net destabilization' of TS (i.e., increase in activation energy), in sharp contrast to the proposals of the Felkin-Anh and the Cieplak models. The equilibrium population between two bridge(C1-C2-C3)-flipping E-Z cation conformers was found to be the origin of facial diastereoselection of these carbocations.  相似文献   

14.
The present paper is aimed at studying the influence of the hydrogen sorption/desorption process occurring on the layered nickel–palladium (Ni/Pd) electrode on the kinetics of the reaction of methanol oxidation in strong alkaline KOH solution. The electrodes were prepared by chemical deposition of a thin layer of porous palladium on a nickel foam support. A scanning electron microscope was used for studying the morphology of both the nickel support and the porous palladium layer. The mechanism of the anodic desorption of hydrogen changes depending on whether or not 6 M KOH electrolyte is admixed with methanol. It was shown that, in the first cycle of the cyclic voltammetry (CV) measurements, the anodic peak current and peak charge related to the oxidative desorption of hydrogen significantly decrease due to the presence of methanol in KOH. This effect is attributed to the obstacles in hydrogen sorption due to the formation of a passivating layer on the Pd surface composed of both adsorbed methanol molecules and the intermediate products involving adsorbed CO. On the other hand, hydrogen desorbing from Pd electrode exerts influence on the kinetics of the reaction of methanol oxidation. Ni/Pd electrode undergoes considerable reactivation due to the potentiostatic saturation with hydrogen at ?1.1 V, followed by the ease in hydrogen desorption. The CV measurements proved that, after such a treatment, the peak of hydrogen desorption partially overlaps the double peak of methanol oxidation and, in consequence, the rate of methanol oxidation is enhanced. The positive effect of hydrogen releasing from the electrode on the kinetics of the reaction of methanol oxidation is ascribed to the anti-poison behavior consisting in the reaction of hydrogen radicals with intermediates adsorbed on the Pd surface.  相似文献   

15.
1-Bromo-2-methoxy-1-phenylpropan-2-yl (3) and 2-methoxy-1-phenyl-1-diphenylphosphatopropan-2-yl (4) were generated under continual photolysis from the respective PTOC precursors in a mixture of acetonitrile and methanol. The radicals undergo heterolytic fragmentation of the substituent in the beta-position to generate the olefin cation radical (5). Z-2-Methoxy-1-phenylpropene (15) is the major product formed in the presence of 1,4-cyclohexadiene, and is believed to result from hydrogen atom transfer to the oxygen of the olefin cation radical, followed by deprotonation. Laser flash photolysis experiments indicate that reaction between 5 and 1,4-cyclohexadiene occurs with a rate constant of approximately 6 x 10(5) M(-1) s(-1). 2,2-Dimethoxy-1-phenylpropane (18) is observed as a minor product. Laser flash photolysis experiments place an upper limit on methanol trapping of 5 at k <1 x 10(3) M(-1) s(-1) and do not provide any evidence for the formation of reactive intermediates other than 5. The use of two PTOC precursors containing different leaving groups to generate a common olefin cation radical enables one to utilize product analysis to probe for the intermediacy of other reactive intermediates. The ratio of 15:18 is dependent upon hydrogen atom donor concentration, but is independent of the PTOC precursor. These observations are consistent with the proposal that both products result from trapping of 5 that is formed via heterolysis of 3 and 4.  相似文献   

16.
17.
Using time resolved Fourier transform EPR spectroscopy the photoreduction of duroquinone by triethylamine in methanol solution was investigated. It is found that the spin-polarized (CIDEP) duroquinone triplet deactivates by electron transfer from triethylamine generating duroquinone radical anion and amine radical cation, and by hydrogen transfer from the solvent generating durosemiquinone radical and hydroxymethyl radical, respectively. All radicals are observed at different conditions and are spin-polarized by triplet mechanism and partially by ST0 radical pair mechanism. The time dependence of FT-EPR intensities of radical cation and radical anion on the amine concentration is investigated in the range of 1 to 100 mM triethylamine. The contribution of the triplet mechanism to the spin polarization of radicals changes with different triethylamine concentrations. The durosemiquinone radical is found to be transformed into duroquinone radical anion in the presence of triethylamine in the solution. CIDNP experiments indicate that the hydrogen back transfer between the durosemiquinone radical and hydroxymethyl radical pair has a significant influence on the time behaviour of duroquinone radical anion. The intensity of triethylamine radical cation is found to be decreased with the increase of triethylamine concentration, which is interpreted that the triethylamine radical cation is deprotonated by the amine. Based on the FT-EPR results, a new complete mechanism is proposed.  相似文献   

18.
Protein motions may be perturbed by altering the properties of the reaction medium. Here we show that dielectric constant, but not viscosity, affects the rate of the hydride-transfer reaction catalysed by dihydrofolate reductase from Thermotoga maritima (TmDHFR), in which quantum-mechanical tunnelling has previously been shown to be driven by protein motions. Neither dielectric constant nor viscosity directly alters the kinetic isotope effect of the reaction or the mechanism of coupling of protein motions to tunnelling. Glycerol and sucrose cause a significant increase in the rate of hydride transfer, but lead to a reduction in the magnitude of the kinetic isotope effect as well as an extension of the temperature range over which "passive" protein dynamics (rather than "active" gating motions) dominate the reaction. Our results are in agreement with the proposal that non-equilibrium dynamical processes (promoting motions) drive the hydride-transfer reaction in TmDHFR.  相似文献   

19.
The decarboxylation of imidazolidin-2-one-1-carboxylate anion 2 has been investigated via combined quantum and statistical mechanics methodology. Monte Carlo statistical mechanics simulations utilizing free-energy perturbation theory and PDDG/PM3 for the QM method yielded free-energy profiles for the reaction in water, methanol, acetonitrile, and mixed solvents. The results for free energies of activation are uniformly in close accord with experimental data and reflect large rate accelerations in progressing from protic to dipolar aprotic media. Structural and energetic analyses confirm that the rate retardation in protic solvents comes from loss of hydrogen bonding in progressing from the carboxylate anion 2 to the more charge-delocalized transition state (TS). The structure of the TS is found to be significantly affected by the reaction medium; it occurs at a 0.2-A shorter C-N separation in protic solvents than in acetonitrile. Characterization of the hydrogen bonding for 2 and the TS also provided insights for design of decarboxylase catalysts, namely, it is desirable to have three hydrogen-bond donating groups positioned to interact with the ureido oxygen along with two hydrogen-bond donors positioned to interact with the ureido nitrogen of the breaking C-N bond.  相似文献   

20.
We have recently proposed a mechanism for the epoxidation of cyclooctene by H2O2 catalyzed by iron(III) [tetrakis(pentafluorophenyl)]porphyrin chloride, (F20TPP)FeCl, in solvent containing methanol [Stephenson, N. A.; Bell, A.T. Inorg. Chem. 2006, 45, 2758-2766]. In that study, we found that catalysis did not occur unless (F20TPP)FeCl first dissociated, a process facilitated by the solvation of the Cl- anion by methanol and the coordination of methanol to the (F20TPP)Fe+ cation. Methanol as well as other alcohols was also found to facilitate the heterolytic cleavage of the O-O bond of H2O2 coordinated to the (F20TPP)Fe+ cation via a generalized acid mechanism. In the present study, we have shown that catalytic activity of the (F20TPP)Fe+ cation can be achieved in aprotic solvent by displacing the tightly bound chloride anion with a weakly bound triflate anion. By working in an aprotic solvent, acetonitrile, it was possible to determine the rate of heterolytic O-O bond cleavage in coordinated H2O2 unaffected by the interaction of the peroxide with methanol. A mechanism is proposed for this system and is shown to be valid over a range of reaction conditions. The mechanisms for cyclooctene epoxidation and H2O2 decomposition for the aprotic and protic solvent systems are similar with the only difference being the mechanism of proton-transfer prior to heterolytic cleavage of the oxygen-oxygen bond of coordinated hydrogen peroxide. Comparison of the rate parameters indicates that the utilization of hydrogen peroxide for cyclooctene epoxidation is higher in a protic solvent than in an aprotic solvent and results in a smaller extent of porphyrin degradation due to free radical attack. It was also shown that water can coordinate to the iron porphyrin cation in aprotic systems resulting in catalyst deactivation; this effect was not observed when methanol was present, since methanol was found to displace all of the coordinated water.  相似文献   

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