乙烯醇钠的从头算研究(英文)

在ＲＨＦ／３－２１Ｇ和ＲＨＦ／６－３１＋Ｇ水平上优化了乙烯醇钠的的平衡构型及过渡态，比较了不同构型的稳定性。在ＲＨＦ／６－３１＋Ｇ水平上探讨了气相中由乙醛和氢氧化钠生成乙烯醇钠的机理。并在ＭＰ２（ｆｕｌ）／６－３１＋Ｇ／／ＭＰ２（ｆｕｌ）／６－３１＋Ｇ水平下计算了反应热     

A computational study of the reactions of thiiranes with ammonia and amines

The relative rates of reaction of thiirane and thiirane derivatives with NH3, a series of secondary amines including aziridine, and trimethylamine were determined in the gas phase by means of B3LYP/6-31+G(d)//HF/6-31+G(d) computations and transition state theory. Convergence of the results was selectively tested using the 6-311++G(d,p) basis set. Comparison with MP2/6-31 + G(d)//MP2/6-31G(d) computations was made in model cases. These results are significant in that they supplement the only reported gas-phase experimental study of this type of reaction. The reaction rates of thiirane with secondary amines can best be rationalized by means of an interplay of steric and polarizability effects. While beta-halo substituents retard S(N)2 reactions in solution, both 2-fluorothiirane and its acyclic model react more than l0(6) times faster with NH3 than the unsubstituted compounds in the gas phase. 2-Fluorothiirane was calculated to react with NH3 at C2 by a factor of 0.142 with respect to thiirane itself; attack at C3 was found to be 3.42 x 10(6) times faster than the parent compound. 2-Methylthirane reacts with NH3 at 0. 230 the rate of thiirane with a 12.8-fold regioselectivity for C3. In the reaction of 2,2-dimethylthirane and NH3, this preference for C3 increases to a factor of 124. Ground-state destabilization of cis-2,3-dimethylthiirane is sufficient to account for its calculated rate acceleration with respect to the trans isomer.     

Theoretical investigation of ion pair SN2 reactions of alkali isothiocyanates with alkyl halides. Part 1. Reaction of lithium isothiocyanate and methyl fluoride with inversion mechanism

The gas‐phase ionic S_N2 reactions NCS^‐ + CH₃F and ion pair S_N2 reaction LiNCS + CH₃F with inversion mechanism were investigated at the level of MP2(full)/6‐311+G**//HF/6‐311+G**. Both of them involve the reactants complex, inversion transition state, and products complex. There are two possible reaction pathways in the ionic S_N2 reaction but four reaction pathways in the ion pair S_N2 reaction. Our results indicate that the introduction of lithium significantly lower the reaction barrier and make the ion pair displacement reaction more facile. For both ionic and ion pair reaction, methyl thiocyanate is predicted to be the major product, but the latter is more selective. More‐stable methyl isothiocyanate can be prepared by thermal rearrangement of methyl thiocyanate. The theoretical predictions are consistent with the known experimental results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Cyclic vinyl p-tolyl sulfilimines as chiral dienophiles: theoretical study on the stereoselectivity, Lewis acid catalysis, and solvent effects in their Diels-Alder reactions

The theoretical study reported in the present work deals with chiral cyclic vinyl sulfilimines and their reactivity as dienophiles in [4 + 2] cycloaddition reactions, using B3LYP/6-31G(d)//AM1 and B3LYP/6-31G(d)//B3LYP/6-31G(d) model chemistries. Consideration of Lewis acid catalysis, illustrated by BF(3), decreases the activation energies of the cycloaddition process while the charge transfer from the diene to the sulfilimine is augmented. The [4 + 2] cycloaddition reactions of sulfilimines with both furan and cyclopentadiene occur in the gas phase with endo stereoselectivity, which is more pronounced with the latter diene. Endo-exo energy differences in the gas phase with the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31G(d)//AM1 model chemistries are almost the same. Solvent effects are responsible for the inversion of the stereoselectivity in the reactions of sulfilimines with furan because of the great difference in the dipole moments in endo and exo approaches.     

Addition reaction of adamantylideneadamantane with Br2 and 2Br2: a computational study

Ab initio calculations were carried out for the reaction of adamantylideneadamantane (Ad=Ad) with Br2 and 2Br2. Geometries of the reactants, transition states, intermediates, and products were optimized at HF and B3LYP levels of theory using the 6-31G(d) basis set. Energies were also obtained using single point calculations at the MP2/6-31G(d)//HF/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31+G(d)//B3LYP/6-31G(d) levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Only one pathway was found for the reaction of Ad=Ad with one Br2 producing a bromonium/bromide ion pair. Three mechanisms for the reaction of Ad=Ad with 2Br2 were found, leading to three different structural forms of the bromonium/Br3- ion pair. Activation energies, free energies, and enthalpies of activation along with the relative stability of products for each reaction pathway were calculated. The reaction of Ad=Ad with 2Br2 was strongly favored over the reaction with only one Br2. According to B3LYP/6-31G(d) and single point calculations at MP2, the most stable bromonium/Br3- ion pair would form spontaneously. The most stable of the three bromonium/Br3- ion pairs has a structure very similar to the observed X-ray structure. Free energies of activation and relative stabilities of reactants and products in CCl4 and CH2ClCH2Cl were also calculated with PCM using the united atom (UA0) cavity model and, in general, results similar to the gas phase were obtained. An optimized structure for the trans-1,2-dibromo product was also found at all levels of theory both in gas phase and in solution, but no transition state leading to the trans-1,2-dibromo product was obtained.     

Uncatalyzed transfer hydrogenation of quinones and related systems: a theoretical mechanistic study

Quantum chemistry calculations have been used to study the uncatalyzed transfer hydrogenation between a range of hydrogen donors and acceptors, in the gas phase and in solution. Our study shows in the first place that in order to obtain reliable condensed-phase transition structures, it is necessary to perform geometry optimization in the presence of a continuum. In addition, the use of a free energy of solvation obtained with the UB3-LYP/6-31+G(d,p)/IEF-PCM/UA0 combination, in conjunction with UMPWB1K/6-311+G(3df,2p)//B3-LYP/6-31+G(d,p) gas-phase energies, gives the best agreement with experimental barriers. In condensed phases, the geometries and energies of the transition structures are found to relate to one another in a manner consistent with the Hammond postulate. There is also a correlation between the barriers and the energies of the radical intermediates in accord with the Bell-Evans-Polanyi principle. We find that in the gas phase, all the transfer-hydrogenation reactions examined proceed via a radical pathway. In condensed phases, some of the reactions follow a radical mechanism regardless of the solvent. However, for some reactions there is a change from a radical mechanism to an ionic mechanism as the solvent becomes more polar. Our calculations indicate that the detection of radical adducts by EPR does not necessarily indicate a predominant radical mechanism, because of the possibility of a concurrent ionic reaction. We also find that the transition structures for these reactions do not necessarily have a strong resemblance to the intermediates, and therefore one should be cautious in utilizing the influence of polar effects on the rate of reaction as a means of determining the mechanism.     

An investigation of keto–enol tautomerism in N-vinyl-2-, and 3-pyrrolidinones using ab initio and density functional theory calculations

We investigated the protomeric tautomerism of N-vinyl-2-pyrrolidinone (NV2P) and N-vinyl-3-pyrrolidinone (NV3P) molecules, and considered the three neutral tautomers for NV2P (1a, 1b, 1c) and the five for NV3P (2a, 2b, 2c, 2d, 2e). Full geometry optimizations were carried out at the HF/6-31G**, HF/6-31+G** and B3LYP/6-31+G** levels in the gas phase and in water. Additionally, single-point MP2/6-31+G** calculations were performed on the HF/6-31+G** optimized geometries. The tautomerization processes in water (=78.54) were studied using the self-consistent reaction field theory. According to our estimations, the tautomerization of NV2P and NV3P molecules are not strongly influenced by the polar solvents, the improvement of the basis set quality and the electron correlation effects in the gas phase and in water. The calculated relative free energies (ΔG) predict that 1a and 2a are the energetically preferred tautomers in the gas phase and in water.     

Theoretical studies on the gas-phase pyrolysis of 2-phenoxycarboxylic acids: an ONIOM approach

Various ONIOM combinations-ONIOM(HF/6-31G*: PM3), ONIOM(B3LYP/6-31G*: PM3), ONIOM(MP2/6-31G*: PM3), and ONIOM(MP2/6-31G*: HF/3-21G)--were applied to investigate thermal decomposition mechanisms of four 2-phenoxycarboxylic acids (2-phenoxyacetic acid, 2-phenoxypropionic acid, 2-phenoxybutyric acid, and 2-phenoxyisobutyric acid) in the gas phase. All the transition states and intermediates of the reaction paths were optimized. The reaction pathway of four reactants yielding the phenol, CO, and the corresponding carbonyl compound was characterized on the potential energy surface and found to proceed stepwise. The first step corresponds to the elimination of phenol and the formation of alpha-lactone intermediate through a five-membered ring transition state, and the second step is the cycloreversion process of alpha-lactone intermediate to form CO and the corresponding carbonyl compound. The reaction pathway of latter three compounds to produce the carboxylic acid and phenol via a four-membered cyclic transition structure was also examined theoretically. Comparison with experiment indicates that the activation parameters for the fist reaction channel are accurately predicted at the ONIOM(MP2/6-31G*: HF/3-21G) level of theory.     

Theoretical study on the hydrolysis mechanism of N,N -dimethyl- N ′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

The hydrolysis mechanisms of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine (FA-3TC) in the gas phase and in aqueous solution were studied by use of the density functional theory B3LYP/6-31+G(d, p) method. Two possible reaction pathways in the title reaction were considered. In one pathway water attacks the C=N double bond first (path A) while in the other water attacks the C-N single bond first (path B). The calculated results indicate that the first step in both pathways is the rate-limiting process and path A is more favorable than path B in the gas phase. The effect of solvent water on the title reaction was assessed at the B3LYP/6-31+G(d, p) level of theory based on the polarizable continuum model (CPCM). In water the first mechanism (path A) is also favored. Supported by the National Natural Science Foundation of China (Grant Nos. 20473055 and 20773089) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry (Grant No. 20071108-18-15)     

乙烯醇锂的从头算研究

用限制的HF/3-21G和HF/6-31G^*优化乙烯醇锂的几种可能构型,比较了它们的稳定性.用限制的HF/3-1G,从乙醛开始,探讨了气相反应生成乙烯醇锂的机理,并在MP2水平上用6-31G^*基组计算了反应热.     

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction

To investigate fundamental features of enzyme catalysis, there is a need for high-level calculations capable of modelling crucial, unstable species such as transition states as they are formed within enzymes. We have modelled an important model enzyme reaction, the Claisen rearrangement of chorismate to prephenate in chorismate mutase, by combined ab initio quantum mechanics/molecular mechanics (QM/MM) methods. The best estimates of the potential energy barrier in the enzyme are 7.4-11.0 kcal mol(-1)(MP2/6-31+G(d)//6-31G(d)/CHARMM22) and 12.7-16.1 kcal mol(-1)(B3LYP/6-311+G(2d,p)//6-31G(d)/CHARMM22), comparable to the experimental estimate of Delta H(++)= 12.7 +/- 0.4 kcal mol(-1). The results provide unequivocal evidence of transition state (TS) stabilization by the enzyme, with contributions from residues Arg90, Arg7, and Arg63. Glu78 stabilizes the prephenate product (relative to substrate), and can also stabilize the TS. Examination of the same pathway in solution (with a variety of continuum models), at the same ab initio levels, allows comparison of the catalyzed and uncatalyzed reactions. Calculated barriers in solution are 28.0 kcal mol(-1)(MP2/6-31+G(d)/PCM) and 24.6 kcal mol(-1)(B3LYP/6-311+G(2d,p)/PCM), comparable to the experimental finding of Delta G(++)= 25.4 kcal mol(-1) and consistent with the experimentally-deduced 10(6)-fold rate acceleration by the enzyme. The substrate is found to be significantly distorted in the enzyme, adopting a structure closer to the transition state, although the degree of compression is less than predicted by lower-level calculations. This apparent substrate strain, or compression, is potentially also catalytically relevant. Solution calculations, however, suggest that the catalytic contribution of this compression may be relatively small. Consideration of the same reaction pathway in solution and in the enzyme, involving reaction from a 'near-attack conformer' of the substrate, indicates that adoption of this conformation is not in itself a major contribution to catalysis. Transition state stabilization (by electrostatic interactions, including hydrogen bonds) is found to be central to catalysis by the enzyme. Several hydrogen bonds are observed to shorten at the TS. The active site is clearly complementary to the transition state for the reaction, stabilizing it more than the substrate, so reducing the barrier to reaction.     

Monomolecular decay of anion-radicals of isomeric chlorobenzonitriles. Quantum chemical analysis

Regularities for the reaction courses of the monomolecular decay of anion-radicals (AR) of isomeric chlorobenzonitriles have been considered basing on the ab initio investigation by ROHF/6-31+G*, MP2/6-31+G*//ROHF/6-31+G*, and B3LYP/6-31+G* methods. Stable structures corresponding to initial AR, final products of the decay, and combining them transition states (TS) of the reaction were localized. The TS found have a substantially non-planar structure. The main factor determining a relative ability of isomeric AR to remove chloride anion is the difference in the density of the unpaired electron on the breaking bond in the initial AR. In the case of para-isomer, whose SOMO is maximally localized on the C atom bonded to Cl, it is likely to expect “ early” TS and low barriers of the reaction both in the gas phase and polar solvents. The fragmentation of ortho-and meta-isomers is forestalled by remarkable structural modifications resulting in the redistribution of electron density with its localization on the breaking bond C—Cl.     

Determination of the origin of stereoselectivity in multiple-transition-state reactions using DFT calculations: enantioselective synthesis of homoallylic alcohols from aliphatic methyl ketones via an auxiliary-mediated allylation

Computational investigations on the highly stereoselective allylation of butanone in the presence of a chiral norpseudoephedrine-derived auxiliary have been performed. They suggest an SN1-type mechanism via the attack of allyltrimethylsilane to an intermediately formed oxocarbenium ion. The identification of preferred transition states (TSs) leads to a straightforward rationalization of the observed selectivity which can be extended to analogues of the auxiliary. A screening process has been devised to select 61 potentially relevant TSs from a total of almost 300 theoretically possible TSs. Final results were obtained from gas-phase calculations employing the B3LYP/6-31+G(d) level of theory as well as in dichloromethane solution using the B3LYP/6-311++G(2d,p)//B3LYP/6-31+G(d) level of theory in combination with polarizable continuum model and the UAKS set of radii. The agreement of theoretically predicted and experimentally observed selectivities is very good in both cases. However, the relative energy differences for several relevant TSs differ significantly when going from gas phase to solution, thus illustrating the necessity of performing calculations in solution to draw correct conclusions.     

The 1,3-dipolar cycloaddition of 1H-pyridinium-3-olate and 1-methylpyridinium-3-olate with methyl acrylate: a density functional theory study

The 1,3-dipolar cycloaddition reaction of 1-substituted pyridinium 3-olates with methyl acrylate is studied using density functional theory (DFT) method at the B3LYP/6-31G(d) level. The molecular mechanisms of the possible stereo- and regio-chemical pathways are characterized and explored. Solvent effects are also evaluated by the polarizable continuum model (PCM). Analysis of the results shows that there are relevant differences in the reaction pathways between the gas phase and with solvent. Only results in solvent phase are in accord with literature experimental results where 6-substituted 8-azabicyclo[3.2.1]oct-3-en-2-ones are formed preferentially. These polar cycloaddition reactions take place through highly asynchronous transition states in which nucleophilic attack by C2/C6 of the pyridinium-3-olates on the more electrophilic centre of the methyl acrylate initiates the process. Analysis of global and local indexes of the reactants is evaluated in order to explain the observed regioselectivity. Rate constants are calculated at room temperature using conventional transition state theory.     

Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution

Ab initio geometry optimizations were carried out at the HF/3-21G and HF/6-31+G^** levels for the six tautomeric forms of 2-thiouracil (2TU, 2TU1, 2TU2, 2TU3, 2TU4, 2TU5) in the gas phase and in solution. To obtain a more definitive estimate of the relative stabilities for 2-thiouracil tautomers in the gas phase, single-point MP2/6-31+G^** calculations were performed on the HF/6-31+G^** optimized geometries. The tautomeric equilibria in 1,4-dioxane (=2.21), acetonitrile (=38), and in water (=78.54) were studied using the self-consistent reaction field (SCRF) theory. The calculated relative free energies indicated that 2TU is the energetically preferred tautomer in the gas phase and in solution. The stability order of 2-thiouracil tautomers depends on the level of theory and the dielectric constant of the solvent. The obtained results are compared with the available experimental data.     

Mechanical and kinetic studies of the formation of polyhalogenated dibenzo-p-dioxins from hydroxylated polybrominated diphenyl ethers and chlorinated derivatives

Hydroxylated polybrominated diphenyl ethers (OH-PBDEs),which may be generated from PBDEs, are more toxic than their matrix and have been detected in organisms. In this article, we have focused on the gas phase formation of polyhalogenated dibenzo-p-dioxins from several OH-PBDEs and their chlorinated derivatives. All of the geometries and frequencies are calculated at the MPWB1K/6-31+G(d,p) level of theory. The single point energy is obtained at the MPWB1K/6-311+G(3df,2p) level. Rate constants of each step have been calculated over a wide range of 200-2000 K using the canonical variational transition state (CVT) theory with small curvature tunneling (SCT) contribution. The rate equations are shown through Arrhenius formulas. The presence of chlorine atoms increases the reaction barrier for the formation of major products.     

Comprehensive mechanistic study of ion pair SN2 reactions of lithium isocyanate and methyl halides

The anionic S_N2 reactions NCO^? + CH₃X and ion pair S_N2 reactions LiNCO + CH₃X (X = F, Cl, Br, and I) at saturated carbon with inversion and retention mechanisms were investigated at the level of MP2/6‐311+G(d,p). There are two possible reaction pathways in the anionic S_N2 reactions, but eight in the ion pair S_N2 reactions. Calculated results suggest that the previously reported T‐shaped isomer of lithium isocyanate does not exist. All the retention pathways are not favorable based on the analysis of transition structures. Two possible competitive reaction pathways proceed via two six‐member ring inversion transition structures. It is found that there are two steps in the most favorable pathway, in which less stable lithium cyanate should be formed through the isomerization of lithium isocyanate and nucleophilic site (N) subsequently attacks methyl halides from the backside. The thermodynamically and kinetically favorable methyl isocyanate is predicted as major product both in the gas phase anionic and the ion pair S_N2 reactions. In addition, good correlations between the overall barriers relative to separated reactants, ΔH , with geometrical looseness parameter %L^≠ and the heterolytic cleavage energies of the C? X and Li? N (or Li? O) bonds are observed for the anionic and ion pair S_N2 reactions. The trend of variation of the overall barriers predicts the leaving ability of X increase in the order: F < Cl < Br < I. The polarized continuum model (PCM) has been used to evaluate the solvent effects on the two inversion pathways with six‐member transition structures for the reactions of LiNCO + CH₃X. The calculations in solution indicate that solvent effects will retard the rate of reactions and the predicted product, methyl isocyanate, is same as the one in the gas phase. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical study of the addition and abstraction reactions of hydroxyl radical with uracil

The addition as well as abstraction reactions of hydroxyl radical (OH) with the nucleic acid base, uracil (U), in the gas phase has been explored at the B3LYP/6-31+G(d,p) level of density functional theory (DFT). The energy barrier of the OH addition to both the C5 and C6 positions of the uracil is less than 1 kcal/mol while the hydrogen abstractions (H-abstractions) from either the N1 or the N3 positions are ∼9.5 kcal/mol. Further the energetics of these reactions are assessed by applying the effect of aqueous medium through the polarizable continuum model (PCM). Both the gas and the solution phase data established that the thermodynamic and kinetic factors are more favorable for the OH addition to either C5 or C6 positions of the uracil than the H-abstraction reactions. Moreover, calculations at the MPW1K/6-31+G(d,p), CCSD(T)/6-31+G(d,p)//B3LYP/6-31+G(d,p) and CCSD(T)/6-31+G(d,p)//MPW1K/6-31+G(d,p) levels of theoretical methods qualitatively supported the B3LYP/6-31+G(d,p) results.     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: water-assisted mechanism and cluster-continuum model

The hydrolysis reaction of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2', 3'-dideoxy-3'-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H2O to the C=N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H2O to the C atom of the C=N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C-N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution.     

Computational study on the aminolysis of beta-hydroxy-alpha,beta-unsaturated ester via the favorable path including the formation of alpha-oxo ketene intermediate

The possible mechanisms of the aminolysis of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone (beta-hydroxy-alpha,beta-unsaturated ester) with dimethylamine are investigated at the hybrid density functional theory B3LYP/6-31G(d,p) level in the gas phase. Single-point computations at the B3LYP/6-311++G(d,p) and the Becke88-Becke95 1-parameter model BB1K/6-311++G(d,p) levels are performed for more precise energy predictions. Solvent effects are also assessed by single-point calculations at the integral equation formalism polarized continuum model IEFPCM-B3LYP/6-311++G(d,p) and IEFPCM-BB1K/6-311++G(d,p) levels on the gas-phase optimized geometries. Three possible pathways, the concerted pathway (path A), the stepwise pathway involving tetrahedral intermediates (path B), and the stepwise pathway via alpha-oxo ketene intermediate due to the participation of beta-hydroxy (path C), are taken into account for the title reaction. Moreover, path C includes two sequential processes. The first process is to generate alpha-oxo ketene intermediate via the decomposition of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone; the second process is the addition of dimethylamine to alpha-oxo ketene intermediate. Our results indicate that path C is more favorable than paths A and B both in the gas phase and in solvent (heptane). In path C, the first process is the rate-determining step, and the second process is revealed to be a [4+2] pseudopericyclic reaction without the energy barrier. Being independent of the concentration of amine, the first process obeys the first-order rate law.