Modeling the reaction mechanisms of the amide hydrolysis in an N-(o-carboxybenzoyl)-L-amino acid

Reaction mechanisms of the amide hydrolysis from the protonated, neutral, and deprotonated forms of N-(o-carboxybenzoyl)-l-amino acid have been investigated by use of the B3LYP density functional method. Our calculations reveal that in the amide hydrolysis the reaction barrier is significantly lower in solution than that in the gas phase, in contrast with the mechanism for imide formation in which the solvent has little influence on the reaction barrier. In the model reactions, the water molecules function both as a catalyst and as a reactant. The reaction mechanism starting from the neutral form of N-(o-carboxybenzoyl)-l-amino acid, which corresponds to pH 0-3, is concluded to be the most favored, and a concerted mechanism is more favorable than a stepwise mechanism. This conclusion is in agreement with experimental observations that the optimal pH range for amide hydrolysis of N-(o-carboxybenzoyl)-l-leucine is pH 0-3 where N-(o-carboxybenzoyl)-l-leucine is predominantly in its neutral form. We suggest that besides the acid-catalyzed mechanism the addition-elimination mechanism is likely to be an alternative choice for cleaving an amide bond. For the reaction mechanism initiated by protonation at the amidic oxygen (hydrogen ion concentration H(0) < -1), the reaction of the model compound with two water molecules lowers the transition barrier significantly compared with that involving a single water molecule.     

Solvent effects on the reaction coordinate of the hydrolysis of phosphates and sulfates: application of Hammond and anti-Hammond postulates to understand hydrolysis in solution.

The mechanism of the alkaline hydrolysis of phosphate and sulfate esters is of great interest. Ab initio quantum mechanical calculations and dielectric continuum methods are used to investigate the effect of the solvent on the associative/dissociative and the in-line/sideways character of the hydrolysis reaction of ethylene sulfate (ES) and ethylene phosphate (EP(-)), and their acyclic counterparts, dimethyl sulfate (DMS) and dimethyl phosphate (DMP(-)). The gas-phase reaction coordinates are determined by Hartree-Fock and density functional theory. For ES, the reaction coordinate in solution is determined; for the other three reactions only the transition state in solution is obtained. The alterations in the reaction induced by solvent are interpreted by use of the Hammond and anti-Hammond postulates.     

3-甲基环状乙撑磷酸二酯醇解的反应途径的理论研究

采用密度泛函理论和MP2方法研究了3-甲基环状乙撑磷酸二酯(MEP)与甲醇的反应途径:(Ⅰ)CH3O-+MEP;(Ⅱ)CH3OH+MEP;(Ⅲ)CH3O-+HMEP(MEP的质子化形式);(Ⅳ)CH3OH+HMEP.在B3LYP/6-31++G(d,p)水平上优化了四条反应途径的反应物、中间体、过渡态及产物的几何构型,并在同水平上进行了自然电荷分析,然后在MP2/6-311++G(3df,2p)水平上计算了各驻点的单点能.采用极化连续介质模型(PCM)研究了各途径在苯、甲醇和水溶液中的溶剂化效应.计算结果表明,溶剂效应使途径(Ⅰ)的自由能垒降低,而使途径(Ⅱ)和(Ⅳ)的决速步骤的自由能垒升高.在气相和苯溶剂中途径(Ⅳ)是反应的优势途径,在甲醇和水溶剂中途径(Ⅰ)则成为最优.研究结果进一步表明实验条件下途径(Ⅱ)与(Ⅳ)对总醇解反应的贡献相当.     

Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis

Pseudorotation reactions of biologically relevant oxyphosphoranes were studied by using density functional and continuum solvation methods. A series of 16 pseudorotation reactions involving acyclic and cyclic oxyphosphoranes in neutral and monoanionic (singly deprotonated) forms were studied, in addition to pseudorotation of PF5. The effect of solvent was treated by using three different solvation models for comparison. The barriers to pseudorotation ranged from 1.5 to 8.1 kcal mol(-1) and were influenced systematically by charge state, apicophilicity of ligands, intramolecular hydrogen bonding, cyclic structure and solvation. Barriers to pseudorotation for monoanionic phosphoranes occur with the anionic oxo ligand as the pivotal atom, and are generally lower than for neutral phosphoranes. The OCH3 groups were observed to be more apicophilic than OH groups, and hence pseudorotations that involve axial OCH3/equatorial OH exchange had higher reaction and activation free energy values. Solvent generally lowered barriers relative to the gas-phase reactions. These results, together with isotope 18O exchange experiments, support the assertion that dianionic phosphoranes are not sufficiently long-lived to undergo pseudorotation. Comparison of the density functional results with those from several semiempirical quantum models highlight a challenge for new-generation hybrid quantum mechanical/molecular mechanical potentials for non-enzymatic and enzymatic phosphoryl transfer reactions: the reliable modeling of pseudorotation processes.     

Theoretical investigation of the gas-phase kinetics active during the GaN MOVPE

Quantum chemistry investigations have been performed to study the gas-phase chemistry active during the MOVPE of GaN when Ga(CH3)(3) and NH3, diluted in a H2 carrier gas, are used as precursors. Optimized molecular geometries, energies, and transition-state structures of gas-phase species have been determined with density functional theory at the B3LYP/6-311+g(d,p) level. On the basis of the similarity with the soot formation mechanism active during hydrocarbon combustion, we propose that in this system a gas-phase chemistry is active and its reactivity is enhanced by a radical chain mechanism started from methyl radicals. Initiation reactions are surface processes or the pyrolysis of Ga(CH3)(3). A propagation mechanism composed of fast radical reactions, most of which without an activation energy, was identified, and kinetic constants were determined for each step. The proposed mechanism is able to describe the formation of large GaN adducts formed by up to three R-Ga-NH units. These molecules can give fast cyclization reactions that lead to the formation of six-membered cyclic species, which, similar to benzene for combustion, are thermodynamically stable in vast temperature and pressure ranges and can thus be considered as the first GaN nuclei. We also found that the presence of H2 as a carrier gas can greatly enhance the rate of formation of gas-phase particles because it is a major source of atomic hydrogen, a promoter of gas-phase reactivity.     

Theoretical Investigation of CH3CF2O2+HOO Reaction

The reactions of CH3CF2O2 with HOO are important chemical cyclic processes of photochemical contamination. In this paper, the reaction pathways and reaction mechanism of CH3CF2O2+HOO are investigated extensively with the Gaussian 98 package at the B3LYP/6-311++G** basis sets. The use of vibrational mode analysis and electron population analysis to reveal the reaction mechanism is firstly reported. The study shows that CH3CF2CO2+HOO→IM1→TS1→CH3CF2O2H+O2 channel is the energetically most favorable, CH3CF2CO2H and O2 are the principal products, and the formation of CH3OH and CF2O is also possible.     

Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of diazomethane to ethene

The electronic mechanism for the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane (CH2N2) to ethene (C2H4) is described through spin-coupled (SC) calculations at a sequence of geometries along the intrinsic reaction coordinate obtained at the MP2/6-31G(d) level of theory. It is shown that the bonding rearrangements occurring during the course of this reaction follow a heterolytic pattern, characterized by the movement of three well-identifiable orbital pairs, which are initially responsible for the pi bond in ethene and the C-N pi bond and one of the N-N pi bonds in diazomethane and are retained throughout the entire reaction path from reactants to product. Taken together with our previous SC study of the electronic mechanism of the 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne (C2H2) (Theor. Chim. Acc. 1998, 100, 222), the results of the present work suggest strongly that most gas-phase concerted 1,3-dipolar cycloaddition reactions can be expected to follow a heterolytic mechanism of this type, which does not involve an aromatic transition state. The more conventional aspects of the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane to ethene, including optimized transition structure geometry, electronic activation energy, activation barrier corrected for zero-point energies, standard enthalpy, entropy and Gibbs free energy of activation, have been calculated at the HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p), QCISD/6-31G(d) and CCD/6-31G(d) levels of theory. We also report the CCD/6-311++G(2d, 2p)//CCD/6-31G(d), MP4(SDTQ)/6-311++G(2d,2p)//CCD/6-31G(d) and CCSD(T)/6-311++G(2d, 2p)//CCD/6-31G(d) electronic activation energies.     

CH2=CHCl与O(3P)反应的理论研究

用量子化学密度泛函理论和QCISD(Quadratic configuration interaction calculation)方法,对0(^3P)与CH2CHCl的反应进行了理论研究．在UB3LYP／6—311 G(d,p),UB3LYP／6—31 (3df,3pd)计算水平上,优化了反应物、产物、中间体和过渡态的几何构型,并在UQCISD(T)／6—311 G(2df,2pO)水平上计算了单点能量．为了确证过渡态的真实性,在UB3LYP／6—311 G(3df,3pd)水平上进行了内禀坐标(IRC)计算和频率分析,并确定了反应机理．研究结果表明,反应主要产物为CH2CHO和Cl．     

Theoretical survey of the gas-phase reactions of allylamine with Co+

Density functional theory calculations have been carried out to survey the gas-phase reactions of allylamine with Co+. The geometries and bonding characteristics of all the stationary points involved in the reactions have been investigated at the B3LYP/6-311++G(d,p) level. Final energies are obtained by means of the B3LYP/6-311+G(2df,2pd) single-point calculations. The performance of these theoretical methods is valuated with respect to the available thermochemical data. Co+ strongly binds allylamine by forming a chelated structure in which the metal cation binds concomitantly to the two functional groups of the neutral molecule. Various mechanisms leading to the loss of NH3, NH2, C2H2, and H2 are analyzed in terms of the topology of the potential energy surface. The most favorable mechanism corresponds to the loss of NH3, through a process of C-N activation followed by a concerted beta-H shift. The accompanying NH2 elimination is also discussed. The loss of C2H2 is also favorable, through C-C activation and stepwise beta-H shift, giving Co+(NH2CH3) and Co+H(NH2CH2) as the product ions. Various possible channels for the loss of H2 are considered. The most favorable mechanism of the H2 loss corresponds to a pathway through which the metal acts as a carrier, connecting a hydrogen atom from the methylidyne group of allylamine with a hydrogen atom of the terminal methylene group. The product ion of this pathway has a tricoordinated structure in which Co+ binds to the terminal two Cs and N atoms of the NH2CH2CCH moiety.     

钐(II)类卡宾CH_3SmCH_2I与乙烯环丙烷化反应及溶剂化效应(THF)对反应途径影响的理论研究

用密度泛函B3LYP方法研究了过渡金属钐类卡宾与乙烯的环丙烷化反应的机理.对钐类卡宾试剂CH3SmCH2I和CH2CH2反应的反应物、中间体、过渡态和产物构型的全部结构几何参数进行了优化,并计算了THF溶液的溶剂化效应,用内禀反应坐标(IRC)计算和频率分析方法,对过渡态进行了验证.结果表明:CH3SmCH2I与CH2CH2环丙烷化反应按亚甲基转移机理(通道A)和卡宾金属化机理(通道B)都可以进行,与锂类卡宾的反应机理相同,通道A比通道B反应的势垒降低了14.65kJ/mol.溶剂化效应使通道B比通道A的反应势垒大幅度提高,更有利于反应沿通道A进行,而不利于通道B.     

o-Quinone methide as alkylating agent of nitrogen, oxygen, and sulfur nucleophiles. The role of H-bonding and solvent effects on the reactivity through a DFT computational study

The reactivity of the alkylating agent o-quinone methide (o-QM) toward NH(3), H(2)O, and H(2)S, prototypes of nitrogen-, oxygen-, and sulfur-centered nucleophiles, has been studied by quantum chemical methods in the frame of DF theory (B3LYP) in reactions modeling its reactivity in water with biological nucleophiles. The computational analysis explores the reaction of NH(3), H(2)O, and H(2)S with o-QM, both free and H-bonded to a discrete water molecule, with the aim to rationalize the specific and general effect of the solvent on o-QM reactivity. Optimizations of stationary points were done at the B3LYP level using several basis sets [6-31G(d), 6-311+G(d,p), adding d and f functions to the S atom, 6-311+G(d,p),S(2df), and AUG-cc-pVTZ]. The activation energies calculated for the addition reactions were found to be reduced by the assistance of a water molecule, which makes easier the proton-transfer process in these alkylation reactions by at least 12.9, 10.5, and 6.0 kcal mol(-1) [at the B3LYP/AUG-cc-pVTZ//B3LYP/6-311+G(d,p) level], for ammonia, water, and hydrogen sulfide, respectively. A proper comparison of an uncatalyzed with a water-catalyzed reaction mechanism has been made on the basis of activation Gibbs free energies. In gas-phase alkylation of ammonia and water by o-QM, reactions assisted by an additional water molecule H-bonded to o-QM (water-catalyzed mechanism) are favored over their uncatalyzed counterparts by 5.6 and 4.0 kcal mol(-1) [at the B3LYP/6-311+G(d,p) level], respectively. In contrast, the hydrogen sulfide alkylation reaction in the gas phase shows a slight preference for a direct alkylation without water assistance, even though the free energy difference (DeltaDeltaG(#)) between the two reaction mechanisms is very small (by 1.0 kcal mol(-1) at the B3LYP/6-311+G(d,p),S(2df) level of theory). The bulk solvent effect, evaluated by the C-PCM model, significantly modifies the relative importance of the uncatalyzed and water-assisted alkylation mechanism by o-QM in comparison to the case in the gas phase. Unexpectedly, the uncatalyzed mechanism becomes highly favored over the catalyzed one in the alkylation reaction of ammonia (by 7.0 kcal mol(-1)) and hydrogen sulfide (by 4.0 kcal mol(-1)). In contrast, activation induced by water complexation still plays an important role in the o-QM hydration reaction in water as solvent.     

氯乙基亚硝基脲烷化碱基导致DNA单链断裂的机理研究

采用密度泛函理论(DFT)和MΦller-Pleset微扰理论(MP)方法对氯乙基亚硝基脲(CENUs)烷化DNA碱基导致单链断裂的机理进行了研究. 对包括CENUs的分解、DNA碱基的烷化、糖苷键的水解、脱嘌呤位点的开环以及最终导致单链断裂的磷酸二酯的消除在内的多步反应过程进行了探讨. 在B3LYP/6-31++G**水平上对各驻点(反应物、中间体、过渡态和生成物)进行了全几何结构优化; 为了模拟细胞环境, 采用自洽场连续极化模型(CPCM)在相同计算水平上对各驻点进行了水相中的单点能计算或全几何结构优化. 分别在B3LYP/6-31++G**和MP2/6-311++G**水平上绘出反应势能曲线, 结果显示, 在整个反应过程中, 磷酸二酯的消除反应能垒最高, 而氯乙基重氮盐离子烷化DNA碱基的反应能垒最低. 理论分析结果表明, CENUs 一旦分解便很容易烷化DNA碱基, 随后生成的氯乙基化鸟嘌呤会迅速从DNA链上脱去, 尽管如此, 脱嘌呤位点最终导致DNA单链断裂的一系列反应则是一个缓慢的过程, 这与断链反应的动力学实验结果相符合.     

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.     

单分子水对CH_2SH+NO_2反应机理影响的理论研究

在B3LYP/6-311++G(2df,p)水平下对单分子水参与下的CH_2SH+NO_2反应的微观机理进行了研究.为了获得更准确的能量信息,采用HL复合方法和CCSD(T)/aug-ccpvtz方法进行单点能校正.结果表明,加入单分子水后的CH_2SH+NO_2反应体系,共经过10条不同的反应路径,得到6种反应产物.与裸反应(CH_2SH+NO_2)相比,水分子在反应中起到了明显的正催化作用.不仅使生成产物trans-HONO的能垒(-52.84kJ·mol~(-1))降低了176.94kJ·mol~(-1),而且不需经过复杂的重排和异构化过程便可得到产物cis-HONO.在生成产物cis-HONO通道(Path3和Path4)中,活化能垒分别为143.65和126.70kJ·mol~(-1),而其裸反应的活化能垒却高达238.34kJ·mol~(-1).生成HNO_2的通道中(Path5和Path6)活化能垒分别为295.23和-42.19kJ·mol~(-1).其中Path6的无势垒过程使HNO_2也成为该反应的主要产物.另外,单分子水还可通过氢迁移的方式直接参与CH_2SH+NO_2的反应,活化能垒(TS7-TS10)分别为-10.62,151.03,186.22和155.10kJ·mol~(-1).除直接抽氢通道中的(Path8-Path10)外,其余反应通道均为放热反应,在热力学上是可行的.     

CH3SS与XO (X＝F,Cl, Br)反应过程的电子密度拓扑研究

利用MP2/6-311＋＋G(d,p)//B3LYP/6-311＋＋G(d,p)对CH3SS与XO (X＝F, Cl, Br)的反应机理进行了研究. 着重从电子密度拓扑分析角度讨论了化学键的生成和断裂. 计算结果表明单线态反应为主要反应通道, 且由于该通道的反应能垒低、放热明显, 说明CH3SS与XO在大气中比较容易进行. 电子密度拓扑分析表明, 在单线态抽氢反应通道中存在着四元环状过渡结构, 随着反应进行, 此四元环状过渡结构通过一个T-型结构变为三元环状过渡结构, 最后环状结构消失得到产物.     

CH2F自由基与HNCO反应机理的理论研究

The reaction mechanism of CH2F radical with HNCO was investigated by density functional theory (DFT)at the B3LYP/6-311++G(d,p) level. The geometries of the reactants, the intermediates, the transition states and the products were optimized. The transition states were verified through the vibration analysis.The relative energies were calculated at the QCISD(T)/6-311++G**//B3LYP/6-311++G(d,p) level. Seven feasible reaction pathways of the reaction were studied. The results indicate that the pathway (5) is the most favorable to occur, so it is the main pathway of the reaction.     

Investigation on mechanism of the decomposition reaction of CH3OF with vibrational mode analysis

All species involved in the multi-channel decomposition reaction of CH(3)OF have been investigated using density functional theory. The molecular geometries for various species are optimized employing B3LYP method implementing 6-311++G** basis set. The potential energy surface is drawn out for this reaction. The vibrational mode analysis is used to elucidate the relationships of the transition states, intermediate and the products. The extensive investigation shows that the reaction mechanism is reliable.     

CH3NO2+X(X=H,OH, CH3, CH2[^3B1], O[^3P])→CH2NO2+XH吸氢反应过渡态 结 构和反应位垒的DFT计算研究

采用DFT(B3LYP)方法,分别在6-311g(d,p),6-311++g(d,p)和自洽相关基组cc-pVIZ水平上优化了基态硝基甲烷和自由基H,OH,CH3,CH2[^3B1]以及O[^3P]等发生吸氢反应时的过渡态结构,并计算了反应的位垒。研究表明,对同一反应,不同基组下优化得到的过渡态几何结构基本一致;反应位垒数值的大小也基本接近,经校正,硝基甲烷同自由基反应位垒的理论计算值同实验结果基本吻合。     

Water-catalyzed hydrolysis of the radical cation of ketene in the gas phase: theory and experiment

Both theoretical and experimental investigations are reported for the gas-phase hydrolysis of the radical cation of ketene, H(2)CCO(*+). Density functional theory (DFT) with the B3LYP/6-311++G(d,p) method indicates that a second water molecule is required as a catalyst for the addition of water across the C=O bond in H(2)CCO(*+) by eliminating the activation barrier for the conversion of [H(2)CCO.H(2)O](*+) to [H(2)CC(OH)(2)](*+). Theory further indicates that [H(2)CC(OH)(2).H(2)O](*+) may recombine with electrons to produce neutral acetic acid. Experimental results of flow-reactor tandem mass spectrometer experiments in which CH(2)CO(*+) ions were produced either directly from ketene by electron transfer or by the chemical reaction of CH(2)(*+) with CO are consistent with formation of an (C(2),H(4),O(2))(*+) ion in a reaction second-order in H(2)O. Furthermore, comparative multi-CID experiments indicate that this ion is likely to be the enolic CH(2)C(OH)(2)(*+) cation. The results suggest a possible mechanism for the formation of acetic acid from ketene and water on icy surfaces in hot cores and interstellar clouds.