2-羟基咪唑在气相和水中的异构平衡和质子迁移的从头算计算和Monte Carlo模拟

采用从头算方法在MP2/6-31＋G^*水平上研究了2-羟基咪唑分子在孤立分子和一水合物的异构体的相对稳定性和可能的质子迁移反应, 分析了一个水分子的参与对2-羟基咪唑分子异构体的相对稳定性和质子迁移速率的影响, 采用Monte Carlo模拟方法研究了反应体系在水溶液中反应的溶剂化效应. 结果表明: 2-羟基咪唑分子的孤立分子和一水合物的最稳定异构体相同, 都为酮式. 直接质子迁移反应在水溶液中活化能垒有轻微增加, 但产物能量得到降低; 水助催化质子迁移反应在水溶液中的活化能垒和产物能量都得到明显降低. 综合气相和水相的计算结果, 2-羟基咪唑水助催化的质子迁移反应较易进行, 且在水溶液中进行容易, 可以很容易被实验观察到.     

2-巯基苯并咪唑及其类似物互变异构的理论研究

采用B3LYP/6-311G**方法, 计算了2-巯基苯并咪唑及其类似物(2-巯基苯并噁唑、2-巯基苯并噻唑、2-羟基苯并咪唑、2-羟基苯并噁唑、2-羟基苯并噻唑以及2-巯基咪唑、2-巯基噁唑、2-巯基噻唑、2-羟基咪唑、2-羟基噁唑、2-羟基噻唑)的(硫)醇式与(硫)酮式结构进行质子迁移的3种可能途径: (a)分子内质子迁移; (b)水助质子迁移; (c)甲醇助质子迁移．结果表明, 途经b和c所需要的活化能较小, 氢键在降低反应活化能方面起重要作用．采用PCM方法研究了反应体系的溶剂化效应．结果表明孤立分子、一水合物和一甲醇合物的最稳定异构体相同, 都为(硫)酮式, 与气相结论一致．溶剂化效应对异构化能垒的影响较小.     

2,6-硫代黄嘌呤质子互变异构反应机理的理论研究

在密度泛函B3LYP/6-311G~(**)理论水平上,对气相和水相中2,6-硫代黄嘌呤各烯醇式与酮式水助质子互变异构体及其过渡态进行几何构型全自由度优化,获得它们在气相和水相中的几何结构和电子结构,PCM反应场溶剂模型用于水相计算.结果显示在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但是没有改变各异构体的稳定性顺序,其顺序为W1＞W3＞W2.进一步研究了2,6-硫代黄嘌呤各烯醇式与酮式水助质子互变异构的反应机理,提出了2,6-硫代黄嘌呤各烯醇式与酮式互变异构质子迁移的反应为平面六元环的过渡态结构.探讨了溶剂化效应对互变异构体的几何结构、能量、电荷分布以及互变异构反应活化能的影响等.     

3-氨基-2-吡啶酮互变异构的密度泛函理论计算

采用密度泛函理论,在B3LYP/6-3 l1G**基组水平上,计算并考察了3-氨基-2-吡啶酮分子酮式和烯醇式结构进行结构互变的质子迁移过程中的2种可能途径:(a)分子内质子迁移,(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小,氢键在降低反应活化能方面起着重要作用.     

2-(2-甲基烯丙基)-3-(3-甲基-1,2-丁二烯基)环己-2-烯酮重排生成八元环化合物反应机理的理论研究

采用密度泛函理论B3LYP/6-31G(d,p)方法研究了2-(2-甲基丙烯基)-3-(3-甲基-1,2-丁二烯基)环己-2-烯酮重排生成八元环化合物在气相中的反应机理. 考虑了两条可能的反应途径: 途径1包含5个过程, 途径2包含两个过程. 从能量上看, 两条途径的决定速度步均是[1,5]氢迁移. 采用自洽反应场极化连续模型(PCM模型)和极化导体模型(CPCM模型)研究了反应体系在甲苯溶液中的溶剂效应. 结果表明, 气相和溶液中途径2均是较优途径, 并且甲苯对该反应的溶剂化效应不明显. 理论研究结果与实验观察结果一致, 并很好地解释了有关实验现象.     

2-巯基吡啶质子迁移过程的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了2-巯基吡啶分子硫醇式结构和硫酮式结构进行结构互变质子迁移过程中的4种可能途径:(a)分子内质子迁移,(b)水助质子迁移,(c)同种二聚体双质子迁移和(d)异种二聚体间双质子迁移.计算结果表明,途经c所需要的活化能最小(9.73 kJ.mol-1,逆反应则为55.28 kJ.mol-1),而过程a所需要的活化能最大(106.02 kJ.mol-1),途径b和d的活化能居中间(分别为32.05和15.91 kJ.mol-1).研究还表明,氢键在降低反应活化能方面起着重要的作用.     

S→N烷基重排反应的机理和溶剂化效应

采用密度泛函理论的B3LYP方法、从头算的MP2方法和自洽反应场极化连续模型(PCM),在6-311++G(2d,2p)基组水平上研究了N,N’-二甲基-S-异苯并呋喃在气相和溶液中发生S→N烷基重排反应的机理、溶剂效应和取代基效应.结果表明:该反应通过四元环机理和双位迁移机理生成产物,在气相和溶剂水中,双位迁移途径的能垒均比四元环途径低,反应主要通过双位迁移途径生成产物.在气相,苯环上发生-Cl,-NO2和-OCH3取代时,双位迁移途径的能垒在MP2/6-311++G(2d,2p)水平上比没有取代时分别低4.18,7.61,4.96kJ/mol,反应的取代基效应不明显.而在溶剂水中,苯环上发生-Cl,-NO2和-OCH3取代时,双位迁移途径的能垒在PCM-MP2/6-311++G(2d,2p)水平上比气相时分别低37.73,39.96和37.17kJ/mol,反应的溶剂化效应非常明显.理论研究结果与实验观察结果一致.     

尿嘧啶水助质子转移反应机理的研究

用密度泛函理论,在B3LYP/6-311++G**计算水平下分别对尿嘧啶所有的气相、液相、过渡态和质子转移异构体的结构进行全优化,获得它们在气相和水相中的几何结构和电子结构,PGM反应场溶剂模型用于水相计算.结果显示:在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但...     

2-(3-巯基-2-吡啶基)苯并咪唑分子内质子转移及溶剂化效应

在B3LYP/6-31G(d,p)和TD B3LYP/6-31++G(d,p)//CIS/6-31G(d,p)水平上,研究了2-(3-巯基-2-吡啶基)苯并咪唑(MPyBI)在气相和七种溶剂(环己烷、苯、三氯甲烷、乙醇、乙腈、二甲亚砜和水)中基态和激发态的分子内质子转移(GSIPT和ESIPT)过程.在基态势能面的研究中发现,该化合物存在分子内双质子转移,其中分步的双质子转移在动力学上具有优势.同时对激发态质子转移势能面及激发态转移过程中的光物理现象进行了研究,结果表明该化合物存在快速的无能垒的激发态分子内质子转移,随着溶剂极性的增强,可以降低基态过渡态的能垒,改变硫醇式与硫酮式互变异构体的比例,从而灵敏地控制荧光的强度.     

亚硝基化合物与甲醛的反应机理和溶剂效应的理论研究

采用密度泛函方法B3LYP/6-311++G(d,p)研究了亚硝基苯C₆H₅-NO和2-甲基-2-亚硝基丙烷(CH₃)₃C-NO与甲醛分别在气相和溶剂中的反应机理. 在气相中均找到两条反应通道, 即协同机理和分步机理, 均生成实验产物氧肟酸, 而且分步机理均为优势通道; 除2-甲基-2-亚硝基丙烷的反应没有协同途径外, 在溶剂中反应机理与气相中的类似. 采用导电极化连续介质模型分别研究了在乙腈与水溶液中反应的溶剂化效应, 发现这些溶剂可降低反应的活化能, 但降低的程度比较小, 反应速率变化不大.     

DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water

Density functional theory (DFT) and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques have been used to study the tautomeric proton transfer reaction of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. Two reaction pathways were considered: the direct and water-assisted transfers. The optimized structures and thermodynamic properties of stationary points for the title reaction system in the gas phase were calculated at the B3LYP/6-311+G(d, p) level of theory. The potential energy profiles along the minimum energy path in the gas phase and in water were obtained. The study of the solvent effect of water on the proton transfer of 2-amino-2-oxozoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline indicates that water as a solvent is favorable for the water-assisted process and slows down the rate of the direct transfer pathway.     

Reaction mechanism and tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution: a combined Monte Carlo and quantum mechanics study

A combined Monte Carlo and quantum mechanical study was carried out to analyze the tautomeric equilibrium of 2-mercaptopyrimidine in the gas phase and in aqueous solution. Second- and fourth-order M?ller-Plesset perturbation theory calculations indicate that in the gas phase thiol (Pym-SH) is more stable than the thione (Pym-NH) by ca. 8 kcal/mol. In aqueous solution, thermodynamic perturbation theory implemented on a Monte Carlo NpT simulation indicates that both the differential enthalpy and Gibbs free energy favor the thione form. The calculated differential enthalpy is DeltaH(SH)(-->)(NH)(solv) = -1.7 kcal/mol and the differential Gibbs free energy is DeltaG(SH)(-->)(NH)(solv) = -1.9 kcal/mol. Analysis is made of the contribution of the solute-solvent hydrogen bonds and it is noted that the SH group in the thiol and NH group in the thione tautomers act exclusively as a hydrogen bond donor in aqueous solution. The proton transfer reaction between the tautomeric forms was also investigated in the gas phase and in aqueous solution. Two distinct mechanisms were considered: a direct intramolecular transfer and a water-assisted mechanism. In the gas phase, the intramolecular transfer leads to a large energy barrier of 34.4 kcal/mol, passing through a three-center transition state. The proton transfer with the assistance of one water molecule decreases the energy barrier to 17.2 kcal/mol. In solution, these calculated activation barriers are, respectively, 32.0 and 14.8 kcal/mol. The solvent effect is found to be sizable but it is considerably more important as a participant in the water-assisted mechanism than the solvent field of the solute-solvent interaction. Finally, the calculated total Gibbs free energy is used to estimate the equilibrium constant.     

DFT investigation on the intramolecular and intermolecular proton transfer processes in 2-aminobenzothiazole (ABT) in the gas phase and in different solvents

DFT at the B3LYP/6-311++G(d,p) level of theory was performed to geometrically, thermodynamically, and kinetically investigate the tautomerism process of 2-aminobenzothiazole (ABT) with n water molecules (n = 1–3) and without water in the gas phase and in different solvents with a gradual increase in their dielectric constants. The geometries of the envisaged tautomers were optimized in the gas phase and in solution with the polarized continuum model (PCM). Equilibrium and rate constants for the forward and reverse intra-/intermolecular isolated and water-assisted tautomerism reactions were also calculated. The results suggest that the activation energy of the transition state of direct proton transfer in the isolated reaction is very high and that the rate constant is very slow (~ 10^?24 s), reflecting that the reaction is thermodynamically unfavored, whereas the barrier differences between the transition states of the tautomers decrease gradually as the number of water molecules increases from one to three. Moreover, the rate constants of the proposed reactions are ~ 10²³–10²⁵ faster than those of the isolated reaction, and the water-assisted tautomerism paths can be performed quickly, especially with the assistance of two molecules of water.

     

喹唑啉酮互变异构的理论计算

采用密度泛函理论B3LYP/6-311+G(d,p)方法,计算并考察了喹唑啉酮进行结构互变的质子迁移过程的两种可能途径:(a)分子内质子迁移,(b)水助质子迁移.结果表明,途经b所需要的能垒小,氢键在降低反应能垒方面起重要作用.     

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.     

Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G(d,p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.     

别嘌醇质子迁移过程的理论研究

别嘌醇(Allopurinol)是次黄嘌呤的位置异构体,是唯一在临床上应用的黄嘌呤氧化酶抑制剂.