6-甲基-4-羟基嘧啶单体及二聚体质子转移过程的理论研究

应用密度泛函理论的B3LYP/6-311+G(d)方法研究了6-甲基-4-羟基嘧啶单体及二聚体质子转移的异构化反应.对反应势能面的研究发现,该化含物可能存在9种单体异构体,对其最稳定的单体构型进行分析.各单体间异构化反应的过渡态共有9种,反应的活化能最小为22.06 kJ/mol,最大为356.55 kJ/mol,最可能的反应路径在室温下即可进行. 研究了2种二聚体及其异构化反应的过渡态,发现二聚体均比其对应的单体稳定,而且质子转移所需要的活化能仅为20.13 kJ/mol,比单体低很多. 氢键在这种变化中起了主要作用,由单体和二聚体的总能量计算了氢键的键能.     

白藜芦醇清理羟基自由基夺氢机理的量子化学研究

在DFT方法的B3LYP/6-31G水平下, 对反式白藜芦醇分子的所有可能构象进行了优化, 并对最稳定构象进行了自然键轨道分析. 键级数据表明, 白藜芦醇清理羟基自由基最活泼反应位点应为其单羟基环上的羟基, 对产物白藜芦醇自由基的优化结果表明, 单羟基环氧自由基的稳定性最高. 在B3LYP/6-31G水平下寻找白藜芦醇单羟基环羟基清理羟基自由基的过渡态, 频率分析结果表明只存在一个虚频. 对该过渡态结构进行内禀反应坐标反应路径解析(IRC), 结果表明, 过渡态沿反应坐标方向分别指向反应物络合物和产物络合物, 反应通道各个能量驻点显示反应物与反应物络合物的能量差为E1=173.5193 kJ/mol, 反应物络合物与过渡态、反应物络合物与产物的能量差分别为Ea=16.5143 kJ/mol, E2=51.8799 kJ/mol. 可见反应物的能量远高于过渡态及产物, 因此, 反应物络合物的形成应是整个反应的驱动力.     

2-羟基吡啶质子转移过程的理论研究

采用量子化学中的密度泛函理论,在B3LYP/6-31G(d)基组水平上,计算并考察了2-羟基吡啶分子醇式结构和酮式结构进行结构互变的质子转移过程中的4种可能途径:(a)分子内质子转移,(b)水助催化质子转移,(c)同种二聚体双质子转移和(d)异种二聚体间双质子转移.计算结果表明,途经c所需要的活化能最小(2.6 kJ•mol－1,逆反应则为27.1 kJ•mol－1),而过程a所需要的活化能最大(137.2 kJ•mol－1),途径b和d的活化能居中间(分别为38.7和17.3 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.     

3,6-二羟基哒嗪质子转移过程的理论研究

为了探索3,6-二羟基哒嗪分子醇式和酮式结构互变异构化的反应机理,本研究组采用DFT B3LYP/6-311+G(d)方法对标题化合物异构化反应的势能面进行了研究,在探讨各种可能的反应途径中,发现至少有34种异构体和43种过渡态.结果表明,6-羟基-3(2H)-哒嗪酮不论是单体,与水形成配合物,还是二聚体,比其相对应的异构体能量低,表明在通常情况下是以6-羟基-3(2H)-哒嗪酮形式稳定存在的,这与前人通过实验数据对互变异构体的比率进行预测的结果是一致的;在考察的可能反应途径中,直接进行的分子内质子转移过程需要的活化能为142.2 kJ·mol^-1,水助催化时,反应活化能为41.3 kJ·mol^-1,考虑溶剂效应后,其活化能为59.2 kJ·mol^-1,二聚体双质子转移的活化能为16.8 kJ·mol^-1,二聚体双质子转移所需活化能最低,在室温下就可以进行.由此可见氢键在降低反应活化能方面起着重要的作用.     

二氧化三氮(N3O2)中性分子和离子的一些重要反应过程的理论研究

二重态的N3O2中性分子作为中间体, 在N3O2阴离子的光解离反应和NO+N2O←→N2+NO2反应中均起重要作用. 在CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPE的水平上, 对这两个反应进行了理论计算. 结果表明, 在N3O2阴离子的光解离反应中, 该阴离子先在光照下解离为与其具有相同的W构型的中性分子和一个电子, 这个中性分子是一个过渡态, 它将打破C2v构型变成具有Cs对称性的W型中间异构体, 然后再经过一个过渡态, 裂解成N2O+NO两个小分子. 这个裂解过程的能垒非常低(5.96 kJ/mol), 因此在实验中很难检测到W型的中间异构体. 在另一个重要的[N3O2]体系的反应(NO+N2O←→N2+NO2)中, 找到了两条反应通道, 其中不经过中间异构体的一步转化通道更为可行.     

CH3NO异构体及异构化反应机理的量子化学研究

在CCSD(T)/6-311＋＋G(d,p)//B3LYP/6-311＋＋G(d,p)水平上对CH₃NO的异构体及各异构化反应机理进行了详细的理论研究. 包括CH₃NO共找到了23种异构体, 这23种异构体间通过24个过渡态相互转化. 用振动频率分析证实了过渡态的真实性, 内禀反应坐标跟踪(IRC)计算验证了过渡态与各异构体的连接关系. 计算结果表明, 在CH₃NO的各种异构体中, 分子骨架中存在N—C—O结构是最稳定的, 而C—O—N, C—N—O结构能量最高, 不稳定. 异构体间的异构化反应主要通过化学键的旋转, H迁移, C, N, O骨架的重组及包含上述两种机理的混合型机理等4种方式完成.     

3-卤代吡唑质子转移过程的理论研究

采用密度泛函B3LYP/6-311G**方法,对3-卤(-F、-Cl、-Br)代吡唑几何构型进行了全自由度优化,获得了它们的几何结构和电子结构。计算结果显示,N1-H型的稳定性大于N2-H型。计算并考察了3-卤代吡唑进行结构互变的质子转移过程的四种可能途径:(a)分子内质子转移;(b)水助质子转移;(c)同种二聚体双质子转移;(d)异种二聚体双质子转移。计算结果表明(以3-氟代吡唑为例),途径d所需要的活化能最小(54.89 kJ/mol),而途径a所需要的活化能最大(198.83kJ/mol),途径b和c的活化能居中间分别为(104.05 kJ/mol和69.05 kJ/mol)。研究还表明氢键在降低活化能方面起着重要的作用,卤素(-F、-Cl、-Br)对活化能的影响不大。     

HSCCS自由基势能面的理论研究

在CCSD(T)/6-311G(d,f)//MP2/6-311G(d,f) ZPE水平下,计算得到含有8个异构体和11个过渡态的HSCCS自由基体系势能面,讨论了异构体的结构与稳定性及异构体之间的异构化过程.结果表明异构体m1的能量最低,除m1以外,异构体m2和m3的能量也比较低,在MP2水平上,过渡态TS1的能量比异构体m2仅高3.9kJ/mol,而在CCSD(T)水平上,TS1的能量比m2低14.6 kJ/mol,这说明异构体m2可以迅速转化为能量更低的m1.异构体m3的能量比异构体m1高49.99 kJ/mol,可以推断,在合适的实验条件下可以观测到异构体m1.     

n‐Butane Monomolecular Cracking on Acidic Zeolites: A Density Functional Study

采用5T簇模型,利用密度泛函理论在B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d)水平下研究正丁烷在酸性分子筛上的单分子催化裂解反应。本文重点详细研究了正丁烷在分子筛表面不同C位的脱氢反应。在B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d)水平下计算所得第一和第二位C-C键裂解的活化能垒分别为 238、217 kJ/mol。而第一第二序位脱氢反应能垒分别为296、242 kJ/mol。正丁烷不同序位脱氢反应的活化能垒相差54 kJ/mol。从计算结果可以看出,正丁烷在分子筛上催化裂解脱氢反应优先发生在第二位C原子上。此外,本文还讨论了簇模型结构与酸性的关系,结果显示改变封端Si-H键的键长的方法可以用来模拟分子筛酸性变化。最后研究了分子筛酸性变化与正丁烷催化裂解反应能垒的关系。     

NC2S+离子的结构和稳定性的理论研究

在密度泛函和从头算理论水平下计算了单重态的NC2S+离子的结构、能量、光谱以及稳定性. 在B3LYP/6-311G(d)水平下, 得到8个异构体, 它们由15个过渡态相连接. 在CCSD(T)/6-311+G(2df)//QCISD/6-311G(d)+ZPVE水平下, 得到能量最低的异构体是直线型的具有1Σ电子态的NCCS+(1)(0.0 kJ/mol), 其次是直线型的异构体CNCS+(2)(54.8 kJ/mol). 两个低能量的异构体1和2及另外一个高能量的直线型异构体CCNS+(3)(323.8 kJ/mol)都具有相当大的动力学稳定性, 这三个异构体在具备一定条件的实验室和星际条件下是可以进行观测的. 分析了这3个异构体的成键性质.     

Computational study of the deamination reaction of cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.     

Mechanisms for the deamination reaction of cytosine with H2O/OH(-) and 2H2O/OH(-): a computational study

Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).     

Transition state structure and energetics of the N(2)O + X (X = Cl,Br) reactions

The structural and vibrational properties of the transition state of the N(2)O + X (X = Cl,Br) reactions have been characterized by ab initio methods using density functional theory. We have employed Becke's hybrid functional (B3LYP), and transition state optimizations were performed with 6-31G(d), 6-311G(2d,2p), 6-311+G(3d,2p), and 6-311+G(3df,2p) basis sets. For the chlorine atom reaction the coupled-cluster method (CCSD(T)) with 6-31G(d) basis set was also used. All calculations resulted in transition state structures with a planar cis arrangement of atoms for both reactions. The geometrical parameters of transition states at B3LYP are very similar, and the reaction coordinates involve mainly the breaking of the N-O bond. At CCSD(T)/6-31G(d) level a contribution of the O-Cl forming bond is also observed in the reaction coordinate. In addition, several highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction energetics. All model chemistries predict exothermic reactions. The G3 and G2 methods result in the smallest deviations from experiment, 1.8 and 0 kcal mol(-1), for the enthalpies of reaction for N(2)O reaction with chlorine and bromine, respectively. The G3//B3LYP and G1 methods perform best among the composite methods in predicting energies of the transition state, with a deviation of 1.9 and 3.0 kcal mol(-1), respectively, in the activation energies for the above processes. However, the B3LYP/6-311+G(3df,2p) method gives smaller deviations of 0.4 and -1.0 kcal mol(-1), respectively. The performance of the methodologies applied in predicting transition state energies was analyzed.     

Mechanistic study of the deamination reaction of guanine: a computational study

The mechanism for the deamination of guanine with H(2)O, OH(-), H(2)O/OH(-) and for GuaH(+) with H(2)O has been investigated using ab initio calculations. Optimized geometries of the reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), B3LYP/6-31G(d), and B3LYP/6-31+G(d) levels of theory. Energies were also determined at G3MP2, G3MP2B3, G4MP2, and CBS-QB3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Thermodynamic properties (ΔE, ΔH, and ΔG), activation energies, enthalpies, and Gibbs free energies of activation were also calculated for each reaction investigated. All pathways yield an initial tetrahedral intermediate and an intermediate in the last step that dissociates to products via a 1,3-proton shift. At the G3MP2 level of theory, deamination with OH(-) was found to have an activation energy barrier of 155 kJ mol(-1) compared to 187 kJ mol(-1) for the reaction with H(2)O and 243 kJ mol(-1) for GuaH(+) with H(2)O. The lowest overall activation energy, 144 kJ mol(-1) at the G3MP2 level, was obtained for the deamination of guanine with H(2)O/OH(-). Due to a lack of experimental results for guanine deamination, a comparison is made with those of cytosine, whose deamination reaction parallels that of guanine.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Transition state for the gas-phase reaction of uranium hexafluoride with water

Density functional theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transition states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF 6, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F 5, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structures and relative energies of the reacting complex and transition state. However, a significant change in the structure of the product complex was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF 4, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF 6 with water.     

硝酸溴与三重态氧原子反应机理的密度泛函研究

The theoretic study of reaction between BrONO2 and O(3P) is reported by using the molecular orbital ab initio and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energy and zero energy of reactants, transition states, inter mediates and products during reactions are computed by B3LYP theory level with the basis set 6-311+G(d,p). The transition states and inter mediates of the reaction are verified by frequency analysis, and the relation ship of reactants, transition states, intermediates and products is affirmed by Intrinsic Reaction Coordinate(IRC) calculation. The activation energy of the reaction has also been calculated. Based on the optimized structure, the single point energy of all species is obtained by CCSD(T) with the basis set 6-311+G(d,p). The results show that there are three exothermic channels and their corresponding products are: cis-Br ONO + 3O2, trans-BrONO + 3O2 and BrOO+NO2. The activation energy of three channels is 91.58, 101.25, 51.17kJ/mol under B3LYP and 141.19, 148.39, 103.21 kJ/molunder CCSD(T) theory level. The third channel is the dominant channel.     

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.     

苯并氧化呋咱稳定性和异构化的DFT和ab initio研究

运用B3LYP/6-31G(d)密度泛函理论（DFT）方法对苯并氧化呋咱、邻二亚硝基苯及其间的异构化反应进行了计算研究。结果表明,苯并氧化呋咱的分子总能量比邻二亚硝基苯的低;由苯并氧化呋咱异构为邻二亚硝基苯的正向反应活化能（Ea+=51.0kJ/mol）,与文献实测值（58.6kJ/mol）较接近,而其逆向反应活化能（Ea-=4.6kJ/mol）很小,从而揭示了苯并氧化呋咱比邻二亚硝基苯更稳定·此外,进行了HF/3-21G、HF/6-31G(d)和MP2/6-31G(d)//6-31G(d)水平下相应的计算,发现B3LYP-DFT的结果较abinitio为优。谐振动频率的B3LYP/6-31G(d)计算还支持了邻二亚硝基苯为苯并氧化呋咱“自-自”互变重排反应的中间体。     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。