氨力农互变异构的理论研究

采用B3LYP/6-311G方法,对氨力农分子的烯醇式构型作构象分析。再采用相同方法计算并考察烯醇式与酮式结构互变时质子迁移的2种可能途径:(a)分子内质子迁移,(b)水助质子迁移。结果表明,b所需的活化能较小,氢键在降低反应活化能方面起着重要作用。     

用密度泛函理论研究苦参碱质子转移的异构化

采用密度泛函B3LYP/6-311G(d,p)方法和分子内质子迁移及水助质子迁移2种途径,计算苦参碱酮式与烯醇式互变异构反应,得到各异构体和过渡态的结构及变化过程中的活化能、反应焓、活化吉布斯自由能等性质。结果表明:苦参碱结构中有3个椅式和1个近扭船式六元环。无论是孤立分子还是一水合物,其酮式是最稳定结构。水助质子迁移可以大大降低反应活化能,其氢键起重要作用。得到了非平面四元环及六元环的过渡态,其碳原子杂化方式均为sp~3。     

1-(4-硝基苯基)-3-(5,6-二甲基-1,2,4三氮唑)-三氮烯质子迁移的理论研究

采用密度泛函B3LYP在6-31G*基组下,对有机显色剂1-(4-硝基苯基)-3-(5,6-二甲基-1,2,4三氮唑)-三氮烯(NPDMTT)的各种可能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)甲醇助质子转移的计算,得到了各种途径异构体的相对能,获得了它们的互变异构过程的活化能、活化吉布斯自由能和质子转移反应的速率常数等性质。计算结果表明,分子内质子转移形成的各种异构体相对能量较大,当水分子或甲醇分子参与反应时,异构体的相对能量明显减小,但无论是孤立分子、一水合物还是一甲醇合物,其最稳定的异构体都相同,均为A2。溶剂化效应对异构化能垒的影响较大。最稳定的异构体分子内质子转移在N11和N13间转移的速控步骤的活化能为130.9 kJ.mol-1,反应速度常数为2.172×10-11s-1;当水分子参与反应以双质子转移机理异构化时,活化能显著降低,有利于三氮异构化,其中异构体质子在N11和N13间转移的速控步骤的活化能为22.55 kJ.mol-1,反应速度常数为3.617×107s-1;当醇分子参与反应以双质子转移机理异构时,活化能减小得更多,其中异构体质子在N11和N13间转移的速控步骤的活化能为2.384 kJ.mol-1,反应速度常数为9.032×1011s-1。计算结果还表明,氢键作用在增大NPDMTT一水合物和NPDMTT一甲醇合物相对稳定性、降低质子转移异构化反应活化能等方面起着重要作用。     

论1-吡啶-3-[4-(苯基偶氮)苯基]-三氮烯的三氮异构化

采用3种不同泛函(B3LYP,BP86,PBE1PBE)在6-31G*和6-311+G*基组下,计算有机材料1-吡啶-3-[4(苯基偶氮)苯基]-三氮烯(PYPAPT)不同结构上三氮异构化的途径有2种可能:(a)分子内质子迁移,(b)水助质子迁移,因此获得它们的互变异构过程活化能、活化吉布斯自由能和质子转移反应的速率常数等性质.采用PCM法研究反应体系的溶剂化效应.证明孤立分子和一水合物最稳定的异构体相同都为[J],计算结果也与实验值符合得很好,溶剂化效应对异构化能垒的影响较大.最稳定的异构体分了内质子转移的速控步骤的活化能为170.48 kJ/mol,速率常数为3.86×10-15s-1:当水分子参与反应以双质子转移机理异构化时,活化能显著降低,有利于三氮异构化,其最稳定异构体的速控步骤的活化能为47.41kJ/mol,速率常数为9.73×104s-1.计算结果还表明,氢键作用在增大PYPAPT水合物相对稳定性、降低质子转移异构化反应活化能等方面起着重要作用.     

理论计算5-氟尿嘧啶三水复合物质子转移的异构化

为了研究5-氯尿嘧啶三水复合物异构体的相对稳定性和异构体之间的转变机理,以至于了解药理性质,对实验进行指导,故本文采用密度泛函B3LYP/6-311+G(d,p)法,研究计算5一氟尿嘧啶6种三水复合物的稳定性及质子转移而引起的双酮式-双醇式或酮醇式互变异构的反应机理,获得零点能、总能量及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.IPCM反应场溶剂模型用于计算水相.本文与文献[9]的区别在于重点研究3个水分子存在下及三水复合物在整体溶剂中的质子专移规律,而文献[9]仅讨论了分子内和-水催化时的规律.本文证明在三水复合物中,双酮式Fu1a-3w最稳定,与已有实验结果相符.由双酮式三水复合物通过双质子转移向双醇式或酮醇式异构化中,找到3条反应通道(P1,P2,P3),其速控步骤活化吉布斯自由能分别为71.6、74.3和83.6kJ·mol-1,是文献报道分子内质子转移所需活化能垒的近三分之一,却均比文献报道-水催化所需活化能垒高.还表明,整体溶剂效应使三水复合物(FU6-3w除外)的偶极矩均增大且质子转移所需活化能垒也相应增大,质子转移反应反而更困难.     

密度泛函方法的ZSM-5分子筛上苯与乙烯烷基化反应机理研究

采用密度泛函(DFT)方法对于ZSM-5分子筛上苯与乙烯的烷基化反应机理进行研究。选取了包含酸性质子的8T原子簇模型代表ZSM-5分子筛的部分结构。采用B3LYP/6-31G(d)水平从生成能与反应活化能角度对于烷基化反应发生时可能存在的2种联合机理和一种分步机理进行了计算与比较。结果表明,联合反应机理中乙烯的质子化和C-C键的形成同时发生,而分步机理开始于乙醇盐中间体的生成,随后与苯反应生成反应产物。分步机理中乙醇盐中间体生成步骤的活化能(124.55 kJ/mol)低于联合机理的反应活化能(168.98 kJ/mol和156.06 kJ/mol),而烷基化步骤的活化能(209.35 kJ/mol)高于联合机理的反应活化能,由此可以推断ZSM-5分子筛上苯与乙烯的烷基化反应时2种机理同时发生,存在竞争关系。     

6-巯基嘌呤质子转移异构化的量子化学计算研究

采用密度泛函B3LYP方法,在6-311G(d,p)基组水平上对6-巯基嘌呤质子转移引起的硫酮式与硫醇式互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数。计算结果表明,6-巯基嘌呤无论是孤立分子还是一水合物,其硫酮式TP2是最稳定的异构体。计算结果同已有实验结果相符。由硫酮式通过分子内质子转移向硫醇式异构化找到4条反应通道(P1,P2,P3,P4),各通道的活化能分别为114.0,133.9,128.0,95.1 kJ·mol~(-1)。当水分子参与反应以双质子转移机理异构化时,活化能垒显著降低,各通道的活化能依次降为51.2,63.0,70.5,42.8 kJ·mol~(-1),可见,水助催化有利于硫酮式向硫醇式转变。计算结果还表明,氢键的强弱对TP2一水合物的稳定性会有一定的影响。     

HA和HYP分子内质子传递模式差异的理论研究

采用量子化学从头算的计算方法,研究了竹红菌素(HA)4种异构体发生分子内质子传递(IPT)的过程。结果表明,在竹红菌素分子内质子传递的过程中不会发生碳骨架结构的变化,这与之前文献中的猜测是不一致的,利用CIS和TD方法计算研究了竹红菌素激发态分子内质子传递的过程.结果表明,竹红菌素顺式结构的IPT过程是一个～10ps的瞬态过程,而竹红菌素反式结构的IPT过程则是一个～50～250ps的瞬态过程.根据计算结果我们对竹红菌素和金丝桃蒽酮分子内质子传递模式之间的差异做出了初步的解释.     

分子筛合成过程中三聚铝硅酸盐生成机理的DFT研究

采用密度泛函理论研究了在分子筛合成的碱性环境中铝硅酸盐三聚体的生成机理.在B3LYP/6-31 G(d,p)计算水平上对反应物、过渡态和产物分别进行了几何结构的全优化和频率计算,通过内禀反应坐标的方法验证了反应路径,并计算了反应的活化能.采用COSMO-RS模型考虑了溶剂效应.结果表明,二聚硅酸分子SiOSi(OH)6和单体铝酸根离子Al(OH)**的缩聚反应可以按照协同方式进行,SiO-Al桥键的形成与水分子的脱除同时发生,最终生成铝硅酸盐的三聚体.计算得到的缩聚反应活化能为80.1 kJ/mol.     

分子筛催化甲苯歧化SE1反应机理的分子模拟研究

应用分子模拟半经验量子力学Mopac 6．0-AM1近似计算方法分析了分子筛催化甲苯歧化反应的S_E~1反应历程,确定了反应历程中的反应态、过渡态和产物态,得到了反应活化能和反应热等相关信息,对内禀反应坐标的计算进一步验证了反应过程中的能量变化。计算结果表明,分子筛催化的甲苯歧化反应沿S_E~1反应历程可通过两步基元反应完成；质子由分子筛向甲苯分子转移的过程为反应的快速步骤,其活化能达到428．54 kJ·mol~(-1),需要在高温下进行；甲苯歧化总反应的热效应很小,与实验数据相吻合。     

Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase

Saccharopine dehydrogenase (SDH) is the last enzyme in the AAA pathway of l-lysine biosynthesis. On the basis of crystal structures of SDH, the whole catalytic cycle of SDH has been studied by using density functional theory (DFT) method. Calculation results indicate that hydride transfer is the rate-limiting step with an energy barrier of 25.02 kcal/mol, and the overall catalytic reaction is calculated to be endothermic by 9.63 kcal/mol. Residue Lys77 is proved to be functional only in the process of saccharopine deprotonation until the formation of product l-lysine, and residue His96 is confirmed to take part in multiple proton transfer processes and can be described as a proton transfer station. From the point of view of energy, the SDH catalytic reaction for the synthesis of l-lysine is unfavorable compared with its reverse reaction for the synthesis of saccharopine. These results are essentially consistent with the experimental observations from pH dependence of kinetic parameters and isotope effects.     

Preliminary density functional calculations on the formic acid dimer

The utility of density functional theory (DFT) to simulate the energetics of intermolecular rearrangement, dissociation energy, and, as well as the fine topological features of the molecular charge distribution has been tested for the formic acid dimer. The equilibrium and transition state structures are optimized using adiabatic connection method (ACM) and the barriers to the double proton transfer reaction have been also evaluated. The ACM results are compared with those obtained from SCF, MP2 and various DFT functionals. Preliminary results indicate that there is perhaps a significant role of the correlation effects in determining the barrier height for this reaction. The formic acid dimer dissociation energies calculated from the non-local gradient corrected or ACM functionals are in reasonable agreement with experimental estimates.Comparison of the DFT, SCF and MP2 electrostatic molecular potentials derived from cumulative atomic multipole moments (CAMM) for the formic acid dimer indicates that the correlation effects are reproduced correctly, providing that DFT atomic charges are supplemented by higher atomic multipole moments.     

Solvent effect on hydrogen bonded ammonia-hydrogen halide complexes: continuum medium versus cluster models

The influence of water and dinitrogen environment on the structures of hydrogen bonded XH-NH3 (X = F, Cl, and Br) complexes has been investigated using the self-consistent isodensity polarizable continuum solvent model (SCI-PCM) with two values of dielectric constants, 1.5 and 78.0, respectively. The geometrical parameters, along with the interaction energies as well as harmonic frequencies were calculated at the B3M-LYP/6-311 + + G(d,p) level of theory. The results from dielectric continuum model were compared with those obtained by traditional supermolecule approach. In order to model the proton transfer in XH-NH3 systems by supermolecular approach, one should add from two to four explicit water or dinitrogen molecules to the calculations. The dielectric continuum model provides similar effect using less effort. As our results shown, the SCI-PCM model, where a solvent is treated as a continuum medium, reproduces quite accurately the molecular properties of investigated medium strong hydrogen bonded systems both with dinitrogen and water environment. In order to represent solvent effects on hydrogen-bonded complexes with less acidic HX subunit it is necessary to take explicit solvent molecules into account.     

Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

QM cluster and QM/MM protein models have been employed to understand aspects of the reaction mechanism of plant allene oxide synthase (pAOS). In this study we have investigated two reaction mechanisms for pAOS. The standard pAOS mechanism was contrasted with an alternative involving an additional active site molecule which has been shown to facilitate proton coupled electron transfer (PCET) in related systems. Firstly, we found that the results from QM/MM protein model are comparable with those from the QM cluster model, presumably due to the large active site used. Furthermore, the results from the QM cluster model show that the Fe^III and Fe^IV pathways for the standard mechanism have similar energetic and structural properties, indicating that the reaction mechanism may well proceed via both pathways. However, while the PCET process is facilitated by an additional active site bound water in other related families, in pAOS it is not, suggesting this type of process is not general to all closely related family members.     

Simulation of carbon dioxide absorption process by aqueous monoethanolamine in a microchannel in annular flow pattern

The process of carbon dioxide absorption by aqueous monoethanolamine solvent was simulated in a microchannel in an annular flow pattern. This simulation has been carried out as a multiphase and three-dimensional process. The effects of different operating parameters such as temperature, superficial gas and liquid velocities, aspect ratio, and concentrations of solvent and solute have been investigated on the mass transfer flux and carbon dioxide conversion. The results of simulating mass transfer flux based on the calculated mass transfer coefficient were well consistent with the experimental data. The result of this study indicated that the mass transfer flux shall increase with the superficial gas and liquid velocities, temperature, concentration of solvent, and increment in the aspect ratio. It also revealed that increasing the concentration of solute would lead to an increase in the mass transfer flux and a decrease in the conversion.