米力农互变异构的理论计算

采用B3LYP/6-311G(d,P)法,分析米力农分子的酮式与烯醇式构型的构象.再采用相同方法,在气相和水相中计算并考察烯醇式与酬式结构互变时,质子迁移的两种可能途径:(a)分子内质子迁移,(b)水助质子迁移.结果表明,后者所需的活化能较小,氢键在降低反应活化能方面起重要作用,PCM溶剂化对分子几何结构参数和反应活化能的影响较小.     

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.     

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.     

甲基取代效应对甘氨酸质子迁移的作用

采用MP2/6-31++G^**//B3LYP/6-31++G^**方法研究了丙氨酸和甘氨酸在水分子作用下质子迁移的相对难易,探讨了甲基取代效应。得到2个主要结论:（1）甲基取代甘氨酸中的α-H后,削弱了迁移质子所在的化学键,有利于质子迁移;（2）通过比较甲基取代前后的质子迁移过程,发现甲基效应使反应能垒降低了3.076 kJ·mol^-1,使反应吸热减少了5.221 kJ·mol^-1。     

三唑烯醇手性分离的密度泛函研究

利用密度泛函B3LYP/6-31G*方法,分别将E-三唑烯醇的对应异构体ER、ES,Z-三唑烯醇的对应异构体ZR、ZS,手性固定相(CSP)以及三唑烯醇的4个异构体与手性固定相(CSP)络合后的分子结构构型全优化.计算结果,三唑烯醇的这4个异构体均能以氢键的形式,与CSP形成复合体;计算表明由于空间效应,E-三唑烯醇的2个手性异构体分子与CSP的结合能力各不相同,因可以通过手型固定相去分离,而Z-三唑烯醇的2个手性异构体分子都能与CSP形成双氢键,结合能相近,却不能通过手性固定相去分离;实验可以证明.     

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.     

Reactions in complex biologically relevant systems: challenges for computational approaches

The ever increasing power of computational architectures allows to investigate reactive phenomena in complex biomolecular systems and environments. Results from such calculations can be compared with experiment and give important insight into microscopic aspects of chemical reactions. We discuss two examples of biologically relevant reaction mechanisms: double proton transfer in a DNA–base pair analogue for which detailed experimental information is available and ligand (re)binding in myoglobin (Mb). For the double proton transfer in the DNA–base pair analogue ab initio molecular dynamics simulations provide direct information on the infrared spectrum that has also been observed experimentally. In the case of ligand rebinding in MbNO, we discuss results from reactive molecular dynamics simulations to investigate the rebinding probability after photodissociation of the NO from myoglobin and compare the findings with experiment. Both reaction types pose different challenges and we highlight and address the computational difficulties in each case. In particular, we explore and discuss the possibilities and limitations of current computational methods to understand reactive processes in systems where several degrees of freedom are important.     

Theoretical studies on the common catalytic mechanism of transketolase by using simplified models

Transketolase is a convenient model system to study enzymatic thiamin catalysis. By using density functional theory (DFT) method, the transfer mechanism of a 2-carbon fragment between a donor ketose X5P and an acceptor aldose R5P catalyzed by transketolase has been studied on simplified models. The calculation results indicate that the whole reaction cycle contains several proton transfer processes as well as CC bond formation and cleavage steps. Each CC bond formation or cleavage step is always accompanied by a proton transfer process, which follows a concerted but asynchronous mechanism. The CC bond formation is always prior to the proton transfer, and the CC bond cleavage is always later than proton transfer, suggesting that the CC bond ligation facilitates the proton transfer, and proton transfer promotes the CC bond cleavage. In the first half- and second half-reactions, the energy barriers of CC bond formations are always higher than those of CC bond cleavages. The 4-amino group of cofactor ThDP and histidine residue can act as the proton donor/acceptor during the catalytic reaction.     

A theoretical study on reaction pathways to carbanions

Different substituents (NO2, C6H5, NH2, NH-CH=CH-CHO) to a methylene group were taken into account to investigate under which conditions the mechanism of formation of carbanions by proton transfer to a base (methylamine) can be favorable, as a preliminary study of the reaction catalyzed by semicarbazide-sensitive amine oxidases. Three different approaching paths of methylamine to C(alpha) in NO2-C(alpha)H2-NO2, and the relevant potential energy surfaces, were examined at the SCF/3-21G and 6-31G* levels. The proton transfer along the first two paths occurred with a similar barrier, which became fairly consistent after including the MP2 correlation correction, with either basis set, while the last approaching path was abandoned. For the other model systems the minimum was searched only at the 3-21G level in the vicinity of the first reaction path. The substitution of a nitro group with a phenyl group sharply raised the barrier for the proton transfer to methylamine. Also by substituting the second nitro group with either -NH2 or -NH-CH=CH-CHO, a steep uphill pathway was found. A more realistic model of the substrate-cofactor complex, namely the Schiff base between benzylamine and pyridoxal, again produced a barrier, almost matching that obtained for C6H5-C(alpha)H2-NO2. In both cases, the energy profiles for the rotation about the CC(alpha)NC dihedral and the proton shift tautomers were also considered at the 3-21G and 6-31G* levels. A preliminary scan of the effect of methyl (or methylphosphate) substitutions to the pyridoxal ring was performed and the stability of the Schiff bases involving other cofactors was also considered.