甲基重氮烷阳离子(CH_3N_2~ )与DNA碱基的甲基化反应

在B3LYP/6-31G**和MP2/6-311G**水平上,计算了终致癌物甲基重氮烷阳离子(CH3N2 )在气相和水溶剂中与四种DNA碱基上10个亲核位发生甲基化过程的反应机理.结果表明:在气相和溶剂中,终致癌物CH3N2 对碱基上相应亲核位的甲基化反应过程,活化能都比较小(<33.5kJ/mol),是容易进行的放热反应.所以,二甲基亚硝胺一旦形成终致癌物,则很容易与碱基形成癌变物.     

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。     

甲基重氮烷阳离子（CH3N2^＋）与DNA碱基的甲基化反应

在B3LYP／6．31G^＊＊和MP2／6．311G^＊＊水平上,计算了终致癌物甲基重氮烷阳离子（CH3N2^＋）在气相和水溶剂中与四种DNA碱基上10个亲核位发生甲基化过程的反应机理．结果表明：在气相和溶剂中,终致癌物CH3N2^＋对碱基上相应亲核位的甲基化反应过程,活化能都比较小（〈33．5kJ／mol）,是容易进行的放热反应．所以,二甲基亚硝胺一旦形成终致癌物,则很容易与碱基形成癌变物．     

H-ZSM-5催化环己酮肟制ε-己内酰胺反应机理的ONIOM研究

采用ONIOM和DFT方法研究了H-ZSM-5分子筛催化环己酮肟制ε-己内酰胺的贝克曼重排反应机理.所有的构型优化使用ONIOM(B3LYP/6-31+G(d):PM3)方法进行,并在此基础上对得到的最优构型应用多种密度泛度方法,如B3LYP/6-31+G(d),PBE/6-31+G(d),M062X/6-31+G(d)和ωB97XD/6-31+G(d)进行完整46T簇模型的单点能计算.B3LYP,PBE和M062X泛函使用dftd3程序计算了额外色散校正,以考虑分子筛内部的弱相互作用.计算结果显示,经色散校正的DFT方法的计算精度被大大提高,达到一个与MP2方法相媲美的精度.反应的决速步是由第一步1,2-H转移和重排步共同决定,内部反应能垒为44.5 kcal/mol.反应速率常数表明,在293~393 K时,在H-ZSM-5上贝克曼重排反应进行得相当缓慢;当温度达到423 K时,正逆反应速率相当,反应开始发生;当达到623 K时,反应速率常数为130 1/s.     

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.     

O6-鸟嘌呤和O4-胸腺嘧啶甲基化与DNA碱基异常氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对顺(cis-)、反式(anti-)O⁶-甲基鸟嘌呤(O⁶-MeG)和O⁴-甲基胸腺嘧啶(O⁴-MeT)与DNA碱基(腺嘌呤A、鸟嘌呤G)的非Watson-Crick氢键二聚体进行了优化. 在MP2/cc-pVXZ (X＝D,T)//B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 此外, 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)和电子密度拓扑方法分析了碱基间的弱相互作用. 计算结果显示, 甲基化使碱基对间的氢键作用模式发生了明显的扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小, 甲基化对O⁶-MeG和O⁴-MeT与DNA碱基间的氢键作用是去稳定化的, 这种影响主要来自于大体积的甲基的空间效应和给电子效应, 且对顺式的影响明显大于反式. 计算结果与文献给出的实验结论基本一致.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

SAPO-34分子筛中多甲基苯分子与卤代甲烷偕甲基化反应的密度泛函理论研究

利用周期性密度泛函理论研究了SAPO-34分子筛催化转化卤代甲烷制取低碳烯烃反应的碳池主要成分多甲基苯分子的偕甲基化反应。氯甲烷和溴甲烷分子在SAPO-34分子筛内的吸附能分别是–18和–22 kJ/mol,由于氯和溴原子相似的电负性,氯甲烷和溴甲烷分子的吸附能并未被精确区分。以氯甲烷和溴甲烷为甲基化试剂,得到了几种多甲基苯分子的偕甲基化反应能及能垒,结果表明,六甲基苯分子(HMB)的偕甲基化反应为放热反应,而其余甲基苯分子的偕甲基化反应为吸热反应。对于上述两种甲基化试剂,体积最大的HMB均表现出最低的偕甲基化反应能垒,这可能是由于分子筛骨架与多甲基苯分子之间的静电相互作用增强了HMB的反应活性所致。     

过充电保护添加剂1,4-二甲氧基苯的反应机理

采用密度泛函理论(B3LYP/6-311+G(d,p))和MP2/6-311+G(d,p)方法,研究锂离子电池过充电保护添加剂1,4-二甲氧基苯(p-DMOB)的作用机理.计算结果表明,在过充时,p-DMOB优先于溶剂分子(乙基甲基碳酸酯、二甲基碳酸酯、碳酸乙酯)发生氧化反应.用B3LYP和MP2计算所得的p-DMOB理论氧化电位接近,分别为4.12和4.05V(vsLi/Li+).p-DMOB氧化时首先失去一个电子,生成p-DMOB+·正离子自由基,用B3LYP和MP2方法计算所得的相应能量变化分别为701.24和728.27kJ·mol-1.失去电子后苯环的共轭性受到破坏,随后p-DMOB+·苯环上的C―H键发生断裂,失去H+并形成p-DMOB·自由基.用B3LYP和MP2方法计算所得的相应能量变化分别为1349.78和1810.99kJ·mol-1.p-DMOB·自由基很不稳定,会在电极表面发生聚合反应形成聚合物膜,用B3LYP和MP2方法计算所得的相应能量变化分别为-553.37和-1331.20kJ·mol-1.     

F原子与瞬态自由基CH_2SH反应的理论研究

用量子化学从头算和密度泛函理论（DFT）对F原子与自由基CH_2SH在势能面上 的反应进行了研究。在B3LYP/6-311G水平上计算出了各物种的优化构型、振动频率 和零点振动能(ZPVE);各物种的总能量由B3LYP/6-311 + G(2df, pd)//B3LYP/6- 311G计算,另外对反应物和产物还计算了其G3能量。结果表明：首先F通过与C或S 结合的两种途径与CH_2SH相配位,再通过H（4）原子转移形成甲基,然后甲基再旋 转,甲基中H（4）原子最终与F结合,反应产物为HF和CH_2S。反应为放热反应,分 别为ΔH_r = -370.7 kJ/mol (DFT)和-396.94 kJ/mol (G3)。此外依据计算出的反 应热,可得自由基·CH_2SH的生成热Δ_fH°_(298.15) = 146.44 kJ/mol (DFT), 而Δ_fH°_0 = 167.36 kJ/mol (G3)。它们与以前的实验和理论值是一致的。     

烷基自由基β位裂解反应类反应势垒与速率常数的精确计算

提出反应类等键方法并用于高温燃烧机理中一类重要反应——烷基自由基β位裂解反应的反应势垒和速率常数的精确校正计算. 通过10种不同从头算水平对类反应中5个代表反应的反应势垒的计算发现, 用反应类等键反应方法和直接从头算方法获得的5 个代表反应的反应势垒最大绝对偏差的平均值分别为5.32 和16.16 kJ·mol^-1, 表明反应类等键反应方法计算的反应势垒对不同水平从头算方法的依赖性小, 可在较低从头算水平计算得到精确的反应势垒, 解决大分子体系反应势垒的精确计算问题. 此外应用反应类等键反应方法在BHandHLYP/cc-pVDZ 从头算水平计算了3 个代表反应的速率常数, 并与文献报道的实验值进行了比较, 其在500-2000 K温度区间内计算速率常数与实验速率常数中较大值与较小值的比值k_max/k_min的平均值为1.67, 最大值也仅有2.49. 表明应用反应类等键反应方法在较低从头算水平即可对同类反应的速率常数进行精确计算.最后在BHandHLYP/cc-pVDZ从头算水平用反应类等键反应方法计算了13个烷基自由基β位裂解反应的速率常数.     

烷烃与氢过氧自由基氢提取反应类反应能垒与速率常数的精确计算

氢过氧自由基从烷烃分子中提取氢的反应是碳氢燃料中低温燃烧化学中非常重要的一类反应。本文用等键反应方法计算了这一类反应的动力学参数。所有反应物、过渡态、产物的几何结构均在HF/6-31+G(d)水平下优化得到。以反应中的过渡态反应中心的几何结构守恒为判据,该反应类可用等键反应处理。本文选取了乙烷和氢过氧自由基的氢提取反应为参考反应,其它反应作为目标反应,用等键反应方法对目标反应在HF/6-31+G(d)水平的近似能垒和反应速率常数进行了校正。为了验证方法的可靠性,选取C5以下的烷烃分子体系,对等键反应方法校正结果和高精度CCSD(T)/CBS直接计算结果进行了比较,最大绝对误差为5.58k J?mol~(-1),因此,采用等键反应方法只需用低水平HF从头算方法就可以再现高精度CCSD(T)/CBS计算结果,从而解决了该反应类中大分子体系的能垒的精确计算。本文的研究为碳氢化合物中低温燃烧模拟中重要的烷烃与氢过氧自由基氢提取反应提供了准确的动力学参数。     

Comparison of the kinetics and thermodynamics for methyl radical addition to C=C, C=O, and C=S double bonds

The barriers, enthalpies, and rate constants for the addition of methyl radical to the double bonds of a selection of alkene, carbonyl, and thiocarbonyl species (CH(2)=Z, CH(3)CH=Z, and (CH(3))(2)C=Z, where Z = CH(2), O, or S) and for the reverse beta-scission reactions have been investigated using high-level ab inito calculations. The results are rationalized with the aid of the curve-crossing model. The addition reactions proceed via early transition structures in all cases. The barriers for addition of methyl radical to C=C bonds are largely determined by the reaction exothermicities. Addition to the unsubstituted carbon center of C=C double bonds is favored over addition to the substituted carbon center, both kinetically (lower barriers) and thermodynamically (greater exothermicities). The barriers for addition to C=O bonds are influenced by both the reaction exothermicity and the singlet-triplet gap of the substrate. Addition to the carbon center is favored over addition to the oxygen, also both thermodynamically and kinetically. For the thiocarbonyl systems, addition to the carbon center is thermodynamically favored over addition to sulfur. However, in this case, the reaction is contrathermodynamic, addition to the sulfur center having a lower barrier due to spin density considerations. Entropic differences among corresponding addition and beta-scission reactions are relatively minor, and the differences in reaction rates are thus dominated by differences in the respective reaction barriers.     

反应类等键反应方法及类反应热动力学参数计算

本文提出了反应类等键反应方法,将通常用于热力学性质计算的等键反应方法推广用于类反应中反应势垒和反应焓变的计算. 对碳氢燃料低温燃烧反应机理中的一类重要反应类：?烷基自由基过氧化氢裂解生成烯烃和HO2自由基的反应势垒和反应焓变进行了计算. 通过对该类16个反应中的5个代表反应分别在不同计算水平HF、DFT、MP2、CCSD(T)的比较计算发现,采用等键反应方法可在较低从头算级别计算得到类反应较高精度的反应势垒,提高了计算的效率和精度. 本文采用反应类等键反应方法在B3LYP/6-311G(d,p)计算水平对该类16个反应进行了反应势垒和反应焓变的计算,并建立了反应势垒和反应能的线性自由能关系：delta V=71.02+0.41?delta E.     

Valence bond calculations of hydrogen transfer reactions: a general predictive pattern derived from theory

Hydrogen abstraction reactions of the type X(*) + H-H' --> X-H + H'(*) (X = F, Cl, Br, I) are studied by ab initio valence bond methods and the VB state correlation diagram (VBSCD) model. The reaction barriers and VB parameters of the VBSCD are computed by using the breathing orbital valence bond and valence bond configuration interaction methods. The combination of the VBSCD model and semiempirical VB theory leads to analytical expressions for the barriers and other VB quantities that match the ab initio VB calculations fairly well. The barriers are influenced by the endo- or exothermicity of the reaction, but the fundamental factor of the barrier is the average singlet-triplet gap of the bonds that are broken or formed in the reactions. Some further approximations lead to a simple formula that expresses the barrier for nonidentity and identity hydrogen abstraction reactions as a function of the bond strengths of reactants and products. The semiempirical expressions are shown to be useful not only for the model reactions that are studied in this work, but also for other nonidentity and identity hydrogen abstraction reactions that have been studied in previous articles.     

Base-catalyzed hydrogenation: rationalizing the effects of catalyst and substrate structures and solvation

Ab initio molecular orbital calculations have been used to study the base-catalyzed hydrogenation of carbonyl compounds. It is found that these hydrogenation reactions share many common features with S(N)2 reactions. Both types of reactions are described by double-well energy profiles, with deep wells and a low or negative overall energy barrier in the gas phase, while the solution-phase profiles show very shallow wells and much higher barriers. For the hydrogenation reactions, the assembly of the highly ordered transition structure is found to be a major limiting factor to the rate of reaction. In the gas phase, the overall barriers for reactions catalyzed by Group I methoxides increase steadily down the group, due to the decreasing charge density on the metal. On the other hand, for Group II and Group III metals, the overall barriers decrease down the group, which is attributed to the increasing ionic character of the metal-oxygen bond. The reaction with B(OCH(3))(3) has an exceptionally high barrier, which is attributed to pi-electron donation from the oxygen lone pairs of the methoxy groups to the formally vacant p orbital on B, as well as to the high covalent character of the B-O bonds. In solution, these reactivity trends are generally the opposite of the corresponding gas-phase trends. While similar barriers are obtained for reactions catalyzed by methoxides and by tert-butoxides, reactions with benzyloxides have somewhat higher barriers. Aromatic ketones are found to be more reactive than purely aliphatic ketones. Moreover, comparison between catalytic hydrogenation of 2,2,5,5-tetramethylcyclopentanone and pivalophenone shows that factors such as steric effects may also be important in differentiating their reactivity. Solvation studies with a wide range of solvents indicate a steady decrease in barrier with decreasing solvent dielectric constant, with nonpolar solvents generally leading to considerably lower barriers than polar solvents. In practice, a good balance between polarity and catalyst solubility is required in selecting the most suitable solvent for the base-catalyzed hydrogenation reaction.     

叔丁氧基自由基引发氢迁移过程的理论研究

采用多种密度泛函理论方法(如CAM-B3LYP, M062x和wB97x方法), 并辅以极化连续介质模型对叔丁氧基自由基(^tBuO·)与一系列胺类、 烷烃、 醇类和醚类反应物之间氢迁移反应的反应机理进行研究. 计算结果表明, 这类氢迁移反应主要受熵的控制. 通过对液相平动熵和气相平动熵得到的活化自由能数据进行对比, 可以看出, 使用气相平动熵得出的活化自由能明显偏高于实验测量值, 而以液相平动熵计算的反应活化自由能垒与实际结果相近, 3种方法对胺类和烷烃类反应物体系得出的结果更可靠, 对醇类和醚类反应物体系自由能垒则略低.     

Reactivity of alkanes on zeolites: a computational study of propane conversion reactions

In this work, quantum chemical methods were used to study propane conversion reactions on zeolites; these reactions included protolytic cracking, primary hydrogen exchange, secondary hydrogen exchange, and dehydrogenation reactions. The reactants, products, and transition-state structures were optimized at the B3LYP/6-31G level and the energies were calculated with CBS-QB3, a complete basis set composite energy method. The computed activation barriers were 62.1 and 62.6 kcal/mol for protolytic cracking through two different transition states, 30.4 kcal/mol for primary hydrogen exchange, 29.8 kcal/mol for secondary hydrogen exchange, and 76.7 kcal/mol for dehydrogenation reactions. The effects of basis set for the geometry optimization and zeolite acidity on the reaction barriers were also investigated. Adding extra polarization and diffuse functions for the geometry optimization did not affect the activation barriers obtained with the composite energy method. The largest difference in calculated activation barriers is within 1 kcal/mol. Reaction activation barriers do change as zeolite acidity changes, however. Linear relationships were found between activation barriers and zeolite deprotonation energies. Analytical expressions for each reaction were proposed so that accurate activation barriers can be obtained when using different zeolites as catalysts, as long as the deprotonation energies are first acquired.     

Proton exchange and transesterification reactions of acetate enolates with alcohols in the gas phase

Transesterification reactions and proton exchange reactions between acetate enolates and alcohols were studied both separately and together. Kinetic analysis shows that transesterification and proton exchange happen in a single collision event. The transesterification reaction is best viewed as an endothermic proton transfer, followed by an exchange of alkoxide and an exothermic proton transfer. Reaction barriers were modeled by Rice-Ramsperger-Kassel-Marcus theory and compared to quantum calculations. CBS-QB3 achieves good agreement whereas B3LYP and MP2 give slightly higher barriers. Quantum calculations also predict that the transition state for these transesterification reactions is the same as that for direct transesterification reactions between alkoxides and esters.     

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.