半经验分子轨道法的电子密度拓扑分析（Ⅱ）

化学反应过程中的过渡态结构及氢键的拓扑性质,是近年来刚刚涉及的课题,本文讨论了文献[1]的方法对偏离平衡构型的过渡态结构及超分子体系的可用性问题及对计算精度较敏感的电子密度拉普拉斯量的拓扑特性。     

CH3SH与CN·自由基的反应机理及电子密度拓扑分析

在B3LYP/6-311＋＋G（d,p）水平上研究了CH3SH与CN·自由基的反应机理.找到了三个可能的反应通道,得到了各反应通道的反应物、中间体、过渡态和产物的优化构型、谐振频率.通过内禀反应坐标（IRC）跟踪确认了稳定点与过渡态的连接关系.在CCSD/6-311＋＋G（d,p）水平上进行能量校正,成功地解释了Brian等的实验结论.通过对反应进程中一些重要点的电子密度拓扑分析,讨论了反应进程中化学键的变化规律,发现了六元环状过渡结构.     

BrO与CH3SH反应机理的量子化学及拓扑研究

利用密度泛函和电子密度拓扑分析方法对BrO与CH₃SH反应的微观机理进行了理论研究. 在B3LYP/6-311G (d, p)水平上对反应势能面上的各驻点进行几何构型的全优化; 振动分析和IRC计算证实了中间体和过渡态的真实性和相互连接关系; 计算得到了各反应通道的活化能, 并进行了零点能校正. 计算结果表明: 该反应存在7个反应通道, 其中生成CH₃S＋HOBr和CH₃SO＋HBr的通道为主要反应通道. 通过对反应过程中部分驻点的电子密度拓扑分析, 首次发现了接近平面的四元环状过渡态, 从而拓展了原来对环状结构过渡态定义的适用范围.     

BrO与CH3SH反应机理的量子化学及拓扑研究

利用密度泛函和电子密度拓扑分析方法对BrO与CH₃SH反应的微观机理进行了理论研究. 在B3LYP/6-311G (d, p)水平上对反应势能面上的各驻点进行几何构型的全优化; 振动分析和IRC计算证实了中间体和过渡态的真实性和相互连接关系; 计算得到了各反应通道的活化能, 并进行了零点能校正. 计算结果表明: 该反应存在7个反应通道, 其中生成CH₃S＋HOBr和CH₃SO＋HBr的通道为主要反应通道. 通过对反应过程中部分驻点的电子密度拓扑分析, 首次发现了接近平面的四元环状过渡态, 从而拓展了原来对环状结构过渡态定义的适用范围.     

CH3SH与CN·自由基的反应机理及电子密度拓扑分析

在B3LYP/6-311++G(d,p)水平上研究了CH3SH与CN·自由基的反应机理.找到了三个可能的反应通道.得到了各反应通道的反应物、中间体、过渡态和产物的优化构型、谐振频率.通过内禀反应坐标(IRC)跟踪确认了稳定点与过渡态的连接关系.在CCSD/6-311++G(d,p)水平上进行能量校正,成功地解释了Brian等的实验结论.通过对反应进程中一些重要点的电子密度拓扑分析,讨论了反应进程中化学键的变化规律,发现了六元环状过渡结构.     

CH3SH与CN·自由基的反应机理及电子密度拓扑分析

在B3LYP/6-311++G(d,p)水平上研究了CH3SH与CN·自由基的反应机理. 找到了三个可能的反应通道, 得到了各反应通道的反应物、中间体、过渡态和产物的优化构型、谐振频率. 通过内禀反应坐标(IRC)跟踪确认了稳定点与过渡态的连接关系. 在CCSD/6-311++G(d,p)水平上进行能量校正, 成功地解释了Brian等的实验结论. 通过对反应进程中一些重要点的电子密度拓扑分析, 讨论了反应进程中化学键的变化规律, 发现了六元环状过渡结构.     

电子定域函数(ELF)理论方法简介——一种描述化学键的新模型

电子定域函数理论可以清晰和定量化描述理论化学研究的基本对象——化学键,已在原子、分子及固体体系中得到广泛应用。本文系统介绍了电子定域函数(ELF)理论方法的基本物理思想;对ELF函数的一些特点如数值稳定性、ELF与分子中的原子理论(AIM理论)方法的异同及ELF的拓扑分析进行了说明;对电子定域函数在研究原子壳层结构、化学键的性质、孤对电子的位置、反应过程化学键的断裂和生成等方面的应用进行了介绍。     

CH3SH与H2O2气相反应机理的理论研究

采用密度泛函理论的B3LYP方法, 在6-311＋G(d,p)基组水平上研究了CH₃SH与H₂O₂的微观反应机理, 全参数优化了反应势能面上各驻点的几何构型, 振动分析和内禀反应坐标(IRC)分析结果证实了中间体和过渡态的真实性, 计算所得的键鞍点电荷密度的变化情况也确认了反应过程. 结果表明, 反应共分三大步进行, 包含两条反应通道, 第二步由IM1到CH₃SO₂H的反应为决速步骤, 其中的第一条通道是主要反应通道, 相应活化能为157.3和109.7 kJ/mol.     

吡咯与HX(X=F,Cl,Br)分子间多种氢键的电子密度拓扑研究

采用密度泛函B3LYP/6-311＋＋G(d,p)方法, 对吡咯与HX (X＝F, Cl, Br)形成的经典氢键和π型氢键, 从其几何参数、电子密度的拓扑性质和电子积分等方面进行了研究. 在对π型氢键的讨论中我们将π电子与σ电子分离, 得到了π型氢键体系的π电子的密度等值线和拉普拉斯量等值线图以及各原子的π电子积分, 形象地说明了π型氢键的作用本质.     

Coordination of methanol clusters to benzene: a computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1,S2,S3和S4).其中,在复合物S1和S3中,HOCl单体的5H原子作为质子供体,与HCOCl单体中作为质子受体的10原子相互作用,形成红移氢键复合物;在复合物S4中,HOCl单体的7Cl原子作为质子供体,与HCOCl单体中作为质子受体的IO原子相互作用,形成红移卤键复合物;而在复合物S2中,同时存在2C-3H…6O蓝移氢键和4Cl…5O相互作用.在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正,其值在-5.05与-14.76 kJ·mol-1之间.采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems

Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superpusition error (BSSE) and CP-uncorrected (normal) gradient opfimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople‘s standard 6-31G(d), 6-31G(d,p) and 6-311 G(d,p) basis sets in order to assess the importance of CP-corrected gradient optimiTation in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1, S2, S3和S4). 其中, 在复合物S1和S3中, HOCl单体的5H原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移氢键复合物; 在复合物S4中, HOCl单体的7Cl原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移卤键复合物; 而在复合物S2中, 同时存在2C—3H…6O蓝移氢键和4Cl…5O相互作用. 在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-5.05与-14.76 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Structures and Electronic Properties of HOCl···HCOCl Complexes

B3LYP/6-311++G** and MP2/6-311++G** calculations were used to analyze the interaction between hypochlorous acid (HOCl) and formyl chloride (HCOCl). The results showed that there were four equilibrium geometries (S1, S2, S3, and S4) optimized at B3LYP/6-311++G** level, and all the equilibrium geometries were confirmed to be in stable states by analytical frequency calculations. Complexes S1 and S3 use the 5H atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift hydrogen bond systems. However, the blue-shifted hydrogen bond (2C-3H···6O) coexists with 4Cl···5O interaction in structures S2. As for S4, it uses the 7Cl atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift halogen bond system. Interaction energies between monomers in the four complexes corrected with basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE) lie in the range from −5.05 to −14.76 kJ·mol⁻¹ at MP2/6-311++G** level. The natural bond orbital (NBO) and atoms in molecules (AIM) theories have also been applied to explain the structures and the properties of the complexes.     

Estimation on the intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies in glycine and alanine peptides

Computation of accurate intramolecular hydrogen-bonding energies for peptides is of great importance in understanding the conformational stabilities of peptides and developing a more accurate force field for proteins. We have proposed a method to determine the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies in glycine and alanine peptides. In this article, the method is further applied to evaluate the intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies in peptides. The optimal structures of the intramolecular 10-membered ring N-H...O=C hydrogen bonds in glycine and alanine tripetide molecules are obtained at the MP2 level with 6-31G(d), 6-31G(d,p), and 6-31+G(d,p) basis sets. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are then evaluated based on our method at the MP2/6-311++G(3df,2p) level with basis set superposition error correction. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are calculated to be in the range of -6.84 to -7.66, -4.44 to -4.98, and -6.95 to -7.88 kcal/mol. The method is also applied to estimate the individual intermolecular hydrogen-bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, formamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen-bonding energies in the four dimers are calculated to be -1.77, -1.67, -6.35, and -4.82 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -6.23, and -4.93 kcal/mol predicted by the supermolecular method.     

甲醛与甲酰胺相互作用的从头算研究

The optimizations geometries and vibrational frequencies of H2CO,HCONH2 and acquired 3 complexes between H2CO?HCONH2 have been calculated by using the ab initio method at the MP2/6-31G（ d）and MP2 （FC）/6-311++G（d,p）level. The non-minimum structures with negative vibrational frequencies are excluded. The lowest energy conformer of these complexes is a cyclic structure with N - H?O and C - H?O hydrogen bonds in a common plane. No significant changes are observed in the geometries of the monomers in their complexed state. The most characteristic geometrical properties of the complex are the lengthening of the contacting N-H bonds by 0.4-1.1 pm,and the general shortening of the contacting C-H bonds by 0.3-0.4 pm with respect to the monomers. The interaction energies of complexes have been corrected by the basis set superposition error （BSSE）using the full Boys-Bernardi counterpoise correction scheme. The corrected complex interaction energies of 3 structures at MP2/6-311++G（2df,3p）/ / MP2（FC）/6-311++G（d,p）level are -29.94, -16.10 and -18.45 kJ/mol,respectively. The interaction energies indicate that C - H?O is a weak hydrogen bond. The results of natural bond orbital population analysis reveals that there is only a small charge-transfer in the process of forming the complexes. The results of natural bond orbital analysis and atom in the molecule scheme appear quite significant in view of their importance for understanding the mechanisms of intermolecular interaction leading to hydrogen bonding. The results of molecular interaction energy decomposition analysis show that the electrostatic interaction plays an essential role in stabilizing the H2CO?HCONH2 complexes.     

H2CO与双卤分子间卤键的电子密度分析

运用B3LYP和MP2方法在6-311++G(d,p)基组水平上, 对H2CO-XY(XY=F2、Cl2、Br2、ClF、BrF、BrCl)卤键体系进行构型全优化, 得到了O…X—Y型卤键复合物. 结果表明, MP2/6-311++G(d,p)计算结果与实验值较吻合. 并在MP2水平下计算了分子间的相互作用能, 用完全均衡校正CP(counterpoise procedure)方法对基函数重叠误差(BSSE)进行了校正. 利用电子密度拓扑分析方法对卤键复合物的电子密度拓扑性质进行了分析研究.