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。     

化学反应过渡态的结构和动力学

化学反应过渡态决定了包括反应速率和微观反应动力学在内的化学反应的基本特性,而无论是从理论还是实验上研究和观测化学反应过渡态都是极具挑战性的课题.近年来,我国科学家们利用交叉分子束-里德堡氢原子飞行时间谱仪,结合高精度的量子动力学计算,对H＋H2和F＋H2这两个教科书式的典型反应体系进行了全量子态分辨的反应动力学研究,从中得出了关于这两个反应体系的过渡态的结构和动力学性质的结论性的研究成果.     

CH2ClO与NO反应机理的理论研究

采用B3LYP,MP2方法在6-31 (d,p)和6-311 G(d,p)水平研究了CH2ClO自由基与NO反应的微观机理,找到了三个可能的反应通道.并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.成功地解释了Wu等的实验结论.从电子密度拓扑分析的角度,讨论了化学反应过程中化学键的变化规律,为实验研究大气化学反应提供理论依据.找到了该反应的结构过渡态(结构过渡区)和能量过渡态,发现了反应热与结构过渡区之间的关系.     

CH2ClO与NO反应机理的理论研究

采用B3LYP, MP2方法在6-31＋(d,p)和6-311＋＋G(d,p)水平研究了CH₂ClO自由基与NO反应的微观机理, 找到了三个可能的反应通道. 并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. 成功地解释了Wu等的实验结论. 从电子密度拓扑分析的角度, 讨论了化学反应过程中化学键的变化规律, 为实验研究大气化学反应提供理论依据. 找到了该反应的结构过渡态(结构过渡区)和能量过渡态, 发现了反应热与结构过渡区之间的关系.     

化学反应散射共振态的实验检测与理论模拟

化学反应中的散射共振态（或称反应性共振）控制着化学反应的分支比、产物的态分布及空间分布等。反应性共振的实验检测分为间接法和直接法。从理论上,一是构造反应体系的势能面,从势能面过渡态的结构来研究散射共振态;二是计算态-态反应动力学,尤其是用寿命矩阵来研究散射共振态。本文介绍反应性散射共振态的实验检测及理论模拟方法,并对今后的发展动向作出展望。     

乙醇分子内及分子间脱水反应机理的计算化学实验研究

介绍了一个面向大三下或大四上本科生的计算化学探索性实验。通过研究乙醇分子内及分子间脱水反应机理,从分子水平理解醇脱水反应过程中酸催化剂的作用机制和反应的能量路径。通过本实验,使学生初步掌握量子化学计算通用软件高斯(Gaussian)的使用方法,掌握结构优化、频率计算、过渡态搜索等基本计算操作,并学会采用量子化学计算手段来研究化学反应的基本过程,为将来科研工作打下重要基础。     

化学反应的价键理论研究

根据价键波函数的对称性及基态、激发态化学键与键表的对应 ,可以把轨道对称守恒原理和键对称规律表述成“价键结构对称性匹配” .价键结构对称规则通过对反应物和产物的价键结构进行对称性分析 ,可以直接预测化学反应活性 ,无需依赖理论计算结果 .在价键结构对称性分析的基础上 ,应用多VB结构计算方法 ,建立了反应H HLi→H2 Li和H LiH→HLiH(cyclic)→HLi H的曲线交叉VB图 ,讨论了能垒及过渡态的形成机制 .计算结果表明 ,H原子交换反应H LiH HLi H是一个两步过程 .     

化学反应速率的过渡态理论

由海森堡运动方程证明了过渡态几率稳定定理.假设化学反应均经过过渡态,由此定理推导了化学反应的微观速率常数.再假设反应的始志处于热平衡,由微观速率常数推导了宏观速率常数.     

一种确定反应中间态几何特征和能量的综合性方法

通过综合使用传统的过渡态优化算法、数学统计工具以及人工神经网络算法(ANN)找到一种不依赖于反应物起始构象而得到化学反应中过渡态结构和能量的方法. 在两个反应物互相接近的过程中, 每一步的几何构象都对应着一个系统能量值. 本研究的目的是尽可能地收集处在反应能量面上的这种能量点值. 通过采用几何参数作为自变量对势能面进行模拟研究, 得到了势能面上对应过渡态结构的一阶鞍点. 采用乙醛负离子和甲醛作为反应物, 对经典的醛醇缩合反应中的亲核进攻步骤进行了研究. 对内禀反应坐标(IRC)路径的计算是从反应物的三组不同起始构象出发, 最终获得了反应势能面上的96个点. 本研究中的势能面采用人工神经网络算法进行模拟研究, 并利用交叉验证方法评估得到的结果, 避免了采用人工神经网络算法时过度拟合情况的发生.     

CH2XH→CH3X (X＝O, S, Se)异构化的量子拓扑研究

利用从头算和量子拓扑方法讨论了CH₂XH→CH₃X (X＝O, S, Se)异构化过程的反应机理. 着重从电子密度拓扑分析计算了反应进程中的各点, 讨论了反应进程中键的断裂和生成, 上述反应都经历了三元环过渡结构, 找到了这类反应的"能量过渡态"和"结构过渡态", 且结构过渡态均在能量过渡态之后出现. 三元结构过渡态结构出现的范围与反应热成正比.     

Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.     

Efficient methods for finding transition states in chemical reactions: comparison of improved dimer method and partitioned rational function optimization method

A combination of interpolation methods and local saddle-point search algorithms is probably the most efficient way of finding transition states in chemical reactions. Interpolation methods such as the growing-string method and the nudged-elastic band are able to find an approximation to the minimum-energy pathway and thereby provide a good initial guess for a transition state and imaginary mode connecting both reactant and product states. Since interpolation methods employ usually just a small number of configurations and converge slowly close to the minimum-energy pathway, local methods such as partitioned rational function optimization methods using either exact or approximate Hessians or minimum-mode-following methods such as the dimer or the Lanczos method have to be used to converge to the transition state. A modification to the original dimer method proposed by [Henkelman and Jonnson J. Chem. Phys. 111, 7010 (1999)] is presented, reducing the number of gradient calculations per cycle from six to four gradients or three gradients and one energy, and significantly improves the overall performance of the algorithm on quantum-chemical potential-energy surfaces, where forces are subject to numerical noise. A comparison is made between the dimer methods and the well-established partitioned rational function optimization methods for finding transition states after the use of interpolation methods. Results for 24 different small- to medium-sized chemical reactions covering a wide range of structural types demonstrate that the improved dimer method is an efficient alternative saddle-point search algorithm on medium-sized to large systems and is often even able to find transition states when partitioned rational function optimization methods fail to converge.     

Using bonding to guide transition state optimization

Optimization of a transition state typically requires both a good initial guess of the molecular structure and one or more computationally demanding Hessian calculations to converge reliably. Often, the transition state being optimized corresponds to the barrier in a chemical reaction where bonds are being broken and formed. Utilizing the geometries and bonding information for reactants and products, an algorithm is outlined to reliably interpolate an initial guess for the transition state geometry. Additionally, the change in bonding is also used to increase the reliability of transition state optimizations that utilize approximate and updated Hessian information. These methods are described and compared against standard transition state optimization methods. © 2015 Wiley Periodicals, Inc.     

几种过渡态结构的有效优化方法

通过双桥反应机理、电环合反应和催化反应三个不同类型的过渡态优化，说明当标准方法难以给出结果时，对物理问题本身的分析有助于给出过渡态优化的线索．第一个例子根据化学问题给出限制条件，通过平衡几何构型优化方法优化得到过渡态；第二个例子是在使用标准过渡态优化方法失败后，根据物理问题从反应途径上用平衡几何构型优化方法选择过渡态优化的初始结构；第三个例子通过Gaussian 98程序中的标准方法QST2直接得到过渡态．     

Broadened glass transition in a liquid-crystalline polymer studied by thermally stimulated currents,AC dielectric,dynamic mechanical,and DSC methods

Thermally stimulated currents (TSC), a. c. dielectric, dynamic mechanical (DMTA), and differential scanning calorimetry (DSC) methods were used to study the glass transition in a thermotropic liquid-crystalline copolyester. All the techniques were consistent in the determination of the main glass transition temperature. Using the high sensitivity of the TSC thermal sampling method, it was shown that cooperative glass transition-like relax-ations occur down to 100°C below the main glass transition. DSC was sensitive only to a broadening of the glass transition to about ca. 30°C, so it was concluded that the thermal sampling method is sensing a very small fraction of cooperatively relaxing species which cannot be detected by DSC. Ac dielectric measurements and DMTA also indicated that the glass transition was broad, but difficulties with overlapping transitions prevented quantitative determination of the breadth of the glass transition. The results suggest that the broad glass transition, in this mostly amorphous LCP, is due to chemical heterogeneity of the copolyester chain. Other evidence indicates that the broadening is not due to the oriented nature of the glassy state. Some discussion is presented concerning how the heterogeneous nature of the LCP glass leads to compensation of the Arrhenius curves obtained by the thermal sampling method. © 1993 John Wiley & Sons, Inc.     

Quantum-chemical analysis of the thermodynamic isotope effect in quasi-one-dimensional H-bonded Pb(H/D)PO<Subscript>4</Subscript> ferroelectrics

The thermodynamics of the structural phase transition of H-bonded ferroelectric materials, Pb(H/D)PO₄, were considered in terms of the pseudo-spin Ising model with inclusion of tunneling and longrange effects. The pseudo-spin Hamiltonian parameters needed for analysis of the transition were determined by a procedure based on an independent quantum chemical method. A simplified scheme for the selection of model clusters was proposed, which allows the application of various quantum chemical methods, including high-level methods (CCSD/6-311+G** and so on), in the calculations of double-well potential profiles and Slater parameters. The calculation results were discussed in terms of two statistic models: molecular field approximation (MFA) and Bethe cluster method (BCM). The theoretical estimates of critical transition temperature for both systems are discussed and it is shown that the (semi)quantitative reproduction of experimental data is possible only in terms of BCM taking into account the tunneling effects. The explanation is given for the observed isotope effect caused by very pronounced increase in the critical transition temperature upon deuteration (ΔT_с ≈ 140 K). The crucial role belongs to the difference between tunneling effects in the ferroelectric crystals in question. It is emphasized that the observed differences between the crystal lattice and H/D bond geometries, including the mutual orientation of the bonds, must be accurately included in the calculations.     

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.     

Multicoordinate driven method for approximating enzymatic reaction paths: automatic definition of the reaction coordinate using a subset of chemical coordinates

We present a generalization of the reaction coordinate driven method to find reaction paths and transition states for complicated chemical processes, especially enzymatic reactions. The method is based on the definition of a subset of chemical coordinates; it is simple, robust, and suitable to calculate one or more alternative pathways, intermediate minima, and transition-state geometries. Though the results are approximate and the computational cost is relatively high, the method works for large systems, where others often fail. It also works when a certain reaction path competes with others having a lower energy barrier. Accordingly, the procedure is appropriate to test hypothetical reaction mechanisms for complicated systems and provides good initial guesses for more accurate methods. We present tests on a number of simple reactions and on several complicated chemical transformations and compare the results with those obtained by other methods. Calculation of the reaction path for the enzymatic hydrolysis of the substrate by dUTPase for an active-site model with 85 atoms, including several loosely bound water molecules, indicates that the method is feasible for the study of enzyme mechanisms.     

Water: From Clusters to the Bulk

Water is of fundamental importance for human life and plays an important role in many biological and chemical systems. Although water is the most abundant compound on earth, it is definitely not a simple liquid. It possesses strongly polar hydrogen bonds which are responsible for a striking set of anomalous physical and chemical properties. For more than a century the combined importance and peculiarity of water inspired scientists to construct conceptual models, which in themselves reproduce the observed behavior of the liquid. The exploration of structural and binding properties of small water complexes provides a key for understanding bulk water in its liquid and solid phase and for understanding solvation phenomena. Modern ab initio quantum chemistry methods and high-resolution spectroscopy methods have been extremely successful in describing such structures. Cluster models for liquid water try to mimic the transition from these clusters to bulk water. The important question is: What cluster properties are required to describe liquid-phase behavior?     

Effect of conformational rigidity on the glass transition and initial decomposition temperatures of polyimides

The dependence of the glass transition and initial decomposition temperatures of polyperyleneimide and polynaphthylimide on the conformational rigidity was studied by the Monte Carlo, Kuhn segment, and quantum chemical AM1 methods. The corresponding linear plots can be used for estimation of the glass transition and initial decomposition temperatures when experimental determination is difficult.