大基组在价键计算中的处理

编写了普适性的多键表自洽场程序，该程序能对单电子轨道展开系数和键表系数同时优化，其中单电子轨道的展开空间可任意定义，实际计算建议采用“杂化”轨道形式，即每个单电子轨道只对一个原子的基函数展开。对Ｈ２、Ｌｉ２及ＨＬｉ采用不同基组进行计算，结果表明用３个键表自洽计算所得能量与ＭＰ２结果相近，且我们的计算对键的共价性和离子性分析非常直观。     

过渡金属羰基簇合物的键价计算和分析

本文运用原子簇化合物键价计算公式 ,对过渡金属羰基簇合物成键情况进行了分析 ,利用金属键轨道数 ,价非键轨道数和金属配体成键轨道数计算簇合物价轨道总数 .计算结果表明 :簇合物价轨道总数与金属键轨道数成线性关系 ,BT=9N -Bn.对于一般簇合物其价轨道总数与Lauher的EHMO计算结果 ,与唐敖庆的结构拓扑规则一致 ,对于反常的高核簇合物其价轨道总数与按化学式计算的 1/ 2VE相吻合     

价键方法中的非活性轨道优化新算法

本文通过引进一组正交的辅助非活性轨道和与它正交的辅助活性轨道,将价键理论方法中的冻核近似推广到轨道非正交的情形,得到了体系能量及其对非活性轨道的梯度解析表达式,简化了价键自洽场方法中非正交轨道能量梯度的计算．该方法的标度为（Na＋1）m^4,其中Na和m分别是活性轨道和基函数的个数．分析表明,与现有的其他算法相比较,该方法具有更低的计算标度,因而计算效率更高．     

键长与价层轨道平均能的关系

关于键长的计算方法颇多。本文试从键长与原子价层轨道平均能的关系建立一个简单且更接近实验值的计算公式。我们知道,对于每个成键原子来说,一方面作为带电体使对方电子云发生变形;另一方面在对方的作用下,本身发生变形。如果成键原子吸引键合电子的能力相等,各自的电荷分布将很少变化,键长就等于成键     

价键理论的不变式方法的新算法

价键理论的不变式方法的新算法吴玮，莫亦荣，张乾二（厦门大学化学系，厦门，３６１００５）关键词价键理论，群论，不变式近年来，我们提出了闭壳层的价键（ＶＢ）计算的不变式（或称正行列式）方法［１，２］．将置换群ＳＮ对ＶＢ结构的对称子群Ｑ进行陪集分解。每一个...     

理论化学在中国的发展

本文回顾1949年以来,我国理论化学的发展历史.全文始于“荒漠渐成绿洲”的总体概括,进入主体全面的论述.按1978年划分为前、后两期.前期为学科的成长成熟期,以创业人及少数从业者的科教活动为中心,后期为学科的繁荣期,以本学科现阶段中青年精英创造佳绩、进入学科主流领域为中心.按时间进程将前后期最有代表性的10个方面研究成...     

有机化学教学中使用共振式描述超共轭效应的探索

有机化学教学中通常使用分子轨道理论和价键理论中的共振论来描述π轨道的共轭效应,而对于类似的σ轨道的超共轭效应,通常只用轨道理论来描述,而基本不采用价键理论中的共振式描述。尝试用共振式来描述σ键的超共轭效应,发现不仅能够获得清晰易懂的图像,还能将有机化学中多个跨章节的知识点联系在一起,有利于知识的融会贯通,以及对电子结构和共振论的深入理解。     

超价分子中的d轨道

通过对一些典型超价分子进行计算和分析,得出了超价分子"d轨道参与"(即外层d轨道杂化和d-pπ键概念)不尽合理的结论,并提出了能与实验事实相符的解释方法。此外,本文还阐述了计算化学中基组d函数与d轨道的关系:二者并不等价。     

碳原子价轨道电负性对化学键性能的影响

研究了同一类型化学键X―C的键能、键长和H―C键的酸性等性能与碳原子价轨道电负性的定量关系。结果表明,X―C键能随碳原子价轨道电负性增加而线性增大;H―C与C―C键的键长随碳原子价轨道电负性增加而线性减小;H―C的酸性随碳原子价轨道电负性增加而线性增大。因而,对结构类似的有机化合物,可以采用碳原子价轨道电负性对实验测定的化学键性能作图,判断其测定结果正确与否。     

量子力学和分子力学组合方法及其应用

QM/MM组合方法在研究凝聚态中的化学反应及生物大分子的结构和活性之间的关系等方面已取得重要进展。这一方法的要点在于将大体系配分成几部分,根据需要对不同部分进行不同级别的处理,因此既利用了量子力学的精确性,又利用了分子力学的高效性。对QM/MM组合理论及其一些最新进展作一简单介绍,并以最近进行了几个工作为例说明QM、MM组合方法的应用。     

Ab initio quantum mechanical charge field (QMCF) molecular dynamics: a QM/MM – MD procedure for accurate simulations of ions and complexes

A new formalism for quantum mechanical / molecular mechanical (QM/MM) dynamics of chemical species in solution has been developed, which does not require the construction of any other potential functions except those for solvent–solvent interactions, maintains all the advantages of large simulation boxes and ensures the accuracy of ab initio quantum mechanics for all forces acting in the chemically most relevant region. Interactions between solute and more distant solvent molecules are incorporated by a dynamically adjusted force field corresponding to the actual molecular configuration of the simulated system and charges derived from the electron distribution in the solvate. The new formalism has been tested with some examples of hydrated ions, for which accurate conventional ab initio QM/MM simulations have been previously performed, and the comparison shows equivalence and in some aspects superiority of the new method. As this simulation procedure does not require any tedious construction of two-and three-body interaction potentials inherent to conventional QM/MM approaches, it opens the straightforward access to ab initio molecular dynamics simulations of any kind of solutes, such as metal complexes and other composite species in solution.     

Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages

The newly implemented quantum‐chemical/molecular‐mechanical (QM/MM) functionality of the Groningen molecular simulation (GROMOS) software for (bio)molecular simulation is described. The implementation scheme is based on direct coupling of the GROMOS C++ software to executables of the quantum‐chemical program packages MNDO and TURBOMOLE, allowing for an independent further development of these packages. The new functions are validated for different test systems using program and model testing techniques. The effect of truncating the QM/MM electrostatic interactions at various QM/MM cutoff radii is discussed and the application of semiempirical versus density‐functional Hamiltonians for a solute molecule in aqueous solution is compared. © 2012 Wiley Periodicals, Inc.     

Calculation of wave‐functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation

The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009 , 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self‐consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree–Fock–Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self‐consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave‐function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. © 2013 Wiley Periodicals, Inc.     

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules

A robust approach for dealing with electrostatic interactions for spherical boundary conditions has been implemented in the QM/MM framework. The development was based on the generalized solvent boundary potential (GSBP) method proposed by Im et al. [J. Chem. Phys. 114, 2924 (2001)], and the specific implementation was applied to the self-consistent-charge density-functional tight-binding approach as the quantum mechanics (QM) level, although extension to other QM methods is straightforward. Compared to the popular stochastic boundary-condition scheme, the new protocol offers a balanced treatment between quantum mechanics/molecular mechanics (QM/MM) and MM/MM interactions; it also includes the effect of the bulk solvent and macromolecule atoms outside of the microscopic region at the Poisson-Boltzmann level. The new method was illustrated with application to the enzyme human carbonic anhydrase II and compared to stochastic boundary-condition simulations using different electrostatic treatments. The GSBP-based QM/MM simulations were most consistent with available experimental data, while conventional stochastic boundary simulations yielded various artifacts depending on different electrostatic models. The results highlight the importance of carefully treating electrostatics in QM/MM simulations of biomolecules and suggest that the commonly used truncation schemes should be avoided in QM/MM simulations, especially in simulations that involve extensive conformational samplings. The development of the GSBP-based QM/MM protocol has opened up the exciting possibility of studying chemical events in very complex biomolecular systems in a multiscale framework.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.