密度泛函活性理论中的Rényi熵, Tsallis熵和Onicescu信息能

根据密度泛函理论,分子的电子密度确定了该体系基态下的所有性质,其中包括结构和反应活性.如何运用电子密度泛函有效地预测分子反应活性仍然是一个有待解决的难题.密度泛函活性理论(DFRT)倾力打造这样一个理论和概念架构,使得运用电子密度以及相关变量准确地预测分子的反应特性成为可能.信息理论方法的香农熵和费舍尔信息就是这样的密度泛函,研究表明,它们均可作为反应活性的有效描述符.本文将在DFRT框架中介绍和引进三个密切相关的描述符, Rényi熵、Tsallis熵和Onicescu信息能.我们准确地计算了它们在一些中性原子和分子中的数值并讨论了它们随电子数量和电子总能量的变化规律.此外,以第二阶Onicescu信息能为例,在分子和分子中的原子两个层面上,系统地考察了其随乙烷二面角旋转的变化模式.这些新慨念的引入将为我们深入洞察和预测分子的结构和反应活性提供额外的描述工具.     

密度泛函活性理论中的信息论方法

密度泛函活性理论(DFRT)运用简单的密度泛函探讨和定量化分子的反应活性,是近来发展起来的一个关于分子活性理论的新方法。在新近的文献中,这样的简单密度泛函的例子包括香农熵,费舍尔信息以及其它来自信息论中的密度泛函。本文综述了DFRT信息论方法的原理,包括物理信息极小原理、最小信息增益原理和信息守恒原理。总结了DFRT信息论方法在电子密度、形态密度和分子中的原子三种表述下的理论框架。此外,还介绍了运用信息论方法在定量描述空间位阻效应、亲电性、亲核性和区域选择性中的突出应用,以及对亲电芳香取代反应的邻对间位取代效应的起源和本质提供的一个全新诠释。最后简要地展望了该领域的几个可能的未来发展方向。     

密度泛函活性理论中的信息论方法（英文）

密度泛函活性理论(DFRT)运用简单的密度泛函探讨和定量化分子的反应活性,是近来发展起来的一个关于分子活性理论的新方法。在新近的文献中,这样的简单密度泛函的例子包括香农熵,费舍尔信息以及其它来自信息论中的密度泛函。本文综述了DFRT信息论方法的原理,包括物理信息极小原理、最小信息增益原理和信息守恒原理。总结了DFRT信息论方法在电子密度、形态密度和分子中的原子三种表述下的理论框架。此外,还介绍了运用信息论方法在定量描述空间位阻效应、亲电性、亲核性和区域选择性中的突出应用,以及对亲电芳香取代反应的邻对间位取代效应的起源和本质提供的一个全新诠释。最后简要地展望了该领域的几个可能的未来发展方向。     

双光子吸收材料的分子设计研究

介绍了双光子吸收材料分子设计原理.为了设计有大的双光子吸收响应的材料,对多种分子进行了系统的理论研究.用量子化学密度泛函理论和AM1方法进行分子几何构型优化.在优化结构的基础上,用ZINDO和自编程序求得分子的单、双光子吸收性质.设计了一些未知化合物,以期为合成新的具有大的双光子吸收截面的材料提供理论根据.以双层二聚二甲苯邻甲酸衍生物、铂乙炔化物、卟啉衍生物、C60、C70、八极矩分子为例,报道了我们在这方面的研究结果.     

取代苯甲酸羧基上H和O原子的部分电荷与Hammett常数之间的线性关系

采用密度泛函分析了取代苯甲酸中羧基上的H1原子和2个氧原子O2和O3的电荷与取代基的Hammett常数之间的线性关系. 比较了不同密度泛函和电荷计算方法B3LYP/6-311G*/(NBO, Mulliken), (BLYP, BP, PWC)/DNP/(Hirshfeld, Mulliken)对上述线性相关系数的影响. 结果表明, BLYP/DNP/Hirshfeld方法的计算精度高且计算速度快. 使用BLYP/DNP/Hirshfeld方法计算了70个取代苯甲酸的部分电荷, 发现H1, O2和O3原子的电荷与取代基Hammett常数σ_p和σ_m之间的线性相关系数可达到0.98以上, 其中O2的电荷和Hammett常数的线性相关性最好. O2的电荷值可以作为Hammett常数的替代, 用于结构性能定量分析, 也可以用于预测取代基的Hammett常数.     

Gaussview在化学教学中的一些应用

Gaussian量子化学计算程序包是美国Gaussian公司开发的一个功能强大的量子化学综合软件包。可执行各类不同精度的分子轨道计算(包括Hartree-Fock水平从头算(HF)、Post-HF从头算、密度泛函理论(DFT)以及多种半经验量子化学方法),进行分子和化学反应性质的理论预测。目前已成为国     

1,3-二氮杂薁类衍生物电子结构和光谱性质的理论研究

对1,3-二氮杂薁类衍生物采用密度泛函理论(DFT)在B3LYP/6-31G(d)的水平上进行了几何构型的全优化, 在此基础上探讨了分子结构和前线分子轨道能量等性质的变化规律, 采用含时密度泛函理论(TD-DFT)计算了分子的电子跃迁性质, 采用二维平面图和三维立体图来直观表示激发态的性质, 研究分子内电子转移特性. 跃迁密度矩阵的二维等高线图反映了电子-空穴相干性, 三维跃迁密度图反映了跃迁偶极矩的方向和强度, 三维电荷差异密度图说明了激发过程中分子内电子转移性质.     

基于两分子和三分子相互作用的流体界面张力研究

提出了一个改进的密度泛函理论模型.该模型同时考虑了流体中两分子和三分子相互作用对体系Helm hlotz自由能的贡献,对Ar,N2,CH4,CO2等四种流体的气液界面张力进行了预测,结果与实验值均吻合良好.通过与仅考虑两分子作用的理论计算值和分子模拟值进行比较,表明流体中的三分子相互作用对描述非均相流体的结构与性质有重要影响.     

扩展苯基衍生物分子器件的电子输运的理论研究

通过结合杂化密度泛函和前线轨道理论与弹性散射格林函数方法研究了三种苯基衍生物分子器件的电子输运性质. 基于杂化密度泛函方法计算扩展分子电子结构的基础上, 计算了苯基衍生物三分子结的输运性质. 计算结果表明, 在低偏压下, 电流与电压呈线性变化; 分子结的电阻的对数与苯环的数目呈线性增加关系.     

有机杂环分子的双光子吸收特性

利用少态模型和密度泛函理论计算了新近合成的三个具有有机杂环结构的苯并噻唑衍生物的非线性光学性质. 计算结果表明，随着有机分子的分子电子离域结构的增大，最大吸收峰红移.当共轭链较长时，共轭链的增长对增强分子双光子吸收截面的影响远大于吸电子基强度变化的影响.该类分子具有较好的双光子吸收特性.最后给出了三个分子的电荷转移过程.     

Modeling molecular acidity with electronic properties and Hammett constants for substituted benzoic acids

Molecular acidity is an important physiochemical property essential in many fields of molecular studies, but an efficient and reliable computational approach to make accurate predictions is still missing. In this work, based on our previous studies to use gas phase electronic properties such as molecular electrostatic potential and valence natural atomic orbitals of the acidic atom and leaving proton, we demonstrate here that different approaches can be employed to tackle this problem. To that end, we employ 196 singly, doubly, and triply substituted benzoic acids for the study. We show that two different approaches are possible, one focusing on the carboxyl group through its localized electronic properties and the other on the substituting groups via Hammett constants and their additivity rule. Our present results clearly exhibit that with the linear models built from the singly substituted species, one can accurately predict the pK(a) values for the doubly and triply substituted species with both of these two approaches. The predictions from these approaches are consistent with each other and agree well with the experimental data. These intrinsically different approaches are the two manifestations of the same molecular acidity property, both valid and complementary to each other.     

Correlations and predictions of carboxylic acid pKa values using intermolecular structure and properties of hydrogen-bonded complexes

Density functional theory calculations have been preformed on a series of hydrogen-bonded complexes of substituted aliphatic and aromatic carboxylic acids with ammonia. Molecular properties, particularly those related to hydrogen bonding, have been carefully examined for their interdependence as well as dependence on the acidity of the acid. The bond length and stretching frequency of the hydroxyl group and the hydrogen-bond length and energy of the complex are shown to be highly correlated with each other and are linearly correlated with available literature pKa values of the carboxylic acids. The linear correlations resulting from the fit to the available pKa values can be used to predict the pKa values of similar carboxylic acids. The pKa values so predicted using the different molecular properties are highly consistent and in good agreement with the literature values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations. This approach is unique in its capability to determine the acidity of a particular functional group or the local acidity within a large molecular system such as a protein.     

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge

In this work we have developed a hybrid QM and MM approach to predict pKa of small drug-like molecules in explicit solvent. The gas phase free energy of deprotonation is calculated using the M06-2X density functional theory level with Pople basis sets. The solvation free energy difference of the acid and its conjugate base is calculated at MD level using thermodynamic integration. We applied this method to the 24 drug-like molecules in the SAMPL6 blind pKa prediction challenge. We achieved an overall RMSE of 2.4 pKa units in our prediction. Our results show that further optimization of the protocol needs to be done before this method can be used as an alternative approach to the well established approaches of a full quantum level or empirical pKa prediction methods.     

二苯二硫和二苄二硫润滑性能的量子化学研究

The molecular geometries optimization and electronic structures of diphenyl disulfide (DPDS) and dibenzyl disulfide (DBDS) compounds were investigated by density functional theory (DFT) and ab initio method at the 6-31G basis set level. The active atoms and bonds of reaction were provided by frontier molecular orbital theory. The molecular orbital parameters of DPDS and DBDS compounds and iron atom cluster were calculated by using density functional theory. The interaction pattern between the organic disulfide compounds and iron atom cluster was discussed based on the approximate rule of orbital energy. Some parameters characterizing the action strength between the organic disulfide compounds and iron atom cluster, including the bonding strength, reactive strength and static action strength, were analyzed by using frontier electron density, super de-localizability, net atomic charge and the interaction energy of chemical adsorption as criteria. The results indicate that S-S chemical bond and C-S chemical bond of the compounds are inclined to be broken when DPDS and DBDS interact with the metal. The anti wear ability order of DPDS and DBDS compounds is DPDS>DBDS, and the extreme pressure ability order of DPDS and DBDS compounds is DBDS>DPDS, and the prediction results based on quantum chemistry calculations are in good accordance with the friction and wear test results.     

Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers

Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low latency such that unprecedented scaling is achieved. As a benchmark, a system of 32 water molecules, a common system size employed in the study of the aqueous solvation and chemistry of small molecules, is shown to scale on more than 1500 processors, which is impossible to achieve using standard approaches. This degree of parallel scaling is expected to open new opportunities for scientific inquiry.