醇及脱氧核糖与水分子间三体作用强度的快速准确计算

快速准确预测醇及脱氧核糖分子与水形成的氢键复合物的三体作用强度, 对准确模拟水环境下蛋白质和DNA的结构和功能至关重要. 基于对多体极化作用的理解, 在可极化偶极-偶极作用模型(PBFF)基础上, 将体系中的极性化学键视为化学键偶极, 通过模拟键偶极的极化计算了醇及脱氧核糖与水分子形成的氢键复合物的三体作用能. 通过拟合甲醇与水氢键复合物的三体作用能随分子间距离变化的能量曲线确定了所需的参数. 将模型和所确定的参数应用于计算更多的甲醇、 乙醇及脱氧核糖与水氢键复合物的三体作用能, 检验了模型的准确性和参数的可转移性. 计算结果表明, 可极化偶极-偶极作用模型及所确定的参数能够较好地预测具有不同结构的氢键复合物的三体作用强度, 其精度可与MP2方法的计算精度相当.     

给受共聚物链上与链间极化子的光谱特性

给受体共聚物具有重要的光伏效应,载流子在其中的传输机理一直备受关注. 近来聚（吡咯并吡咯二酮-噻吩[3,2-b]并噻吩联二噻吩）[poly（DPP-DTT）]在其场效应晶体管器件中表现出高达10.5 cm²/（V·s）的空穴迁移率,有实验表明链上的极化子传输是主要途径,但也有光谱数据表明链上与链间极化子共存. 单链或链间传输机制是目前大家关注的问题. 本工作从计算化学的角度给出单链与双链极化子的光谱特征,为澄清载流子传输的机制提供依据. 首先采用长程密度泛函理论计算不同结构的寡聚链的吸收光谱,通过与实验比较,找到能合理描述poly（DPP-DTT）单链中空穴/电子极化子及激子的有效模型. 然后,通过格点能修正的方法,计算不同堆积情况下链间的电荷转移积分,阐述poly（DPP-DTT）链间不同堆积方式对极化子离域性的影响. 转移积分大的空穴/电子双链极化子的理论吸收光谱与实验吻合. 计算结果表明,在poly（DPP-DTT）中同时存在一维极化子和不同堆积结构的二维极化子,同时也说明载流子的一维和二维传输是同时进行的,而不同堆积结构会影响载流子链间的传输特性.     

生物大分子全量子力学方法:显性极化(X-Pol)模型

显性极化模型(X-Pol)是片段化的量子化学方法,准确描述了体系中的静电相互作用及极化效应,可以用来研究分成片段的溶液或者生物大分子体系.本文介绍了X-Pol模型向多尺度电子结构方法组合的扩展,以及在Gaussian09程序中的实现.应用X-Pol模型,本文研究了两个氢键复合物的分子间相互作用.同时介绍了基于X-Pol模型在半经验方法层次上进行的水溶液中的牛胰胰蛋白酶抑制剂蛋白(BPTI)分子动力学模拟.     

密度泛函理论下的分子电负性——Ⅵ.原子键电负性均衡模型

以密度泛函理论和电负性均衡原理为基础 ,将体系的单电子密度分割为原子的单电子密度和键的单电子密度 ,得到了分子总能量、分子中原子以及键的有效电负性的表达式 .基于这些表达式 ,提出了直接计算体系的总能量和体系中电荷分布的新方法 .此模型比其他电负性均衡方法更合理 .对大量分子的总能量和电荷分布所进行的计算结果表明所提出的原子 键电负性均衡模型是可行的 ,可以应用于确定各类生物和有机大分子的总能量和电荷分布 ,给出较EEM和MEEM模型更近于从头计算的结果     

应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

过氧烷基自由基分子内氢迁移反应类速率常数的计算

过氧烷基自由基分子内氢迁移是低温燃烧反应中的一类重要基元反应. 本文用等键反应方法计算了该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B3LYP/6-311+G(d,p)水平下优化得到. 本文提出了用过渡态反应中心几何结构守恒作为反应类判据, 并将该分子内氢迁移反应分为四类, 包括(1,3)、(1,4)、(1,5)、(1,n) (n=6, 7, 8)氢迁移类. 分别将这4 类反应类中最小反应体系作为类反应的主反应, 并分别在B3LYP/6-311+G(d,p)低水平和CBS-QB3 高水平下得到其近似能垒和精确能垒. 其余氢迁移反应作为目标反应, 在B3LYP/6-311+G(d,p)低水下计算得到其近似能垒, 再采用等键反应方法校正得到目标反应的精确反应势垒和精确速率常数. 研究表明, 采用等键反应方法只需在低水平用从头算计算就可以得到大分子反应体系的高精度能垒和速率常数值, 且本文按等键反应本质的分类方法更能揭示反应类的本质, 并对反应类的定义给出了客观标准. 本文的研究为碳氢化合物低温燃烧模拟中重要的过氧烷基分子内氢迁移反应提供了准确的动力学参数.     

Al(H2O)63+水交换反应溶剂效应的量子化学团簇模型-密度泛函理论方法研究

在气相模型、极化连续模型、超分子模型和超分子-极化连续模型的基础上,采用量子化学团簇模型密度泛函理论方法,在B3LYP/6-311+G(d,p)基组水平下系统地开展了以下研究:优化得到Al(H2O)63+水交换反应的反应物、过渡态和产物构型,采用MP2方法在相同基组水平下计算得到相应的单点能,考虑零点振动能、热力学校正项和熵等参数的影响,计算得到Al(H2O)63+水交换反应的Gibbs自由能变和反应速率常数kex.计算结果表明:GP-SM//MP2-PCM和GP-SM-PCM//MP2-PCM模型得到的kex相近,并且与文献值相符,说明GP-SM//MP2-PCM模型可以充分考虑真实溶剂效应和主体溶剂效应,适用于Al(H3O)63+体系水交换反应的模拟.     

基于电负性均衡理论快速计算多肽分子中原子电荷的新方法（英文）

原子电荷在深入理解和模拟蛋白质的化学行为中发挥了重要的作用。通过校正电负性均衡方法(EEM)可快速计算大分子中原子电荷的分布情况。为进一步提高电负性均衡方法的准确性,本文根据Bader提出的分子区域片段中原子电荷高度转移理论,提出了一种校正电负性均衡理论的新方法,专门用于快速、准确计算生物大分子多肽或蛋白质中分子中原子电荷(AIM)。在EEM参数优化过程中,本方法不仅包括了不同原子间的连接性和价键的杂化属性,还考虑了分子片段或基团的区域化学环境因素对校正的影响。本研究对变量优化方法进行了深入讨论,微分进化算法被证明对目标函数有较好地表现。本方法计算的AIM电荷,与密度泛函理论的计算结果进行了比较。结果表明,与原来的EEM模型相比较,本方法计算的AIM电荷的精确度得到了大幅提高,为具有重复分子片段或基团的生物大分子体系(如多肽或蛋白质等)的原子电荷的快速计算提供了一种更为准确的方法,同时也为EEM的校正提供了一种新的思路。     

C60分子的非线性元激发和电子能谱

1 计算方法在本文中我们利用推广的SSH 模型,采用自洽迭代的数值计算方法,得到C_(60)分子基态、激发态的电子能谱和几何结构.这与分子轨道和密度泛函理论的计算结果是极相符的.在研究导电聚合物,特别是trans-polyacetylene 链的电子态时,苏武沛等提出了著名的SSH 模型,从理论上阐明了非线性元激发(孤子、极化子、双极化子)的物理图象.鉴于C_(60)分子与PA 链有某些相似之处,实验证实了C_(60)分子中的每个C 原子,通过三个σ电     

利用浮动电荷力场对N-甲基乙酰胺水溶液的分子动力学模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对N-甲基乙酰胺(NMA)分子的水溶液体系进行了分子动力学模拟. 与经典的力场模型相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理体现了分子中的电荷分布. 相对其它极化力场模型, 该模型具有计算量较小的特点. 在该模型下对NMA纯溶液和其水溶液体系进行了分子动力学模拟, 得到的径向分布函数、汽化热和偶极矩等物理量与实验值和其它极化力场方法符合很好, 合理描述了溶质与溶剂之间的静电极化和分子内的电荷转移.     

Density-functional-based molecular-dynamics simulations of molten salts

The physicochemical properties of two molten salts, namely, KCl and NaCl, have been studied with a molecular-dynamics approach using a density-functional-based tight-binding (DFTB) model. The obtained results have been compared with a number of previously reported simulations, carried out on smaller systems and using classical force-field techniques. A good agreement has been found for both structural parameters and macroscopic properties, such as self-diffusion coefficients. Furthermore, our DFTB results are very close to the available experimental data. From a more general point of view, our results demonstrate the applicability of DFTB as an efficient tool in the modeling of melts. At the same time, the quality of the obtained results supports the use of this as a reliable alternative to the more expensive ab initio dynamics approaches, if accurate parameters are provided.     

Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules

The polaron might play an important role in the process of charge migration through duplex DNA stack. In the present work, we investigate properties of hole polarons in DNA molecules containing identical base pairs, such as poly(G)-poly(C) and poly(A)-poly(T), An extended tight-binding model (extended Su-Schrieffer-Heeger model), which involves the effect of an electric field in the direction of DNA stack, will be introduced. The transfer integral and electron-phonon coupling parameters in this model are obtained according to ab initio calculation for different base pair dimers. Calculations reveal that the polaron in poly(A)-poly(T) has a wider shape and a higher mobility under a specific electric field than that in poly(G)-poly(C) DNA stack.     

Self-interaction and strong correlation in DFTB

The density functional based tight-binding (DFTB) method can benefit substantially from a number of developments in density functional theory (DFT) while also providing a simple analytical proving ground for new extensions. This contribution begins by demonstrating the variational nature of charge-self-consistent DFTB (SCC-DFTB), proving the presence of a defined ground-state in this class of methods. Because the ground state of the SCC-DFTB method itself can be qualitatively incorrect for some systems, suitable forms of the recent LDA+U functionals for SCC-DFTB are also presented. This leads to both a new semilocal self-interaction correction scheme and a new physical argument for the choice of parameters in the LDA+U method. The locality of these corrections can only partly repair the HOMO-LUMO gap and chemical potential discontinuity, hence a novel method for introducing this further physics into the method is also presented, leading to exact derivative discontinuities in this theory at low computational cost. The prototypical system NiO is used as an illustration for these developments.     

Electronic and structural properties of Si10 cluster

Possible structures for Si₁₀ cluster are considered using a tight-binding model and drawing on significant work done in the past. It is shown that the tight-binding parametrization, fitted to the bulk, is also valid for smaller systems. This model is found to essentially reproduce other published results, but requires much less effort thanab initio techniques—thus, allowing the study of a wide variety of structures and their ions. However, unlike classical force-field calculations, it yields information about the electronic structure of clusters. A new geometric structure for Si₁₀ is found, which is not only of lowest energy, but which also matches the experimental photoelectron band gap and explains the experimental reactivity data. Because of the Jahn-Teller effect, the photoelectron spectrum is very sensitive to geometry. Also, ionization of the cluster alters the geometry slightly.     

Tight-binding cluster Bethe lattice model studies of chemisorption

The surface Green's function which is used in model calculations for chemisorption systems has been approximated by the tight-binding cluster Bethe lattice model (TBCBLM). It is shown that for chemisorption of a single-orbital atom on a simple cubic lattice this model yields results in good agreement with Einstein and Schríeffer's results. The effects of cluster size on the chemisorption properties are explored.     

计算饱和醇异构体标准生成焓的新方法

基于极性叠加原理,在成功设计烷烃异构体和多氯代烷烃生成焓计算新方法的基础上,设计了一种计算多元醇异构体生成焓的新方法,并合理地假定任一异构体的原子化焓等于三种键(C-C、C-H和C-O-H键)的键能、极性叠加能项以及氢键能项的加和.用这一模型拟合24种原子化焓数据,得到了标准生成焓的估算公式.为了检验预测的精确性,又设计了一种预测方法,使用在排除被预测的化合物条件下回归得到的参数,预测该化合物的生成焓.按这种方法,预测了24种异构体的生成焓.通过该5参数预测的相对于实验值的各种误差(平均绝对误差、均方根误差和最大绝对误差)不仅比7参数的基团法预测的对应误差小得多,而且比相应实验数据的误差还要小.与键加和法比较,该方法的模型包含了极性叠加能和氢键能量,该两项代表了主要的非键相互作用能,表征了不同异构体的结构差异,并大大减少了参数.     

Controlling the transmission line shape of molecular t-stubs and potential thermoelectric applications

Asymmetric line shapes can occur in the transmission function describing electron transport in the vicinity of a minimum caused by quantum interference effects. Such asymmetry can be used to increase the thermoelectric efficiency of molecular junctions. So far, however, asymmetric line shapes have been only empirically found for just a few rather complex organic molecules where the origins of the line shapes relation to molecular structure were not resolved. In the present, work we introduce a method to analyze the structure dependence of the asymmetry of interference dips from simple two site tight-binding models, where one site corresponds to a molecular π orbital of the wire and the other to an atomic p(z) orbital of a side group, which allows us to characterize analytically the peak shape in terms of just two parameters. We assess our scheme with first-principles electron transport calculations for a variety of t-stub molecules and also address their suitability for thermoelectric applications.     

Electronic states of an infinite polyene under local perturbations

A perturbation theory method is developed in the tight-binding LCAO MO treatment of a one-dimensional polymer under local perturbation with the aid of the Wannier function. As the first step, electronic states of an infinite polyene under a few of significant cases of perturbation are formulated in the scheme of the Hückel MO approach, giving the changes in total energies, electron densities, and bond orders of the perturbed systems.     

Crystallization kinetic of fluoro- zirconate glasses by non-isothermal analysis

Fluoride glasses have been extensively studied due to their high transparency in the infrared wavelength. The crystallization kinetics of these systems has been studied using DTA and DSC techniques. Most of the experimental data is frequently investigated in terms of the Johnson-Mehl-Avrami (JMA) model in order to obtain kinetic parameters. In this work, DSC technique has been used to study the crystallization of fluorozirconate glass under non-isothermal conditions. It was found that JMA model was not fit to be applied directly to these systems, therefore, the method proposed by Málek has been applied and the Šesták-Berggren (SB) model seems to be adequate to describe the crystallization process. This revised version was published online in July 2006 with corrections to the Cover Date.