Ni2Fe2P团簇结构及电子性质的DFT研究

利用DFT(密度泛函理论)方法对原子簇模型Ni2Fe2P的二十余种可能构型分别在二、四重态下进行优化计算，分析比较了优化结果的能量、成键及电荷分布情况。结果表明：原子簇Ni2Fe2P二重态比四重态稳定，二重态时以变形的四方锥构型最稳定，四重态时以变形的三角双锥构型最稳定；无论是二重态，还是四重态，Fe-P间的成键能力均要强于其它键；随着P原子周围成键金属原子的增加．P原子所带正电荷逐渐增加。     

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     

分子ABEEM电荷分布的图形表示

利用Matlab软件编写程序, 将基于密度泛函理论和电负性均衡原理发展的原子-键电负性均衡方法σ-π模型(ABEEM σ-π)计算的电荷分布, 特别是键电荷和孤对电子的电荷分布, 用图形表现出来, 对分子的电荷分布给出直观形象的认识, 并以腺嘌呤、腺嘌呤脱氧核苷酸以及丙烯与氯化氢的马氏亲电加成反应为例, 进行应用说明.     

ABEEMσπ和OPLS-AA力场对蛋白质GA88/GB88的分子动力学模拟

将原子与键电负性均衡方法融入分子力学方法,即利用ABEEMσπ浮动电荷力场与ABEEM-7P水模型相结合的方法及OPLS-AA固定电荷力场方法,对GA88和GB88蛋白进行了水溶液(温度295 K)和真空中的分子动力学模拟.比较两种方法得到的两个蛋白质的结构与实验结构的均方根偏差,分析了两种方法得到的两个蛋白质的回旋半径、氢键分布、径向分布及电荷分布情况.结果表明,ABEEMσπ和OPLS-AA力场均能正确模拟蛋白质结构,得到的各项偏差值接近,但从各偏差的波动大小可见,ABEEMσπ力场的模拟更稳定;回旋半径模拟很好地体现了蛋白质的"电致紧缩"现象;氢键分布、径向分布及电荷分布表明,与OPLS-AA固定电荷力场相比,ABEEMσπ浮动电荷力场能更好地体现蛋白质和周围水分子的极化效应.     

致癌性胺离子反应过程中电荷和化学位移的计算

应用原子-键电负性均衡方法中的σπ模型(ABEEMσπ)计算了由致癌性胺离子所参与的反应过程中的电荷分布,所计算出的电荷分布可以和从头算很好的相关联,并且所需要的时间也大大的缩短;同时应用从头计算程序计算致癌性胺离子反应过程中的NMR化学位移.结果表明,在反应过程中电荷的变化和NMR化学位移的变化有很好的对应关系.     

应用ABEEM模型计算铁(Ⅱ)配合物的电荷分布

以密度泛函理论和电负性均衡原理为基础,在原子-键电负性均衡模型中,利用最小二乘法,并结合自编程序,拟合确定了氢、碳、氮、硫以及铁(Ⅱ)等各种类型的原子及相关化学键区域的参数.利用上述参数计算了一些铁(Ⅱ)配合物的电荷分布,计算结果可以和从头算结果很好地相关联.     

Ni(111)表面Pt原子对噻吩吸附影响的密度泛函理论研究

采用密度泛函理论方法,运用平板模型对噻吩分子在PtNi2/Ni(111)表面的水平吸附进行了结构优化和能量计算.结果表明:bridge-hollow-1位的吸附最稳定,但是bridge位吸附对噻吩的影响最大.噻吩吸附在表面上时,S原子向上翘起,C原子与表面Ni原子的作用比与Pt原子紧密,表面原子与噻吩的匹配程度决定了吸附的强度和吸附后S—C键和C—C键的活泼性.噻吩以bridge-hollow-1和bridge位吸附时分子与表面之间的电子给予与反馈最多,分子最活泼,而且除了C(1)—S键以外,环上C(1)—C(2)键活化程度也较好,而bridgehollow-2位吸附后噻吩分子中C(2)—C(2)键比较容易发生断裂.     

Au(111)面甲烷硫醇吸附的密度泛函理论研究

采用基于密度泛函理论的第一性原理方法和平板模型研究了CH₃SH分子在Au(111)表面的吸附构型和电子结构. 系统地计算了S原子在不同位置以不同方式吸附的系列构型, 计算结果表明, CH₃SH分子倾向于吸附在top位上, S-C键相对于Au表面法线的夹角为62°～78°|而S-H键断裂后CH₃S_H则倾向于吸附在bri-fcc位上, S-C键相对于Au(111)表面法线的夹角为49°～57°. 比较分析CH₃SH分子和CH₃S_H的吸附, 发现CH₃SH分子倾向于不解离吸附, 表面温度的提升和缺陷的出现可能促使S-H键的断裂. 通过比较S原子在独立的CH₃SH分子和吸附状态下的局域态密度, 发现S-H键断裂后S原子和表面的键合强于S-H键未断裂时S原子和表面的键合. 扫描隧道显微镜(STM)图像模拟显示了CH₃SH和CH₃S_H在Au(111)表面吸附的3个典型的STM图像.     

甲硫醇在Cu(111)表面的解离吸附: 密度泛函理论研究

采用基于密度泛函理论的第一性原理方法和平板模型研究了CH₃SH分子在Cu(111)表面的吸附反应.系统地计算了S原子在不同位置以不同方式吸附的一系列构型, 第一次得到未解离的CH₃SH分子在Cu(111)表面顶位上的稳定吸附构型,该构型吸附属于弱的化学吸附, 吸附能为0.39 eV. 计算同时发现在热力学上解离结构比未解离结构更加稳定. 解离的CH₃S吸附在桥位和中空位之间, 吸附能为0.75-0.77 eV. 计算分析了未解离吸附到解离吸附的两条反应路径, 最小能量路径的能垒为0.57 eV. 计算结果还表明S―H键断裂后的H原子并不是以H₂分子的形式从表面解吸附而是以与表面成键的形式存在. 通过比较S原子在独立的CH₃SH分子和吸附状态下的局域态密度, 发现S―H键断裂后S原子和表面的键合强于未断裂时S原子和表面的键合.     

簇合物中锥形四重桥硫3d轨道成键的EHMO研究

运用EHMO方法对四个[M_4S_2]（M＝Co，Nb）型簇合物的电子结构进行了计算，通过对硫原子3d轨道引入前后体系总能量、轨道能级、电荷分布和Mulliken键级等性质的比较，发现簇合物中锥形四重桥硫原子的3d轨道参与了成键，对稳定[M_4S_2]结构单元有重要的作用．     

Preparation of hexacoordinated tris(bidentate) phosphorus compounds with 1,3,2-dioxaphosphorinane rings. NMR and X-ray crystallographic studies of their conformation

A series of new unstable tris(bidentate) hexacoordinated phosphorus compounds 1 with 1,3,2-dioxaphosphorinane rings was prepared and studied by NMR and X-ray crystallography. The X-ray crystal structures showed that the 1,3,2-dioxaphosphorinane ring adopts different conformations depending on the number and size of substituents at the carbon atom C14. Substituents are deployed around the phosphorus atom in a slightly deformed octahedral structure. Deviations in bond lengths around the phosphorus atom depend on the character of the bonds and the distribution of the negative charge. (1)H and (13)C NMR measurements showed that in solution the flexibility of 1,3,2-dioxaphosphorinane ring depends on the size of substituents at the carbon C14.     

Calculation of the average properties of atoms in molecules. II

This article describes an algorithm for the calculation of the average properties of an atom in a molecule. The atom is defined within the topological theory of molecular structure, a theory which defines atoms, bonds, structure, and structural stability in terms of the topological properties of a system's charge distribution. The average properties of the atom so defined are uniquely determined by quantum mechanics. Results for a number of hydrocarbon molecules, obtained by the program PROAIM (properties of atoms in molecules) which implements this algorithm, are given. In general, this program enables one to calculate the average energy of an atom in a molecule to an accuracy of ±1 kcal/mol.     

Biotransformation,spectroscopic investigation,crystal structure and electrostatic properties of 3,7α‐dihydroxyestra‐1,3,5(10)‐trien‐17‐one monohydrate studied using transferred electron‐density parameters

The biologically transformed product of estradiol valerate, namely 3,7α‐dihydroxyestra‐1,3,5(10)‐trien‐17‐one monohydrate, C₁₈H₂₂O₃·H₂O, has been investigated using UV–Vis, IR, ¹H and ¹³C NMR spectroscopic techniques, as well as by mass spectrometric analysis. Its crystal structure was determined using single‐crystal X‐ray diffraction based on data collected at 100 K. The structure was refined using the independent atom model (IAM) and the transferred electron‐density parameters from the ELMAM2 database. The structure is stabilized by a network of hydrogen bonds and van der Waals interactions. The topology of the hydrogen bonds has been analyzed by the Bader theory of `Atoms in Molecules' framework. The molecular electrostatic potential for the transferred multipolar atom model reveals an asymmetric character of the charge distribution across the molecule due to a substantial charge delocalization within the molecule. The molecular dipole moment was also calculated, which shows that the molecule has a strongly polar character.     

Effects of Electronic Structure of Adjacent Carbon on the Strength of C─F⋯H─F Organofluorine Hydrogen Bonds

We investigate the effects of the electronic structure of carbon atom on the organofluorine hydrogen bonds, C─F⋯H─F. Our results show that we can modulate the strength of organofluorine hydrogen bonds by adjusting the volume of fluorine atom in C─F via changing the electronic structure of adjacent carbon atoms. Different with the conventional hydrogen bonds, we found that instead of carbon rehybridization and hyperconjugative effects, the magnitude of fluorine atomic volume plays important roles in determining the strength of the C─F⋯H─F organofluorine hydrogen bonds. The lone pair electrons at both the proximal and the vicinal carbon dramatically reinforce the strength of C─F⋯H─F organofluorine hydrogen bond with its interaction energy in the range of about 15–25 kcal/mol, that is, the carbanion-mediated organofluorine hydrogen bond could be very strong. Due to the high electronegativity of fluorine atom, it easily attracts the excess electron from the proximal and vicinal carbon, which results in the increase of its volume and negative charge. The enhanced volume of fluorine atom gives rise to the large polarization energy, and its enhanced negative charge favors the large electrostatic interaction, both of which substantially contribute to making the organofluorine hydrogen bonds strong. © 2019 Wiley Periodicals, Inc.     

Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations

We performed geometry optimizations using the tuned and balanced redistributed charge algorithms to treat the QM-MM boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. In the tuned and balanced redistributed charge (TBRC) scheme, the QM boundary atom is terminated by a tuned F link atom, and the charge of the MM boundary atom is properly adjusted to conserve the total charge of the entire QM/MM system; then the adjusted MM boundary charge is moved evenly to the midpoints of the bonds between the MM boundary atom and its neighboring MM atoms. In the tuned and balanced redistributed charge-2 (TBRC2) scheme, the adjusted MM boundary charge is moved evenly to all MM atoms that are attached to the MM boundary atom. A new option, namely charge smearing, has been added to the TBRC scheme, yielding the tuned and balanced smeared redistributed charge (TBSRC) scheme. In the new scheme, the redistributed charges near the QM-MM boundary are smeared to make the electrostatic interactions between the QM region and the redistributed charges more realistic. The TBRC2 scheme and new TBSRC scheme have been tested for various kinds of bonds at a QM-MM boundary, including C-C, C-N, C-O, O-C, N-C, C-S, S-S, S-C, C-Si, and O-N bonds. Charge smearing is necessary if the redistributed charges are close to the QM region, as in the TBSRC scheme, but not if the redistributed charge is farther from the QM region, as in the TBRC2 scheme. We found that QM/MM results using either the TBRC2 scheme or the TBSRC scheme agree well with full QM results; the mean unsigned error (MUE) of the QM/MM deprotonation energy is 1.6 kcal/mol in both cases, and the MUE of QM/MM optimized bond lengths over the three bonds closest to the QM-MM boundary, with errors averaged over the protonated forms and unprotonated forms, is 0.015 ? for TBRC2 and 0.021 ? for TBSRC. The improvements in the new scheme are essential for QM-MM boundaries that pass through a polar bond, but even for boundaries that pass through C-C bonds, the improvement can be quite significant.     

Crystal Structure of Melaminium Orthophosphate from High‐Resolution Synchrotron Powder‐Diffraction Data

The crystal structure of melaminium orthophosphate (MP) has been determined from high‐resolution synchrotron powder‐diffraction data. The crystal packing consists of melaminium layers and pairs of orthophosphate chains connected by H‐bonds almost perpendicular to the layers. The distance between melaminium layers is 3.62 Å. Neighboring melaminium molecules do not lie in the same plane, but in two parallel planes at close distance (0.79 Å), and are shifted with respect to each other. The orthophosphate chains are connected by both intra‐chain and inter‐chain H‐bonds. The melamine is singly protonated at an endocyclic N‐atom. The powder‐diffraction data were corroborated by solid‐state NMR experiments.     

Probing the Crystal Structure Landscape by Doping: 4‐Bromo, 4‐Chloro,and 4‐Methylcinnamic Acids

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4‐bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4‐methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4‐chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii, all but two of the multiple solid solutions obtained in the methyl‐doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of π⋅⋅⋅π interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen.     

Probing the Crystal Structure Landscape by Doping: 4‐Bromo, 4‐Chloro,and 4‐Methylcinnamic Acids

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4‐bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4‐methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4‐chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii, all but two of the multiple solid solutions obtained in the methyl‐doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of π???π interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen.     

Understanding the planar tetracoordinate carbon atom: spiropentadiene dication

The atoms in molecule theory shows that the spiropentadiene dication has a planar tetracoordinate carbon (ptC) atom stabilized mainly through the sigma bonds and this atom has a negative charge. The bonds to the ptC atom have less covalent character than the central carbon from neutral spiropentadiene. The total positive charge is spread along the structure skeleton. The analysis of the potential energy surface shows that the dication spiropentadiene has a 2.3 kcal/mol activation barrier for ring opening.