一种新的分子拓扑指数及其在QSPR/QSAR研究中的应用

通过引入量子数、键参数,认为分子的性质与其中各原子的电负性、价电子数、成键电子数、价层主量子数及各化学键的键长有关,提出了一种新的分子拓扑指数mAY.采用该拓扑指数对饱和烷烃、烷基苯、烷氧氯硅烷、卤代苯、含氮杂环化合物、碱金属卤化物及卤化锡的性质/活性进行了相关关系的研究.结果表明,mAY与有机物和无机物的性质/活性间具有良好的相关性.     

一个新的分子拓扑指数

通过将键参数和量子数引入原子点价,重新定义原子点价δiY,认为分子中某一原子的δiY与该原子的杨氏电负性力标、价电子数、成键电子数及最外层主量子数有关.由此提出新的分子拓扑指数mXY.并用一级指数1XY与饱和烷烃的沸点、液体热容、气体热容、蒸发热、临界温度、临界压力,卤代苯的辛醇/水分配系数,烷氧氯硅烷的气相色谱保留指数、含氮杂环化合物的毒性,碱金属卤化物的晶格焓与F心能带,卤化锡的119Sn Mossbauer等性质/活性进行相关关系的研究.结果表明,1XY与有机物和无机物的性质/活性间具有广泛良好的相关性.     

多氯代二苯并呋喃的结构信息连接性指数与其在不同柱上的气相保留行为的关系

 在分子连接性指数的基础上 ,建立了化合物结构信息连接性指数 nχH(n =0 ,1,2 ,… ,m) ,即 nχH =∑(δiH·δjH·δkH·… ·δmH) -0 5,其中 1阶和 2阶结构信息连接性指数为 :1χH =∑(δiH·δjH) -0 5,2 χH =∑(δiH·δjH·δkH) -0 5,并计算了 135个多氯代二苯并呋喃分子的1χH 和2 χH 值。发现1χH 或2 χH 或1χH 和2 χH 与多氯代二苯并呋喃在不同柱上的气相保留指数 (RI)和相对保留时间 (RRT)有很好的相关性。各样本总体模型即定量结构 保留关系 (QSRR)相关模型的相关系数均在 0 96以上 ,且物理意义明确 ,计算简单.     

Modification of Wiener Index and its application

A novel topological index based on the Wiener Index is proposed as W* = 1/2 sigma (n)(i,j=1) S(*)(ij), the element S(*)(ij) of the distance matrix is defined either as S(*)(ij) = alpha x square root of I(i)I(j)/R(ij) (atoms i and j are adjacent) or as S(*)(ij) = = alpha x (j-i+1)square root of I(i) x x x x x I(j)/R(ij) (atoms i and j are not adjacent), where I(i) and I(j) represent the electronegativity of vertices i or j, respectively, R(ij)() is the sum of the bond length between the vertices i and j in a molecular graph, and alpha = (Z(i)/Z(j))(0.5), where Z(i) and Z(j) are the atomic numbers of the positive valence atom i and the negative valence atom j, respectively. The properties and the interaction of the vertices in a molecule are taken into account in this definition. That is why the application of the index W to heteroatom-containing and multiple bond organic systems and inorganic systems is possible. Correlation coefficients above 0.97 are achieved in the prediction of the retention index of gas chromatography of the hydrocarbons, the standard formation enthalpy of methyl halides, halogen-silicon, and inorganic compounds containing transition metals.     

脂肪醇气相色谱保留指数与结构的相关性研究

在分子图的邻接矩阵基础上,构建了一个化合物均价连接性指数mL,mL=∑(Ai·Aj·Ak…)-0.5,其中一阶指数1L及定位基参数β与25种脂肪醇在6种固定相(SE-30,OV-3,OV-7,OV-11,OV-17和OV-25)上的气相色谱保留指数I显著相关,相关系数均大于0.98。所建定量结 构-保留关系(QSRR)模型具有良好的稳定性和预测能力,较好地揭示了脂肪醇在不同固定相上气相色谱保留指数的变化规律。     

On molecular polarizability: 3. Relationship to the ionization potential of haloalkanes, amines, alcohols, and ethers

The relationship between the ionization potential and the parameters molecular electronegativity and molecular polarizability for haloalkanes, amines, alcohols, and ethers was investigated. There is no good linear correlation between the ionization potential Ip and molecular electronegativity chi(eq) alone for these compounds. Ip can be modeled well with three parameters: chi(eq), polarizability effect index (PEI) of an alkyl group, and atomic polarizability (P). Further, a single expression for predicting the Ip values of aldehydes, esters, nitriles, and carboxylic acids was developed: Ip(Rz)(eV) = Ip(MeZ) + 1.4544delta chi(eq) - 1.6435delta sigmaPEI(Ri). Here Ip(MeZ) is the experimental ionization potential of monosubstituted methane MeZ. Delta chi(eq) and delta sigmaPEI(Ri) are the difference in the molecular electronegativity and the difference in the polarizability effect index of alkyl groups attached to the functional group Z between molecules MeZ and RZ, respectively.     

分子价连接性指数中杂原子价点价计算新方法及应用

对分子价连接性指数中杂原子点价δ^v~i的计算方法进行了改进,提出了一种计算杂原子价点价δ^h~i的新方法,认为分子中某一杂原子i的价点价δ^h~i值不仅与它的价层电子数Z~i、最高主量子数n~i以及结合的氢原子数目h~i有关,还与它所在的族烽N~i、陷氢图中连接的其他原子的数目m~i以及杂化方式L~p有关。杂原子i的δ^h~i值与原子i的Pauling电负性具有相近的物理意义。用由δ^h~i构成的分子价连接性指数^nχ^h(n=0,1,2)研究了取代芳烃和烃衍生物的物理化学性质和生物活性,结果表明,^1χ^h比^1χ^v有显著的改善,计算值与实验值接近的程度更高。     

Modification of the Wiener Index. 2

A novel topological index based on the Wiener Index is proposed as W = 1/2, summation(n/ij)=S*(ij) the element S*(ij) of the distance matrix is defined either as S*(ij)= square root (E(i)E(j)/R(ij) (atoms i and j are adjacent) or as S*(ij)=(j-i+1)square root (E(i)...xE /R(ij) (atoms i and j are not adjacent), where E(i) and E(j) represent the total energy of the valence electrons of vertexes i and j, respectively, R(ij) is the sum of the distance between the vertexes i and j in a molecular graph. The distance and the energy of the vertexes in a molecule are taken into account in this definition. Hence the application of the index W to multiple bond and heteroatom-containing organic systems and inorganic systems is possible. Good correlation coefficients are achieved not only in the standard formation enthalpy of methyl halides, halogen-silicon, but also in the retention index of gas chromatography of the hydrocarbons.     

Skeletal structures of hexa-organo substituted triatomics R3XYZR3: A rationalisation using the second-order Jahn—Teller effect

In compounds of type R₃XYZR₃ (R  phenyl, methyl, benzyl; X, Z  Al, Si, P, Ge, Sn; Y  C, N, O, F) linearity of the XYZ skeleton is predicted by the second-order Jahn—Teller effect in those examples where the valence orbitals of X and Z are much less tightly bound than those of Y. When the X and Z orbitals are bound more tightly than those of Y, the XYZ skeleton is predicted to be non linear at Y. The effects of varying R, X and Z, and the contribution of π-interactions are discussed.     

人工神经网络法预测炸药组分的色谱保留值参数

 以分子拓扑指数作为炸药组分的结构描述符 ,利用反向传播算法 (BP)人工神经网络 ,以Sigmoid函数为传递函数 ,分子连接性指数0 χ ,1χ ,2 χ与边邻接指数 (ε)为输入向量 ,反相高效液相色谱保留值参数logkw 和S为输出向量 ,将输入向量归一化至 - 3～ 3区间 ,输出向量归一化至 0～ 1区间 ,网络精度取 0 5 ,学习步长 η的初始值取0 2 ,动量因子α取 0 5 ,通过对 2 0种炸药的网络模型进行训练 ,建立了炸药分子结构与logkw 和S之间的定量模型。结果表明 ,该模型较好地反映了炸药分子结构与保留值之间的关系。     

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     

价电子轨道能量拓扑指数mZ及其应用

受Randic分子连接性拓扑指数^mZ的启发,本文构建了价电子轨道能量拓扑指数^mZ。用^mZ的0、1阶指数分别与无机氢化物的pKa1值、20种碱金属卤化物的晶格能U、生成焓△rHm、水化能△rG^0m和气态碱金属卤化物核间距R0关联,拟合的回归方程的相关系(指)数,满足优级或良级标准。预测取得较好的结果。     

Ternary rare earth osmium aluminides R(7+)(x)Os(12)Al(61+)(y) belonging to a structural family with layered topology

The 10 intermetallic compounds R(7+)(x)Os(12)Al(61+)(y) (R = Y, Nd, Sm, Gd-Tm) were prepared by arc-melting of the elemental components. They crystallize with a hexagonal structure very similar to that of Y(7.28)Re(12)Al(61.38). The structure was determined from four-circle diffractometer data of Y(7+)(x)Os(12)Al(61+)(y): P6(3)/mcm, a = 1301.5(2) pm, c = 903.0(2) pm, Z =1. Four atomic sites, all located on the 6(3) axis, show fractional occupancy, resulting in the composition Y(7.86(1))Os(12)Al(61.51(4)), corresponding to the Pearson symbol hP90-8.63. The structure may be viewed as consisting of alternating atomic layers of two kinds, although chemical bonding within and between the layers is of similar character as can be judged from the near-neighbor environments, where all of the 11 atomic sites have high coordination numbers. One kind of layers (A). is relatively loosely packed and contains the yttrium and some aluminum atoms. The other kind (B). consists of the osmium and the remaining aluminum atoms in a nearly hexagonal close-packed arrangement. These layers are stacked in the sequence ABAB. A similar building principle has recently been recognized for several other structures of ternary intermetallic compounds of rare earth and transition metals with a high content of aluminum or gallium, where the structures of CeOsGa(4), Ho(3)Ru(4)Ga(15), and Y(2)Pt(6)Al(15) are the most recent examples. This structural family is briefly reviewed. The cell volume of Yb(7+)(x)Os(12)Al(61+)(y) indicates a mixed or intermediate valence character +2/+3 for the ytterbium atoms of this compound.     

Electronic properties of multifurcated bent hydrogen bonds CH3...Y and CH2...Y

H-bonding angle angleYHX has an important effect on the electronic properties of the H-bond Y...HX, such as intra- and intermolecular hyperconjugations and rehybridization, and topological properties of electron density. We studied the multifurcated bent H-bonds of the proton donors H3CZ (Z = F, Cl, Br), H2CO and H2CF2 with the proton acceptors Cl(-) and Br(-) at the four high levels of theory: MP2/6-311++G(d,p), MP2/6-311++G(2df,2p), MP2/6-311++G(3df,3pd) and QCISD/6-311++G(d,p), and found that they are all blue-shifted. These complexes have large interaction energies, 7-12 kcal mol(-1), and large blue shifts, delta r(HC) = -0.0025 --0.006 A and delta v(HC) = 30-90 cm(-1). The natural bond orbital analysis shows that the blue shifts of these H-bonds Y...HnCZ are mainly caused by three factors: rehybridization; indirect intermolecular hyperconjugation n(Y) -->sigma*(CZ), in that the electron density from n(Y) of the proton acceptor is transferred not to sigma*(CH), but to sigma*(CZ) of the donor; intramolecular hyperconjugation n(Z) -->sigma*(CH), in that the electron density in sigma*(CH) comes back to n(Z) of the donor such that the occupancy in sigma*(CH) decreases. The topological properties of the electron density of the bifurcated H-bonds Y...H2CZ are similar to those of the usual linear H-bonds, there is a bond critical point between Y and each hydrogen, and a ring critical point inside the tetragon YHCH. However, the topological properties of electron density of the trifurcated H-bonds Y...H3CZ are essentially different from those of linear H-bonds, in that the intermolecular bond critical point, which represents a closed-shell interaction, is not between Y and hydrogen, but between Y and carbon.     

Novel atomic-level-based AI topological descriptors: application to QSPR/QSAR modeling

Novel atomic level AI topological indexes based on the adjacency matrix and distance matrix of a graph is used to code the structural environment of each atomic type in a molecule. These AI indexes, along with Xu index, are successfully extended to compounds with heteroatoms in terms of novel vertex degree v(m), which is derived from the valence connectivity delta(v) of Kier-Hall to resolve the differentiation of heteroatoms in molecular graphs. The multiple linear regression (MLR) is used to develop the structure-property/activity models based on the modified Xu and AI indices. The efficiency of these indices is verified by high quality QSPR/QSAR models obtained for several representative physical properties and biological activities of several data sets of alcohols with a wide range of non-hydrogen atoms. The results indicate that the physical properties studied are dominated by molecular size, but other atomic types or groups have small influences dependent on the studied properties. Among all atomic types, -OH groups seem to be most important due to hydrogen-bonding interactions. On the contrary, -OH groups play a dominant role in biological activities studied, although molecular size is also an important factor. These results indicate that both Xu and AI indices are useful model parameters for QSPR/QSAR analysis of complex compounds.     

Born-Haber-Fajans cycle generalized: linear energy relation between molecules, crystals, and metals

Classical procedures to calculate ion-based lattice potential energies (U(POT)) assume formal integral charges on the structural units; consequently, poor results are anticipated when significant covalency is present. To generalize the procedures beyond strictly ionic solids, a method is needed for calculating (i) physically reasonable partial charges, delta, and (ii) well-defined and consistent asymptotic reference energies corresponding to the separated structural components. The problem is here treated for groups 1 and 11 monohalides and monohydrides, and for the alkali metal elements (with their metallic bonds), by using the valence-state atoms-in-molecules (VSAM) model of von Szentpály et al. (J. Phys. Chem. A 2001, 105, 9467). In this model, the Born-Haber-Fajans reference energy, U(POT), of free ions, M(+) and Y(-), is replaced by the energy of charged dissociation products, M(delta)(+) and Y(delta)(-), of equalized electronegativity. The partial atomic charge is obtained via the iso-electronegativity principle, and the asymptotic energy reference of separated free ions is lowered by the "ion demotion energy", IDE = -(1)/(2)(1 - delta(VS))(I(VS,M) - A(VS,Y)), where delta(VS) is the valence-state partial charge and (I(VS,M) - A(VS,Y)) is the difference between the valence-state ionization potential and electron affinity of the M and Y atoms producing the charged species. A very close linear relation (R = 0.994) is found between the molecular valence-state dissociation energy, D(VS), of the VSAM model, and our valence-state-based lattice potential energy, U(VS) = U(POT) - (1)/(2)(1 - delta(VS))(I(VS,M) - A(VS,Y)) = 1.230D(VS) + 86.4 kJ mol(-)(1). Predictions are given for the lattice energy of AuF, the coinage metal monohydrides, and the molecular dissociation energy, D(e), of AuI. The coinage metals (Cu, Ag, and Au) do not fit into this linear regression because d orbitals are strongly involved in their metallic bonding, while s orbitals dominate their homonuclear molecular bonding.     

Bonding between strongly repulsive metal atoms: an oxymoron made real in a confined space of endohedral metallofullerenes

Endohedral metallofullerenes (EMFs) are able to encapsulate up to four metal atoms. In EMFs, metal atoms are positively charged because of the electron transfer from the endohedral metal atoms to the carbon cage. It results in the strong Coulomb repulsion between the positively charged ions trapped in the confined inner space of the fullerene. At the same time, in many EMFs, such as Lu(2)@C(76), Y(2)@C(79)N, M(2)@C(82) (M = Sc, Y, Lu, etc.), Y(3)@C(80), or Sc(4)O(2)@C(80), metals do not adopt their highest oxidation states, thus yielding a possibility of the covalent metal-metal bonding. In some other EMFs (e.g., La(2)@C(80)), metal-metal bonding evolves as the result of the electrochemical or chemical reduction, which leads to the population of the metal-based LUMO with pronounced metal-metal bonding character. This article highlights different aspects of the metal-metal bonding in EMFs. It is concluded that the valence state of the metal atoms in dimetallofullerenes is not dependent on their third ionization potential, but is determined by their ns(2)(n- 1)d(1)→ns(1)(n- 1)d(2) excitation energies. Peculiarities of the metal-metal bonding in EMFs are described in terms of molecular orbital analysis as well as topological approaches such as Quantum Theory of Atoms in Molecules and Electron Localization Function. Interplay of Coulomb repulsion and covalent bonding is analyzed in the framework of the Interacting Quantum Atom approach.     

SN1‐SN2 and SN2‐SN3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides

Hydrolysis reactions of benzyl chlorides and benzenesulfonyl chlorides were theoretically investigated with the density functional theory method, where the water molecules are explicitly considered. For the hydrolysis of benzyl chlorides (para‐Z? C₆H₄? CH₂? Cl), the number of water molecules (n) slightly influences the transition‐state (TS) structure. However, the para‐substituent (Z) of the phenyl group significantly changes the reaction process from the stepwise (S_N1) to the concerted (S_N2) pathway when it changes from the typical electron‐donating group (EDG) to the typical electron‐withdrawing one (EWG). The EDG stabilizes the carbocation (MeO? C₆H₄? CH₂⁺), which in turn makes the S_N1 mechanism more favorable and vice versa. For the hydrolysis of benzenesulfonyl chlorides (para‐Z? C₆H₄? SO₂? Cl), both the Z group and n influence the TS structure. For the combination of the large n value (n > 9) and EDG, the S_N2 mechanism was preferred. Conversely, for the combination of the small n value and EWG, the S_N3 one was more favorable. © 2014 Wiley Periodicals, Inc.     

QSAR结合人工神经网络预测取代氯苯酚生物毒性

取代氯苯酚类化合物是有机化学工业中必不可少的重要原料,现已有邻氯苯酚等4种酚类化合物被美国环保局定为优先控制的有机污染物[1].对此,国内外有关专家对取代氯苯酚的生物毒性进行了广泛研究,但都没有得到有效的构效关系[2-3 ].因此,通过建立取代氯苯酚生物毒性与分子结构间的定量关系,对于预测其生物毒性有着实际的意义.