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.     

扩展的距离矩阵指数W~*及其应用研究

重新定义了距离矩阵及距离矩阵拓扑指数W~*，该定义考虑分子中每一原子的 性质和成键情况以及分子中每一原子与所有其它原子的结合情况。拓扑指数W~*对 于饱和碳氢体系可还原为Wiener的距离矩阵指数W，同时，W~*还可一般地应用于含 多重键及杂质原子的有机体系和无机体系。本研究用W~*相关的卤代甲烷标准生成 焓、SiX_n（X = F，Cl，Br，I，n = 1～4）体系的标准生成焓，相关系数均在0. 99以上，置信度大于99.9%。并用W~*研究了含苯环的碳氢体系气相色谱保留指数， 含氧原子的醛酮体系的标准生成焓以及卤代苯体系的辛醇/水分配系数。对饱和碳 氢体，W为W~*的特殊形式。     

Binding of polyanions by biogenic amines. III. Formation and stability of protonated spermidine and spermine complexes with carboxylic ligands

The formation and stability of protonated spermidine and spermine-carboxylic ligand complexes (seven systems) were studied potentiometrically (H(+)-glass electrode). ALH(r) species are formed (A=spermidine, spermine, L(z-)=acetate, malonate, 1,2,3-propanetricarboxylate, 1,2,3,4-butanetetracarboxylate; r=1...m+n-1, where m and n are the maximum degree of protonation of the amine and of the carboxylic ligand, respectively), and their stability is a function of charges involved in the formation reaction. For the equilibrium H(i)A(i+)+H(j)L((j-z))=ALH(i+j)((i+j-z)) the linear relationship logK(ij)=0.46 zeta (zeta=mid R:i(z-j)mid R:) was found. By means of this simple equation a mean free energy value can be obtained per salt bridge (n), namely -DeltaG degrees =5.25+/-0.15 kJ mol(-1)n(-1). Species formed by the highest charged ligands are quite stable (K>10(3) mol(-1) dm(3)) and potentially play an important role in the speciation of biofluids, as shown by speciation diagrams and simulated experiments.     

Novel topological index F based on incidence matrix

Based on incidence matrix W, the novel topological index F is defined by the matrices L, W, X as F = LWX. The properties, the chemical environments, and the interaction of the vertexes in a molecule are taken into account in this definition. Several good QSPR models in the hetero-atom-containing organic compounds and inorganic compounds are obtained. Moreover, based on the definition of F and the values C(i) of the vertexes or the values (m)F(ij) of the chemical bonds, we have obtained serial indices, (m)F(v), (m)F(b), and F(w). They are successfully applied to QSPR models and good correlation results have been obtained as well.     

蛋白质分子的HNP格点模型

从 6 0种球形蛋白质的结构出发 ,采用Miyazawa Jernigan相互作用矩阵 ,计算了蛋白质分子中氨基酸之间的相互作用能 .发现构成蛋白质分子的 2 0种氨基酸可分成疏水 (Hydrophobic ,H)、中性 (Neutral,N)、亲水(Hydrophilic ,P)基团 .在计算它们之间相互作用能的基础上 ,建立了蛋白质分子的HNP格点模型 .用这个模型计算了二维蛋白质分子在自然态 (Nativestate)时的构象性质 .同时研究了氨基酸序列为HHNHNPNHPP HPNPPHPHPPHHPHNH的折叠过程 ,得到其基态能量为 - 6 4 89RT .这能为研究球形蛋白质的构象性质及折叠过程提供一种更合理的格点模型     

[(C2H5)4N]2{Fe4S4[S2CN(C2H5)2]4}的晶体和分子结构

[(C2H5)4N]2{Fe4S4[S2CN(C2H5)2]4}单晶样品在Nicolet-R3四圆衍射仪上收集X射线衍射数据. 分析结果给出其晶胞参数: a=22.125(6), b=11.313(3),c=25.053A; β=118.05(2)°; V=5534.19A^3, Z=4, 空间群Cc. 衍射数据经过Lρ因子和经验吸收效应校正. 分子中铁原子的位置从三维Patterson图上得到. 接着经过若干轮Fourier和差Fourier电子云密度合成, 发现全部其余非氢原子的坐标.氢原子位置根据理论模型计算. 结构修正最后收敛至R=0.073, Rw=0.069. 标题化合物是由[(C2H5)4N]^+和{FeS4[S2CN(C2H5)2]}^2^-组成的离子型化合物. 结构的主要特点表现在阴离子上, 而在阴离子中含有类立方烷型簇核Fe4S4. 该簇核中每个铁原子与五个硫原子配位, 其配位多面体构型均为畸变的四方锥.     

Predicting internal protein dynamics from structures using coupled networks of hindered rotators

Internal motions in proteins, such as oscillations of internuclear vectors u(N(i)H(i) (N)) of amide bonds about their equilibrium position, can be characterized by a local order parameter. This dynamic parameter can be determined experimentally by measuring the longitudinal and transverse relaxation rates of (15)N(i) nuclei by suitable NMR methods. In this paper, it is shown that local variations of order parameters S(ii) (2) can be predicted from the knowledge of the structure. To this effect, the diffusive motion of the internuclear vector u(N(i)H(i) (N)) is described in a potential that takes into account the deviations of the angles theta(ij) between u(N(i)H(i) (N)) and neighboring vectors u(N(j)H(j) (N)) from their average value and similarly of deviations of the angles subtended between u(N(i)H(i) (N)) and u(X(j)Y(j)), where X(j) and Y(j) are heavy atoms in the vicinity of the u(N(i)H(i) (N)) vector under investigation. It is shown how the concept of vicinity can be defined by a simple cutoff threshold, i.e., by neglecting vectors u(X(j)Y(j)) with distances d(N(i),X(j))>7.5 A. The local order parameters S(ii) (2) can be predicted from the structure using a limited set of coordinates of heavy atoms. The inclusion of a larger number of heavy atoms does not improve the predictions. Applications to calmodulin, calbindin, and interleukin 4 illustrate the success and limitations of the predictions.     

Electron bubbles in helium clusters. I. Structure and energetics

In this paper we present a theoretical study of the structure, energetics, potential energy surfaces, and energetic stability of excess electron bubbles in ((4)He)(N) (N=6500-10(6)) clusters. The subsystem of the helium atoms was treated by the density functional method. The density profile was specified by a void (i.e., an empty bubble) at the cluster center, a rising profile towards a constant interior value (described by a power exponential), and a decreasing profile near the cluster surface (described in terms of a Gudermannian function). The cluster surface density profile width (approximately 6 A) weakly depends on the bubble radius R(b), while the interior surface profile widths (approximately 4-8 A) increase with increasing R(b). The cluster deformation energy E(d) accompanying the bubble formation originates from the bubble surface energy, the exterior cluster surface energy change, and the energy increase due to intracluster density changes, with the latter term providing the dominant contribution for N=6500-2 x 10(5). The excess electron energy E(e) was calculated at a fixed nuclear configuration using a pseudopotential method, with an effective (nonlocal) potential, which incorporates repulsion and polarization effects. Concurrently, the energy V(0) of the quasi-free-electron within the deformed cluster was calculated. The total electron bubble energies E(t)=E(e)+E(d), which represent the energetic configurational diagrams of E(t) vs R(b) (at fixed N), provide the equilibrium bubble radii R(b) (c) and the corresponding total equilibrium energies E(t) (e), with E(t) (e)(R(e)) decreasing (increasing) with increasing N (i.e., at N=6500, R(e)=13.5 A and E(t) (e)=0.86 eV, while at N=1.8 x 10(5), R(e)=16.6 A and E(t) (e)=0.39 eV). The cluster size dependence of the energy gap (V(0)-E(t) (e)) allows for the estimate of the minimal ((4)He)(N) cluster size of N approximately 5200 for which the electron bubble is energetically stable.     

簇合物〔WOS_3Cu_3(V-pic)_6〕Br 的合成和晶体结构

簇合物〔ＷＯＳ３Ｃｕ３（γ－ｐｉｃ）６〕Ｂｒ（Ｃ３６Ｈ４２ＢｒＯＮ６Ｓ３Ｃｕ３Ｗ, Ｍｒ＝ １１２５．３４） 属于三方晶系,空间群为Ｐ３,晶胞参数为：ａ＝ １２．２６４（５）, ｃ＝ １５．９０５（８） , γ＝ １２０．００°, Ｖ＝２０７１（２）３, μ（ＭｏＫα）＝ ５．４９０ｍ ｍ － １, Ｚ＝ ２, Ｄｃ＝ １．８０４ｇ／ｃｍ ３, Ｆ（０００）＝ １１０４ , Ｒ＝ ０．０５２ , ｗ Ｒ＝ ０．０５３． 可观察衍射点１９０１ （Ｉ≥２σ（Ｉ））。该簇合物的分子由游离的阴离子Ｂｒ－ 和簇阳离子〔ＷＯＳ３Ｃｕ３（γ－ｐｉｃ）６〕＋ 构成。阳离子中的Ｗ 原子、Ｓ原子和Ｃｕ原子构成１ 个巢状骨架结构,且该结构中存在一个通过Ｗ 和Ｏ原子的Ｃ３ 轴。     

Estimation of electronic coupling in pi-stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of V(da) because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a pi stack, where donor and acceptor are separated by a bridging unit, can be obtained as V(da) = (E(2)-E(1))mu(12)R(da) + (2E(3)-E(1)-E(2))2mu(13)mu(23)R(da) (2), where E(1), E(2), and E(3) are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, mu(ij) is the transition dipole moments between the states i and j, and R(da) is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model.     

The effective surface energy of heterogeneous solids measured by inverse gas chromatography at infinite dilution

Inverse gas chromatography (IGC) at infinite dilution has been widely used to access the nonspecific surface free energy of solid materials. Since most practical surfaces are heterogeneous, the effective surface energy given by IGC at infinite dilution is somehow averaged over the whole sample surface, but the rule of averaging has thus far not been established. To address this problem, infinite dilution IGC analysis was carried out on mixtures of known heterogeneity. These materials are obtained by mixing two types of solid particles with significantly different surface energies as characterized individually with IGC, and results are obtained for binary combinations in varying proportions. It is found that when all surface components have the same accessibility by probe molecules, the effective surface energy of such a heterogeneous surface is related to the surface energy distribution by a square root linear relationship, square root sigma(eff)(LW)= summation operator (i)phi(i) square root sigma(i)(LW), where sigma(i)(LW) refers to the nonspecific (Lifshitz-van der Waals) surface energy of patches i, and phi(i) to their area fraction.     

Anisotropic interaction and stereoreactivity in a chemi-ionization process of OCS by collision with He*(2(3)S) metastable atoms

Ionic-state-resolved collision energy dependence of Penning ionization cross sections for OCS with He*(2(3)S) metastable atoms was measured in a wide collision energy range from 20 to 350 meV. Anisotropic interaction potential for the OCS-He*(2(3)S) system was obtained by comparison of the experimental data with classical trajectory simulations. It has been found that attractive potential wells around the O and S atoms are clearly different in their directions. Around the O atom, the collinear approach is preferred (the well depth is ca. 90 meV), while the perpendicular approach is favored around the S atom (the well depth is ca. 40 meV). On the basis of the optimized potential energy surface and theoretical simulations, stereo reactivity around the O and S atoms was also investigated. The results were discussed in terms of anisotropy of the potential energy surface and the electron density distribution of molecular orbitals to be ionized.     

Prediction of 31P nuclear magnetic resonance chemical shifts for phosphines

Quantitative relationships of the (31)P NMR chemical shifts of the phosphorus atoms in 291 phosphines with the atomic ionicity index (INI) and stereoscopic effect parameters (epsilon(alpha), epsilon(beta), epsilon(gamma)) were primarily investigated in this paper for modeling some fundamental quantitative structure-spectroscopy relationships (QSSR). The results indicated that the (31)P NMR chemical shifts of phosphines can be described as the quantitative equation by multiple linear regression (MLR): delta(p)(ppm)= -174.0197-2.6724INI+40.4755epsilon(alpha)+15.1141epsilon(beta)-3.1858epsilon(gamma), correlation coefficient R=0.9479, root mean square error (rms)=13.9, and cross-validated predictive correlation coefficient was found by using the leave-one-out procedure to be Q(2)=0.8919. Furthermore, through way of random sampling, the estimative stability and the predictive power of the proposed MLR model were examined by constructing data set randomly into both the internal training set and external test set of 261 and 30 compounds, respectively, and then the chemical shifts were estimated and predicted with the training correlation coefficient R=0.9467 and rms=13.4 and the external predicting correlation coefficient Q(ext)=0.9598 and rms=10.8. A partial least square model was developed that produced R=0.9466, Q=0.9407 and Q(ext)=0.9599, respectively. Those good results provided a new, simple, accurate and efficient methodology for calculating (31)P NMR chemical shifts of phosphines.     

5-氯水杨醛缩乙醇胺合铜(Ⅱ)的微波直接合成、晶体结构及抑菌活性

以5-氯水杨醛、乙醇胺和氯化铜为原料,在微波作用下合成了5-氯水杨醛缩乙醇胺合铜(Ⅱ)配合物。 利用红外光谱、元素分析和单晶X射线衍射方法对目标化合物进行了表征,标题配合物为单斜晶系,P21/n空间群。晶胞参数：a=0.49793(6) nm,b=1.7037(2) nm,c=1.07120(12) nm,β=94.579(3)°,F(000)=470,Z=2,V=0.905(8) nm3,Dc=1.689 mg/m3,R[I＞2σ(I)],R1=0.0624,ωR2=0.1555。 配合物分子中,2种Schiff碱配体中的2个O原子和2个N原子参与配位,Cu(Ⅱ)处于四边形配位中心。 用MTT法测得标题配合物对6种革兰氏细菌（B.subtilis、S.aureus、S.faecalis、P.aeruginosa、E.coli和E.cloacae）的最小抑制浓度分别为12.25、25、12.5、12.5、6.25和6.25 mg/L。     

不饱和链烃沸点的拓扑研究

基于邻接矩阵与边价 (fi)定义边价连接性指数 ( mF) ,其中的0 F ,1 F与 2 94种不饱和链烃 (包括烯烃、炔烃及烯炔烃 )的沸点 (Tb)关联 ,得到良好的数学模型 :ln( 70 0 -Tb) =6 5 2 3 3 1-0 0 0 4880 F2 -0 3 46771 F0 5(n =2 94,R =0 9979,R2 =0 995 8,F =3 490 4,S =5 12 ) ,该回归模型经Jackknife法检验具有总体稳健性 .可以预示 ,该指数将在定量构效关系研究中成为重要参数 .     

Is E112 a relatively inert element? Benchmark relativistic correlation study of spectroscopic constants in E112H and its cation

We report the first results of relativistic correlation calculation of the spectroscopic properties for the ground state of E112H and its cation in which spin-orbit interaction is taken into account non-perturbatively. Studying the properties of E112 (eka-Hg) is required for chemical identification of its long-lived isotope, (283)112. It is shown that appropriate accounting for spin-orbit effects leads to dramatic impact on the properties of E112H whereas they are not so important for E112H(+). The calculated equilibrium distance, R(e) (calc)=1.662 Angstrom, in E112H is notably smaller than R(e) (expt)=(1.738+/-0.003) Angstrom and R(e) (calc)=1.738 Angstrom in HgH, whereas the dissociation energy, D(e) (calc)=0.42 eV, in E112H is close to D(e) (expt)=0.46 eV and D(e) (calc)=0.41 eV in HgH. These data are quite different from R(e) (NH)=1.829 Angstrom and D(e) (NH)=0.06 eV obtained for E112H within the scalar-relativistic Douglas-Kroll approximation. Our results indicate that E112 should not be expected to behave like a noble gas in contrast to the results by other authors.     

Development of a cooled He*(23S) beam source for measurements of state-resolved collision energy dependence of Penning ionization cross sections: Evidence for a stereospecific attractive well around methyl group in CH3CN

A low-temperature discharge nozzle source with a liquid-N(2) circulator for He*(2(3)S) metastable atoms has been developed in order to obtain the state-resolved collision energy dependence of Penning ionization cross sections in a low collision energy range from 20 to 80 meV. By controlling the discharge condition, we have made it possible to measure the collision energy dependence of partial ionization cross sections (CEDPICS) for a well-studied system of CH(3)CN+He*(2(3)S) in a wide energy range from 20 to 350 meV. The anisotropic interaction potential energy surface for the present system was obtained starting from an ab initio model potential via an optimization procedure based on classical trajectory calculations for the observed CEDPICS. A dominant attractive well depth was found to be 423 meV (ca. 10 kcal/mol) at a distance of 3.20 A from the center of mass of CH(3)CN in the N-atom side along the CCN axis. In addition, a weak attractive well (ca. 0.9 kcal/mol) surrounding the methyl group (-CH(3)) has been found and ascribed to the interaction between an unoccupied molecular orbital of CH(3)CN and 2s atomic orbital of He*(2(3)S).     

簇合物〔WOS_3 Ag_3 Br(PPh_3)_3〕·(OPPh_3)的合成和晶体结构

报道了〔WOS3Ag3Br(PPh3) 3〕·(OPPh3)簇合物 (C72 H6 0 Ag3BrO2 S3P4W ,Mr=176 4.6 1)单晶的合成和结构。该晶体属于三方晶系 ,空间群为R3 ,晶胞参数 :a =16 .14 0 (3) ,c =2 3 .0 0 3(4) ,V =5 189.4(15 ) 3,μ(MoKα) =3 .2 98mm- 1 ,Z =3 ,F(0 0 0 ) =2 5 98,Dc=1.6 94g/cm3。独立衍射点 2 181,可观察衍射点 195 2 (I≥ 2σ(I) ) ,R =0 .0 496 ,wR =0 .12 48。该晶体由簇合物分子〔WOS3Ag3Br(PPh3) 3〕和以P为中心的扭曲四面体结构的中性分子OPPh3 构成 ,其中的簇合物分子的骨架为由1个W原子、3个S原子、3个Ag原子和 1个Br原子构成的立方烷状。W、O(1)和Br原子位于C3轴上。     

4，6-二甲基-2-巯基嘧啶乙酸·邻菲咯啉双核铜配合物的合成及晶体结构

合成了标题化合物[Cu2（phen）2（C8H9N2O2S）（H2O）（OH）]·（ClO4）2,用元素分析和X射线单晶衍射法对其进行了表征和结构分析．该化合物为单斜晶系,空间群：P2（1）．晶胞参数a=8．2295（7）nm,b=18．0274（15）nm,c=24．5459（19）nm,β=96．240（2）°,V=3620．0（5）nm^2,Z=4,Dc=1．686g／cm^3,Mr=918．64,F（000）=1864,μ（Mo—Kα）=1．452mm^-1,R1=0．1091,ωR2=0．1380．两个铜原子通过来自羟基的氧、水分子和4,6-二甲基-2-巯基嘧啶乙酸根桥连．2个铜原子的配位环境基本相同,都具有5配位扭曲的四方锥构型,Cu…Cu之间的距离为0．30189（8）nm．