Transition state geometry in radical abstraction reactions: comparison of interatomic distances in the intersecting parabolas and Morse curves models with quantum-chemical calculations

Interatomic distances in the transition state were estimated for the reactions of radical abstraction: H^· + H₂, H^· + HCl, H^· + CH₄, N^·H₂ + NH₃, HO^· + H₂O, HO₂ ^· + HOOH, and C^·H₃ + SiH₄. The calculation was performed by the quantum-chemical density functional method or coupled clusters method (QCH), as well as by the methods of intersecting parabolas (IPM) and Morse curves (IMM), using experimental data (activation energies and reaction enthalpies). The results of the latter two methods are close to the quantum-chemical calculation and differ only by the increment a: r(IPM or IMM) = a + r(QCH), where a = –4.5·10^–12 m for IPM and a = +1.9·10^–12 m for IMM.     

Solvothermal Synthesis, Crystal Structure and Electrochemical Property of Complex [Co(p-MBA)2(2,2''-bipy)(H2O)]·(H2O)

One novel complex [Co(p-MBA)2(2,2'-bipy)(H2O)]·(H2O) has been synthesized by the reaction of p-methylbenzoic acid with 2,2'-bipyridine in the solvent mixture of water and methanol. It crystallizes in triclinic, space group P-1 with a=0.70479(14), b=1.1211(2), c=1.6718(3) nm, α=103.806(3), β=90.795(3), γ=104.207(3)°, V=1.2399(4) nm3, Mr=512.41, Dc=1.373 g/cm3, Z=2, F(000)=532, μ=0.733 mm-1, R=0.0432 and wR=0.0957. The crystal structural analysis shows that the cobalt atom is coordinated with three oxygen atoms from two p-methylbenzoic acids and one water molecule and two nitrogen atoms from one 2,2'-bipyridine,forming a distorted square-pyramidal coordination geometry. The cyclic voltammetry behavior of the complex is also reported.     

C_(74)的结构、电子光谱及三阶线性光学性质的理论研究

用密度泛函（DFT）方法（BLYP/3－21G~*）研究了C_(74)的稳定几何构型。用 ZINDO及ab initio GIS两种方法对C_(74)的电子光谱进行了计算，预测C_(74)在红 外区域有光谱吸收。计算了C_(74)的三阶非线性光学系数<γ>为1.483 * 10~(-32) esu，它比C_(60)的<γ>（8.84 * 10~(-34) esu）要大得多。预测C_(74)亦将是 一种有很好应用前景的磁性材料。     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

烷基吡啶及氯化铝正负离子结构的密度泛函研究

采用量子化学密度泛函方法对N-烷基吡啶阳离子和阴离子AlCl4-,Al2Cl7-和Al3Cl10-进行了全优化计算,得到了阴阳离子的几何构型和净电荷分布.计算发现,吡啶环上的电子数符合4n 2规则,具有芳香性.吡啶阳离子的LUMO轨道主要由环上原子的2pz所贡献,是反键π分子轨道.AlCl4-,Al2Cl7-和Al3Cl10-的HOMO轨道主要由Cl原子的2px所贡献.推测吡啶阳离子的LUMO与阴离子的HOMO相互作用形成离子液体分子.     

Isomers of C20: an energy profile III

Semiempirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C(20) isomers that are predicted to exist in and around the ring and cage isomers. Using the optimized Cartesian coordinates for the ring and the cage isomers, a saddle-point calculation was performed. The resulting energy profile, consisting of a series of peaks and valleys, is used as a starting point for the identification and location of fifteen additional isomers of C(20) that are predicted to be energetically stable, both via geometry optimizations and force constant analysis. These additional isomers were subsequently determined to lie adjacent to one another on the potential surface and establish a step-wise transformation between the ring and the cage. Transition-state optimization of the Cartesian coordinates at the saddle point between adjacent isomers was performed to quantify the energy of the transition state. The step-wise process from one isomer to another, which extends out over the three-dimensional surface, is predicted to require approximately 15% less energy than that of the direct, two-dimensional transformation predicted in the bowl-cage profile. However, the net atomic rearrangement for the step-wise process is about four times greater than that of the direct process. Although less in energy, the amount of atomic rearrangement in the step-wise process would make the occurrence of such a route prohibitive. Utilizing the direct distance separating the three primary isomers (ring, bowl, cage), the method of triangulation is performed to quantitatively position other C(20) structures on the potential surface, relative to the ring, bowl, and cage isomers.     

Image analysis in the electron microscopy of cellulose protofibrils II. Digital correlation methods

Electron micrographs of parallel arrays of negatively stained ramie cellulose protofibrils were analyzed using the two-dimensional digital autocorrelation function (ACF). The method is based upon the statistical analysis of images in real space. The ACF shows strong parallel streaks of high correlation, and the lateral distance between adjacent streaks allows the mean interfibrillar distance to be estimated as 3.7 nm. The intensity profile along the streaks shows a weak modulation with peaks occurring at integral multiples of 3 or 6 nm. These results provide direct evidence that there is a regular axial texture in the protofibrils, and corroborate the conclusions previously drawn from optical diffraction analysis. Using the difference vectors found in the ACF it has been possible to reduce the picture noise level by linear integration, thereby obtaining an enhanced image. A preliminary result obtained in this way suggests that the projected protofibril morphology associated with the observed axial periodicity is a ribbon-like zigzag structure. Possible applications of the method for future work are discussed.     

LaCO几何、电子结构和化学键的研究

长期以来 ,人们对希土羰基化合物的存在一直持怀疑态度[1 ] ,尽管 Slater[2 ] 等用基质隔离法合成部分希土羰基化合物的成功消除了这种疑问 ,但由于此类化合物高度的不稳定性 ,其几何结构至今尚未确定 ,希土羰基化合物的电子结构和化学键更是困扰人们的重要课题。希土羰基化合物是具有 L n- C键的最简单希土有机金属化合物 ,其结构和性能具有一定的代表性 ,探讨其化学键合本质及其不稳定的原因对深入了解希土金属有机化合物结构和性能的关系具有十分重要的意义。一 .研究方法本文采用洪功义、黎乐民等[3 ] 改进的高精度求解密度泛函理论方…     

Geometries and electronic structures of W4 and W clusters

Geometries and electronic structures of W₄ and W clusters were studied by use of density functional methods B3LYP, B3P86, B3PW91, BHLYP, BLYP, and MPW1PW91. The calculated results indicate that the three‐dimensional structure of singlet state with either D_2d symmetry (B3LYP, B3P86, B3PW91, BLYP, and MPW1PW91) or C_2v symmetry (BHLYP) is the ground state for the W₄ cluster. For the W cluster, the doublet state is preferred, and the most stable structure is also 3D with either D_2d symmetry (B3LYP, B3PW91, BHLYP, BLYP) or C_2v symmetry (B3P86 and MPW1PW91). The calculated electron affinity at B3P86 gives the best performance compared with experiment. For the dissociation channel, W + W₃ is suggested to be the possible route for the W₄ cluster. For the W cluster, W + W is the most likely route for dissociation, in agreement with experiment. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Simultaneous measurement of glucose and glutamine in aqueous solutions by near infrared spectroscopy

A method is described for measuring the concentrations of both glucose and glutamine in binary mixtures from near infrared (NIR) absorption spectra. Spectra are collected over the range from 5000–4000/cm (2.0–2.5μm) with a 1-mm optical path length. Glucose absorbance features at 4710, 4400, and 4300/cm and glutamine features at 4700, 4580, and 4390/cm provide the analytical information required for the measurement. Multivariate calibration models are generated by using partial least squares (PLS) regression alone and PLS regression combined with a preprocessing digital Fourier filtering step. The ideal number of PLS factors and spectral range are identified separately for each analyte. In addition, the optimum Fourier filter parameters are established for both compounds. The best overall analytical performance is obtained by combining Fourier filtering and PLS regression. Glucose measurements are established over the concentration range from 1.66–59.91 mM, with a standard error of prediction (SEP) of 0.32 mM and a mean percent error of 1.84%. Glutamine can be measured over the concentration range from 1.10–30.65 mM with a SEP of 0.75 mM and a mean percent error of 6.67%. These results demonstrate the analytical utility of NIR spectroscopy for monitoring glucose and glutamine levels in mammalian and insect cell cultures.