Comments on the symmetry-adapted perturbation treatments of molecular interaction

Symmetry-adapted perturbation theories published so far are criticised. Extra conditions imposed in most of these formalisms are found to be not always physically adequate. We conclude that the formalism proposed by Hirschfelder and Silbey is the most appropriate.     

TGSA: A molecular superposition program based on topo‐geometrical considerations

In this article, a new molecular alignment procedure to provide general‐purpose, fast, automatic, and user‐intuitive three‐dimensional molecular alignments is presented. This procedure, called Topo‐Geometrical Superposition Approach (TGSA), is only based on comparisons of atom types and interatomic distances; hence, the procedure can handle large molecular sets within affordable computational costs. The method is able to accurately align 3D structures using the common molecular substructures, as inferred by the bonding pattern (atom correspondences), where present. The algorithm has been implemented into a program named TGSA99, and it has been tested over eight different molecular sets: flavilium salts, amino acids, indole derivatives, AZT, steroids, anilide derivatives, poly‐aromatic‐hydrocarbons, and inhibitors of thrombine. The TGSA algorithm performance is evaluated by means of computational time, number of superposed atoms, and index of fit between the compared structures. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 255–263, 2001     

Mathematical basis of approximate MO theories: Origin of mulliken's magic formula

The mathematical basis for the Ruedenberg's and Mulliken's approximations is given in a general framework.     

Quantum chemical study of the geometrical and electronic structure of niobium pentafluoride

The geometrical and electronic structure of various configurations of niobium pentafluoride is studied in the nonrelativistic approximation of the DV-X_α method. It is shown in a cluster approximation that the presence of the NbF₅ monomer in various geometrical configurations and of the cyclic [NbF₅]₃ trimer (D_3h symmetry) is most probable for the liquid and gaseous phases. Formation of infinite [NbF₅]_n chains is unlikely. For the most stable clusters, the calculated geometrical parameters are in satisfactory agreement with the available experimental data.     

量子化学计算中基组效应对几何结构和性质影响的研究

本文选择28个有代表性的化合物,在20种基组下进行量子化学计算,用Gaussian98(A.11)和AIM2000(V2.0)对它们进行研究。在分子成键性质的分析和判断中,使用AIM和NBO方法得到的结果比采用Mu llik-en集居分析方法更合理。通过系统化学计算表明,高级别的方法和基组是获得可靠的分子几何结构和性质的必要保证。采用6-31 G*以上的基组可以得到可信的分子几何结构。高级别的振动频率计算是确定分子稳定存在的一项必不可少的工作。b31yp/cc-pVDZ是一种经济的、各种体系下计算结果可靠的计算水平。在分子成键性质的分析和判断中,AIM和NBO方法可以给出合理可靠的结果。采用Mu lliken集居分析方法,可能会给出不可靠的结果。     

The molecular basis of electroporation

Background  

Electroporation is a common method to introduce foreign molecules into cells, but its molecular basis is poorly understood. Here I investigate the mechanism of pore formation by direct molecular dynamics simulations of phospholipid bilayers of a size of 256 and of more than 2000 lipids as well as simulations of simpler interface systems with applied electric fields of different strengths.     

Ab initio calculations on large molecules using molecular fragments. Generalization of the molecular fragment basis at the minimum basis set level

By determining basis set parameters in molecular environments using other criteria than total energy, it is shown that a generalization of the molecular fragment basis can be obtained in which calculated geometric and electronic structural properties are predicted substantially better than with other basis sets of similar size. As a first step in the development of a series of basis sets having successively greater flexibility and accuracy, several single-zeta basis sets are created, using a two-Gaussian contraction for each basis orbital. The best of these basis sets produced calculated geometric and electronic properties for a series of molecules that model a wide variety of organic molecules that are of better accuracy than the corresponding STO -2G basis, and similar in most cases to STO -3G. In addition, the basis set is shown to be applicable in either a Cartesian Gaussian basis or a floating spherical Gaussian basis.     

Polymer and organic molecules ordered via epitaxy: geometrical and molecular interactions

Control of structural order at the molecular level for both conventional linear polymers and conjugated polymers with valuable opto‐electronic properties has major consequence on the macroscopic properties of these polymers. Though the traditional means of orientation of polymer was mechanical deformation, presently extensive works are concerned with a more controlled way of orientation: epitaxial crystallisation. Most of the first documented examples of epitaxial growth of conventional polymers on single crystals followed the well‐established geometrical rules of best matching. However, recent examples show off more subtle rules of selection. Analogous cases, following or breaking the matching rules, have been observed for diacetylenes ordered via epipolymerisation on single crystals. Hereafter, representative examples of the structural matching rules are depicted first, and then recent examples, which depart from the simple geometrical fitting, are described. The analysis of the former leads to define the subtle matching rules applying for polymers linked to their conformational adaptability. The analysis of the latter gives the opportunity to discuss the relative influence of geometrical and molecular interactions between the deposit and the substrate.     

Influence of chemical treatments on adhesion properties of hemp fibres

In addition to be an environmentally friendly material, hemp fibres are also inexpensive reinforcements in thermoplastics or concrete composites, due to their intrinsic mechanical, thermal and acoustic properties. The morphology of hemp fibres has been chemically modified in order to enhance the matrix/fibre interface and has been examined by Scanning Electron Microscopy (SEM). In this paper, Gas Chromatography (GC) and Atomic Force Microscopy (AFM) were used to investigate the influence of treatments on the composition of hemp fibres and also on the micro-adhesive interactions between a silica colloidal probe and the surface of the fibres using Chemical Force Microscopy (CFM). Microscopy studies and chemical analysis showed that each treatment tends to lead to a morphology of interconnected web-like structure of hemp fibres. It was found that on an average, the adhesion force, contribution of capillary force and Van der Waals' forces, is higher in the case of NaOH treatment.     

The molecular basis of the adsorption of xylans on cellulose surface

In order to model the adsorption of xylan on cellulose, we have simulated, at the atomic level, the gas phase adsorption of small xylan fragments having 5 skeletal β (1 → 4) xylosyl residues (X₅), using molecular dynamics simulations. A first regime was considered, corresponding to a low surface coverage, with the adsorption of isolated X₅ in various initial orientations. In this regime, the simulation indicated that X₅ moved toward extended conformations, some of them being helical, with the possibility of either 2₁ or left-handed 3₁ helices. During the simulation, the X₅ fragments became preferentially oriented, parallel or anti parallel with respect to the cellulose chain axis. Substitution of the X₅ backbone by either GlcA and/or Araf side chains had no major influence on either the conformation or the efficiency of the interaction. However, the presence of side chains favored orientations of the X₅ backbone inclined with respect to the cellulose chain axis. In a second regime corresponding to monolayer coverage, the geometrical features of the adsorption of the xylan fragments on cellulose was roughly the same as that in the individual coverage situation. In this case, the monolayer became equilibrated at 0.14 g of xylan fragments for each g of cellulose, a figure that compared favourably with the values obtained in experimental adsorption of xylan on bacterial cellulose.