Substructure, subgraph, and walk counts as measures of the complexity of graphs and molecules.

In discussions of unsaturated compounds represented by multigraphs it is necessary to distinguish between the notions of substructure and subgraph. Here the difference is explained and exemplified, and a computer program is introduced which for the first time is able to construct and count all substructures and subgraphs for a colored multigraph (a molecular compound which may contain unsaturation and heteroatoms). Construction of all substructures and subgraphs is computationally demanding; therefore, two alternatives are pointed out for the treatment of large sets of compounds: (i) Often it will suffice to consider counts of substructures/subgraphs up to a certain number of edges only, information which is provided by the program much more rapidly. (ii) It is shown that information equivalent to that gained from substructure or subgraph counts is often far more easily available using walk counts. Some problems and their consequences for substructure/subgraph/walk counts are discussed that arise from the models used in organic chemistry for certain compounds such as aromatics and from the necessity to express qualitative features of molecular structures numerically.     

Analytical parameter estimation by a general non-linear regression software package with user-defined mathematical model implementation

Summary A general purpose non-linear regression program is presented, particularly allowing an easy implementation of user-defined models of analytical signals and responses. Considerations about using non-linear regression in practice are made. The structure of the program is explained. The different modules show the convenient use of the package. Some typical applications of the method with different mathematical models are shown.

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Bestimmung von analytischen Parametern durch ein Programmpaket basierend auf nicht-linearen Regressionen und einem Benutzer-definierten mathematischen Modell

     

Perturbed enantiomorphic-site model

The perturbed enantiomorphic-site (E) model was developed for the analysis of tacticity of Ziegler-Natta polymers. Theoretical probability expressions for tacticity diads, triads, tetrads and pentads were derived, and a computer program incorporating perturbed enantiomorphic-site and Bernoullian models was written to facilitate NMR analysis. Examples are shown of the use of the perturbed models to study the ¹³C NMR tacticity of poly(propylene) made with homogeneous metallocene catalysts. The perturbed E model is shown to be a suitable theoretical framework for the analysis of many polymers made with these catalysts.     

A multipole approximation of the electrostatic potential of molecules

The problem of approximating three-dimensional spatial distributions of quantum-mechanical electrostatic potentials of molecules by analytic potentials on the basis of atomic charges, real dipoles, and atomic multipoles up to quadrupoles inclusive was considered. Real dipole potentials are created by pairs of point charges of opposite signs, and the search for their arrangement in the volume of a molecule is part of the approximation problem. A FitMEP program was developed for the optimization of the parameters of models of the types specified taking into account molecular symmetry. It was shown for the example of several molecules (HF, CO, H₂O, NH₃, CH₄, formaldehyde, methanol, formamide, ethane, cyclopropane, cyclobutane, cyclohexane, tetrahedrane, cubane, adamantane, ethylene, and benzene) that the real dipole and atomic multipole models gave errors in approximated quantum-mechanical electrostatic potential values smaller by one or two orders of magnitude compared with the atomic charge model. The atomic charge model was shown to be virtually inoperative as applied to saturated hydrocarbons. Real dipole models were slightly inferior to atomic multipole models in quality but had all the advantages of the potential of point charges as concerned simplicity and compactness, and their use in potential energy calculations did not require changes in the existing program codes.     

Appraisal of an Empirical Model for Simulation of Retention from Structure in Temperature-Programmed Gas Chromatography

The solvation parameter model and response surface methodology are evaluated for the prediction of retention in temperature-programmed gas chromatography. A large and varied group of compounds were separated at a constant flow rate on three columns of different selectivity (DB-1701, DB-210 and EC-Wax) with initial temperature in the range 60–120 °C and program rates of 1–15 °C min^?1. The solvation parameter model provides an acceptable fit to the experimental retention factors independent of column identity, initial temperature and program rate. The system coefficients of the solvation parameter model are shown to fit a second order program rate model of the form system coefficient = a_o + a₁ X + a₂ X ² where X is the program rate (°C min^?1) and a_o, a₁ and a₂ are fitting coefficients with no physical significance. Response surface methodology was used to derive empirical models to predict system coefficients with program rate and initial temperature as variables. These models explain the experimental data quite well but are local models that depend on the average properties of the solutes used for their derivation. Since they dependent on solute identity, these models are unsuitable for the general prediction of retention from structure, but may prove useful for estimating retention associated with variation in experimental variables for a defined group of compounds.     

Thermal explosion model and calculation of sphere fireworks and crackers

In order to analyze thermal safety of fireworks and crackers, thermal explosion models of three kinds of sphere fireworks and crackers with different structures are achieved on the basis of thermal explosion theory, and thermal resistance of shell and effective Biot number are deduced as for boundary conditions. Two models are calculated with target-shooting method in Matlab program, and the rationality is proved through comparison of numerical solution and classical solution. Meanwhile, calculation steps are shown about a type of firework. The study has a great significance to thermal safety analysis of fireworks and crackers.     

Modelling light diatomics trapped in rare gas matrices: H2, HD and D2 in Ar,Kr and Xe

The different models allowing the calculations of the rovibrational frequency shifts with respect to the free molecule of a molecular impurity embedded in a rare gas crystal are reviewed. It is shown that models which account for the translational motion of the impurity yield reliable results, the effects of the rare-gas translation seem to be less important. The different models currently used are described in detail and the computational procedures are discussed. Finally, it is shown that for heteronuclear diatomics, the translation-rotation coupling could play an important role.     

Computer implementation of simulation models for non-linear,non-ideal chromatography: Part 2. Numerical Experiments and Results [l]

The more practical aspects of simulation of discrete mathematical models are described. Particular attention is given to the model describing the behaviour of mass transport m Chromatographic columns with a non-linear isotherm and with or without longitudinal dispersion. Rules for building general usable simulation software are explained. An outline of the program, without extensive treatment of program listings and flow diagrams, is given and experimental conditions and results are discussed.     

ThermoData Engine (TDE) software implementation of the dynamic data evaluation concept. 7. Ternary mixtures

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present paper describes the first application of this concept to the evaluation of thermophysical properties for ternary chemical systems. The method involves construction of Redlich-Kister type equations for individual properties (excess volume, thermal conductivity, viscosity, surface tension, and excess enthalpy) and activity coefficient models for phase equilibrium properties (vapor-liquid and liquid-liquid equilibrium). Constructed ternary models are based on those for the three pure component and three binary subsystems evaluated on demand through the TDE software algorithms. All models are described in detail, and extensions to the class structure of the program are provided. Reliable evaluation of properties for the binary subsystems is essential for successful property evaluations for ternary systems, and algorithms are described to aid appropriate parameter selection and fitting for the implemented activity coefficient models (NRTL, Wilson, Van Laar, Redlich-Kister, and UNIQUAC). Two activity coefficient models based on group contributions (original UNIFAC and NIST-KT-UNIFAC) are also implemented. Novel features of the user interface are shown, and directions for future enhancements are outlined.     

测定晶体结构的系统试差法的研究(Ⅲ)──SYSTEM 90程序系统和应用

介绍了最近研究的系统试差法的基本公式和它的程序系统SYSTEM90的构成．应用该程序系统对收集到的5个难解结构进行了成功的测定．实验结果显示了SYSTEM90程序系统的威力．最后在分析的基础上，提出了系统试差法程序系统不同于其它直接法的四个特点．     

测定晶体结构的系统试差法的研究(III) SYSTEM 90程序系统和应用

介绍最近研究的系统试差法的基本公式和它的程序系统ＳＹＳＴＥＭ９０的构成，应用该程序系统对收集到的５个难解结构进行了成功的测定，实验结果显示了ＳＹＳＴＥＭ９０程序系统的威力，最后在分析的基础上，提出了系统试差法程序系统不同于其它直接法的四个特点。     

O/F-substitution in BiVO4: Defect structures,phase stability and optical properties

In a recent experimental study it has been shown, that fluorine-containing bismuth vanadate (F:BiVO₄) reveals enhanced photoelectrochemical activity compared to pristine BiVO₄. This work is a combined experimental and theoretical analysis of structural and electronic properties of F:BiVO₄. A theoretical analysis of three different possible defect models for F:BiVO₄ was carried out. The structures are optimized with the PBE + U method employing the GPAW program code. The most stable defect configuration corresponds to fluorine incorporation accompanied by the formation of cation vacancies, which is in good agreement with experimental results. The diffraction pattern of the calculated defect structure is compared to measured XRD data. Both, experiment and theory, predict a small band gap narrowing under O/F-substitution. For the measurements diffuse reflectron spectra were collected. Furthermore the influence of fluorine incorporation on the phase stability was investigated experimentally by high-temperature X-ray powder diffraction measurements at different temperatures and compared to theoretical results collected by DFT calculations.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

A new computer program for QSAR-analysis: ARTE-QSAR

A new computer program has been designed to build and analyze quantitative-structure activity relationship (QSAR) models through regression analysis. The user is provided with a range of regression and validation techniques. The emphasis of the program lies mainly in the validation of QSAR models in chemical applications. ARTE-QSAR produces an easy interpretable output from which the user can conclude if the obtained model is suitable for prediction and analysis.