The lifetime of CFC substitutes studied by a network trained with chaotic mapping modified genetic algorithm and DFT calculations

The hydrohaloalkanes have attracted much attention as potential substitutes of chlorofluorocarbons (CFCs) that deplete the ozone layer and lead to great high global warming. Having a short atmospheric lifetime is very important for the potential substitutes that may also induce ozone depletion and yield high global warming gases to be put in use. Quantitative structure–activity relationship (QSAR) studies were presented for their lifetimes aided by the quantum chemistry parameters including net charges, Mulliken overlaps, E _HOMO and E _LUMO based on the density functional theory (DFT) at B3PW91 level, and the C-H bond dissociation energy based on AM1 calculations. Outstanding features of the logistic mapping, a simple chaotic system, especially the inherent ability to search the space of interest exhaustively have been utilized. The chaotic mapping aided genetic algorithm artificial neural network training scheme (CGANN) showed better performance than the conventional genetic algorithm ANN training when the structure of the data set was not favorable. The lifetimes of HFCs and HCs appeared to be greatly dependent on their energies of the highest occupied molecular orbitals. The perference of the RMSRE comparing to RMSE as objective function of ANN training was better for the samples of interest with relatively short lifetimes. C₂H₆ and C₃H₈ as potential green substitutes of CFCs present relatively short lifetimes.     

The lifetime of CFC substitutes studied by a network trained with chaotic mapping modified genetic algorithm and DFT calculations

The hydrohaloalkanes have attracted much attention as potential substitutes of chlorofluorocarbons (CFCs) that deplete the ozone layer and lead to great high global warming. Having a short atmospheric lifetime is very important for the potential substitutes that may also induce ozone depletion and yield high global warming gases to be put in use. Quantitative structure-activity relationship (QSAR) studies were presented for their lifetimes aided by the quantum chemistry parameters including net charges, Mulliken overlaps, E(HOMO) and E(LUMO) based on the density functional theory (DFT) at B3PW91 level, and the C-H bond dissociation energy based on AM1 calculations. Outstanding features of the logistic mapping, a simple chaotic system, especially the inherent ability to search the space of interest exhaustively have been utilized. The chaotic mapping aided genetic algorithm artificial neural network training scheme (CGANN) showed better performance than the conventional genetic algorithm ANN training when the structure of the data set was not favorable. The lifetimes of HFCs and HCs appeared to be greatly dependent on their energies of the highest occupied molecular orbitals. The perference of the RMSRE comparing to RMSE as objective function of ANN training was better for the samples of interest with relatively short lifetimes. C(2)H(6) and C(3)H(8) as potential green substitutes of CFCs present relatively short lifetimes.     

Reactions of a stable silylene with halocarbons

An unusual product formation is observed for the insertion reaction of the thermally stable silylene Si[(NCH(2)Bu(t))(2)C(6)H(4)-1,2][abbrev. as Si(NN)] into the carbon-halogen bond of alkyl or aryl halides RHal (Hal=Cl, Br). In general, depending on the halogen, the reaction either results in a disilane of type (NN)Si(Hal)-(R)Si(NN) for Hal=Cl or a mixture of disilane and the monosilane (NN)Si(R)(Hal) for Hal=Br. The results are put into context to previously suggested mechanisms. The disilane (NN)Si(Hal)-(R)Si(NN)(Hal=Cl or Br) is thermally labile and mild thermolysis yields the corresponding monosilane (NN)Si(R)(Hal) and silylene 1. Additionally, strong evidence is presented for a radical pathway for the reaction of 1 and RHal.     

Oxygen adsorption on Mo(112) surface studied by ab initio genetic algorithm and experiment

Density functional theory in combination with genetic algorithm is applied to determine the atomic models of p(1x2) and p(1x3) surface structures observed upon oxygen adsorption on a Mo(112) surface. The authors' simulations reveal an unusual flexibility of Mo(112) resulting in oxygen-induced reconstructions and lead to more stable structures than any suggested so far. Comparison of the stabilities of the predicted models shows that different p(1x2) and p(1x3) structures may coexist over a wide range of oxygen pressures. A pure p(1x2) structure can be obtained only in a narrow region of oxygen pressures. In contrast, a pure p(1x3) structure cannot exist as a stable phase. The results of simulations are fully supported by a multitude of experimental data obtained from low energy electron diffraction, x-ray photoelectron spectroscopy, and scanning tunneling microscopy.     

Explosive reactions of liquid mixtures of chlorine trifluoride with hydrocarbons and halocarbons

Combinations of liquid ClF₃ with several hydrocarbons and halocarbons have been caused to explode by sudden mixing at various temperatures from 25° downward. The mixtures occasionally detonate.By fast recording of pressure, flame ionization, and carbon deposition it is found that mixtures derived from all of the fuels tested except perfluorohexane initiate in less than 1 ms at all temperatures down to −70°. An ionic mechanism is proposed. Analysis of the explosion gases indicates that all chemical bonds including CH are labilized owing to the extremely high temperature. Calorimetric measurements agree with calculated heats of explosion.     

Formation of disilanes in the reaction of stable silylenes with halocarbons

Reactions of stable silylenes 1 and 2 with a variety of halogenated organic compounds have been studied. Depending on the nature of the halocarbon, the products can be disilanes, LSiX-LSiR, or monosilanes, LSiXR, or a mixture of both types of products. Hexachloroethane reacts with the silylenes to give mainly the dichlorodisilane, LSiX-LSiX. The experimental results are rationalized in terms of several related free-radical chain mechanisms.     

Problems connected with the analysis of halocarbons and hydrocarbons in the non-urban atmosphere

The problems connected with the measurement of hydrocarbons outside urban areas are considerable: The atmospheric mixing ratios of most of the hydrocarbons are very low--from a few ppb down to some ppt; the mixture of hydrocarbons is extremely complex, ranging from light n-alkanes to alkyl benzenes and terpenes; for measurements in remote areas the logistic conditions often restrict the instrumentation which can be used for sample collection or in situ measurements (such as lack of electric power supply, weight restrictions etc.). Nevertheless, sensitive and sufficiently reliable measurements of hydrocarbons in the non-urban atmosphere are important. Hydrocarbons are important factors in the tropospheric photochemistry (e.g. ozone formation) and can be used as valuable tracers for man-made atmospheric pollutants etc. Other useful tracers for anthropogenic emission are halocarbons such as dichlormethane, tri- and tetrachloroethen etc. The impact of man-made hydrocarbons on the chemistry of the troposphere can only be understood if the extent of natural (biogenic) contributions is known. From measurements of a large variety of hydrocarbons and halocarbons it is often possible to obtain information about the sources of the most important atmospheric hydrocarbon species, even for trace gases with both significant anthropogenic and biogenic sources. In this presentation some of the problems and their solutions connected with such measurements of atmospheric hydrocarbons and halocarbons are presented and discussed. Some of the results obtained by several series of measurements are described, indicating that man-made as well as biogenic hydrocarbons can be important factors for the chemistry of the atmosphere.     

Evaluation of the relationship between spectral and structural similarity in IR spectroscopy

Representation of a structural formula of a compound as a complete set of nonisomorphic k-vertex (2 ≤k≤7) connected fragments is used to evaluate the structural similarity of compounds. The spectra and structures of spectrally or structurally alike compounds are compared statistically using a database containing 32,000 IR spectra and structures. This study reveals some tendencies typical for both full IR spectra and their abbreviated versions represented by sets of most characteristic peaks. Applicability of IR databases to spectrum simulation for compounds with a specified structure is justified statistically. A method is proposed for evaluating the efficiency of a search algorithm selecting structural analogs of the compound from an IR database according to the query spectrum. Translated fromZhurnal Strukturnoi Khimii, Vol. 41, No. 2, pp. 379–390, March–April, 2000.     

Inference of gene regulatory networks with multi-objective cellular genetic algorithm

Reverse engineering of biochemical networks remains an important open challenge in computational systems biology. The goal of model inference is to, based on time-series gene expression data, obtain the sparse topological structure and parameters that quantitatively understand and reproduce the dynamics of biological systems. In this paper, we propose a multi-objective approach for the inference of S-System structures for Gene Regulatory Networks (GRNs) based on Pareto dominance and Pareto optimality theoretical concepts instead of the conventional single-objective evaluation of Mean Squared Error (MSE). Our motivation is that, using a multi-objective formulation for the GRN, it is possible to optimize the sparse topology of a given GRN as well as the kinetic order and rate constant parameters in a decoupled S-System, yet avoiding the use of additional penalty weights. A flexible and robust Multi-Objective Cellular Evolutionary Algorithm is adapted to perform the tasks of parameter learning and network topology inference for the proposed approach. The resulting software, called MONET, is evaluated on real-based academic and synthetic time-series of gene expression taken from the DREAM3 challenge and the IRMA in vivo datasets. The ability to reproduce biological behavior and robustness to noise is assessed and compared. The results obtained are competitive and indicate that the proposed approach offers advantages over previously used methods. In addition, MONET is able to provide experts with a set of trade-off solutions involving GRNs with different typologies and MSEs.     

Optimization of Carbó molecular similarity index using gradient methods

A steepest descent method for optimizing the Carbó molecular similarity index was implemented and evaluated. Comparisons were made between this procedure and the extensively used simplex method. Several data sets were considered, and in each case the gradient method showed a substantial improvement in the time taken for the optimization to converge while comparable similarity values were obtained. In some cases, performance enhancements of up to an order of magnitude were observed. © 1997 by John Wiley & Sons, Inc.     

19F and 1H NMR spectra of halocarbons

19F NMR chemical shifts and coupling constants are reported for 215 compounds. For 77 of these compounds, 1H NMR spectral data are also given. Long-range couplings, including 8J(F,F) and 5J(F,H), are reported. The complexity of halocarbon spectra owing to the presence of rotational isomers, asymmetric centers, long-range couplings, and chlorine isotope effects are illustrated, and the methods used for analyzing such complex spectra are briefly discussed.     

Library search of mass spectra with a new matching algorithm based on substructure similarity.

A new matching algorithm for library searches of mass spectra is presented in this paper. The algorithm is based on the substructure similarity of substances. It emphasizes m/z positions rather than abundance values. 32 spectra, whose corresponding molecular weights are less than 200, were randomly selected from a mass library of 61,993 spectra and taken as targets of library search to illustrate the availability of this algorithm. The results show that the algorithm is better than the one built in a commercial instrument when there is no spectrum of the unknown in the library but there are similar ones.     

Theoretical comparison of conformational properties of molecules: Conformational probability maps and similarity index

The conformational analysis for a molecule is often performed by assuming that the total conformational energy is a function of two dihedral angles. The resulting conformational energy map is sometimes not easy to interpret because what counts is not energy differences but rather the probability distribution map at a given temperature. In the present article, an algorithm to calculate such a map is given. An example concerning N-substituted amino sugars shows how the conformational probability map may be interpreted. In addition, a similarity index is proposed to get a measure of similarity of the conformational properties of two molecules. The index is based upon the analysis of the conformational probability maps for both molecules. © 1993 John Wiley & Sons, Inc.     

The calculation of intermolecular similarity coefficients using an inverted file algorithm

A procedure is described for calculating the similarity between molecules characterised by lists of substructural fragments. The method is very much faster in operation than the conventional method and permits data sets containing some thousands of compounds to be processed.     

醛酮化合物结构与保留指数关系的研究

以非氢原子自身及非氢原子之间的关系为分子结构描述符,对35个醛酮类化合物进行了结构表征。采用多元线性回归和偏最小二乘回归的方法建立了该类化合物结构与色谱保留指数之间的关系模型,两模型的复相关系数(R)分别为0.987和0.981,标准偏差(SD)分别为25.259和32.240。采用"留一法"交互检验和外部样本预测的方法对模型的稳健性和预测能力进行了评价,交互检验的复相关系数(RCV)分别为0.981和0.958,标准偏差(SDCV)分别为34.292和39.652;外部预测的复相关系数(Rtest)分别为0.991和0.990,标准偏差(SDtest)分别为25.749和26.776。结果表明所构建的分子结构描述符能够恰当表现该类化合物结构特征,所建模型具有良好的稳健性和预测能力。     

Calculation of the similarity index of crystal structures: Algorithm,program, and examples

Institute of Inorganic Chemistry, Siberian Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 1, pp. 104–109, January–February, 1991     

Molecular similarity of potential endocrine disruptors: Structural index control of pharmacological clustering

A series of 37 substituted indoles for which estrogen receptor binding data had been reported were studied from a quantitative structure–activity relationship (QSAR) viewpoint. The structures were represented by an established unitary mathematical index, the molecular transform (FT_m), whose derivation is entirely from the geometry‐optimized structure. Data clusters were generated by a primary numerically descending sort of the structure indices and a concurrent secondary numerically descending sort of the binding data. Reversal of numerical descent of the latter served to generate the cluster boundaries. Analysis within and across the clusters permitted a definitive and detailed picture of the influence of substituents and substituent positions on the molecule, and their effect on the biodata, and suggested the structure of a molecule of greater binding ability than any in the database. The relationship of the electronic and charge nature of the molecules to their binding ability was considered. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Thermal electron capture in the mixtures of halocarbons and atmospheric gases

The electron capture processes in the mixtures containing halocarbon (CH₂F₂ or CHF₃) and nitrogen as well as halocarbon, oxygen and carbon dioxide have been investigated. The mechanism has been revealed and the corresponding rate constants have been determined.     

Quantum similarity superposition algorithm (QSSA): a consistent scheme for molecular alignment and molecular similarity based on quantum chemistry

The use of the molecular quantum similarity overlap measure for molecular alignment is investigated. A new algorithm is presented, the quantum similarity superposition algorithm (QSSA), expressing the relative positions of two molecules in terms of mutual translation in three Cartesian directions and three Euler angles. The quantum similarity overlap is then used to optimize the mutual positions of the molecules. A comparison is made with TGSA, a topogeometrical approach, and the influence of differences on molecular clustering is discussed.