Solving incomplete inorganic chemical systems through a fuzzy knowledge frame

A model for the completion and balancing of inconsistent inorganic reactions is presented. A series of fuzzy parameters is proposed. These parameters are considered within a knowledge frame representing inorganic reactions via a semantic/functional network and, through the calculation of possibility measures, allow the completion and solution of such reactions by considering new inorganic species to be added to the reaction. Species to be added are formulated on the basis of atoms present and/or absent in the reaction, along with valence, system features, and a series of flags that determines the cardinality of the possible solution set. Incorporation of the proposed model into an inorganic chemistry formulation system would contribute to the development of powerful computer-assisted learning systems, given the extent of information extracted from a reaction.     

Quantum chemical methods and their applications to chemical reactions

This review is concerned with the impact of quantum chemistry on chemical reactions. Starting from the mid-sixties it focusses on those developments which have enabled us to predict essential features of simple chemical reactions. Thus model theories and computational methods are presented which provide the tools for these predictions. Then procedures to characterize potential surfaces and search methods for reaction paths are described. It is also attempted to relate these features to the terminology of the experimentalist. Finally a systematic survey of the main types of reaction (rearrangement, addition, elimination, substitution) is given.     

Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials

The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.     

Automated chemical resonance generation and structure filtration for kinetic modeling

This work discusses efficient and automated methods for constructing a set of representative resonance structures for arbitrary chemical species, including radicals and biradicals, consisting of the elements H, C, O, N, and S. Determining the representative reactive structures of chemical species is crucial for identification of reactive sites and consequently applying the correct reaction templates to generate the set of important reactions during automated chemical kinetic model generation. We describe a fundamental set of resonance pathway types, accounting for simple resonating structures, as well as global approaches for polycyclic aromatic species. Automatically discovering potential localized structures along with filtration to identify the representative structures was shown to be robust and relatively fast. The algorithms discussed here were recently implemented in the Reaction Mechanism Generator (RMG) software. The final structures proposed by this method were found to be in reasonable agreement with quantum chemical computation results of localized structure contributions to the resonance hybrid.     

Autocatalytic and other general networks for chemical mechanisms,pathways, and cycles: Their systematic and topological generation

Methods to generate a priori all the finite number of possible mechanisms of chemical reactions and/or synthetic pathways or thermodynamic cycles, which we represent by general networks, are given for any number of reaction steps or total number of species (reactants, products, catalysts, and intermediates). General networks do not place limitations on the types of species, e.g. intermediates can be short-lived, thereby participating in at most two elementary reaction steps, or longer-lived, participating in more than one way. Step stoichiometric coefficients can be more than unity. Reactants or products may also act as catalysts or inhibitors. Species vertices and the general networks themselves in which they occur are classified topologically. Topological invariants of the networks with respect to the number of reaction steps are found. Mechanisms with desired features, e.g. containing certain numbers of generalized catalysts, chains, autocatalysts, etc., are generated using the invariants, from the simplest prototypes, for successively larger numbers of reaction steps. Special emphasis is given to autocatalytic networks due to their role in chemical oscillations, dynamical instabilities and in selfreplicating reactions. Examples given include the malic acid cycle, oscillatory cycles in glycolysis, Lotka-Volterra-Prigogine-Glansdorff models, and others. Oscillating and/or self-replicating cycles that have been invoked in various contexts are shown to have a common topological feature. The methods are useful also in the many autocatalytic processes of chemical engineering importance.     

Skeletal and reduced chemical mechanism for hydrogen fluoride chemical laser

The chemical kinetics of supersonic hydrogen fluoride (HF) chemical lasers determines combustion characteristics and output power. However, the inherent complexity of chemical reactions and complex structure still challenge the numerical simulations involving a comprehensive chemical mechanism. Therefore, a high fidelity and low computational consuming model is important for design purpose. This paper presents a strategy to generate a reduced mechanism for HF chemical lasers. Based on a detailed HF chemical mechanism consisting of 16 species and 153 elementary reactions, a specific skeletal mechanism including 11 species and 58 elementary reactions is generated. Finally, we obtain a further reduction mechanism including 11 species and 39 elementary reactions by combining sensitivity analysis and rate of production analysis. The computational cost for simulation of supersonic HF chemical lasers with the reduced mechanism is less than that with the detailed model. The principal contribution of the work is to provide a low computational consuming model.     

Application of chemical graph theory for automated mechanism generation

We present an application of the chemical graph theory approach for generating elementary reactions of complex systems. Molecular species are naturally represented by graphs, which are identified by their vertices and edges where vertices are atom types and edges are bonds. The mechanism is generated using a set of reaction patterns (sub-graphs). These subgraphs are the internal representations for a given class of reaction thus allowing for the possibility of eliminating unimportant product species a priori. Furthermore, each molecule is canonically represented by a set of topological indices (Connectivity Index, Balaban Index, Schulz TI Index, WID Index, etc.) and thus eliminates the probability for regenerating the same species twice. Theoretical background and test cases on combustion of hydrocarbons are presented.     

The application of oscillating chemical reactions to analytical determinations

Oscillating chemical reactions, which are far from equilibrium, are extremely sensitive to certain species and may provide new analytical methods using the regular oscillations as well as the non-equilibrium stationary state after system bifurcation. This review of their application to analytical chemistry from 2005 to 2012 includes other appropriate references. Both organic and inorganic analytes are included.     

Visual valence bond rules for chemical reactions

A symmetry-adaptation rule of the valence bond structure for concerted reactions was developed within the bonded tableau valence bond formalism. According to a symmetry analysis of the valence bond structure segments accounting for the reaction, one can predict whether a chemical process is favored or unfavored. This method is based on conceptual resonance theory and the visual valence bond approach, without carrying out any explicitly theoretical calculations to know orbital details. Furthermore, by imposing a phase factor on each bonding pair, namely, the phase alternation postulate, the mechanisms of the concerted reactions can be easily outlined. These rules have been applied to organic and inorganic reactions including the participation of biradicals and species with multi-reference character. Received: 7 September 1998 / Accepted: 9 November 1998 / Published online: 1 February 1999     

A study of chemical reactions in coarse-grained simulations

We introduce a reaction model for use in coarse-grained simulations to study the chemical reactions in polymer systems at mesoscopic level. In this model, we employ an idea of reaction probability in control of the whole process of chemical reactions. This model has been successfully applied to the studies of surface initiated polymerization process and the network structure formation of typical epoxy resin systems. It can be further modified to study different kinds of chemical reactions at mesoscopic scale.     

Geometric description of chemical reactions

We use the formalism of Geometrothermodynamics to describe chemical reactions in the context of equilibrium thermodynamics. Any chemical reaction in a closed system is shown to be described by a geodesic in a 2-dimensional manifold that can be interpreted as the equilibrium space of the reaction. We first show this in the particular cases of a reaction with only two species corresponding to either two ideal gases or two van der Waals gases. We then consider the case of a reaction with an arbitrary number of species. The initial equilibrium state of the geodesic is determined by the initial conditions of the reaction. The final equilibrium state, which follows from a thermodynamic analysis of the reaction, is shown to correspond to a coordinate singularity of the thermodynamic metric which describes the equilibrium manifold.     

Computer-assisted bilateral solution of chemical problems and generation of reaction networks

The theory of the bond/electron and reaction matrices, a mathematical model of the logical structure of constitutional chemistry, serves as the basis of a new generation of strictly logic-oriented programs for the solution of a variety of chemical problems without the use of any detailed empirical chemical information. These programs are interactive, have comfortable usermenus, and are implemented under the operating system MS-DOS on an IBM-compatible personal computer. The first representatives of the new generation are an improved version of IGOR (interactive generation of organic reactions) which “invents” chemical structures and reactions, and RAIN (reaction and intermediates networks) which generates, in a bilateral approach, pathways of chemical reactions and sequences of reactions from their given starting materials and products.     

致癌性胺离子反应过程中电荷和化学位移的计算

应用原子-键电负性均衡方法中的σπ模型(ABEEMσπ)计算了由致癌性胺离子所参与的反应过程中的电荷分布,所计算出的电荷分布可以和从头算很好的相关联,并且所需要的时间也大大的缩短;同时应用从头计算程序计算致癌性胺离子反应过程中的NMR化学位移.结果表明,在反应过程中电荷的变化和NMR化学位移的变化有很好的对应关系.     

A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays

Several real-world systems, such as gene expression networks in biological cells, contain coupled chemical reactions with a time delay between reaction initiation and completion. The non-Markovian kinetics of such reaction networks can be exactly simulated using the delay stochastic simulation algorithm (dSSA). The computational cost of dSSA scales with the total number of reactions in the network. We reduce this cost to scale at most with the smaller number of species by using the concept of partial reaction propensities. The resulting delay partial-propensity direct method (dPDM) is an exact dSSA formulation for well-stirred systems of coupled chemical reactions with delays. We detail dPDM and present a theoretical analysis of its computational cost. Furthermore, we demonstrate the implications of the theoretical cost analysis in two prototypical benchmark applications. The dPDM formulation is shown to be particularly efficient for strongly coupled reaction networks, where the number of reactions is much larger than the number of species.     

Strategies for chemical reaction searching in SciFinder

The bibliographic, chemical structure, and chemical reaction databases produced by Chemical Abstracts Service allow a number of possibilities for chemical reaction searching. While these same databases may be searched through the STN network, many end-users find the intuitive software interface SciFinder simpler, but there still are issues to address. Searching may be performed through keywords, chemical structures, or chemical reactions, and the answers may vary with respect to precision and comprehension. Often combinations of search options may be needed to best solve the problem. Retrosynthetic analyses are easily performed in the chemical reaction database and can give unique insights into synthetic alternatives.     

Thermal reactions of selected solids including reactants that melt during chemical change

Selected kinetic and mechanistic studies of thermal reactions of initially solid substances are reviewed with emphasis on the evidence that some of these chemical changes proceed with the essential participation of melting. The reactions considered are classified on the extent and the role of such melting and the various types of behaviour observed are discussed with reference to solid state rate processes in crystals. It is stressed that melting is an important feature in theoretical considerations of crystal reactivity because chemical changes often proceed more rapidly in a melt than in the solid state. However, literature reports concerned with reactions of solids do not always explicitly mention the possibility of melting during discussions of reactions mechanisms. The present paper comments on methods capable of detecting liquefaction during reaction, a feature of behaviour that is not always easily identified experimentally. Also considered here is the recognition of reaction intermediates, which provide important evidence concerning the course of the chemical changes through which the reactant is transformed into product. This short review draws attention to the considerable value of chemical evidence in elucidating mechanisms of reactions of solids including the necessity for identifying intermediates and the role of any melt or liquid participating.