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.     

Internal thermal reactions in minerals and materials

Rebuilding reactions of the internal structure of minerals and their artificial analogues are considered. Solid products of these reactions are formed within the structure of the parent substance. This factor determines the course of the reactions and product formation. The mechanism of internal thermal dissociation and rebuilding reactions of internal structure connected with segregation of chemical components and their redistribution (crystallization of multicomponent amorphous solids) is discussed. The internal pressure of gaseous decomposition products and rate of diffusion of chemical components are critical factors influencing kinetics of these processes. Diffusional mass transfer during internal structure rebuilding reactions is directed by acid-base interaction of the parent-structure components; this determines the stages of the reaction pathway.     

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization

By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well. We elucidate the global phase-space structure which gives rise to the non-Markovian dynamics or the dynamical correlation of sequential multisaddle chemical reactions. The phase-space structure relevant to the controllability of the product state in chemical reactions is also discussed.     

ReaxFF MD局部区域反应追踪与物理性质可视化分析

Recently, the application of ReaxFF based reactive molecular dynamics simulation (ReaxFF MD) in complex processes of pyrolysis, oxidation and catalysis has attracted considerable attention. The analysis of the simulation results of these processes is challenging owing to the complex chemical reactions involved, coupled with their dynamic physical properties. VARxMD is a leading tool for the chemical reaction analysis and visualization of ReaxFF MD simulations, which allows the automated analysis of reaction sites to get overall reaction lists, evolution trends of reactants and products, and reaction networks of specified reactants and products. The visualization of the reaction details and dynamic evolution profiles are readily available for each reactant and product. Additionally, the detailed reaction sites of bond breaking and formation are available in 2D chemical structure diagrams and 3D structure views; for specified reactions, they are categorized on the basis of the chemical structures of the bonding sites or function groups in the reacting species. However, the current VARxMD code mainly focuses on global chemical reaction information in the simulation system of the ReaxFF MD, and is incapable of locally tracking the chemical reaction and physical properties in a 3D picked zone. This work extends the VARxMD from global analysis to a focused 3D zone picked interactively from the 3D visualization modules of VARxMD, as well as physical property analysis to complement reaction analysis. The analysis of reactions and physical properties can be implemented in three steps: picking and drawing a 3D zone, identifying molecules in the picked zone, and analyzing the reactions and physical properties of the picked molecules. A 3D zone can be picked by specifying the geometric parameters or drawing on a screen using a mouse. The picking of a cuboid or sphere was implemented using the VTK 3D view libraries by specifying geometric parameters. The interactive 3D zone picking was implemented using a combination of observer and command patterns in the VTK visualization paradigm. The chemical reaction tracking and dynamic radial distribution function (RDF) of the 3D picked zone was efficiently implemented by inheriting data obtained from the global analysis of VARxMD. The reaction tracking between coal particles in coal pyrolysis simulation and dynamic structure characterization of carbon rich cluster formation in the thermal decomposition of an energetic material are presented as application examples. The obtained detailed reactions between the coal particles and comparison of the reaction between the locally and globally picked areas in the cuboid are helpful in understanding the role of micro pores in coal particles. The carbon to carbon RDF analysis and comparison of the spherical region picked for the layered molecular clusters in the pyrolysis system of the TNT crystal model with the standard RDF of the 5-layer graphene demonstrate the extended VARxMD as a chemical structure characteristic tool for detecting the dynamic formation profile of carbon rich clusters in the pyrolysis of TNT. The extended capability of VARxMD for a 3D picked zone of a ReaxFF MD simulation system can be useful for interfacial reaction analysis in a catalysis system, hot spot formation analysis in the detonation of energetic material systems, and particularly the pyrolysis or oxidation processes of coal, biomass, polymers, hydrocarbon fuels, and energetic materials.     

Reaction Dynamics with Molecular Beams and Oriented Molecular Beams: A Tool for Looking Closer to Chemical Reactions and Photodissociations

Experimental studies on reaction dynamics by use of molecular beams and oriented molecular beams are reviewed in order for looking closer to chemical reactions as well as photodissociations at the molecular level. We discuss about versatility and usefulness of the electrostatic hexapole sate‐selector as a non‐destructive selector for molecular structure analysis. Some experimental evidences on novel reaction dynamics in photodissociation and stereodynamics are presented followed by concluding remarks and future perspectives for controlling chemical reactions from the point of view of green chemistry, by manipulating molecular orientation without any catalyst nor by applying any external forces like intense electromagnetic field.     

有机催化不对称Michael/环化串联反应的研究进展北大核心CSCD

串联反应能够减少反应步骤、简化操作、降低成本、实现高效率转化,符合原子经济性和绿色化学理念.特别是有机催化的不对称串联环化反应以一锅法连续催化多个化学反应,为高效合成多手性中心环状结构提供了新方法.不对称Michael/环化串联反应是构建光学活性状化合物的常用方法之一,近些年,各种有机小分子催化剂应用于不对称Michael/环化串联反应的报道不断增加,并且取得了重大进展.我们根据不同的催化剂类型综述了近5年来关于不对称Michael/环化串联反应的研究进展,并对有机催化不对称Michael/环化串联反应的发展趋势进行了展望.     

Steepest descent reaction path integration using a first-order predictor-corrector method

The theoretical treatment of chemical reactions inevitably includes the integration of reaction pathways. After reactant, transition structure, and product stationary points on the potential energy surface are located, steepest descent reaction path following provides a means for verifying reaction mechanisms. Accurately integrated paths are also needed when evaluating reaction rates using variational transition state theory or reaction path Hamiltonian models. In this work an Euler-based predictor-corrector integrator is presented and tested using one analytic model surface and five chemical reactions. The use of Hessian updating, as a means for reducing the overall computational cost of the reaction path calculation, is also discussed.     

Terpenoid Biosynthesis Off the Beaten Track: Unconventional Cyclases and Their Impact on Biomimetic Synthesis

Terpene and terpenoid cyclizations are counted among the most complex chemical reactions occurring in nature and contribute crucially to the tremendous structural diversity of this largest family of natural products. Many studies were conducted at the chemical, genetic, and biochemical levels to gain mechanistic insights into these intriguing reactions that are catalyzed by terpene and terpenoid cyclases. A myriad of these enzymes have been characterized. Classical textbook knowledge divides terpene/terpenoid cyclases into two major classes according to their structure and reaction mechanism. However, recent discoveries of novel types of terpenoid cyclases illustrate that nature’s enzymatic repertoire is far more diverse than initially thought. This Review outlines novel terpenoid cyclases that are out of the ordinary.     

Transition‐state spectroscopy using ultrashort laser pulses

To gain a complete understanding of a chemical reaction, it is necessary to determine the structural changes that occur to the reacting molecules during the reaction. Chemists have long dreamed of being able to determine the molecular structure changes that occur during a chemical reaction, including the structures of transition states (TSs). The use of ultrafast spectroscopy to gain a detailed knowledge of chemical reactions (including their TSs) promises to be a revolutionary way to increase reaction efficiencies and enhance the reaction products, which is difficult to do using conventional methods that are based on trial and error. To confirm the molecular structures of TSs predicted by theoretical analysis, chemists have long desired to directly observe the TSs of chemical reactions. Direct observations have been realized by ultrafast spectroscopy using ultrashort laser pulses. Our group has been able to stably generate visible to near‐infrared sub‐5‐fs laser pulses using a noncollinear optical parametric amplifier (NOPA). We used these sub‐5‐fs pulses to study reaction processes (including their TSs) by detecting structural changes. We determine reaction mechanisms by observing the TSs in a chemical reaction and by performing density‐functional theory calculations. DOI 10.1002/tcr.201000018     

AIM Study on the Reaction of CH2SH Radical with Fluorine Atom

The reaction of CH2SH radical with fluorine atom was studied at the levels of B3LYP/6-311G(d,p) and MP2(Full)/6-311G(d,p). The computational results show that the reaction has three channels and proceeds by the addition of fluorine atoms on carbon or sulfur sites of CH2SH, forming initial intermediates. The calculated results show that the channel in which fluorine attaches to the carbon atom to form CH2S and HF, is the most likely reaction pathway. Topological analysis of electron density was carried out for the three channels. The change trends of the chemical bonds on the reaction paths were discussed. The energy transition states and the structure transition regions (states) of the three channels were found. The calculated results show that the structure transition regions are broad in unobvious exothermic reactions or unobvious endothermic reactions, and are narrow in obvious exothermic reactions or obvious endothermic reactions.     

MNDO calculation of reaction heats determininig the mechanism of antioxidant action of the phenols in polyolefins

The quantum chemical substantiation of antioxidant action of the substituted phenols in polyolefins is presented. The electronic structure of the phenols, phenoxy radicals, and model products of polyolefin destruction was calculated by the MNDO method. On the basis of the presumed chemical reactions, the electronic structure criteria determining the antioxidant activity are selected. These are the O—H bond dissociation energy in phenols and the charge on the atoms of π-system in phenoxy radicals. The competition between these reactions takes place, and the calculation of the reaction heats shows that the reactions with the formation of the substituted quinones are in preference to the reactions in which the peroxycyclo-hexadienones are formed.     

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.     

Mimosa and chestnut tannin extracts reacted with hexamine in solution

Autocondensation reactions of mimosa and chestnut tannin extracts solutions have been analysed at several pH by differential scanning calorimetry (DSC). Alkaline pH promotes autocondensation reaction of these tannins. Curing reactions between these tannins and hexamine at acid and not strongly alkaline pH have been proved by DSC. Thermal analysis gives insights not only on reactions between tannin and hexamine, but also about water presence on solutions and degradation reactions of tannins. Products obtained from reactions between tannins and hexamine have been analysed by Fourier transform infrared spectroscopy (FTIR). The obtained chemical structures are influenced by both chemical structure of tannin and pH of solution. For mimosa tannin amine and ether groups are obtained while for hydrolysable chestnut tannin amide groups have been detected.     

Mechanism of inhibiting action of quinones in oxidizing polymers and model compounds

Quinones (Q) do not affect the liquid-phase oxidation of hydrocarbons and retard the solid-phase oxidation of polymers terminating chains in reactions with alkyl macroradicals. This difference is the result of specific influence of a polymer matrix on the kinetics of free radical reactions. Quinones were found to terminate chains in oxidizing polypropylene containing hydroperoxide groups by the reaction with hydroperoxyl radicals. This is the result of peroxide group's decomposition with hydrogen peroxide production and chain termination in the following reactions: The equilibrium reaction between hydroquinone (QH₂) and quinonimine (QI) was evidenced to proceed as a chain reaction with chain propagation in reactions of •QH with QI and HQI• with QH₂. Analysis of the reactions of quinone with phenols (ArOH) proved that it can be important as an additional way of chain termination in oxidizing polymers and hydrocarbons at elevated temperatures.     

Significance of crystallochemical factors in chemical reactions into the structure of solids

The chemical reaction of the formation of compounds within the structure of solid as a reaction medium??internal reactions??is the subject of the article. The mechanism of these reactions on the example silicate mineral structure and nanocrystallization of oxide glasses is considered. Local atoms interaction analysis based on the electronegativity of and ionicity of the chemical bonds values helps to understand this mechanism and predict course of intrastructural thermal processes.     

吸附胶团和吸附胶团催化

介绍了吸附胶团的结构特点、影响吸附胶团催化的一些因素和在固体表面上的固定化表面活性剂体系的催化作用。吸附胶团是表面活性剂在固-液界面形成的缔合结构,它可以是吸附单层、双层、半球形、球形等。吸附胶团和利用接枝等技术在固体表面形成的不溶性表面活性剂体系,在一定条件下,可对某些反应起催化作用,有利于提高反应产率并使反应产物分离变得容易,这将使胶团催化的实际应用成为可能。     

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.     

Complexity index for the linear mechanisms of chemical reactions

A complexity measure is proposed for the kinetic models of chemical reactions with linear mechanisms. The index is related to the structure of fractional-rational kinetic laws for chemical reactions, as well as to the structure of cyclic graphs used to describe them. The complexity index is shown to be closely related to the detailed hierarchical classification and to the code of linear reaction mechanisms, recently introduced. A number of index properties are proved for two- and three-reaction routes. They reflect the influence of the various classification criteria, such as the number of reaction routes and intermediates, the type, class and subclasses of the mechanism, and the number of intermediates in each reaction route. Hierarchical levels of mechanisms with the same complexity (isocomplex mechanisms) are specified. Standard tables are presented with complexity indices for all topologically distinct linear reaction mechanisms having one to three reaction routes, two to six intermediates, and reversible elementary steps.[/p]     

VET: a tool for reaction plausibility checking

Production of chemical reaction databases is a multistep process, with the possibility of errors at each of these steps. VET is a tool developed to trap errors in the chemical reactions identified as a part of this process. VET has been designed to minimize the acceptance of incorrect reactions, while still supporting various common practices in reaction depiction, including unbalanced reactions, suppressed components, and reactions with alternative products. We discuss the assumptions made in its construction, a general overview of its structure, and some performance characteristics.