New Applications of Computers in Chemistry

The mathematical model of constitutional chemistry described here is based on a concept of isomerism which has been extended from molecules to ensembles of molecules. A chemical reaction is the conversion of an ensemble of molecules into an isomeric ensemble. An ensemble of molecules is representable by an atomic vector and an associated bond and electron (BE)- matrix, and a reaction by a reaction (R)-matrix. These BE-and R-matrices serve as a basis for computer programs for the deductive solution of chemical problems. We present here algorithms and computer programs based on the theory of BE- and R-matrices. They enable the classification and documentation of structrues, substructures and reactions, the prognosis of reaction products,the design of syntheses, the construction of networks of mechanistic and synthetic pathways and the prediction of chemical reactions.     

Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

土壤有机氯脱氯转化的界面交互反应*

有机氯杀虫剂、除草剂等难降解有机物是重要的土壤污染物。近年来,有机氯脱氯转化的界面过程已成为土壤环境科学的研究热点。本文综述了土壤有机氯脱氯转化的界面非生物过程、界面生物过程以及界面生物－非生物交互反应过程。界面脱氯转化过程与主要土壤化学过程、土壤根际过程相互关联,该过程中,铁物种循环与铁氧化物的异化还原溶解扮演了重要角色。     

Transformative two-dimensional layered nanocrystals

Regioselective chemical reactions and structural transformations of two-dimensional (2D) layered transition-metal chalcogenide (TMC) nanocrystals are described. Upon exposure of 2D TiS(2) nanodiscs to a chemical stimulus, such as Cu ion, selective chemical reaction begins to occur at the peripheral edges. This edge reaction is followed by ion diffusion, which is facilitated by interlayer nanochannels and leads to the formation of a heteroepitaxial TiS(2)-Cu(2)S intermediate. These processes eventually result in the generation of a single-crystalline, double-convex toroidal Cu(2)S nanostructure. Such 2D regioselective chemical reactions also take place when other ionic reactants are used. The observations made and chemical principles uncovered in this effort indicate that a general approach exists for building various toroidal nanocrystals of substances such as Ag(2)S, MnS, and CdS.     

The computer processing and interpretation of mass spectral information. V—generation of a table of isotopic spectra of structural fragments

A package of dialogue programs intended for generation of isotopic spectra from specified elemental compositions containing any number of elements is described. Structural fragments (super-elements), once in the table, acquire the status of a separate chemical element. All operations with super-elements are analogous to those with polyisotopic elements of the periodic table. The user can modify the table at his discretion to suit his purpose. The table increases the flexibility of interactive data processing programs and thus the dialogue is made to approach the natural chemist's language. The programs written in FORTRAN IV are intended for a minicomputer with a core memory of about 24 K words.     

In‐situ Chemiluminescence‐Driven Reversible Addition–Fragmentation Chain‐Transfer Photopolymerization

The power of chemical light generation (chemiluminescence) is used to drive polymerization reactions. A biphasic reaction is developed such that light‐generating reactions are confined to the organic phase and photopolymerization occurs in the aqueous phase. Well‐defined RAFT‐capped polymers are synthesized and the kinetics are shown to be dictated by light generation.     

Constraining molecules at the closest approach: chemistry at high pressure

The purpose of this tutorial review is to illustrate the effects that the application of high pressures can have on chemical reactions involving highly compressible molecular materials. The essentials of the high-pressure technology (generation and in situ control of high pressures) are described with particular attention to the versatile diamond anvil cell (DAC) apparatus. The general effects of pressure on chemical equilibrium, reaction rate and reaction mechanism are discussed. The motivation for application of high-pressure methods (in the 1-300 MPa range) to chemical synthesis and in biochemistry are illustrated focusing the attention on environmental effects and with an excursus on developing biotechnological applications. The peculiarities and the unexpected outcomes of chemical reactions occurring at very high pressures (>or=300 MPa) are discussed considering the extraordinary results obtained in polymerization and amorphization of simple molecules and of unsaturated hydrocarbons. The possible connection of the high temperature-high pressure thresholds for chemical reactions with microscopic counterparts (intermolecular distances, molecular orientations) is also discussed.     

Acoustic emission in solid-liquid decomposition reactions

The chemical acoustic emission method was used to study solid-liquid decomposition reactions for the example of the interaction of potassium carbonate pellets with solutions of hydrochloric acid (HCl). The reaction was shown to follow different mechanisms at different hydrochloric acid concentrations (the concentration was varied from 0.12 to 12 M). An increase in the concentration of HCl not always caused an increase in the rate of generation of acoustic emission signals and, therefore, the reaction rate. The generation of acoustic emission was studied at various reaction stages. The advantages of the chemical acoustic emission method include measurements in real time (this is of importance for fast reactions, the reaction studied took no more than 5 min) and the possibility of determining rates at separate reaction stages. An automated acoustic emission unit was tested. The unit showed high reproducibility of measurement results, reliability, and rich possibilities for studying chemical acoustic emission in solids.     

Release of Singlet Oxygen from Aromatic Endoperoxides by Chemical Triggers

The generation of reactive singlet oxygen under mild conditions is of current interest in chemistry, biology, and medicine. We were able to release oxygen from dipyridylanthracene endoperoxides (EPOs) by using a simple chemical trigger at low temperature. Protonation and methylation of such EPOs strongly accelerated these reactions. Furthermore, the methyl pyridinium derivatives are water soluble and therefore serve as oxygen carriers in aqueous media. Methylation of the EPO of the ortho isomer affords the parent form directly without increasing the temperature under very mild conditions. This exceptional behavior is ascribed to the close contact between the nitrogen atom and the peroxo group. Singlet oxygen is released upon this reaction, and can be used to oxygenate an acceptor such as tetramethylethylene in the dark with no heating. Thus, a new chemical source of singlet oxygen has been found, which is triggered by a simple stimulus.     

Formation and role of colloid material structures and surfaces in chemical reaction system: Part II

In a thermodynamically open, non-isotherm, non-continuous, multicomponent, initially homogeneously distributed chemical reaction system far from equilibrium, quasi-stationary states and a heterogeneous spatial structure divided by surface boundaries may emerge spontaneously by self-organisation. This structure emerges, evolves and devolves over time as chemical reactions are completed. During this process, reactants segregate themselves in space, the rate of the mass transport and the chemical process partly decreases, both processes become periodic, new types of material exchange mechanisms unusual in inanimate nature arise, and feedback and self-regulation occur which promote the survival of the structure produced. Roles of boundary surfaces and solubility in generation of new type periodic or cyclic phenomena were discussed.     

The remarkable chemistry of trannulenes: green fluorinated fullerenes with unconventional aromaticity

We report the first reaction of trannulenes involving their thermal isomerization to a new class of compounds termed "triumphenes". The thermodynamically controlled conversion of trannulenes into triumphenes is accompanied by an unprecedented migration of three organic addends from one hemisphere of the fullerene cage to another. The reaction products, bearing aliphatic substituents, might find applications in materials science as strong electron acceptors due to the presence of fifteen electron-withdrawing fluorine atoms in their molecular framework. It was revealed that the isomerization of trannulenes can be affected by the presence of unsaturated compounds in the reaction mixture. Heating of trannulenes C(60)F(15)R(3) with C(60), C(70), anthracene, or pentacene at reflux in 1,2-dichlorobenzene yields fluorinated derivatives C(60)F(14)R(2)A, which possess a fused cyclic addend A. The products of this reaction have "triumphene-type" addition patterns and seem to be formed through an unprecedented sequence of elimination, addition, and isomerization steps. The molecular structure of a representative triumphene was proven unambiguously by X-ray single-crystal diffraction analysis and by NMR spectroscopy. The reactions revealed here open up numerous opportunities for chemical derivatization of fluorinated fullerenes. This method promises to provide a new path towards valuable photoactive materials and a new generation of fullerene-based compounds that are suitable for biomedical applications.     

Direct observation of single-molecule generation at a solid-liquid interface

Direct observation of single-molecule generation from a chemical reaction was achieved at a solid-liquid interface. The reaction between fluorescamine and immobilized N'-(3-trimethoxysilylpropyl)diethylenetriamine (DETA) was studied at the single-molecule level. Time-lapse fluorescence images of single-molecule products, excited by the evanescent field generated at a quartz-liquid interface, were recorded to follow the chemical reaction to its completion. The reactions were restricted to the approximately 1 nm thick layer nearest to the interface. Analysis of the photoelectron intensity of the fluorescent product of the reaction and its distribution shows that the reaction kinetics goes through a transition from zeroth-order to first-order as the reaction proceeds. This approach offered a novel means to study single-molecule reactions at the solid-liquid interface. It also enabled the investigation of reaction kinetics and chemical mapping of surface heterogeneity at the single-molecule level.     

Development of Microdroplet Generation Method for Organic Solvents Used in Chemical Synthesis

Recently, chemical operations with microfluidic devices, especially droplet-based operations, have attracted considerable attention because they can provide an isolated small-volume reaction field. However, analysis of these operations has been limited mostly to aqueous-phase reactions in water droplets due to device material restrictions. In this study, we have successfully demonstrated droplet formation of five common organic solvents frequently used in chemical synthesis by using a simple silicon/glass-based microfluidic device. When an immiscible liquid with surfactant was used as the continuous phase, the organic solvent formed droplets similar to water-in-oil droplets in the device. In contrast to conventional microfluidic devices composed of resins, which are susceptible to swelling in organic solvents, the developed microfluidic device did not undergo swelling owing to the high chemical resistance of the constituent materials. Therefore, the device has potential applications for various chemical reactions involving organic solvents. Furthermore, this droplet generation device enabled control of droplet size by adjusting the liquid flow rate. The droplet generation method proposed in this work will contribute to the study of organic reactions in microdroplets and will be useful for evaluating scaling effects in various chemical reactions.     

New Aspects of Protein‐film Voltammetry of Redox Enzymes Coupled to Follow‐up Reversible Chemical Reaction in Square‐wave Voltammetry

Protein‐film square‐wave voltammetry of uniformly adsorbed molecules of redox lipophilic enzymes is applied to study their electrochemical properties, when a reversible follow‐up chemical reaction is coupled to the electrochemically generated product of enzyme's electrode reaction. Theoretical consideration of this so‐called “surface ECrev mechanism” under conditions of square‐wave voltammetry has revealed several new aspects, especially by enzymatic electrode reactions featuring fast electron transfer. We show that the rate of chemical removal/resupply of electrochemically generated Red(ads) enzymatic species, shows quite specific features to all current components of calculated square‐wave voltammograms and affects the electrode kinetics. The effects observed are specific for this particular redox mechanism (surface ECrev mechanism), and they got more pronounced at high electrode kinetics of enzymatic reaction. The features of phenomena of “split net‐SWV peak” and “quasireversible maximum”, which are typical for surface redox reactions studied in square‐wave voltammetry, are strongly affected by kinetics and thermodynamics of follow‐up chemical reaction. While we present plenty of relevant voltammetric situations useful for recognizing this particular mechanism in square‐wave voltammetry, we also propose a new approach to get access to kinetics and thermodynamics of follow‐up chemical reaction. Most of the results in this work throw new insight into the features of protein‐film systems that are coupled with chemical reactions.     

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.     

Non-carbonyl-stabilized metallocarbenoids in synthesis: the development of a tandem rhodium-catalyzed bamford-stevens/thermal aliphatic claisen rearrangement sequence

A tandem rhodium-catalyzed Bamford-Stevens/Claisen rearrangement is presented. The tandem reaction uses Eschenmoser hydrazones for the in situ generation of non-carbonyl-stabilized diazo alkanes, which are presumably intercepted by Rh(II) catalysts to induce a 1,2-hydride migration. This sequence provides high levels of stereocontrol for the generation of simple acyclic (Z)-enol ethers. These enol ethers undergo either thermal or Lewis acid accelerated Claisen rearrangements to provide products of high diastereopurity. Also presented are cascade reactions, wherein a third chemical step occurs after the initial tandem sequence (i.e., Bamford-Stevens/Claisen/ene and Bamford-Stevens/Claisen/Cope).     

Design and development of computer-aided chemical systems: representation and balance of inorganic chemical reactions

A model for the tracking of inorganic chemical reactions is proposed. Designed to acquire, process, and solve a great number of inorganic reactions, this model will hopefully contribute to the development of powerful computer-aided chemistry teaching systems for use within or without the environment of a virtual laboratory. Using full representation of an inorganic reaction to allow the extraction of chemical knowledge, incomplete reactions (where species are absent) may be completed by adding the necessary species, and reactions may be solved and balanced. Various types of reaction are classified, and a layer-based model is defined for the solution of different reaction types, establishing the basis for the construction of a system which, based on a wide set of production rules, is capable of solving an incomplete inorganic chemical reaction.     

Rehybridization and the Chemical Reaction: POAV and 3D-HMO Analysis

In this study chemical reactions are examined from a new standpoint — rehybridization. With the possible exception of oxidation-reduction processes, all chemical reactions involve rehybridization. Bondmaking and bond-breaking processes are nothing more than changes in hybridization. ln the present study two categories of pericyclic reactions are examined with the π-orbital axis vector (POAV) analysis and-the three-dimensional (3D) HMO theory. The first makes use of a series of related molecular structures derived from X-ray crystallography which provide information on the reaction pathway between the valence tautomers 1,6-methano[10]annulene (1a) and the bisnorcaradiene (1b). The second category involves structures calculated by Dewar and coworkers along the minimum energy reaction pathway of the Cope rearrangement of 1,5-hexadiene (2). The analysis provides a clear delineation of the structural and electronic changes which accompany chemical reaction. The sense of the π-orbital axis vectors at the bridgehead atoms is shown to be the determining feature in dividing the potential surface of 1 between bridged-[10]annulene (1a) and bisnorcaradiene (1b).     

基本化学反应形式的系统分类

The old classification of basic chemical reactions was evaluated and a new systematic classification of basic reactions was proposed.In the new classification,all the chemical reactions were divided into oxidation-reduction reactions and non-oxidation-reduction reactions,and both can be divided into combination reaction,decomposition reaction and replacement reaction,respectively.In addition,a new class of basic reactions,the complicated decomposition reaction,was appended to reaction system.     

Real time monitoring of accelerated chemical reactions by ultrasonication‐assisted spray ionization mass spectrometry

Ultrasonication has been used to accelerate chemical reactions. It would be ideal if ultrasonication‐assisted chemical reactions could be monitored by suitable detection tools such as mass spectrometry in real time. It would be helpful to clarify reaction intermediates/products and to have a better understanding of reaction mechanism. In this work, we developed a system for ultrasonication‐assisted spray ionization mass spectrometry (UASI–MS) with an ~1.7 MHz ultrasonic transducer to monitor chemical reactions in real time. We demonstrated that simply depositing a sample solution on the MHz‐based ultrasonic transducer, which was placed in front of the orifice of a mass spectrometer, the analyte signals can be readily detected by the mass spectrometer. Singly and multiply charged ions from small and large molecules, respectively, can be observed in the UASI mass spectra. Furthermore, the ultrasonic transducer used in the UASI setup accelerates the chemical reactions while being monitored via UASI–MS. The feasibility of using this approach for real‐time acceleration/monitoring of chemical reactions was demonstrated. The reactions of Girard T reagent and hydroxylamine with steroids were used as the model reactions. Upon the deposition of reactant solutions on the ultrasonic transducer, the intermediate/product ions are readily generated and instantaneously monitored using MS within 1 s. Additionally, we also showed the possibility of using this reactive UASI–MS approach to assist the confirmation of trace steroids from complex urine samples by monitoring the generation of the product ions. Copyright © 2014 John Wiley & Sons, Ltd.