Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction

The purpose of the EROS 6.0 system is to predict the products of chemical reactions and to model reaction mechanisms. This is accomplished by elementary reaction steps that are selected through the rules that constitute the knowledge base of the EROS 6.0 system. These rules are derived by methods of machine learning. The learning process is based on reaction in data bases. An overview of the EROS 6.0 system is given and the structure of the knowledge as well as the generation of reaction rules are described.     

Lowering Energy Barriers in Surface Reactions through Concerted Reaction Mechanisms

Any technologically important chemical reaction typically involves a number of different elementary reaction steps consisting of bond‐breaking and bond‐making processes. Usually, one assumes that such complex chemical reactions occur in a step‐wise fashion where one single bond is made or broken at a time. Using first‐principles calculations based on density functional theory we show that the barriers of rate‐limiting steps for technologically relevant surface reactions are significantly reduced if concerted reaction mechanisms are taken into account.     

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.     

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     

Automatic polarographic elucidation of electrode mechanisms by means of a knowledge-based system : Part 1. Sampled d.c. polarography

A knowledge-based system has been developed for the automatic elucidation of electrochemical mechanisms. The system is based on sampled direct current (or Tast) polarography at a dropping mercury electrode as a technique for collecting experimental information and consists of a general expert system shell for the reasoning process, the specific set of rules and experimental modules. The set of rules allows the elucidation of eight relatively simple electrode reaction mechanisms fully atomatically. The computer system has been validated with chemical systems the electrochemical behaviour of which is well established. All parts of the program are written in FORTH language for Apple II microcomputers. This expert system has an open character and new rules can be added to extend the set of mechanisms that can be determined.     

Haptic quantum chemistry

We present an implementation designed to physically experience quantum mechanical forces between reactants in chemical reactions. This allows one to screen the profile of potential energy surfaces for the study of reaction mechanisms. For this, we have developed a interface between the user and a virtual laboratory by means of a force‐feedback haptic device. Potential energy surfaces of chemical reactions can be explored efficiently by rendering in the haptic device the gradients calculated with first‐principles methods. The underlying potential energy surface is accurately fitted on the fly by the interpolating moving least‐squares (IMLS) scheme to a grid of quantum chemical electronic energies (and geometric gradients). In addition, we introduce a new IMLS‐based method to locate minimum‐energy paths between two points on a potential energy surface. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

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.     

Towards Design Rules for Covalent Nanostructures on Metal Surfaces

The covalent molecular assembly on metal surfaces is explored, outlining the different types of applicable reactions. Density functional calculations for on‐surface reactions are shown to yield valuable insights into specific reaction mechanisms and trends across the periodic table. Finally, it is shown how design rules could be derived for nanostructures on metal surfaces.     

The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems

Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as “name reactions”. This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical‐mediated, and rearrangements, which are subdivided by name reactions.     

Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions

The EC (Enzyme Commission) numbers represent a hierarchical classification of enzymatic reactions, but they are also commonly utilized as identifiers of enzymes or enzyme genes in the analysis of complete genomes. This duality of the EC numbers makes it possible to link the genomic repertoire of enzyme genes to the chemical repertoire of metabolic pathways, the process called metabolic reconstruction. Unfortunately, there are numerous reactions known to be present in various pathways, but they will never get EC numbers because the EC number assignment requires published articles on full characterization of enzymes. Here we report a computerized method to automatically assign the EC numbers up to the sub-subclasses, i.e., without the fourth serial number for substrate specificity, given pairs of substrates and products. The method is based on a new classification scheme of enzymatic reactions, named the RC (reaction classification) number. Each reaction in the current dataset of the EC numbers is first decomposed into reactant pairs. Each pair is then structurally aligned to identify the reaction center, the matched region, and the difference region. The RC number represents the conversion patterns of atom types in these three regions. We examined the correspondence between computationally assigned RC numbers and manually assigned EC numbers by the jackknife cross-validation test and found that the EC sub-subclasses could be assigned with the accuracy of about 90%. Furthermore, we examined the correlation with genomic information as represented by the KEGG ortholog clusters (OC) and confirmed that the RC numbers are correlated not only with elementary reaction mechanisms but also with protein families.     

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]     

Classification of Clock Reactions

Autocatalytic systems are sometimes designated as clock reactions or reactions that exhibit clock behavior. To resolve the recent dispute over the term clock reaction, we describe a new approach to classify systems featuring clock behavior into three distinct groups: substrate‐depletive clock reactions, autocatalysis‐driven clock reactions, and systems that have pseudo clock behavior. Many of the well‐known classical and recently discovered reactions can conveniently be put into these categories. We also provide a convincing argument for classifying some autocatalytic processes as clock reactions, but it does not necessarily mean that all autocatalytic processes should be classified as autocatalysis‐driven clock reactions. This classification can be conveniently performed if the kinetic nature of the given system has been completely elucidated and understood.     

Bifunctional Metal Nanocrystals for Catalyzing and Reporting on Chemical Reactions

Bifunctional nanocrystals with integrated plasmonic and catalytic activities hold great promise for analyzing chemical reactions by in situ surface‐enhanced Raman spectroscopy. This Minireview gives a brief introduction to the general strategies for designing such nanocrystals, followed by four typical examples, including their fabrication, characterization, and potential limitation. We then use the reduction of 4‐nitrothiophenol and oxidation of 4‐aminothiophenol as two model systems to demonstrate the capabilities of these bifunctional nanocrystals to monitor chemical reactions for the elucidation of reaction mechanisms and measurement of kinetics. We conclude with perspectives on further development of these bifunctional nanocrystals into a viable platform for investigating other types of catalytic reactions.     

Woodward-Hoffmann rules in density functional theory: initial hardness response

The Woodward-Hoffmann rules for pericyclic reactions, a fundamental set of reactivity rules in organic chemistry, are formulated in the language of conceptual density functional theory (DFT). DFT provides an elegant framework to introduce chemical concepts and principles in a quantitative manner, partly because it is formulated without explicit reference to a wave function, on whose symmetry properties the Woodward-Hoffmann [J. Am. Chem. Soc. 87, 395 (1965)] rules are based. We have studied the initial chemical hardness response using a model reaction profile for two prototypical pericyclic reactions, the Diels-Alder cycloaddition of 1,3-butadiene to ethylene and the addition of ethylene to ethylene, both in the singlet ground state and in the first triplet excited state. For the reaction that is thermally allowed but photochemically forbidden, the initial hardness response is positive along the singlet reaction profile. (By contrast, for the triplet reaction profile, a negative hardness response is observed.) For the photochemically allowed, thermally forbidden reaction, the behavior of the chemical hardness along the initial stages of the singlet and triplet reaction profiles is reversed. This constitutes a first step in showing that chemical concepts from DFT can be invoked to explain results that would otherwise require invoking the phase of the wave function.     

LED‐Illuminated NMR Studies of Flavin‐Catalyzed Photooxidations Reveal Solvent Control of the Electron‐Transfer Mechanism

Mechanistic insights into chemical photocatalysis are mainly the domain of UV/Vis spectroscopy, because NMR spectroscopy has been limited by the type of illumination so far. An improved LED‐based illumination device can be used to obtain NMR reaction profiles of photocatalytic reactions under synthetic conditions and perform both photo‐CIDNP and intermediate studies. Flavin‐catalyzed photooxidations of alcohols show the potential of this setup. After identical initial photoreaction steps the stabilization of a downstream intermediate is the key to the further reaction mechanism and the reactivity. As a chemical photocatalyst flavin can act either as a one‐ or a two‐electron mediator when the stability of the zwitterionic radical pair is moldulated in different solvents. This demonstrates the importance of downstream intermediates and NMR‐accessible complementary information in photocatalytic reactions and suggests the control of photoorganic reactions by solvent effects.     

Chemical and thermal stability of N‐heterocyclic ionic liquids in catalytic C–H activation reactions

¹H‐NMR spectrum analyses are applied to study the chemical and thermal stability of selected N‐heterocyclic ionic liquids within the reaction system that can highly efficiently activate a C–H bond of methane and convert it into the C–O bond in methanol. Our results indicate that under such reaction conditions involving using a powerful Pt‐based catalyst and strong acidic solvent, the aromatic ring of an imidazolium cation becomes unstable generating an ammonium ion (NH₄⁺). Our results also suggest that the instability of the imidazolium ring is more chemically (participation in reactions) than thermally based. Modifications of the aromatic ring structure such as pyrazolium and triazolium cations can increase the chemical/thermal stability of ionic liquids under these reaction conditions. Copyright © 2014 John Wiley & Sons, Ltd.     

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.     

Should the Woodward–Hoffmann Rules be Applied to Mechanochemical Reactions?

Since decades, pericyclic reactions have been well‐understood by means of the Woodward–Hoffmann rules and their classification as thermally or photochemically “allowed” or “forbidden”. Recently, stunning results on such reactions subject to mechanochemical activation by external forces instead of heat or light have revealed reaction pathways at sufficiently large forces, which are not expected from the Woodward–Hoffmann rules. This led to the much reiterated idea that the “Woodward–Hoffmann rules are broken in mechanochemistry”. Here, by studying ring‐opening of cyclopropane, we show that the electronic structure underlying the dis‐ and conrotatory pathways, which are greatly distorted upon applying forces to an extent that eventually the “thermally forbidden” process becomes “mechanochemically allowed”, does not change along both pathways. It is rather the mechanical work that lowers the activation barrier of the thermally forbidden conrotatory process relative to the disrotatory one at large forces.     

Optimization criteria for a single bead-string reactor in flow injection analysis based on consecutive kinetic reactions

In flow-injection methods based on chemical reactions, simple one-step reactions are desirable, but more complex kinetics cannot always be avoided. The consecutive reaction considered here is A + reagent (s)→B→C. The response signal depends on the dispersion of the sample zone in the system and on the kinetics of the chemical reaction. The dispersion in a single-bead-string vector is described by the tanks-in-series model. The reaction of paracetamol with hexacyanoferrate (III) and phenol is used for experimental verification. Rules for optimum reactor design are given, the reactor length being used as the optimization parameter. Comparison of the experimental and calculated peak heights at different reactor lengths confirms the optimization rules.     

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.