Transparent formal methods for reducing the combinatorial abundance of conceivable solutions to a chemical problem : Computer-assisted elucidation of complex reaction mechanisms

Restraining the combinatorial flood of conceivable solutions to chemical problems by formal means is discussed. An algebraic model of the logical structure of constitutional chemistry not only serves as the theoretical foundation of the inference engines in strictly logic-orientated chemical computer programs, but also provides a conceptual framework for non-arbitrary, transparent procedures for reducing the combinational abundance of conceivable solutions to given chemical problems. Diverse procedures are available to provide efficient guidance on routes from a chemical problem to its chemically most meaningful solutions. The division of problems into subsidiary problems, the bilateral alternative to monolateral approaches, and the hierarchic classification of results, prior to selecting individual solutions, is highly effective in computer-assisted problem-solving.     

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.     

MCR XVI. Mathematical support for combinatorial chemistry

The algebra of the s- and r-vectors is an adequate formal tool to describe chemical objects in an abstract way. Compounds as well as reactions are represented, including all constitutional and configurational aspects. The stereochemistry of simple organic molecules as well as those of metal-organic compounds may be described in a unique way. Ionic bonds, covalent bonds, aromatics, and electron-deficiency compounds can formally be described without loss of information. Even reaction types and the flow of electrons can be described by this algebra. The biggest benefit of this approach is its intrinsic group theoretical structure. This does not bother the chemist for its use but allows a computer to handle and structure huge amounts of chemical data. This is especially important for combinatorial chemistry, which deals with huge sets of chemically distinct molecules, the so-called molecular libraries.     

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.     

Echtzeit-Datenerfassungssystem mit minimaler hardware für den Einsatz in der Routine-Massenspektrometrie im organischen Laboratorium

A low-cost on-line digital computer system for data acquisition and reduction of mass spectral information from a single focusing mass spectrometer is described. The data system is designed to handle the problems most commonly encountered in routine applications in organic chemistry. By using sophisticated programming concepts a versatile user oriented system is realised on a minimal hardware configuration. Detailed information about data flow and logical structure of the programs is given.     

Note on the Repeat Space Theory

This note provides a chronological sketch of the development from the early 1990s of the Repeat Space Theory (RST), which had originated in the study of the zero-point energy additivity problems of hydrocarbons in 1985. Interacting with the theories of dynamical systems, operator algebra, and so forth, the RST has developed into a comprehensive theoretical framework of axiomatic nature, which unites and solves, in particular, what we call globally-pertaining-type problems, or, for short, g-type problems; these constitute physico-chemical problems for whose solutions global mathematical contextualization is essential. In conjunction with the author's communications with Prof. Kenichi Fukui, the genesis of the notion of g-type problems has also been presented in this note. Through the vision the RST provides, it is foreseeable that investigations of the peripheral research domains of g-type problems in chemistry will play a significant role for future investigations, especially for those related to macromolecules, physico-chemical network systems, and biochemical network systems, in the vast uncharted interdisciplinary regions between chemistry and modern mathematics.     

探讨二元颗粒混合物取样误差的新的数学模型

采用新的数学模型研究二元颗粒混合物的取样误差,首次提出了取样的逻辑质量单元的理论,探讨了逻辑质量单元的物理意义,建立了按质量取样的标准偏差的计算公式.应用颗粒药品二元混合物的取样实验,证实了该公式的正确性.     

Computer Algebra Systems in Physical Chemistry

It is argued that a computer algebra system should replace the FORTRAN-like languages in the undergraduate and graduate programs in chemistry. To support the argument example applications from physical chemistry are used to display the symbolic, numerical, and graphical capabilities of one such system. The code for the more complex applications is given in an appendix.     

将生物信息学与有机化学结合初探酶促反应原理与实践——介绍一个国外本科生实验并讨论其相关问题

21世纪是生命科学与信息科学高速发展的时代,化学作为理科的中心学科与此二者均有紧密的联系。伴随着各种交叉学科的诞生与发展,将信息科学技术整合有机化学方法并用于认知生物大分子进而解决生命科学问题也是大势所趋,而在生物化学与化学生物学基础教学中引入相关内容也具有前瞻性与必要性。国外化学本科的基础教育也切合时宜地以一个生物信息学的最常用软件PyMOL为例设计相关实验,让学生在了解反应中的有机化学机理的基础上,学习酶的三维结构,并探究酶催化该反应的原因。此设计结合了有机化学、生物化学、生物信息学、蛋白质结构生物学等多学科,可以加深学生对多肽与蛋白质的高级结构的认识,并为今后的生物化学学习与研究打下基础,同时有利于培养学生对于化学的兴趣,可谓一举多得。这对于培养交叉学科人才,做出开创性研究极为重要。对国内生物有机化学实验的设计有借鉴作用。     

Stereocontrol in Organic Synthesis Using the Diphenylphosphoryl Group

In 1959, Horner showed that metalated alkyldiphenylphosphane oxides react with aldehydes or ketones to give alkenes. With this reaction, the diphenylphosphoryl (Ph₂PO) group made its entrance into synthetic organic chemistry. In the thirty-six years since that date, extensive research has shown that this olefination, the Horner–Wittig reaction, has unique properties that make it much more than simply the phosphane oxide cousin of the more famous phosphorus-based olefinations—the Wittig reaction (based on phosphonium salts) and the Wadsworth–Emmons reaction (based on phosphonate esters). Early work on the Horner–Wittig reaction concentrated on the reactivity of phosphane oxides and the regioselectivity of their reactions, but more recently the power of the Ph₂PO group to control the stereochemistry of alkenes, and to produce “on demand” either stereoisomer in high stereochemical purity, has emerged. From the study of these stereocontrolled Horner–Wittig reactions arose the realization that the Ph₂PO group is useful not only for the control of the two-dimensional stereochemistry of alkenes, but also of three-dimensional stereochemistry in general. After a brief introduction to phosphane oxide chemistry, this review will examine the Horner–Wittig reaction, in both its original and “stereocontrolled” varieties. From there, we will move on to an account of the stereoselective construction of molecules containing the Ph₂PO group, concentrating on the stereochemical directing effects of the Ph₂PO group and on the role of its unique combination of attributes—steric bulk, electronegativity, and Lewis basicity—in controlling these reactions. Finally, we will present what is intended as a practical guide to this chemistry, covering the type of functionalized alkenes that have been made with the help of the Ph₂PO group and giving guidelines that we hope will help the organic chemist to make the most of the chemistry the Ph₂PO group has to offer.     

Computer modeling of the chemical-power engineering process of roasting of a moving multilayer mass of phosphorite pellets

A mathematical model and a computer model were developed for the multistage chemical and energy engineering process of roasting of phosphorite pellets, which includes the reactions of dissociation of carbonates and the processes of sintering in a moving dense multilayer mass of phosphorite pellets in a complex chemical and energy engineering system—travelling grate machine. The adequacy of the developed mathematical model was tested. Computational experiments were performed to determine the roasting process parameters at various physicochemical characteristics of the phosphate feedstock and the external heattransfer gas flow.     

Current trends in the development of A. M. Butlerov’s theory of chemical structure

The chemical structure concept developed by A. M. Butlerov supplemented by the views on spatial (J. H. van’t-Hoff and J. A. Le Bel) and electronic (G. Lewis) configurations of molecules constitute the basis of the classical theory of chemical structure. The advent of quantum mechanics and development of the computer chemistry extended and enhanced the conceptual basis of theoretical chemistry, which nevertheless retains its independent value and cannot be reduced to direct physical definitions. The review deals with the evolution of the key concepts of the classical theory of chemical structure and introduction of new notions and approaches to analysis of the structure and reactivity problems, which is associated with the advent of the quantum mechanics and quantum chemistry views and methods.     

A mathematical model of the logical structure of chemistry. A bridge between theoretical and experimental chemistry and a general tool for computer-assisted molecular design

Summary A mathematical model of the logical structure of chemistry is suggested. The model is based on the phenomenon of convertibility between chemical species which is expressed by the so-called convertibility function . In the center of the model there is the potential energy (hyper)surface, PES. A heuristic modification of the general convertibility function is presented. Several algorithms have been developed for an analysis of PES which is described by paths, and for heuristic obtaining of PES paths. The notion ofK-barrier of conformational PES is introduced as well as an algorithm for its computation.     

化学结构正规编码及其信息处理功能

自从计算机在化学领域中应用以来,化学结构的正规编码已广泛用来作为一种化学文献的信息索引,它还在开发化学智能系统中发挥着重要作用。正规编码生成是以化学结构图的拓扑性质为基础的。本文首先概述编码的基本原理及其生成的方法,随后分析这种编码在当今文献数据库、化学反应数据库、分子设计以及合成反应路线规划等化学信息系统中的功能。     

Artificial intelligence in chemistry

The techniques and tools of artificial intelligence are reviewed. Chemical problems can serve as test domains for the development of new artificial intelligence methods. Artificial intelligence techniques can also be applied to the solution of practical problems in chemistry. Applications in chemistry include problems where it is necessary to encode chemical expertise, and where chemistry is merely an additional domain to which standard artificial intelligence techniques can be applied. Programs exploiting encoded chemical expertise can assist in solving problems of structure elucidation, synthesis planning, and experiment design. Robotics methods based on artifical intelligence and expert systems can enhance the performance of chemical instrumentation. Systems understanding natural language could improve the handling of chemical information, and artificial intelligence techniques may extend the capabilities of computer-assisted instruction.     

Computing minimal entropy production trajectories: an approach to model reduction in chemical kinetics

Advanced experimental techniques in chemistry and physics provide increasing access to detailed deterministic mass action models for chemical reaction kinetics. Especially in complex technical or biochemical systems the huge amount of species and reaction pathways involved in a detailed modeling approach call for efficient methods of model reduction. These should be automatic and based on a firm mathematical analysis of the ordinary differential equations underlying the chemical kinetics in deterministic models. A main purpose of model reduction is to enable accurate numerical simulations of even high dimensional and spatially extended reaction systems. The latter include physical transport mechanisms and are modeled by partial differential equations. Their numerical solution for hundreds or thousands of species within a reasonable time will exceed computer capacities available now and in a foreseeable future. The central idea of model reduction is to replace the high dimensional dynamics by a low dimensional approximation with an appropriate degree of accuracy. Here I present a global approach to model reduction based on the concept of minimal entropy production and its numerical implementation. For given values of a single species concentration in a chemical system all other species concentrations are computed under the assumption that the system is as close as possible to its attractor, the thermodynamic equilibrium, in the sense that all modes of thermodynamic forces are maximally relaxed except the one, which drives the remaining system dynamics. This relaxation is expressed in terms of minimal entropy production for single reaction steps along phase space trajectories.     

Chemoinformatics: a new field with a long tradition

Chemoinformatics is the application of informatics methods to solve chemical problems. Although this term was introduced only a few years ago, this field has a long history with its roots going back more than 40 years. Work on chemical structure representation and searching, quantitative structure–activity relationships, chemometrics, molecular modeling as well as computer-assisted structure elucidation and synthesis design was initiated in the 1960s. These different origins have now merged into a discipline of its own that is in full bloom. All areas of chemistry from analytical chemistry to drug design can benefit from chemoinformatics methods. And there are still many challenging chemical problems waiting for solutions through the further development of chemoinformatics.     

Half a Century of Polystyrene—A Survey of the Chemistry and Physics of a Pioneering Material

Hermann Staudinger, the founder of polymer chemistry, would have been 100 years old this year. One of the key materials with which he elucidated the structure of high polymers was polystyrene.—Polystyrene, one of the most important thermoplastics, has now been manufactured industrially for some 50 years. Not only has it simplified our daily lives in a variety of ways, it has also been a model substance for the development and expansion of polymer chemistry and polymer physics, and it was the pioneering material for handling polymer solutions and melts. This article surveys the development and present state of knowledge of the polymerization of styrene and of the relationships between structure and properties.     

Symbolic Algebra in Quantum Chemistry

Complex symbolic algebra, such as the manipulation of second-quantized operators, Slater determinants, Feynman diagrams, is inevitable in quantum chemistry. Increasingly, these operations are performed by the computerized systems that can handle higher mathematical constructs than just numbers and simple arithmetic. This article reviews these new algorithms that automate the algebraic transformation and computer implementation of many-body quantum-mechanical methods for electron correlation. They enable a whole new class of highly complex but vastly accurate methods, the manual development of which is no longer practical