Molecular computation languages

Jiri Cizek s research program centers on the quantum theory of molecular electronic structure and related developments in quantum chemical methodology, coupled-cluster approaches to many-electron correlation problems,105 large-order perturbation theory,106 dynamical groups and exactly solvable models, lower bounds, and the use of symbolic computation language in physics and in chemistry. 

The whole concept of modern chemistry is based on the usage of drawings or other visual models of molecular structures. These simplified models of real molecules provide us with a framework that helps us understand the behavior of chemical compounds. With the development of computers, scientists had to face the problem of transferring molecular models into computer language. 

If the chromatogram is not equipped with a microcomputer for data treatment, one can easily determine results on any available PC. Programs for data treatment have been written in various computer languages. One such program, written in Pascal language, is offered to students who may wish to practice calculations and familiarize themselves with molecular weight determinations. It can be found in Appendix A.2 at the end of this chapter. 

As was said in the introduction (Section 2.1), chemical structures are the universal and the most natural language of chemists, but not for computers. Computers woi k with bits packed into words or bytes, and they perceive neither atoms noi bonds. On the other hand, human beings do not cope with bits very well. Instead of thinking in terms of 0 and 1, chemists try to build models of the world of molecules. The models ai e conceptually quite simple 2D plots of molecular sti uctures or projections of 3D structures onto a plane. The problem is how to transfer these models to computers and how to make computers understand them. This communication must somehow be handled by widely understood input and output processes. The chemists way of thinking about structures must be translated into computers internal, machine representation through one or more intermediate steps or representations (sec figure 2-23, The input/output processes defined... 

The investigation of molecular structures and of their properties is one of the most fascinating topics in chemistry. Chemistry has a language of its own for molecular structures which has been developed from the first alchemy experiments to modem times. With the improvement of computational methods for chemical information processing, several descriptors for the handling of molecular information have been developed and used in a wide range of applications. 

Both the language of valence bond theory and of molecular orbital theory are used in discussing structural effects on reactivity and mechanism. Our intent is to illustrate both approaches to interpretation. A decade has passed since the publication of the Third Edition. That decade has seen significant developments in areas covered by the text. Perhaps most noteworthy has been the application of computational methods to a much wider range of problems of structure and mechanism. We have updated the description of computational methods and have included examples throughout the text of application of computational methods to specific reactions. 

To a computer scientist, VS is nothing but another text mining, only the bits and bytes stored that contain molecular information adopt a format quite different from natural language and without adequate warning cannot be quickly interpreted. It is not that modem day text does not contain text that is not natural language, but that they are adequately flagged and do not stop the NLP software. For example,... 

In excerpt 3Y, the authors refer to computational results performed with the Gaussian suite of programs, a computational package used to calculate molecular ab initio or semiempirical electronic structure theory. Computational parameters (e.g., the basis set and level of theory) are included in the description. Do not worry if you do not understand the content of excerpt 3Y the language is intended for chemists with a computational or theoretical background. 

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