Chemical representation, problems

A Formal Representation of Chemical Genomics Problems 2.1. Pharmacogenomics of Gene Expression... 

Substances. Less common in drug discovery, but very useful for material science and polymer chemistry, is the ability to store "substances." These include unspecified or uncertain chemical structures, polymers, and other chemical entities that cannot be classed with the other chemical representations (42). Polymers pose particular problems, as discussed in the article by Schultz and Wilks (43). 

The need for concise chemical representation also applies to the work described in Chapters 6 and 7, so that the links between these chapters and the present one are crucial if chemical mechanisms, based on the type of understanding of elementary reactions discussed in Chapters 1 to 3, are ever to be incorporated in models of real combustion devices. At present, the generation of such concise mechanisms directly from full mechanisms has not been widely achieved. Most of the objective techniques described here are in their infancy, and this is evident from the need to use the hydrogen/oxygen example as an illustration, rather than one more appropriate to a volume on hydrocarbon oxidation. Therefore, one aim of the chapter is to give a comprehensive account of the mathematical techniques available, with the expectation that they will indeed be applied, before long, to the problems that lie at the heart of this book. 

This said, the number of the local expansions, their location, the number of expansion terms for each centre, and the method to get the numerical coefficients for each expansion term must be defined. There are no formal constraints, and the strategy should be selected on the basis of its efficacy computer time and precision. A detailed and clear exposition of the problems involved in, and of the options open to the definitions of local expansions has been recently done by F. Vigne-Maeder and the late P. Claverie [72]. We shall follow in part this exposition, giving more emphasis, at the end, to the use of atomic monopole expansions (i.e. atomic charges) and to mixed representations, which represent, in our opinion, the most versatile method for chemical reactivity problems. 

A significant problem in the universe of Markush chemical structures is the matter of extreme complexity. Markush chemical representations leave room for ambiguity, and often extremely complex Markush structures are created that become very difficult for Markush database producers to code. Additionally, the scope of these Markush claims can be excessively broad, making establishment of the prior art essentially impossible to determine for purposes of a meaningful and defensible patent examination. Sibley has commented most eloquently on this subject, as have others. " ... 

Other than using the electron equivalence of the substrate and the biomass to construct anabolic equations as described in Section 2.3.6, carbon equivalence has also been used, examples of which are found in references [26, 27]. In this latter method, the carbon in the quantity of substrate used to form the biomass is equivalent to the quantity of carbon in the biomass. Whereas this can be done as a chemical representation, the problem exists that unless the substrate and the cells have exactly the same degree of reduction, 02(aq) will be either a reactant or a product of anabolism. Except to the negligible extent noted in Section 2.4.6., OjCaq) does not enter into anabolism. 

In the next two sections, I examine some of the issues in chemical representation, and demonstrate by example problems that inhibit smooth integration of chemical structures among systems. 

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... 

Finding the adequate descriptor for the representation of chemical structures is one of the basic problems in chemical data analysis. Several methods have been developed in the most recent decades for the description of molecules including their chemical or physicochemical properties [1]. 

Two-Dimensional Representation of Chemical Structures. The lUPAC standardization of organic nomenclature allows automatic translation of a chemical s name into its chemical stmcture, or, conversely, the naming of a compound based on its stmcture. The chemical formula for a compound can be translated into its stmcture once a set of semantic rules for representation are estabUshed (26). The semantic rules and their appHcation have been described (27,28). The inverse problem, generating correct names from chemical stmctures, has been addressed (28) and explored for the specific case of naming condensed benzenoid hydrocarbons (29,30). 

The computational problem of polymer phase equilibrium is to provide an adequate representation of the chemical potentials of each component in solution as a function of temperature, pressure, and composition. 

If teaching and learning about the submicro is complex, then that about the symbolic is even more so. In Chapter 4, Taber unpicks in detail the ranges of symbolisms used in chemistry the spread of types invoked, those used to represent chemical entities and those used to represent reactions between them. In each case, he analyses the educational problems that they present. He concludes with some broad precepts about how symbolic representations might best be presented in chemical education. 

This diagram may appear trivial to the expert chemist but for a novice it contains much information about the chemical reaction at both the sub-micro and symbolic levels presented in multiple representational formats. Unless teachers are explicit in their use of these representations it is umealistic to assume that students would develop the same ability to choose an appropriate representation for a given process. It is possible that students can use and understand the representations without being able to see how they are related. Several authors (Hinton and Nakhleh, 1999 Kozma and Russell, 1997 Nurrenbem and Pickering, 1987) suggest that students are made aware of all three levels of representations and given opportunities to use them in solving problems. 

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