Chemical reaction representations

Substance information such as chemical structures, molecular formulas, and chemical names Is stored in the REGISTRY database. This is the largest collection of chemical substance Information worldwide (see Section 3,1,2), While REGISTRY contains information on specific substances, generic substances are covered by MARPAT, Generic structures are called Markush structures after the American chemist Eugene Markush, who introduced these structures in the patent literature in 1924, MaRPAT comprises generic structures from the patent literature since 1988 (see Structure Representation). Chemical reactions or molecular transformations are covered by CASREACT (see also Reaction Databases). CASREACT has been indexed since 1985 and currently holds 2.9 million chemical reactions from the chemical and patent literature,... 

First, the objects of investigation, chemical compounds or chemical reactions, have to be represented. Chemical compoimds wUl mostly be represented by their molecular structure in various forms of sophistication. This task is addressed in Chapter 2. The representation of chemical reactions is dealt with in Chapter 3. The vast number of compounds known can only be managed by storing them... 

In chemoinformatics, chirality is taken into account by many structural representation schemes, in order that a specific enantiomer can be imambiguously specified. A challenging task is the automatic detection of chirality in a molecular structure, which was solved for the case of chiral atoms, but not for chirality arising from other stereogenic units. Beyond labeling, quantitative descriptors of molecular chirahty are required for the prediction of chiral properties such as biological activity or enantioselectivity in chemical reactions) from the molecular structure. These descriptors, and how chemoinformatics can be used to automatically detect, specify, and represent molecular chirality, are described in more detail in Chapter 8. 

Representation of Chemical Reactions 1185 Table 3-2. The 16 possible unit exchanges at any skeletal carbon atom. 

The representation of a chemical reaction should include the connection table of all participating species starting materials, reagents, solvents, catalysts, products) as well as Information on reaction conditions (temperature, concentration, time, etc.) and observations (yield, reaction rates, heat of reaction, etc.). However, reactions are only Insuffclently represented by the structure of their starting materials and products,... 

It is essential to indicate also the reaction center and the bonds broken and made In a reaction - In essence, to specify how electrons are shifted during a reaction. In this sense, the representation of chemical reactions should consider some essential features of a reaction mechanism. 

The main characteristics of the method, developed in our group for reaction classification arc 1) the representation of a reaction by physicochemical values calculated for the bonds being broken and made during the reaction, and 2 use of the unsupervised learning method of a self-organi2ing neural network for the perception of similarity of chemical reactions [3, 4],... 

Figure 10.3-16. Graphical representation of the chemical structure of the reactants and products of a chemical reaction a) as a 2D image b) with structure diagrams showing all atoms and bonds of the reactants and products to indicate how this information is stored in a connection table.

Representation of Atmospheric Chemistry Through Chemical Mechanisms. A complete description of atmospheric chemistry within an air quaUty model would require tracking the kinetics of many hundreds of compounds through thousands of chemical reactions. Fortunately, in modeling the dynamics of reactive compounds such as peroxyacetyl nitrate [2278-22-0] (PAN), C2H2NO, O, and NO2, it is not necessary to foUow every compound. Instead, a compact representation of the atmospheric chemistry is used. Chemical mechanisms represent a compromise between an exhaustive description of the chemistry and computational tractabiUty. The level of chemical detail is balanced against computational time, which increases as the number of species and reactions increases. Instead of the hundreds of species present in the atmosphere, chemical mechanisms include on the order of 50 species and 100 reactions. 

Descriptions of Physical Objects, Processes, or Abstract Concepts. Eor example, pumps can be described as devices that move fluids. They have input and output ports, need a source of energy, and may have mechanical components such as impellers or pistons. Similarly, the process of flow can be described as a coherent movement of a Hquid, gas, or coUections of soHd particles. Flow is characterized by direction and rate of movement (flow rate). An example of an abstract concept is chemical reaction, which can be described in terms of reactants and conditions. Descriptions such as these can be viewed as stmctured coUections of atomic facts about some common entity. In cases where the descriptions are known to be partial or incomplete, the representation scheme has to be able to express the associated uncertainty. 

With a reactive solvent, the mass-transfer coefficient may be enhanced by a factor E so that, for instance. Kg is replaced by EKg. Like specific rates of ordinary chemical reactions, such enhancements must be found experimentally. There are no generalized correlations. Some calculations have been made for idealized situations, such as complete reaction in the liquid film. Tables 23-6 and 23-7 show a few spot data. On that basis, a tower for absorption of SO9 with NaOH is smaller than that with pure water by a factor of roughly 0.317/7.0 = 0.045. Table 23-8 lists the main factors that are needed for mathematical representation of KgO in a typical case of the absorption of CO9 by aqueous mouethauolamiue. Figure 23-27 shows some of the complex behaviors of equilibria and mass-transfer coefficients for the absorption of CO9 in solutions of potassium carbonate. Other than Henry s law, p = HC, which holds for some fairly dilute solutions, there is no general form of equilibrium relation. A typically complex equation is that for CO9 in contact with sodium carbonate solutions (Harte, Baker, and Purcell, Ind. Eng. Chem., 25, 528 [1933]), which is... 

Villermaux, J. and Devillon, J.C., 1975. Representation de la coalescence et de la redispersion des domains de segregation dans un fluide par un modele d interaction phenomenologique. In Proceedings of the second international conference of chemical reaction engineering. Amsterdam, pp. Bl-13. 

Equation (1-7) is a general representation of any balanced chemical reaction, where A, represents reactants and products, and v, is negative for reactants and positive for products. 

This representation is ordinarily used for solid and for liquid systems and rarely for gases. In the absence of chemical reactions the mass composition of an isolated system remains unchanged. Any consistent set of units for mass (or volume) may be selected in interpreting the compositions expressed on a mass (or volumetric) basis. 

Stoichiometry in Reactive Systems. The use of molar units is preferred in chemical process calculations since the stoichiometry of a chemical reaction is always interpreted in terms of the number of molecules or number of moles. A stoichiometric equation is a balanced representation that indicates the relative proportions in which the reactants and products partake in a given reaction. For example, the following stoichiometric equation represents the combustion of propane in oxygen ... 

We conclude that corrosion is a chemical reaction (equation 10.1) occurring by an electrochemical mechanism (equations 10.2) and (10.3), i.e. by a process involving electrical and chemical species. Figure 10.1 is a schematic representation of aqueous corrrosion occurring at a metal surface. 

Explicit mechanisms attempt to include all nonmethane hydrocarbons believed present in the system with an explicit representation of their known chemical reactions. Atmospheric simulation experiments with controlled NMHC concentrations can be used to develop explicit mechanisms. Examples of these are Leone and Seinfeld (164), Hough (165) and Atkinson et al (169). Rate constants for homogeneous (gas-phase) reactions and photolytic processes are fairly well established for many NMHC. Most of the lower alkanes and alkenes have been extensively studied, and the reactions of the higher family members, although little studied, should be comparable to the lower members of the family. Terpenes and aromatic hydrocarbons, on the other hand, are still inadequately understood, in spite of considerable experimental effort. Parameterization of NMHC chemistry results when NMHC s known to be present in the atmosphere are not explicitly incorporated into the mechanism, but rather are assigned to augment the concentration of NMHC s of similar chemical nature which the... 

Learning various kinds of chemical reactions and physical processes is an important element of all chemistry curricula. Earlier in this chapter we conunented on how students could recite the verbal definition of a strong acid but yet failed to select a visual representation that best illustrates the complete ionization of hydrogen chloride molecules. Another part of this study, conducted by Smith and Metz (1996), was probing students microscopic representation of the reaction... 

Consider the examples of some of the forms of chemical equations (and related representations) met in school and college (i.e. middle and senior high school) science and chemistiy classes that are shown in Table 4.1. For the purposes of this chapter half-equations (Example 11) and symbolic representations of processes such as ionisation (Example 10) will be included under the generic heading of chemical equations . Table 4.1 does not include examples of chemical reactions and reaction schemes that include stmctural formulae, as are commonly nsed in organic chemistiy. 

Both of these forms of representation are symbohc although words are more familiar symbols to students. Both of these forms present difficulties to learners. Although word equations may seem a more direct way for novices to represent chemical reactions, they may sometimes make more demands on learners. So, for example in completing equations, non-systematic names - such as ammonia - may not provide strong clues to the elements present, and there is a need to learn, recall and apply such rules as -ate implies oxygen present, etc. 

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