Chemical structures, generating conversion

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). 

Another approach in generating molecular insulating layers without the need of chemical conversion after deposition is the use of preliminarily modified molecules which can form dense self-assembled monolayers. To create dense self-assembled monolayers with sufficient robustness and insulating properties, a modified alkyltrichlorosilane with an aromatic end-group (18-phenoxyoctadecyl)tri-chlorosilane (PhO-OTS chemical structure Fig. 6.15a) was synthesized and tested [50]. The SAMs were created in a one-step process from vapor phase or solution. On self-assembly on a natively oxidized silicon surface the n-n interaction between the phenoxy end-groups of adjacent molecules creates an intermolecular top-link, leading to a more closely packed surface compared to monolayer than when linear end groups are used. 

Our intention in this chapter is to examine the challenges of extracting identihers from chemistry-related documents and the conversion of those identihers into chemical structures. The authors of this work each have well over a decade of experience in chemical structure representation and systematic nomenclature. We have been deeply involved in the development of software algorithms and software for the generation of systematic names and the conversion of chemical identihers into chemical structures.9 Although we have our own biases concerning approaches to the problem of N2S conversion, we have done our utmost to be objective in our review of the subject and comparison of approaches and performance. 

One of the primary issues with systematic nomenclature is that some names can appear systematic in nature but, in fact, are not. They can have the expected structure of a chemical name generated according to a rules-based system but are false systematic names, at least in their specific context. When the N2S conversion algorithms... 

The chemical energy generated by the combustion of energetic materials is converted to thermodynamic energy used for propulsion and explosion. As described in Chapter 2, the chemical energy is determined by the chemical structure of the molecules of the energetic materials. However, the thermodynamic energy is determined by the conversion of the heat and combustion products to pressure as de-... 

Database preparation is an important aspect of virtual screening. Molecules must be represented by one or more chemically sensible states and must be formatted appropriately for the virtual screening tool to be used. Relevant considerations include storage format(s), 2D-3D conversion or 3D structure generation, stereochemistry, charge, tautomers, protonation, and conformers. The impact of different database preparation protocols has not been thoroughly evaluated. Limited information in this area indicates that database preparation does impact final screening... 

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