Chemical Topology Program

A new generation of software for in-house processing of chemical structures arrived with topological programs like DARC and MACCS in the early 1980s. It became possible to store a chemical structure directly in a database, to search for structures and... 

The name Quantum Chemical Topology, refers to a research program originating in the theory of Atoms in Molecules (AIM), developed by Bader and co-workers. Over the last decade or so this research program has been carried out by about a dozen groups worldwide, while up to a himdred groups have benefited from its applications. 

Chemical information can be expressed in a number of ways. Chemical descriptors are commonly used in QSAR. There are thousands of chemical descriptors possibly used in QSAR. Indeed, programs such as DRAGON and CODESSA, just to name a couple, can calculate thousands of parameters [7, 8]. Chemical descriptors have different complexities. Some of them do not require any information on the structure, such as molecular weight. Others refer to the bidimensional structure, such as the number of double bonds. While some others require tridimensional information, such as molecular volume. Chemical descriptors can be geometrical, topological, quantum-mechanical, electrostatical, etc. There are a few books describing chemical descriptors [7, 8],... 

Descriptors based on the 2D structure or simply on the connectivity matrix of a structure have long been used for chemical similarity and for property correlations. Because they often lack any relationship to mechanism, these descriptors are best used within a congeneric series or at least a set of similar structures. They may be empirically useful for cluster analysis and chemical library design, because they are effective at representing structure differences and similarities. A few programs and providers of topological descriptors include the following ... 

Figure 2.2 Selected families (DDj(aj)) of density domains of the water molecule, as calculated with the GAUSSIAN 90 ab initio program [253] and the GSHAPE 90 molecular shape analysis program [254], using a 6-3IG basis set. There are only two topologically different types of families of density domains either a single density domain, or a family of three density domains. The sequence of topologically distinct cases provides a topological description of chemical bonding.

Simulation and Evaluation of Chemical Synthesis (SECS) is a program for organic synthesis that uses heuristic methods similar to LHASA but puts special emphasis on stereochemistry, topology, and energy minimization. 

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