Chemical structures, graphical

The ability to index a specific chemical structure graphically has been available for quite some time. Telesystemes-DARC launched a commercial system for this purpose in 1979 CAS has been doing this type of indexing in-house since the late 1960s. However, the structures reported in patents present some unique problems chemicals are described not as individual entities, but as famihes of compounds represented by a base structure with variable groups and some possibilities of the compounds protected by the patent are represented as generic terms only. 

Offline preparation and presentation of chemical structure graphics is now possible on a PC using a variety of query editor programs (7), such as those listed in Figure 3. In most cases these are specific to a single system, and use a proprietary format for transmission of the query structure between the PC and the mainframe computer. For example, STN Express allows query structures to be built offline and then, after connection to STN, uploaded and searched against the STN online structure files. Retrieved structures can be downloaded onto the PC and browsed offline in STN Express. Similarly, CHEMLINK is now available for Telesystemes-DARC, while in the case of in-house systems, ChemBase provides similar capabilities for MACCS. 

In the ancient times" the 1950s), data were transferred to computers by using punched cards. But already in 1959 Ascher Opier from Dow Chemical Company reported the use of a light pen for graphical entiy of chemical structures into a computer. Light pens were also used in the Chemical Abstracts Service in the 1970s. 

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

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.

And last not least, we will have to see further improvements in the graphical user interfaces of software systems and the retrieval systems of databases in order to make software and databases more acceptable to the chemical community at large. Software and databases should speak the language a chemist is used to, with hand-drawn chemical structures and reaction equations, or even imderstand the spoken word - and only provide the desired information selectively, not buried in a phe of unnecessary output. 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

Corey EJ, Wipke WT, Cramer RD HI, Howe WJ. Computer-assisted synthetic analysis. Facile man-machine communication of chemical structure by interactive computer graphics. J Am Chem Soc 1972 94 421-30. 

Because the chemical structure of a molecule encodes its biological properties, structure has long served as the primary variable and determinant for the discovery of new drugs by medicinal chemists. For this reason, systematic structural modification has been the primary tool of choice to isolate and enhance a desired biologic activity. Moreover, with the relatively recent development of in vitro receptor-binding assays, combinatorial methods of chemical synthesis, and computer graphics, the overall approach to structural modification has become increasingly sophisticated. 

Weininger D (1990) SMILES. 3. DEPICT. Graphical depiction of chemical structures. J. Chem. Inf. Comput. Sci. 30 237-243. 

It is remarkable that, in the space of less than two decades, the structural theory of organic chemistry should have moved from the first hesitant steps, where the chemical structure was considered to be separate and distinct from the physical structure of the molecule, and represented only the "affinities" of the atoms within the molecule, to the point where those same formulas were now viewed as representations of the actual physical locations of the atoms in the molecule (76). What was left undone at the end of the nineteenth century, by which time three-dimerrsional graphical formitlas for organic compoimds were in routine use, was, of coruse, a description of exactly what the "chemical affinities" of the atoms composing the molecules were. The answer to this problem would have to await the new century, and the development of modem theories of the atom and bonding. 

Feldman, R. J., "Interactive Graphic Chemical Structure Searching," in Computer Representation and Manipulation of Chemical Information, ed. W. T. Wipke, John Wiley, N.Y., 1974. 

Dittmar, Paul G. and Joseph Mockus, "An Algorithmic Computer Graphics Program for Generating Chemical Structure Diagrams," submitted to Journal of Chemical Information and Computer Science. 

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