Structure computer graphics

This example of side-chain alkylation of toluene with methanol serves not only to demonstrate the interaction between basic and acidic centers in a zeolite but also to illustrate another type of zeolite catalysis or of catalysis in general. The key phrases "computer graphics" or "computer-aided catalyst design" are used to describe this novel catalyst research. With the aid of computer graphics, it is possible to simulate zeolite structures and produce images of these structures. Computer graphics can also be used to produce pictures of molecules such as toluene in the zeolite pores or cages. 

In the early days of protein crystallography the determination of a protein structure was laborious and time consuming. The diffracted beams were obtained from weak x-ray sources and recorded on films that had to be manually scanned and measured. The available computers were far from adequate for the problem, with a computing power roughly equal to present-day pocket calculators. Computer graphics were not available, and models of the protein had to be built manually from pieces of steel rod. To determine the... 

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. 

Once an electron density map has become available, atoms may be fitted into the map by means of computer graphics to give an initial structural model of the protein. The quality of the electron density map and structural model may be improved through iterative structural refinement but will ultimately be limited by the resolution of the diffraction data. At low resolution, electron density maps have very few detailed features (Fig. 6), and tracing the protein chain can be rather difficult without some knowledge of the protein structure. At better than 3.0 A resolution, amino acid side chains can be recognized with the help of protein sequence information, while at better than 2.5 A resolution solvent molecules can be observed and added to the structural model with some confidence. As the resolution improves to better than 2.0 A resolution, fitting of individual atoms may be possible, and most of the... 

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. 

KARMA is an interactive computer assisted drug design tool that incorporates quantitative structure-activity relationships (QSAR), conformational analysis, and three-dimensional graphics. It represents a novel approach to receptor mapping analysis when the x-ray structure of the receptor site is not known, karma utilizes real time interactive three-dimensional color computer graphics combined with numerical computations and symbolic manipulation techniques from the field of artificial intelligence. 

The increased use of computer graphics for modeling molecular structures and chemical reactions has opened a path for the synthesis of tailor-made extractants. Thus the future promises new varieties of extractants with highly selective properties for the desired process. 

Important quantities which come out of molecular mechanics and quantum chemical models are typically related in terms of numbers , e.g., the heat of a chemical reaction, or in terms of simple diagrams, e.g., an equilibrium structure. Other quantities, in particular those arising from quantum chemical models, may not be best expressed in this way, e.g., the distribution of electrons in molecules. Here computer graphics provides a vessel. This is addressed in the concluding chapter in this section. Graphical Models. 

When we have access to an interesting protein structure and we would like to engineer the molecule, it is not enough to limit one s preparations to a computer graphics study of the local 3-D environment around the residue(s) in question. It... 

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