Molecular modelling computer graphics

Molecular Modeling, Computer Graphics and, in the Analysis of Synthetic... 

Fletterick, R., and Zoller, M., eds. (1986). Current Communications in Molecular Biology, Computer Graphics and Molecular Modeling. Cold Spring Harbor Laboratory Cold Spring Harbor, New York. 

Figure 8. Model of the dopamine receptor, with the (- -)-isobutactamol molecule superimposed, generated by the MMS-X computer-based molecular modeling and graphic display system. (Courtesy of Dr. G. Marshall, Washington University, St. Louis).

Not only should many techniques be included under the umbrella of molecular modeling/computational chemistry, but also the non-theoretically trained bench scientist must be welcomed to apply the techniques. In addition, it is obvious that as computational chemistry techniques packages become easier to use through sophisticated graphical user interfaces (gui) with pulldown menus and point-and-click buttons, it is incumbent on the developers to make sure their software is foolproof and not easily inappropriately applied. 

We do not view the terms theoretical chemistry and computational chemistry as synonymous. Computational chemistry sometimes involves application of computerized algorithms from quantum theory, but computational chemistry is certainly more than quantum chemistry. In fact, in an industrial setting, the latter is a very small part of it. Molecular mechanics, molecular dynamics, computer graphics, molecular modeling, and computer-assisted molecular design are other important aspects of computational chemistry. In industry, a... 

New ways to represent structure data became available through molecular modeling by computer-based methods. The birth of interactive computer representation of molecular graphics was in the 196Ds. The first dynamic molecular pictures of small molecules were generated in 1964 by Lcvinthal in the Mathematics and Computation (MAC) project at the Electronic Systems Laboratoiy of the Massachusetts... 

The era of the Evans and Sutherland computer systems vanished in the first half of the 1980s, when powerful and more economical workstations were introduced. In spite of advances in computer graphics and in CPU power, these workstations dominate the everyday life of molecular modeling even today. 

Computer graphics has had a dramatic impact upon molecular modelling. It should always be remembered, however, that there is much more to molecular modelling than computer graphics. It is the interaction between molecular graphics and the imderlying theoretical methods that has enhanced the accessibility of molecular modelling methods and assisted the analysis and interpretation of such calculations. 

This German stamp depicts a molecular model of urea and was issued in 1982 to commemorate the bun dredth anniversary of Woh ler s death The computer graphic that opened this in troductory chapter is also a model of urea... 

Thermodynamic properties such as heats of reaction and heats of formation can be computed mote rehably by ab initio theory than by semiempirical MO methods (55). However, the Hterature of the method appropriate to the study should be carefully checked before a technique is selected. Finally, the role of computer graphics in evaluating quantum mechanical properties should not be overlooked. As seen in Figures 2—6, significant information can be conveyed with stick models or various surfaces with charge properties mapped onto them. Additionally, information about orbitals, such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), which ate important sites of reactivity in electrophilic and nucleophilic reactions, can be plotted readily. Figure 7 shows representations of the HOMO and LUMO, respectively, for the antiulcer dmg Zantac. 

The use of graphic displays as an essential element of computer-based instmctional systems has been exploited in a number of ways. Molecular modeling and visualization techniques have supplemented the traditional set of stick models in courses on organic and inorganic chemistry, and animation of molecular motion and of the progress or mechanism of chemical reactions has been a useful classroom tool. 

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