Computer representation of molecules

Computer Representations of Molecules, Chemical Databases and 2D Substructure Searching... 

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... 

An important approach to the graphic representation of molecules is the use of a connection table. A connection table is a data base that stores the available bond types and hybridizations for individual atoms. Using the chemical formula and the connection table, molecular stmctures may be generated through interactive graphics in a menu-driven environment (31—33) or by using a linear input of code words (34,35). The connection table approach may be carried to the next step, computer-aided molecular design (CAMD) (36). 

The next most important aspect of a molecular compound is its shape. The pictorial representations of molecules that most accurately show their shapes are images based on computation or software that represents atoms by spheres of various sizes. An example is the space-filling model of an ethanol molecule shown in Fig. C.2a. The atoms are represented by colored spheres (they are not the actual colors of the atoms) that fit into one another. Another representation of the same molecule, called a ball-and-stick model, is shown in Fig. C.2b. Each ball represents the location of an atom, and the sticks represent the bonds. Although this kind of model does not represent the actual molecular shape as well as a space-filling model does, it shows bond lengths and angles more clearly. It is also easier to draw and interpret. 

XuE, L, Godden, J., and Bajorath, J. Database searching for compounds with similar biological activity using short binary bit string representations of molecules./. Chem. Inf. Comput. Sci. 1999, 39(5), 881-886. 

Although the concept of pharmacophores constituting a simple representation of molecules and chemical groups in certain order was introduced nearly a century ago [1], there has been increasing interest and focus on pharmacophores in recent years following the advances in computational chemistry research. The historical development of the pharmacophore concept has recently been reviewed [2],... 

The past two decades have seen a marked change in the reporting of the application of various techniques to the determination of structure. Most papers relating to the synthesis of organic molecules now confine comments on UV and IR data to a minimum. While NMR data are presented in more detail, much 13C NMR spectral information is often presented simply as a catalogue of chemical shifts with little or no attempt at assignment. X-Ray structural determinations have become more commonplace and many papers now contain ORTEP representations of molecules. In addition, proposed structures are frequently supported by calculations and computer-assisted representations. 

Fig. 3.41 Computer representation of the structure of acetylcholine in its free solution-state conformation, in which oxygen atoms appear on opposite sides of the molecule (top), and of acetylcholine in its receptor-bound state, in which oxygen atoms appear on the same side (bottom). (Reprinted from Fig.

When one inserts an image of molecule from the Molecule Editor into a ChemText document, one actually inserts a computable representation of the structure. As this is a new concept, let me illustrate with an example. Suppose you have a ChemBase data base of your compounds. (See Fig. 1.8) You pull out the structure of your new compound and insert it into your manuscript which you... 

Henry W. Davis, Computer Representation of the Stereochemistry of Organic Molecules With Application to the Problem of Discovery of Organic Synthesis by Computer, Birkhauser Verlag, Basel, 1976. 

The DARC notation (see, for example, ref. 228) is a system of computer representation of chemical compounds rather than a system for the input of molecules into the computer. It will thus not be discussed here. 

Around 1967 three groups1-3 started to attack this problem in a way not restricted to special classes of molecules. In handling the formal aspects of chemical reactions by computers, one has to decide on representations for molecules and reactions. While the choice of the representation of molecules is more or less a technical problem, provided that no information of chemical interest is disregarded, the selection of a representation for chemical reactions is of central importance and can be decisive for the inventiveness of the program system. All three systems which were conceived in 1967 — LHASA1, SECS2, and SYNCHEM3 — have in common that the synthetic reactions are taken from a collection of known reactions, a library which has to be built up in the computer. 

One way to study the shapes of cellulose chains is to construct models that accommodate the available experimental data. There are many approaches to modeling, and comprehensive studies require extensive computations. The first computer model of a carbohydrate was a part of the experimental diffraction studies of cellulose [176]. Since then, there have been substantial improvements in both computers and their representations of molecules. 

Fig. 5 Structural formulas are the best representation of molecules for chemists - numerical descriptors are preferred by computers.

An important fact has been pointed out by Parr and Berk the bare nuclear potential Vn(r) shows many similarities with the electronic density function p(r). The computed isopotential contours of the composite nuclearpotential VnC lwere remarkably similar to some of the molecular isodensity contours (MIDCOs) of the electronic ground states in several simple molecules. One may regard the composite nuclear potential as the harbinger of electronic density, and isopotential contours of the composite nuclear potential V (r) can serve as surprisingly good approximations of MIDCOs. The nuclear potential contours (NUPCOs) are suitable for an inexpensive, approximate shape representation of molecules. 

Computer representation of methane and ethane molecules inside one of the hexagonal pores of MCM-41. Red = oxygen blue = silicon light blue = hydrogen brown = carbon. 

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