Representation of Molecular Structures

such as SDF molfiles3 or PDB4 files are commonly used to represent molecular structures. The data in these files contain information about the atoms, atom charges and aromaticity, and bonds between the atoms. It is possible to define a relational table where each of the data fields in the file is stored in a separate column. One could write structured query language (SQL) to store and search data in such tables, but there is a more succinct way to represent the same information. 

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Representation of Molecular Structures by Electron Systems 2.6.2.1 General Concepts... 

Fig. 32 Schematic representation of molecular structure and morphology observed in PS-fo-PB-fc-PS linear and star-block copolymers. Oblique lines between blocks for LN2 and ST2 indicate tapered transition of dissimilar blocks. From [102], Copyright 2003 Wiley...

Figure 4. Views of DMBA, BP, 5,6-dimethylchrysene, 5,12-dimethyl-chrysene and 5-methyl chrysene. These illustrate the distortions that occur as a result of steric effects. These and many subsequent representations of molecular structure are stereoviews and may be viewed with stereoglasses alternatively the reader can focus his eyes on the two images until an image between them begins to form and then allow his eyes to relax until the central image becomes three-dimensional. This process calls for patience and may take a minute or so. The reader who does not wish to do this may simply inspect one of the two diagrams for each structure.

Figure 3 (Plate 2). Representation of molecular structure in MD simulations. Shown here is the SOPC lipid, discussed in the text. The numbers at each atom indicate the partial charge on the atom. The space-filling picture on the left gives insight into the van der Waals radii of the various groups, and thus into the shape of the molecule. Reproduced from (58) with permission from the Biophysical Society...

Fig. 1. Schematic representation of molecular structures used for the photoseparation of charges, (a) Molecular monolayers on the base of fatty acids (b) lipid bilayers (c) lipid vesicles (d) micelles (e) microemulsions. The circles and ellipses stand for polar fragments the elongated rectangles, the wavy and straight lines depict hydrophobic fragments. Examples of substances forming the depicted structures are given in Fig. 3.

One critical task of any compound registration system is to make sure molecular structures are compliant with chemistry conventions. This ensures consistent representations of molecular structures in the database so that structure searches can find, and only find, the right compounds. Although different organizations may have slightly different conventions, the following ones are some of the most common that the Chemistry Intelligence API takes care of. 

The Web offers affordances to students that more traditional means of teaching cannot offer, such as the use of three-dimensional user-manipulable representations of molecular structures and animated molecular-level representations. While the use of on-screen three-... 

The skeletal branching index, published by Randic, motivated significant research to enlarge its applicability to chemical systems other than alkanes and to predict properties other than boiling point. Kier and coworkers developed the molecular connectivity idea into a full paradigm for the representation of molecular structure (Hall and Kier, 2001). 

Hall, L.H., and Kier, L.B., Issues in representation of molecular structure. The development of molecular connectivity, J. Mol. Graphics Modelling, 20, 4-18, 2001. 

Figure 10 Molecular structure of 2a and crystal packing of (a) the chiral inclusion crystal 2a (- )4 and (b) the chiral crystal of 2a on its own. (c) Space-filling representation of molecular structure of 2a as found in the two crystal structures. Conformations are similar in the two cases.

Graph representation of molecular structures with polycentric bonds... 

This way of hypergraph representation of molecular structures disregards the structure of ligands in the complexes. Yet it gives unambiguos descriptions, because the incidence matrices of the hypergraphs differ ... 

LCR uses a graph theoretic representation of molecular structures, wherein nodes are atoms and edges are bonds. Three modeling elements are employed to create and describe chemical structures. Each modeling element has been implemented as a class, in an object-oriented programming environment, and is described by a set of attributes and a set of procedures. 

Dietz, A. (1995). Yet Another Representation of Molecular Structure. J.Chem.lnf.Comput.ScL,... 

Robinson, D.D., Barlow, T.W. and Richards, W.G. (1997a). Reduced Dimensional Representations of Molecular Structure. JChem.InfComput.Sci., 37, 939-942. 

The concept of orbital hybridization deserves a few summary comments. The method is used throughout basic and applied chemistry to give quick and convenient representations of molecular structure. The method provides a sound quantum mechanical basis for organizing and correlating vast amounts of experimental data for molecular structure. The simple examples discussed earlier all involved... 

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