Substructure representation

One of the most widely used - and successful representations of the constitution, the topology, of a molecule is the HOSE code (Hierarchical Ordered description of the Substructure Environment) [9]. It is an atom-centered code taking into account... 

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

Substantive substructure, a chemical toolbox for the selected practices with macroscopic phenomena as relevant properties as a starting point the toolbox consists of those representations identified as stractures , relevant features of the stmctures and explicit relations between stractures and properties . 

Within the computational scheme described in the course of this work, the available information about the atomic substructure (core+valence) can be taken into account explicitly. In the simplest possible calculation, a fragment of atomic cores is used, and a MaxEnt distribution for valence electrons is computed by modulation of a uniform prior prejudice. As we have shown in the noise-free calculations on l-alanine described in Section 3.1.1, the method will yield a better representation of bonding and non-bonding valence charge concentration regions, but bias will still be present because of Fourier truncation ripples and aliasing errors ... 

Figure 3.42. Schematic representation of a double layer composite structure. Two substructures (1 and 2) are sketched. The composite structure (1 + 2) resulting from the mutual intermingling of the two substructures has a period corresponding to six subcells 1 commensurate to seven subcells 2.

Observe how a double bond with one thin and one thick line has appeared, a graphic representation that this bond can be single or double in the target molecule. The CHAOS program will detect the presence of this substructure provided it finds either of the two atom groupings in the following figure ... 

An heuristic program written by Shelley (10) has been adapted for our computer system to display molecular structures and substructures from connectivity tables. Since the molecular structure and substructure representations are stored in a unique, irredundant form, the structure drawings facilitate visual comparison for commonalities. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

A consequence of screening dissimilar libraries is that by their very nature they should contain only a small representation of any particular scaffold. As a result, there are usually few actives of similar structure this prevents the formulation of hypotheses as to the possible substructure responsible for activity. Thus, similarity searching around initial hits is very important to permit sufficient information to be acquired to allow such hypotheses to be made and... 

For comparative purposes, the spectrum for the DHP polymer from [2-13C] coniferyl alcohol 2b is also included (Fig. 3c) (24,29). As readily noted, the guaiacyl resonances at 127.6 (substructure A), 83.8 (substructure B) and 55.5 ppm (substructures C-E) show some similarity to L. leucocephala tissue. However, even in this case, the DHP polymer is not an adequate representation since relative intensities are essentially inverted between both spectra (Fig. 3b and 3c). 

Figure 10.11 Schematic representation of the VB-structure of a l,4,ll,14,15,30-hexahydro[60]fullerene derivative involving a cyclopentadiene substructure (cyclopentadiene addition pattern).

With the variety of chemical substance representations, i.e., fragment codes, systematic nomenclature, linear notations, and connection tables, a diversity of approaches and techniques are used for substructure searching. Whereas unique, unambiguous representations are essential for some registration processes, it is important to note that this often cannot be used to advantage in substructure searching. With connection tables, there is no assurance that the atoms cited in the substructure will be cited in the same order as the corresponding atoms in the structure. With nomenclature or notation representation systems, a substructural unit may be described by different terms or... 

Depending on the sophistication needed, substructure searching can be accomplished with a variety of the representations of a chemical substance. Some substructure searches can only be adequately answered by a complete atom-by-atom and bond-by-bond search for which a connection table, with its explicit description of full structural detail, is essential. 

Substantial attention and progress has been made in the development of procedures to effect conversion between chemical substance representations. Zamora and Davis [26] describe an algorithm to convert a coordinate representation of a chemical substance (derived from input by a chemical typewriter) to a connection table. An approach for interactive input of a structure diagram and conversion of this representation to a connection table suitable for substructure searching is discussed by Feldmann [27]. The conversion of systematic nomenclature to connection tables offers a powerful editing tool as well as a potential mechanism for conversion of name files to connection tables this type of conversion is described by Vander Stouw [28]. 

The conversion from a connection table to other unambiguous representations is substantially more difficult. The connection table is the least structured representation and incorporates no concepts of chemical significance beyond the list of atoms, bonds, and connections. A complex set of rules must be applied in order to derive nomenclature and linear notation representations. To translate from these more structured representations to a connection table requires primarily the interpretation of symbols and syntax. The opposite conversion, from the connection table to linear notation, nomenclature, or coordinate representation first requires the detailed analysis of the connection table to identify appropriate substructural units. The complex ordering rules of the nomenclature or notation system or the esthetic rules for graphic display are then applied to derive the desired representation. 

It can therefore be inferred that 0(3) electrodynamics is a theory of Rieman-nian curved spacetime, as is the homomorphic SU(2) theory of Barrett [50], Both 0(3) and SU(2) electrodynamics are substructures of general relativity as represented by the irreducible representations of the Einstein group, a continuous Lie group [117]. The Ba> field in vector notation is defined in curved spacetime by... 

Fig. 6. Schematic representation of the tail domains in Type IV intermediate filament chains. The rod domain, indicated by a shaded rectangle, does not show its known substructure. The four chains illustrated here are, from the top downwards, a-intemexin, and the low (NF-L), medium (NF-M), and high molecular weight chains (NF-FI) from neurofilaments. The characters of the segments are indicated by the one letter code. Figure is redrawn from Parry and Steinert (1995) and is based on an original by Shaw.

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