Representation of Organic Structure

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

To save space and time in the representation of organic structures, it is common practice to use condensed formulas in which the bonds are not shown explicitly. In using condensed formulas, normal atomic valences are understood throughout. Examples of condensed formulas are... 

Representation of Organic Structure Descriptions Arranged Linearly SimpUfled Molecular Input Line Entry Specification ... 

FIGURE 20.4 Representation of organic structural formulas with lines the structural formulas showing atoms are on the left and the corresponding line formulas on the right. Each line corner and end represents a carbon atom unless otherwise specified. Each C atom has four covalent bonds or equivalent attached, and the presence of H atoms is implied to provide the required bonds. 

Two-Dimensional Representation of Chemical Structures. The lUPAC standardization of organic nomenclature allows automatic translation of a chemical s name into its chemical stmcture, or, conversely, the naming of a compound based on its stmcture. The chemical formula for a compound can be translated into its stmcture once a set of semantic rules for representation are estabUshed (26). The semantic rules and their appHcation have been described (27,28). The inverse problem, generating correct names from chemical stmctures, has been addressed (28) and explored for the specific case of naming condensed benzenoid hydrocarbons (29,30). 

Figure 4.1 Representation of the structure of MOF-5 (a) six carboxylic acid groups from terephthalic acid are connected to four Zn" cations to form a metal-organic elementary zinc carboxylate cluster (only...

There is increased emphasis throughout Part B on the representation of transition structures to clarify stereoselectivity, including representation by computational models. The current practice of organic synthesis requires a thorough knowledge of molecular architecture and an understanding of how the components of a structure can be assembled. Structures of enantioselective reagents and catalysts are provided to help students appreciate the three-dimensional aspects of the interactions that occur in reactions. 

Figure 2.3 Representation of organized assemblies (a) bilayers, (b) cylindrical micelles, and (c) lamellar structure.

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. 

Figure 3.42 Solution behaviour of [18] crown-6, (a) in an organic solvent such as dichloromethane (the crown resembles a droplet of water in oil), and (b) extreme representation of the structure in a hydrophilic medium (droplet of oil in water).

FIGURE i Diagrammatic representation of the structure and function of bacterial biofilms. Dissolved organic matter (DOM) is sorbed onto the biofilm (1), additional DOM is released from algae and organic particles (2). The organic matter is cleaved by extracellular enzymes (3). Interactions can occur between clones of syntrophic or competing bacteria (4). See Section II for details. 

You have seen several examples of curly arrows so far and you may already have a general idea of what they mean. The representation of organic reaction mechanisms by this means is so important that we must now make quite sure that you do indeed understand exactly what is meant by a curly arrow, how to use it, and how to interpret mechanistic diagrams as well as structural diagrams. 

Despite the vast array of tools available today for structure drawing and representation, each tool is lacking in some way for the representation of complete structure space. Small organic molecules have been well supported, but the needs... 

Figure 2.2 Schematic representation of the structures of a solid, a smectic phase (SmA), the nematic phase and the isotropic liquid state formed by calamitic organic molecules with a large length-to-breadth ratio.

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... 

Martini S, Silvotti L, Shirazi A, Ryba NJP, Hrindelli R (2001) Co-expression of putative pheromone receptors in the sensory neurons of the vomeronasal organ. J Neurosci 21 843-848 Meijerink J, Carlsson MA, Hansson BS (2003) Spatial representation of odorant structure in the moth antennal lobe a study of structure-response relationships at low doses. J Comp Neurol 467 11-21... 

Figure 63 Schematic representation of molecular structure of discotic molecules and three examples of organic discotic molecules.

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