Molecular structure generation

Efficient generators of structural formulas such as the various MOLGEN versions available are required for several applications  

We first describe formula-based generation of molecular structures. This starts with a molecular formula and takes further restrictions into account, which often allow an enormous and necessary - reduction of the search space. Then we discuss the handling of restrictions, i.e. constrained generation. 

Another question concerns the transformation of molecular graphs by chemical reactions. This leads to reaction-based generation of molecular structures used in the simulation of combinatorial chemistry. 

A third issue is the definition of search spaces arising from a generic formula using variable substructures which allow the variation of substituents, homology, position and length of chains. 

For all these tasks, molecules are required to be canonized to avoid duplication. Therefore we also describe the canonizer MOLGEN-CID that is used in MOLGEN. 

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The as-spun acrylic fibers must be thermally stabilized in order to preserve the molecular structure generated as the fibers are drawn. This is typically performed in air at temperatures between 200 and 400°C [8]. Control of the heating rate is essential, since the stabilization reactions are highly exothermic. Therefore, the time required to adequately stabilize PAN fibers can be several hours, but will depend on the size of the fibers, as well as on the composition of the oxidizing atmosphere. Their are numerous reactions that occur during this stabilization process, including oxidation, nitrile cyclization, and saturated carbon bond dehydration [7]. A summary of several fimctional groups which appear in stabilized PAN fiber can be seen in Fig. 3. 

Since these constraints are the same, the same 2691 molecular structures generated for the single compound solvent design are generated in sub-problem 1. 

Pearlman, R.S. (1993) 3D molecular structures generation and use in 3D searching, in 3D QSAR in Drug Design. Theory Methods and Applications, 1st edn (ed. H. Kubinyi), FSCOM Science Publishers, Leiden, pp. 41—79. 

CpCo(CO)2 under UV irradiation and from the polymerizations of metallolyl (57 and 58) and silyldiynes (66-70) catalyzed by tantalum halides [86-91]. The homopolycyclotrimerizations of other aromatic diynes (38-56) all proceeded very rapidly, giving polymeric products that were only partially or totally insoluble in common organic solvents due to the involved cross-linking reactions. The large free volumes and irregular molecular structures generated by the nonlinear carbazolyl, diphenylamine, metallolyl and silyl groups may have helped endow the homopolymers (hb-P57 to hb-P70) with the excellent solubility. 

Pearlman, R. S. 3D Molecular Structure Generation and Use in 3D Searching, in 3D QSAR in Drug Design-Theory Methods and Applications, Kubyni, H. Ed., Escom Science Publishers, Leiden,... 

Many important therapeutics, in use in clinics today, are biosynthesized by the nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) paradigm. For example, many of the antibiotics (penicillin, cephalosporin, vancomycin, erythromycin, etc.), immunosuppressors (cyclosporine, rapamycin), antiviral agents (luzopeptin A), antitumor agents (bleomycin), and toxins (thaxtomin) are NRPS and PKS derived.20-22 Figure 1 displays a small selection of natural products that are NRPS and PKS derived and illustrates the diversity of molecular structures generated by these biosynthetic paradigms. 

When the state of a molecule evolves under the influence of a time-independent H, structure and dynamics are two sides of the same coin. Since the same H appears in the time-independent and time-dependent Schrodinger equations, an Heff-based intuitive picture of the molecular structure generates an intuitive, causal, mechanistic picture of molecular dynamics. 

Molecular structure generated from GIF data.) (CSD416317 obtained from the Crystal Structure Deposition at Fachinformationszentrum Karlsruhe, www.fiz-karlsruhe.de/ crystal structure dep.html)... 

FIGURE 15.11 Chromium(l) Complexes with Extremely Short Metal-Metal Bonds. (Molecular structures generated with CIF data, with hydrogen atoms omitted for clarity.)... 

Figure 9.5 Procedure of the molecular structure generation and conformational search.

Molecular structure generation. Combinatorial chemistry requires the generation of virtual molecular libraries, usually defined by given reactants and reactions. For this reason we shall describe algorithms for reaction-based structure generation. 

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