Database of structures

A useful empirical method for the prediction of chemical shifts and coupling constants relies on the information contained in databases of structures with the corresponding NMR data. Large databases with hundred-thousands of chemical shifts are commercially available and are linked to predictive systems, which basically rely on database searching [35], Protons are internally represented by their structural environments, usually their HOSE codes [9]. When a query structure is submitted, a search is performed to find the protons belonging to similar (overlapping) substructures. These are the protons with the same HOSE codes as the protons in the query molecule. The prediction of the chemical shift is calculated as the average chemical shift of the retrieved protons. 

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

There are now extensive databases of molecular structures and properties. There are some research efforts, such as drug design, in which it is desirable to hnd all molecules that are very similai to a molecule which has the desired property. Thus, there are now techniques for searching large databases of structures to hnd compounds with the highest molecular similarity. This results in hnding a collection of known structures that are most similar to a specihc compound. 

The program allows the user to create a database of structures. Calculations can then be run on the whole set of structures. These databases may also be used by some separately sold software packages. 

CHEOPS is based on the method of atomic constants, which uses atom contributions and an anharmonic oscillator model. Unlike other similar programs, this allows the prediction of polymer network and copolymer properties. A list of 39 properties could be computed. These include permeability, solubility, thermodynamic, microscopic, physical and optical properties. It also predicts the temperature dependence of some of the properties. The program supports common organic functionality as well as halides. As, B, P, Pb, S, Si, and Sn. Files can be saved with individual structures or a database of structures. 

Reference 13 is recommended for its large database of structured packing infonnation. One parameter for structured packing within the narrative of Reference 13 is that the minimum w etting rate is 0.1 to 0.2 gpm/ft compared to 0.5 to 2gpm/fT for random packings. 

See Reference 39 for its large database of structured packing information. One parameter for structured packing... 

A much more common and probably more successful approach to the prediction of shifts are those derived from databases. Here, a database manager searches a database of structures for those containing sub-structures within the postulated structure. The key elements necessary for this approach are ... 

Structure and Nomenclature Search System. This system links the collection of chemical databases found in the Chemical Information System (CIS), one of the first interactive systems for structure and substructure searching. References from the separate files can be retrieved by SANSS using CAS Registry Numbers, and the database of structures may be searched for structures or substructures. An adaptation of the SANSS software for substructure searching has been incorporated in the Dmg Information System of the National Cancer Institute for its own use (54). 

What is lacking at this point in theories relating lattice restraints and chemical reactivity is the identification of specific steric interactions which alter reactivity and an estimation of their magnitude. This requires an extensive database of structure-reactivity information for a series of closely related compounds. This we have from our studies on the solid state photochemistry and X-ray crystallography of a large number of variously substituted bicyclic dienones of general structure L (5). In this series, we recently observed a photorearrangement... 

TABLE 6.11 Buspirone metabolite database of structures identified with LC/MS and LC/MS/MS with a standard method... 

Full-featured structure drawing and presentation program. Supports IUPAC nomenclature (names to structures, structures to names). Integrated with CBIS. Supports personal databases of structures, reactions, and graphics. 

Structure building, manipulation. Van der Waals and electrostatic energy minimization by MM2 and MNDO. Stick or ball-and-stick display. Report generation, interface to ChemDraft for drawing chemical structures. Database of structures of compounds used in the development of the semiempirical methods in MOPAC and AMPAC. PC. 

Figure 10.1 Basic polypeptide geometry. The upper panel shows a short peptide sequence of three amino acids joined by two peptide bonds. A relatively rigid planar structure, indicated by dashed lines, is formed by each peptide bond. The relative positions of two adjacent peptide bond planes is determined by the rotational dihedral angles

A similar pair-wise comparison can be used to evaluate the self-similarity of a database of structures. This approach also allows direct visual comparison of databases or database subsets if the coefficient distributions are plotted as a graph or histogram and this approach can be used for either self-similarity or for database comparison (Chart 1). 

Exact Match Search. One type of structure searching in which a query molecule is searched for in a database of structures. To exactly match the query, the target structure must be topologically identical and not be a substructure or superstructure of the query. 

Hohn, L. and Sander, C., The FSSP database of structurally aligned protein fold families. Nucleic Acids Res., 24, 206, 1996. 

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