Generation of molecular structures

Kier, L.B. and Hall, L.H. (1993b). The Generation of Molecular Structures for a Graph Based QSAR Equation. Quant.Struct.-Act.Relat., 12, 383-388. 

Kier, L.B. and HaD, L.H. (1993) The generation of molecular structures for a graph based QSAR equation. Quant. Struct. -Act. Rdat., 12, 383—388. 

Computer Generation of Molecular Structures by the Smog Program. 

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. 

The QSRR study was performed in three stages (1) entry and storage of the structures and the associated retention indices, (2) generation of molecular structure descriptors, and (3) generation and testing of linear model equations. The compounds structures and associated retention indices were entered into computer files using the structure entry capabilities of the ADAPT software system.The study was limited to the 144 compounds listed in Table 1. 

A, Bertrand, R. Barone, M. Arbelot, and M. Chanon, J. Chem. Res. (S), 158 (1994). Desmol—A Subroutine for the Generation of Molecular Structures with Stereochemical Information from Connectivity Data. 

RAMSES is usually generated from molecular structures in a VB representation. The details of the connection table (localized charges, lone pairs, and bond orders) are kept within the model and are accessible for further processes. Bond orders are stored with the n-systems, while the number of free electrons is stored with the atoms. Upon modification oF a molecule (e.g., in systems dealing with reactions), the VB representation has to be generated in an adapted Form from the RAMSES notation. 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

Two of the widely used programs for the generation of 3D structures are CONCORD and CORINA. CONCORD was developed by Pearlman and co-workers (17, 18] and is distributed by TRIPOS (19). The 3D-structure generator CORINA originates from Gasteiger s research group [20-23] and is available from Molecular Networks [24],... 

The potential of such reaction sequences for the generation of molecular diversity was also demonstrated by the synthesis of a library of heterocycles. Epoxide ring-opening with hydrazine and subsequent condensation with (3-diketones or other bifunctional electrophiles gave rise to a variety of functionalized heterocyclic structures in high purity [34]. A selection based on the substrate derived from cyclohexene oxide is shown in Scheme 12.12. 

Desorption/ionisation techniques such as LSIMS are quite practical, as they give abundant molecular ion signals and fragmentation for structural information. In the conditions of Jackson et al. [96], all the molecular ion and/or protonated molecule ion species were observed in the LSIMS spectrum when only 1 pmol of each additive was placed on the probe tip. However, as mentioned above, in LSIMS/MS experiments the choice of the matrix (e.g. NBA, m-nitrobenzylalcohol) is very important. Matrix effects can lead to suppression of the generation of molecular ions for some additives. LSIMS is not ideal for the quantitative detection of polymer additives, as matrix effects are very important [96]. 

Today it is an alternative method for alignment of molecular structures that maximizes the steric and electrostatic overlap using randomly generated starting configurations and keeping only the best results based on the value of the alignment function. 

Because of the large number of chemicals of actual and potential concern, the difficulties and cost of experimental determinations, and scientific interest in elucidating the fundamental molecular determinants of physical-chemical properties, considerable effort has been devoted to generating quantitative structure-property relationships (QSPRs). This concept of structure-property relationships or structure-activity relationships (QSARs) is based on observations of linear free-energy relationships, and usually takes the form of a plot or regression of the property of interest as a function of an appropriate molecular descriptor which can be calculated using only a knowledge of molecular structure or a readily accessible molecular property. 

Aluminophosphate-Based Molecular Sieves In 1982 a major discovery of a new class of aluminophosphate molecular sieves was reported by Wilson et al. [26]. By 1986 some 13 elements were reported to be incorporated into the aluminophosphate frameworks Li, Be, B, Mg, Si, Ti, Mn, Fe, Co, Zn, Ga, Ge and As [27]. These new generations of molecular sieve materials, designated AlP04-based molecular sieves, comprise more than 24 structures and 200 compositions. 

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