Molecular Editor

The WLN was applied to indexing the Chemical Structure Index (CSI) at the Institute for Scientific Information (ISI) [13] and the Ituiex Chemicus Registry System (ICRS) as well as the Crossbow System of Imperial Chemical Industries (ICl). With the introduction of connection tables in the Chemical Abstracts Service (CAS) in 1965 and the advent of molecular editors in the 1970s, which directly produced connection tables, the WLN lost its importance. 

A structure drawn by a molecular editor such as ISIS Draw) can be translated by the data conversion program AutoNom into a lUPAC name, and vice versa, by exchanging structure information through a ROSDAL string [18, 19]. 

Early implementations of the CIP rules for computer detection and specification of chirality were described for the LHASA [105], CHIRON [106], and CACTVS [107] software packages. Recently, several commercial molecular editors and visualizers (e.g., CambridgeSoft s ChemOffice, ACD s I-Lab, Accelrys WebLab, and MDL s AutoNom) have also implemented the CIP rules. 

The molecular editor consists of a java applet that is embedded in the HTML document. It encodes the drawing into a connection table in inol-format, which is sent to the web server. 

Model Building. CHEMLAB offers a variety of ways to build a model and insert it into its molecular workspace. This includes structure calculation from standard bond lengths and bond angles as well as a true three-dimensional molecular editor. Molecules can be joined in three-space or built from three dimensional fragments. 

Leatherface is a 2-D molecular editor that modifies properties of atoms and bonds in molecular connection tables according to rules specified by the user. Unlike Permute, Leatherface encodes no chemical knowledge and neither processes nor generates 3-D structures. Its real strength is that it allows the user to impose a very detailed and precisely specified chemical view on large numbers of connection tables. 

International Uniform Chemicals Information Database Java Molecular Editor... 

Lastly in this section, a new improvement to the JME molecular editor (see above, http //www.molinspiration. com/cgi-bin/properties) permits prediction of bioactivity. 

JME molecular editor JME is a free Java applet which allows generation and editing of molecules and reactions, and creation of molecule SMILES. The JME applet, written by Peter Ertl from Novartis, has become a standard for molecule structure input on the internet. http //www.molinspiration.com/ jme/index.html... 

A variety of molecules were constructed using the molecular editor of the CAChe program and their properties were calculated using MOPAC (AMI) after optimizing... 

JME molecular editor JME Molecular Editor is a Java program (firee for non-commercial use), which enables drawing and editing of molecules and reactions in a stand-alone mode or as an applet directly within an HTML page. The Editor can generate SMILES of created structure, so it can be used as a firont-end to molecular and reaction databases or property calculation services http //www.ch.ic.ac.uk/vchemlib/mol/search/spurt/... 

We have used Molecular Editor as a display program, and it is modesdy priced. capacity of this application to permit the manipulation and... 

A. Smith, Molecular Editor, Intellimation, P.O. Box 1530, Santa Barbara, California 93116-1530. 

Computational chemistry, which can predict the spectra of a variety of compounds that cannot be obtained in their pure form, was used to study the highly sensitive detection of bromate in ion chromatography. Several possible ions, molecules and their complexes were constructed by a molecular editor, and optimized by MM2 and MOPAC (PM3) calculations. Their possible electronic spectra were then obtained by the Zerner s Intermediate Neglect of Differential Overlap (ZINDO) (INDO)-Visualyzer in the CAChe program. The Amax of the spectra and the transition dipoles were calculated using the ProjectLeader program. Comparison of the experimental and predicted results indicated that Brs" was the probable reaction product, and that N02 and ClO accelerated the reaction. ... 

The surface conditions of the bonded phase and the densities of the chiral recognition groups are not known. Therefore, three-dimensional structures of chiral phases were constructed using the Molecular Editor program, and... 

Underivatized amino acids form complexes with copper(II). A variety of copper(II)-trapped phases have been developed for the enantiosepara-tion of amino acids. N-Salicylidene-(J )-2-amino-l,2-6is(2-buto Q -5-fe/t-bu(yl-phenyl)-3-phenyl-l-propanol was coated on an octadecyl-bonded silica gel column and copper sulfate solution was used as the eluent. The structure was constructed using the Molecular Editor program and optimized by MM2 calculations. The optimization was performed as the energy change was less than 10 kcal mol. The molecular weight of the chiral phase was 1449, and the final and van der Waals energies were 77.04 and —8.77 kcal mol, respectively. 

Correct recognized structures using the JME Molecular Editor. 

Fig. 10.17 JME molecular editor loading with smiles window...

The Java Molecular Editor (JME) is used to input answers to questions in the multimedia activities. Java is copyright of Novartis AG, Switzerland. 

The final program provides probiems >which require the interpretation of the infrared and IMMR spectra for a series of unknovwi compounds. The solutions to these problems are entered using a molecular editor. To complete the study there is a set of interactive self-assessment questions. 

There are a variety of desktop or Web-based molecular editors available that can be used to generate a ligand file for a novel compound not found in any of the databases. The Web-based molecular editors allow users to sketch molecules in 2D, while desktop tools such as Avogadro [15] can draw molecules in 3D. 

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