Chemical software programs

For all the different methods of chemical visualization, a lar e number of special techniques arc available, depending on the purpose of visualization. These software programs can be installed on a local computer or can be operated via the Internet. An ovemew of these programs is given in Section 2.12.3. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

The use of color graphics is also an effective means for displaying chemical stmctures. This method is far better than typesetting the three-dimensional architecture of complex multimolecule assembly (112). For developing in-house CAD software programs, the three-dimensional, sohd-modeling capabiUties of SdverScreen can also be utilized either in monochrome or color for constmction of such stmctures (113). 

Schecher, W. D. and D.C. McAvoy, 1994, MINEQL+, A Chemical Equilibrium Program for Personal Computers, User s Manual, version 3.0. Environmental Research Software, Inc., Hallowell, ME. 

Nomenclature resources help the user give correct names to chemical structures. Visualization resources allow the user to build molecules from scratch or display molecular structures imported from databases or other software programs (like the Protein Data Bank, PDB, for example). 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/home/home.do is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 4.5 include the facihty to visualize imported data however, two free software programs operate well in this regard. One is MDL Chime described previously in this section. Chime, a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator, supports a wide variety of molecule coordinate formats, including PDB (protein data bank), Molfile (from ISIS/Draw), MOP (MOPAC input hies), and GAU (Gaussian Input hies). 

Numerous computer software programs are available today to streamline design calculations. Of course, such software can be structured only after very careful analysis is made of the chemical dynamics of a given application. Calculations are particularly complex and difficult in the instances of azeotropic and reactive distillation. Software programs are described in some detail in the Kumana. Morris, and VenkuUiramkan references listed. 

The third fundamental component in the QSAR model is the mathematical algorithms. Many methods have been used, and in the last years, there has been an increase of the methods, and hence, quite probably this trend will continue, introducing many other methods [4—6]. Classical QSAR methods, used decades ago, were simple linear relationships. Corwin Hansch has been a pioneer of these methods [2]. An example can be the linear relationship between the fish toxicity and the partition coefficient between octanol and water, called Kow [3]. Kow, and its logarithm, called log P, is still the most popular chemical descriptor used in QSAR models for fish toxicity, and it is the base of software programs used by the US Environmental Protection Agency for fish toxicity [11]. The theoretical assumptions for the use of log P are that (1) octanol mimics the lipophylic component of the fish cell, and (2) the toxic effect is due to the adsorption of the chemical substance into the cell. 

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