Computational Chemistry Tools

If the assertion that VD is driven by non-specific interactions between drugs and macromolecular structures in tissues, then it logically follows that VD would be correlated to physiochemical parameters. Since such parameters are amenable to computation from structure alone, the prediction of human VD from chemical structure is feasible. Such in silico approaches have only been described over the past few years, as computational chemistry tools have advanced. 

This chapter 3,64 covered many programs, but it is by no means exhaustive. Many new computational chemistry tools have become available in the last few years. These codes are so new that there is not yet sufficient data to judge their impact on the scientific literature. It will be of interest to perform analyses similar to this one in the future. 

The development during the last decades has been breathtaking and today physical organic chemists like my co-authors and myself have access to useful quantitative computational chemistry tools for prediction of structures and reactivity on our desktops. 

For all compounds in the CIDB, a number of pre-calculated properties or predicted endpoints are stored. These pre-calculated properties allow, for example, for an efficient assembly of property-filtered subsets of the different compound collections. Additionally, important parameters have to be calculated only once for each compound and can then be used multiple times. This saves computational resources and ensures that all users rely on standardized structures and descriptor values that have been calculated in a consistent way. The stractures from the CIDB are therefore also used for updates of computational chemistry tools that maintain compound sets internally (e.g., pharmacophore search software). The calculation of the properties is facilitated by a number of workflows that are automatically triggered whenever structures are added or updated in a compound collection. For some structures, not all properties can be calculated successfully—this case is captured by an error tracking mechanism. Furthermore, a version backing procedure notes which version of a property calculator was used to generate certain property value and permits recalculations of properties if necessary. 

The analysis techniques used were FTIR to study this effect and the optional use of theoretical calculations to justify the obtained results by means of computational chemistry tools. Using QSAR properties, we can obtain an estimate of the activity of a chemical from its molecular structure only. The QSARs have been successfully applied to predict soil sorption coefficients of non-polar and nonionizable organic compounds, including many pesticides. Sorption of organic chemicals in soils or sediments is usually described by sorption coefficients. The molecular electrostatic potential (MESP) was calculated using the AMBER/AM 1 method. These methods give information about the proper region by which compounds have intermolecular interactions between their units. 

Of the three primary computational chemistry tools, two (molecular mechanics and semiempirical molecular orbital theory) rely on embedded empirical parameters, while the third [ab initio quantum chemistry) is potentially capable of reproducing experiment without such parameters. Since the first two methods depend on the availability of reliable experimental data, they are best applied in situations requiring an interpolation between known experimental quantities. The quality of the fundamental parameters on which these models are based depends on the quality and quantity of experimental data. 

Chemical Abstracts Service Information System Electronic Laboratory Notebooks Internet Internet-based Computational Chemistry Tools Laboratory Information Management Systems (LIMS) Online Databases in Chemistry Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure and Substructure Searching. 

The medium Internet is a medium created by hundreds of developments that mark our movement toward the new millennium (see Internet and Internet-based Computational Chemistry Tools). The number of Internet resources reached the mark of four million in 1995. According to an estimate of the Internet society the number of computers connected to the Internet will be around 120 million in the year 1999. World-wide commercial online services attracted seven million people world-wide in 1995. Internet has served an estimated 20 million people so far. Growth in usage for the commercial services is estimated to be about 40% through 1997. Internet growth is estimated at being roughly twice the rate of the commercial online services. ... 

Chemical Abstracts Service Information System Chemical Engineering Databases Chemical Safety Information Databases Factual Information Databases Inorganic Chemistry Databases Internet Internet-based Computational Chemistry Tools Online Databases in Chemistry Reaction Databases Structure Databases. 

In this category can be found a great (and increasing) number of collections of data, nearly all free of charge, and available on the World Wide Web (WWW) (see Internet and Internet-based Computational Chemistry Tools). The contents generally show two characteristics, apart from the very small number of compounds listed ... 

This article focuses on the technical aspects of the Internet. For chemical applications, please refer to Internet-based Computational Chemistry Tools in this encyclopedia. 

Efforts are currently being undertaken to standardize the MIME types of a number of popular structure and spectral information exchange file formats. Even without the official blessing of the standardization organizations, the proposed chemical MIME data types are already used in a consensual fashion. This topic is continued in Internet-based Computational Chemistry Tools. The article includes an extensive table of the important chemical MIME format identifiers and their corresponding file formats and typical extensions. 

The most important Plug-In for chemistry is Chime from MDL Information Sy.stems. Chime contains all the functionality of rasmol plus 2D-display features and extended script-ability for animations. A professional version which interfaces to MDL databases is also available. Chime is available for IRIX, PC, and Macintosh platforms, but not for anything else. Chime applications are described in Internet-based Computational Chemistry Tools. 

An interesting encoding format called CML (chemical markup language) which aims at structuring chemical information in a form far beyond what is possible within HTML, has been proposed." CML is based on XML and consequently has some similarity to HTML. The automatic indexing of chemical information from the original document without human intervention becomes much more feasible with this type of approach. Please refer to Internet-based Computational Chemistry Tools for a more detailed discussion. 

VRML has been found to be a very useful visualization format for chemistry. The only major disadvantage is that VRML files do not contain easily recognizable structures, only balls, cylinders, and triangle strips. The automatic recovery of structure data from these files suitable for further processing is difficult, but has been performed,An increasing number of computational chemistry programs add VRML output support in order to make their visualizations usable for WWW presentation, especially in the context of electronic publishing. More about this topic can be read in Internet-based Computational Chemistry Tools in this encyclopedia. 

Chemical Abstracts Service Information System Computer Graphics and Molecular Modeling Electronic Publishing of Scientific Manuscripts Factual Information Databases Internet-based Computational Chemistry Tools Molecular Models Visualization Nucleic Acids Qualitative Modeling Online Databases in Chemistry Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Reaction Databases Spectroscopic Databases Structure Databases. 

First Generation Internet-based Computational Chemistry Tools 1430... 

FIRST GENERATION INTERNET-BASED COMPUTATIONAL CHEMISTRY TOOLS... 

The rather abstract concepts discussed above, and also their limitations, are best illustrated by dissecting in detail how two simple Web-based computational chemistry tools can be constructed. The first will illustrate how a molecule can be selected from a database, visualized, and if desired used to initiate further database queries. The second example will show how infrared data presented in the form of a spectrum can be linked to theoretically computed normal vibrational modes as part of an animated model. The concepts illustrated here were originally described by us as hyperactive chemistry . No attempt here is made to explain every detail of the syntax employed in these examples, but rather to illustrate the basic concepts behind these tools. It is probable in any event that the syntax may change in the future, and these models should be taken as a snapshot of the state of Internet-based tools in early 1997 rather than as definitive examples. 

As computational chemistry tools have developed over the last decade or so, molecular graphics and visualization have played a prominent role in expressing complex three-and higher-dimensional properties of molecules, such as, e.g., wavefunctions. Just as structured languages such as HTML and its incorporation of URL descriptors were used to achieve structure and context for text-based documents, so there came a realization that a three-dimensional object description language was needed to express the context in more complex 3D scenes, or worlds as they became known. 

Computer Graphics and Molecular Modeling Electronic Publishing of Scientific Manuscripts Internet Internet-based Computational Chemistry Tools Molecular Surface and Volume. 

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