Internet tools, computational chemistry

Donald B. Boyd, Appendix Compendium of Software and Internet Tools for Computational Chemistry. 

Boyd DB. Compendium of software and Internet tools for computational chemistry. In Lipkowitz KB, Boyd DB, eds. Reviews in Computational Chemistry. Vol. 11. New York Wiley-VCH, 1997 373-399. 

See URLs listed by D. B. Boyd, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 373-399. Appendix Compendium of Software and Internet Tools for Computational Chemistry. 

New ideas about howto teach chemistry are constantly being developed, and many of them are reflected in how our textbook is organized and in the ways in which topics are presented. This edition incorporates a number of new methodologies to assist students, including use of the Internet, computer-based classroom tools, Web-based tools, particularly MasteringChemistry , and more effective means of testing. 

The need to establish more effective mechanisms for collaboration has become evident in our previous work under eu cost Action d9. Therefore, in parallel with further development of accurate multireference quantum chemical methods, we decided to investigate the use of web-based and internet tools for remote scientific collaboration. In the past, some of the participants have exchanged data, draft manuscripts and the like by e-mail, supplemented by occasional correspondence by post and face-to-face meetings. By exploring alternative mechanisms, in particular, real-time collaboration procedures, we aim to establish a more productive environment. This includes remote execution of computer programs, the use of web-based interfaces for remote collaboration. The intention has been to use only a publicly accessible and user-friendly software for making the expertise accumulated in this project profitable for national and international collaborations in other domains of chemistry and physics. 

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. 

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