Digital Briefs | October 20, 2008 Issue - Vol. 86 Issue 42 | Chemical & Engineering News
Volume 86 Issue 42 | p. 60
Issue Date: October 20, 2008

Digital Briefs

New Software and Websites for the Chemical Enterprise
Department: Science & Technology

Websites 5.0 is a free, integrated single-search gateway to science and technology information from 17 organizations within 13 federal science agencies. The site is home to 200 million pages of government science resources. Users are able to search collections of valuable science information and readily find links to a variety of topics. Recent improvements include seven new databases and portals that allow researchers access to information, including thousands of patents resulting from Department of Energy research and development, documents and bibliographic citations of DOE accomplishments, millions of electronic (Eprint) documents from around the world, comprehensive and peer-reviewed toxicology data for thousands of chemicals, more than 3 million references to worldwide literature on the adverse effects of chemicals on living organisms, and a digital archive of biomedical and life sciences journal literature. The site also provides cancer-related information for a diverse audience, including support and treatment resources for patients, comprehensive descriptions of research programs and clinical trials for health care professionals and the general public, and funding opportunities for researchers. Links to related EurekAlert! Science News items and to Wikipedia entries are also included on the site. OSTI,

Academy Savant has two new e-Learning modules aimed at safety available on its website, The modules, called “Practical Lab Skills,” were created in a real lab and show demonstrations of the correct and safe methods of carrying out laboratory procedures. The videos in the new modules cover purification techniques such as gravity filtration, suction filtration, recrystallization, sublimation, and refluxing, as well as extraction techniques such as solvent extraction, soxhlet extraction, continuous flow extraction, and sample drying. Each module contains about 30 minutes of video with voice-over that can be displayed as text and in print form. Assessment of a user’s skills is accomplished through automatically scored multiple-choice quizzes and reviews with open-ended questions. Licenses can be obtained on the website for online viewing in a variety of forms. Academy Savant,


STR3DI32 v3.000.2.D is a molecular modeling program that features comprehensive molecular recognition algorithms. The software can generate simulations of organic molecules just from coordinate data and atom types because it automatically detects bond type, bond polarization, and other stereoelectronic effects. The simulation embraces all the stereoelectronic features of the molecule, including all steric, dipolar, and hydrogen-bonding interactions. The structure-recognition properties of the program effectively minimize the user’s required input when working with pregenerated atomic coordinate data, as from diffraction studies, and rapidly enable the user to detect inconsistencies in these data. The program also enables users to easily build, link, dock, and modify the models. Other functions include automatic detection of delocalized π-systems and substructure searching of complex molecules. The software uses the completely new molecular mechanics force field, QVBMM, which is parameterized for n-n, n-σ, and n-π interactions, affording the handling of complex biomolecules, such as double-stranded DNA, and biomolecular clusters. The program calculates molecular features such as molecular volumes and enthalpies of formation. STR3DI32 works on computers that run any Windows operating system. Exorga,

Jmol v11.6 comes in two flavors: an application and an applet. Both use efficient internal graphics code that can render live 3-D views of large proteins or molecular assemblies without the need for a graphics accelerator. Jmol has display features for chemicals, crystals, materials, and biomolecules. Features include reading a variety of file types and outputs from quantum chemistry programs, as well as animation of multiframe files and computed normal modes from quantum programs. As a Web browser applet, Jmol can be integrated into Web pages for development of Web-based courseware and Web-accessible chemical databases. As a Java application, it is quite flexible and can translate into 19 different languages, automatically adopting the language of the system it is being used on. It supports more than 25 file formats and exports five different file types. Jmol is capable of displaying vibrations and animations and can measure parameters such as molecular distances and torsion angles. Jmol is designed for students, educators, and researchers in chemistry and biochemistry. The applet and application are supported by Macs (OS X), PCs (any Windows version), and Linux—any machine with Java 1.4. Jmol,


Noah U. Shussett writes Digital Briefs. Information about new or revised electronic products can be sent to

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