Information • Textbooks • Media • Resources
Chemical Information Instructor
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Introduction to Structure Searching with SciFinder Scholar Damon D. Ridley School of Chemistry, University of Sydney, N.S.W. 2006, Australia;
[email protected] More than 26 million substances have been registered by CAS and each has a unique CAS Registry Number. While search terms based on names or formulas can be valuable, often the easiest way to find a substance that has a clearly defined structure is by a structure search. This particularly applies when substances related by part structure are required. We run a basic course on SciFinder Scholar in two parts: the first deals with subject searching, (1) and the second with structure searching. Here we describe the latter component.
Three other useful hints in structure drawing are discussed here, including: 1. Shortcut symbols may save time and should be used particularly in cases such as the nitro group (which has a donor bond and hence is subject to a special representation); 2. Substitution is blocked at positions by adding hydrogen substituents; and 3. System ring and chain defaults are overridden using the locking tool.
Course Requirements We conduct this component at senior undergraduate or junior postgraduate level, and it takes the place of a threehour laboratory session. The course is particularly relevant to students in chemistry, pharmacy, pharmacology, and related disciplines who wish to find substances by structure search queries. This component contains a number of exercises that require access to SciFinder Scholar. Students work in small groups and the major restriction is the number of computers available in the laboratory and the number of simultaneous subscriptions held by the institution.1 Course Outline After a brief discussion of CAS Registry Numbers, the course takes up the major issues relating to substance registration in the substance database in SciFinder Scholar. In particular, the issues of multicomponent substances and of structure connection tables for aromatic compounds, tautomers, and π- and donor-bonding are addressed, and students are required to retrieve representative examples to illustrate the indexing issues. Structure-drawing options are mentioned next, although today most students are familiar with the workings of structure drawing packages. Nevertheless, important shortcuts can be exploited through quick examination of the structure drawing Help messages. In particular, a problem is set that illustrates the ability to copy a CAS Registry Number from any record within Scholar and to paste it into the structure drawing screen. Here it is pointed out that nearly all the hydrogen atoms in the original substance have been removed in this Copy and Paste operation, and hence that a substructure search on this pasted structure will automatically give substituted derivatives.
Relevant to the last issue is that ring atoms in SciFinder Scholar default to isolated or embedded values, and that chain atoms default to ring or chain values. When clicked, the locking tool displays the balloon message “Lock out ring fusion or ring formation” and this is precisely how it works, although generally the implications need further explanation and an actual example is presented. The course next summarizes the various structure and reaction search options and their implications, and finally a number of issues relating to searching general structures are discussed. Students then undertake six exercises which illustrate: 1. The use of templates, the use of unspecified bonds, results of EXACT/RELATED and substructure searches, and results of obtaining references which list a group of substances as reactants; 2. A precise reaction search leading from starting material to product; 3. The use of a molecular formula search followed by a refinement with a chemical structure (particularly relevant in the case of searching for radicals, cations, etc.); 4. The use of the precision option to refine answers in cases where SciFinder Scholar in the first instance interprets issues relating to resonance and tautomerism in a very general way; 5. The use of Real-atom Attachments as a tool for refining answers; and 6. The use of the precision option to refine answers in questions that contain metals (for example, in coordination compounds).
JChemEd.chem.wisc.edu • Vol. 78 No. 4 April 2001 • Journal of Chemical Education
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Information • Textbooks • Media • Resources
After the mechanics and options within Chemical Structure and the CAS Registration policies for structures are understood, the challenge is to search for the structure that best meets the user’s requirements. When contemplating a structure search it is important to consider the scope and size of the database. With more than 26 million substances currently registered, the database contains quite extraordinary varieties of structures and there may be many hundreds of structures of a given type. So sometimes very specific structures need to be searched in order to obtain the specific information required. On the other hand, the particular substance of interest may not be in the database, in which case it is necessary to search for related substances or even for synthetic precursors. Finding literature on related substances may help with the specific problem, so at times relatively general structures may need to be searched. The solution is to try a few options, to see what results, and to modify queries as appropriate. Course Materials The course materialsW include full student notes and comprehensive instructors’ notes, which provide answers to the problems and comments on the various teaching points made. The materials, which have been used successfully in a
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number of Australian and New Zealand Universities, may easily be modified to meet local needs. Additional information is available at the SciFinder Scholar web site (2). Acknowledgments We acknowledge assistance from Fred Winer from the Chemical Abstracts Service, Columbus OHIO, U.S.A., and from Paul Peters, SIIL, The Netherlands. W
Supplemental Material
Information and instructions for the students and notes for the instructor are available in this issue of JCE Online. Note 1. The Institution’s key contact should explore the option with CAS of obtaining some temporary additional access for specific training classes.
Literature Cited 1. Ridley, D. D. J. Chem. Educ. 2001, 78, 557–558. 2. Chemical Abstracts Services. SciFinder Scholar; http:// www.cas.org/SCIFINDER/SCHOLAR/ (accessed Feb 2001).
Journal of Chemical Education • Vol. 78 No. 4 April 2001 • JChemEd.chem.wisc.edu
