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C471 Exercise 3: Science Writing Aids

Updated: 2 September 2004
Key Points: There are very good free structure drawing programs that can be downloaded from the Web. At least one of them should be available to students on one or more of the institution's computers. The nomenclature program Autonom is a standard part of the Beilstein CrossFire package. You will use these programs to draw and formally name the compound isatin.

Two important ACS products are introduced in this exercise: The ACS Style Guide and CASSI. In addition, the in-class exercise will show you how to download records into EndNote, one of two Citation Management Software packages available at very low cost to IU students (See: http://iuware.iu.edu).

Researchers in chemistry have to publish documents about their research. This exercise introduces you to some software tools that make the task of writing chemical papers less tedious. There are writing standards that must be followed in every scientific field: style guides and conventions for putting the references into a standard form so that later researchers can more easily locate the material and build on it. There are also specific rules for naming a chemical substance, and most editors require authors to conform to the standard nomenclature conventions of IUPAC, the International Union of Pure and Applied Chemistry. CASSI and The ACS Style Guide will be essential partners in your scientific writing endeavors.


Isatin image

It's ok to work in groups on this exercise. If you work in a group, be sure that everyone signs the sheet to be handed in. Write your answers to the questions below on the printout that you get for question 1.

The image above is the molecule Isatin. We are going to do several things with isatin in this exercise. (Note that it is a GIF image, so no additional helper or plug-in applicaton is needed to see it on this page.)

1. ISIS/Draw and ACD/ChemSketch are very powerful free drawing packages.

Either download one of the programs to your own computer or use ISIS/Draw or ChemSketch on one of the university computers in the IUB Chemistry Library (See: http://www.indiana.edu/~libchem/pcr.html) or in a Student Technolgoy Center.

If you are using ISIS/Draw, hold the left mouse button down on each of the tool icons along the left side and pay attention to the function of each icon. It's generally the bond tool that you will want to select when not drawing one of the pre-drawn rings. Also, look at the large number of templates from which you can choose. A template is selected by clicking on one of the nodes in the molecule.

Draw the Isatin molecule, type in the name "Isatin," and your name and obtain a printout to be handed in.

What drawing package did you use for this exercise?

2. A program to assist in naming organic compounds is AUTONOM. You will find a version of AUTONOM as one of the choices in the Beilstein Commander program. (It's a blue icon once in Commander.)

Double-click on the Structure window in AUTONOM and draw the picture of isatin (with or without the H attached to the N). You'll need to click the "-->BC" icon in the Beilstein CrossFire structure editor to get the structure pasted into AUTONOM. Hit the Name button, and AUTONOM should name it for you.

What is the name assigned to the compound by the program?

3. The ACS Style Guide; A Manual for Authors and Editors (QD8.5.A25 1997 on Reserve) and CASSI (Chemical Abstracts Service Source Index) are two very important works for those who are writing manuscripts to be published in American Chemical Society journals.

Glance through the table of contents of The ACS Style Guide and pay special attention to the pages dealing with "References" starting on page 173. Note that only the abbreviated forms of journal titles are used in bibliographies. Thus, it is frequently the case that you encounter in the bibliographies of scientific articles abbreviated journal titles that may be difficult to find in a library catalog because you don't know the full name. We're going to assume that we found a reference to an old German journal and want to get the full form of the title so we can look it up in IUCAT.

Use CASSI to search for the abbreviated title: Ber.Dtsch.Chem.Ges.

What is the full form of the journal title?

Use IUCAT to determine if any Indiana University libraries hold the journal. Which IU libraries have it?

4. In the bound journal section of the IUB Chemistry Library (to the right of the wooden fire exit doors) where materials are arranged by title, not call number, find the volumes of student report papers for Chemical Research (Undergraduate) (C409) and Introduction to Research (C500). Examine one of the most recent report papers for Chemical Research (Undergraduate) (C409) and Introduction to Research (C500). Notice the abbreviated references in the bibliographies of the papers, with no titles for the journal articles and only abbreviations for the journal titles.