C571/696 Exercise: Chemical Structure Searching

Department of Chemistry
Updated: 30 September 2004

Fall 2004

Your name:

Include the numbers in brackets on any printouts you hand in.

1. Using SciFinder Scholar, draw the compound below. The question marks in the depiction indicate unspecified or indefinite bonds.

R1=O or S
R2=H, OH, OMe, CH3, or CO2H
X = any halogen
? = any bond value

Preview a sample of answers, accepting the option to Autofix your structure if it is offered.

[1] How many structures does the system predict for your search (use the Preview option)?

[2] Of the halogens that occur at the point defined as X on the above depiction, which is the most frequent halogen encountered in the retrieved structures according to the Preview option?

[3] What percentage of the compounds have that halogen atom in that position?

[4] Are there structures in the sample answers that seem not to match the search criteria you input?

[5] If so, print out any one of them to be handed in.

[6] Run the full substructure search. How many answers did you retrieve?

[7] Refine the search to limit it to those substances that are commercially available.

[8] How many did you find?

Choose the View option at the top of the screen and Reverse Order of the substances. Look at the 3-D model of the substance on that screen that has the most references. (If you don't see five icons, one of which is a water molecule, then the installation of SciFinder Scholar was not done in a way that lets it recognize that ViewerLite is present. If you do see the molecule icon, then clicking it should cause ViewerLite to kick in with a 2D model of the compound.] Use the View option in ViewerLite to change the display style to ball and stick and rotate the molecule by holding down the left button on the mouse and moving it.

2. Now search Beilstein CrossFire for the substance depicted in question 1.

While in the structure drawing window, click on the template file icon (the one to the left of the benzene ring), and open the template files (they're in the directory xfire/templates).

[9] What are the templates provided by Beilstein for structure drawing?

[10] Obtain a printout of the first three porphyrin templates provided, and hand it in with your homework.

[11] Build the structure from question 1, run the search and write down how many substances you found.

You should find a little over 60 answers. Scan through the structures using the multiple view option.

[12] Did you find any that do not match the structure search criteria?
[13A] If so, print out any one of those in the Substance (IDE) format.

[13B] If not, print the first answer in your answer set in the Substance (IDE) format.

3. Use the free ChemIDplus at for this question.

Try a structure search on the molecule below (Isatin) while in this system. Hold down your right mouse button anywhere in the structure input box (Do not click on the link "Structure Input Box"), choose "Edit," and select "Transfer to ISIS/Draw tool." [NB: If you are using the free plug-in ISIS/Draw on your computer, once the molecule is drawn, you will have to manually transfer it to the ChemIDplus search window by clicking on the icon at the upper left-hand corner.] Another option is to choose to "Display chemical structures using Java," and that will bring up a structure drawing pane that allows you to draw and search the molecule in an easier manner.

[14] How many compounds did you find?