C471 Problem Set 4: Chemical Structure Searching

Fall 2003

Your name:

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?

[2] Of the halogens that occur at the point defined as X on the retrieved structures, which is the most frequent halogen one encounters in the molecules of this structure?

[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 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?

Look at the 3-D model of the substance that has the most references. Use the View option in WebLab Viewer Lite 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 file list with the File --> Open command. If you don't see any template files after doing the File --> Open command, change the directory to group and then templates. If you still cannot find any template files, check your own username directory under template.

[9] What are the fifteen 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.

• Once in the structure window, build the structure of the molecule, with all nodes initially carbon.
• The R groups will have to be designated G# or A# groups. You first click on the appropriate node you have drawn and type in for example A1 (atoms) or G1 (groups).
• You then need to define the variable atoms or functional groups. That is done by drawing each to the side of the molecule you have drawn and selecting that group (encircling all of them at once for either A1 or G1) with the selection tool (lasso or dotted square).
• Once selected the A_n or G_n option is chosen, and the appropriate A# or G# entered.
• Now the hard part. Each of the atoms that will be attached to the drawn molecule at the variable points must be clicked on, and the Attachments box clicked for one point of attachment. Assuming that you have done this correctly, the number 1 should appear directly under those atoms that could attach at the A1 or G1 points on the molecule.
• Return to the commander [click on the crossed red arrows] and run the search.

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 ChemIDplus at http://chem.sis.nlm.nih.gov/chemidplus/ to find out if the substance Columbium appears in the Listing "Toxic Substances Control Act Chemical Substances Inventory" (TSCA).

[14] Is there an exclusion for this substance? If so, why?

[15] What is Columbium, and what is its CAS Registry Number?

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." 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. [The Chime plugin might not display correctly or may not be on the computer you are using, so instead of using Isis/Draw in this problem, use the ChemSymphony Applet to draw Isatin and run your substructure search in this way.]

[16] How many compounds did you find?

[17] What type of structure search appears to be the default on this system? (That is, are you getting an exact match, a substructure search, etc.?)