C471 Problem Set 4: Chemical Structure Searching

Fall 2004

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 preview system predict for your search?

[2] Of the halogens that occur at the point defined as X on the retrieved preview 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. (Be aware of the use of shortcut symbols in the depictions!)

[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?

Choose the View option at the top of the screen and Reverse Order 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.

[9] Indicate whether you were able to use ViewerLite on the computer on which you did this exercise: [ ] Yes [ ] No.

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, follow the procedures below:

If the template icon in the structure drawing window doesn'’t connect to the templates:

1. Doubleclick on the template icon.
2. The file directory into which you are thrown will be empty, so drop down the window and go up to the level where the CrossFire Commander program is located. Click on that.
3. Select the group folder, then within that, select the template folder. You should see Porphyr.bsd there.

1. Choose File, then Open to see a list of all template sets available to you.

[11] Obtain a printout of the first three porphyrin templates provided, and hand it in with your homework. Be sure to write your name on the printout.

[12] 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# groups. You first click on the appropriate node you have drawn and type in for example G1 or G2. [Do not use the A option to define R1 even though it consists of two atoms, O and S.]
• 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 with the selection tool (lasso or dotted square), encircling all of them at once for either G1 or G2.
• Once selected the G_n option is chosen, and the appropriate 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 G1 or G2 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.

[13] How many did you find?

Scan through the structures using the multiple view option.

[14] Did you find any that do not match the structure search criteria? [ ] Yes [ ] No

[15A] If so, print out any one of those, making sure that the View is set to the ID format.

[15B] If not, print the first answer in your answer set, making sure that the View is set to ID format.

3. Use the free ChemIDplus at http://chem.sis.nlm.nih.gov/chemidplus/ to find the substance Columbium.

[16] What is another name for Columbium?

[17] What is its CAS Registry Number?

[18} How many records in the Medline database are tied to this substance?

Try a structure search on the molecule below (Isatin) while in this system.

[19] How many compounds did you find?

[20] What types of structure search are possible on this system, and what are the different results likely to be found with each?