C371 Chemical Informatics I
Updated: 25 September 2004
SMILES Exercise 2: SMILES as input in the
1. Link to the page on the Fisher site that allows you to do structure
Draw the Isatin molecule below:
Perform both an exact search and a substructure search for the substance.
HINT: the search options for the structure searches are below the drawing
window. You may have to scroll down to find them.
How many did answers did you find in each case?
One of the answers found in the substructure search should be Isatin. Look
at that answer. Is it exactly like the molecule you drew for the search? Did
you find it when you did an exact search? If not, why do you think it was missed?
Note that the Fisher record provides both an IR spectrum for the Isatin entry.
Look at the IR spectrum. Note that you can zoom in on
parts of the spectrum, and that you can get the actual values for the peaks
by moving your mouse over the spectrum.
What is the value of the highest peak?
Click on the 3D Model option. When the molecule appears,
hold down the left mouse, and move it around all three axes.
Try the "View molecule using a plugin" option. Download the file to your
computer, use Wordpad to open it, and obtain a printout to hand in with your
answers. What kind of file is this?
2. Change the file type of the file to .mol, using the procedure that was sent
to you on Oncourse mail.
Now try to open the file. Did it open and display a 2-D structure? If so,
obtain a printout. What program opened it?
Now use the ViewerLite program that should be on your computer. (Get it from
the IU Chemistry SciFinder Scholar download site if not.) Open the file.
Try all of the options under the Tools menu of ViewerLite. Obtain a printout
of the molecule from ViewLite.
3. Use the site at
Molinspiration, but use the SMILES INPUT option for the following molecule:
Do a Pharmacophore similarity search on the SMILES string and see what you get.
Print out the first page of your results. [If your SMILES search does not work,
input the structure, do the pharmacophore similarity search, and get a printout of