Beilstein and Gmelin Structure Searching; Cambridge Structural Database
1. Using Beilstein CrossFire 2000, look for the Markush compound below. Do not allow isotopes, multifragment compounds, charges, or radicals in the answer set, but do permit implicit ring closures. You'll need to define a G group where the R is and to draw the "Rs" as separate functional groups. Then select them and define as the same G# you put on the ring. The final step is very important. With the pencil active, click on each point of attachment in the functional groups, and set the attachment number to 1.
How many answers did you find?
What are the lowest and highest melting points you found?
2. Organophosphates have the potential for transferring their phosphate unit to another molecule. Some of these are involved in the production of chemical energy in the body.
O
|
O-P=O
|
O
with anything besides hydrogen attached to one and only one of the singly-bonded oxygens and with hydrogens on the other two. Use the "Set Free Sites" option under Query. (Do you need to do more than one search to determine this?)
b. How many compounds in Gmelin have a C attached to one and only one of the singly-bonded oxygens? (Again, the "Set Free Sites" option is critical.)
c. How many of those from b are the "type of substance" (HINT: that's the field name in a Fact search) "Coordination Compound"?
d. How many of the Coordination Compounds in c have a Molecular Weight greater than 1000?
e. Obtain a complete printout of the first answer in d.
3. Search the following reaction in Beilstein.
Hints: The "3" in the product refers to the maximum number of free sites. You can only link the reaction centers after you have defined the reactant and product. Allow implicit ring closures under query options.
Run the search and display the answers. Obtain a printout of any one of your results that shows the reactants and products.
While in the record for one of the reactions, click on the various hotkeys for the product and references and see how you can learn additional information (or if you're like me, get lost very quickly!).
Now delete the atom mappings and run the same search (must be in Reaction Editmode to do this). How many did you find without atom mapping, as compared to with atom mapping?
4. Search the Beilstein CrossFire database for the capsaicin molecule (as depicted below).
How many substances did you retrieve?
At least two of the compounds in the answer set have references to articles which describe the isolation of capsaicin from a natural product. One of those references is:
Lapworth; Royle; JCSOA9; J.Chem.Soc.; 115; 1919; 1111.
Use the Web of Science to find newer articles that have cited Lapworth and Royle's 1919 article. How many did you find?
5. Search the Cambridge Structural Database to find compounds that include Chlorpromazine in the Chemical Name.
How many answers did you find? Choose the compound that is the unsubstituted Chlorpromazine. In the File menu, select the option to "Write PDF file to view/print" and be sure to choose the "Current entry only". Obtain a printout to hand in. Use the 3D Visualiser and right click outside the molecule. Investigate the options for obtaining additional information on the compound. What did you think of the CSD in comparison to other frontend client software such as STN Express or Beilstein Commander? 6. Search the CSD for Aconitase With Isocitrate. Did you find it? If not, what does that indicate to you about the CSD's coverage of biomolecules?