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Virtual Molecular Model Kit: Exercises |
Exercise 11 Return to Index
Introduction
In the previous exercise we used two of AKA's query constructors to retrieve spectral data from two different databases. Now let's turn our attention to the other 5 query constructors and see what other types of information are available through AKA. The power of AKA lies in its ability to provide more focused searches than traditional search engines such as Google, Bing, and AOL. For example, a normal Google search of tyrosine returns 12,800,000 hits. An AKA Wikipedia search returns 1!!!!
Figure 11.1 provides a recap of the structures first introduced in Exercise 3 and is repeated here to refresh your memory regarding the biochemical pathway from tyrosine to norepinephrine.
Figure 11.1
The biosynthetic pathway from tyrosine to norepinephrine
Instructions
1. Make or load a model of L-dopa into AKA.
You can make a model using the VMK and load it into AKA from the Tools control panel, or you can enter the name L-dopa directly into the Compound Identifier field of AKA, or you can draw the structure using the JSDraw utility in AKA.
2. Click the Action:Search option and select the Wikipedia link.
This returns a single link to a Wikipedia article about L-dopa. If you are curious, you might want to see how many hits a simple Google search for L-dopa generates.
3. Make or load a model of dopamine into AKA.
4. Click the Action:Search option and select the ChEBI link.
ChEBI is the acronym for Chemical Entities of Biological Interest. As the name implies, this site provides links to information about bioactive molecules such as dopamine.
In the final part of this exercise, we'll kill two birds with one stone, using JSDraw to load a model of norepinephrine and ChemSpider to find some information about that compound.
5. Click the JSDraw icon in the lower left hand corner of the AKA window.
6. Draw the structure of norepinephrine, but do not specify the stereochemistry at the chiral carbon.
7. Click the Load button at the bottom of the window.
Note that the 2D drawing of norepinephrine that appears does not specify stereochemistry.
8. Click the Action:Search option and select the ChemSpider link.
ChemSpider (spider webs...get it?) provides links to patents as well as articles in the primary literature about the compound of interest.
9. Return to the AKA Query Constructor and click the Search link followed by the General option.
As you might expect, a general search returns many more hits-650 or so in the case of norepinephrine. Still, a regular Google search for this compound returns 5,210,000. Given that Google displays 10 links per page, you would have to click the Next link 521,000 times to get to the last link in the list.
10. Close the AKA Query Constructor pop-up. Select the Load source:Resolver button if it is not already active. Open the JSDraw utility again.
11. Select the "wedge bond" tool and click on the C-O bond of your drawing. Then load the drawing into AKA.
The 2D drawing that loads includes the stereochemical designation at the chiral carbon.
12. Perform a ChemSpider search and a General search on this stereoisomer. Compare the results with those you obtained in steps 8 and 9.
13. Repeat steps 10-12 using the "hash bond" tool rather than the "wedge bond".
Now that we've seen how to make compounds and how to find out some information about them, it's time to look at some additional features of the VMK before moving on to the remaining exercises in this manual.