Questions

Note: There is a Printable PDF of these Questions at the top of Module 5
http://olcc.ccce.divched.org/2015OLCCModule5P1

1. Go to the PubChem database (http://pubchem.ncbi.nlm.nih.gov) and search for omeprazole and esomeprazole. Fill in the table below with appropriate chemical representations for the two molecules and answer the following questions.

(1) What is the structural difference between omeprazole and esomeprazole?

(2) Do omeprazole and esomeprazole have the same InChI and InChIKeys as each other?

(3) Do omeprazole and esomeprazole have the same canonical SMILES? Explain why.

Omeprazol (from PubChem)
CID
IUPAC name
Canonical SMILES
Isomeric SMILES
InChI
InChIKey
Esomeprazole (from PubChem)
CID
IUPAC name
Canonical SMILES
Isomeric SMILES
InChI
InChIKey

2. Go to ChemSpider (http://www.chemspider.com) and search for omeprazole and esomeprazole. Fill in the table below with appropriate chemical representations for the two molecules and answer the following questions.

(1) Are the systematic names from ChemSpider the same as those from PubChem?

(2) Are the canonical SMILES from ChemSpider the same as those from PubChem?

(3) Are the InChI and InChIKeys from ChemSpider the same as those from PubChem?

Omeprazol (from ChemSpider)
ChemSpider ID
IUPAC name
Canonical SMILES
Isomeric SMILES
InChI
InChIKey
Esomeprazole (from ChemSpider)
CID
IUPAC name
Canonical SMILES
Isomeric SMILES
InChI
InChIKey

3. Compare the SMILES strings from PubChem with those from ChemSpider for the following compounds, in terms of how the two databases deal with perceived aromaticity of the molecules. Explain an advantage and a disadvantage of the SMILES strings used in each database.

	SMILES from PubChem	SMILES from ChemSpider
Benzene
pyridine
Pyrrole
Furan
Thiophene
Selenophene
Tellurophene

4. Suppose that you are a project manager at Google, who are in charge of implementing a chemical search algorithm to the Google search. This algorithm accepts a chemical structure as an input through the search box on the Google homepage (http://www.google.com), but the input needs to be a text string that represents a chemical structure. Therefore, you need to choose a line notation that is most appropriate for this search system, among the canonical SMILES, InChI, and InChIKey. Choose only one and justify your choice over the others, based on what you have learned from this module and from Questions 1, 2 and 3).

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In PubChem, why doesn't the

In PubChem, why doesn't the structure of Omeprazole contain a squiggly line showing that it can exist as either the (S) or (R) enantiomer?

Depends on whether you want to add emphasis on stereochemistry

Below is from “Graphical representation of stereochemical configuration” (IUPAC, Pure and Applied Chemistry 2006, 78, 1897–1970). <a href="http://www.iupac.org/publications/pac/2006/pdf/7810x1897.pdf">http://www.iupac.org/publications/pac/2006/pdf/7810x1897.pdf</a> === Beginning of the excerpt === If configuration is unknown, this can be indicated explicitly by a wavy line . The waves in such a line may be rounded or angular, but they should be of constant amplitude. The use of “wedged wavy” bonds is discouraged. In most cases, a wavy bond is conceptually identical to a plain bond, and a plain bond should be used instead. Wavy bonds are most often used in general usage when an author wants to place special emphasis on the unknown nature of the configuration at a specific position; the wavy bond would usually be accompanied by additional explanatory text in that case. === End of the excerpt === Simply put, a wavy bond is acceptable, but not necessary. Of course, both wavy bonds and plain bonds are okay. Which one to choose depends on whether you want to add emphasis on an undefined stereocenter or not, which is subjective. (I understand that some people think a wavy bond make a structure representation clearer.)

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