Molecule Project CHEM 1140
Each student is assigned a biochemically active molecule. This project is worth 100 points of
your grade. Points assigned for each part are shown in brackets[]. Organize the material in
the following way when turning in your project:
a) The Lewis structure (Be sure to show all bonds, spare pairs of electrons and formal
charges) [15]
b) Identify the organic functional group(s) present. These should be indicated on the
Lewis structure. [10]
c) Provide a computer generated three dimensional perspective ball-and-stick model of
the molecule. A key to the colors should be included. Some websites are included below
to assist you in locating a model. [12]
d) Identify the chiral centers on the Lewis structure and the 3-D model with an asterisk(*).
If there are no chiral centers on the molecule, you should state this. Otherwise, I don’t
know that you looked. [10]
e) Predict the molecule’s solubility in water. This should be based on your knowledge of
polar and nonpolar functional groups and the golden rule of solubility, “like dissolves
like”, not on a number found in one of your references. You should make a statement
like: “(your molecule) is predicted to be soluble/insoluble in water because. . .” This
statement may be included in the summary (part f). [10]
f) Provide a summary (no more than one and a half pages typed, double spaced) of the
molecule’s biological function. This should include whether: (a) the body can make this
molecule, (b) it is an essential nutrient, or (c) it is a drug. For nutrients, you should
include information on the effects of a deficiency. This part should include at least one
specific chemical reaction (This means molecules written or printed out and an arrow
between reactants and products) which should be described in the accompanying text.
If your molecule is a proprietary drug, a chemical reaction may be difficult to find, if so
you must describe the mechanism of action for the drug and potential side effects. [30]
g) OTHER: At the beginning of the report provide a title page (No fancy cover is required).
At the end of the report provide references for both the model in part c) and the
summary in part f) [13].
Preferred formats for references are given below:
Book
Authors, Title of Book, Edition, Publishing company, location, date of publication, pages used.
Journal Article
Authors, “Title of article”, Journal, Vol (No.):pages, Date.
Website
Title of webpage. www.webaddress.com, (accessed mm/dd/yr).
A preliminary submission of parts a) and b) above will be due mid-semester after the material is
covered in class. This must be hand-written. You may not turn in a print out. If your molecule
contains a ring, rings can be drawn in line structures, otherwise, all atoms, bonds, and spare
pairs of electrons must be shown in the Lewis structure. This preliminary submission is worth
25 points of the 100 points allocated for the project.
Finding a 3-D computer generated structure represented in Ball-and-Stick form.
Before you begin, you should have some idea of what class of molecules yours belongs to and what it
does. You should be able to find a 3-D image of your molecule on one of the websites below or through
the other options listed below the websites.
Note: Some of the websites require plug-ins. To view the molecules on your computer, you will need to
download the software to your own computer. All the plug-ins are installed in the chemistry computer
lab, Rm 2216 on the second floor of the Chemistry building.
www.chemfinder.com “Chemfinder.com”
This website will provide the Lewis structure for most molecules and with a plug-in that must be
downloaded, will provide a 3-d representation (select View Chem3D Model).
http://www.nyu.edu/pages/mathmol/library/ “MathMol Library”
This website has lots of biological structures. If you know the class of your biological molecule,
you may find it here. No plug-in needed
http://www.iconbazaar.com/molecules/ “Icon Bazaar”
Several prescription drugs are shown here as well as the amino acids. No plug-in needed.
http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html “Alphabetical Listing of Molecules”
Wellesley College site. Many small organic molecules listed here. Need Chime plug-in.
Other Ways to Find a 3-D image of your Molecule:
� To find even more listings than the websites above, search with words like chemical structure or
3D molecule or even ball and stick molecule for a search listing.
� To get more specific, you may find your molecule by simply typing in the name of your molecule
followed by the words chemical structure in a search engine. For example, if your molecule was
caffeine, type in “caffeine chemical structure”, or “caffeine 3D molecule”
� Last resort, come see me for assistance.
Suggestions on finding a Chemical Reaction for your molecule
� Use words like metabolism, (molecule name) OR metabolic pathway, (molecule name) OR
reactivity (molecule name) to get started.
� Go to the KEGG database at http://www.genome.jp/kegg/pathway.html#metabolism .
This database shows lots of interconnected pathways. Once you find a pathway that contains
your molecule, you will find the individual reactants and products (circles on diagram) connected
by arrows. The four place numbers in the boxes represent the enzymes that catalyze the given
reaction. Clicking on the numbers will provide the name of the enzyme.
� If you can not interpret the information on the KEGG site, come see me for
assistance.