CHEMISTRY 211
Fall 2008
Molecule Library Project
Goals:
This project is designed to give you a chance to apply your developing understanding of organic
molecules to learn about an interesting substance and acquire a feeling for the diversity of structures
and properties among organic compounds. Another objective is for you to learn how to use
Chemical Abstracts, which you will access on-line through SciFinder Scholar software, as well as
other reference materials commonly used by chemists. Completion of this project is required to pass
CHEM 211 and your completed project will account for 2 % of your course grade in the course.
Library Orientation:
In class in on Wednesday, September 17, librarian Amy Dumouchel will meet with us to help us
learn to use the tools available through Reeves Library that are required to complete this project.
The date will be announced and attendance at this session is required.
The Report:
The report is organized into the nine sections enumerated below. More information on each
section is provided in the attached report form.
Report Outline
1. Compound Names:
2. Physical Properties
3. Structure
4. Molecular Model
5. Functional groups
6. Aqueous Solubility
7. Stereochemical Features
8. Infrared Spectrum
9. Essay:
10. References
Use the attached paper copy of the report form to collect information as you do your research. Use
the electronic version of the report form (MolRpt.doc on the course website) for your report; it must
be word-processed (Times or Times New Roman, 12 point with 1 in. margins: top, bottom and both
sides). Do NOT change the order of the questions or their page placement; that is, do not change
the page breaks provided in the file.
Your report will be submitted in two phases. Phase one will include sections 1->8 & 10. Phase two
will consist of a corrected version of sections 1->8, the essay for section 9 and an expanded
reference list in section 10. On the dates specified below for phase one and phase two, turn in your
report in a folder of the style used for class groups. Place the report in the left side pocket. In the
right side pocket, assemble all records related to your literature search. Records should include
any printouts you made of source materials, your hand written “working” report form, and any other
notes documenting your search path.
There are specific requirements for citing the references that you use to find the required information
about your molecule. Include all of your references in a numerical list in section 10 at the end of the
report. You do not have to cite the suggested CGWW readings. For sections 1-8 of your report, cite
specific references for each section by including their numbers from the section 10 reference list
in the space designated for references. (On the right side of the first line of each section) For section
9, place citation numbers as superscripts at the end of the sentence in which you report
information from a particular reference. For example a citation for information from reference 3
(See list below) would appear as:
Even though acetaminophen is considered an effective and safe over-the-counter
analgesic, it is the preferred method of suicide for adolescents in Great
Britain.3 This research paper examines other safety concerns related to this
commonly used medication.
The sample Reference List below shows the required format for citing books, periodicals and
Internet pages. If you are unable to find required information about your molecule, list all the
references you searched in the answer space on the report form.
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Molecule Library Project
Sample Reference List
1. Physician's Desk Reference, 58th edition, Thomson PDR, 2004.
2. The Merck Index, 11th edition, Susan Budavari, ed., Merck & Co., 1989.
3. “Acute acetaminophen overdose in adolescents and adults.”, Hamm J., Critical Care Nurse,
2000, 20, 69-74.
4. “The effect of analgesic agents on the healing rat medial collateral ligament.”, Hanson C. A.,
Am J Sports Med., 2005, Feb. 16. (abstract only).
5. MedScape DrugInfo: ACETAMINOPHEN ORAL.
http://www.medscape.com/druginfo/Pharm?id=11866&name=ACETAMINOPHEN+ORAL&DrugType=1&MenuID=PHM&ClassID=N&Ge
neralStatement=N(accessed March 13, 2004).
Explanation of Reference Formats above:
# 1 shows the format for citing a book with an author: book title, edition (both in italics), author,
publisher, year of publication.
# 2 shows the format for citing a book with an editor: book title, edition (both in italics), editor
name (followed by ed.), publisher, year of publication.
# 3 shows the format for a periodical reference: “article title” (in quotation marks), authors,
periodical title, publication year, volume, inclusive pages. (all in italics)
# 4 shows a periodical reference in the format of #3 above, but only the abstract of the article
was read.
# 5 shows the format for citing an Internet reference: Author (if any). Title of Site. URL
(accessed date).
Note: When citing information found using online resources, provide the information for the
actual source (web page or journal), NOT the search engine or database URL.]
Classification of References
from Dartmouth Medical Libraries http://www.dartmouth.edu/~biomed/resources.htmld/primarylit.shtml
Accessed 8/20/08
Primary Sources: contain original data and ideas and are generally the first published record of
an investigation. Examples include research articles, research monographs, preprints, patents,
dissertations, and conference proceedings. E.g. #’s 3 & 4 above
Secondary Sources: information about primary sources, usually a compilation or synthesis of
various ideas and data. Secondary sources may rearrange or modify data and include such
sources as indexes to the primary literature, reference works derived from primary research,
and reviews. Examples include encyclopedias, review articles, handbooks, bibliographies,
and abstracts/indexes. E.g. #’s 1, 2 & 5 above
Tertiary Sources: discuss science rather than contribute or are indirect sources. Examples include
textbooks, directories, and literature guides. Molecule Library Project
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Fall 2008
Dates and Deadlines
9/4
Wed.
Sign up for molecule outside 213 Collier. Only 1 person per
9/5
Thurs.
molecule.
You are required to sign up by Thursday 4:00 PM. Make sure that you record the complete
correct name of your molecule
9/17 Wed.
9:10 AM
Library orientation in class: Be sure to bring the assignment and
report form to class.
10/20 Mon.
4:00PM
Phase one of report due: complete sections 1 – 8 and 10.
11/17 Mon.
4:00PM
Phase two of report due: turn in the original copy of your phase 1
report and a new copy of your report with the essay for section #9
and modifications of Phase one.
Compounds
1,8-Cineole
D-Mannitol
8-Hydroxyquinoline
Ectoine
Acetaminophen
Epinephrine
Acetylene
Ethanolamine
Acetylsalicylic acid
Ethylene glycol
Acridine orange
Eugenol
Acrylic Acid
Folic acid
Adenosine triphosphate
Fructose
Allyl Isocyanate
Glycerine
Anandamide
Heparin
Anatoxin-a
Hydroxyproline
Ascorbic acid
Lactic acid
Atorvastatin
Loperamide
Benzene
Lycopene
Benzoyl Peroxide
Methyl Paraben
Betulinic acid
Minoxidil
Bisabolol
Nitroglycerin
Carminic Acid
Ozone
Ceramide
Permethrin
Chlorophyll a
Piperine
Citric acid
Raloxifene
Cubane
Sorbic Acid
Cyclopentadiene
Sucrose
Desloratadine
Taxol
Dihydroxyacetone
trans-Cinnamaldehyde
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Report Form
Molecule Library Project
Molecule Library Project
Chem 211
Name
1. Compound Names
My molecule
Fall 2008
References:
Molecular Formula
CAS Registry Number [see Lehman Appendix VII]
CA Index Name
Other names. What type of name is it? (IUPAC, systematic, common, generic or trade)
Name
IUPAC or
systematic
Common,
Generic or
Trade
2. Physical Properties
References:
(at normal laboratory conditions, 20-25oC and 1 atmosphere)
Boiling point
Melting point
Refractive index
Color
Density
Under normal lab conditions, would your compound be a solid, liquid or gas? Why do you
say so?
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Molecule Library Project
3. Structure
References:
(draw by hand, a skeletal representation of your molecule using wedges and dashes as needed
to specify unique structure)
4. Molecular Model
Make a molecular model of your compound. If your model kit doesn’t have enough atoms,
use the model kits provided so you can make a complete structure. Hold your model in your
hands. Manipulate it. What do you learn about your molecule from the model? You might
comment on shape, distribution of heteroatoms, flexibility, etc. (~100 words)
Look at and manipulate the model of a classmate’s molecule. In what ways are the
molecules alike? How are they different? (~50 words) Only write about what you learn by
considering the molecular model.
Comparison molecule
Alike:
Different:
belongs to
(classmate’s name)
Chem 211
Molecule Library Project
Fall 2008
5. Functional groups
References:
Draw your molecule using molecular drawing software or paste in the structure from an
online source. Then indicate functional groups present by circling (or highlighting) them on
the structure and by drawing arrows to them and labeling them. Functional groups you
should consider are those in CGWW Table at the bottom of p. 36 and if you have nitrogen in
a ring, see CGWW pp. 1180-1181.
6. Aqueous Solubility
References:
Would you predict that your compound is soluble in water? Why or why not? Consider the
number and distribution of any polar heteroatoms present.
Might your compound be more soluble in aqueous sodium hydroxide or aqueous
hydrochloric acid than it is in water? (see Chem 211 Lab Manual Appendix B). Why or why
not?
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Molecule Library Project
7. Stereochemical Features
References:
Draw the structure of your molecule (hand drawn, created using molecular drawing software, or
pasted in from an online source) in which stereochemical features
are clearly indicated, for example using wedges and dashes.
Circle (or highlight) and draw an arrow to label any cis-trans structures or chiral centers.
Label any chiral centers correctly as R or S
(See http://www.acdlabs.com/iupac/nomenclature/93/r93_630.htm and
http://www.chemhelper.com/enantiomers.html for explanations of how to determine the
configuration of a chiral center.
If your molecule has no cis-trans features or any chiral centers, write none and explain how
you came to that conclusion. Then label the cis-trans structures and chiral centers of the
following structure.
H
O
H
Cl
8. Infrared Spectrum
References:
Draw the structure of your molecule (hand drawn, created using molecular drawing software,
or pasted in from an online source). Circle the bonds with distinctive IR absorbance.
List the characteristic IR frequencies expected or reported for your compound. Be as precise
as possible with “cm-1” (for ex. an ester C=O absorbs at different cm-1 than a ketone C=O)
Bond or structural feature
, cm-1
Bond or structural feature
, cm-1
Chem 211
Molecule Library Project
Fall 2008
9. Essay:
Write a short essay about your compound (300-400 words) at a level that would interest other
young scientists; consider your audience to be a senior chemistry or biology major. You might
address these questions or anything else that intrigues you: What is it? How was it discovered?
Isolated? Identified? Why is it interesting to scientists? What sort of research is being carried
out on this compound? Among your references you must include a primary source (mark
with *), secondary source, (mark with #), and tertiary source (mark with ^). You must provide
documentation in your report folder of the primary source you used (either the first page or the
entire research article if you copied it all).
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10. Reference List
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Molecule Library Project