CHEMISTRY 211
Fall 2010
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 3 % of your course grade in the course.
Library Orientation:
In class in on Wednesday, September 15, we will explore the tools available through Reeves
Library and on the Internet that allow you to complete this project.
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. Infrared Spectrum
8. Essay
9. References
Use the attached paper copy of the report form (pp. 5-10) or the electronic version (MolRpt.doc on
the course website) to collect information as you do your research. Use an electronic version of the
report form for your report; it must be word-processed (Times or Times New Roman, 12 point with
1 in. margins: top, bottom and both sides). In your report, do NOT change the order of the questions
or their page placement; that is, do not change the page breaks provided in the file. If you require
more space than is available on a given page, allow it to spill over to a new page, but leave the next
page break in the original position.
Your report will be submitted in two phases. Phase one will include sections 1->6 with cited
references in section 9 and a copy of your original information gathered. Phase two will consist of a
corrected version of sections 1->6, section 7, the essay for section 8 and an expanded reference list
in section 9. 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 or electronic “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 9 at the end of
the report. You do not have to cite the suggested CGWW readings. For sections 1-7 of your report,
cite specific references for each section by including their numbers from the section 9 reference
list in the space designated for references in each section. (On the right side of the first line of
each section) For your section 8 essay, 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.
(See citation for 3 in the Sample Section 9 reference List on p.2)
Fall 2010
2
Molecule Library Project
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.
Molecule Library Project
3
Fall 2010
Sample Section 9 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 University of Maryland Libraries http://www.lib.umd.edu/guides/primary-sources.html
Accessed 8/12/09
Primary Sources: original materials. They are from the time period involved and have not been
filtered through interpretation or evaluation. Primary sources are original materials on which
other research is based. They are usually the first formal appearance of results in physical,
print or electronic format. They present original thinking, report a discovery, or share new
information. E.g. #’s 3 & 4 above
Secondary Sources: less easily defined than primary sources. Generally, they are accounts
written after the fact with the benefit of hindsight. They are interpretations and
evaluations of primary sources. Secondary sources are not evidence, but rather
commentary on and discussion of evidence. Examples include encyclopedias, review
articles, handbooks, bibliographies, and abstracts/indexes. E.g. #’s 1, 2 & 5 above
Tertiary Sources: consist of information that is a distillation and collection of primary and
secondary sources. Comparative Examples:
SUBJECT
PRIMARY
Chemistry/Life Sciences
Einstein's diary
SECONDARY
Book on Einstein's life
TERTIARY
Dictionary on Theory
of Relativity
Fall 2010
4
Molecule Library Project
Dates and Deadlines
9/9
Thurs.
Sign up for molecule outside 213 Collier. Only 1 person per
9/10 Fri.
molecule and one molecule per person.
You are required to sign up by Friday 4:00 PM. Make sure that you record the complete
correct name of your molecule
9/22 Wed.
9:10 AM Library orientation in class: Be sure to bring the assignment and
report form to class.
10/25 Mon.
4:00PM Phase one of report due: complete sections 1 – 6 w/ references in 9.
11/29 Mon.
4:00PM Phase two of report due: turn in the original copy of your phase 1
report and a revised copy of your phase 1 report (1-6) with section 7,
the essay for section 8 and expanded references, section 9.
Compounds
Adamantane
Lisdexamfetamine
Adenosine
Lophine
Aflatoxin B1
Melamine
Amphetamine
Methadone
Anabasine
Methylphenidate
Atrazine
N-Methyl-2-pyrrolidone
Bis(2-ethylhexyl) phthalate
Morphine
Bombykol
Neotame
Capsaicin
Niacin
Carbofuran
Oxalic acid
Cortisone
Paroxetine
Coumarin
cis-Pellitorin
Cyanuric Acid
Phenothiazine
β-Damascenone
Pyruvic acid
Diphenhydramine hydrochloride
Quinine
Dimethylformamide
trans-Resveratrol
Dimethyl fumarate
trans-Retinol
Domoic Acid
Sarin
Ephedrine
Serotonin
Ethanethiol
Sulfasalazine
Finasteride
Succinic acid
Fuchsine
α-Tocopherol
Galanthamine
L-(+)-Tartaric acid
Geraniol
Taurine
5-(Hydroxymethyl)furfural
Thalidomide
Imidazolidinyl urea
L-Theanine
Isocytosine
Trichloroisocyanuric acid
Isoprene
Trichoviridin
Levulinic acid
Tyrosol
Linalool
Zoledronic acid
Molecule Library Project
5
Report Form
Fall 2010
Chem 211
Molecule Library Project
Name
1. Compound Characteristics
Name of my molecule
Fall 2010
References from section 9:
Molecular Formula
CAS Registry Number
CA Index Name
Other names. What type of name is it? (IUPAC, systematic, common, generic or trade)
Name
IUPAC or
systematic
2. Physical Properties
(at 1 atmosphere)
Common,
Generic or
Trade
References from section 9:
Boiling point
Melting point
Refractive index
Color
Density
Based only on the physical properties listed in this section, do you expect your compound to
be a solid, liquid or gas under normal lab conditions (20-25oC and 1 atmosphere)? Provide a
warrant to support your claim.
Fall 2010
2
Molecule Library Project
3. Structure
References from section 9:
(draw by hand, a skeletal representation of your molecule)
4. Molecular Model
Make a molecular model of your compound. If your model kit doesn’t have enough atoms,
use the model kits provided in the lab 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 name
Alike:
Different:
belongs to
(classmate’s name)
Chem 211
3
Fall 2010
5. Functional groups
References from section 9:
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 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 from section 9:
Would you predict that your compound is soluble in water? Consider the number and
distribution of any polar heteroatoms present and provide a warrant to support your claim.
Might your compound be more soluble in aqueous sodium hydroxide or aqueous
hydrochloric acid than it is in water? (Recall results from Experiment 3). Provide a warrant
to support your claim.
3
Fall 2010
4
Molecule Library Project
7. Infrared Spectrum
References from Section 9:
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) (See 211 Lab Manual Appendix C)
Bond or structural feature
, cm-1
Bond or structural feature
, cm-1
Chem 211
5
Fall 2010
8. 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 the following 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 at least one
primary source (mark with *). You must provide documentation in your report folder of the
primary source(s) you used (either the first page with the citation or the entire research article if
you copied it all).
5
Fall 2010
9. Reference List
6
Molecule Library Project