CHEMISTRY 211
Fall 2011
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 14, 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 the original information you gathered. Phase two will consist
of a corrected version of sections 1->6, sections 7and 8, and an expanded reference list in section 9.
On the dates specified below for phase one and phase two, turn in your report with all records
related to your literature search attached with a binder clip. Your 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. The pages of the report are to be stapled together,
but the attached record sheets should not be stapled.
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 at the beginning of 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)
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Molecule Library Project
All references used to prepare your report are listed in Section 9. These references are numbered
and listed in the order they are cited in your report. 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.
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 October 13, 2011).
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 8/18/11
Primary Sources: original materials. They have not been filtered through interpretation or
evaluation. Primary sources are original materials based on research. They are usually the
first formal appearance of results in 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. 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 such as textbooks.
Comparative Examples:
SUBJECT
PRIMARY
Chemistry/Life Sciences
Einstein's diary
SECONDARY
Book on Einstein's life
TERTIARY
Dictionary on Theory
of Relativity
Molecule Library Project
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Dates and Deadlines
9/8
Thurs.
Sign up for molecule outside 213 Collier. Only 1 person per
9/9
Fri.
molecule and one molecule per person.
You are required to sign up by Friday, September 9 at 4:00 PM. Make sure that you record the
complete correct name of your molecule
9/21 Wed. 8:50 AM Library orientation in class: Be sure to bring the assignment and report
form to class.
10/31 Mon. 4:00PM Phase one of report due: complete sections 1 – 6 w/ references in 9.
12/5 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 sections 7, 8
and expanded references, section 9.
Compounds
abscisic acid
lidocaine
abyssinone II
linalool
adapalene
α-linoleic acid
alizarin
luteolin
amentoflavone
lutein
astaxanthin
metformin
1,2-benzenedithiol
octocrylene
benzoic anhydride
octyl methoxycinnamate
bisphenol a
oseltamivir
bupivacaine
2,6-nonadienal
butylated hydroxytoluene
pantothenic acid
carbon disulfide
phenolphthalein
celecoxib
propranolol
cerivastatin
rosiglitazone
cetirizine
sanguinarine
cholecalciferol
sulfanilamide
complanadine A
sulfolane
curcumin
tafamidis
3,4-diaminopyridine
2,3,7,8-tetrachlorodibenzo-p-dioxin
docetaxel
Δ9-tetrahydrocannabinol
epicatechin
thiourea
eriochrome black T
triptycene
fexofenadine
urushiol
ganoderic acid
warfarin
gemifloxacin
whiskey lactone
gossyplure
p-xylene
z-guggulsterone
yohimbine
indigo
yuccagenin
(+)-kavain
zingerone
levoglucosenone
zymosterol
Report Form
(next 6 pages)
Chem 211
Molecule Library Project
Name
1. Compound Characteristics
Name of my molecule
Fall 2011
References from section 9:
Molecular Formula
CAS Registry Number
CA Index Name
Other names. What type of name is it? (IUPAC or systematic names– define the structure of
the compound; common, generic or trade names – do not provide structural information)
Name
2. Physical Properties
(at 1 atmosphere)
Boiling point
Refractive index
IUPAC or
systematic
Common,
Generic or
Trade
References from section 9:
Melting point
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.
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Molecule Library Project
3. Structure
References from section 9:
(draw by hand, a bond-line 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 chemistry reading room (2** Collier) 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)
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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
for ring names.
6. Aqueous Solubility
References from section 9:
(Consult Appendix A1 of the lab manual and your results from Experiment 5 for guidelines
on solubility in water, acid and base.)
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? Provide a warrant to support your claim.
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Molecule Library Project
7. Infrared Spectrum
References from Section 9:
Draw the structure of your molecule (hand drawn, create it using molecular drawing
software, or pasted it 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
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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, biology, neuroscience or
environmental studies 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 is it used for? 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 of the primary source(s) you used in the records related to your literature
search (either the first page with the citation or the entire research article if you copied it all).
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9. Reference List
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Molecule Library Project