Chemistry 2LA3 – Tools for Chemical Discovery I
Course Instructors Primary
W.J. Leigh (ABB-158)
and
x 23485; leigh@mcmaster.ca
Secondary D.J.H. Emslie (ABB-267) and
x 23307; emslied@mcmaster.ca
2009/10
P. Britz-McKibbin (ABB-231)
x 22771; britz@mcmaster.ca
G. Goward (ABB-268)
x 24176; goward@mcmaster.ca
Teaching Assistants
Adroha Bhattacharya (ABB-111; x23715; bhatta9@mcmaster.ca)
Lawrence Huck (ABB-111; x23715; huckl@mcmaster.ca)
Naomi Janson (ABB-205W; x26337; TBA)
Lana Kostina (ABB-111; x23715; kostins@mcmaster.ca)
Karen Lam (ABB-302; x24864; lamkp3@mcmaster.ca)
Farah Lollmahomed (ABB-111; x23715; lollmafb@mcmaster.ca)
Anika Louie (ABB-466; x27128; louieas@mcmaster.ca)
Technical Administrators
Leah Allan (ABB-113; x22486; allanle@mcmaster.ca)
Karen Neumann (ABB-412; x26084; neumann@mcmaster.ca)
Course webpage
on McMaster’s WebCT
Lectures
Mondays & Wednesdays at 11:30 pm; ABB-165
Laboratories
Mondays at 1:30-5:30 pm; ABB-402
Wednesdays at 1:30-5:30 pm; ABB-402
Required Course Materials
Text:
Catalyst: Tools for Chemical Discovery. Laboratory Techniques and Other Useful
Information for the Experimental Chemist; Pearson Custom Publishing, 2008 (“TCD”)
Hardbound “Physics Notes” laboratory notebook (2)
Safety goggles
Lab coat
Course Objectives. The primary goal of Chemistry 2LA3 and its 2nd-term partner course, Chemistry
2LB3, is to train students in the fundamental techniques of modern experimental chemistry: the
synthesis and spectroscopic characterization of organic and inorganic molecules and materials,
chemical analysis, the measurement of physical properties of molecules and materials, and
computational chemistry. Secondary goals include training in proper record-keeping and safe
laboratory practices, and the development of critical thinking and time-management skills. The
specific experiments to be carried out in the courses have been designed to give students
experience in the fundamental aspects of both molecular and materials chemistry, thus providing
them with a sound basis for selecting their individual area of specialization in Levels 3 and 4 of the
Honours Chemistry program, and preparing them for the Level 3 laboratory courses, where more
advanced techniques will be learned and there is a greater emphasis on inquiry. An emphasis has
been placed on the design of integrated laboratory experiments, that emphasize the interplay
between the traditional sub-disciplines of analytical, inorganic, organic, and physical chemistry.
Course Structure. Four chemistry faculty members are responsible for Chem 2LA3 and 2LB3, with
two playing the leading roles in Chem 2LA3 (Leigh & Britz-McKibbin) and the other two in Chem
2LB3 (Goward & Emslie). Day-to-day instruction and supervision, and weekly evaluation of
laboratory notebooks will be provided by a team of graduate teaching assistants, with technical
support from undergraduate laboratory staff members. Both the primary faculty course instructors
and the teaching assistants contribute to student evaluation in the courses.
The laboratory manual is available as a series of pdf files on the course WebCT site.
Evaluation.
Pre-lab preparation
Laboratory notebook & supplementary material
Skills Assessment
Mid-term assignment
Final assignment
20%
40%
16%
12%
12%
Grades for pre-lab preparation will be assigned continuously throughout the course, and on an
experiment-by-experiment basis. Each experiment in the laboratory manual provides explicit
instructions in regards to pre-lab preparation, which takes two forms in every case:
Readings. The description of the experiment itself must obviously be read from start to
finish before entering the laboratory. Chapters in the 2LA3/2LB3 course textbook (“TCD”)
that constitute essential reading in advance of the experiment are indicated in boldface
under the heading “Techniques” (Note: “TCD-1” refers to Chapter 1 in TCD; see the
Revised Table of Contents pages). Other relevant chapters may also be indicated.
Notebook preparation. The “Pre-lab” section of each experiment lists specific things that
are to be entered into the notebook prior to entering the laboratory for that experiment.
A grade out of 5 for pre-lab preparation will be assigned by the TAs during the first hour of every
laboratory session, based primarily on inspection of the lab notebook. The grade will be derived
using the following guidelines:
5/5 – student has read the experiment and essential readings, the notebook has been prepared as
instructed, and the student is clearly well-organized.
4/5 – student has read and understands the experiment and the essential readings and prepared the
notebook as instructed, but there are minor deficiencies.
(2-3) /5 – student has read the experiment and the essential readings and prepared the notebook as
instructed, but there are major deficiencies in the notebook preparation.
1/5 – student has read the experiment, but has recorded nothing in the notebook beyond the title
and purpose of the experiment.
0/5 – student is completely unprepared – there are no notebook entries and it is clear that the
student hasn’t even read the experiment.
Students who receive a grade of 1/5 or less will be required to withdraw from the laboratory, and
meet with one of the course instructors, who will decide whether the circumstances warrant allowing
the lab to be made up on an alternate date. If a make-up is permitted, it will be the student’s
responsibility to arrange a date and time that is acceptable to the technical staff and a TA. If a
make-up is not permitted, the student will receive a grade of zero for the experiment.
Students compelled to be absent from a scheduled laboratory session due to religious reasons are
to inform one of the instructors by 1 pm on the Friday preceding the session, and an alternate date
for completing the experiment will be arranged.
Students are expected to be fully prepared for the experiment of the day, when they arrive for the
pre-lab lecture where (usually) some of the finer details of the experiment will be presented.
The assignments will each consist of a 10-15 page written report on a selected experiment from the
course, in which students will interpret the results of the experiment in detail and explore some of the
broader ramifications of the experiment. These assignments will provide students with experience in
preparing reports based on their experimental work, for consumption by the broader chemical
community. Some experiments are more suitable for this than others, so students will be provided
with a list of experiments from which to select. The first report will be assigned during Week 5 and
due at the end of Week 6, while the second will be assigned during Week 11 and due at the end of
Week 12. LATE ASSIGNMENTS WILL NOT BE ACCEPTED FOR GRADING.
The skills assessment will be carried out by the course instructors, in consultation with the teaching
assistants, throughout the course but with emphasis on the latter half. Grades will be assigned
based on the following guidelines:
< 8/16 (Insufficient) - Student required continuous assistance while ignoring safety hazards
12/16 (Reasonable) - Student performed experiments competently with some assistance
14/16 (Good) - Student showed good skills at performing experiments
16/16 (Excellent) - Student showed excellent skill, performed work independently, and had an
excellent understanding of the basic principles involved.
Missed Laboratory Experiments. Failure to hand in an assignment or complete a laboratory
experiment will result in a zero grade unless a valid reason has been filed with and accepted by the
Associate Dean’s office. It is the responsibility of the student to ensure that medical slips etc.
are filed with the Associate Dean, and that the appropriate Permission Slip is issued and filed
with the Course Instructor. There will be no exemptions to these rules.
The Laboratory Notebook is the permanent record of the experiments a chemist carries out. The
required laboratory notebook (“Physics Notes”) is available in Titles Bookstore. It is to be purchased
new, and not used for any purpose other than Chemistry 2LA3 and (if space permits) 2LB3.
The first two pages of the notebook are to be reserved for an Index that will contain the title of the
experiment and the page number on which it starts. Note that you will have to number the pages in
the notebook yourself; please do this prior to the first lab (the first 100 pages should be plenty).
The remainder of the book will contain your lab notebook entries for each of the experiments you do.
The right-hand pages are to be used for the text associated with the write-up (purpose, procedure,
conclusions, etc.), tables, and hand-entered data that you acquire, while the left-hand pages are to
be used for rough calculations, sketches of apparatus, original hard-copies of spectra or any other
instrumental data that are acquired during the experiment (stapled or taped in place). Your TAs and
course instructors will provide you with additional instructions as time goes on in the course – the
basic rule, however, is that everything goes in the lab book, and never on loose scraps of paper that
can be misplaced.
Use a pen for all entries in the lab book, and cross out (with a single line) any errors that are made.
It is a mortal sin to tear or otherwise remove pages from a laboratory notebook, punishable by the
loss of 2% of the course grade per page removed.
The format to be used in recording the details of an experiment will vary somewhat depending on
whether the experiment is primarily synthetic or focuses on analytical or physical measurements, but
will take the following generic form:
DATE
Experiment Number – Title of the Experiment
Objective – A concise (2 sentences at most) description of the purpose of the experiment.
Chemical equations should be included here as well.
Reagents table – a table which gives the name, molecular weight, target amount, actual amount,
moles, and other relevant information about each reagent to be used in the experiment.
Product table (if applicable) – a table which gives the name, molecular weight, amount isolated (crude
and recrystallized, if applicable), percent yield, melting point, and description of the target product(s)
for the lab.
Data table (if applicable) – a table in which quantitative measurements made during the experiment
will be recorded.
Procedure and Observations – a point-form description of what you actually did. This includes,
but is not limited to, glassware set-up, order in which reagents were added, temperatures used, how
the product was isolated and purified. Observations made during the experiment (e.g. colour
changes, precipitation of solids, evolution of gases) or problems that are encountered along the way
should be included here as well.
Spectra – all spectra acquired during the experiment are to be folded and taped neatly on the left
hand pages in your lab book so they can be opened and viewed readily but won’t fall out.
Conclusions – a short paragraph that describes the outcome of the experiment. Here you can
discuss things such as the product yield in synthetic experiments (whether it is reasonable), what
could be done differently if you had to repeat it, any problems that were encountered (“HUMAN
ERROR” IS NOT A VALID PROBLEM). For sections of the lab that do not involve synthesis (e.g.
chemical tests), state what was learned from the results. If a question is posed at the end of the lab,
it should be answered here as well.
References – you should at least reference the procedure in the lab manual. Other sources used
for your conclusions (such as text books, journals, etc.) should be added here as well.
------------------------------------------------------------Some experiments may require that a separate 1-2 page summary report be submitted, along with
(or rather than) the laboratory notebook.
An example of the lab notebook description of a synthetic experiment, showing what the book
should look like at the beginning and at the end of the experiment, is given on the following pages.
Before the lab…
10 September 2008
p21
Experiment 0 – Synthesis of phenacetin
Objective: Synthesize phenacetin (N-(4-ethoxyphenyl)acetamide) through the
reaction of p-phenetidine (para-ethoxyaniline) and acetic anhydride in water.
O
NH2
O
+
O
! (50 oC)
O
H2O
OCH2CH3
MW
(g/mol)
Target
[g (mol)]
p-phenetidine
137.18
1.0 g (7.3 mmol)
acetic anhydride
102.09
0.74 g (7.5 mmol)
distilled water
+ CH3CO2H
OCH2CH3
Reagents:
Name
HN
Actual
[g (mol)]
Hazards
toxic
corrosive
10 mL (solvent)
Products:
Name
phenacetin
Procedure:
MW
(g/mol)
Theoretical Yield
179.22
7.1 mmol (1.27 g)
Actual
Yield
% yield
mp
After the lab…
10 September 2008
p21
Experiment 0 – Synthesis of phenacetin
Objective: Synthesize phenacetin (N-(4-ethoxyphenyl)acetamide) through the
reaction of p-phenetidine (para-ethoxyaniline) and acetic anhydride in water.
O
NH2
+
O
O
! (50 oC)
O
H2O
OCH2CH3
+ CH3CO2H
OCH2CH3
Reagents:
Name
HN
MW
(g/mol)
Target
[g (mol)]
Actual
[g (mol)]
p-phenetidine
137.18
1.0 g (7.3 mmol)
0.98 g (7.1 mmol)
toxic
acetic anhydride
102.09
0.74 g (7.5 mmol)
0.75 g (7.3 mmol)
corrosive
10 mL (solvent)
10 mL
distilled water
Hazards
Products:
Name
phenacetin
MW
(g/mol)
Theoretical Yield
Actual
Yield
% yield
mp
179.22
7.1 mmol (1.27 g)
0.55 g
43 %
124 – 131 oC
Procedure:1
-
50 mL round-bottom flask equipped with a stir-bar
distilled water added to flask
phenacetin (colourless liquid) was added in one portion with
stirring
amine did not dissolve, added two drops of conc. HCl - amine
dissolved
flask warmed in a water bath to ~50oC
p22
Wt. beaker: 87.16 g
Beaker+prod: 87.71 g
Diff: 0.55 g
-
(this will be on the facing
page)
-
acetic anhydride (colourless liquid) added in one portion;
mixture turned light brown
stirred 5 min.
stirring stopped and flask was cooled in ice bath
pale yellow precipitate formed; isolated by vacuum filtration
(**spilled about half of the mixture prior to filtering**)
recrystallized from water to yield white crystals, which were
vacuum filtered and left to dry in funnel for 10 min.
dry crystals transferred to clean, tared 50 mL beaker &
weighed
mp recorded (apparatus #5): 124 - 130 131 oC
Conclusions:
Phenacetin was successfully prepared and isolated. The yield (43%) was low because of
the loss of sample during the procedure. Aside from that, the yield could have been
improved by isolating a second crop of crystals from the mother liquor. The melting
range is wide and lower than the theoretical melting point of 133-136oC – this suggests
either impurities are present or the crystals weren’t completely dry before recording
the melting point.
References:
1. Chemistry 2LA3 Laboratory Manual, McMaster University, p 0-1, 2008.
The instructors and university reserve the right to modify elements of the course during the term.
The university may change the dates and deadlines for any or all courses in extreme circumstances.
If either type of modification becomes necessary, reasonable notice and communication with the
students will be given with explanation and the opportunity to comment on changes. It is the
responsibility of the student to check their McMaster email and course website weekly during the
term and to note any changes.
McMaster’s Policy on Academic Dishonesty
Academic dishonesty consists of misrepresentation by deception or by other fraudulent means and
can result in serious consequences, e.g., a grade of zero on an assignment, loss of credit with a
notation on transcript and/or suspension or explusion from university.
It is your responsibility to understand what constitutes academic dishonesty. For information on the
various kinds of academic dishonesty please refer to the Academic Integrity Policy, specifically
Appendix 3:
http://www.mcmaster.ca/univsec/policy/AcademicIntegrity.pdf
The following illustrates only three forms of academic dishonesty most relevant to experimental
research and scientific ethical behavior:
1. Plagiarism: Submission of work (e.g., report, manuscript, presentation) that is not one’s own
work or for which other credit (e.g., citation. permission) has not been obtained. Transcribing
passages from other references in lab reports is an example.
2. Fraudulent Data: The intentional use of fraudulent, inauthentic and misleading data in
experimental research that cannot be reproduced independently by other groups; submitting
data collected by someone else and passing it off as your own.
3. Improper Collaboration: Taking credit for work performed in a group without reasonable and/or
equitable effort consistent with other members of the group .
The university requires that every act of academic dishonesty be reported and subjected to a penalty
depending on specific context.
To avoid any conflicts with this policy:
- Limit any discussion of academic work with your peers, avoiding specific details of assignments
or laboratory reports (unless instructed otherwise)
- Record authentic data and all observations during an experiment in an unaltered laboratory
notebook as a permanent record.
- Consult your instructors or TAs in case of any doubts in these matters