Chemistry 2LA3 Tools for Chemical Discovery I Course Instructors Primary W.J. Leigh (ABB-158) and x 23485; leigh@mcmaster.

ca

2009/10 P. Britz-McKibbin (ABB-231) x 22771; britz@mcmaster.ca G. Goward (ABB-268) x 24176; goward@mcmaster.ca

Secondary D.J.H. Emslie (ABB-267) and x 23307; emslied@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) Leah Allan (ABB-113; x22486; allanle@mcmaster.ca) Karen Neumann (ABB-412; x26084; neumann@mcmaster.ca) on McMasters WebCT Mondays & Wednesdays at 11:30 pm; ABB-165 Mondays at 1:30-5:30 pm; ABB-402 Wednesdays at 1:30-5:30 pm; ABB-402

Technical Administrators Course webpage Lectures Laboratories 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 hasnt 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 students 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 Deans 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 wont 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 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.
NH2 + OCH2CH3 O O O ! (50 oC) H2O OCH2CH3 O HN + CH3CO2H

p21

Reagents: Name
p-phenetidine
acetic anhydride distilled water

MW (g/mol)
137.18 102.09

Target [g (mol)]
1.0 g (7.3 mmol) 0.74 g (7.5 mmol) 10 mL (solvent)

Actual [g (mol)]

Hazards
toxic corrosive

Products: Name
phenacetin

MW (g/mol)
179.22

Theoretical Yield
7.1 mmol (1.27 g)

Actual Yield

% yield

mp

Procedure:

After the lab

10 September 2008 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.
NH2 + OCH2CH3 O O O ! (50 oC) H2O OCH2CH3 O HN + CH3CO2H

p21

Reagents: Name
p-phenetidine
acetic anhydride distilled water

MW (g/mol)
137.18 102.09

Target [g (mol)]
1.0 g (7.3 mmol) 0.74 g (7.5 mmol) 10 mL (solvent)

Actual [g (mol)]
0.98 g (7.1 mmol) 0.75 g (7.3 mmol) 10 mL toxic

Hazards

corrosive

Products: Name phenacetin 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 MW (g/mol) 179.22 Theoretical Yield 7.1 mmol (1.27 g) Actual Yield 0.55 g % yield 43 % mp 124 131 oC

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 werent 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.

McMasters 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 ones 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