chem 336, spring 2021 organic chemistry ii ......1 chem 336, spring 2021 organic chemistry ii...

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CHEM 336, SPRING 2021 ORGANIC CHEMISTRY II LABORATORY

Course Instructor: Prof. Michael Rubin (GL 3152B) [email protected]

Laboratory Director: Dr. Marina Rubin (GL 3142D) [email protected]

Teaching Assistants:

Garg, Gaurav <[email protected]>

Griaznov, Georgii <[email protected]>

Joseph, Ebbin <[email protected]>

Ortiz-Medina, Xavier Alexis <[email protected]>

Vithanage, Dimuthu <[email protected]>

Maliszewski, Mary <[email protected]>

Williams, Jenna <[email protected]>

Organic Stockroom Technician: Bruce Johnston (GL 3142A) [email protected]

Required materials:

• Chemical splash goggles and chemistry lab coats: see below under “Laboratory Safety and

Etiquette”. • ChemDraw software for producing molecular structures. This will be needed for creating molecular

structures for e-notebook and laboratory reports. ChemDraw is a professional grade product that is available free to all KU students. The PC version (ChemBioOffice) includes additional software. Click here for instructions: http://chem.ku.edu/resources/it/chembiooffice. Some students find it more convenient to use ChemDraw online, which does not require installation: https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html. Video tutorial for ChemDraw is available on the course Blackboard in CHEM 331 Materials folder.

• Signals Notebook software for laboratory record keeping. Register at: http://informatics.perkinelmer.com/sitesubscription/ Video and printable tutorials for Signals Notebook are available on the course Blackboard in CHEM 331 Materials folder.

Laboratories: Each laboratory section will be split into two cohorts, A and B. Cohort A schedule is shown in blue, while cohort B schedule is shown in red in the Lab Schedule attached at the end of this document. Due to social distancing requirements, experimental work in the lab will be performed individually by each student in a designated fumehood. Your advance lab preparation, adherence to safety protocol, workplace housekeeping, time management and technical skills will be evaluated by your TA and will be reflected in Lab Technique grade (4 pts per lab period, 24 pts total, see below).

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Make-up Laboratory Policy: If you miss an in-person lab session due to a planned or unplanned emergencies (including COVID quarantine), you should first and foremost notify your TA of your absence. To compensate for a missed lab, you will be offered a make up lab activity at the end of the semester (week of April 26), as indicated in Lab Schedule. The make up lab cannot be used to replace another lab grade. Zero points will be assigned for an unexcused missed lab, where no proper medical or other emergency excuse documentation is provided. If you miss more than two labs, you will receive an F for the course. Lab Lecture: CHEM 336 course has a dedicated weekly lab lecture class that meets on Mondays. There are two lecture sessions (M 3:00-4:15 pm and M 4:30-5:45 pm, Budig 120) and you must be enrolled in one of them. Some of these lecture hours will be used to meet with your TA via Zoom to discuss the upcoming lab activities and to cover theory behind each experiment. Zoom lecture attendance will be taken and participation points (3 pts/lecture) will be given to everyone in attendance. TA zoom meetings will not be recorded, but slides will be posted on Blackboard in corresponding experiment folders. The remaining lectures will be used by Prof. Rubin to cover spectroscopy (NMR, IR, Mass). The spectroscopy lectures can be attended in person (Budig 120), and will also be videorecorded and uploaded on Blackboard, so you will be able to review them later. There will be no participation points awarded for attending spectroscopy lectures.

Safety and Laboratory Etiquette Safety Quiz: Prior to your first laboratory session, you will need to take a safety quiz (administered through Blackboard) and pass with a score of 100% (15/15, these points do not count toward your grade). The quiz will be based on the document entitled "Safety and Standard Operating Procedures for Organic Teaching Laboratories”, as well as video tutorials posted in Safety link on Blackboard. Some important items from the “Teaching Laboratory Dress Code” section of the document are copied below. SAFETY QUIZ IS A PART OF A MANDATORY LAB SAFETY CHECK-IN PROTOCOL AND MUST BE COMPLETED BY ALL STUDENTS. • Chemical Splash Goggles are required at all times in the lab. The wearing of approved safety

goggles with indirect vents is mandated by State Law. Students found in the laboratory without approved goggles will receive a zero grade for this lab period. Note: These are meant to protect the eyes, not the forehead.

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• Clothing must cover your body from the neck to the ankles. You must wear closed-toe shoes

in the lab. Note that skin-tight pants (e.g. leggings, jeggings, etc.), and tights are not considered pants and are, therefore, not allowed in lab (refer to “Safety and Standard Operating Procedures for Organic Teaching Laboratories” document for details on lab dress code).

• Lab Coats are required in organic labs. Current CDC regulations do not allow us to store lab coats

and goggles in lab drawers for the duration of the semester, as we normally do. You will be provided with a plastic Ziploc bag to carry your goggles and lab coat to and from the lab.

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Preparing for, and Documenting, Laboratory Work

Advanced Laboratory Preparation: Before attending each lab, you must review all materials posted in the corresponding experiment folder on Blackboard. These include: the video of the experiment, TA lecture slides and any additional materials posted therein, as well as the experiment handout, and Safety Data Sheets for all chemicals listed for that lab. Although you are not graded directly on the completion of prelab assignments, lack of preparation translates into loss of technique points in the lab. The following easy steps will help you avoid unnecessary frustration and point deduction for lab technique and lab report:

1) Review the prelab lecture

2) Read the handout

3) Watch the experiment video while following along with the handout procedure and make notes

4) Email your TA or lab director if you have any questions

Submitting Products: In experiments that involve synthesis or isolation of compounds, the compounds must be submitted in properly labeled containers at the end of the laboratory period. Proper presentation (e.g. vial labeling), yield and purity of the product will be reflected in the grade for the Laboratory Technique. Refer to the PRODUCT SUBMISSION GUIDELINES document (Course Documents link in Bb) for details.

Documenting your work: We will continue mastering electronic notebook record keeping that we started in CHEM 331. Please make sure you are registered and have an active Signals Notebook account with PerkinElmer (see the link provided above in Required Materials section).

Laboratory Reports: A typed, complete laboratory report (worth 50 pts) will be required for Nitration of Bromobenzene experiment. This report must be formatted in the manner outlined in the document entitled “Lab Report Format” (Course Documents link in Bb). For two other experiments (Grignard Synthesis and Diels-Alder Reaction), you will turn in a partial formal report including only two of the following sections: Abstract & Introduction, or Results and Discussion & Experimental (10 pts each). Formal reports will be collected in electronic format only, in Word document (.doc, .docx) or PDF format, using the template provided. Reports must be posted on SafeAssign before specified deadlines (TBA). Reports submitted after the deadline will be subject to 10% deduction per day (every 24 hrs passed). Zero points will be assigned for reports submitted more than 72 hrs after the deadline, unless they result from a legitimate and documented absence as determined by the course instructor and your TA. Be sure to review Lab Report Submission Guidelines on Blackboard before submitting your work. It is your responsibility to make sure that your file was uploaded successfully and in a correct format, which can be verified by a) checking the SafeAssign score that appears shortly after submission; and b) downloading the file back to your computer. Please carefully review lab report writing guidelines posted in Course Document link on Blackboard. Plagiarism will result in a score of zero for the entire assignment and further disciplinary measures as appropriate.

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http://college.ku.edu/sites/clas.drupal.ku.edu/files/docs/SAS/Policies/Academic%20Misconduct%20Policies%20and%20Procedures%20(Rev.%20Nov.%202012).pdf

Assessment See Grading Summary below for detailed point breakdown.

Lab Technique Grade: (20 points maximum; 4 points per “wet” lab period). This score will be assigned by your TA for each “wet” lab, and will be based on an overall assessment of the following factors: (1) Your understanding of what is going on in the lab. (2) Preparation, and general confidence in performing experiments. (3) Attitude (follow directions, focus on your work, respect TA and your classmates, etc.) (4) Day to day neatness, drawer/hood organization, and efficiency. (5) Product appearance, yield, purity, and proper presentation. (6) Ability to draw conclusions from experimental data and recognize sources of error. (7) Ability to correctly and effectively use laboratory apparatus. Most technique point losses occur as a result of a) lack of preparation and b) messy workplace and poor glassware cleaning skills. Following Advance Lab Preparation steps (page 3 above) and reviewing “PPE and Housekeeping in Chemistry Lab” video (posted in Safety link on Blackboard) will help avoid unnecessary technique point deductions. TA Lab Lecture: (3 pts/zoom session, 18 pts total) Participation in each TA lab lecture will earn you full points for that day’s session Lab Report Grading: Specific grading rubrics will be provided for each lab report. However, it is very important that you also follow General Lab Report Format and Writing Guidelines posted in Course Documents. Point losses can be easily avoided by cross-checking your written work against the above-mentioned documents before submission. All questions about graded lab reports must be brought to the attention of the grading TAs within 2 weeks after the graded work is handed back. Please notify the course instructor if you do not receive timely feedback for your report from your TA. Lab Notebook: (3 pts/notebook, 12 pts total) To receive full credit, a complete e-notebook for each experiment must be submitted on Blackboard before designated deadline. Your TA will communicate specific requirements for e-notebook for each lab. For experiments that also require submission of a lab report, the notebook pages can be turned in as an attachment to your report. Quizzes: (3 pts/quiz, 18 pts total) There will be total of 6 quizzes, each consisting of 3 questions. These quizzes will be administered via Blackboard. One make up quiz will be offered at the end of the semester, which can be counted as an extra credit. Each quiz will cover theoretical background for the experiment discussed in the relevant lab, and the material presented in the corresponding TA lab lectures. Virtual Lab Assignment: A packet of questions based on the virtual lab - Aldol Reaction – and other topics covered within the semester (excluding spectroscopy). Multiple choice and open-ended questions (20 pts).

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Spectroscopy Assignments: Include two problem sets: NMR (10 pts) and Integrated Spectroscopy (15 pts). Practice problem sets for each of these assignments will be provided and discussed in the corresponding Zoom workshops (Experiments 4 and 8).

Grading Summary: Lab Technique 20 pts (5 wet labs x 4 pts) TA Lab Lectures 18 pts (6 x 3 pts) Lab Notebook 12 pts (4 x 3 pts) Partial Lab Reports 20 pts (2 x 10 pts) Full Lab Report 50 pts Spectroscopy 25 pts Lab Quizzes 18 pts (6 x 3 pts) Virtual Lab Assignment 20 pts ____________________________ Total 183 pts

Final Letter Grades: The following grading scale will be used. Grades may be scaled (i.e. cutoffs lowered) if the class average warrants. 93% - 100% = A 73% - 76% = C 90% - 92% = A- 70% - 72% = C- 87% - 89% = B+ 67% - 69% = D+ 83% - 86% = B 63% - 66% = D 80% - 82% = B- 60% - 62% = D- 77% - 79% = C+ Below 60% = F Additional Policies COMMERCIAL NOTE-TAKING: Pursuant to the University of Kansas’ Policy on Commercial Note-Taking Ventures, commercial note-taking is not permitted in this course. Lecture notes and course materials may be taken for personal use, for the purpose of mastering the course material, and may not be sold to any person or entity in any form. Any student engaged in or contributing to the commercial exchange of notes or course materials will be subject to discipline, including academic misconduct charges, in accordance with University policy. Please note: note-taking provided by a student volunteer for a student with a disability, as a reasonable accommodation under the ADA, is not the same as commercial note-taking and is not covered under this policy. DISABILITY ACCOMMODATIONS: The Academic Achievement & Access Center (AAAC) coordinates accommodations and services for all KU students who are eligible. If you have a disability for which you wish to request accommodations and have not contacted the AAAC, please do so as soon as possible. Their office is located in 22 Strong Hall; their phone number is 785-864-4064 (V/TTY). Information about their services can be found at https://achievement.ku.edu/. Please also feel free to contact me privately in regard to your needs in this course.

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ACADEMIC MISCONDUCT: Cheating, or the appearance thereof, including giving or receiving help on a laboratory report, looking at another student’s paper while taking an exam or a quiz, falsifying laboratory reports or data, using unauthorized materials, notes, crib sheets, or the equivalent, will not be tolerated and will be dealt with in accordance with University regulations. The Chemistry Department reserves the right to make and keep copies of individual examination papers. DIVERSITY, INCLUSIVITY, AND CIVILITY: Civility and respect for the opinions of others are very important in an academic environment. It is likely you may not agree with everything that is said or discussed in the classroom. Courteous behavior and responses are expected at all times. When you disagree with someone, be sure that you make a distinction between criticizing an idea and criticizing the person. Expressions or actions that disparage a person’s race, ethnicity, nationality, culture, gender, gender identity / expression, religion, sexual orientation, age, disability, or marital, parental, or veteran status are contrary to the mission of this course and will not be tolerated. CONCEALED CARRY: Individuals who choose to carry concealed handguns are solely responsible to do so in a safe and secure manner in strict conformity with state and federal laws and KU weapons policy. Safety measures outlined in the KU weapons policy specify that a concealed handgun: • Must be under the constant control of the carrier. • Must be out of view, concealed either on the body of the carrier, or backpack, purse, or bag that

remains under the carrier’s custody and control. • Must be in a holster that covers the trigger area and secures any external hammer in an un-cocked

position • Must have the safety on, and have no round in the chamber.

This course takes place in spaces that will require students to leave belongings such as backpacks and purses away and unattended for the duration of class time. Students who choose to carry a concealed handgun in a purse, backpack, or bag must review and plan each day accordingly, and are responsible for making alternate arrangements as necessary. The university does not provide appropriate secured storage for concealed handguns. Individuals who violate the KU weapons policy may be asked to leave campus with the weapon and may face disciplinary action under the appropriate university code of conduct. COVID-19 RELATED POLICIES:

“To protect all of us, everyone must wear a mask in the classroom as required by the Protect KU Pledge and by University policy. Violations of the mask policy in classrooms are treated as academic misconduct. If you come to the lab without a mask, TA will ask you to put one on. If you do not put on a mask when asked, you will have to leave class. Violations will be reported, and consequences will follow, up to and including suspension from the course.” CDC guidelines for face coverings can be found here.

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CHEM 336 SPRING 2021 LAB SCHEDULE

CHEM 336 February 2021

Sunday Monday Tuesday Wednesday Thursday Friday Saturday

1 TA Lab Lecture

2 3 4

5 6

7 8 Spectroscopy Lecture

9 10 11

12 13

14 15 TA Lab Lecture

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17 18 19 20


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EXPERIMENT 1: COHORT A – OXIDATION OF ALCOHOLS (WET LAB)

EXPERIMENT 1: COHORT B - OXIDATION OF ALCOHOLS (WET LAB)

EXPERIMENT 2: COHORT A - GRIGNARD SYNTHESIS (WET LAB)

EXPERIMENT 2: COHORT B - GRIGNARD SYNTHESIS (WET LAB)

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CHEM 336 March 2021 Sunday Monday Tuesday Wednesday Thursday Friday Saturday

Feb 28 1 TA Lab Lecture

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3 4

5 6


9

10 11

12 13


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26 27


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EXPERIMENT 3: COHORT A – DIELS-ALDER REACTION (WET LAB)

EXPERIMENT 3: COHORT B – DIELS-ALDER REACTION (WET LAB)

EXPERIMENT 4:

EXPERIMENT 5: COHORT A - NITRATION OF BROMOBENZENE PART 1 (WET LAB)

EXPERIMENT 5: COHORT B - NITRATION OF BROMOBENZENE PART 1 (WET LAB)

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CHEM 336 April 2021 Sunday Monday Tuesday Wednesday Thursday Friday Saturday

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2 3

4 5 TA Lab Lecture

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7 8 9

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EXPERIMENT 7:



EXPERIMENT 6: COHORT A - NITRATION OF BROMOBENZENE PART 2 (WET LAB)

EXPERIMENT 8: