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Syllabus for Chemistry 852 - Spring 2022 (PDF version)

Course content:   "In-depth coverage of the principle reactions leading to carbon-carbon bond formation, along with functional group transformations. Strategies and methods for organic synthesis."

Lecture Times:     MWF 9:10–10:00 am, January by zoom (meeting ID & passcode will be sent by email), then room 127 Chemistry
                               Mondays 7–9 pm, January 31 by zoom, then room 581W Chemistry 

Course Website:   https://www.chemistry.msu.edu/courses/cem852/index.html   


Instructor:

Professor Robert E. Maleczka, Jr.  
phone: 353-0834
email: maleczka@msu.edu 
zoom office hours: by appointment

Course Coordinator:

Ms. Nancy Lavrik
email: lavrik@chemistry.msu.edu 


Recommended Texts:

            1. Your undergraduate organic text.

            2.   George S. Zweifel, Michael H. Nantz, and Peter Somfai, Modern Organic Synthesis: An Introduction, 2017, Wiley.  ISBN-978-1-119-08653-6.

            3.   Paul Wyatt & Stuart Warren, Organic Synthesis: Strategy and Control, Wiley, 2007.  ISBN-978-0-470-92963-5.

            4.   K. C. Nicolaou & E. J. Sorensen, Classics in Total Synthesis, Targets, Strategies, Methods, VCH, 1996.  ISBN-3-527-29231-4. (On reserve in the MSU library)

            5.   The ACS Organic Division recently released a new resource for organic chemists: https://organicchemistrydata.org/.  The Reich Collection of Resources includes ~700 Total Syntheses searchable and categorized by compound name, named reactions used, chemoselectivity, rings formed, reaction types, and reagents used, etc.; a comprehensive Topics in NMR database, and information on pKa tableselectron pushingA-valuesnomenclatureorganometallic chemistry, etc.


Announcements:  Here you will find important information, course up-dates, and additional materials.  Please check frequently as items will be placed there as the course progresses.




Dates
Tentative Lecture Schedule*
Reading Suggestions
January 10
Course Intro
January 12
Rapamycin & Methyl Homosecodaphniphyllate Nicolaou & Sorensen
January 14–31 Classics in Total Synthesis Nicolaou & Sorensen
February 2
Synthetic Design
Zweifel/Nance Chapter 1
February 4, 7
Conformational Analysis Zweifel/Nance Chapter 2
February 9, 11
Protective Groups / Chemoselectivity
Zweifel/Nance Chapter 3
February 14 (am), 16, 18
Oxidations and Reductions
Zweifel/Nance Chapter 4
Feb. 21 (6:00 – 9:00 pm) Exam 1 to be held in room 127 100 pts
February 23, 25, 28, March 2
Reactions of C–C pi-Bonds Zweifel/Nance Chapter 5
March 4, 14
Formation of C–C pi-Bonds Zweifel/Nance Chapter 7
March 16, 18, 21 Formation of C–C bonds via Enolate Anions Zweifel/Nance Chapter 6
March 23, 25 Formation of C–C bonds via Organometallics Zweifel/Nance Chapter 7
March 28 (6:00 – 9:00 pm)
Exam 2 to be held in room 127
100 pts
March 30–April 1 Pericyclic Reactions Zweifel/Nance Chapter 9
April 4, 6
Asymmetric Catalysis
Warren Chapter 25, 26
April 8
Organocatalysis Warren Chapter 28, 29
April 11 (am), 13, 15 Aromatic Substitution / CH activation Warren Chapters 7, 33
April 11 (pm) Synthesis Presentations I 10 pts
April 18, 20, 22 Reactive Intermediates Zweifel/Nance Chapter 9
April 25, 27, 29 Heterocycles
Warren Chapters 32, 34, 35
April 25
Written Reports Due, 6 pm, Room TBD 40 pts
April 25, 26, 27 Synthesis Presentations II, 6 pm, Room TBD 50 pts
Tues. May 3 (Time TBD) All inclusive Final Exam to be held in room TBD 150 pts
 

*Subject to Change.

Note: The links will take you to the start of the related chapter in Professor William Reusch's Virtual Textbook of Organic Chemistry


Classic Syntheses (50 points):

  Students will each present a synthesis from Nicolaou's "Classics in Total Synthesis" (on reserve in the MSU library).  In years past, these presentations would be spread out over the semester.  However, owing to President Stanley’s mandate, these presentations will occur throughout the month of January.  Plan for your presentation to take about 20 minutes, excluding questions.  Your lecture will be graded using the same criteria used for the Organic Seminars, including input from your classmates.  I also expect you to provide a PDF file no later than three days following your presentation for placement on the web.  (Note: please use white backgrounds for your presentation.)
Dates
Molecule (Chapter)
Lecturer
January 12 Rapamycin (Chapter 31) Robert Maleczka
January 12 Methyl Homosecodaphniphyllate (Chapter 26) Robert Maleczka
January 14 Erythronolide B (Chapter 11) Nick Wills 
January 14 Reserpene (Chapter 4) Nikita  
January 19 Strychnine (Chapter 2) Sodiq Nafiu  
January 19 Strychnine (Chapter 33) Nathan Slater  
January 21
Monensin (Chapter 12) Hanin Sarhan
January 21
Monensin (Chapter 15) Vindula Alwis  
January 24 Periplanone (Chapter 13) Sonam Shivtarkar
January 24 Periplanone (Chapter 21) Nethma Wethalawe
January 26 Progesterone (Chapter 6) Rosemary Augustine
January 26 Endiandric Acids A–D (Chapter 17) Shannon Cartwright
January 28 Amphotericin B (Chapter 24) Bahareh Ghaffari
January 28 Zaragozic Acid (Chapter 35) Sydney Cobb
January 31 (am) Indolizomycin (Chapter 27) Keyvan Pedrood   
January 31 (am) Indolizomycin (Chapter 27) Keshav Prahaladi  
January 31 (pm) Asteltoxin (Chapter 20) Milad Pedarpourvajargahy     
January 31 (pm) Hirsutene  (Chapter 23) Salma Begum  


 

(Clicking on the molecule's name will down load that student's presentation as a pdf file)

Total Synthesis (100 pts):

In early March, each of you will be given a natural product for which you are to design a synthesis.  We will first meet on at 7 pm on Monday April 11.  At that meeting, you are to present a retrosynthesis (10-minutes max!) of your molecule highlighting what you view will be the key points of your proposed synthesis, including the means by which your synthesis will be made asymmetric.  An electronic copy of your retrosynthesis is due at 7 pm that day. A written report describing your synthesis is part of this assignment.  This report should resemble a second-year oral exam written report with a ≤4000-word limit, not counting Scheme captions and references (no limit on the number of Schemes).  An electronic of your written report is due at 6 pm on April 25.  On the evenings of April 25–27 we will meet at 6 pm (room TBD) for a full presentation of your synthesis (30 minutes maximum!) .  Each synthesis will be graded on the basis of your presentation, how you respond to questions, chemical soundness, creativity, thoroughness, the clarity of your final report, and your attendance.  More details on this assignment will be given later in the semester.

Total Synthesis Schedule: 

First Oral Report (10 pts): Presented April 11 starting at 6 pm.

Written Report: (40 pts):  An electronic copy is due at 6 pm Monday April 11

Final Oral Report (50 pts):  Presented over three evenings  Monday April 25, Tuesday April 26, and Wednesday April 27, starting at 6 pm each night.  These meetings are tentatively scheduled to take place in-person in room 136 (subject to change).  Electronic copies (PDF) of all presentations are due at 6 pm on April 25.  Those giving their oral report on April 26 or 27 are not to present an edited version of what was handed in on April 25.  Doing so will result in a 0 for the assignment.




Grading Scheme:


Two examinations = 200 points
Classic Synthesis Presentation = 50 points
Total Synthesis First Oral Report = 10 points
Total Synthesis Final Oral = 50 points
Total Synthesis Written Report = 40 points
Final examination = 150 points
Total = 500 points
No makeup exams will be given. If you miss an hourly examination due to religious holidays, unavoidable personal commitments, illness, etc., your course grade will be calculated by adding the point value (100 pts) of each missed exam to the Final Exam.  (If you know you will have a conflict with the dates indicated above AND you let me know by January 17 I will arrange for a makeup date.)

Grade Scale (I reserve the right to adjust this scale downward):

        Grade                    pts

        4.0                      >400

        3.5                300–400

        3.0                200–299

        2.5                150–199

           0.0                      <150
  

Homework:  Homework may be assigned periodically, but will not be considered directly in the grading of the course.


Supplemental MaterialOld exams are available. You may also find Professor Reusch's Virtual Textbook of Organic Chemistry helpful. Furthermore, please check the "announcements" link on the 852 web page frequently as important information, course up-dates, and additional materials will be placed there as the course progresses.

Special Assistance:  Any students requiring special assistance must identify themselves to the instructor at the beginning of the semester.

Class Conduct:  Professional, courteous, and ethical conduct is expected of all students at all times.  Likewise, diversity among students should be respected.  Finally, please turn off your cell phones before entering the classroom.

Policy on Cheating:  In order to discourage cheating, the instructor may make copies of some pages of some exams. Any student caught cheating will receive a grade of 0.0 for that test. In addition, a letter describing the incident will be sent to the chairperson of the Chemistry department, as well as that student's Department Chair, College Dean, and each memeber of the student's Ph.D. committee.


COVID-19 Information:  The novel coronavirus, which causes the disease COVID-19, has been declared a worldwide pandemic.  The COVID-19 virus is extremely contagious and is believed to spread mainly from person-to-person contact.  The COVID-19 pandemic represents an unprecedented public health crisis that has impacted every facet of life, including the classroom environment.  The most up to date information from MSU is available at: https://msu.edu/together-we-will/covid19-guidance/.

Instructional format: In response to omicron, instruction will be by zoom throughout the month of January.  Come February, significant changes in how we conduct in-person classes may be on the horizon.  Should in classroom attendance be impacted by COVID-19, modifications may be made to the class format and/or instructor.  Similarly, were MSU to halt in-person graduate study modifications will be made to the class format. 

Face coverings: Face coverings must be worn by everyone (including all faculty, staff, students, vendors, and visitors) indoors while on property owned or governed by MSU and while participating in MSU-related or MSU-sponsored activities.  Thus, unless you have a University issued exemption, you must wear a face covering in class. This face covering must cover your mouth and nose.

Physical distancing: As best as our room assignment allows, we will be practicing physical distancing in the classroom.  Thus, all students should attempt to maintain at least six feet distance between themselves and others (excluding those with whom they live).  This applies to all aspects of the classroom setting, including seating arrangements, informal conversations, and dialogue between faculty and students.

Exposure to COVID-19:  If a student is exposed to someone who is ill or has tested positive for the COVID-19 virus, they will stay home and follow MSU guidelines (see below) to determine what steps should be taken.  Students who miss assignments or exams will have their final pro-rated.  Cases of extended absence will be handled on an individual basis

Self-Monitoring: Students will self-monitor for flu-like symptoms (for example, cough, shortness of breath, difficulty breathing, fever, sore throat or loss of taste or smell). If a student experiences any flu-like symptoms, they will stay home and follow MSU guidelines (see below) to determine what steps should be taken.

Personal Hygiene. All students must maintain proper hygiene and health practices, including:

Adherence to Signage and Instructions: Students will (a) look for instructional signs posted by MSU or public health authorities, (b) observe instructions from MSU or public health authorities that are emailed to my “msu.edu” account, and (c) follow those instructions.

Compliance and reporting: Those who come to MSU facilities must commit to the personal responsibility necessary for us to remain as safe as possible, including following the specific guidelines outlined in this syllabus and provided by MSU more broadly (see below). There may be times when action will be necessary to reinforce expectations. If you do not wear appropriate face coverings (see MSU’s guidelines), do not wear your face covering appropriately (i.e., over your mouth and nose), or do not adhere to physical distancing guidelines (i.e., six feet apart), you will be asked to correct the situation or leave the facility. In addition, MSU will utilize the processes already in place to respond to any issues of noncompliance with standards established for the health and safety of our community. For classroom disruptions or issues, the responses and processes that have been used previously remain the first line of action. If necessary, the student conduct system will be the avenue used to adjudicate student disciplinary situations.

Additional COVID-19 information. See https://msu.edu/together-we-will/keeping-spartans-safe/ for details about these new policies and procedures and see https://ehs.msu.edu/_assets/docs/fact-sheets/cloth-face-covering-fact-sheet.pdf for more details about the cloth face coverings guidelines.