Organic Chemistry II (CHEM*3750)

Code and section: CHEM*3750*01

Term: Fall 2023

Details

General Information

Department of Chemistry
University of Guelph
Fall 2023

Calendar Description

CHEM*3750  Organic Chemistry II  Summer and Fall  (LEC: 3, LAB: 3)  [0.50]  
This course provides continued coverage of fundamental aspects of organic chemistry using an assimilation of carbonyl chemistry, unsaturated systems and carbon-carbon bond forming processes to acquaint students with methods of organic synthesis. Topics also include an introduction to spectroscopic methods for the identification of organic compounds.

Prerequisite(s): CHEM*2700  
Restriction(s): This is a Priority Access Course. Enrolment may be restricted to particular programs, specializations or semester levels during certain periods. Please see the departmental website for more information.  
Department(s): Department of Chemistry  
Location(s): Guelph  

 

Course Materials Delivery and Support

Note: Although in-person/face-to-face instruction is planned for the F2023 semester, face-to- face instruction may be suspended and pivoted to virtual instruction at any time in response to a directive from Public Health Ontario

1. Course instructor, time and location information are available on CourseLink or WebAdvisor.
2. Virtual Office Hours: office hour (~1 hour on Zoom) on Mondays (1-2 PM), Wednesdays (8PM-8h30PM). These are subject to change (without revising the course outline) depending on various factors like student availabilities. See CourseLink for details
3. Online Assistant: Readily available online mainly via email (also via Zoom/Teams/ CourseLink)
4. This class is listed as in-person and synchronous, and as such, class attendance is strongly encouraged

 

Course Objectives

CHEM*3750 provides continued coverage of fundamental aspects of Organic Chemistry. CHEM*2700 and CHEM*3750 have been designed to provide a comprehensive introduction to Organic Chemistry. This will properly serve the students who require a year of Organic Chemistry in addition to their first year General Chemistry. In CHEM*3750, the emphasis is on the understanding of the factors that control reactions and the reaction products, as well as the introduction to spectroscopic methods for the identification of organic compounds. This course is a prerequisite for CHEM*3760.

Specific Learning Objectives

1. To make the students knowledgeable about the fundamentals of Organic Chemistry.
2. To understand the consequences (reactivity, properties) of the 3-dimensional structures of molecules.
3. To be able to interpret patterns of reactivity on the basis of mechanistic reasoning.
4. To be able to design syntheses of organic molecules of moderate complexity.
5. To be able to identify structure of simple organic compounds using IR and NMR techniques, as well as other complementary techniques.

 

Course Materials

Textbooks

1. Organic Chemistry, 13th Edition by T. W. G. Solomons and C. B. Fryhle, John Wiley & Sons, Inc. I recommend that you purchase the textbook as it will effectively supplement the lecture material.
2. Study Guide and Solutions Manual to Organic Chemistry, 13th by T.W.G. Solomons, C. B. Fryhle and S.A. Snyder, John Wiley & Sons, Inc. This guide provides answers to all problems in the text and also offers addition self test problems. **A combine package of the textbook and the study guide, as well as two molecular model kits, and the Wiley Plus Access Code, is available at the Bookstore for a substantially reduced price. You are encouraged to consider this package. Solomons is also the textbook for CHEM*2700 (Organic Chemistry I).
3. If you already have an older edition of the textbook (9th/10th/11th, 12th ed.), I do not recommend you to purchase the 13th edition as there is only very little difference between them.

Lecture Slides

The lecture slides for CHEM*3750, Organic Chemistry II, will be available for download through CourseLink before each lecture (note that a series of preliminary slides may be available for the entire semester, and will be subject to modification prior to a given lecture without notification). It is assumed that students are familiar with the organic chemistry materials covered in CHEM*2700 and you may wish to have the notes available to review topic as needed (see CourseLink).

Course Web Page

You can access the course website through Courselink: https://courselink.uoguelph.ca/shared/login/login.html.

This web page will be updated regularly. Lecture slides, assignments, answer for assignments, tutorial and revision materials, practice exam papers and answers, as well as midterm exam grades will be posted. Please visit this website regularly, especially before exams.

 

Course Outline, Reading Assignments and Problem assignments

An outline of the course is shown below. The reading assignments (see below) from the Solomons textbook will provide a more detailed perspective of the course material. The number of lectures allocated for each topic is approximate. Problem assignments and answers for the assignments can be downloaded through Courselink. These are instrumental for midterms and final exam preparation.

Part I: Introduction to Structural Determination of Organic Compounds

Topics:

• Elemental Analysis
• Mass Spectrometry (very briefly, more details in CHEM*3760) 
• Degree of Unsaturation
• Infrared Spectroscopy
• ¹H Nuclear Magnetic Resonance (NMR) Spectroscopy
• ¹³C Nuclear Magnetic Resonance (NMR) Spectroscopy

Reading Assignments (Solomons 12th Ed. and 13th Ed):Chapter 2, Sections 2.15 – 2.17 Chapter 9, Sections 9.1 – 9.15

Part II-1: Aldehydes and Ketones: Synthesis & Enolate Chemistry

Topics:

• Synthetic Routes to Aldehydes and Ketones (a brief review from CHEM*2700)
• Nucleophilic Addition Reactions (a brief review from CHEM*2700) 
• Wittig Olefination
• Acidity and Enolization
• Halogenation at the  Carbon
• Enolates and Alkylation Reactions
• Enolates of Beta-Dicarbonyl Compounds, Acetoacetate Synthesis, Malonate Synthesis 
• Imines and Enamines

Reading Assignments (Solomons 12th Ed. and 13th Ed):Chapter 16, Sections 16.4 – 16.11 Chapter 18, Sections 18.1 – 18.10

Part II-2: Condensation and Conjugate Addition Reactions of Carbonyl Compounds: More Chemistry of Enolates

Topics: 

• Carbonyl condensation reactions – Claisen, Dieckmann 
• Aldol Reactions
• Conjugate Additions of Enolates 
• The Mannich Reaction
• Robinson Annulation

Reading Assignments (Solomons 12th Ed. and 13th Ed):Chapter 19, Sections 19.1 – 19.9 Chapter 20, Sections 20.6 – 20.8

Part III: Conjugation

Topics: 

• Conjugated Systems 
• Allylic Systems
• UV-Vis Spectroscopy (very briefly, more details in CHEM*3760)
• Conjugated Dienes – Electrophilic Additions and The Diels-Alder Reaction
• Frontier Orbital and Molecular Orbital of Ethene, Butadiene and Allyl Systems

Reading Assignments (Solomons 12th Ed. and 13th Ed.):Chapter 13, Sections 13.1 – 13.10 

Part IV-V: Benzene Chemistry

Topics:

• Aromaticity
• Electrophilic Aromatic Substitution (a brief review from CHEM*2700) 
• Reactions of the Side Chain of Alkylbenzenes
  – RadicalHalogenationandOxidation
• Birch Reaction
• Aromatic Amines – Use of Protecting and Blocking Groups, Diazonium Salts 
• Aromatic Halides – Nucleophilic Aromatic Substitution, Benzyne

Reading Assignments (Solomons 12th Ed. and 13th Ed):Chapter 14, Sections 14.1 – 14.11 Chapter 15, Sections 15.1 – 15.15
 

Molecular Model Kit

A molecular model kit can be purchased from the Bookstore. It is very useful to those who have difficulty with stereochemistry.

 

Laboratory

The lab manual will be available for sale in the Department at the beginning of the semester. Students are also required to have a “Blue Lab Note book” and must provide their own safety goggles (both of these may be purchased in the Department). Students are also required to provide their own lab coats. A student without eye protection will not be permitted to work in the laboratory. Contact lenses are extremely hazardous in a laboratory environment and their use is prohibited in the lab. SAFETY GOGGLES MUST BE WORN AT ALL TIMES IN THE CHEM*3750 LABORATORY.

• For any problems associated with the lab please contact the lab coordinator.
• For TA’s Names, emails, office locations and office hours, please contact the lab coordinator.
• Organic Chemistry II labs location: SC2111/2112.
• Attendance is mandatory for all labs. Failure to attend and complete 3 or more of the labs regardless of reason (emergency, illness, etc.) may result in automatic lab grade of zero. Contact your TA and the Lab Coordinator before your scheduled lab period if you cannot attend your weekly lab.
• The Organic Chem Lab Survival Manual” by J. W. Zubrick, contains helpful hints on a variety of techniques and apparatus employed in the organic chemistry laboratory. It is available in the Library on 2-hour reserve.
• IMPORTANT NOTE: Students can only get lab exemptions if the course was taken within the past 12 months. Any student who would like to get lab exemption must get approval from the lab coordinator within the first week of the semester.

 

Assessments and grades

1. Sign and submit “Consent form”
   You MUST submit a signed consent form otherwise we (me and the TAs) will not be able to grade your quizzes, exams and other assessments. (Please see CourseLink for more details).
2. Lab Grades (30%):
   Please see your Lab Manual for details. If you have any questions concerning your Lab Grades, please contact your TA or our lab coordinator, Dr. Robert Reed (E-mail: rwreed@uoguelph.ca).
3. On-line Quizzes F2023 (15%): 3% × 5 quizzes. Due dates are subject to change by the instructor depending on material covered in class, without requiring amendment of the course outline. Must-Know Quiz (strongly recommended). Available Sept 11th to Sept 22nd
   Quiz 1 (3%): (coverage: Part 1). Available Oct 3rd (6AM)
   Tentative due Date: Oct 4th, 2023 by 11:30 PM
   Quiz 2 (3%): (coverage: Parts 1-2). Available Oct 16th (6AM)
   Tentative due Date: Oct 17th, 2023 by 11:30 PM
   Quiz 3 (3%): (coverage: Parts 1-3). Available Nov 2th (6AM)
   Tentative due Date: Nov 3rd, 2023 by 11:30 PM
   Quiz 4 (3%): (coverage: Parts 1-4). Available Nov 13th (6AM)
   Tentative due Date: Nov 14st, 2023 by 11:30 PM
   Quiz 5 (3%): (coverage: Parts 1-5). Available Nov 30th (6AM)
   Tentative due Date: Dec. 1st, 2023 by 11:30 PM
   (Quizzes will be open the day prior to the due date and you will be allotted a time limit (and an attempt limit) to complete and submit your answers to CourseLink. See CourseLink for more details)
4. Midterm Examination (20%) (Expected coverage: Parts 1, 2, and 3 depending on progress) (a closed-book, **in-person exam**)|
   Oct 28th, 2023 (Saturday) expected time: 1:00pm-3:00pm location: TBA
   (See CourseLink for details)
5. Final Examination (35%) (Coverage: Parts 1-5) (a closed-book, **in-person exam**) Date and time: Dec. 8th (Friday), 2023 11:30 am – 1h30 pm location: TBA.
   (See CourseLink for details)

The mid-term and final exams are currently scheduled as closed-book, **in-person exams**. However, due to the ongoing COVID-19 pandemic, these in-person exams may not be allowed and pivoted to online exams through Crowdmark in response to a directive from Public Health Ontario and the decision by the University of Guelph.

As long as the University allows exams to be conducted “in-person”, the mid-term and final exams will be conducted as closed-book, **in-person exams**, and NO online exam option will be offered. At any time, if the University does not allow an exam to be conducted “in-person” anymore, then the scheduled exam will be conducted through Courselink or another examination software. Please check the “Announcements” in CourseLink regularly for any updates and change of plans.

Students must pass the laboratory part of the course to obtain credit for the course. To pass the lab portion, an overall grade of 50% must be achieved on the lab part of the grades. Otherwise a mark of 47% or the mark calculated from the above distribution, whichever is lower, will be the reported grade.

Policy for Re-grading of Exams

All of the exams in this course will be graded by TAs and the instructor. Although TAs will have been given detailed instructions concerning grading schemes for each question of the exams, and I should have meetings with them and explained to them how each questions should be graded, it is uncommon that sometimes TAs could make some mistakes in grading. After you have looked over your exam, and believe there is anything wrong with the gradings, you are more than welcome to email me and let me know which question(s) you think may have error(s) in gradings, and I will re-grade your exam paper. However, I would like to make it clear that when I re-grade an exam paper, I will re-grade the entire exam paper (and not just the question(s) that you think may have grading errors), and the results of the re-grading of the exam paper may result in an increase of your grade, no change of the grade, or a decrease of your grade. The principle is that a student should get what they are supposed to get based on the answers that they have given in the exam papers.

Important information concerning exams

1. You must sign and submit the “Consent form” (available on CourseLink) before writing the first assessment.
2. Only valid excuses on medical or compassionate grounds will prevent a grade of zero for a missed examination/quiz. Midterm exams may be submitted to the instructor for correction of grading errors within 5 days of the return of the graded papers.
3. If you missed a quiz due to the above valid excuses, please email me ASAP and we will schedule a date and time so that you can write a makeup quiz. If a quiz is not written by the last day of lecture classes (Dec 1st, 2023), it will automatically receive a grade of zero.
4. If you missed a mid-term exam due to the above valid excuses, please email me ASAP. Only ONE makeup/alternate mid-term exam will be scheduled one week after the regular, scheduled mid-term exam (typically the same time on the Saturday after the regular, scheduled mid-term exam). If you are still unable to write the scheduled makeup exam due to the above valid excuses, then you must contact me and make further arrangements. Failing to do so will results in a grade of zero. The weighting of the missed mid-term exam will be moved to the final exam (i.e. your final exam will weigh more). Please consult the University guidelines for valid excuses. Note that the pending grade for a midterm that is not written will be 0, until the grade change has taken into effect.
5. If you did not do well in a mid-term exam (or a quiz), I will NOT be able to “re-weight” the percentage of the exam, i.e. moving certain percentage of a mid-term exam to the final exam. (Point 5 is subject to change without amendment to the course outline).
6. If an assessment is not submitted, re-written, and arrangement with me have not been made, a grade of zero will awarded for that assessment.

Important information for students registered with Student Accessibility Services (SAS)

1. If you plan to write any examination at SAS, please arrangement with SAS within the first two weeks of classes. Do not wait till the week before any exam to schedule with SAS as they may not be able to accommodate your request in such a short notice.
2. Please send me an e-mail within the first two weeks of classes to inform me that you will be writing exams at SAS. I usually make up seating plan for exams, so if you are going to write any exam at SAS, I will not assign a seat for you in the exam room. Also, I will make sure I will send the exam paper to SAS so that you can write the exam there.

Contingency Plan

In case of severe weather or other unforeseeable disruptions, it may be necessary to change course materials delivery methods, or change in assessments/evaluation methods and academic schedules. Any such changes will be announced via CourseLink and/or class email.

 

Weekly Lecture^b Schedule

^a Revisions classes will also serve as catch up classes if material was not fully covered in previous classes.
^b This schedule is tentative and is subject to change without amendment to the course outline.

 

Course Statements

Communications

The primary communication between the students and the lecturer concerning issues with the course is through discussions during the lectures (e.g. exams and quizzes coverage, due dates for quizzes, and other announcements related to the course). Although most of the time, announcements and information related to the course will also be made through the course website and/or e-mails to the students, students are expected to attend EVERY lecture. This is NOT a DE course. If you miss a lecture, make sure you talk to your classmate to see if there is any important announcement during the lecture that you missed or you are welcome to contact me by phone or e-mail.

 

University Statements

Covid Information

Please note that the ongoing COVID-19 pandemic may necessitate a revision of the format of course offerings, changes in classroom protocols, and academic schedules. Any such changes will be announced via CourseLink and/or class email. This includes on-campus scheduling during the semester, mid-terms and final examination schedules. All University-wide decisions will be posted on the COVID-19 website and circulated by email.

Students are encouraged to wear a face mask in order to attend class and lab.

Please note, these guidelines may be updated as required in response to evolving University, Public Health or government directives.

Appropriate Online Behaviour

Inappropriate online behaviour will not be tolerated. Examples of inappropriate online behaviour include:

• Posting inflammatory messages about your instructor or fellow students
• Using obscene or offensive language online
• Copying or presenting someone else's work as your own
• Adapting information from the Internet without using proper citations or references
• Buying or selling term papers or assignments
• Posting or selling course materials to course notes websites
• Having someone else complete your quiz or completing a quiz for/with another student
• Stating false claims about lost quiz answers or other assignment submissions
• Threatening or harassing a student or instructor online
• Discriminating against fellow students, instructors and/or TAs
• Using the course website to promote profit-driven products or services
• Attempting to compromise the security or functionality of the learning management system
• Sharing your username and password
• Recording lectures without the permission of the instructor

E-mail Communication

As per university regulations, all students are required to check their <uoguelph.ca> e-mail account regularly: e-mail is the official route of communication between the University and its students.

When You Cannot Meet a Course Requirement

When you find yourself unable to meet an in-course requirement because of illness or compassionate reasons, please advise the course instructor (or designated person, such as a teaching assistant) in writing, with your name, id#, and e-mail contact. See the undergraduate calendar for information on regulations and procedures for Academic Consideration.

Illness

Medical notes will not normally be required for singular instances of academic consideration, although students may be required to provide supporting documentation for multiple missed assessments or when involving a large part of a course (e.g. final exam or major assignment).

Drop Date

Courses that are one semester long must be dropped by the end of the last day of classes; two-semester courses must be dropped by the last day of classes in the second semester. The regulations and procedures for Dropping Courses are available in the Undergraduate Calendar.

Copies of out-of-class assignments

Keep paper and/or other reliable back-up copies of all out-of-class assignments: you may be asked to resubmit work at any time.

Accessibility

The University promotes the full participation of students who experience disabilities in their academic programs. To that end, the provision of academic accommodation is a shared responsibility between the University and the student.

When accommodations are needed, the student is required to first register with Student Accessibility Services (SAS). Documentation to substantiate the existence of a disability is required, however, interim accommodations may be possible while that process is underway.

Accommodations are available for both permanent and temporary disabilities. It should be noted that common illnesses such as a cold or the flu do not constitute a disability.

Use of the SAS Exam Centre requires students to book their exams at least 7 days in advance, and not later than the 40th Class Day.

Academic Misconduct

The University of Guelph is committed to upholding the highest standards of academic integrity and it is the responsibility of all members of the University community – faculty, staff, and students – to be aware of what constitutes academic misconduct and to do as much as possible to prevent academic offences from occurring. University of Guelph students have the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff and students have the responsibility of supporting an environment that discourages misconduct. Students need to remain aware that instructors have access to and the right to use electronic and other means of detection.

Please note: Whether or not a student intended to commit academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of assignments does not excuse students from responsibility for verifying the academic integrity of their work before submitting it. Students who are in any doubt as to whether an action on their part could be construed as an academic offence should consult with a faculty member or faculty advisor.

The Academic Misconduct Policy is detailed in the Undergraduate Calendar.

Recording of Materials

Presentations which are made in relation to course work—including lectures—cannot be recorded or copied without the permission of the presenter, whether the instructor, a classmate or guest lecturer. Material recorded with permission is restricted to use for that course unless further permission is granted.
By enrolling in a course, unless explicitly stated and brought forward to their instructor, it is assumed that students agree to the possibility of being recorded during lecture, seminar or other “live” course activities, whether delivery is in-class or online/remote. If a student prefers not to be distinguishable during a recording, they may:

1. turn off their camera
2. mute their microphone
3. edit their name (e.g., initials only) upon entry to each session
4. use the chat function to pose questions.

Students who express to their instructor that they, or a reference to their name or person, do not wish to be recorded may discuss possible alternatives or accommodations with their instructor.

Resources

The Academic Calendars are the source of information about the University of Guelph’s procedures, policies and regulations which apply to undergraduate, graduate and diploma programs.