Mechanisms of Organic & Inorganic Reactions

Chemistry 465

Prof. Simon J. Meek & Prof. Alexander J. M. Miller

REACTION MECHANISMS Fall 2013 Instructor: Office:

Professor Simon Meek ([email protected]) Kenan Laboratories C648 (919-962-0359)

Instructor: Office:

Professor Alexander J. M. Miller ([email protected]) Kenan Laboratories A400 (919-962-4618)

Schedule:

Monday, Wednesday, and Friday 11:00 am – 11:50 am; Kenan 121

Discussion:

Friday 1:00 pm – 1:50 pm; Kenan 121 (required)

Office Hours: By appointment. Do not hesitate to contact us; we are eager to help everyone understand the material. Textbooks: Required: Recommended:

Required:

Organic: “Modern Physical Organic Chemistry”, Eric V. Anslyn and Dennis A. Dougherty “The Art of Writing Reasonable Organic Reaction Mechanisms”, Grossman “Advanced Organic Chemistry/Part A: Structure & Mechanisms”, Carey & Sundberg Inorganic: “Inorganic and Organometallic Reaction Mechanisms”, Jim D. Atwood

Recommended:

“The Mechanisms of Reactions at Transition Metal Sites”, Henderson “Reaction Mechanisms of Inorganic and Organometallic Systems”, Jordan “The Organometallic Chemistry of the Transition Metals”, Crabtree

Course Website:

sakai.unc.edu

Course Number: CHEM465.001.FA13

“Cannot we be content with experiment alone? No, that is impossible; that would be a complete misunderstanding of the true character of science. The man of science must work with method. Science is built up of facts, as a house is built of stones; but an accumulation of facts is no more a science than a heap of stones is a house…” –Henri Poincaré COURSE DESCRIPTION Chem 465 will provide a framework of experiment and theory for the understanding organic and inorganic reaction mechanisms. The first section will cover structure and reactivity towards drawing reasonable electron-pushing reaction mechanisms as well as the tools of fundamental kinetic analysis. Foremost, students in this course should endeavor to develop an understanding of experimental analysis available for studying mechanisms, and the situations where each is appropriate. In second part we will use the tools of mechanistic analysis to examine a wide variety of organic and inorganic reactions through case studies, including: substitutions, eliminations, reactive intermediates, photochemical reactions, and electron transfer reactions. Grappling with unfamiliar mechanisms, predicting the products of reactions, and applying mechanistic tools will be significant and recurring themes.

Chemistry 465


CHEM 465 LEARNING OBJECTIVES After completion of this course, students should feel confident in assessing the mechanism of any chemical reaction. Specifically, students will be able to: 1. Propose reasonable reaction pathways using arrow-pushing concepts from mechanisms based on Frontier Molecular Orbital theory and an understanding of metal oxidation state and electron count. 2. Predict whether a reaction is exo- or endo-thermic based on bond dissociation energies. 3. Describe Interpret a qualitative energy surfaces for a reaction using a reaction coordinate diagrams. 4. Understand the difference between ground states and transition states of molecules. 3. Derive rate laws for single and multiple step reactions, including catalytic reactions. 4. Differentiate between thermodynamic and kinetic reaction products. 5. Use isotopic labeling studies to differentiate mechanistic possibilities. 6. Understand mechanistic subtleties of catalytic reactions (including enantioselective catalysis). 7. Utilize the tools of mechanistic analysis to determine the mechanisms of substitution and elimination reactions, photochemical and electron transfer reactions, and the behavior of reactive intermediates such as carbocations, radicals, and carbenes. 8. Search and understand primary literature. 9. Communicate ideas clearly and effectively in written and oral formats. APPROXIMATE COURSE OUTLINE:

SCHEDULED TOPIC

DATES (TENTATIVE)

READING

INSTRUCTOR

Part 1: Tools of the Trade Week 1: Organic: Arrow-pushing

August 21, 23, 23

A&D Ch. 1 App. 5

Meek

Week 2: Inorganic: Structure & Reactivity

August 26, 28, 30, 30

A&D Ch. 12

Miller

LABOR DAY

SEPTEMBER 2

NO CLASS

Week 3: Kinetics 1 – 1 and 2 order

September 4, 6, 6

A&D Ch. 7

Meek

Week 4: Kinetics 2 – Complex systems

September 9, 11, 13, 13

Atwd Ch. 1

Miller

Week 5: Reaction Coordinate Diagrams

September 16, 18, 20, 20

A&D Ch. 7 & 8

Meek

Week 6: Transition State Theory

September 23, 25, 27

A&D Ch. 7

Meek

EXAM 1

SEPTEMBER 27 (11:00 AM)

Week 7: Catalysis

Sept. 30 & Oct. 2, 4, 4

A&D Ch. 9

Miller

A&D Ch. 8

Meek

A&D Ch. 8

Miller

st

nd

Week 8: Organic Linear Free Energy Relationships October 7, 9, 11, 11 Week 9: Kinetic Isotope Effects

October 14, 16, 25

REACTION MECHANISM PROPOSAL INTENT

OCTOBER 16

FALL BREAK

OCTOBER 18

NO CLASS

Part 2: Case Studies in Assessing Mechanism Case studies: Organic Substitution Reactions

October 21, 23

Meek

Case studies: Inorganic Substitution Reactions

October 25, 28

Miller

Halloween Lecture

October 30

Miller

Case studies: Organic Elimination Reactions

November 1, 1

Meek

Case studies: Organic Reactions

November 4, 6

Meek

Case studies: Oxidative Addition

November 8, 8

Miller

Chemistry 465


EXAM 2

NOVEMBER 11 (11:00 AM)

Case studies: Electron transfer

November 13, 15, 15

REACTION MECHANISM REPORTS DUE

NOVEMBER 15

Student Presentations

November 18, 20, 22, 22


November 25, 27

THANKSGIVING BREAK

NOVEMBER 29


December 2

Review Session

December 4

Final Exam

December 6, 12:00 pm

Miller

NO CLASS

All Material Covered

GRADING Your course grade will be determined from three components: I. In-Class Exams (2): 50 min, 100 points each, totaling 200 points (40%) II. REACTION MECHANISM REPORT AND Presentation (1): Due November 15th; 100 points (20%) III. Final Exam (1): 2 hours, 200 points (40%). Friday December 6th, 12–2pm. EXAMS There will be a total of two In-Class Exams, worth 100 points each. No makeup exams will be given. A Final Exam will be given that is worth 200 points. The final exam will be cumulative, covering all of the material from the semester. Note that the Final Exam date is fixed and cannot be changed; make sure that your schedule can accommodate the exam time. REACTION MECHANISM REPORT AND PRESENTATION Each student will choose a literature reaction, which has not been studied in detail. A copy of the paper accompanied by a very short explanation for why the reaction was chosen will be submitted for instructor approval. A written report suggesting mechanistic experiments that could be performed (and outlining the possible outcomes) will be handed in towards the end of the semester. A short oral presentation on the report will be given in the last few weeks of the semester. For a detailed explanation see additional handout. PROBLEM SESSIONS (FRIDAYS AT 1 PM) Each Friday, the second-class period (1 pm) will be used as a problem session. These required sessions will be used to work problems individually and in groups, recap course material introduced during the week, and prepare for the various examinations. The problems worked in the problem sessions are presented in lieu of homework assignments; these should be taken seriously as the problem sessions are your primary preparation for the questions to be encountered on examinations. STUDYING Reaction Mechanisms is a course that builds upon key concepts that you have previously learned in inorganic and organic chemistry classes. In this course, you will be asked to learn additional concepts, to recall and to apply these concepts to solve problems. It is vital to your success that you review basic reactions and concepts from undergraduate inorganic and organic chemistry at the beginning of the semester in order to be adequately prepared for Chem 465. To aid in understanding the material, it is advisable that you review your notes daily as opposed to waiting until the night before the exam to study. In addition to reviewing your notes, you are strongly encouraged to work through the assigned problems in the text. The best advise for obtaining a good grade in this class: practice, practice, practice.

Chemistry 465


NOTES AND CLASS TIME This will be a lecture-based course and you will be responsible for taking notes during class. Although attendance is not factored into your final grade, it is highly encouraged that you do not miss any classes. If you miss a class, it is your responsibility to copy the notes from one of your classmates. Reading assignments for each section are given above, as are the hourly exam dates. The final exam date is scheduled by the University Registrar. COURSE WEBSITE Please refer to the Sakai Website (sakai.unc.edu) for all class assignments and announcements as well as the syllabus and exam schedule. Our class site can be found under the following section: CHEM465.001.FA13 CLASS CITIZEN ETIQUETTE Please be respectful of both the instructor and your classmates; pay attention, sit quietly, turn off your cell phones and computers, and put away reading literature not pertinent to class (i.e. The Daily Tar Heel). Repeat offenders will be asked to leave the classroom. HONOR CODE: “Since all graded work (including homework to be collected, quizzes, papers, mid-term examinations, research proposals, laboratory results and reports, etc.) may be used in the determination of academic progress, no collaboration on this work is permitted unless the instructor explicitly indicates that some specific degree of collaboration is allowed. This statement is not intended to discourage students from studying together or working together on assignments, which are not to be collected.” As you know, the Honor Code (http://honor.unc.edu/) is a cornerstone in maintaining academic integrity at Carolina. I take it extremely seriously and expect you do as well. All suspected Honor Code violations will be reported promptly. ABOUT THIS COURSE In order to understand the mechanism of organic and inorganic reactions, considerable background knowledge of the two fields is needed, which will be augmented by a variety of new methods and concepts. To master the course material, a few tips may come in handy: •

•

Come to class prepared. This is a no-brainer. Reaction Mechanisms introduces a number of new, high-level concepts and if you’ve read the textbooks and handouts before lecture, you will be better prepared to absorb and discuss the material. The class sessions should be active learning environments, with complex discussions, rather than passive information exchange. Study in groups. Group studying can be effective when everyone is working hard and at a similar level of understanding. It can also give a false sense of understanding if the group comes up with an answer that is not completely obvious to the individual. If you study in groups, do not fall into the trap of feeling that your understanding of the material is more advanced than it is. Get help early. If you are having problems with the material, seek help early in the semester. Halfway through the course is way too late. Simon and Alex are always happy to make appointments to discuss the course.

Disclaimer: The professor reserves the right to make changes to the syllabus, including project due dates and tests (excluding the officially scheduled final examination), when unforeseen circumstances occur. These changes will be announced as early as possible so that students can adjust their schedules