CHEM 741 - Physical Organic Chemistry I - Fall 2006
Class Hours & Details || Exams || Grading for the Course || Text books and Supplementary materials || Course goals || Course overview || Standard Course Policies || Syllabus outline (Week by week) || Lectures || Class Presentation Evaluation ||Assignments and Exams (PDF files)
Room: |
152 DUNBAR Hall |
| Class time : | Mondays: 3-3.50 PM Tuesdays and Thursdays: 2-3.15 PM |
| Office Hours: | Open. It is adviced to e-mail me in advance. |
Exam 1 |
Tuesday, October 3, 2006, 2.00-4.00PM |
Exam 2 |
Tuesday November 7, 2006, 2.00-4.00PM |
| Final Exam | Thursday, December 14, 2006. 2.00-5.00PM |
Grading for the courses :
- Two term-time exams (20% each).
- Final exam (35%).
- Oral presentation in class and Write up of a related recent research paper. (10%). Topics must be given a month in advance. (Due date for topics: Nov 02, 2006)
- Assignments (15%).
- Homework problems will not be graded or collected, but will provide the background for tests and serve to stimulate student-led discussion in the classroom.
- The grades will not be determined based on statistics (curve), given the limited sampling pool. Instead, grades will be assigned based on the absolute total scores.
- Attendance – Mandatory.
Text books and Supplementary materials:
Text book:
Modern Physical Organic Chemistry, by Anslyn and Dougherty. The books will be available at the bookstore. Required reading assignments will be given during the lecture.
Supplementary READING materials: (will be available in the Library).
Carey and Sundberg’s Advanced Organic Chemistry, part A, and the 5th edition
March, Advanced Organic Chemistry, 4th ed. or 5th ed.
Turro, Molecular Photochemistry, 2nd edition.
Carpenter, Determination of Organic Reaction Mechanisms
Provide you with a set of tools / principles to rationalize, control, and predict the behavior and outcome of organic reactions.
CHEM 741 is intended to be an overview of aspects of physical organic chemistry – understanding the nature of organic reactions and mechanisms. This course will not focus on memorizing organic reactions and mechanisms, but will concentrate instead on using physical organic techniques to come up with viable mechanisms, solve mechanistic problems, and rationalize outcomes of organic reactions. Many of the reactions covered in this course will not be new to many of you. However, we will be looking how they function in more detail to gain a better understanding of physical organic principles and how they can be used in a practical sense.
The intent of CHEM 741 is to provide new organic graduate students with all the fundamental tools and concepts for understanding advanced organic chemistry.
The first aspect of CHEM 741 will review basic principles for qualitiatively analyzing and writing organic reaction mechanisms. Also in this section, useful qualitiative relationships in physical organic chemistry will be presented and examined. A systematic approach to provide some ground rules for formulating plausible mechanisms, which is a critical component of advanced organic chemistry.The second aspect of the course will be devoted to examining how qualitiative aspects of physical organic chemistry such as steric effects, stereoelectronic effects, conformation analysis, orbital symmetry, etc. can be used to rationalize the outcomes of organic reactions. In addition to overviews of these areas, we will be looking at specific examples of organic transformations where these principles apply in practice.
The third aspect of the course will concentrate on understanding and applying methods for the experimental determination of organic reaction mechanisms. This will concentrate on the "physical" part of physical organic chemistry. That is, equation solving, kinetic and thermodynamic analyses; and data interpretation. A good calculator is recommended for this section of the course.
The fourth part of the course will expose students to modern Organic chemistry, organic and polymer chemistry, molecular recognition, photochemistry and supramolecuar chemistry.
(1) Examinable material: Students will only be responsible for knowing the material covered in the lectures, suggested study problems, and any handouts. The assigned reading sections in the textbook and supplementary textbooks are to be used to supplement the information provided in class.
(2) Requests for special exam writing conditions: Requests for special exam writing conditions (e.g., separate room, extra time) will be accommodated as long as formal documentation from the Disability Services Office is received. No other office on campus is authorized to validate a disability.
(3) Late problem sets, missed exams, and extenuating circumstances: Late problem set solutions will be penalized 20% for each day late. Late problem sets will not be accepted once the answer key has been posted. Any person who does not had in a problem set or misses the midterm exam will automatically be given a zero for the assignment or midterm exam. Any person who misses the final exam without a documented, valid reason will automatically be given an F for the class. Students who are passing the course and miss the final exam for reason of documented illness or similar catastrophe will be given an Incomplete.
(4) Cheating: Any student caught cheating, or helping someone cheat, will be reported to the NDSU Honor Code Council and to the Department of Chemistry and Molecular Biology for punitive action, as described below. Plagiarism also constitutes as cheating in this course. Any discovered act of academic dishonesty by a student in this course will be reported to the NDSU Honor Code Council. Additionally, the incident will be reported to the Academic Ethics Committee of the Department of Chemistry and Molecular Biology. This Committee will recommend if a sanction should be applied to the student. It is expected that students will abide by the NDSU Honor Code for all exams and problem sets. For problem sets, students must work independently on their solutions. Students must abide by the NDSU Honor Code for the problem sets in that they are not allowed to simply copy solutions and answers from each other.
Syllabus Outline (Week by week):
Note: This outline below is to guide through the way the class will be conducted week by week. We will try to follow the schedule although some deviation is expected.
Tue Aug 22: Over view of Molecular Structure – VB and MO theory – General introduction. Thu Aug 24: Ch 2: Strain and Stability. Thermochemistrry. Thermochemistry of Reactive Intermediates and thermodynamics, structure and bonding theories. Mon Aug 28: Ch 2: Ch 2: Reactive Intermediates – Radicals, Carbocations and Carbanions. Tue Aug 29: Ch 2: Ch 2: Reactive Intermediates – Radicals, Carbocations and Carbanions. Thu Aug 31: Conformational analysis, electronic effects, Strained molecules,
Ch 3: Non-covalent interactions and binding forces (overview).Mon Sept 04: No Class. Labor Day – University Holiday. Tue Sept 05: INDEPENDENT PROBLEM SESSION on Chapeter 2 and 3. Thu Sept 07: Ch 5: Acid Base chemisry. Pka, Predicting acid and basic strength. Applications to molecules of Biological interest. Mon Sept 11: Ch 5: Lewis acid, Nucleophiles and electrophiles. Ch 6: Stereochemisty, Terminology. Tue Sept 12: Ch:6: Symmetry and Stereochemistry, Stereoselective and stereospecific reactions. Adavance stereochemical aspects. Thu Sept 14: INDEPENDENT PROBLEM SESSION / Review for exam. Ch 7: Reactivity, Kinetics and Mechanism, Hammond Postulate, Kinetic analysis and principle Mon Sept 18: Ch 7: Kinetic Analysis. Ch 8: Reactivity, Kinetics and Mechanism. Tue Sept 19: Ch 8: Reactivity, Kinetics and Mechanism. Hammett Equations/Plots and Linear Free energy relationships. Thu Sept 21: Hammett Equations/Plots and Linear Free energy relationships (Contd).
INDEPENDENT PROBLEM SESSION / Review for the exam.Mon Sept 25: No class Tue Sept 26: Experiments related to thermodynamics and kinetics (Isotope effects and substitution effects). Thu Sept 28: Ch 10: Organic reaction mechanisms (Electrophilic additions) Mon Oct 02: Ch 10: Organic reaction mechanisms (Nucleophilic additions), Radical reactions. Tue Oct 03: EXAM ONE - 2.00 PM to 4.00 PM. Thu Oct 05: Ch 10: Radical reactions (contd.), Carbenes, Nitrenes, Benzynes. Mon Oct 09: Ch 10: Elimination reactions. Tue Oct 10: Ch 10: Elemination, Acyl Transfer reactions. Thu Oct 12: Ch 10: Electrophilec Aromatic Substitutions Mon Oct 16: Ch 11: Substitution at Carbonyl center, Enol and enolate chemistry. Tue Oct 17: Ch 11: Substitution at aliphatic centers Thu Oct 19: Ch 11: Substituion reactions, (Radicals) and OVERVIEW of reaction mechanisms Mon Oct 23: Ch 11: Isomerization and Rearrangements. Tue Oct 24: Ch 11: Isomerization and Rearrangements. (Contd.). Thu Oct 26: Ch 9: Catalysis Mon Oct 30: Ch 12: Organo transition metal reactions, Mechanisms and Catalysis. Tue Oct 31: Ch 4: Molecular Recognition and Supramolecular Chemistry. Thu Nov 02: Ch 4: Molecular Recognition and Supramolecular Chemistry (Contd.). Mon Nov 06: Ch. 15: Pericyclic reactions and and symmetry correlations. INDEPENDENT PROBLEM SESSION / Review for the exam Tue Nov 07: EXAM TWO - 2.00 PM to 4.00 PM Thu Nov 09: Ch. 15: Pericyclic reactions and symmetry correlations. Mon Nov 13: Ch. 15: Photochemistry – Photophysical processes. Tue Nov 14: Ch. 15: Photochemistry – Photophysical processes (Contd.). Photochemical reactions. Thu Nov 16: Ch. 15: Photochemistry – Photochemical reactions. Mon Nov 20: Ch. 15: Photochemistry – Photochemical reactions, Chemi luminescence, singlet oxygen. Tue Nov 21: Ch 17: Organic Materials, Polymers. Thu Nov 23: No Class. Thanksgiving – University Holiday. Mon Nov 27: Ch 17: Organic Materials, Polymers. Tue Nov 28: Overview / Problem session. Thu Nov 30: INDEPENDENT PROBLEM SESSION/Review for the exam. Mon Dec 04: ORAL PRESENTATIONS OF RECENT LITERATURE / Write up Tue Dec 05: ORAL PRESENTATIONS OF RECENT LITERATURE / Write up Thu Dec 07: ORAL PRESENTATIONS OF RECENT LITERATURE / Write up Thu Dec 14: FINAL EXAMINATION - 2.00 PM to 5.00 PM Friday Dec 15: Final Grades - 3.00 PM – Meet at 104H Ladd.