R340: Survey of Organic Chemistry Fall 2014

Instructor: Dr. Ben Burlingham Phone: 856-7782 Office: Chemistry A206 Email: bburling@indiana.edu Office Hours: M 10-11AM, T 10-11AM, W 2:30-3:30PM, R 11-noon Associate Instructor: Xiaoxiao Qiao will be your AI for this course. Please take advantage of the AI’s help during discussion sections and other times. Her office hours will be Thursdays, 6-7PM, in C046. Contact her at xiaoqiao@indiana.edu. Course Description: Organic chemistry is the study of the structure and reactivity of carbon-containing compounds. In this survey course, we will discuss the structure and reactivity of most major functional groups from a mechanistic perspective. Students will be able to describe basic reactivity of molecules in terms of electrophilic addition, elimination, nucleophilic substitution, nucleophilic addition, and acyl substitution. An understanding of biological redox chemistry and decarboxylation will allow students to apply structure and reactivity principles to biochemical systems. Text Materials: Required: Klein, David R. “Organic Chemistry as a Second Language 2nd ed.” ISBN978-0-470-12929-6 Suggested: “Organic Chemistry Models” molecular modeling kit (You may find it helpful to share a kit.) Course website: Go to the following website for all handouts and class information: http://courses.chem.indiana.edu/r340/ Grade record: Grades will be posted on Oncourse. Class Organization: Lecture: In this three-credit course, there will be classroom lectures 9:05-9:55AM MWF in BH347. Attendance will not be taken, but is highly recommended. Discussion: Students will meet once a week for discussion section. Students must attend the section for which they are registered. If there is an extenuating circumstance that prevents this, please talk to Sarah.

Grading: Discussion quizzes: 100 pts Exams: 300pts Final Exam: 150pts Total 550 pts

Anticipated grading scale: A = above 90%, B = 80-89.9%, C = 70-79.9%, D = 55-69.9%, F=below 55%. Plus/minus grades will be awarded. Homework: Working out problems is the only way to be successful in Organic chemistry. There will be a worksheet available on the course website for most lectures, which reviews the major concepts and expectations, then gives practice problems. To help in your studying, I have broken out the problems into three sets. Daily Homework is intended to be a small subset of problems that cover the main ideas of each lecture. Consider them the minimum that you should do every day to keep up in the class. Even if you get behind a little bit, never miss doing these problems. Cumulative problems are given so that you can see how topics connect to previous material. These are more like exam questions, because they incorporate what you have learned over weeks and months rather than just one day. Extension problems help you to think about applying what you have learned into a new situation. These are important for two reasons. First, they are more similar to A-level exam questions because they test a level of understanding that is at the application level. Second, they help you to prepare for the next class, so that you will be more prepared and allow you to learn more quickly. Quizzes: Quizzes will be made up of Daily Homework problems from the previous 2-3 days of class. Eleven 10-point quizzes will be given during discussion section. The lowest score will be dropped, and the remaining ten will be totaled out of 100 points. If a quiz is missed due to absence, that score will be dropped. If you know you will miss a quiz ahead of time, you can contact the AI PRIOR to class for options of taking the quiz. Any other absences must be appealed to the instructor. The score for a quiz with an excused absence will be the average of the other ten scores. Exams: Three midterm exams, each worth 100 points, will be given in class on September 26, October 31, and December 5. Because organic chemistry is a subject that builds upon previously learned material, all exams will be cumulative, but will focus on the material covered since the previous exam. No makeup exams will be given; if a valid excuse is given for missing an exam, the percentage grade on the final will be substituted for the missed exam grade. Please talk to the instructor at least a week ahead of the exam if there is a university approved conflict with one of the exams. Final Exam: The final exam will be cumulative and worth 150 points. The final will be given during the time assigned by the University, Monday, December 15, 8-10AM. There will be no excused absences from the final.

Academic Honesty: The determination of academic misconduct is at the discretion of the instructor. The sanctions may range from deduction of points to a failing grade for the class. In all cases, the infraction will be immediately reported to the Dean of Students as well as the dean or director of the student’s school. Please read the Code of Student Rights, Responsibilities, and Conduct for further detail. Withdrawals The last day to withdraw with an automatic W is October 26. After that date, you must seek permission from the Dean’s office. If the Dean allows you to withdraw, you will be assigned a “W” if passing at that time, or an “F” if not passing, according to the policy of the College of Arts and Sciences. Tips for maximum success:

You need to attend all classes and discussions. Practice, practice, practice. Organic chemistry requires drawing many structures,

so you must write out every homework problem. Do not simply look at it and think that you know how to do it.

Develop and use your own study aids, such as flashcards and study guides. Be persistent in asking questions. Take advantage of discussion sections. Come

to office hours as soon as you are having problems. Form study groups. Many different skill sets are needed to comprehend the

material, including visual/spacial reasoning, logic, abstract reasoning, memorization, organization, and drawing. Few individual students have strengths in all of these areas, but a group of students probably will. At the beginning of the semester, form a 3-4 person study group to meet weekly to review homework and major topics.

Don’t get behind! One day behind puts you two days behind because you won’t understand the next day because you missed the previous.

I want to see you succeed! My personal goal is to see every individual student succeed to the level he or she is willing to work. Please feel free to talk with me any time you want—keep me up to date with how you are doing.

This schedule may be changed by the instructor to better meet the needs of the class. Lecture Topic Aug 25 Typical Bonding in Organic Chemistry Aug 27 Structural representations Aug 29 Functional Groups and reactivity Sept 3 Nomenclature Sept 5 Atypical bonding and stability Sept 8 Resonance Concepts Sep 10 Drawing Resonance structures Sep 12 Drawing resonance structures and VSEPR Sep 15 Hybridization and atomic orbital overlap pictures Sep 17 sp3 systems: enantiomers and R/S Sep 19 sp2 systems: pi bonds, conjugation Sep 22 sp2 systems: delocalization, Aromaticity and Nucleobases Sep 24 Review: Structure determines electron distribution in molecules Sep 26 Exam 1 Sep 29 Intermolecular Forces Oct 1 IMF and properties (bp, solubility, molecular recognition) Oct 3 Acid/base reactions Oct 6 Acid/base stability principles Oct 8 pKa, acid/base relative strength Oct 13 Addition reactions: HX and basics of mechanisms Oct 15 Enol tautomerization

Oct 17 Mechanism, energy diagrams, thermodynamics Oct 20 Mechanism, energy diagrams, kinetics Oct 22 Elimination Reactions Oct 24 Elimination reactions Oct 27 Substitution reactions Oct 29 Review: Applying acid/base chemistry to substitution reactions Oct 31 Exam 2 Nov 3 Nucleophilic addition of strong Nu, Aldol Rxn Nov 5 Imine formation/hydrolysis Nov 7 Hemiacetal and acetal formation Nov 10 Carbohydrates Nov 12 Addition/elimination under basic conditions Nov 14 Addition/elimination under acidic conditions Nov 17 Hydrolyxix of ketone/aldehyde derivatives Nov 19 Hydrolysis of ketone and carboxylic acid derivatives Nov 21 Phosphate esters and anhydrides Dec 1 Review: Comparing reactivity of nucleophilic reactions Dec 3 Grouping reactions and compounds by Redox Dec 5 Exam 3 Dec 8 Redox in biological systems/ Decarboxylation Dec 10 Decarboxylation and cofactors Dec 12 Review—Metabolic reactions