Honors Organic Chemistry I MWF 9:05 9:55 Baker Room 335 Instructor: Yimon Aye (Assistant Professor) ya222@cornell.edu, www.ayelab.org Office hour: Sat 1-2 pm Location: Baker 219 Teaching Assistant: Somsinee (Sine) Wisitpitthaya (Graduate Student, Aye Lab) sw739@cornell.edu, www.ayelab.org Office hour: Fri 4-5 pm Location: Baker 158 Important Dates Wednesday, January 22 Sunday, January 26 Thursday, February 13 Saturday, February 15 Wednesday, February 19 Thursday, March 13 Saturday, March 29 Monday, Apr 7 Tuesday, April 8 Thursday, May 8 Sunday, May 11 TBA Spring term instructions begin Vote for office hours preference by Prelim 1 (7:30 pm) Fall break begins Classes resume Prelim 2 (7:30 pm) Spring Break begins Classes resume Prelim 3 (7:30 pm) Study Period begins Study Period ends Scheduled Final Exam 1
Learning Outcomes Gain an intensive introduction to organic chemistry as a solid foundation for subsequent study in chemical, biological and materials sciences. Learn a set of important tools and concepts that enable appreciation and powerful application of modern organic chemistry. Academic integrity Each student in Chem 3590 is expected to abide by the University s Code of Academic Integrity. Please familiarize yourself with the Code, which is posted on the University s website: http://cuinfo.cornell.edu/academic/aic.html Diversity & Inclusive Excellence Chem 3590 is open to the views of each and every student in the classroom. Please honor the uniqueness of your fellow classmates and appreciate the opportunity to be in an environment where we can all learn from each other. Responsibility to Notify All students are expected to promptly notify the TA of any issues that may interfere with the performance and participation in all course-related matters. 2
Textbook, study guide and solutions manual & molecular model kit (3 in 1 set) Note: this Textbook will be the same text used for CHEM3600 in the fall. Required: 9781256151111 Bruice - 4 PKG Organic Chemistry w/ SG + Model Kit + Study Skills Website - 6 - Pearson Education The least expensive places to purchase the Chem 3590 textbook and its accompanying study guide, model kit, and study skills website are at the Cornell Store and on Amazon.com. Please see the buying options and prices below for each. Cornell Store 1. Buy New * 4 Pkg Organic Chemistry W/ Sg + Model Kit + Study Skills Website - $189.50 Amazon 1. Buy New * Organic Chemistry textbook - $59.98 * Organic Chemistry Study Guide and Solutions Manual - $29.90 (loose leaf) or $105.41 (paperback) * Organic Chemistry Model Kit #3 by Darling Models - $29.03 2. Buy Used * Organic Chemistry textbook - $22.00 * Organic Chemistry Study Guide and Solutions Manual (paperback) - $30.00 (loose leaf) or $22.85 (paperback) * Organic Chemistry Model Kit #3 by Darling Models - $14.85 3. Rent * Organic Chemistry textbook - $17.79 * Organic Chemistry Study Guide and Solutions Manual (paperback)- $16.70 The textbook bundle is only available through the Cornell Store, therefore you would need to purchase all items separately through Amazon.com. Also, access to the Study Skills Website is not available on Amazon.com; it is only available through the bundle at the Cornell Store. 3
Molecular Models (come with the Text above) These models are indispensable for understanding stereochemical problems in organic chemistry that often define fundamental properties of materials, biomolecules and drugs. You are allowed to bring the model kit to the exam. Web Site https://piazza.com/cornell/spring2014/9087_2014sp/home The course web site is Piazza linked through blackboard. The web site will contain all materials handed out in class, as well as problem sets, exams, and their solutions. We will also post copies of hand-written notes and power point slides from all lectures and review sessions, and all handouts given out in individual sections. The site also contains recent chemistry news, and digital chemistry animations expressing various key concepts. Studying Throughout the semester, we will be discussing a large amount of difficult material in a short amount of time. It is critical that you do not fall behind in your studies. Often, understanding of new material in organic chemistry relies upon mastery of ideas previously discussed. We urge you to review your class notes immediately after class and to clear up ambiguities while the subject is still fresh in your mind. An important component of your study will be the practice problems from the recommended, a copy of which will be posted on Piazza. It is often said that you cannot study organic chemistry without a pencil in your hand. Please make the effort to use these problems in your study and consult the solutions only after you have worked out your own answers. 4
TA office hours Office hours will begin the 2nd week. See page 1 for time/day and location. The final time/day selected was based on the class votes. Regular attendance at section is strongly encouraged. In order to get the most out of your office hours, always review the material before coming to office hours. Homework There will be 9 assigned problem sets over the course of the semester. 1 or 2 questions will be arbitrarily picked from each PSet and graded. These grades will make up of the entire class. Problem sets will be will be made available on Piazza. Problem sets will be due precisely on the dates/times listed on the PSet. Answer key will be posted on the course web site 24 hours after the due date. "late" hand-ins will receive only 50% of the credit they would have received had they been on time. No credit will be given to the Psets handed in after answer key has been posted. They will not be graded either. Some of the homework problems will be difficult, and you are advised not to wait until the last moment to begin working on your assignments. Although working with classmates on homework sets is encouraged, it is to your own benefit to make an effort on each problem before collaborating with others. Copying another student's solutions will not be tolerated. Prelims Three written exams will be given during the course of the semester (dates above). Material discussed in the lecture immediately preceding the exam will not be covered on the exam (see course syllabus). Use of molecular models will be permitted. Exams 2 and 3 will be comprehensive. Although emphasis will be placed on recent material, knowledge of any topic previously discussed is expected. The final exam is also comprehensive (date and time: TBA). No make up exams will be administered. In the event of a missed exam, the lowest hour exam score will be replaced with the final exam score. For all students, the final exam score will automatically replace the lowest hour exam score, if this is advantageous in the calculation of the course grade (see Grades). 5
Regrades You will have one week from the day a graded homework or exam is returned to request a regrade. Homework regrades should be submitted directly to your TA (not to the instructor). Requests for exam regrades should be given to the TA with a brief note attached explaining the problem. Please note, students submitting an exam for regrade will necessarily submit the entire exam for regrading. Grades Grades will be determined based on the total numeric score. You will be allowed to drop either your lowest hourly exam or half of your final exam, whichever is to your advantage. These two options are delineated below; the more advantageous option will be determined and applied automatically. Option 2* Option 1 Exam 1 Exam 2 Exam 3 Homework Final Best Exam 2nd Best Exam Homework Final 40% Total 100% Total 100% *Option 2 applies automatically in the event of a missed hourly exam. Ways to gain bonus points (up to 30%) (1) In-class quizzes and breakout sessions (https://learningcatalytics.com) (up to ) (see next page) Think-Pair-Solve (2) End-of-semester flash talks and games (more information: TBA) (up to 10%) (Peer evaluated) 6
You MUST register for Learning Catalytics. Registration is FREE: Before the first lecture, register for a student account at Learning Catalytics using access code: USLCSX-TRAIL-POIND-SPINA-TAROT-PULSE Do not pay with a credit card! This is a free trial graciously provided by Pearson Education. If possible, bring a web-enabled device to each lecture, such as a smart phone, ipod Touch, tablet, or laptop. Smaller is better, so you don't need a laptop if you have a smart phone or ipod Touch. 7
Lecture Date 1 W Jan 22/ F Jan 24 2 F Jan 24/ M Jan 27 3 W Jan 29 4 F Jan 31 5 M Feb 3 6 W Feb 5 7 F Feb 7 Due PS 1 Out PS 1 Due PS 2 Out Topics Introduction What is organic chemistry? What is special about carbon? Course mechanics Structure and Bonding What do organic molecules look like? Atomic orbitals, molecules Covalent bonds, Resonance structures The Nature of the Chemical Bond Electronegativity, MO-Theory The Shapes of Organic Molecules Bond lengths, Bond angles, Hybridization Conformational Analysis The shapes of organic molecules Energies, Transition state theory Newman projections Chemical Reactions Homolysis, Heterolysis Arrow-pushing conventions Lewis Acidity/Basicity Nucleophilicity, Electrophilicity Acids and Bases Brönsted Acidity/Basicity, definition of pka Strengths of acids and bases Predicting trends in acidity Introduction to Alkenes Orbital description, Alkene stereoisomers Nomenclature, Cahn-Ingold-Prelog convention Alkene hydrogenation, Catalysis, Alkene stability Reading Suggested Problems (posted on (posted on Piazza and/or in Piazza and/or in class) class) p. 8-13, 1921, 281-286 p. 10-13, 2125, 35-39, 50 p. 97-100 p. 61-62, 132-136, 470-471 p. 41-54 p. 125-132, 183-187, 224 8
Lecture Date Due 8 M Feb 10 *End of Material for Prelim1 PS 2 Due 9 W Feb 12 ** Th Feb 13 Prelim 1 10 F Feb 14 PS 3 Out 11 M Feb 17 W Feb 19 F Feb 21 Lecture M Feb 24 slides 11 Lecture W Feb 26 slides 11 PS 3 Due PS 4 Out Topics Reactivity of Alkenes Addition of HX Mechanism of the addition Carbocations, Markovnikov s Rule Carbocation rearrangements Prelim 1 Review Lecture (please review the exam material before attending this lecture) Malott Hall 228 Bache Aud (7:30-9:00 pm) Alkene Addition Reactions Thermodynamics, Bromination Solvent participation, Hydration, Regiochemistry, Stereochemistry Oxymercuration February Break Further Reactions of Alkenes Hydroboration, Dihydroxylation Ozonolysis Oxidation states Introduction to Stereochemistry Chirality and Enantiomers Configurational stability, Racemates Stereochemistry Diastereomers, Resolutions using diastereomers, Meso compounds Chiral recognition Achieving Enantioselectivity Diastereoselectivity, Enantioselectivity Enantio/diastereospecific, Enantio/diastereotopic rxns Reading Suggested Problems p. 156-158, 162, 168-170 p. 159-166, 175-177 p. 179-183, 900, 902-904 p. 195-205, 210 p. 212, 216 9
Lecture Date Lecture F Feb 28 slides 11 Lecture M Mar 3 slides 12 Lecture W Mar 5 slides 13 Due Topics M Mar 10 Stereochemistry (continue) *End of material for Prelim 2 PS 4 Due W Mar 12 ** Some evening time Th Mar 13 Suggested Problems Stereochemistry (continue) F Mar 7 Special Lecture Reading Prelim 2 Cycloalkanes Ring strain, Conformational Analysis, Cyclohexane (Chair, twist- boat and boat, A- values), Cyclopentane, Other Cycloalkanes, Bicyclic Structure Non-covalent Forces Steric interactions, Hydrogen bonding Solubility, Miscibility Van der Waals interactions Chemistry Technology Session p. 102-113 Nucleophilic Substitution Nucleophilicity, Some chemistry of alcohols Occam s razor, Mechanistic analysis, Kinetics Prelim 2 Review Lecture (please review the exam material before attending this lecture) p. 333, 339 p. 91-92, 95 Baker Laboratory 119 & 135 (7:30-9:00 pm) F Mar 14 PS 5 Out Nucleophilic Substitution MO analysis, Stereochemistry Solvent effects, Competing processes p. 336, 341342 10
Lecture Date Due M Mar 17 W Mar 19 F Mar 21 M Mar 24 W Mar 26 F Mar 28 Mar 29Apr 6 M Apr 7 *End of Material for Prelim 3 Topics Substitution vs. Elimination Mechanistic analysis, Alignment of HX Regioselectivity (Saytzeff s rule), Kinetic isotope effects, Nucleophilicity vs. basicity SN2 vs E2, SN1 vs E1 Chemistry of Alcohols Williamson Ether Synthesis, Epoxide formation Pinacol rearrangement, Conversion of the hydroxyl group into a leaving group Chemistry of Alcohols Nomenclature, Oxidation reactions Synthesis of alcohols and glycols Carbonyl Compounds Oxidation states, Reduction, MO analysis, Hydride reduction, Alkylation, Retrosynthetic analysis Ethers and Epoxides Structure, Cyclic ethers Synthesis of epoxides Reactions of Epoxides Epoxide opening, Grignard/cuprate additions Selectivity issues Reading Suggested Problems p. 333-341, 347-352, 435437 p.178-179, 400-401 p. 83-85, 425427, 900 p. 706-708, 782-787, 809811, 844-847 p. 82-83, 178179 p. 452 Spring Break PS 7 Out Retrosynthesis analysis Epoxide opening, epoxide synthesis, diastereo and enantioselective epoxidation Practice Problems on Learning Catalytics 11
Lecture Date ** Some evening time Tu Apr 8 Due Prelim 3 F Apr 11 M Apr 14 W Apr 16 F Apr 18 F May 2 Reading Suggested Problems Prelim 3 Review Lecture (please review the exam material before attending this lecture) W Apr 9 M Apr 21 W Apr 23 F Apr 25 M Apr 28 W Apr 30 Topics PS 7 Due Malott Hall 228 Bache Aud (7:30-9:00 pm) Spectroscopy Introduction UV-Vis, Mass spectrometry, IR Nuclear Magnetic Resonance (NMR) Spectroscopy Physical basis, NMR spectrometers, Chemical shift Integration, Spin-spin splitting, Second-order splitting, Karplus relationship, Chemical equivalence Continue with spectroscopy (case studies) p. 501-515, 535-536, 1211-1216 p. 553-564, 567, 569-572, 580, 583-586 Integrating Structure and Spectroscopy in Synthetic Organic Chemistry and Retrosynthetic Analysis (More case studies) Central role of Organic Chemistry + Flash Talks in Biology and Medicine Central role of Organic Chemistry + Flash Talks in Materials & Polymers Science End of Semester In-Class Activity & Games Your Favorite Molecule Flashcards Concluding Lecture p. 290-292 12