Syllabus


Course description

Organic chemistry studies the properties of the compounds of carbon, which alone of all the chemical elements can form the numerous, strong, and directional bonds essential to the construction of biomolecules such as fats, carbohydrates, proteins and nucleic acids. This course focuses on gaining an understanding of the fundamental concepts of the science. Important learning goals that the student will wish to achieve are: (1) familiarity with classical and quantum mechanical theories of bonding; (2) the ability to deduce the structures of organic molecules by interpreting spectroscopic data; (3) developing an appreciation for the interplay of an organic molecule’s three-dimensional structure and that molecule’s chemical properties; (4) the ability to apply concepts of physical organic chemistry (e.g., thermodynamics and kinetics) to predict the properties and reactivity of organic compounds. A few reactions (acid–base, radical substitution, addition to carbon–carbon multiple bonds, nucleophilic substitution, elimination) are covered. The relevance of organic chemistry to biological systems, medicine, environmental science and industry is discussed. In the laboratory portion of the course, students gain experience in conducting organic reactions, purifying products, and interpreting and reporting organic chemical phenomena.

Instructors

Lecturer

Bruno I. Rubio, Ph.D.
E-mail birubio@bu.edu
Office hours Sundays, 3pm–4:00pm, Room 613A, Center for Student Services, 100 Bay State Road and by appointment

Laboratory coordinator

Rebecca Loy, Ph.D.
E-mail rnloy@bu.edu

Discussion leaders

TBA

Times & locations

Lecture

TR 5:00 p.m.–6:30 p.m. in STO B50 (CA)

Discussion

Discussions begin the week of M 9 Sep.

T 3:00 p.m.–4:00 p.m. in PRB 150 (C0)

T 4:00 p.m.–5:00 p.m. in PRB 150 (C1)

T 6:30 p.m.–7:30 p.m. in PRB 150 (C2)

W 2:00 p.m.–3:00 p.m. in SOC B63 (C3)

W 3:00 p.m.–4:00 p.m. in SOC B59 (C4)

R 1:00 p.m.–2:00 p.m. in PSY B42 (C5)

R 2:00 p.m.–3:00 p.m. in MCS B21 (C6)

R 3:00 p.m.–4:00 p.m. in SCI 115 (C7)

R 4:00 p.m.–5:00 p.m. in PSY B50 (C8)

R 6:30 p.m.–7:30 p.m. in PSY B33 (C9)

Pre-lab lecture

Pre-lab lectures begin the week of M 2 Sep.

R 1:00 p.m.–2:00 p.m. in KCB 101 (P1)

W 5:00 p.m.–6:00 p.m. in SCI 109 (P2)

F 12:00 p.m.–1:00 p.m. in SCI 109 (P3)

Lab

Labs begin the week of M 9 Sep in SCI 342.

M 12:00 p.m.–3:30 p.m. (F1)

M 5:30 p.m.–9:00 p.m. (F2)

T 1:00 p.m.–4:30 p.m. (F3)

T 5:30 p.m.–9:00 p.m. (F4)

W 1:00 p.m.–4:30 p.m. (F5)

W 6:00 p.m.–9:30 p.m. (F6)

R 1:00 p.m.–4:30 p.m. (F7)

R 5:30 p.m.–9:30 p.m. (F8)

F 1:00 p.m.–4:30 p.m. (F9)

F 5:00 p.m.–8:30 p.m. (G1)

Required materials

Textbook

Brown, William; Foote, Christopher; Iverson, Brent; Anslyn, Eric. Organic Chemistry, 7th B.U. ed. Cengage Learning.

On-line homework module

The Sapling Learning on-line homework module is required. Access instructions can be found at http://www2.saplinglearning.com; create an account under higher education.

Molecular models

Many suitable styles (e.g., space-filling, ball-and-stick, framework) are available.

Scientific calculator

Must display results in scientific notation and exponentiate e (2.71828…) to an arbitrary power.

Lab manual

D.L. Pavia, G.M. Lampman, G.S.Kriz, Jr. and R.G. Engel, Introduction to Organic Laboratory Techniques, A Microscale Approach, 5th B.U. ed. W.B. Saunders, 2014.

Safety glasses

Must have side shields and be approved for lab use. Safety glasses must be worn in the lab at all times!

Lab notebook

Must make carbon-copy pages.

Lab coat

Lab safety dictates a rigorously enforced dress code whose essence is: Don’t show any skin except your face and hands. Wear a lab coat. Be aware that even if you wear a lab coat, open-toe shoes, sandals, shorts and skirts (i.e., any article of clothing that exposes bare skin) are not acceptable lab attire.

Grading policies

Point distribution

CH 203
On-line homework (7%), discussion quizzes (3%), lecture exams (50%), final exam (25%), lab (15%)

CH 205
On-line homework (7%), discussion quizzes (3%), lecture exams (60%), final exam (30%)

On-line homework

Problem sets based on the Sapling Learning module are assigned. You must complete and submit the assignments on-line: no paper transcriptions are accepted. On-line homework is due 6:00 p.m. T 17 Dec.

Discussion quizzes

Three 10-min quizzes are administered in the discussion section during the weeks of 16 Sep, 7 Oct, and 11 Nov. Discussion quizzes are graded on a 10-point basis. No make-up discusion quizzes are given for any reason.

Lecture exams

Three 80-minute exams are administered on T 24 Sep, T 29 Oct, and T 3 Dec during the lecture meeting time. All lecture exams are cumulative.

Lecture exams are graded on a 100-point basis and scaled to a 75-point class median by adding a maximum of 15 points to raw scores. No points are added if the class median is 75 points or higher.

You must take all three lecture exams. No make-up exams are given for any reason: please do not ask to take a make-up exam nor ask to take an exam at other than the scheduled time.

If you miss a lecture exam, the score you earn on the final exam is counted as the score of the exam you missed.

Final exam

A cumulative 2-hour final exam is administered 6:00 p.m.–8:00 p.m. on T 17 Dec. Final exams are graded on a 100-point basis and scaled to a 75-point class median by adding a maximum of 15 points to raw scores. No points are added if the class median is 75 points or higher. See the “Incompletes” section of this syllabus for policies concerning missed final exams.

Lab grades

The laboratory coordinator gives full details concerning lab grades in a separately prepared lab syllabus.

Letter grades

Course grades are calculated by the following formulas:

CH 203
(1.67 * X) + (2.5 *F) + (1.5 * L) + (0.7 * H) + Q

CH 205
(2 * X) + (3 *F) + (0.7 * H) + Q

where X is the sum of the scaled scores of your three lecture exams, F is the scaled score of your final exam, L is your lab score based on 100 points, and H is your on-line homework score based on 100 points, and Q is the sum of the scores of your three discussion quizzes. Grade ranges are:

A ≥ 925

925 > A- ≥ 875

875 > B+ ≥ 850

850 > B ≥ 775

775 > B- ≥ 750

750 > C+ ≥ 675

675 > C ≥ 625

625 > C- ≥ 550

550 > D ≥ 500

500 > F

There are no extra-credit projects to offset poor performance on exams. Please do not ask to have the course grade you earn raised gratuitously because you fail to satisfy the GPA requirements of your program of study, scholarship, etc.

Regrades of exams

You may request that exams be regraded if you suspect errors in grading. The exam in question, accompanied by a note explaining the nature of the grading dispute, must be submitted no later than one week after the exam is returned. This is a firm deadline. Answers in pencil, in ink over pencil, and on the back of exam pages are not regraded.

Other policies

Rules for taking exams

(1) Expect to place all personal belongings (e.g., backpacks, clothing that you will not be wearing) at the front of the room. You may not refer to books or notes of any kind. You may not have any electronic devices (e.g., laptops, iPods, cell phones) in your possession. Silence all telecommunication equipment including the vibrator function. You should bring a functioning stand-alone (i.e., not the calculator built in to your cell phone) scientific calculator to the exam when instructed to do so. You may use molecular models but only if they are contained in a clear plastic bag.

(2) Do not look at anyone else's exam. There is no talking to other students or sharing of any materials such as writing instruments or molecular models. Scratch paper is not allowed.

(3) Do not sit for the exam if you are ill, sneezing or coughing. Do not sit for the exam if you are psychologically unprepared to complete it. Once the exam is distributed, you are officially taking the exam and whatever score you attain stands. Do not consume food or beverages and refrain from asking to go to the restroom. Do not wear hats, caps or other headgear unless you do so for religious reasons.

(4) If you arrive late, you are not given additional time to complete the exam. If you finish the exam early, hand it in and leave the examination hall with the minimum disturbance. Do not congregate in the common area immediately outside the examination hall waiting for your friends.

Academic misconduct

Cases of suspected academic misconduct (e.g., cheating on exams, plagiarism of lab reports) are reported to the Academic Conduct Committee, which investigates and takes appropriate action.

Incompletes

If, for a valid reason that is corroborated by documentation and communicated to the lecturer in advance, you miss the final exam, you will be given an incomplete (I) grade. You must be in good academic standing (i.e., not failing the course) to be considered for an incomplete. You must meet with the lecturer to draw up a schedule for making up a missed final exam. An incomplete grade automatically and permanently changes to a failing grade (F) 12 months after the completion of the course. Incompletes based on your failing to satisfactorily complete the laboratory portion of the course are left to the discretion of the laboratory coordinator.

Withdrawals

The last day to withdraw from the course without a W grade is M 7 Oct; the last day to withdraw from the course with a W grade is F 8 Nov.

Students with disabilities

Students having disabilities and whom the Boston University Office of Disabilities Services approves for special accommodation should present documentation to that effect to the lecturer by T 17 Sep so that acceptable arrangements for taking exams can be made. Students presenting such documentation must take all exams at a special venue arranged by the lecturer.

Lecture topics, reading & homework

To derive the maximum benefit from the lecture do the assigned reading from the text or the on-line version of the lecture notes before class: in this way, you can pay more attention to what is being said in the lecture. The on-line lecture notes are intended to supplement, not replace, the textbook and coming to lecture.

Studying organic chemistry means doing problems. Yes, you must read and memorize, but most of your study time should be devoted to solving problems. Do not peek at the answer until you have given the problem a serious try.

Work the in-chapter problems pertaining to the assigned sections in the text, do as many end-of-chapter problems and problems in the on-line lecture notes as needed to gain mastery of the material. Recall that there are also mandatory on-line homework problem sets to be submitted.

Please keep current with the lecture material: cramming the night before an exam usually fails to produce adequate results because most students cannot effectively absorb the subject matter in a short amount of time. If you are having trouble with the course material, see the lecturer or the discussion leaders for extra help.

Citations in the following list of reading assignments and end-of-chapter problems refer to the 7th edition of Brown, Foote, Iverson, and Anslyn.

Classical & quantum mechanical theories of bonding
Topics Electronic structure of atoms; Lewis structures; polar and nonpolar bonds; dipole moments; hybridization; molecular orbital theory of bonding; resonance; functional groups
Reading 1.1–1.10
Problems 1.20–1.63

Conformational analysis
Topics Constitutional isomerism; condensed and bond-line (line-angle) structures; degrees of unsaturation; angle, torsional and steric strain; Newman projections; conformational analysis of acyclic and cyclic alkanes; cis,trans isomerism in cycloalkanes; homodesmotic reactions
Reading 2.1, 2.2, 2.5, 2.6 (homodesmotic reactions are not covered in the text; refer to lecture notes); 5.1.A
Problems 2.16, 2.17, 2.19–2.23, 2.25, 2.32–2.34, 2.37, 2.39, 2.42, 2.45–2.48, 2.50–2.52; 5.32, 5.33(c), 5.34(d); 13.9

Stereochemistry
Topics Chirality; molecular symmetry; enantiomers and diastereomers; chirality centers; the R,S system; meso compounds; optical activity; resolution of enantiomers system; the E,Z system
Reading 3.1–3.9; 5.2
Problems 3.13, 3.16–3.32, 3.34–3.37; 5.15–5.18, 5.20, 5.23, 5.24, 5.33(b), 5.34(a), 5.35, 5.36; 7.7

Spectroscopy
Topics Proton magnetic energy states; proton chemical shifts; chemically equivalent and non-equivalent protons; spin–spin splitting; coupling constants; integration; structure determination using nuclear magnetic resonance spectroscopy
Reading 13.1–13.10, 13.12
Problems 13.15–13.18, 13.23, 13.24, 13.28

Acids and bases
Topics Definition of protic and Lewis acids and bases; trends in protic acid and base strength; the concept of reaction mechanism; reaction coordinate diagrams
Reading 4.1–4.7
Problems 4.9–4.23, 4.30–4.34, 4.38, 4.41–4.43

Reactions of alkenes
Topics Hydrohalogenation; hydration; halogenation; halohydrin formation; hydroboration–oxidation; osmylation; ozonolysis; hydrogenation
Reading 6.1–6.7
Problems 6.14–6.16, 6.17(a)–(f), 6.18, 6.19(a)-(d), 6.21-6.24, 6.26–6.42, 6.44, 6.45, 6.46 (omit (a)), 6.47, 6.48

Reactions of alkynes
Topics Deprotonation of terminal alkynes; hydration; reduction
Reading 7.4, 7.7–7.9
Problems 7.8 (omit (a))– 7.10, 7.11 (omit (g), (i), (j)), 7.12–7.14, 7.17, 7.21–7.23, 7.30–7.33

Radical reactions
Topics Radical halogenation of alkanes: mecanism, thermodynamics, and stereochemistry; allylic halogenation using N–bromosuccinamide; anti-Markovnikov hydrobromination of alkenes
Reading 8.4–8.8
Problems 8.13–8.29d, 8.30 (omit f), 8.32

Nucleophilic substitution and elimation
Topics SN1 and SN2 reactions; variables in nucleophilic substitution (leaving groups, substrates, nucleophiles); E1 and E2 reactions; competition between substitution and elimination
Reading 9.1–9.10
Problems 9.10–9.14, 9.16–9.46, 9.47 (omit (g), (h))–9.51, 9.55(d)


Posted 3 Sep 2013

This page is maintained by Bruno I. Rubio