Chemistry 030.205.

01 – Introductory Organic Chemistry I

Section 1, Fall 2015

Instructor: Professor J. D. Tovar (email: tovar@jhu.edu)

Lead TA: Reid Messersmith (email: rmesser2@jhu.edu)

Lectures: M/W/F 9:00 – 9:50 am in Mudd Hall 26

Discussion section: Th 9:00 – 10:20 am in TBA

Office Hours: JDT: M/T 12:30-2 pm in NCB 316

TAs: TBA

This course is an introduction to the chemistry of carbon-containing compounds. You

experience and/or produce these compounds continuously, so it is important to understand their
properties and reactivities.

We will develop conceptual frameworks to understand the electronic properties of organic

compounds, the structures they adopt, and how the two converge to explain reactivity. I will put
many of these topics in historical context, to reveal the humanity of organic chemistry.

It is important to read the text, follow the lectures and consult outside sources. You will often
find significant deviations from my lectures and the texts (both in choice and depth of topics).
You may find that another textbook is more in resonance with your own learning style.

Prerequisites: I will assume familiarity with introductory chemistry (030.101/102 or the

equivalent). It will be to your advantage to review the material presented in Chapters 1 and 2
immediately and concurrently with the first week of lectures.

“Required” Text: Bruice, Organic Chemistry (7th)

“A” textbook is required, but it need not be Bruice’s. I will reference subject topics and assign
problems relative to this text, so you should at least have access to a copy. Reserve copies will
be placed in the library for your reference, but I cannot guarantee their availability.

Grading: Three midterm exams (3 x 100 points): Thursdays 10/1, 10/22 and 11/12
Final Examination (200 points): DECEMBER 15 (2 pm – 5 pm)
Discussion section attendance (42 points)

While the three midterm exams will focus on material covered since the last one, all exams
should be considered cumulative. Concepts introduced in the beginning will be used throughout.

You will be credited with 6 points for each attendance at your assigned section (not counting
exams), up to 42 points. This allows two absences. No make-up, alternative arrangements, etc.

Recommended end-of-chapter problems will be assigned periodically. Some of these may be

discussed in the Thursday sections, but they will not be graded.

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General policies and comments

Lectures. Lectures are MWF in Mudd 26. You should attend, pay attention, and take notes.
Read relevant material BEFORE lecture, and again AFTER.

Do not use electronic devices during lecture unless you have a specific learning-related reason
for doing so. Keep up with Facebook, Twitter, email and your other classes on your own time.
It is inconsiderate to me and more importantly, to classmates sitting next to you. Much of what
we cover in organic chemistry is graphical in nature, and it will be in your best interest to do as
much freehand note taking as possible rather than try to use a computer to draw structures. Note
takers are available for those with disabilities that might interfere with this process.

Discussion sections and exams. Discussion sections are held on Thursdays with your TAs.
You must attend your assigned section at all times: attendance will be recorded.

Problems will be assigned periodically and subject to discussions in your section. Copies of the
chapter problems are posted on the MSEL e-reserves (https://ares.library.jhu.edu/shib/)

Midterm exams are held during the Thursday discussion sections. You must show up for the
section to which you are assigned. You may be asked to present a JHU ID card before and/or
after an exam. TAs will only distribute exams to test-takers formally assigned to their sections
unless prior arrangements have been made with me. It is your responsibility to know which
section you are assigned to and where this section reports for meeting.

Exams will be taken with closed notes and closed books. No cheat sheets. You may bring an
unassembled molecular model set provided that it is free from any writing or inscriptions. All
non-medical electronic devices must be turned off, and they must be surrendered to your TA
should you need to leave the exam room for any reason. Chemistry affiliates around the testing
areas will inform me of anyone found violating this.

Make up exams. I do not offer them. If you can document a University-sanctioned absence for
one midterm, the AVERAGE of the other two midterms will be used (WITHOUT
WEIGHTING). Should you document University-sanctioned absences for two midterms, the
RAW SCORE of the third exam will be credited in their place (WITHOUT WEIGHTING).
Should you miss all three midterms due to University-sanctioned absences, the RAW
PERCENTAGE of the final exam will be used for all exams (WITHOUT WEIGHTING). You
must take the final exam to pass the course. The date and time are scheduled by the University
and are not subject to change. It is your responsibility to resolve any other University-sanctioned
conflicts directly.

A University-sanctioned absence is one approved by and reported to me directly by the Dean of

Student Life. You must initiate the process to secure University approval of an absence
BEFORE the scheduled exam. Health-related absences must be cleared through the Student
Health and Wellness Center or other non-relative medical professionals.

No credit will be granted for unexcused absences, such as oversleeping, attending the wrong
section, forgetting, etc. In special circumstances, documented but otherwise unsanctioned
absences may be excused but only with prior authorization from the instructor.

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Cheating. You are expected to abide by the ethical guidelines that have contributed to the
academic strengths of Johns Hopkins University. All incidents of academic misconduct will be
reported to the appropriate authorities and pursued to the best of my abilities. By default, any
observed academic dishonesty or misconduct during or after the completion of any exam will
result in the score for that exam being dropped to ZERO. I reserve the right to personally grade
future exams of any student caught cheating on a prior exam, or to administer oral examinations
in lieu of written ones for serious offenders. A CHEATER WILL NOT PASS THIS COURSE.

What constitutes cheating: the use of any unauthorized aids during an exam (calculator, phone,
tablet, laptop, any notes), forgery/falsification/lying on any part of an exam, copying from
someone else’s exam or willfully allowing your own exam to be copied, otherwise facilitating or
engaging in academic dishonesty, etc. This is not an all-inclusive list.

The university reserves the right to punish cheaters with failure in the course, permanent
transcript notation, suspension or expulsion. Offenses may be reported to medical, law, or other
professional and graduate schools that a cheater applies to. I as a professor am considered a legal
extension of the University, and I will personally ensure such notifications are made should the
University elect not to do so.

Office hours and appointments. The TAs and I will hold office hours throughout the semester
as an opportunity to address questions about course content. Should these not be sufficient to
address your content questions, you should arrange to meet privately with your assigned TA.
Should this not be sufficient to address your content questions, your TA will suggest an
appointment with me and will notify me as such. I cannot make individual appointments to go
over content-related issues until your TA has the chance to address your questions first. Your
TAs are very busy outside of this course and are NOT to be considered personal tutors. They
can however recommend private tutors or other JHU resources should you need more
personalized attention.

Confidential concerns not about course content should be discussed by appointment with your
TA or with me. Questions about exam preparation or how to better master the material are
usually best figured out on your own, and I will direct you to study the textbook and lecture
notes and do practice problems. Everyone has their own unique way to learn, and strategies that
work for me very likely will not work for all of you. This is why your TAs are great resources:
they took this course much more recently than I did!

Announcements. All course–related communications will be sent to email addresses provided to

me by the registrar. It is your responsibility to ensure that their information is accurate. I am not
obligated to email or otherwise re-broadcast any verbal announcements made in class.

Email and etiquette. I receive dozens/hundreds of emails every day, so your TA is the best
resource for day-to-day administrative or topical questions. I will only respond to course-related
emails of a personal or confidential nature if they originate from your JHU account. I will not
provide lengthy responses to emailed questions about the subject matter. The more difficult the
question, the more effective talking to the TA or me directly in office hours will be. I will not
respond to emails that do not conform to standard professional English. Start the subject line
with 030.205.

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Regrade policy

The teaching assistants will uphold a reasonable standard for exam grading that will be executed
consistently. However, people do make mistakes. If you feel your exam was scored in error,
you have the following recourses that must be pursued within 24 hours after the distribution of
graded exams.

(1) Report mathematical errors in tabulating exam scores to your TA immediately. You must
surrender your exam to your TA.

(2) If you feel that you deserve more credit for an answer, submit directly to me one and only
one hard-copy one-paragraph justification no longer than 300 words per each challenged
question along with your graded exam. Note that multiple subsections within a particular
question still count as one question and therefore are allowed only one paragraph in total. Each
paragraph must state the question under dispute and the specific grievance. You are strongly
advised to pursue this recourse only if you are asking for full credit for a question or for a
particular subsection(s). Regrade requests not adhering to this format will be refused.

(3) If you feel that a classmate was given a higher score than you for what appears to be the same
answer, submit directly to me a description of the discrepancy described as in (2) along with
your exam AND your classmate’s exam. Your peer must give written consent.

At your initiation for recourses (2) and (3) above, I will carefully consider your arguments and
determine if they justify a revised score. I reserve the right to regrade the entire exam under
stricter criteria for partial credit that will override the standards used during the initial grading. I
may determine that your argument was valid and award you more credit. However, I may also
deduct points elsewhere on questions that you did not challenge. After a regrade, it is possible
that you will receive a LOWER score, even if I agreed with your point of contention.
Similarly, if you pursue recourse (3) above, it is possible that your peer’s exam will be reduced
in score if I deem something was overlooked during the initial grading. Regardless, the grade I
assign will stand as final. Under no circumstances may the results of a regrade serve as a basis
for you or your peers to articulate other challenges.

Should you be caught cheating, I will personally manage the future grading of your exams.
Grades I assign in these cases are final and not subject to regrading except for math errors.

On the exams, you will be asked to sign the following statement:

“My signature hereby affirms that I honestly completed this exam to the best of my innate
abilities without the use of unauthorized aids. I furthermore accept the grading procedures in
place for this course.”

If your exam is not signed, you will be given a ZERO.

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If you intend to initiate a discussion about an exam or final grade with the TA or with me, a
selection of introductory phrases that have proven ineffective are as follows:

“ I understood the question, but … ”

“ I misinterpreted the question … ”
“ My performance does not reflect my understanding … ”
“ I ran out of time, but my unfinished answer was on the right path … ”
“ I wrote the right answer but then crossed it out … ”
“ I was tired on the day of the exam … ”
“ I had [an athletic/cultural/sorority/fraternity event, work] the night before/during the term … ”
“ There was a [birth, death, wedding, other major life event] in the family during the term … ”
“ I need [a certain grade] to [graduate, maintain a scholarship, participate in athletics, stay
enrolled at JHU, re-take the course, stay in parent’s favor, stay in advisor’s favor, etc.] … ”

I value each of my students as the interesting individuals that they are, and I take genuine interest
in seeing everyone develop a solid grasp of the course material. If you finish the semester with a
firm understanding of the concepts and material presented in this course, you will have
succeeded regardless of what your final grade may be or what circumstances led to your grade.

There are several mechanisms for you to avoid the conversation openers above.

STUDY THE MATERIAL IN ADVANCE, and WORK THROUGH PROBLEMS!

ATTEND OFFICE HOURS, and ASK QUESTIONS!

Just reading and understanding the material (passive understanding) is insufficient; you should
be able to use the just learned concepts in situations not previously encountered, and make
logical connections with concepts learned previously (active understanding). You should
constantly probe your understanding by asking (and answering) the question "why?" in relation
to all statements and logical constructions.

Form a study group with a few classmates.

Ad-hoc review sessions may be held, led by me and/or by the TAs.

Pilot Groups. Join a PILOT group (a peer facilitated problem solving group). PILOT LINK:
http://academicsupport.jhu.edu/pilot-learning/registration/

Small Group Tutoring. The Learning Den is in Gilman Hall. Sign up online at
http://tutoring.jhu.edu (Your User ID and password is your 6-character Hopkins ID (not JHED
ID); the two fields are identical)
Sundays - Thursdays, 6 pm - 10 pm. Visit the web site for more information:
http://jhu.edu/academic-assistance/tutoring.html.
410-516-8216, tutoring@jhu.edu

Study Consulting. 385 Garland Hall Suite 3A

http://jhu.edu/academic-assistance/studyconsulting.html
410-516-5506, fday2@jhu.edu

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Topics to be covered
1. Structure, Bonding & Molecular Properties (5 lectures*)
·  Structure of atoms, atomic orbitals
·  Chemical Bonding (ionic bonds, covalent bonds)
·  Valence-bond theory (hybridization)
·  Molecular Orbital (MO) theory (HOMO and LUMO)
·  Resonance
·  Electronegativity, dipole moments
·  Acids and bases
Sections covered: 1.1 - 1.16; 2.1-2.12
Suggested problems: 1.46-1.73, 2.47-2.70

2. Alkanes (3 lectures *)
·  Alkanes as building blocks (constitutional isomers)
·  Functional groups
·  Nomenclature
·  Conformational analysis of alkanes and cycloalkanes (strain)
Sections covered: 3.1-3.15
Suggested problems: 3.52-3.58, 3.61-3.63, 3.65- 3.76, 3.78-3.79, 3.82-3.86

3. Stereochemistry (3 lectures*)
·  Optical activity – enantiomers (asymmetric centers)
·  Diastereomers, meso compounds,
·  R, S Nomenclature, absolute configuration
·  Fischer projections
·  Chiral molecules without asymmetric centers
Sections covered: 4.1-4.16
Suggested problems: 4.53-4.67, 4.69-4.87

4. Alkenes, Overview of Organic Reaction Mechanisms, Addition of HX (3 lectures*)

·  Cis-trans (E, Z) isomerism and degrees of unsaturation, nomenclature, structure
·  Nucleophilic substitution on methyl halides, Radical chlorination of methane, Addition of HBr
to ethylene
·  Thermodynamics, kinetics, energy diagrams , transition states, rate-determining step
·  Writing reaction mechanisms
·  Hammond postulate
Sections covered: 5.1-5.12
Suggested problems: 5.37-5.39, 5.41, 5.42, 5.44-5.50, 5.52-5.58

5. Electrophilic Addition to π  Bonds (5 lectures*)

·  Hyperconjugation and regioselectivity (Markovnikov’s rule)
·  Addition of X2 and HX to p  bonds in alkenes, alkynes and dienes
·  Carbocations and their rearrangements
·  Preparation (mechanistic details are covered under section 9)
·  Addition of halogens and water
·  Hydration of the double bond
·  Epoxide formation

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·  Catalytic Hydrogenation
Sections covered: 6.1-6.18
Suggested problems: 6.59-6.95, 6.98-6.107

6. The Reactions of Alkynes; Organic Synthesis (2 lectures*)

·  Structure and Nomenclature
·  Reactions of alkynes: addition of hydrogen halides, halogens, hydrogen
·  Hydroboration-oxidation and acid ion catalyzed addition of water
·  The acidity of terminal alkynes, acetylide ions, and synthesis of organic molecules
Sections covered: 7.1-7.12
Suggested problems: 7.27-7.37, 7.40-7.57

7. Conjugated Dienes and Aromaticity, (4 lectures*)

·  Delocalization of Electrons (Resonance Structures)
·  Benzene and Hückel’s Rule
·  Aromaticity and Antiaromaticity
·  Electrophilic additions of dienes
·  Kinetic vs. thermodynamic control
·  UV and visible spectroscopy, conjugation, and the chemistry of vision
·  Diels-Alder Reaction
Sections covered: 8.1-8.21
Suggested problems: 8.57-8.108

8. Structure Determination (6 lectures*)

·  Mass Spectrometry
·  UV spectroscopy (review)
·  Infrared Spectroscopy
·  Nuclear Magnetic Resonance Spectroscopy (1H, 13C)
Sections covered: 14.1-14.22; 15.1-14.24
Suggested problems: 14.44-14.73, 15.46-15.78

9. Nucleophilic Substitutions and Eliminations (5 lectures*)

·  SN1 and SN2
·  E1 and E2; E1cb
·  Effects of solvent, substrate structure, and nucleophile (base) on reactivity
Sections covered: 9.1-9.9, 10.1-10.10, 11.1-11.12 (as time allows)
Suggested problems: 9.35-9.68; 10.35-10.63

10. Alcohols, Ethers, Epoxides, and Amines (As time allows)

·  Substitution reactions of alkanes
·  Radical Halogenation: Reactivity-Selectivity Principle
·  Radical addition to alkenes
·  Allylic bromination
Sections covered: 11.1-11.4, 11.6, 11.9, 11.11
Suggested problems: 11.48-11.70, 11.72, 11.76-11.78, 11.82, 11.84, 11.89

*The number of lectures and the order within each main topic are approximate; adjustments may
be made as necessary. All in-chapter problems should be worked out.