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Chemistry 242-002. Organic Chemistry II with Professor Virgil Percec Tue. And Thu. 9:00 AM-10:30 AM. Calendar. Professor Virgil Percec E-mail: Office: Vagelos Labs Room 4003 Office hours: T-Th 10:30 am - 12:30 pm or by appointment. Brad Rosen

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Chemistry 242-002

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Chemistry 242 002

Chemistry 242-002

Organic Chemistry II

with Professor Virgil Percec

Tue. And Thu. 9:00 AM-10:30 AM



Contact and other information

Professor Virgil Percec


Office: Vagelos Labs Room 4003

Office hours: T-Th 10:30 am - 12:30 pm or by appointment

Brad Rosen


Office: Vagelos Labs Room 4080

Office Hours Thu Jan 17th and Tue Jan 24th 10:30 am – 12:30 pm

Contact and Other Information

Class info on Blackboard:

Sign-up for Workshops:

Course policy

Course Policy

  • Text & Other Requirements: (packaged at considerable price savings): Solomons, Organic Chemistry, 9th Edition (John Wiley & Sons); Solomons, Study Guide and Solutions Manual for Solomons 9th Edition (John Wiley & Sons); Hehre, Shusterman & Nelson; Stull, Science on the Internet; John Wiley & Sons Molecular Model Set for Organic Chemistry. Students must read the assigned chapters before and after lectures for complete understanding of the material. Problem solving is an essential part of the course, and you should always try to do the problems before looking up the answers. Always read questions carefully when solving problems, both in the homework and in the tests.

  • Recitations & Workshops: teaching assistants and specific rooms are assigned for recitations and workshops and you are encouraged to take advantage of as many of these sessions as you can.

Some more course policy

Some more Course Policy

  • Exams, Grading & Regrading: there will be four exams and one cumulative final. There are no re-exams and no exams are dropped. However, in case of illness, etc. with an appropriate excuse, given before rather than after the exam, a student may be allowed to miss and reschedule one exam. I expect that A- to A+ will be given for final scores of 80 or 85 to 100% and B- to B+ for final scores of 60 or 70 to 80 or 85%. A very good class is expected to obtain up to 65 or 70% A and B. Regrading must be done within two days from the time the exam is returned. Questions must be directed to the grader in writing. You must not write on your exam in any fashion until after it has been regraded. Mid-Term Exams are scheduled for 5:00 – 7:00 PM in the locations posted above.

  • Drops, Withdrawals, or Incompletes: the deadlines for dropping or withdrawing must be rigorously observed.

  • Final grades: Final exams are scheduled by the Registrar’s office. Students missing a final examination must obtain permission to take the make-up exam the following semester (also scheduled by the registrar’s office) from an advisor in the SAS Dean’s office. The organic faculty has adopted a policy of not posting grades. You must obtain your grade by requesting in writing via email.

Please Direct all Questions Regarding Course Policy to Professor Percec

Lecture 1 conjugated unsaturated systems

Lecture 1: Conjugated Unsaturated Systems

Chapter 13 in Solomons 9/e

What are conjugated unsaturated systems

What Are Conjugated Unsaturated Systems

  • Any system where there is a p-orbital adjacent to a double (or triple) bond

Motivation synthetic target

Motivation: Synthetic Target

  • One often desires to make or study Medicinal Natural Products Containing Conjugated Unsaturated Systems

Motivation unique reactivity

Motivation: Unique Reactivity

Motivation biology

Motivation: Biology

  • Vision

Allylic substitution and the allylic radical

Allylic Substitution and the Allylic Radical

Allylic substitution and the allylic radical1

Allylic Substitution and the Allylic Radical

Why Allyl versus Vinyl or Alkyl Substitution ?

Allylic versus vinylic substitution

Allylic versus Vinylic Substitution

Allylic Proton is easier to homolyze by 96 kJ/mol

Allylic bromination

Allylic Bromination

Note: N-chloro-succinimide and N-iodo-succinimide exist and react in a similar way

Rules of resonance

Rules of Resonance

1) The most important rule of resonance is that resonance structures are not real. They are merely a tool for rationalizing chemical behavior. We will revisit this in terms of the allylic and other conjugated systems.

Rules of resonance1

Rules of Resonance

2) In resonance we move only electrons, not atoms. And when we do it is usually π electrons.

Processes which involve “resonance” of atoms such as keto-enol

tautomerization (Chapter 17) are true chemical equilibria with where each

Isomer truely exists in solution

Rules of resonance2

Rules of Resonance

3) All resonance structures must be true Lewis Structures (Chapter 1.5)

4) Resonance structures must have the same

number of unpaired electrons.

Rules of resonance3

Rules of Resonance

5) Another very important rule is that systems in resonance need to be coplanar.

However 2,3-di-tert-butyl-1,3-

Butadiene is twisted out of plane

and is not in resonance

transoid 1,3 Butadiene coplanar

and in resonance

Rules of resonance4

Rules of resonance

6) For reason which will be explained shortly, the energies of structures in resonance are always lower than those of their prototypical resonance forms.

7) Equivalent resonance structures make equivalent contributions to energies of the resonating compound

8) The more stable the resonance structure

the larger its contribution

Assessing resonance structure stability

Assessing Resonance Structure Stability

  • The more covalent bonds the better the structure.

  • The more complete valance shells the better the structure.

  • The less charge separation the better.

Source of allylic radical stability resonance

Source of Allylic Radical Stability: Resonance

One explanation for the peculiar stability of the Allyl Radical is through implications of resonance.

Allyl cation also stabilized via resonance

Allyl Cation also Stabilized via Resonance ?

Indeed according to suggested stability via resonance , the allyl cation is unusually


Resonance structures are just a tool

Resonance Structures are Just A Tool

  • Keep in mind that resonance structures do not really exist.

  • Resonance Structures allow a chemist to quickly ascertain stabilities and relativities of compounds from their line drawings.

  • More accurate energies and electron distributions require computational chemistry.

Molecular orbital description of ethene

Molecular Orbital Description of Ethene



The molecular orbital mo approach to the allyl system

The Molecular Orbital (MO) Approach to the Allyl System




Polyunsaturated systems nomenclature and classification

Polyunsaturated Systems:Nomenclature and Classification

AKA isolated dienes

Molecular orbital description of 1 3 butadiene

Molecular Orbital Description of 1,3 Butadiene







Conformations of 1 3 butadiene

Conformations of 1,3 Butadiene

Stability of conjugated dienes

Stability of Conjugated Dienes

Conjugative Stability

Uv vis spectroscopy

UV-Vis Spectroscopy

Beer’s Law

A=ε x c x l = log (Io/I)

ε=extinction coefficient/molar absorptivity


l= path length

Uv vis of extended trans systems

UV-VIS of Extended trans π-systems

All π π* transitions

Electrophillic attack on conjugated dienes

Electrophillic Attack on Conjugated Dienes

Expected Markovnikov Product

Mechanism of electrophillic addition to conjugated dienes

Mechanism of Electrophillic Addition to Conjugated Dienes

Comparison of 1 4 addition

Comparison of 1,4 Addition

Kinetic versus thermodynamic control

Kinetic versus Thermodynamic Control

Kinetic Control



Diels alder reaction the basics

Diels-Alder Reaction:The Basics

S-cis diene required,

s-trans does not work

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