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CHEM201: Advanced Organic Chemistry

Unit 2: Stereochemistry and Reaction Mechanisms   Many of these topics will be a review from the first two semesters of organic chemistry.  However, you will look deeper into stereochemistry with topics such as pro-s and pro-r hydrogens, re/si faces of carbonyls, along with the relationship of reacticity and stereochemistry.  This unit will cover sections on reaction mechanisms, including kinetics (the study of chemical reaction rates).           

Unit 2 Time Advisory
This unit should take you approximately 33.5 hours to complete.

☐    Subunit 2.1: 19 hours

☐    Subunit 2.1.1: 4 hours

☐    Subunit 2.1.1.1: 4 hours

☐    Subunit 2.1.2: 3 hours

☐    Subunit 2.1.3: 3.5 hours

☐    Subunit 2.1.4: 3 hours

☐    Subunit 2.1.5: 2.5 hours

☐    Subunit 2.1.6: 3 hours

☐    Subunit 2.1.6.1: 1.5 hours

☐    Subunit 2.1.6.2: 1.5 hours

☐    Subunit 2.2: 14.5 hours

☐    Subunit 2.2.1: 4.5 hours

☐    Subunit 2.2.1.1: 1.5 hours

☐    Subunit 2.2.1.2: 1.5 hours

☐    Subunit 2.2.1.3: 1.5 hours

☐    Subunit 2.2.2: 3 hours

☐    Subunit 2.2.3: 2 hours

☐    Subunit 2.2.4: 3 hours

☐    Subunit 2.2.5: 2 hours

☐    Subunit 2.2.5.1: 1 hour

☐    Subunit 2.2.5.2: 1 hour

Unit2 Learning Outcomes
Upon successful completion of this unit, the student will be able to:

  • Define stereochemistry.
  • Identify enantiomers and diastereomers.
  • Explain the role of optical activity in stereochemistry.
  • Explain how enantiomers can be separated using kinetic resolution.
  • Define prochirality and explain its role in organic reaction.
  • Define reaction mechanism.
  • Show how arrows can be used to explain the mechanism of a reaction.
  • Define and explain the factors that affect a chemical reaction.
  • Explain the mechanism of SN1, SN2, E1, and E2 reactions.
  • Describe reaction mechanisms in terms of variousparameters (i.e.,kinetics, Curtin-Hammet principle, Hammond postulate,etc.).

2.1 Stereochemistry   - Reading: University of California at Los Angeles: Steven Hardiner’s “Organic Chemistry Tutorials: Stereochemistry” Link: University of California at Los Angeles: Steven Hardiner’s “Organic Chemistry Tutorials: Stereochemistry” (PDF)
 
Instructions: Please click on the above link and look up “tutorials” on the left section of the page. Click on “tutorials” and the “Organic Chemistry Tutorials” menu will appear. Scroll down and click on the “Stereochemistry Lecture Chem 30A Fall 2002” pdf file.  You may also want to click the other links under the “Stereochemistry” section and further your reading.
 
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2.1.1 Enantiomers   - Reading: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Enantiomers” Link: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Enantiomers” (HTML)
 
Instructions: Please read the section titled “Enantiomers” to gain a general understanding of enantiomers and how to identify them.  Please take the time to answer the questions at the end of the chapter.
 
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2.1.1.1 Optical Activity   - Reading: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Optical Activity” Link: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Optical Activity” (HTML)
 
Instructions: Please read the section titled “Optical Activity” to gain a general understanding of optical activity and how to measure it.  This section also provides the method to determine optical purity.
 
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2.1.2 Diastereomers   - Reading: UC Davis ChemWiki: “Diastereomers” Link: UC Davis ChemWiki: “Diastereomers” (HTML or PDF)
 
Instructions: Please read this section beginning with the title “Section 3.7: Diastereomers” to gain a general understanding of the difference between enantiomers and diastereoisomers.  You can access a PDF version by clicking the “Make PDF” button near the top of the page.

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2.1.3 Kinetic Resolution   - Reading: Chem Europe: “Kinetic Resolution” Link: Chem Europe: “Kinetic Resolution” (HTML)
 
Instructions: Please read this section beginning with the title “Kinetic Resolution” to gain a general understanding the techniques available to resolve enantiomers.

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2.1.4 Pro-S and Pro-R Hydrogens   - Reading: UC Davis ChemWiki: “Prochirality” Link: UC Davis ChemWiki: Prochirality (HTML or PDF)
 
Instructions: Please read this section beginning with the title “Section 3.10: Prochirality” to learn how to recognize prochiral hydrogens.  Please make sure you note the difference in properties between an enantiomeric hydrogen and a diastereomeric hydrogen.  You can access a PDF version by clicking the “Make PDF” button near the top of the page.

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2.1.5 Re/Si Faces   - Reading: ABitAbout: “Cahn–Ingold–Prelog Priority Rules” The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

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2.1.6 Conformational Analysis   2.1.6.1 Newman Projections and Free Energy Diagrams   - Reading: Michigan State University: Brian Modders and Abby Parrill’s “Organic Chemistry: The Conformation of Ethane” Link: Michigan State University: Brian Modders and Abby Parrill’s “Organic Chemistry: The Conformation of Ethane” (HTML and QuickTime)
 
Instructions: Please read the section titled “The Conformation of Ethane.”  In this section, ethane is used as an example to explain how to drawn Newman Projections and to determine the energy associated with each projection.
 
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2.1.6.2 Hyperconjugation   - Reading: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: What Is Hyperconjugation?” Link: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: What Is Hyperconjugation?” (HTML)
 
Instructions: Please read the section titled “What Is Hyperconjugation?” to gain a general understanding of what hyperconjugation is with respect to alcohols and alkyl halides.
 
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  • Assessment: The Saylor Foundation’s “Stereochemistry in Action” Link: The Saylor Foundation’s “Stereochemistry in Action” (PDF)
     
    Instructions: Please complete the entire assessment.  You can check your answers against the Answer Key (PDF).

2.2 Reaction Mechanisms   - Reading: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Reaction Mechanisms” Link: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Reaction Mechanisms” (HTML)
 
Instructions: Read the entire webpage linked here on the “Reaction Mechanisms” chapter.  You may also want to click the hyperlinks in the online text to review some of the terms and further your reading.
 
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2.2.1 Kinetics   2.2.1.1 Rate Laws   - Reading: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Reaction Rates and Kinetics” Link: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Reaction Rates and Kinetics” (HTML)
 
Instructions: Please read the section titled “Reaction Rates and Kinetics” to learn how to calculate the rate of zero, first, and second order reactions.
 
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2.2.1.2 Rate Determining Step   - Reading: UC Davis ChemWiki: “Rate Determining Step” Link: UC Davis ChemWiki: “Rate Determining Step” (HTML or PDF)
 
Instructions: Please read this section beginning with the title “Rate Determining Step” togain a general understanding of the rate determining step in a multi-step chemical reaction.  You can access a PDF version by clicking the “Make PDF” button near the top of the page.

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2.2.1.3 Steady-State Approximation   - Reading: University of Waterloo: Chung Chieh’s “Organic Chemistry: Steady-State Approximation” Link: University of Waterloo: Chung Chieh’s “Organic Chemistry: Steady-State Approximation” (HTML)
 
Instructions: Please read this section beginning with the title “Deriving Rate Laws Using the Steady-State Approximation—Part II”  to gain a general understanding on how to calculate rate laws using the steady-state approximation.

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2.2.2 Hammond Postulate   - Reading: Chem Europe: “Hammond’s Postulate” Link: Chem Europe: “Hammond’s Postulate” (HTML)
 
Instructions: Please read the section titled “Hammond’s Postulate” to gain a general understanding of the postulate and how to apply it in kinetics.

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2.2.3 Curtin-Hammett Principle   - Reading: Chem Europe: “Curtin-Hammett Principle” Link: Chem Europe: “Curtin-Hammett Principle” (HTML)
 
Instructions: Please read this section titled “Curtin-Hammett Principle” to gain a general understanding of the principle and how to apply it in stereoselective reactions.

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2.2.4 Factors That Influence the Rate of a Reaction   - Reading: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: Factors That Influence Reactions Link: Michigan State University: Professor William Reusch’s Virtual Textbook of Organic Chemistry: Factors That Influence Reactions (HTML)
 
Instructions: Please read the section titled “Reaction Variable” (you may need to scroll up to find the title) to gain a general understanding of factors that will affect the outcome of organic chemical reactions.
 
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  • Assessment: The Saylor Foundation’s “Exploring Reaction Mechanisms” Link: The Saylor Foundation’s “Exploring Reaction Mechanisms” (PDF)
     
    Instructions: Please complete the entire assessment.  You can check your answers with the answer key provided here. (PDF)

2.2.5 Reactions of Alkyl Halides   - Reading: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Substitution and Elimination” Link: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Substitution and Elimination” (HTML)
 
Instructions: Read the entire webpage linked here on the “Substitution and Elimination” chapter.  You may also want to click the hyperlinks in the online text to review some of the terms and further your reading.
 
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2.2.5.1 SN1 and SN2 Mechanisms   - Reading: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Substitution Reaction Mechanisms” Link: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Subtitution Reaction Mechanisms” (HTML)
 
Instructions: Please read the section titled “Mechanisms of Nucleophilic Substitution Reactions” to gain a general understanding of the mechanism behind nucleophilic substitution reactions.  You may also want to click the hyperlinks in the online text to review some of the terms and further your reading.  Although you have covered both SN1 and SN2 mechanisms,we find that these mechanisms are not as definite as we learned before.  Many times a reaction has characteristics for both SN1 and SN2 reactions.  Remember to also pay attention to the solvent effects in the mechanisms.
 
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2.2.5.2 E1 and E2 Mechanisms   - Reading: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Elimination Reactions” Link: Michigan State University: Professor William Reusch’s “Virtual Textbook of Organic Chemistry: Elimination Reactions” (HTML)
 
Instructions: Please read the section titled “Elimination Reactions of Alkyl Halides” to gain a general understanding of the mechanism behind the elimination reactions for alkenes.  Just as with SN1 and SN2 mechanisms, we will go deeper into the mechanisms of E1 and E2.  Please pay close attention to the regiochemistry involved in the E2 mechanism. 
 
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  • Assessment: The Saylor Foundation’s “Substitutions and Eliminations” Link: The Saylor Foundation’s “Substitutions and Eliminations” (PDF)
     
    Instructions: Please complete the entire assessment.  You can check your answers with the answer key provided here. (PDF)