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Advanced Organic Chemistry

Purpose of Course  showclose

Remember that organic chemistry is the discipline that studies the properties and reactions of organic, carbon-based compounds.  This course is intended to be taken after the first two semesters of organic chemistry.  Many of the topics within this outline have been covered in the first two semesters of organic chemistry; however, this course will explore these topics in much greater depth.  It is important to make sure that you have a good grasp of the concepts from earlier organic chemistry courses before moving on to this course.

We begin by studying a unit on ylides, benzyne, and free radicals.  Many free radicals affect life processes.  For example, oxygen-derived radicals may be overproduced in cells, such as white blood cells that try to defend against infection in a living organism.  In the first unit, you will learn about free radicals, including oxygen-containing compounds.  Afterward we move into a comprehensive examination of stereochemistry, as well as the kinetics of substitution and elimination reactions.  After learning the information in that unit, you will be able to describe reaction mechanisms.  The course wraps up with a final unit, which is a survey of various hetereocyclic structures, including their MO theory, aromaticity, and reactivity.

Course Information  showclose

Welcome to CHEM 201.  Below, please find general information on this course and its requirements.  

Course Designer: Rachel Lerebours

Primary Resources: This course is composed of a range of free online materials.  However, the course primarily makes use of the following materials:

Requirements for Completion: In order to complete this course, you will need to work through each unit and all of its assigned materials.  You will also need to complete the Final Exam.  In order to “pass” this course, you will need to earn a 70% or higher on the FinalExam.  Your score on the exam will be tabulated as soon as you complete it.  If you do not pass the exam, you may take it again.

Time Commitment: This course should take you a total of 60 hours to complete. Each unit includes a “time advisory” that lists the amount of time you are expected to spend on each subunit.  These should help you plan your time accordingly.  Please look at the time advisories prior to starting the course to determine how much time you have over the next few weeks to complete eachunit.

Tips/Suggestions: This is a very difficult course, so allow time to “digest” the material. When needed, review relevant information from the prerequisite courses.  Take plenty of notes and review daily.



Learning Outcomes  showclose

Upon successful completion of this course, you will be able to:
  • Describe free radicals in terms of stability, kinetics, and bond dissociation energies.
  • Describe the stereochemistry and orbitals involved in photochemical reactions.
  • Describe enantiomers, diastereomers, pro-S and pro-R hydrogens, and Re/Si faces of carbonyls. 
  • Perform conformational analysis of alkanes and cyclohexanes.
  • Describe reaction mechanisms in terms of variousparameters (i.e.,kinetics, Curtin-Hammet principle, Hammond postulate,etc.).
  • Describe the chemistry of the heterocycles listed in Unit 3in terms of molecular orbital theory, aromaticity, and reactions. 

Course Requirements  showclose

In order to take this course, you must:
 
√    Have access to a computer.

√    Have a basic understanding of computers.

√    Have continuous broadband Internet access.

√    Have the ability/permission to install plug-ins or software (e.g., Adobe Reader or Flash).

√    Have the ability to download and save files and documents to a computer.

√   Have the ability to open Microsoft files and documents (.doc, .ppt, .xls, etc.).

√    Be competent in the English language.

√    Have read the Saylor Student Handbook.

√    Have completed the following courses: CHEM101: General Chemistry I, CHEM102: General Chemistry II, CHEM103: Organic Chemistry I, CHEM104: Organic Chemistry II

Unit Outline show close


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  • Unit 1: Reactive Reaction Intermediates  

    A reaction intermediate is a short-lived compound that is generated in a chemical reaction.  These intermediates are very important because their isolation, though difficult, can provide very important insight into the mechanism of the reaction.  When the intermediate cannot be isolated, evidence of its existence can be seen through spectroscopic methods. 
               
    In this unit,we study the chemistry behind some of the important reaction intermediates. We will first discuss ylides, their preparation, and reactions.  We will then study benzynes, and finally we will discuss free radicals.

    Unit 1 Time Advisory   show close
    Unit 1 Learning Outcomes   show close
  • 1.1 Ylides  
    • Reading: Metropolitan State College of Denver: Professor Milton Weider’s “Advanced Organic Chemistry: Ylides”

      Link: Metropolitan State College of Denver: Professor Milton Weider’s “Advanced Organic Chemistry: Ylides” (PowerPoint)
       
      Instructions: Click on the file named “Ylides.ppt” to view the file titled “Ylides.”  This presentation will provide a general overview of ylides and how to prepare them (Section 1.1.1). In this presentation, reaction of ylides will also be discussed. This section also provides method and preparation of nitrogen and sulfur ylides (Sections 1.1.2 and 1.1.3).
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.1.1 Preparation of Ylides and Wittig Reaction  

    Note: This subunit is covered by the reading assigned beneath subunit 1.1.  Focus specifically on slides 1–5 as they focus on the preparation of ylides and the Wittig reaction.

  • 1.1.2 Sulfur Ylides  

    Note: This subunit is covered by the reading assigned beneath subunit 1.1.  Focus specifically on slides 7–8 as they focus on the preparation of sulfur ylides.

  • 1.1.3 Nitrogen Ylides  

    Note: This subunit is covered by the reading assigned beneath subunit 1.1.  Focus specifically on slide 6 as it focuses on the preparation and reactions of nitrogen ylides.

  • 1.2 Benzynes  
    • Reading: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Benzyne”

      Link: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Benzyne” (HTML)
       
      Instructions: Please read the section titled “Benzyne” to gain a general understanding of benzyne.  This section provides an explanation of the geometry of benzyne, which is the main reason for its high reactivity.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.2.1 Preparation of Benzynes  
    • Reading: Metropolitan State College of Denver: Professor Milton Weider’s “Advanced Organic Chemistry: Benzynes”

      Link: Metropolitan State College of Denver: Professor Milton Weider’s “Advanced Organic Chemistry: Benzynes” (PowerPoint)
       
      Instructions: Click on the file named “Benzynes.ppt” to view the file titled “Benzynes.”  This presentation will provide a general overview of benzynes and how to prepare them. In this presentation, reaction of benzynes will also be briefly discussed.  For a more detailed presentation of the reactions of benzynes, please refer to the links in section 1.2.2.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 1.2.2 Reactions of Benzynes  
  • 1.2.2.1 Nucleophilic Reactions  
  • 1.2.2.2 Cycloadditions  
  • 1.3 Free Radicals  

    A radical is an unpaired electron that arises from homolytical cleavage of a chemical bond.  Free radicals are extremely important for many reactions and life processes, such as the function of our immune systems.  When your body is attacked by foreign invaders, your immune system recognizes this through free radicals, and therefore, it is able to defend against the attack.  The introduction to this course mentions how white blood cells, which overproduce oxygen-based free radicals, defend against infection.
     
    Note: Free radicals are an example of homolytic bond cleavage, as you learned in your previous organic chemistry course.  Here, we go into more detail about radicals, their bond dissociation energies, and the mechanisms of radicals.   

  • 1.3.1 Stability of Radicals  
  • 1.3.2 Free Radical Initiators  
  • 1.3.2.1 Oxygen Containing Compounds  

    Note: This subunit is covered by the reading assigned beneath subunit 1.3.2.  Focus specifically on slide 9 as it focuses on the initiation of oxygen containing compounds.

  • 1.3.2.2 Decomposition of Azo Compounds  

    Note: This subunit is covered by the reading assigned beneath subunit 1.3.2.  Focus specifically on slide 10 as it focuses on the decomposition of nitrogen containing compounds.

  • 1.3.3 Reactions of Radicals  

    Note: The reaction section of this unit covers all of the common reactions, such as oxidation, addition, rearrangements, and substitution reactions commonly found to involve radicals. This subunit is covered by the reading assigned beneath subunit 1.3Please scroll down to the section titled “Reactions of Free Radicals” to gain a general understanding of the reactions of free radicals. 

  • 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   show close
    Unit 2 Learning Outcomes   show close
  • 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.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 2.1.1 Enantiomers  
  • 2.1.1.1 Optical Activity  
  • 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.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 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.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 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.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 2.1.5 Re/Si Faces  
    • Reading: ABitAbout: “Cahn–Ingold–Prelog Priority Rules”

      Link: ABitAbout: “Cahn-Ingold-Prelog Priority Rules” (HTML)
       
      Instructions: Please read this section beginning with the title “Cahn-Ingold-Prelog Priority Rules” to learn the rules behind naming molecules with stereochemistry.  This section provides a series of rules to distinguish between prochical hydrogens and the faces of prochiral molecules.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

      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.

      Submit Materials

  • 2.1.6 Conformational Analysis  
  • 2.1.6.1 Newman Projections and Free Energy Diagrams  
  • 2.1.6.2 Hyperconjugation  
  • 2.2 Reaction Mechanisms  
  • 2.2.1 Kinetics  
  • 2.2.1.1 Rate Laws  
  • 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.

      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 2.2.1.3 Steady-State Approximation  
  • 2.2.2 Hammond Postulate  
  • 2.2.3 Curtin-Hammett Principle  
  • 2.2.4 Factors That Influence the Rate of a Reaction  
  • 2.2.5 Reactions of Alkyl Halides  
  • 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.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 2.2.5.2 E1 and E2 Mechanisms  
  • Unit 3: Organometallics and Heterocycles  

    Remember that organometallics is the study of metals bonded to nonmetals, and there is an overlap of studying organometallics in both organic and inorganic chemistry.  In your previous organic chemistry courses, you have seen organometallic reagents in the form of Grignards, metal hydrides, and so forth.  Here, we will discuss organometallics more in depth, more specifically as carbon nucleophiles.  We will then examine the classes of organic heterocyclic compounds, which are compounds that contain at least two different elements as ring-member atoms. 

    Unit 3 Time Advisory   show close
    Unit 3 Learning Outcomes   show close
  • 3.1 Organometallics  
    • Reading: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Organometallic Compounds”

      Link: University of Calgary: Professor Ian Hunt’s “Organic Chemistry: Organometallic Compounds” (HTML)
       
      Instructions: Please read the section titled “Organometallic Compounds” to gain a general understanding of this very complex class of compounds.  Please also click on the links on the page to gain a more in-depth understanding of this class of compounds.  The links will also provide rules for nomenclature, the general structure and reactivity of this class of compounds.
       
      Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • 3.1.1 Organometallics as Carbon Nucleophiles  
  • 3.1.1.1 Addition to Carbonyls  
  • 3.1.1.2 Conjugate Addition  
  • 3.2 Classes of Organic Heterocyclic Compounds  
  • 3.2.1 Pyridine  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of pyridines are presented.

  • 3.2.2 Quinoline  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of quinolines are presented.

  • 3.2.3 Isoquinoline  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of isoquinolines are presented.

  • 3.2.4 Pyrroles  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of pyrroles are presented.

  • 3.2.5 Azoles  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of azoles are presented.

  • 3.2.6 Furan  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of furans are presented.

  • 3.2.7 Thiophene  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of thiophenes are presented.

  • 3.2.8 Pyridazine  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of pyridazines are presented.

  • 3.2.9 Pyrimidine  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of pyrimidines are presented.

  • 3.2.10 Pyrazine  

    Note: This subunit is covered by the reading assigned beneath subunit 3.2.  Nomenclature and preparation of pyrazines are presented.

  • Final Exam  

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