In addition to the specific and more detailed goals listed for each topic we study, we have overall goals, things that we want to take away with us from the course. The individual study topics and goals are simply a means to the more general end. We want to:

• Understand what organic chemistry is, and how it impacts scientific enterprises from the manufacture of bulk chemicals like gasoline and paper to the interpretation of enzyme structure and behavior;

• Understand the connection between molecular structure and chemical reactivity;

• Learn to think more clearly and logically;

• Improve our problem solving skills, learning methodology that works with many kinds of problems;

• Learn to communicate scientific information clearly and accurately, with both words and pictures.

Chapters 1 and 2

1. Review structural ideas from general chemistry, including:

   • the Octet Rule and Lewis structures;

     

     • formal charges;

     • predicting molecular shape from Lewis structures

   • electronegativity;
     • Ionic vs covalent bonding

   • polar bonds and polar molecules;

   • Bronsted acid-base chemistry;

     

   • Lewis acid and bases

     

   • resonance and delocalization of electrons;

   • Structure of atomic orbitals

     

   • Hybridization of atomic orbitals

     

2. Be able to use several new notations for describing molecular structure
   • condensed notation

   • line notation

   • dash-wedge notation for 3-D pictures

Chapter 3

When you have finished this chapter you should

• Be able to identify the common functional groups in organic molecules

• Classify organic reactions according to
  • Overall transformation: addition, elimination, substitution, or rearrangement

  • Nature of the reagent: electrophilic or nucleophilic

Chapter 4

When you have finished this chapter, you should

• Know what an alkane is, and be able to write structures for alkanes in condensed and line notation

• Be able to provide names for alkanes and haloalkanes using the systematic IUPAC scheme

  (We will name other kinds of organic molecules as we study their chemistry)

• Be able to explain what isomers are, and determine if two molecules are isomers

• Be able to write structures for the isomers of a given formula

• Know what is meant by the term "stereoisomer"

• Be able to describe the conformational stereoisomers (conformers) of simple alkanes using a new kind of structure representation - the Newman projection

• Be able to explain what "strain" is and be able to identify the structural features that result in:
  • angle strain

  • torsional strain

  • van der Waals strain

• Be able to rationalize the relative energies of alkane conformers in terms of the different kinds of strain

• Be able to describe the shapes of the cycloalkanes from 3-6 carbons, and explain the sources of strain in them

  • Be able to draw neat, clear projections in line notation of cyclohexane chair conformations that show axial and equatorial bonds

• Describe the chair-chair conformational interconversion in cyclohexane, and describe how it affects the orientation of substituents on the ring

• Be able to rationalize the energies of the different conformers of a cyclohexane derivative

• Be able to recognize configurational stereoisomers of cycloalkane derivatives

• Be able to write structures in line notation describing the shapes of some simple polycyclic molecules.

Chapter 5

This chapter introduces us to chirality, the property of being non-superposable on one's mirror image. It involves much manipulation of 2-D images as if they were 3-D. Use your model kit both while reading the chapter and while working the problems.

When we have finished the Chapter, you should:

• Understand what chirality is and be able to recognize objects, including molecules, that are chiral

• Be able to use the IUPAC system for specifying the absolute configuration (handedness) of chiral molecules

  Students in the various "bio" disciplines will have encountered an earlier scheme for specifying configuration. Here is why it should be abandoned and wiped from the face of the planet:

  

  Be able to classify stereoisomers as enantiomers or diastereomers, and relate differences in their chemical and pysical properties to their classification

  Here's the classification scheme and some problems:

  

  Be able to draw correct stereoprojections of chiral molecules

  Be able to describe the stereoisomerism of cycloalkane derivatives

  Be able to test for chirality using a symmetry plane, and use the plane to identify objects that are chiral without containing stereogenic centers

Here is a summary of the principal ideas in this chapter.

Chapter 13

We're jumping out of order here to begin to answer the question, "How do they know the molecule looks like that?" How do we know the structures of the complex molecules we have been writing?

When you finish this Chapter, you should:

• Be able to describe qualitatively how a mass spectrometer works, including what happens to molecules when they are injected into one

• Be able to obtain molecular formulas from mass spectra
  using the M, M+1, and M+2 peaks
  • using exact masses

• Be able to describe qualitatively how an infrared spectrometer works, and how infrared radiation is absorbed by organic molecules

• Be able to use infrared spectra and data tables to:
  • Identify functional groups

  • Identify some skeletal features

Chapter 6

When you have finished this chapter, you should be able to:

• Describe how bond breaking may occur homolytically and heterolytically

• Identify the kinds of carbo-based species produced by such bond breaking

• Use curly arrows to show electron flow during bond making and breaking

• Be able to use bond dissociation energies to calculate DH of reaction

• Explain the difference between equilibrium and rate of a chemical reaction

• Write the algebraic expressions describing equilibria and rates

• Draw potential energy diagrams for a variety of types of organic reactions

Chapters 7 and 8

We consider Chapters 7 and 8 together because the reactions in them are inseparable, largely occuring in the same reaction mixture at the same time. In your text, Chapter 7 focuses on substitution, Chapter 8 on elimination.

When you have finished these Chapters you should

• Write examples of the four mechanisms for nucleophilic substitution and elimination, using curly arrows to represent bond-making and bond-breaking steps accurately.

• Describe these reactions employing the "filled-empty" orbital interaction terminology

• Explain how the mechanism that occurs in a particular case is determined by:
  • the structure of R

  • the nature of the solvent

  • the basicity of the nucleophile

  • the basicity of the leaving group, X

• Predict the products, including stereochemistry, of these reactions for any given RX

• Examine the product of an S_N or E reaction and determine the reactants from which it can be made

Use this flow chart to help in making predictions.

Chapter 14

• Understand how radiofrequency radiation is absorbed by organic molecules

• Understand qualitatively how nmr measurements are performed

• Be able to judge qualitatively the relative absorption frequencies (the "chemical shifts") of both ¹H and ¹³C nuclei

• Be able to get connectivity information from ¹H-¹H coupling

• Use ¹H and ¹³C nmr data to solve molecular structures

Chapter 9

When we have finished this chapter you should be able to:

• Write equations for the synthesis of alcohols and ethers from alkyl halides and other organic molecules

• Write curly arrow mechanisms for the reactions involved in those syntheses

• Write equations for the dehyration of alcohols by strong acid and the conversion of alcohols to halides by HX

• Write curly arrow mechanisms for those reactions, including any carbocation rearrangements that may occur

• Explain the stereoselectivity and regioselectivity of the above reactions

• Write equations for the reactions of oxiranes with bases (nucleophiles), including stereochemistry, and for the acid-catalyzed ring opening of oxiranes.

• Write curly arrow mechanisms for both of those reactions that account for the difference in regio- and stereoselectivity.

• Provide systematic names for simple alcohols, ethers, and oxiranes

Here is a summary of reactions of alcohols; it includes some oxidation reactions that you will not see until next semester.

Chapter 10

When we have finished this chapter, you should be able to:

• Name and specify the stereochemistry of alkenes by the IUPAC methods

• Write equations for the electronphilic additions of HX, X₂, H₂O (three ways), H₂O+X₂ including appropriate regio- and stereospecificity

• Write curly arrow mechanisms for those reactions, explaining the observed regio- and stereospecificity

• Write equations for the preparation of specific alcohols, selecting appropriate starting alkenes and reagents

Here is a summary of the reactions of alkenes; again, it includes some oxidation reactions that you will not see until next semester: