CHEM104: Organic Chemistry II

Course Syllabus for "CHEM104: Organic Chemistry II"

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This course is a continuation of CHEM103: Organic Chemistry I.  As you progress through the units below, you will continue to learn the different chemical reactions characteristic of each family of organic compounds.  We will focus on the four most important classes of reactions: electrophilic substitution at aromatic rings, nucleophilic addition at carbonyl compounds, hydrolysis of carboxylic acids, and carbon-carbon bond formation using enolates.  The enolate portion of this course will cover the reactivity of functional groups. We will also look at synthetic strategies for making simple, small organic molecules, using the knowledge of organic chemistry accumulated thus far.  At the end of this course, you will possess the tools you need to plan the synthesis of fairly complicated molecules, like those used in pharmaceutics.  From the perspective of a synthetic organic chemist, the two most challenging aspects of synthesizing drug molecules are the incorporation of  "molecular rings" (rings of 5, 6, 7, or more atoms) and/or fused ring systems into the structure of the molecule and the configuration of the chiral center, which will ensure the desired optical activity.  For example, the drug Zantac contains amines, disulfides, and an oxole ring.  By the end of this course, you will be able to rationalize your way through the synthesis of this drug. This course also introduces biological molecules, including carbohydrates, peptides and proteins, lipids, and nucleic acids, from a molecular perspective.  You will learn how chemical reactions, especially oxidation and reduction reactions, form the basis of all life.  In fact, plants reduce carbon dioxide to produce carbohydrates (sugars), whereas animals and humans oxidize the food eaten to produce energy. Humans store this produced energy  in the form of "chemical bonds" (ATP, etc.). Note that in biology, you would study the functionality of these structures by asking, “How do they operate?” whereas in the field of organic chemistry, we ask: “What are they made of?”  We will conclude this course with a unit on spectroscopy in which you will learn how to characterize and identify an unknown organic molecule based on its functional group’s vibrational modes (IR), mass (MS), light absorption (UV-Vis), and nuclei resonance (NMR). ****

Learning Outcomes

Upon successful completion of this course, the student will be able to:

  • identify the chemistry and basic mechanisms of the following functional groups: ethers, epoxides, thiols, sulfides, benzene, amines, aldehydes, ketones, and carboxylic acids and their derivatives;
  • plan the synthesis of ethers, amines, and carboxylic acid derivatives (esters, amides, etc.);
  • predict the product(s) of an electrophilic addition reaction involving conjugated dienes;
  • use the Diels-Alder reaction on conjugated dienes to form new carbon-carbon bonds and chiral centers of a desired configuration (R or S);
  • determine whether a molecule is aromatic, non-aromatic, or anti-aromatic;
  • indicate the position in which an electrophile will be added on an aromatic ring, given the other substituents present;
  • identify the products and mechanisms of electrophilic and nucleophilic aromatic substitution reactions;
  • demonstrate mastery of enolate chemistry and techniques for C-C bond formation;
  • plan the synthesis of simple molecules using the reactions learned throughout both the Organic Chemistry I and Organic Chemistry II courses;
  • describe the chemistry associated with biological molecules such as amino acids, nucleic acids, lipids, and carbohydrates;
  • identify different monosaccharides, disaccharides, aldoses, and ketoses, as well as reducing and non-reducing carbohydrates;
  • identify the twenty naturally occurring amino acids and describe the mechanisms associated with peptide cleavage and synthesis; and
  • use spectroscopy (mass spectrometry, UV-Vis spectrometry, infrared spectrometry, and nuclear magnetic resonance) to characterize an organic molecule. 

Course Requirements

In order to take this course, you must:

√    have access to a computer;

√    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; and

√    have completed the following courses as prerequisites: CHEM001/PHYS101, CHEM002/PHYS102, CHEM003/MA101, CHEM004/MA102, CHEM101, CHEM102, and CHEM103.

Course Information

Welcome to CHEM104: Organic Chemistry II.  Below, please find general information on this course and its requirements. 

Primary Resources: This course is comprised of a range of different free, online materials. However, the course makes primary use of the following materials:

Requirements for Completion: A solid understanding of CHEM103: Organic Chemistry 1 is required in order to do well in CHEM104.  In order to complete this course, you will need to work through each unit and all of its assigned materials.

You will need to complete at least one set of practice problems in all units (except units 2 and 10) as well as a Final Exam.  Note that you will only receive an official grade on your Final Exam.  However, in order to adequately prepare for this exam, you will need to work through the aforementioned problem sets.

In order to “pass” this course, you will need to earn a 70% or higher on the Final Exam.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 126.25 hours **** to complete; this time estimate includes optional resources. 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.  It may be useful to take a look at these time advisories and to determine how much time you have over the next few weeks to complete each unit, and then to set goals for yourself.  For example, Unit 1 should take you 8.75 hours.  Perhaps you can sit down with your calendar and decide to complete subunits 1.1 through 1.3 (a total of 4.75 hours) on Monday night; subunit 1.4 (4 hours) on Tuesday night; etc.

Tips/Suggestions: As noted in the “Course Requirements,” Organic Chemistry I is a pre-requisite for this course.  If you are struggling with the basic functional group structure and nomenclature as you progress through this course, try taking a break to review CHEM103. As you read, take careful notes on a separate sheet of paper.  Draw each reaction type, including both reagents and products.  Then, you can use this sheet to review for your Final Exam. 

Table of Contents: You can find the course's units at the links below.