Marshall University, College of Science

Chemistry 254

Section 201

Basics of Organic Chemistry

Spring 2011

3 Credit Hours




Dr. Robert J. Morgan
Department of Chemistry 
Marshall University 
Huntington, WV   25755 


Office:  S-486

Phone:  304-696-3159

Prerequisites: Chemistry 212. 

Course Description: The course covers approximately 90% of the material contained in an Organic I course, with a strong emphasis on the basics. It is designed for:

1. Students who have struggled in Organic Chemistry

2. Students who have not had General chemistry in a number of years, and would like a preview of Organic Chemistry I

3. Anyone who feels uncomfortable entering Organic Chemistry I.

4. Anyone who needs a refresher in Organic Chemistry I



Policy for Students with Disabilities:

Marshall University is committed to equal opportunity in education for all students, including those with physical, learning and psychological disabilities. University policy states that it is the responsibility of students with disabilities to contact the Office of Disabled Student Services (DSS) in Prichard Hall 117, phone 304 696-2271 to provide documentation of their disability. Following this, the DSS Coordinator will send a letter to each of the student's instructors outlining the academic accommodation he/she will need to ensure equality in classroom experiences, outside assignment, testing and grading. The instructor and student will meet to discuss how the accommodation(s) requested will be provided. For more information, please visit or contact Disabled Student Services Office at Prichard Hall 11, phone 304-696-2271.

Note for students with visual impairments: This course contains a substantial number of graphics files that cannot be adequately described as text equivalents. If you contact the instructor arrangements can be made to provide the source files for the graphics and/or Braille embossed high resolution graphics.

Since this syllabus is rather long, I have included some hyperlinks to help you find specific information.

Academic Honesty and Plagiarism:

University policy states that any act of a dishonorable nature which gives the student engaged in it an unfair advantage over others engaged in the same or similar course of study is prohibited. You must do you own work inside and outside of this class. Cheating/plagiarism in or out of this class is prohibited.

You will be given a final grade of F for any instance of academic dishonesty. I am happy to assist you with anything you do not understand or have questions about. Cheating in this course includes, but is not

limited to:

l.  Recording identical answers and screen captures as a classmate for your assignments.

lI.  Plagiarizing material from the textbook or readings. To avoid plagiarism, read all assigned material first; complete your exercises second; then base your written answers to review questions on yourexperience; only refer to the textbook or readings as necessary.

Required Materials
Computer and Software Requirements
Contacting the Instructor
Course Objectives
How This Course Is Organized
List of Topics to Be Covered
Time Requirement
Target Dates and Deadlines
Grading Policies
Instructor Biographical Information

Required Materials:

1. David R. Klein, Organic Chemistry I, translating the basic concepts, 2nd Ed, John Wiley and Sons, 2008 ISBN: 978-0470-12929-6 This book can be ordered online from the Marshall University Bookstore or they will take phone orders at 304-696-2461.

2. William Reusch, Virtual Textbook of Organic Chemistry, (This work is licensed under a Creative Commons License. Virtual Text of Organic Chemistry 1999. An interactive textbook covering the usual topics treated in a college sophomore-level course. Links are offered to advanced discussions of selected topics.)

Molecular Models:  If you have a hard time visualizing some of the three-dimensional aspects you may want to purchase an inexpensive set of molecular models but I would recommend that you not pay more than about $15.  And, I would suggest that you wait until you find that you really need them before buying them.

Suggested Materials:

It is recommended that you have a textbook in Organic Chemistry. This book will be used for background reading. Nearly any textbook designed for a one year sequence in Organic Chemistry will do. e-mail me if you have a doubt as to whether the one you have will be sufficient. If you are taking this course in preparation of a course in organic chemistry choose the book that will be used in that course. This way you will become familiar with it.

I also have included references to Professor William Reusch's, Virtual Textbook of Organic Chemistry. I have found this to be a convenient and wonderful source of background information. Best of all, it's free.


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Computer and Software Requirements:

  • You will need ready access to the internet.  Home access is highly recommended. Your computer should meet the minimum requirements listed at Broadband access such as DSL or cable modem is desirable but modem dialup access at 56K will work. There are very few files that will take more than a minute to download even at 56K.
  • You will need a web browser.  Internet Explorer 7.0 is the browser of choice but IE 5.0 or IE 5.5(sp2) IE 6.0 will work also.  I have also tested much of the course with Firefox 2.0. It is usable, but some of the graphics in the lecture notes are a little difficult to read.
  • You will also need the Sun Virtual Java Machine and you can download that from the link on the Computer Requirements page
  • Be sure to run the browser tuneup to make sure that you have all the correct browser settings. Note well that it is very important to have the correct cache settings for your browser.  If the cache is not set properly you may have problems accessing portions of the course. 
  • You may find it useful to send chemical structures in questions you ask me. You can get a free chemical drawing program called Isis draw. There are both Windows and Mac versions  at  Simply attach your structure to the e-mail message.
  • If you have technical problems, please go to the Help Desk:

    • (304) 696-3200 (Huntington, WV)
    • (304) 746-1969 (Charleston, WV)
    • (877) 689-8638 (Toll free)

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Contacting the Instructor:

Whenever you need help with the course or just want to ask a question about anything, you should feel free to contact me. I am a full time professor in the Chemistry Department at Marshall University. I have an office on the fourth floor of the Science building at the Huntington Campus.


The best method for contacting me is by e-mail. I tend to check my email a couple of times a day on regular class days. I tend to reply to e-mail as I receive it. On weekends or when classes are not in session, this is by far the best way to contact me. I usually check e-mail in the evenings. You may use the e-mail that is internal to the course by clicking on the MAIL icon on the main page.  Alternately, you may send e-mail to On weekends or evenings.  CC: your message  to (Especially if you believe the Marshall servers are down) I will normally respond by whichever method you used to send your message.  If you do not receive a response to an e-mail message within 48 hours you should assume that either your original message or my reply has gone astray in the e-mail system and you should resend the message.  Don't feel you are nagging me I'm there to answer your questions. It is helpful to me if you find errors in the course. I can’t fix things I’m unaware of!

Please note that while we tend to think of e-mail as being a nearly instantaneous means of communication there are times that there are significant delays in e-mail transmissions.  Under certain circumstances it has been known to take as much as 48 hours for an e-mail message to get between a Marshall University account and an account at a local internet service provider. 


I will also often be available in the evenings on Blackboard. If I am visible and available send me a chat invitation. Be patient, as I might have wandered from the computer.


    I will establish an e-mail list that will be used to make general announcements.  Your Marshall University e-mail account will automatically be placed on this list.  If you wish to have an alternate e-mail address added to this list you should send me an e-mail message requesting this.  If this address changes it is your responsibility to make sure to send me an e-mail message asking me to change the address in the mailing list.  General announcements are also posted on the course bulletin board.

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Course Objectives:

    This course is a basic course in organic chemistry, and it is aimed specifically at students who have struggled in organic chemistry I, feel they need a refresher course in Organic Chemistry I, or want to have a self-paced preview of Organic Chemistry I. This course only assumes you have a basic knowledge of General Chemistry. The introductory units will give you most of the background you need. At the end of this course, it is expected that you will have learned the basic skills required to be successful in Organic Chemistry. These include:

  • A knowledge of bonding and Lewis structures
  • The ability to read and write all the basic types of structural formulae
  • Have an understanding and an appreciation for the 3-D nature of organic molecules
  • Have an understanding of  isomers and stereoisomers
  • Have a basic understanding of the IUPAC nomenclature system
  • Be able to recognize all the common functional groups
  • Have an understanding of acid/base reactions
  • Gain confidence in the substitution and elimination reactions of alcohols and alkyl halides.


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Using the course materials

This course is strongly based on the included lecture notes. They are your primary source of information in the course. They follow a, “How to approach”, and are designed to teach you the basic skills required for success in organic chemistry. This is primarily a skills course, and I have not included that much, theoretical content. My aim here is not to teach you all of Organic Chemistry I, but to show you how to succeed in that course.

The book by Klein is also a book aimed at helping you to develop all the basic skills required in Organic chemistry. It's a great companion to any organic chemistry text.  The book focuses on the basic skills needed to succeed in organic chemistry. I tend to skip around in that book. Follow the reading references contained in each unit.

For background information you can use  Dr. Reuch's text or any other organic text.

Organization of the Course:

Chemistry is a subject that builds on a foundation.  You cannot understand the later topics unless you understand the earlier topics.  You cannot go on to a new topic until you have mastered the current one.  This is especially true of organic chemistry. Having a poor understanding of the early topics will haunt you throughout the course. To prevent this I stop you at the end of each topic and give you one or more quizzes. You must make 80% (or higher) to go on to the next quiz or unit. Only the highest score will count so you can never lower your grade by attempting to improve your score on a quiz, and you may take the quiz as many times as you wish. Most students read the lecture nots and try the quiz. If you find you are guessing, go back to the lecture notes and then try the quiz again. Use the quizzes in your studying. The only requirement is that you wait a few minutes between each attempt.

When you first start the course, only one topic will be available to you.  Whenever you complete a topic, a new one will become available.  All of the older ones will stay available so that you can review them as needed. You can find a list of all the quizzes and exams below.

    I divided the course into 26 units, with 43 quizzes. -- Essentially starting a new topic at the point where I would normally end a lecture session in a regular course (“Brick and mortar”), although a few units are longer and a few are shorter.   Each unit will have between one and three quizzes associated with it. You should be able to complete some topics in a few minutes but some will take an hour or more.

More on the quizzes, exams and final

The course is divided into three roughly equal sized parts.  There is an hour exam after you complete each of these parts.  Each of these parts is about the size of one lecture exam in an Organic chemistry course. Click here for a detailed list of the topics.

The quizzes are your main learning vehicle. They have between 5 and 10 questions, and there is no time limit. Your object is not to get the questions correct! Your object is to figure out why you are getting questions wrong. Use the quizzes to learn the material in the lecture notes.

The exams are longer, and are based on the quizzes. The final is based on the exams.

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Time Requirement

    NOTE WELL:  In a normal classroom setting for this course you would be expected to attend approximately 45 hours of lectures. You would also be expected to spend roughly double that amount of time studying for the course outside of class.  The e-course format does not work magic -- you should expect to spend at least the same number of hours completing this course.  Do not put off working on the course and then expect to be able to complete it in a couple of days.  Be sure to try to meet the target dates so that you can successfully complete the course.

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Target Dates:

  Students in this course have a maximum of one semester (session) to complete the course.  As is mentioned in the grading section of this syllabus, there is a target date for each of the hour examinations. You should try very hard to meet these targets.  Otherwise, you will probably have trouble completing the course. Important dates for the Spring of 2011 are:

  • January 10, 2011   First day of classes. 
  • February 11, 2011  Target date for completing Part I and taking Exam I.  If you take this exam on or before February 4, 2011,  I will add 1% to your final average. 
  • March 25, 2011  Target date for completing Part II and taking Exam II.  If you take this exam on or before March 18, 2011 I will add 1% to your final average. 
  • April 30, 2011 Target date for completing Part III and taking Exam III.  If you take this exam on or before April 23, 2011 I will add 1% to your final average. 
  • May, 4, 2011 Target date for taking the Final exam.  If you take this exam on or before May, 1, 2011, I will add 1% to your final average.  The absolute deadline for taking this exam is May 6, 2011.  Failure to complete this exam by that date will result in a grade of zero.


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    There will be three hour exams and a final exam in addition to the quizzes.  The quizzes will count for one third of the final average.  The three hour exams will all have the same weight and will account for one half of the final average.  The final exam will account for the remaining one sixth of the final average.

Letter grades will be then be assigned based on the following scale for the final average.

  •  Greater than 90% = A
  •  80-89% = B
  •  70-79% = C
  •  60-69% = D
  •  Less than 60% = F
  • In a Cr/NCr format, a Score of 70% results in a Grade of Cr.

   I want to encourage students to complete this course in a timely manner. If you take full advantage of the incentives outlined above, you can raise your grade by almost half a letter grade.

    The hour exams will be given on-line.  There is a time limit on the exams and it will be enforced by the computer -- no answers will be accepted after the time limit on an exam.  You will get the graded exam back with your score and feedback on your errors.  Exams are closed book, closed notes. You are on your honor to take the exams without any assistance and without referring to any materials other than a basic periodic table.
    The final exam will be handled the same way as the hour exams. You only get one attempt on each exam.
    The quizzes are all taken on-line and the scores and the correct answers are available to you as soon as you complete the quiz. 

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Biographical Information:

 I received my B.S. in Chemistry from Queens College, and completed my Ph.D. at The City University of  New York in 1992.  My dissertation research was in the area of the synthesis of Ru(II) based photocatalysts. I also taught for four years at Long Island University, before joining the Marshall University faculty in 1997.  I have taught a wide variety of courses at LIU and MU including instrumental analysis, and all levels of organic chemistry.  I have taught Organic Chemistry I at a total of four Universities, and have taught this course in the classroom three times.

My research interests are currently in synthesis of ligands and development of fluorescent dyes, for which I hold two Patents.  My hobbies include is raising Koi, and growing fruit, for which I have been known to make a gallon or two of wine a year. 

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 Topics to Be Covered in This Course

The Structure of Organic Compounds (Unit I)

      • 1-Valence and Bonding
      • 2-Formula Writing
      • 3-Formal Charges
      • 4-Resonance Theory
      • 5-Curved Arrows
      • 6-Hybridization
      • 7-Functional Groups
      • 8-Nomenclature of Alkanes

Isomerism (Unit II)

      • 9-Classification
      • 10- Constitutional Isomerism
      • 11- Conformations of Alkanes
      • 12- Stereoisomers I. Cis and trans
      • 13-Conformations of Cycloalkanes
      • 14- Stereoisomers II. Stereocenters
      • 15- Stereoisomers III. The R/S system
      • 16-Stereoisomers IV. Diasteomers and meso stereoisomers

Organic Reactions (Unit III)

      • 17-Bronsted Acid/Base Theory
      • 18-Lewis Acids
      • 19-Substitution Reactions
      • 20-The SN2 Mechanism
      • 21- The SN1 Mechanism
      • 22-SN1 vs SN2
      • 23-Alcohols in Substitution Reactions
      • 24-E1 Reactions
      • 25-E2 Reactions
      • 26-Elimimination Vs. Substitution

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