TEXTS

1. Organic Chemistry, 7th ed. upgrade, Graham Solomons & Craig Fryhle
2. The Organic Chem Lab Survival Manual, 5th ed., Zubrick
(Recommended) Study Guide to Organic Chemistry,7th ed. upgrade, Solomons & Fryhle

ADDITIONAL MATERIALS

1. Bound notebook for laboratory
2. Safety goggles as required by Department
3. Protective gloves
(Recommended) Darling Flexible Stereochemical Models

MODES OF EVALUATION

Organic Chemistry is very much like a language. As with any language, mastery is only possible with regular practice. Accordingly, homework assignments following the enclosed Class Schedule will be given daily. It is expected that the assignment will be completed before the next lecture. Homework will be assigned to help clarify important concepts; however, homework will not be collected and will not directly affect the course grade. Homework does, of course, affect the grade in that it is unlikely that the course content can be mastered without significant practice. Self-evaluation of homework will be possible through the use of the Study Guide.

A brief quiz covering recent lecture material will normally be given at the beginning of every other class period. The first quiz will occur on the fourth day of class. Regular attendance is, thus, necessary to achieve success in the course. The three lowest quiz scores will be discarded when calculating the final quiz score. Make-up quizzes will not be administered under any circumstances. All quizzes are closed-book, closed notes.

Since the ability to communicate effectively is a key to success in scientific endeavors, a writing assignment (the Digital Organic Library) is an important element in this course. This paper will be ten to twelve pages of double-spaced text (plus any tables, figures etc.), word-processed, laser-printed, with end-notes, annotated bibliography, end-of-chapter questions and their solutions. Important note : this is not a standard research paper. Please refer to the section below which describes the style of the paper before proceeding! A list of possible topics is provided; however, individual interests may be pursued with permission. While content is extremely important, this assignment will also be evaluated in terms of form of presentation. Due to the complexity of this project, several intermediate milestones are due (sse handout). Failure to observe these due dates will result in a one-half letter grade reduction in the final paper grade for each milestone missed. Handwritten milestones will not be accepted. The final paper is due as shown on the Class Schedule below. Late submissions will be penalized one letter grade for each day (or portion thereof) late - "Big mistake. Big. Huge."

Three Opportunities will be administered on the dates listed below. Make-ups will be given only under extreme circumstances (illness, serious personal difficulty).

The final examination will be a multiple choice standardized American Chemical Society examination which is cumulative over both courses. Any student scoring at the national 90th percentile or higher on the this exam will automatically receive a grade of A in the course provided all laboratory work has also been completed.

Laboratory work will be assessed in the following way. A student is expected to attend all labs (or makeup assignment if missed through excusable absence), properly utilize a laboratory notebook (which will be subject to examination without notice), show evidence of preparation for lab (through lab quizzes, flowcharts, etc.), and strictly adhere to all chemical hygiene rules. It is usually very difficult to make up missed labs, thus it is essential that lab attendance be very faithful. The lab grade begins at 100% and will be decreased by 10% for each nonperformance of the expected standards. After a one time grace period (no penalty), upon violation of a chemical hygiene rule, the student will be asked to leave the lab for the remainder of the class period. This will result in two reductions to the lab grade (chemical hygiene violation, nonexcused absence).

Laboratory notebooks will be prepared by the student and will be assessed by a combination of self-evaluation and peer-evaluation (neither of which will affect the actual grade in the course) and by evaluation by the lab instructor. Students who perform all laboratory work, observe all chemical safety regulations, and maintain an acceptable laboratory notebook will receive full credit for laboratory effort (representing 67% of the lab grade). During the final laboratory session, a laboratory examination will be administered. The score on this examination represents 33% of the lab grade.

Scores on graded materials are not curved. Final grades will be computed as follows:

      25% - Three Opportunities
      20% - Quizzes (drop three low scores)
      20% - Laboratory (includes lab exam)
      20% - Paper
      15% - Final examination (curved)

DIGITAL ORGANIC LIBRARY WRITING ASSIGNMENT

The choice of your topic for this paper is a vital key to your success. You need to choose a topic which is of interest to you in order to be able to present it in an interesting manner (believe it or not, scientific writing should be interesting as well as informative!).

Note carefully: your paper's audience is not the instructor but rather a group of your fellow classmates. Everything in the paper should be readily understood by another organic chemistry student. You may assume that this reader is an excellent student who has just completed the CH212 course. Consequently, any other material from outside this course (or the normal course of study for a sophomore college student) must be explained to this reader. Remember, for example, that not all organic chemistry students have attended a college biology course. Depending upon the topic it may be helpful to include solved example problems within the chapter.

When writing your paper, it may help to compose it as the text for a lecture to an audience filled with such students. This should insure that the paper is organized and developed in a very logical manner ). It is also a very good idea to read your paper aloud to insure that sentence structure,etc. is correct. Feel free to try it out on a friend, also, to determine whether you have gone overboard. Papers that present material beyond the audience described will be penalized even if they are technically accurate.

Several important dates apply to the various milestones in this project. The timely submission of all items is essential to success in the project. Details of the milestones follow.

Milestones

1. January 27 - Title and Outline

This milestone requires the selection of a specific focussed topic, along with the outline for the presentation of that topic in the paper. The final paper may deviate from this tentative structure; however, this milestone requires the author to think about what they will be presenting and in what order.

2. February 17 - Annotated Bibliography

This milestone requires the submission of a list of references that have been obtained for preparation of the paper. For each reference you must give a brief (1 paragraph) description of the article/book/etc. Important! You may not simply copy the output from an online search. You are to describe the article - not its abstract! In a second paragraph you will then explain how this reference will be useful in the preparation of your paper. This is an extremely important milestone.

Please note: web sites may provide much valuable background material for your work; however, the quality of content and permanence of this information must be considered before placing a web site into a bibliography. In general only .edu or .org web sites will be acceptable sources. In special cases a .com web site may be appropriate. In any case, every web site included in the bibliography must be approved in advance by the professor. The only way to receive approval is to email the following to the professor far enough in advance to receive approval before this deadline:

Title of the web page
Author of the web source (if known)
Date of the publication (if known)
Annotation (i.e. description of content and how it is useful)
Exact web address as it will be entered on a browser

3. March 3 - Revised Outline

This milestone requires the resubmission of the outline - probably in finer detail than the original. For each outline entry, you must also list the references (from the annotated bibliography and other new materials) which you currently plan to use for that section.

4. March 31 - Critique of Draft by classmate

This milestone requires a word-processed draft of your paper to be submitted to a student in the class (as directed by the instructor). The student is responsible to read and critique this draft and return it to you by April 3.

5. April 16 - Paper Due in class

Prepare a packet in a manila file folder with the following items in the order indicated

1. Cover page with title, author and a two or three paragraph abstract of the paper
2. Revised outline
3. Actual text of the paper including figures, graphs and tables.

   Important! Do not include any text, figures, graphs or tables from external sources without including proper attribution. This is extremely important!

4. End of chapter questions
5. Solutions key to end of chapter questions
6. Annotated bibliography
7. Written comments of the peer reader
8. An envelope containing a CD with the final version of the paper and all other needed items. The text document must be saved in Word or Wordperfect format. If you store your files with another word-processor you will receive a grade of incomplete. The paper will not be evaluated until it is in the correct format. Late penalties will be assessed.

   Important! All files must be saved in the following manner. Any deviation will result in an incomplete paper.

   Filename on CD	Contents of the file
   cover	the title, author and abstract page
   outline	the revised outline
   paper	the text of the paper, including figures, graphs or tables
   prob	end of chapter questions
   sol	solutions to end of chapter questions
   bib	the annotated bibliography with suggested "Further Reading" list

9. (Optional) Literature source material which you Xeroxed and no longer wish to keep

The following list of topics is meant to indicate the intended scope of the projects. The most common error is the pursuit of an enormously large topic, for example "biochemistry." Given the brief length of these papers, it is much more appropriate to present a thorough introduction to a very specific area of research. Another very common error is the choice of a topic in which the organic chemistry is clearly secondary to other interests. For example, some students have written papers which would be much more appropriate for a biology course. Accordingly, if you wish to pursue a topic of personal interest which is not on the list, be sure to inform me as soon as possible (lest your work be in vain). I will be happy to provide key references for the topics listed below.

ILLUSTRATIVE SAMPLE TOPICS

• RETIRED: Interstellar Organic Chemistry
• RETIRED: Ethnobotany: Drug Discovery
• The SYNGEN program for organic synthesis design
• Olive Oil and Garlic: Organic Chemistry Perspectives
• Photochemical Synthesis
• Ionomers - Ion Containing Polymers
• Molecular Structure-Property Relationships
• Automated Protein Synthesis
• Organic Flavors and Fragrances - Theory of design
• Mass Spectroscopy
• Chemical Communication by Insects
• Carbon-13 NMR Spectroscopy
• Woodward-Hoffmann Rules
• The Organic Chemistry of Night Vision
• Phase Transfer Catalysis
• Transition Metal Organometallic Compounds
• Alkaloids: Structure and Physiological Properties
• Degradable Polymers
• Luciferin: Firefly Bioluminescence - Mechanism
• Hyperconjugation
• Computer Aided Retrosynthesis - LHASA
• Molecular circuits: Building computers at a molecular scale
• Chemical Graph Theory
• Computer Aided Mechanistic Evaluation of Organic Reactions - CAMEO
• Organolanthanides as Synthetic Reagents
• Reactions Involving Orbital Symmetry
• Polyaniline: An Organic Semiconductor
• Use of Lanthanide Shift Reagents in NMR Spectroscopy
• Incorporation of Radioactive Isotopes in Organic Molecules
• Organosulfur Chemistry - Garlic Chemistry
• Taxol - Pharmaceutical Discovery and Development
• The Discovery of the Structure of Benzene
• Nondeterminism in the Lab - The HBr Addition Experiment
• Total synthesis of any organic compound

Make-up examinations will be allowed only if the absence is previously cleared with the instructor or in the event of an emergency. In the case of illness, a written excuse from the health center is required. In the case of a personal emergency, a note from the Center for Student Development is required.

Make-up quizzes are not administered under any circumstances.

Students with documented disabilities must identify themselves in writing no later than the second Friday of classes in order for an accommodation to be made available.

USEFUL WEB RESOURCES

General resources

Aldrichimica Acta	journal
Organic Syntheses	books
US Patent Office	documents
ChemFinder	database
ChemSketch: All-Purpose Chemical Drawing and Graphics Software	download
IUPAC Naming Tool	download
Laboratory Notebook Guidelines	handout
Calculating limiting reagents and percentage yield	handout
Aldrich Chemical Company Search Page	database
ChemExper Chemical Directory	database
Acros Chemicals	database
NIST Chemistry Webbook	database

Special topics

Please note that these resources are all managed by other institutions. Consequently, the links may not work depending on the whim of the creators of these web resources.

IUPAC Rules of Nomenclature
WEB-ster's Organic Chemistry, A List of Lists
Visualizing Aids For Organic Chemistry
The Organic Laboratory
Named Reactions in Organic Chemistry
Basic Organic Nomenclature
Organic Structure Elucidation
NMR Made Simple
Stereochemistry Online

Royal Society of Chemistry - Multiple Choice Exam
    Solutions

Illinois/Chicago
UCLA
Maryland, Organic 1
Maryland, Organic 2
Wisconsion/Osh Kosh
California/Santa Cruz
Wisconsin/Madison
Nebraska/Lincoln

Note: Laboratory is preceeded by a mandatory pre-lab lecture. Reading: Handouts will be provided online (links below) or in hard copy. Failure to read the required material before arrival at lab may result in a reduction in the laboratory grade. Unannounced laboratory quizzes will be used as necessary. These will be graded on a Pass/Fail basis. Passing grades will not affect the laboratory grade; however, each failing grade will reduce the final laboratory score by 1/2 letter grade.

Meeting	Reading	Topic
Jan 21	handout	Check-in Light as reagent: Photochemical synthesis of benzopinacol
Jan 28	handout	Light as product: Synthesis and chemiluminescence of luminol
Feb 4	handout	The Grignard syntheis of a 3° alcohol: Synthesis of triphenylmethanol
Feb 11	handout	The Diels-Alder reaction: Synthesis of endo-norbornene-5,6-dicarboxylic anyhdride
Feb 18	handout	Electrophilic aromatic substitution: Synthesis of p-nitroaniline
Feb 25	handout	Nitroaniline workup
Mar 4	handout	Identification of an unknown organic compound
Mar 18	handout	Claisen-Schmidt condensation
Mar 25	Solomons ch. 9 handout	NMR lecture video Problem solving with NMR spectra
Apr 1	handout	Unknown lab continues
Apr 8	handout	Unknown lab continues
Apr 15	handout	Unknown lab continues
Apr 22	handout	Unknown lab continues
Apr 29	---	Laboratory Exam; Check-out
May 6	---	Thursday schedule of classes