Organic Special Projects Laboratory 
Chemistry 336
Fall 2004



Professor Fryhle
Department of Chemistry
Pacific Lutheran University
Tacoma, WA 98447

Office: Rieke Science Center 240
Phone: 206-535-8314


About the Organic Special Projects Laboratory:



Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Organic Special Projects Lab

An Overview

Welcome to the Organic Special Projects Laboratory!  Each of you in the small group of students selected for the Organic Special Projects Laboratory will undertake a set of multi-week projects. Significant independence and self-motivation will be required on your part. While the first project will be very similar for the entire class, its variation on a theme motif will acquaint you with use of the FTNMR, FTIR, GCMS and other spectroscopic techniques and equipment available in the department. Beginning with the second project, students will embark on their own journey.  The second and third projects may involve a multistep synthesis, may contribute in some way to an ongoing research project, or may be a reaction which gives an "unknown" product.   In each case, you will utilize your general background in organic reactions and mechanisms and spectroscopic tools to full characterize the products formed.

The Organic Special Projects Lab meets on Friday afternoons between 1:45 and 5:30 PM. Since there is usually much to do during that period, you should carefully plan in advance what you will need to accomplish each Friday. Prior preparations typically include familiarizing yourself with procedures to be carried out, setting up your notebook with preliminary information and calculations, preparing glassware,etc. It will occasionally be necessary to work at other times than Friday. For example, you may need to purify a reagent, obtain a spectrum of one sort or another, or measure a physical constant. If you do work during an Open Laboratory time other than Friday it is imperative that you inform the Open Lab instructor when you arrive and when you depart. Lab work during unsupervised times is not allowed, except after securing my permission to obtain spectral data from an instrument.

On some Fridays, especially near the beginning of the semester, we will meet in room 224 at the beginning of the afternoon to discuss things of general importance to the group. Also, in order to make your overall time in the lab as productive as possible and to help me keep abreast of what each person is working on (this is quite a challenge!), I expect each of you will take it upon yourself to keep me informed of your activities each week and to discuss the status of your current project with me. Sometimes a simple email message from you will suffice ( At other times, an office appointment may be helpful.

All projects are to be thoroughly documented in your lab notebook. Suggestions on notebook style are provided below in the section entitled Notebook Format. Use a soft-cover bound notebook with quadrilled pages. Write balanced equations for all pertinent reactions. Use your notebook as a record of exactly what you do as you are doing it, such that someone else could repeat your work and obtain comparable results by following your notes. In general, be as thorough and as neat as you can, all the while using your notebook as a "living document".   Copies of pages from your lab notebook will be due periodically during the semester (see the section below regarding the schedule for specific dates).

Reaction products are to be fully characterized by appropriate spectroscopic methods (NMR, IR, MS) and useful physical constants (e.g. mp or bp). Spectra for each experiment should be given reference numbers relating to your notebook entries and printed spectra should be hole-punched and catalogued in a three-ring binder. You should turn your spectra in with your laboratory notes for grading at the conclusion of each project. 

Each project will be graded on the basis of your lab notes, spectroscopic data, and samples. In addition, you will write one formal paper in the style of an article in the Journal of Organic Chemistry. A draft of this paper will be due several weeks before the final version.  An evaluation of the draft will be worth 10% of the overall grade for the paper.  See the “ACS Style Guide” and the Journal of Organic Chemistry for guidance in preparing formal papers.  You should submit both a hard copy and an electronic version of your paper. 

You will also prepare a poster presentation and a brief (15-20 minute) Powerpoint oral presentation about one of your projects.  On either the last class meeting or during the final exam period we will hold a mini-symposium at which time the oral presentations will be given.   Your finished posters will be hung for display at the symposium, and also saved so that you can present the poster at the Division of Natural Sciences Academic Festival in late April. You should submit electronic versions of your poster and your oral presentation. 

The Organic Special Projects Laboratory is a course quite atypical of sophomore lab courses. If you invest your time, creativity, and initiative in this course you will have much to gain from it. 

Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Fall 2004 Organic Special Projects Lab Schedule





Friday September 10 

Check-In and Instrument Instruction

Friday September 17

Begin Project I

Friday October 1

Complete work on Project I

Friday October 8

Begin Project II;

Notebooks and Project I Spectra Due

Friday October 15

Draft Formal Papers on Project I Due and Distributed

Friday October 22 

Mid-semester Break

Friday October 29

Complete work on Project II;

Student Comments on Project I Paper Drafts Due

Friday November 5

Begin Project III;

Final Draft of Project I Paper Due

Friday November 28


Friday December 3

Complete work on Project III;

Lab Check Out

Friday December 10

Organic Special Projects Lab Symposium 
(Project II Poster and Oral Presentations)
Notebooks due

Tuesday December 14

Final Exam Period (Symposium Conclusion)

April or May 2005

Division of Natural Science "Academic Festival"
Presentation of Posters from Chem 336


Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Laboratory Safety:

You must complete a Chemistry Department Laboratory Safety Tour before you can begin work in the Organic Special Projects Laboratory. You must also read and sign the Department's safety policies sheet, titled "Laboratory Safety", and turn it in at the Stockroom at the end of your safety tour.

Laboratory Notebook Style and Information

From years of our own experience, we find that the following format works well. Your notebook should be a complete and continuously updated diary or journal for your work in the laboratory. Your notebook is the only place where notes about your laboratory work should be kept, and it should be a thorough record of your work. A stranger with approximately your level of training should be able to read your notebook and repeat your work without any additional assistance, and obtain similar results to your own. The style that is used should have the following characteristics: information needs to be recorded in an organized, complete and logical manner, with a clear statement regarding the outcome of the experiment, yet without long wordy discussions and observations (it wastes time and neither you nor anybody else will want to read it). In research and industrial situations, a laboratory notebook is a legal document that is signed daily by the author and frequently by a witness. You should ascribe corresponding importance to your laboratory notebook.

Format for Lab Notes:

Your notebook format should be basically that described in Pavia et al., pp. 22-29. The Pavia model as well as a few additional required sections are listed by the headings below. Be sure to begin the notebook with the Table of Contents, Safety and Hazard Information, and List of Abbreviations pages, as specified above.

Prelab Portion 



Reference (e.g., the specific literature references used)

Goal or Purpose (brief)

Main Reaction [balanced equation(s), including likely side reactions] (Note that this section might not be appropriate for non-preparative experiments.)

Table of Relevant Physical Constants or "Reaction Table" Format - MW, mp or bp, density (for liquids), planned weights and moles, actual amounts and moles (filled in after experiment is begun), ratio of molar equivalents, and Registry Numbers for organic and hazardous inorganic reagents. Hazard information may also be noted in this table, if not placed in a separate section as described below. 

Separation Scheme (Usually a flow chart - not a written duplicate of the planned lab procedure copied from the book. - Be concise but complete.) The goal of this section is to show where actual physical separations of materials occur (and what the materials are) as you move through the experiment to obtain a pure, isolated material. For the case of non-preparative experiments (where a synthesis is not conducted), the Separation Scheme is logically replaced by a simple flowchart of the procedures to be conducted. 

HAZARDS (of the chemicals and/or the procedures) In addition to the lab manual, you will need to consult the Material Safety Data Sheets (MSDS's) available in the Open Lab. Recurring hazards and safety considerations can be documented once in the preliminary notebook pages described above, and simply referenced in the prelab as being noted there. This is another place where Registry Numbers could be listed, if not provided elsewhere already. 



In-lab Portion 

In-lab Notes, Data, and Observations - Written continuously during the lab period documenting your work in your notebook as you do the work, not at some later time or date. Your notes should be sufficient for someone else to duplicate your work, although they might not necessarily be in perfect prose. It is often helpful to note the time of each operation in the left margin. This can allow easy determination of the length of various steps or procedures. When taking numerical data, organize them into neatly labeled tables so that later it is obvious what the data means. 

Spectroscopic Data (NMR, IR, GCMS Etc.) - All spectra (NMR, IR, GCMS, UV/VIS, etc.) should be labeled fully on a copy of the spectrum, including the date and page number from the notebook, indicating the origin of the sample. Interpretation of the spectral data should be written in the notebook, as well as on a copy of the spectrum itself if appropriate. Spectra should be catalogued in a three-ring binder. Each spectrum and its notebook reference must be cross-referenced with identifying information about the notebook page on which the sample originated. 

Calculations - include the actual calculations in the notebook, in a clear fashion, so that they can be understood easily and checked at a later date.

Exercises (if any are included)

Conclusions - Brief statement or restatement of key results and conclusions, and perhaps suggestions for future repetition of the work. Editorial comments such as "I think the experiment went well.", etc., are not appropriate. 

Date of Completion

Your Signature

Reaction Products

Products requiring further work at a later time should be stored in a labeled vial and left in a stable place in your lab cabinet for storage. Final products should be stored in your lab cabinet and labeled fully with the compound name, your name, the date, tare weight of the container, net weight of product, and experiment number.

Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Format and Style for Papers

See the information about formal reports posted on eCourse for Chemistry 336.   Submit both a printed copy and an electronic copy of your report. 

Format and Style for Posters

See the “American Chemical Society Style Guide”, 2nd edition, for information about preparing posters.  Your poster will be presented at the end of the semester and at the Division of Natural Sciences Academic Festival in the spring. 

Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Chem 336 Grading


Percentage of Total



Project I 


Project II 


Project III


Formal Report


Poster Presentation


Oral Presentation


Grand Total


Top || Overview || Schedule || Notebook Format || Paper Format || Presentation Style || Grading

Copyright 2004, Craig B. Fryhle