Pointers on Doing Good Research
It's much more than following a recipe!!



1. Always
know what you are going to do before entering the laboratory. This means:

  • being familiar with all relevant literature references
  • understanding the mechanism of the reaction to be run
  • being aware of any appropriate safety precautions.
This means that, if I or anyone else should ask you what's going on in a certain reaction flask, you must be able to whip out a blank sheet of paper and lay it out for them.

[By the way, I know you've heard this warning in organic teaching labs you've already been through.  The big difference here is that, this time, WE REALLY MEAN IT!!!  You're doing chemistry that has never been done before, sometimes via reactions whose outcome is questionable, and you cannot make decisions on what to do if the reaction misbehaves if you're just playing cook-for-a-day.]

The top section of your laboratory notebook (reaction, reference, reagents) must be filled out prior to beginning any lab work. This is not optional, not a matter of style, and not a negotiating point. Do not let me catch you running a reaction without the lab book entry already filled out, as described on the next page.

2. Set up your reaction equipment with great care, ensuring (when appropriate) tight connections, safety-wired rubber hoses, stability, dryness, etc.

3. Accurately measure all reagents, including solvents and catalysts. Discrepancies which may seem unimportant at the time can drastically alter the course of a reaction. When you're discovering new chemistry, it's impossible to tell beforehand what's important and what isn't!

4. Follow the (hardbound) notebook format illustrated on the following page. Before beginning experimentation, fill in the reaction you intend to run (either use a template or draw very neatly), the literature precedent, and all reagent quantities. Reagents should be listed by name, followed by the density (if it's a liquid), mass (g or mg), and mmoles.


NOTE on E-NOTEBOOK
 
Starting in Fall of 2004, we will begin using CambridgeSoft's E-Notebook® system for maintaining records of past reactions, spectra, experimental results (including SAR-type studies for new reactions), experimental descriptions, etc.  It will calculate all reagents, solvents, times, etc.  The first group meeting of the semester will cover this important upgrade in our operation.


5. Record the progress of your reaction meticulously, beginning with a description of your reaction setup. Note all observations - you can not assume any change (i.e., temperature, viscosity, color, gas evolution, stirring rate, etc., etc.) to be unimportant! If any environmental variables are unusual (cold or hot in the lab, extra-high humidity, etc.), note that too.

6. Describe workup/purification conditions in detail - they are important!

7. When you isolate a compound in crude (impure) form, record its physical characteristics, weight, and usually at least one spectral or chromatographic measurement. How complete your analysis should be depends on the compound's purity (this just makes sense - why do lots of analysis on impure stuff?). The following table outlines some of these differences:

    Minimal Data to be Collected on ALL Isolated Compounds
    Crude Material Purified Product
    mass: in g or mg; (percent yield)
    Same as for crude, but adding the following:
    phys. appearance: color, crystallinity, viscosity, etc. m.p. or b.p. (@vacuum, if applicable)
    TLC information: eluant; how many spots, Rf of each NMR data (follow standard format)
    IR data:important absorptions only ( <6) , and the fnc. grp. to which they correspond. Also, note the lack of a certain peak if it represents a fnc. grp. which was successfully converted to another (e.g., for a C=O to a C=C bond transform, the C=O absorbence should be gone).

    Note: physical constants and spectral data should be compared to literature values, if it's a known cmpd. IR: choose 4-6 impt. absorptions. NMR: compare d and multiplicity for the functional groups which confirm the compound's identity.

       If it's NOT a known cmpd., be sure to intensely purify 100-200mg to be sent out for CHN combustion analysis.  Talk to me about this.

8. Assign each compound a unique number, which has four parts, each separated by a dash: your (two-letter) initials, which # lab book you're on (Roman numeral), the page no., and a letter (assigned sequentially: A..B..etc.). So, a compound of mine might have the number HB-II-123-B. This unambiguously states that I made it, in my second lab book, on page 123, and it it the second compound isolated on that page. Often, a crude product will be A, and, after purification, will be designated as BThe idea is that if a sample vial of yours is discovered years after you leave, it can be quickly matched with your notebook, and its identity discovered without trouble.

9.
End your notebook entry with a sentence or two describing your conclusion(s) concerning the experiment's outcome. Was it a success? If not, what do you think went wrong? What should be tried next? On what notebook page is the next trial in the experimental series?

10. Overall - BE COMPLETE! Someone should be able to reproduce your experiments exactly using only your notebook as a guide.

11. When you are finished with an experiment, including its notebook entry, please ask another group member to look over the notes to be sure that they conform to the guidelines and then to sign and date the page in the spaces provided at the bottom.  It is especially important that the notebook contain all appropriate yield and analytical data, as well as a clear, brief conclusion.

    When you are asked to sign someone's book, please take the responsibility seriously!  If I find a page which is not complete, it's the signer that I'll look for first! 

     By the way, if you don't understand how important this is, you just haven't been around long enough to be intensely frustrated by trying to follow someone's book who left the group years ago, and find poor record keeping, no yield, no physical or spectral data, a failed reaction with no conclusion, etc.

12. Finally - keep a positive attitude and have fun!

Additional Notes and Observations - Important!

    It is very tempting to skip some of the steps outlined above, in the desire to keep things moving.  However, in the end, skipping or glossing over any of these steps will come back to haunt you, especially when it's time to write a semesterly report.  Incredibly, however, during any year, every single group member has usually violated most of the guidelines provided above. The following are the most egregious examples, in approximate order of importance and thus ability to annoy me when I find out (going from worst to least):

    Before you run a reaction, the top part of your lab notebook must be filled out completely,  with the information outlined previously. It should be legible, and include all data specified. If you are repeating a previous, successful reaction, it's fine to outline the reaction, as usual, and then, for the reference, write "Page XX, this book (or book X, if you've already filled one). You can also write "Reagents/solvents exactly as before", or "Reagents/solvents 3x scaled up", etc.


    For repetition of unsuccessful reactions, if only one variable is being changed (which is how it should be), you can write something like "Reagents/solvents exactly as before, except that the quantity of (for instance) thionyl chloride was increased to XX mL (XX g, XX mmol)."  A few more specifics:

  • When you isolate a crude product, obtain its weight/yield, mp (if solid), and TLC. It doesn't matter if this is the 25th time you've run the same reaction. Incredibly, I see this guideline ignored time after time!
  • Write a cohesive, thoughtful conclusion at the end of every single reaction! Unfortunately, you won't appreciate the importance of this until it's time to write your thesis, semester report, etc., when it's too late to gain the time savings this allows.
  • Store samples only in vials, test tubes, etc. Do not use standard taper glassware to store samples!! It's too expensive to use as store containers, and you are depriving others of the use of that piece of equipment.
  • Parafilm7 has only one use - to seal screw-top jars from air and moisture!  It is not cheap, and is not to be used to seal flasks (especially standard taper joints - what do you think the ground glass joint is for?!), beakers, etc. And, it just needs to be pulled/pressed around the lid-jar interface - NOT plastered all over the entire top of the container!  I have seen reagent or sample vials virtually mummified with Parafilm - it's wasteful (and looks really dumb).