First of all, welcome new graduate students!

Let’s start September with a topic near and dear to everyone’s heart, proper lab book maintenance.  I’m not the first to take a crack at this subject (the most important book for 1st year graduate students has a section, as does the book of standard reaction conditions, the website Not Voodoo and Jon Chui’s blog), but repetition is at the heart of every good lesson.

In an academic setting your lab books are your long term memory.  For those of us who have trouble remembering what we ate for lunch yesterday the lab book is a place to hold all the little details of an experiment, so that five days or five months later the results can be reproduced or (hopefully) a paper can be written.  As a result, most of my advice is focused around keeping the lab book accessible and complete [1].

Books designed specifically for use in the lab are generally larger than the standard 9.5″x11″, which makes it easy to write most experiments on  single page, and makes it possible to tape/staple in printouts from the MS/HPLC/etc.  They also tend to be a little pricy, so if you’re on a budget just grab whatever bound composition book is handy in the local bookstore.  While you’re there, also grab a gel ink pen.  Gel ink isn’t soluble in water or organic solvents, which makes it the perfect choice for a research notebook [2].

Like any good tome your lab book should start with a table of contents, listing broadly where key experiments can be found and when each project began and ended.  The format is up to you, but I like to also leave a few pages for brief project summaries, where I list key findings.

The general format of an experiment page is easier to show than explain.

Important points:

A) The date.  This can be very important if IP ever becomes an issue.  Every page should have a date at the top left, with more spaced throughout the page for when extractions, columns, etc. were performed.

B) The scheme.  You don’t have to draw structures if your compounds are huge, but the scheme lets you flip through pages quickly and easily.  Very useful when there’s more than a hundred reactions per book, and a dozen books to go through.  Leave the product slot blank until after the reaction is complete, just in case it doesn’t work or an unexpected compound is formed.

C) The reference.  If your reaction has been done before or you’re borrowing someone’s conditions write a brief citation here.  If you’re referencing a previous experiment you  did, put that too (ie. BF4-103).

D) The chemicals.  This table is broken down by chemical name, molecular weight, comments (density, molar equivalents, melting point, etc.), amount required for the reaction, and amount actually used in the reaction.

E) The procedure.  Everything required to prefectly repeat the reaction ten years later should be written down here.  I generally note the beginning and end of a reaction, colour changes, and techniques performed (together with relevant variables like extraction solvents, column gradients, recrystallization solvents, etc.).  There’s a bit of shorthand involved, but I hope nothing that’s too hard to decode.

F) The followup.  Codes for each related NMR, MS, etc.  A brief summary is also useful, especially for MS (ie. Calc 780.5, found 780.9).  Yield goes here too, both theoretical and actual.  This area is a little compact in my example, as I’d only budgeted a single page for this reaction, instead of the usual two.  Most reactions, especially in the beginning, are going to require two letter sized lab book pages.

Tests that use compounds from multiple reactions go into the back of the book, working backwards from the last page.  I like to number my books Arabic numerals (Roman numerals and letters are other popular choices), with samples recorded in the format BF#-Page#-experiment.details (my initials are BF).  So, if an NMR sample is labelled BF4-103-col2.12-15 I know that it was from the fourth lab book, page 103, second column, fractions twelve through fifteen.   Always link your compounds to the technique used to create them, not to an arbitrary label like “pure compound” or “pure compound (for real this time!),” and don’t carry forward numbering schemes across multiple experiments.  Trust me, it’s easier this way.

Once every page is used it’s time to write up the table of contents and summary pages and doublecheck that every yield is filled in that all your external tests (NMR, MS, etc.) are mentioned.  After that I take each book down to the campus print centre (ask your supervisor first), and have them cut off the binding and scan each page.  The resulting pdf goes onto my computer and backup discs, and the book is rebound with a nice fancy cover and gifted to my supervisor for his bookcase.  It’s a little pricy, sure, but having every book on hand no matter where I am is incredibly useful.

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[1] Industry of course has its own needs, based around intellectual property laws and large teams of chemists and biologists working together.  I’d be interested in how keeping a lab book differs in such a setting, but have no direct experience.

[2] Bloggers from days gone by have shown that gel ink has an Rf of 0, regardless of solvent.

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