There’s odd tidbits in the synthetic lab that everyone seems to err, and then learn, on their own.  For these, one of these was writing stuff down in the lab: I’ve seen my fair share of spectra coming out from the NMR that says “unknown solid“, as well as samples from the freezer whose labels fell off or became illegible.  Here’s some notes on what my solution to them are – since they’re very much tied to the kind of thing I work with and has available, you’ll need to use good judgment in their adaptation.  And I certainly don’t have all/most of the best practice – post your own discoveries/practices in the comments!


Here’s a page from one of my books…

A page from lab notebook

Annotated page from lab notebook

Every researcher has an initial, every lab-book needs an ID, and every page should have a page number.  The dash-separated conjunction of these give each experiment a unique identifier in the form of JCR24 (A). I try to not have multiple experiments on the same page — pages are cheap, confusion in the lab is expensive.

I tried both labeling lab-books with numbers (1, 2,…) as well as letters (P, Q,…), and I prefer the latter: JC-R-24 is clearer to me than JC-2-24.

The same ID is used to refer to compounds generated in the experiment, with a period to separate their origins.  As a synthetic chemist there are certain suffixes I use.  As an example, a crude sample from a reaction may be JC-R-24.crude, which then becomes JC-R-24.ppt(hex) when it’s crystallized from hexanes, and JC-R-24.f(34-56) when it went through the column.  I use the same ID for spectroscopic characterization (B) and sample labeling (more on that later).  For the love of ice-cream, don’t run an NMR/UV with “final compound” as the title — first you likely have several targets, and second, you’re probably going to end up with “final compound (REAL)” and “final compound!!!” for the same “final compound” ;)

The dot/bracket notation came from thinking ahead that “one day” I’ll process things programmatically, and it would be easier to parse.  So far it hasn’t happened yet.

I like to keep paper copies of spectra in the lab-book (C), so years later I can come back and everything is in one place.  Two paperclips works well enough.  I’ve known others who shrink-photocopy their spectra to fit in a standard-size lab-book; I just use a larger-than-A4 sketchpad (I also like the big surface and no lines).  I find this size works very well — larger ones (11×17″) is unwieldy.  Since it’ll get thicker as spectra get clipped in there, don’t try to get the thickest one you could get.

Do check in with your advisor/group before using something with spiral-bound — and esp. perforated, unnumbered pages (D) — where pages could get teared off.  I sequentially number all my pages the moment I start a new book on the lower-right.

And yea.  While we’re on spectra, write-up your (potentially) publishable spectra immediately.  I did not do this and by the end of a PhD found myself with a smatter of paper trails with no electronic copy, or electronic files that no software will now open.  Bad place to be in.  Don’t be like me.

I picked up this particular “Reagents and Products” formatting as an undergrad co-op at Merck-Frosst (E).  It had pretty much fulfilled everything I need in the decade since.  From left the right, it reads:

  1. Material (name of reagent/solvent)
  2. FW/d (formular weight/density if applicable)
  3. Amount (gram/ml…)
  4. mmol (millimoles gives convenient numbers for synthesis)
  5. eqv (equivalent; ratios of reagents)
  6. properties (catch-all.  I usually indicate the ID for intermediates I’ve made, or safety data for particularly nasty chemicals.)

TLC plates are drawn in (F) — when they’re developed with acid-sprays, fixing them to paper will eventually give a hole in the lab-book.  Or so I was told.  It certainly prevents your lab-book from smelling like vanillin or anisaldehyde.

You should definitely get yourself some pigment pens (G).  (Copic, micron, and Staedtler are equally good.)  Once the ink from these pen dry, they’re flippin’ amazingly permanent.  You can soak the pages in water, acetone, chloroform, and the lines stay every bit as clean as it were before the negligence.  0.3mm is good for writing in lab-books.


These pigment pens are equally awesome for labelling samples, even though they smudge on labels before drying.  The following picture shows four vials with labels written by different pens, and the labels are wrapped over with tape (otherwise they’ll fall off eventually from freeze-thaw).  All of these samples were made in ~2005/6: from left to right they were written with (i) sharpie, (ii) ball-point pen, (iii) pigment pen (0.05mm), and pencil.  So, pigment pen or pencil for sample labels.  Note also the same unique ID on the vials.

Labelling samples

If you’re not going to be touching a vial for some years, and don’t need to go through the hassle of putting the samples in flame-sealed ampules, HPLC vials work very well for storage (much better than sample vials shown here; notice the second vial says “3.9mM” — it used to be a solution. Yes, it was teflon taped and parafilmed.).  If the septa has not been pierced, even chloroform solutions can last for years without evaporation.  I have not tried storing samples in Eppendorfs for extended periods — I have a general mistrust for the use of plastics in synthesis. (But of course, glass vials are a good source of sodium ions -.-)

If you have any hints/tips/questions/best practice for writing lab-shtufff, let’s hear them!