How to use LabArchives as your Electronic Lab Notebook for Organic Synthesis Research

LabArchives—love it or hate it, a growing number of academic institutions are adopting it (reviewed here). As a “jack-of-all-trades” electronic lab notebook, it tries to cater to every field of science. If you do organic synthesis research, you may be disappointed at first as you struggle with the silly chemical sketcher widget, complete lack of integration with ChemDraw, and weak stock spreadsheet widget. Once you learn to use it, however, LabArchives isn’t half-bad. While it may not offer all of the chemistry-specific bells and whistles that come with Perkin-Elmer’s offerings or the slick ease-of-use that comes with (more biology-focused) Benchling, LabArchives is a serviceable option for synthetic chemists with the right tricks.

A good notebook entry for a reaction consists of three parts:

1. Structure drawing,
2. Table of reactants, and
3. Experimental write-up and characterization data.

Here’s how to tackle all 3:

1. Structure drawing

1. Just make it in ChemDraw!
2. From there, copy and paste the structures and arrow into a Word document.
3. Copy and paste from the Word document into a rich text entry in LabArchives.
4. In ChemDraw, select the product, and use the Structure → Convert Structure to Name command (⌥⌘N (Mac) or Ctrl + Alt + N (Windows)). Double-click it to resize.
5. Then, use View → Show Analysis Window → Paste to add formula, molecular weight, and exact mass to the document.
6. Copy the text box near the structure containing the IUPAC name, formula, MW, and exact mass, and paste into the LabArchives rich text entry.
7. (Optional, but makes searching easier) Copy the structure as a SMILES string (Edit → Copy As → SMILES (⌥⌘C (Mac) or Ctrl + Alt + C (Windows)), and paste.

2. Table of reactants

1. Create a Google sheet.
2. Starting in cell B7, make columns for the following:
   1. Compound
   2. Abbrev.
   3. Amount
   4. Unit (narrow column—just big enough to fit “mg” or “µL”)
   5. mmol
   6. MW (g/mol)
   7. d (g/mL)
   8. (Optional) CAS
   9. (Optional) Source
3. Use formulas to make all of the calculations (e.g, for mmoles, just do =[amount]*[density]/[MW]). I like to calculate the theoretical amounts of all solids I’m supposed to weigh out, then go back and fill in the actual amounts as I weight them.
4. Press “Share” in the upper right. Change the sharing settings to “Anyone with the link can edit,” then copy the link.
5. In LabArchives, insert a Google Doc and paste the link. When you hit “save to page,” you’ll have a decent spreadsheet you can edit in your notebook.

Bam!

3. Text and characterization data

1. Write up an experimental.
   

   Acetic anhydride (150. µL, 1.59 mmol, 2.2 eq) was added to a solution of salicylic acid (100.3 mg, 726.2 µmol) in anhydrous pyridine (2.5 mL). The reaction mixture was stirred for 10 h at ambient temperature. It was diluted with 0.1 N HCl (20 mL) and extracted with EtOAc (3 x 15 mL). The pooled organic phase was dried (Na2SO4), filtered, and concentrated in vacuo, affording acetylsalicylic acid as a white solid in 87% yield (113.8 mg, 631.8 µmol).

2. Upload all relevant data (I do PDFs exported from TopSpin for NMR). FolderMonitor could be good here (if you install it on the computer where you collect a lot of data and set it up to upload it automatically), but I find it’s easier to just upload to each individual page.
3. For TLC plates, take a photograph of the plate with your phone. For UV-absorbing compounds, I like to cut a ~1″ square hole in the top of a shoebox-sized box, cut a ~3″ x 6″ “door” in the side to shine in a UV lamp, and then photograph the plate inside the box. My photos automatically upload to Google Photos. Then, I quickly crop the images in Google Photos, right-click and copy them, and paste them into my notebook entries (the rich text portion). I double-click them to resize them to something reasonable (e.g., 300 pixels in height).

Organization

I prefer to put each compound on its own page and number each page. Every now and then, I get characterization data for reagents, which I put into a “Reagents” folder.

Conclusion

LabArchives is a versatile platform for lab notebooks. It can be useful for synthetic organic chemistry if you make the proper tweaks and take advantage of other applications’ functionality (e.g., ChemDraw, Google Sheets, and Google Photos) to make it work.