by Nessa Carson
Drawing with Flair
After much tweaking, I have a set of ChemDraw® settings, not unlike the sturdily-bonded Totally Synthetic stylesheet that went around the chemistry community a few years ago – but with a fetching pink background. In various workplaces, I’ve become famous for that bold look.
Robinson’s total synthesis of tropinone, in my style1
My settings include:
• Thick bonds that give a crisp look to the molecules on screen, and are clear at the back of a presentation room
• Explicit labels on terminal carbons, a requirement kept from my grad school supervisor’s rules
• And even a special font such that serifs are present only on capital ‘I’, to distinguish it from nearby vertical bonds.
However, the only comment when anyone sees my drawings is, “why is your ChemDraw pink?!”
I’m sure this is sometimes said with a hint of derision, but get over it. If I’m going to be staring at a screen for a portion of my day, it might as well be colorful. This is what I love about ChemDraw® : the chance to make it your own.
Personalization is not only about the aesthetics. Features I typically suggest to newbie organic chemists include enabling autosave, snapping only the desired toolbars to the window edges, and switching default ChemNMR solvent from DMSO to CDCl3. And if you’re in pink, turning off ‘Print Background Color’ - though this option might only affect me. Once you’ve set these options, remember to save your personal stylesheet in the ChemDraw Items folder, so you are ready to go.
Perfect Molecules, Every Time
Every chemist is unique, but most of us can be fussy about how our precious molecules look on screen. To this end, I recommend the Clean Structure feature. Highlight the molecule, or part of it, and press Ctrl+Shift+K (on Windows). Most of the time, if your bonds aren’t already perfect, they’ll snap to the default length, and optimize angles to avoid overlapping substituents. In particularly crowded structures, any computational effort may not match your individual preferences, and you’ll have to do some post-clean tinkering to get it exactly how you want. Luckily, this further personalization is not hard!
As an example, I’ve drawn blockbuster chemotherapy drug taxol. Just kidding: I pressed Ctrl+Shift+N to automatically produce a structure from the name.
The structure of this natural product is too complex to depict with the usual 120° bond angles, particularly with its bridged 6-8 ring system. Sadly, my personal stylesheet falls down here. The molecule looks worse than with default settings – those explicit methyl groups have something to answer for!
Since this compound is so complex, I like to use abbreviations to keep the groups from taking up too much space. I’ve condensed COPh groups to ‘Bz’ and COMe groups to ‘Ac’ – ChemDraw® recognizes these common abbreviations and continues to determine molecular weight and other properties correctly. You’ll notice, I’ve removed some of my explicit methyls for clarity’s sake.
That looks better, but my abbreviations still overlap, and there are one or two portions I’d like to adjust. At this point, I reorient some of the groups. I can rewrite the NHBz as BzNH, then center it with Ctrl+Shift+C. I’ve also right-oriented the benzoyl group with Ctrl+Shift+R, and added in a new bond for the southeast acetate to avoid overlap. I selected any straggling atoms and the entire ester side-chain, and tweaked their exact positions with the arrow keys, to achieve my own variant of perfection.
Lastly, I like to present important molecules with a frame, which can be sized automatically by selecting the entire molecule (double-clicking on any atom or bond), right-clicking, and choosing Add Frame.
My final tip is for thesis-writers. If your reactions are too long to fit into a word processor document without being annoyingly resized, keep all bonds to identical length by using the Ctrl+K Scale feature at any time.
Standardization Isn’t Always a Bad Thing
Don’t throw away your default settings yet! Default stylesheets look great in print, and are required for publication in major journals. Most chemists will also agree on roughly standard ways to transcribe flatter, more linear molecules to a 2D screen. For the majority of your drawings, ChemDraw® will provide perfect chain bond angles (press 1 or 0 when an atom is selected) and Kekulé structure aromatic rings (press 3 with an atom selected) without effort – saving you time for the perfecting strokes that matter.
1 Robinson, R. LXIII.–A synthesis of tropinone. J. Chem. Soc., Trans., 1917, 111, 762–768
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About the Author
Nessa Carson is a synthetic organic chemist based in southeast England. Nessa graduated from the University of Illinois at Urbana-Champaign with an MS degree in organic chemistry, working with Prof Scott E Denmark.
Nessa is also a freelance writer, with a regular column in Chemistry World. She tweets as @SuperScienceGrl, where she mostly enthuses over new papers and complains about fluorine.
Nessa can be reached at supersciencegrl.co.uk.