Friday, August 26, 2011

Handwritten structures

What's wrong with that phosphorus, anyway? 
One of the most charming things about Carmen Drahl's posts on The Haystack is her photos of handwritten structures. For example, here are her structures for her article on anesthetics in this week's Chemical and Engineering news.

A chemist's structures, while adhering to the "1996 ACS" Chemdraw style (or whatever it's called) cannot help but be a signature of sorts. I've written up Carmen's structures to show the differences (hers are a lot neater and some of my bond angles are funny.)

Readers, critique my bond angles!... and have a good weekend! 

24 comments:

  1. My favorite part is the scribbled-out "H" of the phenol in the last structure. I do that ALL THE TIME, and it causes my (GLP-notebook-oriented) analytical coworkers to have fits.

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  2. Dude, what's with your predilection for trigonal bipyramidal phosphorous?

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  3. I notice that you don't draw your phenyl rings in one motion, the pen comes off the paper at some point.

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  4. your drawing would be much cooler if you had it autographed by Michael Jackson

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  5. CJ, please tell me your chair cyclohexanes don't resemble lightning bolts! At least your drawings imply that you're a happy-go-lucky person. Back in grad school, the anger, despair, and (rare) elation of my colleagues could be inferred from the thickness of their hand-drawn stereochemical wedges and hatches.

    On a tangent, one old-school drawing convention that has ALWAYS annoyed me is writing out all the methylenes in an alkyl chain, e.g, -CH2CH2CH3.

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  6. That benzene rings look a lot like sad faces.

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  7. Aww, thanks for the shout-out, CJ. I never quite matched the awesomeness of the boss's hand-drawn structures in grad school (he used sidewalk chalk). @SeeArrOh my foible is not so much scribbling out the H in a phenol, but forgetting that I'm drawing a heterocycle and then sorta slipping the nitrogen into an already-drawn aromatic ring. On another random structure-drawing related note, anyone out there see Phil Baran talk circa 2005? He used Ryan Shenvi's notebook drawings in his talk about chartelline.

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  8. "forgetting that I'm drawing a heterocycle and then sorta slipping the nitrogen into an already-drawn aromatic ring"

    I am a repeat offender in this area too.

    Re Baran: are you talking about the two-headed hydra drawing?

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  9. They do look like sad faces. :(

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  10. @Anon 11:21:

    wow- I don't remember the two-headed hydra, though I bet that looks pretty awesome. I was thinking about Shenvi's structure drawings-- I remember them being picture perfect.

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  11. I confess that a trip through my notebook reveals a 'sad face' problem. Uh-oh.

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  12. @CJ
    This was a really great idea for a post, and I thoroughly enjoyed it!
    That is all ...

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  13. You can avoid the sad face by using the circle instead of each individual double bond. Faster too, FYI.

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  14. Verily, verily, I aesthetically object to the circle (even though it may be more accurate.)

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  15. @Carmen, @Anon11:21 - I saw Phil (yes, he's mighty enough to go by just his first name now!) speak twice between 2005-2007. I recall that one time, he wore a tan leisure suit, and the other a leather jacket for pictures later.

    Anyway, those were talks in which he indicated strain in molecules (like haouamine) by building models and stretching the bonds to near-breaking, so they got the distorted plastic stress marks.

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  16. If you wanna see some *real* structures: Woodward in 1961

    (whiskey3) ch.ic.ac.uk (slash) video (slah) woodward (slah) index_embed (dot) (hotel tango mike lima)

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  17. Actually, CJ, your phospropofol looks more cheery than its associates to the left. I also object to indiscriminately drawing pi-electron circles for all aromatics. This lazy method does not sufficiently represent the unequal electron distributions in heterocycles or heteroatom-substituted phenyl rings. Furthermore, stereoelectronic effects in electrophic and nucleophilic aromatic substitutions are easier to convey with discrete pi electrons.

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  18. when you draw your pi-electrons keep in mind that there are 3.141 double bonds in benzene molecule

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  19. @milkshake - So, what, you just draw one of them 15% longer? Or all three 5% longer? :)

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  20. I don't really like the linear O between the phenoxy moiety and the phosphonoxymethyl group, though it isn't the same as the tribipy P. The structures aren't bad though.

    I've never managed to draw benzenes in one motion - I have to stop while drawing the hexagon. I don't really like the circle for aromaticity, though my first organic chem book uses that notation.

    I like drawing structures a lot. I'm slightly afraid of the all-electronic world because I won't have paper to draw on.

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  21. Ooof -- I didn't even see the linear O. That IS ugly.

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  22. @CJ, @Hap - I almost wonder if you drew the linear O subconsciously...after all, in order to maintain the 110 deg bond angle and avoid sterics of the 2,6 di-iPr-phenyl (while still keeping one of the lone pairs roughly in conj. with the aromatic), it'd have to be rotated 120 deg away from you "into" the page, which would make the line a lot more "straight" from our viewpoint.

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  23. It's possible, but generally for prettiness I draw flat structures, if I can, and for accuracy I draw perspective. I don't know what others do.

    If I were drawing for prettiness, even though the CH2 interaction with the isopropyl is a problem, I would probably have drawn the CH2 and isopropyl Me close anyway (the vertex of the CH2, the Me and CH of the isopropyl, the ipso and ortho benzene carbons, and the O forming roughly a six-membered ring). If accuracy were the object, I would have figured that the benzene-O-CH2 bond angle in an overhead view of the structure wouldn't be quite linear, probably like 30 degrees from vertical, to maximize conjugation between the lone pair and the phenyl while avoiding the syn-pentane (?) between the CH2 and isopropyl groups.

    Has anyone worked through the structure drawing part of Michael Smith's Organic Synthesis? I think I tried once, and got shipwrecked.

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  24. CJ: Thank you you for avoiding 1,3-strain and syn-pentane-like interactions in your structures. (Beatnik-style snapplause for you!)

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