Review: ChemBioDraw 14.0

Dear ChemBioDraw* Ultra 13.0,

Listen, we had a good run together. But I've fallen for another: ChemBioDraw Ultra 14.

My good friends at PerkinElmer (PKI) were kind enough to grant me trial access to their spiffy new chemistry drawing software. As an avid user since, oh, say, ChemDraw Pro 4.5, I feel confident in stating that this version wins all around for smoother operation, better templates, easier file export, and better shortcut keys.

So, I figured what PKI really wanted me to do most was to try and BREAK ChemBioDraw 14.0
 . . .if I could. Did I succeed? Let's talk a walk through the software and find out.

CBD 14.0 means NEVER seeing this screen again (hooray!)

Starting at the top, I figured I'd check the "What's New?" link in the help menu. One thing I appreciated more than I thought? ChemBioDraw 14.0 directing "Help" queries into the appropriate section of the User Guide. Version 13 still spawned its help window inside Windows help, with the infamous purple booklets leading you down wild goose chases of clunkily-presented information.

Drawing hasn't changed much since 13.0. At least the text direction auto-correct -- which drove me batty in former iterations -- seems to have been tweaked; the system now opens my older drawings the way I typed 'em in originally (hence, below, attaching pasta sauce to a scaffold in place of a sugary placeholder).

I promise this made sense in earlier ChemDraw versions...

The CBD 14.0-to-SciFinder jump works much more smoothly than I had anticipated. For those of us who shuddered through dial-up desktop versions of SciFinder in the late '90s, this version feels like the sleek Lamborghini of the search world. After drawing (or importing) my structures of choice, I lassoed them up and pressed the little "SciFinder diamond" on the top toolbar. Within about 5 seconds, a new window opened with the standard exact / substructure motif. Two clicks later, I'd be deep into the primary literature.

So, my goal was to break the system, right? Here's a logical place to try - I attempted to load each and every complex structure I had drawn since starting my fledgling blogger's career, around 2009 or thereabouts. Again, I was amazed by the speed and accuracy of the SciFinder pop-out, which returned roughly 90% of the correct molecules I'd searched for (below):

From this 2011 post

From this 2013 post

From this 2014 post

However, it's not all bubbles and sunshine. Two of my molecular queries bore no fruit**; perhaps they're too new to have been uploaded into CAS's databases yet. But one thing remains tricky: drawing and searching for metallocenes. Along with their new push into biology clip art, ChemBioDraw has a renewed focus on making sure you've got those sandwich compounds properly aligned.

Sigh. If only I remembered what they were all supposed to be...

Now, even after aligning my query using the proper template, SciFinder makes a mess out of it.

From this 2012 post

So, obviously I went looking for things to break, and found some rather limited examples. Honestly? The rest of the program works pretty well. And writing this review gave me a wonderful opportunity to poke and prod at the product in ways I hadn't in far too long.*** I finally realized you could change the solvent on the NMR predictor! I played around with expanding and collapsing peptide and RNA strings. And the post-drawing mods to more complex peptides, like disulfide and lactam cross-linking? Much better.

Found on p. 126 of the User Guide. (Get it?)
I'd like to shake the hand of the person who slipped this in...

R.I.P., Optimizing Octopus

I will take this final moment to remember a long-lost piece of ChemDraw lore. Once upon a time, to "clean up" one's structures, the icon looked something like this (right). I've heard it referred to as a jellyfish, a squid, a broom (no!), but I always knew it as a friendly little octopus. With CBD 14, any doubt about its brushiness has been cast aside with a full-out icon redesign.


Looks great, guys. Now let me think about more ways to use it for actual work!

Thanks again to Philip Skinner and PerkinElmer for the chance to review the software.

---
*For other blog reviews of ChemDraw products, see Jess The Chemist, Andre the Chemist (no relation), or Chemjobber.

**Here's the structures that returned empty SciFinder searches. Both compounds (left, right) were first reported in 2014.

***P.S. I never knew you openly solicited beta testers for these products...gimme a call sometime, PKI!

Stock Photo Science - Colchicine

Our tiny company doesn't have a true marketing or business development staff, so publicity often falls to the scientists - y'know, during our "down time." : )

For the past month, I've been trawling stock photo sites and "how-to" guides to assemble some company brochures for an upcoming event. Yesterday, I dug up this stock photo gem:

Source: iStockphoto

Now, Just Like Cooking 1.0 might have beleaguered the graphic artist, decrying his lack of experience and shouting about why we need more chemists in design departments. 

But I'm tryin', Ringo. I'm tryin' real hard to be the shepherd. Let's go piece by piece and try to figure out why we can't print this on our marketing materials.

For starters: the molecule I think they're looking for, colchicine, isn't exactly unknown. Doctors and healers have prescribed this plant extract for centuries to treat gout and local inflammation, despite concerns over its toxicity. Chemists have known how to make colchicine since at least the mid-1950s. 

So, here's how the molecule should look. There's some important differences here, perhaps most importantly that the acetamide (the "top" functional group, CH3-C=O-NH) should actually have a bond to the central ring. 

Next, let's move to the bottom right ring, which I'd call a cycloheptatrienone ("hepta" = 7, "trien" = 3 double bonds, "one" = ketone functional group). See how the double bonds are shuffled around in the stock photo? That would be OK, since the system does have other resonance structures, forms where just the electrons move around without breaking the carbon framework. But this structure, where the C=O and C=C bonds overlap, makes 5 bonds at that carbon. That only happens under very specific conditions, but certainly not in this drug.

Finally, check out those bonds on the left. We organic chemists use bond notation to infer a lot of crucial details, not least which atoms connect to which other atoms! Note the line drawn from the 6-membered ring to the "C" of the bottom methoxy (H3CO-) group. Perhaps an artistic choice, centering the group over the bond, but the real molecule shows a C-O bond. 

I know photographers don't often consult chemists before they take these shots, but I'd invite their input here. Wouldn't their business do better if their photos were accurate? 

Speaking as a scientist-cum-designer, it would make my job easier.

Happy Friday, everyone.

-SAO

WWWTP? "Third-Party" Edition

Source: Kishida Chemical

A blog buddy sent along this puckish reminder of customer perception in the crowded chemical sourcing market. Seems Oakwood Chemical, a U.S.-based supplier, recently partnered with Kishida, a Japanese fine chemicals company.

Kishida specializes in med-chem building blocks, but seems to have a problem with their structure-drawing program (right)...where did all the hydrogens go? Don't think it's just on the website - the catalog goes 50/50 for abnormal heteroatom saturation.*

Readers, am I missing something (other than those "H" atoms)? Is this part of some common fragment representation, or is it just lazy drawing?

Comments welcome.

*For a good time, check cyclobutylhydrazine dihydrochloride (PK0-13441), which seems to be missing a record five (5) hydrogens! Can anyone top that?

Whimsy

Walking through a used book store today, I happened across the "Science and Math" section (hardly by coincidence). One of the better collections I've seen in awhile, it had a few copies of Feynman's QED and Six Easy Pieces, Kaku's Physics of the Impossible, and even biographies of Niels Bohr and Jane Goodall.

I ended up with a copy of Dawkins' The Blind Watchmaker, for $7.14.

An inveterate "skimmer," I often leaf through the old books before I pick them up. Many times, they have handwritten notes from a class, business cards, sometimes even personal photographs or "to-do" lists. On this particular occasion, I happened across a special surprise in a book titled Elementary Chinese.

I left it in the book. Maybe someday you'll find it [wink].

Chemical Rosetta Stone

Clever ad, or linguistic marvel?

The other night, while eating at a fine American gourmet restaurant, I happened upon some "found chemistry" on a soda cup (see right).


At first, I downplayed it to sketchbook advertising gone mainstream. After thinking about it some more, though, I realized it was really a clever little doodle. Consider the Rosetta Stone, a stone version of "Hieroglyphics for Dummies" that allowed Egyptologists to begin deciphering the ancient script via Greek, which they knew. 


This graphic bridges four linguistic worlds: English, Spanish, chemistry, and symbolism (see how it's drawn in the shape of a water droplet?). Naturally, I couldn't get the concept out of my head, and decided to try my hand at a few of my own.


*DISCLAIMER - I am a scientist, not an artist. WYSIWYG.

Memes and Bandwagons

I'm interested in how internet memes get started; it's probably the same mob psychology that drives events like Black Friday or stock market bubbles. Either way, when I read Carmen Drahl's Haystack post with the handwritten chemical structures, followed by Chemjobber's homage, I felt the urgent need to actively participate in what is, undoubtedly, the next big thing on the internet: structure drawing!!!



Perhaps I should link this to a catchy jingle, or a flashing banner ad?

 So, there you go, now I'm part of the groundswell. Feel free to comment or critique, I'll even start you off: yes, I know my hydrogens look like "4's", and the persnickety demands of my postdoc advisor for exactness drove my desire to cap off those alkyl stereocenters with an actual group. 

'Til we all meet again on YouTube, 14,000,000 hits later...