Tuesday, June 4, 2013

One inorganic chemist's thoughts on ChemDraw app for iOS

I have a "go to" molecule whenever I download a new version of ChemDraw. It's molybdenum hexacarbonyl, drawn like this:

Sheer octahedral beauty, no?

The reason I feel the need to have a test molecule speaks to the love/hate relationship I have with the program, which I imagine is shared by many inorganic chemists. For many years, ChemDraw (or whatever it's called now: ChemBioPhilosoDraw or some such) neglected the inorganic community. To give you one example, if I wanted to draw molybdenum hexacarbonyl, I could do it in a few ways:

Small, large, and super-sized molybdenum hexacarbonyl.

Each is a valid structure, although the one on the right is extremely clumsy due to its size and the time it takes to fully draw. I often use the middle depiction because I used Mo(CO)6 as a precursor to other hexavalent Mo compounds and can easily replace the CO ligands with whatever new ligands I add. However, if you were to look at the analysis window in for that depiction of Mo(CO)6 in older versions of ChemDraw, you would see the following:


ChemDraw would secretly add hydrogens to all the carbonyl ligands, making them, unknown to the user, formyl ligands. There is an option in the ChemDraw preferences that says "Automatically Rectify Hydrogens in Atom Labels" that, if unselected, would not add these phantom hydrogens.

However if you were to save your structure and open it at a later time, the hydrogens would secretly be there! (No matter the settings in your preferences.) Arrgh! Even worse, if you copied and pasted within the same document, the phantom hydrogens would also be present again!

This may sound like a little thing, but it means every time I would run a mass spec or elemental analysis of my compounds and the results came back awry, I would have to go back and recalculate my structures making sure there weren't any phantom hydrogen atoms present on my CO ligands. I always double checked before submitting my samples, but I always had to check one more time just to be sure.

Oh, I almost forgot. I'd also have to check any phosphorus and sulfur ligands, if present, to make sure the program hadn't just randomly added (in these cases non-phantom) hydrogens to these atoms as well. Because, yeah, that happened sometimes too.

I was extremely glad that the phantom hydrogen problem with carbonyls seems to have been cleared up with the release of ChemDraw 13 (I know it affected versions 10 through 12 at least), but I keep checking for similar mistakes because I've gotten the notion that there aren't a lot of inorganic chemists over there testing their products before release.

Which brings us to today and the release of the ChemDraw app for iOS. Let me just start off by saying that it's great that ChemDraw finally put out a mobile app. Ever since I first got my iPad I've been looking for ways to incorporate it into the lab and my work in general. Unsurprisingly, there haven't been a lot of apps released with the serious chemist in mind, so it's nice to see that changing.

That being said, today comes and I buy the ChemDraw app right when I'm awake enough to notice it's a thing I can buy, and I open the app on my iPad and start drawing moly hexacarb (as I like to call it because I'm cool like that). I get this far lickety split:*

Quick and easy!

The drawing is straight forward for those used to the iOS interface and ChemDraw in its other iterations. I will point out that the "clean-up" functions seems to work well on the app (my hexamethyl molybdenum wasn't quite this octahedral to being with), although you sometimes have to hit it a couple of times to get the desired result.**

But then I try to figure out how to reduce this sucker down to the carbonyl and it takes me 15 minutes to realize I have to do this:

So much work, the blog cannot even contain it!

And then I have to do it five more times, which doesn't take too long, but man is it annoying to put all those triple bonds in, and I'm left with the super bulky and clumsy depiction of Mo(CO)6 that I do not like.

The reason you have to do this can be found in the FAQs on the app itself:
Text input is not currently implemented. Atom labels can be modified using the Atom or Functional Group tools only. If you wish to add captions or make other modifications to labels within the document you should export the document to the desktop application.
Well sucks for us non-organic chemists. Every included functional group included is organic: Ac, Bu, CN, CONH2, COOH, Et, Me, NO2, OMe, Ph, Pr, and tBu. Also included are generic labels A, M, R, and X.

What if we want something with pyridine ligands? Something from the cyclopendatienyl (Cp) family? I occasionally use Tp as a ligand. I'm not drawing that out, nosiree.

This is what I love about my desktop version. It handles a lot of complicated inorganic structures without too much trouble (especially now that I'm using version 13). This starts with being able to input your own text into the atom labels. I'd much rather type in "SCN" at the end of a bond than draw out the structure of the thiocyanate ligand. It's faster and I'm that lazy.***

It's not that I expect them to be able to handle all the really tricky metal bonding stuff that is out there: fully drawn out Cp rings and phenyl rings in sandwich compounds or detailed depictions of dihydrogen and dinitrogen compounds, but the text input seems like a really basic feature (so basic that it took me a while to realize it wasn't there, even though I use it so much in desktop ChemDraw).

Their FAQ answer makes me believe that they will add this functionality in the future, which I hope they do. I was looking for an app that I could use in the lab to help me make notes, teach students, or determine molecular masses (which it does quite nicely for any drawn structure, btw). But unfortunately, the app does only one job well, and that's draw organic molecules. Even organic chemists cannot write out reaction schemes with their reagents over the arrows of the reactions yet, so there are limitations all around. But the limitations are too much for me to recommend this to any inorganic chemists who are looking for a useful tool for their work.

That being said, at $9.99 (for those of us in the US) it's not the astronomical price of a ChemDraw application that we've all grown to expect, so you can probably buy it anyway and not feel too bad it doesn't do everything you ever wanted... yet.

* All chemical drawings in this post purported to be from the iPad were painstakingly recreated in exquisite detail on my desktop ChemDraw program because I'm not tech savvy enough to get the files transferred between devices quickly yet. I'll probably need some teenage children to show me how.

** I will note that after drawing pentane in the "M" fashion as I prefer, the clean up button switched it to the "W" orientation, which I dislike. But it made the angles nice and 120 degrees.

*** Plus, I probably would mess the bonding up on the first go around and put it as all double bonds between the atoms or some similar abomination.

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