Org Prep Daily

July 12, 2010

Look ma, no bromine!

Filed under: mechanisms — milkshake @ 3:57 pm

After heating up some simple 2-chloro-4-amino-5-bromopyrimidines with an excess of p-MeS-aniline, I got the corresponding 2-anilino-substituted products  - but with the bromine clipped off. The aniline was apparently the reducing agent in this case, producing lots of deep-blue colored oxidized aniline stuff in the process.

I suppose it has to do with the chemical similarity of this aniline with the leuco form of methylene blue, a known reducing agent.

July 7, 2010

All your structure are belong to us

Filed under: Uncategorized — milkshake @ 7:02 pm

I downloaded Symyx Draw this morning, it is offered as a free program for academia. It is used for drawing reaction schemes, creating SMILES strings, entering structures into Symyx databases, etc. and I am quite anxious to get rid of it: Symyx Draw automatically assigned Chemdraw files to a default association with itself (all files, not just those accessed by/copied into Symyx Draw).  And now when I try to reset the file association back to Chemdraw with the help of Chemdraw file connection prompt my computer would ignore the change. A newly drawn Chemdraw file then comes out with a cheerful Symyx icon and will reopen with Symyx Draw too (unless I rightclick and select Chemdraw from the list)….  I do not wish to have all my Chemdraw files appropriated by Symyx Draw without myself deciding to do so. And its not like that they would have asked during the installation. And I resent that in this way they try to mess with a functionality of a (better) competing software that we have already purchased.

I have had some experience with this company: after Symyx acquired MDL, Symyx stopped offering standalone ACD access subscription. (Available Chemical Directory – the most complete database of commercially-available chemicals, their pricing and vendor contact info). Symyx wanted the MDL customers to switch to their Symyx Discovery Gate “all inclusive” chemical search package which also bundled ACD access in it. The cost of the Discovery gate is so high that many academic institutions cannot afford it; for example my current employer does not have it. But I had the misfortune of struggling with the  Discovery Gate in my previous job – its  Java-heavy web-based interface provides the ACD search functionality too – but for me the most important difference was that a regular search that used to take one or two click per compound with the standalone ACD database from MDL was now taking about ten clicks per compound  in the Discovery Gate (with the extra download delays in between): now try to browse through few hundred compounds in the ACD database with this dog. A Symyx customer service representative informed me that they were not offering the standalone access anymore but I could put my concerns into writing (I wrote them an e-mail and I never received a reply to it).

Also, several times I spoke with our chem-informatics guy at the previous job, about our compound submission database – we used to have a simple one from MDL that worked perfectly well  - before it got integrated into a spiffy new Symyx database. And he too has been really frustrated with the Symyx chemical inventory and bio data integrated database that we were using thereafter for our compounds and biology data and chemical collections and high-throughput screening – all in one unwieldy mammoth database. He told me that he had to eventually get a third party software and write a new interface for us in chemistry just to help us with viewing and searching our compounds after we had entered them into the Symyx database (for which our employer paid hundreds of thousands USD). He said he felt hamstrung by having to work with this enormous and poorly designed package that someone high above in the management had chosen for us.

I suppose is always the same – a ginormous all-inclusive package that hardly does any of its basic functions well – and the company that does not care about the needs of the users and promotes its “complete solutions” to the management folks who actually decide about purchasing this stuff… I have the impression that when Symyx bought MDL it set out to max up the profits while riding on the popularity of MDL software; I think in the long run Symyx will drive away many MDL customers by these tactics and will not create too many new ones because eventually the word gets around. For example the ACD access is pretty important but in the end one can get a list of vendors and commercial availability/pricing info from alternative sources.


The individual Chemdraw licence complete with a decent manual costs about $170 for academia and private users (I bought one for myself last year when I needed to prepare my job presentations). I have no special love for CambridgeSoft but at least they never pulled a surprise like this on me and never told me to go and stuff myself with my concerns.

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