A scent of fresh soil

Our lab has been smelling a lot like disturbed soil lately, due to my work with 2-ethylfenchol. The flavor and fragrance division of Aldrich is a good place to start when you need highly hindered tertiary alcohols. While many of the low-molecular weight tertiary alcohols are minty and camphor-like, Et-fenchol smells like dirt. Actually in the concentrated state it reeks similar to TBS-silanol, but stronger. In more diluted form though it has a clean smell of freshly dug-up moist earth –  the smell is persistant and very convincing; a colleague asked me if he could wear ethylfenchol on his shroud when he goes to a Halloween party dressed as a mummy.

Turns out, 2-ethylfenchol prepared from (+)-enantiomer of fenchone has been developed with a specific purpose: as a substitute for geosmin – the terpenoid metabolite produced by soil bacteria that makes soil smell earthy. The earthy note is desirable in some compositions, i.e. for pipe tobacco flavoring, and since geosmin is rather hard to make cheaply a semisynthetic substitute was found. (Water utility companies are less fond of geosmin; the odor threshold of geosmin is incredibly low. Together with 2-methylisoborneol – another dirty-smelling terpenoid from soil bacteria/fungi – geosmin lends awful taste to tap water).

Et-fenchol from Aldrich comes in kosher grade, with a large seal from rabbi Gershon Segal on the bottle:

Last post

Today is my first day with a small privately held biotech company that is developing self-assembling polymers for targeted drug delivery. The group and the projects are awesome – and as much as I am excited about the research and the company, for obvious reasons I shouldn’t be writing about it. So there will be nothing new to add here. This is it – thank you for visiting!

All your structure are belong to us

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.

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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.

Back in the lab

Today was my first day at the new job.

A job interview

I just got first job interview invitation, end of this month. Its for a medicinal chemistry position – at a good place and with a group that I want to work in, and the project is also very interesting  - so please keep your fingers crossed for me.

Also, there won’t be that many updates here in the next few weeks. Maybe I can dig up some procedures from old notebooks but for now I decided put up here an ancient recording (like 40 years old) of a Czech blues song that I am quite fond of. Sorry for the incomprehensible language and less-then-awesome sound quality.

Update (4/2/10): It’s a boy!

Predetermined Conclusions 2

I suddenly found myself in HR office this Wednesday in front of assembled top four bosses, faced with immediate dismissal. The story was that I supposedly yelled at a security guard and chased him around the lab  - which I have not done - but they already had it all prepared nicely (you see, they investigated it quietly for almost three weeks and they kept the meeting secret to the last minute) and there they would not allow any facts get in a way of their neat story. They threatened and bullied - that I better shut up and sign the papers they are giving me to sign or they will fire me right there. Needles to say, the HR meeting did not go down too well but it became noticebly nicer towards the end, especially after the boss of the translational research institute screamed on top of his voice that he is in control of the entire budget and that I am messing with the wrong guy – and then stormed out. (He threatened to leave the meeting unless I apologize for saying that their story makes no sense - and I observed that it would be perhaps helpful if he could leave the meeting).

What they insisted on was that I must undergo anger management treatment with therapist of their own choosing and they handed me a consent form – to sign away all my confidentiality over to HR, and to confirm that this is actually an employer-mandated psychiatric treatment that I am taking voluntarily so that HR could receive regular status reports from my therapist.

I guess they just tried to find out if I have any interesting personal problems and see how I am struggling through with the help of their therapist – who would then send a nice summary to HR about my treatment plan and attendance and they would just add it in the file…

I knew that they were considering layoffs next January because of the funding problems and from their nastiness I figured out that this was a cute method to have me certified as a nut so as to not to have worry about wrongful dismissal case from me in the future. Bending over and taking it from both ends would only save me couple weeks at best. So I boxed up my stuff, loaded it in my car and wrote back that  I can see someone if they insist but I am not signing away my shrink’s confidentiality over to HR. I also wrote  that it was a fine inquisition meeting – and that they should check the facts because there are people who can easily confirm that the guard story is a fabrication and that I hope they will at least have the decency to clear my name with the same eagerness with witch they have now besmirched it.

The next day my e-mail client stopped working and the PC logged itself off. That gave a hint that I should probably head down to HR so I said the goodbyes to my colleagues, handed back my keys + keycard and it was over in a civil way within few minutes.

As to why this has been staged the way it happened, there are several reasons but I think the main one was that the people I worked for got from me all what they needed, my salary just got past six figure and they were faced the financial pressure to have someone let go - in our group the potdocs cannot find staff jobs anywhere (and are willing to survive on indefinite postdoc-ship often due to the visa situation). I have had complained too much about the people here being left intentionally off the publications and cheated from their co-authorship on patents. I have been with the institute from the beginnig, and I am not an easy person to put up with, over the five years they had plenty about me on file - so they thought they can easily make it look like it I am creating some serious trouble and therefore they had no other choice but to let me go…

The reason why I wrote down all this unpleasant story is to firsthand inform my colleagues and friends who are reading this page because I did not have the time to speak with everybody before leaving.