Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: derekb.lowe@gmail.com
Twitter: Dereklowe
I've been evaluating an interesting and useful piece of equipment the last few days, and getting a lot of things done with it. At about 8:20 this morning, though, I marched into the lab and proceeded to clog, mis-plumb, and generally absurdify the thing, and I've spent the rest of the day trying to get back to the way things were at 8:15. You know, before I laid my magic hands on the apparatus and gave it the healing touch. Honestly, I couldn't have done a more complete job if I'd been wearing a rainbow wig and honking a horn.
At the moment, all seems to be working, but I've labored under that illusion several times today. If this doesn't do the trick, I'm going to bring in a troupe of Pomeranians and train them to jump over the thing. Sheesh.
3. Anonymous BMS Researcher on May 29, 2009 3:37 PM writes...
Ah yes, I call such days my "left-handed baboon" days (meaning an ape would have done a better job than I did on such a day).
In his book Memoirs of a Computer Pioneer, Maurice Wilkes describes the moment when he "realised how much of the rest of my life would be spent fixing my own mistakes." In other words, he was among the first programmers to learn the painful art of debugging.
My usual take on these days is the disastrous reverse-phase column. You know the type - load your gear on, and start the run, finding that all the components come out together, over eighty fractions. And then spend the rest of the day removing the sodding methanol / water, and dealing with the times it decides to crash-out and bump, or form a gelatinous foam, and evenatually, eight hours later, end out with exactly the same crude, except minus 20% mass, and brown for some reason. Argh.
Do not despair. There are always the undergraduates in teaching labs who use magnesium sulfate in a futile attempt to dry and then proceed to rotovap their aqueous layer. Oopsie!
Everyone is entitled to their share of mistakes. Just don't let me catch you rotovapping your aqueous layer too often..............
Its not your fault: Nature resists the inquiry on some days more vigorously and any attempt to overcome the spell by persistence and hard labor only makes things worse. But few early-afternoon drinks, a big steak and a good sleep sometimes help to break the curse.
By the way, are you setting up a chiral prep HPLC column? It would be very nice if you could share the experience.
#4 - I learned the hard way that my greaseball compounds do not run on C18 reverse-phase HPLC. Nothing is quite like having to switch between about four different solvent systems to get the thing out...
#4, #9 - I work with really non-polar compounds, and i ended up just giving up on reverse phase HPLC.
I switched to semi-prep normalphase and, while it has some problems, i can actually separate the stuff i want out in a reasonable (~30 minutes) amount of time, using 6:1 HX:EA.
Course, we have a multiuser HPLC and i end up spending an hour at the beginning and end just cleaning it out, but i did separate the regioisomers.
Methinks Derek was describing a flow reactor of some type. Perhaps hydrogenation? Oxidation? The first gen versions of these things (as recent as 2-3 years ago were desperately inadequate. Anyone had good experiences with them recently?
Over the years various devices have shown up in the lab in which unanticipated precipitation can have catastrophic (ie. lots of time and compound lost) results. There's always one person who gets it to work and pushes it but after a while even he gets tired of fixing it for every one else and the device goes to storage.
13. RandDChemist on June 1, 2009 7:23 AM writes...
Yes I have....one instance that always come to mind from the days of yore was one where I had a bad feeling about the day, right from the start. It eventually involved me starting a fire (unintentionally)! I did stick with it and got the chemistry done though.
Another vote for the flow reactor here too. The only ones that seem to be reliable are the one ones custom made for a specific process -- like the ones occasionally mentioned in OPRD. I've tried out a few of the newer off-the-shelf ones in the past year and they've all been junky.
15. wackyvorlon on June 17, 2009 7:12 PM writes...
There is a term that was popular in the 19th century that I like to use for this sort of situation. That is "derange the mechanism". Indeed, you appear to have deranged its mechanism. My sympathies are with you.
I did something similar with a Vapourtec flow reactor yesterday, mainly out of inexperience with the system. Looked like it was going well for a little while, then DIPEA.HCL crashed out during the course of the reaction (in AcN). Learned the hard way that I should have either used DABCO, wet AcN, or tributylamine according to my colleagues. Anyway, clogged the thing and managed to get all the solids flushed through the PTFE tubing. Solids appeared to be clogging the one pump head - the check valves and pump head were carefully cleaned and free flowing. Re-assembled everything, and it's not working. Can't prime the pump, has alot of trapped air and isn't pumping anything. Has anyone had this happen? Advice? We're trying to contact UK, but those guys have all gone home by now.
1. Sili on May 29, 2009 2:35 PM writes...
I've had days where the diffractometer (and/or the crystals) just refused to coƶperate.
And of course I've had days where it took me three or four hours to realise I'd forgotten to turn up the generator ...
Permalink to Comment2. Fred on May 29, 2009 3:21 PM writes...
Absurdify will be another useful addition to my vocabulary.
Permalink to Comment3. Anonymous BMS Researcher on May 29, 2009 3:37 PM writes...
Ah yes, I call such days my "left-handed baboon" days (meaning an ape would have done a better job than I did on such a day).
In his book Memoirs of a Computer Pioneer, Maurice Wilkes describes the moment when he "realised how much of the rest of my life would be spent fixing my own mistakes." In other words, he was among the first programmers to learn the painful art of debugging.
Permalink to Comment4. Tot. Syn. on May 29, 2009 4:14 PM writes...
My usual take on these days is the disastrous reverse-phase column. You know the type - load your gear on, and start the run, finding that all the components come out together, over eighty fractions. And then spend the rest of the day removing the sodding methanol / water, and dealing with the times it decides to crash-out and bump, or form a gelatinous foam, and evenatually, eight hours later, end out with exactly the same crude, except minus 20% mass, and brown for some reason. Argh.
Permalink to Comment5. JMB on May 29, 2009 7:25 PM writes...
When stuff like that happens on Friday, it's a sign that it's a good day to go home early.
Permalink to Comment6. T on May 29, 2009 8:42 PM writes...
Do not despair. There are always the undergraduates in teaching labs who use magnesium sulfate in a futile attempt to dry and then proceed to rotovap their aqueous layer. Oopsie!
Everyone is entitled to their share of mistakes. Just don't let me catch you rotovapping your aqueous layer too often..............
Permalink to Comment7. milkshake on May 29, 2009 8:52 PM writes...
Its not your fault: Nature resists the inquiry on some days more vigorously and any attempt to overcome the spell by persistence and hard labor only makes things worse. But few early-afternoon drinks, a big steak and a good sleep sometimes help to break the curse.
By the way, are you setting up a chiral prep HPLC column? It would be very nice if you could share the experience.
Permalink to Comment8. dorf on May 30, 2009 6:36 AM writes...
Murphy was an Optimist...
Permalink to Comment9. Norepi on May 30, 2009 4:37 PM writes...
#4 - I learned the hard way that my greaseball compounds do not run on C18 reverse-phase HPLC. Nothing is quite like having to switch between about four different solvent systems to get the thing out...
Permalink to Comment10. Erich on May 30, 2009 6:14 PM writes...
#4, #9 - I work with really non-polar compounds, and i ended up just giving up on reverse phase HPLC.
Permalink to CommentI switched to semi-prep normalphase and, while it has some problems, i can actually separate the stuff i want out in a reasonable (~30 minutes) amount of time, using 6:1 HX:EA.
Course, we have a multiuser HPLC and i end up spending an hour at the beginning and end just cleaning it out, but i did separate the regioisomers.
11. PorkPieHat on May 30, 2009 9:05 PM writes...
Methinks Derek was describing a flow reactor of some type. Perhaps hydrogenation? Oxidation? The first gen versions of these things (as recent as 2-3 years ago were desperately inadequate. Anyone had good experiences with them recently?
Permalink to Comment12. anon the II on May 31, 2009 2:13 PM writes...
Flow reactor was my first guess also.
Over the years various devices have shown up in the lab in which unanticipated precipitation can have catastrophic (ie. lots of time and compound lost) results. There's always one person who gets it to work and pushes it but after a while even he gets tired of fixing it for every one else and the device goes to storage.
Permalink to Comment13. RandDChemist on June 1, 2009 7:23 AM writes...
Yes I have....one instance that always come to mind from the days of yore was one where I had a bad feeling about the day, right from the start. It eventually involved me starting a fire (unintentionally)! I did stick with it and got the chemistry done though.
Permalink to Comment14. Bombauer on June 1, 2009 3:34 PM writes...
Another vote for the flow reactor here too. The only ones that seem to be reliable are the one ones custom made for a specific process -- like the ones occasionally mentioned in OPRD. I've tried out a few of the newer off-the-shelf ones in the past year and they've all been junky.
Permalink to Comment15. wackyvorlon on June 17, 2009 7:12 PM writes...
There is a term that was popular in the 19th century that I like to use for this sort of situation. That is "derange the mechanism". Indeed, you appear to have deranged its mechanism. My sympathies are with you.
Permalink to Comment16. anon on July 1, 2009 1:56 PM writes...
I did something similar with a Vapourtec flow reactor yesterday, mainly out of inexperience with the system. Looked like it was going well for a little while, then DIPEA.HCL crashed out during the course of the reaction (in AcN). Learned the hard way that I should have either used DABCO, wet AcN, or tributylamine according to my colleagues. Anyway, clogged the thing and managed to get all the solids flushed through the PTFE tubing. Solids appeared to be clogging the one pump head - the check valves and pump head were carefully cleaned and free flowing. Re-assembled everything, and it's not working. Can't prime the pump, has alot of trapped air and isn't pumping anything. Has anyone had this happen? Advice? We're trying to contact UK, but those guys have all gone home by now.
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