Category Archives: Chemistry

Friday Link-o-Rama

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The Russian cruise missile submarine Kursk went down in the Barents Sea, killing all aboard.  The first link has interesting pictures of the remains of the sub after it had been recovered. The second has interesting background information.

Need a spectrograph for your backyard telescope?  Check out this cool instrument from SBIG.  The good folks at Brookhaven have a table of nuclides online as well as a “Nuclear Wallet Card“. Golly, maybe one day we’ll have electricity too cheap to meter…

Check out the Deep Space Exploration Society- DSES.  They have resurrected a pair of dishes for the purpose of amateur radio astronomy.  They have been doing a sky survey at 1420 MHz.

Looking for something more refractory than the head of Karl Rove?  Check out FiberFrax.

Where are all the BA/BS organic chemists?

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Over the years I have interviewed many hopeful candidates for a position of entry level BS/BA bench chemist in a synthesis lab.  Recently, I have interviewed a couple of candidates for synthesis chemist position and have refreshed myself with the challenge. 

It is surprisingly difficult to find and hire a decent candidate for position as a synthetic chemist at the bachelors level.  In fact, I am having trouble finding fresh BS/BA graduates that can show me the mechanism for the acid catalyzed hydrolysis of an ester, or can suggest a reagent for the reduction of benzaldehyde to benzyl alcohol.  These are fundamental transformations and a BA/BS in chemist should be able to go to the board and noodle through a little bit of arrow pushing.

Most of the candidates sent in by our favorite temp agency are analysts either by temperament or by experience.  Granted, analysts may be the meat and potatoes of the temp chemist trade.  But what astonishes me is the small number of candidates out there with more than 2 semesters of organic chemistry and an even smaller number with any inorganic lab experience at all. 

In previous searches we have looked for BA/BS people from an ad in C&EN.  Rarely did we find that students had taken an advanced organic class/lab, let alone an organic qual class.  I know that such classes are offered out there.  Are all of these bachelors level students who take advances coursework going to grad school or med school?  Maybe most of them are.

As a former supervisor of undergraduate research, I am tickled pink that bachelors students are getting experience with advanced equipment, but we still need to graduate people who can make a target molecule and fish it out of a product mixture.  I’m glad that Bobby or Suzie can do capillary electrophoresis or use a peptide synthesizer to make a decapeptide.  I just hope that a few students are learning how to take a substrate through at least two steps of a literature procedure synthesis and then purify by fractional distillation or a recrystallization.  Furthermore, I hope that chemistry departments are still hiring an occasional mainstream organic chemist or inorganic chemist who can pass along lab techniques.

Perhaps the bachelors organikkers are drawn to grad school for advanced education.  That is what I did.  But I’m still shocked by the number of bachelors level candidates I see that show very little retention of organic concepts, apparently the result of disuse in their junior or senior years. 

Part of this problem might be geography as well.  My region does not have the industrial legacy that other regions have.  Perhaps the situation might be different in NJ, CT, or TX. 

Sorry. I’ve filled the position, so don’t send a resume.

Boron Cosmochemistry

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Next time you wash your laundry with borax, pause for a moment and consider the path those boron atoms took to get to your dirty shirts.  The Big Bang started the universe with H, He, and maybe a bit of Li.  The rest of the periodic table had to be produced by nuclear reactions within the core of a star or during the explosion of a star.  This occurs through either the fusion of charged nuclear particles (nuclei included) or absorbed neutrons to nuclei, perhaps followed by a decay cascade.  Note to reader: astronomers are in the habit of referring to elements heavier than helium as a “metal”. 

In the core of a star there exists a complex kinetic circus of multiple simultaneus synthetic channels involving both atomic weight buildup and disintegration.  Nuclei less sensitive to the reaction conditions may accumulate and delicate nuclei like boron have but a fleeting existance and are consumed.  In addition to stability to the reaction conditions, particular combinations of protons and neutrons tend to be more stable and accumulate if only by the lack of propensity to decay. 

While the elements C, N, and O are cosmically quite abundant, at least in comparison to the rest of the elements (3 to 92), the elements Li, Be, and B (LiBeB) are relatively scarce. 

Because boron was too heavy for Big Bang nucleosynthesis and too reactive to accumulate in a stellar core, it’s cosmic abundance is low.  What little that is found did not arise as simple boron ejecta mechanically boosted into the interstellar medium by an explosion or as entrained mass from stellar wind.  It was formed from more abundant elements like CNO that had already been ejected- elements that would be subjected to a barrage of highly energetic particles.

LiBeB are thought to be “spallation” products from interstellar CNO collisions with cosmic rays.  From the linked chart, we can see that C, N, and O are relatively abundant.  So over a multibillion year timeframe of stellar evolution, early massive stars can live and die, dispersing metals into nearby space.  Accumulated heavy elements can then be exposed to cosmic ray fragmentation.  The source of the cosmic ray particles in these collisions is somewhat up in the air.  Some of the latest thinking suggests that these energetic cosmic rays yielding spallation products are from especially energetic sources like Wolf-Rayet stars or type II supernova events.  There is an indication that boron can come from two spallation channels- cosmic ray and neutrino-induced spallation of carbon. 

So, the picture thus far- boron arises from the energetic collision of particles outside of a star.  Heavier nuclei will fragment under cosmic ray bombardment and some combination of B-11 and B-10 are formed.  What is interesting is that this is a dispersive phenomenon.  By contrast, on earth, boron is found in deposits as the hydrate of the alkali metal salt of the oxide- Borax.  There are a variety of distinct mineral compositions that contain boron.  On earth, a bit of the dispersed boron was somehow concentrated into ore bodies.  This is where geology kicks in.

Hydrothermal action near subduction zones can dissolve borates in hot, pressurized water and deposit them at the surface where the solid borates come out of solution on cooling.  This process evidently partitions the isotopes of Boron slightly.  Over time the process continues until geological events interrupt the deposition process.  If the solubility of the borates is relatively low at surface temperatures and pressures, then weathering will not further disperse them into the hydrological cycle.  Thus they form a deposit.  Layers of sediment accumulate over the borax deposit and eventually geological processes move the layer underground. Eventually, uplifting, weathering, and mining makes the deposit accessible.  Through the miracle of marketing, distribution, and 18-wheeler trucks, this spallation product can be used to clean that unsightly mustard stain from your shirt.

News Flash! Most energetic supernova ever observed was detected in the galaxy NGC-1260 by Chandra.

Blam!

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There are quite a number of YouTube videos featuring explosions.  One that caught my eye recently features the reactions (explosions) of the heavier alkali metals, Rb and Cs.  The “experiments” could be legitimate, but with television you never know.  Then there is the lab demo of the reaction betwen bromine and potassium.  My personal favorite is the combustion of Magnesium in CO2 (Dry Ice).

Some years back I decided that I would treat my class to a demo on the reduction of CO2 with magnesium.  I had already done the Mg/CO2 demo before, but I learned in Bassam Shakhashiri’s book on demonstrations that the addition of a smidgen of potassium chlorate to the magnesium would assure that the Mg would ignite properly.  Make no mistake, Shakhashiri is much beloved in the chem educator field and rightfully so. His demonstrations are legendary.

I was a little uncertain of the wisdom of using potassium chlorate, so I decided it would be prudent to try out Shakhashiri’s modification in advance. One evening in my research lab I chiseled out a small indentation in a block of dry ice and added a Mg ribbon “fuse”, Mg turnings, and the recommended mass of potassium chlorate.  I ignited the ribbon and held the second dry ice block in front of me, ready to place it on the burning Mg.  As the burn reached the chlorate there was a blinding flash and a loud BLAM! When I opened my eyes I saw that the papers on the benchtop were ablaze and that the block of dry ice I was holding prevented burning Mg frags from lodging in my clothing. The air was cloudy with MgO dust, my ears were ringing, and expletives were flying out of my mouth.

Better that it happened in private than in front of 65 students. The students’ burns would heal.  But, more importantly, the damage to my reputation would have been horrific.

A few years later at an ACS meeting, in the mens room at the convention center in San Diego, I was standing at the urinal when who should take the urinal right next to me?  Bassam Shakhashiri.  I pondered the opportunity this might present.  Suddenly the moment passed and we both finished our business and went on with our day.  One of us nearly left with a wet shoe.

Melamine in Pet Food

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The issue of melamine in pet food has come up again as more lots of pet food are found to be contaminated with it.  At least a few news outlets have published a proposed reason for this contamination by a monomer from another industrial sector.  Melamine is very nitrogen rich- 6 equivalents per mole- so if you spike grain products with it you can cause the nitrogen analysis to read higher than it normally would.  Protein content is one of the factors in the pricing of animal feed, so an additive that would contribute to an uptick in nitrogen content would raise the price or even make a non-saleable lot of feed qualify for sale. 

The nitrogen test that most people think of is the Kjeldahl test.  It is a digestion-distillation-titration method that affords total nitrogen.  This test is still in wide use and is inexpensive to conduct.  A friend who has an Ag Lab still does the test on a bank of burners in his lab for total nitrogen in feed samples.

The practice of adulteration of foodstuffs not limited to China.  As an undergraduate I worked in a dairy processing plant lab and we had to screen for several kinds of mischief.  Dilution of milk with water is an old trick, given that pricing is on a per pound basis, so we had to test each raw milk tanker for total solids content.  We also tested for pH and temperature.

Neutralization of partially fermented raw milk with NaOH was also practiced at one time, so we taste tested each tanker as well since neutralization could not mask off-flavor.  Finally, we had to carefully screen raw milk for residual antibiotics.  Mastitis is an inflamation of the udder and has many causes. One aggravating factor is the common practice of milking ol’ Bessie three times a day.  A sick cow has to be taken off-line to recover. This reduces the productivity of the cow.

Farmers were often tempted to give sick cows a big jolt of antibiotic and get her milking again before the time needed to fully recover and clear the system of antibiotic. This could lead to antibiotic contamination in the tanker.  We performed two tests for penicillin at our plant. The microbiological test we performed was the Bacillus stearothermophilus disk assay. The other was a radiological assay called the Charm test utilizing C-14.  This test could be performed in 20 minutes, whereas the B. stearothermophilus test took 6 hours or so.  The newer Charm tests now take only a few minutes.

Residual antibiotics found in dairy products on the Grocers shelf could put a dairy out of business for repeated infractions. The state health authorities took (take) a dim view of penicillin in milk.

Nanosquat

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Th’ Gaussling is getting an eye-opening introduction to the maddening world high purity products and trace element analysis.  Multiple analytical methods seems to translate to multiple layers of confusion.  I’m a 3-Nines pilgrim in a 4-Nines land of opportunity.  Ya picks yer analytical method and ya stays with it.  Cripes.

It’s an alphabet soup of methods- GDMS, ICPMS, and XRF.  Gonna hafta crack the books again. Watch out. That shadow darkening the library stacks could be cast by a trustee of the f-block.

KSR Int’l v Teleflex, Inc. SCOTUS No. 04-1350

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The authors at Anticipate This! provide a good resource for those of us interested in IP and patents.  They have posted a summary of the recent KSR decision by the US Supreme Court.  If you’ve never read oral argument transcripts from the Supreme court, I would urge the reader to do so.  It’s fascinating.  No matter what you may think of the Supreme Court Justices politically, as a rule they are exceptionally sharp characters. 

We scientists spend very little time with lawyers and judges, other than for the usual public drunkenness or bitter divorce proceedings, so we may not have a calibration point for gauging their scholarly expertise.  Certainly reading transcripts or an actual decision will give the reader insights into who turns the big boat and what the rationale was.

I’m not a legal scholar- I’m more like a NASCAR fan.  I like to watch the legal wreckage go flying through the air and the pit crews scrambling for cover.  In this case, it looks like the USPTO may have to scramble to recalibrate the measure of obviousness.  Hey, pass me a beer …

BLEVE- Boiling Liquid Expanding Vapor Explosion

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There is kind of fire behaviour called a BLEVE– Boiling Liquid Expanding Vapor Explosion.  A BLEVE is what happens, for instance, when a closed container of flammable liquid is exposed to strong heating.  It can be caused by an external source, like a pool of burning liquid around the container, or it can result from a runaway reaction within a drum, cylinder, or tank.  The internal pressure builds up more rapidly than it can be vented and the containment fails, often explosively. It is interesting to note from the above link that boiling action of the liquid phase in the container absorbs energy and has a cooling effect, but there may come a point where the vapor pressure rise above the liquid exceeds the capacity of the relief discharge capacity and the vessel fails, discharging liquid and vapor across the burn zone.  At minimum, discharge and ignition will lead to a large flare, or if conditions are right, an actual detonation of the fuel/air mix could happen over a relatively large space.

These things often begin with some kind of tank or tanker accident (link updated 6/10/16) resulting in a discharge and ignition of flammable liquid.  As responders arrive they find a burning pool under or next to the tank(er).  Naturally, firemen and bystanders try to help those who may be hurt. As the minutes tick away and the fire becomes more aggressive and the tank gets hotter, the firefighters get their equipment in place and attempt to cool the tanker and suppress the fire.  Suddenly the tank fails and there is a prompt bulk discharge of liquid and vapor yielding a large fireball which may include an explosive shock, flying metal debris and a dangerous heat pulse.  It is at this point that the surviving bystanders and responders see the error of their ways.

Containers of flammable liquids rarely explode in a symmetric fashion so the container or its fragments are likely to be sent flying at high velocity, possibly spewing flammable material as it moves.  Even a relatively small volume of flammable liquid dispersed explosively can fill a large surrounding space with a fireball.

All chemical plants have their protocols for emergency response.  It is important for those in charge to recognize an incipient BLEVE and respond accordingly.  But even academic chemists should familiarize themselves with the phenomenon.  A fire in the lab engulfing closed containers of flammable solvents is extremely dangerous and very quickly firefighting may become your last earthly act, especially without personal protective equipment.  It is easy to under estimate the violence of these things.

Every lab person needs to look inward and decide what their personal limit is for dropping the fire extinguisher and running for the exit.  In my sophomore organic labs, the seed I planted in the students mind was this: The main purpose of a fire extinguisher was to fight your way to an exit.

Mixing and Unmixing

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Today was take-your-kid-to-work-day.  In honor of this we put on a chemistry show in one of the labs.  Burned some Mg ribbon, shrunk some balloons in LN2, blew up some balloons with dry ice, reduced iodine with ascorbic acid, and we unmixed some NaCl and carbon black. 

One of the barriers to teaching chemistry is a level of physical abstraction that is hard to get around.  It is hard to get around trivial explanations when the audience is not ready to discuss electrons.  Many of the really insightful concepts in chemistry are inherently abstract and age inappropriate for the younger crowd, so to compensate, chemistry demonstrations are often heavy in the whizbang components.  That’s fine.  It should be fun and visually appealing, especially for K-6. 

I like to do mixing and unmixing because it demonstrates something about materials handling.  It also represents an activity that occupies much of our time.  Separation science is not commonly called “unmixing”, but for chemistry demonstrations it causes kids to ponder the problem for a bit.  They all have experience in mixing things- we talk about that.  Then I ask the question “What if I asked you to unmix that KoolAid”?  A few of the more worldly ones might suggest boiling off the water.  But most kids seem to be stumped- they will admit that they would have never considered the possibility of unmixing. 

So we dissolve some NaCl in water and make a solution.  The use of a magnetic stirrer and stirbar makes way for a minor diversion with magnets and iron filings. Then we blend in a bit of carbon black. Using a Buchner Filter, filter paper, and Celite, we do the vacuum filtration, showing the remains of the carbon in the Celite.  The filtrate is then treated with some “Anti-Solvent” like acetone and the salt comes crashing out. 

Yeah, I know. It is pretty tame.  But it can be done cheaply in 45 minutes and the kids can see their parents actually doing something. 

Happy 100th Birthday Albert Hoffmann!!

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Albert Hoffmann, the discoverer of LSD, turned 100 years old this year on Juanary 11th.  Happy Birthday, Albert!  Scienceblogs.com relates the story of Hoffmann’s first deliberate LSD trip on April 19th, 1943.  You might recall that Hoffmann was the Sandoz chemist who stumbled upon the psychotropic activity of lysergic acid diethylamide.  

Just this last week, the medical journal The Lancet called for an end to the “demonization” of psychedelic drugs, according to Guardian Unlimited.  The motivation behind the editorial in the Lancet was to urge a loosening of taboo’s connected with the use of psychedelic compounds.  The widespread criminalization of psychedelics has made research with these interesting molecules quite problematic. 

Perhaps the day will come when such materials are decriminalized and it will be possible to visit a psychedelic spa where one could go to have a safe dosage administered by qualified staff.  But it wouldn’t be all fun and games, though.  While the euphoric experience can be prolonged and profoundly vivid, there is a dark side.  An account of the experience of the psychiatrist Werner Stoll is described in Chapter 4 of Hoffmanns book “LSD. My Problem Child”.

Hoffmann and Sandoz would watch their discovery move from a psychiatric adjunct to a full fledged inebriant adopted by a counter culture movement.  In his book, Hoffmann laments-

    This joy at having fathered LSD was tarnished after more than ten years of uninterrupted scientific research and medicinal use when LSD was swept up in the huge wave of an inebriant mania that began to spread over the Western world, above all the United States, at the end of the 1950s. It was strange how rapidly LSD adopted its new role as inebriant and, for a time, became the number-one inebriating drug, at least as far as publicity was concerned. The more its use as an inebriant was disseminated, bringing an upsurge in the number of untoward incidents caused by careless, medically unsupervised use, the more LSD became a problem child for me and for the Sandoz firm.

    It was obvious that a substance with such fantastic effects on mental perception and on the experience of the outer and inner world would also arouse interest outside medical science, but I had not expected that LSD, with its unfathomably uncanny, profound effects, so unlike the character of a recreational drug, would ever find worldwide use as an inebriant. I had expected curiosity and interest on the part of artists outside of medicine-performers, painters, and writers-but not among people in general. After the scientific publications around the turn of the century on mescaline-which, as already mentioned, evokes psychic effects quite like those of LSD-the use of this compound remained confined to medicine and to experiments within artistic and literary circles. I had expected the same fate for LSD. And indeed, the first non-medicinal self-experiments with LSD were carried out by writers, painters, musicians, and other intellectuals.

Today, psychedelic substances are considered to be drugs of abuse and their use will lead to a long stay at the Gray Bar Hotel. Our Puritanical heritage seems everlasting. But rather than wallow in pity for my unenlightened brothers and sisters, I look forward to a brighter future where one could sit in a licensed psychotropic suite and explore the deepest recesses of consciousness brought out in full non-linear display, say, while listening to music. Everybody associates acid rock with LSD. That’s too easy. I’ve often wondered what it’d be like to listen to Leon Redbone in an altered state of consciousness.  Kinda curious about what a baritone sax does to a brain on acid.  Or David Bowie- Major Tom.  I’m showing my age.