Photophobic Chemistry

Ugg… what a pain.  The reaction I’m doing today produces a low molecular weight, light-sensitive α,β-unsaturated ketone as a product.  It’s a derivative of methyl vinyl ketone.  Not only is it low-boiling, it also polymerizes upon standing in light.  Ugg…

Now, I’ve worked with light-sensitive reagents (like the iodomethane and methallyl iodide) before, so I’m comfortable turning off the light and covering the reaction with foil to keep out extraneous photons.  That’s not so bad, because when the reaction’s done, you can flip on the light to work up the reaction.

Not so when the product is light sensitive.  Gotta keep the light off.  Gotta extract in the dark.  Gotta dry the organic layer with foil around the flask.  Gotta rotovap in the dark with foil around the flask.  Worst of all, gotta run a column in the dark.  For that, I cut off some of the sides of a cardboard box and used them as a shield to block the light and holed myself up in the dark corner of my hood to run the column.  Then gotta rotovap the fractions corresponding to product in the dark in foil.  Take the mass in the dark…  Ugg.  Pain all around.  Oh yeah, I forgot I gotta keep the NMR samples in the dark while I acquire the spectra, too.

Plus, gotta keep the product away from light until I set up the next reaction (which is going on right now)… and that’s gotta be in the dark.  At least when this reaction’s done, I can turn the lights back on.

Fortunately, the first reaction worked quite well.  I ran two multi-gram reactions side by side in the dark and got quantitative yield on both.

So while I run off to find some vitamin D supplements, tell me what the most operationally painful experiment you’ve set up is.  I’m sure many of you have stories that make mine seem trivial.  What experiment’s the biggest pain to run?  I think any reaction involving FOOF (the most awesome, most onomatopoeic molecular formula evah) has to be up there.

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Astrobiology: The Search for Life on Mars

Photo: Techchee.com

This doesn’t exactly fit in with the direction I was planning on taking with the posts on space science, but a story on MSNBC.com on Wednesday got my attention.  The story discusses NASA’s long endeavor into the search for life outside of Earth.  It used to be called exobiology (which I find to be an awesome name), but is now referred to as astrobiology.

NASA has previously attempted to find life on Mars with the Viking program in the 1970s.  Probes were sent to Mars to look for life… Earth life, that is.  The tests the probes ran attempted to find life that would exist at physiological conditions on Earth, a supposition that perhaps seems silly in hindsight.

An option in line with NASA’s recent change in direction could have the potential to bring Martian samples back to Earth for another attempt to find life on Mars.  The program – still in theoretical infancy – would last some 3-4 years and could begin in 2018 with sending a joint US/European rover to Mars to collect samples.  In 2020, a return vessel would go to Mars, get the samples, and return.

The story talks about the potential hazards of bring unknown astrobiological samples to Earth and the need to handle them in the equivalent of a Biosafety Level 4 Lab.

Anyway, my point in bringing this up is to share with you a short story – a commentary, really – by one of my favorite science fiction writers ever: Isaac Asmiov.  Asimov (also a former biochemist at Boston University) developed the Three Laws of Robotics and is the author of the original robot series that inspired movies such as I, Robot and Bicentennial Man.  If you haven’t read any of his work, I highly recommend one of his collections of short stories, such as The Complete Robot.

The commentary you should read is titled “Not as We Know It: The Chemistry of Life” and outlines what NASA scientists should keep in mind: life outside of Earth probably won’t look like life on Earth.

(in talking about life on Jupiter): An objection that might, however, be raised against the whole concept of an ammonia background for life, rests on the fact that living organisms are made up of unstable compounds that react quickly, subtly and variously. The proteins that are so characteristic of life-as-we-know-it must consequently be on the edge of instability. A slight rise in temperature and they break down.

A drop in temperature, on the other hand, might make protein molecules too stable. At temperatures near the freezing point of water, many forms of non-warm-blooded life become sluggish indeed. In an ammonia environment with temperatures that are a hundred or so Centigrade degrees lower than the freezing point of water, would not chemical reactions become too slow to support life?

The answer is twofold. In the first place, why is “slow” to be considered “too slow?” Why might there not be forms of life that live at slow motion compared to ourselves? Plants do.

He continues on to describe, in his opinion, what life might look like under the natural conditions of the various planets.  What the background medium would have to be and what the life-sustaining molecules would have to look like.  A fascinating read and a must read, in my opinion.

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Good News: Lancet Article Author Cooks Data on Vaccine/Autism Link Updated and Bumped: Lancet Retracts Wakefield’s 1998 Paper

(See important update, below)

The Times of London yesterday ran a story that Jenny McCarthy needs to read (h/t HotAir.com).  The article details an investigation of the results of the 1998 paper in the Lancet medical journal which shows a link between thimerosal in MMR vaccines and autism.  The investigation concludes the author, Andrew Wakefield, manipulated data to show the link.

Confidential medical documents and interviews with witnesses have established that Andrew Wakefield manipulated patients’ data, which triggered fears that the MMR triple vaccine to protect against measles, mumps and rubella was linked to the condition.

The research … claimed that the families of eight out of 12 children attending a routine clinic at the hospital had blamed MMR for their autism, and said that problems came on within days of the jab. The team also claimed to have discovered a new inflammatory bowel disease underlying the children’s conditions.

However, our investigation … reveals that: In most of the 12 cases, the children’s ailments as described in The Lancet were different from their hospital and GP records. Although the research paper claimed that problems came on within days of the jab, in only one case did medical records suggest this was true, and in many of the cases medical concerns had been raised before the children were vaccinated. Hospital pathologists, looking for inflammatory bowel disease, reported in the majority of cases that the gut was normal. This was then reviewed and the Lancet paper showed them as abnormal.

How convincing was Dr. Wakefield’s article?  Vaccination rates in the UK dropped from 98% to below 80%.  Some 1350 cases of measles have been confirmed in the UK, a 2400% increase over the number of confirmed cases in 1998.

Besides the obvious implications of manipulated data, no one seemed too concerned that Dr. Wakefield’s sample in the 1998 paper included only 12 children.  Time after time after time, studies have tried to replicate Dr. Wakefield’s results.  Not surprisingly (anymore), no one was able to.  Yet, that doesn’t stop parents from receiving news time warning about vaccines, the CDC from needing to issue a statement on the safety of thimerosal, the HHS from issuing money from the vaccine injury fund (!), and major presidential candidates from telling town hall attendees that there is a “strong link” between thimerosal and autism.

I don’t even think this qualifies for an Ig Nobel award.  It’s just infuriating.

Update (2/2/10): Today, the Lancet Medical Journal officially retracted Dr. Wakefield’s original 1998 paper.  The retraction was the final domino to fall in officially discrediting the specious claim linking thimerosal and autism.  How long will it take to rid the vaccine-autism link from the minds of worried parents?  That’s a different question.  Hopefully, though, doctors can now use this to help persuade overly-worried parents that vaccines are indeed safe.

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Boiling in Space: What Happens in the Absence of Gravity?

(for other entries in the Chemistry in Space series, click here)

Who knew boiling a liquid was so complicated?  When you put a pot of water on the stove or heat your reaction-in-toluene solution in an oil bath several things happen.  The liquid closest to the heating element starts to get hot.  Convection circulates the hot liquid up and the cold liquid down due to the density differences of hot and cold liquids.  Eventually, the liquid near the heating element becomes hot enough to move into the vapor phase and bubbles start to form.  Buoyancy causes the bubbles to float to the surface and pop, while more convection continues to circulate the water.  Eventually, you get a rolling boil.

Everything changes in the microgravity environment of space.  Buoyancy and convection no longer play a role.  The heated fluids no longer circulate and the bubbles no longer naturally rise to the surface.  So what happens when you try to heat a liquid to boil in microgravity?  Astronauts tested this during the course of several space shuttle missions during the 1990s.  They arrived at some very interesting conclusions.

First, the liquid nearest the heating element starts to get hot, just as it does on Earth.  But it doesn’t rise and circulate due to convection.  It just gets hotter and stays next to the heating element.  It eventually gets hot enough to move into the vapor phase, just as it does on Earth, but the bubbles don’t rise to the surface and pop.  Instead, they stay next to the heating element and coalesce into one giant bubble.  Eventually, the size of the bubble becomes larger than the heating element and there is no longer any liquid in contact with the heating element.  This insulates the liquid from the heating element and leads to a “dry out” where there is no more boiling and the temperature of the heating element “begins to soar.”

(click on the image to go to the NASA page describing Zero G Boiling and to see an awesome movie of boiling in action)

All of this is predicted by theory, but it’s nice to have the chance to do some of those proof of principle experiments for the first time ever.  It reminds me of what some of the pioneers of science must have felt when working out some of the fundamental theories of chemistry and physics that we don’t even realize we take for granted today.

An interesting variation of this experiment was conducted impromptu by an astronaut on the International Space Station in 2003.  Don Pettit* was performing repair operations using a soldering iron.  He decided to put a few milliliters of water on the hot surface.  The water droplet formed a blob around the soldering iron and kinda wobbled there.  As expected, the water heated up and began to boil.  Surprisingly, though, this time the boiling looked much similar to boiling on Earth.

My working theory is the small amount of water and the inherent jostling of the system (the soldering iron looks like it was held by hand in front of the camera) caused enough motion in the water to move the bubbles around.  The bubbles could bump into each other and coalesce.  The size of the bubbles quickly reached the surface (unlike the bulk boiling experiment described above) and were allowed to pop.  Thus, it is by accident, in my opinion, that the boiling looks like it would on Earth.  It’d be interesting to repeat the experiment with the soldering iron held steady by vice grips or something.

(click on the image to go to the NASA page on the soldering iron boiling experiment and to see an awesome movie of this microgravity microboiling in action)

Here’s an overview page of boiling in space.
Here’s the NASA page on the 1990s boiling experiments.
Here’s the NASA page on the impromptu soldering iron boiling experiment.

*Also inventor of the super awesome zero-g coffee mug.

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Sodium Chloride

(for other entries in the Chemistry in Space series, click here)

The below picture is of sodium chloride crystals.  I’ve made them dozens of times in left over aqueous layers that have been in my hood so long that all the water evaporated.

Crystalline sodium chloride is one of my favorite crystals to grow.  Very easy (although it takes a while), the crystals can get quite large and beautiful.  And they have the characteristic X running through them.  Especially awesome to me, because I did my undergrad at Xavier University.  It’s nice to know that even my chemistry loves XU

What makes this picture so cool, though, is the crystals were grown in space.  The picture is from NASA’s Image of the Day.  The crew aboard the International Space Station’s Destiny lab grew the crystals in a water bubble as part of the program to do chemistry in space.  From NASA:

Looking for all the world like a snowflake, this is actually a close up view of sodium chloride crystals. The crystals are in a water bubble within a 50-millimeter metal loop that was part of an experiment in the Destiny laboratory aboard the International Space Station and was photographed by the Expedition 6 crew.

Space has long fascinated me, and I’ve been trying to get the info and motivation to start a miniseries on chemistry in space.  So I guess today’s IotD is a good way to begin.  Stay tuned over the next several weeks to hear more about awesome chemistry in space!

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Funny Flasks

During a recent group clean up, I came across these gems drying in an oven.  No one knew where they’d come from or how we obtained them:

Looks like the glass blower just capped some broken-off joints to make tiny flasks.  Although, I gotta say, if you’re going to do chemistry on that small of scale, why not just grab a 1 dram vial?

Merry Christmas, all!  Safe travels and well wishes in the new year

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More SEM fun

Happy Thanksgiving, all!

ASPEX is initiating a Name That Sample contest.  Head over to the ASPEX site to cast your vote.  Voting ends 11:59pm Friday night.  The winner will win a 1Gb flash drive courtesy of ASPEX.  Here’s Volume 1’s mystery picture:

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Ditch the Dimetapp?

I just finished up the teaching part of my teaching fellowship.  I got to teach five weeks of an undergrad organic class, and I had a blast!  As the seasons started to change, though, I started to hear more and more coughing and sneezing and sniffling.  Everyone’s all concerned with the swine flu, but we’re also entering cough and cold season, too.

The news I’m presenting today from ScienceDaily is old news, but I hadn’t heard it before… That makes it news to me   In an article published in 2004 in the journal Pediatrics (DOI: 10.1542/peds.114.1.e85), Dr. Ian Paul of Penn State Children’s Hospital studied the effect of dextromethorphan and diphenhydramine versus placebo in providing nighttime relief from cough symptoms as a result of upper respiratory infection.

Dextromethorphan is sold as an antitussive (cough medicine) in just about every cough formulation known to man.  The study specifically tested cough syrups in children ages 2-18.  Parents were given a survey to used to rate severity of symptoms.  The following morning, parents filled out a second survey re-rating the same symptoms.  The follow up survey also asked how both the children and parents slept during the night.

The double blind study showed that while symptoms did improve with the active ingredients, there was no statistical improvement over placebo.  On the scoring scale used in the study, children taking dextromethorphan improved 10.06 points, while those taking diphenhydramine improved an average of 11.79 points.  By comparison, children in the placebo group improved 10.85 points.

Given that dextromethorphan can easily be abused when taken in high doses, one wonders whether a spoonful of sugar (in the form of honey) might be as good of a cough syrup as any.  Keep this in mind when you browse the shelf at the drug store this winter.

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Close up Pictures of Stir Bars (with a Wide Angle Lens!)

A while ago, we had an offer from ASPEX, a microanalysis company, to provide a free SEM scan of an object of our choosing (that post being a follow up to our M&M mystery post).  The stir bar won and was sent away, never to return.

The results are in, and they are as cool as expected.  Analyst Ben Abraham captured several images of our very, very old stir bar, with corresponding chemical composition analysis.  The stir bar contains several elements, some expected, some not.  At various sampling points around the stir bar, carbon, oxygen, aluminum, silicon, iron, sodium, magnesium, sulfur, chlorine, calcium, zinc, fluorine, and chromium (!)  were identified.  Clearly, after several good years of wear and tear, the surface of the stir bar becomes irregular and several impurities remain on the stir bar.

As a follow up, it would be interesting to see what a brand new stir bar looks like.  Also, it would be interesting to see what two old stir bars look like after a lifetime of cleaning by only soap and water, versus one cleaned regularly with aqua regia or piranha mix or some such cleaning solution.  I don’t know how this analyzed stir bar was cleaned.  Most likely soap and water.

Make sure you click over to the ASPEX site to see the rest of the images and results.  You can also check out the rest of the site, including their desktop SEM.

PS, if you don’t get the joke in the title, watch this.

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LHC at Operating Temperature

ScienceInsider is reporting news out of CERN today that all sectors of the LHC have reached operating temperature of 1.9 K.  You’ll recall we went through this buildup of emotion last year, only to be disappointed when the particle accelerator broke down.  Now that the magnets are cool, the team is slowly building up the current to the desired 6 kA needed for correct particle guidance.

Also in place are new detection systems aimed to prevent another disaster like last year.  Readings will be taken in closer to real time to allow better overall monitoring of the various components of the system.

ScienceInsider claims beams will be in orbit sometime in November, followed by low energy collisions sometime in December.  They’ll ramp up the energy of the collisions slowly and probably won’t get to the cool collisions until January at the earliest. (/sarc)

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