Post-Doc Stories

When a post-doc joins your group, you’re never sure exactly what you’re going to get. I’ve known both good ones and some not-so-good ones. The following is a story about one of the latter, whom I met during my graduate school days in Illinois.

He was not in my group, but belonged to a research group whose lab space I was sharing. The post-doc, whom I shall call Dr. Orange (only members of the group would understand the significance of that nickname), was from Sweden. His area of expertise was multinuclear NMR of transition metals and that was exactly what the professor desired. Everything seemed to be working out okay with Dr. Orange, until he was asked to prepare some sodium decavanadate (Na₆V₁₀O₂₈) for some simple V⁵¹ NMR measurements. It is a rather simple prep. You basically dissolve some vanadium(V) in water and manipulate the pH until beautiful orange crystals fall out of solution. I had made this stuff years before as an undergraduate and hadn’t had a problem. Unfortunately this prep was beyond Dr. Orange’s capabilities. Either the crystals failed to appear, or they appeared and then disappeared, or if they stayed around long enough to be filtered, the crystals would quickly decompose. (I think he had neglected to rinse his fritted glass filter after a sulfuric acid washing). I volunteered to do the prep myself, but the professor said no, that it was Dr. Orange’s responsibility.

Things started to turn ugly and he began blaming other members of his group for sabotaging his synthesis. For example, he was sure the now-you-see-them-now-you-don’t crystals had been stolen. He believed someone had actually gone through the trouble of filtering out the crystals when he was away, throwing them out (he was convinced he found a trail of orange drops leading to a wastebasket), and then returning everything back the way it was. Of course, he also thought his labmates were stealing his mail too. Rather paranoid if you ask me. Eventually the professor instructed Dr. Orange not to make any more accusations and to just finish the damn prep. We later discovered that the guy had gotten his PhD mostly by grabbing compounds off the shelf, or synthesized by other people, and running them through an NMR. He didn’t know much about chemicals themselves.

Of course, an NMR jock doesn’t have to be good at synthesis, as long as the NMR jock is good with NMRs. Unfortunately, Dr. Orange was not. He was given permission to use the departmental multinuclear NMR, but that ended just as badly as the decavanadate prep. He could never get the instrument to shim properly, he had trouble understanding the software, his spectra were often ugly, and he managed to somehow wipe out the entire operating system. Along with everyone else’s spectra. Twice. That’s a lot of angry grad students. After the second data wiping, he was only allowed to use the instrument during the day, and only under the supervision of one of the NMR techs. You can imagine how embarrassing this was to the professor who had hired him. Besides, all the best NMR data is taken after midnight anyway.

He disappeared at the end of the year, much like his crystals.

Back on the Air Again

Here’s hoping that my long hiatus from blogging is about over. I returned from my Grand Canyon trip several weeks ago, but I just spent the last two weeks in Missouri with my family. After a long battle with Parkinson’s disease, my father passed away last week. He taught me a lot about life and I’ll miss him. Who knows how my life would have turned out had not my parents bought that chemistry set for my birthday back in grade school? Thanks for everything, Dad.


In a lighter bit of news, my wife came across Mythbusters the other night, a television show dedicated to proving or disproving various myths, commonly accepted beliefs, and stunts enacted on TV. I haven’t seen many episodes, but in this one the hosts were attempting to reenact a scene from an old MacGiver show, where MacGiver used the sodium+water reaction to blow up a masonry wall. Chemical experiments on TV? Okay, I’ll watch for a while. Unfortunately, anyone who has ever handled sodium would know the small piece of sodium which they were using (duplicating the MacGiver episode) was doomed to failure. I threw larger pieces than that into buckets of water back in high school. (Not that that means it’s a particularly smart thing to do, I might add). The safety precautions used by the show’s hosts were a little over the top, but then again, I don’t know how much experience these guys have with chemicals. When the sodium failed to make more than a loud noise, they eventually turned to using potassium (which is much more reactive) while also increasing the amount of metal to 500 grams. The explosion was more impressive visually, but as expected, the wall wasn’t even touched.

Of course the reason why sodium or potassium explodes is due to its reaction with water to form hydrogen and heat, which then proceeds to ignite with the oxygen in air. Despite the rather impressive sound produced by hydrogen explosions, the actual explosive force is rather low, unless large quantities are present (or if one tries to constrain it within a vessel that might shatter). Two summers ago, my kids attended a demonstration where hydrogen and air were bubbled through dishwashing soap to create a pile of foam which was scooped up by the demonstrator and ignited while still clinging to his hand. Impressive noise, but no damage to the fingers. Now I’m not knocking the potential dangers of hydrogen here. After all, I work on fuel cells, and we pipe pure hydrogen all over the lab, so our detection and alarm systems are quite elaborate, let me assure you. But hydrogen is usually only a problem if large amounts of it collect somewhere, like near the ceiling, which is why hydrogen detectors are always placed up there.

Hydrogen explosions are interesting in that most explosives, such as TNT, work because their ignition produces a huge volume of gas (much of it carbon dioxide) which rapidly expands. The combustion of hydrogen

H₂ + 0.5O₂ ----> H₂O

actually results in the loss of ½ molecule of gas, which might be expected to create an implosion instead, except that the large amount of energy released during the reaction heats the gas, causing it to expand rapidly per the ideal gas law. The thing that makes hydrogen particularly dangerous is its extremely fast flame propagation speed, which allows all the hydrogen to react nearly simultaneously, greatly increasing its explosive power.



I didn’t watch the whole show. Can anyone tell me if they were successful in making a working hang glider using the motor from a portable cement mixer?

A Real Sabbatical

You may have noticed I haven't posted in a while. Basically, I've been busy with a lot of other things, including a recent vacation. My other projects require a fair amount of writing, and I can only do so much writing in a day before I explode. As a result, I have not been as diligent with posting on this blog as I should have been. Since the family and I are leaving tomorrow for the Grand Canyon, I'm pretty sure there will be no more posts next week either. Anyway, thanks for having checked in.

Note: It's apparently much easier to post when the weather is less than ideal.

Are You Ready for the Digital Transition?

As most of you should know by now, the U.S. government mandated switch to digital television transmissions will occur tomorrow (Friday) at midnight. I’ll be stopping by the Comcast office on my way home tonight, picking up an extra converter box or two for our secondary TVs. We already have one for the main television. All the polls indicate there is still a lot of confusion out there about what needs to be done to prepare for the transition, and while I was initially amused by all this confusion, I have since learned just how easily it can be to get it wrong. I know, because I also got it wrong at first thanks, in part, to some badly worded announcements put out by Comcast.

Several months ago, Comcast was telling everyone (in this area at least) that if you were a subscriber with them, you would still receive all the same analog channels without being required to do anything.. We wouldn’t even notice the transition, they said. About a month and a half ago, the announcements changed. Only the over-the-air based analog channels would remain untouched. All the other analog channels, History Channel, Nickelodeon, Disney, Animal Planet, etc. (yes, we have kids) would disappear, reappearing in a digital format which would require a converter box to access. Although these channels are also analog based, at least by the time they arrive at our house, Comcast no longer refers to them as analog channels. That distinction is now reserved for over-the-air channels. Analog channels which do not originate from local broadcasting stations are now referred to as cable channels, a point which was missed by the people writing the earlier announcements.

At least the extra DTV boxes are free for a year.

Do We Really Need Another Element?

Just great. They’ve officially decided to add element 112 to the periodic table. Like I really needed another name to memorize.

A Babelfish for Chemists

As an undergraduate, I fulfilled my foreign language requirements by taking German. I found it moderately useful for translating a few chemistry papers needed for my research, but the process was admittedly painful. Scientific German is a lot different (read: harder) than conversational German. By the time I entered the job market, my translating ability had atrophied to the point where it was nothing more than a bullet on my resume. And unless you are very good at it, it’s more economical for the company to pay someone else to perform translations for you.

A report has been released in the Journal of Chemical Information and Modeling describing Lexichem, computer software designed to translate over 250,000 English chemical names into seven other languages and back again. Hmmmm…… I suspect I might have found this useful back in the day, not only for me, but for some professional translators as well. I recall reading through a compilation of abstracts on ceramic materials translated from Japanese articles several years ago. I kept running into the term “basic soil elements” which had me totally bewildered until I finally realized the translator was trying to say “alkaline earth elements”.

Original source: New Scientist

Arsenic (Again) and Drugs

Following up on last week's post concerning the relationship between elevated levels of arsenic in drinking water and a diminished immune response to certain types of influenza (swine flu?), I ran across the following article describing the use of nanorust (actually tiny particles of iron oxide coated on sand) to provide a possible low cost means of removing arsenic from water. You can’t get much more inorganic than this.


In a previous post, I discussed my general reluctance for taking drugs, somewhat skeptical that it might be possible to develop a drug which didn’t cause some problem somewhere else in the body. Now, Derek Lowe has written a column describing how much we don’t know about drugs and their mechanisms inside the body. He even says:” I try not to take any medication unless I feel it's absolutely needed, and I'm often not very happy about taking it even then.” A man after my own heart! I just might finally consider throwing out all that aspirin I’ve been suspicious of for a while now.

Mediterranean Cyclones

According to this article, scientists have developed a new method of forecasting cyclones in the Mediterranean Sea. This has nothing to do with chemistry, and I don't really care about the subject, but it does give me a chance to post a (rather poor) picture I took in Malta years ago.

This waterspout appeared near the town of Mellieha (where we were staying) during the last day of our trip. As far as I know, it's the closest I've ever been to a tornado. We felt pretty safe from our vantage point, but I'm not sure the crew of the freighter (not shown) felt the same way. We flew out of Malta early the next morning -- fortunately -- since the resulting torrential rains shut down much of the island along with the airport.

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Two new elemental podcast are now available at Chemistry World. This week's elements are zinc and radon.

Poisons of the Day - Part Ib

When I started the “Poisons of the Day” series last year, I was hoping to update it a bit more regularly, but one post a year (plus an addendum) is pretty pathetic. I’ve had several partially written entries since last year, but general laziness has prevented me from finishing them up. Perhaps they’ll see the light of day in June. In the meantime, here is an addendum to the addendum to the original post concerning arsenic. Besides its well-established toxicity, it appears arsenic also makes us more susceptible to the flu.

It is already known that arsenic disrupts a large number of hormone pathways in the body, which may link it with a variety of hormonal related diseases. The link with cancer has already been established. Now, Joshua Hamilton and Courtney Kozul have demonstrated that, after five weeks of drinking water containing 100 ppb of arsenic, mice exposed to the H1N1 influenza virus are only able to generate a rather poor immune response (compared with non-arsenated mice). Several days are required to reach appropriate response levels and that delay can be costly. According to Hamilton, “One thing that did strike us, when we heard about the recent H1N1 outbreak, is Mexico has large areas of very high arsenic in their well water, including the areas where the flu first cropped up. We don't know that the Mexicans who got the flu were drinking high levels of arsenic, but it's an intriguing notion that this may have contributed,”

Perhaps. So it may be worth noting that arsenic concentrations of 100 ppb and higher can also be found in well water in many areas of the United States.

Fortunately, unlike heavy metals such as lead and mercury, arsenic does not accumulate in the body. “Arsenic goes right through us like table salt,” Hamilton says. “We believe for arsenic to have health consequences, it requires exposure day after day, year after year, such as through drinking water.”

If it weren't for BPA, I'd be drinking bottled water all the time.

The End of the Hydrogen Economy?

Most of you probably missed it, but about two weeks ago, the Obama administration announced the cutting off of funds for research into the use of hydrogen fuel cells to power the next generation of cars and trucks. The reasoning? The technology was not expected to be viable within the next 10-20 years and the administration wanted to spend its (our) money on projects with a quicker payoff. The difficulties with using PEM (proton exchange membrane) fuel cells in cars and trucks are many. Problems with on-board hydrogen storage, the need to use high purity hydrogen (ppm levels of CO poison PEM fuel cells), low power densities, and the lack of a hydrogen infrastructure (e.g. filling stations) all have to be solved first. Basically, this is an admission that we’re still a long way off from the much touted hydrogen economy.

And it doesn't help that hydrogen may not be as "green" a fuel as first thought.

Note: Fortunately, this has no effect on my work on SOFCs (solid oxide fuel cells). SOFCs can utilize both H₂ and CO as fuels, both of which are produced by on-board reforming of gasoline or diesel fuel. SOFCs have their own set of difficulties, but they’re much closer to being solved.

The Science News Cycle

PhD Comics has some interesting comics relating to science and the news. Here's one example:

Go check out the site.

Francium -- Probably Only Good For About One and a Third PhDs

Two new elemental podcasts are available for download at chemistryworld. This week's elements of interest include Francium and Aluminum. The Fr podcast is especially interesting. Considering that Fr has a halflife on the order of 20 minutes, it's probably not a good idea to base your thesis on its chemistry. All the quick experiments have already been done. And it cannot be classified as a disappearing element since it's continually being generated by radioactive decay. It's estimated that the steady state amount of Fr on the earth at any one time is about a kilogram, which is another reason not to base your thesis on it.

^* Post title was edited based on Mitch's comment.

A Fear of Drugs

My wife recently recovered from a lower respiratory infection which she picked up during our trip to Missouri. The source of the infection cannot be confirmed, but the woman who sat in the adjacent row on the plane with the severe cough who couldn’t bother to cover her mouth should probably avoid any dark alleys where my wife might be waiting. Anyway, one antibiotic, two steroids, and two weeks later, the wife is back to normal. As usual, I escaped unscathed, much to my wife’s annoyance.

It’s probably best that I don't get sick very often. My wife will dutifully take any and all pills prescribed by the doctor without the slightest hesitation, while I tend to avoid medicines and drugs like the plague, especially those to which I’ve never been exposed before. Maybe I’ve seen too many doctor/hospital/ER shows where the entire episode revolved around the life and death struggle of a patient who had either experienced a rare, life threatening reaction to some commonly prescribed medicine or else experienced a common, life threatening reaction to a incorrectly prescribed medicine. (Perhaps I just watch too much TV -- but that’s another issue). But the main reason I don’t relish the idea of taking drugs is that, as a chemist (admittedly with a limited biochemical background), I have some idea of just how insanely complex the chemistry is inside our bodies. It seems utterly impossible to me that the introduction of a new chemical into our systems wouldn’t cause havoc somewhere. Just think about how easy it is for small impurities to crap up a reaction in the lab. While the general success of the pharmaceutical industry does allay my fears to a certain extent, I am still cautious since most doctors will admit that taking a drug is always a compromise. The idea/hope is that the benefits outweigh the negative effects. And if we are lucky, the negative consequences go unnoticed by the patient and are eventually repairable by the body. As a result, my doctor, the pharmacist, and myself have come to an uneasy truce over the years.

Unfortunately, that truce has become a bit more shaky thanks to a talk I attended at a local chemistry group, brewingchemistry. The lecturer was Felix Schneider, a retired FDA chemist, and his talk was entitled “What Happened to the FDA?” Without giving a lot of details, the politicalization of the FDA in the last decade, along with attempts to outsource some of its responsibilities, has led to a less effective organization (to put it mildly). It sounds as though the FDA is attempting to fix itself, beginning with a move back toward directors wiwth more of a science background, but it will be an uphill climb.

Scary fact¹: Most of the large pharmaceutical companies do not make the active ingredients in the drugs we buy – they license them out to other manufacturing facilities. If I recall correctly, something like 75% of these plants are outside the United States, mostly foreign corporations. At the present rate of inspection, it has been estimated that it will require nearly 50 years before all these plants can be visited by the FDA. Just what I needed to hear, especially after hearing stories about what the FDA has found in sites they have visited.
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¹Some alcohol was consumed during the talk, so take these numbers with a grain of salt -- the inorganic kind.

Bioelectricity

The “corn into ethanol as automotive fuel” supporters received another bit of bad news the other day. They were already smarting from criticisms that corn based ethanol would not only dramatically drive up the price of food but would also generate more greenhouse gas emissions than fossil fuels (once you take into account the entire life-cycle of corn growing/ethanol manufacturing). Now, Elliot Campbell (UCM), David Lobell (Stanford), and Chris Field (Stanford) have calculated you can get more energy per acre by simply burning the biomass (corn, switchgrass, or whatever you’re growing) to make electricity. Converting the biomass into ethanol just wastes a significant portion of its energy content. The authors also point out that an additional benefit of “bioelectricity” might be in the area of carbon sequestration. You can sequester carbon at a stationary power plant, but not for mobile sources like automobiles.

Of course, this only helps lower our dependence on oil if we’re all using electric cars.

Bad Science -- Toxic Salt

The great promise of the Internet is that it allows everyone to share their opinions with the public. The curse of the Internet is that it allows everyone to share their opinions with the public. I occasionally run into web-based articles discussing some aspect of science written by people who obviously don’t know the first thing about the subject. Recently, I found myself greatly amused by the following article on table salt. Excessive salt intake is apparently bad for your health – not because it increases your blood pressure, but because refined salt contains dangerous chemicals the industry doesn’t want you to know about. Here’s a typical quote:

“One or two servings of refined salt won`t send you to the grave. But continued almost daily use will avail you to the perils of aluminum toxicity.”

Aluminum toxicity?

The author’s suggestion: Use only “organic” salt. An amusing oxymoron, to say the least. There are many more such pearls of wisdom within this article. For example, he seems to have a fear of NaF, which he describes as “a synthetic, poisonous fluoride.” Unless I’m misreading it’s LD₅₀, the amount of NaF you’d have to ingest for it to be toxic would probably cause your heart to explode due to a super elevated blood pressure brought on by all that sodium.

I’m sure the author means well, but this article could be the poster child for why chemistry should be a required course in high school.

Ruthenium Compound Splits Water

If you work in the energy sector and your focus is on hydrogen, then chances are you spend a lot of time thinking about this reaction:

2H₂ + O₂ --> 2H₂O

Researchers in this field tend to fall into one of two groups. The first group wants to use hydrogen to generate energy, usually in the form of electricity via a fuel cell, and devotes its energies into driving the above reaction as far to the right as possible. The second group wants to use energy to generate hydrogen, usually by electrolysis, possibly using solar photons, and strives to drive the reaction as far to the left as possible. (A third group is concerned with hydrogen storage, using high surface area materials such as MOFs, but that’s a topic for another discussion). Although these the two groups would appear to be diametrically opposed, they have at least one thing in common. In both cases, the efficiencies of the processes are often dependent on the oxygen side of the reaction. During electrolysis, forming the O₂ is the hard part, which explains why most of the advancements in this area are related to the anode. The cobalt phosphate electrode coating announced by MIT last year would be one example. And in fuel cells, it’s the cathode that causes most of the headaches, since it’s more difficult to reduce O₂ then it is to oxidize H₂ (at the anode).

In an attempt to negate the need for electrodes, much work has been devoted to identifying transition metal complexes which might catalyze the photochemical splitting of water in solution. The results have been generally disappointing. In many cases, sacrificial reagents are required, usually to facilitate the formation of O₂, obviously limiting the usefulness of the process. In addition, since the H₂ and O₂ are usually co-generated at the same location, an additional step is required to isolate the H₂. Not good at all.

In a recent article in Science , David Milstein describes some ruthenium chemistry which may have some implications in the solar energy field. When water was added to a ruthenium compound they’ve been working with, a new hydrido-hydroxo complex was formed.



Upon heating, this new complex continues to react with water to produce a dihydroxo ruthenium complex along with free H₂. Irradiating this dihydroxo complex with a halogen lamp causes it to revert back to the original hydrido-hydroxo complex, along with the formation of O₂. Catalytic photochemical splitting of water without the use of sacrificial reagents. Not bad. Even better, since the H₂ and O₂ are produced during different steps, there are no separation issues to be dealt with. This process is a loooong way from being commercially viable, but I enjoy any chemistry where an organometallic compound reacts constructively with water without simply igniting or decomposing into an ugly pile of goo.

Osmium, Osmium, Everywhere

I don’t use osmium much. In fact, I don’t think I’ve ever used an osmium compound, although I’m fairly certain I once picked up a bottle of OsO4. The sum total of my osmium knowledge consists of knowing OsO4 (osmium tetroxide) is quite toxic. However, it now appears that if I ever do have need of osmium, I can just go outside and grab some. A group of researchers has studied the distribution of osmium across the globe and found that a surprising amount of the element is now present in rain, in snow, and in our rivers.

Osmium naturally occurs along with copper and nickel and is a by-product of their manufacture. But all this osmium in our water system comes from another source – during the production of platinum – much of which is used for the manufacture of automotive exhaust catalysts. During the process of refining platinum, the ore is subjected to high temperatures to burn out sulfur impurities. But volatile OsO4 is also produced and it has been spreading. According to the researchers, the levels of osmium are still small enough that this may not be a health concern, at least so far….

Russia and South Africa produce over 90% of the world’s supply of platinum and neither country regulates these osmium emissions. The demand for platinum may have dropped temporarily due to the worldwide plunge in car and truck sales, but it will return eventually. In addition, the current generation of hydrogen fuel cells also depend upon platinum for their electrodes, which means the rate of osmium release will probably only increase in the future.
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Since I did mention platinum, I’ll point out that this week’s Chemistry In Its Element podcast covers platinum and its chemistry. Podcasts for many other elements are also available, including osmium, so feel free to see if your favorite element has been discussed yet.

Error Analysis

I just ran across a discussion of errors, R values, and Gaussian distributions over at “The Curious Wavefunction” blog. Being able to estimate, understand, and interpret sources of experimental error is perhaps one of the most important skills you can develop. It can save your career, for one thing. I once attended an in-house presentation by a coworker who felt the need to explain what he was currently doing for the company. The coworker presented the following chart to summarize his data.

No, I’m not giving away valuable corporate data here. This chart is just something I whipped up using a random number generator, which, as it turns out, makes it a damn good representation of what we were shown at this presentation. Seriously. Members of the audience began looking at one another, wondering where this talk might be heading. Basically, the black dots represented the data under standard conditions (obviously noisy data), while the red dots represented the data after changing the variable of interest. After spending ten minutes describing the experimental procedure, he summed up his results by comparing the average of the standard data (black) with the average of the four red data points and then had the audacity to conclude that the variable did indeed have a small effect. Audacity is probably not the correct term here since that implies a certain knowledge on the part of the speaker as to the outrageousness of his statement. He was totally surprised by the general outrage displayed by certain members of the audience and the discussion became rather heated, which is rare at this company. Eventually, he countered with “Well, this is the data I got. What else can I say?”

A simple “My data is inconclusive” would have sufficed.

By the way, the guy no longer works at this company. To be honest, he left of his own accord and jumped to a new company, one which is actually in better financial shape than this one. He’s actually a nice guy and I wish him luck, especially since I may be calling on him for a job some day.

Miscellaneous Friday

I was temporarily unemployed for a couple of months at the end of last year, but I never considered expressing my disappointment in the same manner as this unemployed chemist. I cannot imagine this sort of thing looking good on a resume, but I’ve been wrong before.
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Now I need to rant a bit.

Yesterday, I needed to download a software driver for a National Instruments GPIB interface card from the company’s website. It should have been a quick 50K download at most, requiring only about a minute of my “valuable” time. Annoyingly, the entire process took 45 minutes -- time that could have been better spent searching the Web for more antics by unemployed chemists. First, the website required me to register before downloading the file. Swine! I already paid for the hardware! Forcing me to register just to download the accompanying software is sooooooo last millennium. Check out your competitors’ web sites. And what’s with all the “required” questions? I can understand asking for my email address so I can be spammed, but do you really need the name of my firstborn?

After being granted access to the download page, I discovered the “driver” file was over 108MB. WTF??? Are they sending an operating system along with the driver? Please: make non-essential utilities a separate download. If I had been downloading this from home, it would have not been that big a deal, but my company’s firewall insisted on scanning the entire 108MB file for porn and viruses, and the scanner is not very fast.

Anyway, I feel better now.
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Our governor here in Michigan has been desperately trying to make the state less reliant on the automotive industry. For the past few years, she’s been pushing to make Michigan the biodiesel capital of the world. Last year, she was promoting solar cell technology, partly since we have several companies (Dow Corning, for example) which are in the photovoltaic arena. And yesterday, she announced a program designed to (hopefully) make Michigan the nation’s leader in the manufacturing of lithium ion batteries for electric and hybrid cars. $300M in tax credits, among other things, with an eye on grabbing a piece of the $2 billion earmarked by the federal government for advanced battery projects. Basically, she want s Michigan to be the "alternative energy" state -- not to be confused with the "alternative lifestyle" state. According to Governor Granholm, “We are going from rust to green.” Will this work? I don’t know, but all three areas have need of inorganic chemists and that’s definitely okay by me. All the chemistry based jobs listed around here are pharmaceutical based.

PAHs -- Not Found at Your Local Health Food Store

Yesterday, my family and I returned from a five day visit with my parents in southwestern Missouri. This, of course, means I’ll be spending most of today actually recovering from the “vacation”. You have to love how that works. The travel part of the trip went smoothly, thankfully. No one got sick, the plane was on time, and there were no traffic problems; so we arrived in Springfield at the appointed time – only two hours before the tornadoes passed through. Ah, the joys of traveling!
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Several of the houses in our neighborhood (not mine) have asphalt driveways. They’re a popular option since they cost less to build than concrete driveways, but they require a yearly application of sealant for protection from the elements. Apparently, that sealant contains polycyclic aromatic hydrocarbons (PAHs). PAHs (sometimes referred to as polynuclear aromatics or PNAs) consist of three or more fused aromatic rings (anthracene is one example), and as you might guess, are not always the most healthy of chemicals. And according to a recent study, the PAHs from these sealants are making their way into the water system. Since many PAHs are carcinogenic, you can kind of understand the concern.

As an inorganic chemist, I never really had much contact with PAHs, but I did run into them a few years ago while working on reforming catalysts. These catalysts convert air and hydrocarbons (like gasoline or diesel fuel) into CO and H2, along with smaller amounts of methane. I began to notice the buildup of an orange/yellow/brown solid all throughout my vent lines, sometimes as far as 10 feet away from the reactor. This necessitated not only the periodic replacement of these lines, but also, to my great joy, a massive clean out of my mass spectrometer. An NMR revealed this solid to be a mixture of PAHs. A little research revealed that under hot (700C), reducing conditions, methane forms PAHs quite happily. A little more research revealed that PAHs have been found responsible for the higher than usual rates of testicular cancer among workers in the metal cutting industry. Cutting fluids contain PAHs, and wearing clothes which are constantly soaked with them was found to be a bad idea.

I elected to start wearing gloves. Anybody else have any interesting stories about carcinogenic materials with which they’ve worked?


On the lighter side, David Bradley has managed to convince a few people to reveal some of the more stupid things they have done in the lab. .
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I’ve decided to add a verification check in the comments section. I apologize for the inconvenience, but this blog seems to have been targeted by a bot which feels the need to leave garbage in the comments section and I’m getting tired of deleting it. Hopefully I’ll be able to drop it again in a couple of weeks.

New Chemistry Game!

If you enjoyed playing the Spectral Game , here’s another one for you. The people over at Useful Chemistry have created the Chem Tiles Game. If you enjoy Newman projections, Lewis structures, and nomenclature, this is the game/quiz for you. Reminds me how much organic chemistry I’ve forgotten since my sophomore year.

Also, I congratulation the Michigan State basketball team on their amazing season. The Spartans went a lot farther in the tournament than most prognosticators had predicted. Unfortunately, they appeared to run out of gas last night when they were pretty much pounded by North Carolina. I’m not a particularly big fan of college basketball, but I can still appreciate the tenacity of underdogs.

Potassium Ferrate - The "Green" Oxidant

K₂FeO₄ is pretty cool stuff. It’s relatively easy to make, has a nice purple color, and it’s a stronger oxidant than permanganate. Oh… and it reacts with water. You can dissolve it in water, but unless the solution is fairly alkaline, it will decompose rapidly, generating O₂ as a product. It is being investigated for use as a cathode material for so-called “super-iron” batteries (using zinc anodes) and for its use as an oxidant for organic reactions. But its biggest claim to fame is its role in the area of water treatment.

A description of the methods used in water treatment facilities is too large to describe here, but one common method is flocculation, a technique used by both the Egyptians and Romans. The addition of alum and/or iron salts to the water to be treated, along with some lime, results in the precipitation of Al(OH)₃, Fe(OH)₂, and Fe(OH)₃. As these precipitates sink, they drag undesirable particulate material along with them, resulting in cleaner water. Chlorine (or chloramines) is then added for disinfection purposes. Chlorine treatments are very successful at removing harmful bacteria, but there has always been a concern that its reaction with organic material still present in the water might form harmful compounds.

This concern has been confirmed by a recently completed 10-year study. Michael Plewa, a geneticist at the University of Illinois, has quantified the toxicity, genotoxicity, and carcinogenicity of these disinfectant by-products (DBPs) using a mammalian cell line specifically developed for this study. He found not only that these DBPs are harmful, but that the degree of toxicity can depend on other factors. For example, it was found that water which contained bromine and iodine (seawater or aquifers associated with ancient sea beds) generated even more toxic DBPs. And DBPs which contained nitrogen were more toxic, genotoxic, and carcinogenic than DBPs which contained no nitrogen.

Plewa is especially concerned with swimming pools and hot tubs, which he refers to as DBP reactors. Organic material from swimmers -- sweat, urine, sunscreen, cosmetics, as well as some disgusting stuff – sits in contact with the chlorinated water for long periods of time, generating DBP levels up to ten times higher than drinking water. This may explain the higher levels of bladder cancer found in people who spend a lot of time swimming in pools.

This is where potassium ferrate comes into play, at least for water treatment applications. If all the organic material could be removed prior to the application of chlorine, then DBPs couldn’t form. So instead of adding iron salts and lime to the water, one could just throw in some K₂FeO₄. Ferrate would chew up the organic material in the water and then decompose to form the Fe(OH)₃ precipitant which removes the particulate matter as usual. And unlike chlorine, you cannot really add too much ferrate – you’ll just end up with more harmless Fe(OH)3. For this reason, ferrate is often referred to as a "green" oxidant. And once the ferrrate has done its work, you can add chlorine without the fear of forming DBPs.

The use of ferrate for this purpose has been investigated for over thirty years. One of the big drawbacks has always been the cost of manufacturing K₂FeO₄, but last year Battelle announced a lower cost method for its production, so it may yet come to pass.

Chemists vs. Engineers

One of the guys in our group at work is a co-op student from a local university. As part of his engineering degree, he spends every other semester working in our lab receiving a massive dose of industrial reality and forced indoctrination into the world of engineering. His current stint ends this week, so yesterday he presented a summation of this semester’s work to the group. It wasn’t supposed to be a big deal -- a quick, informal 15 minute talk -- but the head of our division (3 or 4 steps up the corporate ladder) decided she’d attend the presentation, and the intensity level ratcheted up a notch or two. Of course, the division head ended up asking all the questions while the rest of us just smiled and watched the student sweat.

The questions were all good, although many of them concerned engineering protocols and methodologies of which I am woefully (and thankfully ignorant). Unfortunately for the student, there wasn’t much data with which to defend himself, due to situations mostly beyond his control. There had been a two month delay in getting the equipment up and running, due to the time required to implement various safety features in our labs. For some unfathomable reason, the safety guys had been (and still are) very nervous about the prospect of piping pure hydrogen and carbon monoxide throughout the building. They take safety much more seriously in industry than they do in graduate school, where safety protocols often involve nothing more than wearing safety glasses and not eating food in the lab, both of which are largely ignored anyway.

Anyway, the presentation ended, 90 minutes later, with very little blood spilt, and with the conclusion that several of the test variables would need to be quantified (by me, unfortunately) before the student’s return in July. So less than two hours later I was attending a meeting to discuss the quantification of these variables – a meeting attended by myself and 3 engineers. I recall the various good-natured rivalries between chemists and chemical engineers back in school, but we all generally thought alike. But these guys are process engineers. Acronyms like DFSS, MCE, Green Y, Red X, and MFEA were flying fast and furious. Process engineers have a very different way of approaching these types of problems. As a chemist, I just want to understand which variables are of interest and how they affect the final results. Process engineers are more interested in maximizing the reproducibility and repeatability of those variables.

For example, let’s suppose I were tasked with improving a known chemical synthesis. I would try to understand the chemical steps involved, I would isolate the important variables, and I would systematically make changes to the procedure to increase the product yield. Process engineers would be more interested in making the prep more reproducible and operator independent (meaning that everyone who followed the written procedure would get exactly the same yield). As a chemist, I might try different methods of cleaning/drying/purifying the starting materials/solvents. Process engineers would rather write solvent specifications and protocols to ensure that the level of impurities were reproducible, although not necessarily lower. They would sacrifice yield for the holy grail of repeatability. In their world, attempts to maximize yields shouldn’t occur until later. Process engineers feel this mindset allows them to solve chemical related problems without having to actually understand the chemistry.

In yesterday’s meeting, these engineers actually wanted to devote almost half of our allotted time just verifying the repeatability of our test as a function of which of us was actually running the test. An analysis of the test variables in question would be squeezed in later. It’s going to be a long three months.
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Note: I'm not trying to rag on process engineers too much here. Their techniques are exactly what you need when you are trying to design and operate an industrial process. I would fail miserably were I to ever attempt such a thing. But these techniques don't work so well in the research arena. There is a reason why advanced development groups and product development groups are generally kept apart.

The CIMS -- No, Not the Sims

So far, my new job appears to be working out pretty well. My official job title is "test engineer" although I'm neither an engineer nor well versed in the testing protocols so beloved by product engineers, but it's a job and it allows me to get my feet wet in the world of fuel cells. It's a good time to be getting in on this project, as the number of chemistry-related subprojects is beginning to grow quickly and most of the people in the group are engineers (non-chemical). Now don't misunderstand me, these engineers are very good process engineers and they've picked up a fair amount of chemical knowledge over the years, but some of these chemistry projects really need a chemist's touch to finish them in a timely fashion.

With these projects in mind, I've already been grabbing some of my old equipment from the company's storage facility. This equipment is still in storage after all these months partly because the shiny, new lab my old group was supposed to move into is still not completed and partly because there really aren't any chemists left in that group capable of using the equipment. Anyway, I never know exactly what I'm to find during these salvage excursions. Remember the warehouse scene at the end of the "Raiders of the Lost Ark"? That's what our storage site looks like. This week I struck paydirt and I brought back the CIMS unit.

CIMS stands for Chemical Ionization Mass Spectrometer and it's great for analyzing the products typically generated during gas phase heterogeneous catalysis. In general, mass spectrometers operate by ionizing molecules using a variety of methods, followed by their separation via magnetic fields. Most mass spectrometers are electron impact types, which means they ionize molecules by bombarding them with electrons. Unfortunately, a fair number of molecules, especially organic ones, do not take kindly to this technique and tend to fragment into smaller pieces before the spectrometer can detect them. The CIMS alleviates some of this problem by first ionizing an inert gas like Kr and then letting the Kr⁺ ions do all the ionization. This kindler, gentler approach allows many organic molecules to remain intact and thus detectable. As an additional bonus, the appropriate selection of source gas allows you to choose which molecules to ionize. For example, detecting CO in the presence of nitrogen is problematic as they both have the same mass. This usually leaves you with four choices: find another analytical method, ignore the CO, use helium for all your experiments, or choose a new project. But with the CIMS, Xe⁺ only ionizes the CO, allowing the N₂ to sail blissfully past the detectors.

It's not a high resolution instrument , so it only costs about $250K, but it is small (a cube about 2.5 feet per side), portable (it has wheels), and the software is sweet. The unit started right up without a hitch, but the xenon source gas cylinder is essentially empty. Xenon isn't cheap and the CIMS requires an isotopically pure sample ($$$) and so we're talking $3000 here. I haven't told the boss yet how much this free mass spectrometer is going to cost him.

I still miss working with lab glassware and synthetic chemistry, but I do have to admit this instrument does rock.
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It's old news, but I'd like to add my congratulations to M. Frederick Hawthorne for having been awarded the 2009 Priestley medal for his work on boron. I admit to not having paid much attention to boron chemistry since grad school, but Hawthorne is currently located at the University of Missouri (my alma mater) and anyone who can make a water soluble boron cluster is okay in my book.

Being Flexible as a Chemist

My freshman year was almost over. Final exams would take place in about two weeks and I was already beginning to prepare myself mentally. Almost as an afterthought, the chemistry professor assigned us one last chapter to read on solid-state chemistry. It wasn’t a real assignment – the professor never mentioned the chapter again and as I correctly surmised, it wasn’t going to be covered on the final exam. It should have been a meaningless blip in my academic career, quickly forgotten, but I still remember that chapter after all these years, or at least the section which covered the concept of non-stoichiometric materials.

I remember absolutely hating it.

We had just spent the entire year having the “Law of Multiple Proportions” hammered into our brains. “Atoms combine in ratios of natural numbers,” they would say. “If you can’t grasp this basic concept, you’ll never get a job as a chemist. You’ll just have to settle for being a doctor or lawyer or telemarketer.” Frightening words indeed! But now, just weeks before the final, I was discovering that this law was more of a suggestion.

I think I even remember one of the provided examples. It was NiO_1.03. WTF? 1.03? What sort of sick joke was this? It looked like something a freshman engineer would write, one who hadn’t yet grasped the concept of rounding. This deviation from stoichiometry was within the experimental error associated with an elemental analysis. I cannot begin to imagine what my thesis advisor would have done had I submitted an article discussing the properties of the V₁₀O_27.97^6- ion. The beatings would have been severe. The whole idea seemed stupid to me.

Fast forward to the present and my mind is now quite a bit more receptive to this concept. The field of non-stoichiometric materials is huge, incredibly huge, due to their special properties (catalytic, electronic, and optical). As a transition metal chemist, I now understand that the many oxidation states available to most transition metals can lead to mixed oxides, many of which are non-stoichiometric. I’ve also come to the realization that over half of my projects over the years have involved non-stoichiometric oxides in some fashion. Examples would include ZrO₂/CeO₂ solid solutions, various doped metal oxide catalysts, zeolites, and, at the present time, fuel cell cathodes. (Strictly speaking, zeolites are not really considered non-stoichiometric materials since there are no mixed oxidation states available, but with formulae such as Na_xAl_xSiO_(2+2x), where x can be < 0.01, I’m still counting them.)

The defect sites in these non-stoichiometric oxides make them wonderful catalysts, especially for redox reactions. The vacancies left by the loss of oxygen atoms in the crystal structure can create materials with the ability for ion conduction (usually at higher temperatures). This leads to their use in gas sensors, batteries, and fuel cells. (La_1-xSr_x)_yMnO_3-z is a typical oxide used in fuel cell cathodes. Non-stoichiometric oxides are here to stay.

And I'm loving it.



The moral of the story: Don’t dismiss new concepts in chemistry until you’ve had a chance to work with them first.