One of the Keys to a Good Presentations is...

One thing (amon many) that bothers me during a presentation is a lack of consistency between graphs. Perhaps I’m just being a bit anal here, but it seems to me that talks should be designed so as to allow the listener to grasp what you are trying to say as quickly as possible. If the audience has to work too hard to understand a series of graphs, then the audience will stop paying attention.

Now I’m not talking about colors and fonts, although maintaining a consistent color scheme for data sets throughout a talk is a very good thing. (If you use red for sample #1 and blue for sample #2 on the first slide, keep it that way throughout the rest of the talk. I know that seems fairly obvious, but you’d be surprised how many people don’t pay attention to this. Far too many people who should know better just use whatever colors Powerpoint gives them.) No, I’m talking about inconsistencies in the way the data is plotted. For example, plotting some of your data using weight% and others using mole% (unless there is some special reason for doing so.)

This almost always happens because the presenter is too lazy to convert one (or more) of the plots. I’ve seen this at group meetings at work as well as at talks given at our local catalysis society meetings. In these cases, it’s obvious the presenter just tossed in a bunch of plots drawn by their students (or group members) and figured that was good enough.

I bring this up now since my current project involves lots of meetings with lots of presentations with lots of data and we’re running into the same problem. In this case, the problem stems from a lack of an agreed upon format. We work on fuel cells and it’s common to evaluate a cell by measuring its current output as a function of voltage. It’s called a polarization curve and is commonly plotted as amps versus voltage. That’s fine, but we have people from many different backgrounds - materials people, electrochemists, product engineers, graduates students from a local university, PhDs from one of the national labs – and everyone has their own preferences. Some like to plot watts (amps x volts) versus volts. Others plot current density (amps/cm2) versus volts while still others plot power density (watts/cm2) versus volts. If that wasn’t bad enough, sometimes the axes are flipped, so that voltage is now on the y-axis. And when they start mixing up these plots in their project updates – and they always do -- I spend half my time doing conversions in my head, just to figure out what the data really means.

So please keep your plots consistent. I may be in your audience one day and I’ll greatly appreciate it!

I would also like to apologize for the long delays between posts. I promise to start posting more often, like I used to do.

Bacteria - The New Chemists

A new wave of chemists is on the horizon – and they are called microbiologists. Every day, it seems, I read an article about the use of bacteria to perform chemical synthesis, a job that rightly belongs to chemistry graduate students. Hydrogen, biodiesel fuels, drugs, and a few other organic compounds whose names I don’t remember are being produced by trained bacteria. I don’t know how many of these processes are commercially viable.... yet.... but I’m afraid it’s only a matter of time before graduate students will have nothing left to do other than caring for the bacteria in their labs.

In a similar and yet totally unrelated vein, here is another report detailing the use of bacteria to remove uranium from waste water.

According to the report:
“Bacteria, in this case, E. coli, break down a source of inositol phosphate (also called phytic acid), a phosphate storage material in seeds, to free the phosphate molecules. The phosphate then binds to the uranium forming a uranium phosphate precipitate on the bacterial cells that can be harvested to recover the uranium.”

While I’m sure we can probably always use another new technique for the removal of toxic heavy metals, I cannot help but wonder if having radioactive bacteria running around out in the open is such a good idea. I realize the radiation levels are pretty low, but this still seems like the basis for a movie on the Science Fiction channel.
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On another note, the 2009 Ig Noble awards have been announced and they are as funny as ever. The Chemistry prize goes to Javier Morales, Miguel Apátiga, and Victor M. Castaño for creating diamonds from tequila. I sure hope they have an MSDS for the starting material. The link is here. Thanks to Anne Marie Helmenstine's blog for the original link.

Modern Chemistry (Sets)

My neighbor is planning to buy a chemistry set for her son (second grade) and she asked me for some suggestions. It was a chemistry set that I received back in second or third grade many years ago that sent me down the path to a career in chemistry, so I thought I’d spend a little time trying to find a good one. I’ve talked about this before, but they just don’t make chemistry sets the way they used to. Perhaps for safety reasons, perhaps for environmental reasons, perhaps for liability concerns – there just are not that many chemicals in chemistry sets any more. And that’s a real shame.

My chemistry set (Chemcraft) had plenty of chemicals in it, and there were plenty more you could order. These days, you are lucky to find ten chemicals in a set, sometimes as few as two or three. I did find a Thames and Kosmos set which contained 20 different chemicals, but many of them were boring and the set cost about $250! I finally suggested a less expensive version of the Thames and Kosmos set to my neighbor. Of all the sets I checked out, it appeared to be the best one. The deciding factor was the inclusion of potassium permanganate. Even my old chem. set didn’t have that one. How did permanganate slip through the safety police?

New World Order?

Not really chemistry related, but….

There was one of these so-called “town hall” meetings in my area yesterday to discuss President Obama’s proposed health care plan. Turns out it was less than a mile from my house, which meant that all the streets in our neighborhood were filled with parked cars and frantic drivers attempting to find parking spaces. It took a while for me to drive my daughter to soccer practice.

Debates like this always bring out the crazies. I noticed one sign that read something like “This is the USA, not the USSR.” Ignoring the fact that the USSR no longer exists, comparing attempts to ensure that some kind of health care exists for the millions of people who cannot get it now to communism or socialism is beyond stupid. Might as well hold up a sign that says “I’m a moron.” Try to put a little thought into this debate people. There are plenty of valid reasons to like or dislike the plan. Let’s try and stick to the real issues, okay?

My wife tried going to the meeting, but she was turned away, along with hundreds of others, since the auditorium filled up quickly. On the way back home, she ran into one guy who explained why he was against the health plan -- because it was basically a government plot for population control. This plot was apparently a part of the world takeover by the New World Order. Implemented by the Illuminati, I suppose. Shades of Sarah Palin. I certainly hope he did not contribute to the gene pool.

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.

Donut Powered Solar Cells

I came across the following video this weekend. Apparently powdered donuts are an important constituent in the drive to harness the power of the sun. Yes, nano-chemists will do anything for attention. And yes, magnetic stirrers DO rule!



So the powdered sugar in donuts can contain up to 1% TiO₂? I guess organic chemistry always benefits from the addition of some inorganic chemicals.

This video is one of the entries in the ACS Nanotation Video contest. If you want to see more, click here.


EDIT: I now see that this video was already posted over at the Chemistry Blog earlier last week. Not sure how I missed it, but this demonstrates the importance of keeping up with the literature when writing about current events.

Disappearing Elements? - Part IV

Yet another element has turned up on the “Where’s it going to come from in the future?” list. (See my earlier posts). Recently, Fetzthechemist discussed the use of Nd-Fe-B magnets slated to be used in upcoming wind-to-energy conversion devices. His point was that the world’s current capacity for producing neodymium was insufficient to meet these future needs. This doesn’t mean the project is necessarily doomed. As a general rule, the inevitable price spikes which occur whenever demand exceeds supply often leads to the discovery of new, albeit more expensive, sources and methods of extraction. But at what point does the difference between running out of an element and being unable to use it due to cost become moot? Developers of new technologies will need to start paying more attention to the future availability of their starting materials. Maybe those alchemists obsessed with the transmutation of metals were just preparing for the future.

I’ve also noticed that many of these disappearing elements seem to be associated with new energy technologies. My first post on this subject came after reading a stock analysis criticizing a company’s (First Solar) plan to significantly increase their solar cell production – a plan which would have required using 16% of the world’s current capacity of tellurium. Hopefully this is not a trend which will continue.
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On the brighter side, my son no longer needs training wheels for his bike. My enthusiasm, however, is somewhat dampened by the soreness which I’m now experiencing after having spent yesterday running along side his bike, trying to help him maintain balance, while accelerating down our street. (Our sub has no sidewalks) He was probably ready to learn this last summer, but we never got around to it. So it took him less than a day to learn, to my great relief.

The Alchemy of Zinc

Back in the day, alchemists apparently spent all their time attempting to turn base metals into gold. I say apparently, since that is the common perception of alchemists. In reality, most alchemists were devoted to what was often referred to as the “Great Work.” According to alchemical theories, much of what is created by nature is imperfect, and by applying the art of alchemy, natural substances can be brought to a higher state of perfection. Since gold was the height of perfection for metals, it was thought that base metals could be transmuted into gold merely by removing these imperfections. The Philosophers Stone wasn’t just about making gold or the “Elixer of Life”, it was a process/device/concept for bringing about perfection.

Color was very important to the alchemists, perhaps since it was one of the few clues with which they had to go on during their experiments. Colors and color changes were rigorously recorded and eventually incorporated into many of the alchemical theories. Certain color sequences were expected during the path towards perfection. In the transmutation of base metals into gold, for example, a color sequence of black to white to yellow to purple was thought to be required. Later theories redefined the sequence as black to white to red. While this fascination with colors may have led them astray on occasion, it has also led to a vast array of wonderful, full color illustrations, intricately drawn and full of alchemical symbolism. Here is one such example.

An experiment often touted as reminiscent of alchemy and demonstrating the relative ease of generating color changes involves the apparent conversion of a copper penny into silver or gold. Simply dissolve some Zn powder in warm NaOH solution, toss in a penny, and watch the penny turn silver as a coating of Zn forms on its surface. Heating the penny turns it gold as the Zn and Cu alloy to form brass. (My kids were duly impressed when I performed this experiment for them, informing me that it was “awesome”, but considering they said the same thing when I turned phenolphthalein red, the “awesomeness” bar may be set pretty low.)

But why does this work? I’ve coated pennies with silver and mercury before, but zinc is more electropositive than copper. Based on electrochemical potentials, zinc shouldn’t plate out on copper -- copper should be plating out on zinc. Apparently I’m not the only person to wonder about this, as web pages devoted to this effect can be found throughout the Internet, for example, here and here.

First of all, Zn dissolves in NaOH to make zincate ion and hydrogen.

Zn + 2OH^- + 2H₂O ----> Zn(OH)₄^2- + H₂

Okay, that’s straightforward chemistry. But how does the copper reduce the Zn(OH)₄^2-? The answer is that it doesn’t. Surprisingly, copper is not the reductant . Copper is not oxidized and it does not go into solution. Copper’s role is to create a galvanic cell with the undissolved portion of the zinc powder. Zinc does not plate out on the penny until the copper is in direct contact with zinc metal. It turns out that zinc metal is the reductant, which sounds bizarre, at least to me. Once the zinc and copper metals are in contact and the galvanic cell is created, the zinc begins to oxidize…

Zn + 4OH^- ----> Zn(OH)₄^2- + 2e^-

And its electrons are now available to reduce the zincate ion near the surface of the penny...

Zn(OH)₄^2- + 2e^- ---> Zn + 4OH^-

So the overall reaction is:

Zn + Zn(OH)₄^2- ----> Zn(OH)₄^2- + Zn

Basically there is no net reaction! Which means the zinc is essentially just migrating from the surface of the zinc powder to the surface of the penny. At first glance, this would appear to violate the laws of thermodynamics, but obviously it doesn’t. I assume there is some sort of entropy effect here, perhaps related to the galvanic cell, but I don’t know the exact cause. In any case, this reaction appears just as mystical as alchemy itself!

If anyone happens to know any more about this process, I’d be happy to hear from you.

Should the American Automotive Industry Be Saved?

Despite living in the Detroit area and working in the automotive sector, I’ve never mentioned the current plight of the American automakers, despite it being a major news story for the past several months. I have no idea if anyone outside of Michigan really cares one way or another about the subject, but what the heck – this is a blog and I have no chemistry items ready for today, so here’s my take….

As you might imagine, I’m generally for the idea of helping out the ailing auto industry. I admit to having a certain financial incentive in keeping the local economy from tanking even more than it already has. I also admit I probably wouldn’t care as much about the subject if I lived somewhere else. But I don’t, and since I’ve had a chance to see how the auto industry operates, up close and personal, I do perhaps have a little better idea about what’s happening than most people outside the state of Michigan, especially southern Republicans.

I’m certainly not an apologist for domestic automakers. I’ve laughed at, or cursed, many of their decisions over the years, and there have been plenty of instances in which I’ve thought the UAW should be blown up, but even I have to admit that things have indeed been changing (albeit slowly) over the last decade. Before I begin, I going to have to rant a little…

rant mode on
Forget all the crap you hear from politicians claiming that domestic automakers:
1. Haven’t changed for decades (hire a competent staff who has at least a clue about the auto industry)
2. haven’t worked on alternative energy vehicles (they could finance small countries with what they’ve spent in that area)
3. have been resisting tighter emissions and fuel economy requirements. (Okay, so that last one is definitely true, but name an industry that hasn’t. Energy related industries (a Republican favorite) like coal have resisted emissions and safety regulations for decades but haven’t been bashed for it the last 8 years. We’ll see if that changes now).
rant mode off

Look, had this crisis occurred ten years ago, I probably would have said, “Let them fail” too. They were behemoths, unable or unwilling to change, so perhaps a bankruptcy is what they needed. But after all the changes the automakers have gone through in the last 5-10 years to make themselves leaner, more responsive, and more cost effective, it would be a shame for them to fail now because of bad timing. Even the unions were beginning to understand that changes were coming, which I believe is one of the signs Armageddon is close at hand. It appeared that GM had turned things around. Their new cars were getting good reviews, they were selling well (before the credit crisis), the company’s cost structure was much better, the time required to design, develop, and build a new car was approaching that of their foreign competitors, and surveys indicated that they had pretty much matched the Japanese in terms of initial quality (it will be a few years before we know if how their 1-3 year quality grades out). Had the credit crisis not occurred when it did, we might well be reading glowing stories about how GM had turned it all around. But it did and so now certain decisions have to be made.

Do the automakers deserve to be saved? I don’t think they “deserve” it, but after all the changes they’ve made, they probably don’t “deserve” to fail either. Unfortunately, many of the U.S. Senators who bashed the automakers back in January were woefully ignorant (or pretending to be woefully ignorant -- surely their staffs can’t have been that misinformed) of these changes along with some basic facts about the automotive industry. Even if you ignore all the factual errors, the fact that the Senators which are pushing hardest for a domestic bankruptcy represent states which enjoy the presence of foreign auto plants and thus might benefit from such a bankruptcy lessens the validity of their arguments. Already, the argument that there is something inherently wrong with domestic automakers if they need to ask for government aid has been blown apart by the fact that even Toyota is doing the same thing. By the way, I should mention that those same foreign automakers have been quietly telling these Congressmen to tone down their rhetoric about the evils of government bailouts and the benefits of bankruptcy. A bankruptcy at GM would wipe out the already strained supplier base, which also supplies parts to the foreign automakers. Shutting down foreign owned auto plants in the south would not be particularly good for the people down there either.

Of course the real question is “What is in the best interests of the country?” Which will cost the country more? Bankruptcy or financial aid? And this is a question everyone must answer. If you don’t think a GM bankruptcy is going to affect you, you are kidding yourself. The domino effect of from a GM bankruptcy will take out a huge section of the economy, including areas that may not be apparent to people working in non-automotive areas. I’m not an economist, but it wouldn’t surprise me if such a collapse would prolong the current financial crisis by another 6 months, and that may be optomistic. Let’s make sure we get this right. Playing politics with this decision has the potential to damage the country even further.

OK, I’ll get down off the soapbox now.

Colorful Chemistry

I suspect that one of the reasons I chose Inorganic chemistry as my major was due to the colorful chemistry of transition metal complexes. Organic compounds, at least the ones I saw during my first several years in college, were almost always white. And in those instances where some color was present, usually a rather boring pale yellow or brown, it was often due to the presence of impurities.

Unfortunately, the electronic transitions responsible for most of the transition metal colors are d-d transitions, which are generally forbidden under the rules of quantum mechanics, so it often requires fairly concentrated solutions to generate rich colors. There are the occasional exceptions – e.g. MnO₄^-, whose color is due to a quantum mechanically allowed electronic charge transition (the electron jumps from a metal orbital to an oxygen orbital) -- but generally, the extinction coefficients of most inorganic molecules are low.

So it’s rather ironic that a majority of the most deeply colored compounds are organic molecules. No forbidden electronic transitions here, just conjugated systems that can be tailored to absorb just about any wavelength of light in the visible and UV spectrum. This property has led to their use as dyes for over 4000 years. A list of the early dyes would include:

Alizarin – produced by the madder root
Carmine - obtained from the bodies of cochineal insects
Indigo – obtained from the indigo plant
Tyrian Purple – a brominated version of indigo, obtained from the Murex (a type of shellfish) in minute amounts, so quite expensive. Only affordable to the uber-wealthy, it eventually became seen as a symbol of royalty (thus the saying “born to the purple”). In Roman times, it was a capital offense to wear it if you were not a noble. Exposure of the dye to alkali turns it crimson, producing the color worn by Cardinals in the Catholic church.

Starting in the 1800s, many of these natural dyes were replaced with aniline based compounds produced from coal tar. Some of these are considered safe enough to eat, which is why Blue No. 2 (indigotine) is found both in your blue jeans and in your blue M&Ms. Not all of today’s dyes are synthetic. Carmine, which is still obtained from insects, is still used to impart a reddish color to some foods in the US, which is creating a bit of an uproar. Not surprisingly, the food industry is not enthused about telling consumers that some of their products are made from bugs.

The blue food coloring referred to as Brilliant Blue FCF (or Blue No. 1) has a noticeable side effect of which most parents are aware. Green poop. I remember the first time my six month old son presented me with such a gift. Unfortunately, he was suffering from some unknown intestinal disorder at the time which already had us a little worried. The only reason I didn’t immediately panic was that the bright Kelly green color was so artificial looking that it was hard to believe it was physiological in origin. Apparently purple goldfish crackers have Blue No. 1 in them.

Clustered Water Chemistry

As an aqueous inorganic chemist by training (at least in grad school, although my horizons have expanded quite a bit due to my time in industry), I’ve spent a fair amount of time investigating and understanding the role of water in chemical reactions. When working with transition metals, this usually translates into accounting for aqueous coordination complexes, pH, and solvent effects. However, after perusing the Net these last few years, I now realize I have been woefully ignorant concerning the chemistry of water. I knew water tends to form loose clusters of molecules (due to hydrogen bonding), which accounts for some of its unusual properties, but I wasn’t aware of the immense importance of these clusters to its chemistry.

I am particularly upset that neither my professors nor my chemistry textbooks felt it necessary to cover this important aspect of aqueous chemistry. As a result, I’ve been forced to learn about clustered water on my own by visiting some rather arcane web sites – web sites that for some reason appear to contain a high percentage of viruses, bots, and other spyware. To make it even worse, most of the my information comes from sites which make a profit by selling devices or elixirs based on the unique properties of these water clusters, which means that the scientific basis for these properties are often poorly explained. (These people really need some spell checkers!)

Here is what I’ve been able to deduce from my research:

1. There is a form of clustered water which has very unusual properties. Scientists are generally unaware of this form of water since it disappeared from the earth in the distant past. However, it can still be found naturally in very old glaciers and newborn babies. Yes, we are born with our own supply of the stuff, but we lose it as we age (being replaced by ordinary water) and this leads to disease and the overall decay of our bodies. I can only assume the major pharmaceutical companies are working feverously on this in secret as I type.

2. Clustered water has a different surface tension than normal water. Unfortunately, there is disagreement as to whether it’s higher or lower. Regardless, this difference in surface tension allows it to permeate cell membranes more readily which keeps our cells more hydrated… and healthy… and happy.

3. Clustered water retains a memory of the impurities which were trapped inside these clusters in the past. Although this sounds suspiciously like the failed theory of "water memory" proposed by Jacques Benveniste, this time it’s for real! Unfortunately, this has led to some confusion amongst the makers of clustered water products. Some marketers want you to ingest water clusters which have been exposed to very dilute solutions of vitamins to help replenish the body. Others feel it is the ingestion of clustered water which has been previously exposed to toxins which causes all our problems. These people want to sell you devices for purging your body of bad clusters. The scientific world is still debating this one.

4. Clustered water can impart its properties to ordinary water. So it’s cheaper to buy a concentrated bottle of clustered water and dilute it with ordinary tap water.

5. Changing the bond angle within the water molecules results in a burst of light which affects your DNA. Apparently, this turns out to be a good thing. I’m not quite sure I understand everything that was explained on the web site, but I believe changing the bond angle can be done using sound vibrations. Gregorian chants are particularly good. In any case, we should all be aware of the possible effects of MP3 players on our lab experiments.

6. Clustered water is not to be confused with the fictional compound Ice-Nine, mentioned in Kurt Vonnegut’s book, Cat’s Cradle. Clustered water is real.


If you wish to read more about this fascinating area, visit the Water Cluster Quackery page.

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Woohoo! We now have vending machines at work! Our work site now is relevant!

Adatoms?

A few weeks ago, I attended a talk given by Professor John Yates at the local Michigan Catalysis Society meeting. John Yates (University of Virginia) is a well respected figure in the area of surface chemistry and catalysis. I hadn’t heard him speak before, but I was looking forward to it since, according to a friend of mine, John could make a talk on life insurance interesting. I was not disappointed. On a side note, he looks pretty damn good for someone in his 70's. His talk centered on self-assembled thiol complexes on gold surfaces. Interested parties might read the following paper: P. Maksymovych, D. C. Sorescu and J. T. Yates, Jr., “Gold-Adatom-Mediated Bonding in Self-Assembled Short-Chain Alkanethiolate Species on the Au(111) Surface,” Phys. Rev. Lett. 97, 146103 (2006).

John spent a fair amount of time discussing gold “adatoms.” What are adatoms, you ask?

No. Not this guy.

An adatom is an “adsorbed atom” and is usually described as a single atom sitting on a crystal surface. Adatoms have been around for years, but I’d never heard of the term before, despite the fact that I’ve apparently been making them for years. Simply exposing Pt to a hydrogen molecule, for example, will lead to the formation of hydrogen adatoms on the Pt surface. Of course, many of us who work on catalyst development would not think of these as adatoms, since in our line of work, exposure to even tiny amounts of hydrogen would essentially cover the entire surface of the platinum with a layer of hydrogen atoms, which doesn’t really fit the adatom definition.

What I found interesting was that Au, Ag, and Cu have the ability to generate their own adatoms. Due to structural strains in the crystal packing of these metals, individual atoms tend to pop out of the bulk to form single atoms on the surface. Assuming I understand this correctly, these adatoms tend to appear in a regularly repeating two dimensional pattern across the surface. Molecules (such as thiols) can bind to these adatoms, creating a surface layer with unique chemical properties. (Note: It’s possible that exposure to these binding molecules actually helps cause the adatoms to appear on the surface in the first place, but I don’t know. Perhaps someone else can answer that question.) Interesting chemistry indeed.
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I see that I passed the one year anniversary of this blog back in January. It’s unfortunate that it occurred during a dry spell, but I’m happy the blog is still going. The percentage of blogs that last more than a year is fairly low, so I can’t complain.

First Week Back At Work

Well, I'm a week into my new job and things are beginning to settle down.

A little.

Even though I'm working for the same company as before, I'm working at a totally different location on a totally different project under a whole new set of rules and regulations. Although I know I'm working on fuel cells, my specific duties have yet to be fully determined. One of my initial assignments is to get the various testing facilities up and running, but I can see that I'm going to be needed in many different areas. The manager of the project has apparently decided to let me decide where I should be focusing my efforts. Hopefully I don't disappoint. I'm certainly not going to be bored. Here are the pros and cons so far:

Pros
--I'm getting paid. Yeah!!!!!!!! (Come on, what did you expect?)
--The project looks like fun. There's a lot of interesting chemistry happening here.
--Sorry, that's all I've got.

Cons
--Long commute. It's a 55 minute commute each way now, but it could be worse, so I won't complain too much. Some of my coworkers have even longer commutes. Such is your fate when you work for a company in the midst of a significant downsizing.
--No phone number, computer logon ID, email address, or computer! I have to request these things and the response time is yet to be determined. I'm currently borrowing a computer for making notes and browsing the net, but someone else has to log me in on their account every day for this to work. The lack of ID means I can't be the first person to arrive in the morning or the last person out at night, else I'll be setting off alarms.
--There are no vending machines here! Not even for soda! Not enough people here to support them I suppose, but I was under the impression that OSHA regulations required their presence at all work facilities. ;)

I previously wrote that I needed more structure in my life in order to keep up with this blog. Beware of what you wish for! I definitely have structure in my life now, but at the expense of free time. We'll see how this translates into blog entries.

Photo Chemistry

A few weeks ago, my wife began taking a photography class at a local college. Although her real interest is in the area of digital photography, course prerequisites require her to take an initial course using real film. One of the things the course is designed to teach is how to develop your own film, so she's getting some hands-on experience in some basic chemistry. She may never use any of this knowledge, but she does seem to be enjoying the class.

In any case, she's reached the section of the textbook which covers the chemical aspects of film development and she's already asked me for help on her homework questions. Unfortunately, the questions turned out to be a little bit more difficult than I expected. This was due in part to the fact that the chemistry questions were written by someone who obviously was not a chemist, which always adds to the degree of difficulty. This meant I spent a lot of time trying to determine exactly what the instructor "thought" he was asking and what type of answer he was hoping for. (Now I don't mean to suggest that the non-chemist is always to blame in situations like this. Sometimes it's the chemist who is the problem. I recall trying to answer a Trivial Pursuit question many years ago which read "Glass is made out of what?" The answer, of course, was "sand", but all I could think of were answers like "silica" or other more esoteric chemical terms, despite being given the hint not to think like a chemist.)

The other difficulty arose when I came to the realization that I knew less about the chemistry of film than I thought. I knew that silver halide salts (the main ingredient in film) are light sensitive, decomposing to black silver metal upon exposure to light. After all, that's why silver salts are always shipped in dark brown bottles. And I had known about the role of sodium thiosulfate in the fixer (dissolving and removing unreacted silver halide) since I was a freshman. But what did the developer do? And what is a stop bath?

Apparently, the initial exposure to light only reduces a small fraction of the silver halide in the film -- not nearly enough to make a negative. The developer operates by magnifying the amount of silver reduced to the metallic state. The developer contains organic compounds (such as hydroquinone or p-aminophenol) which are good at reducing silver halides in the film, but only when catalyzed by the presence of small metallic silver clusters (such as Ag₄^o) which were formed during the initial exposure to light. The grain size of the silver halide particles are an important determiner of the amount of silver reduced by the developer, and this fact is used to produce films with different speeds.

And the stop bath? It's basically a solution of acid which lowers the pH of the developer and essentially halts the further reduction of silver halide.

At least my wife is experiencing the joys of using graduated cylinders in her lab. Maybe I'll make a chemist out of her yet!

Why Free Time and Blogs Do Not Mix

The biggest reason why I haven't been updating my blog lately (other than laziness) is apparently due to having too much free time. Strange as it may seem, I am finding I require a certain minimum level of structure in my life in order to post anything on this blog. Back when I lived in the land of employment, there was structure. Searching the net for interesting science articles at work (during lunch, of course) was a regular routine and this process generated most of the ideas about which I posted. When I'm home all day, I never get around to performing this ritual until late at night, and then I feel obliged to work on my resume, or rearranging my office, or any of the other tasks I managed to avoid during the day.

Well it looks like that practice is about to stop.

Unless something unforeseen occurs, I should be entering the land of the employed in about a week. Now before you all start cheering too loudly, I should point out this job is not a permanent position. It's a contract position, with a length of one year, and the salary is significantly less than my prior job. And it's not going to involve a lot of interesting research on my part either, at least not for a while. I'll be developing computer automated test reactors for the evaluation of fuel cells. Not what I'd call an ideal position, but it will help keep us financially secure until I do locate a more favorable, permanent position. To say the national job market for inorganic chemists has fallen off a cliff is an understatement. The trick will be to ride it out for a couple of years until the job market opens up.

The funny thing is -- I am going to be working for the same company I was laid off from two months ago. I was only able to pull this off because:
1. it's a contract position, which means they can cut me loose at any time, and considering the precarious state of the company, that time could be measured in months or weeks.
2. it's at a different facility, which unfortunately means a 50-60 minute commute each way.
3. it involves a product area in which they are very excited. And the fact that this project is partially funded by the government actually allowed them to hire someone.

Anyway, I hope to be spending lunch breaks posting in a more regular fashion soon.

More Bad News

I just learned that there are going to be more layoffs at my former company. Unfortunately, one of the guys I worked closely with was tapped this time. All the competent researchers from that particular division are now basically gone. This does not bode well for the future of that division or the company overall.

Hydrate Chemistry

As I've previously indicated on this blog, I am primarily an AQUEOUS inorganic chemist. As such, I've prepared a wide variety of aquated metal complexes over the years, but I've never paid much attention to solid hydrate chemistry. And that's a shame, since there is a lot of good chemistry in that area, some of which I'm dealing with right now.

A few months ago, we decorated our ceilings with crown molding. Unfortunately, the original builders of our house placed the water pipes too close to the ceiling, which meant that two months after the crown molding was added, the FOUR nails which had punctured the pipes rusted and caused the pipes to leak. The resulting repair left a hole in the ceiling which was my job to fix. The material of choice for this type of repair is drywall (sometimes called sheetrock). Drywall is prepared by mixing CaSO4 · 1/2H2O with water to form CaSO4 · 2H2O, a hydrate with enough strength to be used to construct walls. Considering the fact that the added water forms no bonds other than hydrogen bonds, it's a little surprising that the resulting hydrate is so stable.

Of course, the strength of CaSO4 · 2H2O is nothing compared to that of another well-known hydrate. Cement begins as a mixture of CaO and SiO2 in various proportions, which is then reacted with water to form a calcium silicate hydrate.

2 Ca3SiO5 + 7 H2O —> 3 CaO · 2 SiO2 · 4 H2O +3 Ca(OH)2

Actually there is an entire series of hydration reactions which occur during the hardening of cement, with reaction times ranging from hours to weeks. Again, the strength generated by the formation of a hydrate is simply amazing.

Another hydrate with interesting chemistry is methane hydrate. Containing 5-6 molecules of water for every molecule of methane, this material can be found in huge quantities along the ocean floor. Wiki link here. It has been described as both a huge, untapped energy reserve and a major source of greenhouse gas. The latter description has become more significant as the temperature of the oceans continues to rise, since methane hydrate is only stable at low temperatures. It's also been used to explain the disappearance of ships in the Bermuda Triangle. What more could you ask from a simple compound?

Anyway, the ceiling is fixed.