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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