This blog is my attempt to reconnect with the world of chemistry. I have a PhD in Inorganic Chemistry and make a living doing research for a large company in Michigan. As times have changed, that company has changed its focus and I no longer have as much chance to do the basic, fundamental research which I most enjoy. Through this blog, I am hoping to recapture the magic which I felt during my graduate (and undergraduate) days in college. Expect topics on chemistry and alchemy along with some non-chemistry related items which I think might be interesting.

"The chymists are a strange class of mortals, impelled by an almost insane impulse to seek their pleasure among smoke and vapour, soot and flame, poisons and poverty; yet among all these evils I seem to live so sweetly that may I die if I would change places with the Persian King."

Johann Joachim Becher (phlogistonist)
Acta Laboratorii Chymica Monacensis, seu Physica Subterranea, (1669).

Thursday, August 28, 2008

We're Moving.... Sometime.... Maybe.....

Today we received word that our lab will be moving to the new research site at the end of October. Even though this pronouncement was delivered by upper management, it can be considered nothing more than a rumor until it actually happens. Too many unknowns exist for anyone to even guess at our move date. For one thing, the construction crews haven't even begun work on our lab yet. We are part of the third (and final) phase in the rollout plan and they haven't even finished the first two phases yet. As a further complication, our current building is being taken over by another set of tenants in the near future. If they show up early, we may find ourselves being thrown out early. And of course, knowing how this company works, it would not be surprising if some clueless upper manager somewhere arbitrarily changes the move date with little regard for how it might affect our projects.

I've talked about our move before, and while it will be great to get all of us (chemists, physicists, engineers, purchasing, IT, marketing, etc.) together in one building, I'm still going to have to endure some pain before everything is settled. Our group is not the only group waiting for their new labs to be finished. But those groups have not been given permission to stay in their labs any longer, so they will be moving into our already crowded lab for a few months.

Since I do stop over at the new location occasionally, I've begun to notice some of the annoyances that the new place will have to offer. First, while remodeling the building for our use, it was decided that a wireless intranet was the way to go. We still have network jacks at all our desks, but that's about it. None of the conference rooms had internet jacks installed. This isn't a problem if your laptop is wireless, but mine isn't. Nothing can quite describe the pure horror of having to attend a group meeting without having access to the internet. What the hell are we supposed to do during the boring parts of the meeting? Everyone else uses these meetings to go through their mail, read Dilbert cartoons, and check stock prices. It's just not fair! I've ordered a new laptop computer so hopefully this will not a problem by the time I move to the new location.

Parking is also going to be a problem at the new site. It's not like there aren't plenty of spaces available, it's just a matter of how far away you'll be from the building when you find a spot. This can be a significant issue during Michigan winters.

You have to use your magnetic security badges to unlock doors in order to go anywhere in the new building. No more just sticking it in your pocket and leaving it there all day.

Finally, there is this one guy at the main desk who insists on checking my laptop every time I leave in the evening. He actually checks the serial number on the bottom of the laptop with the number on my security badge. It's not like he hasn't seen me before with a laptop, and it's not like it would take me more than 5 minutes to fake the serial number on the laptop, but he insists on doing it every time. I can bypass this problem by exiting through one of the unmanned, security badge accessible side exits, but that puts me a lot farther from my car and will not be a favored option during the winter.

Additional note: Our old location is located within three miles of the four plant nurseries where I buy most of the flowers I plant every year. The new site has no nurseries anywhere near it. Damn! Obligatory garden picture follows:

Wednesday, August 27, 2008

Golden Health

Gold has been used for medicinal purposes since the time of the Romans. Rightly or wrongly, gold was often used as a medical treatment for a variety of conditions. It does appear to have anti-bacterial properties, much like silver. In medieval Europe, pills were often coated with gold to "enhance" the benefits of the medicine. Paracelsus, the alchemist, developed a solution of colloidal gold which he named "Aurum Potable". He considered it a powerful elixer capable of curing all sorts of ills.

In recent years, gold has experienced a bit of a renaissance in the form of nano-particles. Gold nano-particles are being used for drug delivery systems, biosensors, optical devices, and catalysts, among other things. It's hard to get through a chemistry journal without seeing at least on paper on nano-gold. In retrospect, gold nano-particles aren't really all that new. First of all, they apparently already existed in nature. They were also used by the Romans to create red stained glass. In bulk form, gold is yellowish since it reflects light at the blue end of the spectrum less efficiently than other colors. However, if the size of the gold particles is significantly smaller than the wavelength of visible light, new interactions occur between the light and the gold surface, resulting in a red color. In aqueous suspensions, purple and yellow colors can also be obtained if the particles are allowed to aggregate. In fact, Paracelsus's purple "Aurum Potable" was a simple suspension of gold nano-particles.

As you can imagine, colloidal gold is now available all over the net (for example, here and here) for boosting your physical and mental health. Don't feel like drinking gold? No worries. They also sell nano-silver, nano-copper, nano-platinum, nano-palladium, nano-iridium, nano-titanium, and nano-zinc too.

Why am I mentioning gold's supposed health benefits? Apparently the Romans were on to something back in the day since it turns out their gold nano-particle based stained glass windows are good at removing volatile organic compounds from the air. Will we be seeing gold-based air purifiers in the stores soon? I can only imagine what the web marketeers are going to do with this information.

Thursday, August 21, 2008

Hooray! Aqueous Transition Metal Chemistry Talks

I really miss going to ACS meetings, but with chemistry not being as big a focus at my company anymore, it can be difficult to justify (to upper management) the expense of going to one unless there is a session directly related to my current project. I attended a session on reforming catalysts several years ago, but that’s been it for a while. Besides, my true love is aqueous transition metal chemistry and those types of talks can be few and far between. So imagine my surprise and delight when I ran across blogs discussing, not one, but two such talks being presented at this week’s national ACS meeting.

The first talk was mentioned on the Chemistry Blog, concerning a study to use chelating agents like EDDA to extract actinides from nuclear waste. YES! Good, old-fashioned aqueous transition metal chemistry. Okay, actinides aren't strictly transition metals, but they're close enough. I did find it amusing when Mitch wrote "These types of systems look promising and are a nice upgrade over traditional old-school extractors like tributylphosphate(TBP)." Any reference to classic chelating agents as "new-school" is music to my ears. To be honest though, I would have thought that these chelators, especially EDDA, would have been tested for this application a long time ago. At least it shows there are still applications for this type of chemistry yet to be discovered.

The second talk involved the use of Fe-TAML complexes to facilitate the oxidation of organic pollutants by hydrogen peroxide. Apparently these complexes are good mimcs of peroxidase enzymes. Here is the structure of the compound taken from the Collins group website:

Although I haven't had the chance to read the mechanistic and kinetic work on these reactions yet, this seems like a classic example of the TAML group basically locking the Fe into a square planar configuration and keeping it stable while it’s shuttling back and forth between the +2 and +3 states as it facilitates the transfer of electrons between the H2O2 and the target molecule. I've always had a soft spot for chelating agents that lock themselves around metals in tight, specific configurations, significantly changing the metal's properties in the process. My first undergraduate project used an amine oxime to wrap itself around cobalt in a manner resembling the structure of cobalamin (B12 vitamin). Classic aqueous transition metal chemistry. It brings a tear to my eye.

Tuesday, August 19, 2008

The Value of Toxic Metals

These's a body of water in Montana known as the Berkeley Pit. This lake is a remnant of an old open-pit copper mine that closed down in 1982 when it was no longer profitable to operate. It has since filled with water, about 37 billion gallons worth, and that's when the real chemistry began. Pyrites and other sulfides dissolved in the water and oxidized, forming sulfuric acid, and lowering the pH of the water to less than 3. This led to the steady leeching of metals out of the surrounding rocks, and after 25 years the Berkeley "Lake" has high levels of arsenic, lead, zinc, manganese, iron, copper, aluminum, and cadmium. It's a place only an inorganic chemist could love. It's also a part of one of the largest Superfund sites in the U.S. Nothing lives there - no fish, no birds, no plants - it's a dead zone, or at least that's what everybody thought. In 1995, someone spotted some green slime on the surface of the lake, which turned out to be a form of green algae.

Organisms which manage to survive extremely harsh conditions are called extremophiles. They have been found under the ice in the Arctic, around deep sea vents, and in the boiling water of hot springs. Their ability to survive these conditions makes them of interest to biologists. In particular, many extremophiles demonstrate a superior ability to repair their DNA, which makes them of great interest to cancer researchers. Andrea and Don Stierle have been studying the organisms which have been living in the pit, looking for new compounds which may have anti-cancer activity. And they have been successful, having discovered berkeleydione, berkeleytrione, and berkeley acid, all of which have shown anti-cancer activity. The structures for berkeleydione and berkeleytrione are shown below.

Thought #1:
Makes you look at toxic metals in the environment a little differently now, doesn't it? Perhaps we should be harvesting more of the toxic waste dumps we have created over the years. It could be one of this country's biggest resources.

Thought #2:
Microorganisms are better at making new and novel organic compounds than grad students. Soon, the only reason why faculty members will continue to hire grad students instead of microorganisms will be because grad students are usually paid less than what microorganisms would accept.

Sunday, August 17, 2008

Disappearing Elements? - Part III

In what is shaping up to be a recurring theme, there is yet another report warning of the possible future scarcity of an element. This time it's lithium.

The biggest sources of lithium are salt pans and salt lake deposits, mostly in Chile and Argentina. There is also a large, relatively untapped reserve of lithium salt is in the Bolivia salt pans. The Bolivian reserves are thought to contain 5.4 million tonnes of lithium (nearly 50 per cent of the global lithium salt reserves). Since the annual worldwide production of lithium is about 70,000 tonnes (lithium carbonate), this would seem to indicate we have plenty of lithium for the near future, assuming that demand does not significantly increase. Unfortunately, demand may be about to increase drastically. Lithium ion batteries are becoming all the rage, especially as automakers attempt to mass produce hybrid and electric vehicles.

According to William Tahil, the report's author: "to make 60 million plug-in hybrid vehicles a year containing a small lithium-ion battery would require 420,000 tonnes of lithium carbonate – or six times the current global production annually. But in reality, you'd want a decent-sized battery, so it's more likely you'd have to increase global production 10-fold. And this excludes the demand for lithium in portable electronics." At that rate, lithium is going to run out a lot more quickly.

However, this is not a universally accepted opinion. Keith Evans, a geologist with some expertise in lithium mining, disputes Tahil's conclusions. Evans believes that the available lithium reserves are much larger. His critique of Tahil's report is given here, and additional details can be found at his blog, which is named Lithium Abundance.

I don't use lithium very much in the lab, although I have occasionally used LiAlH4 and LiBH4. Still, I would be rather bummed out if we ever ran out of lithium, or any element for that matter. Let's hope Evans is correct.

In more lighthearted news, John Swain of Northeastern university has a video demonstrating that the iron which is used to enrich cereals like Total is actually in the metallic form. The link to the story is here and a link to a commercial free version of the video is here. I assume this isn't some sort of joke.

Wednesday, August 13, 2008

Chemistry Journalism?

I try to spend some time every day browsing through the various science reporting websites so as to receive my daily dose of science. I generally find them informative, but today I was greatly disappointed with the level of their quality. Science Daily reported the discovery of “an unusual molecule that is essential to the atmosphere's ability to break down pollutants, especially the compounds that cause acid rain.” "Okay," I thought, "that sounds interesting. I'll check it out." So I read through the entire article, several times, looking for the new molecule until I finally realized the molecule was never identified.

"Okay," I thought, "the writer screwed up. I'll just google some other articles."

Googling did indeed reveal many, many other sites which had covered this story. Unfortunately, it quickly became obvious that other sites weren't describing the molecule either. In fact, the articles were all identical copies of the original Purdue press release. No additional explanations, no deep dives into the subject matter, nothing but simple copying and pasting.

Now that is just plain laziness. I realize the internet is one huge morass of plagiarism -- it's not uncommon to find the same page duplicated over and over again when googling -- but I expect a little more from science news sites that are updated on a daily basis. At the end of the Science Daily article it reads: "Adapted from materials provided by Purdue University." By adapt, I assume they mean reformatted.

Of course, all this occurred because the Purdue press release had failed to identify the molecule. A full color ball and stick model of the molecule was presented, which the science sites dutifully reproduced, but there was a problem. I present the figure and its caption here.

Image caption: Scientists at Purdue and Pennsylvania universities have discovered an atmospheric molecule that is essential to the breakdown of pollutants in the atmosphere. The molecule, which had not been seen before, is unusual because it has two hydrogen bonds. This image shows the structure of the molecule, with the blue ball being a nitrogen atom, red representing hydrogen atoms, white representing oxygen atoms, and the yellow clouds showing the location of the double hydrogen bonds. (Purdue News Service image/Joseph Francisco)

So the molecule was O-H-NH2? That sure looks like one hell of a reactive molecule. Who cares about a double hydrogen bond? We have a hydrogen with two covalent bonds -- a much bigger story. Or maybe the person writing the caption just got the colors for hydrogen and oxygen switched. I was able to figure out the molecule's identity by looking at the title of the abstract tacked on at the end of the press release. If any of the website writers had actually bothered to read this press release while pasting, this mistake would have easily been caught. BTW, the new molecule is an HONO2 + OH moiety, held together by hydrogen bonding.

I'm not trying to dump on Purdue here, mistakes like this can happen. I’m just disappointed that none of the science sites I frequent picked up on it.


Note: while writing this I noticed that the Science Daily report did list a link to the paper which included the terms OH and HONO2, so it wasn't totally necessary to go to the Purdue site to figure out what was going on.

Tuesday, August 12, 2008

Humility is Good for the Soul

One of the reasons I started this blog was to sharpen my chemical skills -- skills which have been steadily declining over the years as my job has required less and less chemistry. I just played the “Can You Name the Elements in the Periodic Table in 15 Minutes” game and was reminded of just how little attention I’ve paid to the periodic table in the last 10 years. I expected that my score was going to be rather poor, and I was not disappointed. I only remembered 70% of the elements. I knew I’d have trouble with the actinides and lanthanides, but I also had trouble with the heavier main group elements. And even though I nailed all the transition metals, it required an embarrassingly long time -- embarrassing because transition metals are supposed to be my area of expertise. And it hasn't been that long since I've worked with the precious metals (Pt, Pd, etc.), so why did it take so long to remember rhodium, dammit? That’s pathetic. I also missed a few elements because I couldn’t remember how to spell them. Damn that praseodymium. Where’s the spell checker when you need one? Try the game at your own risk.

Maltese Water Problems

Reverse osmosis is the technique generally used for the desalination of seawater. Unfortunately, the polyamide-based membranes typically used in these processes are attacked by chlorine, which complicates the purification process (meaning more expensive). Polysulfone-based membranes are resistant to chlorine, but their hydrophobicity means that water does not move well through them. Extra hydrophilic sulfone groups can be added to the polymer, but they tend to attach to the least stable sites, which limits their effectiveness. Now, two research groups have combined to solve these problems -- by using the remarkably simple idea of adding the polysulfone groups to the original monomers before polymerization.

Reaction diagram obtained from patent application

Considering the lack of fresh water at locations around the world, anything that can help lower the cost of desalination can be a big deal. As I read this article, one country immediately came to mind -- Malta. Located 50 miles south of Sicily, the islands of Malta are the home country of my wife's parents. As a result, my wife and I have already visited Malta three times in the past 12 years. And believe me – it is hot! Since I think Michigan summers are too hot, you can only imagine what I think about our summer visits to Malta. Here is a family picture taken last summer in Malta.

Not a lot of greenery around. Mars probably has more water in the soil than Malta. Notice my daughter's T-shirt. Never too early to start influencing them.

It turns out that due to the quantity and quality of their beaches, Malta is a common vacation spot for many Europeans, especially the British and Germans, who tend to spend all day at the beach before showing up later in the evening looking remarkably like broiled lobsters. The water quality was fine 12 years ago during our first visit, but the influx of tourists, along with an increased demand for water by the local residents, has apparently stressed the desalination plants. 5 years ago, during our second trip to Malta, the water was really too salty to drink and we essentially lived off of bottled water for two weeks. Last summer, although the water was getting better, we still stuck with the bottled water. It's weird being surrounded by all that water and yet having to import water from the mainland. I hope this new membrane will allow Malta to build a few more desalination plants before our next visit.

Thursday, August 7, 2008

Textbooks Are Becoming Old School

Question. How many of you still have your old chemistry (or physics or whatever) textbooks from your undergraduate years? I think I still have nearly all of mine. And although I'm sure this is at least partly due to my being a packrat who can't throw anything away, it's also due to the fact that I like books. I may still go to the web first if I need some piece of information, but sometimes it's easier to go back to your textbooks for more detailed explanations. Besides, there is just an intrinsically good feeling when holding a book in your hands. But after reading this article, I'm beginning to wonder how much longer this trend will continue. Apparently, it's becoming just as easy to download textbooks illegally as it is to download ripped music and warez. And publishers are beginning to react in various ways. Unfortunately, one of their strategies is to offer the texts in ebook format, with subscriptions that run out at the end of the semester. So much for using that text as a reference a year from now.

Publishers, please let us keep our paper-based books!

BTW, this only applies to real textbooks. Textbooks for classes like psychology or sociology can be burned or thrown into an acid bath for all I care.

Wednesday, August 6, 2008

MIT Propaganda Machine

No doubt, many of you have heard of the recent “MIT Breakthrough”TM which provides a dramatic new way to store solar energy. Using a simple catalyst consisting of cobalt and phosphate, Daniel Nocera has supposedly removed the biggest road block holding back mass utilization of solar power. This story has been making its way through the web and the blogosphere for several days now and since I’m not an electrochemist, I’m not sure how much more I could add. However, my first reaction after reading the article was a sense of annoyance, and I found myself becoming more irked every time I read another article on the “breakthrough.” Part of my irknessTM was due to the authors themselves. I’m not sure how much information MIT released to the press, but several of the writers really had no clue about what the invention really was or why it was novel. Perhaps I'm a poor reader, but it required reading several articles before I was even sure exactly what Nocera had and had not done.

Irksome point #1. The constant references to solar energy, despite the fact that this catalyst has nothing to do with solar energy per se. The invention makes the electrolysis of water more efficient, nothing more. Nocera hopes that one day his invention may work in conjunction with solar power, using electrolytically generated hydrogen as an energy storage material, but right now, it doesn’t really have that much to do with solar energy, despite MIT's press release.

Irksome point #2. Many of the article writers appeared to be unfamiliar with the process of electrolysis, marveling at the novelty of being able to electrolyze water at room temperature. Hmmmm, I vaguely seem to recall hooking up a battery to salt water back in high school. Why wasn’t I referenced in these articles? The problem is that the efficiency of electrolysis is poor under these conditions, which I believe is due to the overpotential required when generating gases. (Please let me know if I am mistaken here.) Commercial electrolysis devices have been around for awhile, although to keep the efficiencies high, they are often run at high temperatures and pressures, using expensive electrodes and basic solutions. The novelty of Nocera’s breakthrough is that the cobalt-phosphate material allows for higher efficiencies at room temperature using cheaper materials.

Irksome point #3. The Scientific American writer who referred to both cobalt and phosphate as metals needs a refresher course in chemistry.

Irksome point #4. The MIT press machine set off the BS (Blatant Statement) meter way too often for my taste. Nocera didn’t do himself any favors either, with quotes like:

“This is the nirvana of what we've been talking about for years"

I've gotten rid of all the goddamn [power] grids."
Probably not during your lifetime, Daniel.

"Solar power has always been a limited, far-off solution. Now we can seriously think about solar power as unlimited and soon."
Sorry, but as I understand it, one of the big problems with solar power is the low conversion efficiency of sunlight into electricity. This invention does nothing to solve that problem.

Irksome point #5. I don’t really have one, but I really wanted to use “irk” as many times as possible. I’ll probably never use the word again.

Snarkier blog posts on this subject can be found here and here.