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).

Friday, February 29, 2008

Ode to "The Professor"

Last night, my wife and daughter were reading one of the “Magic School Bus” books (an excellent series if your kids like science at all) and came upon a section describing Marie Curie and her discovery of radium. The book explained that it required 3 years and several tons of pitchblende to isolate a few grams of radium.

“What’s pitchblende?” my wife asked me.

Damn. I didn’t know the answer, at least not for sure. What’s the point of being a chemist if I can’t answer simple questions like this, especially since I used to know the answer. Eventually I told her pitchblende was probably a uranium ore, but I wasn't really sure. So, of course, as soon as the story was over and the kids were in bed, I ran downstairs to look it up on the computer. (Seriously, does anyone use an encyclopedia anymore?) To my relief, pitchblende was indeed described as a uranium ore, composed mostly of UO2, with a little UO3 mixed in.

And that, my friends, is one of the main reasons I started this blog. Back in undergraduate land I would have known the answer immediately, but years of focused research have dulled much of my general chemistry knowledge. Writing this blog forces me to recall chemical facts which I’ve forgotten over the years. Of course, the downside is that writing this blog continually reminds me of the number of chemical facts I have forgotten over the years. I've always prided myself on knowing or wanting to know about all areas of chemistry, not just my favorite areas like aqueous transition metal chemistry. My only failing has been that I've never taken a single biochemistry course, much to my regret.

In other words, my role model would probably be “The Professor” from Gilligan’s Island. I’m not sure what his main area of expertise was supposed to be, but the scope of his knowledge was impressive. According to his website the Professor’s expertise included medicine, dentistry, biology, agriculture, astronomy, marine biology, botany, psychology, physics, law, and zoology. (Hey, what about chemistry? Almost everything he did involved chemistry). And his ability to build anything (except, of course, a boat patching kit) would put MacGyver to shame. If Gilligan's Island had lasted more than 3 years, I’m sure the Professor would have solved cold fusion. Now this is a guy I could pattern myself after. I doubt that I would have brought science textbooks along on a 3 hour cruise as he did, but since he apparently has 6 degrees (according to the website), I guess he can be accorded a little slack.

In a slightly more bizarre bit of news, eye-tattooing is now available. You can read about it here and if you really want, you can see far more gruesome pictures here. Damn, I can't even type this without imagining a needle approaching my eye.

Tuesday, February 26, 2008

The Roundabout Conspiracy

Yesterday, I drove through our local roundabout, carefully avoiding the confused driver who had stopped inside the roundabout desperately trying to decide what he should do. I live near a road which apparently has one of the highest incidents of traffic accidents in the state of Michigan. There are three main reasons for this distinction. First, this road is the only real access into this area from the main beltway and so traffic density can be quite high at times. Second, the first 4 miles of this road are lined with nothing but shopping malls and office buildings, which results in lots of drivers attempting left-hand turns across 3 lanes of traffic. Third, drivers in this area are generally stupid and do not understand why reason #2 is a bad thing. In an attempt to decrease the number of accidents as well as to facilitate traffic flow during rush hour, local governments have spent years trying to find a solution. Part of their solution involves the use of roundabouts.

Now I have nothing against roundabouts. They can do a great job solving traffic problems, and the increase in heart rate you get while looking out for other drivers is probably good for your heart. Nevertheless, placing them in this area of Michigan would seem to be a very bad idea. The viability of a roundabout depends upon drivers not only knowing who has the right of way but also knowing when they have it. Around here, the concept of right of way means that making left-hand turns across 3 lanes of oncoming traffic is allowed if you are aggressive (or oblivious) enough. Apparently realizing this problem, the construction plan called for only 2 roundabouts to be built initially, with more to be constructed after a suitable evaluation period. Those 2 roundabouts were completed a few months ago and surprisingly, the number of accidents has been less than I expected, and traffic flow seems to be faster than before, although this may be due to the avoidance of these intersections by a fair number of drivers. Of course, my wife has actually seen a car driving the wrong way around the roundabout, so there is still some excitement to be found here, but overall, it appears to be a success.

Since these roundabouts opened, I have felt a growing suspicion that there was something odd about them. These suspicions have continued to grow and a few days ago, I finally figured out what's going on here. Take a close look at a typical roundabout sign.

See anything familiar about it? No? Let's try looking at the traffic flow pattern.

Look familiar yet? Still not seeing it? Does this help?

Coincidence? I think not!

Now I don't know why, but I think it's pretty obvious that roundabouts are part of some sort of conspiracy perpetrated by biochemists. Why? Who knows? Perhaps to prepare children for the inevitable biochem classes? Perhaps as a subliminal method to instill public trust in biochemists? I'm not sure what other explanation there can be. In addition, you will notice that biochemical cycles are almost always drawn in a clockwise fashion, which is the opposite of our traffic patterns here in the US. Obviously, British biochemists are behind this plot. There are numerous roundabout configurations out there - 5 way intersections, double roundabouts, etc. and I'm currently in the process of determining which biochemical cycles each type represents. The most complicated roundabout that I've found is located in Swindon, England and is known as the Magic Roundabout. It's traffic flow is shown here:

Now, I want the biochemists out there to tell me which biochemical cycle this roundabout represents.

Monday, February 25, 2008

Chemistry Free Zone

I spent part of today looking for interesting science and/or chemical related webpages to discuss on this blog. Instead, all I found were bizarre stories.

First on the list is an article about a 150 pound hamburger developed by the owners of a sports grill named Mallie's. They are attempting to set a new record for the largest hamburger ever served. 150 pounds! That is basically a whole cow (admittedly a small one). How many people do you need to eat this thing? Since this restaurant only has a 240 person capacity, they are going to have to bring people in off the street to finish this burger. After reading this article, I started thinking to myself, "In what part of the country do these guys live?" and "What kind of joke can I make about the local residents?" I check out the article for details. Crap! This place is less than 30 miles from my house. End of story!

You will find me periodically discussing videogames on this site. It will not be very often since I don't play them as much as I did several years ago, and as a result, very little of what I could say would be either useful or timely. Anyway, here is some retro gaming action for you. A group of people got together to make a video of the Space Invaders game (plus some others) using stopped motion photography and with people representing the screen pixels. Utterly bizarre and utterly enjoyable! Go here to see it.

Enjoy The Lord of the Rings trilogy? The Hubble telescope has discovered "The Eye of Sauron." See the image here.

Finally, on a sports related note, the Detroit Pistons pretty much demolished the Phoenix Suns yesterday. You really cannot tell much from any single basketball game, but this game just reinforces what Pistons fans have known for years. The Pistons have one of the best starting fives in the NBA, but their ability to win depends almost completely upon their motivation. The instant they get bored and/or arrogant, and that has happened distressingly often ever since they won the championship in 2004, they can lose badly to any team in the league. But if they are motivated to play, they can crush any team out there. Sunday's game was the perfect storm, playing on national TV, going against one of the top teams in the West, facing a team that's been getting a lot of attention lately because of their acquisition of Shaq, and getting to play against Steve Nash. (Ever since getting edged out of the MVP voting by Nash a couple of years ago, Chauncey Billips has taken a certain delight in punishing Nash every time they play). What does this mean to the Pistons' playoff chances? Who knows? I've given up understanding how this team works.

Saturday, February 23, 2008

Miscellaneous Saturday

Know of any chemicals with funny or bad names? Paul May has an exhaustive list on his website. This list can be found mirrored all over the web, but I believe this is the original version. Certainly it has the best pictures and diagrams.

These scientists can tell your age by measuring proteins in your eyes. The procedure is a little involved, so don't expect it to replace the practice of carding underaged drinkers.

I've also added my first chemistry related link to the blog list, Curly Arrow. He may be an organic chemist, but any chemist who enjoys the colors of chemistry or uses chemical equipment as Christmas decorations must have a little inorganic chemist in him.

Thursday, February 21, 2008

Missing Ammonia Chemistry

Cats are great pets, but having them around means occasionally having to deal with cat pee. Years ago I had a male cat that for some reason began to spray inside the house. The problem eventually resolved itself, but not before I had plenty of urine-soaked towels that needed to be cleaned (or burned). Without thinking too much about it, I threw them in the washing machine along with some bleach. Now even my wife knows not to mix ammonia and bleach, but I didn’t make the connection until a rather noxious odor began emanating from the laundry room. Apparently, the amount of nitrogen in those towels was considerable.

While airing out the house, I was struck by the fact that I was unaware of the actual chemical reaction that had occurred. AFAIK, it had never been mentioned in any of my chemistry classes. In fact, I do not recall ever hearing much about ammonia chemistry at all, other than vague statements about ammonia being the nitrogen analogue of water. We covered amines in organic chemistry, but that was about it. Apparently, the chemistry of ammonia was just not considered important enough to teach. Other than using a metric ton of ammonium hydroxide over the years for raising pHs or making transition metal ammine complexes, I really had not had much interaction with ammonia. Anyway, as most of you probably already know, the ammonia/bleach reactions are:

NH3 + HOCl → NH2Cl + H2O Toxic
NH2Cl + HOCl → NHCl2 + H2O Toxic
NHCl2 + HOCl → NCl3 + H2O Toxic and explosive

(Cat urine is mostly urea, I believe, but apparently Cl2 can react with that too.)

In retrospect, I should have been aware of these reactions based on my “familiarity” with their iodine analogues. NI3 is prepared using ammonia and iodine in exactly the same manner. Once dry, a slight touch is often sufficient to cause it to explode, producing a loud crack and a plume of purplish smoke. It’s probably fairly difficult to make it through undergraduate chemistry without learning this reaction (perhaps less so for organic chemists who have their own set of explosive materials with which to work). I admit to having used NI3 in rather unprofessional ways as an undergraduate, but I was an amateur compared to the guy down the hall, who was known for producing rather large batches of NI3 for his entertainment. My closest encounter with NI3 occurred one evening, when this guy stopped by my lab to ask if I had enjoyed “the show.” Seeing the puzzled look on my face, he pointed to the various undetonated piles of NI3 he had left throughout the lab which, by some miracle, I had managed to avoid. He also pointed to what appeared to be the remains of an already detonated batch of NI3 on the inside of the doorknob - remains that I attempted to brush off with my finger. Well, my finger only tingled for a little while and it took some work to remove the iodine coating my hand, but otherwise I was no worse for wear. Needless to say, that guy never brought NI3 into my lab again.

We definitely need to start teaching ammonia chemistry in school again.

Tuesday, February 19, 2008

Cold Season

Recovering from a cold today, so I’ll keep it short.

First, I spent several minutes looking through our medicine closet today, trying to find a simple cough medicine. Unfortunately, due to market forces, it is getting harder and harder to find one that does not also contain antihistamines, decongestants, or pain relievers. The best I could do was a combination cough suppressant and expectorant ("to make your coughs more productive!"). Why do they need to make my cough more productive if their medicine is supposed to stop my cough in the first place? Have they that little faith in their product?

Second, I would like to recommend the book “Oxygen: The Molecule that Made the World” by Nick Lane. The book discusses the role of oxygen during the last 4 billion years on Earth, including its effect on both planetary chemistry and the development of life. It’s a great read, and includes both currently accepted ideas as well as less accepted hypotheses. The author may spend a little too much time discussing oxygen’s role in aging in the later stages of the book, but it was still hard to put down. It is not a new book (it was written in 2004) and I actually read it last year, but I highly recommend it.

Monday, February 18, 2008

It's a Nano-World

Since I have gotten back into reading journals again, or at least perusing their table of contents for papers in which I might be interested, I have noticed a large increase in the number of papers dealing with nano-materials. Perhaps they have been there all along for the past 10 years and I just haven’t been paying attention, but lately it seems that every journal I read has at least one article relating to either carbon nanotubes or nano-titania, if not both. In one week I found reports covering nano-magnets, nano-gold wire, nano-silver, nano-fibers, and nano DNA particles.

The last time I paid any attention to an article about nano-somethings was about 15 years ago, when the authors were proclaiming the advantage of some newly developed alumina nano-powders for use as substrates in automotive catalytic converters. Smaller particles typically have higher surface areas, and high substrate surface areas are often the Holy Grail when it comes to creating highly dispersed Pt or Rh metal catalysts. Unfortunately, it doesn’t matter what the surface area is when you make these catalysts, what matters is the surface area after the catalytic converter has seen 600oC for many, many miles while experiencing alternating lean and rich environments. Not surprisingly, the alumina nano-powders lost most all their surface area under these conditions, eventually looking very similar to the regular old alumina powders prepared by traditional methods.

Nevertheless, nano-materials sound like an exciting field, but I wonder how often these materials are really novel and how often it is just sexy to use the term “nano.” Samsung has developed a washing machine with supposedly antibacterial properties. Using a silver plate and some electrolysis, apparently 1 trillion silver ions are released into the wash water, supposedly killing bacteria and possibly bonding to the clothes for further antibacterial action over the next 30 days. The general idea is not particularly new, of course. An entire industry has built up around the concept of using very minute amounts of silver as an antibacterial agent, including (very expensive) soaps and food storage containers. What caught my interest was Samsung’s reference to silver ions as nanoparticles. Now it would not surprise me if those 1 trillion silver ions get reduced to metal (nano?) particles with time, but Samsung is specifically applying the word “nanoparticles” to silver ions, which seems, at least to me, to be an incorrect use of the word. Of course Samsung’s marketing department is hardly alone in this. For example, according to Invision International, promoter of Opti-Silver, "’Nano silver’ is the sexy new term for ionic silver." Hmmm… water molecules are less than a nanometer in length (water clusters would be on the order of a few nanometers), I wonder when some bottled water company is going to start calling their product NanoWater (Note to self: trademark the term “NanoWater”). Air molecules are pretty small also – perhaps another marketing opportunity?

Btw, while searching the net for information on alchemical information, I have come across several discussions concerning the benefit of drinking water containing gold nanoparticles. Supposedly, it cures a variety of aliments. Of course, companies have sprung up to meet this important demand.

Friday, February 15, 2008

Cooking With Chemicals

A friend of mine (non-chemist) once told me that chemists should make great cooks. To reinforce this idea, he has given me several books on cooking over the years which, to be honest, I have not taken advantage of fully. Cooking can be enjoyable, but only when you have the time to do it right, and I haven’t had that in a looooong time. Perhaps it might be more accurate to say that good synthetic chemists should make good cooks. Cooking is not so much about carefully measuring out ingredients or following recipes to the letter, it’s about knowing how to improvise and knowing what you can and cannot get away with. It’s the same with chemical preps. Be honest, how many of you start taking liberties with a prep once you became familiar with it? You no longer needed to time your steps, you just knew when to stop heating or when to add the next reagent. Subtle color changes have often been enough to tell me exactly what to do next. (Color changes are more of an inorganic thing. When your reactants, products, and intermediates are all clear or white, it’s a lot harder to do this.)

HervĂ© This is a well-known chemist/chef in France. He’s made a career out of understanding the chemistry of cooking. Want to know why pepper should be added to a stock only eight minutes before it is taken off the heat? Ask this guy. I’ve read stories explaining the chemistry of foods before, but this guy is amazing. Read about him yourself.

Thursday, February 14, 2008

Rube Goldberg Lives Again!

As a part of my Master’s thesis, I was tasked with measuring the rate of oxygen exchange between VO2+ and H2O18 labeled water. Unfortunately, the VO2+ exchange rate is insanely fast, much better suited to NMR based studies which were beyond the capabilities of our group. I managed to slow the exchange reaction by complexing the VO2+ with oxalate, but with a resulting half-life on the order of 2 seconds, it was still a bitch of an experiment to do. Basically the procedure involved injecting a known amount of O18 enriched water into about 1 ml of VO2(C2O4)23- solution followed by the injection of a solution of Co(en)3Cl3 to precipitate the vanadium complex and stop the O exchange. Subsequent isotopic analysis of the Co(en)3VO2(C2O4)2 gave me the exchange rate. Due to the rapid reaction rate, the time between the 2 injections ranged between 0.5 to 8 seconds and since both my hands were busy holding the injectors (a plastic syringe and a 100uL pipettor), I used a foot activated electronic timer to measure the time interval. Although my results looked pretty good, my advisor informed me that I would need to find a way to automate the timer or else no one would believe my results. I’m not sure that was really true, but when your advisor suggests something…. Since our group didn’t have a lot of money to spend, I ended up scavenging around for old switches and devices which I could take apart and attach to my injectors. After much trial and error, I concocted a device which actually worked (much to my surprise), but which was also rather frightening to behold. (I wish I still had a picture of it) The injectors were held locked into place on a ring-stand assembly with electrical contacts attached in bizarre ways so that the timer would be started and stopped by the acts of injection. Even though it appeared ready to fall apart, it worked surprisingly well, allowing me to routinely perform 0.5 second runs with reproducible results. The first time my advisor saw it, he simply smiled and said: “Nice job, Rube,” referring to Rube Goldberg, the cartoonist known for depicting ridiculously complex devices that perform simple tasks in indirect, convoluted ways. The building of that injector system is still one of my best memories from graduate school. In memory of that system, here is a link to an amusing advertisement based on Rube’s ideas.

Wednesday, February 13, 2008

Valentine's Day Stuff

Just a few miscellaneous items today. First is a link to a site which is somewhat related to the chemistry of Valentine’s day.
A quick Walmart rant. Several days ago, I stopped by a local Super Walmart to buy a Valentine’s Day card for my wife. Before it became “super” it used to be fairly easy to find the items you wanted. After the expansion, however, the floor layout is so badly designed that you can easily take 10 minutes just trying to find/get a few items. Instead of putting the items that most people want in close proximity like it used to be, now they’re spread as far apart as possible. The grocery section is on one side of the store while common household items like deodorant, cat litter, etc. is on the other. What’s in the middle of the store? Clothes. And very few people. Either the floor designers are idiots or they believe that forcing you to walk past the clothes section multiple times will entice you into an impulse purchase (which still makes them idiots). Put the low traffic items on the side of the stores, you fools.
I originally heard this radio commercial during Christmas, but caught a variation of it just recently for Valentine’s Day. It sounded something like this:

Having trouble picking out a present for your wife or girlfriend? You haven’t done too well in that department lately, have you? That dress you bought her 2 years ago didn’t fit. The faux jewelry didn’t go over too well either, did it? And the vacuum cleaner last year was an absolute disaster. Well worry no more. We have the perfect gift for you. Show her you care by giving her a gift certificate for cosmetic surgery.

I wish I could say that the commercial was intended to be funny, but the tone was way too serious. Seriously, this cosmetic surgery place must be a front for a divorce firm.

Happy Valentine’s Day!

Monday, February 11, 2008

Revisiting Chalcogenides

Today I came across an article detailing how Intel and STMicroelectronics are teaming up to produce flash memory with significantly faster speeds. They are utilizing a PCM (phase change material) which alternates between liquid and crystalline states using the application of electric pulses. The sentence which caught my eye was “PCM memory uses a chalcogenide gas that is kept in one of two states, liquid or crystalline.” Besides the fact that I’m pretty sure they meant to say “glass” instead of “gas,” I am slightly embarrassed to admit that I was no longer sure which elements could be described as “chalcogens.” Since I have never used or studied Se, Te, or Po at any time in my life, I suppose that I shouldn’t feel too bad about not recalling the term from graduate school. (I’ve used O and S extensively, but frankly, no one really calls them chalcogens unless Se or Te is a part of the conversation). However, one of the guys I shared a house with in graduate school (his name was Gregg) did work extensively with S and Se and it was from him that I learned the definition of chalcogenides. In addition, his advisor, Tom Rauchfuss, graciously allowed me to complete my PhD work in his group’s lab space when my lab space was taken over by another professor. I was literally surrounded by chalcogens for a 2 year period and yet I managed to forget them after spending time in the “real world.” I would like to humbly apologize to both Gregg and Tom.

Btw, while looking up the term “chalcogenide” I was surprised to see that the “ch” is pronounced like a “k”. Perhaps my memory is failing me, but I’m fairly sure that I’ve always heard it pronounced like the “ch” in “chalice.”

Thursday, February 7, 2008

Progress in the Lab

I apologize for not updating this blog the last several days. I tend to wordsmith these posts far too much and as a result, it can take a couple of hours for me to write these posts. Watching TV while I’m writing these things doesn’t help either. In my first ever post on this blog, I mentioned that I would be chronicling my attempts to create a lab in my basement where I could perform some basic, fundamental experiments that I can no longer do at work. Hey, if mechanical engineers can put together a metal fabricating shop in their basement, what’s wrong with me having a lab? Anyway, I haven’t mentioned this project at all since, mostly because there has been little progress. I’ve been somewhat successful scrounging around for equipment, but I have yet to decide exactly where I’m going to be doing this. Since we have a finished basement, the decision is not going to be easy. I have an office downstairs which already looks like a cross between an alchemist’s lab and an office in Hogwarts, but I don’t relish the idea of working with chemicals in close proximity to bookshelves, computers, and carpeting. The other choice is in the furnace/toolbench/litter box/storage room, but it may be a tight fit. Ultimately, however, the decision will probably depend upon the WAF.

In the world of media center computers, there are those who seek to create the perfect HTPC (home theatre pc). By outfitting a computer with TV tuners, capture cards, remote controls, and the appropriate software, you can build the equivalent of a TIVO on steroids, with far better control over the image quality. There are plenty of websites and forums where posters (guys mostly, go figure) can share their attempts at building the perfect HTPC. Due to the sometimes less than friendly user interfaces, the success or failure of these projects can often be tied to one overriding consideration -- the WAF, or Wife Acceptance Factor. Entire threads are devoted to this subject. Such is the power of the WAF.

The two main areas I’ll be focusing on will be aqueous transition metals, which often require the presence of strong acids, and recreation of alchemical experiments, which can result in the generation of noxious gases. My lab will have to be able to handle both problems, which probably limits it to the furnace room. I’ll let you know when I figure it out.

Tuesday, February 5, 2008

Want to Learn Chemistry Fast?

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Saturday, February 2, 2008

The "Science" of UFOs

Last night I watched a show called “UFO Files” on the History Channel. Basically, a bunch of guys from UFO magazine run around the country investigating various UFO sightings and trying to sound scientific while doing so. Now I’ve always enjoyed reading about or watching shows that deal with unexplained phenomena, conspiracy theories, or alternative explanations, especially if they’re done well. In this case, the show was standard fare, using ominous music and slow motion videos to turn everyday occurrences into mysterious events. And as you might expect, their results were “inconclusive”.

What I found most amusing however, was their attempt to make everything sound as scientific as possible. Now trying to dress up somewhat dubious theories with the cloak of science is not particularly new. Try Googling “chakras,” for example, and you’ll find that each of us is apparently surrounded with colored auras which indicate our well being. You will also find the name “Isaac Newton” invoked fairly often due to his work with light. Isaac may not have known anything about chakras, but chakras sure sound a hell of a lot more scientific after mentioning his name.

I won’t go into detail about some of the crazier things they tried, although having one guy attempt to search over 6000 square feet of lake bottom for “suspicious” slag-like material that may have been left 60 years ago gives you the general idea. But like I said earlier, sounding scientific was more important than actually finding any real evidence of UFOs. Unfortunately, the UFO investigators are fairly clueless about science. X-ray analysis of an aluminum sample revealed the presence of (gasp!) aluminum oxide and was considered very significant. Several minutes were spent explaining ground penetrating radar and its use, despite the fact that their GPR failed to work properly and generated no data. And to prove the theory that UFO-based slag can burn through aluminum (don’t ask), an expert apparently used the thermite reaction to impress the viewers with pyrotechnics. Now I do not begrudge these guys’ their attempt at making a living, but if you’ve ever wondered how the general public thinks science works, just watch this show.

Edit: I watched another episode and discovered that a UFO encounter happened less than 10 miles from where I work. Yikes! Perhaps I need to pay more attention to this stuff!