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).

Monday, June 30, 2008

Vacation!

I had hoped to put up a new post by Monday, but it was not to be. We will be going out of town for a family vacation for several days, so don't expect to see any new posts until next week. Wish us luck!

Hope everyone gets a chance to see a little pyrotechic chemistry this week.

Friday, June 27, 2008

Chemophobia Part II – MSDS’s

Note: A three minute storm was sufficient to knock out our power again for about 5 hours on Thursday evening, so this post was somewhat delayed.

Wow! The post on chemophobia evoked more comments than any other topic I've come up with. Must be a lot of pent-up emotion, I guess. During that post I failed to mention an article that covers the subject in much greater depth. The writer jokes that if everyone were required to obtain an MSDS for everything, they’d eventually get over chemophobia. Possibly, but I’d be more concerned that making the general public aware of the existence of MSDS’s might just backfire on us. I mean, has anyone here actually read an MSDS sheet for commonly used lab chemicals? Even the most benign material can sound like a potential terrorist weapon after reading through those things. I once looked up the MSDS for “oil of wintergreen” (ingredient in Icy Hot and mint toothpaste) and capsaicin (active component of chili peppers, also used for muscle pain relief). Despite the fact that these materials are meant to be eaten and/or placed on our skin, their MSDS’s tended to scare me away from their use. ("Sorry, honey, I can't really bring myself to brush my teeth anymore"). Here are a few sentences taken from an MSDS for another common chemical usually found in the lab:

Mutagenic for mammalian somatic cells, bacteria, and yeast.
May cause cancer based on animal data.
May cause adverse reproductive effects and birth defects.
May be toxic to heart, gastrointestinal tract, central nervous system.
Repeated or prolonged exposure can damage target organs.
Hazardous in case of skin contact (irritant), of ingestion, or inhalation.

May cause gastrointestinal (digestive) tract irritation with epigastric pain, abdominal cramps, nausea, vomiting and diarrhea. Affects metabolism and cardiovascular system with symptoms including increase in metabolism, flushing, palpitations, rapid heart rate, dysrhythmias, hypotension, blood pressure elevation and weight loss, metabolic acidosis. May affect brain and behavior/central nervous system.. Symptoms may include nervousness, anxiety, restlessness, insomnia, dizziness, tremor, seizures, convulsions, hallucinations, somnolence, toxic psychosis, tremors, convulsions, ataxia. May also affect blood, respiration (hyperventilation), and urinary system (mild increase in urinary volume and urinary sodium excretion), and may directly produce hypokalemia.


Whoa, that sure sounds like something I should handle with some care! Now I don’t know how many of you actually use 1,3,7-trimethylxanthine in the lab, but I’d suggest being very careful with it. Even non-organikers may have cause for alarm since it is commonly found in aqueous solutions of coffee, tea, Mountain Dew, Coke, and various energy drinks.

So do we really need non-scientists reading these things? I’ve run across plenty of websites where people (obviously not science majors) were misusing MSDS’s to support their argument (e.g., anti-fluoridation groups). The fact that they occasionally used the wrong MSDS's (fluorine instead of fluoride or hexafluorosilicate) did not help their cause, IMO.

By the way, the idea for using caffeine as an example originally came from this website.

Wednesday, June 25, 2008

Chemophobia

“So what do you do for a living?” asked the guy standing next to me. “I’m a chemist,” I said, expecting to see his face light up with a mixture of admiration and envy. “Oh…. So you work with chemicals, then?” he said, and his emphasis on the word “chemicals” indicated both repulsion and pity for my unfortunate career choice. I thought about saying, “Everyone works with chemicals, since everything is a chemical,” but I can usually spot a lost cause when I see one so I just nodded and began talking to myself until he decided he wanted to be somewhere else. Why does the term ”chemical” evoke such negative feelings in some people? I suspect that much of the reason has to do with the media (and those who use the media, e.g. politicians). It’s pretty much an unwritten rule in the media that the word “chemical” is only to be used when negative connotations are required. If a chemical is found to be beneficial, words like “substance” or “ingredient” or “compound” or “drug” will be used instead. Here's an article I found discussing the use of chemical alternatives to chlorine in swimming pools. These alternatives include ozone, Cu2+, and Ag+ to kill bacteria. The pool owners are happy that they no longer have to deal with the problems inherent with chlorine and there’s no problem with that. But you’ll notice that many of these owners (and the writer of the article) indicate they are glad to be in a chemical-free pool. What? Copper and silver aren’t chemicals?

Want to get someone’s attention? Just invoke a chemical name – the longer and the more scientific sounding, the better. There’s been a series of hoaxes over the years based on the supposed necessity of banning DHMO (dihydrogen monoxide). The most recent incarnation occurred last year in New Zealand when an MP was tricked into believing that DHMO might be harmful to the public. DHMO was described to her as colorless, odorless, tasteless, causing the death of uncounted thousands of people every year, and yet so addicting that, for those who become dependent on it, its withdrawal means certain death. Not bad for a substance which covers over two thirds of the planet’s surface.

Monday, June 23, 2008

Weird Water Chemistry

Recently, Honda announced the Clarity, a fuel cell based vehicle that is advertised as a clean car which only emits H2O. The fuel, of course, is hydrogen. Now the concept is not new and fuel cell cars have been around for a while, but Honda’s decision to make 200 of them and releasing them to the public is a first step into understanding how well they might work in the real world. There are plenty of obstacles to overcome and so it should be an interesting trial. Of course, there’s a reason (actually quite a lot of them) why hydrogen fuel cell cars haven’t taken off yet, and it has nothing to do with conspiracy theories between the auto and oil companies.

1. Very few hydrogen filling stations
2. No large sources of hydrogen until you reach Jupiter. You either make it from hydrocarbon fuels like natural gas (which negates the zero CO2 emissions claim) or by electrolysis. And if the electricity isn’t coming from a renewable source, then what exactly are you gaining? (OK, you should still be producing less NOx, CO, and hydrocarbon emissions. That’s a good thing)
3. No one likes the idea of driving around with a 5000 psi hydrogen tank sitting next to them. That is why so many researchers are feverishly looking for materials that can store hydrogen safely at low pressures with good volumetric efficiencies.
4. Price?

However this post is not about cars that produce H2O emissions, it is about cars that claim to use H2O as the fuel. The most recent announcement has come from Genepax, which claims to have just such a car. According to Genepax, their car converts water into hydrogen which is then utilized by a fuel cell (along with air) to produce water and electricity. Now think about this. They are taking water, mixing in a little air, and using that to produce water and energy. I would hope that this would set off BS detectors for anyone who is at all familiar with science. Are they converting matter into energy, or what? What is their secret? They pass the water through a special top secret membrane that converts the water into hydrogen. (The reports actually say hydrogen and oxygen, but I doubt they mean oxygen gas as it would just recombine with the hydrogen at the fuel cell electrode with no production of electricity.) Not surprisingly, Genepax is tight-lipped about this membrane, but indications are that it is similar to a metal hydride. Adding water to a metal hydride produces H2 and a metal oxide. Of course, this means the hydride is the fuel, not the water. Genepax does grudgingly admit that the membrane will have to be periodically replaced (although they do not mention how often that will be needed). Basically it would be like an automaker saying “We have built a car that runs on air only. All you need is a tank full of a liquid hydrocarbon catalyst to make it work.”

The idea of running a car on water instead of a hydrocarbon fuel has been around for a long time, despite the obvious problem with the laws of thermodynamics. But as the price of gasoline has continued to rise, these reports of water-based fuels have dramatically increased. Try googling the term “HHO,” which is the term generally used by the “water-as-fuel” supporters to represent the “improved” form of water. There are several variations on this concept. In one version, HHO is actually supposed to be a high energy form of water, apparently containing H-H bonds. I’m sure the spectroscopists would be very excited to work with this molecule. In the most common variation, however, HHO is a fancy way of saying “a 2:1 molar ratio of H2 and O2 gases,” basically the standard product of electrolysis, otherwise known as Brown’s gas. In this incarnation, water is electrolyzed into H2 and O2 and this mixture is added to the gasoline/air mix in the engine. The extra energy from H2 combustion results in better fuel economy. Of course, you have to provide at least as much energy to split the water as you get back, but that doesn’t seem to bother the “scientists” working on these projects. As is typical in these situations, there is just enough truth in there to keep these ideas from dying. Automakers have long known that adding H2 to an engine allows you to run the engine leaner, which can help gas mileage somewhat in certain circumstances (although your emissions may no longer meet EPA requirements). The best way of producing H2 is not by an electrolysis device in your car, but by reforming a small amount of gasoline to make H2 and CO. We'll see if the auto companies can get this concept to work.

Sunday, June 22, 2008

Garden Complete

Finally, the gardening project around our house is done. We still have a lot of outdoor (and indoor) projects in the works, but the major project is finished which means I will once again have more time to devote to blogging. In what has developed into a tradition over the years, I signal the end of gardening by posting a sign in the garden.




At this point, everything is on automatic. I've done my part. I've fertilized, mulched, and set up the automatic watering system. Now its up to the plants. It's like setting up a chemical synthesis and letting it reflux for a couple of days while you wait for the product to form. All you can do is wait and hope that the chemicals behave in the manner you believe they should. I'm not going to spend a lot of time weeding. Should a weed manage to thrive, that's not my problem. I've given the flowers a head start. It's up to them. Survival of the fittest, I say. I'll post some pictures in July, when everything starts filling in. Otherwise, back to Chemistry again!

Thursday, June 19, 2008

Miscellaneous Thursday

This will be one of those miscellaneous, rambling posts I write when I’m too lazy to actually put any critical thought into a subject.

First Item: Looks like I’ll have about 5 minutes less a day to accomplish anything at work since the spam filter on our firewall has apparently died a horrible death. I used to get about one email a day suggesting that I buy certain stocks, but that was about it. Since Monday morning, I’ve suddenly been averaging about 10 spams a day. I’m not sure if my name suddenly appeared on a list somewhere, but I’ve been deluged with offers from:

eHarmony and various other dating services. Hmmm... why?
Help in obtaining credit cards.
Debt relief services – for when I max out those credit cards.
Unbelievably cheap insurance.

I’ve generally been immune to spam both at work and at home, which is a surprise considering all the web sites I visit. I have a coworker, however, who used to regularly receive several Viagra-type emails a day at work. Not sure what sites he was visiting.

Second Item: New Scientists has a video of robots whose forms were inspired by animals. It’s not chemistry related at all, but my daughter, who is into both animals and building robots, thought it was great.

Third Item: Over at Practical Transmutations, there is a picture of a T-shirt with the “original” periodic table printed on it. Very cool! Perhaps we also need an alchemical periodic table with only the original seven elements.

Finally, we have the top ten list of scientists killed or maimed by their experiments. Really makes you want to run into the lab and try that crazy experiment you dreamed up last weekend over that pitcher of beer. Reminds me of how na├»ve I was about the dangers in the lab back when I was an undergrad. Good thing my mom never knew about these things or she never would have let me get into science in the first place. She certainly wouldn’t have left me alone with my first chemistry set.

P.S. I don’t remember how I found this link, so apologies to whomever I might have slighted by not mentioning them.

Wednesday, June 18, 2008

Poisons of the Day - Part Ia

News Flash! Napoleon probably did not die of arsenic poisoning. I would like to say that I’m surprised by this, but I can’t since I had never heard of the “Napoleon was poisoned by arsenic” theory in the first place. Apparently, arsenic had previously been found in a sample of Napoleon’s hair, and when combined with reports of his severe stomach pain (a symptom of arsenic poisoning), it had been speculated that Napoleon was either poisoned by the British during his captivity or had been exposed to poisonous arsenic fumes generated by mold infested wallpaper containing an arsenic-based dye. But a team of Italian scientists has now cast considerable doubt on this theory. By collecting samples of Napoleon’s hair at various stages of his life, along with hair from his son and first wife, they were able to show that all three of them had had elevated levels of arsenic in their bodies long before Napoleon’s imprisonment.

What made the story interesting was that the levels of arsenic in Napoleon’s hair were 100 times greater than expected today. Apparently, back in the day, consuming small amounts of arsenic was a highly regarded practice. It was supposed to make the body more vigorous, it was believed to be a sexual stimulant, and its tendency to produce bright, rosy cheeks was much in demand by the women of the time. (The rosy cheeks were a result of blood vessel damage in the skin.) The knowledge that arsenic was a poison, and that it caused severe stomach pain, was apparently not much of a deterrent. (To make things worse, facial powders were often loaded with white lead, Pb3(CO3)2(OH)2, in order to make the face more pale -- a sign of nobility.)

Now the reason I mention this story relates to the “Poisons of the Day” post from last week in which I mentioned that much of arsenic’s toxicity arises from its tendency to replace phosphorus in the body. My question was: How could people continue to survive the continuous ingestion of arsenic if it’s slowly replacing the body’s phosphorus? In fact, anecdotal reports suggest that it is possible to build up some immunity to arsenic by regularly ingesting it -- although some experts reject that possibility. Now, I know that you can build up an immunity to the poison "iocane" (warning: Princess Bride reference ;) ), but how would that work with arsenic? One theory involves metallothioneins, which are proteins produced by the body that seem to bond to ions of dangerous elements like arsenic and cadmium and help minimize their effects. Constant exposure to arsenic might increase the levels of metallothioneins produced by the body. I don’t think anyone knows the answer just yet.

By the way, I found a few references to a second mechanism by which arsenic can be toxic. It tends to bind to the sulfhydryl (thiol) groups (-SH) in proteins, which as you can imagine, really screws up the operation of these proteins.

Monday, June 16, 2008

The Power Returnth!

Finally! As of 7:20pm, on Saturday the 14th, electrons are once again running through every corner of our house. Not the artificial kind created by our generator, but honest to goodness real electrons, captured in the wild by Detroit Energy (DTE) and sent to our house. I would like to thank DTE for getting us back online, but I will temper my thanks with the following two caveats. First, I realize that we were placed at the end of the queue due to the complexity of the repair job and the fact that only 25 houses were affected in our area, but I did not appreciate being pushed back in the queue in order to work on houses which lost their power two days later during a second storm. Let them wait their turn. Second, when the repair crew did finally show up, we were not at all impressed by the arrival of six trucks when only two were needed. Watching 10 DTE guys sitting around doing nothing for 3-4 hours while the 2 tree guys cut down a branch (eventually one of the DTE guys did spend about 10 minutes fixing the line itself) pretty much explained why it had taken DTE 6 days to fix our area. Hint: actually keep track of your crews and explain to them that it is possible to work on different jobs simultaneously. Audiences are not required.

Here is an accounting of our costs associated with the power outage:
Item: Several gallons of lemonade consumed. Cost: $10
Item: Eating out at restaurants. Cost: $47
Item: 36 gallons of gasoline for generator. Cost: $148
Item: Hearing the power come back on, turning on the air conditioning to its lowest possible temperature, sitting back, and watching icicles form on the window. Cost: Priceless.

In more important news, Venezuelan researchers have identified another chemical pathway which causes beer to lose some of it flavor during storage. They have even managed to inhibit this reaction (which generates phenylacetaldehyde, by the way) by blocking the pathway with diaminobenzene. Unfortunately, diaminobenzene is toxic, so the current solution would probably not be considered optimal. After all, if beer drinkers start keeling over, then it’s just going to take longer to go through the world’s supply of beer and thus lead to longer beer storage times and additional flavor loss. Fortunately, they are continuing to work on the problem.

Friday, June 13, 2008

Still Without Power, But Blogging Anyway!

What can I say? Life without electricity is teh suck. We've been without power for 5 days now and DTE (Detroit Energy) still has no idea when they will be getting around to our block. I suppose I shouldn't complain too much since we have a gas powered generator, but I'm getting tired buying 5-7 gallons of gas everyday to keep it running. About every 6 hours I have to shut down the computer, disconnect the generator from our circuits, shut down the generator, refill the gas tank, start it back up, reconnect it to our circuits, unplug/replug the router (since the cable modem box most likely has a new IP address), restart the computer, and start the 6 hour timer. Amazingly, the novelty has disappeared -- just like my patience. Fortunately, after the first 2 days, the temperatures have dropped to the point where it's comfortable in the evening.

Both of the kids had their last half-day of school today and we celebrated by buying gasoline going to see the new Indiana Jones movie. I won't bother reviewing it in any detail, but it was your classic over-the-top escapist movie. It kept us entertained and the theatre was air conditioned, so it was a success by any definition.

After much procrastination, I've finally started adding links to other chemistry blogs I read on a regular basis. You probably already know about most of them, but I've been remiss in not listing them before. Happy Friday!

Thursday, June 12, 2008

Poisons of the Day - Part I

I’ve decided to start a little series called “Poisons of the Day.” This series is not to discuss the use of poisons to remove irritating coworkers in the chemical laboratory, but to understand why many elements and simple compounds are poisonous, something I’ve never really thought about before. Ever since I ran into an article describing the mechanism of arsenic poisoning, I’ve been interested in the subject. After doing some research I have come to the conclusion that there appears to be four main ways in which an element can be poisonous.

1. It binds to and/or removes necessary elements or compounds from the body
2. It replaces an element already in the body, but cannot fulfill the same role.
3. It’s a necessary element for life in small amounts but causes trouble when too much is around.
4. It interferes with the chemical reactions in the body.

I’ll start out with four poisons today.

ARSENIC
This is the element which got me started on this series. Arsenic does not attack the body directly, it operates by replacing the phosphorus in the body. Since it sits just below P in the periodic table, it tends to bind to the same compounds that phosphorus does. As you might expect, the arsenic analogues do not work very well, if at all. ATP, the molecule responsible for storing and releasing energy, is particularly susceptible to arsenic poisoning. In the presence of arsenic, cells tend to die from energy starvation.

LEAD
Lead is another poison which works by slowly replacing other metals used by the body, in particular, calcium, iron, and zinc which are cofactors in many enzymatic reactions. Lead tends to bind to the same enzymes as these metals, but the resulting molecules fail to function properly, usually because the shape of the protein is no longer correct. It is known to interfere both with the production of heme (Zn replacement), which leads to anemia, as well as the transmission of electrical impulses in the brain (Ca replacement) which impairs brain function.

BARIUM
Barium apparently causes problems in a lot of ways, but its primary role occurs because it interferes with the sodium-potassium pump used by our muscles. Apparently it reduces the permeability of muscles to potassium entry. This can lead to paralysis, and if the affected muscles include the heart and respiratory muscles, death. Barium does also appear to replace calcium in the body, but this is a minor effect.

I hadn’t really appreciated how toxic barium is, assuming that it’s in the form of a soluble salt. Barium carbonate is a common rat poison. Barium sulfate is so insoluble that you can drink it with no ill effects.

D2O
I include this compound because I used D2O (deuterated or heavy water) back as an undergraduate for isotope labeling experiments. My undergraduate advisor used to tell me that if you drank enough of it, it would kill you. Apparently he was correct, although you would have to work really hard to get your body deuterated enough to have an effect. If you can replace between 25 and 50% of the water in your body with D2O, then you’ll notice the health effects, but this will require the drinking of nothing but large quantities of D2O for at least a week according to Wikipedia. The poisoning mechanism is pretty simple. Deuterium has slightly different hydrogen bonding properties than hydrogen (which is why we use D2O in the lab in the first place). Our bodies consist of large number of proteins, including DNA, which depend upon hydrogen bonding to hold them in the rather complicated conformations which are necessary for certain enzymatic reactions to occur. Start changing the hydrogen bonding in our bodies and you can imagine what kind of problems would result.

I’ll have more poisons to discuss at a later date.

Wednesday, June 11, 2008

When the Elements are Against You

The elements are conspiring against me. I’m finally ready to start posting again and then we lose power here on Sunday due to the storms that swept through the Midwest. It’s been a little hectic around here to say the least, and at the present time, DTE is not expecting our power to come back until late Thursday. Fortunately, we have a gasoline powered generator and so we have enough power to run the important things: TV, computer, internet, fans and…, oh yeah, the refrigerator, microwave, and freezer.

It’s my six year old son who is having the roughest time. He experienced his first blackout this winter, when we lost power while I was giving him a shower. Without warning, the bathroom went pitch black and he started panicking. I was reluctant to leave him to go open the door because he was covered in soap and I was afraid he was going to slip and fall during his panic attack. Eventually I got him out of there, but afterwards he started using the term “power outage” several times a day for several weeks. After Sunday, he’s added “thunderstorms” to his daily vocabulary. He’s even learned how to bring up a local area weather radar map on the computer, which he now does constantly to check for any indication of an impending storm, despite our assurances that nothing is imminent. (He’s apparently already reached the age where he believes what he sees on the Internet more than what his parents tell him.) Even a partially overcast sky now starts to worry him, which makes me feel a little guilty since I actually enjoy rainy days and thunderstorms as opposed to hot summer days (northern European ancestry, no doubt). My wife, whose ancestry is Maltese, thinks I’m crazy. Who’s to say she isn’t right?

Friday, June 6, 2008

Better Living Through Chemistry

Wouldn't you just know it. I'm finally back to blogging on a regular schedule and then I come down with a severe head cold. I'm getting better, but I just came into work long enough to move my boxes from my temporary cubicle to my new permanent desk. And I'm now exhausted. As soon as the customer meeting is finished, I'm outta here.

Here's a note I received from a coworker who is lucky enough to have a pool.

"Still not feeling well? Maybe, you can sweat it out this weekend. Opened the pool yesterday to see the Black Lagoon. Already put 8 gallons of Chorine in. Hit it with every chemical known to man. Still going to take a couple of days before I risk catching the plague."

It makes me proud that chemistry is such a boon to mankind. Sniff...Sniff.. Sorry, I've got to go now, there's something in my eye. Yeah, that's it...

Tuesday, June 3, 2008

Garden Chemistry

Considering all the time I’ve spent gardening, it’s amazing how little I’ve thought about all the chemistry that surrounds me in the garden. Of course I realize there is a lot of organic and bioinorganic chemistry going on in the plants, but there is actually a fair amount of inorganic chemistry occurring in the soil itself. Almost 99% of a typical fertilizer consists of nitrogen, phosphorus, and potassium, but in order to survive, however, plants also need small amounts of magnesium, iron, calcium, boron, sulfur, copper, zinc, and manganese. Although these elements are usually present in the soil, their bioavailability isn’t always guaranteed. Most plants perform best in a pH range of 6-7.5 and much of this has to do with the availability of these trace elements as shown on the following chart obtained from this website.



Much of this availability has to do with the form of the element. To be useful to the plant, the elements generally have to be in an ionic form, which is why some fertilizers chelate their metals. Nice healthy soils with lots of organic matter or clay essentially behave like ion exchange resins, holding on to and stabilizing the ionic species for eventual use by the plant. If the pH is too high, insoluble metal oxides (Cu, Fe, Mn) can form. If it’s too low, too much Al3+ is released from rocks, which displaces all the other elements on the ion exchange sites.

Redox properties can also have an effect. Well aerated and well drained soils tend to be oxidizing while wet, decomposing, clay soils tend to be reducing. In the presence of sulfur, anaerobic conditions lead to formation of insoluble metal sulfides. Anaerobic conditions also increase Fe availability by changing its oxidation state from Fe3+ to Fe2+ (which I assume makes it easier for its release from the ion absorption sites. There is a lot of complicated chemistry going on here.
I admit that I was totally unaware of any of this when I started gardening. In fact, the only reason I even know this much is due to having to understanding how to change soil pH. Lime is used to raise soil pH while iron salts and elemental sulfur are used to lower soil pH. The lime and iron reactions I understood from freshman chemistry, but sulfur? Gardeners would simply tell me that sulfur is acidic, but that obviously wasn't true. Eventually I guessed (correctly) that the sulfur oxidizes to SO2 which dissolves in water to make H2SO3.
What do I do with all this knowledge? Well, nothing really. I just plant the flowers, add Miracle-Gro, and hope everything grows.