The ACS national conference is coming up. The theme is sustainability. The keynote speech is Green Chemistry: Chemical Solutions for a Sustainable World. The whole "green" thing reminded me of a post I wrote almost 2 years ago. Since I'm semi-retired from blogging, I thought I'd do a little reposting to fill up the space.

Here is my opinion of "going green" from a May 2008 post.

=======================

I think of a lot of things. Recently, when the trees were finally forming leaves[1], I was thinking about chlorophyll. The area is finally turning green and the amount of chlorophyll being produced by trees is no doubt in the "ton" range.[2]

I got to thinking about the visible spectrum of chlorophyll a and b. Here is a picture from Wikipedia:
Do you notice anything? Look at the spectrum again and think about it for a second.

Let me ask you this: Why do leaves (most of them) look green?

Yup, because they don't absorb the green wavelengths of light. They don't absorb anything in the 500-550 nm range. In other words, green plants reject the color green!!!!

Allow me to personify. Plants hate green and they will have nothing to do with it. That is why they do not absorb green wavelengths of light. Plants DO like blue and red light. They absorb those wavelengths with glee. Plants hate green and love blue and red.

If you care about plants (and I hope you do because your survival depends on them) you should have the courtesy to reject what plants reject: GREEN.

I'm in favor of plants so I will not "Go Green" for anything. I will "Go Red and Blue". That's what plants like, and I like plants.


[1] We're still waiting for solid Spring weather.
[2] That would be an interesting calculation to figure out what mass of chlorophyll (all types) are stored in one tree.

And I call myself a chemist

I hate it when I do things that #1 result in the destruction of my toys and #2 are a direct result of me not applying sound chemical principles to the task at hand.

A few days ago I was going to rack 4 different beers. To do so, I needed to clean and sanitize an empty carboy. The empty carboy was sitting on my basement floor. The outside temperatures are currently around 0°F here in Minnesota and anything on my basement floor is around 50°F, including the aforementioned carboy. I placed the carboy in my utility sink and turned the water on. I only turned the hot water on. My intent was to turn the hot water on, get the sanitizer, turn the cold water on and start sanitizin'. Before I got a chance to turn the cold water on, I heard the most terrible and unmistakable sound. I can't really describe what it sounded like. It was more of a pop that a shatter sound, but I knew exactly what had happened. My carboy was dead.

The hot water on the cold carboy shattered the bottom of my 6.5 gallon glass carboy. It was irreparable. Thankfully, the whole thing remained intact enough for me to lift the whole thing into the garbage can and get it outside without getting glass everywhere.

I should have known better.

******************

Science section:

******************

Glass primer. So, what is glass? Why did the carboy shatter?

Glass is an amorphous solid composed of silica (SiO₂). That's right. I said "solid," Contrary to popular belief, glass is not a "highly viscous" liquid. It is an amorphous solid meaning it is a solid that does not have an organized crystal structure.

The primary glass making material is SiO₂, but this silica is not that great for making glass. It has a high melting point (1723°C) and is highly viscous when molten. That makes it difficult to work with. To make the silica more useable, chemicals known as fluxing oxides are added. These fluxes can affect the properties significantly and are responsible for the different types of glass.

Soda-lime glass is the most common type of glass and the type that was used in my carboy. This glass is also found in windows. It is made by mixing sodium oxide (soda, Na₂O) and calcium oxide (lime, CaO) with the silica. This does two things. First it lowers the melting point of the glass to around 1300°C. That makes it much more workable. The soda and lime also make the glass more robust and resistant to corrosion. However, soda-lime glass has a high coefficient of thermal expansion. That means it expands significantly when it gets hot. Inconsistent expansion can create stress points and result in cracks. This can be demonstrated very well using the cold carboy in hot water trick!!!

Borosilicate glass is much more thermally robust. It is made by adding boron oxide (B₂O₃), among other things, to the silica. The boron oxide also reduces the melting point, but more importantly,it also reduces the thermal expansion significantly and makes the glass highly resistant to cracking as a result of temperature changes. Any glass you use for cooking is borosilicate glass. Pyrex and Kimax are two brand names. Science glassware is almost always borosilicate glass. My carboy was NOT made of this type of glass.

There are other types of glass, but these are the most common.

WT-WTF?

There are not enough 'WTFs' for this one.

A chemistry student in the Ukraine was found dead with his jaw blown off by what is believed to be exploding chewing gum, according to reports.

It gets a bit more interesting:

The student apparently had a bizarre habit of chewing gum after dipping it into citric acid, Russian news agency Ria Novosti said.

Officers found both citric acid packets and a similar-looking unidentified substance, believed to be some kind of explosive material, on a table near the body, the agency continued.

Investigators suspect that the student simply confused the packets and put gum covered with explosive material into his mouth.

WHAT THE HARTREE-FOCK!!!!!! What did have sitting next to his citric acid that was capable of blowing his jaw off?

Horseradish: Kick ass chemistry

I like horseradish. It is used in cocktail sauce, spicy mustards, wasabi sauces and Arby's horsey sauce.

Several years ago I planted horseradish in my backyard. Horseradish is essentially a weed and grows with little attention. During October, the roots can be harvested and ground up into a most delightful condiment. I recently did that.

Here's the dirty roots:

Here they are after cleaning. One of them (top left) has been peeled:

I do everything outside so I don't die from the strong fumes. Using a food processor, I grind up the roots and add enough water to make a grindable paste. This is when the odor gets strong. To stop the enzymatic action (see below) I add a few tablespoon of a 5% aqueous acetic acid solution (vinegar) and bottle it. Here is the prepared horseradish:

Yes, I made a quart and a half. That's a lot.

So, what about the chemistry? Glad you asked.

Horseradish is not pungent until you start destroying cell walls. When that happens, enzymes are released and they go into action and start breaking down glucosinolates. The result is a number of compounds in the isothiocyanate class such as allylisothiocyanate and 2-phenyl ethyl isothiocyanate as shown:

These compounds are noxious and irritating.

But, they also have a special place in my heart. I used isothiocyanates regularly in my graduate work. I spent some time functionalizing amino terminated dendrimers with isothiocyanates. What is great about the isothiocyanate group is that it reacts exclusively with amino groups in the presence of alcohols. The isothiocyanate is tuned just right to react with the more nucleophilic N instead of the less nucleophilic O. Cool (see above and ignore the misspelled isothiocyanate).

NOS

#1

Dear chemists,

Should I spend $1000+ of my faculty development money to attend the National Organic Symposium in Boulder, CO?

*******

#2

Dear beer enthusiasts,

Should I spend $1000+ of my faculty development money to attend a chemistry conference near a hot bed of craft breweries and brewpubs?

*******

What would you do?

What would you do if you (or a student in your Organic lab) spilled about 150 mL of solution containing DMSO, DME, water, ~6 M HCl, iron (II) chloride and ferrocene all over your lab notebook?

I dunked it in a tub of water with sodium bicarbonate followed by a dunk in clean water. I'll let you know how it turns out. Wrinkly, I'm sure.

UPDATE: Yup, it's wrinkly. Crunchy too, but legible and perhaps usable. The pages are a little brown from the residual iron which I'm sure has settled into a +3 oxidation state.

A bit of success

I'm feeling less troubled about the organic chemistry problems I encountered recently. I returned the exams today and spent the whole period covering it. I was expecting some weeping and gnashing, but I got a lot of "Oh, now I understand." I also did a fairly in-depth review of what nucleophiles and electrophiles are. I hope it sticks.

I had a bit of success in my Biochemistry class. They are analyzing a dipeptide. The goal is to ID the two amino acids present and the sequence. To ID the N-terminus amino acid they functionalize it with a dinitrophenyl group. Then after hydrolysis under 6M HCl conditions they analyze it by TLC and compare to standards. In years past, we've had modest success for various reasons (usually student error). Today we batted 1.000 (which is really 100%).That made me happy.
************************

On a related note, for any of you teachers, lab TAs or similar folk, have you ever given the entire class the same unknown? I have. They tend to freak out, but it teaches them to have confidence in their lab technique.

Annoying frustration

As a teacher, I occasionally experience situations that make me wonder if I am the worst teacher ever. There are times when, despite what seem to be my best effort, the point I am trying to make never sinks in. Sometimes after a bit of contemplation, I can figure out what went wrong and do something to correct the situation. But, occasionally there seems to be no solution. It is even more frustrating when the topic is fairly simple.

I recently had one of these frustrating episodes. In my Organic Chemistry class we have been covering substitution and elimination.

***disclaimer: To any non-chemists out there, much of this may not make sense. I'm not going to try to explain what I'm talking about, because based on the response of my students, I'd fail miserably.***

I put the following reactions on the board:

Many of you will recognize this as a classic question posed to organic chemistry students since Alexander first described his ether synthesis. One route will work quite nicely as written, but the other route is fraught with failure. Do you know which is which? If you've read this far, I'm sure you do.

Route A will work. Route B, however, will fail to make the desired product because elimination (to form 2-methylpropene) will predominate.

I put both reactions on the board and asked my students which one will work and which one won't.

Dead silence.

I rephrase the questions to something like, "one of these is a valid strategy and one is not. Which one will work and which one will fail to make the ether?"

More dead silence.

I start asking leading questions, but nothing is clicking. I finally get annoyed and ask, "how many carbons do you need to form a double bond?"

A student timidly answers, "2?" I say, "exactly. Which reaction will undergo successful substitution?"

Nothing.

It went on like this for about 15 minutes. I could not get them to realize that in route A, elimination is impossible. Or, if they did, they could not explain it to me.

This has really annoyed me, because if the entire class fails to figure something out, the most likely culprit is me. Besides, the example I describe above is NOT a difficult concept. I spent about half of a class period describing the difference between the two.

I'll find our tomorrow if it worked. This is the first question on tomorrow's exam.

UPDATE: Only 20% of my students got the answer correct. The others chose B. This is preposterageous!!! They will learn.

Learning things...twice.

Have you ever learned something twice?

Have you ever learned something, forgot it, and learn about it later only to realize you already knew that?

Sometimes, it can be kind of embarrassing. Especially if you tell something you are convinced is true only to find out you knew better. That happened to me today.

At The Curious Wavefunction, Ashutosh posted about an article in the New York Times about radio signals and early stars. He identified a rather curious statement in the article:

Dust grows over time as stars manufacture heavy elements called metals, like carbon, silicon and oxygen, that make up dust and then spit them out into space.

I checked out the article and found the offending sentence and it offended my delicate chemistry teacher sensibilities. Carbon, silicon and oxygen are most decidedly NOT metals, nor are they "heavy elements."

I decided I had finally found my purpose on this planet and decided to send the author an email and personally advance his education. This is what I sent him:

Mr. Overbye,
In a recent article you wrote: "Dust grows over time as stars manufacture heavy elements called metals, like carbon, silicon and oxygen, that make up dust and then spit them out into space." Carbon, silicon and oxygen are most certainly NOT metals nor are they heavy elements.
Best wishes,
Eric Woller, Ph.D.

I added the Ph.D. part to make sure he knew I wasn't messing around. I felt good. I had taught some big shot NYT science correspondent some damn fine chemistry. He was nice enough to reply. This is what he sent me:

Astronomers refer to anything heavier than helium as metals.
Thanks for writing,
Dennis

That was when I slapped my forehead and realized...I knew that. I'm such an idiot.

While one can argue that labeling anything heavier than helium as a metal is silly, that's what astronomers and the like do. I knew that, but it didn't stop me from displaying some degree of ignorance.

So, I learned that little fact...again.

Midterm exams

It is midterm time. Time for exams.

I'm writing an Organic exam for tomorrow. It covers cycloalkanes and an overview of organic reactions.

Feel free to suggest a question you think I should include on the exam. I'm not opposed to letting other people do my work for me.

Tales of Biochemistry

Some of the comments in my last post got on the subject of Biochemistry courses. The comments reminded me of a couple stories from when I took Biochemistry.

I have had the "pleasure" of taking an undergraduate Biochemistry course not once, not twice, but three times. The latter two were cross listed as graduate courses, so don't go thinking I'm a moron. That should have been obvious long before this post.

I have two stories about my experiences in Biochemistry.

The second time I took it, it was team taught by two professors at a large state university. He was a good teacher, and she was not. One day she was scheduled to teach, but he showed up. The class of about 100 undergrads burst into applause and cheering when they realized he was going to teach and not her. A few class periods when she showed up, the groans and moans were hardly subtle. As a grad student, I didn't think she was that bad. She wasn't good, but not deserving of that treatment. Yet, it was humorous to observe that.

The second story comes from when I took the third time. By this time, I was just going through the motions. I knew most of the stuff and was bored. Sadly, the teacher this time was less interested in accurate chemistry. She would do a lot of things that would make chemists cringe. One day, she decided to deprotonate something with a chloride ion. I don't remember what she was deprotonating, but it doesn't matter. Chloride will never deprotonate anything, especially in an aqueous environment since water is a base about 1,000,000 times stronger than chloride. And that's if you ignore everything else that is even more likely to act as a base. OK, she may have just been trying to simplify things, but when we asked her about it, she would not back down. She tried to convince us that chloride was the base. We decided to not push the issue. The effort was just not worth it.

An analogy is sort of like a....

I'm a big fans of analogies in teaching. I think they can be useful at simplifying complex concepts. They help by putting the general ideas of a concept into more familiar forms. This is gives the student something to grasp and contemplate. The ultimate goal is that the simplified version incubates and eventually provides a foundation for the understanding of the complex concept.

The danger is that the student never gets past the analogy, and the full understanding never develops. So, analogies must be used carefully and judiciously.

With that said, I like to use analogies using kindergarteners (figuratively, not literally).

For example (my apologies to any non-chemists; this is going to get nerdy), I use kindergarteners to explain the stability provided by resonance.

The following carbanion is very unstable and highly reactive because the charge is localized on one carbon.
Whereas, this next molecule, while still quite reactive, is more stable and less reactive because the negative charge is delocalized through the pi system.

The first structure is analogous to being locked in a small room with 20 hyper adn overly energetic kindergarteners. That would be a high stress and uncomfortable situation for everyone involved. What the kindergarteners need is room to run. The second structure is analogous to being in a gymnasium with the same 20 kindergarteners. When the kindergarteners have room to run around, things are a lot less stressful. In other words, kindergarteners are nonbonded electrons.

Fluorene, what's it good for?

I've been culling items from our organic stockroom. This task has been long overdue. I have bottles of things that were filled before the EPA and OSHA even existed. They were filled before benzene started causing cancer.

I found a 1 pound bottle of fluorene. Fluorene puts the F in FMOC and the F in a lot of other things.

My question is, does anybody know what uses plain, old, ordinary 9H-fluorene has?

I know the proton can be removed relatively easily and then it probably acts as a nucleophile.

It can also be oxidized to fluorenone using a phase transfer catalyst.



What else can I do with my newly discovered stash of fluorene?

What do you want?

So, I've been really bad at posting on this blog. I'm not sure what my problem is. Oh! I know. I've been really busy at work with an impending accreditation review coming up in October.

So much for my summer.

Back in the day when I was pretending to be a premed, I had a med school interview. I was ready to answer all possible questions. So, I was taken aback when the doctor interviewing me asked me, "so, what do you want to know?" That was his first and only question. I didn't expect to be asked to ask questions. Perhaps I was naive. When all was said and done, I went to grad school. However, even before then, I was convinced I wanted to be a chemist. At the time I was just going through the premed motions.

So, I thought I'd ask you, my readers (both of you), what do you want to know?

What do you want to know about brewing beer? About teaching Chemistry? About holding your high school high jump record for 18 years (and running).

I know some things about these areas and will dispense whatever information I have about them free of charge.[1]

So, what do you want to know?

[1] I realize I'm overcharging you, but deal with it!

That would have bought a lot of beer

It's presidential election season here in the good ol' USA (and has been for about 3 years now). In a few weeks the Republican National Convention will be held in St. Paul, MN [1]. Being a Minnesota boy, I am quite proud of the fact that my state will be hosting this national convention.

I don't care if it is the RNC or the DNC. The flavor of the politics doesn't really matter to me. This is good for the local economy and it's good for exposure to the rest of the country.
Of course, any political convention of this magnitude comes with many challenges. One obvious challenge is security. The St. Paul police have been very busy preparing.

One big security challenge is the protests and the potential that these protests can escalate into riots. All of the protesters deserve to have their safety and their first amendment rights preserved. However, the protesters do not have the right to put the public or property at risk of harm.

To be prepared for any potential riots, the St. Paul police will be spending $1.9 million on chemical irritants, or as the budget request says "public order agents."

$1,900,000 would buy a lot of beer. That would buy at least 100,000 cases of beer, though I'm sure we could get a volume discount.

I don't know how much chemical irritant/public order agent $1.9 million actually buys, but I bet it's a lot.

The most common riot control agent is what is know as CS gas (2-chlorobenzalmalononitrile)
This 'tear gas' is not a gas but a solid with low water solubility. It is dispersed as an aerosol usually combined with an organic solvent such as dichloromethane. It really sucks when it gets in your eyes and on your skin. I've never experienced it. I'm just not into the riot scene.

I don't know if the St. Paul P.D. is going to have $1.9 million worth of CS gas specifically on hand, but they will have a lot of something. Incidentally, they are also going to spend $1 million on gas masks. That's probably a good idea.

Let's hope they don't need to use any of it.



[1] Not in Minneapolis as the ever intelligent Katie Couric believes.

pH crash course

Herein, in as few words as possible, I will attempt to describe what pH is and why every aqueous solution has a pH.

pH is mathematically defined as the negative log of the hydronium concentration. Or:

pH = –log[H₃O⁺]

So, what is H₃O⁺? Simply put, it is the active ingredient of acid. A more concentrated acid will produce more H₃O⁺.
Water spontaneously reacts with itself to form hydronium (H₃O⁺) and hydroxide (OH^-):

2H₂O <----> H₃O⁺ + OH^-

At 25°C, the concentration of hydronium times the concentration of hydroxide is always 1x10^-14 moles per liter (M). Mathematically:

[H₃O⁺][OH^-]= 1x10^-14

To make a long story short, [H₃O⁺] cannot be zero and will never be zero. So, any and all aqueous solutions must have a pH value. Besides, the log of 0 is really big. I mean really, really big.

A neutral solution has equal amounts of hydronium and hydroxide:

[H₃O⁺] = [OH^-] = 1x10^-7 M (at 25°C)

The pH of a neutral solution is 7 since -log(1x10^-7) = 7.

So, it is inaccurate to say a solution does not have a pH.

In addition:

A solution can have a negative pH. For example a pH of -1.0 would correlate to a hydronium concentration of 10M.

Every common usage of pH is at 25°C. pH is temperature dependent. For example a neutral solution of pure water at 100°C has a pH of 6.14!!! Even though the pH is <7, this is neutral solution!!!!

negative log of what, exactly?

I love the show How It's Made. But tonight, I was annoyed. They were showing how aluminum cans are made. Nothing too fancy. What I did find interesting is that after the can is made, it is rinsed out with hydrofluoric acid. The acid etches away some of the metal and any aluminum oxide as a way of preparing it for the sprayed on can liner. The sprayed on can liner puts a barrier between my beer and the aluminum metal.

OK, so what annoyed me? The narrator said that after the acid bath, the cans were rinsed 4 times with deionized water "which does not have a pH."

For those of you in the know, I'm sure you will join in my annoyance with how basic chemical concepts have been totally ignored.

For those who don't know what I'm talking about, don't worry. I'm going to write a post about it in a day or two.

Methylene chloride

I've always wondered and now I am asking the world: Why does methylene chloride hurt when I get it on my skin? It's especially bad under a ring.

Here's another question, what is your preferred name for CH2Cl2?

Carbon Tet is back on the air

Greg is back and posting again at Carbon Tet. That's good, because he usually[1] has something worth reading.

Thanks Greg.



[1] I would say 'always' but it's nice to have the freedom to post completely worthless stuff every now and then. This blog is a perfect example of worthless stuff.

Moving pictures of Thermite

Finally, here it is: Thermite.

At about 2:00 I almost die. Well, OK, not really, but I did almost get a lot of liquid iron on my legs.

We tried to melt a tower of Al cans below the reaction, but it just got knocked over. I will need to support it next time.