Olympicene: just to see if we can

Not too long ago, a picture from the world's most sensitive atomic force microscope was published, which showed the internal structure of a fairly small organic molecule: a 5-ring snippet of graphene, which is currently a hot and sexy topic in carbon chemistry.

The AFM in question has a sensor "needle" made of a single carbon monoxide molecule, and it's small enough to measure the gap in the middle of a six-carbon hexagonal ring structure, of which olympicene has five.

Will olympicene be a useful compound? I don't know. It's one of a class of potentially useful compounds. Even if it turns out not to be useful itself, learning how to control the reactions to create it is useful in learning how to create other molecules, and learning how to get a clear image of it is useful in learning how to get clear images of other molecules, so we can directly see what shape they are.

And here's an interview with the people who made it:

A Tale of Two Studies

While looking up information on how ammonia takes the sting out of stings, I ran across two studies, both double-blinded, placebo-controlled trials of a sting relief formulation. The one that mentioned ammonia was the one I read first, because that's what I was looking for. The other one named a product brand name I'd never heard of before; I read it by accident, clicking on the wrong link in the search results. These two trials came up as the top two results when I searched google scholar for ammonia mosquito bite relief.

The two studies are: Effectiveness of Ammonium Solution in Relieving Type I Mosquito Bite Symptoms: A Double-blind, Placebo-controlled Study and The efficacy of Prrrikweg® gel in the treatment of insect bites: a double-blind, placebo-controlled clinical trial.

Go ahead and read only the abstract; those are all I'm going to talk about, not the rest of the papers. The abstracts say it all.

How to be repellent

The chemical I want to talk about today is a widely used and very useful chemical called N,N-diethyl-3-methylbenzamide. Most people know it by its acronym, DEET.

I was recently wondering just how DEET does its thing of making mosquitoes not bite people. (Why yes, the recent gap in my posts means I was on vacation. There may have been mosquitoes involved.) Obviously, I started by searching Google Scholar.

Orange Juice Flavour

I ran across yet another news item about processed food the other day, and decided to find out a bit more about what was behind it.

For those who didn't click the link above: I'm not talking about twinkies, I'm talking about orange juice. Because make no mistake about it, unless you cut and juice oranges yourself, the orange juice you drink is chemically processed. It has to be—fresh squeezed orange juice goes bad on a time scale of a couple of days even with refrigeration. (Apparently you can buy unpasteurized OJ, but it has a "use by" date about 2-3 days after the oranges are juiced at the processing plant. I don't recall seeing it for sale in Canada, which is about a 24-hr drive nonstop from the orange groves... Doesn't mean it isn't here, only that I haven't seen it.)

Where to put the carbon?

You may have seen a few articles lately about a nuisance of a chemical called carbon dioxide, namely, that it's the waste product of a number of very common chemical reactions and doesn't itself react with much (other than plants, but that reaction isn't fast or extensive enough to keep up with our current production rate) meaning it accumulates in the environment.

So, we're trying to make sure less of it gets into the environment. One class of methods which you may have heard of is carbon capture and sequestration, where after production it's captured, compressed, and often pumped deep underground—sometimes into retired oil wells, sometimes into the deep ocean, or many other places.

Before it can be stored, however, it has to be captured. Scrubbing can be highly effective at removing CO₂ from smokestacks and other concentrated sources, traditionally with amine solutions. Then there was a new discovery about the CO₂ absorption of polyethylenimine, which was what caused me to start researching this post.

One of the issues with a reaction that is very effective at grabbing a chemical out of the air is making it let go again. Most of the chemicals that are good at grabbing CO₂ are too expensive to use only once. Polyethylenimine is of great interest because it releases the CO₂ easily by heating it up, which can let the CO₂ be collected in concentrated form for use elsewhere.

Sunshine? What's that?

It's a long weekend Monday... go play outside :-)

Overflowing with math

New toy!

After discussing the options with one of my co-workers, I installed SciPy and all its associated dependencies, because it was free and had more than enough computational power to do what I wanted to play with. I don't know enough about any of the computer-math programs to make a case for work buying me one of the very expensive programs, and I couldn't rationalize buying such a program for myself at home to play with, so open source it is.

My first "project", such as it was, was both somewhat practical and relevant to my work, while still being easy enough for a first project: calculating how long it takes for the flow to reach steady state in a series of tanks with a pump at one end (step change input) and gravity flow all the way through.

Chemical wires

For the ever-shrinking world of micro-electronics, I hear the size of the wires themselves are a tricky problem to handle. For one thing, how do you place and solder a wire that's only a dozen atoms across? I don't work in micro-electronics (or any kind of electronics) so that's all I'll say about that.

However, a new nanowire has recently been connected between two tiny electrodes. It's so tiny it can only be seen under an atomic force microscope, and this is what it (well, a whole series of them) looks like:

They conduct nearly as well as copper, and made extremely low-resistance contact with the electrode surfaces they're connecting. Even better? They're self-assembling with an easy to control "on" switch, and charging the electrodes before triggering the self-assembly means the wires build themselves between the charged electrodes and nowhere else.

Bioreactor growth rates

My home bioreactor took 48 hours to get going where the instructions said 24-36 hours was typical, but it got going. About two weeks after startup the active cell culture had matured and I decided to put it into production. The instructions indicated that 1.5 hours at room temperature would be an adequate first stage reaction period. Four hours into it the first reaction stage wasn't finished, so I put the lot into the fridge and went to bed; clearly the time estimates were not representative.

I knew putting it in the fridge would slow the reaction down to the point where I could pick it up again the next day, because it's a bioreactor and they're sensitive to temperature - specifically, the reproduction rate of the cell culture slows down dramatically when cooled.

That's when I realized that my bioreactor had been reacting more slowly than the instructions suggested was normal every step of the way.

Calcium Catastrophe

Generally speaking, a sudden drastic change in the chemistry of your environment is catastrophic. From bacteria to humans, there is a range of chemistry we can tolerate, and outside that range we tend to die.

I mentioned one major geochemical event last year, when free atmospheric oxygen first became common. That was a pretty catastrophic change for the living creatures (bacteria) who were adapted to the pre-oxygen conditions of the early earth.

Some time after that, another major geochemical event happened. Some researchers now think that this led directly to the cambrian explosion and to more complex life on earth. Even so, it was a catastrophic change—from the point of view of the creatures who didn't survive it.