Computer researcher

Looks like computers are opening up even more areas of chemistry!

Earlier this year I posted about some software that can predict crystal growth conditions.

Now, there's new software coming out that can predict organic chemistry reactions.

Organic chemistry isn't my field, so unlike the crystal software I probably won't be able to justify a purchase to my boss, but I can still think that this is pretty amazing. The researchers spent a good solid ten years putting the sum total of all organic chemistry knowledge from the past 250 years into a database.

Not only can the computer search possible reaction pathways to make whatever compound you want, you can also filter those results. For example, pathways that use only non-toxic ingredients, or pathways with fewer reaction steps.

In one excellent example, the software came up with what they're calling a "one-pot" reaction for an asthma drug, which is normally produced with four separate reaction and separation steps. The suggested one-pot reaction said that they could put all the ingredients in the same flask in a specific order with specific timing—but with no separation steps, which are often complicated and expensive—and get the asthma drug they wanted—so they tried it.

It worked.

This software sounds like it can lead to the truly ideal case that chemical engineers wish for: faster, cheaper, and safer all at the same time. There are a lot of reactions that use dangerous chemicals, because we don't know of alternate reactions to produce the same thing. Sometimes, research eventually reveals an alternate; for an inorganic example, the production of sodium hydroxide used to involve mercury, which is very toxic even in very small amounts. Now, the mercury process is rarely if ever used, because better and safer processes have been found.

Lazy citations

One thing I've complained about many times in the past with respect to internet searches is the way blogs will link to the blog where they found a link to something interesting, not to the something interesting itself.

I understand the desire to acknowledge the source of your information, and kudos to them for doing so. But from the point of view of somebody searching for information, what this means is that a google search will find a lot of blogs talking about this cool thing, all linking to each other in a long chain of clicks which is sometimes broken in the middle by a blog being long abandoned and taken down. This happens often enough that it has its own term (linkrot) and it makes it very hard to follow the clicks to the "something interesting" you're looking for. (This has been improving in the last few years, fortunately; either people are getting better at linking to both the original and their source, or google is getting better at filtering out the link chains in their search results.)

But, like everything on the internet, this is just a computerized, digitized version of something that is not new at all, as I have been discovering since starting this blog a bit over a year ago. I saw a perfect example of it while doing the reading for an earlier post, in fact, though fortunately (this time) not the linkrot aspect of it.

One paper I read made a claim, and had a citation for it. I searched Google Scholar for the paper cited, found it, and looked for the information to back up the claim. Instead, I found the exact same claim, using almost the exact same phrasing, with a citation listed. So, after shaking my head in mild disbelief and wondering if the author was just copying without verifying, I searched for this other citation. Fortunately I did eventually find the original paper, and it did say more or less what the cite-upon-cite said.

Useful blindness

I've run across the term "double-blind studies" in reference to medical research. In the operations and research that I've done myself, I've made use of "blind testing" as needed. It is widely considered both in medicine and in my own field of chemistry to be the most accurate way to get results uncontaminated by our own wishful thinking.

I wrote earlier about the placebo effect, and blinding the studies is probably the best way to counter it.

In chemistry, we really only need single blinding: the person running the lab tests doesn't know what the sample is supposed to be: a sample, a duplicate, a standard, or a blank. To do this, I hand over a set of sample bottles with nothing but code numbers written on them and tell them to test the lot for a particular set of compounds. A chemical reaction is a chemical reaction; if the same sample doesn't react the same way to the same test, it means somebody did something wrong somewhere along the way. In medicine, it's not so easy because there are patients involved, and their reactions (chemical, biological, and psychological) are all slightly different, and some of them will get better on their own no matter what is given to them.

Two rovers

Once again, there are two rovers alive and well on the surface of Mars.

Just over eight hours ago, Curiosity landed on Mars. It was an odd mixture of tension and knowing that no matter what we saw, it was all 14 minutes in the past and there was absolutely nothing anybody could do.

Two rovers? You haven't forgotten Opportunity, have you? Eight and a half earth years old (five martian winters) and still going strong.

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 :-)