Chemistry Literature Feature, Vol. VIII

Have you seen a good paper lately? Written one? Send it in and have it featured here! treetownchem@gmail.com

In this episode of the Chemistry Literature Feature, we'll take a look at sticky slides that trap bacteria for disease identification, cheap iron catalysts that make expensive chiral molecules, and an experiment with way too many lasers. But first, how precise is your day-to-day performance?

Overheard at Michigan

"I feel like I don't suck at science today. Yesterday, I definitely did, but today I actually know what I'm doing."

Analytical - Supramolecular Scaffolds on Glass Slides as Sugar Based Rewritable Sensor for Bacteria [sic]

Methods for detecting diseases are expensive. On top of the materials cost, a trained technician must be paid to perform the analyses, so both the cost of the device and the cost of the labor needed to run it factor in to the price tag of a diagnostic procedure. As part of an effort to address that concern, the authors of this paper ($, advance article) in Chemical Communications (RSC) have developed a simple procedure for detecting troublesome microbes. The authors coated glass slides with a specially-designed binding agent and a type of ring-shaped sugar called cyclodextrin.The researchers took advantage of the fact that bacteria naturally bind to certain sugars to show selective adhesion of certain cells to the slides based on which types of sugar they prefer. This simple device has the potential to quickly detect and identify infectious microorganisms in a very simple fashion.

Chemical Biology - Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: fluorescent light-up probes for DNA-binding proteins
Scientists often use fluorescence-based methods to detect when important biological molecules are interacting with one another. This molecule goes to this molecule and then boom - they light up. However, for DNA-protein interactions, these methods are only well-developed for proteins that change the DNA. The authors of this paper (open access), published in Chemical Communications (RSC), investigated a new type of fluorescence probe capable of reporting on non-enzymatic DNA-protein interactions. These probes are sensitive to the viscosity of their environment. Water near big biomolecules ($) like proteins and DNA tends to be more viscous. The authors showed that their probes lit up much more brightly in viscous environments. Probes of this nature could allow researchers to learn more about hugely important cell processes such as DNA transcription and coiling/uncoiling.

Inorganic - Silica-Supported Tungsten Carbynes (≡SiO)_xW(≡CH)Me_y (x=1, y=2; x=2, y=1): New Efficient Catalysts for Alkyne Cyclotrimerization
Traditionally, catalysts for chemical reactions have been soluble molecules that react with soluble starting materials to produce the desired product. But separating products out of solutions after the reaction is over can be a pain, which translates to higher processing costs at industrial scale. Binding catalysts to solid surfaces to create a heterogeneous catalyst, which can be simply filtered from the reaction, is a growing trend in many areas of chemistry. In a recently-published paper ($) in Organometallics (ACS), researchers bound tungsten-based catalysts to a silica surface and demonstrated that their hybrid catalyst had high activity for cyclotrimerization reactions with alkynes. Additionally, by making the safe assumption that tungsten catalysts were far away from one another (molecularly speaking), the authors were able to shed some more light on the mechanism by which the tungsten catalyst achieves cyclotrimerization.

Inorganic students who love extended solids might also love the Physical paper.

Materials - Controlling the Size of Hot Injection Made Nanocrystals by Manipulating the Diffusion Coefficient of the Solute
Nanocrystalline materials are extremely useful. In addition to showing great promise in a number of different technical applications, their extremely small sizes allow chemists and physicists to investigate fundamental questions related to light-matter interaction. Making nanocrystals uniformly and in specific sizes, then, is very important. The authors of this paper ($) in the Journal of the American Chemical Society delve into the very popular hot injection method for the synthesis of cadmium selenide nanocrystals. They conduct a detailed investigation of what makes this reaction work. Their data shows that cadmium and selenium ions bind to carboxylate additives in solution, and that those carboxylates in turn determine how fast the ions can travel throughout the solution. Using a rigorous model based on classic theories of crystal nucleation, the authors show that control of the diffusion coefficient, or how fast the ions float around solution, is what establishes control over nanocrystal size.

Organic - Relay Iron/Chiral Brønsted Acid Catalysis: Enantioselective Hydrogenation of Benzoxazinones
Like your right and left hands, chiral molecules are mirror images of one another and cannot be superimposed. Unlike your right and left hands, separating a mixture of chiral molecules into batches of a specific handedness, or chirality, is extremely difficult. In fact, chemists have usually avoided this problem entirely by developing stereoselective synthesis methods that produce exclusively molecules of a given chirality (stereoisomers). Methods that selectively produce one stereoisomer over another are always in high demand. The authors of this paper ($), published in the Journal of the American Chemical Society, have developed a method by which an iron carbonyl catalyst can be used along with a chiral acid to stereoselectively hydrogenate molecules called benzoxazinones. This method improves on other known syntheses by using an extremely cheap iron catalyst as opposed to expensive metals like palladium or ruthenium.

Physical - Channeling Vibrational Energy To Probe the Electronic Density of States in Metal Clusters
Electronic structure describes the energy levels available for compounds to move electrons to and from when making and breaking bonds. Seems important for chemists, right? When it comes to electronic structure, molecules behave one way, bulk solids behave another way, and we know a great deal about both of those regimes. However, when it comes to metal clusters - molecules containing only tens of metal atoms - things get very blurry. The authors of this recent study ($) in the Journal of Physical Chemistry Letters (ACS) used a highly sophisticated laser apparatus to vaporize cobalt metal into small clusters of about ten cobalt atoms. These clusters were then heated by an infrared laser, then hit with an ultraviolet laser. By studying how the clusters' interactions with the ultraviolet laser changed with temperature, the authors were able to experimentally map out the clusters' electronic structure. Information of this nature typically comes from computer simulations, so an experimental verification of those simulations is extremely important.

Author's note: If you're keeping track at home, yes, that was three lasers. This paper has quite possibly the coolest methods section I have ever read.

Remember, if you come across an article that you think should be featured here, send it in! treetownchem@gmail.com

ACS - American Chemical Society
RSC - Royal Society of Chemistry
$ - subscription required to access

ICYMS 3, Student Edition: Get More Out of Your Salts with Bijay Bhattarai

In the past, In Case You Missed Seminar has focused on the achievements of a traveling scholar who recently visited Michigan for a talk. This time, though, we'll take a look at some research done by a second-year student gearing up for their departmental seminar. 

Bijay Bhattarai is a second-year organic chemistry student in Dr. Pavel Nagorny's research group. Dr. Nagorny's group pursues natural product synthesis with particular emphasis on the chemistry of sugars and other carbohydrates. Bijay, along with co-author Jia-Hui Tay, recently published the results ($) of his research with Dr. Nagorny in Chemical Communications (RSC).

Ion Activation: Splitting Salts to Increase Reactivity

The structure of diphenyliodonium
triflate, which the authors used as
one of their phenyl-ring donors for
their experiments.

Organic chemists are always looking for newer and better ways of building up small molecules piece by piece. Often, the starting materials for organic reactions take the form of salts, which are composed of positive and negative ions. The positive ion is called the cation, and the negative ion the anion. The picture at the left shows an example of one salt, diaryliodonium triflate, used in the authors' paper.

When reactions are carried out in non-polar solvents such as toluene and hexanes, the ions in salts tend to stay close to one another. The attraction of positive and negative charges keeps them together. When another molecule tries to come in and react with either the cation or anion, the strong salt bond must be overcome first, which can prevent the reaction from happening at all.

Enter "ion activation." The focus of Bhattarai and Tay's paper is the use of a cooperative reaction additive that is known to bind to anions. The specific type of molecule they employed is called a thiophosphoramide. After the thiophosphoramide has partnered up with the anion, the bond between cation and anion is weakened, and the cation can more easily participate in reactions.

Bijay and Tay used this scheme to attempt to improve upon a known reaction ($) in which benzoic acid is transformed to its phenyl ester via a copper(II) catalyst. The results? Adding in the thiophosphoramide not only greatly increases the yield of the products, but also reduces the temperature needed to activate the reaction. They show that the reaction works for a variety of different diaryliodonium and copper reagents. Under their optimized conditions, they were able to esterify several different kinds of carboxylic acids, including some steroid compounds.

For Bhattarai, it was rewarding to see some of the same principles at work in his reaction flask that are so important to protein function in biology. "Proteins do the exactly the same thing. It's cool to think of it that way," he said. Proteins have highly specific binding pockets that isolate molecules and orient them in a certain way to direct their reactivity. Often, ion pairing is an important part of that process.

All According to Plan

Bijay Bhattarai, the paper's first author.

According to Bhattarai, the results were not very surprising. "When I started, we already knew something like that might happen," he said. The project grew out of results published previously by another lab member ($) and some further preliminary experiments conducted by Tay.

In fact, the authors were surprised that their method was not more widely applicable. It was originally anticipated that the ion activation scheme would work for a wider variety of nucleophiles, not just carboxylic acids. When the results did not come right off the bat, Dr. Nagorny suggested building on the results his students already had with carboxylic acid esterification. "We just took this reaction and said, yeah, we're just going to make it bigger and do a lot of substrate scope, do some catalyst scope," said Bhattarai.

For this type of paper, the short form of a communication worked out nicely. "We were just looking for an initial picture of the activity of the thiophosphoramides," said Bhattarai. With so much promise on the project, it was appropriate to submit the communication right away. After two months of hard work, the paper was well-outlined.

Onward and Upward
Bhattarai credits his quick success in publishing to a combination of luck and long hours spent in the lab. "I just got lucky that I had a working project," he said. "But then, of course, we work late into the night, and that is the only factor that really matters. When you work long hours, you get more results, and more data," which, he added, allows you to sort through the uninteresting results more quickly.

"This is just a starting point," he said of the publication. He seemed excited to pursue further research on the subject in the future, rather than moving to something new after writing the paper. "We have a bigger picture of [this reactivity], and we just started small to see if it would work." As always, there is a whole pile of science left to be done.

With a smile, Bijay added, "Hopefully the bigger picture is going to work as well."