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Tuesday, January 6, 2015

Chemistry Literature Feature Vol. VII

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

In 2015's very first Chemistry Literature Feature, we'll take a look at a lot of interesting, technique-based studies for new types of analyses. We'll see mass spectrometers that can track drugs through fingerprints, detection of tiny protein intermediates that might lead to Alzheimer's, real-time tracking of single proteins through cells, and more. But first, a little snapshot of what it's like to be a first-year grad student:

Overheard at Michigan:
"I mean, there's a lot to take in here. This is the first time that I've had to think about what a volt actually is."
Analytical - Mass spectrometry imaging of fingerprint sweat on nanostructured silicon
In mass spectrometry, analytes must be ionized before they can be detected. The energies used in ionizing techniques can be quite high - high enough to destroy the molecule entirely. So-called "soft" ionization techniques such as MALDI have been developed to avoid complete decomposition of analyte molecules, but these are most useful for very large molecules such as proteins. For small molecules such as illicit drugs, extra compounds needed for soft ionization techniques can actually confound analysis. This study ($), recently published in Chemical Communcations (RSC) uses a relatively new ionization technique called DIOS, or desorption ionization on (porous) silicon, to analyze for the presence of drug molecules in human sweat. Using their technique, the authors are able to create 2D maps of the fingerprints of smokers and non-smokers, confirming the presence or absence of nicotine (or nicotine metabolites) and determining its distribution throughout the fingerprint.

Chemical Biology - Single-molecule tracking in live Vibrio cholerae reveals that ToxR recruits the membrane-bound virulence regulator TcpP to the toxT promoter
Cells are immensely complicated. To figure out how they work, scientists of all disciplines have invented scores of techniques in order to grow the toolbox at humanity's disposal for understanding why cells make food or cause diseases. In this paper ($), published in Molecular Microbiology (Wiley), the authors use single-molecule fluorescence microscopy to study the movements of three critical proteins through living cholera cells. Two mutant cell lines lacking one or another of these critical proteins are studied as well. The findings suggest that cholera toxin is only produced through a complex interaction involving these three critical proteins. One membrane-bound protein reaches out and "recruits" a second from the cell's cytoplasm, and the protein dimer then binds to a third membrane-bound protein to form the toxin-producing complex. Interrupting this interaction could lead to new cholera treatment therapies.
-University of Michigan research conducted in Dr. Julie Biteen's group

Chemical Biology readers may also be interested in the Physical chemistry paper.

Inorganic - Calculation of Ionization Energy, Electron Affinity, and Hydride Affinity Trends in Pincer-Ligated d8-Ir(tBu4PXCXP) Complexes: Implications for the Thermodynamics of H2 Addition
Hydrogenation chemistry and its reverse, dehydrogenation, are big business in the chemical industry. Catalysts that can reliably and selectively rearrange carbon feedstocks into long-chain hydrocarbons suitable for use as fuel are constantly under development. An important part of the operation of these catalysts is their ability to bind and release a molecule of hydrogen. In a recent study ($) published in Inorganic Chemistry (ACS), the authors seek to understand how a specific class of iridium catalysts binds hydrogen. This can be extremely difficult to determine experimentally, so the authors turned to computer modeling, which is commonly used to understand phenomena that are too small, too fast, or too expensive for experimentalists to see. Their findings reveal that the addition reaction can be understood relatively simply as a sequential addition of a hydride (H-) and a proton (H+), and physical insight into the activity of these complexes is offered.

Materials - Water in Ionic Liquids at Electrified Interfaces: The Anatomy of Electrosorption
Ionic liquids, or salts that are liquid around room temperature, have received a great deal of attention in chemistry recently. They are under study for everything from solvents for chemical reactions to liquid media for ion batteries. However, because ionic liquids are so highly charged, they tend to absorb water very quickly from the air and hang on to that water rather tenaciously. According to the abstract of this paper ($) published in ACS Nano, "[c]omplete removal of water from [...] ionic liquids is nearly impossible." Instead, the authors turn to molecular dynamics calculations to understand how water behaves within an ionic liquid, particularly near the surface of an electrode experiencing an applied voltage. Their findings suggest that water migrates quickly to the charged surfaces, particularly positively charged ones. This observation may inform future observations as ionic liquids are used for wider and wider applications.

Organic - Thiophosphoramides as cooperative catalysts for copper-catalyzed arylation of carboxylates with diaryliodonium salts
In organic chemistry, which is concerned with building highly specialized small molecules step-by-step, an arylation reaction is one in which a benzene ring (or modified benzene ring) is attached to the substrate of interest. The authors of this study ($), recently published in Chemical Communications (RSC), observed that the yield of copper-catalyzed arylation reactions was increased in the presence of a strong hydrogen bond donor. Their findings demonstrate that a thiophosphoramide reagent, which contains an N-P=S central group, works together with the traditional copper catalyst to provide the highest yields of the final arylated product. They demonstrate this  method and explore functional group tolerance for a few small molecules and also for larger steroids.
-University of Michigan research conducted in Dr. Pavel Nagorny's group

Physical - Intermediates caught in the act: tracing insulin amyloid fibril formation in time by combined optical spectroscopy, light scattering, mass spectrometry and microscopy
Large, fiber-like clusters of proteins called amyloid fibrils have been associated with Alzheimer's, Alzheimer's and a number of other neurodegenerative diseases. However, recent thinking in the field suggests that it is not these large fibrils themselves, but their smaller precursors that are the culprits in these diseases. The catch: the large fibrils are very easy to detect. The smaller clumps of only a few proteins ("oligomers") that lead to the formation of the fibrils are not. With so little known about this subject, the authors of this study ($) in Physical Chemistry Chemical Physics (RSC) studied insulin, which forms fibrils under certain conditions in vitro. Using a wide range of characterization techniques, the authors are able to describe the oligomerization process using insulin as a model and suggest that these smaller intermediates are directly connected to the formation of larger fibrils. Their methodology lays the groundwork for future studies on proteins whose fibrils are connected with disease states.

Physical chemistry readers may also like the Inorganic chemistry paper.

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

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1 comment:

  1. The imidazole ring, shown in Figure 1, is a versatile ionic liquid scaffold. Imidazole-based ionic liquids have been used in a variety of applications including potential water treatment agents because they have the ability to coordinate with metal atoms and are not volatile. Imidazolium ionic liquids