Chemistry Literature Feature Vol. VI

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 some new developments in molecular wires, track individual atoms through a catalyst that cleans your gasoline for you, meet some protein labels with interesting and useful functionalities, and more. But first, a quote from an education research seminar that recently happened in the department:

Overheard at Michigan:

"When we think about meaningful learning, we have to think about what we want our students to go out into the world and do. Do we want our students to be able to think about and tackle difficult problems? Or do we want them to play an awesome game of Trivial Pursuit?"

Analytical - Visualizing the Stoichiometry of Industrial-Style Co-Mo-S Catalysts with Single-Atom Sensitivity
Hydrodesulfurization is a very important industrial process for purifying natural gas and petroleum products. Molybdenum disulfide is a well-known catalyst for this process, and the activity of MoS₂ is enhanced by the addition of cobalt ions. The structural causes of that enhancement are not well-understood for this important class of catalysts. Using an extremely powerful microscopy technique called scanning tunneling microscopy (STM) in combination with electron energy loss spectroscopy (EELS), the authors of this Angewandte Chemie (GDCh) study ($) were able to determine the precise location of cobalt atoms within the MoS₂ catalyst particles. Their conclusion that cobalt exists in a tetrahedrally-coordinated environment at the particle edges may help to design more effective catalysts in the future. However, the truly interesting part of the paper is the methodology, which allows the geography of small particles to be described on an atomic level.

Chemical Biology - De Novo-Designed Enzymes as Small-Molecule-Regulated Fluorescence Imaging Tags and Fluorescent Reporters
Living cells are really hard to understand. Proteins move around in immensely complicated ways, catalyzing a reaction here, moving a molecule across the membrane there, and so on and so forth. As a result, methods of understanding what's going on within a cell are always being developed. One such method is described by the authors of this study ($) in the Journal of the American Chemical Society (ACS). The authors use a de novo-designed protein (one which is not found in nature) to label a native protein they are interested in studying. The de novo protein tag has a number of advantages over other tags. Particularly interesting is the ability of the de novo tag to become fluorescent in the presence of a small molecule activator - all while preserving the reactivity of the original protein, which is very important. The fluorescence causes the protein-tag complex to light up, which means its location in the cells can be tracked, providing clues to its function.

Inorganic - Iridium Complexes of N-Heterocyclic Carbene Ligands: Investigation into the Energetic Requirements for Efficient Electrogenerated Chemiluminescence
There are a lot of ways to make a molecule light up. We've most often talked about fluorescence on this blog, but another phenomenon that causes chemicals to glow is electrochemiluminescence. During electrochemiluminescence, a luminescent molecule (luminophore) exists in an oxidized state. It then reacts with a reductant, which is either a reduced form of the luminophore or some sacrifical reductant, and the resulting release of energy causes the luminophore to glow. In this study ($), published in Organometallics (ACS), the authors study the electrochemiluminescent properties of a series of iridium N-heterocyclic carbene (NHC) complexes. Due to the easily-modified NHC ligand framework, five related iridium complexes were synthesized and their basic physical properties were measured alongside their luminescence activity. The authors are able to uncover some underlying factors controlling the brightness, color (wavelength), and mechanism of electrochemiluminescent materials. (Bonus points for a super dorky graphical abstract.)

Inorganic students might also be interested in the Materials paper, as they so often are.

Materials - Crystallization of Methyl Ammonium Lead Halide Perovskites: Implications for Photovoltaic Applications
An important aspect of solar cells is their crystallinity. Crystalline materials have few defects or particle boundaries for excited charges to bounce off of and get lost on their way to the electric circuit. For thin film devices that are compositionally complex, figuring out how to make uniform and comparatively crystalline layers of solar cell materials is a huge and important synthetic challenge. In a recent paper ($) published in the Journal of the American Chemical Society (ACS), the authors examine synthetic conditions that control the very beginnings of crystal growth, called nucleation, for the organic-inorganic perovskite solar cell materials methylammonium lead bromide and methylammonium lead iodide. They find via microscopy investigations that the addition of lead chloride makes for well-behaved nucleation, and then see the effects of the improved synthesis pay off in the increased performance of their solar cells.

Organic - Vanadium-Catalyzed Solvent-Free Synthesis of Quaternary α-Trifluoromethyl Nitriles by Electrophilic Trifluoromethylation The trifluoromethane functional group (-CF₃) is an important structural component for a wide variety of interesting organic molecules, including prescription drugs and agricultural products. Methods for installing trifluoromethyl groups can include some harsh conditions and are constantly improving. A particularly rare feat for organic chemists thus far has been creating quaternary carbon centers (carbons with 4 carbon-carbon bonds) that contain -CF₃ groups. A recent development ($) reported in Angewandte Chemie (GDCh) shows the activity of an oxovanadium catalyst towards installing -CF₃ groups to form products with quaternary trifluoromethylated centers.

Physical - Electron transfer through rigid organic molecular wires enhanced by electronic and electron-vibration coupling
Certain biological systems are capable of moving electrons over surprisingly large distances, and there are research efforts in a variety of fields to figure out how that is and whether we can build systems to emulate it. The emerging field of molecular electronics is one such research area. The authors of this recent paper ($) published in Nature Chemistry (NPG) examines the charge transfer between a zinc porphyrin complex tethered to a C60 fullerene by means of both rigid and flexible molecular wires. Their data, taken from electrochemistry experiments as well as ultrafast electronic transient absorption spectroscopy, quantifies the rate of charge transfer from the zinc to the fullerene, and also the rate of the back electron transfer. The authors also identify a vibrational component to the charge transfer through rigid wires by which recombination (backwards electron transfer) of the charges is accelerated relative to flexible wires. While the recombination isn't the best, the fast initial charge transfer is an exciting prospect for future research.

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

ACS - American Chemical Society
GDCh - Gesellschaft Deutscher Chemiker
NPG -  Nature Publishing Group

ICYMS 1: MOFs and More with Dr. Joe Zhou

Welcome to the first installment of In Case You Missed Seminar! This time, we'll be talking about the MOF-centered research of Dr. Hong-Cai (Joe) Zhou, a professor of chemistry at Texas A&M University.

MOFs - Don't I Put Those on My Ears?

Cartoon depicting copper hexamine formation (in
the box) with simple MOF formation (outside box).
The product MOF is shown in 2-D for clarity.

Dr. Zhou cares a lot about metal organic frameworks, or MOFs for short. We've addressed MOFs briefly in this blog before. If you aren't familiar with MOFs, it might be helpful to think of them as bigger, more complicated versions of simple inorganic complexes. For example, when copper ions (Lewis acidic) react with ammonia (Lewis basic), they make a very simple copper hexamine complex. To make the basic ingredients for a MOF, we can replace the ammonia with a different ligand - one with a rigid shape and at least two Lewis basic sites. This new ligand, called a linker, can in principle bind multiple copper ions. However, the copper ions can also bind multiple linkers, so extended 3-D frameworks can form (see above).

For an analogy, picture a 3-D molecular net; where the ropes cross, a copper ion sits, and the ropes in-between are the linker molecules.

The resulting MOF is a crystalline solid compound. Because of its net-like structure, most of the MOF is empty space - and that makes MOFs very useful as a class of substances. Dr. Zhou's group and many others in the scientific community are investigating MOFs towards applications such as hydrogen storage for alternative energy, carbon dioxide storage for emissions reduction, and gas purification. Due to their high porosity and surface area, MOFs might also make excellent heterogeneous catalysts, gas-phase sensors, and drug delivery agents as well.

The Latest: Light-up MOFs

The most recent paper ($) from Dr. Zhou's group, published in the Journal of the American Chemical Society, details still another application for MOFs: fluorescence emitters, or fluorophores. Chances are good that you're experiencing the benefits of efficient fluorophores as you read this article off of your computer or phone screen.

Crash course on radiative vs. non-
radiative decay modes following the
absorption of light by an active
molecule. Green means go - the authors
want lots of radiative decay!

The central focus of the paper is to investigate the optical absorption spectra and fluorescence spectra of the molecule H₄ETTC and also of the group's new MOF PCN-94, which uses H₄ETTC as a linker. H₄ETTC itself is a highly-conjugated ethylene-based aromatic system featuring four terminal carboxylic acids. In solution, its fluorescence profile is unremarkable, with a quantum yield (photons emitted divided by photons absorbed) of only 30% in air. That means that 70% of the photons are dissipated non-radiatively, probably as wasted heat. A display made only out of H₄ETTC wouldn't be very bright.

However, when H₄ETTC is used to make a MOF with zirconium, the fluorescence picture changes drastically. Optical absorptions attributed to the H₄ETTC linker move higher in energy, as does the fluorescence resulting from those absorptions. Fluorescence from PCN-94 is in the blue region of the spectrum, which is a sweet spot for technological applications. The quantum yield also increases drastically to 76% in air. When the air (which contains oxygen, a common inhibitor of fluorescence) is displaced with argon gas, the quantum yield reaches effectively 100%.

Wait, but Why?

The explanation for the improved fluorescence properties of the PCN-94 MOF over the free H₄ETTC ligand comes down to a very important concept in physical organic chemistry: conjugation. Conjugation is a stabilizing effect by which free p-orbitals in unsaturated atoms can share electron density. Conjugated systems tend to absorb lower energies of light because the extended ("delocalized") p-orbital network spreads out the excited state over a wider area. Only planar molecules can be conjugated. In PCN-94, the arms of the H₄ETTC molecule must twist in order to bind appropriately to 4 zirconium atoms. The twisting action disrupts the planarity of the molecule, which in turn breaks the conjugation. So, the excited state energy is higher, and the fluorescence is of higher energy ("blue-shifted") as well.

The twisted conformation of H₄ETTC in PCN-94 explains the higher quantum yield as well. The MOF freezes the molecule in place, which forces the excited state to decay through fluorescence rather than by vibrational (non-radiative) relaxation. Another effect mentioned by the authors is called concentration quenching, where fluorescence in one H₄ETTC molecule can be shut off by another nearby H₄ETTC. Concentration quenching is prevented in the MOF structure because each H₄ETTC is frozen in place relatively far away from the nearest-neighbor H₄ETTC.

MOFs Are for Everyone!

Dr. Zhou's group's most recent paper showcases an important stride forward in research into the technological applications of MOFs. These versatile structures are a hot research topic in chemistry. With more developments like this, MOFs may break out of the lab and into our daily lives (or, if they make it into our phone screens, our minute-ly lives).

The most striking part of Dr. Zhou's research, and research into MOFs in general, is its interdisciplinarity. The skills required to publish the paper outlined above are spread - delocalized, if you will - among organic, inorganic, physical, and materials chemistry. There's something in there for every chemist.

Introducing ICYMS: In Case You Missed Seminar

Fellow chemistry grad students, this one's for you.

Seminar talks are important. Everyone knows that. But, as a graduate student, you've got fifty-six other obligations during a day. Sometimes you've got a class, sometimes your reaction goes out of control, sometimes that damned eluent just doesn't come out fast enough - and we've all had times where we look at the clock only to find in horror that it's 4:45 and you've missed the whole talk already.

I've got you covered.

Starting this coming Monday, I'll be running a bi-weekly series that covers the latest publication from seminar speakers visiting the University of Michigan Department of Chemistry. If there happens to be more than one seminar speaker during the two-week period, I'll pick my favorite; if there aren't any speakers, I will cover someone I missed during a previous week.

You know, just ICYMS.*

*Tree Town Chemistry is not responsible for advisor-rage that will result from your skipping seminar.