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Monday, December 15, 2014

Astrochemistry in Action: The Rosetta Observation

Last Wednesday, the European Space Agency (ESA) released the results of measurements conducted by the Rosetta space probe, currently in orbit of a 2.5-mile wide comet designated as 67P/Churyumov-Gerasimenko. The measurements are the newest development in the quest to determine the origins of Earth's water - specifically, whether it was delivered by impacts from comets or asteroids. The findings revealed that the chemical composition of the water on the comet 67P was significantly different than that found in Earth's oceans.

"Wait, what? Isn't water H2O, no matter where you find it?" If you find yourself wondering how comet water could be different from Earth water, or if you're interested in how chemistry can be applied in space, read on.

Isotopes: Not All Atoms Are Created Equal

Atoms are composed of three basic subatomic particles: positively-charged protons, negatively-charged electrons, and neutrons, which have no charge. Atoms of different elements always have different numbers of protons, and atoms of the same element always have the same number of protons. Electrons are much messier, but they don't play much of a role in this story, so we'll leave them for another day.

Hydrogen (H) and deuterium (D) both
form water, but they are made of
different stuff on the subatomic level.
Neutrons add to the mass of an atom without changing its chemical identity. Atoms of the same element can have different numbers of neutrons. The simplest (and most relevant) example is the difference between hydrogen (H) and deuterium (D). The average hydrogen atom contains only a proton and an electron. Deuterium, on the other hand, has a proton, an electron, and a neutron, so it is heavier than a regular hydrogen atom, but because it still has only one proton, it still acts like hydrogen. Hydrogen and deuterium are called isotopes of one another - same element, different mass.

You may have heard the word "isotope" connected with radioactivity, such as the famous plutonium-239 used in nuclear bombs, or carbon-14 used for radiocarbon dating. Radioactive isotopes are unstable and decompose at predictable rates. However, there are plenty of stable, non-radioactive isotopes that do not decompose on their own. Hydrogen and deuterium are two examples. A very important consequence of their stability: once a sample containing hydrogen and deuterium is isolated from its environment, the ratio of hydrogen to deuterium will never change.

Stable isotopes have (almost) the same chemistry as one another. Hydrogen can react with oxygen to form water, and so can deuterium. H2O, D2O, and HDO all exist, and all are colorless, odorless, tasteless liquids at room temperature. On Earth, about 16 of every 1,000 hydrogen atoms are actually deuterium. So, if these three kinds of water are so similar to each other, how do scientists figure out the difference?

The Measurement: Mass Spectrometry

A mass spectrometer at the University of Michigan
Department of Chemistry. This instrument also uses a gas
chromatograph (GC) in conjunction with the MS to identify
complex mixtures of compounds.
One very common method for determining the amount of an isotope present in a sample is to measure the mass of a molecule of that sample using a technique called mass spectrometry, often abbreviated MS. In mass spectrometry, molecules are hit by a high-energy spark of electricity to charge them up. Then, the molecular ions (charged molecules) are flown through a tube in the presence of an electric or magnetic field. The field is adjusted to allow only ions of a certain mass-to-charge ratio to pass through to the detector, which measures how many of the ions got through. Different mass-to-charge ratios are permitted through the tube one-at-a-time as the instrument continually adjusts the field strength. In this way, an analyst can measure the relative amounts of chemicals of different masses within the original sample. Mass spectrometry can be coupled with other separation or chemical analysis techniques to give even more information about the sample.

The ESA's Rosetta probe contains two very sophisticated mass spectrometers. Since there is no easy way to bring the water on the comet to Earth for analysis, the ESA brought the mass spectrometer to the comet. The readings that were sent back to Earth showed that the water on comet 67P contains three times more deuterium than the average value in Earth's oceans. Since deuterium is stable, and since the comet is an isolated system that does not exchange water with other bodies in the solar system, the findings suggest that water from comet 67P and related comets was not the primary source for Earth's water.

Problem Solved! ...Right?

Of course not! Science is never over!

The Rosetta measurement is just one piece of an extremely large and complicated puzzle. It is strong, but not conclusive, evidence that Earth's oceans could not have come from cometary collisions. For starters, Rosetta has only measured the composition of the comet's outer layer, so the deeper water could potentially be different. Secondly, 67P is only one comet among many. According to Dr. Nicholas Dauphas at the University of Chicago, quoted by Dan Vergano at National Geographic, this "is a very exciting study that raises more questions than it answers."

One intriguing facet of the Rosetta measurement, though, is its simplicity. Even though the ESA spent millions on launching the probe to comet 67P in an unprecedented feat of aeronautics, the chemistry that the probe examined in these measurements is fairly basic. The next time you're sitting in General Chemistry picturing a chemist toiling behind a benchtop somewhere in a sterile lab, maybe try picturing that scene in space.

Everything is cooler in space.

Friday, October 10, 2014

When Mentoring Undergraduates, Educate, Don't Regulate

This post was originally published on the University of Michigan Rackham Graduate School's "student voices" blog. I've reposted the first bit here, and you can find the full text here.

"Universities often advertise student to faculty ratios in publicity pamphlets. Would you want to go to a class where the ratio was 1,000 to 1? How about 20 to 1? 8 to 1?

What about 1 to 1?

Undergraduate students who get involved in research put themselves in a unique position. They typically work under the direct supervision of an older graduate student or, in some cases, a faculty member. At a school as large as the University of Michigan, such a close student/teacher relationship is difficult to come by and provides a rare experience to workshop creative and critical thinking skills.

Undergraduate research can be a transformative experience for young students who don’t know what opportunities are out there for them. However, on the other side as graduate student mentors, it’s unfortunately easy to downplay the importance of the mentorship as a teaching experience, especially in the face of the laundry list of other obligations that comes with graduate education.

In a recent post over at Tree Town Chemistry, I interviewed Dr. Ginger Shultz of the Chemistry Department. “Modern educational psychology says that knowledge is constructed by the learner,” she wrote in reference to classroom teaching (read the whole article here). That idea is even more powerful in a mentor/mentee relationship and has been central to my approach over my last two years mentoring undergraduate researchers. And, while I make no claims to perfection or anything close to it, I will use this post to pass on a few ideas that I feel have helped me to be more successful as a graduate student mentor."

Check out the rest of this article at the student voices portal by following this link. While you're there, support student bloggers and check out a few of the other articles!

Friday, October 3, 2014

ICYMS 2: Dr. Ryan Bailey's Structurally-Controllable Scaffolds Influence Stem Cell Differentiation

In this installment of In Case You Missed Seminar, we'll look over the latest research from Dr. Ryan C. Bailey's group at the University of Illinois at Urbana-Champaign. Dr. Bailey and his group care about developing new biomaterials to aid in the separation and analysis of heterogeneous tissue samples, meaning samples composed of many different kinds of cells in varying disease states. If successful, the materials developed in his lab could allow clinicians to crank a lot more information out of simple measurements while diagnosing a wide range of diseases, in addition to being useful tools in further fundamental scientific studies.

Adult Stem Cells Get a Lot of Mixed Signals

Mesenchymal stem cells ("adult" stem cells) are promising research targets in the world of biomedicine. They can be harvested safely from umbilical cord blood, amniotic fluid, and a long list of other places in the adult body as well. Compared to embryonic stem cells, which are harvested from growing embryos in a process that usually destroys the embryo, the ethical issues surrounding mesenchymal stem cells are greatly reduced.

However, an important term in stem cell research is "potency." The most potent cells, called pluripotent, can be chemically coaxed to turn into any tissue that exists in the human body through a process called differentiation. Embryonic stem cells are pluripotent. Mesenchymal stem cells (MSCs), on the other hand, are only multipotent, which means that they can be forced to differentiate into only a handful of cell types. Scientists are determining just how potent MSCs can be and are working out methods of inducing desired differentiations.

One surprising factor that appears to influence the differentiation of MSCs is the stiffness of the surface, or "matrix," on which they are growing. Researchers have shown that, when chemical signaling molecules responsible for starting cell differentiation are immobilized on various solid supports, the responses of MSCs to the signaling molecules are different depending on the mechanical stiffness of the supports (see here and here, $).

So what does that mean? Well, it's a little like telling your son or daughter you want them to be a doctor when they grow up. The words that you say are important, just like the signaling molecule. But when and where you let that expectation known can help butter your kid up for a more favorable response. The environment that a stem cell experiences while interacting with signaling molecules seems to matter in an analogous way.

A mesenchymal stem cell contemplates the future.

The Latest: Building the Toolset

Published in the journal Biomaterials (Elsevier), the most recent publication from Dr. Bailey's group (first authors: Jessica M. Banks and Laura C. Mozdzen) examines the effects of two variables on the behavior of MSCs: matrix stiffness and amount of signaling molecule present. A specific method of synthesis developed in Dr. Bailey's group allows the researchers to control the stiffness of the matrix independently from the concentration of signaling molecules, a key advantage which is not possible through other methods of synthesizing these kinds of biomaterials. The matrix is synthesized with a desired stiffness in one step without any signaling molecules incorporated. Then, a separate chemical step is used to incorporate signaling molecules. Two flavors of signaling molecule are attached to the biomaterials: BMP-2 (bone morphogenetic protein 2), which encourages undifferentiated MSCs to turn into bone cells (osteocytes), and PDGF-BB (platelet-derived growth factor BB), which signals MSCs to grow and divide (proliferation).

The authors quantify the proliferation for cells growing on each kind of biomaterial. The biochemical activity for each group of cells is also quantified by measuring how much of five different genes the cells express. Two genes in particular are contrasted: ALP (alkaline phosphatase) and PPARG (peroxisome proliferator-activated receptor gamma). When undifferentiated MSCs are expressing a high amount of ALP, they are likely to become osteocytes; when MSCs are expressing a high amount of PPARG, they are becoming adipocytes (fat cells). By measuring the differences in gene expression, the researchers get clues as to how the cells will eventually differentiate.

The findings were a little surprising. The researchers found that the presence or absence of BMP-2, the signal for MSCs to become osteocytes, did not have a very profound effect on the biochemical activity of the MSCs. The matrix stiffness played a much more dominant role in influencing the MSCs to become osteocytes, even in the complete absence of BMP-2. Conversely, when less stiff matrices were used in the experiments, the MSCs displayed biochemical activity more similar to adipocytes - again, even in the presence of BMP-2.

Wait, but Why? 

Well, nobody really knows. The relationship between stem cell differentiation and matrix stiffness is still a new observation, and several groups are working together to try to figure out why cells care about the mechanical properties of their environment when there are chemical cues floating around to tell them what to do. The measured effects are significant enough to warrant further investigation, so further investigation there shall be.

The authors are quick to point out some limitations of their study. First, they acknowledge that the range of BMP-2 concentrations they used was not exhaustively wide, and they are still exploring how BMP-2 can be incorporated into the biomaterial scaffold that they have built. Testing a wider range of BMP-2 loading and matrix stiffness will help to strengthen their conclusions. Secondly, the authors point out that the materials used in the study were only two-dimensional. Repeating the experiments on a three-dimensional biomaterial scaffold will more accurately replicate the environment for developing MCSs and in turn allow researchers to more accurately describe the factors that influence differentiations in real biological systems.

Biomaterials for Better Science and Better Medicine

Dr. Bailey's most recent paper highlights only one facet of the potential applications for the types of biomaterials he and his group are developing. Boosting stem cell research is exciting, but certainly not the only application for their research. Spatially sensitive chemical scaffolds could find applications in the fields of clinical medicine and biological analysis. They could also be used as tools by future generations of scientific researchers looking to easily separate complex groups of cells or establish greater control over their behavior. Dr. Bailey's research is an example that shows that science is a tool-driven process. The science behind developing experimental tools is just as exciting as the research that the perfected tools will produce.

Friday, September 26, 2014

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

Wednesday, September 10, 2014

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.

Friday, September 5, 2014

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.

Monday, August 25, 2014

How to Survive (and Excel) as a Graduate Student Instructor

The #SciBlogReaders survey is still underway! If you enjoy this blog or another science blog, click here to learn how you can help bloggers and win some cool prizes for yourself.


It's a critical task of academia to produce new educators for the future, but for many students starting graduate school this semester, the word inspires groans and feelings of dread.

The first graduate student teaching assignment might force you out of your comfort zone. It is true that teaching for the first time is a big adjustment, but with the right attitude and preparation, you might just
discover a skill you never knew you had.

To learn more about what makes a good graduate student instructor (GSI) and how to adjust to the position, I interviewed Dr. Ginger Shultz and Grace Winschel at the University of Michigan. Dr. Shultz (top photo) is a postdoctoral teaching fellow and educational researcher in the chemistry department with 4 years of experience working with freshman GSIs. Grace (bottom photo) is a 5th-year graduate student in Dr. Pavel Nagorny's lab and has also co-authored research on chemistry education with Dr. Shultz.

Dr. Shultz jumped right into teaching when she got to graduate school, serving as a GSI for General Chemistry during her first year as a Ph. D. student. "I was intimidated to teach [Organic Chemistry] or [Physical Chemistry]," she writes. "I really sold myself short because I was afraid." She also obtained a fellowship that enabled her to teach a hands-on science lecture once per week at elementary schools in her area. "Once I got over my initial fears, teaching turned out to be the easiest part of my first year of graduate school. After that it was just something else to balance."

Teaching is More than Lecturing; Teachers are More than Answer Banks

Shultz's experiences as a GSI contributed to her teaching philosophy. "I had it in my head that I had to know all of the answers. One time I gave a student a wrong answer and they complained to the instructor," she writes. Uh-oh. Big trouble coming, right?

Well, not really. "The instructor met with me and explained that I wasn't supposed to be providing students the answers. It's the teacher's job to model thinking for the students and to help them learn." Shultz challenges students by facilitating their thinking so that they guide themselves to the answers to their questions. She encourages the GSIs teaching in her classes to do the same. "Changing your thinking about your role as a teacher is the first step toward becoming a good one. Some people are naturals at teaching, but effective teaching can also be learned."

Grace Winschel is an experienced GSI and has worked closely with Dr. Shultz both in instruction and in education research. She echoes Dr. Shultz's sentiments. Even for experienced GSIs teaching within their field of study, it is possible to be stumped by a student's question. "Of course, it is ideal to know the answers," Winschel writes. "But if you don't know, you can say, 'This isn't my field, let me point to you some places I think you can find the answer,' or, 'I'm not 100% sure I'll give you the most thorough answer here, so why don't you come to my office hours and we'll work on it together?'" Winschel also suggests asking a student to pose the question to their lab group to see whether the students can collaborate and come up with a solution on their own.

While it is not the end of the world for a GSI not to know the answer to a question, Winschel does stress one thing: "Be helpful. That is the goal. We want to avoid you saying, 'I'm not answering that question because it's dumb and you should know the answer.'"

Advice for Your First Class

Whether you are teaching a lab section or a discussion/lecture, having to perform a new task in front of strangers can be very stressful. Dr. Shultz stresses that, when nerves are a problem, Socratic teaching is still your friend. "You're not helping students by giving them the answer. It takes some of the pressure off when you let go of that expectation." She goes on to say that students do not learn simply by sitting passively - "like Neo in The Matrix" - and likewise, faculty do not teach effectively simply by lecturing. "Modern educational psychology says that knowledge is constructed by the learner. Once you understand your role as an instructor - a facilitator of learning and not a transmitter of knowledge - you can be much more effective." Shultz suggests that teachers merely need to present material and construct an environment that is conducive to learning and to questioning, to students building their own knowledge, and that "ultimately, [students] are the architects of that knowledge."

Winschel has taught both labs and discussions at the University of Michigan and offers loads of advice for both. One important and relatively easy thing is to stay on top of your grading. "It's easy to not bother to grade your worksheets one afternoon, but if you're teaching two sessions a week with 20 students per section, it backs up really quickly until you are buried in worksheets and then you die." She also adds that keeping up with grading is helpful to the students, as they always know exactly how they are doing in the class. Nothing throws a student into panic mode more than receiving three weeks of failing-quality work all at one time - and it can lead to administrative problems as well.

Of course, basic people skills come in handy too. "I tend to be extremely peppy, and that works for me," writes Winschel. She adds that all personality types can make for great GSIs. However, it is always important to consider the image you project to your students. "From a student's perspective, GSIs can be a little intimidating, so having an abrasive approach to your [teaching] can be difficult for your students to handle. There's a difference between being sarcastic and being mean or unapproachable."

Lastly, GSIs should be prepared for the fact that the way students have the material presented to them in lecture might be very different from the way the GSI was taught at their undergraduate institution. That fact can lead to confusion for students when the GSI is teaching them one way and the lecturer another. "Going to lectures with the undergrads definitely helped me see what they were learning from a Michigan perspective," writes Winschel. She writes that doing so also helps you to bone up on the material for yourself, which can ease some of your tension in presenting it to students during your own class.

Lab Sections: A Special Beast

Grace Winschel oversees a lab during the WISE
 (Women in Science and Engineering) summer workshop
at the University of Michigan. Image credit: WISE.
Teaching lab presents a unique set of challenges. While the pressure to deliver expert knowledge is not quite as high since students are mostly following pre-written directions, there is an entirely new set of issues associated with making sure that students get through the lab session safely and efficiently. It can be overwhelming. How am I going to keep everyone safe? What do I do if an accident happens - will I handle it correctly? Do I actually know chemistry at all? "Serious stage fright can happen in your first day teaching lab," writes Winschel.

But there are simple things you can do to prepare, and the "stage fright" does not last forever. Winschel wrote that bad nerves were her biggest obstacle going into her first lab, but stresses the importance of being comfortable in the classroom lab environment. "I showed up to my first lab session early to explore the lab and make sure I knew where things were." Simply being able to direct students to the right part of the room quickly and easily means that you will be able to field most of their questions on the first day without any problems.

With teaching labs, safety takes precedence over everything else. The primary responsibility of a lab GSI is to get all of the students in the door, through the lab, and back out again with no injuries or accidents. "The biggest difference between an experienced GSI and a new one is the steps taken towards preventing [safety] incidents. Over time, you develop a sort of second vision [for safety violations]." One of the best things you can learn as a lab GSI is how to casually patrol your lab, looking for small things like unlabeled vials, loose hair, and missing goggles. Check in with your students regularly to see how they are doing. In addition to making the lab session go by a little faster, it goes a long way towards preventing the kinds of large accidents that you have nightmares thinking about. Your students will also feel that you are more actively involved in helping them, which makes them feel better about the class.

It's Not as Hard as You Think. Really.

All in all, teaching is not as bad as you think it is going to be, suggests Winschel. "Relax! And when that's impossible, act relaxed. Engage with your students, try to be helpful, be friendly. That will usually calm the nerves and build rapport with students - all positive things!"

For GSIs, a little effort goes a long way towards improving the learning experience for students. When asked what makes a good GSI, Dr. Shultz responded, "They care whether a student is learning and want to do a good job teaching. They are respectful of students' time and effort. They are flexible and will adapt to the needs of their students in real time. They are approachable, but at the same time aren't afraid to hold students accountable for their part."

Now, that doesn't sound so hard, does it? You might even like it.

For University of Michigan students who have already found that teaching is their thing and are interested in getting involved with research in chemical education, contact Dr. Shultz. ("Talk to me! I have projects and ideas coming out of my ears.") She can be reached at gshultz@umich.edu. Also, check out the U of M SLAM (Student Learning and Analytics at Michigan) Seminar Series and the School of Education Events Calendar for more information on how to get involved in other departments.

Tuesday, August 19, 2014

Chemistry Lit Feature Vol. V

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

Tree Town Chemistry is back! After a mostly unintended summer hiatus, I am gearing up to blog throughout the semester once again. What better way to start back than with a literature feature?

Before we jump into that, I would like to announce that I will also be blogging for the Rackham Graduate School this semester as part of the Student Voices series. The posts there will be for a more general audience and the content will be more on the life side of the work-life spectrum, but I will be sure to cross-post when relevant.

In this episode of the Chemistry Literature Feature, we will look at large-scale characterization of graphene sheets, mechanisms of catalysis by gold complexes, new breakthroughs on the mysteries of energy transfer in photosynthesis, and more. But first:

Overheard at Michigan:
"So I have this black stuff on my platinum and I don't know how to clean it off."
(Labmate takes a quick look.) "Oh yeah, I always just light that on fire. Comes right off."

Analytical: Nondestructive Characterization of the Structural Quality and Thickness of Large-Area Graphene on Various Substrates
Materials chemists spend a lot of time worrying about surfaces - how clean they are, how flat they are, how well-coated they are, etc., and how all of those factors can be controlled. One significant challenge in this process is understanding how microscopic inhomogeneities (nanometer-micrometer size scale) are distributed throughout a macroscopic object. In this study ($), published in Analytical Chemistry (ACS), the authors apply a technique called spectroscopic ellipsometry to quickly build a topological map of graphene films synthesized by chemical vapor deposition on a variety of surfaces. By measuring how the films absorb polarized light, the authors are able to learn about the films' thickness and structural features over macroscopic (millimeter) size scales.

Chemical Biology: The Au clusters induce tumor cell apoptosis via specifically targeting thioredoxin reductase 1 (TrxR1) and suppressing its activity
As chemists, when we think of drugs, we tend to think of organic molecules - some large, some small. However, metals are sometimes used as pharmaceuticals as well, with a well-known example being the platinum-containing chemotherapeutic molecule cisplatin. A recent study ($) published in Chemical Communications (RSC) examines the cancer-fighting properties of well-defined clusters of 25 gold atoms. These clusters, stabilized and disguised from the cell by a peptide wrapper, were shown to enter cancerous cells and trigger their self-destruction by blocking the TrxR1 protein, which keeps the levels of reactive oxygen species inside the cell in check.

Inorganic: An Ultrastable Anode for Long-Life Room-Temperature Sodium-Ion Batteries
Odds are good that you use at least one lithium-ion battery every day of your life, and those odds are only going to get better. The catch? Lithium is rare, which makes it expensive. Chemists, such as the authors of this study ($) from Angewandte Chemie International Edition (GDCh), are investigating replacing the expensive lithium-containing parts of the battery with components made from more common elements such as sodium. In the paper, the authors describe the synthesis, structure, and long-term test behavior of a new sodium-ion battery negative electrode. The material efficiently exchanges sodium ions during charging and discharging up to 3,000 times while retaining ~85% of its capacity.

Materials: Molecular doping of graphene as metal-free electrocatalyst for oxygen reduction reaction
Fuel cells are a hot topic; particularly, a cheap and efficient hydrogen fuel cell would enable us to use hydrogen as a fuel with only pure water as a combustion product. Oxygen reduction is the kinetically limiting step in hydrogen fuel cells, so the faster oxygen reduction becomes, the more energy the fuel cell can pump out. The authors of this study ($), published in Chemical Communications (RSC), investigated a new graphene catalyst chemically modified by small amounts of nitrobenzene ("nitrobenzene-doped graphene"). The catalyst is tested for oxygen reduction activity using several electrochemical methods. The authors found that, although their catalyst was not as active as traditional platinum catalysts, their method of doping graphene significantly increases its activity compared to clean graphene and is worth taking a look at.

Organic: Role of Gold(I) α-Oxo Carbenes in the Oxidation Reactions of Alkynes Catalyzed by Gold(I) Complexes
A particular family of gold(I) complexes is known to catalyze the oxidation of alkynes to vinyl ketones in the presence of an O-atom donor and a nucleophile. However, side products are observed. The reactivity could accounted for if a particularly reactive gold oxo-carbene intermediate was forming, but no direct experimental evidence for that species has been published. To further understand the reaction pathway as catalyzed by gold(I) carbenes, the authors of this paper ($) in the Journal of the American Chemical Society (ACS) carried out a sophisticated study involving mass spectrometry and quantum chemistry calculations. The authors chase after the gold oxo-carbene intermediate and are able to demonstrate that it does indeed form during alkyne oxidations. Based on the difficulty of directly and conclusively identifying short-lived reaction intermediates, this study represents as significant achievement for the field.

Physical: Vibronic coherence in oxygenic photosynthesis
Photosystem II (PSII) is a very special complex. As the authors of this recent study in Nature Chemistry (NPG) point out, it is "the only known natural enzyme that uses solar energy to split water," which makes it a key player in solar energy fixation. With the advent of ultrafast spectroscopic methods (specifically 2-dimensional electronic spectroscopy, 2DES), groups have begun to paint a detailed picture of how the complex interacts with light in hopes of learning what makes it so effective. The authors of this particular paper observe the formation of a coherent excited state in PSII after the complex absorbs light. The coherence, which is a quantum mechanical superposition of two states, was determined to involve both electronic and vibrational states. This "teamwork" between electronic and vibrational motion could be an important factor in what makes PSII so good at charge separation, an important step in photosynthesis.
-University of Michigan research from the Ogilvie group. To read more about this article, check out the press release. Hat tip to Kimberly Daley for discussing coherences.

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
RSC - Royal Society of Chemistry

Friday, May 30, 2014

#FF: Using Twitter for Good (Chemistry)

Anyone who knows me personally will by now have been exposed to my (relatively) new Twitter obsession. For that, I apologize.

Only a little bit, though.

The fact remains that Twitter is a powerful engine for rapidly sharing news about any topic in headline format, allowing the reader to make a decision on whether to delve deeper in a matter of seconds. Why humanity has chosen to inundate these spaces with Bieber and pictures of cats is beyond me, but that doesn't mean that your Twitter feed has to experience the same fate.

In the spirit of #FF (Follow Friday), here are 7-ish Twitter accounts you can add to your feed to bring yourself some great chemistry content every day.

Socializing Scientists
I'm going to go out on a limb here and say that you didn't join Twitter to get work done. Scientists, being humans, enjoy having fun with social media. Of course, scientists, being nerds, think that the best way to have fun with social media is to share pictures of their science with as many people as possible. In chemistry, these pictures are all curated and retweeted by @RealTimeChem (#RealTimeChem). From jury-rigged glassware setups to celebrations of that one triumphant spectrum, you're bound to find something interesting here. For example:

However, scientists on social media aren't only concerned with having fun. There has been a great deal of effort devoted to meeting the needs of underrepresented groups in the sciences in order to promote further participation. Obviously these problems are not yet solved, and conversations continue in a number of venues, Twitter included. The handle that I see most often is @BLACKandSTEM (#BLACKandSTEM), which provides amplification for the voices of black scientists across all disciplines. The handle also hosts frequent chats on universally important topics such as self-promotion and strategies for finding employment.

The American Chemical Society
Most scientific publications and organizations are on social media in some capacity, but the American Chemical Society does a particularly good job of it among chemistry-related organizations. Following @AmerChemSociety will get you access to tweets about high-profile publications from the flagship ACS journals. The best part about following the ACS, though, is that all of the different sub-handles all retweet each other, so by following @AmerChemSociety you'll get information about opportunities for employment, news targeted at graduate students, outreach activities, and more.

Another interesting facet of the ACS social media presence is @ACSReactions, which publishes short pop-science videos giving a chemical explanation for everyday curiosities. It hasn't been active for long, but has already made a big splash with a video about the chemistry of bacon smell.

Chemical & Engineering News
Tweets from Chemical & Engineering News (C&EN) probably make up the bulk of my feed, and they definitely get the bulk of my clicks. As with the main ACS account, the main C&EN account, @cenmag, retweets a large volume of content from its associates. If you're into materials chemistry and emerging technologies, you can't miss.

Additionally, C&EN reporter Carmen Drahl (@carmendrahl) hosts the short podcast Speaking of Chemistry (#speakingofchem), which gives bite-sized recaps of news items in a very accessible video format.

Strictly Business
Do you love to read papers all the time? I'll admit that I've had lunch breaks cut short by a tweet about an interesting paper that inspired me to go out and be productive again. Go ahead and search for your favorite journals - odds are, if they're from the ACS, RSC, or Nature Publishing Group, they're on Twitter. You can use Twitter's Lists function to sort all of the journal tweets out of your feed, which is surprisingly helpful for staying on top of things if you're already on social media fairly often.

While it might be a long way from convincing your advisor that sitting on Twitter is helping you with your degree, following these accounts will give your feed a healthy variety of science news and happenings that you might have missed otherwise. Happy #FF!

Did I miss a good one? If you're following someone great that I haven't mentioned here, feel free to leave a comment!

Tuesday, May 20, 2014

The Giant De Novo Peptide Review: An Interview with Fangting Yu

The #SciBlogReaders survey is still underway! If you enjoy this blog or another science blog, click here to learn how you can help bloggers and win some cool prizes for yourself.

For researchers breaking into the field of protein design, life just got a whole lot easier.

In late March, a massive review of rational protein design ($) entitled "Protein Design: Towards Functional Metalloenzymes" hit the web. Scientists of all levels and disciplines use reviews to figure out where to start on new research projects or to gain a wider perspective of their field, so writing good review articles is an essential part of scientific research. The review was published in Chemical Reviews (ACS) as part of a specially-themed issue on enzymology and authored by Dr. Vince Pecoraro's group at the University of Michigan, along with collaborator Dr. Matteo Tegoni.

Enzymology, or the study of how enzymes do their jobs, is a diverse field of science that intersects chemistry, biochemistry, and biology (for example). Some enzymologists are interested in cataloguing existing functional proteins. Some take those proteins and, by changing their structure or the chemicals available for them to react with, learn the intimate mechanism of their function. Still others apply what is known about how the enzymes work in an attempt to create new enzymes or enzyme-like molecules that function even more efficiently than the natural structure.

The latter group of enzymologists most often utilize the two methods covered by the review: protein redesign/engineering, in which an existing protein is modified to enhance its function; and de novo protein synthesis, in which a functional protein that does not exist in nature is dreamt up and created in the lab.

Dr. Pecoraro's "Protein Design" review was a massive undertaking involving ten authors and over 1,000 cited papers. I sat down with Fangting Yu, the article's lead author and a 5th-year graduate student in Dr. Pecoraro's lab, to learn more about the process of putting the review together.

Fangting Yu, explaining how she uses a device in the lab to synthesize new proteins.
Image credit: Sung-Hei Yau; used with permission.
Getting into the Research
Fangting originally joined the Pecoraro group to work on making inorganic manganese complexes to model the reactivity of the oxygen-evolving complex in photosystem II (PSII). The calcium-manganese cluster in PSII is essential for the final step of photosynthesis in which water is oxidized to the oxygen that we breathe. The mechanism of its action has been debated since the structure of PSI and PSII began to become more clear in the late 1980's (see links).

Fangting got a publication ($) out of the project. However, the manganese project would soon run out of funding. Because of a broad interest in the reactivity of transition metal small molecule centers in proteins, she decided to take up a new project dealing with a more biologically relevant system. At the time, Dr. Matteo Tegoni, an Italian researcher currently at the University of Parma, Italy, and also an author on the review, was a visiting scholar in Dr. Pecoraro's lab. He made progress on a new aspect of de novo protein design involving copper reaction centers. Fangting took over the project as he left and devoted her interests to de novo protein synthesis, resulting in two papers thus far (1 and 2, $).

The All-Important First Draft
Writing a good review can be a huge undertaking, and most graduate students do not have the time to pursue it with hectic schedules and workloads. Fangting was no exception. "We got to write this because of [Dr. Pecoraro]," she said. In addition to de novo design, Dr. Pecoraro has worked on understanding the role of manganese and vanadium in biological systems for the bulk of his 30-year career at the University of Michigan. As one of the leading experts in the field, he was invited by Chemical Reviews to write the article.

Dr. Pecoraro left the first author position open to the student who made the best case for authorship. "I was debating whether or not to take it because that was my fourth year of grad school, and in that summer you can generate a lot of data," said Fangting. However, an instrument critical to moving her research forward broke down near the start of the summer, and she decided to make a bid for authorship.

The writing process began in earnest in May 2013. It took 3 months to put the first draft together for submission, which means it spent about 7 months in review before its publication online.

Collaboration, Here and Abroad
Reviewing a topic as deep and well-studied as protein design requires a ton of reading, and for one person to do it all would be an astronomical task. As such, the paper ended up with ten authors, nine of which are currently in the Pecoraro lab. However, Dr. Tegoni's appointment in Italy put the Atlantic Ocean between him and the rest of the authors.

When I asked if the international collaboration was difficult, Fangting waved the question off. "[Dr. Tegoni] is the person who started my thesis project. We're pretty close - we're both friends and collaborators." Electronic communication made the collaboration easy.

Fangting went on to say that managing multiple authors was not the hardest part of the process. Collaboration is essential for putting together a project of this scale. "One thing that I would advise on multi-author papers is, when you are the point person, you want to be as specific as possible when you give people assignments, and be firm about deadlines."

The Review Experience, In Review
The toughest part of the review for Fangting was deciding what to include. "There's so much out there," she said. "For example, say this protein design paper cites a few other papers that are kind of protein design, kind of engineering, kind of a directed evolution approach." The line of what is in the scope of a review and what is not is never black and white, and those papers fall into the grey area. "It takes time and energy to make a decision on what kind of material you want to include and how you want to connect them together."

Writing the review certainly brought benefits with it. First, in assembling all of the material, Fangting learned a great deal and feels more on top of her field than she did before.

Perhaps more tangibly, though, she feels like she has gotten a head start on her thesis. "Any Ph. D. student is going to have to go through writing a review chapter," she said, referring to the introduction of the final Ph. D. thesis. "It's just a matter of when. I personally think that the intro chapter is the most difficult to write. Deciding what context you want to put your thesis in is the most difficult."

Lessons Learned
Writing the review has certainly given Fangting a head start on her thesis, but has also taught her some valuable skills for tackling large writing projects in general. When I asked her what advice she would pass along to other students engaging their theses or similar publications, she paused and her face became much more serious. "Outline," she said.

"You need to think more than you need to write," she added. "At least for me. I would spend time just shutting down everything and thinking." She paused again. "And outline it."

To learn more about the other authors of the review, and for more specifics on what a rational protein design research project actually looks like, check out the Pecoraro group web page.

ACS - American Chemical Society
PSI/II - photosystem I/II

Monday, May 12, 2014

Join the Fun!

I started Tree Town Chemistry as a way to spread news about graduate student researchers, the social side of science, and other interesting tidbits that interest scientists of all levels, all while building a professional portfolio. So far, it has been a lot of fun and I would call it a success.

But why just me? There has to be someone else out there looking to test the waters, right?

This is an official invitation for guest posts and collaborators - a call for papers, if you will. If you're interested in science writing and want to give blogging a quick try, contact me. Whether you have an idea for a one-shot post or you would like to join the blog long-term, I am interested in hosting your work. More authors means more points of view and a deeper perspective.

Send your ideas in to treetownchem@gmail.com and let's get started.

Wednesday, April 23, 2014

Chemistry Lit Feature Vol. IV

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

In case you're looking for a little school pride to give you a boost for your end-of-semester activities, for this edition of the Chemistry Literature Feature I've managed to find recent publications in every cluster by University of Michigan students. This month, we'll take a look at inorganic complexes that act like proteins, nanowire solar cells deposited from aqueous solution, and more.

But first, some truth told by a recent seminar speaker:

Overheard at Michigan:
"This is what assistant professors do - just dump a lot of information on you and try to convince you that we know what we're doing."
Analytical: Unveiling the Membrane-Binding Properties of N-Terminal and C-Terminal Regions of G-Protein Coupled Receptor Kinase 5 by Combined Optical Spectroscopies
Some of the most important proteins in your body operate within the cell membrane, and figuring out how membrane proteins work is notoriously complicated. Analytical and biological chemists are always looking for new techniques to help. In a recent paper ($) published in Langmuir (ACS), the authors describe the binding modes and secondary structure of a membrane-bound kinase using two flavors of surface-sensitive infrared spectroscopy (sum frequency generation and attenuated total reflectance). These techniques reveal the equilibrium structure of the protein in the membrane, and are also applied to probe how the structure changes over the course of normal signaling events.
-University of Michigan research from Dr. Zhan Chen's group

Analytical chemists experienced in electrochemistry might enjoy the Materials paper.

Chemical Biology: Model complexes of key intermediates in fungal cytochrome P450 nitric oxide reductase (P450nor)
The reduction of nitric oxide (NO) to nitrous oxide (N2O) is an important biological pathway in the denitrification arm of the global nitrogen cycle. In cells, the reaction is catalyzed by cytochrome P450 nitric oxide reductases (P450nor) in a process that is not fully understood. One way to shed light on the mechanism is to create synthetic molecular complexes that look and act like the P450nor active sites. These model complexes are much easier to interrogate. In a recent review ($) in Current Opinion in Chemical Biology (Elsevier), the authors review findings from several projects attempting to learn about P450nor's nuts and bolts by making and studying model organometallic complexes.
-Review written by the University of Michigan's Dr. Nicolai Lehnert's group

Fans of Chem Bio may also enjoy the Analytical paper and, if you're involved in simulations, the Physical paper.

Inorganic: A 3-Fold-Symmetric Ligand Based on 2-Hydroxypyridine: Regulation of Ligand Binding by Hydrogen Bonding
Organometallic chemistry has historically focused its efforts on elucidating how chemical reactions take place at the metal center of a complex. However, a newer direction in the field is to exploit the second coordination sphere - parts of the organic ligand that are in proximity to the metal center - to provide new reactivity. In this short communication ($) published in Inorganic Chemistry (ACS), the authors describe the synthesis and characterization of a new three-fold symmetric tautomerizable ligand. The ligand is successfully reacted with copper to create metal complexes with second coordination spheres suited for reacting with small molecules.
-University of Michigan research from Dr. Nathaniel Szymczak's group

Readers specializing in Inorganic chemistry might also like the Chem Bio paper.

Materials: Electrochemical Liquid-Liquid-Solid Deposition of Crystalline Ge Nanowires as a Function of Ga Nanodroplet Size
Synthesizing electrodes of pure germanium, which may be useful in both batteries and solar cells, can be very expensive. Harsh reagents and high temperatures are required. A recent effort ($) published in the Journal of the Electrochemical Society (ECS) continues the work of Dr. Stephen Maldonado's group in synthesizing materials for solar cells via an aqueous solution-based electrochemical process much closer to room temperature. In this work, the authors find that the size of the liquid gallium catalyst employed in the deposition directly controls the morphological properties of the germanium nanowires grown. These nanowires may find applications in lithium batteries, similar to the silicon wires discussed in this post.
-University of Michigan research from Dr. Stephen Maldonado's group

Organic: Directing Group-Controlled Regioselectivity in an Enzymatic C-H Bond Oxygenation
Biocatalysis is a field of chemistry in which naturally-occuring enzymes are used to effect chemical transformations, often on substrates with which they do not typically react. A common line of investigation is to mutate the enzyme of interest, deducing the important parts of its structure by observing how the mutations affect the reactivity for common substrates. In this Journal of the American Chemical Society paper ($), the authors take the reverse approach. Using so-called "substrate engineering," the authors demonstrate that, by changing a specific part of the structure of their macrocyclic substrate, they can effect changes in stereoselectivity several carbon centers away. They provide several useful synthetic observations, but also comment on the prospect of using this approach as a platform to learn more about protein function.
-University of Michigan research collaboration between Dr. Montgomery's and Dr. Sherman's groups

Physical: WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm
Molecular dynamics simulations are often used to model the mechanisms of proteins and other biological systems. A classic problem in the field is that it is difficult for a simulation to access rare events, such as large conformational changes in a protein's structure, that are often critical to its function. A recent article ($) featured on the cover of the Journal of Physical Chemistry B (ACS) describes a new algorithm, called WExplore, which allows a simulation to more easily access these exotic regions of configurational space. The algorithm works by assigning a weight to configurations experienced by the simulation. High-probability states are weighted down and are thus less likely to be visited again. Low-probability states are weighted up. The authors use a small peptide simulation to show that the WExplore method accesses protein configurations not often seen in normal simulations.
-University of Michigan research from Dr. Charles Brooks, III's group.
-suggested by Jessica Gagnon

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

ACS - American Chemical Society
ECS - The Electrochemical Society 

Monday, March 31, 2014

Making Sense of Multiple Sclerosis Research (Blogroll)

(For a brief primer on multiple sclerosis, skip to the end of this article.)

March was National Multiple Sclerosis Awareness Month in the United States.
Kim and I at Bike MS 2013 with a Fighting
Shamrocks sign that sums up our feelings. Scientific
research is the only way to improve quality of life
for current and future MS patients.

Were you aware?

With any chronic illness, clear communication between patients, doctors, and researchers is a critical concern. Patients in particular, most of whom are scientific laypeople, have an extremely difficult time keeping up with developments in research. The multiple sclerosis (MS) community is no exception. Cutting-edge research is being conducted along a myriad of avenues related to MS, from the cause to the mechanism of disease progression to treatment development.

However, keeping patients informed of these cutting-edge developments in a way that is easily understood is a tough item for researchers. Blogging can help to change that by making research details available - and accessible - to everyone.

The Research Blogroll
Dr. Karen Lee, the vice president of research at the Multiple Sclerosis Society of Canada, keeps a blog detailing the major goals of studies funded by the Society (and more). In particular, this post builds understanding from the ground up to explain in layman's terms how three research teams are pursuing one facet of the MS problem.

It is easy to think of doctors, patients, and researchers as three mutually exclusive sets of people, but that is not always the case. In a series of posts entitled "MS Patient, Ph. D.," Dr. Griselda Zuccarino-Catania and Dr. Emily Willingham provide unique insights on all three realms based on their personal experiences both as scientists and as MS patients. They give information on everything from digesting exciting research findings to the frustrations of making sense of diagnoses from multiple doctors. The Multiple Sclerosis Discovery Forum, which hosts the series, is in itself an excellent resource for those interested in learning more about MS research.

Dr. Gavin Giovannoni of Barts and The London Neuroimmunology Group and another blogger by the name of MouseDoctor maintain a blog designed to keep the public informed of research findings across the MS community. If you are a biochemist looking for scientifically heavier reading material, then the blog is a gold mine for you. However, many of the posts are philosophical in nature and accessible to everyone, such as this post about how potentially harmful therapies fit in with the Hippocratic Oath.

We're All in This Together
A problem like MS requires minds to solve it, and not just a few. By improving communication between researchers and patients, just as these bloggers and many more are trying to do, the number of people in the huddle grows larger and larger. Improved communication carries a second benefit, however, which is articulated perfectly by the Multiple Sclerosis Society of Canada: "[...] Hearing directly from a researcher about their work provides a powerful tool of hope, of better understanding of what the future could promise through research."

About MS
Multiple sclerosis (MS) is a chronic disease in which a patient's central nervous system is slowly degraded. Specifically, the protective coating of myelin nerve cells is worn away, which throws a wrench in the body's communication systems. A wide variety of symptoms results, ranging from impaired memory to loss of motor skills. The National Multiple Sclerosis Society estimates that 400,000 Americans are afflicted with MS.

The cause of MS is not known. This fact makes researching possible treatments for the disease extremely difficult. For an excellent review of known trends in MS diagnosis, check out this 2008 paper in The Lancet ($). The National Multiple Sclerosis Society also offers this list of potential causes (read: research targets) for MS, along with a very interesting list of factors shown not to be the cause of MS.

Scientists of all sorts are involved in MS research. In particular, chemists and biochemists have developed several commercially available drugs that are used in MS treatment. These drugs can take the form of small molecules or large tailored antibodies; which drugs are applicable depends on how far the MS has progressed.

Friday, March 14, 2014

I Make My Pi with Silicon Nanowires

As this is the first Pi Day (3.14 ~ March 14) of Tree Town Chemistry's life, I felt that I would be remiss if I were to go through it without putting up a celebratory post. But what to write about?

Like any good chemist, I turned to my periodic table for answers. Element 3 is lithium. Element 14? Silicon.

Happy Pi Day, everyone. Let's make some batteries.

One Way Your Phone Battery Destroys Itself*

The lithium (Li) cycle for
the + electrode in a Li-ion
One of the classic problems in lithium ion batteries - the kinds of batteries currently powering your phone or laptop - is the instability of the compounds that make it up. The electrode materials in a lithium ion battery must be able to suck lithium ions out of the electrolyte while charge is flowing in one direction, and then spit them back out when the polarity of the battery is reversed (charging versus discharging). In a perfect substance, the process is totally reversible.

However, in most substances, the size of one crystal unit grows substantially during the lithiation process (see the cartoon at left). This causes the individual particles of the material to swell. The strain induced on the particles, either from the growth process itself or from bumping into neighboring particles, mechanically crushes the battery material. As a result, pieces of the battery material fall off of the electrode and are rendered useless.

This presents a huge problem for chemists and materials scientists. There are two main ways to look at it. One could imagine screening hundreds of compounds, looking for ones where the percent expansion during lithiation is as small as possible, thereby minimizing the strain. Another solution to the problem is to study exactly how these compounds expand, and then try to shape them on the nanoscale in such a way that the strain forces are minimized.

Silicon Solutions

Silicon is most famous for its applications in solar energy technologies, but it has also been identified as a lithium-ion battery anode (negative electrode) with record capacity for storing electrical energy. However, silicon also undergoes huge expansion once it accepts lithium ions - on the order of 400%. That fact makes it inapplicable to traditionally-structured lithium-ion electrodes.

A 2007 study led by Professor Yi Cui at Stanford University found a way around silicon's volume expansion. Professor Cui's research team developed a method of synthesizing electrodes composed of ordered silicon nanowires. The electrode structure is not unlike your toothbrush; each bristle is a silicon wire that is directly connected to the base of the electrode, called the current collector.

The unique electrode structure brings about two major improvements. First of all, the electrical conductivity of the entire electrode is improved, since all of the silicon is directly connected to the current collector. Secondly, the silicon wires have plenty of room to expand in length and in width without clashing against one another. Cui's team observed that their silicon nanowire electrodes exhibit record-breaking storage capacity and are stable over several charge/discharge cycles.

The result made an impressive impact in the battery community and is slated for limited commercialization soon. This paper is a great example of how materials chemists can solve problems by addressing concerns that fall outside of the chemical identity of the material. In this case, changing the shape of the material particles took an unimpressive substance and made it into something industrially relevant. And who knows? If these batteries are successful commercially, we might all be celebrating Pi Day with lithium and silicon in the future.

*Disclaimer: The pulverization issue is, of course, not the only method by which lithium ion batteries fail. There are many physical and chemical changes that take place within a battery cell as it is charged and discharged repeatedly, and each material presents its own special problems. Additionally, the anode is only one half of the battery, so there is still a lot of good research going on solving similar problems for cathodes as well.

If you're interested in reading more about nanowire electrodes, U of M researchers published a similar result using germanium nanowires in 2012. This research comes from the Maldonado group and the first author was Junsi Gu.

Monday, March 10, 2014

'Tis the Season for Tough Decisions

The acceptance letters are out, and students all over the country will be traveling from school to school to make sure they are as informed as possible when they make the decision. It's a big one - one that will set the stage for the rest of their careers.

The decision is where or whether to pursue a Ph. D. in chemistry.

Everyone approaches their decision a little bit differently, and to gain some perspective on that fact, I reached out to a few graduate students in the department and asked them about the factors they considered most strongly when making their choice.*

Department Size and Variety
All respondents agreed on one thing: when it comes to choosing a school, a big department with a lot of variety is always better. This idea is one that graduating students often haven't considered when they arrive for visitation. "A big program often offers a wider selection in terms of research, which I decided was critical in making my decision since I wasn’t 100% sure exactly what type of research I wanted to do [when selecting a school]," wrote Charles Lhermitte. Additionally, students aiming for spots in specific labs should acknowledge that there can be many other students vying for those spots, and the chances of not landing your first choice are real. A Ph. D. is a long and difficult degree, and if you get stuck working on a research project that you are not passionate about, it will be even more so. Choosing a school where there are several labs that are attractive to you makes having a good backup plan easy. Students also view schools that feature research rotations very favorably for the same reasons.

A varied department also offers a safety when it comes to student/advisor relationships. As graduate students, we're offered the somewhat unique opportunity of choosing our boss, and in many ways choosing the right advisor is just as critical as choosing research that you are passionate about. "One advising style is not right for all graduate students and can lead to 5 long and miserable years," writes one respondent. "I'd recommend really talking to professors and asking students about advisor/student relationships and mentor styles."

Program Rank
Each student considers the prestige of a school's program when deciding whether or not to apply there, and program rank is just as important in the final selection process. An advanced degree from an elite institution is certainly a lofty goal, and building one's academic pedigree in that way has obvious benefits when it comes to landing a great job after graduate school. The Ph. D. is a huge investment of time and effort. Everyone wants to get a job that makes that investment worthwhile.

However, some respondents viewed rank as a less important consideration when reviewing their decision process in retrospect. Choosing a school based on rank alone is risky. Be sure to weigh program rank carefully against other factors such as those outlined above.

Personal Factors
"I like to be involved in where I live, so it was important that there are opportunities for that," writes Kim Daley. Visitation weekends just as much about getting a feel for the research as they are about experiencing the town surrounding the school, the social atmosphere of the department, and your potential lab mates. It is important to find people that you can get along with. Additionally, the other members of the department will turn into your mentors and collaborators, so it is worthwhile to check your own work habits against theirs to see how they mesh. "Fitting in with a group is semi-important since so much time is spent in the lab. Work style and work ethic are important," notes one respondent.

Moving on to graduate school usually means packing up and shipping off to a new part of the world, and for students in relationships, that can be especially stressful. There is a lot of pressure to make a decision that is in the best interest of your professional life. "However," writes Daley, "your personal life is also important. When I was picking, I felt like considering my boyfriend would somehow make me a weak person. But it's okay."

School or Work?
For some students, the decision involves not only choosing between graduate schools, but choosing between graduate school in general or entering the workforce directly. Working for a few years after undergrad can provide invaluable experience and perspective, especially for those just looking to take a break before returning to advanced education later on. (And, of course, the pay is often significantly better than a graduate student stipend.) Working in industry can also win you contacts and references that distinguish you from other applicants when applying for future positions.

For those with aspirations of managing research projects, however, a Ph. D. is undoubtedly the way to go. "Those with a B.S. may hit a sort of promotional 'ceiling' a lot sooner than a Ph. D.," writes Lhermitte, who interned at Procter & Gamble before applying to graduate school. "I discussed this with my bosses and they agreed that a Ph. D. would allow me to move more quickly up the ranks in the company. If you want to go far in a technical company, then you have to get a Ph. D." Managing a research project is a skill that must be learned like any other. Over the course of a Ph. D., you will not only gain focused knowledge and become an expert in your field, but you will also develop your skills as a manager of research - training that is very difficult to find elsewhere. The Ph. D. is a certification of that training.

It's Your Decision - Nobody Else's!
Choosing what to do after getting your undergraduate degree is a big professional decision, and it is necessarily stressful. That stress can be compounded by other figures in your life - parents, undergraduate advisors, etc. - telling you what is and is not important in a school. To some extent, their advice is necessary to help inform your decision, but remember that the final decision is yours alone. Your choice should reflect the best compromise among all of the factors that are truly important to you, no matter what those factors are.

*comments lightly edited for clarity

P.S. Thank you to everyone who responded for this post! Input like yours makes these kinds of pieces possible. Showcasing student opinion is an important part of the project for me. If you have more to add, feel free to leave a comment!