Editorial: What's the Point of Organic Chemistry Education?

On Monday, the American Chemical Society National Meeting hosted a presidential symposium entitled "Is There a Crisis in Organic Chemistry Education?" This is a provocative question that has been floating around the community of chemistry educators for some time.

The panel of presenters consists mostly of representatives for academic publishers like Elsevier and McGraw-Hill, and their 15-minute talks focused on what their respective companies are doing to innovate and enable learning in new ways for students. From the publishing perspective, changes in curriculum seem motivated by changes in the assessment of that curriculum - namely, standardized tests like the GRE and MCAT which are used as metrics for admission into more advanced degree programs.

The audience, however, seemed to consist mostly of academics and educators largely responsible for teaching the content. The symposium concluded with a panel-style discussion between the presenters and the audience in which audience members picked brains, voiced concerns, and shared experiences regarding organic chemistry instruction. But the symposium's central question never really got answered.

Instead, the discussion between the panelists and attendees revealed a bit of a gray area on what the purpose of the organic chemistry course is or, perhaps, should be. Is it to prepare pre-meds for medical school and increase their MCAT scores? Is it to prepare chemistry students for graduate education? Is it to challenge them with a new way of thinking? Do we actually anticipate that students will remember the intimate details of reactivity presented in organic chemistry classes two or three years later? Should we have one or two semesters - or more?

The comments exchanged between panelists and audience members suggested that all of these purposes are at play. One audience member with over thirty years of experience in teaching actually surveyed medical schools and asked why they even require organic chemistry. According to him, the most insightful reply he received was that organic chemistry tends to be the first time that students are forced outside of their comfort zone. Contrasted with general chemistry, which is very algebraic, organic chemistry introduces the language of molecular architecture.

Another audience member corroborated, adding that organic chemistry forces students to develop spatial reasoning and study habits that they did not need to get by in previous courses. She actually claimed that these skills were the most important take-aways from an organic chemistry course.

To me, the discussion suggested that individual academics and publishers may approach organic chemistry with different goals or different sets of goals in mind. Maybe, in the quest to optimize organic chemistry courses to best serve students, organic chemistry educators need to come to a consensus on what particular way students are best served. For example, if the goal is truly to introduce foreign concepts of molecular architecture, should courses cover a more narrow scope of reactions and functional groups to make more time to hammer that concept home?

The question isn't only important to academics. Publishers are essentially communicators of scientific education materials, and the first step in any effective communication is sitting down and deciding what the goal of that communication ought to be.

Is there a crisis in organic chemistry education? I don't know. But what I did see during the presidential symposium was an opportunity for publishers and educators to work more closely on refining organic chemistry education's identity and the goals it seeks to accomplish.

Oxygen's Alchemical Origins: The Phlogiston Story

Today, everybody knows about oxygen. We know that it fuels fires and keeps us breathing. It seems to us one of the most basic elements of life, ubiquitously available, irrefutably present. Oxygen is obvious.
But it wasn't always.

Maybe you would have liked chemistry a little more
if your book looked like this. Photo credit: Paul K./flickr.com

Let's rewind the clock to the late 1660's, when chemistry texts still looked like spellbooks. At that time, the practice of chemistry was still very much rooted in alchemy - a rich mixture of science, occultism, and superstition. In his 1667 publication of Physica Subterranea, German alchemist Johann Joachim Becher outlined the theory of a fundamentally flammable element called terra pinguis. Substances that burned easily in air, like oils, waxes, and metals, were rich in terra pinguis. Becher's theory was taken up again and refined in the early 1700s by Georg Ernst Stahl, who renamed terra pinguis to phlogiston (from Greek, "burning up").

Great Blogs by Women in Science

What's the day-to-day like for women in science or engineering?

I don't know, ask them. They're out there, doing science, living life, and blogging about it.

For chemistry aficionados, Michelle Francl-Donnay (@MichelleFrancl) at The Culture of Chemistry has a real knack for finding topics in language, teaching, and politics that relate to chemistry in an exciting way. Raychelle Burks (@DrRubidium) of Thirty-Seven is an analytical chemist who does fantastic outreach in support of increasing STEM's inclusiveness towards women, people of color, and LGBTQ folks. Kat Day (@chronicleflask) of the chronicle flask has already called BS on one overhyped health article this year (and blogs a lot of other great chemistry stuff). Beth Haas (@belehaa) at Casual Science and Jenny Martin at cubistcrystal blog their reflections on their careers as chemists and educators, and Anna (@Lady_Beaker) at Chemistry Intersection is documenting her quest for a Ph. D. Jyllian Kemsley (@jkemsley) covers chemical safety in industry and academia for Chemical & Engineering News's The Safety Zone. Stephani Page (@ThePurplePage) runs the blog #BLACKandSTEM. The husband and wife team of Geoffrey and Ruth Bowers (@CarChemProf) is behind Understanding Chemistry through Cars, which has a great perspective combining knowledge of the automotive industry with some of its fundamental chemistry. Last, but not least, Carmen Drahl (@carmendrahl) covers exciting and timely chemistry news at Forbes.

There are great blogs covering topics in other areas of science as well. Thus Spake Zuska (@TSZuska) writes beautifully, relaying stories and perspectives from STEM, politics, personal life, and the areas between. Ulli Hain (@ulli_hain) at Science Extracted covers a range of topics in research with an emphasis on ethics. The women of Portrait of the Scientist document their lives as they pursue a number of different science and science-adjacent paths.

Finally, leveling the playing field for women in STEM is an area for activism and outreach as well as personal reflection. STEM Women (@STEMWomen) is a team of three scientists who aim to bring female scientists together and increase their visibility to the public through blogs, videos, and other great content. Soapbox Science (@SoapboxScience) is a media initiative doing much the same by bringing scientists from around the UK "to the soapbox" to talk about their lives and careers in public presentations. And, unless you just plain hate joy, you've got to follow GeekGirlCon (@GeekGirlCon).

I originally wanted to put this blogroll together to raise awareness of sexual harassment and sexual assault in scientific workplaces. But here's the whole story on that: it happens. A lot. It happens in lecture halls and on research cruises and in meetings and on archaeological digs. It happens to women and scientists of all demographics. Sometimes it's not a secret. It has almost assuredly happened to someone you know. It's unacceptable, it's repugnant, it needs to stop.

So don't sit and think smugly "oh, biology is OK! Chemistry is free of sexual harassment! It's just those astronomers!"

— Matthew R. Francis (@DrMRFrancis) January 12, 2016

The links above are, for the most part, to stories from larger outlets dealing with statistics and responses to well-publicized cases. I wanted to go out and find survivors who have shared their stories, to point out that yes, this happens to real people and it's an intensely personal issue.

I abandoned that search without having found very much. And of course not, I thought. The stakes of publishing a post like that are too high, the emotions too real, and the internet atmosphere too hostile. In the event an investigation actually does get started, it can be a nightmare for the complainant, and it's too easy to misstep.

But how about this stunning revelation? Scientists don't want to write about sexual harassment. These women didn't start science blogs so they could write posts about how hostile their work environments are. They didn't sign up to be scientists so that they could be harassed or worse. We - all of us - became scientists because we're fascinated by some aspect of the material or social world and we want to poke it with a stick. That experience is what scientist-bloggers are publishing about.

Normalizing marginalized voices in our scientific community is critical to achieving equality. Add some of these excellent writers to your feeds. They all speak for themselves.

Special thanks to Beth Haas, Jyllian Kemsley, Chemjobber, Renee Webster, and the rest of Chemistry Twitter for helping me find all of these bloggers. If you know of someone else that I've left off, feel free to add in the comments.

SLACkers: University of Michigan Chemists Experience Premier Research Facility

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From left to right: Nick Miller, Ted Wiley, and Laura Kiefer,
the graduate students who carried out experiments at
SLAC-LCLS last month.

Inside an underground tunnel about thirty miles south of San Francisco, electrons scream by at nearly the speed of light. Suddenly, they find themselves jerked back and forth along their mile-long path by magnets. As they veer around turns, they spit out high-energy X-rays that are the light source for one of the most advanced lasers humans have ever built.

Just another day at the lab.

The Stanford Linear Accelerator Center, or SLAC, is a nationally funded laboratory dedicated to helping scientists answer fundamentally difficult questions about the matter our universe is made of. At SLAC, the Linac Coherent Light Source (LCLS) is home to one of the world's most advanced X-ray lasers - a billion-dollar device about a kilometer long. What is it like to use an instrument that pushes the boundaries of human technology? A group of University of Michigan researchers found that out for themselves this past October.

The proposal that took the group to SLAC was headed up by Roseanne Sension, in collaboration with Jim Penner-Hahn and Kevin Kubarych, all professors at the University of Michigan, and with University of Louisville professor Pawel Kozlowski. Nick Miller and Ted Wiley, graduate students in the Sension group, and Laura Kiefer, a student of Kubarych's, traveled out to California to conduct the experiments with their advisors. Also accompanying the group was Aniruddha Deb, a staff scientist in the Penner-Hahn group.

Nick Miller in one of SLAC-LCLS's long,
long, long hallways. Image credit: Laura Kiefer

While that might seem like a large group for a science experiment, the shared pool of expertise was instrumental for the group's success. "Each member of the team had something to contribute that the other members didn't know that much about, so it strengthened the proposal," said Wiley. These experiments will make up a large part of his and Miller's theses.

The application process is very competitive. The group found out in June that the proposal, titled "Investigating Structural Changes in Short-lived Excited States of Vitamin B12," had been accepted and that they would be making the trip. During the time between that and their October 14 start date, they planned for lodging, and also went through several online training modules not unlike what would be required of new employees at any lab. "It's a government lab, so it's under a lot of scrutiny," said Wiley. "So, you know, you have to be able to use a stepladder correctly."

There were a few more training modules on-site at SLAC-LCLS. Then, the marathon began.

The group performed measurements between 9 PM and 9 AM for four straight days. "You get delirious on the night shift," said Kiefer. But no time could be wasted. Although the expenses for the actual measurements are paid by grants from the United States Department of Energy, the bill is extremely high - to the tune of tens of thousands of dollars per hour. "So we got to this point where we were just goofing off, talking, and it was like, 'It's eleven dollars a second for you to say that!'" Wiley recalled of the late night experiments.

The technique the group used is called X-ray pump-probe spectroscopy. The measurement involves "pumping" the sample with a green laser, putting it into an electronic excited state. Then, a pulse of X-ray light, the "probe," comes in, allowing the experimenter to measure the X-ray absorption spectrum of an electronically excited molecule. "These experiments weren't possible a few years ago," notes Wiley.

This area of the laser performs diagnostics on the incoming X-ray beam
before hitting the sample at the far right. Image credit: Laura Kiefer. [enlarge]

SLAC-LCLS technicians had built the experiment preceding the group's arrival based on the specifications of their proposal. Once they arrived, all the group had to do to begin measurements was prepare a sample at a nearby laboratory. That's probably for the best, though, notes Wiley. "It's one of the only two free electron lasers on Earth. They're not going to just let some turkey that doesn't know what they're doing do anything for them."

Even though the experiment was pre-built, the first day still involved a lot of setup in which the group worked closely with technicians. "During the first day, they have to get both the optical beam and the X-ray beam overlapped in space and time," Miller said. The sample, a jet of solution which shoots downwards through the crossed laser beams, has to be positioned very accurately as well; an error of even 10 micrometers, less than the width of a human hair, is enough to ruin the measurement.

The green-themed control room for X-ray pump probe. Each
measurement at SLAC-LCLS is color-coded. "The red was
just obnoxious," said Miller. Image credit: Laura Kiefer

After the first day of setup, the group became much more independent. From 9 to 9 solid, the entire group, professors included, was buzzing in the control room. Miller credits the group's diverse expertise for their success. "[...] It made us a lot stronger while we were there," he said. Some people worked on conducting the measurements, while others, particularly Kubarych and Deb, built computer programs to analyze the data on-the-fly. Without the ability to quickly analyze data, "we would have been lost," said Miller.

At that point, the technicians let the researchers do their thing. "It's actually amazing how much freedom you have. Once things are going, you can do it," said Kiefer.

"It was an exhausting experience," said Wiley. "First of all, you're jet-lagged by three hours by flying to California. Then you invert your sleep schedule and try to sleep during the day." Never mind the four consecutive twelve-hour work days.

Despite the endurance contest, Miller, Kiefer, and Wiley seem to think that their efforts were a success. The proposal contained a strong plan with all sorts of contingencies laid out in case things went wrong or data didn't come out as anticipated. "I think the thing that we didn't think about was, well, what do we do if it goes really well?" said Wiley. "And it did go well," added Miller. "We ended up doing some unexpected experiments on the third and fourth day, and those actually are going to be maybe some of the most significant results that we found."

As if performing cutting-edge science wasn't enough, the three were exposed to some of the most advanced devices on Earth just by walking through the LCLS facility. "Seeing the technology that they have is un-freaking-believable," said Kiefer. Wiley added, "They had the world's [smoothest] surface for x-ray lasers. The [smoothest] surface on Earth, ever made, being kept in a vacuum that's a thousand times lower pressure than outer space."

X-ray pump-probe is just one of the types of measurements that can be conducted at SLAC-LCLS. Overall, there are six different types of experiments available, and a seventh to be added in 2016. With evocative names like Macromolecular Femtosecond Crystallography and Matter in Extreme Conditions, these experiments sit on the fringe of what is possible in experimental science.

Ted Wiley takes a long draw off of the sample
jet depicted on the video monitor. Image credit:
Laura Kiefer

When asked about his favorite part of the experience, Wiley got poetic. "Messing around with all the gizmos, man," he said.

"My favorite part was being at the helm," Miller said, "being in control of the two million-dollar experiment." Kiefer added, "It's pretty amazing that you can be hands-on at this facility."

The group wasn't ready to talk about the scientific results yet, but you'll probably be hearing about them soon. SLAC reported last year that 341 scientific publications have come out of LCLS in the five years between 2009 and 2014. Of those, 31% were published in high-profile journals - not surprising, considering that the measurements available there can only be performed in a few other places on the planet.

Now that the data has been collected and they've settled back in Ann Arbor, Miller, Wiley, and Kiefer talk about their trip with obvious enthusiasm. (Kiefer's library of photos is testament to that as well.) "It's big science," Wiley said. "In every sense of the word."

Chemistry Literature Feature, Vol XI: University of Michigan Edition

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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 celebrate chemistry at the University of Michigan! Keep scrolling to learn about chemical reactions happening high in the clouds, how to teach a bad catalyst to keep itself together for longer, and new developments in small molecule cancer treatments. But first, check out the Chem Lit Feature's newest addition: CLFPic!

This volume's CLFPic comes to us from Aaron Goodman, who graduated from the University of Michigan with a B.S. in chemistry and went on to graduate school at MIT. His photo, taken through a microscope eyepiece, shows flakes of molybdenum disulfide, MoS₂. MoS₂ can be separated into sheets that are only a few atomic layers thick, much in the same way that graphite can be made into graphene. The blue flake in the picture is only 3 atomic layers! Such thin MoS₂, which is a semiconducting material, could find applications in miniaturized electronics or light-emitting diodes.

ICYMS 4: Mirkin and Schatz's Gold Nanoparticle Lattices Mess with Light in New Ways

What do stained glass windows, single molecule sensing, and light-emitting diodes have in common?

Right now, not much. But research from the laboratories of Northwestern University chemists Dr. George Schatz and Dr. Chad Mirkin are trying to change that. Together, they have published several papers on a new breed of nanoparticle superlattices - materials that are turning out to do unique tricks with light. Their research contributes to the field of plasmonics, which encompasses optical phenomena that give stained glass windows their color and could find application in futuristic devices.

"Chasing Molecules" Has a Green Message for Chemists and Consumers

I have synthesized over 2,500 compounds! I have never been taught what makes a chemical toxic! I have no idea what makes a chemical an environmental hazard! I have synthesized over 2,500 compounds! I have no idea what makes a chemical toxic!

Chasing Molecules, xxiii

Elizabeth Grossman, the author of Chasing Molecules: Poisonous Products, Human Health, and the Promise of Green Chemistry (Island Press, 2011), quotes the above from Dr. John Warner, who is the co-founder of the Warner Babcock Institute for Green Chemistry.

Chemistry Buzzword Dictionary

Understanding scientific literature can be hard. Let's face it: scientists, despite all our claims to the contrary, love words. We love making words up and flaunting them about - and bonus points if they're pronouncable acronyms.

Some chemistry words, however, are unnecessarily flashy and find their way into headlines a little too often. Buzzwords can be misleading at worst, and tiresome at best.

If you're trying to understand the chemical literature but keep getting tripped up in the jargon, have no fear. Because I care about you, my dearest readers, I've assembled a list of some of the most common chemistry buzzwords along with clear, concise definitions or, where quotations are used, what the authors probably could have said instead. Armed with this reference, you'll be an unstoppable scientific critic from this point forward.

asymmetric catalysis/reaction: "We spent a lot of money on ligands. A lot."

biomimetic: has the same metal as a protein that does the reaction faster and better than the molecule under study

challenge: something scientists collectively have not figured out yet; what the authors think about to prevent themselves from getting too happy

divergent synthesis: "Turns out you can do more than one reaction on the same molecule!"

(photo)electrochemical: (even more) questionably relevant

elusive: "difficult to make, but come on, that's not our fault."

"from first principles": "We have successfully avoided wet labs since undergrad."

ionic liquid: salts that are liquid at or near room temperature; definitely not a fad

limitation: what happens when physics gets in the way

"mechanistic insight": the next best thing to guessing

nano[noun or adjective]: oh god please publish this

novel: a meaningless adjective

public engagement: Twitter

serendipitous: accidental

synthesis: what the authors do when they're not on Facebook

transformation: seriously just a reaction

ultrafast: The last time the authors came to your party, they just repeated, "I work with a big fancy laser" until they were either unanimously acknowledged as the coolest person in the room or were later found repeating "I work with a big fancy laser" shakily to themselves in a corner with their drink and all of your chips.

I hope that this will serve as a valuable tool for your future forays into the scientific literature. No citations will be necessary; everyone knows that scientists don't really care about their H-indexes.

This article has been submitted to Nature BuzzChem, pending review by its prestigious board of editors.

Chemistry Literature Feature, Vol. X

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

It's the tenth blog-o-versary of the Chemistry Literature Feature! In celebration, here are ten (minus four) cool chemistry papers, one from each of the chemical disciplines. This time, we'll learn what gives the "sea sapphire" its color, see single molecules of proteins stick to a platinum surface, and see a new technique for learning about the fate of photoexcited electrons in an important photocatalyst material.

Don't know what a sea sapphire is? Neither did I!

Analytical - Observation of Single-Protein and DNA Macromolecule Collisions on Ultramicroelectrodes
Chemistry is typically understood "in the ensemble" - that is, a large number of atoms or molecules are observed simultaneously. Recently, particularly in spectroscopic fields, researchers have gone to great lengths to investigate single-molecule systems where ensemble behavior is impossible. The authors of this communication ($) in the Journal of the American Chemical Society designed an experiment where large molecules - proteins, polystyrene beads, and strands of DNA - were placed in solution with an extremely small platinum electrode (linked photo shows a carbon fiber ultramicroelectrode). These "insulating objects" block the flow of electric current from the electrode. The study examines how the size and shape of the objects contribute to the observed changes in the current and paves the way for further investigation into macromolecule behavior in solution via electrochemical methods - without the use of a complicated laser.

Chemical Biology - Structural Basis for the Brilliant Colors of Sapphirinid Copepods
I never thought I would learn of an animal's existence from the Journal of the American Chemical Society, but the authors of this communication ($) took an interest in figuring out what gives color to the sapphirinid copepod. Sappirinid copepods are millimeter-sized animals similar to plankton that inhabit oceans around the globe. The males have crystalline shells that scatter light, creating brilliant flashes of color when the sun hits them just right - an evolutionary adaptation known as "death wish."* The communication explains why different copepods flash different colors. The authors used scanning electron microscopy to examine the crystal sizes in the copepod shells and also the thickness of the liquid cytoplasm layer between the crystal layers, finding that copepods of different colors show differences in the cytoplasm layer thickness rather than crystal size. The variance in spacing between the crystals in the copepod shells gives rise to the observed colors via photonic effects similar to what gives opals their colors.

*: editorial, sort of

Inorganic - A Stable Planar-Chiral N-Heterocyclic Carbene with a 1,1'-Ferrocenediyl Backbone
N-heterocyclic carbenes (NHCs) are some of the most interesting ligands in organometallic chemistry. Sad graduate students have synthesized hundreds of NHCs by varying the size and electronic properties of substituents near the carbene site, and the fruits of these modifications are often made manifest in the catalytic properties of metal-NHC complexes. Traditional NHC ligands are based on a 5-membered imidazole ring. Lately, however, synthetic chemists have explored NHCs with larger rings, showing that straining the bond angles near the carbene increases its reactivity. The authors of this recent paper ($) in Inorganic Chemistry (ACS) perform a thorough investigation of a new series of 6-membered NHCs made chiral by a ferrocene backbone. Their NHC molecule is extremely reactive and is capable reacting with dichloromethane and acetonitrile. The authors go on to characterize the compound electrochemically in preparation for future synthetic work to take advantage of its chirality.

Materials - Fabrication of Self-Cleaning, Reusable Titania Templates for Nanometer and Micrometer Scale Protein Patterning
Biological sensing technologies are becoming smaller and smaller, and nanopatterned arrays created using laser etching methods are emerging to the forefront of miniaturization efforts. Both for research and commercial applications, easily-renewed biosensor arrays are cost-effective and attractive. The authors of this paper ($) in ACS Nano present a method for decorating a titanium dioxide surface with organic groups capable of binding proteins. A separate step makes the rest of the surface inert to proteins, allowing the authors to bind proteins in an array pattern in specific locations on the film. This is supported with fluorescence microscopy, which causes the proteins to light up and determines where they are. The protein-bound film can function as a biosensor. Importantly, though, the authors demonstrate that shining strong ultraviolet light on the film causes the titanium oxide to chew up all the proteins, leaving the film surface free to bind a new set of proteins and create a new biosensor from the recycled surface.


Materials chemistry readers will get an especial kick out of the Chemical Biology article as well.

Organic - Base-Promoted β-C(sp³)-H Functionalization of Enaminones: An Approach to Polysubstituted Pyridines
If you've ever studied or practiced organic chemistry, you know that the reactions can quickly become an excessive soup of starting materials, acids or bases, catalysts, solvents, and additives. In addition to adding up in terms of complexity, all of these reagents contribute to the cost of a reaction, both energetically, monetarily, and environmentally. The group who published this recent paper ($) in the Journal of Organic Chemistry (ACS) has discovered a very simple base-promoted route for joining ynones to ethylamines for the production of pyridine rings. With only two equivalents of base, the two molecules snap together like Legos, then eliminate water to yield the pyridine product. Pyridines are useful throughout organic chemistry, both as structural motifs and also as common binding sites for metals, so a convenient and versatile route (34 pyridines reported!) such as this could be quite useful.

Physical - Chronoabsorptometry To Investigate Conduction-Band-Mediated Electron Transfer in Mesoporoous TiO₂ Thin Films
Photochemical processes - like solar cells, for example - depend on the ability of an excited-state electron to move throughout a material to a site where it can do useful work. However, a bunch of things can happen to it along the way, and simple methods to understand these various processes and, critically, how quickly they happen relative to one another, are in short supply. A new paper ($) in the Journal of Physical Chemistry C (ACS) provides a thorough mathematical introduction to a technique called chronoabsorptometry, in which optical spectroscopy is used to keep track of the state of a probe molecule bound to the surface of the TiO2 under study. The electronic properties of the TiO₂ film are controlled separately by an electrical potential. The authors vary the potential while watching the probe to learn more about how photoexcited electrons move through the film. By matching their results with previously published conclusions from other, more widely-used techniques, the authors are able to verify the validity of their method.

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 (German Chemical Society)
RSC - Royal Society of Chemistry
$ - subscription required to access full text

Winter is Coming: Icy Lab Monitors Toxic Gases in Atmosphere

Congratulations to the winner of the first Tree Town Chemistry photo contest! The photo and the original caption are below. Read to the end of the article to see the runners-up and other entries from this year's contest.

Every day in lab is a winter wonderland. I operate two gas chromatography-mass spectrometers, analyzing ambient air samples for toxic materials. Each system uses almost an entire tank of liquid nitrogen a day to cool the preconcentrator gas traps. The amount of snow and ice formed on the tanks and transfer lines each day are enough to have a full snowball fight, and once a tank is empty, it can take up to 24 hours to melt enough to swap out for a new tank.

Crystals in Chemistry: The How and (Some of) the Why

Welcome to Crystals in Chemistry, Part II. In this installment, we'll talk about how crystals are made and a few of the things that chemists and physicists use them for. For the previous installment, in which we covered some basics about what crystals are and how they form defects, click here.

A few of Dr. David Chow's crystallization reactions in the Pecoraro lab.
For puzzling out crystallization conditions, quantity equals quality.

One of the most painstaking parts of being an inorganic chemist is crystallization. When it comes time in your research to crystallize a new compound so you can study its structure, that task becomes the dark beast lurking in your lab that you have to think about facing every day. Crystallizations are difficult because the conditions for growing high-quality crystals are not always obvious.

It's Time to Face Your Fear of Scorpionates

Scorpions.

The little arachnids are one of the most recognizable members of the animal kingdom. Just reading the word conjures images - perhaps of monsters with fangs and spines dripping with venom, perhaps of a household pe(s)t, perhaps of Dwayne Johnson. No matter the association, the scorpion is an iconic figure.

For inorganic chemists, scorpions are associated with a broad class of metal-organic complexes with a unique molecular shape. These molecules are called scorpionates.

Chemistry Literature Feature, Vol. IX

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

Overheard at Michigan: Snapchat Edition

These results not sponsored by Dell, but I can't
really understand why.

Once again, it's time to look at six cool papers from five cool fields and also organic chemistry! In this ninth episode of the Chemistry Literature Feature, we'll take a look at a paper that pulls the old bait-and-switch on drug-resistant cancers, a one-step experimental verification of some really old kinetics thinking, and a new look at how frustrated Lewis pairs catalyze hydrogen activation. But first, at your left, a simulation gone horribly wrong!

Crystals in Chemistry: Wait, What?

This is the first in a multi-part post about crystals in chemistry. Stay tuned for more!

I have been spending a lot of time on crystallizations lately. (Read: I have been a very sad chemist lately.) Last week, as I was hanging dejectedly out of the glove box like some shamed medieval peasant, peering into impossibly dark solutions looking for the smallest sign of a crystal, it occurred to me that these little nuggets of perfection might be the kind of thing that people want to read about.

What are crystals? Why do chemists care about them so much? Why am I trying so hard to make one? How are they made, and what do we do with them after we have them? For all this and more, read on.

Crystals - Not (Exactly) Magic

Whether you know it or not, you've seen a crystal in your lifetime. The salt and sugar in your kitchen, gemstones in jewelry, and the tip of Gandalf's staff are all crystalline materials. But not all crystals are shiny, pretty things. The solar cell in your high school calculator was probably a crystal. Metals, drugs, and all kinds of other things can form crystals.

Let's start with a definition. A crystal is a collection of atoms, ions, or molecules that comes together

The crystal structure of sodium chloride, called the "rock salt"
structure (rather appropriately).

to form a regular, repeating pattern in three-dimensional space. Crystals are most frequently made out of small species like atoms or molecules, such as is the case with diamonds (crystalline carbon). However, some fields of science have labored painstakingly to produce crystals of much larger species like proteins and an entire ribosome.

Sodium chloride, table salt, has a fairly simple crystal structure, shown here at the right. The red cube shows the smallest repeating unit of the crystal, called the unit cell. The entire crystal, no matter how big it gets, is just many copies of this tiny unit cell stacked over and over and over again in three dimensions.

Crystals form because they force their constituent atoms or molecules to pack in as closely and as tightly as possible to one another. The extended network of bonds gives the crystal extraordinary stability. We'll talk more about crystal formation in another installment.

Red crystals of an iron phenanthroline complex prepared
by my labmate Kayla. Crystals containing transition metals
like iron are often brightly colored.

Damn It, Entropy! This Is Why We Can't Have Nice Things!

Of course, the packing isn't always 100% perfect. By the second law of thermodynamics, processes that increase entropy are favored. Crystals, with their regular packing and rigid bonds, are not very entropic, so defects form readily and increase the crystal's overall entropy.

There are many different ways a crystal can be imperfect or defective. Atoms or groups of atoms can switch places, get swapped out for other atoms, or be missing entirely. Another defect that can appear in crystals is the grain boundary. A grain boundary is a line usually formed when two crystals fuse together to become part of the same particle, or when a crystal changes orientation during growth.

This means that a single particle of a given material can be composed of more than one grain, also called a crystalline domain. In the case where each particle of a material is composed of only one crystalline domain, we call the material a single crystal. In the other case, where each particle of a material is composed of several crystalline domains all stuck together, we call the material polycrystalline. If a material has totally random ordering at the molecular level, it is called amorphous

Needle-like crystals of tetrabutylammonium
hexafluorophosphate. These crystals have poor clarity and
are probably polycrystalline - lots of grain boundaries.

One Grain or Many?

Outside of the analytical world, both single crystalline and polycrystalline materials have important uses. Generally speaking, single crystalline materials are more conductive of heat and electricity because heat and electricity both have a hard time transferring through grain boundaries. That's why solar cells are often made from highly crystalline silicon wafers.

Polycrystalline materials, on the other hand, tend to respond better to stress and strain than single crystals. The grain boundaries stop the spread of dislocations and other signs of stress that eventually end in material failure. The bones in your body and metal support beams for buildings are both polycrystalline; a single crystalline material would be far too brittle.

Get Ready to Go Deeper...

We've only scratched the surface of the properties of crystals and what they can do for scientists. Next time, we'll talk about techniques used by lab workers for crystal growth, both in research and in industry.

Chemistry Literature Feature, Vol. VIII

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

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

Overheard at Michigan

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Ion Activation: Splitting Salts to Increase Reactivity

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

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

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

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

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

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

All According to Plan

Bijay Bhattarai, the paper's first author.

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

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

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

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

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

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

Faculty Panel Gives Advice for Grad Students Seeking Academic Postdocs

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Last week at the University of Michigan, the department's Chemistry Professional Development Organization (CPDO) organized a seminar called "Ascending the Summit: How to Make the Best Postdoc Application and Interview." The goal of the seminar was to prepare current graduate students in chemistry for the process of landing a postdoctoral position after graduation.

Viewed by many as a stepping stone to a faculty position, a postdoctoral fellowship allows a newly-minted doctorate to stretch their legs and apply themselves in a new research lab, sometimes dedicated to drastically different research. Choosing where to do a postdoc, figuring out which research labs to approach, and getting hired are often critical steps for a chemistry graduate looking to continue along an academic career track.

The seminar was composed of a faculty panel of four chemistry professors, ranging in experience from the newly-hired Professor Corinna Schindler ([bio]organic) to Professor Carol Fierke (chemical biology), who has served as chair of the department since 2005. The panel was rounded out by Professors Nicolai Lehnert ([bio]inorganic) and Brandon Ruotolo (analytical/chemical biology). CPDO presented a list of questions compiled from suggestions by seminar registrants. Once the room settled down, it was off to the races.

The following is a summary of the seminar, which was dense with good advice and important information. Use the list below to jump to the question that interests you most, or read the whole post top-to-bottom. And when you finish, feel free to leave a comment! Many of these questions are open-ended, and more voices answering means more perspective for everyone reading.

Q1: When hiring a postdoc for your own lab, what do you look for?
Q2: Do you have a preference as to whether your potential postdoc wants to end up in academia or industry?
Q3: How much involvement do you expect postdocs to have? What role do you typically expect them to play?
Q4: In transitioning from graduate studies to postdoctoral research, how much of a change should you make in terms of entering a new field?
Q5: How involved do you expect postdocs to be in the teaching process?
Q6: How long is too long for a postdoc?
Q7: What should a postdoc do as far as procuring their own funding?
Q8: As a graduate student, how early is too early to start lining up a postdoctoral position?
Q9: How much independence does a postdoc have to pursue new ideas/discoveries (perhaps off the path of the grant)?
Q10: Are there disadvantages inherent to doing a postdoc outside of the USA if your Ph. D research was conducted there, or vice versa?

Q1: When hiring a postdoc for your own lab, what do you look for?
The panel's responses to this question dealt mostly with the way in which a postdoc's application was presented. "Make your email exciting to the PI," said Professor Ruotolo. The panel agreed that the onus was on the potential postdoc to make plain what they were going to add to the PI's lab, regardless of the postdoc's field of origin. These ideas would be fleshed out more in the fourth question.

Other suggestions during this discussion came from Professor Schindler, who suggested sending a paper letter along with an electronic application to the PI of interest. For Schindler, the tangible paper letter makes a postdoc application a little more difficult to forget, increasing the applicant's chances of landing an interview. Professor Fierke also stressed that postdocs would do well to meet their prospective PIs in person at conferences or seminars. Additionally, a letter of reference from the postdoc's previous advisor goes a lot further when both the previous advisor and the prospective advisor are in good contact.
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Q2: Do you have a preference as to whether your potential postdoc wants to end up in academia or industry?
Discussion on this point was very concise, with the panel members agreeing that from the perspective of a PI, the postdoc's future plans were not very relevant. However, Professor Ruotolo stressed the importance of potential postdocs considering how taking on a postdoctoral fellowship will benefit their careers. In some industries, such as pharmaceuticals, having done a postdoc can give you an edge in landing what is sure to be a competitive position. However, in other industries, the experience may carry less weight (or none at all).
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Q3: How much involvement do you expect postdocs to have? What role do you typically expect them to play?
As could be expected, different professors on the panel had different ideas about how to answer this question. Professor Fierke expects postdocs to bring maturity and scientific perspective to her group, but does not expect postdocs to be responsible for directly mentoring graduate students. Professor Ruotolo agreed, noting that he prefers a "flat architecture" for intellectual hierarchy in his lab.

Professor Lehnert offered a contrasting opinion. He expects postdocs to take on direct leadership roles, contribute to grants, and develop management skills. His view is that the postdoctoral experience is a critical intermediate step between ending one's career as a graduate student and beginning one's career as an independent principal investigator. Even if a postdoc comes to his lab from a different field and does not know how to do a certain reaction, for example, the postdoc's broader experience as a researcher allows them to learn and troubleshoot the reaction faster than a graduate student.
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Q4: In transitioning from graduate studies to postdoctoral research, how much of a change should you make in terms of entering a new field?
Professor Lehnert jumped on this question. He advised researchers seeking postdocs to primarily look for something that they're really excited about. He acknowledged that getting a position might be harder the further a postdoc moves from their original field of research, but said, "You just have to get the interview. Once you get the interview, everything changes."

The panel also reiterated (as in Q2) that it is critical for postdocs to consider how taking a particular position will set them up for the next step of their career. For postdocs considering branching out, the options are many, so careful decision-making is critical.

A4, C. Fierke: There are so many directions, and the more u know what you want, the more you'll be able to make sure u get the right skills.
— Tree Town Chemistry (@treetownchem) January 12, 2015

Q5: How involved do you expect postdocs to be in the teaching process?
The panel agreed that they prefer postdocs to be uninvolved in teaching. Postdocs are typically hired as researchers, so PIs want to maximize the benefit of their hire by maximizing the time available for research. However, if a postdoc is interested in getting more teaching experience, perhaps in preparation for applying for a job at a primarily undergraduate institution, then that can be made to happen as well. Again, though, the onus is on the postdoc to shape their own experiences in preparation for the professional future they envision for themselves.
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Q6: How long is too long for a postdoc?
"This is probably going to be very discipline-specific," said Professor Ruotolo. His own postdoc was 4 years. At the outset, he had expected it to be shorter, but "there are lots of things that can complicate timelines for postdocs." He stressed that the most important thing is for postdocs to leave having accomplished something. If it takes an honest 4 or 5 years for a promising project to pan out, and if the funding holds up, there is nothing wrong with that.

Professor Schindler noted that postdocs in organic chemistry are significantly shorter. She looks for postdocs with the expectation that they will work for a year with the option to renew their contract after that year, with a two-year average.
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Q7: What should a postdoc do as far as procuring their own funding?
None of the four panel members expected postdocs to be able to arrive at the job with funding. It requires an unrealistic amount of anticipation to think that a postdoctoral researcher will know where they will end up and what they will be working on early enough in advance to secure an appropriate grant. However, all of the panel members voiced expectations that postdocs will contribute to grant applications to help renew or procure new funding for the laboratory.
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Q8: How early is too early to line up a postdoc as a graduate student?
Between six months and a year from the potential postdoc's projected graduation date was acknowledged as the ideal time to look for and lock down a postdoctoral position. Any earlier than that, and it becomes uncertain whether a project will still be funded by the time a postdoc arrives. (Professor Fierke, the most experienced member of the panel, noted that the one year maximum is an unfortunate consequence of recent changes in the funding climate.) Any later, and job applications get jumbled up with thesis requirements, which can make for a hectic, stressful, and ultimately less effective final semester.
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Q9: How much independence does a postdoc have to pursue new ideas/discoveries (perhaps off the path of the grant)?
The panel members had somewhat differing opinions on this subject. Professor Ruotolo jumped at the question, explaining that the postdoctoral phase is one of the best times for researchers to explore "lateral space" in science. In his lab, exploration of new discoveries is met with excitement and encouragement. However, Professor Lehnert pointed out that this kind of creativity is limited by the money, and that he would ask postdocs to find a balance between pursuing new ideas and ensuring that enough progress is made on established projects to keep the funding coming in. At the end of the day, primary investigators have to get their grants renewed to keep the lab running, and postdocs have to be part of that.

Professor Fierke stressed the importance of having a conversation with the PI about how much of the research a potential postdoc will be able to take with them, and having that conversation as early as possible. Particularly if the postdoc wants to seek an independent research position at a high-level institution such as an R1 school, tensions can arise when a postdoc comes across an idea that they might use to found their own lab, but the postdoc's PI wants to hold onto it. The best way to avoid that tension is to communicate clearly, early, and often.
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Q10: Are there disadvantages inherent to doing a postdoc outside of the USA if your Ph. D research was conducted there, or vice versa?
Professor Ruotolo, whose postdoctoral research was conducted at the University of Cambridge in the United Kingdom, was very enthusiastic about recommending that students considering postdocs outside of their country of origin at least try to make it happen. Ruotolo's advisors in the United States were worried that he would have a difficult time getting a job back in the USA if he took a postdoc position at Cambridge due to the lack of a strong network. To remedy that concern, Ruotolo recommended that students seeking postdocs in other countries look at their potential PI's track record for placing researchers in jobs, whether the students are interested in working back in their country of origin or in the foreign country in which they want to do their postdoc. "The advantages of trying far outweigh the disadvantages," he said.

Professor Schindler echoed his sentiments and added some of her own. She recommended that students looking to transition from the USA to elsewhere in the world specifically seek out postdoc advisors with strong ties to the USA. As with any career search, networking plays a big role, and the stronger the network overlap is on either side of the ocean (Atlantic or Pacific), the easier the career search will be.
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The Conversation Continues
The CPDO seminar was very motivating and contained great advice for graduate students starting their postdoc searches or considering whether to postdoc at all. However, this seminar just scratches the surface of the conversation happening now in chemistry on postdoctoral researchers, tenure-track faculty, and the job climate for newly-minted chemistry doctorates in general. As with a new research project, there is a wealth of information out there, and it falls to us as students to find it, process it, and use it to make the best choices we can. Of course, seminars like "Ascending the Summit" are great places for that research to start.

For more perspective on this issue, you might start with this post from Chemistry Blog, this post from Prof-Like Substance, and another post here (and linked posts) from Anna Armitage. Update 2/3: I found another good article at ACS Graduate & Postdoctoral Chemist.

Was this information useful to you? Does it contradict your own advice or experience? The comment section is wide open for further discussion on this important topic!

Chemistry Literature Feature Vol. VII

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

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

Overheard at Michigan:

"I mean, there's a lot to take in here. This is the first time that I've had to think about what a volt actually is."

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

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

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

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

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

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

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

Physical chemistry readers may also like the Inorganic chemistry paper.

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

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