New Vistas in Reaction Kinetics

As a holdover from grad school, I still get a little pain in my stomach whenever someone mentions “kinetics studies.” I never had the displeasure of running one myself, but I’ve heard many stories of others’  painful nights camped out at the NMR, running hours-long kinetics runs on slow reactions. And really, not a whole lot has changed with respect to reaction kinetics over the years. Sampling rates have gotten larger, and the repertoire of analytical methods used to follow concentration(s) has grown, but the underlying theory of reaction kinetics has largely remained the same.

Historically, the development of reaction kinetics has been a story of increasing cleverness. At some point, someone figured out that using a reactant in “drowning” concentrations causes its concentration to remain basically constant over the course of the reaction, removing its influence on the reaction rate—and thus was born the “isolation method.” Yet another clever chemist figured out that only initial rates are necessary to determine kinetic orders, provided multiple runs of a reaction are feasible—and thus emerged the “method of initial rates.”

Why stop there? Increasingly complicated mechanisms (especially catalytic mechanisms) have created a demand for ever more clever methods of kinetic study. Plus, technological advancements are pushing the Δt between data points ever smaller and the sizes of data sets ever larger. Concentration versus time data are basically continuous these days (as are rate versus time data), so why not use the entire span of a kinetics run to the best of our ability? A recent article by Blackmond shows just how far this approach can take chemists studying reaction mechanisms. With data for just a couple of cleverly structured reaction runs, one can propose pretty good guesses for reaction mechanisms. Continue reading →


Organic Chemistry Curriculum: A Step in the Right Direction

Alison Flynn’s latest in the Journal of Chemical Education is an instant classic. She describes a redesign of the organic chemistry curriculum at the University of Ottawa that tackles head on the issue of “curved arrows as decorations” that has been well documented by Cooper, Bhattacharyya, and others.

Her approach begins with four units on the basics of organic structure and physical properties, which is standard stuff. An entire unit on reaction mechanisms that precedes the first reaction covered comes next, and this is really the pièce de résistance of the design. Acid-base reactions come next (pretty standard), followed by nucleophilic additions to π electrophiles and electrophilic addition to π electrophiles, including reactions of alkenes and arenes. That’s organic 1. Note the complete absence of substitution and elimination—a huge plus in my opinion!

Organic 2 begins with eliminations and oxidations—love how these two are grouped together, as many oxidations are glorified eliminations. Next come activated π nucleophiles (enols and enolates), π electrophiles with a leaving group (e.g., acid chlorides), and π electrophiles with a “hidden” leaving group (e.g., imine formation). Seems a little odd to loop back to carbonyl chemistry at the end of organic 2 after hitting nucleophilic addition to carbonyls near the beginning of organic 1, but let’s not allow “we’ve always done it this way” to rationalize away the change. Continue reading →

Lone Electron Pairs: Beyond the Rabbit Ears

In chemistry, quantum mechanics and orbital theory often rub up uncomfortably against more naïve bonding theories, such as VSEPR and Lewis structures. For example, VSEPR tends to give the impression that the positions of lone pairs (or better yet, the orientations of filled non-bonding orbitals) are dictated by the number of electronic domains around the atom. Water, then, which has four electronic domains around oxygen—two single bonds and two lone pairs—apparently has lone pairs at 109.5º angles in a plane perpendicular to the H–O–H plane. The carbonyl oxygen, which VSEPR suggests is “really” trigonal, has two “rabbit-ear” lone pairs at 120º angles. These pictures make the lone pairs look equivalent, and helps us slot these structures in mentally with analogous structures, like imines (for the carbonyl) and ammonia (for water).

MO theory suggests that the lone pairs shown are not equivalent.

MO theory suggests that the lone pairs shown are not equivalent.

Yet, MO theory suggests that the lone pairs shown are not in equivalent orbitals! The simplest explanation for water is that the atomic 2p orbital on oxygen perpendicular to the H–O–H plane cannot interact with the 1s orbitals on hydrogen (there’s zero net overlap), so one of the 2p orbitals on oxygen must show up as a non-bonding molecular orbital. But this orbital can only hold two electrons, so the other lone-pair-bearing orbital on oxygen must be a hybrid. In a nutshell, one lone pair is best characterized as a π MO (the pure 2p orbital) while the other is a σ MO. The two lone pairs are not equivalent. As it turns out, this situation holds up even for lone-pair-bearing atoms in larger molecules. The inequivalency holds for both canonical and natural bond orbitals (NBOs), but the paper that inspired this post focuses on the usefulness of NBOs in the correct description. Continue reading →

Make Your Move: Understanding Strategies for Teaching Chemistry

Remember middle-school dances? I have fond memories of the gym floor transforming into a capacitor of sorts, flanked by rows of pubescent boys and girls pressed as far apart from one another as possible. Although a few daring couples would wander out to the dance floor, generally action would happen only when a sufficiently large clique worked up the collective courage to form an awkward dancing circle. Talking to the opposite sex—aptly called “making one’s move”—was positively painful back then.

My teaching career could aptly be described as a series of moments getting incrementally less awkward.

My teaching career could aptly be described as a series of moments getting incrementally less awkward.

Eventually we all get over our fear of the opposite sex (or the same sex, if that’s your gig) for the most part and move on with our lives. For me, that process of building up a solid conversational repertoire and comfort in my own skin took years. Imagine how a teacher feels, who must use his or her conversational skills and set of “moves” to help a new crop of students learn a complex topic in the matter of a semester! It can be just as painful to watch a teacher barking at a disengaged student as it is to watch middle schoolers blow it at a dance. And yes, it can be just as awkward and gut wrenching when you’re the teacher doing the barking (or the middle-school dancer failing hard with your crush).

How do teachers decide what to say? How can we distinguish good moves from bad? What are the motives behind different types of moves? I was reminded of these questions while reading an excellent J. Chem. Educ. article last week. Warfa and co-workers studied the moves used by teachers in a POGIL classroom—where new norms for teaching and learning can make both students and teachers uneasy. They categorized teachers’ moves according to whether the move occurred in a monologic or dialogic context. Monologic discourse involves a one-way transfer of information from teacher to student, with little to no student input (think Hamlet’s “to be or not to be”). Dialogic discourse, on the other hand, involves a social dimension and sharing of ideas between teacher and student (think Socrates). Both types of discourse are important in the chemistry classroom, but figuring out the proper balance to meet the needs of students in a particular classroom environment is tricky. Continue reading →

S**t My Undergrads Say

I’m very fond of “ranking problems” that ask students to order a series of compounds in some way and provide an explanation. One of my all-time favorites is the famous “rank these acids from most to least acidic…” problem, which might include compounds like the following.

Rank the compounds shown from most to least acidic. Explain your response.

Rank the compounds shown from most to least acidic. Explain your response.

To really understand a problem like this deeply, the student has to be able to connect the structures provided with either physical/chemical properties or theoretical constructs (such as electron-donating and electron-withdrawing groups). Structure-property relationships are at the root of the appropriate thinking here. Unfortunately, as was pointed out by a recent paper that caught my attention in J. Res. Sci. Teach., students often struggle with structure-property relationships. Without experience under one’s belt, the incredible utility packed into a Lewis structure can be lost on students. It’s staggering, really—what other devices in science approach the information density of a chemical structure?! Continue reading →

Should Hybrid Orbitals Sell the Farm and Move to Florida?

Should hybrid atomic orbitals be placed alongside ancient scientific misconceptions like phlogiston?An interesting controversy has emerged in the Journal of Chemical Education this month, following a paper by Grushow calling for the retirement of the hybrid orbital concept from the chemistry curriculum. The flurry of rebuttals that followed Grushow’s letter are an excellent summary of current thought about the relationship between canonical, delocalized molecular orbitals and localized MOs. The latter, although derived qualitatively from hybrid atomic orbitals, are just as legitimate as the canonical MOs that result from traditional quantum chemical calculations. A wonderful description of the idea with just the right amount of math has been provided by Hilberty, Volatron, and Shaik.

An important point of almost all of the rebuttals is that the traditional photoelectron spectroscopy argument in support of canonical MOs (and arguing against localized MOs) is totally bogus. I mention this particular aspect of the debate because I learned something myself! The traditional argument goes that because methane possesses two different ionization energies, its filled MOs must sit at two different energy levels. The two different ionization energies observed are the result of pulling an electron from MOs of two different energies. Hilberty et al. and DeKock + Strickwerda both point out that localized MO theory may be used with success to explain the two different ionization energies—and that the premises of those who claim otherwise are false. From Hilberty:

The reasoning of those people eager to retire the LMO model, is as follows: since the [Hybrid Atomic Orbital] model puts four electron pairs into four equivalent localized orbitals…then extracting an electron from anyone of these four orbitals should always cost the same energy, leading to a single unique ionization potential (IP). The error in this reasoning is simple: it completely ignores the quantum mechanical requirement that any wave function must match the symmetry of the molecule.

Hilberty goes on to illustrate that when the localized MO approach is applied to this problem, although the filled MOs of CH4 all reside at the same energy, the MOs of ionized CH4+ must bear two different symmetries and sit at two different energies. Hence, two ionization energies should be expected on the localized MO model as well. Continue reading →

Deslauriers, Schelew, and Wieman vs. “Hard Science”

Science education is the angsty teenager of the scientific research field. Assaulted on all sides with strict demands from the “patriarchal” hard sciences, education research holds its ground by echoing cries of “you don’t understand me!” and basing its claims on past literature, much of which was probably subject to the same criticisms that present-day educational research is! Where does the vicious cycle end?

A little background first—as regular readers of my blog may be vaguely aware (assuming these “readers” exist), Science has begun to include science education studies in its pages lately. This is a very good thing. Not only does it put important research in the spotlight, it also attracts science educators to the journal, and an army of science educators who read Science is much better than one that does not! A recent educational research paper by Deslauriers, Schelew, and Wieman published in the pages of Science made some sweeping claims about improved learning in a large physics class thanks to a course intervention based on the idea of “deliberate practice.” Exam scores and attendance were both higher in the section that used deliberate practice; the “old school” section’s scores and attendance were lower. The sections were “matched” using several metrics, including the Brief Electricity and Magnetism Assessment and Colorado Learning Attitudes about Science Survey. Matched sections, differing only in the presence or absence of deliberate practice…everything seems peachy, right?

Not according to Derting et al. and Torgerson, who both wrote letters to Science criticizing the study. The bulk of Torgerson’s argument is that the study is not properly controlled, and does not take into account teacher effects (maybe the control group teacher just sucks in general, in addition to using “bad, old school” methods), selection bias, whether students knew they were being treated differently, etc. Derting et al. echo many of these points. One of their more intriguing ideas in common is that, really, the original study is the equivalent of a “single data point,” or a clinical trial involving a single placebo patient and a single treatment patient. Replication, echo the throngs of hard scientists, is needed.

The original authors responded by supplying evidence that their experimental design was good enough to be generalized. Randomized, hyper-controlled trials are not, they claim, necessary in collegiate science courses. Teacher personalities tend to not affect the amount of learning that occurs in collegiate courses (?!). Finally, they raise the point that replications of their experiment may introduce ethical issues, as investigators should expect to replicate their result, which would involve putting the control group at an intrinsic disadvantage.

Where to fall on this debate? It’s tough for me to decide. Both sides advance good arguments. Theoretical ideas and educational psychology research do support the practices used by the experimental section from the original paper. It would have been very bad if the authors’ results had not supported this existing literature, and what they did was almost certainly good from an educational perspective. However, like a sparrow sitting on a giant’s shoulder, the work does little to advance the field of physics education. There are some very subtle issues at play in the classroom, not all of which can be addressed by sweeping labels like “deliberate practice” and even “active learning.” Practical ideas that real educators can take away are hard to find in the paper, and that lowers its value. It’s a shame, because one can tell that their hearts are in it, but the long-term usefulness of the work just doesn’t stand up to scrutiny! The most valuable literature in education (at least to me) has always been the stuff with the most practical value. This paper will at best fade away and be remembered as little more than a blip on the radar—and at worst have a negative effect on the practicing scientist’s view of education research.