Notes Toward a User's Guide to Synthetic Chemistry Talks

Reading Dylan Stiles's blog yesterday reminded me of a post I wrote last summer about how to approach student talks about synthetic chemistry. Since evil spammers have forced us to turn off comments to the old site, I'll reproduce the original below the fold:

Summer days are here again, which means the return of the
annual summer student research seminar. There's a local tradition
of having all the students doing on-campus research give 15-minute
talks to all the other summer students. In principle, I think this
is a very good idea, as it gives the students some practice at
public speaking, and can help form some sense of community among
the sciences.

In practice, I'm less happy about it, because I wind up sitting
through a lot of nearly incomprehensible talks, most of them
dealing with the synthesis of some molecule or another. Over the
past several years, I've slowly begun to develop an understanding
of how to interpret these talks, but the students who are new to
summer research are completely at sea. This has a tendency to make
them sort of cynical about the whole business, and undercut the
very sense of community that the talks are supposed to be

Anyway, the following is a somewhat flippant summary of my
conclusions about synthetic chemistry talks by way of (not
entirely serious) guidance for non-chemistry students attending
these talks.

Recognizing a Synthetic Chemistry Talk

There's no foolproof way to know for sure what you're in for
(though the word "synthesis" in the title is a dead giveaway), but
knowing some key classes of words can help you spot talks that are
likely to be about chemical synthesis. Various "-tion" words
("methylation," "intercalation," "purification") are pretty good
markers, though they occasionally show up in molecular biology
talks as well. Active verbs are likewise a hint.

A good rule of thumb might be: If there's more than one word in
the title that you're not sure how to pronounce, odds are good it
will deal with chemical synthesis.

The Four Stages of Synthetic Chemistry Talks

These talks always follow the same basic form, and can be
broken down into four stages:

Stage One: "Here's this thing we're trying to
make." This is usually accompanied by a picture consisting of a
bunch of hexagons, and maybe a ribbon diagram or some other
three-dimensional model. Stage One will occasionally include an
explanation of why they're trying to make
whatever the thing is, but don't count on it.

Stage Two: "Here's the stuff we start with."
This will include a couple of diagrams showing different
arrangements of hexagons. The jargon will get pretty thick, here,
but almost all the strange words will be names of different parts
and sub-parts of molecules. See the "Guide to Jargon" below.

Stage Three: "Here are the steps in the
process." This will include at least one slide showing multiple
diagrams of hexagons, with arrows between them. The jargon will
again be pretty thick, but here, all the strange words will refer
to methods of sticking pieces of molecules together. See the
"Guide to Jargon" below.

Stage Four: "Here are some graphs to prove we
ended up what we wanted." This is the stage with the greatest
variety of slides. Data graphs may include (but are not limited
to) pictures of chart recorder traces, blobby photographs of
electrophoresis gels, or pictures of pencil marks made on
chromatography films. You'll also get the occasional bar graph or
scatter plot.

If you listen carefully, you can easily identify these four

Guide to Jargon

The key here is, don't sweat the details. The confusing jargon
terms all break down into two categories:

Pieces of Molecules: Words like "ligand" and
"R-group" and "imidazole" and "aromatic ring" all refer to pieces
of molecules. These are things that need to be stuck to other
things in order to get to the end final product. These usually
occur in Stage 2.

You might find it helpful to construct a mental look-up table
mapping chemical terms to bits of apparatus:

"Benzene Ring" ⇒ "Vacuum Chamber"
"R-Group" ⇒
"Ion Pump"
"Ligand" ⇒ "Vacuum Window"

And so forth. Every time you hear a new term, assign it the
name of another piece of apparatus.

Assembly Methods: Words like "Grignard
reaction" or "ligand exchange" or "catalysis" refer to different
methods for getting the various pieces of molecules to stick to
one another, and indicate that you're reached Stage 3. Think of
these terms as different tools used to connect the bits of

You might find it helpful to construct a look-up table as you
go along:

"Grignard Reaction" ⇒ "Pipe
"Ligand Exchage" ⇒ "Phillips-Head
"Catalysis" ⇒ "Five-Minute Epoxy"

And so forth. Every time you hear a new term,
assign it the name of a new tool.

Using these tables, you can easily translate sentences like "We
attach the imidazole to the aromatic ring with a Grignard
reaction" into "We bolted the ion gauge onto the vacuum chamber
with a pipe wrench." The resulting constructions might not
actually make sense in experimental-physics terms, but it will get
you the basic idea.

The key thing to remember here is that this information is not
at all essential unless you plan to replicate the experiment.
Hence the analogy: the fact that you bolted the ion gauge to the
vacuum chamber is absolutely critical; the fact that you did it
with a pipe wrench is really interesting only to specialists.

Guide to Data Plots

The key to interpreting the data plots is that they always come
in pairs (at least). There will be one picture showing the signal
from the initial reactants, which will consist of a set of peaks,
or little photographic blobs, or pencil marks. Then there will be
a second set, showing the signal from the same method applied to
the products of the reaction. This will be a different set of
peaks, blobs, or pencil marks.

The entire point of this section of the talk is to note that
the peaks, blobs, or pencil marks in the second picture are in
different places than the peaks, blobs, or pencil marks in the
first picture. Success is defined as the disappearance of the
peaks, blobs, or pencil marks corresponding to the reactants, and
the appearance of the peaks, blobs, or pencil marks corresponding
to the products.

Peaks, blobs, or pencil marks that are in the same places in
both pictures are invariably due to solvents. The speaker will
often pretend that these don't exist. Humor them.

Guide to Questions

There are innumerable questions of the form "Why did you use
that reaction, rather than this reaction?" that can be asked, and
probably will be asked by somebody. These are functionally
equivalent to "Why did you use a pipe wrench for that? Wouldn't a
socket wrench be easier?" The answers will be really technical,
and you probably won't understand them, but if you keep the tool
analogy in mind, you'll at least have a sense of what's going on.

If you absolutely need to ask a question,
remember that the crucial figure of merit for these talks is the
"yield," which basically means "How much product do you get for a
given volume of reactant?" If the speaker hasn't mentioned the
yield specifically, you can't go wrong asking "What's the yield

If they have stated the yield, ask "How does the yield stack up
against other methods of producing this stuff?"

If they have stated the yield, and compared it to existing
methods, and you still feel a need to ask a question, ask about
the solvent peaks/ blobs/ pencil marks.

Questions of the form "Why are you trying to make this stuff in
the first place?" are usually considered unsporting.

(Of course, similar guides could easily be prepared for various
categories of physics talks (as I remarked to some peope at the
Gordon Conference, the Generic Quantum Information Question is
either "What about scalability?" or "What about the decoherence
rates?"). Offended academic chemists should feel free to retaliate
with snarky physics guides.)

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Well, one common element for any physics talk or even a p.chem talk is that there is bound to be some equation or number of equations in the first stage of the talk, then the talk will move into how they investigated a parameter that corresponds to one or more of the variables in the equation(s). A good physics paper or talk will have at least one equation (preferably in tensor notation), at least three x-y plots or even a 3D plot (preferably one that compares theory with experiment), a spectrum of some sort (preferably one that came from homemade equipment that no one will be able to easily reproduce), and if the paper is really cool, a 3D plot in multicolor that has so much information in one plot it would take a physics degree to decipher it all.

In the physicsy talks, I always grin in confusion at the log-log plots and energies in units of eV (rather than the organic-chemist-favored kcal/mol). Photos of experimental apparatus (esp. if they involve vacuum chambers & flanges & diamond windows) are also enjoyable.

(Synthetic organic talks can be deadly -- my usual strategy is to fall asleep after the intro slides. And I have certainly put plenty of people to sleep with polymer chemistry talks, so who am I to talk.)

Questions of the form "Why are you trying to make this stuff in the first place?" are usually considered unsporting.

Dammit! You made me snort my nightcap! Whisky stings when it hits your sinuses...

I am synthetic organic chemist so your post is particularly funny to me - I used to be the perpetrator of this kind of thing and I have sympathy with the victims (of badly presented technical stuff like org synthesis).

A good presentation should be made into a coherent story ("This is what was wanted but things went terribly wrong and and we could not make this intermediate and all kinds of thing were tried and we had to go all the way back to beginnig and re-design the scheme and eventualy we got these impressive yelds/activities/results and as a side deal we found that this encountered complictation is general to this kind of situation but it could be actualy employed to make something else that is also useful, or the trouble can be circumvented by using this nifty protection strategy and this would be usefull to other things too, etc."

It is also important to avoid temptation of Powerpoint Prevarocation.

Many competent people do not learn how to present their research and they end-up giving stupefying presentation even at their job interviews. So, if you become a victim of such a talk at student colloquium, remind yourself that your serve as a necessary practice audience. Better you then them.

By secret milkshake (not verified) on 24 Mar 2006 #permalink

Being a syntheic organic chemist, I'm going to love bomb you and your kind (sounds aggressive, eh?).

William A. Little proposed excitonic high temperature superconductors, [-C(Ph)=(Ph)C-]n

Phys. Rev. A 134 1416 (1964)
Phys. Rev. B 13 4766 (1976)

Little's 1964 PRA paper has been cited 840 times, including 16 times in 2005. There is sustained interest. Ph is phenyl, generic arenes and derivatives; chromophores, fluorophores... Your satiric hexagons are elevated to chickenwire with occasional flashes of color.

Replace Bardeen-Cooper-Shrieffer large mass BCS phonons (quantized lattice vibrations characterized by Debye temperature) with small mass excitons (quantized electron excitation) possessing characteristic energies around 2 eV or 23,000 K. Exciton-mediated electron pairing suggests superconductor critical temperatures exceeding 300 K even with weak coupling. Perhaps. Theory is elegant but experiment is definitive.

The foregoing is for physicists pontificating with tensor indices, groupoids, foliation, simplectic manifolds, and other excuses for not getting a real job. "8^>) Now comes the love...

There exist two straightforward paper syntheses of a broad variety of Little's fully substituted high polymer polyacetylenes. Modeling gives energies varying from -600 kcal/mole to +1200 kcal/mole for 16-mers (32-carbon polyacetylene backbones). Varying backbone hybridization, doping with a terminal carbocation... are interesting.

HyperChem mm+ calculates Little 16-mers (up to about 1500 atoms) to minimized energy in acceptable run times. Negative is good. A single carbon-carbon bond is about -175 kcal/mole. (b. grubbs wasn't kidding about kcal/mole. He enjoyed a 2005 trip to Sweden for diddling them downhill.)

kcal/mole Species
-2.677 benzene
+2.288 isopropenyl benzene
+73.231 32X isopropenyl benzene
+39.997 poly(diphenylacetylene) 16-mer
Little's undoped polymers are helical...
...with distortions possible. Interesting minima are abundant.

Physicists pontificate. Screw that. Benzil costs $(US)0.16/gram. Let's do Little,

benzil + McMurry coupling --> Little
One step, one weekend, so cheap it's off budget. Mechanical stirring or external vortex mixer. Magnetic stir bars might be counterproductive given the Meissner effect.

O=C(Ph)-(Ph)C=O --> [=C(Ph)-(Ph)C=]n
that is Little's [-C(Ph)=(Ph)C-]n (Shift the braketted window one carbon)

ADMET living polymerization is more elegant and useful,

arene aldehyde --> diarenyl benzoin --> diarenyl benzil
diarenyl benzil + Tebbe methylenation --> 2,3-diarenylbutadiene
2,3-diarenylbutadienes + ADMET (probably Schrock, maybe Grubbs) --> Little + ethylene

A chemist could secure tenure for all you physicists. Are ya feelin' lucky? Somebody should look.

Seriously, somebody should look.