{"id":138,"date":"2006-03-24T15:19:55","date_gmt":"2006-03-24T15:19:55","guid":{"rendered":"http:\/\/scienceblogs.com\/principles\/2006\/03\/24\/notes-toward-a-users-guide-to\/"},"modified":"2006-03-24T15:19:55","modified_gmt":"2006-03-24T15:19:55","slug":"notes-toward-a-users-guide-to","status":"publish","type":"post","link":"http:\/\/chadorzel.com\/principles\/2006\/03\/24\/notes-toward-a-users-guide-to\/","title":{"rendered":"Notes Toward a User’s Guide to Synthetic Chemistry Talks"},"content":{"rendered":"

Reading Dylan Stiles’s blog<\/a> 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:
\n<\/p>\n

Summer days are here again, which means the return of the
\nannual summer student research seminar. There’s a local tradition
\nof having all the students doing on-campus research give 15-minute
\ntalks to all the other summer students. In principle, I think this
\nis a very good idea, as it gives the students some practice at
\npublic speaking, and can help form some sense of community among
\nthe sciences.<\/p>\n

In practice, I’m less happy about it, because I wind up sitting
\nthrough a lot of nearly incomprehensible talks, most of them
\ndealing with the synthesis of some molecule or another. Over the
\npast several years, I’ve slowly begun to develop an understanding
\nof how to interpret these talks, but the students who are new to
\nsummer research are completely at sea. This has a tendency to make
\nthem sort of cynical about the whole business, and undercut the
\nvery sense of community that the talks are supposed to be
\nbuilding.<\/p>\n

Anyway, the following is a somewhat flippant summary of my
\nconclusions about synthetic chemistry talks by way of (not
\nentirely serious) guidance for non-chemistry students attending
\nthese talks.<\/p>\n

Recognizing a Synthetic Chemistry Talk<\/strong><\/p>\n

There’s no foolproof way to know for sure what you’re in for
\n(though the word “synthesis” in the title is a dead giveaway), but
\nknowing some key classes of words can help you spot talks that are
\nlikely to be about chemical synthesis. Various “-tion” words
\n(“methylation,” “intercalation,” “purification”) are pretty good
\nmarkers, though they occasionally show up in molecular biology
\ntalks as well. Active verbs are likewise a hint.<\/p>\n

A good rule of thumb might be: If there’s more than one word in
\nthe title that you’re not sure how to pronounce, odds are good it
\nwill deal with chemical synthesis.<\/p>\n

The Four Stages of Synthetic Chemistry Talks<\/strong><\/p>\n

These talks always follow the same basic form, and can be
\nbroken down into four stages:<\/p>\n

Stage One<\/strong>: “Here’s this thing we’re trying to
\nmake.” This is usually accompanied by a picture consisting of a
\nbunch of hexagons, and maybe a ribbon diagram or some other
\nthree-dimensional model. Stage One will occasionally include an
\nexplanation of why<\/strong> they’re trying to make
\nwhatever the thing is, but don’t count on it.<\/p>\n

Stage Two<\/strong>: “Here’s the stuff we start with.”
\nThis will include a couple of diagrams showing different
\narrangements of hexagons. The jargon will get pretty thick, here,
\nbut almost all the strange words will be names of different parts
\nand sub-parts of molecules. See the “Guide to Jargon” below.<\/p>\n

Stage Three<\/strong>: “Here are the steps in the
\nprocess.” This will include at least one slide showing multiple
\ndiagrams of hexagons, with arrows between them. The jargon will
\nagain be pretty thick, but here, all the strange words will refer
\nto methods of sticking pieces of molecules together. See the
\n“Guide to Jargon” below.<\/p>\n

Stage Four<\/strong>: “Here are some graphs to prove we
\nended up what we wanted.” This is the stage with the greatest
\nvariety of slides. Data graphs may include (but are not limited
\nto) pictures of chart recorder traces, blobby photographs of
\nelectrophoresis gels, or pictures of pencil marks made on
\nchromatography films. You’ll also get the occasional bar graph or
\nscatter plot.<\/p>\n

If you listen carefully, you can easily identify these four
\nstages.<\/p>\n

Guide to Jargon<\/strong><\/p>\n

The key here is, don’t sweat the details. The confusing jargon
\nterms all break down into two categories:<\/p>\n

Pieces of Molecules<\/strong>: Words like “ligand” and
\n“R-group” and “imidazole” and “aromatic ring” all refer to pieces
\nof molecules. These are things that need to be stuck to other
\nthings in order to get to the end final product. These usually
\noccur in Stage 2.<\/p>\n

You might find it helpful to construct a mental look-up table
\nmapping chemical terms to bits of apparatus: <\/p>\n

\n

“Benzene Ring” \u21d2 “Vacuum Chamber”
“R-Group” \u21d2
\n“Ion Pump”
“Ligand” \u21d2 “Vacuum Window” <\/p>\n<\/blockquote>\n

And so forth. Every time you hear a new term, assign it the
\nname of another piece of apparatus.<\/p>\n

Assembly Methods<\/strong>: Words like “Grignard
\nreaction” or “ligand exchange” or “catalysis” refer to different
\nmethods for getting the various pieces of molecules to stick to
\none another, and indicate that you’re reached Stage 3. Think of
\nthese terms as different tools used to connect the bits of
\napparatus.<\/p>\n

You might find it helpful to construct a look-up table as you
\ngo along:<\/p>\n

\n

“Grignard Reaction” \u21d2 “Pipe
\nWrench”
“Ligand Exchage” \u21d2 “Phillips-Head
\nScrewdriver”
“Catalysis” \u21d2 “Five-Minute Epoxy”<\/p>\n<\/blockquote>\n

And so forth. Every time you hear a new term,
\nassign it the name of a new tool.<\/p>\n

Using these tables, you can easily translate sentences like “We
\nattach the imidazole to the aromatic ring with a Grignard
\nreaction” into “We bolted the ion gauge onto the vacuum chamber
\nwith a pipe wrench.” The resulting constructions might not
\nactually make sense in experimental-physics terms, but it will get
\nyou the basic idea.<\/p>\n

The key thing to remember here is that this information is not
\nat all essential unless you plan to replicate the experiment.
\nHence the analogy: the fact that you bolted the ion gauge to the
\nvacuum chamber is absolutely critical; the fact that you did it
\nwith a pipe wrench is really interesting only to specialists.<\/p>\n

Guide to Data Plots<\/strong><\/p>\n

The key to interpreting the data plots is that they always come
\nin pairs (at least). There will be one picture showing the signal
\nfrom the initial reactants, which will consist of a set of peaks,
\nor little photographic blobs, or pencil marks. Then there will be
\na second set, showing the signal from the same method applied to
\nthe products of the reaction. This will be a different set of
\npeaks, blobs, or pencil marks.<\/p>\n

The entire point of this section of the talk is to note that
\nthe peaks, blobs, or pencil marks in the second picture are in
\ndifferent places than the peaks, blobs, or pencil marks in the
\nfirst picture. Success is defined as the disappearance of the
\npeaks, blobs, or pencil marks corresponding to the reactants, and
\nthe appearance of the peaks, blobs, or pencil marks corresponding
\nto the products.<\/p>\n

Peaks, blobs, or pencil marks that are in the same places in
\nboth pictures are invariably due to solvents. The speaker will
\noften pretend that these don’t exist. Humor them.<\/p>\n

Guide to Questions<\/strong><\/p>\n

There are innumerable questions of the form “Why did you use
\nthat reaction, rather than this reaction?” that can be asked, and
\nprobably will be asked by somebody. These are functionally
\nequivalent to “Why did you use a pipe wrench for that? Wouldn’t a
\nsocket wrench be easier?” The answers will be really technical,
\nand you probably won’t understand them, but if you keep the tool
\nanalogy in mind, you’ll at least have a sense of what’s going on.<\/p>\n

If you absolutely need to ask<\/strong> a question,
\nremember that the crucial figure of merit for these talks is the
\n“yield,” which basically means “How much product do you get for a
\ngiven volume of reactant?” If the speaker hasn’t mentioned the
\nyield specifically, you can’t go wrong asking “What’s the yield
\nlike?”<\/p>\n

If they have stated the yield, ask “How does the yield stack up
\nagainst other methods of producing this stuff?”<\/p>\n

If they have stated the yield, and compared it to existing
\nmethods, and you still feel a need to ask a question, ask about
\nthe solvent peaks\/ blobs\/ pencil marks.<\/p>\n

Questions of the form “Why are you trying to make this stuff in
\nthe first place?” are usually considered unsporting.<\/p>\n

(Of course, similar guides could easily be prepared for various
\ncategories of physics talks (as I remarked to some peope at the
\nGordon Conference, the Generic Quantum Information Question is
\neither “What about scalability?” or “What about the decoherence
\nrates?”). Offended academic chemists should feel free to retaliate
\nwith snarky physics guides.)<\/p>\n","protected":false},"excerpt":{"rendered":"

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:<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"1","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8,11,24],"tags":[],"class_list":["post-138","post","type-post","status-publish","format-standard","hentry","category-academia","category-science","category-silliness","entry"],"_links":{"self":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts\/138","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/comments?post=138"}],"version-history":[{"count":0,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts\/138\/revisions"}],"wp:attachment":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/media?parent=138"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/categories?post=138"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/tags?post=138"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}