The Awful Chemical Language

I was often asked to explain chemical nomenclature in the context of such and such intellectual property law matter and one day I surprised a trial lawyer — an elderly gent — with my knowledge. He was actually annoyed at first, perhaps because he felt hostage to knowledge which he did not possess. Actually, he probably just resented that I could bill time for knowledge which I already possessed — just like he could. Had he known what it had cost me to acquire my art, he would also have known that it would break any law firm to buy it. Meanwhile, I had been hard at work learning legal terminology for several weeks, and although I had made good progress, it had been accomplished under great difficulty and annoyance. But he was greatly impressed and after I had explained a while, he said my explanation of the chemical language was very rare, possibly "unique" and he wanted to add me to his litigation team.

Friedrich Wöhler, the father of modern organic chemistry, already remarked in 1835:

Organic chemistry just now is enough to drive one mad. It gives me the impression of a primeval forest full of the most remarkable things, a monstrous and boundless thicket, with no way of escape, into which one may well dread to enter.

A person who has not studied chemistry — especially organic chemistry — can form no idea of what a perplexing language describes that thicket. Or perhaps they can, but can come up with no logical explanation for why things are so. I aim here to simplify.

The Germans invented modern organic chemistry and they logically fashioned the nomenclature in their own image — and just as the German language is troublesome for the beginner — having so many parts of speech — it's no wonder organic nomenclature is so troublesome.

An average organic chemical name is a sublime and impressive curiosity; it may occupy several lines and comprise several unfamiliar names and numbers — things called moieties — and even Greek letters; it is built mainly of compound words synthesized by the writer around a core or parent name; it's quite often a word not to be found in any normal dictionary — several words compacted into one, but with joints and seams — that is, with hyphens; it may treat of up to umpteen different subunits, each enclosed in a parenthesis of its own, with here and there extra parentheses which reinclose three or four of the minor parentheses, making pens within pens: finally, all the parentheses and re-parentheses are massed together between a couple of king-parentheses, one of which is placed in the first line of the majestic structure and the other in the middle of the last line of it — after which comes the parent compound name, and you find out for the first time what the molecule is or at least what some chemical lexicographer thought it should be derived from. Sometimes, often as an afterthought — merely by way of differentiation — the writer shovels in the name of a salt, or in patent parlance "or salts thereof," signifying that the delicate molecular flower has been preserved as a salt, and the monument is finished. I suppose that this closing hurrah is often the doing of patent attorneys seeking to claim more broadly; it's not necessary, but covers the doctrine of equivalents.

To repeat, organic chemistry nomenclature was invented by 19th century Germans who wanted to create a simple system which closely mimicked the logic of their own language. Full stop. Therein lies the secret why that nomenclature is so seemingly obtuse — it is patterned after German syntax. In linguistics, syntax refers to the way in which morphemes are arranged. By analogy, "chemical morphemes" are irreducible units of metaphor — core words like "meth-," eth-," "prop-," and "but-" and ringed ones like "phen-" or "benz-" represent chemical entities. [1]  The studied reader may already recognize these morphemes in methane, ethane, propane, butane, phenyl, and benzene and the like. The endings "ane," "yl," and "ene" are, in a linguistic sense, inflections of the morphemes. Another word related to morphemes commonly used by chemists is moiety. Moiety refers to small clusters of recognizable function, for example, "acyl," carboxyl," "alkyl," etc.

By way of example, consider the common pain reliever ibuprofen which more properly goes by the name
RS-2-(4-(2-methylpropyl)phenyl)propanoic acid.

Chemical names are easier to read when you hold them next to the actual structure which is like a pictograph (hold that thought for later) or read them backwards in a mirror or stand on your head — so as to reverse the construction -- but because many refuse to learn the real language of chemistry — structural short hand — I'll muddle through the name of ibuprofen by way of example.  It's not a particularly elaborate molecule or name, but it strikes a nice balance between complexity and simplicity.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

First comes "R,S." The "R" stands for rectus (Latin for right) and the "S" stands for sinister (Latin for left). This gives the enlightened reader notice that chirality is at hand — more on this later.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

The second element in the name is the number 2, and because this number stands alone — outside of parentheses — the reader is asked to hold its meaning in abeyance until such a time as the parent morpheme is finally reached after much exhaustion of patience. Putting the "2" in front resembles the dreaded separable prefix verbs so common to German. Mark Twain wrote in his delightful essay, The Awful German Language:

The Germans have another kind of parenthesis, which they make by splitting a verb in two and putting half of it at the beginning of an exciting chapter and the other half at the end of it. Can any one conceive of anything more confusing than that? These things are called "separable verbs." The German grammar is blistered all over with separable verbs; and the wider the two portions of one of them are spread apart, the better the author of the crime is pleased with his performance.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

The third element, (4-(2-methylpropyl)phenyl) is a microcosm of the whole name writ larger; in it we have a 2-methylpropyl corralled by parentheses, which is itself corralled by "4-" and "phenyl." The name is starting to look like a matryoshka doll.

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

At long last we arrive at the parent morpheme, which like the verb in a German sentence, tells us the key information: propanoic acid. In the lexicographer's mind, ibuprofen is a derivative of propanoic acid.

We have the germanic parenthesis disease in our language, too; also often expressed with em dashes and sometimes elipses and one may see cases of it every day in our books and blog posts: but with us it is — unless botched — the mark and sign of a practiced writer or a clear intellect, whereas with the Germans and chemical lexicographers it is doubtless the mark and sign of a practiced pen and of the presence of that sort of luminous intellectual fog which stands for clearness among these people. For surely it is not clearness — it necessarily can't be clearness.

Now dear reader, allow me to introduce a better way to depict all the foregoing and to illustrate the  foolishness:

Ibuprofen

R,S-2-(4-(2-methylpropyl)phenyl)propanoic acid

I have color-coded the three main parts of the molecule, both in name and in the depiction. The reader immediately grasps that the red propanoic acid portion has a three carbon chain. The red number "2" in the name describes wherefrom the rest depends. The "R,S" refers to the two possible ways that the invisible hydrogen atom attached to carbon 2 may point: either out of or into to the screen or page. The portion circled in light blue is a phenyl moiety having six carbons numbered as shown. The curious reader can attest that the portion in green indeed appends from carbon 4 of the blue phenyl. The left-most portion — circled in green — is the "2-methylpropyl" portion: it's really a 3-carbon propyl chain having a methyl affixed to carbon 2.

Lastly, it is perhaps now apparent (to me at least) where the trivial name ibuprofen comes from: I parse ibuprofen into three separable pieces: ibu/pro/fen

"ibu" is short for "isobutyl (another name for 2-methylpropyl;"
"pro" is short for "propanoic acid;"
"fen" stands for "phenyl."

Have you got a headache yet?
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Suggested further reading:

[1] An Algorithm For Translating Chemical Names To Molecular Formulas
[2] Development Of Systematic Names For The Simple Alkanes

Madonna's Woes and Tramping Abroad

Madonna got into a bit of trouble overseas in France. link  I'm mostly bored with the details and won't go into them. The crowd's reaction reminded me of a Patti Smith concert I saw in Florence, Italy, back in 1979.  Smith really riled the crowd and retired from performing afterwards.

My mother salvaged an old diary I kept on that trip and returned it to me last month. Here's what I said about that concert then.

Martedì 10 settembre [1979]
Rome, Villa Borghese 

Wow what a night last night. I went to the Patti Smith concert at the stadium in Florence. The stadium looked like a huge bathtub. I couldn't believe it when I arrived. It was as if Led Zeppelin were playing. There were people all over 5 hours before the concert began. We waited away from the noisy mob collecting near the gates. I caught some sleep. Then there was a shout--the gates were opening. We made for the nearest gate.
After waiting in the hot noisy crowd (like so many grains of sand all trying to get through the neck of an hourglass) we broke through to the inside and picked ourselves some good seats.
Below it was like pigs to a feeding trough, pushing shoving, shouting, etc. I remember laughing as we watched people scaling the fence around the field track. At the top there was 3 wires of barbwire and some people would get their shirts or pants caught.
Well after some length of time the music began. First it was tapes. Lynyrd Skynyrd "Street Survivors" and then Dire Straits--"Down By The Waterfront."
When the equipment was tested, I thought at first it was just the roadies tuning up stuff, but then they played songs, rock like "You Really Got Me" and then quit--the tapes continued. But when the real band began I realized it was the same musicians.
Patti Smith had a hard time with the audience. First of all she barely knew a word of Italian, only "ti capisc" which she pronounced like "ti capeach."  Secondly the audience couldn't understand a word of English.
She had a problem with people climbing up on the stage--the crowd was absolutely unruly.
"Hey man, you wanna climb the stage, get your own stage, man."
The last song they played was "My Generation."  Before this though the guitarist played the first few notes of the Star Spangled Banner (like Hendrix at Woodstock) and a big American flag came up behind them. Then all the Italians gave it the finger. Then the Who song--then a finale and then chaos; people surged up onto the stage like the pressure of being pushed forward reached a breaking point.
Then "Hey man, get the fuck off the stage" but there was nothing that could be done.
Patti tried to talk with them. "Hey you know" she said to one, "you light up my life." She tried to get him to sit down at the piano "fucking sit down, asshole....how do you say sit down in Italian" she said through 80,000 pairs of ears--but to no avail.
The chaos ended when the road crew swept the undesirables off the stage and then, like a giant bathtub, the moment came when the plug was pulled and it started to drain, not without leaving a residue of paper, cans, and bottles though. So went the concert in Italy.

My own recollection of the same concert, written a year and a half ago from memory is here.
It's interesting for me to compare the two accounts--one fresh and the other filtered by 30 years of  experience and memory.

My All Time Favorite...

...ride at Disneyland: The Mark Twain:

A Tale of Two Picket Fences

Wallace Carothers, American chemist and inventor extraordinaire, had a brief teaching and research appointment at Harvard before leaving to make history at DuPont.  I wrote about him here.  Carothers' mentor at Harvard was Professor E. P. Kohler, a veteran teacher by the time Carothers got there in 1926.  A contemporary of Carothers remembers Kohler:

But after I met him [Kohler]..we sat around listening, waiting for the words of wisdom. He was a bachelor, and he had an old New England house down in some town south of Boston. He had a picket fence around his house, and he talked at great length about what a great thing it was to paint a picket fence. He got enormous joy and satisfaction out of this, and I thought it was awfully stupid. Finally he said, 'The reason this is so wonderful: it's the only thing that I do that has a beginning, has an end, and at anytime I know exactly where I stand.' Twenty years later it finally dawned on me that I'd heard some words of wisdom.' Kohler, now 62, was in his sixteenth year at Harvard when James Conant and Roger Adams presented to Kohler--'the King' he was called--the convincing case for Wallace Carothers as a new Harvard instructor. 

Enough for One Lifetime by Matthew E. Hermes.

Carothers lasted just three semesters before leaving Harvard for DuPont in 1927.  The rest is history. I bring up the story because Professor Kohler's peculiar (and real-life) attitude about fence painting contrasts so starkly with that of the fictional Tom Sawyer, forever captured by Mark Twain:

Tom appeared on the sidewalk with a bucket of whitewash and a long-handled brush. He surveyed the fence, and all gladness left him and a deep melancholy settled down upon his spirit. Thirty yards of board fence nine feet high. Life to him seemed hollow, and existence but a burden. Sighing, he dipped his brush and passed it along the topmost plank; repeated the operation; did it again; compared the insignificant whitewashed streak with the far-reaching continent of unwhitewashed fence, and sat down on a tree-box discouraged.

Of course the guileful Tom goes on to convince his friends to paint the fence for him, and that of course is part of his charm.

What sort of character do we reward in workers and leaders today?  Which traits do we admire in ourselves when faced with such a task?

Letters Home: Greetings From Marktredwitz

A postcard my father sent home during his Army service in Germany 1951-53 (click on the tag "Letters Home" for the whole series):

Click to enlarge. Clockwise from top left: [1] Schlageterstrasse, [2] Kreuzstrasse, [3] Krankenhaus, [4] Schillerstrasse. Note the name Marktredwitz is in the old Fraktur script lettering. The Nazis had a love-hate relationship with that style and ultimately sought to limit its use.

The reverse reads:

July 12, 1953

Hi Mom,

I am spending the weekend in Marktredwitz. I have been swimming twice. I am staying at my girlfriends house. They live in a small rented apartment. I will sign off for now.

Love V.

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[1] Schlageterstrasse was named after Albert Leo Schlageter who was heralded by the Third Reich. Many German streets were renamed Schlageterstrasse or Albert-Leo-Schlageterstrasse during the NS times. After the war, many were subsequently renamed. By 1953, de-nazification had not yet reached the smaller towns.

[2] Kreuzstrasse, which means, I believe, simply Crossroad.

[3] Krankenhaus, literally the "Sick House", or the hospital.

[4] Schillerstrasse was named after Friedrich Schiller, the great German poet and philosopher.

Why The German Language Is So Difficult

From Mark Twain's hilarious essay "The Awful German Language":

An average sentence, in a German newspaper, is a sublime and impressive curiosity; it occupies a quarter of a column; it contains all the ten parts of speech—not in regular order, but mixed; it is built mainly of compound words constructed by the writer on the spot, and not to be found in any dictionary—six or seven words compacted into one, without joint or seam—that is, without hyphens; it treats of fourteen or fifteen different subjects, each inclosed in a parenthesis of its own, with here and there extra parentheses which reinclose three or four of the minor parentheses, making pens within pens: finally, all the parentheses and reparentheses are massed together between a couple of king-parentheses, one of which is placed in the first line of the majestic sentence and the other in the middle of the last line of it—after which comes the VERB, and you find out for the first time what the man has been talking about; and after the verb—merely by way of ornament, as far as I can make out—the writer shovels in "haben sind gewesen gehabt haben geworden sein," or words to that effect, and the monument is finished. I suppose that this closing hurrah is in the nature of the flourish to a man's signature—not necessary, but pretty. German books are easy enough to read when you hold them before the looking-glass or stand on your head -- so as to reverse the construction—but I think that to learn to read and understand a German newspaper is a thing which must always remain an impossibility to a foreigner.

The whole essay is here: link

Past and Present: Now The Twain Shall Meet

Now, if I wanted to be one of those ponderous scientific people, and `let on' to prove what had occurred in the remote past by what had occurred in a given time in the recent past, or what will occur in the far future by what has occurred in late years, what an opportunity is here! Geology never had such a chance, nor such exact data to argue from! Nor `development of species', either! Glacial epochs are great things, but they are vague--vague. Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. This is an average of a trifle over one mile and a third per year. Therefore, any calm person, who is not blind or idiotic, can see that in the Old Oolitic Silurian Period, just a million years ago next November, the Lower Mississippi River was upward of one million three hundred thousand miles long, and stuck out over the Gulf of Mexico like a fishing-rod. And by the same token any person can see that seven hundred and forty-two years from now the Lower Mississippi will be only a mile and three-quarters long, and Cairo and New Orleans will have joined their streets together, and be plodding comfortably along under a single mayor and a mutual board of aldermen. There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.

~Mark Twain, The Atlantic Monthly, 36, 193 (1875)

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Mark Twain's autobiography is finally coming out after 100 years of waiting: link.  I'm expecting the unexpected, based on conjecture.