Back here somewhere I commented that new chemical terms were relatively rare -- infrequent enough to keep up with them. Well here's a new one: "agostomer." Classics scholars and word lovers should like the origin of this new word.
The word agostic was coined about 30 years or so ago to describe how certain two-point bonding occurs. The Greek word agostos (ἀγοστός) means the "flat of the hand" and is apparently very rare and only occurs once in Homer's Iliad (it took me some doing to find that Greek link). The metaphor is that the bonding resembles a man's bent arm with the flat of one hand on a hip such that there are two points of arm attachment to the body: a strong one at the shoulder and a weaker one between the hand and the hip.
Recently, an old friend of mine co-discovered and reported on a remarkable new compound which crystallized in two subtly different ways, one analogous to having the palm on the hip and the other with the back of the hand on the hip. The two isomers are termed "agostomers" and also show the interesting property that one agostomer crystal is orange and the other one is blue. Here's a depiction:
Saturday, August 24, 2013
Sunday, August 11, 2013
What Should Be Forgiven?
Trespasses, sins, guilt, debts, shoulds?
Palladian's version of the Lord's Prayer (evolved from a machine) struck me because of how the words "trespasses" and "trespassed" survived wholly intact:
Or father
court in heaven
shall be dining biking them,
but I will be done
on corporate as it is in heaven
give us this day ordeal the bride
and for guests are trespasses
as a brief for give those who trespassed against its
and leave us not into temptation
to deliver us from evil
for design to step forward
and glory forever,
on and.
The Lord's Prayer has appeared in English since the latter's earliest recorded times but the word "trespass" did not appear until the 16th century. Originally, we used the word gyltas which is cognate with the modern English word "guilt":
Fæder ure þu þe eart on heofonum
si þin nama gehalgod
tobecume þin rice
gewurþe þin willa
on eorðan swa swa on heofonum
urne gedæghwamlican hlaf syle us to dæg
and forgyf us ure gyltas
swa swa we forgyfað urum gyltendum
and ne gelæd þu us on costnunge
ac alys us of yfele soþlice.
By the 14th century, the word had evolved to a combination of dettis and synnys, which are cognate with modern English words "debts" and "sins;" Middle English had clearly felt the influence of the Norman Conquest (1066):
Oure fadir þat art in heuenes halwid be þi name;
þi reume or kyngdom come to be.
Be þi wille don in herþe as it is doun in heuene.
yeue to us today oure eche dayes bred.
And foryeue to us oure dettis þat is oure synnys
As we foryeuen to oure dettouris þat is to men þat han synned in us.
As we foryeuen to oure dettouris þat is to men þat han synned in us.
And lede us not into temptacion but delyuere us from euyl.
By the 16th century, "trespasses" had supplanted guilt, sin, and debt to give the verses we know by heart:
Our Father which art in heaven, hallowed be thy name.
Thy kingdom come.
Thy will be done in earth as it is in heaven.
Give us this day our daily bread.
And forgive us our trespasses, as we forgive them that trespass against us.
And lead us not into temptation. But deliver us from evil.
Amen.
___________________"Trespass" has an archaic meaning of sin or transgression but the word today largely means to stray into another's territory--like being "offsides" -- 5 yard penalty. The OED instructs on the origin of trespass; it is French in origin, meaning to transgress or literally to go beyond. It's odd that we use a word of French origin when the French themselves use the word debit or debt and apparently always have done so: link
The Italians use debito and the Latin Mass uses the identical concept: link
I once wrote a blog post on this topic (which originated in an Althouse comment). There is a curious convolution of monetary debt and sin in the German language (Nietzsche is involved) and I wrote about it here.
[Cross-posted with a question here]
Thursday, August 8, 2013
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:
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.
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 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:
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?
________________________
Suggested further reading:
[1] An Algorithm For Translating Chemical Names To Molecular Formulas
[2] Development Of Systematic Names For The Simple Alkanes
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.
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?
________________________
Suggested further reading:
[1] An Algorithm For Translating Chemical Names To Molecular Formulas
[2] Development Of Systematic Names For The Simple Alkanes
Wednesday, July 31, 2013
Friday, July 26, 2013
Sunday, July 21, 2013
Trade Secrets
I'm not certain what to make of this study which asserts that 90+% of truly useful innovations are not patented. I have my doubts because in the chemical arts--and pharmaceutical inventions in particular--the converse is more likely the case. The paper takes a minute to load so here's the abstract:
Trade secrecy is the default setting for intellectual property law. It's what the system reverts to when things get ugly, costly and when openness is abused. Trade secrecy is not what Thomas Jefferson wanted for us.
Abstract
It is well known that not all innovations are patented, but the exact volume of innovative activities undertaken outside the coverage of patent protection and, relatedly, the actual propensity to patent an innovation in different contexts remain, to a major degree, a matter of speculation. This paper presents an exploratory study comparing systematically patented and unpatented innovations over the period 1977-2004 across industrial sectors. The main data source is the ‘R&D 100 Awards’ competition organized by the journal Research and Development. Since 1963, the magazine has been awarding this prize to the 100 most technologically significant new products available for sale or licensing in the year preceding the judgments. We match the products winners of the R&D 100 awards competition with USPTO patents and we examine the variation of patent propensity across different contexts (industries, geographical areas and organizations). Finally we compare our findings with previous assessments of patent propensity based on several sources of data.
Trade secrecy is the default setting for intellectual property law. It's what the system reverts to when things get ugly, costly and when openness is abused. Trade secrecy is not what Thomas Jefferson wanted for us.
Saturday, July 20, 2013
Changing Of The Guards (2007)
Another Dylan cover:
Labels:
1978,
2007,
50 years of myTunes,
Dylan,
Patti Smith
Friday, July 19, 2013
On The Roof (1986)
I know
I said you can't (even) fly
On your way
I hope you'll be OK
Stop for a while
Talk about it
For a while
From now on
Sooner or later
Sing a new song
Call me when you're better
Stop for a while
Talk about it
For a while
In a while
In a while
For a while
For a while
I said you can't (even) fly
On your way
I hope you'll be OK
Stop for a while
Talk about it
For a while
From now on
Sooner or later
Sing a new song
Call me when you're better
Stop for a while
Talk about it
For a while
In a while
In a while
For a while
For a while
Inspired By Amba
Amba wrote this a while back on her blog Ambiance:
For too long I've behaved like water or electricity -- always seeking the path of least resistance. If I wish to channel my thoughts -- to steer them in a meaningful direction-- I must also do the work of building the embankments to contain them. I'll have to move a few atoms. I've done this before and so am no stranger.
Matter is a corrective. Matter exerts a resistance, a counterforce, like wood to a carving knife or water to a ship’s keel or air under an airplane’s wings, that paradoxically enables us to get somewhere by making it more difficult. linkTo which I responded:
OK, this is way off-topic and perhaps I should write it as another “inspired-by-Amba” blogpost, but I had to mention two connections this triggered for me. The first was the old-fashioned way that nations used to settledtrade imbalances: there might be trade exchanges in one direction: goods or services for example. At the end of the day, there would be a reckoning and something like gold would flow in the other direction. In this way gold, having gravitas, kept thing[s] grounded.
The second was the way chemical reactions occur. Chemistry is valence electrons exchanging and rearranging. The nuclei hardly change at all (unless we’re talking nuclear chemistry). Anyways, electrons, being flighty and fleet, are forever waiting around for the heavier nuclei to get into the right configurations for exchange. When the laggard atoms finally are…zip…the electrons are already there like magic. linkShe responded:
Anyways, electrons, being flighty and fleet, are forever waiting around for the heavier nuclei to get into the right configurations for exchange. When the laggard atoms finally are…zip…the electrons are already there like magic.
That is totally what it’s like to write, or perhaps to create in any medium. You have to do the heavy, lumbering work of getting yourself properly aligned, then–inspiration is there. link_______________________
For too long I've behaved like water or electricity -- always seeking the path of least resistance. If I wish to channel my thoughts -- to steer them in a meaningful direction-- I must also do the work of building the embankments to contain them. I'll have to move a few atoms. I've done this before and so am no stranger.
Monday, July 15, 2013
I Believe In You (2008)
This is a cover of a Bob Dylan song from his 1979 album "Slow Train Coming"
Her cover version retains the same words and lyrics of Dylan's orginal but taken out of context of Dylan's album, she could be singing about faith in another person.
I saw Cat Power perform this song at San Diego's "Street Scenes" music festival a few years ago. Here are links to that which I want to watch later on. link Her guitar player was a guy named Judah Bauer who played in the Jon Spencer Blues Explosion.
Her cover version retains the same words and lyrics of Dylan's orginal but taken out of context of Dylan's album, she could be singing about faith in another person.
I saw Cat Power perform this song at San Diego's "Street Scenes" music festival a few years ago. Here are links to that which I want to watch later on. link Her guitar player was a guy named Judah Bauer who played in the Jon Spencer Blues Explosion.
Notes on "The Disappearing Spoon"
[continuation in part]
I'm reading Sam Kean's book "The Disappearing Spoon" and posting comments about it. I'm on page 29:
_________________________________
Next up, Chapter 2: "Near Twins and Black Sheep: The genealogy of Elements C, Si, Ge" wherein I pretend to get nasty.
I'm reading Sam Kean's book "The Disappearing Spoon" and posting comments about it. I'm on page 29:
Reading the periodic table across each row reveals a lot about the elements, but that's only part of the story, and not even the best part. Elements in the same column, latitudinal neighbors, are actually far more intimately related than horizontal neighbors. People are used to reading from left to right (or right to left) in virtually every human language, but reading the periodic table up and down, column by column, as in some forms of Japanese, is actually more significant. Doing so reveals a rich subtext of relationships among elements, including unexpected rivalries and antagonisms. The periodic table has its own grammar, and reading between its lines reveals whole new stories.Very very nice. I call the up down periodic relationship between elements "rhyming;" each element rhymes with the one above and below it. The table is written in 2n2 meter, where n = 1, 2, 3, 4... link
_________________________________
Next up, Chapter 2: "Near Twins and Black Sheep: The genealogy of Elements C, Si, Ge" wherein I pretend to get nasty.
Sunday, July 14, 2013
More notes on "The Disappearing Spoon"
[continuation in part]
I'm reading a book and posting comments about it. I'm on page 27:
Years ago, I corresponded with Jacob Bigeleisen, the doyen of that branch of science. He was her junior coworker at Columbia U on the Manhattan Project and was a coauthor of the 1947 paper I mentioned above. I happened to ask him about his role in isotope chemistry and he opened up, telling me a great story involving her which I already blogged on here. It's long, but well worth a read. I'm just going to re-post the part where he later told a reporter about the amazing moment when he was briefly overwhelmed by Goeppert-Mayer's brilliance. Bigeleisen had been struggling to derive an equation and to simplify it. Goeppert-Mayer glanced at his work and instantly finished it for him:
I'm reading a book and posting comments about it. I'm on page 27:
Electron behavior drives the periodic table. But to really understand the elements, you can't ignore the part that makes up more than 99 percent of their mass---the nucleus. And whereas electrons obey the laws of the greatest scientist never to win the Nobel Prize, the nucleus obeys the dictates of probably the most unlikely Nobel laureate ever, a woman whose career was even more nomadic than Lewis's.Maria Goeppert-Mayer. I blogged about her here. She was the poster girl for how badly science used to treat women. Kean tells a good story, but mischaracterizes one aspect which I'd like to correct and add to. At page 28, middle of the second paragraph:
After the Depression lifted, hundreds of her intellectual peers gathered for the Manhattan Project, perhaps the most vitalizing exchange of scientific ideas ever. Goeppert-Mayer received an invitation to participate, but peripherally, on a useless side project to separate uranium with flashing lights. No doubt she chafed in private, but she craved science enough to continue to work under such conditions.I object to the characterization of "useless side project to separate uranium with flashing lights," or whatever that means. What Goeppert-Mayer was working on was the separation of uranium isotopes, under the direction of H.C. Urey at Columbia University. I suppose that work could be characterized as "useless" because ultimately gaseous diffusion solved the problem. But Goeppert-Mayer did make a valuable contribution to science during the war. The results were declassified and finally published in 1947 and became the seminal paper for the science of isotope effect chemistry.
Years ago, I corresponded with Jacob Bigeleisen, the doyen of that branch of science. He was her junior coworker at Columbia U on the Manhattan Project and was a coauthor of the 1947 paper I mentioned above. I happened to ask him about his role in isotope chemistry and he opened up, telling me a great story involving her which I already blogged on here. It's long, but well worth a read. I'm just going to re-post the part where he later told a reporter about the amazing moment when he was briefly overwhelmed by Goeppert-Mayer's brilliance. Bigeleisen had been struggling to derive an equation and to simplify it. Goeppert-Mayer glanced at his work and instantly finished it for him:
She looked at my work and asked 'why don't you finish it up by taking out the classical part?' Without a pause, she wrote the simplified equation, saying 'Now you have it; it's all done.' I didn't immediately understand what she meant when she said to cut out the classical part. I went home. I worked on it, and eventually I got the same result. linkI suppose that those with an ax to grind could subtitle that moment in time "superior female intellect briefly overwhelms male dominance." I'm sure that she had other moments later on. But all the players are now dead and together somewhere, I suppose.
Saturday, July 13, 2013
More notes on "The Disappearing Spoon"
[continued from previous post]
Part I "Orientation: Column By Column, Row by Row"
Part I "Orientation: Column By Column, Row by Row"
1. Geography Is Destiny: H, He, B, Be, Sb
__________________________
Page 21, bottom of page:
which sort of resembles an upside down version of the female symbol.
________________________
Kean writes at length about Gilbert N. Lewis, as have I. My take on him is here and here.
_______________________
Now on to some substantive descriptive chemistry: Page 24, bottom:
What Aufbau builds on is how electrons self-organize around an increasingly charged nucleus in moving from hydrogen to higher and higher elements. Start with the simplest atom having one proton and one electron. The very first electron goes into a spherical shaped 1s orbital surrounding the proton. Now if we add another proton to that picture to get to the next element (helium), we must add a second electron. It too goes into the same 1s-orbital and two electrons are happy as clams--perfectly-paired. The pairing of electrons is one of the most sublime aspects of electronic theory and is one which I struggle to understand.
Now move on to element 3, lithium: the third electron cannot occupy the same orbital space as its first two, so it must go into a higher energy orbital, the so-call 2s orbital. The 2s orbital is not exactly just a larger s-orbital; it actually interleaves with the 1s orbital as I drew attention to here:
The fourth electron in element 4, beryllium, perfectly pairs with the third one and fills the 2s orbital. Now, the fifth electron in boron could go into what's called a 3s orbital depicted above, i.e., electrons could just keep building higher and higher energy shells of spherical symmetry, but something else happens. A different type of node appears which breaks the spherical symmetry, creating what's called a p-orbital:
The 2p-orbitals are lower in energy than the 3s orbitals and that's why the next 6 electrons fill those first. There are 6 spaces because the electrons pair and go into 3 different p-orbitals -- one for each Cartesian dimension, x, y, and z.
[more soon]
__________________________
Page 21, bottom of page:
Egyptian women were applying a different form of antimony as mascara, both to decorate their faces and to give themselves witchlike powers to cast the evil eye on enemies.They used stibnite in which you can still see the Latin origin of antimony's chemical symbol, Sb. Stibnite gave the blueish black look which is still alluring, though antimony has been removed from reformulated modern eyeliner. The alchemist's symbol for antimony is:
which sort of resembles an upside down version of the female symbol.
________________________
Kean writes at length about Gilbert N. Lewis, as have I. My take on him is here and here.
_______________________
Now on to some substantive descriptive chemistry: Page 24, bottom:
As we move horizontally across the periodic table, each element has one more electron than it neighbor to the left. Sodium, element eleven, normally has eleven electrons; magnesium, element 12, has twelve electrons; and so on. As elements swell in size, they not only sort electrons into energy levels, they also store those electrons in different shaped bunks, called shells.Early German quantum mechanics called this Aufbau or building up. Kean describes how electrons build shells -- s, p, d, and f orbitals -- in a logical way. His descriptions of p-orbitals as a "misshapen lung" and "d-orbitals" as balloon animals is amusing, but I would explain it differently. They more resemble blobs with 0, 1, 2, and 3 nodes as described here.
What Aufbau builds on is how electrons self-organize around an increasingly charged nucleus in moving from hydrogen to higher and higher elements. Start with the simplest atom having one proton and one electron. The very first electron goes into a spherical shaped 1s orbital surrounding the proton. Now if we add another proton to that picture to get to the next element (helium), we must add a second electron. It too goes into the same 1s-orbital and two electrons are happy as clams--perfectly-paired. The pairing of electrons is one of the most sublime aspects of electronic theory and is one which I struggle to understand.
Now move on to element 3, lithium: the third electron cannot occupy the same orbital space as its first two, so it must go into a higher energy orbital, the so-call 2s orbital. The 2s orbital is not exactly just a larger s-orbital; it actually interleaves with the 1s orbital as I drew attention to here:
The fourth electron in element 4, beryllium, perfectly pairs with the third one and fills the 2s orbital. Now, the fifth electron in boron could go into what's called a 3s orbital depicted above, i.e., electrons could just keep building higher and higher energy shells of spherical symmetry, but something else happens. A different type of node appears which breaks the spherical symmetry, creating what's called a p-orbital:
The 2p-orbitals are lower in energy than the 3s orbitals and that's why the next 6 electrons fill those first. There are 6 spaces because the electrons pair and go into 3 different p-orbitals -- one for each Cartesian dimension, x, y, and z.
[more soon]
Labels:
Antimony,
Boron,
electrons,
Helium,
The Disappearing Spoon
Friday, July 12, 2013
Pere Ubu, Final Solution (1976)
A proto-angst ridden number from the past with direct links to bands like Sonic Youth in the future. I don't think Pere Ubu ever had a commercial success, but that doesn't matter, they're still great. They're still around too.
Divide And Conquer
Strangely prophetic for 1985:
Well they divided up all the land
And we've got states and cities
Cities have their neighborhoods
And more subdivisions
There's countries divided by walls
Oceans and latitudes
And longitude, longing to find out
Just what they're missing
They're lots of area codes
And nine digit zip codes
Secret decoder ring codes
Arteries, shopping nodes
We'll invent some new computers
Link up the global village
And get AP, UPI, and Reuters
To tell everybody the newest news
We'll be one happy neighborhood
Spread out across the world
But who's going to stop that burglar
From breaking in my house
If he lives that far away
We'll be just like old friends
No means to your ends
The police state is too busy
And the neighborhood's getting out of hand
Big Brother on every wall
Muzak plays in all the halls
Empires see the rise and fall
They divide, conquer
It's not about my politics
Something happened way too quick
A bunch of men who played it sick
They divide, conquer
It's all here before your eyes
Safety is a big disguise
That hides among the other lies
They divide, conquer
Well I expect I won't be heard
Because my silence is assured
Never a discouraging word
They divide, conquer
They divide and conquer
Special Secret Song Inside
I know it sounds like an urban legend, but these guys incited a riot in Fort Collins, CO after they played there in 1987. This was on the play list:
More Notes on "The Disappearing Spoon"
[continuation in part]
I'm reading a book and posting comments about it:
Sam Kean wrote a book a couple years back called "The Disappearing Spoon And Other True Tales Of Madness, Love, And The History Of The World From The Periodic Table Of The Elements."
I am at:
Part I "Orientation: Column By Column, Row by Row"
I'm reading a book and posting comments about it:
Sam Kean wrote a book a couple years back called "The Disappearing Spoon And Other True Tales Of Madness, Love, And The History Of The World From The Periodic Table Of The Elements."
I am at:
Part I "Orientation: Column By Column, Row by Row"
1. Geography Is Destiny: He, B, Sb, Tm, O, Ho
_____________________________
This chapter is an excellent introduction but risks alienation from the start. Page 12, line 1:
I, like most people, first encountered the periodic chart in high school. And I was unaware of any beauty behind the periodic chart or chemical theory. I was somewhat attracted to the mechanical aspects of the chemistry lab -- the glassware, the Bunsen burners -- and all the tangible aspects. But instead of focusing on experiments, I built elaborate rubber gas lines snaking under desks in order to "gas out" other students according to some WW I trench warfare reenactment going on in my head. Seriously, I don't remember much from high school chemistry. I may have learned the names of a few elements, but I was pretty much a smart ass in my first two years of high school and I paid a price for that. It probably didn't help that I had a terrible teacher who didn't know much chemistry himself (he was an earth science teacher). My high school had a regular chemistry teacher with a chemistry background (Mr. Z), but space was limited in his class and I didn't make the cut. The irony. But I digress. Getting back to the book: yes I too associated chemistry with dweebs. I fought the dweebs and the dweebs won. I became a dweeb or as we affectionately called ourselves in grad school "chem nerds."
Page 12, middle:
The author is keen on stressing the rectilinear grid structure -- the Cartesian qualities. And for good reason: the chart is the form we all know -- but still, it is just a convention. There is nothing intrinsic about that flat tabular presentation. I "co-invented" an alternative version here.
There is a rich history of how the grid was assembled. First came columns in the early 19th century: Döbereiner's triads --though the column metaphor presumes a vertical relation which didn't yet exist. Then came Newlands with his rows and notions of repeating layers. And then came Mendeleev who envisioned the whole thing well enough to predict where holes were for missing elements.
Page 13, last paragraph:
Page 17, middle paragraph:
...Doodle du jour:
_____________________________
This chapter is an excellent introduction but risks alienation from the start. Page 12, line 1:
Probably the biggest frustration for many students was that the people who got the periodic chart, who could really unpack how it worked, could pull so many facts from it with such dweeby nonchalance.Dweeb: noun: an insignificant student who is ridiculed as being affected or studying excessively.
I, like most people, first encountered the periodic chart in high school. And I was unaware of any beauty behind the periodic chart or chemical theory. I was somewhat attracted to the mechanical aspects of the chemistry lab -- the glassware, the Bunsen burners -- and all the tangible aspects. But instead of focusing on experiments, I built elaborate rubber gas lines snaking under desks in order to "gas out" other students according to some WW I trench warfare reenactment going on in my head. Seriously, I don't remember much from high school chemistry. I may have learned the names of a few elements, but I was pretty much a smart ass in my first two years of high school and I paid a price for that. It probably didn't help that I had a terrible teacher who didn't know much chemistry himself (he was an earth science teacher). My high school had a regular chemistry teacher with a chemistry background (Mr. Z), but space was limited in his class and I didn't make the cut. The irony. But I digress. Getting back to the book: yes I too associated chemistry with dweebs. I fought the dweebs and the dweebs won. I became a dweeb or as we affectionately called ourselves in grad school "chem nerds."
Page 12, middle:
Before introducing the periodic table, every teacher should strip away all the clutter and have students just stare at the thing, blank.Hey! I made a similar point back here, except I proposed actually testing such knowledge.
The author is keen on stressing the rectilinear grid structure -- the Cartesian qualities. And for good reason: the chart is the form we all know -- but still, it is just a convention. There is nothing intrinsic about that flat tabular presentation. I "co-invented" an alternative version here.
There is a rich history of how the grid was assembled. First came columns in the early 19th century: Döbereiner's triads --though the column metaphor presumes a vertical relation which didn't yet exist. Then came Newlands with his rows and notions of repeating layers. And then came Mendeleev who envisioned the whole thing well enough to predict where holes were for missing elements.
Page 13, last paragraph:
For each element, its geography is destiny. In fact, now that you have a sense of what the table looks like in outline, I can switch to a more useful metaphor: the periodic table as a map. And to sketch in a bit more detail, I'm going to plot this map from east to west, lingering over both well-known and out-of-the-way elements.This reminded me of lecture I heard at the UW-Madison ca. 1982 given by a guest lecturer (I wasn't a grad student but rather a precocious undergrad). He put up a periodic table in which he likened it to a US map and showed how certain university research groups were working on the chemistry of elements in a "geographic" way: "Oh look, there's Jack Halpern in Chicago working on rhodium which sits in the "midwest"; and just north of him on the chart is Chuck Casey at Madison, working on iron; out west on the leftern edge is the Bercaw group exploring scandium; out east there's so and so." The modern periodic table is iconic.
Page 17, middle paragraph:
The repose of the noble gases is rare, however. One column to the west sits the most energetic and reactive gases on the periodic table, the halogens. And if you think of the table wrapping around like a Mercator map, so east meets west and column eighteen meets column one, even more violent elements appear on the western edge, the alkali metal. The pacifist noble gases are a demilitarized zone surrounded by unstable neighbors.I love that. I made the identical point about the Mercator aspect back here (and this was before Kean published, WTF?). But none of this is original, so far...
...Doodle du jour:
Wednesday, July 10, 2013
Remembering Elizabeth Reed Redux
I ran across an excellent YouTube video of the classic Fillmore East live version of the Allman Brother's "In Memory Of Elizabeth Reed." It's actually video footage of another night overlayed on the original sound track. There is no extant footage of that live version that I know of. I am in love with this song, having written about it at length once before: link It haunts me somehow.
Duane Allman introduces the song, snapping his fingers to mark time (you can clearly hear this in the remastered CD version). Duane was a dirty hippy but there is something very southern gentleman in his voice: "A song Dickey Betts wrote from our second album....uh, In Memory of Elizabeth Reed...ready gentlemen? 1..2..3..."
Duane Allman introduces the song, snapping his fingers to mark time (you can clearly hear this in the remastered CD version). Duane was a dirty hippy but there is something very southern gentleman in his voice: "A song Dickey Betts wrote from our second album....uh, In Memory of Elizabeth Reed...ready gentlemen? 1..2..3..."
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