Protecting Groups

The whole family was at camp last week, living in tents, sleeping on cots, eating in the mess hall. Every camp has them, squirrels and chipmunks that survive on the crumbs of campers' treats (or sometimes the whole banana). We were warned - no food in the tents except in metal boxes.

The boys had the tent next door to ours. I came back from dinner one night to find a very happy squirrel just making off with a chip container from the kids tent. At which point I remembered the dried fruit I'd left in my pack after the morning hike. Whew...it was still there. The rodents had been attracted to the far more tasty snack leavings next door. The boys tent is serving as (a chemist would say) a protecting group.

Chemical protecting groups work similarly. Say you have two sites on a molecule that can react with a reagent, but you only want one to undergo the reaction. If you can put a protecting group on the site you want left unmolested, like a cover, you can run the reaction, change the other site and then take off the protecting group. (See the scheme for an example.)

It works wonderfully for many reactions, and is keeping my pack safe from marauders.

Weird Words of Science: isotope

The periodic table is the map of the chemical world. Columns collect atoms which share properties - all of the elements on the far right - He, Ne, Ar… - are all gases and all nearly chemically inert. The region at the bottom harbors elements more likely to be radioactive. Metals pool in the middle.

Each atom of an element has a characteristic number of protons - positively charged particles - in their nucleus. An atom with five protons is boron. One with 82? Lead.

Most atoms also have a number of uncharged particles - neutrons - in their nuclei as well. The sum of the number of protons and neutrons in a given nucleus is called its mass number. A boron atom with six neutrons has a mass number of 11: five protons and six neutrons. Take away a neutron and it’s still boron, but the mass number is now 10.

Atoms with different mass numbers but the same number of protons are termed isotopes. Most elements have several naturally occuring isotopes. The most abundant form of the element carbon has a mass number of 12. One percent of carbon atoms, however, have an extra neutron and a mass number of 13.

Scottish novelist and physician Margaret Todd coined the term for her distant relative Frederick Soddy at a dinner party in 1913. He had described his research to her and she responded that any good discovery need a Greek term to describe it. She suggested combining the Greek “iso” for same and “topos” for place - to emphasize that the mass number of an element doesn’t affect it’s place in the periodic table: argon-36 and argon-40 are both inert gases. Soddy went on to win the Nobel Prize in 1921 for his discovery - perhaps because his distant relation had coined him a such good term?

Writing in Santa Fe

In about 8 hours, I should be taking off for Santa Fe and the 2008 Santa Fe Science Writing Workshop. I'm bringing some of the work I've done on the blog, trying to shape a longer and coherent narrative. There are about 40 students coming - from a range of backgrounds. Scientists, journalists, students. My instructor will be Laura Helmuth - the science editor for the Smithsonian.

How to tell if you're really a chemist

You pronounce unionized as UN-ionized not union-ized.
When you hear the word mole, you don't think of an animal.
Milli is a prefix, not a girl's name.

This Sceptical Chemist blog post suggests a new test to tell if you're really a chemist. What do you see when you look at this illustration by Joon Mo Kang? If the first things you see are five bonds to carbon, and three bonds to a hydrogen, you're a chemist. If that's all you see - you are really a chemist.

A couple of chemists missed the point of the illustration so completely they wrote to the NY Times to let them know of their chemical illiteracy. Another blogger was also vexed by the nonsensical molecule.

I'll admit it -- I saw five bonds.

The Grecian Bends: Ladies' Corsets and Henry's Law

In an earlier post I suggested there was a connection between ladies' corsets and Henry's Law. A general statement of Henry's Law is that the solubility of a gas in a liquid depends on the pressure of the gas above the liquid. An everyday example is soda. A can of soda is pressurized by exposing it to carbon dioxide having equivalent of about 2.5 times atmospheric pressure at room temperature. When you quickly lower the pressure of carbon dioxide over the liquid, say by opening the can, the solubility decreases and the gas adjusts by rapidly coming out of solution. Fizzing results (and eventually the soda goes flat).

When a diver dives the pressure of the gases breathed increases, and the amount dissolved in the blood increases. Diving to just 50 feet increases the total pressure to roughly that of the carbonated soda! Rapidly ascending reduces the pressure, just like opening the can of soda, and the gas rapidly comes out of solution - the diver's blood can "fizz". Bubbles in the blood and body tissues are clearly not a great thing, and the physiological effects range from the relatively minor (bubbles in the skin layers) and joint pain, to potentially lethal embolisms in the brain and lungs.

This phenomenon was first observed by Robert Boyle in 1670 who noted the formation of bubbles in the eyes of a snake that had been placed in a high pressure environment, then rapidly decompressed. "I once observed a viper furiously tortured in our exhausted receiver… that had manifestly a conspicuous bubble moving to and fro in the waterish humour of one of its eyes." Before the effects was widely understood, many construction workers suffered from "caisson workers' disease" while working in pressurized environments (caissons) under rivers.

Dive tables - a schedule for ascending from a dive that reduces the chance of decompression sickness - were first created for use by British Navy divers in the early 20th century. How do whales and dolphins cope without dive tables? Half-mile deep, hour long dives are not uncommon - and a rapid ascent from depth could cause a massive case of the bends. They may not be immune - recently researchers have found evidence for chronic decompression injuries in sperm whales. The whale bone in the photo above shows evidence of dysbaric osteonecrosis (bone death caused by rapid decompression).

What does this all have to do with ladies' corsets? In the 1870s tight corsets and big bustles were all the rage. The posture forced upon women wearing these fashionable undergarments was called the Grecian Bend. As decompression injuries caused a similar posture, workers on the Brooklyn Bridge christened the syndrome "the Grecian bends", soon shortened to "the bends".

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The photograph of the whale bone is by Tom Kleindinst, Woods Hole Oceanographic Institution and is used with permission.

The image of the Grecian Bends is from the Library of Congress

Concentrated Chemistry: American Chemical Society National Meeting

The American Chemical Society national meeting is on in New Orleans this week. Somewhere on the order of 10,000 chemists will be here for at least some of the week - it's noticeable on the streets to be sure.

The Nature Chemistry group win the prize for most challenging travel. Read the teaser at the Sceptical Chymist - and place your bet on whether United Airlines will get them home again. A road trip to London isn't going to be the solution to return travel woes (unless that Bering Strait tunnel project gets off the drawing board much sooner than anticipated...).

The ACS has an oral history project going...and I'm signed up to be videotaped this afternoon.

My favorite t-shirt seen at the meeting: The name's Bond. Ionic bond. Taken, not shared.

Random Facts about Ludwig B.

Not that Ludwig B. - the other Ludwig B: Ludwig Boltzmann, an Austrian physicist.

Boltzmann's name is familiar to many science students through the eponymous constant: 1.381 x 10^-23 Joules/mole-Kelvin, which appears in many equations. The constant (usually written as k) arises from the proportionality between the absolute entropy of a system (S) and the number of possible arrangements of that system (W). Boltzmann's expression of the entropy, S=k ln W, is inscribed on Boltzmann’s tombstone in Vienna, Austria. Boltzmann did not write it in this form, however, Planck did.

Boltzmann also has two other equations named for him, the first is a diffusion equation used in neutron transport theory and the second describes particles in a gravitational field. In 1904, Boltzmann gave lectures on mathematics at the World’s Fair in St. Louis. He was also a popular lecturer in philosophy at the University of Vienna. Boltzmann is considered the founder of statistical mechanics, and a strong proponent of the “atomistic” view that underscored the importance of understanding the behavior of atoms and molecules in order to understand the bulk.

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Loosely, the entropy is a measure of the "randomness" in a system.

Allotropes and architects: buckminsterfullerene

Responding to an earlier post on inert gases, a commenter wondered if buckminsterfullerene might act as an inhalation anesthetic - given that, like xenon, it's a large, polarizable ball of electron density. It might, if you could get enough to inhale. At room temperature, the vapor pressure is 5 x 10^-6 torr. Very roughly, that's about a billionth of atmospheric pressure. For comparison's sake, the pressure of xenon necessary to induce anesthesia is about 500 torr, or 65% of normal atmospheric pressure. If you want higher pressures, you need higher temperatures: buckminsterfullerene sublimes (goes directly from the solid to the gas phase, like dry ice) just above 1000F. Not great to breathe...

While likely impractical as an anesthetic, buckminsterfullerene has asthetic properties. It's a highly symmetric molecule - having iscosohedral symmetry. Kroto and Smalley discovered the new allotrope of carbon, C₆₀, in vaporized graphite and named it for the architect (Buckminster Fuller) who made famous the geodesic domes it resembled. Two more familiar allotropes of carbon are graphite and diamond.

Allotropes are differing forms of the same element. The roots of the word are Greek - allos for different and tropos for "turn of mind". A different turn of mind? It's what Smalley needed to propose the now iconic structure, over a beer at his kitchen table.

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Another allotrope of carbon is lonsdaleite - named for Kathleen Lonsdale, an Irish crystallographer who determined the structure of benzene and my brother-in-law's godmother.

Inert gases aren't always inert

Earlier this week I posted about the intoxicating effects of nitrogen gas at high pressures, which leads divers to substitute helium for nitrogen. An astute reader wondered in the comments why argon wasn't used, as it is substantially cheaper. It turns out that argon is even more potent intoxicant than nitrogen at high pressures! But aren't argon and helium inert gases?

The elements in the last column in the periodic table comprise what IUPAC (the International Union of Pure and Applied Chemists is to chemists what the IOC is to sports) calls Group 18, but what most of us learned in high school to call the noble or rare, gases. Helium, argon, neon, krypton, xenon and radon are indeed all gases under standard conditions, but the modifier misses the mark by a bit.

Rare? Take a deep breath, you've just inhaled about 100 mg of argon. Almost 1% of the atmosphere is argon; there is almost three times as much argon in the air as there is CO₂. "Noble" generally means "unreactive" to a chemist. The noble metals, such as gold and platinum are resistant to oxidation - they don't rust - unlike the "base" metals such as iron and copper. Much like gold and platinum, under the right conditions these inert gases can be made to react. The first noble gas compound - xenon hexafluoroplatinate - was synthesized in 1962, but there were earlier clues that these gases might not be completely unreactive. The anesthetic effect of xenon had been observed in the 1930s, and reports of its use in clinical settings appeared in the late 1940s.

The mechanism by which nitrogen, argon and xenon behave as anesthetics isn't completely understood. The best theories at the moment suggest that the gases interact with ion channels - but whether they binding chemically or physically is not clear.

Breathing Deeply

The tunnels deep beneath New York that bring crystal clear water from the reservoirs upstate to the city are aging. Divers are busy assessing the infrastructure - and it's literally a high pressure job. In order to avoid time consuming daily decompressions, the divers are living in a high pressure environment for weeks at time, almost 20 times normal atmospheric pressure. As AP reports, the pressures require that the men breathe a helium-oxygen mixture. Unfortunately, the reason given in the article for breathing the squeaky voice inducing mix: "the nitrogen in regular air is too heavy at 600 feet and their lungs could not handle the pressure." is utter nonsense.

Nitrogen does not weigh more under pressure, and the total pressure of the gas in the divers lungs is high, regardless of the identity of the gas (oxygen gas weighs more than nitrogen does, in fact). The real reason has to do with Dalton's law of partial pressures, and the fact that at high pressures, neither oxygen nor nitrogen are benign substances.

Dalton's law says that the pressure of each gas in a mixture is a function of the percentage of that gas and the total pressure of all the gases. For example, at 30,000 ft, where the total pressure is 0.3 atm and the fraction of oxygen in the air is 21%, the partial pressure of oxygen is 0.063 (humans need a partial pressure of about 0.1 atm to oxygenate their blood).

At the depth of the NYC tunnels, the total pressure is just over 18 atm, so the partial pressure of oxygen would be 3.8 atm. Above a partial pressure of roughly 1.5 atm oxygen gas is seriously toxic. The partial pressure of nitrogen 600 feet below the surface is about 14 atm. Nitrogen narcosis, rapture of the deep, sets in at pressures above 4 atm. At these depths, nitrogen is essentially an anesthetic!

Introducing an inert gas into the breathing mix, such as helium, reduces the percentage of oxygen and nitrogen in the air, thus reducing their partial pressure and reducing the danger of oxygen toxicity and nitrogen narcosis. The need for the specialized breathing mix has nothing to do with the heaviness of the nitrogen and everything to do with the toxic effects of these gases at high partial pressures.

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Eliminating nitrogen completely from the mix can also reduce the potential for developing the bends (bubbles of gas that form in the tissues when pressure is reduced) - but that has to do with Henry's Law and ladies corsets, and is another blog post!