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May 10, 2013 at 8:00 AMComments: 0 Faves: 0

The ABCs of Chemistry: Part 7

By Lydia from SLN More Blogs by This AuthorFrom the Science Bits in a World of Bytes Blog Series

“Here we are again, last as usual.” That line, uttered by Thompson or Thomson from the Tintin books, makes me chuckle. If the last four letters of the alphabet were people, I imagine they would say that with a despondent sigh. Not to worry, though. There are plenty of concepts and chemicals to go around for all.

W is for Williamson Ether Synthesis

The Epoxide's Second Appearance!

Ethers are a class of compounds distinguished by an oxygen single bonded to two carbons or carbon groups. The picture shows a special kind of ether called an epoxide, which is about as simple an ether as you can get. The ether that comes to most people’s minds is diethyl ether , which first found popularity as an anesthetic. Who can forget that scene in Curious George where George inhales the ether and thinks he’s flying? I used it in organic lab because it was polar like water but held on to its hydrogens, unlike water. Another organic solvent I used was tetrahydrofuran , a cyclic ether that’s basically diethyl ether with its ends joined to make a pentagonal heterocycle.

How do you make such useful molecules? You use a process named for its brilliant inventor, Alexander Williamson. Williamson lost an arm in childhood, but he still got his PhD and worked as a professor for 38 years. The reaction, in essence, is between an alcohol and an alkyl halide (carbon group plus F, Cl, Br, or I). The initial step uses a strong base like sodium hydride, NaH to pull the hydrogen off the oxygen of the alcohol. The oxygen is left with a bunch of electrons, and it uses those to pull the carbon group away from the halide. Boom, ether. Alternatively, the reaction can be done in one step if silver oxide, AgO2, is used in place of NaH. A sample reaction from John McMurry’s Organic Chemistry, 7th edition is shown below.

Ether Synthesis

This reaction is subject to certain restrictions. The reaction rate slows if there are a lot of groups near the reaction site. This property has been exploited to make non-symmetrical ethers. For example, the gas additive tert-butyl methyl ether is prepared by reacting the t-butoxide ion with iodomethane (CH3I).

Gas additive

The bulk provided by the methyl groups ensures that nothing can swoop in and change the product of the reaction. The added methyl group can go only to the t-butoxide ion.

X is for Xylene


Xylene is the common name for dimethylbenzene. Although the picture shows only one form (isomer), it has three in all. If the two methyl groups are on adjacent carbons, the molecule is called o-xylene. If there is a carbon atom between the two, as in the picture, it is called m-xylene. If there are two carbons between the methyl groups, it is called p-xylene. The three isomers have slightly different properties. The melting points range from -54 degrees Fahrenheit for m-xylene to 55 degrees Fahrenheit for p-xylene. O-Xylene has the highest boiling point, 291 degrees Fahrenheit,  and the boiling points decrease to 282 degrees for m-xylene and then to 280 degrees for p-xylene. This happens because the intermolecular forces are strongest with o-xylene. One side of the molecule is ever so slightly more negative than the other, so it can grab other o-xylene molecules with a little more strength.

Xylene has a variety of uses. P-xylene is used as a precursor in plastics manufacturing; this usage represents about half of all xylene produced.  It is used as a solvent in the printing, rubber, and leather industries and a cleaner in the electronic industry. The art world has embraced it as a paint thinner that takes longer to dry than toluene.

Xylene is not as toxic as other substances but nevertheless carries its own set of health hazards. It is normally converted in the body to an acid that is excreted in the urine. Some xylenes are exhaled unchanged. The level of xylene and length of exposure to it have a great effect on severity of symptoms. Xylene vapor depresses the central nervous system (brain and spinal cord), resulting in dizziness, headaches, nausea, and vomiting. The hypothesis says that xylene disrupts the lipid part of the cell membrane and might even interact with proteins in the membrane. Long-term exposure has many symptoms, such as insomnia, depression, irritability, tremors, and inability to concentrate. Xylene irritates various parts of the body, such as the liver, kidneys, and GI tract, but the damage is often found with high exposure and is often reversible. Xylene is not carcinogenic.

Y is for Yttrium


This element is named for a mining town and is pronounced “Yittrium.” Carl Arrhenius found a black rock near the town of Ytterby. He thought it was a new mineral containing the new element, tungsten, and sent it on to chemists for analysis. Johan Gadolin found a new oxide in there in 1789; a few years later, another chemist confirmed his findings and called the new oxide “yttria.”  The actual metal was first prepared in 1828 by Friedrich Wohler by heating the metal chloride with potassium. Its symbol was Yt at first, but this was changed to Y in the early 1920s.

Yttrium is classified as a rare earth metal, like the ones in the two rows under the periodic table, due to its chemical similarity. Its concentration in the crust ranges from 10 to 150 ppm, where it is 400 times more common than silver. Its concentration in seawater is 9 ppm. It makes up parts of several rare earth minerals, such as monazite (rare earth phosphates), gadolinite (Y2Fe++Be2Si2O10), and Fergusonite (YNbO4), to name a few. Although it is of no biological importance, it accumulates in the body, particularly in the liver, kidney, spleen, lungs, and bones. Acute exposure can irritate the lungs, causing coughing and shortness of breath. Soluble yttrium compounds are slightly toxic.

Yttrium has found use in many applications. A radioactive isotope, 90Y, is used in the medical field, particularly in tumor treatment. It produces intermediate-energy beta decay reliably, has a short half-life of 2.67 days, and decays to a stable daughter product, 40Zr. Old cathode ray tube (CRT) TVs and monitors used it to produce a red color. Have you ever heard of the YAG laser? The “YAG” stands for the crystal used in it, yttrium-aluminum-garnet. When doped with cerium, YAG makes a fine white-light LED.

The latest and greatest yttrium usage, however, is high-temperature superconductors. Don’t get out your shorts yet, though. The highest temperature superconductors have worked is at a brisk -220 degrees Fahrenheit. There are various compounds containing yttrium found to work. The premier one is yttrium barium copper oxide, YBa2Cu3Ox, which was the first material discovered to superconduct above the boiling point of liquid nitrogen.


The structure was found to be pyramids of CuO5 linked by squares of CuO4, with barium and yttrium cations in the empty spaces. Although the amount of oxygen can vary, without a minimum amount of it, the material is an insulator. The optimum amount of oxygen is slightly under 7 atoms, meaning that almost all the spaces in the lattice for oxygen are filled with oxygen. This compound is fairly reactive. Water, strong acids, and strong bases all do a number to it. Humidity, for example, will cause the slow growth of cracks in the crystals.

Z is for Zwitterion

As you might have guessed, “zwitterion” has its roots in German. It’s fun to say and a useful concept to boot. It includes a form of “zwei,” showing that there are two ions on the same molecule. This is important, because different groups in molecules often have a charge that depends on pH. For example, a common zwitterion is one of the amino acids. Amino acids have a carboxylic acid end (COOH) and an amine one (NH2).

Both have hydrogens (also called protons) that can be pulled off. However, the losing does not occur at the same time. The carboxylic acid loses its proton at a far lower pH, often to the amine. This gives the carboxyl end a negative charge and the amine a positive one, maintaining the charge balance. Take a look at the amino acid above, phenylalanine. Notice that the oxygen atoms (red) have no hydrogen on them, while the nitrogen atom (blue) has three. This is how the molecule looks in your body at this point.

The point at which the amino acid becomes a zwitterion varies from one molecule to the next. Many make the transition at a pH of 2.0 to 2.3. Phenylalanine has a fairly low transition pH of 1.83. Once a zwitterion, the molecule stays that way until a certain pH is passed, and then it takes on a negative charge. There is a greater range for this because different groups that give the amino acid its identity can have their own effect on the process. For example, acidic amino acids decrease the pH range in which the zwitterions exist by easily giving up protons, while basic ones increase the range by clutching their protons close. Aspartic acid loses its zwitterionic character at a low pH, 2.77, while arginine has to be brought up to pH 10.76 to become a negative species.

There is a chemistry class for everyone. School offered lower-level, less-intense ones for people who needed chemistry for something like nursing. General and organic chemistry branched out into various sub disciplines. I like analytical chemistry and found Environmental Geochemistry particularly interesting and useful. For those who excelled at organic, Structures, Dynamics, and Synthesis offered the opportunity to gain even more knowledge of mechanisms. Future computational chemists felt at home in Physical Chemistry II.  I found something useful and interesting in every class that helped to explain the world around me, and I hope I have given you tasty tidbits of several different disciplines of chemistry.

Capponi, J, C Chaillout, et al. "Structure of the 100 K Superconductor Ba2YCu307 between (5 300) K by Neutron Powder Diffraction." Europhysics Letters. 3.12 (1987): 1301-1307. Web. 1 Apr. 2013.

Frase, KG, EG Liniger, and DR Clarke. "Environmental and Solvent Effects on Yttrium Barium Cuprate (Y sub 1 Ba sub 2 Cu sub 3 O sub x)." Advanced Ceramic Materials. 2.3 (1987): 698-700. Web. 1 Apr. 2013.

Hnatowich, DJ, F Virzi, and PW Doherty. " DTPA-Coupled Antibodies Labeled with Yttrium-90." Journal of Nuclear Medicine. 26.5 (1985): 503-509. Web. 1 Apr. 2013.

Kandyala, Reena, Sumanth Raghavendra, and Saraswathi Rajasekharan. "Xylene: An Overview of Its Health Hazards and Preventative Measures." Journal of Oral and Maxillofacial Pathology. 14.1 (2010): 1-5. Web. 1 Apr. 2013.

McMurry, John. Organic Chemistry. 7th ed. Belmont, CA: Brooks/Cole, 2008. Print.
"Mineral Species Containing Yttrium (Y)." Mineralogy Database. N.p., 1 Apr 2013. Web. 1 Apr 2013.

Nerz-Stormes, Maryellen. "Forces and Factors Influencing Melting Points, Boiling Points and Other Physical Properties ."  Bryn Mawr College. Web. 1 Apr 2013.

Wikipedia and Pubchem Sketcher version 2.4

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Previously:The ABCs of Chemistry: Part 6

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