Indolent Molecules chemistry

I heard a colleague talk today at the MidAtlantic Regional Meeting of the ACS about his work with fluoroquinones. These molecules (which despite their name contain no fluorine) fluoresce, that is they "glow" when exposed to light. The process can be short circuited by binding another molecule, a quencher, to fluoroquinone. The research discussed the quenching behavior of tryptophan. Tryptophan is an amino acid, one of the building blocks of proteins. Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.

The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.

Perils of Summer 2: Mephitis Squared chemistry

It's war on my dad's farm: humans versus Mephitis mephitis, night time maneuvers complete with chemical weapons. Currently the skunks hold the high ground.

Last night my brother's dog threatened a skunk, with predictable results. The collateral damage included my shoes and feet. The Reverend's Wife produced a bottle of something guaranteed to elminate the smell and we decontaminated me and the dog on the lawn. I was more cooperative about being hosed down. The odor was overpowering, and even after twice deskunking me, my kids swore I still smelled of skunk.

Skunk musk is a mixture of low molecular weight thiols, sulfur containing compounds that have the basic structure ☐-S-H (where the box represents a functional group, such as methyl or butyl), and related compounds called thioacetates. Most thiols have a characteristic, and awful, odor. (Thioacetates don't smell quite so badly.) The simplest thiol is methane thiol, also known as methyl mercaptan, which is used to spike methane (natural gas) so that leaks can be detected. (Methane is actually odorless.) Humans can detect thiols at very low concentrations, less than 1 ppm, which explains why my kids could still pick up the odor.

Skunk odor can be neutralized by converting the thiols to less odiferous molecules. One way this can be accomplished is by reacting the thiols with hydrogen peroxide, which oxidizes the thiol to a sulfonic acid ( ☐-SO₃H), which has virtually no odor. Bleach (a strong oxidizing agent) will work as well. A similar technology is used to remove thiols from industrial waste water, where the thiols are converted to disulfides ( ☐-S-S- ☐), which are oils that separate easily from the water.

---

Mercaptan comes from the Latin mercurium captans, something that seizes or captures mercury. Sulfur reacts very effectively with mercury, and one way to clean up a mercury spill is to sprinkle sulfur on the mercury. Thiol is Greek for sulfur.

If you need a recipe to remove skunk odor, try Humbolt's list. I can personally vouch for the effectiveness of the pet/human version. Note that tomato juice is not particularly effective.

1-para-methen-8-thiol is an uncharacteristically and pleasantly scented thiol more commonly known as grapefruit mercaptan.

More demystified chemical perils of summer...

Melting Points chemistry

Pain perdu - a delicious part of my New Orleans heritage and better known in most of the US as french toast - has a long history. The earliest extant recipe is in Latin and dates to the 4th or 5th century! Friday brought a snow day for my kids, and come evening, some experimental time for me in my favorite home lab.

After a day spent teaching and shoveling in the sleet, I made pain perdu aux pommes from Simon Hopkinson's Second Helpings of Roast Chicken. Think french toast, vanilla custard, apples and caramel sauce. The first step in making the caramel sauce is to melt sugar over high heat. As I stirred the dry sugar in my heaviest sauce pot, alert for the first sign of melting, I flashed back to my days in an organic chemistry research lab. Melting points were used both to identify products (though even then, spectroscopic methods such as NMR were the gold standard) and to verify purity. Taking an accurate melting point required patience - and being attentive to the appearance of that first glistening drop of liquid in the fine capillary tube. It looked almost as if the crystals were sweating.

How is the purity of a compound related to its melting point? An impure sample will tend to melt over a few degree range, pure samples will melt at a sharp temperature. Impurities in a solid will also depress its melting point, in the same way that applying salt to ice (another application of chemistry appropriate for a snow day) lowers the freezing point. This phenomena also offers a low tech way to confirm the identity of a compound. Make a mixture of the sample to be identified and a known sample of (presumably) the same stuff. If the melting point is sharp and the same as the pure compound, the unknown is certain to be what you think it is. This will work even if the melting points of the two compounds are fortuitously the same.

A nice film of a melting in a capillary tube can be found at Wellesley's organic chem lab site.

Campus Technology Article about Molecules in Second Life chemistry

Linda Briggs wrote a nice article in Campus Technology about using Second Life to teach and highlighted the chemistry application that I used last term:
Creating Life-Size Molecules in Second Life

A Conversation with Drexel University's Jean-Claude Bradley

1/9/2008

By Linda L Briggs

CT: Conversely, what are some things that work really well in Second Life?

JCB: One thing new that I've done this term is have students do a project in Second Life.

CT: Yes, you recently wrote in your blog that one of your students created a life-size model of a molecule as part of that. That sounded really cool.

JCB: Right. To be able to stand next to a molecule that is as tall as you are, and to have your teacher be able to walk around it with you and comment,... that's pretty useful.

[....]

CT: Do you have advice for instructors who want to integrate Second Life into their course?

JCB: You should have a really good reason to do it. The best advice is to find another teacher who is actually using it, and try to experience what the student is experiencing. You'll get some ideas and advice from that. I was just talking to another teacher an hour ago who might be doing some things in Second Life. She's also an organic chemistry teacher. I told her, just send your students to Drexel Island; have them interact with my students, click around on the quizzes, and if you think it might make sense, you can spawn off from that.

A lot of people have bad experiences in Second Life because they don't have a good reason for going there. It's like having people go to the Internet without a Web address. You want to be guided. That's the best possible scenario.

It's just another tool. I wouldn't teach exclusively on Second Life. We have WebCT Blackboard; I have my wiki; I have my blogs; and those things all have their strengths. You've got to leverage them all.

Electrochemical Uses Of Carbon from chemistry notes

Carbon is one of the most abundant elements found on earth. It occurs freely in crystalline forms such as diamond and graphite.The diamond crystal is cubic, with the atoms arranged in a tetrahedral configuration. This arrangement of carbon atoms produces a solid that is the hardest known substance. Consequently, it is used as an industrial abrasive. In addition, diamond has a very high refractive index, hence it produces brilliant cut gems. Graphite, on the other hand, is soft, has a hexagonal structure, with the carbon atoms arranged in layer planes. The spacing between the layer planes in graphite is 0.3354 nm (nm = billionth of a meter). This layer structure facilitates easy cleavage along the planes, which makes it desirable as a solid lubricant. There are variations of the graphite structure. When the dimensions of the layer planes are small and the separation between the layer planes becomes large, the carbon is referred to as amorphous carbon (for example, charcoal, coke, and soot). Because of their difference in structures, diamond is an electrical insulator, whereas graphite is a good electrical conductor. The high conductivity of graphite and its good chemical stability are attractive features for its use in electrochemistry.

Read More :- http://electrochem.cwru.edu/ed/encycl/art-c01-carbon.htm

Why do we assume that other beings must be based on carbon? Why couldn't organisms be based on other substances? from chemistry notes

[A portion of this entry is based on a lecture by Alain Leger (IAS) at
the SPIE Astronomical Telescopes and Instrumentation 2000 Conference.]

As far as SETI, the search for extraterrestrial intelligence, is
concerned, we do not assume that other being must be based on carbon.
In fact, SETI is a bit of a misnomer. We are searching for
extraterrestrial *technological* intelligences, technological
intelligences capable of broadcasting their existence over
interstellar distances. Whether the technological civilizations is
based on carbon or some other substance is largely irrelevant. (Of
course, one might worry that intelligences based on some substance
other than carbon might have such different perspectives on the
Universe that, even if they broadcast electromagnetic radiation, they
would do so in a fashion that we would never consider.)

However, when one moves to finding life on other bodies in the solar
system or traces of life on extrasolar planets, there is a definite
carbon chauvinism in our thinking. The most commonly mentioned
alternate to carbon (C) is silicon (Si). It has similar chemical
properties as C, lying just below C in the periodic table of the
elements.

Carbon chauvinism has arisen because C is able to form quite
complicated molecules, in part because its atomic structure is such
that C can bond with up to four other elements. Not only can it bond
with up to four other elements, but C can form multiple bonds with
other elements, particularly itself. (Atoms bond by sharing
electrons, when two atoms share more than one electron they have a
multiple bond. For instance, water is formed by an oxygen atom
sharing the two electrons from two hydrogen atoms. In contrast, there
are many C compounds in which a single C atom shares multiple
electrons with other atom.)

A clear indication of the versatility of C is found in interstellar
chemistry. Interstellar chemistry typically occurs on the surface of
microscopic dust grains contained with large clouds of gas between the
stars. The physical conditions are much different than anything on
the surface of a habitable planet. Nonetheless, of the molecules
identified in interstellar space as of 1998, 84 are based on C and 8
are based on Si. Moreover of the eight Si-based compounds, 4 also
include C.

Thus, while there is definitely a C bias in our thinking, there is at
least some evidence from Nature supporting this bias.

Indolent Molecules

I heard a colleague talk today at the MidAtlantic Regional Meeting of the ACS about his work with fluoroquinones. These molecules (which despite their name contain no fluorine) fluoresce, that is they "glow" when exposed to light. The process can be short circuited by binding another molecule, a quencher, to fluoroquinone. The research discussed the quenching behavior of tryptophan. Tryptophan is an amino acid, one of the building blocks of proteins. Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.

The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.

Perils of Summer 2: Mephitis Squared

It's war on my dad's farm: humans versus Mephitis mephitis, night time maneuvers complete with chemical weapons. Currently the skunks hold the high ground.

Last night my brother's dog threatened a skunk, with predictable results. The collateral damage included my shoes and feet. The Reverend's Wife produced a bottle of something guaranteed to elminate the smell and we decontaminated me and the dog on the lawn. I was more cooperative about being hosed down. The odor was overpowering, and even after twice deskunking me, my kids swore I still smelled of skunk.

Skunk musk is a mixture of low molecular weight thiols, sulfur containing compounds that have the basic structure ☐-S-H (where the box represents a functional group, such as methyl or butyl), and related compounds called thioacetates. Most thiols have a characteristic, and awful, odor. (Thioacetates don't smell quite so badly.) The simplest thiol is methane thiol, also known as methyl mercaptan, which is used to spike methane (natural gas) so that leaks can be detected. (Methane is actually odorless.) Humans can detect thiols at very low concentrations, less than 1 ppm, which explains why my kids could still pick up the odor.

Skunk odor can be neutralized by converting the thiols to less odiferous molecules. One way this can be accomplished is by reacting the thiols with hydrogen peroxide, which oxidizes the thiol to a sulfonic acid ( ☐-SO₃H), which has virtually no odor. Bleach (a strong oxidizing agent) will work as well. A similar technology is used to remove thiols from industrial waste water, where the thiols are converted to disulfides ( ☐-S-S- ☐), which are oils that separate easily from the water.

---

Mercaptan comes from the Latin mercurium captans, something that seizes or captures mercury. Sulfur reacts very effectively with mercury, and one way to clean up a mercury spill is to sprinkle sulfur on the mercury. Thiol is Greek for sulfur.

If you need a recipe to remove skunk odor, try Humbolt's list. I can personally vouch for the effectiveness of the pet/human version. Note that tomato juice is not particularly effective.

1-para-methen-8-thiol is an uncharacteristically and pleasantly scented thiol more commonly known as grapefruit mercaptan.

More demystified chemical perils of summer...

Melting Points

Pain perdu - a delicious part of my New Orleans heritage and better known in most of the US as french toast - has a long history. The earliest extant recipe is in Latin and dates to the 4th or 5th century! Friday brought a snow day for my kids, and come evening, some experimental time for me in my favorite home lab.

After a day spent teaching and shoveling in the sleet, I made pain perdu aux pommes from Simon Hopkinson's Second Helpings of Roast Chicken. Think french toast, vanilla custard, apples and caramel sauce. The first step in making the caramel sauce is to melt sugar over high heat. As I stirred the dry sugar in my heaviest sauce pot, alert for the first sign of melting, I flashed back to my days in an organic chemistry research lab. Melting points were used both to identify products (though even then, spectroscopic methods such as NMR were the gold standard) and to verify purity. Taking an accurate melting point required patience - and being attentive to the appearance of that first glistening drop of liquid in the fine capillary tube. It looked almost as if the crystals were sweating.

How is the purity of a compound related to its melting point? An impure sample will tend to melt over a few degree range, pure samples will melt at a sharp temperature. Impurities in a solid will also depress its melting point, in the same way that applying salt to ice (another application of chemistry appropriate for a snow day) lowers the freezing point. This phenomena also offers a low tech way to confirm the identity of a compound. Make a mixture of the sample to be identified and a known sample of (presumably) the same stuff. If the melting point is sharp and the same as the pure compound, the unknown is certain to be what you think it is. This will work even if the melting points of the two compounds are fortuitously the same.

---

A nice film of a melting in a capillary tube can be found at Wellesley's organic chem lab site.