Category: Chemistry

In chemistry, hydrophobicity (from the combining form of water in Greek hydros and for fear phobos) is the physical property of a molecule that is repelled from water. Hydrophobic molecules tend to be non-polar and thus have a greater affinity for other neutral molecules and non-polar solvents. Hydrophobic molecules in water often cluster together forming tiny bubble-like structures known as micelles.

The opposite of hydrophobic is hydrophilic. A hydrophilic substance, from the Greek hydros for water and philia love, is a molecule or other molecular entity that is attracted to, and tends to be dissolved by, water. A hydrophilic molecule is one that has a tendency to interact with or be dissolved by water and other polar substances including solvents; the interactions are more thermodynamically favourable.

Water always was a slippery character. Now, scientists at Pacific Northwest National Laboratory have made an incredible thin layer of water, just a single molecule thick, that sits on a slab of platinum metal and refuses to freeze. Strictly speaking, the monolayer held at just 60 Kelvin becomes hydrophobic and will not allow ice crystallites to form on its surface.

What’s that you say, “hydrophobic water”?

Denial doesn’t get any more profound than that, even if we are talking about molecules.

According to Physics News Update: “Weaker bonding results in a “classic” hydrophobic state, in which the water merely balls up immediately.” So, it’s a balls up, is it? That explains a lot.

Diethylstilbestrol (DES) is a synthetic nonsteroidal estrogen that was first synthesized in 1938. Human exposure to DES has allegedly occurred through diverse sources, such as dietary ingestion from supplemented cattle feed and medical treatment for certain conditions, including breast and prostate cancers.

From 1940 to 1970, DES was actually given to pregnant women in the belief that it would reduce the risk of pregnancy complications and losses. In 1971, DES was shown to cause a rare vaginal tumour in girls and young women who had been exposed to this drug in utero and the US FDA subsequently withdrew DES from use in pregnant women.

Dan Lednicer offered us a guest editorial some time ago that mentioned the ill-fated drug diethyl stilbestrol (DES) and the toxicity of this and other compounds. Here’s the 3D chemical structure of DES for recent visitors to Sciencebase who were looking for it!

Diethylstilbestrol is an orally active non-steroidal estrogen first made in 1938 and originally approved for use in gonorrheal vaginitis, atrophic vaginitis, for menopausal symptoms, and in postpartum lactation suppression to prevent breast engorgement.

However, in 1971 it was found to be a teratogen – causing birth defects – when given to pregnant women and later a carcinogen. It is currently used only in veterinary practice at very low (hypocarcinogenic) doses for treating female canine incontinence.

Quite a lot of visitors to Sciencebase hit the site asking questions of the search engines, but a recent spate of similar questions would suggest lots of students doing a science assignment: What does boron smell like? What does carbon smell like? What is molecules plasma? (sic) Picture of zinc element etc etc.

As the question about boron seems to come up the most frequently and has garnered the most comments on this post, I thought I would get a definitive answer from boron expert John Kennedy Professor of Inorganic Chemistry at the University of Leeds, UK. This is what he has to say and it pretty much confirms my own suspicions about boron, although I am still curious as to why this question comes up so often and wonder whether there are volatile compounds formed when boron comes into contact with your skin in the same way that metallic BO arises.

“Elemental boron is a ceramic, and completely involatile,” Kennedy told me, “So it should have no smell associated with it, just like porcelain.” He points out that very fine boron dust might stimulate the nostrils in the same way that any dust would and could feasibly have a particular nuance of flavour. “As I recall when I did handle some course boron powder,” adds Kennedy, “there was no smell, just like sand.”

So there you have it, volatility is the key. If something is involatile, then it cannot reach the smell (olfactory) receptors in your nose to stimulate them. If it is finely powdered, particles could conceivably reach your nose, but would stimulate it in a similar way to any other fine dust. Some time ago, we discussed on Sciencebase.com an odd theory that the nose acts as a sophisticated natural spectrometer rather than a straightforward detector. This theory suggests that different compounds smell differently because they vibrate with different frequencies, a property observed by vibrational spectroscopy.

As a chemistry student, I was always taught to flute my filter papers, but a heated debate about another method of using your filter paper is raging on the Chemed-l discussion group about why others fold their paper and then tear off the corner. Hal Harris University of Missouri-St. Louis reckons the little corner tear improves the filtering process and also speeds it up significantly. So much so, he says, that “Over a lifetime in chemistry, I’m sure that this has saved me a cumulative 20 msec, at least.”

Meanwhile, here’s the standard method of fluting filter paper. The technique is used when you wish to separate a liquid and a solid, keeping the liquid and discarding the solid. The specific arrangement of folds (flutes) in the filter paper will allow the liquid to pass through it very quickly and at the same time provide a large surface area on which to collect the solid impurities.

According to this week’s C&EN many cats are unaffected by catnip.

Apparently, only 50% of cats respond to catnip. Catnip sensitivity is inherited, says Carolyn McDaniel, a veterinarian at the Feline Health Center at Cornell University in Ithaca, NY.

Catnip is available as a herb or the essential oil of Nepeta cataria, and it’s the compound nepetalactone that is one of several chemicals known to set off the characteristic behaviour of cats exposed to it. This behaviour generally starts with sniffing, licking and chewing, followed by head shaking, body and head rubbing, and then repeated head-over-heels rolling.

No one is sure why cats respond to nepetalactone in this way, but it sounds like it’s doing something not dissimilar to the action of cocaine. (I defer to the experts on that presumption though).
If you’d like a print-quality molecular structure of nepetalactone to accompany an article you may be writing on this compound please check out my molecular modeling service.

Apparently, the recent patent using the non-word “chene“, I mentioned last week is older than my original source suggested. More to the point, says UCSF’s John Irwin on CHMINF-L, the patent examiners failed to recognize a whole tranche of prior art from Daylight, MDL, Tripos, and Acelrys, among others. The patent will be invalidated, he adds. Irwin also suggests that we, “Spare a thought for overworked USPTO examiners.”

So, chenomics may not emerge in the way the Japanese patent application hoped. But, watch out next week for yet another patent on a gene, this time by a Canadian company exploiting US university research…can’t say any more for now…