Saturday, June 27, 2009
Friday, June 19, 2009
I was fascinated by Bonnie Brasler's TED talk on Quorum-Sensing, and being a chemist I wanted to know more about the molecules involved. She did put up a slide with structures during the talk, but I wanted more so I did a search on PubMed and found this Perspective written by Brassler and Michael Federle.
Federle, M. (2003). Interspecies communication in bacteria Journal of Clinical Investigation, 112 (9), 1291-1299 DOI: 10.1172/jci200320195
Monday, June 15, 2009
Saturday, June 13, 2009
You can search by product name, product category, manufacturer, or ingredient. All ingredients in the product are listed along with a safety rating of 0-10 and what type of hazard may caused by the ingredient, as well as a “Data Gap” which indicates the lack of safety information on the ingredient as a percent.
Of course, toxicity is a complex issue and not simple to nail down precisely. It depends on the dosage and the route of exposure (skin, oral ingestion, inhalation, etc). It would be nice to see the actual test data that they used to develop their ratings. Many ingredients are listed as (possible) carcinogens or as neurotoxins, but I can't tell how this was determined. If the actual test were based on oral ingestion or whole cell screens they may not be very informative about how the compound would behave when applied to the skin.
The other problem is dosage – most of the compounds in a cosmetic are likely to be found in small amounts – were the tests done with low concentrations to accurately reflect the “dosage” in a cosmetic? The pigments in particular seem to get the higher toxicity ratings – the thing about pigments is that it only takes a small amount of pigment to get a significant color. It may be difficult to measure the behavior of really small amounts accurately, higher dosages would be easier to measure but may not be good indications of the effects when exposed to only small amounts.
Particularly telling is the “Data Gap” rating which is "is a measure of how much is unknown about an ingredient. " A search for a common shampoo listed one of the ingredients as "Fragrance," which was given a hazard score of 8 (out of 10) with concerns about "Neurotoxicity, Allergies/immunotoxicity, Miscellaneous " and a Data Gap of 100%. The Data Gap score suggests to me that their toxicity rating is a not at all reliable. Most fragrances in commercial products are fairly simple compounds of a floral nature, and probably only present in a fairly small concentration. Although allergy concerns are probably sensible, I really doubt that washing my hair with shampoo is much of a risk for neurotoxic or immunotoxic side effects. Most people with a little common sense would probably tell you the same thing.
Skin Deep is probably a good place to start looking for information about the substances found in cosmetic products, but I don't know how much you should really trust the toxicity ratings that are given.
Wednesday, June 10, 2009
They also have a Rock Ballad video.
Tuesday, June 9, 2009
Crystals are generally rigid and brittle, but this paper describes microcrystals of dimethylamino trans azobenzene that bend into a semicircle when a light is shined on them. That the azobenzene molecule responds to light is no real surprize, but the fact that the whole crystal changes shape, and reversibly to boot, was pretty cool.
Take a look at the video's of this that are provided, for free, in the supplemental information for the paper. The movie 002 shows the bending motion most clearly. This crystal is about 0.5 mm by 0.28 mm and 0.005 mm thick, so it is really tiny. A larger crystal probably would not do this.
So what's going on? The N=N double bond can be in either the trans orientation or the cis orientation. The trans version is preferred - the cis version suffers from steric crowding as the two benzene rings bump into one another. By shining light with the proper wavelength on the molecule, you can convert the trans into the cis molecule. Turn off the light, and the molecule can revert back the the trans version.
The authors were able to confirm that when they shine light on their crystals they convert about 1% of the molecules from the trans form to the cis form. This was readily apparent in proton NMR, but evidence could also be seen in changes in the UV-vis spectrum and the melting point of the crystals. After turning off the light source, the molecules in the crystal return slowly to all-trans.
So, how does this cause the crystal to bend almost in half? It seems to have to do with the way the molecules arrange themselves in the crystal lattice. The trans molecules are flat and stack into a very regular herring-bone type of pattern. The cis molecules don't fit this pattern - in addition to the U-shape, the cis molecules have a twist in them to reduce some of the steric strain between the benzene rings. The twist make the molecules much bulkier than the flat trans form As a result the cis molecules don't fit into the crystal lattice and cause the unit cell to be longer than the unit cell for only the trans molecules.
When the light source converts some of the molecules to the cis form, the side of the crystal nearest the light source appears to expand - because of the larger unit cell of the cis molecules. The side of the crystal away from the light source does not experience this and stays the same size. To accommodate the expanding surface facing the light source, the whole crystal bends away from the light source. When the light is turned off, the cis molecules slowly revert to the (more stable) trans form and the crystal un-bends.
Koshima, H., Ojima, N., & Uchimoto, H. (2009). Mechanical Motion of Azobenzene Crystals upon Photoirradiation Journal of the American Chemical Society, 131 (20), 6890-6891 DOI: 10.1021/ja8098596
Monday, June 8, 2009
The June issue of Popular Science has an image of the 3D molecular structure of the protein capsid for the Penicillium stoloniferum virus (PsV-F). This is the protein outer shell of the virus that acts as a container for the genetic information of the virus. The image doesn't appear to be on the Popular Science web site, so I went looking for the protein structure at the Protein Databank.
If you can't find a copy of Popular Science, you can see the original article at PNAS or Pubmed Central in September, since PNAS makes articles available for free 6 months after print publication.