Scientific Literature for Everyone

Some recent snippets that I could forward to my non-science friends:

Microbacterium hatanonis sp. nov., isolated as a contaminant of hairspray

Scientists isolate bacteria from hairspray!
I know its not unheard of to have growth in cosmetics, but I just wonder whose idea it was to test the hairspray.

Paradoxical Facilitatory Effect of Low-Dose Alcohol Consumption on Memory Mediated by NMDA Receptors

Shutting your brain off every once in a while improves your memory.
"Epidemiological studies have suggested a negative correlation between alcohol intake and Alzheimer's disease. In vitro, ethanol negatively modulates NMDA receptor function. We hypothesized that chronic moderate alcohol intake leads to improved memory via adaptive responses in the expression of NMDA receptors and downstream signaling."


I'll drink to that!

Asprin: Development and Mechanism of Action

The pain reliving power of salicylic acid has been known for hundreds of years. Hippocrates recommended willow bark to relieve the pain of childbirth. (1) The active ingredient was later isolated by Leroux. Sodium salicylate was used as a treatment for rheumatiod arthritis in the late 1800s, but chronic patients suffered from severe stomach irritation. The father of a Baeyer chemist asked his son to search for a less irritating drug than sodium salicylate. Many derivatives were made, and the acetylated version found to be the best. Before the end of the century Baeyer had acetylsalicylic acid, or asprin, on the market.
The mechanism of action for asprin was determined much later. Asprin inhibits prostaglandin biosynthesis. Prostaglandins are released when cells are damaged and result in inflammation and fever. Asprin inhibits palatlet cyclooxygenase for the life of the platelet. Asprin acetylates a serine hydroxyl group in the active site of cyclooxygenase buy what can be thought of as a transesterification reaction. (2)
(1) Gross, M. and Greenberg, L. A. "The Salicylates: A Critical Bibliographical Review." Hillman: New Haven, CT.
(2) Van der Ouderaa, F. J., Buytenhek, M., Nugteren, D. H., and Van Dorp, D. A. 1980, Eur. J. Biochem. 109, 1.

Book Review Review

I was somewhat interested in reading a review of Mary Roach's new book-I read Stiff and was grossed-out and intrigued. Honestly, I couldn't get past the illustration. Has no one at the New York Times taken a course in organic chemistry? Really?
This illustration is wrong in so many ways.

You know you are on the path to fluency with organic chemistry when you quickly take inventory of all the valence mistakes, you are already there if that is all you notice.

The shifting carbonyl stretching frequency

Which of the following structures would you expect to have the strongest (higest wavenumber) streching frequency for the carbonyl stretch?
The key to this type of problem is realizing that there are two contributing forms to any carbonyl compound resonance hybrind. The one shown above, but also the polar charged form below.
You would expect that any group which could cause elctron donation to the carbonyl carbon would favor the polar form (right) and decrease the strecthing frequency. Similarly, any group that causes electron withdraw would enhance the double bond character (left) which increases the stretching frequency.
In this example you are looking at the effects through the conjugation of a phenyl ring. The stongest electron withdrawing group listed above is the nitro group, followed by chlorine, and the methyl group is slightly donating.
You also need to draw the resonance structures. Illustrating the withdraw of the nitro group on both the para and meta substituted phenol rings brings up a good point. You need to be able to draw a resonance strucure where the positive charge build up is next to the carbonyl. Think about what this would look like if you had the dipolar carbonyl-two adjacent positive charges = not a heavily contributing structure, therefore the double bond character is favored by this charge build up. The para substitution allows this but the meta does not (below). The correct answer for the problem above, methyl 4-nitrobenzoate, has a carbonyl strecthing frequency of 1700 cm-1.

Conjugation and Light

Absorbtion of UV light or light from the visible region of the electromagnetic spectrum can promote an electron into its excited state. Without going into MO theory here you can know that some of these transitions are more favored and some have small enough energy barriers that they can be promoted by longer wavelengths. Conjugated dienes have a sufficiently small barrier such that they can transition to excited state (absorb) in the UV and Visible regions.
Allowing our skin to absorb UV rays from the sun puts us at higher risk for skin cancer. The active ingredients in sunblock absorb in the UV region, acting as a shield for our skin. If the suns rays are absorbed by a compound on top of our skin, they will not be absorbed by our skin. A popular active ingtredient for sunblocks is PABA or para-amino benzoic acid. All of the double bonds of the aromatic ring are conjugated, in addition the carbonyl is in conjugation with the aromatic ring. Another active ingredient that has come on the market more recently is Parsol. Parsol is said to block more UVA rays. It takes 1ooX more UVA light to cause the same damage as UVB light, but over the course of your lifetime, it is probably prudent to protect yourself from both. Parsol contains two ketones that are in conjugation with two para substituted aromatic rings.

As you increase the amount of conjugated pi bonds the energy between ground state and excited state is reduced, the absorption is reduced to lower wavelengths in the visible region. When a compound absorbs in the visible region it takes on the color of the wavelengths it does not absorb. Beta-carotene has 11 conjugated double bonds and has a maximum absorbance at 454 nm, the blue region. White light that appears orange once blue has been removed. Beta-carotene gives carrots and many other vegetables their color. Indigo absorbs at the other region of the visible spectrum, around 675 nm. If it is absorbing red and yellow, it will appear blue under white light.

Functional Group Polarity

A molecules polarity depends primarily on

1. The extent to which it can hydrogen bond
2. The number of electronegative atoms
3. The polarizability of the bonds or atoms
4. The net dipole moment of the molecule.


Applying these rules you can make a list for determining the relative polarities of the functional groups when all else is similar.

Alkanes are the least polar. No hydrogen bonding, electronegative atoms, polarizability and the net dipole moment is small at best.
Alkenes are similar to alkanes in all respects except polarizability. The p orbitals of are large and polarizable, making this class of molecules more polar than alkenes.
Conjugated Polyenes and Aromatic Compounds are similar to alkenes but now the pi system (of p orbitals) is even larger, increasing polarity.
Ethers and alkyl halides are more polar than the above classes because of the introduction of a polar atom. Rules higher on the list take precedence over rules lower on the list.
Aldehydes, Ketones, and Esters have a large dipole moment due to the carbonyl. Along with the electronegative oxygens, this makes them more polar than an ether or alkyl halide.
Amines and Alcohols have the ability to hydrogen bond, the first and most important rule on the list. Although it is a close call, everything else similar, an alcohol would be more polar than an amine because oxygen is more electronegative (Rule 2).
Carboxylic Acids are the most polar functional group because they can hydrogen bond extensively, they have a dipole moment and 2 electronegative atoms.

Notice how large the difference is between esters and carboxylic acids-hydrogen bonding counts for a lot.



Obviously the rest of the molecule plays in to any decision. If you have a 30 carbon chain attached to an any group it will be significantly less polar, but this can give you a framework to make an educated decision. The rules aren't perfect, and sometimes lab experience can surprise you. Sometimes you have two compounds that you really couldn't make a good guess about because they seem so similar. In that case, you run the column and figure it out by NMR.

Distinguishing Aldehydes and Ketones using IR

The following two spectra are simple carbonyl compounds. Formaldehyde, the simplest aldehyde, and acetone, the simplest ketone. Students often come to me frustrated because they can not tell one carbonyl compound from the next, or the peak will be right between the two literature values. The aldehyde or ketone question is simple. In both you will see a very prominent C-O stretch around 1700cm-1 area.

Ketone

Aldehyde

But in the aldehyde you should also see see a peaks around 2820 and 2720cm-1. They often look like a doublet and are sometimes referred to as a Fermi doublet. These are the C-H stretches between the aldehydic proton and the carbonyl carbon. The presence of these peaks along with a carbonyl peak is a good indication that you have an aldehyde.