musings on music and life

February 26, 2014

The secret of scent

Filed under: Books, Uncategorized — Tags: , — sankirnam @ 7:16 pm

I recently finished reading Luca Turin’s The Secret of Scent, and wanted to get my thoughts down before they faded to nonexistence. The book is very compelling, being that the subject matter is about human olfaction. The mechanism of how humans and other animals detect odor is still up for grabs, and there are several competing theories, such as the “lock-and-key” mechanism, or shape-based detection. The author’s central thesis is that the nose operates through a mechanism known as quantum electron tunneling, and he gives a detailed history of the development of the theory. The book is aimed at laymen, and is written for a nonscientific audience. As a chemist, I was very impressed by Turin’s coverage of the basics of organic chemistry, given that all the popular fragrance molecules in use today are small organic molecules! It is noteworthy that Turin is not an organic chemist by training; he got his PhD in biophysics. Turin posits that the odor of molecules as detected by the nose can be correlated with their IR (infrared) frequencies, and one of the biggest pieces of evidence he describes is the similarity of the smell of decaborane and thiols (B-H and S-H bonds both have IR frequencies around 2500 cm-1). Any organic chemist will be all too familiar with the vile smell of divalent sulfur compounds, such as H2S, thiols, thiolate salts, disulfides, and sulfides. However, the moment the sulfur is oxidized, the smell vanishes. Sulfoxides and sulfones do not smell bad at all. Recently, I have been working with aryl-SF5 compounds as part of my graduate research work, and those smell very pleasant, often reminiscent of their -CF3 analoges! Thus, according to Turin’s theory, they should have similar IR frequencies, which I am unfortunately too lazy to look up.

Turin explains that deuterated and non-deuterated molecules smell different when properly purified (by GC methods) and that the smell can be distinguished by trained individuals (he writes about his attempt to demonstrate this with acetophenone and acetophenone-d8). This is due to the isotope effect, which is most pronounced with D-H substitution, since deuterium is twice the mass of protium.

He also attempts to explain the difference in odor between the enantiomers of carvone, suggesting that the C=O stretch in one enantiomer may not be detected as well as other (which is entirely feasible when one considers that molecules in the nose are detected in a protein receptor, which is an inherently chiral environment). His experiment to prove this theory involves mixing simple ketones (such as acetone or MEK) and one enantiomer of carvone to see if the smell matches the other.

The above experiments call for reproduction by interested individuals, and it is noteworthy that Dr. Turin has wriiten about these experiments in detail in a book intended for laymen. His passion for the subject shines through every paragraph in the book.

That being said, here’s another shameless plug (for fluorine and fluorine chemistry). Selective fluorination may be another way to intelligently design new fragance molecules. While it is known that C-F bonds, due to their inherent polarity, are stronger than C-H bonds (and thus vibrate differently), organofluorine compounds are also often more volatile than their nonfluorinated counterparts. This could be useful for designing new “headnote” fragrances, which are the smells one initially detects when applying perfume; they only last for a few minutes or so.

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March 22, 2012

Organo Main Group Chemistry

Filed under: Books, Chemistry — Tags: — sankirnam @ 5:30 pm

I recently discovered a good textbook for those interested in organic chemistry: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470450339.html

This is geared towards intermediate undergraduate chemistry majors (preferably after they have finished a year-long course in Organic Chemistry), or can be used by the instructor to supplement the regular sophomore Organic course. The book gives a very broad-based coverage of the organic chemistry of the elements; thus the topic of this book can more correctly be described as “elemento-organic chemistry”. Since the emphasis is on the main-group elements, transition-metal organometallic chemistry is glossed over. Very detailed attention is given to the chemistry of the hypervalent main group elements (such as boron, carbon, silicon, sulfur, phosphorous, germanium, bismuth, iodine, and bromine), since that is the author’s area of expertise. Carbene chemistry (especially that of the stable, NHC (Arduengo) carbenes) has a chapter of its own. Brief mention of stereoelectronic effects as applied to conformation and reactivity of organic substrates is done in the overall context of bonding.

Unfortunately, there is little mention of carbocation chemistry (which is one of my areas of interest). I also feel the author could have been a little bit more attentive in citing the literature appropriately. While I do not doubt his knowledge of the chemistry presented, one of the major uses of a textbook is a primary tool for finding literature citations. To take a random example: If I wanted to find papers on the chemistry of low-valent iron, the first thing I would do would be to find a book or textbook on iron chemistry, flip to the chapter on low-valent iron, and look up the references for that chapter. Also, since this book was translated from Japanese, minor errors in translation and various other typos are scattered throughout. However, they do not impede understanding.

I would recommend this book to interested undergraduate and graduate students in organic chemistry. For instructors, this book can be used as a supplement for sophomore undergraduate chemistry and would make a perfect textbook for undergraduate advanced organic chemistry. At the graduate level, this can serve as an introduction to advanced topics, such as hypervalency, which are not usually taught at the undergraduate level.

It’s not that expensive on amazon: http://www.amazon.com/Organo-Group-Chemistry-Kin-ya-Akiba/dp/0470450339, only $73. This is cheap compared to the astronomical prices I have paid for books in years past.

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