musings on music and life

May 29, 2012

More on trifluoromethylation

Filed under: Chemistry — Tags: , , — sankirnam @ 4:31 pm

For those interested, here’s a link to a presentation made by one of Prof. Scott Denmark’s students last year on trifluoromethylation methods. It gives a good summary of the field, from initial developments to the state-of-the art today.


May 23, 2012

Clip of the week

Filed under: Carnatic Music — sankirnam @ 6:34 pm

I’m slowly starting to get the hang of this blogging thing; if these last few posts seem to have relatively low content, it’s because I’ve been a bit occupied with other stuff lately.

I’ve been watching this clip a lot lately while I’m working. It’s a rendition of the song Atukarada, in ragam Manoranjani. The mrudangist is Bangalore Arjun Kumar, and A. S. Murali and Pramoth Kiran (I think?) are on the ghatam and morsing, respectively. It’s a recording by Jaya TV from a concert in Cleveland in 2007. Arjun Kumar’s playing in this clip is phenomenal, as usual. He’s one of my favorite mrudangists lately; I make it a point to listen to a few of his concerts every year in December. The amount of hard work and practice he has put in shows in every single stroke he plays. His playing for the anupallavi (2nd stanza) of the song is especially noteworthy, with the mel kalam (fast) phrases he plays being highly reminiscent of Karaikudi Mani. It’s not easy to play with that kind of clarity at that speed, and it’s even harder to shuffle phrases around like he does while at that speed (I say this from experience).

I remember vividly that I was going to go to Cleveland that year for the Thyagaraja Aradhana; when I got to the airport, I missed my flight and then ended up misplacing and losing my carry-on bag! I was rescheduled to go on the next flight out, but then decided to cancel my ticket since I had gotten spooked by having 2 mishaps in succession. I ended up using the rest of that day to complete my graduate school applications. Coincidence or intervention by a higher power? We’ll never know…

I really like Jayanthi’s style of veena playing; unfortunately the veena as an instrument is becoming less and less popular lately. Less people seem to be learning it, and so there are less artists to go around, and even lower numbers of rasikas who are willing to listen to a veena concert. The casualties are especially bad outside of India, since foreign students prefer to learn something a little more mainstream (like violin). This also explains the rapid rise in popularity of playing Carnatic music on the keyboard.

I also share the sentiment that the keyboard will not become a classical instrument to rival the violin, mrudangam, veena etc. I say this because there is, in my opinion, a degree of physical training required to become a good musician. In vocal music, voice culture is part and parcel of the training. The long hours of practice required shape the voice and help build breath control and better lung capacity, among other things. Practicing mrudangam, violin, and veena also requires enormous training of the muscles in the fingers for the very fine movements required. In addition, sitting with the instruments is not easy to begin with! Keyboard, on the other hand, requires none of these. This lowers the bar considerably in terms of accessibility for novice students, but because of the relative ease of effort in playing the instrument, more people can reach a “performing” level, so to speak, and it becomes more difficult to impress rasikas.

Of course, I could just be extremely conservative. I’m sure people were saying the same thing about the Mandolin until U. Srinivas came along, and he sure showed them!

May 18, 2012

On flourine and organofluorine chemistry

Filed under: Chemistry, Uncategorized — Tags: , , — sankirnam @ 8:08 pm

Since I had a spare moment today, I thought I would briefly write about fluorine chemistry (especially organofluorine chemistry as it pertains to my research today).

For those not acquainted with it’s basic chemistry, fluorine is element 9 on the Periodic Table, and is the lightest member of the chemical family known as the halogens. Like all the halogens, in it’s elemental state it is diatomic, existing as molecules rather than individual atoms. However, fluorine was the last of the halogens to be isolated, due to its (dare I say obscene?) reactivity. Many people were seriously injured or even killed during attempts to isolate the element, and ultimately Henri Moissan succeeded in the late 19th century. He was later awarded the Nobel Prize for his efforts, and also probably for being the only person to isolate it without being maimed in the process. The weak F-F bond in elemental fluorine, combined with the very strong bonds other elements make with it, make the reactions of fluorine with almost anything extremely energetic.

Thus, for some time, fluorine chemistry, and organofluorine chemistry especially, were considered niche topics of little interest. Reactions of elemental fluorine with organic compounds were difficult to control, often catching fire or just going straight to tar. As most undergraduates learn, the introduction of fluorine into aromatic compounds is a little different from the other halogens. The fluorine atom cannot be introduced by a usual Sandmeyer reaction as is possible for other halogens or pseudohalogens (such as Cl, Br, I, or CN). Instead, the Balz-Schiemann reaction is required.

A few developments helped to spark interest in organofluorine chemistry. The realization that C-F bonds were among the strongest single bonds that carbon makes with other elements led to the discovery of several important inert compounds. One was CFC’s (chlorofluorocarbons). These were found to be extremely unreactive under even very harsh reaction conditions (CFC’s can even be used as solvents for such reactive compounds as SbF5!). They then found extensive use as solvents and especially refrigerants. They were made in multi-tonne quantities worldwide, until the work of the late Prof. F. S. Rowland (more about him later) showed that they were responsible for ozone depletion in the upper atmosphere. Prof. Rowland received the Nobel Prize in chemistry in 1995 for that very work.

Another important discovery was that of Teflon. Teflon is the polymer of tetrafluoroethylene, and so it only contains C-F bonds, making it very inert. The introduction of fluorine into organic molecules also tends to make them lipophilic, or hydrophobic, and so Teflon surfaces were found to be ideal for non-stick cooking ware. The discovery of Teflon was actually an accident (see here).

The Manhattan project sparked further interest in fluorine since it was discovered that the most convenient method of uranium enrichment was through separation of the two isotopes via UF6. UF6 is an extremely reactive, corrosive solid that has a low sublimation temperature, and so separation of the isotopes is done through careful gaseous diffusion. Materials that could handle UF6 were therefore sought, and most such materials were found to have to be fluorinated themselves in order to withstand the reactivity of UF6.

As one can see, fluorine chemistry offers a swath of compounds with extremely varying degrees of reactivity, from the most inert compounds known to man, to the most reactive and toxic compounds known (e.g. HF and fluoroacetate). HF (hydrogen fluoride or hydrofluoric acid when in solution) is an extremely versatile acid and fluorinating reagent, but is not used much in academic research due to difficulties involved with its handling. Prof. Olah (whom I talked about in detail earlier) made a significant contribution to the development of HF chemistry through the introduction of the reagent that now bears his name. Noble gas chemistry also falls under the umbrella of fluorine chemistry, since most of the oxidants required to access the higher oxidation states of Xe, Kr, or Ar are either F2 itself or are fluorinated.

Jumping to the modern day, there is a now a sudden renaissance in medicinal chemistry involving organofluorine compounds. As mentioned earlier, the C-F bond is one of the strongest carbon single bonds known. As such, C-F bonds are typically more difficult to degrade, making compounds containing such bonds longer lasting (as usual, exceptions exist). Dr. Prakash (who was initially a graduate student of Prof. Olah and is now a professor himself alongside Olah at USC) made a significant contribution to the development of modern organofluorine chemistry through the use of the reagent commonly called TMSCF3. The facile introduction of trifluoromethyl groups into organic compounds was a long-standing challenge in organic synthesis due to the instability of organometallic compounds containing CF3. The use of TMSCF3 provided a solution to this problem, and paved the way for numerous other methods for the introduction of trifluoromethyl or other perfluoroalkyl groups into organic molecules. Now, within 20 years, trifluoromethylation chemistry has become rather trivial, in my opinion. Several top-selling medications contain a trifluoromethyl group, including Celebrex and Prozac. The best-selling pharmaceutical in the world, Lipitor, is fluorinated, again highlighting the importance of fluorine in modern medicinal chemistry.

May 15, 2012

Fun with Sulfur Hexafluoride!

Filed under: Chemistry — Tags: — sankirnam @ 8:19 pm

I had mentioned sulfur hexafluoride (SF6) in a previous post, and just thought I would post this video, highlighting some of it’s interesting physical properties:

May 11, 2012

Palghat Raghu links

Filed under: Carnatic Music — Tags: — sankirnam @ 9:31 am

This is a layavinyasam program on Doordharshan (TV) in the 80’s. The violinist, who is putting thalam for most of the program, is Sikkil Bhaskaran.

What one should take note of is his unhurried, thorough treatment of chatusra nadai initially and then tisra gathi. From a superficial perspective, his style may not have the fancy flair or breakneck speed of other mrudangam vidwans; what is noteworthy is his intellectual approach to music. Almost all of this is improvised on the spot, although there are a few bits (like the korvais and mohara) that are prewritten.
He uses a korvai to transition from chatusram to tisram. This is not very commonly done, and takes great skill to pull of in an aesthetically pleasing manner.
Also, one should take note of his posture. Even at his age, he is sitting with the correct posture. Maintaining the correct posture is not a trivial thing, especially with a heavy mrudangam on your leg, but it is necessary in order to be able to deliver the goods, so to speak. Increasingly, more and more artists today are not sitting with the correct posture, setting a bad example for the younger aspirants. This is not a healthy trend, but can be checked if one is informed at an early age.

May 9, 2012

about sankirnam (part 1)

Filed under: Carnatic Music, Uncategorized — sankirnam @ 11:22 am

I thought I would talk a little about the name of this blog, that is, sankirnam. But first, a little background is required.

In Carnatic music, there are two main aspects: raaga (melody) and taala (rhythm). When you delve into Carnatic thalam theory, you will find there are hundreds of thalams, or beat cycles, but only a few of them are used with any frequency. These thalams are: Dhruva, Matya, Rupaka, Jampa, Triputa, Ata, and Eka. In concerts you will also see the thalams misra chapu and kanda chapu used; those are shortened 7 and 5 beat cycles adapted from folk music, respectively.

The seven thalams mentioned above are collectively referred to as the suladi sapta thalams (sapta means 7). Every student of Carnatic music learns fundamental exercises in these thalams, called alankarams. Each one has a unique structure, as shown below:

Dhruva: beat+finger counts (called laghu), beat+wave (called drutham), beat+finger counts, beat+finger counts

Matya: laghu, drutham, laghu

Rupakam: drutham, laghu

Jampa: laghu, single beat (called anudrutham), drutham

Triputa: laghu, drutham, drutham

Ata: Laghu, laghu, drutham, drutham

Ekam: laghu

These are simply frameworks. The actual thalam cycle can be further defined by the introduction of jaathi bedham. In the laghu, one can vary the number of finger counts for further variety. There are 5 variations possible: tisram (3), chatusram (4), kandam (5), misram (7), and sankirnam (9). The number refers to the total number of beats in the laghu, not just the finger counts. So, a chatusra jaathi laghu would be a beat followed by 3 finger counts, while a misra jathi laghu would be a beat followed by 6 finger counts. Taking this further, chatusra jathi triputa thalam would be an 8 beat cycle: 4 beats in laghu, 2 in each drutham. In fact, this is the formal nomenclature for “Adi thalam”, the first thalam cycle that is introduced to students of Carnatic music.

There are several reasons why Adi thalam is introduced first. One is due to the 8 beat structure; units of 4 or 8 are fundamental in almost all systems of music. Adi thalam is also a symmetric 8 beat cycle, with the structure 4+2+2. Other 8 beat cycles are possible, but they are not necessarily symmetric like Adi thalam.

In addition to jaathi bedham, nadai (or gathi) bedham is also possible. This involves varying the number of counts (called matras) in each beat (also called aksharams). Again, the terminology of tisram, chatusram, khandam, misram, and sankirnam is used here to indicate the number of matras per beat. The majority of compositions in Carnatic music are set to chatusra nadai (4 matras per beat), just like in other systems of music. Tisram is the next most common mode (3 per beat; this is akin to 3/4 time in Western Classical music).

I guess I will have to talk about sankirnam later, probably after going through all the nadais in detail first. This is just the basics of laya (rhythm) in Carnatic music. If it seems like a lot, that’s because it is. There is a steep learning curve to being able to understand and appreciate the music at some level, and an even steeper curve to becoming proficient. This is probably one of the reasons why Carnatic music remains a niche art form to this day, even among south Indians.

May 3, 2012

On hypervalence and J. C. Martin

Filed under: Chemistry — Tags: — sankirnam @ 11:33 am

One of the central tenets of structural chemistry is the “octet rule” that is obeyed by first row elements. This was first formulated by G. N. Lewis based on experimental data in the early 20th century, and even though it is simple, it is extraordinarily powerful and allows a quick, rational determination of molecular structures. The lowest-energy electron configuration for first-row elements is an 8-electron configuration, and molecular structures will naturally reflect that. This is what leads to the concept that carbon can have no more than 4 bonds, and why ammonium compounds are ionic rather than pentavalent molecular structures. Of course, the octet rule is just a theory, and in science, if a single experiment can disprove a long-standing theory or law, then the theory needs to be reassessed. Many experiments have therefore been carried out over the years designed to test the limits of bonding in first-row elements and whether the “octet rule” still holds under extreme experimental conditions.

One of the first experiments was conducted by Georg Wittig at the University of Heidelberg in Germany. He added phenyllithium to tetramethylammonium bromide, hoping to make a pentavalent nitrogen compound, which is not completely crazy, since organolithium reagents are very strong nucleophiles. However, he instead obtained a nitrogen ylide, from deprotonation of one of the methyl groups, since organolithium reagents are also strong bases!Image

These nitrogen ylides were not very stable, but did add in a nucleophilic manner to aldehydes and ketones. Wittig then extended this chemistry to the next element below nitrogen, phosphorous, and discovered that phosphonium ylides were exceedingly stable. They also had enormous synthetic value since upon addition to aldehydes or ketones, they yielded the alkene upon extrusion of phosphine oxide. This reaction is now known as the Wittig reaction, and is one of the workhorse reactions in synthetic organic chemistry for the synthesis of olefins. Wittig ended up sharing the Nobel Prize in chemistry in 1979 with H. C. Brown for his work in the development of synthetic methods. More details about his work can be read in his Nobel Lecture.

This is only the beginning of the story of hypervalence, however. While first-row elements cannot take on more than 8 electrons (due to a combination of sterics and orbital constraints), second row and lower elements can (just like in the above example). In fact, one of the long-standing mysteries in chemistry is the stability and lack of reactivity of sulfur hexafluoride. This has also spurred recent interest in the organofluorine community on the synthesis of organic derivatives of SF6, that is, organo-SF5 compounds. For a long time, the only higher-valent derivatives of the main group elements that were known were all main group fluorides (e.g. SF6, ClF3, ClF5, BrF3, BrF5, PF5, IF3, IF5, IF7, and others). These were (and to a degree, still are) considered rather exotic compounds to the traditional practicing synthetic organic chemist. But thanks to the work of J. C. Martin, some of these reagents have been “tamed” for organic synthesis.


J. C. Martin was at the University of Illinois, Urbana-Champaign for most of his career, and built up his reputation in physical organic chemistry and main group chemistry. Over the course of his career, he investigated the hypervalent chemistry of several elements, including sulfur, phosphorous, bromine, and especially iodine. His work on iodine chemistry led to the discovery of the reagent now known as the Dess-Martin periodinane. This is an I(V) reagent, and can be thought of as a “tamed” version of IF5. The reagent is widely used in organic synthesis as a mild and chemoselective oxidant, and the 1983 JOC communication detailing the synthesis and use of the reagent remains J. C. Martin’s most highly cited paper, with over 2,000 citations to date. J. C. Martin also synthesized an organic Br(III) compound, analogous to BrF3.


This reagent is also a strong oxidant, just like BrF3, but it is not widely used in organic synthesis. The study of Br(III) and Br(V) chemistry remains a niche area of research; to the best of my knowledge, there are only 1 or 2 labs worldwide doing research in this area. It is inherently dangerous, but there are some interesting results emerging from this area. Last year, a Japanese group published a paper showing how they could do metal-free amination of alkanes using a Br(III)-nitrenoid reagent! This chemistry is generally dominated by the use of precious metals (see Justin Du Bois’ recent publication in Acc. Chem. Res.). This is due to the fact that the oxidized forms of Br, such as Br(III) or Br(V) have enormous chemical potential energy; there is a very strong thermodynamic driving force for Br to come back to it’s normal valency.

J. C. Martin also did interesting research attempting to synthesize compounds containing pentavalent carbon (analogous to the SN2 transition state) and compounds containing pentavalent and hexavalent boron. These were pioneering studies, and even though they were unsuccessful, revealed a lot of information about structure and bonding. The carbon compound does not really rest in the pentavalent form in the ground state, but undergoes a “bell-clapper” rearrangement. Similarly, although pentavalency and hexavalency were claimed in the case of the boron compound based on boron NMR data, convincing evidence could not be obtained (in the form of an X-ray crystal structure).

Some of his most interesting work (in my opinion) was done towards the end of his career. He disclosed the concept of “σ-aromaticity” and synthesized some model systems that demonstrated this behavior. σ-aromaticity is a theoretically very interesting concept, and studies like this are at the heart of physical organic chemistry. The prototypical compound is the hexaiodobenzene dication, which can accessed by 2-electron oxidation of hexaiodobenzene.

ImageOxidizing hexaiodobenzene does not remove electrons from the aromatic π system; it removes electrons from the iodine atoms. Due to their size and relatively close proximity, they can delocalize the charge through bonding interactions. Theroretical calculations show that the HOMO (highest occupied molecular orbital) of hexaiodobenzene is antibonding between the iodine atoms; removing those electrons allows weak bonding interactions to take place. This is borne out by the 13C NMR shift observed upon oxidation, and the fact that the species is diamagnetic (has no unpaired electrons). Unfortunately, since J. C. Martin’s demise in 1999, this field has languished. More studies on σ-aromaticity would definitely be a welcome addition to the theoretical framework of organic chemistry and more groundbreaking results could serve to revive physical organic chemistry today.

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