Monday, 13 July 2015

In the mood for indigo?

"Mood Indigo" is the name given to one of my all time favourite Duke Ellington compositions. It is also the colour that we associate with Blue Jeans, and remains one of the most important textile dyes in use today. Once it was a major export item of India, derived from the plant Indigofera tinctora, more recently it has become a major natural product of Guatemala and El Salvador. However, the majority of indigo produced today is manufactured by chemical synthesis. It has however been so familiar in the UK as a colour, that Isaac Newton identified indigo as one of the 7 colours of the visible spectrum: red, orange, yellow, green, blue, indigo and violet. Indigo as a molecule offers not only considerable insight into the mechanism of absorbance spectroscopy, but is an important model compound for helping us to understand the subtlety of intramolecular hydrogen bonding 

One of the most enjoyable aspects of the last two years at the UTC, has been my re-acquaintance with textile dyes: my PhD involved the application of triazine dyes in the purification of proteins; but this was over 30 years ago! Indigo is not a triazine dye, but it does help us understand the concept of of electron(ic) transitions in chemistry, which are so important in Biology. Indigo also gives us a beautiful illustration of the importance of Hydrogen bonds in molecular recognition. Indigo is a colour that most people would call blue. Isaac Newton however placed indigo in between blue and violet in the visible spectrum, which he famously published in his book "Opticks" in 1704. However, it wasn't until the middle of the 20th century that the field of quantum mechanics began to offer an explanation for the origins of colour at the molecular level (let's forget transition metal salts for now).   

The electromagnetic spectrum spans over 15 orders of magnitude: from the weak, but tunable wavelengths of radio waves to the powerful energy of X rays and gamma rays, that can tear through covalent bonds. Indigo absorbs light that is in the orange part of the visible spectrum, thereby appearing blue (oops, indigo!). The light absorbed, promotes the reorganization of an electron in the indigo molecule: the relatively low level of energy required to induce an electronic transition in the central double bond, is in part a consequence of the planar structure adopted by indigo. Which is in turn a result of the hydrogen bonds at "12 o'clock" and "6 o'clock" (dotted lines in the structure). Without this hydrogen bond stabilization, it is believed that the molecule would rotate more freely around the central double bond, making the electronic transition much less probable and requiring a higher input of energy. At this point, I should point out that whilst there is undoubtedly a relationship between the intramolecular hydrogen bonding in indigo and its absorbance characteristics, there are experiments in which the oxygen is replaced by sulphur that suggest other factors are at work. Sulphur lacks the electronegativity required to form H-bonds and so suggests perhaps that intermolecular stacking plays an important role in constraining the molecule into planer stacks. This is also a feature found in DNA bases, where stacking interactions also play an important role in stabilising the double helix. There can never be an end to experiments until we obtain the truth! The Book entitled "Organic Photochromes" by A.V. El'tsov provides a detailed discussion of these issues (for aficionados).

I think this is a lovely example of how quantum theory helps us to put the phenomenon of absorbance, and therefore colour on a mathematical footing. However, the hydrogen bonding component, makes me think of the elegant
interactions found in Biological polymers. Recall Watson and Crick base pairs in DNA, the base pairing of the anticodon loop and the triplet codons during translation of mRNA on the ribosome (RHS), or the elegant hydrogen bonding between substrates and protein amino acid side chains in the active sites of enzymes. For me, the last two years of using dyes to demonstrate ion exchange chromatography and spectroscopy has reminded me of the  sheer beauty of their visual appeal and has made me completely re-evaluate the way I will teach the importance of Chemistry in explaining Biology. 

Last week, John and I welcomed a group of primary school children to the Innovation labs and we chose to engage them with some demonstrations of colour in Biology, Chemistry and Physics. The excitement and enthusiasm as they watched a dye change back and forth from yellow to blue, by the sequential addition of an acid and a base, was truly inspirational. I hope I have persuaded at least some of you to share these views and to make more use of colour chemistry in science education.

1 comment:

  1. Your post will be rather good, and I’m sure some will find it interesting because it’s about a topic that’s as widely discussed as others. Some may even find it useful.Thanks so much for your post.

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