The wonders and mysteries of bioluminescence

 Members of my family have been reading Phosphorescence: On awe, wonder, and things that sustain you when the world goes dark, a personal memoir by Julia Baird.

This reminded me of how amazing and fascinating bioluminescence is, stimulating me to read more on the science side. One of the first things is to distinguish between bioluminescence, fluorescence, and phosphorescence.

Bioluminescence is chemical luminescence whereby a biomolecule emits a photon through the radiative decay of a singlet excited state that is produced by a chemical reaction. 

In contrast, fluorescence occurs when the singlet excited state is produced by the molecule absorbing a photon.

Phosphorescence occurs when a molecule emits a photon through the radiative decay of an excited triplet state, that was produced by the absorption of a photon.

Bioluminescence can occur in the dark. Fluorescence cannot as there are no photons to absorb. Phosphorescence is sometimes seen in the dark but this is because the molecule absorbs invisible UV light which produces the triplet state which has a very long radiative lifetime.

Baird gives beautiful and enchanted descriptions of seeing "phosphorescence" on her daily early morning ocean swim. She acknowledges that this is actually bioluminescence not phosphorescence. I should stress that in pointing this out I am not "unweaving the rainbow", as for literary purposes using "bioluminescent" would be clunky.

 

There is a useful webpage from a research group at UC Santa Barbara. They also have a detailed review article from which I took the image above.

Bioluminescence in the Sea
Steven H.D. Haddock, Mark A. Moline, James F. Case

A much shorter review that I read this morning is

Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity, by E.A. Widder

An article in Quanta magazine, In the Deep, Clues to How Life Makes Light by Stephanie Yin

So what is the underlying photophysics and quantum chemistry? The following review is helpful.

The Chemistry of Bioluminescence: An Analysis of Chemical Functionalities 

Isabelle Navizet, Ya-Jun Liu, Nicolas Ferré, Daniel Roca-Sanjuán, Roland Lindh

Almost all currently known chemiluminescent substrates have the peroxide bond, -O-O-, in common as a chemiluminophore. This chemical system facilitates the essential mechanism of chemiluminescence—providing a route for a thermally activated chemical ground-state reaction to produce a product in an electronically excited state. The basics of this process can be understood from studies of ... dioxetanone. [it] contains a peroxide bond, [and] fragments like the firefly luciferin system to carbon dioxide.

The squiggly line denotes the bond that is broken to produce the excited singlet state.
The figure below shows the potential energy surface that describes the dynamics leading to the emissive state. Note the presence of two conical intersections.

 

Much of this photophysics can be understood in terms of a "two-site Hubbard model" discussed in this classic paper that I love.

Neutral and Charged Biradicals, Zwitterions, Funnels in S1, and Proton Translocation: Their Role in Photochemistry, Photophysics, and Vision

Vlasta Bonačić-Koutecký, Jaroslav Koutecký, Josef Michl

In simple terms, all that is different in the biomolecular system is that the enzyme and the larger chromophore tune energy levels so that the energy barriers are much smaller so that the steps needed for bioluminescence become accessible at room temperature.

This highlights two fundamental things. 

Chemistry is local. This is relevant to understanding Wannier orbitals in solid state physics, to hydrogen bonding, and how protein structure aids function.

"Biochemistry is the search for the chemistry that works" [in water at room temperature].

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