What determines the colour of an organic dye?

This week I read most of chapter 4 of the book, Colour and Constitution of Organic Molecules by John Griffiths. I think it is a must-read for anyone working on dye molecules. It is at an elementary level and so accessible to both chemists and physicists, experimentalists and theorists. I fear much of the content has been forgotten or is unknown to many working on these materials, whether quantum chemists or biologists trying to find new molecules for fluorescent marker or people working on dye-sensitised solar cells.

Griffiths gives a nice discussion of resonance theory and then discusses its "failures", stating:

The apparent failure of resonance theory in these systems arises from the assumption that only low energy resonance forms need to be considered as contributing to the ground and first excited states.

Indeed, work by Seth Olsen and I (mostly Seth) shows for methine dyes (including flourescent proteins) how to do this in a systematic manner.

Beware of curve fitting

In a comment on a previous post about charge transport in organic materials Doug Natelson brought to my attention a recent preprint. It is a really nice paper and is a cautionary tale about drawing conclusions from curve fitting.

In a Nature Materials paper last year, Alan Heeger's group at UCSB considered the electric field and temperature dependence of the current in an organic field effect transistor. They fitted the observed dependence to that for a theory which describes slightly dirty long one dimensional conducting wires with strong electronic correlations (Tomonaga-Luttinger liquid theory). This theory gives a good description of charge transport in single carbon nanotubes. However, it is not clear if there is a physical reason to expect the TLL theory to be relevant to "dirty" crystals of small organic molecules.

However, Worne, Anthony, and Natelson show that for their data on similar devices the curve fitting to the TLL theory is problematic. In particular, the apparent "scaling collapse" is fortuitous. They state:

decreasing T moves subsequent temperature data sets up and to the right on the graph, even if the data themselves do not change with temperature at all. In fact, any weakly temperature dependent dataset that resembles a power-law can be made to fit onto a single line if plotted in this way with an appropriate choice of α. Data collapse with this plotting procedure is not sufficient to demonstrate TLL physics.

There is another reason why I am skeptical about any claim of "metalllic" behavior in these systems. Their mobility is much less than than the "minimum mobility"of 1 cm^2/Vsec that is necessary for the coherent transport associated with delocalised electrons and band structure.

Examples of inhomogeneous mixed valence

In contrast, to homogeneous mixed-valence the inhomogeneous mixed-valence case involves a mixture of different integer valence ions which occupy inequivalent lattice sites in a static charge-ordered array. Examples of this are provided by Fe3O4, Eu3O4 and Eu3S4.

The following material and figure is copied from the chemexplore web site

Magnetite (Fe3O4) has the AM₂X₄ spinel structure, of the "inverse" type :

Magnetite has the empirical formula Fe₃O₄, or Fe²⁺(Fe³⁺O₂)₂, “ferrous ferrite”. Its formula as a spinel would be Fe³⁺_tetFe²⁺_octFe³⁺_octO₄ , where "tet" and "oct" stand for tetrahedral and octahedral coordinations by the oxide anions. In the above model, the blue spheres represent the tetrahedral iron(III) cations , and the red spheres are the octahedrally coordinated iron(II) and (III) cations. The oxide anions are shown as the green spheres. Because of the fortuitous inverse nature of the magnetite structure, ferrous and ferric cations are both in the similar octahedral coordination by oxides. In "normal" spinels, such as the mineral spinel itself (magnesium aluminate), the A cation is tetrahedral and the M cations are both octahedral:

However, this inverse-spinel charge ordering has recently been challenged in favour of the normal spinel charge structure where the Fe3+ ions exclusively occupy all the octahedral sites while the Fe2+ ions reside in the tetrahedral sites.

What happens in higher order oxides of cerium is not so simple, as discussed here.

Sell your science not your hyper-activity

One of the most important sections in grant applications in Australia is where applicants have half a page to described their "significant contributions to the field".

Such material is also important in CV's and job applications.

Many people seem to write things like:

-I published a paper in a high impact journal and it has been cited and I got invited to speak on it at a conference.

-I worked on topic XYZ where I learnt how to use technique ABC and then I got offered a job at the prestigious University of Mediocrity.

-I have used state-of-the art software to calculate such and such a property of this exotic material which is a really hot topic right now.

-I previously got a grant. Therefore you should give me another one.

These are all activities not contributions to scientific knowledge.
Grants are inputs not outputs.

Instead you should write something like:

I developed a new technique to measure the position of atoms in crystals to a resolution that was an order of magnitude better than existing techniques. With collaborators from Austria, we were able to show that the actual structure of blah-blah materials was different from that predicted by the standard theoretical model....

This led theoretical chemists to develop a new model which shows that entropic effects are actually important in determining the most stable crystal structure at room temperature.....

Research is all about knowledge creation, not about busyness, metrics, or points scoring.

Bridging the chemistry-physics divide

My UQ colleague Ben Powell has written a nice set of notes An introduction to effective low-energy Hamiltonians in condensed matter physics and chemistry. They will be particularly useful for beginning graduate students. They have already been helpful to theoretical chemists and physicists who struggle to understand each other, when actually talking about the same thing. The notes will be published in a forthcoming book edited by Jeff Reimers.

Are flourescent proteins exotic?

"Biochemistry is the search for the chemistry that works."

Just how special, unique, and fine-tuned are biomolecules?

There are a wide range of proteins which have functionalities based on their optical properties. One outstanding example are flourescent proteins. Seth Olsen and I just completed a paper which uses high-level quantum chemistry calculations to show that the low-lying excited states of the chromophore

molecule in the green flourescent protein has a natural description in terms of the resonant colour theory of organic dyes developed in the middle of the twentieth century by Brooker, Platt, and Moffitt.

[Aside: this is the same Platt of multiple alternative hypothesis fame!].

Brooker showed how one could relate the absorption wavelength of an asymmetric methine dye molecule to the absorption wavelengths of two symmetric parent dyes.

The figure above shows that the anion of the

chromophore for GFP (which is what is responsible for the light emission) is a Brooker dye which is "on resonance", i.e. its ground state and first excited state contain equal superpositions of two valence bond states with electrons displaced to the left and the right of the methine bridge (central carbon atom).

How I use the h-index

I am a big fan of the h-index, when used appropriately.

I review numerous research grant applications and job applications and I find the h-index is a good filter to consider how seriously to take an application.

In comparing theory to experiment any discrepancy by an order of magnitude is usually a pretty good indicator that a theory is in trouble. Factors of 2 to 5 can also be useful.

What I find interesting and useful about the h-index is that there are often differences by factors of as much as 2 to 3 between individuals at the same career stage and applying for the same job or grant. I find it surprising that there are such large variations. Furthermore, there appears to be no correlation between the h-index and how much noise an individual makes about the significance of their work.

Some things I do keep in mind are:

-the younger the person the less reliable and useful the h-index

-differences of less than fifty per cent (e.g., 9 vs. 12 or 20 vs. 24) are of no significance

-different sub-fields have different traditions of citing each others works

One thing I never do is to look up an individual's h-index just out of curiousity. I only look it up if I have to actually evaluate the person.