Wednesday, April 4, 2012

Effective Hamiltonians for a family of organic dyes

Seth Olsen and I have just finished a paper An Effective Hamiltonian for Symmetric Diarylmethanes from a Series of Analogous Quantum Chemical Models.

Finding simple effective Hamiltonians for classes of complex chemical systems is not easy. Justifying them from quantum chemistry is even harder. We consider a family of organic dye molecules related to Michler's hydrol blue, including auramine-O and malachite green. These molecules are increasingly being used as sensors of the local environment in biomolecules.

The three lowest singlet states can be described by a 3x3 matrix Hamiltonian whose parameters vary across the family of the dyes. This variation appears to be correlated with an empirical parameter [Brown-Okamoto] used to characterise the effect of substituents. There is also a subtle and interesting variation in the character of the diabatic states as one traverses the family of dyes.


  1. Hi Ross,
    Nice paper :). I have a few comments, if you like.
    In 2.2, when introducing the Hamiltonian, I think the point that this is the most general 3 state model allowed by the symmetry could be made earlier (and stronger), before writing any of the individual elements.
    The identification of |L>, |R>, |B> as left, right and bridge states could be clearer; possibly even inspired by symmetry arguments when introducing H.
    I think the labeling in Fig 2 might be wrong; should the purple "l2b2" state be "b2r2"?

  2. Thanks Jacko; I'm glad you enjoyed it. You're right about the figure error - thanks again, and I'll give the paragraph in 2.2 some special attention. Hope all's well over yonder.