Classification of Spectra of Cata-Condensed Hydrocarbons

Abstract

The classification of π-orbitals in a cata-condensed aromatic system is like that of the orbitals of a free electron traveling in a one-dimensional loop of constant potential around the perimeter. To take into account electron interaction, certain quantities corresponding to angular momenta may be added or subtracted. Introduction of the cross-links in the molecule removes the degeneracy. The first excited configuration in such systems gives two low frequency singlet weak absorption bands and two higher singlet strong dipole absorption bands. Selection and polarization rules are given. The levels are identified from the spectra and some of their properties are determined. An explanation is given of the regularities found by Klevens and Platt. A systematic nomenclature is given. The results agree qualitatively with LCAO theory, can be applied easily to unsymmetrical molecules, and can possibly be extended to other types of ring systems.

Modeling the Absorption Spectrum of Tryptophan in Proteins

“…The experimentally determined transition energies to 1 48,18 The wave function approach of Somers et al predicts the vertical transition energies well, and the results, with 3-methylindole representing the chromophore, are in good agreement with experiment, particularly for the first 1 L excited state. In contrast, our Kohn-Sham methodology overestimates the transition energies for each mutant.…”

“…In comparison with the experimentally determined vertical transition energies of 4.37 and 4.77 eV for the 1 (Electronic transitions to) Rydberg orbitals play an important role in the excited states of aromatic chromophores, such as indole, 5 where they may mix with (transitions to the) valence orbitals giving excited states of mixed valence-Rydberg character. In the gas phase we find that our basis set is flexible enough to capture the singlet π-σ* Rydberg state described by Dedonder-Lardeux et al, 17 who predict, using TDDFT, a vertical transition energy of 4.72 eV.…”

“…The calculated gas-phase (isolated) indole transition energies are nearly identical for each of the three mutants. Upon addition of just the extended environment represented by point charges (R ) 0.0 Å), the 1 18 whose best results (using an AMBER force field and charges with snapshot geometries) are 4.32 and 4.73 eV for transitions to 1 L b and 1 L a , respectively. These correspond to red shifts of 0.04 and 0.07 eV with respect to vertical transition energies calculated in the gas phase.…”

“…For the structures selected from the dynamics, planarity was reintroduced in the Trp aromatic side chain by steepest descent minimization with protein atoms including the Trp C γ fixed; i.e., 14 atoms in the aromatic ring were unconstrained during energy minimization. These constraints preserve the 1 angles from the dynamics. The ring is made planar to assess the influence of the environment on the electronic transitions, as distinct from any structural effects, such as the influence of ring puckering.…”

“…1 These are observed for indole in the gas phase and in bulk solvent and are responsible for the majority of the spectroscopic bands due to the side chain of the tryptophan (Trp) residue in proteins. We focus on the two 1 L states, as these are more important in a biological context, where they are used as structural probes.…”