Direct INDO/SCI method for excited state calculations

Spectral fine tuning of cyanine dyes: electron donor-acceptor substituted analogues of thiazole orange

The introduction of electron donor and acceptor groups at strategic locations on a fluorogenic cyanine dye allows fine-tuning of the absorption and emission spectra while preserving the ability of the dye to bind to biomolecular hosts such as double-stranded DNA and a single-chain antibody fragment originally selected for binding to the parent unsubstituted dye, thiazole orange (TO). The observed spectral shifts are consistent with calculated HOMO-LUMO energy gaps and reflect electron density localization on the quinoline half of TO in the LUMO. A dye bearing donating methoxy and withdrawing trifluoromethyl groups on the benzothiazole and quinoline rings, respectively, shifts the absorption spectrum to sufficiently longer wavelengths to allow excitation at green wavelengths as opposed to the parent dye, which is optimally excited in the blue.

Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes

Unsymmetrical cyanine dyes are widely used in biomolecular detection due to their fluorogenic behavior, whereby fluorescence quantum yields can be very low in fluid solution but are significantly enhanced in conformationally restricted environments. Herein we describe a series of fluorinated analogues of the dye thiazole orange that exhibit improved fluorescence quantum yields and photostabilities. In addition, computational studies on these dyes revealed that twisting about the monomethine bridge beyond an interplanar angle of 60 degrees leads to a dark state that decays nonradiatively to the ground state, accounting for the observed fluorogenic behavior. The effects of position and number of fluorine substituents correlate with both observed quantum yield and calculated activation energy for twisting beyond this critical angle.

Modeling the Effects of Torsional Disorder on the Spectra of Poly- and Oligo-(p-phenyleneethynylenes)

The absorption spectra of phenyleneethynylene oligomers show an unusual change in shape with oligomer length. The unusual aspects of the spectra arise from rotation of the phenylene rings about the long axis of the oligomer. In the ground electronic state, the barrier to this rotation is low and the spectra in room temperature come from an ensemble of different structures. In the excited electronic state, the barrier to rotation is substantially higher, giving rise to strong nonlinear electron-phonon coupling. A multidimensional semiempirical model that includes these effects is developed for the photophysics of phenyleneethynylene oligomers. The ground-state energy is modeled with a molecular mechanics expression, and the excitation energy is modeled with an exciton model. Intermediate Neglect of Differential Overlap/Singles Configuration Interaction (INDO/SCI) calculations verify the exciton model and provide initial estimates of the model parameters. These parameters generate the qualitative features seen in experimental spectra. Inclusion of entropy effects from the multiple torsional coordinates is essential. Refinement of the parameters yields quantitative agreement with experiment. This agreement shows that coupling to torsional motion is a major factor in the spectroscopy and photophysics of these conjugated polymers.

Optical Properties and Delocalization of Excess Negative Charges on Oligo(Phenylenevinylene)s: A Quantum Chemical Study

A quantum chemical study of the electronic structure of negatively charged phenylenevinylene (PV) oligomers and methoxy-substituted derivatives is presented. The geometries of the PV oligomers were optimized using density functional theory. The geometry deformations are found to be delocalized along the entire oligomer chain without indication of polaron formation. The optical absorption spectra of the negatively charged PVs were calculated using both time-dependent density functional theory (TDDFT) and the singly excited configuration interaction method with an intermediate neglect of differential overlap reference wave function (INDO/s-CIS). The available experimental optical absorption energies are reproduced by the calculations. Introduction of methoxy substituents reduces the transition energies, while this does not have a strong effect on the charge distribution along the chain. DFT calculations yield a more delocalized excess negative charge than that of INDO/s-CIS calculations.