TDDFT Investigation of the Raman and Resonant Raman Spectra of Fluorescent Protein Chromophore Models.

The off-resonance and resonant Raman spectra have been simulated for models of fluorescent protein chromophores, those of the green fluorescent protein (GFP, called FP1) and of DsRed (called FP2), which presents a longer π-conjugated path, with the aim of providing a systematic investigation of structural but also computational aspects. These were performed at the (time-dependent) density functional theory [(TD)DFT] level. The off-resonance intensities have been calculated from the derivatives of the frequency-dependent polarizability with respect to the normal coordinates while the resonant ones have been evaluated using Huang-Rhys factors determined from the gradients of the excitation energies with respect to the normal coordinates.

Simulation of absorption and scattering spectra of crystalline organic nanoparticles with the discrete dipole approximation: Effects of crystal shape, crystal size, and refractive index of the medium.

The effect of the shape (habit) of crystalline organic nanoparticles on their absorption spectra is studied by simulations using the discrete dipole approximation, focusing, in particular, on the vibronic structure of the absorption bands in the spectra. Simulations predict a significant effect that, for sufficiently small particles, can be simply rationalized by the depolarization factor. The crystal size and the refractive index of the medium in which the nanoparticles are embedded are also found to have an effect on the absorption spectra.

Predicting Keto-Enol Equilibrium from Combining UV/Visible Absorption Spectroscopy with Quantum Chemical Calculations of Vibronic Structures for Many Excited States. A Case Study on Salicylideneanilines.

Salicylideneanilines are characterized by a tautomer equilibrium, between an enol and a keto form of different colors, at the origin of their remarkable thermochromic, solvatochromic, and photochromic properties. The enol form is usually the most stable but appropriate choice of substituents and conditions (solvent, crystal, host compound) can displace the equilibrium toward the keto form so that there is a need for fast prediction of the keto:enol abundance ratio. Here we demonstrate the reliability of a combined theoretical-experimental method, based on comparing simulated and measured UV/visible absorption spectra, to determine this keto/enol ratio.

Pigment violet 19 - a test case to define a simple method to simulate the vibronic structure of absorption spectra of organic pigments and dyes in solution.

A typical quinacridone pigment, PV19, has been used to analyze the impact of several computational parameters on the UV/vis absorption band shape in solution, simulated using density functional theory and time-dependent density functional theory levels of approximation. These encompass, (i) the choice of exchange-correlation functional, (ii) the basis set, (iii) the method for non-equilibrium optimization of the excited state geometry, (iv) the approach for evaluating the vibronic band structure, (v) the peak broadening, and (vi) the scaling of the harmonic vibrational frequencies. Among these, the choice of exchange-correlation functional is certainly of the most importance because it can drastically modify the spectral shape.

Multimode simulation of dimer absorption spectra from first principles calculations: application to the 3,4,9,10-perylenetetracarboxylic diimide dimer.

First principles calculations based on density functional theory (DFT) have been combined with the multimode vibronic theory of coupled identical monomers to simulate the absorption spectra of dimers. In comparison to our previous study [J. Guthmuller et al.

Prediction of Vibronic Coupling and Absorption Spectra of Dimers from Time-Dependent Density Functional Theory: The Case of a Stacked Streptocyanine.

Methods based on density functional theory calculations have been used to simulate the absorption spectra of a streptocyanine and of its covalently bonded dimer. Two approaches, based on multimode Franck-Condon overlap integrals, have been employed. In the first approach the monomer and the dimer are treated as single molecules, and the Franck-Condon factors are determined for both systems.