Ana Lilian Montero-Alejo

Understanding rhodopsin mutations linked to the retinitis pigmentosa disease: a QM/MM and DFT/MRCI study.

Retinitis pigmentosa (RP) is a pathological condition associated with blindness due to progressive retinal degeneration. RP-linked mutations lead to changes at the retinal binding pocket and in the absorption spectra. Here, we evaluate the geometries, electronic effects, and vertical excitation energies in the dark state of mutated human rhodopsins carrying the abnormal substitutions M207R or S186W at the retinal binding pocket. Two models are used, the solvated protein and the protein in a solvated POPC lipid bilayer. We apply homology modeling, classical molecular dynamics simulations, density functional theory (DFT), and quantum mechanical/molecular mechanical (QM/MM) methods. Our results for the wild type bovine and human rhodopsins, used as a reference, are in good agreement with experiment. For the mutants, we find less twisted QM/MM ground-state chromophore geometries around the C(11)-C(12) double bond and substantial blue shifts in the lowest vertical DFT excitation energies. An analysis of the QM energies shows that the chromophore-counterion region is less stable in the mutants compared to the wild type, consistent with recent protein folding studies. The influence of the mutations near the chromophore is discussed in detail to gain more insight into the properties of these mutants. The spectral tuning is mainly associated with counterion effects and structural features of the retinal chain in the case of the hM207R mutant, and with the presence of a neutral chromophore with deprotonated Lys296 in the case of the hS186W mutant.

Theoretical study of chlordecone and surface groups interaction in an activated carbon model under acidic and neutral conditions.

Activated carbons (ACs) are widely used in the purification of drinking water without almost any knowledge about the adsorption mechanisms of the persistent organic pollutants. Chlordecone (CLD, Kepone) is an organochlorinated synthetic compound that has been used mainly as agricultural insecticide. CLD has been identified and listed as a persistent organic pollutant by the Stockholm Convention. The selection of the best suited AC for this type of contaminants is mainly an empirical and costly process. A theoretical study of the influence of AC surface groups (SGs) on CLD adsorption is done in order to help understanding the process. This may provide a first selection criteria for the preparation of AC with suitable surface properties. A model of AC consisting of a seven membered ring graphene sheet (coronene) with a functional group on the edge was used to evaluate the influence of the SGs over the adsorption. Multiple Minima Hypersurface methodology (MMH) coupled with PM7 semiempirical Hamiltonian was employed in order to study the interactions of the chlordecone with SGs (hydroxyl and carboxyl) at acidic and neutral pH and different hydration conditions. Selected structures were re-optimized using CAM-B3LYP to achieve a well-defined electron density to characterize the interactions by the Quantum Theory of Atoms in Molecules approach. The deprotonated form of surface carboxyl and hydroxyl groups of AC models show the strongest interactions, suggesting a chemical adsorption. An increase in carboxylic SGs content is proposed to enhance CLD adsorption onto AC at neutral pH conditions.

Theoretical study of γ-hexachlorocyclohexane and β-hexachlorocyclohexane isomers interaction with surface groups of activated carbon model

Activated carbon (AC) is employed in drinking water purification without almost any knowledge about the adsorption mechanism of persistent organic pollutants (POPs) onto it. Hexachlorocyclohexane (HCH) is an organochlorinated contaminant present in water and soils of banana crops production zones of the Caribbean. The most relevant isomers of HCH are γ-HCH and β-HCH, both with great environmental persistence. A theoretical study of the influence of AC surface groups (SGs) on HCH adsorption is done in order to help to understand the process and may lead to improve the AC selection process. A simplified AC model consisting of naphthalene with a functional group was used to assess the influence of SGs over the adsorption process. The Multiple Minima Hypersurface (MMH) methodology was employed to study γ-HCH and β-HCH interactions with different AC SGs (hydroxyl and carboxyl) under different hydration and pH conditions. The results obtained showed that association of HCH with SGs preferentially occurs between the axial protons of HCH and SGs oxygen atom, and the most favorable interactions occurring with charged SGs. An increase in carboxylic SGs content is proposed to enhance HCH adsorption onto AC under neutral pH conditions. Finally, this work presents an inexpensive computer aided methodology for preselecting activated carbon SGs content for the removal of a given compound.

Electron density deformations provide new insights into the spectral shift of rhodopsins

Spectral shifts of rhodopsin, which are related to variations of the electron distribution in 11‐cis‐retinal, are investigated here using the method of deformed atoms in molecules. We found that systems carrying the M207R and S186W mutations display large perturbations of the π‐conjugated system with respect to wild‐type rhodopsins. These changes agree with the predicted behavior of the bond length alternation (BLA) and the blue shifts of vertical excitation energies of these systems. The effect of the planarity of the central and Schiff‐base regions of retinal chain on the electronic structure of the chromophore is also investigated. By establishing nonlinear polynomial relations between BLA, chain distortions, and vertical excitation energies, we are also able to provide a semiquantitative approach for the understanding of the mechanisms regulating spectral shifts in rhodopsin and its mutants.

Similarity measures between excited singlet and triplet electron densities in linear acenes: an application to singlet fission

ABSTRACT A theoretical framework for modelling the electronic structure of absorbing molecules that may contribute to explain and even predict phenomena where a singlet exciton is converted to triplet is reported. The pathway is suggested to occur when the excited singlet and triplet electron density maps are similarly shaped at Frank Condon states. Calculations were carried for some linear acene excitons from their multielectronic wave functions and corresponding charge maps after a configuration interaction of singly excited determinants. For cases where the singlet fission effect has been reported, charge maps of certain higher energy singlet excitons show a relevant shape similarity with the corresponding lowest triplet. This method could enlighten the way for predicting transit between singlets and triplets of very big systems and also may help to explain experimental phenomena at femto and even attosecond scales.