1. |
- Franco, Leandro R., et al.
(author)
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Elucidating the conformational change and electronic absorption spectrum of p-dimethylamino-cinnamaldehyde merocyanine across different solvent polarities
- 2023
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In: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 159:7
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Journal article (peer-reviewed)abstract
- We present a theoretical study on the structural and electronic properties of the p-dimethylamino-cinnamaldehyde (DMACA) merocyanine molecule in solvents of different polarities by combining the free energy gradient and the average solvent electrostatic configuration methods via an iterative procedure based on the sequential quantum mechanics/molecular mechanics hybrid methodology. Studying such a system in solution is a crucial step for understanding the solvent effects on its properties, which can have implications in fields such as optoelectronics and biophysics. We found that the DMACA molecule presents different geometries in nonpolar and polar solvents, changing from a polyene-like structure with a pyramidal dimethylamino group (in gas phase or nonpolar solvents) to a cyanine-like structure with a planar dimethylamino group in water due to the stabilizing effect of hydrogen bonds between DMACA and water. The molecular absorption spectrum showed a significant change, increasing solvent polarity with a large shift of the lower energy band, while the other two low lying bands did not shift significantly. The study accurately described the solvatochromic shift of the lowest-energy band and analyzed the structure of the excited states in terms of the one-electron transition density matrix, which showed that the dominant excited state (associated with the first lower energy band) is characterized by a local excitation on the benzene ring with charge transfer character to the carbon conjugated segment.
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2. |
- Franco, Leandro R., et al.
(author)
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Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration
- 2022
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In: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 12:8, s. 4573-4588
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Journal article (peer-reviewed)abstract
- BP100, a short antimicrobial peptide, produces membrane perturbations that depend on lipid structure and charge, salts presence, and peptide/lipid molar ratios. As membrane perturbation mechanisms are not fully understood, the atomic scale nature of peptide/membrane interactions requires a close-up view analysis. Molecular Dynamics (MD) simulations are valuable tools for describing molecular interactions at the atomic level. Here, we use MD simulations to investigate alterations in membrane properties consequent to BP100 binding to zwitterionic and anionic model membranes. We focused on membrane property changes upon peptide binding, namely membrane thickness, order parameters, surface curvature, lipid lateral diffusion and membrane hydration. In agreement with experimental results, our simulations showed that, when buried into the membrane, BP100 causes a decrease in lipid lateral diffusion and lipid acyl-chain order parameters and sharp local membrane thinning. These effects were most pronounced on the closest lipids in direct contact with the membrane-bound peptide. In DPPG and anionic-aggregate-containing DPPC/DPPG membranes, peptide flip (rotation of its non-polar facet towards the membrane interior) induced marked negative membrane curvature and enhanced the water residence half-life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide. These results further elucidate the consequences of the initial interaction of cationic alpha-helical antimicrobial peptides with membranes.
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3. |
- Franco, Leandro R., et al.
(author)
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Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution
- 2023
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 25:36, s. 24475-24494
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Journal article (peer-reviewed)abstract
- Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2 & PRIME;-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method. Ru-aqua complex in water, showcasing Ru atom, coordinated water, and hydrogen bonds on left; UV-Vis spectrum and comparison to experiment on right. QM/MM approach emphasized.
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4. |
- Franco, Leandro Rezende, et al.
(author)
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Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution
- 2023
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 25:36, s. 24475-24494
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Journal article (peer-reviewed)abstract
- Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2 & PRIME;-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.
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5. |
- Franco, Leandro R., et al.
(author)
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Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand
- 2022
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:17, s. 10222-10240
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Journal article (peer-reviewed)abstract
- Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the 1H-NMR properties, spectroscopy (UV-vis absorption), and the acid–base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical–experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid–base characterization and its effects on the electronic properties of such a molecule in solution. The calculated free-energies allowed the identification of the main species present in solution as a function of the solvent polarity, and its effects on the magnetic shielding of protons (1H-NMR chemical shifts), the UV-vis absorption spectra, and the acid–base equilibrium constants (pKas) in aqueous solution. Three acid–base equilibrium constants were experimentally/theoretically determined (pKa1 = 1.3/1.2, pKa2 = 2.1/2.2 and pKa5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pKa3 = 3.7 and pKa4 = 6.0 were also experimentally determined and assigned to the protonation and deprotonation of dimeric species. The dimerization of the most stable neutral species was investigated by Monte Carlo simulations and its electronic effects were considered for the elucidation of the UV-vis absorption bands, revealing transitions mainly with the charge-transfer characteristic and involving both the monomeric species and the dimeric species. The good matching of the theoretical and experimental results provides an atomistic insight into the solvent effects on the electronic properties of this bis-bidentate bridging ligand.
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6. |
- Mitev, Pavlin D., et al.
(author)
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Different structures give similar vibrational spectra : The case of OH- in aqueous solution
- 2013
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 138:6, s. 064503-
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Journal article (peer-reviewed)abstract
- We have calculated the anharmonic OH-(aq) vibrational spectrum in aqueous solution with a "classical Monte Carlo simulation + QM/MM + vibrational" sequential approach. A new interaction model was used in the Monte Carlo simulations: a modified version of the charged-ring hydroxide-water model from the literature. This spectrum is compared with experiment and with a spectrum based on CPMD-generated structures, and the hydration structures and H-bonding for the two models are compared. We find that: (i) the solvent-induced frequency shift as well as the absolute OH- frequency are in good agreement with experiment using the two models; (ii) the Raman and IR bands are very similar, in agreement with experiment; (iii) the hydration structure and H-bonding around the ion are very different with the two ion-water interaction models (charged-ring and CPMD); (iv) a cancellation effect between different regions of the hydration shell makes the total spectra similar for the two interaction models, although their hydration structures are different; (v) the net OH- frequency shift is a blueshift of about + 80 cm(-1) with respect to frequency of the gas-phase ion.
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7. |
- Silva, Jose Luis, et al.
(author)
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X‑ray Photoelectron Fingerprints of High-Valence Ruthenium−Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment
- 2019
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 10:24, s. 7636-7643
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Journal article (peer-reviewed)abstract
- Recent advances in operando-synchrotron-based X-ray techniques are making it possible to address fundamental questions related to complex proton-coupled electron transfer reactions, for instance, the electrocatalytic water splitting process. However, it is still a grand challenge to assess the ability of the different techniques to characterize the relevant intermediates, with minimal interference on the reaction mechanism. To this end, we have developed a novel methodology employing X-ray photoelectron spectroscopy (XPS) in connection with the liquid-jet approach to probe the electrochemical properties of a model electrocatalyst, [RuII(bpy)2(py)-(OH2)]2+, in an aqueous environment. There is a unique fingerprint of the extremely important higher-valence ruthenium−oxo species in the XPS spectra along the oxidation reaction pathway. Furthermore, a sequential method combining quantum mechanics and molecular mechanics is used to illuminate the underlying physical chemistry of such systems. This study provides the basis for the future development of in-operando XPS techniques for water oxidation reactions.
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