Raman Spectroscopy Study of Skin Biopsies from Patients with Parkinson's Disease: Trends in Alpha-Synuclein Aggregation from the Amide I Region.

Parkinson's disease (PD) is one of the most common neurological pathologies with a high prevalence worldwide. PD is characterized by Lewy bodies, whose major component is the aggregates of α-synuclein (αSyn) protein. Interestingly, recent works have demonstrated that skin biopsy studies are a promising diagnostic tool for evaluating α-synucleinopathies. In this sense, this work focuses on the detection of αSyn in skin biopsies employing Raman spectroscopy, using three different approaches: (i) the in vitro Raman spectrum of α-synuclein, (ii) the ex vivo Raman spectra of human skin biopsies from healthy and Parkinson's disease patients, and (iii) theoretical calculations of the Raman spectra obtained from different model αSyn fragments using density functional theory (DFT). Significant differences in the intensity and location of Raman active frequencies in the amide I region were found when comparing healthy and PD subjects related to α-synuclein conformational changes and variations in their aggregation behavior. In samples from healthy patients, we identified well-known Raman peaks at 1655, 1664, and 1680 cm-1 associated with the normal state of the protein. In PD subjects, shifted Raman bands and intensity variations were found at 1650, 1670, and 1687 cm-1 associated with aggregated forms of the protein. DFT calculations reveal that the shape of the amide I Raman peak in model αSyn fragments strongly depends on the degree of aggregation. Sizable frequency shifts and intensity variations are found within the highly relevant 1600-1700 cm-1 domain, revealing the sensitivity of the amide I Raman band to the changes in the local atomic environment. Interestingly, we obtain that the presence of surrounding waters also affects the structure of the amide I band, leading to the appearance of new peaks on the low-frequency side and a notable broadening of the Raman spectra. These results strongly suggest that, through Raman spectroscopy, it is possible to infer the presence of aggregated forms of αSyn in skin biopsies, a result that could have important implications for understanding α-synuclein related diseases.

Potential of Mean Force Calculations for an SN2 Fluorination Reaction in Five Different Imidazolium Ionic Liquid Solvents Using Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

The use of ionic liquids (ILs) as both catalysts and solvents in a wide range of chemical reactions has received considerable attention over the last few years due to their positive effects in enhancing reaction rates and selectivities. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations were carried out in conjunction with umbrella-sampling techniques to study the bimolecular nucleophilic substitution (SN2) fluorination reaction between propyl-mesylate and potassium fluoride using five ILs as solvents, specifically, 1-butyl-3-methylimidazolium mesylate ([C4mim][OMs]), 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim][BF4]), 1-butyl-3-methylimidazolium trifluoroacetate ([C4mim][CF3COO]), 1-butyl-3-methylimidazolium bromide ([C4mim][Br]), and 1-butyl-3-methylimidazolium chloride ([C4mim][Cl]) at 373.15 K. The QM region (reactive part) in all QM/MM systems was simulated using the Parametric Method 6 (PM6) semiempirical methods, and for the MM region (IL solvent), classical force fields (FF) were employed, with the FF developed within the group. The calculated activation free energy barriers (ΔG‡) for the SN2 reaction in the presence of [C4mim][OMs] and [C4mim][BF4] ILs were in agreement with the experimental values reported in the literature. On the other hand, only predicted values were obtained for the activation energies for the [C4mim][CF3COO], [C4mim][Br], and [C4mim][Cl] ILs. These activation energies indicated that the SN2 reaction would be more facile to proceed using the [C4mim][Cl] and [C4mim][OMs] ILs, in contrast with the use of [C4mim][Br] IL, which presented the highest activation energy. Energy-pair distributions, radial distribution functions, and noncovalent interactions (NCI) were also calculated to elucidate the molecular interactions between the reactive QM region and the solvents or reaction media. From these calculations, it was found that not only the reactivity can be enhanced by selecting a specific anion to increase the K-F separation but also the cation plays a relevant role, producing a synergetic effect by forming hydrogen bonds with the fluorine atom from KF and with the oxygen atoms within the mesylate leaving group. Three interactions are significant for the IL catalytic behavior, FQM-HX, KQM-anion, and OQM-HX interactions, where the FQM and KQM labels correspond to fluorine and potassium atoms from the KF salt, OQM corresponds to oxygen atoms within the mesylate leaving group (reactant), and HX refers to hydrogen atoms within the IL cation. The NCI analysis revealed that KQM-anion interactions are of weak type, indicating the importance of hydrogen bond interactions from the cation such as FQM-HX and OQM-HX for the catalytic behavior of ILs.

Thermodynamic, structural and dynamic properties of ionic liquids [C4mim][CF3COO], [C4mim][Br] in the condensed phase, using molecular simulations.

In this work a series of thermodynamic, structural, and dynamical properties for the 1-butyl-3-methylimidazolium trifluoroacetate ([C4mim][CF3COO]) and 1-butyl-3-methylimidazolium bromide, ([C4mim][Br]) ionic liquids (ILs) were calculated using Non-polarizable Force Fields (FF), parameterized using a methodology developed previously within the research group, for condensed phase applications. Properties such as the Vapor-Liquid Equilibrium (VLE) curve, critical points (ρ c, T c), Radial, Spatial and Combined Distribution Functions and self-diffusion coefficients were calculated using Equilibrium Molecular Dynamics simulations (EMD); other properties such as shear viscosities and thermal conductivities were calculated using Non-Equilibrium Molecular Dynamics simulations (NEMD). The results obtained in this work indicated that the calculated critical points are comparable with those available in the literature. The calculated structural information for these two ILs indicated that the anions interact mainly with hydrogen atoms from both the imidazolium ring and the methyl chain; the bromide anion displays twice the hydrogen coordination number than the oxygen atoms from the trifluoroacetate anion. Furthermore, Non-Covalent interactions (NCI index), determined by DFT calculations, revealed that some hydrogen bonds in the [C4mim][Br] IL displayed similar strength to those in the [C4mim][CF3COO] IL, in spite of the shorter O--H distances found in the latter IL. The majority of the calculated transport properties presented reasonable agreement with the experimental available data. Nonetheless, the self-diffusion coefficients determined in this work are under-estimated with respect to experimental values; however, by escalating the electrostatic atomic charges for the anion and cation to ±0.8e, only for this property, a remarkable improvement was obtained. Experimental evidence was recovered for most of the calculated properties and to the best of our knowledge, some new predictions were done mainly in thermodynamic states where data are not available. To validate the FF, developed previously within the research group, dynamic properties were also evaluated for a series of ILs such as [C4mim][PF6], [C4mim][BF4], [C4mim][OMs], and [C4mim][NTf2] ILs.