Enantioselective synthesis of sulfoxide using an SBA-15 supported vanadia catalyst: a computational elucidation using a QM/MM approach

Vanadium complex as a potential modulator of the autophagic mechanism through proteins PI3K and ULK1: development, validation and biological implications of a specific force field for [VO(bpy)2Cl]

The modulation of autophagy has been presented as a very useful strategy in anticancer treatments. In this sense, the vanadium complex (VC) bis(2,2'-bipyridine)chlorooxovanadium(IV), [VO(bpy)2Cl], is known for its ability to induce autophagy in triple-negative breast cancer cells (TNBC). An excellent resource to investigate the role of VC in the induction of autophagy is to make use of Molecular Dynamics (MD) simulations. However, until now, the scarcity of force field parameters for the VC prevented a reliable analysis. The autophagy signaling pathway starts with the PI3K protein and ends with ULK1. Therefore, in the first stage of this work, we developed a new AMBER force field for the VC (VCFF) from a quantum structure, obtained by DFT calculations. In the second stage, the VCFF was validated through structural analyses. From this, it was possible to investigate, through docking and MD (200 ns), the performance of the PI3K-VC and ULK1-VC systems (third stage). The analyses of this last stage involved RMSD, hydrogen bonds, RMSF and two pathways for the modulation of autophagy. In general, this work fills in the absence of force field parameters (FF) for VC by proposing an efficient and new FF, in addition to investigating, at the molecular level, how VC is able to induce autophagy in TNBC cells. This study encourages new parameterizations of metallic complexes and contributes to the understanding of the duality of autophagic processes.Communicated by Ramaswamy H. Sarma.

Evaluation of autophagy inhibition to combat cancer: (vanadium complex)-protein interactions, parameterization, and validation of a new force field

Autophagy has drawn attention from the scientific community, mainly because of its significant advantages over chemotherapeutic processes. One of these advantages is its direct action on cancer cells, avoiding possible side effects, unlike chemotherapy, which reaches tumor cells and affects healthy cells in the body, leading to a great loss in the quality of life of patients. In this way, it is known that vanadium complex (VC) [VO(oda)(phen)] has proven inhibition effect on autophagy process in pancreatic cancer cells. Keeping that in mind, molecular dynamics (MD) simulations can be considered excellent strategies to investigate the interaction of metal complexes and their biological targets. However, simulations of this type are strongly dependent on the appropriate choice of force field (FF). Therefore, this work proposes the development of AMBER FF parameters for VC, having a minimum energy structure as a starting point, obtained through DFT calculations with B3LYP/def2-TZVP level of theory plus ECP for the vanadium atom. An MD simulation in vacuum was performed to validate the developed FF. From the structural analyses, satisfying values of VC bond lengths and angles were obtained, where a good agreement with the experimental data and the quantum reference was found. The RMSD analysis showed an average of only 0.3%. Finally, we performed docking and MD (120 ns) simulations with explicit solvent between VC and PI3K. Overall, our findings encourage new parameterizations of metal complexes with significant biological applications, as well as allow to contribute to the elucidation of the complex process of autophagy.

Understanding structure-activity relation in VxOy clusters of varied stoichiometry and sizes through conceptual density functional approach

Computations have been performed on V_xO_y clusters (with x = 1-8, y = 1-21) to explore their structure, stability, and reactivity based on local and global reactivity descriptors defined within the formalism of density functional theory (DFT). The vertical and adiabatic ionization energies and electron affinities are in accordance with Franck-Condon principle and suggest that the V_xO_y clusters are more likely to be electron acceptors than donors. The structure and reactivity of V_xO_y clusters delicately depend on their oxygen content and environment. Distinct active sites have been identified for each cluster species on the basis of coordination, symmetry, and charge distribution. The propensity of all the reactive sites towards an approaching electrophile and/or nucleophile has been studied using local reactivity descriptor. In oxygen-poor clusters, the vanadium atoms are more prone to nucleophilic attack. With an increase in oxygen concentration, the coordination number of vanadium increases and reaches four-fold, the site for nucleophilic attack shifts to terminal oxygens. We conclude that of all the stoichiometries, the stable V_xO_y clusters have the (VO₃)_a(V₂O₅)_b formula unit_. The localization of positive charge density in cubic cage structure of V₈O₂₀ successfully traps halide ions (F^-, Cl^-, and Br^-). In view of increasing use of metal oxide clusters in heterogeneous catalysis, the understanding of structure-activity relationship in vanadium oxides' clusters provided in the current study is highly desirable.

Role of ionic liquids on the selectivity and the rate of organic reactions: A computational approach

In the last years, ionic liquids have been used as substitutes to common solvents since they combine good solubility properties with small vapor pressures. Herein, the Diels-Alder reactions of cyclopentadiene (CP) with acrolein, methyl acrylate and acrylonitrile in ionic liquids ([Emim][N(Tf)₂]), ([Hbim][N(Tf)₂]) and ([Bmim][OTf]) have been modeled with density functional theory to explore the effect of ionic liquids on the endo selectivity in the adducts. Besides the hydogen bonding interactions between the cation and the diene in all the structures, endo transition structures are slightly better stabilized than exo transition structures because of the favorable interactions between the H's of the CP ring and the O's of the [N(Tf)₂]^- and [OTf]^- anions of the IL's. In this study, B3LYP/6-31 + G* and M06-2X/6-31 + G* calculations have demonstrated that endo selectivity in the Diels-Alder reactions can be achieved in the presence of ionic liquids in agreement with experiments.