Federico Iribarne

Understanding how surface chemistry controls the physical properties of MXenes is essential for designing multifunctional two-dimensional materials. In this work, we investigate a Ti2C-based Janus MXene with an asymmetric OH/F termination and the corresponding symmetric MXenes using first-principles calculations. Combining OH and F terminations on opposite surfaces of Ti2COHF creates inequivalent bonding environments, reducing the structural symmetry and modifying the charge distribution and vibrational polarization. The monolayer retains metallic character dominated by Ti 3d states and exhibits weak spin polarization. Compared with the symmetrically terminated systems, Ti2COHF features finite phonon angular momentum across a broader portion of the vibrational spectrum. The in-plane components of the angular momentum allow nonzero longitudinal phonon helicity, supporting asymmetric surface termination as a route to axial chiral propagating modes. To the best of our knowledge, this is the first study to identify chiral phonon behavior in a MXene material and provide a comprehensive investigation of the structural, electronic, mechanical, magnetic, and chiral vibrational properties of Janus Ti2COHF. Our findings signal asymmetric surface functionalization as a promising route for engineering chiral lattice dynamics and exploring spin–phonon coupling in MXenes.

The removal of agrochemical contaminants from water and soil is a major challenge in environmental remediation. Adsorption-based treatments are widely used for contaminant removal due to their efficiency, scalability, and relatively low cost, making the understanding at the molecular level of pesticide–surface interactions essential for improving remediation strategies. Here, molecular dynamics (MD) simulations with adaptive biasing force (ABF) were used to evaluate the adsorption free energies of several well-known agrochemicals, including glyphosate, atrazine, chlorpyrifos, aminomethylphosphonic acid (AMPA), glufosinate, rotenone, and paraquat, on graphene, graphene oxide, and hydroxylated silica surfaces. These materials represent model systems for the carbonaceous and mineral components commonly found in environmental matrices. MD simulations reveal systematically stronger adsorption on graphene-based materials (≈ −3 to −13 kcal/mol), driven primarily by dispersion and π-surface interactions, resulting in particularly high affinity for aromatic and compounds with low polarity such as atrazine, chlorpyrifos, and rotenone. In contrast, adsorption on hydroxylated silica is substantially weaker (≈ −1 to −3 kcal/mol) and reflects competition between hydrogen bonding, electrostatic interactions with surface silanol groups, and interfacial hydration. Polar molecules, such as glyphosate, glufosinate, and AMPA, interact mainly through hydration-mediated mechanisms, while other compounds, such as paraquat, exhibit intermediate behavior due to their planar aromatic structure. Overall, these findings provide a thermodynamic rationale at the molecular level for the role of soil organic carbon in limiting pesticide leaching and suggest that carbon amendments designed with complementary mineral phases may enhance the retention capacity of natural substrates.

Anthocyanidin 3-O-glucosyltransferase (UFGT) is a key determinant of anthocyanin stabilization in grape berries. Understanding the molecular basis underlying the distinctive deep-purple pigmentation of Vitis vinifera L. cv. Tannat requires a detailed characterization of the genes encoding this enzyme and their products. Here, we combined comparative genomics, berry-skin expression profiling, sequence and phylogenetic analyses, mutual information mapping, structural modelling, and molecular dynamics (MD) simulations to identify and functionally characterize UFGT candidate genes associated with Tannat berry colour development. From an initial set of 300 genomic hits, seven loci were retained based on sequence features and expression patterns during berry skin pigmentation. These putative Tannat UFGT genes clustered into multiple pre-existing paralogous lineages, mapping mainly to chromosomes 16 and 18, supporting functional diversification rather than a recent lineage-specific expansion. Comparative structural analyses revealed a conserved C-terminal Rossmann-like core and a more variable N-terminal region enriched in substitutions and indels, consistent with differential acceptor recognition. Mutual information analysis further identified co-evolving residue networks linking both domains. Binding free energy estimates, computed using the MM/PBSA method, revealed gene-dependent ligand preferences toward the major Tannat anthocyanidins, driven primarily by non-polar interactions and polar solvation. In this context, the intense coloration of Tannat grapes is likely explained by the coordinated “division of labour” of UFGT genes at veraison, exhibiting favourable affinities for delphinidin and petunidin as acceptor aglycones, consistent with the abundance of their derived anthocyanin in the berry skin. Overall, the typical appearance of this cultivar is not only a trait of oenological importance but also an indicator of the strong antioxidant potential conferred by the accumulation of these bioactive metabolites.

Cholesterol is an essential sterol in cell membranes that regulates organization and fluidity. This biomolecule has been identified as one of the critical factors in the internalization process of various viruses in human cells. Therefore, understanding these mechanisms is crucial for a deeper comprehension of viral pathogenicity in the search for practical therapeutic approaches against viral diseases. The biochemical and biophysical processes related to these diseases are highly complex. For this reason, studying model systems capable of mimicking the interaction of lipid membranes with cholesterol and proteins is fundamental. In this work, we propose to study the structural and elastic changes in mono-, bi-, and tridimensional lipid systems composed of dipalmitoylphosphatidylcholine (PC) with varying amounts of cholesterol in the presence and absence of the S protein (Spike) and its receptor-binding domain (RBD) from SARS-CoV-2. To characterize these systems, we used both experimental and theoretical approaches such as Langmuir trough, atomic force microscopy (AFM), small-angle X-ray scattering (SAXS), electrochemical methods, and molecular dynamics (MD) simulations. With the interpretation of all results obtained in this work, it was possible to propose a structural model of the membrane in the presence of cholesterol and the interaction with the Spike protein and RBD. The behavior of the adsorption isotherm and SAXS data, together with the results provided by MD simulations, led us to conclude that cholesterol in PC monolayers promotes local alterations, inducing the formation of more rigid membrane regions. More importantly, cholesterol plays a crucial role in facilitating the allocation of SARS-CoV-2 proteins in lipid systems. This is especially true for the Spike protein, which displayed a non-ACE2 mediated stable binding to the lipid membrane with high internalization.

Cyclophilins (CyPs) are enzymes involved in protein folding. In Trypanosoma cruzi (T. cruzi), the most abundantly expressed CyP is the isoform TcCyP19. It has been shown that TcCyP19 is inhibited by the immunosuppressive drug cyclosporin A (CsA) and analogs, which also proved to have potent trypanosomicidal activity in vitro. In this work, we continue and expand a previous study on the molecular interactions of CsA, and a set of analogs modeled in complexes with TcCyP19. The modeled complexes were used to evaluate binding free energies by molecular dynamics (MD), applying the Linear Interaction Energy (LIE) method. In addition, putative binding sites were identified by molecular docking. In our analysis, the binding free energy calculations did not correlate with experimental data. The heterogeneity of the non-bonded energies and the variation in the pattern of hydrogen bonds suggest that the systems may not be suitable for the application of the LIE method. Further, the docking calculations identified two other putative binding sites with comparable scoring energies to the active site, a fact that may also explain the lack of correlation found. Kinetic experiments are needed to confirm or reject the multiple binding sites hypothesis. In the meantime, MD simulations at the alternative sites, employing other methods to compute binding free energies, might be successful at finding good correlations with the experimental data.