Exploring the Use of a Lipopeptide in Dipalmitoylphosphatidylcholine Monolayers for Enhanced Detection of Glyphosate in Aqueous Environments.

The growing reliance on pesticides for pest management in agriculture highlights the need for new analytical methods to detect these substances in food and water. Our research introduces a SPRWG-(C18H37) lipopeptide (LP) as a functional analog of acetylcholinesterase (AChE) for glyphosate detection in environmental samples using phosphatidylcholine (PC) monolayers. This LP, containing hydrophilic amino acids linked to an 18-carbon aliphatic chain, alters lipid assembly properties, leading to a more flexible system. Changes included reduced molecular area and peak pressure in Langmuir adsorption isotherms. Small angle X-ray scattering (SAXS) and atomic force microscopy (AFM) analyses provided insights into the LP's structural organization within the membrane and its interaction with glyphosate (PNG). Structural and geometric parameters, as derived from in silico molecular dynamics simulations (MD), substantiated the impact of LP on the monolayer structure and the interaction with PNG. Notably, the presence of the LP and glyphosate increased charge transfer resistance, indicating strong adherence of the monolayer to the indium tin oxide (ITO) surface and effective pesticide interaction. A calibration curve for glyphosate concentration adjustment revealed a detection limit (LOD) of 24 nmol L-1, showcasing the high sensitivity of this electrochemical biosensor. This LOD is significantly lower than that of a similar colorimetric biosensor in aqueous media with a detection limit of approximately 0.3 µmol L-1. Such an improvement in sensitivity likely stems from adding a polar residue to the amino acid chain of the LP.

The effect of the dopant nature on the reactivity, interlayer bonding and electronic properties of dual doped bilayer graphene.

Herein, we report on the structural, chemical reactivity and electronic properties of dual-doped bilayer graphene (DDBG). Only one of the layers was doped with a pair of 3p-2p elements. Aluminum was the only dopant which prefers to interact with the undoped layer. The interlayer interaction energies of DDBG are smaller than those determined for bilayer graphene, except for AlN and AlO DDBG. This effect is due to the presence of weak Al-C interlayer bonds. The dopants increase the reactivity of both the doped and undoped layers. Interestingly, we found that hydrogenation is a method that can be used to switch on/off the interlayer bonding, as it controlled the X-C interlayer distance (X = Al, Si, P, S). The magnetic moment of the systems can be adjusted by the position of the 3p dopant. In effect, when X interacts with the doped layer, the magnetic moment is reduced, while it is maintained when X fails to interact. Finally, we found that the doped layer is able to break the symmetry of the undoped sheet and small gaps can be opened in the band structure of the undoped layer. As observed for single doped monolayer graphene, the most effective element for such purposes is P, which opened gaps close to 0.2 eV. For SiN DDBG, the spin filtering properties are enhanced with respect to the monolayered structure.

A first-principles study on the interaction between alkyl radicals and graphene.

The interaction between alkyl radicals and graphene was studied by means of dispersion-corrected density functional theory. The results indicate that isolated alkyl radicals are not likely to be attached onto perfect graphene. It was found that the covalent binding energies are low, and because of the large entropic contribution, ΔG(298)° is positive for methyl, ethyl, isopropyl, and tert-butyl radicals. Although the alkylation may proceed by moderate heating, the desorption barriers are low. For the removal of the methyl and tert-butyl radicals covalently bonded to graphene, 15.3 and 2.4 kcal mol(-1) are needed, respectively. When alkyl radicals are agglomerated, the binding energies are increased. For the addition in the ortho position and on opposite sides of the sheet, the graphene-CH(3) binding energy is increased by 20 kcal mol(-1), whereas for the para addition on the same side of the sheet, the increment is 9.4 kcal mol(-1). In both cases, the agglomeration turns the ΔG(298)°<0. For the ethyl radical, the ortho addition on opposite sides of the sheet has a negative ΔG(298)°, whereas for isopropyl and tert-butyl radicals the reactions are endergonic. The attachment of the four alkyl radicals under consideration onto the zigzag edges is exergonic. The noncovalent adsorption energies computed for ethyl, isopropyl, and tert-butyl radicals are significantly larger than the graphene-alkyl-radical covalent binding energies. Thus, physisorption is favored over chemisorption. As for the ΔG(298)° for the adsorption of isolated alkyl radicals, only the tert-butyl radical is likely to be exergonic. For the phenalenyl radical we were not able to locate a local minimum for the chemisorbed structure since it moves to the physisorbed structure. An important conclusion of this work is that the consideration of entropic effects is essential to investigate the interaction between graphene and free radicals.

On the applicability of cluster models to study the chemical reactivity of carbon nanotubes.

We have performed a comparative study on the reactivity of metallic and semiconducting nanotubes using infinite and finite models. Infinite models were created using periodic boundary conditions while finite ones were constructed by means of hydrogen terminated nanotubes sections. Cluster models systematically underestimate the reactivity of metallic single wall carbon nanotube (SWCNT)s. We have confirmed that metallic nanotubes are more reactive than semiconducting species, in disagreement with previous works. The differences can be attributed to the presence of an instability in the singlet ground state of the wavefunction corresponding to semiconducting nanotubes clusters. When lower electronic states of the pristine cluster are considered, semiconducting nanotubes become less reactive as compared with metallic SWCNTs. Particularly, if an antiferromagnetic solution is considered for the semiconducting (10,0) SWCNT cluster, it becomes less reactive than the (5,5) SWCNT, as observed for infinite models. Because semiconducting nanotubes are less reactive than metallic counterparts, their reaction energies converge faster to the values observed for graphene. For a 1.6-nm diameter semiconducting nanotube, the addition energy is comparable with graphene. Thus, semiconducting nanotubes with diameters larger than 1.6 nm are going to be as reactive as graphene and the effects of curvature will be unimportant.

Theoretical investigation of carbon-sulfur triple bonds.

By means of first principle calculations we have investigated a set of molecules that are presumed to contain carbon-sulfur triple bonds, namely HCSOH, H(3)SCH, cis-FCSF, F(3)CCSF(3), and F(5)SCSF(3). For HCSOH, FCSF, and H(3)SCH we used the CCSD(T) methodology and the correlation-consistent basis sets. On the other hand, F(3)CCSF(3) and F(5)SCSF(3) were studied at the B3LYP, M06-2X, MP2, and G3 levels of theory. We found that none of these molecules display a carbon-sulfur adiabatic bond dissociation energy (ABDE) as strong as diatomic CS (170.5 kcal mol(-1)), or a diabatic bond dissociation energy (DBDE) larger than the one found in SCO (212.0 kcal mol(-1)), although the DBDE of FCSF comes quite close at 208.3 kcal mol(-1). The CS ABDEs of F(3)CCSF(3), F(5)SCSF(3), and H(3)SCH are comparable to that of a single C-S bond. In contrast with the experimental results, F(3)CCSF(3) and F(5)SCSF(3) are predicted to be linear with C(3v) and C(s) symmetry, respectively, at the B3LYP/6-311+G(3df,2p) level. MP2/6-311+G(2df,2p) calculations support the C(3v) symmetry for F(3)CCSF(3), despite F(5)SCSF(3) not having a perfect linear structure; the CSC angle is 174.6°, which is nearly 20° larger than the experimental value. The analysis of the carbene structures of HCSOH and H(3)SCH revealed that they are not significant, because the triplet state is dissociative in these cases. However, for F(3)CCSF(3) and F(5)SCSF(3) , the carbene triplet states lie 0.81 and 0.77 eV above the singlet state, respectively. In the same vein, our investigation supports the presence of a strong double bond for HCSOH. The conflicting evidence available for F(3)CCSF(3) and F(5)SCSF(3) makes it very difficult to determine the nature of the CS bonds. However, the bond dissociation energies and the singlet-triplet splittings clearly suggest that these compounds should be considered as masked sulfinylcarbenes. The analysis of the bond dissociation energies challenges the existence of a triple bond in these five molecules, but from a strictly thermodynamic standpoint, cis-FCSF is found to be the candidate most likely to exhibit triple-bond character.

Hydrogenated double wall carbon nanotubes.

Herein, we investigate the chemisorption of hydrogen on double wall carbon nanotubes (DWCNT) employing density functional theory and periodic boundary conditions. In agreement with recent investigations based on Lennard-Jones potentials, we found that the (n,m)@(n+9,m) combination is favored for tubes with small diameters. The C-H binding energies determined for the (16,0) single wall carbon nanotubes (SWCNT) are nearly identical to those computed for the (7,0)@(16,0) and (8,0)@(16,0) DWCNTs. For both of the latter we found that interlayer interaction modifies the band structure of the inner tube. In the case of hydrogenated DWCNTs, the electronic structure of the inner tube experiences very small changes at high coverages (50%). However, at lower hydrogen coverages (3%-25%) changes are observed in the electronic structure of the inner tube. In agreement with recent experimental results we conclude that, for heavily functionalized DWCNTs, the electronic properties of the inner tube remain unchanged. For zigzag SWCNTs, the band gap becomes larger upon increase in hydrogen coverage; at 50% of coverage the hydrogenated (16,0) SWCNT has a band gap of 3.38 eV. Finally, based on the fact that high coverages significantly elongate C-H bond distances, we propose that the hydrogenation coverage may be determined measuring the C-H vibrational modes.

Analysis of cyclosporin A and a set of analogs as inhibitors of a T. cruzi cyclophilin by docking and molecular dynamics.

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.

Toward the understanding of the molecular basis for the inhibition of COX-1 and COX-2 by phenolic compounds present in Uruguayan propolis and grape pomace.

Propolis and grape pomace have significant amounts of phenols which can take part in anti-inflammatory mechanisms. As the cyclooxygenases 1 and 2 (COX-1 and COX-2) are involved in said mechanisms, the possibility for a selective inhibition of COX-2 was analyzed in vitro and in silico. Propolis and grape pomace from Uruguayan species were collected, extracted in hydroalcoholic mixture and analyzed. Based on phenols previously identified, and taking as reference the crystallographic structures of COX-1 and COX-2 in complex with the commercial drug Celecoxib, a molecular docking procedure was devised to adjust 123 phenolic molecular models at the enzyme-binding sites. The most important results of this work are that the extracts have an overall inhibition activity very similar in COX-1 and COX-2, i.e. they do not possess selective inhibition activity for COX-2. Nevertheless, 10 compounds of the phenolic database turned out to be more selective and 94 phenols resulted with similar selectivity than Celecoxib, an outcome that accounts for the overall experimental inhibition measures. Binding site environment observations showed increased polarity in COX-2 as compared with COX-1, suggesting that polarity is the key for selectivity. Accordingly, the screening of molecular contacts pointed to the residues: Arg106, Gln178, Leu338, Ser339, Tyr341, Tyr371, Arg499, Ala502, Val509, and Ser516, which would explain, at the atomic level, the anti-inflammatory effect of the phenolic compounds. Among them, Gln178 and Arg499 appear to be essential for the selective inhibition of COX-2.

Docking and molecular dynamics studies at trypanothione reductase and glutathione reductase active sites.

A theoretical docking study on the active sites of trypanothione reductase (TR) and glutathione reductase (GR) with the corresponding natural substrates, trypanothione disulfide (T[S]2) and glutathione disulfide (GSSG), is reported. Molecular dynamics simulations were carried out in order to check the robustness of the docking results. The energetic results are in agreement with previous experimental findings and show the crossed complexes have lower stabilization energies than the natural ones. To test DOCK3.5, four nitro furanic compounds, previously designed as potentially active anti-chagasic molecules, were docked at the GR and TR active sites with the DOCK3.5 procedure. A good correlation was found between differential inhibitory activity and relative interaction energy (affinity). The results provide a validation test for the use of DOCK3.5 in connection with the design of anti-chagasic drugs.