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Four established ReaxFF force fields, trained on biochemical systems, have been systematically benchmarked on 20 proteinogenic amino acids and 11 dipeptides. The force fields were compared with respect to geometries, energetics, and atomic charges of conformers for the amino acids. To assess the performance with respect to reactivity, the condensation reactions for the formation of dipeptides were investigated by calculating the reaction energetics and pathways. We found systematic errors in the torsion angles for the amino acids, with deviations over 100°, and a generally incorrect account of relative energies for amino acid conformers. In describing the reactivity, only one of the force fields could reproduce the reaction energies of amino acid condensations quantitatively. All four force fields predict unphysical mechanisms for these reactions, involving highly unstable intermediate structures, proton transfers involving aliphatic protons, and even five-coordinate carbon atoms. The corresponding energy landscapes exhibit fluctuations on small length scales and artificial minima.The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.Probing structural changes of a molecule induced by charge transfer is important for understanding the physicochemical properties of molecules and developing new electronic devices. Here, we interrogate the structural changes of a single diketopyrrolopyrrole (DPP) molecule induced by charge transport at a high bias using scanning tunneling microscope break junction (STM-BJ) techniques. Selleck Epigenetic inhibitor Specifically, we demonstrate that application of a high bias increases the average nonresonant conductance of single Au-DPP-Au junctions. We infer from the increased conductance that resonant charge transport induces planarization of the molecular backbone. We further show that this conformational planarization is assisted by thermally activated junction reorganization. The planarization only occurs under specific electronic conditions, which we rationalize by ab initio calculations. These results emphasize the need for a comprehensive view of single-molecule junctions which includes both the electronic properties and structure of the molecules and the electrodes when designing electrically driven single-molecule motors.Laser writing as a simple and straightforward method for covalent 2D patterning of graphene remains challenging. Here, we report a facile and efficient approach for a laser-induced 2D patterning of graphene utilizing silver trifluoroacetate, providing an unprecedented high degree of functionalization. The use of laser-triggered photolysis of silver trifluoroacetate to generate trifluoromethyl radicals, confined only to the laser-irradiated region, leads to the selective reaction of graphene, thereby completing direct laser writing on graphene toward a spatially resolved 2D-patterned architecture. This highly 2D-functionalized graphene is completely reversible. Furthermore, a more complex patterned graphene hybrid architecture was constructed, taking advantage of the simultaneously produced/patterned silver nanoparticles during the laser-writing process. Considering the simplicity of this approach and its ability to provide high degrees of functionalization, the prerequisite of 2D patterning of other 2D materials based on this method is provided.Mixed-matrix membranes (MMMs) with an ideal polymer-filler interface and high gas separation performance are very challenging to fabricate because of incompatibility between the fillers and the polymer matrix. This work provides a simple technique to prepare a series of cross-linked MMMs (xMMM@n) by covalently attaching UiO-66-NB metal-organic frameworks (MOFs) within the PEG/PPG-PDMS copolymer matrix via ring-opening metathesis polymerization and in situ membrane casting. The norbornene-modified MOF (UiO-66-NB) is successfully copolymerized and dispersed homogeneously into a PEG/PPG-PDMS matrix because of very fast polymer formation and strong covalent interaction between MOFs and the rubbery polymer. A significant improvement in gas permeability is achieved in membranes up to a 5 wt % MOF loading compared to the pristine polymer membrane without affecting selectivity. The CO2/N2 separation performance of xMMM@1, xMMM@3, and xMMM@5 with 1, 3, and 5 wt % MOF loading, respectively, surpassed Robeson’s 2008 upper bound. In addition, the best performing membrane, xMMM@3 (PCO2 = 585 Barrer and CO2/N2 ∼53), approaches the 2019 upper bound, indicating that the cross-linked MMMs (xMMM@n) are very promising for CO2 separation from flue gas. The experimental results of our study were evaluated and are supported by theoretical data obtained using the Maxwell model for MMMs. Moreover, the developed MMMs, xMMM@ns, displayed outstanding antiplasticization performance at pressures of up to 25 atm and very stable antiaging performance for up to 11 months with good temperature switching behaviors.