Revisiting the carbon mesopore contribution towards improved performance of ionic liquid–based EDLCs at sub-zero temperatures

The important role of mesopores has been investigated in electric double-layer capacitors (EDLCs) operating from 24 °C down to − 40 °C by using two in-house synthesized carbons with hierarchical porosity. These carbons were prepared from colloidal nanoparticles of SiO2 as the template and d-glucose as the carbon source. A decrease in the average diameter of the nanoparticles from 12 to 8 nm results in increased surface area and offers a perfect match between ions of binary mixture of imidazolium-based fluorinated ionic liquids and the pores of carbon. Short-range graphene layers produced with 8-nm silica nanoparticles lead to the creation of transport channels which better accommodate ions. We explain these findings per coulombic interactions among the ions and between the pore wall and the ionic species under confinement and electrochemical polarization conditions. Further, it is shown that a microporous carbon (another in-house produced rice-husk carbon SBET = 1800 m2∙g−1) performs better than hierarchical carbons at room temperature; however, thanks to the large fraction of mesopores, the latter exhibit far higher capacitance down to − 40 °C. While the ordering of ions in confinement is more critical at room temperature and dictated by the micropores, low temperature performance of supercapacitors is determined by the mesopores that provide channels for facile ion movement and keep the bulk ionic liquid–like properties. Graphical abstract

Crystal structures of two copper(I)–6,6′-dimethyl-2,2′-bipyridyl (dmbpy) compounds, [Cu(dmbpy)2]2[MF6]·xH2O (M = Zr, Hf; x = 1.134, 0.671)

The syntheses and crystal structures of two bimetallic molecular compounds, namely, bis[bis(6,6′-dimethyl-2,2′-bipyridine)copper(I)] hexafluoridozirconate(IV) 1.134-hydrate, [Cu(dmbpy)2]2[ZrF6]·1.134H2O (dmbpy = 6,6′-dimethyl-2,2′-bipyridyl, C12H12N2), (I), and bis[bis(6,6′-dimethyl-2,2′-bipyridine)copper(I)] hexafluoridohafnate(IV) 0.671-hydrate, [Cu(dmbpy)2]2[HfF6]·0.671H2O, (II), are reported. Apart from a slight site occupany difference for the water molecule of crystallization, compounds (I) and (II) are isostructural, featuring isolated tetrahedral cations of copper(I) ions coordinated by two dmbpy ligands and centrosymmetric, octahedral anions of fluorinated early transition metals. The tetrahedral environments of the copper complexes are distorted owing to the steric effects of the dmbpy ligands. The extended structures are built up through Coulombic interactions between cations and anions and π–π stacking interactions between heterochiral Δ- and Λ-[Cu(dmbpy)2]+ complexes. A comparison between the title compounds and other [Cu(dmbpy)2]+ compounds with monovalent and bivalent anions reveals a significant influence of the cation-to-anion ratio on the resulting crystal packing architectures, providing insights for future crystal design of distorted tetrahedral copper compounds.

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6–4) photolyase

Photolyases are flavoenzymes responsible for light-driven repair of carcinogenic crosslinks formed in DNA by UV exposure. They possess two non-covalently bound chromophores: flavin adenine dinucleotide (FAD) as a catalytic center and an auxiliary antenna chromophore that harvests photons and transfers solar energy to the catalytic center. Although the energy transfer reaction has been characterized by time-resolved spectroscopy, it is strikingly important to understand how well natural biological systems organize the chromophores for the efficient energy transfer. Here, we comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6–4) photolyase. In silico simulations indicated that a hydrophobic amino acid residue located at the entrance of the binding site dominates translocation of a loop upon binding of 8-HDF, and a mutation of this residue caused dysfunction of the efficient energy transfer in the DNA repair reaction. Mutational analyses of the protein combined with modification of the chromophore suggested that Coulombic interactions between positively charged residues in the protein and the phenoxide moiety in 8-HDF play a key role in accommodation of 8-HDF in the proper direction. This study provides a clear evidence that Xenopus (6–4) photolyase can utilize 8-HDF as the light-harvesting chromophore. The obtained new insights into binding of the natural antenna molecule will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in (6–4) photolyase by spectroscopic studies.

Computational Analysis of the Interactions between the S100B Extracellular Chaperone and Its Amyloid β Peptide Client

S100B is an astrocytic extracellular Ca2+-binding protein implicated in Alzheimer’s disease, whose role as a holdase-type chaperone delaying Aβ42 aggregation and toxicity was recently uncovered. Here, we employ computational biology approaches to dissect the structural details and dynamics of the interaction between S100B and Aβ42. Driven by previous structural data, we used the Aβ25–35 segment, which recapitulates key aspects of S100B activity, as a starting guide for the analysis. We used Haddock to establish a preferred binding mode, which was studied with the full length Aβ using long (1 μs) molecular dynamics (MD) simulations to investigate the structural dynamics and obtain representative interaction complexes. From the analysis, Aβ-Lys28 emerged as a key candidate for stabilizing interactions with the S100B binding cleft, in particular involving a triad composed of Met79, Thr82 and Glu86. Binding constant calculations concluded that coulombic interactions, presumably implicating the Lys28(Aβ)/Glu86(S100B) pair, are very relevant for the holdase-type chaperone activity. To confirm this experimentally, we examined the inhibitory effect of S100B over Aβ aggregation at high ionic strength. In agreement with the computational predictions, we observed that electrostatic perturbation of the Aβ-S100B interaction decreases anti-aggregation activity. Altogether, these findings unveil features relevant in the definition of selectivity of the S100B chaperone, with implications in Alzheimer’s disease.

Modeling of coupled flow, transport and biogeochemical reactions during electrokinetic bioremediation: model development and application

<p>Electrokinetic (EK) remediation is one of the few in-situ remediation technologies that can effectively remove contaminants from low-permeability porous media. Process-based modeling, including the complex multiphysics and biogeochemical processes occurring during electrokinetic remediation, is instrumental to describe EK systems and to assist in their design. In this work we use NP-Phreeqc-EK [1], a multidimensional, multiphysics code which couples a flow and transport simulator (COMSOL Multiphysics) with a geochemical code (PhreeqcRM) through a MATLAB LiveLink interface. The model allows the simulation of coupled fluid flow, solute transport, charge interactions and biogeochemical reactions during electrokinetics in saturated porous media. The process-based code is applied for the modeling of electrokinetic delivery of amendments to enhance bioremediation (EK-Bio) of chlorinated compounds at a pilot test site [2]. We simulate both conservative and reactive transport scenarios and we compute and show the Nernst-Planck fluxes and the velocities of the different species (such as lactate, chlorinated ethenes and degrading microorganisms). To compare remediation performances and model outcomes we define different metrics quantifying the spatial distribution of the delivered reactants and the mass of the organic contaminants in the system. The process-based model allowed the simulation of the key processes occurring during EK-Bio, including 1) multidimensional electrokinetic transport such as electromigration of charged species and electroosmosis, 2) Coulombic interactions between ions in solution, 3) kinetics of contaminant biodegradation, 4) dynamics of microbial populations, 5) mass transfer limitations and 6) geochemical reactions.</p><p> </p><p>[1] Sprocati, R., Masi, M., Muniruzzaman, M., & Rolle, M. (2019). Modeling electrokinetic transport and biogeochemical reactions in porous media: A multidimensional Nernst–Planck–Poisson approach with PHREEQC coupling. <em>Advances in Water Resources</em>, <strong>127</strong>, 134-147.</p><p>[2] Sprocati, R., Flyvbjerg, J., Tuxen, N., & Rolle, M. (2020). Process-based modeling of electrokinetic-enhanced bioremediation of chlorinated ethenes. <em>Journal of Hazardous Materials</em>, <strong>397</strong>, 122787.</p>

Structure-Based Virtual Screening of Essential Mycobacterium Tuberculosis Enzymes AspS and KatG for potential inhibitors

Mycobacterium tuberculosis (TB) is a leading global cause of disease-related death. Recent works have studied metabolic pathways of the mycobacterium, highlighting essential enzymes to target via competitive inhibition through computational molecular modeling to suppress the organism’s life cycle. We used the Protein Databank (PDB), the UniProt Knowledgebase and the iDock server in this study. In vitro toxicity screening and pharmacokinetic properties were assessed to determine potential ligand safety and drug properties. Our results have revealed five and nine potential ligands for the enzymes AspS and KatG respectively. The KatG active site has displayed binding affinities of -13.443 to -12.895 kcal/mol, while AspS ligands range from -6.580 to -6.490kcal/mol. The intermolecular forces responsible for the differing binding affinities of each enzyme are primarily Coulombic interactions for AspS, versus Coulombic and extensive hydrogen bonding interactions in KatG.

Controlling the Film Microstructure in Organic Thermoelectrics

Doping is a vital method to increase the charge carrier concentration of conjugated polymers, thus improving the performance of organic electronic devices. However, the introduction of dopants may cause phase separation. The miscibility of dopants and polymers as well as the doping-induced microstructure change are always the barriers in the way to further enhance the thermoelectrical performance. Here, recent research studies about the influence of molecular doping on the microstructures of conjugated polymers are summarized, with an emphasis on the n-type doping. Highlighted topics include how to control the distribution and density of dopants within the conjugated polymers by modulating the polymer structure, dopant structure, and solution-processing method. The strong Coulombic interactions between dopants and polymers as well as the heterogeneous doping process of polymers can hinder the polymer film to achieve better miscibility of dopants/polymer and further loading of the charge carriers. Recent developments and breakthroughs provide guidance to control the film microstructures in the doping process and achieve high-performance thermoelectrical materials.

Impact of hydration on ion transport in Li2Sn2S5·xH2O

The layered material Li2Sn2S5 forms two hydrated solid phases under increasing humidity. Intercalated water hydrates the interlayer Li+ ions and screens coulombic interactions, leading to a high in-plane mobility of both Li+ and H2O.

The ultrafast onset of exciton formation in 2D semiconductors

The equilibrium and non-equilibrium optical properties of single-layer transition metal dichalcogenides (TMDs) are determined by strongly bound excitons. Exciton relaxation dynamics in TMDs have been extensively studied by time-domain optical spectroscopies. However, the formation dynamics of excitons following non-resonant photoexcitation of free electron-hole pairs have been challenging to directly probe because of their inherently fast timescales. Here, we use extremely short optical pulses to non-resonantly excite an electron-hole plasma and show the formation of two-dimensional excitons in single-layer MoS2 on the timescale of 30 fs via the induced changes to photo-absorption. These formation dynamics are significantly faster than in conventional 2D quantum wells and are attributed to the intense Coulombic interactions present in 2D TMDs. A theoretical model of a coherent polarization that dephases and relaxes to an incoherent exciton population reproduces the experimental dynamics on the sub-100-fs timescale and sheds light into the underlying mechanism of how the lowest-energy excitons, which are the most important for optoelectronic applications, form from higher-energy excitations. Importantly, a phonon-mediated exciton cascade from higher energy states to the ground excitonic state is found to be the rate-limiting process. These results set an ultimate timescale of the exciton formation in TMDs and elucidate the exceptionally fast physical mechanism behind this process.