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We report a parameterization of the density-functional tight-binding (DFTB) method for the accurate prediction of molecular, electronic and vibrational structure of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces.
This study describes cyclometallation as a new metal binding mode for imine-based COFs. The iridacycle decorated COF could be used for catalytic hydrogen evolution from aqueous formate solution with high stability and high efficacy.
The structural and vibrational properties of pristine graphite and point defects in graphite are studied by tight-binding (TB) calculations using a three-center TB potential model. We showed that the three-center TB potential without ‘‘ad hoc’’ van der Waals interaction corrections can accurately describe the inter-layer distance of graphite and the lowest-energy structures and stabilities of typical point defects in graphite. The results from our TB calculations are in good agreement with those from density-functional theory calculations with van der Waals interaction corrections. We also investigated the vibrational properties to gain better understanding on the localization of vibrational states induced by the point defects. Our calculation results show that although localized or quasi-localized vibrational modes can be found in all defected graphite, the localization induced by Frenkel pair, dual-vacancy, and dual-interstitial defects is much stronger. Atomic displacements associated with the localized vibrational modes induced by these three point defects are also analyzed
We associate potentials with the binding of substrates and inhibitors, H + , C 2 H 2 , CO and MeNC, to nitrogenase MoFe protein by coupling electrochemical control with gas chromatography analysis and in situ infrared spectroscopy.
A robust binding between secondary amines and Au atomic contacts is achieved through the creation of Au adatoms by the use of a wax-coated tip.
Non-cognate GTP and dATP nucleotides can be stabilized or trapped upon initial binding to be prevented from further insertion into the active site of SARS-CoV-2 RdRp enzyme in viral genome replication fidelity control.
A detailed chemical understanding of H 2 interactions with binding sites in the nanoporous crystalline structure of metal–organic frameworks (MOFs) can lay a sound basis for the design of new sorbent materials.
The binding properties of DNA-coated colloids are modified by growing new DNA domains on the particles’ surface using an isothermal DNA polymerization reaction.
This study explores the versatile binding properties of a tetrapodal ligand framework with nickel, demonstrating ligand fluxionality through the interconversions of several complexes.
An alkene-terminated ligand self-assembles with rare-earth ions, yielding polymerizable cages and subsequently rare-earth-binding polymer networks.
Elucidating the relationship between metal–ligand interactions and the associated conformational change of the ligand is critical for understanding the separation of lanthanides via ion binding.
The impact of explicit water molecules on the binding of two rare earth nitrate aqua complexes, [X(NO 3 ) 3 (H 2 O) n ] (X = Nd, Yb), has been explored on both the internal pores and external surfaces of MCM-22.
A protein-based model of carbon monoxide dehydrogenase displays distinct X-ray absorption, EPR, and vibrational signatures upon CO and CN − binding that support ligand-dependent electronic rearrangement throughout the nickel–iron–sulfur core.
Efficient cellulose degradation by cellulase enzymes is crucial for using lignocellulosic biomass in bioenergy production. Single-molecule microscopy showed that xylan hinders the efficiency of cellulase by inhibiting its binding to cellulose and impeding the processivity of bound enzyme molecules.
The conversion of alpha-zirconium phosphate, Zr(HPO 4 ) 2 ·H 2 O, to the K-, Rb-, and Cs-phases and the subsequent ion exchange behavior of these alkali metal phases, A-ZrP, with La 3+ and Cr 3+ have been investigated. The conversion to the A-ZrP phases was achieved by reaction with metal chloride, metal hydroxide solution, and confirmed through various techniques, including X-ray powder diffraction, thermogravimetry analysis, IR spectroscopy, scanning and transmission electron microscopy, and X-ray photoelectron spectroscopy. The effect of material hydration, which increased the interlayer distance, was also examined. The ion exchange behavior of the A-ZrP showed strong affinity for both La 3+ , a representative for trivalent lanthanide metals, and Cr 3+ , a representative for the trivalent transition metals, with a rapid, near quantitative removal of the M 3+ ions at a pH of 3 when the ion concentration was ≤25% of the ion exchange capacity of the materials. Additionally, the ion affinity was shown to be pH and concentration-dependent, decreasing with a decrease in pH or an increase in ion concentration. Lastly, the binding strength of La- and Cr-loaded ZrP materials was examined through a series of leaching experiments in a carbonate buffer, phosphate buffer, HEPES buffer, and a series of EDTA solutions at various concentrations. No observable leaching occurred in the carbonate buffer, phosphate buffer, HEPES buffer, or when the EDTA concentration was below 0.1 mM. These results highlight the potential for the A-ZrP materials to provide a platform for trivalent transition metal and trivalent lanthanide radionuclide capture for various applications.
Correction for ‘Interfacial rheology of lanthanide binding peptide surfactants at the air–water interface’ by Stephen A. Crane et al. , Soft Matter , 2024, 20 , 9161–9173, https://doi.org/10.1039/D4SM00493K.
Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.
Virtually all proton-pumping terminal respiratory oxygen reductases are members of the heme-copper oxidoreductase superfamily. Most of these enzymes use reduced cytochrome c as a source of electrons, but a group of enzymes have evolved to directly oxidize membrane-bound quinols, usually menaquinol or ubiquinol. All of the quinol oxidases have an additional transmembrane helix (TM0) in subunit I that is not present in the related cytochrome c oxidases. The current work reports the 3.6-Å-resolution X-ray structure of the cytochrome aa 3 -600 menaquinol oxidase from Bacillus subtilis containing 1 equivalent of menaquinone. The structure shows that TM0 forms part of a cleft to accommodate the menaquinol-7 substrate. Crystals which have been soaked with the quinol-analog inhibitor HQNO (N-oxo-2-heptyl-4-hydroxyquinoline) or 3-iodo-HQNO reveal a single binding site where the inhibitor forms hydrogen bonds to amino acid residues shown previously by spectroscopic methods to interact with the semiquinone state of menaquinone, a catalytic intermediate.