Be3 Ru: Polar Multiatomic Bonding in the Closest Packing of Atoms.
Ontology highlight
ABSTRACT:
SUBMITTER: Agnarelli L
PROVIDER: S-EPMC9210927 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The interplay between spin-orbit coupling and structural inversion symmetry breaking in solids has generated much interest due to the nontrivial spin and magnetic textures which can result. Such studies are typically focused on systems where large atomic number elements lead to strong spin-orbit coupling, in turn rendering electronic correlations weak. In contrast, here we investigate the temperature-dependent electronic structure of [Formula: see text], a [Formula: see text] oxide metal for which both correlations and spin-orbit coupling are pronounced and in which octahedral tilts and rotations combine to mediate both global and local inversion symmetry-breaking polar distortions. Our angle-resolved photoemission measurements reveal the destruction of a large hole-like Fermi surface upon cooling through a coupled structural and spin-reorientation transition at 48 K, accompanied by a sudden onset of quasiparticle coherence. We demonstrate how these result from band hybridization mediated by a hidden Rashba-type spin-orbit coupling. This is enabled by the bulk structural distortions and unlocked when the spin reorients perpendicular to the local symmetry-breaking potential at the Ru sites. We argue that the electronic energy gain associated with the band hybridization is actually the key driver for the phase transition, reflecting a delicate interplay between spin-orbit coupling and strong electronic correlations and revealing a route to control magnetic ordering in solids.
| S-EPMC7355039 | biostudies-literature
Project description:Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.
| S-EPMC5376665 | biostudies-literature
Project description:The recent structural elucidation of about one dozen channels (in which we include transporters) has provided further evidence that these membrane proteins typically undergo large movements during their function. However, it is still not well understood how these proteins achieve the necessary trade-off between stability and mobility. To identify specific structural properties of channels, we compared the helix-packing and hydrogen-bonding patterns of channels with those of membrane coils; the latter is a class of membrane proteins whose structures are expected to be more rigid. We describe in detail how in channels, helix pairs are usually arranged in packing motifs with large crossing angles (|tau| approximately 40 degrees ), where the (small) side chains point away from the packing core and the backbones of the two helices are in close contact. We found that this contributes to a significant enrichment of Calpha-H...O bonds and to a packing geometry where right-handed parallel (tau = -40 degrees +/- 10 degrees ) and antiparallel (tau = +140 degrees +/- 25 degrees ) arrangements are equally preferred. By sharp contrast, the interdigitation and hydrogen bonding of side chains in helix pairs of membrane coils results in narrowly distributed left-handed antiparallel arrangements with crossing angles tau = -160 degrees +/- 10 degrees (|tau| approximately 20 degrees ). In addition, we show that these different helix-packing modes of the two types of membrane proteins correspond to specific hydrogen-bonding patterns. In particular, in channels, three times as many of the hydrogen-bonded helix pairs are found in parallel right-handed motifs than are non-hydrogen-bonded helix pairs. Finally, we discuss how the presence of weak hydrogen bonds, water-containing cavities, and right-handed crossing angles may facilitate the required conformational flexibility between helix pairs of channels while maintaining sufficient structural stability.
| S-EPMC2257885 | biostudies-literature
Project description:BACKGROUND:Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. RESULTS:We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. CONCLUSION:Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.
| S-EPMC3225823 | biostudies-literature
Project description:The vast majority of membrane proteins are anchored to biological membranes through hydrophobic ?-helices. Sequence analysis of high-resolution membrane protein structures show that ionizable amino acid residues are present in transmembrane (TM) helices, often with a functional and/or structural role. Here, using as scaffold the hydrophobic TM domain of the model membrane protein glycophorin A (GpA), we address the consequences of replacing specific residues by ionizable amino acids on TM helix insertion and packing, both in detergent micelles and in biological membranes. Our findings demonstrate that ionizable residues are stably inserted in hydrophobic environments, and tolerated in the dimerization process when oriented toward the lipid face, emphasizing the complexity of protein-lipid interactions in biological membranes.
| S-EPMC3440369 | biostudies-literature
Project description:This paper focuses in the influence of halogen atoms in the design and structural control of the crystal packing of Group VIII halogenated metallocenes. The study is based on the present knowledge on new types of intermolecular contacts such as halogen (X?X, C-X?H, C-X??), ???, and C-H?? interactions. The presence of novel C-H?M interactions is also discussed. Crystal packings are analysed after database search on this family of compounds. Results are supported by ab initio calculations on electrostatic charge distributions; Hirshfeld analysis is also used to predict the types of contacts to be expected in the molecules. Special attention is given to the competition among hydrogen and halogen interactions, mainly its influence on the nature and geometric orientations of the different supramolecular motifs. Supramolecular arrangements of halogenated metallocenes and Group IV di-halogenated bent metallocenes are also compared and discussed. Analysis supports halogen bonds as the predominant interactions in defining the crystal packing of bromine and iodine 1,1'-halometallocenes.
| S-EPMC6278450 | biostudies-literature
Project description:To overcome the fundamental challenge of the weak natural response of antiferromagnetic materials under a magnetic field, voltage manipulation of antiferromagnetic interaction is developed to realize ultrafast, high-density, and power efficient antiferromagnetic spintronics. Here, we report a low voltage modulation of Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction via ionic liquid gating in synthetic antiferromagnetic multilayers of FeCoB/Ru/FeCoB and (Pt/Co)2/Ru/(Co/Pt)2. At room temperature, the distinct voltage control of transition between antiferromagnetic and ferromagnetic ordering is realized and up to 80% of perpendicular magnetic moments manage to switch with a small-applied voltage bias of 2.5?V. We related this ionic liquid gating-induced RKKY interaction modification to the disturbance of itinerant electrons inside synthetic antiferromagnetic heterostructure and the corresponding change of its Fermi level. Voltage tuning of RKKY interaction may enable the next generation of switchable spintronics between antiferromagnetic and ferromagnetic modes with both fundamental and practical perspectives.
| S-EPMC5841336 | biostudies-literature
Project description:In the present work we describe the synthesis and study of a RuII-FeII chromophore-catalyst assembly designed to perform the light-induced activation of an iron bound water molecule and subsequent photo-driven oxidation of a substrate. Using a series of spectroscopic techniques, we demonstrate that excitation of the chromophore unit with 450 nm light, in the presence of a sacrificial electron acceptor, triggers a cascade of electron transfers leading to the formation of a high valent iron(iv)-oxo center from an iron(ii)-bound water molecule. The activity of this catalytic center is illustrated by the oxidation of triphenyl phosphine.
| S-EPMC5488195 | biostudies-literature
Project description:An efficient strategy for designing charge-transfer complexes using coinage metal cyclic trinuclear complexes (CTCs) is described herein. Due to opposite quadrupolar electrostatic contributions from metal ions and ligand substituents, [Au(μ-Pz-(i-C3H7)2)]3·[Ag(μ-Tz-(n-C3F7)2)]3 (Pz = pyrazolate, Tz = triazolate) has been obtained and its structure verified by single crystal X-ray diffraction - representing the 1st crystallographically-verified stacked adduct of monovalent coinage metal CTCs. Abundant supramolecular interactions with aggregate covalent bonding strength arise from a combination of M-M' (Au → Ag), metal-π, π-π interactions and hydrogen bonding in this charge-transfer complex, according to density functional theory analyses, yielding a computed binding energy of 66 kcal mol-1 between the two trimer moieties - a large value for intermolecular interactions between adjacent d10 centres (nearly doubling the value for a recently-claimed Au(i) → Cu(i) polar-covalent bond: Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E5042) - which becomes 87 kcal mol-1 with benzene stacking. Surprisingly, DFT analysis suggests that: (a) some other literature precedents should have attained a stacked product akin to the one herein, with similar or even higher binding energy; and (b) a high overall intertrimer bonding energy by inferior electrostatic assistance, underscoring genuine orbital overlap between M and M' frontier molecular orbitals in such polar-covalent M-M' bonds in this family of molecules. The Au → Ag bonding is reminiscent of classical Werner-type coordinate-covalent bonds such as H3N: → Ag in [Ag(NH3)2]+, as demonstrated herein quantitatively. Solid-state and molecular modeling illustrate electron flow from the π-basic gold trimer to the π-acidic silver trimer with augmented contributions from ligand-to-ligand' (LL'CT) and metal-to-ligand (MLCT) charge transfer.
| S-EPMC8162903 | biostudies-literature
Project description:Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure [Ru(phen)2 dppz]2+ (phen =1,10-phenanthroline and dppz = dipyrido[3,2-a:2´,3´-c]phenazine) and [?-bidppz(phen)4 Ru2 ]4+ (bidppz =11,11´-bis(dipyrido[3,2-a:2´,3´-c]phenazinyl)), on Gram-negative Escherichia coli and Gram-positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while [?-bidppz(phen)4 Ru2 ]4+ only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of [Ru(phen)2 dppz]2+ against B. subtilis was comparable to that of tetracyline. In addition, the ?-enantiomer of [Ru(phen)2 dppz]2+ showed a 2-fold higher bacteriostatic and bactericidal effect compared to the ?-enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
| S-EPMC5248623 | biostudies-literature