Atoms Of Ligand Research Articles

Charge transfer complexation between some transition metal ions with azo Schiff base donor as a smart precursor for synthesis of nano oxides: An adsorption efficiency for treatment of Congo red dye in wastewater

This mentioned article aimed to synthesized of nanostructured CuO, Co3O4 and NiO oxides based on the thermal decomposition of precursors associated from the complexation between azo Schiff base chelate (2,2′-((1E,1′E)-hydrazine-1,2-diylidenebis(methaneylylidene))bis(4-((E)-phenyldiazenyl)phenol) (NNOO)) and metal chloride salts with 1:1 M ratio. The NNOO azo Schiff base chelate, and its Cu(II), Co(II) and Ni(II) complexes were synthesized and discussed using microanalytical, molar conductance, magnetic properties, FT-IR, UV–Vis, 1H NMR, mass, and TGA (thermogravimetric analysis) techniques. According to the microanalysis and spectroscopic results, the coordination mode between azo Schiff base ligand and the central metal ion was occurs through NNOO donating atoms of azo Schiff base ligand. The electronic spectra and magnetic susceptibility analyses concluded that all synthesized metal complexes have an octahedral geometrical structural. The metal oxides (CuO, Co3O4, and NiO) nanoparticles were synthesized after the calcination of azo Schiff base complexes at 800 °C in a static air. The assignments of CuO, Co3O4 and NiO nanostructured oxides were discussed based on the FTIR, XRD, and TEM analysis technique. The ability of CuO, Co3O4 and NiO was compared by catalytic degradation of Congo red azo dye. The decolorization behavioral of Congo red dye was examined using spectroscopic UV–Vis techniques. Furthermore, the rate of catalytic decolorization activity of Congo red dye using prepared metal oxides was successfully performed. The dye has been successfully decolorized by ~57% in the presence of Co3O4 NPs at room temperature.

Bidentate Disilicate Framework for Bis-Grafted Surface Species.

Recent advances in surface organometallic chemistry have enabled the detailed characterization of the surface species in single-site heterogeneous catalysts. However, the selective formation of bis-grafted surface species remains challenging because of the heterogeneity of the supporting surface. Herein, we introduce a metal complex bearing bidentate disilicate ligands, -OSi(Ot Bu)2 OSi(Ot Bu)2 O-, as a molecular precursor, which has a silicate framework adjacent to the metal (Pt) center. The grafting of the precursors on silica supports (MCM-41 and CARiACT Q10) proceeded through a substitution reaction on the silicon atoms of the disilicate ligand, which was verified by the detection of isobutene and t BuOH as the elimination products, to selectively yield bis-grafted surface species. The chemical structure of the surface species was characterized by solid-state NMR, and the chemical shift values of the ancillary ligands and 195 Pt nuclei suggested that the bidentate coordination sphere was maintained following grafting.

Electronic Structure and Donor Ability of an Unsaturated Triphosphorus-Bridged Dimolybdenum Complex.

The triphosphorus complex [Mo2Cp2(μ-η3:η3-P3)(μ-PtBu2)] was prepared in 83% yield by reacting the methyl complex [Mo2Cp2(μ-κ1:η2-CH3)(μ-PtBu2)(μ-CO)] with P4 at 333 K, a process also giving small amounts of the methyldiphosphenyl complex [Mo2Cp2(μ-η2:η2-P2Me)(μ-PtBu2)(CO)2]. The latter could be better prepared by first reacting the anionic complex Na[Mo2Cp2(μ-PtBu2)(μ-CO)2] with P4 to give the diphosphorus derivative Na[Mo2Cp2(μ-η2:η2-P2)(μ-PtBu2)(CO)2] and further reaction of the latter with MeI. Density functional theory calculations on the title complex revealed that its triphosphorus group can be viewed as an allylic-like P3– ligand acting as a six-electron donor via the external P atoms, while coordination of the internal P atom involves donation from the π orbital of the ligand and back-donation to its π* orbital, both interactions having a weakening effect on the Mo–Mo and P–P connections. The reactivity of the title compound is dominated by the electron-donor ability associated with the lone pairs located at the P atoms. Its reaction with CF3SO3Me gave [Mo2Cp2(μ-η3:η3-P3Me)(μ-PtBu2)](CF3SO3) as a result of methylation at an external atom of the P3 ligand, while its reaction with [Fe2(CO)9] enabled the addition of one, two, or three Fe(CO)4 fragments at these P atoms, but only the diiron derivative [Mo2Fe2Cp2(μ-η3:η3:κ1:κ1-P3)(μ-PtBu2)(CO)8] could be isolated. This complex bears a Fe(CO)4 fragment at each of the external atoms of the P3 ligand, and the central P atom of the latter displays the lowest 31P chemical shift reported to date (δP −721.8 ppm). The related complexes [Mo2M2Cp2(μ-η3:η3:κ1:κ1-P3)(μ-PtBu2)(CO)10] (M = Mo, W) were prepared by reacting the title compound with the corresponding [M(CO)5(THF)] complexes in toluene, while reaction with [Mo(CO)4(THF)2] also enabled the formation of the heptanuclear derivative [Mo7Cp4(μ-η3:η3:κ1:κ1-P3)2(μ-PtBu2)2(CO)14]. The interatomic distances in the above compounds indicate that the central Mo2P3 skeleton of these molecules is little modified by the attachment of 16-electron M(CO)n fragments at the external atoms of the P3 ligand.

The Isocyanide Complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd, Pt; X = Cl, Br) as Tectons in Crystal Engineering Involving Halogen Bonds

The isocyanide complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd; X = Cl, Br; M = Pt; X = Br) form isomorphous crystal structures exhibiting the Cl/Br and Pd/Pt exchanges featuring 1D chains upon crystallisation. Crystal packing is supported by the C–X···X–C halogen bonds (HaBs), C–H···X–C hydrogen bonds (HB), X···M semicoordination, and C···C contacts between the C atoms of aryl isocyanide ligands. The results of DFT calculations and topological analysis indicate that all the above contact types belong to attractive noncovalent interactions. A projection of the electron localization function (ELF) and an inspection of the electron density (ED) and the electrostatic potential (ESP) reveal the amphiphilic nature of X atoms playing the role of HaB donors, HaB and HB acceptors, and a nucleophilic partner in X···M semicoordination.

A generalized scheme for characterizing orientational correlations in condensed phases of high symmetry molecules: SF6 and C60

The orientational correlation scheme introduced earlier for tetrahedral molecules is extended for being able to classify orientational correlations between pairs of high symmetry molecules. While in the original algorithm a given orientation of a pair of tetrahedral molecules is characterized unambiguously by the number of ligand atoms that can be found between two planes that contain each centre and perpendicular to the centre-centre connecting line, in the generalized algorithm, the planes are replaced by cones, whose apex angles are set according to the symmetry of each molecule. To demonstrate the applicability of the method, the octahedral-shaped SF6 molecule is studied in a wide range of phases (gaseous, supercritical fluid, liquid and plastic crystalline) using classical molecular dynamics. By analyzing the orientational correlations, a close-contact region in the first coordination shell and a medium-range order behaviour are identified in the non-crystalline phases. While the former is invariant to changes of the density, the latter showed longer-ranged correlations as density is raised. In the plastic crystalline state, fluorine atoms are oriented along the lattice directions with higher probability. To test the method for icosahedral symmetries, the crystalline structures of room temperature C60 is generated by three sets of potentials that produce different local arrangements. The novel analysis provided quantitative result on preferred arrangements.

Synthesis and structure of a mixed ligand copper(II) compound based on a distorted {CuN2O3} square pyramid

The synthesis, spectra, thermal study and crystal structure of a mixed ligand copper(II) compound viz. [Cu(biq)(acac)(NO 3 )] 1 (biq = 2,2′-biquinoline, acac = acetylacetonate) are reported. The {CuN 2 O 3 } coordination sphere is made up of two oxygen atoms of an unique acac ligand, an oxygen of the nitrate group and one N atom of biq ligand which form the basal plane {CuNO 3 } of a square pyramid. A second nitrogen atom of the biq ligand occupies the apical position resulting in a distorted square pyramidal {CuN 2 O 3 } polyhedron. In the crystal structure, each neutral square pyramidal copper(II) species is linked with two symmetry related molecules with the aid of intermolecular C-H×××O hydrogen bonding interactions. A study of fifteen mixed ligand copper(II) acetylacetonates reveals that in this series of compounds, 1 exhibits maximum deviation of the {CuN 2 O 3 } polyhedron from square pyramidal towards trigonal bipyramidal geometry.

Hybrid organoruthenium(II) complexes with thiophene-β-diketo-benzazole ligands: Synthesis, optical properties, CT-DNA interactions and anticancer activity

Two new hybrid half‐sandwiched Ru(II) arene complexes of a general formula [η6-(p-cymene)Ru(L)Cl] (4a,b) {where L = 1-(Benzazol-2-yl)-3-(thiophen-2-yl) propane-1,3-dione} were synthesized and characterized. Spectral and elemental analysis revealed that these complexes have tetrahedral piano stool‐like geometry with a coordination environment composed of two O atoms of ligand, chloride ion, and electron cloud of p‐cymene moiety. The CT-DNA–Ru(II) complexes interactions were evaluated based on absorption and emission titration experiments. The results have shown intercalative modes of interaction between DNA and complexes, with a preferable binding to complex 4b. Based on the in vitro cytotoxicity MTT assay, the complexes exhibit significant inhibitory activity against human breast and lung cancer cells (MCF-7, A549), with lower micromolar IC50 values in comparison to that of clinical drug (cisplatin). In contrast, neither complex shows activity against the normal cell lines (Hela), suggesting that the new hybrid thiophene-β-diketo-benzazole organoruthenium(II) complexes may offer promising safe anticancer agents.

Crystal and Substituent Effects on Paramagnetic NMR Shifts in Transition-Metal Complexes.

Nuclear magnetic resonance (NMR) spectroscopy of paramagnetic molecules provides detailed information about their molecular and electron-spin structure. The paramagnetic NMR spectrum is a very rich source of information about the hyperfine interaction between the atomic nuclei and the unpaired electron density. The Fermi-contact contribution to ligand hyperfine NMR shifts is particularly informative about the nature of the metal–ligand bonding and the structural arrangements of the ligands coordinated to the metal center. In this account, we provide a detailed experimental and theoretical NMR study of compounds of Cr(III) and Cu(II) coordinated with substituted acetylacetonate (acac) ligands in the solid state. For the first time, we report the experimental observation of extremely paramagnetically deshielded 13C NMR resonances for these compounds in the range of 900–1200 ppm. We demonstrate an excellent agreement between the experimental NMR shifts and those calculated using relativistic density-functional theory. Crystal packing is shown to significantly influence the NMR shifts in the solid state, as demonstrated by theoretical calculations of various supramolecular clusters. The resonances are assigned to individual atoms in octahedral Cr(acac)3 and square-planar Cu(acac)2 compounds and interpreted by different electron configurations and magnetizations at the central metal atoms resulting in different spin delocalizations and polarizations of the ligand atoms. Further, effects of substituents on the 13C NMR resonance of the ipso carbon atom reaching almost 700 ppm for Cr(acac)3 compounds are interpreted based on the analysis of Fermi-contact hyperfine contributions.

Synthesis, X-Ray Crystal Structures and Catalytic Epoxidation of Oxidovanadium(V) Complexes with Aroylhydrazone and Ethyl Maltolate Ligands

Two oxidovanadium(V) complexes, [VOL1L] (1) and [VOL2L] (2) (L = ethyl maltolate), derived from the aroylhydrazones 4-bromo-N'-(2-hydroxy-5-methylbenzylidene)benzohydrazide (H2L1) and N'-(3,5-dibromo-2-hydroxybenzylidene)-4-methoxybenzohydrazide (H2L2), respectively, have been synthesized and characterized by elemental analysis, infrared and electronic spectroscopy. Structures of the complexes were further confirmed by single crystal X-ray determination. The V atoms in the complexes are coordinated by the ONO donor atoms of the aroylhydrazone ligand, OO donor atoms of the ethyl maltolate ligand, and one oxido O atom, forming octahedral coordination. The complexes function as effective olefin epoxidation catalysts with hydrogen peroxide as terminal oxidant and sodium hydrogen carbonate as a co-catalyst.

Synthesis and crystal structure of a one-dimensional chain-like strontium(II) coordination polymer built of N-methyldi-ethano-lamine and isobutyrate ligands.

The one-dimensional coordination polymer (I) [Sr(ib)2(H2mda)] n (Hib = isobutyric acid, C4H8O2, and H2mda = N-methyldi-ethano-lamine, C5H13NO2), namely, catena-poly[[(N-methyldi-ethano-lamine-κ3 O,N,O')strontium(II)]-di-μ2-isobutyrato-κ3 O,O':O;κ3 O:O,O'], was prepared by the one-pot aerobic reaction of [Zr6O4(OH)4(ib)12(H2O)]·3Hib with Sr(NO3)2 and H2mda in the presence of MnCl2 and Et3N in aceto-nitrile. The use of MnCl2 is key to the isolation of I as high-quality colorless crystals in good yield. The mol-ecular solid-state structure of I was determined by single-crystal X-ray diffraction. Compound I crystallizes in the monoclinic space group P21/c and shows a one-dimensional polymeric chain structure. Each monomeric unit of this coordination polymer consists of a central SrII ion in the NO8 coordination environment of two deprotonated ib- ligands and one fully protonated H2mda ligand. The C and O atoms of the H2mda ligand were refined as disordered over two sets of sites with site occupancies of 0.619 (3) and 0.381 (3). Compound I shows thermal stability up to 130°C in air.

(1,2,5,6-η)-Cyclo-octa-1,5-diene](1-ethyl-3-isopropyl-1,3-imidazol-2-yl-idene)(tri-phenyl-phosphane)rhodium(I) tetra-fluorido-borate.

A new N-heterocyclic cationic rhodium(I) complex with a tetra-fluorido-borate counter-anion, [Rh(C8H14N2)(C8H12)(C18H15P)]BF4, has been prepared and structurally characterized. The cationic complex exhibits a distorted square-planar environment around the rhodium(I) ion. Two connections are made from rhodium(I) to the carbon atom of an N-heterocylic carbene ligand and to the phospho-rus atom of a tri-phenyl-phosphane ligand. The remaining two coordination sites are made via a bidentate inter-action from the two olefinic bonds of cyclo-octa-diene to the rhodium(I) ion. The compound includes an out-sphere tetra-fluorido-borate counter-anion. Within the crystal of the compound exist several weak inter-molecular C-H⋯F inter-actions.

Deep Scoring Neural Network Replacing the Scoring Function Components to Improve the Performance of Structure-Based Molecular Docking.

Accurate prediction of protein-ligand interactions can greatly promote drug development. Recently, a number of deep-learning-based methods have been proposed to predict protein-ligand binding affinities. However, these methods independently extract the feature representations of proteins and ligands but ignore the relative spatial positions and interaction pairs between them. Here, we propose a virtual screening method based on deep learning, called Deep Scoring, which directly extracts the relative position information and atomic attribute information on proteins and ligands from the docking poses. Furthermore, we use two Resnets to extract the features of ligand atoms and protein residues, respectively, and generate an atom-residue interaction matrix to learn the underlying principles of the interactions between proteins and ligands. This is then followed by a dual attention network (DAN) to generate the attention for two related entities (i.e., proteins and ligands) and to weigh the contributions of each atom and residue to binding affinity prediction. As a result, Deep Scoring outperforms other structure-based deep learning methods in terms of screening performance (area under the receiver operating characteristic curve (AUC) of 0.901 for an unbiased DUD-E version), pose prediction (AUC of 0.935 for PDBbind test set), and generalization ability (AUC of 0.803 for the CHEMBL data set). Finally, Deep Scoring was used to select novel ERK2 inhibitor, and two compounds (D264-0698 and D483-1785) were obtained with potential inhibitory activity on ERK2 through the biological experiments.

Towards mild conditions by predictive catalysis via sterics in the Ru-catalyzed hydrogenation of thioesters

• Milstein's reported discovery of hydrogenation of thioesters directly toward thiols and alcohols catalyzed by a Ru-acridine. • Reaction mechanism and precise description of the rate determining step described by DFT calculations. • Steric maps via%VBur rationalize the path to milder conditions. • Sterical demanding substituents on the P atoms of the PNP pincer ligands reduces the kinetic cost of the rate determining step. The Milstein's reported discovery of hydrogenation of thioesters directly toward thiols and alcohols catalyzed by a Ru-acridine complex has been studied here by DFT calculations to know the origin of the different performance depending on the nature of the substituents. Unveiling the reaction mechanism leads to a deeper understanding of the steric and electronic properties on the nature of the limiting step of the reaction. Steric maps and Conceptual DFT have been the tools to rationalize the reactivity patterns. In addition, the nature of the catalyst has been studied, replacing the substituents on the phosphorous atoms by less sterically demanding groups with the aim to move to milder reaction conditions.

A Porous Copper-Organic Framework Assembled by [Cu12] Nanocages: Highly Efficient CO2 Capture and Chemical Fixation and Theoretical DFT Calculations.

A new porous copper-organic framework assembled from 12-nuclear [Cu12] nanocages {[Cu2(L4-)(H2O)2]·4DMA·2H2O}n (1) (H4L = 5,5'-(butane-1,4-diyl)-bis(oxy)-diisophthalic acid) was successfully prepared and structurally characterized. Compound 1 feathering of a 3D framework with two types of 1D nanotubular channels and a large specific surface area can effectively enrich various harmful dyes. Additionally, due to the carbon dioxide (CO2) interactions with open Cu(II) sites and the electron-rich ether oxygen atoms of ligand in 1, it exhibits a highly selective CO2 uptake. Interestingly, 1 can effectively catalyze the cycloaddition reaction of CO2 with various epoxides under mild conditions, which is ascribed to the Lewis acid Cu(II) sites in the framework of 1. Importantly, 1 acting as a heterogeneous catalyst can be recycled at least 10 times without an obvious loss of catalytic activity, and the CO2 cycloaddition mechanism was further uncovered by density functional theory (DFT) calculations. This study can greatly enrich the MOF catalysts system of CO2 conversion and also provide a valuable guidance for the design of efficient MOFs catalysts.

Ligand Engineered Metal−Organic Frameworks for Electrochemical Reduction of Carbon Dioxide to Carbon Monoxide

The economic feasibility of electrocatalytic carbon dioxide reduction reaction (CO2RR) relies on the development of highly selective and efficient catalysts operating at a high current density. Herein, we explore a ligand engineering strategy involving the use of metal-organic frameworks (MOFs) and combining the desirable features of homogeneous and heterogeneous catalysts for boosting the activity of CO2RR. Zn-based MOFs involving two different azolate functional ligands i.e., 1,2,4-triazole (Calgary Framework-20, CALF-20) and 2-methylimidazole (zeolitic imidazolate framework-8, ZIF-8) were investigated for CO2RR in an alkaline flow cell electrolyzer. The highest CO partial current density of 53.2 mA/cm2 was observed for a Zn-based MOF (CALF-20). CALF-20 showed the highest reported Faradaic efficiency of Zn-based MOFs for CO production (ca. 94% at -0.969 V vs. reversible hydrogen electrode, RHE), with a TOF of 1360.8 h-1 and a partial current density -32.8 mA/cm2. Experimental and density functional theory (DFT) results indicate that the sp2 carbon atoms in azole ligands coordinated with the metal center in the MOFs are the active sites for CO2RR, due to the fully occupied 3d orbital of Zn(II) centers. Ab initio investigation shows that both azolate frameworks in CALF-20 and ZIF-8 have most favorable adsorption sites at the N−sp2 C. Adopting the triazole ligand in CALF-20 enhances the charge transfer (as compared with diazole group in ZIF-8), which induces more electrons in the adjacent active sites at the azole ligand and facilitates *COOH formation, boosting the current density and Faradaic efficiency towards CO production. This study suggests that ligand engineering in MOFs could be a viable approach to design highly efficient CO2RR catalyst.

Crystal structure of di-aqua-(3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosa-ne)copper(II) (3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo[16.4.0.07,12]docosa-ne)copper(II) tetra-bromide dihydrate, [Cu(C22H44N4)(H2O)2][Cu(C22H44N4)]Br4·2H2O.

The crystal structure of the new double CuII complex salt, [Cu(L)(H2O)2][Cu(L)]Br4·2H2O (L = 3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosane, C22H44N4) has been determined using synchrotron radiation. The asymmetric unit contains one half of a [Cu(L)(H2O)2]2+ cation, one half of a [Cu(L)]2+ cation (both completed by crystallographic inversion symmetry), two bromide anions and one water solvent mol-ecule. The CuII atom in the first complex exists in a tetra-gonally distorted octa-hedral environment with the four N atoms of the macrocyclic ligand in equatorial and two aqua ligands in axial positions, whereas the CuII atom in the second complex exists in a square-planar environment defined by the four nitro-gen atoms of the macrocyclic ligand. The two macrocyclic rings adopt the most stable trans-III configuration with normal Cu-N bond lengths from 2.016 (3) to 2.055 (3) Å and an axial Cu-O bond length of 2.658 (4) Å. The crystal structure is stabilized by inter-molecular hydrogen bonds involving the macrocycle N-H or C-H groups and the O-H groups of water mol-ecules as donor groups, and the O atoms of water mol-ecules and bromide anions as acceptor groups, giving rise to a one-dimensional network extending parallel to [100].

Bis(1-methyl-imidazole)[meso-α,α,α,α-tetra-kis(o-nicotinamido-phen-yl)porphinato]iron(II)-1-methyl-imidazole-tetra-hydro-furan (1/1/1.5).

In the title compound, [FeII(C68H44N12O4)(C4H6N2)2]·C4H6N2·1.5C4H8O, the central FeII ion is coordinated by four pyrrole N atoms of the porphyrin core and two N atoms of the 1-methyl-imidazole ligands in the axial sites. One 1-methyl-imidazole and one and a half tetra-hydro-furan solvent mol-ecules are also present in the asymmetric unit. The complex exhibits a near planar porphyrin core conformation, in which the iron centre is slightly displaced towards the hindered porphyrin side (0.01 Å). The average Fe-Np (Np refers to the pyrrole nitro-gen atoms in the porphyrin) bond length is 1.990 (9) Å, and the axial Fe-NIm (NIm refers to the imidazole nitro-gen atoms) bond lengths are 1.993 (3) and 2.004 (3) Å. The dihedral angle between the two coordinated 1-methyl-imidazole planes is 56.6 (2)°. The dihedral angles between the 1-methyl-imidazole planes and the planes of the closest Fe-Np vector are 16.8 (2) and 39.8 (2)°. N-H⋯N and N-H⋯O inter-actions are observed in the crystal structure.

μ-Methyl-ene-bis-[di-bromido(diethyl ether-κO)aluminium(III)]: crystal structure and chemical exchange in solution.

In the title compound, [Al2Br4(CH2)(C4H10O)2], the mol-ecule lies on a crystallographic twofold axis passing through the bridging C atom. Each AlIII atom is four-coordinate, being bonded to two bromide ions, bridging the CH2 group as well as the oxygen atom of a diethyl ether ligand in a slightly distorted tetra-hedral arrangement with angles ranging from 101.52 (8) to 116.44 (5)°. The Al-CH2-Al angle, 118.4 (2)°, is the smallest observed for a structure where this moiety is not part of a ring. In the crystal, weak C-H⋯Br inter-actions, characterized as R 2 2(12) rings, link the mol-ecules into ribbons in the [101] direction. The title compound is monomeric and coordinatively saturated in the solid state, as each aluminum is four-coordinate, but in solution the ether mol-ecules from either or both Al atoms can dissociate, and would be expected to rapidly exchange, and this is supported by NMR data.

Cyclobutanone Inhibitor of Cobalt-Functionalized Metallo-γ-Lactonase AiiA with Cyclobutanone Ring Opening in the Active Site.

An α-amido cyclobutanone possessing a C10 hydrocarbon tail was designed as a potential transition-state mimetic for the quorum-quenching metallo-γ-lactonase autoinducer inactivator A (AiiA) with the support of in-house modeling techniques and found to be a competitive inhibitor of dicobalt(II) AiiA with an inhibition constant of Ki = 0.007 ± 0.002 mM. The catalytic mechanism of AiiA was further explored using our product-based transition-state modeling (PBTSM) computational approach, providing substrate-intermediate models arising during enzyme turnover and further insight into substrate–enzyme interactions governing native substrate catalysis. These interactions were targeted in the docking of cyclobutanone hydrates into the active site of AiiA. The X-ray crystal structure of dicobalt(II) AiiA cocrystallized with this cyclobutanone inhibitor unexpectedly revealed an N-(2-oxocyclobutyl)decanamide ring-opened acyclic product bound to the enzyme active site (PDB 7L5F). The C10 alkyl chain and its interaction with the hydrophobic phenylalanine clamp region of AiiA adjacent to the active site enabled atomic placement of the ligand atoms, including the C10 alkyl chain. A mechanistic hypothesis for the ring opening is proposed involving a radical-mediated process.

Oxygen magnetic polarization, nodes in spin density, and zigzag spin order in oxides

Recent DFT calculations for Ba2CoO4 (BCO) and neutron scattering experiments for SrRuO3 (SRO) have shown that oxygen develops a magnetic polarization. Moreover, DFT calculations for these compounds also unveiled unexpected nodes in the spin density, both along Co-O and Ru-O. For BCO, the overall antiferromagnetic state in its triangular lattice contains unusual zigzag spin patterns. Here, using simple model calculations supplemented by DFT we explain and extend these results. We predict that ligands that in principle should be spinless, such as O$^{2-}$, will develop a net polarization when they act as electronic bridges between transition metal (TM) spins ferromagnetically ordered, regardless of the number of intermediate ligand atoms. The reason is the hybridization between atoms and mobility of the electrons with spins opposite to those of the closest TM atoms. Moreover, for bonds with TMs antiferromagnetically ordered, counterintuitively our calculations show that oxygens should also have a net magnetization for the super-super-exchange cases TM-O-O-TM while for only one oxygen, as in Cu-O-Cu, the O-polarization should cancel. Our simple model also allows us to explain the presence of nodes based on the antibonding character of the dominant singly occupied molecular orbitals along the TM-O bonds. Finally, the zigzag pattern order becomes the ground state mainly due to the influence of the Hubbard $U$, that creates the moments, in combination with a robust easy-axis anisotropy that suppresses the competing 120$^{\circ}$ degree antiferromagnetic order of a triangular lattice. Our predictions are generic and should be applicable to any other compound with characteristics similar to those of BCO and SRO.