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Discovery of Fe7O9: a new iron oxide with a complex monoclinic structure.

ABSTRACT: Iron oxides are fundamentally important compounds for basic and applied sciences as well as in numerous industrial applications. In this work we report the synthesis and investigation of a new binary iron oxide with the hitherto unknown stoichiometry of Fe7O9. This new oxide was synthesized at high-pressure high-temperature (HP-HT) conditions, and its black single crystals were successfully recovered at ambient conditions. By means of single crystal X-ray diffraction we determined that Fe7O9 adopts a monoclinic C2/m lattice with the most distorted crystal structure among the binary iron oxides known to date. The synthesis of Fe7O9 opens a new portal to exotic iron-rich (M,Fe)7O9 oxides with unusual stoichiometry and distorted crystal structures. Moreover, the crystal structure and phase relations of such new iron oxide groups may provide new insight into the cycling of volatiles in the Earth's interior.

SUBMITTER: Sinmyo R

PROVIDER: S-EPMC5015080 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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Discovery of Fe7O9: a new iron oxide with a complex monoclinic structure.

Sinmyo Ryosuke R Bykova Elena E Ovsyannikov Sergey V SV McCammon Catherine C Kupenko Ilya I Ismailova Leyla L Dubrovinsky Leonid L

Scientific reports 20160908

Iron oxides are fundamentally important compounds for basic and applied sciences as well as in numerous industrial applications. In this work we report the synthesis and investigation of a new binary iron oxide with the hitherto unknown stoichiometry of Fe7O9. This new oxide was synthesized at high-pressure high-temperature (HP-HT) conditions, and its black single crystals were successfully recovered at ambient conditions. By means of single crystal X-ray diffraction we determined that Fe7O9 ado ...[more]

PMID: 27605075

Similar Datasets

Author Correction: Discovery of Fe7O9: a new iron oxide with a complex monoclinic structure.

Project description:An amendment to this paper has been published and can be accessed via a link at the top of the paper.

| S-EPMC7160142 | biostudies-literature

Crystal structure of 8-hy-droxy-quinoline: a new monoclinic polymorph.

Project description:In an attempt to grow 8-hy-droxy-quinoline-acetamino-phen co-crystals from equimolar amounts of conformers in a chloro-form-ethanol solvent mixture at room temperature, the title compound, C9H7NO, was obtained. The mol-ecule is planar, with the hy-droxy H atom forming an intra-molecular O-H⋯N hydrogen bond. In the crystal, mol-ecules form centrosymmetric dimers via two O-H⋯N hydrogen bonds. Thus, the hy-droxy H atoms are involved in bifurcated O-H⋯N hydrogen bonds, leading to the formation of a central planar four-membered N2H2 ring. The dimers are bound by inter-molecular π-π stacking [the shortest C⋯C distance is 3.2997 (17) Å] and C-H⋯π inter-actions into a three-dimensional framework. The crystal grown represents a new monoclinic polymorph in the space group P21/n. The mol-ecular structure of the present monoclinic polymorph is very similar to that of the ortho-rhom-bic polymorph (space group Fdd2) studied previously [Roychowdhury et al. (1978 ▶). Acta Cryst. B34, 1047-1048; Banerjee & Saha (1986 ▶). Acta Cryst. C42, 1408-1411]. The structures of the two polymorphs are distinguished by the different geometries of the hydrogen-bonded dimers, which in the crystal of the ortho-rhom-bic polymorph possess twofold axis symmetry, with the central N2H2 ring adopting a butterfly conformation.

| S-EPMC4186174 | biostudies-literature

Discovery of the recoverable high-pressure iron oxide Fe4O5.

Project description:Phases of the iron-oxygen binary system are significant to most scientific disciplines, directly affecting planetary evolution, life, and technology. Iron oxides have unique electronic properties and strongly interact with the environment, particularly through redox reactions. The iron-oxygen phase diagram therefore has been among the most thoroughly investigated, yet it still holds striking findings. Here, we report the discovery of an iron oxide with formula Fe(4)O(5), synthesized at high pressure and temperature. The previously undescribed phase, stable from 5 to at least 30 GPa, is recoverable to ambient conditions. First-principles calculations confirm that the iron oxide here described is energetically more stable than FeO + Fe(3)O(4) at pressure greater than 10 GPa. The calculated lattice constants, equation of states, and atomic coordinates are in excellent agreement with experimental data, confirming the synthesis of Fe(4)O(5). Given the conditions of stability and its composition, Fe(4)O(5) is a plausible accessory mineral of the Earth's upper mantle. The phase has strong ferrimagnetic character comparable to magnetite. The ability to synthesize the material at accessible conditions and recover it at ambient conditions, along with its physical properties, suggests a potential interest in Fe(4)O(5) for technological applications.

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A second monoclinic modification of triphenyl-phosphine oxide hemihydrate.

Project description:In the crystal of the title compound, C(18)H(15)OP·0.5H(2)O, a water molecule links to two adjacent triphenylphosphine molecules by way of O-H⋯O hydrogen bonds. The crystal is twinned, the minor twin component being 36%.

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Structure-guided discovery of new deaminase enzymes.

Project description:A substantial challenge for genomic enzymology is the reliable annotation for proteins of unknown function. Described here is an interrogation of uncharacterized enzymes from the amidohydrolase superfamily using a structure-guided approach that integrates bioinformatics, computational biology, and molecular enzymology. Previously, Tm0936 from Thermotoga maritima was shown to catalyze the deamination of S-adenosylhomocysteine (SAH) to S-inosylhomocysteine (SIH). Homologues of Tm0936 homologues were identified, and substrate profiles were proposed by docking metabolites to modeled enzyme structures. These enzymes were predicted to deaminate analogues of adenosine including SAH, 5'-methylthioadenosine (MTA), adenosine (Ado), and 5'-deoxyadenosine (5'-dAdo). Fifteen of these proteins were purified to homogeneity, and the three-dimensional structures of three proteins were determined by X-ray diffraction methods. Enzyme assays supported the structure-based predictions and identified subgroups of enzymes with the capacity to deaminate various combinations of the adenosine analogues, including the first enzyme (Dvu1825) capable of deaminating 5'-dAdo. One subgroup of proteins, exemplified by Moth1224 from Moorella thermoacetica, deaminates guanine to xanthine, and another subgroup, exemplified by Avi5431 from Agrobacterium vitis S4, deaminates two oxidatively damaged forms of adenine: 2-oxoadenine and 8-oxoadenine. The sequence and structural basis of the observed substrate specificities were proposed, and the substrate profiles for 834 protein sequences were provisionally annotated. The results highlight the power of a multidisciplinary approach for annotating enzymes of unknown function.

| S-EPMC3827683 | biostudies-literature

Zeta-Fe2O3--A new stable polymorph in iron(III) oxide family.

Project description:Iron(III) oxide shows a polymorphism, characteristic of existence of phases with the same chemical composition but distinct crystal structures and, hence, physical properties. Four crystalline phases of iron(III) oxide have previously been identified: α-Fe2O3 (hematite), β-Fe2O3, γ-Fe2O3 (maghemite), and ε-Fe2O3. All four iron(III) oxide phases easily undergo various phase transformations in response to heating or pressure treatment, usually forming hexagonal α-Fe2O3, which is the most thermodynamically stable Fe2O3 polymorph under ambient conditions. Here, from synchrotron X-ray diffraction experiments, we report the formation of a new iron(III) oxide polymorph that we have termed ζ-Fe2O3 and which evolved during pressure treatment of cubic β-Fe2O3 (Ia3 space group) at pressures above 30 GPa. Importantly, ζ-Fe2O3 is maintained after pressure release and represents the first monoclinic Fe2O3 polymorph (I2/a space group) that is stable at atmospheric pressure and room temperature. ζ-Fe2O3 behaves as an antiferromagnet with a Néel transition temperature of ~69 K. The complex mechanism of pressure-induced transformation of β-Fe2O3, involving also the formation of Rh2O3-II-type Fe2O3 and post-perovskite-Fe2O3 structure, is suggested and discussed with respect to a bimodal size distribution of precursor nanoparticles.

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New Phenotype and Mineralization of Biogenic Iron Oxide in Magnetotactic Bacteria.

Project description:Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles originating from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to as magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here, we tackle the question of the organization of magnetosomes, which are always described as constituted by linear chains of nanocrystals. In addition, it is commonly accepted that the iron oxide nanocrystals are in the magnetite-based phase. We show, in the case of a wild species of coccus-type bacterium, that there is a double organization of the magnetosomes, relatively perpendicular to each other, and that the nanocrystals are in fact maghemite. These findings were obtained, respectively, by using electron tomography of whole mounts of cells directly from the environment and high-resolution transmission electron microscopy and diffraction. Structure simulations were performed with the MacTempas software. This study opens new perspectives on the diversity of phenotypes within MTBs and allows to envisage other mechanisms of nucleation and formation of biogenic iron oxide crystals.

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Crystal structure of a new monoclinic polymorph of 2,4-di-hydroxy-benzaldehyde 4-methyl-thio-semi-carbazone.

Project description:The title compound, C9H11N3O2S, is a second monoclinic (P21/c) polymorph of the previously reported Cc form [Tan et al. (2008b ▶). Acta Cryst. E64, o2224]. The mol-ecule is non-planar, with the dihedral angle between the N3CS residue (r.m.s. deviation = 0.0816 Å) and the benzene ring being 21.36 (4)°. The conformation about the C=N bond [1.292 (2) Å] is E, the two N-bound H atoms are anti, and the inner hy-droxy O-bound and outer amide N-bound H atoms form intra-molecular hydrogen bonds to the imine N atom. Crucially, the H atom of the outer hy-droxy group is approximately syn to the H atom of the benzene C atom connecting the two C atoms bearing the hy-droxy substituents. This arrangement enables the formation of supra-molecular tubes aligned along [010] and sustained by N-H⋯O, O-H⋯S and N-H⋯S hydrogen bonds; the tubes pack with no specific inter-actions between them. While the mol-ecular structure in the Cc form is comparable, the H atom of the outer hy-droxy group is approximately anti, rather than syn. This different orientation leads to the formation a three-dimensional architecture based on N-H⋯O and O-H⋯S hydrogen bonds.

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Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery.

Project description:4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery. The unknown binding mode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novel HPPD inhibitor design. Herein, we determined the first crystal structure of Arabidopsis thaliana HPPD (AtHPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 Å. Then, combination of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations confirmed that HPPA takes keto rather than enol form inside the HPPD active pocket. Subsequent site-directed mutagenesis and kinetic analysis further showed that residues (Phe424, Asn423, Glu394, Gln307, Asn282, and Ser267) played important roles in substrate binding and catalytic cycle. Structural comparison between HPPA-AtHPPD and holo-AtHPPD revealed that Gln293 underwent a remarkable rotation upon the HPPA binding and formed H-bond network of Ser267-Asn282-Gln307-Gln293, resulting in the transformation of HPPD from an inactive state to active state. Finally, taking the conformation change of Gln293 as a target, we proposed a new strategy of blocking the transformation of HPPD from inactive state to active state to design a novel inhibitor with K i value of 24.10 nM towards AtHPPD. The inhibitor has entered into industry development as the first selective herbicide used for the weed control in sorghum field. The crystal structure of AtHPPD in complex with the inhibitor (2.40 Å) confirmed the rationality of the design strategy. We believe that the present work provides a new starting point for the understanding of enzymatic reaction mechanism and the design of next generation HPPD inhibitors.

| S-EPMC6750108 | biostudies-literature

Crystal structure of a new monoclinic polymorph of N-(4-methyl-phen-yl)-3-nitro-pyridin-2-amine.

Project description:The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z' = 4) of the previously reported monoclinic (P21/c, with Z' = 2) form [Akhmad Aznan et al. (2010 ?). Acta Cryst. E66, o2400]. Four independent mol-ecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intra-molecular amine-nitro N-H?O hydrogen bond. The differences between mol-ecules relate to the dihedral angles between the rings which range from 2.92?(19) to 26.24?(19)°. The geometry-optimized structure [B3LYP level of theory and 6-311?g+(d,p) basis set] has the same features except that the entire mol-ecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C-H?O, C-H??, nitro-N-O?? and ?-? inter-actions [inter-centroid distances = 3.649?(2)-3.916?(2)?Å].

| S-EPMC4158497 | biostudies-literature

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