Structural response of phyllomanganates to wet aging and aqueous Mn(II)
Abstract not provided
Hinkle, Margaret A. G.↗
SEARCH · Engineering Papers
Results for “structures”
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Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer
The aldehyde dehydrogenase (ALDH) superfamily is a vast group of enzymes that catalyze the NAD + -dependent oxidation of aldehydes to carboxylic acids. ALDH16 is perhaps the most enigmatic member of the superfamily, owing to its extra C-terminal domain of unknown function and the absence of the essential catalytic cysteine residue in certain non-bacterial ALDH16 sequences. Herein we report the first production of recombinant ALDH16, the first biochemical characterization of ALDH16, and the first crystal structure of ALDH16. Recombinant expression systems were generated for the bacterial ALDH16 from Loktanella sp. and human ALDH16A1. Four high-resolution crystal structures of Loktanella ALDH16 were determined. Loktanella ALDH16 is found to be a bona fide enzyme, exhibiting NAD + -binding, ALDH activity, and esterase activity. In contrast, human ALDH16A1 apparently lacks measurable aldehyde oxidation activity, suggesting that it is a pseudoenzyme, consistent with the absence of the catalytic Cys in its sequence. The fold of ALDH16 comprises three domains: NAD+-binding, catalytic, and C-terminal. The latter is unique to ALDH16 and features a Rossmann fold connected to a protruding β-flap. The tertiary structural interactions of the C-terminal domain mimic the quaternary structural interactions of the classic ALDH superfamily dimer, a phenomenon we call “trans-hierarchical structural similarity.” ALDH16 forms a unique dimer in solution, which mimics the classic ALDH superfamily dimer-of-dimer tetramer. Small-angle X-ray scattering shows that human ALDH16A1 has the same dimeric structure and fold as Loktanella ALDH16. Finally, we suggest that the Loktanella ALDH16 structure may be considered to be the archetype of the ALDH16 family.
59 BASIC BIOLOGICAL SCIENCES↗
Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity
Not Available
Manjasetty, Babu A.↗
Three new homochiral coordination polymers involving two three-dimensional structural architectures: Syntheses, structures and magnetic properties
The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. -- Graphical abstract: The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. Highlights: • Three homochiral 3D coordination polymers were synthesized. • 1 and 2 are 3D structure with metal-D-cam helical chains pillared by pyrazine. • 3 shows a 3D homochiral framework involving 1D manganese-carboxylate chains. • Magnetic data analysis indicates that 1–3 exhibit weak antiferromagnetic coupling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structures of Ni{sub 3+x}Sn{sub 4}Zn and Ni{sub 6+x}Sn{sub 8}Zn and their structural relations to Ni{sub 3+x}Sn{sub 4}, NiSn and Ni{sub 5−δ}ZnSn{sub 4}
The crystal structures of two new compounds were determined from single-crystal X-ray diffraction measurements: Ni{sub 3+x}Sn{sub 4}Zn, (x~1.35, a=7.110(2) Å, b=4.123(1) Å, c=10.346(3) Å, β=90.23(2)°, space group I2/m, Z=2. R1=0.025, wR2=0.059 for 748 unique reflections, 35 variable parameters) and Ni{sub 6+x}Sn{sub 8}Zn, x~1.35 (a=12.379(3) Å, b=4.095(1) Å, c=12.155(3) Å, β=116.25(3)°, space group C2/m, Z=2. R1=0.026, wR2=0.052 for 1346 unique reflections, 60 variable parameters). In addition, a structural refinement was performed for Ni{sub 3+x}Sn{sub 4}, x~0.13 (a=12.264(3) Å, b=4.066(1) Å, c=5.223(2) Å, β=104.85(3)°, space group C2/m, Z=2. R1=0.019, wR2=0.046 for 617 unique reflections, 29 variable parameters). The three compounds show pronounced similarities among each other as well as to the crystal structures of surrounding binary Ni–Sn and ternary Ni–Sn–Zn compounds. In particular, the two new compounds form a homologous series with Ni{sub 3+x}Sn{sub 4}, x~0.13. They contain “Ni{sub 4}Sn{sub 4}” and “Ni{sub 2}Sn{sub 4}” building blocks which by different interconnection build up the distinct structures. Topological relations with NiSn and Ni{sub 5−δ}Sn{sub 4}Zn, δ~0.25 are evident. - Graphical abstract: Projection of the structure of Ni{sub 6+x}ZnSn{sub 8}, x~1.35 and constituent building blocks. Display Omitted - Highlights: • The crystal structures of Ni{sub 6+x}Sn{sub 8}Zn and Ni{sub 3+x}Sn{sub 4}Zn were determined using single crystal XRD. • Topological relations to Ni–Sn and Ni–Sn–Zn compounds were established and discussed. • Common structural units were identified and their interconnection patterns described.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structure, electronic, and magnetic properties of NaPd{sub 3}Ge{sub 2}
Highlights: • Correct crystal structure of NaPd{sub 3}Ge{sub 2} is solved by single crystal X-ray diffraction. • NaPd{sub 3}Ge{sub 2} is found to crystallize in the ErRh{sub 3}Si{sub 2} structure type. • NaPd{sub 3}Si{sub 2}, NaPd{sub 3}Ge{sub 2} and NaPd{sub 3}Sn{sub 2} are found to be metals down to 2 K. • All three compounds show a weak diamagnetic response down to 2 K. • Trend of p-block atom dimer breaking as function of size. - Abstract: Crystals of NaPd{sub 3}X{sub 2}, (X = Si, Ge, Sn) were synthesized and their crystal structures investigated by single crystal X-ray diffraction. The previously reported structures of NaPd{sub 3}Si{sub 2} and NaPd{sub 3}Sn{sub 2} were confirmed. NaPd{sub 3}Ge{sub 2} was found to have a different unit cell from that originally reported; therefore the structure was solved. It is an orthorhombically distorted version of the hexagonal CeCo{sub 3}Be{sub 2}-type structure, in space group Imma, with cell parameters a = 7.244(1) Å, b = 9.938(1) Å, c = 5.767(2) Å. The originally reported cell is explained through triple twinning of the true cell. The structure of NaPd{sub 3}Ge{sub 2} fits the trend of decreasing X–X dimerization as a function of increasing period from Si–Sn. All three compounds are metals showing weak diamagnetism with increasing resistivity from NaPd{sub 3}Si{sub 2}–NaPd{sub 3}Sn{sub 2}; no superconductivity is observed down to 2 K.
36 MATERIALS SCIENCE↗
Controlling the structure and ferroic properties of strained epitaxial NiTiO3 thin films on sapphire by post-deposition annealing
Ferroelectrically induced weak ferromagnetism had been predicted earlier in compounds MTiO3 (M = Fe, Mn, Ni) with the LiNbO3-type structure. In order to stabilize this metastable structure by oxide heteroepitaxy, we attempted to grow epitaxial NiTiO3 films on the nonpolar, non-magnetic substrate Al2O3 by pulsed laser deposition. Given the structural imperfections of the as-deposited films arising from the large lattice mismatch, which resulted in weak ferroic ordering, we investigated the effect of post-synthesis annealing on the films’ properties. Our structural data from x-ray diffraction and electron microscopy suggest that the crystalline quality of the NiTiO3 films was greatly improved by annealing the films at 600-1000 oC for 8 hours, with new phase formation along the interface at 1000 oC. Our physical property characterization indicates increased ferromagnetism and polarization after 600 oC, but a change in the magnetic state to likely ferrimagnetism, and a loss of polarization after the 1000 oC treatment. Our results suggest that the ferroic domain properties of the NiTiO3 films can be favorably altered by post-synthesis heat treatment at the proper temperature to manipulate interfacial strain and enhance the multiferroic properties. Improvement in the ferroic properties can be explained by a combination of crystallite growth, interfacial strain relief, and thermodynamic phase stability arguments. At the same time, exceeding temperatures may drive the system to a thermodynamically more favored crystalline order, and eventually to phase segregation and decomposition.
Varga, Tamas↗
Structural Transformations in High-Capacity Li 2 Cu 0.5 Ni 0.5 O 2 Cathodes
Cathode materials that can cycle > 1 Li+ per transition metal are of substantial interest to increase the overall energy density of lithium-ion batteries. Li2Cu0.5Ni0.5O2 has a very high theoretical capacity of ~ 500 mAh/g assuming both Li+ are cycled reversibly. The Cu2+/3+ and Ni2+/3+/4+ redox couples are also at high voltage, which could further boost the energy density of this system. Despite such promise, Li2Cu0.5Ni0.5O2 undergoes irreversible phase changes during charge (delithiation) that result in large first-cycle irreversible loss and poor long-term cycling stability. Oxygen is evolved before the Cu2+/3+ or Ni3+/4+ transitions are accessed. In this contribution, XRD, TEM, and TXM-XANES are used to follow the chemical and structural changes that occur in Li2Cu0.5Ni0.5O2 during electrochemical cycling. Li2Cu0.5Ni0.5O2 is a solid solution of orthorhombic Li2CuO2 and Li2NiO2, but the structural changes more closely mimic the Li2NiO2 endmember. Li2Cu0.5Ni0.5O2 loses long-range order during charge, but TEM analysis provides clear evidence for particle exfoliation and the transformation from orthorhombic to a partially layered structure. Linear combination fitting and principal component analysis of TXM-XANES are used to map the different phases that emerge during cycling ex situ and in situ. Significant changes in the XANES at the Cu and Ni K-edges correlate with the onset of oxygen evolution.
Environmental Molecular Sciences Laboratory↗
Hydrogen Bonding Controls the Structural Evolution in Perovskite-Related Hybrid Platinum(IV) Iodides
In this paper, we describe the solid-state structural evolution in four hybrid hexaiodoplatinate(IV) compounds, demonstrating the increasingly important role that extended hydrogen bonding plays in directing the structure across the series. The compounds are A 2 PtI 6 , where A is one of the following amines: ammonium, NH 4 + ; methylammonium, CH 3 NH 3 + ; formamidinium, CH(NH 2 ) 2 + ; guanidinium, C(NH 2 ) 3 + . These are closely related in structure and properties to the hybrid halide perovskites of lead(II) that have recently established their prowess in optoelectronics. The first three of these compounds crystallize in the vacancy-ordered double perovskite A 2 Pt$\square$I 6 ($\square$ indicates a vacant site) structure in the K 2 PtCl 6 archetype, despite the relatively large perovskite tolerance factors involved. The last compound, (GUA) 2 PtI 6 , crystallizes in a vacancy-ordered variant of the hexagonal CsNiCl 3 structure: the K 2 MnF 6 structure. A combination of solid-state 195 Pt and 1 H NMR spectroscopy and detailed density functional theory calculations helps to reveal structural trends and establish the hydrogen-bonding tendencies. Finally, the calculations and measured optical properties support the surprising observation in these iodosalt compounds that, for smaller A cations, the conduction bands are considerably disperse, despite lacking extended I–Pt–I connectivity.
36 MATERIALS SCIENCE↗
An Efficient Scheme for Crystal Structure Prediction Based on Structural Motifs
An efficient scheme based on structural motifs is proposed for the crystal structure prediction of materials. The key advantage of the present method comes in two fold: first, the degrees of freedom of the system are greatly reduced, since each structural motif, regardless of its size, can always be described by a set of parameters (R, θ, φ) with five degrees of freedom; second, the motifs could always appear in the predicted structures when the energies of the structures are relatively low. Both features make the present scheme a very efficient method for predicting desired materials. The method has been applied to the case of LiFePO 4 , an important cathode material for lithium-ion batteries. Numerous new structures of LiFePO 4 have been found, compared to those currently available, available, demonstrating the reliability of the present methodology and illustrating the promise of the concept of structural motifs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Resolving Atomic-Scale Structure and Chemical Coordination in High-Entropy Alloy Electrocatalysts for Structure–Function Relationship Elucidation
The recent breakthrough in confining five or more atomic species in nanocatalysts, referred to as high-entropy alloy nanocatalysts (HEAs), has revealed the possibilities of multielemental interactions that can surpass the limitations of binary and ternary electrocatalysts. The wide range of potential surface configurations in HEAs, however, presents a significant challenge in resolving active structural motifs, preventing the establishment of structure-function relationships for rational catalyst design and optimization. Here, we present a methodology for creating sub-5 nm HEAs using an aqueous-based peptide-directed route. Using a combination of pair distribution function and X-ray absorption spectroscopy, HEA structure models are constructed from reverse Monte Carlo modeling of experimental data sets and showcase a clear peptide-induced influence on atomic-structure and chemical miscibility. Coordination analysis of our structure models facilitated the construction of structure-function correlations applied to electrochemical methanol oxidation reactions, revealing the complex interplay between multiple metals that leads to improved catalytic properties. Our results showcase a viable strategy for elucidating structure-function relationships in HEAs, prospectively providing a pathway for future materials design.
36 MATERIALS SCIENCE↗
Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer
Abstract not provided
Wei, Jia↗
Compressed glassy carbon maintaining graphite-like structure with linkage formation between graphene layers
Abstract not provided
Shibazaki, Yuki↗
On the relationship between the structural and volumetric properties of solvated metal ions in O -donor solvents using new structural data in amide solvents
The structures of the N , N -dimethylformamide (dmf), N , N -dimethylacetamide (dma), and N , N -dimethylpropionamide (dmp) solvated strontium and barium ions have been determined in solution using large angle X-ray scattering and EXAFS spectroscopy. The strontium ion has a mean coordination number (CN) between 6.2 and 6.8, and the barium ion has a mean CN between 7.1 and 7.8 in these amide solvents. The non-integer numbers indicates that equilibria between different coordination numbers and geometries exist in these systems. Structural information of the alkali, alkaline earth, and selected transition metal and lanthanoid( III ) ions, and the halide ions in water, methanol, ethanol, dimethylsulfoxide, formamide, dmf and dma has been combined with previously reported standard partial molar volumes, V 0 . The ionic radii and charge densities (charge/ionic volume), and corresponding V 0 values have been used to gain information on the relationship between structural and volumetric properties. For the structure-breaking ions, i.e. the alkali metal and halide ions, there is an almost linear relationship between the ionic radius and V 0 . On the other hand, for the structure-making ions, here the alkaline earth, transition metal and lanthanoid( III ) ions, a linear relationship is observed between the charge density and V 0 . Solvents with a well-defined bulk structure through hydrogen bonding, specifically, water, methanol and ethanol, will be more contracted through solvation than aprotic solvents, as the space between the solvent molecules is lost as a result of the hydrogen bonding. In this respect, methanol stands out as the most compressed solvent participating in solvation compared to its bulk structure.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination
In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019) Proc Natl Acad Sci USA , 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure.
59 BASIC BIOLOGICAL SCIENCES↗
Structural analyses of an RNA stability element interacting with poly(A)
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99 GENERAL AND MISCELLANEOUS↗
SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database
The SCOPe (Structural Classification of Proteins—extended, https://scop.berkeley.edu) database hierarchically classifies domains from the majority of proteins of known structure according to their structural and evolutionary relationships. SCOPe also incorporates and updates the ASTRAL compendium, which provides multiple databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. Protein structures are classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.07, we have focused our manual curation efforts on larger protein structures, including the spliceosome, proteasome and RNA polymerase I, as well as many other Pfam families that had not previously been classified. Domains from these large protein complexes are distinctive in several ways: novel non-globular folds are more common, and domains from previously observed protein families often have N- or C-terminal extensions that were disordered or not present in previous structures. The current monthly release update, SCOPe 2.07–2018-10–18, classifies 90 992 PDB entries (about two thirds of PDB entries).
Biochemistry & Molecular Biology↗