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At least 1,225 records · Page 68

Structure and regulation of ZCCHC4 in m 6 A-methylation of 28S rRNA

N 6 -methyladenosine (m 6 A) modification provides an important epitranscriptomic mechanism that critically regulates RNA metabolism and function. However, how m 6 A writers attain substrate specificities remains unclear. We report the 3.1 Å-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m 6 A methyltransferase, bound to S-adenosyl-L-homocysteine. The methyltransferase (MTase) domain of ZCCHC4 is packed against N-terminal GRF-type and C2H2 zinc finger domains and a Cterminal CCHC domain, creating an integrated RNA-binding surface. Strikingly, the MTase domain adopts an autoinhibitory conformation, with a self-occluded catalytic site and a fullyclosed cofactor pocket. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity. Overall, this study unveils unique structural and enzymatic characteristics of ZCCHC4, distinctive from what was seen with the METTL family of m 6 A writers, providing the mechanistic basis for ZCCHC4 modulation of m 6 A RNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172

Recent advances in direct-acting antivirals against Hepatitis C Virus (HCV) have led to the development of potent inhibitors, including MK-5172, that target the viral NS3/4A protease with relatively low susceptibility to resistance. MK-5172 has a P2–P4 macrocycle and a unique binding mode among current protease inhibitors where the P2 quinoxaline packs against the catalytic residues H57 and D81. Furthermore, the effect of macrocyclization on this binding mode is not clear, as is the relation between macrocyclization, thermodynamic stabilization, and susceptibility to the resistance mutation A156T. We have determined high-resolution crystal structures of linear and P1–P3 macrocyclic analogs of MK-5172 bound to WT and A156T protease and compared these structures, their molecular dynamics, and experimental binding thermodynamics to the parent compound. We find that the “unique” binding mode of MK-5172 is conserved even when the P2–P4 macrocycle is removed or replaced with a P1–P3 macrocycle. While beneficial to decreasing the entropic penalty associated with binding, the constraint exerted by the P2–P4 macrocycle prevents efficient rearrangement to accommodate the A156T mutation, a deficit alleviated in the linear and P1–P3 analogs. Design of macrocyclic inhibitors against NS3/4A needs to achieve the best balance between exerting optimal conformational constraint for enhancing potency, fitting within the substrate envelope and allowing adaptability to be robust against resistance mutations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometry Dependence of Magnetization Reversal in Nanocomposite Alloys

The geometrical optimization of aligned hard-soft permanent-magnet nanocomposites is investigated by model calculations. Considered criteria are the shapes of the soft and c-axis-aligned hard phases, the packing fraction of the soft phase, and magnetostatic interactions. Taking into account that the energy product is enhanced via the volume fraction of the soft phase, subject to maintaining coercivity, we find that the best structures are soft-magnetic cubes as well as long rods with a square cross section. Comparing embedded soft cubes with embedded soft spheres of the same size, our nucleation-field analysis shows that the volume fraction of the soft phase is enhanced by 91%, with a coercivity reduction of only 25%. Magnetostatic interactions often but not always deteriorate the permanent-magnet performance, as exemplified by the example of MnBi:FeCo bilayers and multilayers.

magnetization reversal↗

Crystal structure of {approx}RCu{sub 3}S{sub 3} and {approx}RCuTe{sub 2} (R=Gd-Lu) compounds

The crystal structures of ternary compounds TbCu{sub 3}S{sub 3}, Dy{sub 1.06}Cu{sub 2.84}S{sub 3} (space group R3-bar), Ho{sub 0.67}Cu{sub 2}S{sub 2} (space group P3-bar m1), ErCu{sub 3}S{sub 3} (space group P3-bar 1c), Yb{sub 0.80}Cu{sub 1.60}S{sub 2}, Lu{sub 0.67}Cu{sub 2}S{sub 2}, TbCuTe{sub 2}, DyCuTe{sub 2}, Tm{sub 1.07}Cu{sub 0.78}Te{sub 2}, LuCuTe{sub 2} (space group P3-bar m1), Gd{sub 0.75}Cu{sub 1.74}Te{sub 2} (space group P3-bar 1m) were determined by means of X-ray single crystal diffraction. The S(Te) atoms are stacked in a close packed arrangement with the layers in the sequence AB. The R atoms are distributed over octahedral interstices whereas Cu atoms are located in tetrahedral interstices. Disorder of R and Cu atoms in studied chalcogenides is found. Crystal structure comparison showed that TbCuTe{sub 2} and DyCuTe{sub 2} crystallize as superstructure 2a Multiplication-Sign 2a Multiplication-Sign {sub 2}c to CaAl{sub 2}Si{sub 2} structure type, whereas Gd{sub 0.75}Cu{sub 1.74}Te{sub 2}, ErCu{sub 3}S{sub 3} and TbCu{sub 3}S{sub 3} (Dy{sub 1.06}Cu{sub 2.84}S{sub 3}) have superstructure {radical}3a Multiplication-Sign {radical}3a Multiplication-Sign nc with n=1, 2, 3. - Graphical abstract: In the series of the {approx}RCu{sub 3}S{sub 3} and {approx}RCuTe{sub 2} compounds the R and Cu atoms occupy disordered positions. The S(Te) atoms are stacked in a close packed arrangement with the layers in the sequence AB. Highlights: Black-Right-Pointing-Pointer The {approx}RCu{sub 3}S{sub 3} and {approx}RCuTe{sub 2} (R=Gd-Lu) crystallize with layered structure. Black-Right-Pointing-Pointer Superstructure {radical}3a Multiplication-Sign {radical}3a Multiplication-Sign nc (n=1, 2, 3) to CaAl{sub 2}Si{sub 2} structure type is found. Black-Right-Pointing-Pointer TbCuTe{sub 2} and DyCuTe{sub 2} crystallize as superstructure 2a Multiplication-Sign 2a Multiplication-Sign 2c. Black-Right-Pointing-Pointer Disorder of R and Cu atoms in studied chalcogenides is found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recycling the Energy of Indoor Light: Highly Efficient Organic Photovoltaics via a Ternary Strategy

A ternary approach in organic photovoltaics (OPV) is simple and reliable to effectively tune the optical, electrical and morphological properties of the photoactive layer for high efficiency as well as long-term stability under 1 sun. However, there have been few papers reporting spectra and weak illumination compared to outdoor light. In this study, by using two compatible 16 structures, we demonstrate a simultaneous modulation of light absorption and molecular donor polymers (PM7 and PM7 D1) with slightly-different band gaps and similar chemical packing under ambient conditions, which resulted in efficient indoor OPVs exhibiting power conversion efficiency (PCE) over 20% under 1000 lux of warm white light-emitting diode (2900 K). From morphological analysis, we infer that PM7 serves to seed nucleation of PM7 D1 in the ternary blend, templating its crystallization and alignment along the PM7 backbone. Such templating effect leads to increased domain spacing and relative degree of crystallinity (rDoC) compared to those of each binary system. We further show that higher rDoC helps suppress both bimolecular and trap-assisted recombination of photogenerated charges in the ternary devices. As a result, the complementary absorption and synergistic molecular assembly of the two donor polymers enhance the short-circuit current density as to increase the average PCEs from 9.6 to 10.3% under 1 sun and from 18.7 to 20.0% under 1000 lux. We envision that our strategy of incorporating both a planar and a flexible donor polymer with similar chemical structures can be generally applicable to attain a high performance ternary OPV under both 1 sun and indoor light.

14 SOLAR ENERGY↗

Short- and medium-range orders in Al90Tb10 glass and their relation to the structures of competing crystalline phases

Molecular dynamics simulations using an interatomic potential developed by artificial neural network deep machine learning are performed to study the local structural order in Al90Tb10 metallic glass. We show that more than 80% of the Tb-centered clusters in Al90Tb10 glass have short-range order (SRO) with their 17 first coordination shell atoms stacked in a ‘3661’ or ‘15551’ sequence. Medium-range order (MRO) in Bergman-type packing extended out to the second and third coordination shells is also clearly observed. Analysis of the network formed by the ‘3661’ and ‘15551’ clusters show that ~82% of such SRO units share their faces or vertexes, while only ~6% of neighboring SRO pairs are interpenetrating. Such a network topology is consistent with the Bergman-type MRO around the Tb-centers. Moreover, crystal structure searches using genetic algorithm and the neural network interatomic potential reveal several low-energy metastable crystalline structures in the composition range close to Al 90 Tb 10 . Some of these crystalline structures have the ‘3661’ SRO while others have the ‘15551’ SRO. While the crystalline structures with the ‘3661’ SRO also exhibit the MRO very similar to that observed in the glass, the ones with the ‘15551’ SRO have very different atomic packing in the second and third shells around the Tb centers from that of the Bergman-type MRO observed in the glassy phase.

36 MATERIALS SCIENCE↗

Crystal structures of gold, silver, and sodium chalcogenides: Sphenoidal interpretation

The crystal structures of 13 chalcogenides of Na, Au(I), and Ag(I) in the Na{sub 2-n}(Au,Ag){sub n}(S,Se,Te) series, where 0 {<=} n {<=} 2, are interpreted from unified positions based on the sphenoidal representation. Its essence is in the consideration of the entire crystal space (with packing X atoms in the framework of close-packing, body-centered, or hybrid schemes) as a set of elementary space units (sphenoids). Unified one-dimensional associates of sphenoids, the so-called basic rods, with sets of possible atomic positions in them are selected for all structures. The mutual effect of the dimensional and stoichiometric ratios of all components on the features of filling rod positions is analyzed. New possibilities in the crystallochemical and crystal-geometry analysis of inorganic compounds whose structures are characterized by a relatively uniform distribution of atoms are demonstrated by the example of chalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

CdCu{sub 3}(OH){sub 6}Cl{sub 2}: A new layered hydroxide chloride

A new transition metal hydroxide chloride containing kagome layers of magnetic ions, CdCu{sub 3}(OH){sub 6}Cl{sub 2}, has been synthesized and structurally characterized. The actual low symmetry P2{sub 1}/n structure can be derived from the ideal trigonal one with a change in cation distribution and coherent distortions of the anion framework. The result is a fundamentally different Cu{sup 2+} kagome framework than found in the related Herbertsmithite and Kapellasite minerals. Magnetization measurements show no transition to long range magnetic order above T=2 K, despite strong antiferromagnetic interactions with a Weiss temperature of {theta}{sub w}=-150 K. Furthermore, we show that the structure of CdCu{sub 3}(OH){sub 6}Cl{sub 2} and related hydroxide chlorides can be rationalized on the basis of [(OH){sub 3}Cl]{sup 4-} pseudopolyatomic anions that pack and rotate, in much the same way as do traditional polyatomic anions. This opens the door to rational design of new and useful hydroxide chloride materials. - Graphical Abstract: The [(OH){sub 3}Cl]{sup 4-} pseudopolyatomic anion and the kagome lattice of CdCu{sub 3}[(OH){sub 3}Cl]{sub 2}. Highlights: Black-Right-Pointing-Pointer A new understanding of hydroxide chlorides, based on the polyatomic anion [(OH){sub 3}Cl]{sup 4-}. Black-Right-Pointing-Pointer Synthesis and structure of a new layered hydroxide chloride, CdCu{sub 3}(OH){sub 6}Cl{sub 2}, are reported. Black-Right-Pointing-Pointer A new compound is reported with kagome layers of Cu{sup 2+}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Transformation of CuI Nanoparticles Into Oxidation‐Resistant 2D Copper Nanoplates

Unconventional phase transformations reveal new crystallization mechanisms, yet direct observation of such pathways during nanoscale solution-phase synthesis remains challenging. This study uncovers an atypical growth process in which thermodynamically stable CuI nanoparticles (NPs) transform into high-energy 2D Cu plates. Using a combination of in situ transmission electron microscopy, ex situ structural analysis, and density functional theory calculations shows that the formation of structural defects induced by hexadecylamine and chloride ions facilitates the transformation by promoting surface iodine vacancies. The resulting Cu{111} nanoplates, with ultrathin thicknesses (≈4 nm) and exceptionally high aspect ratios (≈450), display enhanced oxidation resistance and long-term stability under ambient conditions. This resistance is attributed to the close-packed {111} facets, which suppress chemical oxidation even after extended exposure to air over 100 days. These findings provide new insights into non-classical crystallization pathways in metal nanomaterials and suggest a versatile approach for preparing oxidation-resistant, structurally defined Cu nanostructures.

36 MATERIALS SCIENCE↗

Crystal structure of strontium Di[bis(iminodiacetato)cobaltate(III)] pentahydrate, Sr[cis(N)-Co(Ida){sub 2}]{sub 2} {center_dot} 5H{sub 2}O

Compound Sr[cis(N)-Co(Ida){sub 2}]{sub 2} {center_dot} 5H{sub 2}O (I) is synthesized and its crystal structure is determined. The crystals are built of [Co(Ida){sub 2}]{sup -} anionic complexes, [Sr(H{sub 2}O){sub 3}]{sup 2+} hydrated cations, and crystallization water molecules. Two independent anions are located on rotation axis 2 and have close structures. A distorted octahedral coordination of Co{sup 3+} atoms is formed by two N atoms and four O atoms of two Ida{sup 2-} ligands [Co-N, 1.932(3) and 1.940(3) Angstrom-Sign ; Co-O, 1.879-1.899(3) Angstrom-Sign ]. [Sr(H{sub 2}O){sub 3}]{sup 2+} cations randomly occupy half of the positions in the vicinity of centers of inversion. In addition to three water molecules, the environment of the Sr{sup 2+} atom includes five O atoms of five Ida{sup 2-} ligands [Sr-O, 2.487(3)-2.889(5) Angstrom-Sign ]. Because of the disordering of [Sr(H{sub 2}O){sub 3}]{sup 2+} cations, the structural function of the Ida{sup 2-} ligands varies from tridentate chelate to pentadentate bridging chelate. Sr-O and hydrogen bonds connect structural elements into a three-dimensional framework. The structure of I is compared with that of a related compound Sr[CoEdta]{sub 2}{center_dot}9H{sub 2}O (II). It is shown that the formation of N-H Horizontal-Ellipsis O hydrogen bonds, which connect [Co(Ida){sub 2}]{sup -} anionic complexes in I into compact chains, is an important factor leading to the difference between packings I and II.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Homophilic Adhesion Mechanism of Neurofascin, a Member of the L1 Family of Neural Cell Adhesion Molecules

The L1 family neural cell adhesion molecules play key roles in specifying the formation and remodeling of the neural network, but their homophilic interaction that mediates adhesion is not well understood. We report two crystal structures of a dimeric form of the headpiece of neurofascin, an L1 family member. The four N-terminal Ig-like domains of neurofascin form a horseshoe shape, akin to several other immunoglobulin superfamily cell adhesion molecules such as hemolin, axonin, and Dscam. The neurofascin dimer, captured in two crystal forms with independent packing patterns, reveals a pair of horseshoes in trans-synaptic adhesion mode. The adhesion interaction is mediated mostly by the second Ig-like domain, which features an intermolecular {beta}-sheet formed by the joining of two individual GFC {beta}-sheets and a large but loosely packed hydrophobic cluster. Mutagenesis combined with gel filtration assays suggested that the side chain hydrogen bonds at the intermolecular {beta}-sheet are essential for the homophilic interaction and that the residues at the hydrophobic cluster play supplementary roles. Our structures reveal a conserved homophilic adhesion mode for the L1 family and also shed light on how the pathological mutations of L1 affect its structure and function.

08 HYDROGEN↗

Cytoskeletal organization in microtentacles

Microtentacles are thin, flexible cell protrusions that have recently been described and whose presence enhances efficient attachment of circulating cells. They are found on circulating tumor cells and can be induced on a wide range of breast cancer cell lines, where they are promoted by factors that either stabilize microtubules or destabilize the actin cytoskeleton. Evidence suggests that they are relevant to the metastatic spread of cancer, so understanding their structure and formation may lead to useful therapies. Microtentacles are formed by microtubules and contain vimentin intermediate filaments, but beyond this, there is little information about their ultrastructure. We have used electron microscopy of high pressure frozen sections and tomography of cryo-prepared intact cells, along with super resolution fluorescence microscopy, to provide the first ultrastructural insights into microtubule and intermediate filament arrangement within microtentacles. By scanning electron microscopy it was seen that microtentacles form within minutes of addition of drugs that stabilize microtubules and destabilize actin filaments. Mature microtentacles were found to be well below one micrometer in diameter, tapering gradually to below 100 nm at the distal ends. They also contained frequent branches and bulges suggestive of heterogeneous internal structure. Super resolution fluorescence microscopy and examination of sectioned samples showed that the microtubules and intermediate filaments can occupy different areas within the microtentacles, rather than interacting intimately as had been expected. Cryo-electron tomography of thin regions of microtentacles revealed densely packed microtubules and absence of intermediate filaments. The number of microtubules ranged from several dozen in some areas to just a few in the thinnest regions, with none of the regular arrangement found in axonemes. Improved understanding of the mechanism of microtentacle formation, as well as the resultant structure, will be valuable in developing therapies against metastasis, if the hypothesized role of microtentacles in metastasis is confirmed. This work provides a significant step in this direction. - Highlights: • Microtentacles can form within minutes of the addition of inducing drugs. Microtentacle diameters are in the range of a tenth of a micrometer. • Microtubules are clearly resolved in microtentacles by cryo-electron tomography. • There is little microtubule-intermediate filament interaction in drug-induced microtentacles.

60 APPLIED LIFE SCIENCES↗

High energy x-ray scattering studies of the local order in liquid Al

The x-ray structure factors and densities for liquid aluminum from 1123 K to 1273 K have been measured using the beamline electrostatic levitator. Atomic structures as a function of temperature have been constructed from the diffraction data with reverse Monte Carlo simulations. An analysis of the local atomic structures in terms of the Honeycutt-Andersen indices indicates a high degree of icosahedral and distorted icosahedral order, a modest amount of body-centered cubic order, and marginal amounts of face-centered cubic and hexagonal close-packed order.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on the monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ~25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. In conclusion, these results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.

36 MATERIALS SCIENCE↗

Microscopic activated dynamics theory of the shear rheology and stress overshoot in ultradense glass-forming fluids and colloidal suspensions

We formulate a particle and force level, activated dynamics-based statistical mechanical theory for the continuous startup nonlinear shear rheology of ultradense glass-forming hard sphere fluids and colloidal suspensions in the context of the elastically collective nonlinear Langevin equation approach and a generalized Maxwell model constitutive equation. Activated structural relaxation is described as a coupled local-nonlocal event involving caging and longer range collective elasticity which controls the characteristic stress relaxation time. Theoretical predictions for the deformation-induced enhancement of mobility, the onset of relaxation acceleration at remarkably low values of stress, strain, or shear rate, apparent power law thinning of the steady-state structural relaxation time and viscosity, a nonvanishing activation barrier in the shear thinning regime, an apparent Herschel–Buckley form of the shear rate dependence of the steady-state shear stress, exponential growth of different measures of a yield or flow stress with packing fraction, and reduced fragility and dynamic heterogeneity under deformation were previously shown to be in good agreement with experiments. The central new question we address here is the defining feature of the transient response—the stress overshoot. In contrast to the steady-state flow regime, understanding the transient response requires an explicit treatment of the coupled nonequilibrium evolution of structure, elastic modulus, and stress relaxation time. We formulate a new quantitative model for this aspect in a physically motivated and computationally tractable manner. Theoretical predictions for the stress overshoot are shown to be in good agreement with experimental observations in the metastable ultradense regime of hard sphere colloidal suspensions as a function of shear rate and packing fraction, and accounting for deformation-assisted activated motion appears to be crucial for both the transient and steady-state responses.

Mechanics↗

Anion Exchange in Cationic Frameworks: Structures of Channel-Forming Triarylpyrylium Tetrafluoroborate Salts

The crystal structure of a co-crystal of 2,4,6-tris(4-methylphenyl)pyridine and 2,4,6-tris(4-methylphenyl)pyrylium revealed a pseudohexagonal motif assembled from π-stacked helices that enclose 1-D channels containing disordered tetrafluoroborate counterions and solvent molecules. Though convoluted by disorder, aperiodicity, and complex twinning patterns, further investigation was motivated by the unique packing arrangement of this material, which enables solid-state anion diffusion, while resisting dissolution in water. Such properties are ideal for the development of anion exchange materials that can be employed for the remediation of agricultural and nuclear waste. Here, to develop a more complete understanding of the intermolecular interactions that give rise to this helical motif, we have compiled and analyzed the local interactions and extended structural motifs of 19 pore- and channel-forming 2,4,6-triarylpyrylium crystal structures. Here, three conserved local interactions were identified, including C–H···X– interactions, the rhombic binding pocket, and four-ring antiparallel dimerization. Development of this library of interaction motifs rationalizes the packing arrangement of the co-crystal and contributes to the informed design of anion exchange materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring Lithium-Cobalt-Nickel Oxide Spinel Electrodes for ≥3.5 V Li-Ion Cells

Recent reports have indicated that a manganese oxide spinel component, when embedded in a relatively small concentration in layered xLi2MnO3(1-x)LiMO2 (M=Ni, Mn, Co) electrode systems, can act as a stabilizer that increases their capacity, rate capability, cycle life, and first-cycle efficiency. These findings prompted us to explore the possibility of exploiting lithiated cobalt oxide spinel stabilizers by taking advantage of (1) the low mobility of cobalt ions relative to manganese and nickel ions in close-packed oxides and (2) their higher potential (~3.6 V vs. Li0) relative to manganese oxide spinels (~2.9 V vs. Li0) for the spinel-to-lithiated spinel electrochemical reaction. In particular, we have revisited the structural and electrochemical properties of lithiated spinels in the LiCo1-xNixO2 (0x0.2) system, first reported almost 25 years ago, by means of high-resolution (synchrotron) X-ray diffraction, transmission electron microscopy, nuclear magnetic resonance spectroscopy, electrochemical cell tests, and theoretical calculations. The results provide a deeper understanding of the complexity of intergrown layered/lithiated spinel LiCo1-xNixO2 structures, when prepared in air between 400 and 800 C, and the impact of structural variations on their electrochemical behavior. These structures, when used in low concentration, offer the possibility of improving the cycling stability, energy, and power of high energy (≥3.5 V) lithium-ion cells.

Environmental Molecular Sciences Laboratory↗