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At least 541 records · Page 30

Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography

Numerous studies have shown how periplasmic binding proteins (PBPs) bind substrates with exquisite specificity, even distinguishing between sugar epimers and anomers, or structurally similar ions. Yet, marked substrate promiscuity is also a feature encoded in some PBPs. Except for three sub-Ångström crystal structures, there are no reports of hydrogen atom positions in the remaining (> 1000) PBP structures. The previous X-ray crystal structure of the maltodextrin periplasmic-binding protein from Thermotoga maritima (tmMBP) complexed with oligosaccharide showed a large network of interconnected water molecules stretching from one end of the substrate binding pocket to the other. These water molecules are positioned to form multiple hydrogen bonds, as well as forming interactions between the protein and substrate. Here we present the neutron crystal structure of tmMBP to a resolution of 2.1 Å. This is the first neutron crystal structure from the PBP superfamily and here we unambiguously identify the nature and orientation of the hydrogen bonding and water-mediated interactions involved in stabilizing a tetrasaccharide in the binding site. More broadly, these results demonstrate the conserved intricate mechanisms that underlie substrate-specificity and affinity in PBPs.

59 BASIC BIOLOGICAL SCIENCES↗

Li 2 GeS 3 : Lithium Ionic Conductor with an Unprecedented Structural Type

Lithium-ion batteries (LIBs) are widely used in electric vehicles, mobile electronic devices, and large-scale stationary energy storage systems. However, their liquid electrolytes present significant safety concerns due to their inherent flammability. To address this, the focus has shifted toward all-solid-state batteries (ASSBs) utilizing inorganic solid electrolytes that promise enhanced safety. In this work, we report the discovery of a new crystal structural type of Li-ion conductor, Li 2 GeS 3 , with a unique structure, synthesized by a solid-state reaction from Li 2 S and GeS 2 . It was first reported in 2000 with an orthorhombic unit cell, but its detailed crystal structure remains veiled. Here, we have unveiled its structure for the first time, employing an ab initio structure determination technique from powder X-ray and time-of-flight neutron diffraction data. The compound has an unprecedented crystal structural type with a hexagonal $P6_1$ symmetry and a unit cell of α = 6.79364(4) Å and c = 17.90724(14) Å. Its structure is comprised of a distorted hexagonal close-packed arrangement of sulfur anions with three asymmetric metal atoms: Li1, Li2, and Ge are in tetrahedral cavities surrounded by sulfur atoms. The ionic conductivity of Li 2 GeS 3 was measured to be 1.63 × 10 –8 S cm –1 at 303 K and 2.45 × 10 –7 S cm –1 at 383 K. Bond valence energy landscape calculations revealed three-dimensional lithium diffusion pathways within the structure. This novel crystal structure in Li 2 GeS 3 holds the potential for developing high-performance ionic conductors through suitable chemical substitution and offers valuable insights into designing new ionic conductors for ASSBs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topochemical Deintercalation of Li from Layered LiNiB: toward 2D MBene

The pursuit of two-dimensional (2D) borides, MBenes, has proven to be challenging, not the least because of the lack of a suitable precursor prone to the deintercalation. Here, we studied room-temperature topochemical deintercalation of lithium from the layered polymorphs of the LiNiB compound with a considerable amount of Li stored in between [NiB] layers (33 at. % Li). Deintercalation of Li leads to novel metastable borides (Li~ 0.5 NiB) with unique crystal structures. Partial removal of Li is accomplished by exposing the parent phases to air, water, or dilute HCl under ambient conditions. Scanning transmission electron microscopy and solid-state 7 Li and 11 B NMR spectroscopy, combined with X-ray pair distribution function (PDF) analysis and DFT calculations, were utilized to elucidate the novel structures of Li~ 0.5 NiB and the mechanism of Li-deintercalation. We have shown that the deintercalation of Li proceeds via a “zip-lock” mechanism, leading to the condensation of single [NiB] layers into double or triple layers bound via covalent bonds, resulting in structural fragments with Li[NiB] 2 and Li[NiB] 3 compositions. The crystal structure of Li~ 0.5 NiB is best described as an intergrowth of the ordered single [NiB], double [NiB] 2 , or triple [NiB] 3 layers alternating with single Li layers; this explains its structural complexity. Here, the formation of double or triple [NiB] layers induces a change in the magnetic behavior from temperatureindependent paramagnets in the parent LiNiB compounds to the spin-glassiness in the deintercalated Li~ 0.5 NiB counterparts. LiNiB compounds showcase the potential to access a plethora of unique materials, including 2D MBenes (NiB).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accuracy of DFT computed oxygen-vacancy formation energies and high-throughput search of solar thermochemical water-splitting compounds

The enthalpy change involved in metal oxide reduction is a key quantity in various processes related to energy conversion and storage, and is of particular interest for computational prediction. Often this prediction involves the simulation of a high temperature reduction process with a 0K methodology like density functional theory (DFT), and it is not infrequent for the high temperature and 0K stable crystal structures to differ. This introduces a conundrum with regards to the choice of crystal structure to utilize in the computation, with approaches in the literature varying and experimental validation remaining scarce. In this work we address both the crystal structure conundrum and the experimental validation, and then apply the insights we gain to guide a high-throughput search for new materials for solar thermochemical water-splitting applications. By computing the DFT+U oxygen vacancy formation energy (ΔE vf ) of a selection of ABO 3 compounds and comparing different crystal structures for each composition, we highlight the issues that arise when the structure utilized in the computation is dynamically unstable at 0K, namely the presence of an artificial lowering of ΔE vf , and the lack of convergence of ΔE vf with cell size. We solve these limitations by identifying and employing a suitable surrogate dynamically stable structure. We then validate the predictive power of our calculations against appositely generated experimental measurements of reduction enthalpy for a series of Hubbard U values, finding an accuracy ranging between 0.2-0.6 eV/O. In light of such conclusions, we revise and expand a previous a high-throughput DFT study on ABO 3 perovskite oxides. As a result, we provide a list of candidate STCH materials, highlight trends with redox-active cation and structural distortion, and identify Mn 4+ , Mn 3+ and Co 3+ as the most promising redox-active cations.

08 HYDROGEN↗

Insight into the structural ambiguity of actinide(IV) oxalate sheet structures: a case for alternate coordination geometries

Plutonium(IV) oxalate hexahydrate (Pu(C 2 O 4 ) 2 ∙ 6H 2 O; PuOx) is an important intermediate in the recovery of plutonium from used nuclear fuel. Its formation via precipitation is well studied, yet its crystal structure remains unknown. Instead, the crystal structure of PuOx is assumed to be isostructural with neptunium(IV) oxalate hexahydrate (Np(C 2 O 4 )­ 2 ∙ 6H 2 O; NpOx) and uranium(IV) oxalate hexahydrate (U(C 2 O 4 )­ 2 ∙ 6H 2 O; UOx) despite the high degree of unresolved disorder that exists when determining water positions in the crystal structures of the latter two compounds. Such assumptions regarding the isostructural behavior of the actinide elements have been used to predict the structure of PuOx for use in a wide range of studies. Herein, we report the first crystal structures for PuOx and Th(C 2 O 4 ) 2 · 6H 2 O (ThOx). This data, along with new characterization of UOx and NpOx, has resulted in the full determination of the structures and resolution of the disorder around the water molecules. Specifically, we identify the coordination of two water molecules with each metal center, which necessitates a change in oxalate coordination mode from axial to equatorial that has not been reported in the literature. Here this work exemplifies the need to revisit previous assumptions regarding fundamental actinide chemistry, which are heavily relied upon within the current nuclear field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Insights into the Complexation of Actinides by Diethylenetriaminepentaacetic Acid from Characterization of the Americium(III) Complex

Diethylenetriaminepentaacetic acid (DTPA) is a frequently used chelator in the nuclear and medical industries, especially for the complexation of trivalent actinides. However, structural data on these complexes in the solid-state have long remained elusive. Herein, a detailed structural analysis of the presented crystal structures of [C(NH 2 ) 3 ] 4 [Nd(DTPA)] 2 · n H 2 O and [C(NH 2 ) 3 ] 4 [Am(DTPA)] 2 · n H 2 O, where [C(NH 2 ) 3 ] + is guanidinium, details the subtle differences in the Lewis acidity between a lanthanide/actinide pair of similar ionic sizes. Contractions in nitrogen–metal bond lengths between neodymium(III) and americium(III) were observed, while the metal–oxygen bonds remained relatively consistent, highlighting the marginal favorability for actinide complexation over the lanthanides with moderately soft N-donors. Spectroscopic analysis shows significant splitting of many transitions and relatively strong electronic interactions with traditionally low-intensity transitions in the americium complex, as is demonstrated in the 7 F 0 → 7 F 5 transitions. Pressure-induced spectroscopic analysis showed surprisingly little effect on the americium complex, with 5 f →5 f transitions either not shifting or marginally shifting from 2 to 3 nm at 11.93 ± 0.06 GPa─atypical of a soft, N-donor americium complex under pressure. Finally, large voids occupied by water molecules in between the complexes within the crystal structure may be responsible for the lack of pressure response in the 5 f →5 f transitions.

absorption spectroscopy↗

New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis provide a framework for a novel catalytic mechanism for the entire class

Class II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of the enzyme in different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn 2+ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in the inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product, and divalent metal cations in the catalytic centers of the enzyme led to a revision of the catalytic mechanism suggested previously for class II FBPases. We propose that phosphate-1 is cleaved from the substrate fructose-1,6-bisphosphate (F1,6BP) by T89 in a proximal α-helix backbone (G88-T89-T90-I91-T92-S93-K94) in which the substrate transition state is stabilized by the positive dipole of the $\langle$-helix backbone. Once cleaved a water molecule found in the active site liberates the inorganic phosphate from T89 completing the catalytic mechanism. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII) containing a bound F1,6BP is presented to further support the substrate binding and novel catalytic mechanism suggested for this class of enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗

K 3 Ir 2 O 6 and K 16.3 Ir 8 O 30 , Low-Dimensional Iridates with Infinite IrO 6 Chains

A previously unreported 1D iridate, K 3 Ir 2 O 6 , has been grown by a flux method in O 2 -rich environment and its crystal structure determined via single crystal structural analysis. It exhibits straight chains of face-sharing [IrO 6 ] octahedra, which are arranged along the crystallographic c axis, separated by nonmagnetic K ions. No magnetic transitions are observed during measured range, and the material is electrically insulating. Potentially interesting electronic behavior for K 3 Ir 2 O 6 is supported by electronic structure calculations. A structurally related material, K 16.3 Ir 8 O 30 , which displays similar fundamental geometric units but in a different spatial arrangement – zigzag chains based on edge and face sharing [IrO 6 ] octahedra, is also reported. Both materials are of interest for probing the properties of a 1D system with strong spin-orbit coupling

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins

We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Automated Identification of Molecular Crystals’ Packing Motifs

Packing motifs—patterns in how molecules orient relative to one another in a crystal structure—are an important concept in many subdisciplines of materials science because of correlations observed between specific packing motifs and properties of interest. That said, packing motif data sets have remained small and noisy due to intensive manual labeling processes and insufficient labeling schemes. The most prominent labeling algorithms calculate relative interplanar angles of nearest neighbor molecules to determine the packing motif of a molecular crystal, but this simple approach can fail when neighbors are naively sampled isotropically around the crystal structure. To remedy this issue, here we propose an optimization algorithm, which rotates the molecular crystal structure to find representative molecules that inform the packing motif. We package this algorithm into an automated framework—Autopack—which both optimally rotates the crystal structure and labels the packing motif based on the appropriate neighboring molecules. In this work, we detail the Autopack framework and its performance, which shows improvements compared to previous state-of-the-art labeling methods, providing the first quantitative point of comparison for packing motif labeling algorithms. Furthermore, using Autopack (available at https://ipo.llnl.gov/technologies/software/autopack), we perform the first large-scale study of potential relationships between chemicals’ compositions and packing motifs, which shows that these relationships are more complex than previously hypothesized from studies that used only tens of polycyclic aromatic hydrocarbon molecules. Autopack’s capabilities help pose next steps for crystal engineering research focusing not only on a molecule’s adoption of a specific packing motif but also on new structure–property relationships.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multipole groups and fracton phenomena on arbitrary crystalline lattices

Multipole symmetries are of interest in multiple contexts, from the study of fracton phases, to nonergodic quantum dynamics, to the exploration of new hydrodynamic universality classes. However, prior explorations have focused on continuum systems or hypercubic lattices. In this work, we systematically explore multipole symmetries on arbitrary crystal lattices. We explain how, given a crystal structure (specified by a space group and the occupied Wyckoff positions), one may systematically construct all consistent multipole groups. We focus on two-dimensional crystal structures for simplicity, although our methods are general and extend straightforwardly to three dimensions. We classify the possible multipole groups on all two-dimensional Bravais lattices, and on the Kagome and breathing Kagome crystal structures to illustrate the procedure on general crystal lattices. Using Wyckoff positions, we provide an in-principle classification of all possible multipole groups in any space group. We explain how, given a valid multipole group, one may construct a consistent lattice Hamiltonian and a low-energy field theory. We then explore the physical consequences, beginning by generalizing certain results originally obtained on hypercubic lattices to arbitrary crystal structures. Next, we identify two apparently novel phenomena: an emergent, robust subsystem symmetry on the triangular lattice, and an exact multipolar symmetry on the breathing Kagome lattice that does not include conservation of charge (monopole), but instead conserves a vector charge. This makes clear that there is new physics to be found by exploring the consequences of multipolar symmetries on arbitrary lattices, and this work provides the map for the exploration thereof, as well as guiding the search for emergent multipolar symmetries and the attendant exotic phenomena in real materials based on nonhypercubic lattices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An Aluminum-Based Metal–Organic Cage for Cesium Capture

Metal–organic cages are a class of supramolecular structures that often require the careful selection of organic linkers and metal nodes. Of this class, few examples of metal–organic cages exist where the nodes are composed of main group metals. Herein, we have prepared an aluminum-based metal–organic cage, H 8 [Al 8 (pdc) 8 (OAc) 8 O 4 ] (Al-pdc-AA), using inexpensive and commercially available materials. The cage formation was achieved via solvothermal self-assembly of solvated aluminum and pyridine-dicarboxylic linkers in the presence of a capping agent, acetic acid. The obtained supramolecular structure was characterized by single-crystal X-ray diffraction (SCXRD), thermogravimetric analysis, and NMR spectroscopy. Based on crystal structure and computational analyses, the cage has a 3.7 Å diameter electron-rich cavity suitable for the binding of cations such as cesium (ionic radius of 1.69 Å). Here, the host–guest interactions were probed with 1 H and 133 Cs NMR spectroscopy in DMSO, where at low concentrations, Cs + binds to Al-pdc-AA in a 1:1 ratio. The binding site was identified from the crystal structure of CsH 7 [Al 8 (pdc) 8 (OAc) 8 O 4 ] (Cs + Al-pdc-AA), and a binding affinity of ~10 6 –10 7 M –1 was determined from NMR titration experiments. The Al-pdc-AA showed improved selectivity for cesium binding over alkali metal cations (Cs + > Rb + > K + >> Na + ~ Li + ). Collectively, the study reports a novel aluminum cage that can serve as a promising host for efficient and selective cesium removal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Polar Magnetic and Insulating Double Corundum Oxide: Mn2MnSbO6 with Ordered Mn(II) and Mn(III) Ions

A new magnetic insulator Mn2MnSbO6 with a polar crystal structure and an ordered Mn2+ and Mn3+ arrangement was synthesized under a high pressure of 7.5 GPa and 1300 degrees C. The crystal structure of Mn2MnSbO6, investigated by synchrotron powder X-ray diffraction, was found to be isomorphous with that of Ni3TeO6-type, space group R3. The non-centrosymmetric structure was confirmed by the second-harmonic generation measurements. The X-ray absorption near-edge spectroscopy measurement confirmed the nominal oxidation states of Mn22+Mn3+SbO6. Magnetic measurements indicate that Mn2MnSbO6 orders antiferromagnetically below 44 K and undergoes a field-induced spin-flop transition at 5 K. First-principles calculations indicate an antiferromagnetic ground state with up/up/up/down/down/down (uuuddd) spin configuration of the six crystallographically unique Mn ions in the c-axis doubled magnetic structure. The density functional theory calculations also substantiate the experimentally observed charge ordering of the Mn2+/Mn3+ ions and the insulating behavior due to a bandgap of 0.52 eV. To the best of our knowledge, this is the first double corundum oxide containing Jahn-Teller active Mn3+ ions.

Feng, Hai L.↗

X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms

The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1–80) fused to the switch region of troponin I (cTnI; residues 138–162). In both crystal forms, the cTnI residues form a six-turn α-helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative to the cTnC groove and completely blocks the calcium desensitizer binding site of the cTnC–cTnI interface.

59 BASIC BIOLOGICAL SCIENCES↗

Twists and Puckers: Tuning Crystal Chemistry in the La(Au x Ge 1– x ) 2 Compositional Series

The physical properties of solid-state materials are closely tied to their crystal structure, yet our understanding of how competing structural arrangements energetically compare is limited. In this work, we explore how small differences in composition affect structure in the La(Au x Ge 1-x ) 2 series of compounds, comprising four unique structure types between LaGe 2 and LaAu 2 . This family includes the previously unknown AlB2-type compound with the stoichiometry La(Au 0.375 Ge 0.625 ) 2 , as well as La(Au 0.25 Ge 0.75 ) 2 , an intergrowth of the AlB 2 and ThSi 2 structure types. We then study the chemical forces driving the structure changes, including using phonon band structure calculations and DFT Chemical Pressure to evaluate atomic size effects. These calculations show that the parent AlB 2 structure type is disfavored in Au-rich compounds due to soft atomic motions along the c axis. The instability of AlB 2 -type LaAuGe is confirmed by the presence of imaginary modes in the phonon band structure that correspond to a ‘puckering’ of the hexagonal AlB 2 -type lattice, resulting in the experimentally observed LiGaGe structure type. The impact of size effects is less clear for Au-poor compositions; instead, ‘twisting’ the AlB 2 structure type to form the ThSi 2 type opens a pseudogap at the Fermi level in the electronic density of states. Here, this investigation demonstrates how crystal structure in solid-state materials can be compositionally tuned based on balancing size and electronics when multiple structure types are in close thermodynamic competition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanisms of Three-Dimensional Solid-Phase Epitaxial Crystallization of Strontium Titanate

Strontium titanate (SrTiO 3 , STO) is a complex metal oxide with a cubic perovskite crystal structure. Due to its easily described and understood crystal structure in the cubic phase, STO is an ideal model system for exploring the mechanistic details of solid-phase epitaxy (SPE) in complex oxides. SPE is a crystallization approach that aims to guide crystal growth at low homologous temperatures to achieve targeted microstructures. Beyond planar thin films, SPE can also exploit the addition of a chemically inert, noncrystallizing, amorphous obstacle in the path of crystallization to generate complex three-dimensional structures. The introduction of this mask fundamentally alters the SPE process, inducing a transition from two- to three-dimensional geometries and from vertical to lateral crystal growth under the influence of the crystal/mask/amorphous boundary. Using a combination of molecular dynamics simulations and experiments, we identify several unique phenomena in the nanoscale growth behaviors in both conventional (unmasked) and masked SPE. Examining conventional SPE of STO, we find that crystallization at the interface is strongly correlated to, and potentially driven by, density fluctuations in the region of the amorphous STO near the crystalline/amorphous interface with a strong facet dependence. In the masked case, we find that the crystalline growth front becomes nonplanar near contact with the mask. We also observe a minimum vertical growth requirement prior to lateral crystallization. Both phenomena depend on the relative bulk and interfacial free energies of the three-phase (crystal/mask/amorphous) system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗