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At least 73 records · Page 4

Multiscale investigations of europium(III) complexation with tetra- n -octyl diglycolamide confined in porous solid supports

The microscopic, short-range coordination environments and mesoscopic, long-range structures of Eu 3+ contacted with tetra-n-octyl diglycolamide (TODGA) confined on ordered mesoporous carbon (OMC) nanoparticles and Amberchrom CG 71 resin were probed using Eu L 3 -edge extended X ray absorption fine structure (EXAFS) as well as small-angle and wide-angle X ray scattering, SAXS and WAXS, respectively. A homoleptic Eu(TODGA) 3 3+ coordination complex typical of liquid-liquid extraction (LLE) chemistry is present under low Eu 3+ loading conditions on both solid supports. Deviations from this traditional structure motif appear at hyperstoichiometric Eu 3+ loadings, above the 1:3 Eu 3+ to TODGA mole ratio. Microcrystalline-like domains with multinuclear Eu speciation are templated by use of these high Eu 3+ loading conditions with the functionalized OMC materials, highlighting a major departure of liquid-solid extraction chromatography (EXC) from the coordination chemistry of LLE. No such long-range spatial coherence was observed for analogous polyacrylic resin materials. Furthermore, these results demonstrate both the similarities and differences between multiscale structures in LLE and EXC, underscoring the opportunities for improved separation techniques based on solid supports with long-range spatial coherence (e.g., OMC systems) and without it (e.g., resin materials). Since crystallization was the first approach to adjacent lanthanide separations, the prospect of templating microcrystalline TODGA-lanthanide complexes that are otherwise not prone to crystallization by use of OMC nanoparticles represents a new entry to addressing long-standing issues in purification by liquid-solid phase separation.

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Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

Non-NASA Center↗

Insights into the Structure–Activity Relationship in Aerobic Alcohol Oxidation over a Metal–Organic-Framework-Supported Molybdenum(VI) Catalyst

The understanding of structure–activity relationships at the atomic level has played a profound role in heterogeneous catalysis, providing valuable insights into designing suitable heterogeneous catalysts. However, uncovering the detailed roles of how such active species’ structures affect their catalytic performance remains a challenge owing to the lack of direct structural information on a specific active species. Herein, we deposited molybdenum(VI), an active species in oxidation reactions, on the Zr 6 node of a mesoporous zirconium-based metal–organic framework (MOF) NU-1200, using solvothermal deposition in MOFs (SIM). Due to the high crystallinity of the NU-1200 support, the precise structure of the resulting molybdenum catalyst, Mo-NU-1200, was characterized through single-crystal X-ray diffraction (SCXRD). Two distinct anchoring modes of the molybdenum species were observed: one mode (Mo1), displaying an octahedral geometry, coordinated to the node through one terminal oxygen atom and the other mode (Mo2) coordinated to two adjacent Zr 6 node oxygen atoms in a tetrahedral geometry. To investigate the role of base in the catalytic activity of these Mo centers, we assessed the activity of Mo-NU-1200 for the aerobic oxidation of 4-methoxybenzyl alcohol as a model reaction. The results revealed that Mo-NU-1200 exhibited remarkably higher catalytic reactivity under base-free conditions, while the presence of base inhibited the catalytic reactivity of this species. SCXRD studies revealed that the molybdenum binding motifs (structures of the supported metal on the Zr 6 node in the MOF) changed over the course of the reactions. Following the oxidation without base, both pristine coordination modes (Mo1 and Mo2) evolved into a new coordination mode (Mo3), in which the molybdenum atom coordinated to two adjacent oxygen atoms from the Zr 6 node in an octahedral geometry, while in the presence of base, the pristine Mo1 coordination mode evolved entirely into the pristine Mo2. Here, this study demonstrates the direct observation of an active species’ structural evolution from metal installation to subsequent catalytic reaction. As a result, these subtle structural changes in catalyst binding motifs led to distinct differences in catalytic activities, providing a compelling strategy for elucidating structure–activity relationships.

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Synthesis and Characterization of Layered Actinide (U, Np, Pu) Oxide and Hydroxide Phases

Systematic structural comparisons across the early actinides remain limited by the scarcity of well-defined transuranic layered oxide and oxyhydroxide phases. Here, we report the synthesis and single-crystal characterization of new layered actinide compounds spanning U, Np, and Pu obtained under mild hydrothermal conditions in concentrated alkali hydroxide media. These include hydrated oxides α-Cs 2 U 2 O 7 •0.5H 2 O and Rb 2 An 2 O 7 •0.5H 2 O (An = Np, Pu), oxy-hydroxides Rb 6 [(AnO 2 ) 6 O 8 (OH) 2 ]•xH 2 O x = 0, 0.5 (An = U, Np) and Rb 4 [(UO 2 ) 5 O 6 (OH) 2 ]•2H 2 O, as well as nitrate-intercalated compounds Cs 6 [(AnO 2 ) 3 O 4 (OH) 2 ](NO 3 ) 2 (An = Np, Pu). Single-crystal X-ray diffraction studies reveal extended two-dimensional architectures constructed from edge- and vertex-sharing actinyl polyhedra, with systematic evolution in equatorial coordination, hydration, and anionic sheet topology across the U–Np–Pu series. Incorporation of nitrate anions within the interlayer region of Cs 6 [(AnO 2 ) 3 O 4 (OH) 2 ](NO 3 ) 2 establishes a previously unobserved structural motif in layered transuranic oxyhydroxides, demonstrating an additional pathway for anion-mediated framework stabilization. Correlation of crystallographic metrics with single-crystal Raman spectroscopy provides new vibrational benchmarks linking differences in An═O yl bond lengths to the equatorial coordination and the interstitial cations. These findings expand the structural hierarchy of layered actinide materials and address clarifying periodic trends governing topology, bonding, and vibrational signatures in high-valent 5ƒ oxide systems.

actinides↗

Hydrogen bonding to the formate ligand: Structural characterization of 2,2′:6′,2″-terpyridine zinc formate·H 2 O

Here, two polymorphs of the 2,2’:6’,2”-terpyridine zinc formate compound (terpy)Zn(O 2 CH) 2 •H 2 O have been structurally characterized by X-ray diffraction. In each case, the formate ligands coordinate via a K 1 -monodentate coordination mode and participate in hydrogen bonding interactions with water molecules. Despite this similarity, however, the polymorphs exhibit different hydrogen bonding motifs. Specifically, while one polymorph forms chains in which water molecules link adjacent (terpy)Zn(O 2 CH) 2 molecules, the other polymorph consists of discrete tetranuclear [(terpy)Zn(O 2 CH) 2 •H 2 O] 4 moieties.

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The GTPase-activating protein p120RasGAP has an evolutionarily conserved “FLVR-unique” SH2 domain

The Src homology 2 (SH2) domain has a highly conserved architecture that recognizes linear phosphotyrosine motifs and is present in a wide range of signaling pathways across different evolutionary taxa. A hallmark of SH2 domains is the arginine residue in the conserved FLVR motif that forms a direct salt bridge with bound phosphotyrosine. In this work, we solve the X-ray crystal structures of the C-terminal SH2 domain of p120RasGAP (RASA1) in its apo and peptide-bound form. We find that the arginine residue in the FLVR motif does not directly contact pTyr1087 of a bound phosphopeptide derived from p190RhoGAP; rather, it makes an intramolecular salt bridge to an aspartic acid. Unexpectedly, coordination of phosphotyrosine is achieved by a modified binding pocket that appears early in evolution. Using isothermal titration calorimetry, we find that substitution of the FLVR arginine R377A does not cause a significant loss of phosphopeptide binding, but rather a tandem substitution of R398A (SH2 position βD4) and K400A (SH2 position βD6) is required to disrupt the binding. These results indicate a hitherto unrecognized diversity in SH2 domain interactions with phosphotyrosine and classify the C-terminal SH2 domain of p120RasGAP as “FLVR-unique.”

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Advanced supramolecular design for direct ink writing of soft materials

The exciting advancements in 3D-printing of soft materials are changing the landscape of materials development and fabrication. Among various 3D-printers that are designed for soft materials fabrication, the direct ink writing (DIW) system is particularly attractive for chemists and materials scientists due to the mild fabrication conditions, compatibility with a wide range of organic and inorganic materials, and the ease of multi-materials 3D-printing. Inks for DIW need to possess suitable viscoelastic properties to allow for smooth extrusion and be self-supportive after printing, but molecularly facilitating 3D printability to functional materials remains nontrivial. While supramolecular binding motifs have been increasingly used for 3D-printing, these inks are largely optimized empirically for DIW. Hence, this review aims to establish a clear connection between the molecular understanding of the supramolecularly bound motifs and their viscoelastic properties at bulk. Herein, extrudable (but not self-supportive) and 3D-printable (self-supportive) polymeric materials that utilize noncovalent interactions, including hydrogen bonding, host–guest inclusion, metal–ligand coordination, micro-crystallization, and van der Waals interaction, have been discussed in detail. In particular, the rheological distinctions between extrudable and 3D-printable inks have been discussed from a supramolecular design perspective. Examples shown in this review also highlight the exciting macroscale functions amplified from the molecular design. Challenges associated with the hierarchical control and characterization of supramolecularly designed DIW inks are also outlined. The perspective of utilizing supramolecular binding motifs in soft materials DIW printing has been discussed. Finally, this review serves to connect researchers across disciplines to develop innovative solutions that connect top-down 3D-printing and bottom-up supramolecular design to accelerate the development of 3D-print soft materials for a sustainable future.

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A tetrahedral neptunium(V) complex

Neptunium is an actinide element sourced from anthropogenic production, and, unlike naturally abundant uranium, its coordination chemistry is not well developed in all accessible oxidation states. High-valent neptunium generally requires stabilization from at least one metal–ligand multiple bond, and departing from this structural motif poses a considerable challenge. Here we report a tetrahedral molecular neptunium(V) complex ([Np 5+ (NPC) 4 ][B(ArF 5 ) 4 ], 1-Np) (NPC = [NP t Bu(pyrr) 2 ] − ; t Bu = C(CH 3 ) 3 ; pyrr = pyrrolidinyl (N(C 2 H 4 ) 2 ); B(ArF 5 ) 4 = tetrakis(2,3,4,5,6-pentafluourophenyl)borate). Single-crystal X-ray diffraction, solution-state spectroscopy and density functional theory studies of 1-Np and the product of its proton-coupled electron transfer (PCET) reaction, 2-Np, demonstrate the unique bonding that stabilizes this reactive ion and establishes the thermochemical and kinetic parameters of PCET in a condensed-phase transuranic complex. The isolation of this four-coordinate, neptunium(V) complex reveals a fundamental reaction pathway in transuranic chemistry.

coordination chemistry↗

Synthesis of Two New Group 13 Benzoato-Chloro Complexes: A Structural Study of Gallium and Indium Chelating Carboxylates

Two new heteroleptic chelated-benzoato gallium (III) and indium (III) complexes have been prepared and structurally characterized. The molecular structures of [GaCl2(4-Mepy)2(O2CPh)]4-Mepy (1) and [InCl(4-Mepy)2(O2CPh)2]4-Mepy (2) have been determined by single-crystal x-ray diffraction. The gallium compound (1) is a distorted octahedron with cis-chloride ligands co-planar with the chelating benzoate and the 4-methylpyridines trans to each other. This is the first example of a Ga(III) structure with a chelating benzoate. The indium compound (2) is a distorted pentagonal bipyramid with two chelating benzoates, one 4-methylpyridine in the plane and a chloride trans to the other 4-methylpyridine. The indium bis-benzoate is an unusual example of a seven-coordinate structure with classical ligands. Both complexes, which due to the chelates, could also be described as pseudo-trigonal bipyramidal, include a three-bladed motif with three roughly parallel aromatic rings that along with a solvent of crystallization and electron-withdrawing chloride ligand(s) stabilize the solid-state structures.

Duraj, Stan A.↗

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗

Revealing Intermetallic Active Sites of PtNi Nanocatalysts for Reverse Water Gas Shift Reaction

Bimetallic nanoparticles have gained great interest due to their potential applications in catalysis. By combining Lattice Boltzmann Modeling (LBM), Density Functional Theory (DFT) calculations, and kinetic Monte Carlo (KMC) simulation, here we rationalize the superior performance of supported Pt-Ni alloy nanostructures over Pt and Ni alone during the reverse Water Gas Shift (rWGS) reaction, which was observed previously. The LBM simulation including the diffusion and flow of the reacting gas molecules within the supporting nanoporous channels in SBA-15 indicates that the simple combination of contributions from Ni and Pt alone is not enough to result in the observed promotion in rWGS activity and selectivity of the Pt-Ni alloy. Instead, the synergy between Pt and Ni via a unique intermetallic motif is responsible according to the DFT and KMC simulation. In conclusion, compared to the monometallic counterparts, the intermetallic-introduced ensemble effect at the low-coordinated Pt-Ni hybrid site of Pt-Ni alloy nanocatalysts enables the enhanced activation of CO 2 and promoted removal of CO/H 2 O as gas phase product.

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Coupled Cluster Study of the Interactions of AnO 2 , AnO 2 + , and AnO 2 2+ (An = U, Np) with N 2 and CO

We report thermochemical and spectroscopic properties for actinyl complexes involving UO 2 2+/1+/0 and NpO 2 2+/1+/0 with N 2 and CO, together with the UO 2 -O 2 , UO 2 + -O 2 , and UO 2 + -NO complexes, have been studied for the first time using an accurate composite coupled cluster approach. Two general bonding motifs were investigated, end-on (η 1 ) and side-on (η 2 ) relative to the metal center of the actinyls. For end-on CO complexes, both C-coordinated (An-C) and O-coordinated (An-O) structures were examined, with the former always being lower in energy. All of the η 1 complexes were calculated to be stable, with dissociation energies ranging from 2 to 36 kcal/mol, except for that of UO 2 + -O 2 (the η 1 orientation for UO 2 + -NO was not amenable to single reference coupled cluster). In agreement with a previous study, the η 2 structure for UO 2 + -O 2 was calculated to be relatively strongly bound, by 22.3 kcal/mol in this work. The closely related NO complex, however, had a calculated dissociation energy of just 4.0 kcal/mol. The binding energy of O 2 to neutral UO 2 in a η 2 orientation was calculated to be very strong, 75.4 kcal/mol, and strongly resembled a UO 2 + (O 2 – ) complex at equilibrium. The N–N and C–O bonds were found to be somewhat activated for all the side-on (η 2 ) neutral An(IV) complexes, with stretching frequencies of N 2 or CO being red-shifted by as much as 480 cm –1 with a 0.06 Å bond length elongation. Dissociation energies for the η 1 complexes are strongly correlated with the extent of electron transfer from ligand to actinyl. The nature of bonding in the actinyl complexes is examined using natural resonance theory (NRT). The correlation between bonding motif and small molecule activation is in agreement with experiments in condensed phases.

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Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase

The N-terminus of nickel-dependent superoxide dismutase (NiSOD) forms a structural motif known as the "Ni-hook," where the peptide wraps around the metal to bring cysteine-2 and cysteine-6 into spatial proximity, allowing these residues to coordinate in a cis-geometry. A highly conserved proline-5 residue in the Ni-hook adopts a cis-conformation that is widely considered important for its formation. Herein, we investigate this role by point mutation of Pro5 to alanine. The results obtained show that the variant exhibits wild-type-like redox catalysis and features a Ni(III) center very similar to that found in enzyme. Structural analysis using x-ray absorption spectroscopy of the nickel sites in as-isolated P5A-NiSOD reveals changes in the variant and are consistent with a six-coordinate Ni site with (N/O) 4 S 2 coordination. These changes are attributed to changes in the Ni(II) site structure. Nickel-binding studies using isothermal titration calorimetry reveal two binding events with K d = 25(20) nM, and 250(60) nM. These events are attributed to i) Ni(II) binding to a preformed Ni-hook containing cis-Pro5 and ii) the combination of trans- to cis- isomerization upon Ni(II) binding, respectively. Finally, the higher-affinity binding event is absent in P5A-NiSOD, an observation attributed to the low abundance of the cis-Ala5 isomer in the apo-protein.

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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↗

Manipulating the Second Coordination Shell of Single-Atom Fe for Enhanced Fenton Reaction

While current methods use oxidizable metals as electron donors to effectively reduce Fe 3+ , they suffer from the irreversible oxidation of these metals, ultimately compromising the catalyst’s longevity. To address this challenge, we engineered the second coordination shell of a single-atom Fe center by doping boron (B) onto a graphene-based support (Fe 1 /B-graphene) and utilized H 2 O 2 as the electron source for efficient Fe 2+ regeneration. Experimental results, supported by theoretical calculations, revealed that the Fe–O–B motif functions like a micro galvanic cell, with intermediary O atoms facilitating electron transfer between electrodes. Specifically, electrons consumed during H 2 O 2 activation at Fe 1 sites (positive electrode) are replenished by electrons extracted from H 2 O 2 at B atoms (negative electrode), where the activation energy for H 2 O 2 oxidation is significantly lower than that at Fe 1 sites. This study offers inspirational insights into the design of Fenton catalysts through precise regulation of the second coordination shell, demonstrating the potential of tailoring the outer coordination environment of single-atom catalysts to enhance catalytic performance across various reactions.

36 MATERIALS SCIENCE↗

The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants

Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.

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Enhancing Substrate–Metal Catalyst Affinity via Hydrogen Bonding: Pd(II)-Catalyzed β-C(sp 3 )–H Bromination of Free Carboxylic Acids

Achieving sufficient substrate-metal catalyst affinity is a fundamental challenge for developing synthetically useful C–H activation reactions of weakly coordinating native substrates. While hydrogen bonding has been harnessed to bias site selectivity in existing C(sp 2 )–H activation reactions, the potential for designing catalysts with hydrogen bond donors (HBDs) to enhance catalyst substrate affinity, and thereby facilitate otherwise unreactive C(sp 3 )–H activation, remains to be demonstrated. Herein, we report the discovery of a ligand scaffold containing a remote amide motif that can form a favorable meta-macrocyclic hydrogen bonding interaction with the aliphatic acid substrate. The utility of this ligand scaffold is demonstrated through the development of an unprecedented C(sp 3 )–H bromination of α-tertiary and α-quaternary free carboxylic acids, which proceeds in exceedingly high mono-selectivity. Furthermore, the geometric relationship of the NHAc hydrogen bond donor and the coordinating quinoline ligand is crucial for forming the meta-macrocyclophane-like hydrogen bonding interaction, providing a guideline for the future design of catalysts employing secondary interactions.

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Inference of principal species in caustic aluminate solutions through solid-state spectroscopic characterization

Tetrahedrally coordinated aluminate Al(OH) 4 – and dialuminate Al 2 O(OH) 6 2– anions are considered to be major species in aluminum-rich alkaline solutions. However, their relative abundance remains difficult to spectroscopically quantify due to local structure similarities and poorly understood effects arising from extent of polymerization and counter-cations. To help unravel these relationships in this paper we report detailed characterization of three solid-phase analogues as structurally and compositionally well-defined reference materials. We successfully synthesized a cesium salt of the aluminate monomer, CsAl(OH) 4 ·2H 2 O, for comparison to potassium and rubidium salts of the aluminate dimer, K 2 Al 2 O(OH) 6 , and Rb 2 Al 2 O(OH) 6 , respectively. Single crystal and powder X-ray diffraction methods clearly reveal the structure and purity of these materials for which a combination of 27 Al MAS-NMR, Al K-edge X-ray absorption and Raman/IR spectroscopies was then used to fingerprint the two major tetrahedrally coordinated Al species. The resulting insights into the effect of Al–O–Al bridge formation between aluminate tetrahedra on spectroscopic features may also be generalized to the many materials that are based on this motif.

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