Wheldone Revisited: Structure Revision Via DFT-GIAO Chemical Shift Calculations, 1,1-HD-ADEQUATE NMR Spectroscopy, and X-ray Crystallography Studies.

Wheldone is a fungal metabolite isolated from the coculture of Aspergillus fischeri and Xylaria flabelliformis, displaying cytotoxic activity against breast, melanoma, and ovarian cancer cell lines. Initially, its structure was characterized as an unusual 5-methyl-bicyclo[5.4.0]undeca-3,5-diene scaffold with a 2-hydroxy-1-propanone side chain and a 3-(2-(1-hydroxyethyl)-2-methyl-2,5-dihydrofuran-3-yl)acrylic acid moiety. Upon further examination, minor inconsistencies in the data suggested the need for the structure to be revisited. Thus, the structure of wheldone has been revised using an orthogonal experimental-computational approach, which combines 1,1-HD-ADEQUATE NMR experiments, DFT-GIAO chemical shift calculations, and single-crystal X-ray diffraction (SCXRD) analysis of a semisynthetic p-bromobenzylamide derivative, formed via a Steglich-type reaction. The summation of these data now permits the unequivocal assignment of both the structure and absolute configuration of the natural product.

Catching a New Zeolite as a Transition Material during Deconstruction.

Zeolites are key materials in both basic research and industrial applications. However, their synthesis is neither diverse nor applicable to labile frameworks because classical procedures require harsh hydrothermal conditions, whereas post-synthesis methods are limited to a few suitable parent materials. Remaining frameworks can fail due to amorphization, dissolution, and other decomposition processes. Nevertheless, stopping degradation at intermediate structures could yield new zeolites. Here, by optimizing the design and synthesis parameters of the parent zeolite IWV, we "caught" a new, highly crystalline, and siliceous zeolite during its degradation. IWV seed-assisted crystallization followed by gentle transformation into the water-alcohol system yielded the highly crystalline daughter zeolite IPC-20, whose structure was solved by precession-assisted three-dimensional electron diffraction. Without additional requirements, as in conventional (direct or post-synthesis) strategies, our approach may be applied to any chemically labile material with a staged structure.

Preparation and Characterization of Metalloporphyrin Tröger's and Spiro-Tröger's Base Derivatives.

A series of metalloporphyrin dimers as Tröger's bases 1 or spiro-Tröger's bases 2 was prepared starting from five different C4-symmetry porphyrin derivatives substituted in meso-positions by Ph, 3-MeO-Ph, 4-MeO-Ph, 3,4-(MeO)2-Ph, or 3,5-(MeO)2-Ph. Free-base porphyrins were converted to metalloporphyrins, which were subsequently nitrated with nickel(II), copper(II), or zinc(II) nitrate to give ß-nitrometalloporphyrins. These were further reduced to ß-aminometalloporphyrins and treated with a methanal equivalent under acidic conditions to selectively obtain Tröger's base 1, spiro-Tröger's base 2, or a mixture of both, in yields up to 41% of 1 and 45% of 2 depending on the reaction conditions used. The ratio of 1 to 2 was influenced by the methanal equivalent used, the strength of the acid, and, above all, the solvent. The presence of a metal ion within the porphyrin core and the use of a chlorinated solvent were found to be essential for the formation of spiro-Tröger's base 2. The molecular structure of spiroTB 2a-Ni2 was proven by electron diffraction.

Cleaving silicene-terminated calcium disilicide in the transmission electron microscope.

Silicene, a monolayer of silicon atoms arranged in a honeycomb lattice, is excellently compatible with the materials used in today's semiconductor manufacturing. In this paper, silicene-terminated CaSi2 is cleaved inside a transmission electron microscope using an in situ manipulator. HRTEM studies on a standard lift-out lamella performed from several crystallographic orientations confirm the cell parameters of a = 3.7 Å and c = 30.60 Å, and allow to determine its exact orientation in the SEM/FIB system. A FIB procedure with corrected tilting and rotating angles has been developed to ensure that the tensile force applied by the manipulator is perpendicular to the (0 0 1) plane, and that the [1 0 0] pole axis could be used for HRTEM imaging. A sharp and flat cleavage interface with a length of more than 1 µm was observed in one in situ experiment. HRTEM images from multiple regions confirm that the flat cleavage follows the (0 0 3) plane of the CaSi2 crystal. The current in situ study demonstrates that a surface sheet with silicene-like atomic arrangement can be mechanically exfoliated from silicide compounds.

Synthesis of Discrete CHA Zeolite Nanocrystals without Organic Templates for Selective CO2 Capture.

Small-pore zeolites such as chabazite (CHA) are excellent candidates for the selective separation of CO2 ; however, the current synthesis involves several steps and the use of organic structure-directing agent (OSDA), increasing their cost and energy requirements. We report the synthesis of small-pore zeolite crystals (aluminosilicate) with CHA-type framework structure by direct synthesis in a colloidal suspension containing a mixture of inorganic cations only (Na+ , K+ , and Cs+ ). The location of CO2 molecules in the host structure was revealed by 3D electron diffraction (3D ED). The high sorption capacity for CO2 (3.8 mmol g-1 at 121 kPa), structural stability and regenerability of the discreate CHA zeolite nanocrystals is maintained for 10 consecutive cycles without any visible degradation. The CHA zeolite (Si:Al=2) reaches an almost perfect CO2 storage capacity (8 CO2 per unit cell) and high selectivity (no CH4 was adsorbed).

Homoleptic Imidophosphorane Stabilization of Tetravalent Cerium.

The homoleptic complexes of cerium with the tris(piperidinyl)imidophosphorane ligand, [NP(pip)3]-, present the most negative Ce3+/4+ redox couple known (<-2.64 V vs Fc/Fc+). This dramatic stabilization of the cerium tetravalent oxidation state [>4.0 V shift from the Ce3+/4+ couple in 1 M HClO4(aq)] is established through reactivity studies. Spectroscopic studies (UV-vis, electron paramagnetic resonance, and Ce L3-edge X-ray absorption spectroscopy), in conjunction with density functional theory studies, reveal the dominant covalent metal-ligand interactions underlying the observed redox chemistry and the dependence of the redox potential on the binding of potassium in the inner coordination sphere.

SSZ-27: A Small-Pore Zeolite with Large Heart-Shaped Cavities Determined by Using Multi-crystal Electron Diffraction.

The high-silica zeolite SSZ-27 was synthesized using one of the isomers of the organic structure-directing agent that is known to produce the large-pore zeolite SSZ-26 (CON). The structure of the as-synthesized form was solved using multi-crystal electron diffraction data. Data were collected on eighteen crystals, and to obtain a high-quality and complete data set for structure refinement, hierarchical cluster analysis was employed to select the data sets most suitable for merging. The framework structure of SSZ-27 can be described as a combination of two types of cavities, one of which is shaped like a heart. The cavities are connected through shared 8-ring windows to create straight channels that are linked together in pairs to form a one-dimensional channel system. Once the framework structure was known, molecular modelling was used to find the best fitting isomer, and this, in turn, was isolated to improve the synthesis conditions for SSZ-27.

At the Gates: The Tantalum-Rich Phase Hf3Ta2O11 and its Commensurately Modulated Structure.

Generic mixtures in the system (Zr,Hf)O2-(Nb,Ta)2O5 are employed as tunable gate materials for field-effect transistors. Whereas production processes and target compositions are well-defined, resulting crystal structures are vastly unexplored. In this study, we summarize the sparse reported findings and present the new phase Hf3Ta2O11 as synthesized via a sol-gel route. Its commensurately modulated structure represents the hitherto unknown, metal(V)-richest member of the family (Zr,Hf) x(Nb,Ta)2O2 x+5. Based on electron, neutron, and X-ray diffraction, the crystal structure is described within modern superspace [Hf1.2Ta0.8O4.4, Z = 2, a = 4.7834(13), b = 5.1782(17), c = 5.064(3) Å, q = 1/5 c*, orthorhombic, superspace group Xmcm(00γ) s00] and supercell formalisms [Hf3Ta2O11, Z = 4, a = 4.7834(13), b = 5.1782(17), c = 25.320(13) Å, orthorhombic, space group Pbnm]. Transmission electron microscopy shows the microscopic structure from film-like aggregates down to atomic resolution. Cation ordering within the different available coordination environments is possible, but no significant hint at it is found within the limits of standard diffraction techniques. Hf3Ta2O11 is an unpredicted compound in the above-mentioned oxide systems, in which stability ranges have been disputably fuzzy and established only by syntheses via solid-state routes so far.

Unusual Relaxor Ferroelectric Behavior in Stairlike Aurivillius Phases.

New ferroelectric layered materials were found in the pseudobinary system Bi5Nb3O15-ABi2Nb2O9 (A= Ba, Sr and Pb). Preliminary observations made by transmission electron microscopy indicate that these compounds exhibit a complex incommensurately modulated structure. A (3 + 1)D structural model is obtained using ab initio phasing by charge flipping based on the analysis of precession electron diffraction tomography data. The (3 + 1)D structure is further validated by a refinement against neutron powder diffraction. These materials possess a layered structure with discontinuous [Bi2O2] slabs and perovskite blocks. While these structural units are characteristics of Aurivillius phases, the existence of periodic crystallographic shear planes offers strong similarities with collapsed or stairlike structures known in high-Tc superconductors and related compounds. Using dielectric spectroscopy, we study the phase transitions of these new layered materials. For A = Ba and Sr, a Vögel-Fulcher-like behavior characteristic of the so-called relaxor ferroelectrics is observed and compared to "canonical" relaxors. For A = Sr, the absence of a Burns temperature separated from the freezing temperature appears as a rather unusual behavior.

On the Use of Dynamical Diffraction Theory To Refine Crystal Structure from Electron Diffraction Data: Application to KLa5O5(VO4)2, a Material with Promising Luminescent Properties.

A new lanthanum oxide, KLa5O5(VO4)2, was synthesized using a flux growth technique that involved solid-state reaction under an air atmosphere at 900 °C. The crystal structure was solved and refined using an innovative approach recently established and based on three-dimensional (3D) electron diffraction data, using precession of the electron beam and then validated against Rietveld refinement and denisty functional theory (DFT) calculations. It crystallizes in a monoclinic unit cell with space group C2/m and has unit cell parameters of a = 20.2282(14) Å, b = 5.8639(4) Å, c = 12.6060(9) Å, and ß = 117.64(1)°. Its structure is built on Cresnel-like two-dimensional (2D) units (La5O5) of 4*3 (OLa4) tetrahedra, which run parallel to (001) plane, being surrounded by isolated VO4 tetrahedra. Four isolated vanadate groups create channels that host K(+) ions. Substitution of K(+) cations by another alkali metal is possible, going from lithium to rubidium. Li substitution led to a similar phase with a primitive monoclinic unit cell. A complementary selected area electron diffraction (SAED) study highlighted diffuse streaks associated with stacking faults observed on high-resolution electron microscopy (HREM) images of the lithium compound. Finally, preliminary catalytic tests for ethanol oxidation are reported, as well as luminescence evidence. This paper also describes how solid-state chemists can take advantages of recent progresses in electron crystallography, assisted by DFT calculations and powder X-ray diffraction (PXRD) refinements, to propose new structural types with potential applications to the physicist community.

Hydrogen Peroxide Coordination to Cobalt(II) Facilitated by Second-Sphere Hydrogen Bonding.

M(H2 O2 ) adducts have been postulated as intermediates in biological and industrial processes; however, only one observable M(H2 O2 ) adduct has been reported, where M is redox-inactive zinc. Herein, direct solution-phase detection of an M(H2 O2 ) adduct with a redox-active metal, cobalt(II), is described. This Co(II) (H2 O2 ) compound is made observable by incorporating second-sphere hydrogen-bonding interactions between bound H2 O2 and the supporting ligand, a trianionic trisulfonamido ligand. Thermodynamics of H2 O2 binding and decay kinetics of the Co(II) (H2 O2 ) species are described, as well as the reaction of this Co(II) (H2 O2 ) species with Group 2 cations.

First Step Towards a Devil's Staircase in Spin-Crossover Materials.

The unprecedented bimetallic 2D coordination polymer {Fe[(Hg(SCN)3 )2 ](4,4'-bipy)2 }n exhibits a thermal high-spin (HS)↔low-spin (LS) staircase-like conversion characterized by a multi-step dependence of the HS molar fraction γHS . Between the fully HS (γHS =1) and LS (γHS =0) phases, two steps associated with different ordering appear in terms of spin-state concentration waves (SSCW). On the γHS ≈0.5 step, a periodic SSCW forms with a HS-LS-HS-LS sequence. On the γHS ≈0.34 step, the 4D superspace crystallography structural refinement reveals an aperiodic SSCW, with a HS-LS sequence incommensurate with the molecular lattice. The formation of these different long-range spatially ordered structures of LS and HS states during the multi-step spin-crossover is discussed within the framework of "Devil's staircase"-type transitions. Spatially modulated phases are known in various types of materials but are uniquely related to molecular HS/LS bistability in this case.

Dynamical refinement with multipolar electron scattering factors.

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petrícek & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

Structure and absolute configuration of natural fungal product beauveriolide I, isolated from Cordyceps javanica, determined by 3D electron diffraction.

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methylpropyl)-1-oxa-4,7,10-triazacyclotridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclodepsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclodepsipeptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Šand ß = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enantiomorphs of beauveriolide I.

Absolute structure determination of Berkecoumarin by X-ray and electron diffraction.

X-ray and electron diffraction methods independently identify the S-enantiomer of Berkecoumarin [systematic name: (S)-8-hydroxy-3-(2-hydroxypropyl)-6-methoxy-2H-chromen-2-one]. Isolated from Berkeley Pit Lake Penicillium sp., Berkecoumarin is a natural product with a light-atom composition (C13H14O5) that challenges in-house absolute structure determination by anomalous scattering. This study further demonstrates the utility of dynamical refinement of electron-diffraction data for absolute structure determination.

Refining short-range order parameters from the three-dimensional diffuse scattering in single-crystal electron diffraction data.

Our study compares short-range order parameters refined from the diffuse scattering in single-crystal X-ray and single-crystal electron diffraction data. Nb0.84CoSb was chosen as a reference material. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms were refined from the diffuse scattering using a Monte Carlo refinement in DISCUS. The difference between the Sb and Co displacements refined from the diffuse scattering and the Sb and Co displacements refined from the Bragg reflections in single-crystal X-ray diffraction data is 0.012 (7) Šfor the refinement on diffuse scattering in single-crystal X-ray diffraction data and 0.03 (2) Šfor the refinement on the diffuse scattering in single-crystal electron diffraction data. As electron diffraction requires much smaller crystals than X-ray diffraction, this opens up the possibility of refining short-range order parameters in many technologically relevant materials for which no crystals large enough for single-crystal X-ray diffraction are available.

Applying 3D ED/MicroED workflows toward the next frontiers.

We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.

Lensless coherent imaging of proteins and supramolecular assemblies: Efficient phase retrieval by the charge flipping algorithm.

Diffractive imaging using the intense and coherent beam of X-ray free-electron lasers opens new perspectives for structural studies of single nanoparticles and biomolecules. Simulations were carried out to generate 3D oversampled diffraction patterns of non-crystalline biological samples, ranging from peptides and proteins to megadalton complex assemblies, and to recover their molecular structure from nanometer to near-atomic resolutions. Using these simulated data, we show here that iterative reconstruction methods based on standard and variant forms of the charge flipping algorithm, can efficiently solve the phase retrieval problem and extract a unique and reliable molecular structure. Contrary to the case of conventional algorithms, where the estimation and the use of a compact support is imposed, our approach does not require any prior information about the molecular assembly, and is amenable to a wide range of biological assemblies. Importantly, the robustness of this ab initio approach is illustrated by the fact that it tolerates experimental noise and incompleteness of the intensity data at the center of the speckle pattern.

Precession electron diffraction tomography for solving complex modulated structures: the case of Bi5Nb3O15.

The crystal structure of the 1D incommensurately modulated phase Bi5Nb3O15 [superspace group X2mb(0b0)000, a = 5.46781(7) Å, b = 5.47381(8) Å, c = 41.9005(5) Å, and q = 0.17588(8)b*] is solved by electron diffraction using a tomography technique combined with precession of the electron beam. The (3 + 1)D structure is further validated by a refinement against powder X-ray diffraction (PXRD). A coherent picture of the true nature of this compound is obtained, conciliating experimental observations made by different groups using transmission electron microscopy and PXRD. Bi5Nb3O15 does not have a mixed-layer Aurivillius-type structure but does contain structural elements, [Bi2O2](2+) slabs, and perovskite-like blocks, characteristic of Aurivillius phases. The presence of aperiodic crystallographic shear planes (CSPs) along the modulated direction b leads to the formation of an original layered structure containing both continuous and discontinuous [Bi2O2](2+) and perovskite-like octahedral layers. Between CSPs, the stacking of these two structural elements exhibits an unprecedented nonuniform sequence referring to Aurivillius phases.

High-aspect-ratio and high-flatness Cu3(SiGe) nanoplatelets prepared by chemical vapor deposition.

Cu3(SiGe) nanoplatelets were synthesized by low-pressure chemical vapor deposition of a SiH3C2H5/Ge2(CH3)6 mixture on a Cu-substrate at 500 degrees C, total pressure of 110-115 Pa, and Ge/Si molar ratio of 22. The nanoplatelets with composition Cu76Si15Ge12 are formed by the 4'-phase, and they are flattened perpendicular to the [001] direction. Their lateral dimensions reach several tens of micrometers in size, but they are only about 50 nm thick. Their surface is extremely flat, with measured root mean square roughness R(q) below 0.2 nm. The nanoplatelets grow via the non-catalytic vapor-solid mechanism and surface growth. In addition, nanowires and nanorods of various Cu-Si-Ge alloys were also obtained depending on the experimental conditions. Morphology of the resulting Cu-Si-Ge nanoobjects is very sensitive to the experimental parameters. The formation of nanoplatelets is associated with increased amount of Ge in the alloy.