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At least 541 records · Page 30

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Thompson, Michael C. (ORCID:0000000260992027)↗

On the dynamic tensile strength of an FCC metal

The tensile response of ductile, polycrystalline metals is often accompanied by the formation of pores within the material, which coalesce and fail a plane within a metal. This large deformation process is broadly progressive, with a physical path consisting of nucleation, growth, coalescence, and failure, which occur individually over short periods of time. Thus distinct micro-mechanisms operate, each influenced by microstructure, loading path, and loading profile, which remains a significant challenge to represent and predict numerically at the macroscale. In a previous study, the influence of loading path on damage evolution in high-purity tantalum has been presented; in this paper, complimentary measurements are made on a pure, FCC copper. Samples were shock loaded to three different peak stresses using both symmetric impact, and two different composite flyer plate configurations, such that upon unloading, the three samples were subject to nearly identical tensile loading. The damage evolution in the soft-recovered copper samples was then quantified using optical metallography and electron-back-scatter diffraction. We shall compare metallurgical observations, velocimetry histories and simulations to discuss the dynamic failure mechanics observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S 2 ). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. Herein we use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S 2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological Transformation of a Metal–Organic Framework Triggered by Ligand Exchange

Metal-organic frameworks (MOFs) have shown to be unsuspectedly dynamic. Here we describe the topological interconversion of a new framework in the bio-MOF-100 family (dia-c) into the known isomer (lcs) by doubling the pore volume, which occurs during post-synthesis modifications. During this transformation, re-assembling of the MOF building blocks into a completely different framework occurs, involving breaking/forming of metal-ligand bonds. MOF crystallinity and local structure are retained, as determined by powder X-ray diffraction (PXRD) and pair distribution function (PDF) analyses, respectively. We have exploited the inherent dynamism of bio-MOF-100 by coupling chemical decorations of the framework using solvent-assisted ligand exchange (SALE) to the topological change. Following this method and starting from the pristine dense dia-c phase, open lcs-bio-MOF-100 was prepared and functionalized in-situ with an iridium complex (IrL). Alternatively, the dia-c MOF could be modified with wide-ranging amounts of IrL up to ca. 50 mol%, as determined by solution 1 H Nuclear Magnetic Resonance (NMR) spectroscopy, by tuning the concentration of the solutions used and with no evidence for isomer interconversion. The single-site nature of the iridium complexes within the MOFs was assessed by X-ray absorption spectroscopy (XAS) and PDF analyses. As a result, ligand exchanges occurred quantitatively at room temperature, with no need of excess of the iridium metallolinker.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation

Crystallographic imperfections can significantly alter material properties and responses to external stimuli, including solute induced phase transformations and crystal growth and dissolution . Despite recent progress in imaging defects using both electron and x-ray techniques, in situ three-dimensional imaging studies of defect dynamics, necessary to understand and engineer nanoscale processes, remains challenging. Here, we report in situ three-dimensional imaging of defect dynamics during the hydriding phase transformation of individual palladium nanocrystals by Bragg Coherent Diffractive Imaging (BCDI) . During constant pressure experiments, we observed that the phase transformation begins after the nucleation of dislocations in large (300 nm) particles. The 3D dislocation network shows that dislocations are close to the phase boundary. The 3D phase morphology resolved by BCDI suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than the core-shell model commonly assumed. We substantiate this conclusion using 3D phase field modeling and demonstrate how phase morphology affects the critical size for dislocation nucleation. We determine the size dependence of the transformation pressure for large (150-300 nm) palladium nanocrystals using variable pressure experiments. Our results reveal a pathway for solute induced structural phase transformations in nanocrystals and demonstrate BCDI as a novel method for understanding dislocation dynamics in phase transforming systems at the nanoscale.

36 MATERIALS SCIENCE↗

High energy electron diffraction instrument with tunable camera length

Ultrafast electron diffraction (UED) stands as a powerful technique for real-time observation of structural dynamics at the atomic level. In recent years, the use of MeV electrons from radio frequency guns has been widely adopted to take advantage of the relativistic suppression of the space charge effects that otherwise limit the temporal resolution of the technique. Nevertheless, there is not a clear choice for the optimal energy for a UED instrument. Scaling to beam energies higher than a few MeV does pose significant technical challenges, mainly related to the inherent increase in diffraction camera length associated with the smaller Bragg angles. In this study, we report a solution by using a compact post-sample magnetic optical system to magnify the diffraction pattern from a crystal Au sample illuminated by an 8.2 MeV electron beam. Our method employs, as one of the lenses of the optical system, a triplet of compact, high field gradients (>500 T/m), small-gap (3.5 mm) Halbach permanent magnet quadrupoles. Shifting the relative position of the quadrupoles, we demonstrate tuning the magnification by more than a factor of two, a 6× improvement in camera length, and reciprocal space resolution better than 0.1 Å –1 in agreement with beam transport simulations.

47 OTHER INSTRUMENTATION↗

Neutron Instruments for Research in Coordination Chemistry

Here, neutron diffraction and spectroscopies offer unique insight into structures and properties of solids and molecular materials. All neutron instruments located at the various neutron sources are distinct, even if their designs are based on similar principles, and thus, are usually less familiar to the community than commercial X–ray diffractometers and optical spectrometers. Major neutron instruments in the USA, which are open to scientists around the world, and examples of their use in coordination chemistry research are presented here, along with a list of similar instruments at main neutron facilities in other countries. The reader may easily and quickly find from this mini–review an appropriate neutron instrument for research. The instruments include single–crystal and powder diffractometers to determine structures, inelastic neutron scattering (INS) spectrometers to probe magnetic and vibrational excitations, and quasielastic neutron scattering (QENS) spectrometers to study molecular dynamics such as methyl rotation on ligands. Key and unique features of the diffraction and neutron spectroscopies that are relevant to inorganic chemistry are reviewed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The laser shock station in the dynamic compression sector. I

The Laser Shock Station in the Dynamic Compression Sector [Advanced Photon Source (APS), Argonne National Laboratory] links a laser-driven shock compression platform with high energy x-ray pulses from the APS to achieve in-situ, time-resolved x-ray measurements (diffraction and imaging) in materials subjected to well-characterized, high stress, short duration planar shock waves. Additionally, the combination of this station and the other DCS experimental stations provides a unique and versatile experimental facility to study condensed state phenomena by undertaking real-time, multi-scale measurements in materials subjected to a wide range of shock amplitudes (to above ~350 GPa) and time-durations (~10 ns to 1 μs). The Laser Shock Station uses a 100 joule, 5-17 ns, 351 nm frequency tripled Nd:glass laser with programmable pulse shaping and focal profile smoothing for maximum precision. The laser is capable of a shot every 30 minutes. The interaction chamber contains multiple ports for simultaneous diagnostics, a sample holder that allows sequential exposure for 14 samples without breaking vacuum, the capability to vary the angle between the x-ray beam and laser beam by 135°, and the ability to translate to select one of two types of x-ray beams. X-ray data can be taken with a temporal resolution of ~90 psec. Highly reproducible, planar shocks can be propagated in samples to undertake precise and well-characterized experiments. In a series of ten shots, the absolute variation in the time the shock breaks out at the back of the sample is less than 500ps and the variation in peak particle velocity at the sample/window interface is 4.3%. Lastly, this paper describes the entire DCS Laser Shock Station, including sample fabrication and diagnostics, as well as representative experimental results from shock compressed tantalum to demonstrate the excellent quality of x-ray diffraction data in solid tantalum and to establish the stress for tantalum melting.

47 OTHER INSTRUMENTATION↗

Phase Transitions in Orthoenstatite and Subduction Zone Dynamics: Effects of Water and Transition Metal Ions

Synchrotron–based high–pressure and temperature single–crystal X–ray diffraction experiments were conducted on two hydrous orthoenstatite samples (oEn#1: Mg 1.004 Si 0.996 O 3 , ~619 ppm water; oEn#2: Mg 0.947 Ni 0.055 Si 0.998 O 3 , ~696 ppm water) to ~34 GPa and 700 K, using resistively heated diamond anvil cells. The α–opx (Pbca space group)→β–opx (P2 1 /c space group) phase transition of oEn#1 occurs at 12.90(2) GPa, and the β–opx phase persists to 34.25(1) GPa. The α–β transition of oEn#2 occurs at 13.50(1) GPa, and a new isosymmetric β–opx→β–opxII transition takes place at 29.80(4) GPa. The β–opxII phase is preserved down to 24.53(3) GPa during decompression. The transition to the monoclinic β–opxII phase is interpreted as a result of incorporation of Ni 2+ into the orthoenstatite structure. Fitting the third–order Birch–Murnaghan thermal equation of state to the single–crystal P–V–T data yields the thermoelastic parameters of the α– and β–opx phases for both orthoenstatite samples. This study is the first attempt to determine the thermal equation of state of the β–opx phase. Our results suggest that several hundred ppm of water has negligible effects on the bulk modulus of orthoenstatite but notably enhances the thermal expansion. The potential effects of metastable orthoenstatite on subduction zone dynamics are discussed, and the possible contributions of displacive phase transitions to enhancement of the transformational faulting mechanism of the deep–focus earthquakes in subducted slabs are considered. In conclusion, the presence of metastable orthoenstatite within cold slabs could promote slab stagnation above the 660–km discontinuity.

58 GEOSCIENCES↗

A Woven Supramolecular Metal‐Organic Framework Comprising a Ruthenium Bis(terpyridine) Complex and Cucurbit[8]uril: Enhanced Catalytic Activity toward Alcohol Oxidation

Abstract The self‐assembly of a diamondoid woven supramolecular metal–organic framework wSMOF‐1 has been achieved from intertwined [Ru(tpy) 2 ] 2+ (tpy=2,2′,6′,2′′‐terpyridine) complex M1 and cucurbit[8]uril (CB[8]) in water, where the intermolecular dimers formed by the appended aromatic arms of M1 are encapsulated in CB[8]. wSMOF‐1 exhibits ordered pore periodicity in both water and the solid state, as confirmed by a combination of 1 H NMR spectroscopy, UV‐vis absorption, isothermal titration calorimetry, dynamic light scattering, small angle X‐ray scattering and selected area electron diffraction experiments. The woven framework has a pore aperture of 2.1 nm, which allows for the free access of both secondary and primary alcohols and tert ‐butyl hydroperoxide (TBHP). Compared with the control molecule [Ru(tpy) 2 ]Cl 2 , the [Ru(tpy) 2 ] 2+ unit of wSMOF‐1 exhibits a remarkably higher heterogeneous catalysis activity for the oxidation of alcohols by TBHP in n ‐hexane. For the oxidation of 1‐phenylethan‐1‐ol, the yield of acetophenone was increased from 10 % to 95 %.

Zhang, Yun‐Chang↗

Unlocking High Capacity and Reversible Alkaline Iron Redox Using Silicate-Sodium Hydroxide Hybrid Electrolytes

Alkaline iron (Fe) batteries are attractive due to the high abundance, low cost, and multiple valent states of Fe but show limited columbic efficiency and storage capacity when forming electrochemically inert Fe 3 O 4 on discharging and parasitic H 2 on charging. Herein, sodium silicate is found to promote Fe(OH) 2 /FeOOH against Fe(OH) 2 /Fe 3 O 4 conversions. Electrochemical experiments, operando X-ray characterization, and atomistic simulations reveal that improved Fe(OH) 2 /FeOOH conversion originates from (i) strong interaction between sodium silicate and iron oxide and (ii) silicate-induced strengthening of hydrogen-bond networks in electrolytes that inhibits water transport. Furthermore, the silicate additive suppresses hydrogen evolution by impairing energetics of water dissociation and hydroxyl de-sorption on iron surfaces. In conclusion, this new silicate-assisted redox chemistry mitigates H 2 and Fe 3 O 4 formation, improving storage capacity (199 mAh g -1 in half-cells) and coulombic efficiency (94 % after 400 full-cell cycles), paving a path to realizing green battery systems built from earth-abundant materials.

36 MATERIALS SCIENCE↗

Determining the influence of temperature and pressure on the structural stability in a polyurea elastomer

The structural response of amorphous elastomers to applied pressure and temperature is of significant interest given their potential for blast and impact protection applications. While understanding disordered structures is often challenging, this study focuses on the ordered correlations that are present at the atomic level even in amorphous materials. This local order was characterized in polyurea elastomers with two molecular weights up to 6 GPa and ~280 °C using in situ energy dispersive X-ray diffraction at the Advanced Photon Source via total scattering techniques. The resulting structure factors and pair distribution functions indicate that the applied pressure reduced the free volume but had little effect on covalent bonds for both molecular weights. Temperature-induced order-disorder transitions that occur readily at ambient pressures within the temperature range studied here were not observed, their onset likely delayed by the limited chain mobility associated with the free volume reduction. In conclusion, this study demonstrates that total scattering offers insights into the high-pressure structure of disordered polymers that are otherwise inaccessible using more conventional X-ray scattering techniques.

42 ENGINEERING↗

Critical Role of Framework Flexibility and Disorder in Driving High Ionic Conductivity in LiNbOCl 4

Understanding Li-ion transport is key for the rational design of superionic solid electrolytes with exceptional ionic conductivities. LiNbOCl 4 is reported to be one of the most highly conducting materials in the recently realized new class of soft oxyhalide solid electrolytes, exhibiting an ionic conductivity of ~11 mS·cm -1 . Here, we apply X-ray/neutron diffraction and pair distribution function analysis - coupled with density functional theory/ab-initio molecular dynamics - to determine a structural model that provides a rationale for the high conductivity that we observe experimentally in this nanocrystalline solid. We show that it arises from unusually high framework flexibility at room temperature. This owes to isolated 1-D [NbOCl 4 ] - anionic chains which exhibit energetically favorable orientational disorder that is - in turn - correlated to multiple, disordered and equi-energetic Li + sites in the lattice. As the Li-ions sample the 3-D energy landscape with a fast predicted diffusion coefficient of 5.1 x 10 -7 cm 2 /s at room temperature (σ i calc = 17.4 mS·cm -1 ), the inorganic polymer chains can reorient or vice versa. The activation energy barrier for Li migration through the frustrated energy landscape is especially reduced by the elastic nature of the NbO 2 Cl 4 octahedra evident from very widely dispersed Cl-Nb-Cl bond angles in AIMD snapshots at 300 K. The phonon spectra are predominantly influenced by Cl vibrations in the low energy range, and there is strong overlap between the framework (Cl, Nb) and Li partial pDOS in the region between 1.2 - 4.0 THz. The framework flexibility is also reflected in a relatively low bulk modulus of 22 GPa. In conclusion, our findings pave the way for investigation of future “flex-ion” inorganic solids and open up a new direction for the design of high conductivity, soft solid electrolytes for all-solid-state batteries.

AIMD↗

Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

Abstract We present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, $$({\hbox {C}}_{10} {\hbox {H}}_8 {\hbox {O}}_4)_n$$ ( C 10 H 8 O 4 ) n , also called mylar) shock-compressed to ( $$155 \pm 20$$ 155 ± 20 ) GPa and ( $$6000 \pm 1000$$ 6000 ± 1000 ) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

36 MATERIALS SCIENCE↗

Pressure-tuned plethora of ferroelectric phases in CuInP 2 S 6

Layered chalcogenides like CuInP 2 S 6 are room temperature ferroelectrics. Modest compression even increases the electric polarization, raising questions about the origin of this unusual trend and other properties under pressure. In this work, we combine synchrotron-based infrared and Raman scattering spectroscopies, x-ray diffraction, and resistivity measurements with first-principles calculations of the lattice dynamics and energy landscape to unravel the influence of pressure on symmetry, polarization, and metallicity. We uncover a remarkable series of phase transitions across a series of polar space groups: monoclinic Cc → trigonal P31c (prismatic sulfur) → P31c (octahedral sulfur). True metallicity develops above 63 GPa, significantly higher than in related MPS 3 materials (M = Mn, Co, Fe, Ni), offering a picture of competing states of matter that is different than previously supposed. Detailed examination of pressure trends within the Cc phase also reveals phonon lifetime changes and streaking of satellite x-ray peaks that correlate with the maximum polarization. We discuss these tendencies in terms of Cu + ion migration, phase formation, and the overall energy landscape. Our findings place the high pressure behavior of CuInP 2 S 6 on a firm foundation and pave the way for the development of structure-property relations in this family of complex chalcogenides.

ferroelectric phases↗

Negative thermal expansion in cubic FeFe(CN) 6 Prussian blue analogues

Negative thermal expansion (NTE) behavior is an interesting physical phenomenon, but the number of NTE materials is limited. In this study, a new NTE compound has been found, FeFe(CN) 6 Prussian blue analogue, where the average linear coefficient of thermal expansion (α l ) is –4.260 × 10 –6 K –1 between 100 and 450 K. The NTE properties and local vibration dynamics have been investigated by joint experiments of synchrotron X-ray diffraction, X-ray pair distribution function, and extended X-ray absorption fine structure spectroscopy. It has been observed that the Fe–C/Fe–N bonds expand with increasing temperature, while the unit cell shrinks in FeFe(CN) 6 . The vibration directions of both Fe–C and Fe–N prefer to be perpendicular to the linkage of Fe–C[≡]N–Fe rather than being parallel. More pieces of evidence indicate that the transverse vibrations of N atoms dominate the NTE behavior of FeFe(CN) 6 . In conclusion, the present results prove directly that the transverse thermal vibrations of C and N atoms are crucial for the occurrence of the NTE of Prussian blue analogues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanoscale organization in the fluorinated room temperature ionic liquid: Tetraethyl ammonium (trifluoromethanesulfonyl)(nonafluorobutylsulfonyl)imide

Fluorinated Room Temperature Ionic Liquids (FRTILs) are a branch of ionic liquids that is the object of growing interest for a wide range of potential applications, due to the synergic combination of specifically ionic features and those properties that stem from fluorous tails. So far limited experimental work exists on the micro- and mesoscopic structural organization in this class of compounds. Such a work is however necessary to fully understand morphological details at atomistic level that would have strong implications in terms of bulk properties. In this work, we use the synergy between X-ray and neutron scattering together with molecular dynamics simulations to access structural details of a technologically relevant FRTIL that is characterised by an anion bearing a long enough fluorinated tail to develop specific morphological features. In particular, we find the first experimental evidence that in FRTILs bearing an asymmetric bis(perfluoroalkyl)sulfonyl-imide anion, fluorous side chains tend to be spatially segregated into nm-scale spatial heterogeneities. This feature together with the well-established micro-segregation of side alkyl chains in conventional RTILs leads to the concept of triphilic ILs, whose technological applications are yet to be fully developed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗