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At least 235 records · Page 13

Decomposition of liquid-liquid extraction organic phase structure into critical and pre-peak contributions

Solution nanostructure induced by amphiphile self-association plays an important role in various chemical and physical processes, including liquid-liquid extraction (LLE). Small angle scattering techniques are an essential means of probing this structure, but, due to non-uniqueness of scattering patterns, their interpretation is not trivial. Here, in this study, we decompose small angle x-ray scattering (SAXS) patterns for a range of binary LLE organic phases into two components: Ornstein-Zernike and pre-peak contributions resulting from, respectively, critical concentration fluctuations and packing of the amphiphilic extractant molecules in the nonpolar aliphatic diluent. While we previously applied Ornstein-Zernike scattering models to similar organic phases, including the pre-peak explicitly in the fit allows us to measure weak fluctuations at high extractant concentration and simultaneously obtain information on the position and intensity of the correlation peak related to amphiphile packing. Scattering patterns and partial structure factors calculated from molecular dynamics simulations support this interpretation. We demonstrate how this minimal scattering model describes nanostructuring for a large number of extractant types over their entire extractant/diluent composition ranges, suggesting simple and universal behavior. The straightforward assignment of these structural contributions facilitates the comparison of these features between different classes of extractant molecules and will enable further studies of organic phase aggregation. Applicability to more complex, process-relevant organic phases is illustrated with post-contact organic phases containing significant quantities of extracted lanthanide nitrate salt, which we find are readily described by this model.

74 ATOMIC AND MOLECULAR PHYSICS↗

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↗

The Pack Method for Compressive Tests of Thin Specimens of Materials Used in Thin-Wall Structures

The strength of modern lightweight thin-wall structures is generally limited by the strength of the compression members. An adequate design of these members requires a knowledge of the compressive stress-strain graph of the thin-wall material. The "pack" method was developed at the National Bureau of Standards with the support of the National Advisory Committee for Aeronautics to make possible a determination of compressive stress-strain graphs for such material. In the pack test an odd number of specimens are assembled into a relatively stable pack, like a "pack of cards." Additional lateral stability is obtained from lateral supports between the external sheet faces of the pack and outside reactions. The tests seems adequate for many problems in structural research.

Aitchison, C S↗

Shear-aligned large-area organic semiconductor crystals through extended π–π interaction

Small molecule-based organic semiconductors are of broad interest in organic field-effect transistors (OFETs) due to their potential for high crystallinity and electrical performance. The 2D molecule, TIPS-peri-pentacenopentacene (TIPS-PPP), which is the vertical extension of the 1D TIPS-pentacene (TIPS-PEN) molecule, offers a lower bandgap, higher aromaticity, and an enhanced π–π interaction with neighboring molecules in the solid state when compared to TIPS-PEN. However, an in-depth understanding of the relationship between the molecule structure, solid-state molecular packing, and the electronic properties has not been reported due to poor control over the TIPS-PPP crystallite size. In this work, we successfully engineered highly oriented large-area TIPS-PPP crystals through the solution shear coating technique. Additionally, compared with narrow ribbon-like TIPS-PEN crystals, TIPS-PPP crystals can grow centimeters long and over 500 μm wide. TIPS-PPP molecules are less susceptible to forming metastable polymorphs than TIPS-PEN molecules upon fast evaporation. The crystal structure of TIPS-PPP is also thermally stable at 250 °C. Notably, the anisotropic charge carrier mobility of TIPS-PPP crystals is resolved through fabricating bottom-gate top-contact devices, with a hole mobility of 3.1 cm 2 V -1 s -1 along the preferred packing direction. Further device optimization using top-gate bottom-contact devices improved the mobility up to 6.5 cm 2 V -1 s -1 , which is among the highest for pentacene-derivative-based organic semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structures of five salt forms of disulfonated monoazo dyes

The structures of five s -block metal salt forms of three disulfonated monoazo dyes are presented. These are poly[di-μ-aqua-diaqua[μ 4 -3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)]disodium(I)], [Na 2 (C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (I), catena -poly[[tetraaquacalcium(II)]-μ-3,3'-(diazane-1,2-diyl)bis(benzenesulfonato)], [Ca(C 12 H 8 N 2 O 6 S 2 )(H 2 O) 4 ] n , (II), catena -poly[[[diaquacalcium(II)]-μ-2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] dihydrate], {[Na(C 12 H 10 N 3 O 6 S 2 )(H 2 O) 2 ]·2H 2 O} n , (III), hexaaquamagnesium bis[2-(4-amino-3-sulfonatophenyl)-1-(4-sulfonatophenyl)diazenium] octahydrate, [Mg(H 2 O) 6 ](C 12 H 10 N 3 O 6 S 2 ) 2 ·8H 2 O, (IV), and poly[[{μ 2 -4-[2-(4-amino-2-methyl-5-methoxyphenyl)diazen-1-yl]benzene-1,3-disulfonato}di-μ-aqua-diaquabarium(II)] dihydrate], {[Ba(C 14 H 13 N 3 O 7 S 2 )(H 2 O) 4 ]·2H 2 O} n , (V). Compound (III) is that obtained on crystallizing the commercial dyestuff Acid Yellow 9 [74543-21-8]. The Mg species is a solvent-separated ion-pair structure and the others are all coordination polymers with bonds from the metal atoms to sulfonate groups. Compound (I) is a three-dimensional coordination polymer, (V) is a two-dimensional coordination polymer and both (II) and (III) are one-dimensional coordination polymers. The coordination behaviour of the azo ligands and the water ligands, the dimensionality of the coordination polymers and the overall packing motifs of these five structures are contrasted to those of monosulfonate monoazo congers. It is found that (I) and (II) adopt similar structural types to those of monosulfonate species but that the other three structures do not.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiscale Crystalline Structure of Confined Polypeptoid Films: The Effect of Alkyl Side Chain Branching

Here we report the effect of alkyl side chain branching on melt-recrystallization of nanoconfined polypeptoid films using poly(N-octyl glycine) (PNOG) and poly(N-2-ethyl-1-hexyl glycine) (PNEHG) as model systems. Upon cooling from the isotropic melt, confined PNOG molecules recrystallize into a near-perfect orthorhombic crystal structure with the board-like molecules stacked face-to-face in the substrate-parallel direction, resulting in long-range ordered wormlike lamellae that occupy the entire film. By contrast, rod-like PNEHG molecules bearing branched N-2-ethyl-1-hexyl side chains stack into a columnar hexagonal mesophase with their backbones oriented parallel to the substrates, forming micron-sized sheaf-like superstructures under confinement, exposing large areas of empty spaces in the film. These findings highlight the effect of alkyl side chain branching on the packing motif and multiscale crystalline structure of polypeptoids under a nanoconfined geometry.

36 MATERIALS SCIENCE↗

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↗

Direct observation of dual-step twinning nucleation in hexagonal close-packed crystals

Design and processing of advanced lightweight structural alloys based on magnesium and titanium rely critically on a control over twinning which, however, remains elusive to date and is dependent on an explicit understanding on the twinning nucleation mechanism in hexagonal close-packed (HCP) crystals. Here, by using in-situ high resolution transmission electron microscopy, we directly reveal a “dual-step” twinning nucleation mechanism in HCP rhenium nanocrystals. It is found that nucleation of the predominant {10 -12} twinning is initiated by disconnections on the Prismatic¦Basal interfaces which establish the lattice correspondence of the twin with a minor deviation from the ideal orientation. Subsequently, the minor deviation is corrected by the formation of coherent twin boundaries through rearrangement of the disconnections on the Prismatic¦Basal interface; thereafter, the coherent twin boundaries propagate by twinning disconnections. The findings provide much-needed high-resolution evidences to the twinning nucleation mechanism in HCP crystals, with crucial implications for engineering advanced structural alloys.

36 MATERIALS SCIENCE↗

Activation of Semicore Electrons in Alkali Metals and Their Role in the B1–B2 Phase Transition under Pressure

Alkali fluorides are often thought of as archetypical ionic compounds whose structures can be understood in terms of the packing of rigid spheres. At ambient pressure, they assume the rocksalt (B1) structure, while under only a few GPa of pressure, the cesium chloride (B2) structure, with higher coordination numbers, is assumed for KF, RbF, and CsF. NaF requires almost 10 times more pressure to undergo this same phase transition, which has not been observed for LiF. Herein, we provide a detailed analysis, based upon quantum chemical calculations, explaining this behavior. We show that for the heavier alkali metals, the semicore p orbitals engage in metal-metal bonding in the B2 phase, facilitating the pressure-induced B1 → B2 structural transition. Furthermore, these findings suggest that the semicore orbitals of heavy alkali metals can be activated without the need of strong oxidants at very mild levels of compression, resulting in the formation of chemical bonds, challenging both traditional and modern core-valence distinctions. In addition, we argue that Cs 5p-5p bonding in CsCl occurs already at ambient pressure, stabilizing the B2 phase, and suggest experiments that may be able to detect signatures of such bonding.

Anions↗

Sealing ceramic material in low melting point glass

A structured device placed in an aerated crucible to pack ceramics molding substance that is to be processed was designed. The structure is wrapped by sealing material made of pyrex glass and graphite foil or sheet with a weight attached on top of it. The crucible is made of carbon; the ceramics material to be treated through heat intervenient press process is molding substance consisting mainly of silicon nitride.

Moritoki, M.↗

Extended-MHD simulations of disruption mitigation via massive gas injection in SPARC

Recent developments to the M3D-C1 code enable higher fidelity modeling of disruptions, and can be applied in the design verification of reactor-scale tokamaks. Among these new capabilities is a method to mesh conducting vessel structures such as coils and passive plates, packing of the toroidal mesh around gas injectors, as well as anisotropic resistivity inside the vessel structures. We present extended-magnetohydrodynamic (MHD) simulations of disruption mitigation via massive gas injection (MGI) in SPARC. The goal of this study is to inform the disruption mitigation layout of SPARC and aid in the design of an effective gas injector configuration. Fully three-dimensional simulations with M3D-C1 are carried out for various injector configurations with the primary goal of determining the effect of different MGI parameters on heat loads and vessel forces. The simulations include a model for impurity ionization, recombination, advection and radiation, as well as spatially resolved conducting structures around the plasma. A localized mixture of deuterium and neon with a small toroidal and poloidal width is injected in up to six locations. We demonstrate that M3D-C1 can model a rapid shutdown via MGI using narrow and more realistic gas plumes than in previous simulations. As a result of the q = 1 surface in the SPARC baseline case a sawtooth is observed early in the simulations. Despite the sawtooth and the onset of edge MHD instabilities, the impurity distribution remains localized around the injector locations, but enables a radiative shutdown of the plasma. We find that using the maximum of six gas injectors results in a lower peaking factor and leads to a more even distribution of radiation toroidally than using two injectors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Microscopic Theory of Long-Time Center-of-Mass Self-Diffusion and Anomalous Transport in Ring Polymer Liquids

We construct a microscopic theory at the level of segment-scale correlated space–time intermolecular forces for the long-time center-of-mass (CM) diffusion constant and intermediate-time non-Fickian transport in dense solutions and melts of ring polymers. The approach combines ideas of polymer, colloid, and liquid-state statistical mechanics to quantify how the multifractal intra-ring conformational structure and inter-ring packing correlations determine dynamic caging constraints and time-dependent friction. Breakdown of Rouse theory is predicted to occur due to length scale-dependent temporal correlation of forces exerted on pairs of tagged ring segments from surrounding polymers. At large enough degrees of polymerization (N), a stronger scaling of the CM diffusion constant (D ∝ N –2 ) is predicted, with a crossover N D proportional to the product of the system-specific macromolecular volume fraction and dimensionless compressibility. In analogy with caging effects in glass-forming fluids, the theory does appear to begin to fail at sufficiently high N/N D for the center-of-mass diffusivity, likely due to another crossover to an even slower activated transport regime. However, use of N/N D with the theoretically predicted N D , in conjunction with dynamic blob scaling ideas for local Rouse friction, collapses semidilute and concentrated solution simulation data onto a master curve. Based on the same physical ideas employed to predict the diffusion constant, a generalized Langevin equation description is formulated for intermediate-time CM transport. It predicts two subdiffusive regimes that emerge due to the self-similar nature of internal ring structure. Analytic and numerical predictions for the apparent non-Fickian exponent as a function of time, N/N D and dimensionless compressibility, the evolution of the maximum degree of subdiffusive motion with N/N D , and the time scale for recovering Fickian diffusion are made, all of which are in good accordance with melt simulations. Furthermore, the present work sets the stage to address activated dynamics and glass formation on the macromolecular scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation of Vertically Oriented Channels during Calcination of Surfactant-Templated Titania-Doped Mesoporous Silica Thin Films

Here, the mesoporous structure development during calcination of titania-doped mesoporous silica thin films is characterized by in situ grazing-incidence small angle x-ray scattering (GISAXS). Varying amounts of titania (≤ 6 mol%) are incorporated in cetyltrimethylammonium bromide (CTAB) templated film by two methods in this study: dispersion of titania in the silica matrix, and fixing titania at the pore surface by complexation of the titania precursor with a sugar-based co-surfactant, dodecyl maltoside (C 12 G 2 ). Before calcination, films templated with only CTAB display a mesoporous structure with a mixture of in-plane 2D hexagonal and randomly oriented porous structure, while C 12 G 2 -complexed film possessed randomly oriented mesostructure only. Both methods yield a final structure of hexagonal close-packed pores orthogonally oriented to the substrate after calcination at 500 °C. This is attributed to weak Si-O-Ti bonds which allow sintering to occur at 500 °C, combined with unidirectional thermal contraction of the film in the vertical direction. Anisotropic stress and annealing of the films allows the randomly oriented pores to merge vertically and form channels with pore diameter of 2.3 ± 0.3 nm. Titania doping greater than 1% is required for this transformation in films with no C 12 G 2 surfactant used while the transformation was observed for films with C 12 G 2 complexation even at low (0.005%) titania doping, perhaps accentuated by orientational disorder introduced by the sugar surfactant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Delineating the Effects of Counterions on the Structural and Vibrational Properties of U(IV) Lindqvist Polyoxometalate Complexes

Herein we conducted a full investigation into the fundamental structural and vibrational properties of uranium(IV) Peacock−Weakley-type lacunary Lindqvist (W 10 ) polyoxometalate (POM) complexes. We recently demonstrated the importance of the secondary lattice elements in tuning the distortion of the D 4d symmetry in W 10 POM complexes, and here, we synthesized eight UW 10 complexes with different alkali metal counterions and evaluated how the composition and packing of counterion species affected complex structural and vibrational properties. Single-crystal X-ray diffraction analysis on complexes 1−8 revealed changes in structural distortion parameters as a function of differences in counterion configurations, while far-infrared and Raman spectra for 1−8 also demonstrated that vibrational mode frequencies were sensitive to changes in counterion composition and packing. To more effectively compare different counterion configurations, we developed counterion effective ionic radius (eIR) as a new structural parameter, and comparisons between structural distortion parameters and eIR values strongly suggested that modulation by the secondary lattice elements can affect structural and vibrational manifolds within POM complexes. Partial least squares (PLS) analysis was used to quantitatively evaluate correlations observed within this investigation, and PLS statistical models showed a strong correlation between counterion eIR and both structural distortion parameters and vibrational mode frequencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗

Folded network and structural transition in molten tin

The fundamental relationships between the structure and properties of liquids are far from being well understood. For instance, the structural origins of many liquid anomalies still remain unclear, but liquid-liquid transitions (LLT) are believed to hold a key. However, experimental demonstrations of LLTs have been rather challenging. Here, we report experimental and theoretical evidence of a second-order-like LLT in molten tin, one which favors a percolating covalent bond network at high temperatures. The observed structural transition originates from the fluctuating metallic/covalent behavior of atomic bonding, and consequently a new paradigm of liquid structure emerges. The liquid structure, described in the form of a folded network, bridges two well-established structural models for disordered systems, i.e., the random packing of hard-spheres and a continuous random network, offering a large structural midground for liquids and glasses. Our findings provide an unparalleled physical picture of the atomic arrangement for a plethora of liquids, shedding light on the thermodynamic and dynamic anomalies of liquids but also entailing far-reaching implications for studying liquid polyamorphism and dynamical transitions in liquids.

36 MATERIALS SCIENCE↗

Toward Computation-Guided Design of Tunable Organic-Inorganic CdS Quantum Dot Binary Superlattices

Combining the advantages of structural programmability in sequence-defined biomimetic molecules and the controllable packing geometry in nanoparticle superlattices, we demonstrate a self-assembled organic-inorganic superlattice whose structure can be altered with the slightest change in the sequence of the organic counterpart. Here, oleate-coated CdS quantum dots (QDs) form a square-packed superlattice with a 1:1 molar equivalence of a di-block amphiphilic peptoid (Nbrpe6Dig) in chloroform. In contrast, no apparent structure is observed in the organic solvent alone. Based on theoretical evidence, we show that the assembly is a binary superlattice where both the CdS QDs and the peptoids serve as building blocks and further predict a correlation between the superlattice structure and the peptoid sequence. The computationally guided prediction is validated by experiments where superlattice transformation is observed with modified peptoids. The mechanism identified in our work inspires new ways to control and tune organic-inorganic hybrid nanomaterial self-assembly.

Qi, Xin↗

High‐Pressure Characterization of Melt‐Castable Energetic Materials: Bis(Nitroxymethylisoxazolyl) Furoxan (DNDIF)

Abstract The high‐pressure behavior of bis(nitroxymethylisoxazolyl) furoxan (DNDIF) was studied at ambient temperature and pressures approaching 30 GPa by Raman spectroscopy and powder X‐ray diffraction. There was no evidence of a phase change observed over this pressure range, indicating that the ambient structure of DNDIF remains stable up to conditions similar to the detonation pressure of the material. Such findings suggest that this melt‐castable explosive may be used in the replacement of 2,4,6‐trinitrotoluene (TNT) in energetic formulations without the concern of uncontrolled polymorphism that might otherwise affect the performance and safety of the munition. Additionally, empirical understanding of the effect of different structural motifs in the crystal packing builds on understanding of what macroscale features are desirable for future materials and gets us closer to the design of future novel energetics.

Bennion, Jonathan C.↗