The Influence of Phosphorus Substituents on the Structures and Solution Speciation of Trivalent Uranium and Lanthanide Phosphinodiboranates
Not Available
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Controlling the Crystal Packing and Morphology of Metal–Organic Macrocycles through Side-Chain Modification
Supramolecular nanotubes constructed from the self-assembly of conjugated metal–organic macrocycles provide a unique collection of materials properties, including solution processability, porosity, and electrical conductivity. Here we show how small modifications to the macrocycle periphery subtly alter the noncovalent interactions governing self-assembly, leading to large changes in crystal packing, crystal morphology, and materials properties. Specifically, we synthesized five distinct copper-based macrocycles that differ in either the steric bulk, polarity, or hydrogen-bonding ability of the peripheral side chains. We show that the electrical conductivity of these macrocycles is highly sensitive to steric bulk, decreasing by 3 orders of magnitude upon introduction of peripheral neopentyl substituents. Here, we further show that the introduction of hydrogen-bonding groups leads to more ordered packing and a dramatic increase in crystallite size. Together, these results establish side-chain engineering as a rich toolkit for controlling the packing structure, particle morphology, and bulk properties of conjugated metal–organic macrocycles.
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Self-Assembled Vesicles from Mixed Brush Nanoparticles in Solution
The self-assembly of binary polymer-grafted nanoparticles (NPs) in a selective solvent is investigated using coarse-grained simulations. Simulations are performed using theoretically informed Langevin dynamics (TILD), a particle-based method that employs a particle-to-mesh scheme to efficiently calculate the nonbonded interactions. Here, the particles are densely grafted with two immiscible polymers, A and B, that are permanently bound to the NP either at random grafting sites (random-grafted) or with all the A chains on one hemisphere of the NP and all the B chains on the other hemisphere (Janus-grafted). For NPs with random grafting, the polymers phase-separate on the surface of the NP to form Janus-type structures in dilute solution, even though some of the chains have to stretch around the particle to form the Janus structure. When the solvent quality is sufficiently poor for the solvophobic chains, the binary grafted NPs assemble into various structures, including double-walled vesicles. In particular, vesicles are formed when the solvophilic volume fraction is between 0.2 and 0.3, in a similar range to that required for vesicle formation in diblock copolymers in a selective solvent. For mixed-grafted NPs, there is considerable variation in the structure of each individual NP, but nevertheless, these NPs form ordered vesicles, similar to those formed by Janus-grafted NPs.
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Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control
Macromolecule sequence, structure, and function are inherently intertwined. While well-established relationships exist in proteins, they are more challenging to define for synthetic polymer nanoparticles due to their molecular weight, sequence, and conformational dispersities. Furthermore, to explore the impact of sequence on nanoparticle structure, we synthesized a set of 16 compositionally identical, sequence-controlled polymers with distinct monomer patterning of dimethyl acrylamide and a bioinspired, structure-driving di(phenylalanine) acrylamide (FF). Sequence control was achieved through multiblock polymerizations, yielding unique ensembles of polymer sequences which were simulated by kinetic Monte Carlo simulations. Systematic analysis of the global (tertiary- and quaternary-like) structure in this amphiphilic copolymer series revealed the effect of multiple sequence descriptors: the number of domains, the hydropathy of terminal domains, and the patchiness (density) of FF within a domain, each of which impacted both chain collapse and the distribution of single- and multichain assemblies. Furthermore, both the conformational freedom of chain segments and local-scale, β-sheet-like interactions were sensitive to the patchiness of FF. To connect sequence, structure, and target function, we evaluated an additional series of nine sequence-controlled copolymers as sequestrants for rare earth elements (REEs) by incorporating a functional acrylic acid monomer into select polymer scaffolds. We identified key sequence variables that influence the binding affinity, capacity, and selectivity of the polymers for REEs. Collectively, these results highlight the potential of and boundaries of sequence control via multiblock polymerizations to drive primary sequence ensembles hierarchical structures, and ultimately the functionality of compositionally identical polymeric materials.
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Gas phase protonated nicotine is a mixture of pyridine- and pyrrolidine-protonated conformers: implications for its native structure in the nicotinic acetylcholine receptor
The infrared (IR) spectra of gas phase protonated nicotine has been measured in the never-before probed N–H “fingerprint region” (3200–3500 cm -1 ). The protonated molecules generated by an electrospray source are thermalized in the first ion trap with water vapor and He gas at a pre-determined temperature prior to being probed by IR spectroscopy in the second ion trap at 4 K. The IR spectra exhibit two N–H stretching bands which are assigned to the pyridine and pyrrolidine protomers with the aid of high-level electronic structure calculations. This finding is in sharp contrast to previous spectroscopic studies that suggested a single population of the pyridine protomer. The relative populations of the two protomers vary by changing the temperature of the thermalizing trap from 180-300 K. The relative conformer populations at 240 K and 300 K are well reproduced by the theoretical calculations, unequivocally determining that gas phase nicotine is a 3 : 2 mixture of both pyridine and pyrrolidine protomers at room temperature. The thermalizing anhydrous vapor does not result in any population change. It rather demonstrates the catalytic role of water in achieving equilibrium between the two protomers. The combination of IR spectroscopy and electronic structure calculations establish the small energy difference between the pyridine and pyrrolidine protomers in nicotine. Finally, one of the gas phase nicotine pyrrolidine protomers has the closest conformational resemblance among all low-lying energy isomers with the X-ray structure of nicotine in the nicotinic acetylcholine receptor (nAChR).
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General Protocol for the Accurate Prediction of Molecular 13 C/ 1 H NMR Chemical Shifts via Machine Learning Augmented DFT
An accurate prediction of NMR chemical shifts at affordable computational cost is very important for different types of structural assignments in experimental studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) are two of the most popular computational methods for NMR calculation, yet they often fail to resolve ambiguities in structural assignments. In this work, we present a new method that uses machine learning (ML) techniques (DFT + ML) that significantly increases the accuracy of 13 C/ 1 H NMR chemical shift prediction for a variety of organic molecules. The input of the generalizable DFT + ML model contains two critical parts: one is a vector providing insights into chemical environments, which can be evaluated without knowing the exact geometry of the molecule; the other one is the DFT-calculated isotropic shielding constant. The DFT + ML model was trained with a data set containing 476 13 C and 270 1 H experimental chemical shifts. For the DFT methods used here, the root mean square deviations (RMSDs) for the errors between predicted and experimental 13 C/ 1 H chemical shifts can be as small as 2.10/0.18 ppm, which is much lower than those from simple DFT (5.54/0.25 ppm), or DFT + linear regression (LR) (4.77/0.23 ppm) approaches. It also has a smaller maximum absolute error than two previously proposed NMR-predicting ML models. The robustness of the DFT + ML model is tested on two classes of organic molecules (TIC10 and hyacinthacines), where the correct isomers were unambiguously assigned to the experimental ones. Overall, the DFT + ML model shows promise for structural assignments in a variety of systems, including stereoisomers, that are often challenging to determine experimentally.
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Ultra-black coatings for space instruments: a comparison of traditional Ebonol C processes and a method for future repeatability
Ultra-black coatings have served various roles in space instrumentation and hardware. The Ebonol C coating has been used for various missions requiring low reflectivity on aluminum substrates that are electrically conducting. This coating is produced through the formation of a cupric oxide structure on an intermediate layer of copper applied to the aluminum. For many years, this commercial formulation has been used ubiquitously for space instruments. The coating relies upon details of the copper base layer that have been trade secret at various finishing companies, and the availability of the Ebonol C formulated chemistry from the chemical supplier. In recent years, this product has been discontinued at various times, leaving vendors to either rely on expired stock or to formulate their own equivalents. Here, we detail the processing methods, chemistries, and resultant coating structures that produce reflectance performance equivalent to baseline historical reflectance data. This process detail will ensure equivalent performance for such coatings for future missions and link the performance to past and currently deployed instruments.
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Probing Interactions between Adsorbed Polymers and γ-Al 2 O 3 Using Solid-State NMR
The interactions between polymers and metal oxide surfaces affect the physical properties of polymer composites and the selectivity of catalysts used for plastic conversion. Gauging the strengths of these interactions and how they depend on adsorption conformations and polymer structure is nevertheless quite challenging. Herein, we evaluate whether a recently introduced dynamic nuclear polarization-based surface-to-atom distance measurement method can be used to gauge the specific interactions between five vinyl polymers and an oxide support (alumina). The adsorption conformations of polymer monolayers were studied using site-specific 13 C{ 27 Al} rotational-echo saturation-pulse double-resonance (RESPDOR) experiments. The method is effective in revealing the average distance between the adsorbed polymer and the surface, as well as the fraction of the monomers that are adsorbed. Polymers that possess larger side chains are more weakly adsorbed, as evidenced by their formation of more numerous loop and tail structures. In conclusion, the measured RESPDOR dephasing data further reveals that polymer adsorption conformations are largely disordered and involve few hydrogen bonding interactions.
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Ferromagnetic Cr 4 PtGa 17 : A Half-Heusler-Type Compound with a Breathing Pyrochlore Lattice
Here, we describe the crystal structure and elementary magnetic properties of a previously unreported ternary intermetallic compound, Cr 4 PtGa 17 , which crystallizes in a rhombohedral unit cell in the noncentrosymmetric space group R3m. The crystal structure is closely related to those of XYZ half-Heusler compounds, where X, Y, and Z are reported to be single elements only, occupying three different face-centered-cubic sublattices. The new material, Cr 4 PtGa 17 , can be most straightforwardly illustrated by writing the formula as (PtGa 2 )(Cr 4 Ga 14 )Ga (X = PtGa 2 , Y = Cr 4 Ga 14 , Z = Ga); that is, the X and Y sites are occupied by clusters instead of single elements. The magnetic Cr occupies a breathing pyrochlore lattice. Ferromagnetic ordering is found below T C ~ 61 K, by both neutron diffraction and magnetometer studies, with a small, saturated moment of ~0.25 μ B /Cr observed at 2 K, making Cr 4 PtGa 17 the first ferromagnetically ordered material with a breathing pyrochlore lattice. A magnetoresistance of ~140% was observed at 2 K. DFT calculations suggest that the material has a nearly half-metallic electronic structure. The new material, Cr 4 PtGa 17 , the first realization of both a half-Heusler-type structure and a breathing pyrochlore lattice, might pave a new way to achieve novel types of half-Heusler compounds.
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Probing the Radial Chemistry of Getter Components in Light Water Reactors via Controlled Electrochemical Dissolution
Getters are among the key functional components in the Tritium Producing Burnable Absorber Rods (TPBARs) of Light Water Reactors, and are used to capture the released tritium gas. They are cylindrical tubes comprised of the alloy zircaloy-4 which is coated with nickel plating both internally and externally. Their exposure to tritium as well as the irradiation environments in the light water reactors changes their structure, chemical composition and chemistry. Understanding the radial tritium distribution is key to gaining insight into the evolution of new chemistry upon irradiation in order to predict getter performance. Consequently, efforts are underway to devise a method that can allow selective probing into the getter core radially to probe the chemistry akin to carefully and selectively peeling of the layers of an onion. We have recently devised an electrochemical dissolution technique for controlled radial dissolution of zirconium based liners; this work describes the first proof-of-concept demonstration of the applicability of this technique on the controlled radial dissolution of nickel plated getters. The technique is complemented with periodic analysis of the electrolyte solution to measure the rates of release of the various elemental components and therefore glean information on their radial distribution across the getter; further complementary microscopy on the exposed surfaces allows us insight into the chemistry at the getter core.
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Structures and Energetics of E 2 H 3 + (E = As, Sb, and Bi) Cations
Not Available
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Crystal Structure and Properties of Layered Pnictides BaCuSi2Pn3 (Pn = P, As)
Two novel layered compounds BaCuSi 2 Pn 3 (Pn = P, As) adopting new structure types are reported. As revealed by single-crystal X-ray diffraction, both compounds are composed of unique Cu–Si–Pn layers featuring CuPn 3 and Si 2 Pn 6 structural motifs found in other archetypal pnictide materials. The stacking of the isostructural Cu–Si–Pn layers is different for phosphide and arsenide compounds. Synthesis from elements aided by in situ synchrotron powder X-ray diffraction resulted in the obtainment of bulk powders with a minimized amount of admixtures. Experimentally measured physical properties of BaCuSi 2 As 3 unexpectedly showed metal-like behavior at temperatures above 15 K, despite the fact that density functional theory calculations predict a small band gap of 0.4 eV. BaCuSi 2 As 3 exhibits ultralow thermal conductivity, which can be explained by the combination of a layered crystal structure with alternating covalent and ionic bonding, which feature rattling of Cu atoms similar to that in tetrahedrites.
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Fermi-Level Engineering of Nitrogen Core-Doped Armchair Graphene Nanoribbons
Substitutional heteroatom doping of bottom-up engineered 1D graphene nanoribbons (GNRs) is a versatile tool for realizing low-dimensional functional materials for nanoelectronics and sensing. Previous efforts have largely relied on replacing C–H groups lining the edges of GNRs with trigonal planar N atoms. This type of atomically precise doping, however, only results in a modest realignment of the valence band (VB) and conduction band (CB) energies. Here, we report the design, bottom-up synthesis, and spectroscopic characterization of nitrogen core-doped 5-atom-wide armchair GNRs (N2-5-AGNRs) that yield much greater energy-level shifting of the GNR electronic structure. Here, the substitution of C atoms with N atoms along the backbone of the GNR introduces a single surplus π-electron per dopant that populates the electronic states associated with previously unoccupied bands. First-principles DFT-LDA calculations confirm that a sizable shift in Fermi energy (∼1.0 eV) is accompanied by a broad reconfiguration of the band structure, including the opening of a new band gap and the transition from a direct to an indirect semiconducting band gap. Scanning tunneling spectroscopy (STS) lift-off charge transport experiments corroborate the theoretical results and reveal the relationship among substitutional heteroatom doping, Fermi-level shifting, electronic band structure, and topological engineering for this new N-doped GNR.
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Intermolecular correlations of liquid and glassy CS 2 studied by synchrotron radiation x-ray diffraction
How is the orientation of molecular liquids ordered on cooling? What are the basic structures of molecular glasses, e.g., close to the crystalline structure or some special structures such as icosahedral cluster? These are long-standing questions in liquid and glass physics. Here, we have constructed a novel cryostat to prepare simple molecular glasses by vapor deposition and performed in situ synchrotron radiation x-ray diffraction experiments. The glassy state of a simple molecule CS 2 , which cannot be vitrified by normal liquid quenching, was successfully prepared with this instrument, and its diffraction data were collected in a wide Q-range of 0.16–25.7 Å -1 with a high-energy diffractometer at BL04B2, SPring-8. The diffraction data of liquid CS 2 were also recorded in a wide temperature range of 160–300 K. These diffraction data were analyzed with molecular dynamics simulations and reverse Monte Carlo modelings to investigate orientational correlation. From the obtained 3D structure models, the orientational correlation between neighboring CS 2 molecules was investigated quantitatively as a function of temperature. At room temperature, the parallel and T-shaped arrangements are preferred for the nearest neighbor correlation. On cooling, these arrangements are developed gradually, and its rate became prominent below the melting temperature (162 K). In the glassy state, the slipped-parallel arrangement is dominant as well as the T-shaped arrangement. Both arrangements appear in the CS 2 crystal, indicating that the structure of glassy CS 2 is close to that of crystalline CS 2 .
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Lattice Dynamics and Structural Phase Transitions in Eu 2 O 3
Using the density functional theory, we study the structural and lattice dynamical properties of europium sesquioxide (Eu 2 O 3 ) in the cubic, trigonal, and monoclinic phases. The obtained lattice parameters and energies of the Raman modes show a good agreement with the available experimental data. The Eu-partial phonon density of states calculated for the cubic structure is compared with the nuclear inelastic scattering data obtained from a 20 nm thick Eu 2 O 3 film deposited on a YSZ substrate. A small shift of the experimental spectrum to higher energies results from a compressive strain induced by the substrate. On the basis of lattice and phonon properties, we analyze the mechanisms of structural transitions between different phases of Eu 2 O 3 .
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Suppression of Disorder in Benzamide and Thiobenzamide Crystals by Fluorine Substitution
Disorder is a common feature of molecular crystals that complicates determination of structures and can potentially affect electric and mechanical properties. Suppression of disorder is observed in otherwise severely disordered benzamide and thiobenzamide crystals by substituting hydrogen with fluorine in the ortho-position of the phenyl ring. Fluorine occupancies of 20–30% are sufficient to suppress disorder without changing the packing motif. Crystal structure prediction calculations reveal a much denser lattice energy landscape for benzamide compared to 2-fluorobenzamide, suggesting that fluorine substitution makes disorder less likely.
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Dynamic Heterogeneity and Kovacs’ Memory Effects in Supercooled Water
Understanding the properties of supercooled water is important for developing a comprehensive theory for liquid water and amorphous ices. Because of rapid crystallization for deeply supercooled water, experiments on it are typically carried out under conditions in which the temperature and/or pressure are rapidly changing. As a result, information on the structural relaxation kinetics of supercooled water as it approaches (metastable) equilibrium is useful for interpreting results obtained in this experimentally challenging region of phase space. Here, we used infrared spectroscopy and the fast time resolution obtained by transiently heating nanoscale water films to investigate relaxation kinetics (aging) in supercooled water. When the structural relaxation of the water films was followed using a temperature jump protocol analogous to the classic experiments of Kovacs, similar memory effects were observed. In particular, after suitable aging at one temperature, water’s structure displayed an extremum versus the number of heat pulses upon changing to a second temperature before eventually relaxing to a steady-state structure characteristic of that temperature. A random double well model based on the idea of dynamic heterogeneity in supercooled water accounts for the observations.
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RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures
The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.
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