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At least 1,333 records · Page 74

CHARGED POINT DEFECTS AND DEFECT COMPLEXES IN PHOSPHORENE AND STRUCTURAL PREDICTION OF TAU-11, A DENSITY FUNCTIONAL THEORY APPROACH

With the advent of powerful computers, first principle calculations have become a robust and reliable tool to complement experiments in the study of materials. First principle calculations such as density functional theory can be used to guide experiments to save time and effort when it comes to new and advanced materials discovery. Study of charge defects in materials and crystal structure prediction are such areas in which density functional theory calculations facilitate the prediction of defect formation energy, charge transition levels and elemental site occupations. Experimentally, studying charge defects requires inferring results from various techniques. Likewise, determining site occupancies for similar elements using experimental techniques is challenging and sometimes impossible. In this work, we study the charged intrinsic and extrinsic defects and defect complexes in phosphorene and determine the site occupancies of Al, Fe and Si in the τ11 phase using density functional theory. In the defect work, we calculate the defect formation energy, charge transition level, binding energies and Stokes shift for vacancy, dopant substitution and dopant-vacancy defect complexes in phosphorene. We found that vacancy defect in phosphorene becomes negatively charged in n-type doping and may passivate the dopants and reduce carrier concentration and mobility. For non-metal dopants in phosphorene, we predict that O, S and Si prefer to form dopant-vacancy complexes removing the vacancy defect states from the band gap. Mn dopant-vacancy defect complex exhibits possibility of switching between two magnetic spin states. Lastly, using density functional theory, we complement the results from neutron powder diffraction to determine the site occupancies of Al and Si in τ11 phase which was used to determine the alloying element to develop a high temperature and low density alloy.

36 MATERIALS SCIENCE↗

Complexation of NpO 2 + with Amine-Functionalized Diacetamide Ligands in Aqueous Solution: Thermodynamic, Structural, and Computational Studies

Complexation of Np(V) with three structurally related amine-functionalized diacetamide ligands, including 2,2'-azanediylbis( N, N'-dimethylacetamide) (ABDMA), 2,2'-(methylazanediyl)bis( N, N'-dimethylacetamide) (MABDMA), and 2,2'-(benzylazanediyl)bis( N, N'-dimethylacetamide) (BnABDMA), in aqueous solutions was investigated. The stability constants of two successive complexes, namely, NpO 2 L + and NpO 2 L 2 + , where L stands for the ligands, were determined by absorption spectrophotometry. The results suggest that the stability constants of corresponding Np(V) complexes follow the trend: MABDMA > ABDMA ≈ BnABDMA. The data are discussed in terms of the basicity of the ligands and compared with those for the complexation of Np(V) with an ether oxygen-linked diacetamide ligand. Extended X-ray absorption fine structure data indicate that, similar to the complexation with Nd 3+ and UO 2 2+ , the ligands coordinate to NpO 2 + in a tridentate mode through the amine nitrogen and two oxygen atoms of the amide groups. Furthermore, computational results, in conjunction with spectrophotometric data, verify that the 1:2 complexes (NpO 2 (L) 2 + ) in aqueous solutions are highly symmetric with Np at the inversion center, so that the f-f transition of Np(V) is forbidden and NpO 2 (L) 2 + does not display significant absorption in the near-IR region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex

The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an “open” and “closed” conformation is also described. With these structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.

Cavalier, Michael C.↗

Driving macro-scale transformations in three-dimensional-printed biopolymers through controlled induction of molecular anisotropy at the nanoscale

Motivated by the need to harness the properties of renewable and biodegradable polymers for the design and manufacturing of multi-scale structures with complex geometries, we have employed our additive manufacturing platform that leverages molecular self-assembly for the production of metre-scale structures characterized by complex geometries and heterogeneous material composition. As a precursor material, we used chitosan, a chemically modified form of chitin, an abundant and sustainable structural polysaccharide. We demonstrate the ability to control concentration-dependent crystallization as well as the induction of the preferred orientation of the polymer chains through the combination of extrusion-based robotic fabrication and directional toolpathing. Anisotropy is demonstrated and assessed through high-resolution micro-X-ray diffraction in conjunction with finite element simulations. Using this approach, we can leverage controlled and user-defined small-scale propagation of residual stresses to induce large-scale folding of the resulting structures.

36 MATERIALS SCIENCE↗

Synthesis and crystal structure of a copper complex with (E)-2-(4-(1H-1,2,4-triazol-1-yl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one ligand

The title compound, C{sub 35}H{sub 23}CuF{sub 6}N{sub 3}O{sub 5}S{sub 2} (1), was synthesized by the reaction of Cu(tta){sub 2} and L{sup 1}, (L{sup 1} = (E)-2-(4-(1H-1,2,4-triazol-1-yl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one) in the dichloromethane solution. It crystallizes in the monoclinic, space group P2{sub 1}/c with a = 33.8388(5), b = 9.3874(2), c = 21.8194(4) Å, β = 95.522(2), V = 6898.9(2) Å{sup 3}, Z = 8, D{sub x} = 1.554 Mg/m{sup 3}, F(000) = 3272, µ = 0.834 mm{sup –1}, R{sub 1} = 0.0639, wR{sub 2} = 0.1637. The copper(II) ion of 1 is in a distorted square-pyramidal environment with four O atoms of the two tta ligands and one N atom of triazole ligand L{sup 1}. Single-crystal X-ray diffraction data revealed that the hydrogen bonds, weak C–H···π and π···π interactions in the crystals link the coordination units to form 3D supramolecular structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unsupervised data mining in nanoscale x-ray spectro-microscopic study of NdFeB magnet

Novel developments in X-ray based spectro-microscopic characterization techniques have increased the rate of acquisition of spatially resolved spectroscopic data by several orders of magnitude over what was possible a few years ago. This accelerated data acquisition, with high spatial resolution at nanoscale and sensitivity to subtle differences in chemistry and atomic structure, provides a unique opportunity to investigate hierarchically complex and structurally heterogeneous systems found in functional devices and materials systems. However, handling and analyzing the large volume data generated poses significant challenges. Here we apply an unsupervised data-mining algorithm known as DBSCAN to study a rare-earth element based permanent magnet material, Nd 2 Fe 14 B. We are able to reduce a large spectro-microscopic dataset of over 300,000 spectra to 3, preserving much of the underlying information. Scientists can easily and quickly analyze in detail three characteristic spectra. Our approach can rapidly provide a concise representation of a large and complex dataset to materials scientists and chemists. For instance, it shows that the surface of common Nd 2 Fe 14 B magnet is chemically and structurally very different from the bulk, suggesting a possible surface alteration effect possibly due to the corrosion, which could affect the material’s overall properties.

36 MATERIALS SCIENCE↗

Synthesis and molecular structure of a manganese tricarbonyl complex based on 5,6-nido-C{sub 2}B{sub 8}H{sub 12} carborane

The anionic manganese tricarbonyl complex [1,1,1-(CO){sub 3}-isonido-1,2,4-MnC{sub 2}B{sub 8}H{sub 10}]–was synthesized in the form of PPN and tmdaH salts (PPN is bis(triphenylphosphine)iminium, tmda is N,N,N’,N’-tetramethyl-1,8-diaminonaphthalene) by the reaction of the deprotonated form of the medium-size non-icosahedral carborane 5,6-nido-C{sub 2}B{sub 8}H{sub 12} with Mn(CO){sub 5}Br. The structure of the complex [tmdaH][1,1,1-(CO){sub 3}-isonido-1,2,4-MnC{sub 2}B{sub 8}H{sub 10}] was deter-mined by X-ray diffraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aromatic 3,5-Di(2′,4′-dicarboxylphenyl)benozoic acid based coordination polymers as luminescent sensor for the sensitive detection of chromate anions in aqueous solution

Highlights: • The novel pentacarboxylate of 3,5-di(2′,4′-dicarboxylphenyl)benozoic acid were firstly introduced here. • Topology analyses reveal that complex 1 is a 2D {6"3}{sub 2}{6"4.8.10}{6"4.8"2}{sub 2} trilayer structure, and complex 2 is a 3D {6.8"2}{sub 2}{6"4.8"2}{sub 2}{8.10"4.12} network. • Two coordination polymers both show highly sensitive sensing of Cr(VI) anions in aqueous solution. - Abstract: Based on the mixed ligands of aromatic pentacarboxylate of 3,5-di(2′,4′-dicarboxylphenyl)benozoic acid (H{sub 5}L) and 1,4-bis(imidazol-1-yl) benzene (bib), two novel coordination polymers, namely, [Ni{sub 1.5}(H{sub 2}L)(bib){sub 1.5}(H{sub 2}O){sub 2}]{sub n} (1), and {[Pb_2(HL)(bib)_1_._5(H_2O)]·H_2O}{sub n} (2) have been synthesized and characterized by EA, IR, TG, PXRD. Structure analyses reveal that complexes 1 and 2 are both (3,4,4)-connected structures with the same stoichiometry of (3-c){sub 2}(4-c){sub 2}(4-c), the 2D {6"3}{sub 2}{6"4.8.10}{6"4.8"2}{sub 2} trilayer for 1, and 3D {6.8"2}{sub 2}{6"4.8"2}{sub 2}{8.10"4.12} network for 2. Complexes 1 and 2 exhibit excellent recyclable, selective, and sensitive detection of Cr(VI) anions in aqueous solution. The possible mechanism for selective luminescence quenching responses toward Cr(VI) anions is also discussed in detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Fluorescent Properties and Electronic Structure of Nd(111) Complexes with Carboxylic Acids

Mixed-ligand neodymium(III) complexes with carboxylic acids and nitrogen- and phosphorus-containing neutral ligands, which luminesce in the near-IR region, are studied by luminescence and X-ray photoelectron spectroscopies. It is found that coordination of neutral ligands through the nitrogen donor atom leads to an increase in the electron density at the neodymium(III) ion.

74 ATOMIC AND MOLECULAR PHYSICS↗

Comparison of the Energy-Transfer Rates in Structural and Spectral Variants of the B800–850 Complex from Purple Bacteria

Photosynthetic light harvesting can occur with a remarkable near-unity quantum efficiency. The B800–850 complex, also known as light-harvesting complex 2 (LH2), is the primary light-harvesting complex in purple bacteria and has been extensively studied as a model system. The bacteriochlorophylls of the B800–850 complex are organized into two concentric rings, known as the B800 and B850 rings. However, depending on the species and growth conditions, the number of constituent subunits, the pigment geometry, and the absorption energies vary. While the dynamics of some B800–850 variants have been exhaustively characterized, others have not been measured. Furthermore, a direct and simultaneous comparison of how both structural and spectral differences between variants affect these dynamics has not been performed. In this work, we utilize ultrafast transient absorption measurements to compare the B800 to B850 energy-transfer rates in the B800–850 complex as a function of the number of subunits, geometry, and absorption energies. The nonameric B800–850 complex from Rhodobacter (Rb.) sphaeroides is 40% faster than the octameric B800–850 complex from Rhodospirillum (Rs.) molischianum, consistent with structure-based predictions. In contrast, the blue-shifted B800–820 complex from Rs. molischianum is only 20% faster than the B800–850 complex from Rs. molischianum despite an increase in the spectral overlap between the rings that would be expected to produce a larger increase in the energy-transfer rate. These measurements support current models that contain dark, higher-lying excitonic states to bridge the energy gap between rings, thereby maintaining similar energy-transfer dynamics. Altogether, these results demonstrate that energy-transfer dynamics in the B800–850 complex are robust to the spectral and structural variations between species used to optimize energy capture and flow in purple bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solving complex nanostructures with ptychographic atomic electron tomography

Abstract Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr 11 Te 50 structure containing a previously unobserved ZrTe 2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.

36 MATERIALS SCIENCE↗

A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD + , which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis , Campylobacter jejuni , and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD + and XMP/NAD + . In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD + -binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD + -binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.

60 APPLIED LIFE SCIENCES↗

Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry

The extent to which noncovalent protein complexes retain native structure in the gas phase is highly dependent on experimental conditions. Energetic collisions with background gas can cause structural changes ranging from unfolding to subunit dissociation. Additionally, recent studies have highlighted the role of charge in such structural changes, but the mechanism is not completely understood. In this study, native top down (native TD) mass spectrometry was used to probe gas-phase structural changes of alcohol dehydrogenase (ADH, 4mer) under varying degrees of in-source activation. Changes in covalent backbone fragments produced by electron capture dissociation (ECD) or 193 nm ultraviolet photodissociation (UVPD) were correlated to structural changes of the ADH 4mer. ECD fragments indicated unfolding started at the N-terminus, and the charge states of UVPD fragments enabled monitoring of charge migration to the unfolded regions. Interestingly, UVPD fragments also indicated that the charge at the “unfolding” N-terminus of ADH decreased at high in-source activation energies after the initial increase. We proposed a possible “refolding-after-unfolding” mechanism, as further supported by monitoring hydrogen elimination from radical a-ions produced by UVPD at the N-terminus of ADH. However, “refolding-after-unfolding” with increasing in-source activation was not observed for charge-reduced ADH, which likely adopted compact structures that are resistant to both charge migration and unfolding. Combined, these results support a charge-directed unfolding mechanism for protein complexes. Overall, an experimental framework was outlined for utilizing native TD to generate structure-informative mass spectral signatures for protein complexes that complement other structure characterization techniques, such as ion mobility spectrometry and computational modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unveiling and Mapping Polymorphs in Fluorite Y2TiO5 Using 4D-STEM and Unsupervised Machine Learning

Y2TiO5 belongs to the Ln2TiO5 (Ln = lanthanide or Y) family of ceramic materials and exhibits a range of desirable material properties such as radiation tolerance, frustrated magnetism, and large dielectric constant. However, understanding the complex crystal structure of Y2TiO5 remains elusive, given that Y2TiO5 can adopt multiple polymorphs such as cubic, orthorhombic, and hexagonal phases within the lattice. In this work, we report a detailed structural analysis of Y2TiO5 using four-dimensional scanning transmission electron microscopy coupled with unsupervised machine learning. The pyrochlore nanodomains, characterized by the ordered arrangement of yttrium cations on the A site of their A2BO5 structure, are present within the matrix of a predominantly fluorite-structured Y2TiO5 along with a third polymorph, the hexagonal phase. The pyrochlore phase is found to form 2 nm boundary regions around hexagonal phase stacking faults, highlighting the potential influence of the hexagonal phase on the occurrence and distribution of the pyrochlore phase. Lastly, we identify a unique pyrochlore phase with asymmetric arrangement of cation ordering along a single planar direction. Our findings provide invaluable insights into the possible mechanisms stabilizing pyrochlore nanodomains within the fluorite lattice of Y2TiO5.

36 MATERIALS SCIENCE↗

Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋ x Tb x VO₃ (x=0 and 0.2)

The spin and orbital ordering in Dy₁₋ x Tb x VO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy 0.8 Tb 0.20 VO 3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dy sublattice by external magnetic fields couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋ x Tb x VO₃.

Yan, J.-Q.↗

Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes

Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O{sub 2} adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N{sub 4} chelation, as well as the molecular and electronic structures for the O{sub 2} adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O{sub 2} on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d{sub z{sup 2}}, d{sub xy}, d{sub xz}, and d{sub yz}) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O{sub 2} adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Creating Binary Cu–Bi Compounds via High-Pressure Synthesis: A Combined Experimental and Theoretical Study

Exploration beyond the known phase space of thermodynamically stable compounds into the realm of metastable materials is a frontier of materials chemistry. The application of high pressure in experiment and theory provides a powerful vector by which to explore this uncharted phase space, allowing discovery of complex new structures and bonding in the solid state. We harnessed this approach for the Cu–Bi system, where the realization of new phases offers potential for exotic properties such as superconductivity. This potential is due to the presence of bismuth, which, by virtue of its status as one of the heaviest stable elements, forms a critical component in emergent materials such as superconductors and topological insulators. To fully investigate and understand the Cu–Bi system, we welded theoretical predictions with experiment to probe the Cu–Bi system under high pressures. By employing the powerful approach of in situ X-ray diffraction in a laser-heated diamond anvil cell (LHDAC), we thoroughly explored the high-pressure and high-temperature (high-PT) phase space to gain insight into the formation of intermetallic compounds at these conditions. We employed density functional theory (DFT) calculations to calculate a pressure versus temperature phase diagram, which correctly predicts that CuBi is stabilized at lower pressures than Cu11Bi7, and allows us to uncover the thermodynamic contributions responsible for the stability of each phase. Detailed comparisons between the NiAs structure type and the two high-pressure Cu–Bi phases, Cu11Bi7 and CuBi, reveal the preference for elemental segregation within the Cu–Bi phases, and highlight the unique channels and layers formed by ordered Cu vacancies. The electron localization function from DFT calculations account for the presence of these “voids” as a manifestation of the lone pair orientation on the Bi atoms. Our study demonstrates the power of joint experimental–computational work in exploring the chemistry occurring at high-PT conditions. The existence of multiple high-pressure-stabilized phases in the Cu–Bi binary system, which can be readily identified with in situ techniques, offers promise for other systems in which no ambient pressure phases are known to exist.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗