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At least 541 records · Page 30

Programming Amphiphilic Peptoid Oligomers for Hierarchical Assembly and Inorganic Crystallization

Natural organisms make a wide variety of exquisitely complex, nano-, micro-, and macroscale structured materials in an energy-efficient and highly reproducible manner. During these processes, the information-carrying biomolecules (e.g., proteins, peptides, and carbohydrates) enable (1) hierarchical organization to assemble scaffold materials and execute high-level functions and (2) exquisite control over inorganic materials synthesis, generating biominerals whose properties are optimized for their functions. Inspired by nature, significant efforts have been devoted to developing functional materials that can rival those natural molecules by mimicking in vivo functions using engineered proteins, peptides, DNAs, sequence-defined synthetic molecules (e.g., peptoids), and other biomimetic polymers. Among them, peptoids, a new type of synthetic mimetics of peptides and proteins, have received particular attention because they combine the merits of both synthetic polymers (e.g., high chemical stability and efficient synthesis) and biomolecules (e.g., sequence programmability and biocompatibility). The lack of both chirality and hydrogen bonds in their backbone results in a highly designable peptoid-based system with reduced structural complexity and side chain-chemistry-dominated properties. Here in this Account, we present our recent efforts in this field by programming amphiphilic peptoid sequences for (1) the controlled self-assembly into different hierarchically structured nanomaterials with favorable properties and (2) manipulating inorganic (nano)crystal nucleation, growth, and assembly into superstructures. First, we designed a series of amphiphilic peptoids with controlled side chain chemistries that self-assembled into 1D highly stiff and dynamic nanotubes, 2D membrane-mimetic nanosheets, hexagonally patterned nanoribbons, and 3D nanoflowers. These crystalline nanostructures exhibited sequence-dependent properties and showed promise for different applications. The corresponding peptoid self-assembly pathways and mechanisms were also investigated by leveraging in situ atomic force microscopy studies and molecular dynamics simulations, which showed precise sequence dependency. Second, inspired by peptide- and protein-controlled formation of hierarchical inorganic nanostructures in nature, we developed peptoid-based biomimetic approaches for controlled synthesis of inorganic materials (e.g., noble metals and calcite), in which we took advantage of the substantial side chain chemistry of peptoids and investigated the relationship between the peptoid sequences and the morphology and growth kinetics of inorganic materials. For example, to overcome the challenges (e.g., complexity of protein- and peptide-folding, poor thermal and chemical stabilities) facing the area of protein- and peptide-controlled synthesis of inorganic materials, we recently reported the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. Moreover, we developed a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped gold nanoparticles (NPs). With this Account, we hope to stimulate the research interest of chemists and materials scientists and promote the predictive synthesis of functional and robust materials through the design of sequence-defined synthetic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Imaging supermoiré relaxation in helical trilayer graphene

In twisted van der Waals materials, local atomic relaxation can alter the underlying electronic structure. Characterizing lattice reconstruction and its susceptibility to strain is essential for understanding emergent electronic states, especially in multilayers in which interference between moiré lattices yields larger supermoiré patterns whose energy is highly sensitive to local stacking. Here, in this study, we image spatial modulations in the electronic character of helical trilayer graphene, which indicate relaxation into a superstructure of large domains with uniform moiré periodicity. We show that the supermoiré domain size is increased by strain and can be altered in the same device while preserving the local properties within each domain. Finally, we observe a higher conductance at the domain boundaries, consistent with predictions that they host counterpropagating edge modes. Our work provides a real-space visualization of moiré-periodic domains, reveals two independently tunable length scales and demonstrates strain engineering as a route towards designing correlated topological networks at the supermoiré scale.

36 MATERIALS SCIENCE↗

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c -type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.

Cytochromes/metabolism↗

Structure retrieval in liquid-phase electron scattering

Electron scattering on liquid samples has been enabled recently by the development of ultrathin liquid sheet technologies. The data treatment of liquid-phase electron scattering has been mostly reliant on methodologies developed for gas electron diffraction, in which theoretical inputs and empirical fittings are often needed to account for the atomic form factor and remove the inelastic scattering background. In this work, we present an alternative data treatment method that is able to retrieve the radial distribution of all the charged particle pairs without the need of either theoretical inputs or empirical fittings. Here, the merits of this new method are illustrated through the retrieval of real-space molecular structure from experimental electron scattering patterns of liquid water, carbon tetrachloride, chloroform, and dichloromethane.

74 ATOMIC AND MOLECULAR PHYSICS↗

Emergent Z 2 Gauge Theories and Topological Excitations in Rydberg Atom Arrays

Strongly interacting arrays of Rydberg atoms provide versatile platforms for exploring exotic many-body phases and dynamics of correlated quantum systems. Motivated by recent experimental advances, we show that the combination of Rydberg interactions and appropriate lattice geometries naturally leads to emergent Z 2 gauge theories endowed with matter fields. Based on this mapping, we describe how Rydberg platforms could realize two distinct classes of topological Z 2 quantum spin liquids, which differ in their patterns of translational symmetry fractionalization. Additionally, we also discuss the natures of the fractionalized excitations of these Z 2 spin liquid states using both fermionic and bosonic parton theories and illustrate their rich interplay with proximate solid phases.

74 ATOMIC AND MOLECULAR PHYSICS↗

A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins

A general formalism to compute configurational properties of proteins and other heteropolymers with an arbitrary sequence of charges and non-uniform excluded volume interaction is presented. A variational approach is utilized to predict average distance between any two monomers in the chain. The presented analytical model, for the first time, explicitly incorporates the role of sequence charge distribution to determine relative sizes between two sequences that vary not only in total charge composition but also in charge decoration (even when charge composition is fixed). Furthermore, the formalism is general enough to allow variation in excluded volume interactions between two monomers. Model predictions are benchmarked against the all-atom Monte Carlo studies of Das and Pappu [Proc. Natl. Acad. Sci. U. S. A. 110, 13392 (2013)] for 30 different synthetic sequences of polyampholytes. These sequences possess an equal number of glutamic acid (E) and lysine (K) residues but differ in the patterning within the sequence. Without any fit parameter, the model captures the strong sequence dependence of the simulated values of the radius of gyration with a correlation coefficient of R{sup 2} = 0.9. The model is then applied to real proteins to compare the unfolded state dimensions of 540 orthologous pairs of thermophilic and mesophilic proteins. The excluded volume parameters are assumed similar under denatured conditions, and only electrostatic effects encoded in the sequence are accounted for. With these assumptions, thermophilic proteins are found—with high statistical significance—to have more compact disordered ensemble compared to their mesophilic counterparts. The method presented here, due to its analytical nature, is capable of making such high throughput analysis of multiple proteins and will have broad applications in proteomic studies as well as in other heteropolymeric systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanoimaging of Electronic Heterogeneity in Bi 2 Se 3 and Sb 2 Te 3 Nanocrystals

Topological insulators (TIs) are quantum materials with topologically protected surface states surrounding an insulating bulk. However, defect-induced bulk conduction often dominates transport properties in most TI materials, obscuring the Dirac surface states. In order to realize intrinsic topological insulating properties, it is thus of great significance to identify the spatial distribution of defects, understand their formation mechanism, and finally control or eliminate their influence. For this study, the electronic heterogeneity in polyol-synthesized Bi 2 Se 3 and chemical vapor deposition-grown Sb 2 Te 3 nanocrystals is systematically investigated by multimodal atomic-to-mesoscale resolution imaging. In particular, by combining the Drude response sensitivity of infrared scattering-type scanning near-field optical microscopy with the work-function specificity of mirror electron microscopy, characteristic mesoscopic patterns are identified, which are related to carrier concentration modulation originating from the formation of defects during the crystal growth process. This correlative imaging and modeling approach thus provides the desired guidance for optimization of growth parameters, crucial for preparing TI nanomaterials to display their intrinsic exotic Dirac properties.

43 PARTICLE ACCELERATORS↗

Direct Exfoliation of Nanoribbons from Bulk van der Waals Crystals

Confinement of monolayers into quasi-1D atomically thin nanoribbons could lead to novel quantum phenomena beyond those achieved in their bulk and monolayer counterparts. However, current experimental availability of nanoribbon species beyond graphene is limited to bottom-up synthesis or lithographic patterning. Here, in this study, a versatile and direct approach is introduced to exfoliate bulk van der Waals crystals as nanoribbons. Akin to the Scotch tape exfoliation method for producing monolayers, this technique provides convenient access to a wide range of nanoribbons derived from their corresponding bulk crystals, including MoS 2 , WS 2 , MoSe 2 , WSe 2 , MoTe 2 , WTe 2 , ReS 2 , and hBN. The nanoribbons are predominantly monolayer, single-crystalline, parallel-aligned, flat, and exhibit high aspect ratios. The role of confinement, strain, and edge configuration of these nanoribbons is observed in their electrical, magnetic, and optical properties. This versatile exfoliation technique provides a universal route for producing a variety of nanoribbon materials and supports the study of their fundamental properties and potential applications.

2D materials↗

The Surface Chemistry of Methanol on Cu 3 Pd(111): Effects of Metal Alloying and Reaction with Hydrogen

Synchrotron-based ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) was used to study the adsorption and surface chemistry of methanol on a Cu 3 Pd(111) model surface. The composition and morphological properties of the pristine Cu 3 Pd(111) substrate were analyzed using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), and low-energy ion scattering (LEIS). The results of ion scattering showed segregation of Pd toward the surface, with a Pd/Cu ratio close to 0.5, a larger value than the ratio of 0.33 expected for a Cu 3 Pd bimetallic structure. The surface of the alloy exhibited a good LEED pattern with three-fold long-range periodicities. In STM, clusters of palladium with hexagonal arrays and Pd- Pd distances of 2.7-2.8 Å were detected. Bonding to copper perturbed the electronic properties of the atoms in the Pd clusters, shifting their 4d states toward higher binding energy with respect to the Fermi level. Further, the valence band spectrum of Cu 3 Pd(111) exhibited a line shape that was very different from those displayed by Cu(111) or Pd(111). At low pressures, the adsorption of methanol on Cu 3 Pd(111) at 300 K mainly produced CH 3 O, CO and CH x species. AP-XPS showed that most Pd atoms in the surface of the Cu 3 Pd(111) alloy interacted with the decomposition products of methanol. No significant changes were observed in the core levels of copper upon the adsorption and dissociation of methanol, suggesting that the molecule mainly interacted with Pd sites of the alloy. Reaction with hydrogen led to fast removal of CH x , C and PdC x species from Cu 3 Pd(111) at moderate (< 450 K) temperatures and prevented a CH x → C transformation. If the stability of adsorbed CH 3 O is used as a descriptor for the hydrogenation of CO 2 to methanol, Cu 3 Pd should be a much better catalyst than monometallic palladium. This may be a consequence of electronic and ensemble effects in the alloy that moderate the reactivity of Pd sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis of a series of rare-earth-based multi-anion chalcogenide iodides RE 3 Si 2 Se x S 8− x I (RE = La, Ce, Pr, and Nd) using the flux-assisted boron–chalcogen mixture method

Single crystals and polycrystalline powders of rare earth mixed chalcogenide iodides La 3 Si 2 Se 1.21 S 6.79 I, Ce 3 Si 2 Se 1.39 S 6.61 I, Pr 3 Si 2 Se 1.22 S 6.78 I, and Nd 3 Si 2 Se 1.18 S 6.82 I were prepared using the reactive flux-assisted boron–chalcogen mixture (BCM) method at 850 °C. All compounds crystallized in the monoclinic crystal system, space group C2/c (space group number 15). The series adopts the La 3 Si 2 O 8 Cl structure type, containing isolated SiQ 4 tetrahedra connected by REQ 8 (RE = La, Ce, Pr and Nd) polyhedra; this arrangement creates tunnels that are filled by I atoms. The partial substitution of S by Se was carried out to modulate the optical properties. Phase pure samples and uniform solid solutions were obtained for all compositions as determined using powder X-ray diffraction patterns. Polycrystalline powders were used for physical property measurements, including magnetic susceptibility and UV-Vis diffuse reflectance. The solid-state UV-Vis data for the polycrystalline La 3 Si 2 Se 1.21 S 6.79 I, Ce 3 Si 2 Se 1.39 S 6.61 I, and Pr 3 Si 2 Se 1.22 S 6.78 I samples revealed band gaps of E g = 2.5(1), 2.2(1), and 2.3(1) eV, typical of semiconductors. Magnetic measurements indicated that Ce 3 Si 2 Se 1.39 S 6.61 I and Nd 3 Si 2 Se 1.18 S 6.82 I exhibit paramagnetic behavior with slightly negative Weiss constants θ = −25 and −38. The photoluminescence spectrum of Ce 3 Si 2 Se 1.39 S 6.61 I exhibits a broad emission band around ∼493 nm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Driving chemical interactions at graphene-germanium van der Waals interfaces via thermal annealing

Despite its extraordinary charge carrier mobility, the lack of an electronic bandgap in graphene limits its utilization in electronic devices. To overcome this issue, researchers have attempted to chemically modify the pristine graphene lattice in order to engineer its electronic bandstructure. While significant progress has been achieved, aggressive chemistries are often employed that are difficult to pattern and control. In an effort to overcome this issue, here we utilize the well-defined van der Waals interface between crystalline Ge(110) and epitaxial graphene to template covalent chemistry. In particular, by annealing atomically pristine graphene-germanium interfaces synthesized by chemical vapor deposition under ultra-high vacuum conditions, chemical bonding is driven between the germanium surface and the graphene lattice. The resulting bonds act as charge scattering centers that are identified with scanning tunneling microscopy. The generation of atomic-scale defects are independently confirmed with Raman spectroscopy, revealing significant densities within the graphene lattice. Furthermore, the resulting chemically modified graphene has the potential to impact next-generation nanoelectronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bonding, elastic and vibrational properties in low and high pressure synthesized diamond-like BCx phases

Recent studies demonstrate that low pressure chemical vapor deposition at 950 K leads to the synthesis of diamond-like boron carbides with high concentrations of boron (0.66 < x < 4) in which the sp 2 fraction depends on the boron concentration [1]. This indicates that the graphitic BC3 (g-BC3) phases obtained by chemical vapor deposition materials are mixtures of diamond-like and graphitic BCx phases. This finding allows us to revise the interpretation of the x-ray diffraction (XRD) patterns of the g-BC3 phases discussed previously [2, 3]. To support the new interpretation, we conducted a laser heating experiment of the g-BC3 phase. We found that after laser heating at 1100 K and 25 GPa in a diamond anvil cell (DAC) almost all graphitic layers of the g-BC3 transform into a cubic structure. The XRD pattern of the cubic BC3 phase (c-BC3) can be indexed with a cubic unit cell a = 3.619 (0.165) Å. Measurements of the equation of state of the g-BC3 phase demonstrated that boron atoms were incorporated into the graphitic B-C network. The linear compressibility along the c axis can be characterized by the value of the linear modulus Bc = 29.2 ± 1.8 GPa. Linear fitting of the experimental data for the a/a o parameter as a function of pressure gives us the value of the linear elastic modulus along the a axes: Ba = 800 ± 75 GPa.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Selective thermal evolution of native oxide layer in Nb and Nb$_3$Sn-coated SRF grade Nb: An in-situ angular XPS study

This contribution discusses the results of an in-situ angular XPS study on the thermal evolution of the native oxide layer on Nb3Sn and pure Nb. XPS data were recorded with conventional spectrometers using an AlK(alpha) X-ray source for spectra collected up to 600 C, and an MgK(Alpha) X-rays source for temperatures above 600 C. The effect of the thickness, composition, and thermal stability of that oxide layer is relevant to understanding the functional properties of superconducting radiofrequency (SRF) cavities used in particle accelerators. There is a consensus that oxide plays a role in surface resistance (Rs). The focus of this study is Nb3Sn, which is a promising material that is used in the manufacturing of superconducting radiofrequency (SRF) cavities as well as in quantum sensing, and pure Nb, which was included in the study for comparison. The thermal evolution of the oxide layer in these two materials is found to be quite different, which is ascribed to the influence of the Sn atom on the reactivity of the Nb atom in Nb3Sn films. Nb and Sn atoms in this intermetallic solid have different electronegativity, and the Sn atom can reduce electron density around neighbouring Nb atoms in the solid, thus reducing their reactivity for oxygen. This is shown in the thickness, composition, and thermal stability of the oxide layer formed on Nb3Sn. The XPS spectra were complemented by grazing incident XRD patterns collected using the ESRF synchrotron radiation facility. The results discussed herein shed light on oxide evolution in the Nb3Sn compound and guide its processing for potential applications of the Nb3Sn-based SRF cavities in accelerators and other superconducting devices.

Cano, Arely↗

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the conformations of oligomers observed from AFM images, the D and T units were more abundantly on mica surface at pH 4.5 because the ESP re-distribution of M units helped to stabilize these larger oligomers. The amino acid side chains involved in the binding interfaces were stabilized by hydrogen bonds and electrostatic interactions. The detailed analysis of the charged side chains at pH 4.5 indicated that the polarized ESPs induced the aggregations among M, D, and T to form larger oligomers. Therefore, the hydrogen bonds and electrostatic interactions worked together to form the stabilized prion oligomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Three dimensional cluster analysis for atom probe tomography using Ripley’s K-function and machine learning

The size and structure of spatial molecular and atomic clustering can significantly impact material properties and is therefore important to accurately quantify. Ripley’s K-function (K(r)), a measure of spatial correlation, can be used to perform such quantification when the material system of interest can be represented as a marked point pattern. This work demonstrates how machine learning models based on K (r)-derived metrics can accurately estimate cluster size and intra-cluster density in simulated three dimensional (3D) point patterns containing spherical clusters of varying size; over 90% of model estimates for cluster size and intra-cluster density fall within 11% and 18% error of the true values, respectively. These K (r)-based size and density estimates are then applied to an experimental APT reconstruction to characterize MgZn clusters in a 7000 series aluminum alloy. Here we find that the estimates are more accurate, consistent, and robust to user interaction than estimates from the popular maximum separation algorithm. Using K (r) and machine learning to measure clustering is an accurate and repeatable way to quantify this important material attribute.

36 MATERIALS SCIENCE↗

Crystal and electronic characterization of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} semiconductors

Highlights: • Crystal and electronic structure properties of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} structure were investigated. • New crystal structures for Nd–Ti complexes are determined. • Distortions in the crystal structure were observed as a result of Boron shortage. • Prominent change in electronic properties of the samples with the increasing Nd amount. - Abstract: Neodymium substituted TiBO{sub 3} samples were investigated according to their crystal, electric and electronic properties. Studies were conducted by X-ray absorption fine structure spectroscopy (XAFS) technique for the samples with different substitutions in the preparation processes. To achieve better crystal structure results during the study, XRD pattern results were supported by extended-XAFS (EXAFS) analysis. The electronic structure analysis were studied by X-ray absorption near-edge structure spectroscopy (XANES) measurements at the room temperatures. Due to the substituted Nd atoms, prominent changes in crystal structure, new crystal geometries for Nd-Ti complexes, phase transitions in the crystals structure were detected according to the increasing Nd substitutions in the samples. In the entire stages of the substitutions, Nd atoms were observed as governing the whole phenomena due to their dominant characteristics in Ti geometries. Besides, electrical resistivity decay was determined in the materials with the increasing amount of Nd substitution.

36 MATERIALS SCIENCE↗

Sodium Cationization Enables Exotic Deprotonation Sites on Gaseous Mononucleotides

In this work, we report observation and photoelectron spectroscopic characterization of sodium cationization on four doubly deprotonated mononucleotide dianions Na + ·[dNMP-2H] 2- (N = A, G, C, or T) in the gas phase. Multiple tautomers with distinct deprotonated sites are identified, in which Na+ enables novel double deprotonation patterns and folds resultant mononucleotide dianions. The most stable isomer for the whole family is derived from detaching one proton from phosphate and the other from nucleobase (amino group for N = A, G and C, but nitrogen atom for T), while a high-lying isomer with protons detached separately from phosphate and hydroxy group of sugar coexist. Particularly, an exotic deprotomer with both protons deprived from guanosine is populated as well. This work thus displays a remarkably diverse binding landscape enabled by sodium cationization, a potentially critical element in developing general formulism to better model metal cation and nucleotide interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

59 BASIC BIOLOGICAL SCIENCES↗