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At least 73 records · Page 4

Confinement of quasi-atomic structures in Ti 2 N and Ti 3 N 2 MXene electrides

Metal carbides, nitrides, or carbonitrides of early transition metals, better known as MXenes, possess notable structural, electrical, and magnetic properties. Analyzing electronic structures by calculating structural stability, band structure, density of states, Bader charge transfer, and work functions utilizing first principle calculations, we revealed that titanium nitride MXenes, namely Ti 2 N and Ti 3 N 2 , have excess anionic electrons in their lattice voids, making them MXene electrides. Bulk Ti 3 N 2 has competing antiferromagnetic (AFM) and ferromagnetic (FM) configurations with slightly more stable AFM configuration, while the Ti 2 N MXene is nonmagnetic. Although Ti 3 N 2 favors AFM configuration with hexagonal crystal systems having 6/ mmm point group symmetry, Ti 3 N 2 does not support altermagnetism. The monolayer of the Ti 3 N 2 MXene is a ferromagnetic electride. These unique properties of having non-nuclear interstitial anionic electrons in the electronic structure of titanium nitride MXene have not yet been reported in the literature. Density functional theory calculations show TiN is neither an electride, MXene, or magnetic.

Anionic electrons↗

Two Polymorphs of BaZn 2 P 2 : Crystal Structures, Phase Transition, and Transport Properties

Here, the novel α-BaZn 2 P 2 structural polymorph has been synthesized and structurally characterized for the first time. Its structure, elu-cidated from single crystal X-ray diffraction, indicates that the compound crystallizes in the orthorhombic α-BaCu 2 S 2 structure type, with unit cell parameters a = 9.7567(14) Å, b = 4.1266(6) Å, and c = 10.6000(15) Å. With β-BaZn 2 P 2 being previously iden-tified as belonging to the ThCr 2 Si 2 family, and with the precedent of structural phase transitions between the α-BaCu 2 S 2 type and the ThCr 2 Si 2 type, the potential for the pattern to be extended to the two different structural forms of BaZn 2 P 2 was explored. Thermal analysis suggest that a first order phase transition occurs at ~1123 K, whereby the low-temperature orthorhombic α-phase transforms to a high-temperature tetragonal β-BaZn 2 P 2 ; the structure of which was also studied and confirmed by single-crystal X-ray diffraction. Preliminary transport properties and band structure calculations indicate that α-BaZn 2 P 2 is a p-type, narrow-gap semiconductor with a direct bandgap (Eg) of 0.5 eV. The Seebeck coefficient, S(T), for the material increases steadily from the room temperature value of 119 µV/K to 184 µV/K at 600 K. The electrical resistivity of α-BaZn 2 P 2 is relatively high, on the order of 40 mΩ·cm, and the ρ(T) dependence shows gradual decrease upon heating. Such behavior is comparable to those of the typical semimetals or degenerate semiconductors. Although the observed values of the as-synthesized samples are not optimal, the carrier concentration can apparently be tuned to fall between the values of metals and semiconductors, thus providing an open window for optimizing this phase towards achieving an enhanced thermoelectric figure of merit zT. The calculated indirect band gap for the β-BaZn 2 P 2 phase is Eg = 0.03 eV which is about an order of magnitude lower than that of α-BaZn 2 P 2 . It is expected that the cage-like structural motif and layered structure possessed by α-BaZn 2 P 2 and β-BaZn 2 P 2 phases, respectively, would promote the realiza-tion of a low thermal conductivity in both compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of peracetic acid on the disruption of lignin packing structure and its consequence on lignin depolymerisation

Peracetic acid (PAA) is an effective oxidant capable of solubilising lignin and efficiently depolymerising it to selective phenolic compounds; however, the specific role by which PAA initiates the depolymerisation is still elusive. Herein, interaction between PAA and the lignin macromolecule and the consequent structural changes of the latter were studied by characterising the lignin packing structure and its associated changes during the oxidation process. While the lignin packing structure and its changes associated with the PAA-mediated oxidation were probed by X-ray diffraction, the impact of the PAA on different chemical functionalities present in the lignin structure was established by 13 C and 1 H– 13 C heteronuclear single-quantum coherence nuclear magnetic resonance (NMR) spectroscopy. Further, combining the NMR spectroscopy results, and the product distribution, we conclude that the predominant reaction pathway for the oxidative depolymerisation of lignin with PAA is the Baeyer–Villiger oxidation of the ketone formed by the oxidation of the benzylic hydroxyl group adjacent to the β-O-4 linkage. The experimental evidence provided herein corroborated that PAA instigates oxygen insertion to the lignin macromolecule resulting in disruption of its packing structures and facilitates depolymerisation. We also investigated various metal oxide and mixed metal oxide catalysts to identify effective catalysts that further enhance the efficiency of PAA-mediated depolymerisation of lignin and produce selective monomeric phenolic compounds. Techno-economic analysis was also conducted to identify the key parameters associated with this oxidative process that need to be considered for possible commercial application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity

Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli ( Ec )-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec- dGTPase, including an X-ray free-electron laser structure of the free Ec- -dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec- dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec- dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.

Barnes, Christopher O.↗

Critical differences in 3D atomic structure of individual ligand-protected nanocrystals in solution

Precise three-dimensional (3D) atomic structure determination of individual nanocrystals is a prerequisite for understanding and predicting their physical properties. Nanocrystals from the same synthesis batch display what are often presumed to be small but possibly important differences in size, lattice distortions, and defects, which can only be understood by structural characterization with high spatial 3D resolution. We solved the structures of individual colloidal platinum nanocrystals by developing atomic-resolution 3D liquid-cell electron microscopy to reveal critical intrinsic heterogeneity of ligand-protected platinum nanocrystals in solution, including structural degeneracies, lattice parameter deviations, internal defects, and strain. These differences in structure lead to substantial contributions to free energies, consequential enough that they must be considered in any discussion of fundamental nanocrystal properties or applications.

Kim, Byung Hyo↗

Reversible structural transformations in supercooled liquid water from 135 to 245 K

Water has many anomalous properties compared to “simple” liquids, and these anomalies are typically enhanced in supercooled water.1-3 While numerous models have been proposed, including the liquid-liquid critical point,4,5 the singularity-free scenario,6 and the stability limit conjecture,1 a molecular-level understanding remains elusive. The main difficulty in determining which, if any, of these models is correct is the limited amount of data in the relevant temperature and pressure ranges. For water at ambient pressures, which is the focus of this work, data is largely missing from 160 – 232 K (“No Man’s Land”) due to rapid crystallization.2,3 Whether rapid crystallization is just an experimental obstacle, or a fundamental problem signaling the inability of water to thermally equilibrate prior to crystallization is also a major unanswered question.5,7 Here, we investigate the structural transformations of transiently-heated, supercooled water with nanosecond time resolution using infrared vibrational spectroscopy. The experiments demonstrate three key results. First, water’s structure relaxes from its initial configuration to a “steady-state” configuration prior to the onset of crystallization over a wide temperature range. Second, water’s steady-state structure can be reproduced by a linear combination of two, temperature-independent structures that correspond to a “high-temperature liquid” and a “low-temperature liquid.” Third, the observed structural changes are reversible over the full temperature range. Taken together, these results show that supercooled water can equilibrate prior to crystallization for temperatures from the homogeneous nucleation temperature, TH ~232 K,3 down to the glass transition temperature (Tg ~ 136 K). Second, the results provide support for the hypothesis that supercooled water can be described as a mixture of two, structurally-distinct, interconvertible liquids from 135 K to 245 K.5,8-18

Kringle, Loni M.↗

Lateral Water Structure Connects Metal Oxide Nanoparticle Faces

When a metal oxide surface is immersed in aqueous solution, it has the ability to bind, orient, and order interfacial water, affecting both chemical and physical interactions with the surface. Structured interfacial water thus possesses time-averaged, spatially varying polarization charge and potential that are comparable to those arising due to ion accumulation. It is well established that interfacial water structure propagates from the surface into bulk solution. Here, we show that interfacial water structure also propagates laterally, with important consequences. The constant pH molecular dynamics was used to impose a pH difference between opposite faces of a model goethite (a-FeOOH) nanoparticle and quantify water polarization charge on intervening faces. We find that the structure of water on one face is strongly affected by the structure on nearby surfaces, revealing the importance of long-range lateral hydrogen bonding networks with implications for particle aggregation, oriented attachment, and processes such as dissolution and growth.

Zarzycki, Piotr P.↗

Adaptive structures for deployment/construction of structures in space

The application of adaptive structures to the structural design of space structures is examined with attention given to facilitating their construction in space and enhancing reliability. A modified approach based on traditional techniques is presented which incorporates the loads analysis by Wada (1979) and the application of adaptive structures to control structural motion. An analytical technique is described for the deployment/construction of the structure in which each step of the assembly sequence is analyzed. The use of adaptive structures is shown to permit the static adjustment of the structure after assembly in its operational environment. The concepts presented to incorporate adaptive structures in the deployment of large space structures are expected to improve the reliability and reduce the cost of the total systems.

Wada, Ben K.↗

Structural identification and damage assessment of large space structures

Two different methods are proposed for identifying the structural properties of large orbiting space structures under ordinary service loads, and for assessing potential damage due to impact or other extreme loadings. It is shown that the behavior of a structure in a weightless environment is nonlinear due to unloaded or lightly loaded connections, an effect which not only complicates structural control, but makes the problem of system identification more difficult than for ground based systems. Both proposed methods assume that the structure is subjected to loads imposed by prescribed self stressing systems sufficient to produce repeatable internal force systems in the structure. The first method is based on statical response and requires a survey of structural displacements produced by the self stressing systems. The displacements do not have to be determined completely (i.e., in three directions at each connection), but more displacement information produces more accurate structural stiffness information. It is anticipated that displacement measurements will be taken using on-board laser measurement devices. The second technique employs dynamic stress wave measurement techniques using on-board loading devices and strain gages to track stress wave propagation through the space structure. This approach, which is in its early stages of development, relies on an analysis of transit times of impulsive stress waves and changes in transit times and wave forms due to changes in structural parameters.

Nelson, Richard B.↗

Structural Qualification Testing of the WindSat Payload Using Sine Bursts Near Structural Resonance

Sine burst tests are often used for structural qualification of space flight hardware. In most instances, the driving frequency of the shaker is specified far below the structure's first resonant mode, such that the entire test article sees uniform acceleration. For large structures, this limits qualification testing to lower parts of the structure, or else it over-tests the lower structure to achieve qualification of the upper structure. The WindSat payload, a 10.5 foot tall graphite/epoxy, titanium, and aluminum radiometer, experiences accelerations at the six foot diameter reflector nearly four times that at the spacecraft interface. Due to size of the payload, the number of bonded joints, and the lightweight reflector support structure design and construction, using static pull testing to qualify all of the bonded joints in the upper structure would result in large, expensive, and extensive test fixturing. Sine burst testing near the first two structural resonant modes was performed on the WindSat payload to achieve the correct load factor distribution up the stack for structural qualification. In this presentation, how finite element method (FEM) sine burst predictions were used in conjunction with low level random and sine burst tests to achieve correct qualification test load factor distribution on the WindSat payload is discussed. Also presented is the risk mitigation approach for using the uncorrelated FEM in this procedure.

Pontius, Jim↗

DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation damage, immune response changes and other risks identified for long-duration Space travel.

vanderWoerd, Mark↗

Modeling and Control of Robot-Structure Coupling During In-Space Structure Assembly

This paper considers the problem of robot-structure coupling dynamics during in-space robotic assembly of large flexible structures. A two-legged walking robot is used as a construction agent, whose primary goal is to stably walking on the flexible structure while carrying a substructure component to a designated location. The reaction forces inserted by the structure to the walking robot are treated as bounded disturbance inputs, and a trajectory tracking robotic controller is proposed that combines the standard full state feedback motion controller and an adaptive controller to account for the disturbance inputs. In this study, a reduced-order Euler-Bernoulli beam structure model is adapted, and a finite number of co-located sensors and actuators are distributed along the span of the beam structure. The robot-structure coupling forces are treated as a bounded external forcing function to the structure, and hence an output covariance constraint problem can be formulated, in terms of linear matrix inequality, for optimal structure control by utilizing the direct output feedback controllers. The numerical simulations show the effectiveness of the proposed robot-structure modeling and control methodology.

Swei, Sean↗

R -Nb 2 O 5 has an ‘idealized’ V 2 O 5 structure and Wadsley–Roth-like structural stability during Li-ion battery cycling

The adoption of batteries across diverse applications requires electrode materials with a wider range of performance metrics, such as cost, safety, and material availability. Along the path to discovering new commercially viable materials, a fundamental understanding of chemical and atomic structure features that provide structural stability and effective ion transport is essential. In support of new understanding, we report the cycling behavior of metastable R-Nb 2 O 5 . R-Nb 2 O 5 adopts an ‘idealized’ V 2 O 5 structure, in which [NbO 6 ] octahedra alternate in edge- and corner-sharing resulting in ReO 3 -like slabs, whereas Wadsley–Roth materials have ReO 3 -like blocks, linked through edge-sharing octahedra at intersecting crystallographic shear planes. We find that this slab structure is stable during cycling, with minor atomic structure changes and cycling curves that are symmetric on discharge and charge, resembling the behavior of Wadsley–Roth materials more than other related materials, such as ReO 3 , V 2 O 5 , or Nb 3 O 7 F. Based on our findings, R-Nb 2 O 5 can serve as a ‘structural bridge’ between Wadsley–Roth block structures and V 2 O 5 , through which we can relate inter- and intra-polyhedral structures to cycling behavior and structural stability during cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

59 BASIC BIOLOGICAL SCIENCES↗

User's guide to computer program CIVM-JET 4B to calculate the transient structural responses of partial and/or complete structural rings to engine-rotor-fragment impact

A user-oriented computer program CIVM-JET 4B is described to predict the large-deflection elastic-plastic structural responses of fragment impacted single-layer: (a) partial-ring fragment containment or deflector structure or (b) complete-ring fragment containment structure. These two types of structures may be either free or supported in various ways. Supports accommodated include: (1) point supports such as pinned-fixed, ideally-clamped, or supported by a structural branch simulating mounting-bracket structure and (2) elastic foundation support distributed over selected regions of the structure. The initial geometry of each partial or complete ring may be circular or arbitrarily curved; uniform or variable thicknesses of the structure are accommodated. The structural material is assumed to be initially isotropic; strain hardening and strain rate effects are taken into account.

Stagliano, T. R.↗