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Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography
This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.
Atomic structure of the i- R -Cd quasicrystals and consequences for magnetism
Not Available
Amorphous W–S–N thin films: The atomic structure behind ultra-low friction
Not Available
Order, disorder and mixing: The atomic structure of amorphous mixtures of titania and tantala
Not Available
Atomic structure calculations of complex atoms: review
This report presents different methods, codes, and theories used in calculating complex atoms.
Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening
Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numerical complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. This technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.
Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta{sub 2}O{sub 5})
Amorphous tantala (a-Ta{sub 2}O{sub 5}) is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta{sub 2}O{sub 5} coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta{sub 2}O{sub 5} and other a-T{sub 2}O{sub 5} studies.
Defects in local atomic structure of ZnO films sensitized with tinto and mangrove organic dyes
Not provided.
Insight into the Atomic Structure of High-Voltage Spinel LiNi 0.5 Mn 1.5 O 4 Cathode Material in the First Cycle
Application of high-voltage spinel LiNi 0.5 Mn 1.5 O 4 cathode material is the closest and the most realistic approach to meeting the midterm goal of lithium-ion batteries for electric vehicles (EVs) and plug-in hybrid electric vehicles (HEVs). However, this application has been hampered by long-standing issues, such as capacity degradation and poor first-cycle Coulombic efficiency of LiNi 0.5 Mn 1.5 O 4 cathode material. Although it is well-known that the structure of LiNi 0.5 Mn 1.5 O 4 into which Li ions are reversibly intercalated plays a critical role in the above issues, performance degradation related to structural changes, particularly in the first cycle, are not fully understood. Here, we report detailed investigations of local atomic-level and average structure of LiNi 0.5 Mn 1.5 O 4 during first cycle (3.5–4.9 V) at room temperature. We observed two types of local atomic-level migration of transition metals (TM) ions in the cathode of a well-prepared LiNi 0.5 Mn 1.5 O 4 //Li half-cell during first charge via an aberration-corrected scanning transmission electron microscopy (STEM). Surface regions (~2 nm) of the cycled LiNi 0.5 Mn 1.5 O 4 particles show migration of TM ions into tetrahedral Li sites to form a Mn 3 O 4 -like structure. However, subsurface regions of the cycled particles exhibit migration of TM ions into empty octahedral sites to form a rocksalt-like structure. The migration of these TM ions are closely related to dissolution of Ni/Mn ions and building-up of charge transfer impedance, which contribute significantly to the capacity degradation and the poor first-cycle Coulombic efficiency of spinel LiNi 0.5 Mn 1.5 O 4 cathode material. Accordingly, we provide suggestions of effective stabilization of LiNi 0.5 Mn 1.5 O 4 structure to obtain better electrochemical performance.
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.
Elucidating the atomic structures of different sources of fly ash using X-ray and neutron PDF analysis
Abstract not provided
Using a spherical crystallite model with vacancies to relate local atomic structure to irradiation defects in ZrC and ZrN
Abstract not provided
Local atomic structure of Pd and Ag in the SiC containment layer of TRISO fuel particles fissioned to 20% burn-up
The structure and speciation of fission products within the SiC barrier layer of tristructural-isotropic (TRISO) fuel particles irradiated to 19.6% fissions per initial metal atom (FIMA) burnup in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) was investigated. As-irradiated fuel particles, as well as those subjected to simulated accident scenarios, were examined. The TRISO particles were characterized using synchrotron X-ray absorption fine-structure spectroscopy (XAFS) at the Materials Research Collaborative Access Team (MRCAT) beamline at the Advanced Photon Source. The TRISO particles were produced at Oak Ridge National Laboratory under the Advanced Gas Reactor Fuel Development and Qualification Program and sent to the ATR for irradiation. XAFS measurements on the palladium and silver K-edges were collected using the MRCAT undulator beamline. Analysis of the Pd edge indicated the formation of palladium silicides of the form Pd x Si (2 ≤ x ≤ 3). In contrast, Ag was found to be metallic within the SiC shell safety tested to 1700 °C. To the best of our knowledge, this is the first result demonstrating metallic bonding of silver from fissioned samples. Knowledge of these reaction pathways will allow for better simulations of radionuclide transport in the various coating layers of TRISO fuels for next generation nuclear reactors. In conclusion, they may also suggest different ways to modify TRISO particles to improve their fuel performance and to mitigate potential fission product release under both normal operation and accident conditions.
Non-phase-separated 2D B–C–N alloys via molecule-like carbon doping in 2D BN: atomic structures and optoelectronic properties
A new way to overcome the phase-separation problem to fabricate 2D B–C–N via molecule-like carbon doping in 2D BN.