Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structural disorder”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Production of the thermal scattering law and neutron scattering cross sections for ice from first principles - 14503

Water ice can exist in many polymorphic phases as a result of the wide range of geometric ordering possible for the hydrogen bonds between H{sub 2}O molecules. Ice Ih, which can form under normal atmospheric pressure at 273 K, is the most common type. Ab initio density functional theory, incorporating the generalized gradient approximation (GGA) for the exchange-correlation energy, is used to simulate the hexagonal structure of ice Ih and calculate phonon dispersion relations with harmonic lattice dynamics. While the unit cell for ice Ih contains four molecules with particular alignments of the H{sub 2}O molecules possible, the structure has globally disordered proton arrangement. To improve capturing this random distribution, a 12-molecule unit cell is incorporated along with a 2x2x2 supercell. The total phonon density of states is determined by randomly sampling dispersion relations in the first Brillouin zone. The translational, librational, bending, and stretching modes are produced with high-quality resolution and are consistent with the optical peaks and ranges observed in Raman, infrared, and inelastic neutron scattering experiments [1]. The phonon spectrum is used to calculate the S(α,β) thermal scattering law for ENDF [2] publication in the incoherent approximation, which is appropriate due to the relatively small coherent nuclear scattering cross section for H{sub 2}O. These theoretical results are compared to experimental S(α,β) at 268 K [3] and trends are found to be in good agreement. Finally, total scattering cross sections are calculated by integrating over S(α,β) to determine the incoherent inelastic cross sections and then separately adding the absorption and incoherent elastic components. These results are compared to experimental total cross sections for ice Ih at 115 K over a range of incident energies [4] and found to provide excellent agreement. (authors)

42 ENGINEERING↗
DOE OSTI2022

Ab Initio Simulation of Amorphous Graphite

An amorphous graphite material has been predicted from molecular dynamics simulation using ab initio methods. Carbon materials reveal a strong proclivity to convert into a sp 2 network and then layer at temperatures near 3000 K within a density range of ca. 2.2–2.8 g/cm 3 . Each layer of amorphous graphite is a monolayer of amorphous graphene including pentagons and heptagons in addition to hexagons, and the planes are separated by about 3.1 Å. The layering transition has been studied using various structural and dynamical analyses. The transition is unique as one of partial ordering (long range order of planes and galleries, but topological disorder in the planes). The planes are quite flat, even though monolayer amorphous graphene puckers near pentagonal sites. Interplane cohesion is due partly to non-Van der Waals interactions. The structural disorder has been studied closely, especially the consequences of disorder to electronic transport. Finally, it is expected that the transition elucidated here may be salient to other layered materials.

42 ENGINEERING↗
DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗
DOE OSTI2016

A $n$-vector model for charge transport in molecular semiconductors

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1972

Quartz and feldspar glasses produced by natural and experimental shock.

Refractive index, density, and infrared absorption studies of naturally and experimentally shocked-produced glasses formed from quartz, plagioclase, and alkali-feldspar confirm the existence of two main groups of amorphous forms of the framework silicates: solid-state and liquid-state glasses. These were apparently formed as metastable release products of high-pressure-phases above and below the glass transition temperatures. Solid-state glasses exhibit a series of structural states with increasing disorder caused by increasing shock pressures and temperatures. They gradually merge into the structural state of fused minerals similar to that of synthetic glasses quenched from a melt. Shock-fused alkali feldspars can, however, be distinguished from their laboratory-fused counterparts by infrared absorption and by higher density.

Stoeffler, D.↗
DOE OSTI2023

Disordered Au Nanoclusters for Efficient Ammonia Electrosynthesis

The electrochemical nitrogen (N 2 ) reduction reaction (N 2 RR) under mild conditions is a promising and environmentally friendly alternative to the traditional Haber-Bosch process with high energy consumption and greenhouse emission for the synthesis of ammonia (NH 3 ), but high-yielding production is rendered challenging by the strong nonpolar N≡N bond in N 2 molecules, which hinders their dissociation or activation. In this study, disordered Au nanoclusters anchored on two-dimensional ultrathin Ti 3 C 2 T x MXene nanosheets are explored as highly active and selective electrocatalysts for efficient N 2 -to-NH 3 conversion, exhibiting exceptional activity with an NH 3 yield rate of 88.3±1.7 μg h –1 mg cat. –1 and a faradaic efficiency of 9.3±0.4 %. Further, a combination of in situ near-ambient pressure X-ray photoelectron spectroscopy and operando X-ray absorption fine structure spectroscopy is employed to unveil the uniqueness of this catalyst for N 2 RR. The disordered structure is found to serve as the active site for N 2 chemisorption and activation during the N 2 RR process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2015

Single atom catalysts on amorphous supports: A quenched disorder perspective

Phenomenological models that invoke catalyst sites with different adsorption constants and rate constants are well-established, but computational and experimental methods are just beginning to provide atomically resolved details about amorphous surfaces and their active sites. This letter develops a statistical transformation from the quenched disorder distribution of site structures to the distribution of activation energies for sites on amorphous supports. We show that the overall kinetics are highly sensitive to the precise nature of the low energy tail in the activation energy distribution. Our analysis motivates further development of systematic methods to identify and understand the most reactive members of the active site distribution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Metal–oxygen decoordination stabilizes anion redox in Li-rich oxides

Reversible high-voltage redox chemistry is an essential component of many electrochemical technologies, from (electro)catalysts to lithium-ion batteries. Oxygen-anion redox has garnered intense interest for such applications, particularly lithium-ion batteries, as it offers substantial redox capacity at more than 4 V versus Li/Li + in a variety of oxide materials. However, oxidation of oxygen is almost universally correlated with irreversible local structural transformations, voltage hysteresis and voltage fade, which currently preclude its widespread use. By comprehensively studying the Li 2-x Ir 1-y Sn y O 3 model system, which exhibits tunable oxidation state and structural evolution with y upon cycling, we reveal here that this structure–redox coupling arises from the local stabilization of short approximately 1.8 Å metal–oxygen π bonds and approximately 1.4 Å O–O dimers during oxygen redox, which occurs in Li 2-x Ir 1-y Sn y O 3 through ligand-to-metal charge transfer. Crucially, formation of these oxidized oxygen species necessitates the decoordination of oxygen to a single covalent bonding partner through formation of vacancies at neighbouring cation sites, driving cation disorder. These insights establish a point-defect explanation for why anion redox often occurs alongside local structural disordering and voltage hysteresis during cycling. Our findings offer an explanation for the unique electrochemical properties of lithium-rich layered oxides, with implications generally for the design of materials employing oxygen redox chemistry.

25 ENERGY STORAGE↗
DOE OSTI2024

Structural, Electrochemical, and (De)lithiation Mechanism Investigation of Cation-Disordered Rocksalt and Spinel Hybrid Nanomaterials in Lithium-Ion Batteries

Significant demand for lithium-ion batteries necessitates alternatives to Co- and Ni-based cathode materials. Cation-disordered materials using earth-abundant elements are being explored as promising candidates. Here, in this paper, we demonstrate a coprecipitation synthetic approach that allows direct preparation of disordered rocksalt Li 2.4 Fe 1.0 Ti 1.0 O 4.7 (r-LFTO·C) and spinel structured hybrid Li 0.5 Fe 1.0 Ti 0.9 O 3.2 ·C (s-LFTO·C) nanoparticles with a conformal conductive carbon coating. High-angle annular dark-field imaging coupled with electron energy loss spectroscopy mapping shows uniform Fe/Ti distribution with minor compositional variation among particles. Cation disorder was confirmed for both of the materials at an atomic level, with a short-range order more pronounced in r-LFTO·C. Operando X-ray absorption spectroscopy, ex situ hard X-ray photoelectron spectroscopy, ex situ soft X-ray absorption spectroscopy, and ex situ synchrotron X-ray diffraction were used to investigate (de)lithiation in the bulk and at the surface. Structurally, the r-LFTO·C demonstrated reversible partial Fe center migration between octahedral and tetrahedral sites during (de)lithiation. The r-LFTO·C evidenced that the redox of O was coincident with iron redox during initial electrochemical cycling, while iron redox dominated later cycling. In contrast, s-LFTO·C electrochemistry involved iron redox throughout the cycling process. The findings rationalize the differences in the electrochemistry where r-LFTO·C shows higher initial capacity yet poorer capacity retention over a voltage window where O redox can be accessed, while the s-LFTO·C shows lower initial capacity yet improved capacity retention.

25 ENERGY STORAGE↗
DOE OSTI2017

Dielectric anomaly and relaxation natures in a Zn-Cr pillar−layered metal−organic framework with cages and channels

A bimetallic metal–organic framework (MOF) with the formula [Zn{sub 3}btc{sub 2}(Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH))]·(DMF){sub 15.5}(H{sub 2}O){sub 8} (H{sub 3}btc=1,3,5-benzenetricarboxylic acid; isonic=isonicotinicate) shows a pillar-layered structure. The monolayer consists of hexagon-like rings formed by the [Zn(isonic){sub 2}(btc){sub 2}] tetrahedral and the consecutive monolayers are pillared by trigonal–prismatic clusters of [Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH)]through the remaining binding sites of the Zn{sup 2+} ions. DMF and water molecules are confined in the cages and channels. TGA indicates that the lattice DMF and water molecules begin to be released at temperatures above 363 K. Dielectric measurements were carried out in the range of 173–363 K and 1–10{sup 7} Hz for three successive thermal cycles. The dielectric spectroscopy obtained in the first thermal cycle was different from that observed in the next two thermal cycles, while the dielectric spectra in the last two thermal cycles were almost identical. The dielectric nature of this MOF is discussed in detail for each thermal cycle. Since MOFs are unique host–guest systems in which the structure of the host framework is designable and the guests are exchangeable, it is no doubt those MOFs are materials with a variety of dielectric natures. This study gives a fresh impetus to achieve MOFs–based dielectric materials. - Graphical abstract: The bimetallic MOF [Zn{sub 3}btc{sub 2}(Cr{sub 3}O(isonic){sub 6}(H{sub 2}O){sub 2}(OH))]·(DMF){sub 15.5}(H{sub 2}O){sub 8}1, shows a pillar-layered open-framework structure. The dielectric spectra of 1 are almost identical in the last two thermal cycles, whereas significantly different from that observed in the first thermal cycle. The novel dielectric anomaly associated with a stacked structure transformation of the disordered guests. - Highlights: • A bimetallic metal-organic framework shows a pillar-layered structure. • The MOF displays novel dielectric anomaly and relaxation behaviors. • The dielectric anomaly arises from the stacking structure transformation of guests. • The dielectric relaxation is related to the dipole dynamics of guests.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Phase transition from fcc to bcc structure of the Cu-clusters during nanocrystallization of Fe{sub 85.2}Si{sub 1}B{sub 9}P{sub 4}Cu{sub 0.8} soft magnetic alloy

A role of Cu on the nanocrystallization of an Fe{sub 85.2}Si{sub 1}B{sub 9}P{sub 4}Cu{sub 0.8} alloy was investigated by X-ray absorption fine structure (XAFS) and transmission electron microscopy (TEM). The Cu K-edge XAFS results show that local structure around Cu is disordered for the as-quenched sample whereas it changes to fcc-like structure at 613 K. The fcc Cu-clusters are, however, thermodynamically unstable and begin to transform into bcc structure at 638 K. An explicit bcc structure is observed for the sample annealed at 693 K for 600 s in which TEM observation shows that precipitated bcc-Fe crystallites with ∼12 nm are homogeneously distributed. The bcc structure of the Cu-clusters transforms into the fcc-type again at 973 K, which can be explained by the TEM observations; Cu segregates at grain boundaries between bcc-Fe crystallites and Fe{sub 3}(B,P) compounds. Combining the XAFS results with the TEM observations, the structure transition of the Cu-clusters from fcc to bcc is highly correlated with the preliminary precipitation of the bcc-Fe which takes place prior to the onset of the first crystallization temperature, T{sub x1} = 707 K. Thermodynamic analysis suggests that an interfacial energy density γ between an fcc-Cu cluster and bcc-Fe matrix dominates at a certain case over the structural energy between fcc and bcc Cu, ΔG{sub fcc} {sub −} {sub bcc}, which causes phase transition of the Cu clusters from fcc to bcc structure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural and magnetic properties of iodide-mediated chemically synthesized L1 2 FePt 3 nanoparticles

In this work, we study the effect of elemental iodine as a halide intermediary in the synthesis of FePt 3 nanoparticles using a co-reduction of Fe(acac) 3 and (NH 4 ) 2 PtCl 2 with 1,2-hexadecanediol. Our study shows that elemental iodine facilitates the formation of FePt 3 nanoparticles with the L1 2 structure. When iodine is not used, the as-made nanoparticles have mostly the disordered fcc FePt 3 structure. The as-made nanoparticles are ferromagnetic and have a Curie temperature close to 380 K. Annealing of the as-made nanoparticles leads to an increased particle size and a transformation to the ordered L1 2 FePt 3 phase. Nanoparticles annealed at 700°C for 30 minutes show a mixture of two magnetic phases, a ferromagnetic phase with a lower ordering temperature of ~300 K and an antiferromagnetic phase with a Néel temperature around 135 K.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Intrinsic disorder in the regulatory N-terminal domain of diacylglycerol acyltransferase 1 from Brassica napus

Proteins with multifunctional regulatory domains often demonstrate structural plasticity or protein disorder, allowing the binding of multiple regulatory factors and post-translational modifications. While the importance of protein disorder is clear, it also poses a challenge for in vitro characterization. Here, we report protein intrinsic disorder in a plant molecular system, which despite its prevalence is less studied. We present a detailed biophysical characterization of the entire cytoplasmic N-terminal domain of Brassica napus diacylglycerol acyltransferase, (DGAT1), which includes an inhibitory module and allosteric binding sites. Our results demonstrate that the monomeric N-terminal domain can be stabilized for biophysical characterization and is largely intrinsically disordered in solution. This domain interacts with allosteric modulators of DGAT1, CoA and oleoyl-CoA, at micromolar concentrations. Furthermore, while solution scattering studies indicate conformational heterogeneity in the N-terminal domain of DGAT1, there is a small gain of secondary structure induced by ligand binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid “molecular chaperones”, which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration

The anisotropy of crystals of glypican-1 was significantly reduced by controlled dehydration using the HC1 device, allowing the building of previously disordered parts of the structure. The use of controlled dehydration for improvement of protein crystal diffraction quality is increasing in popularity, although there are still relatively few documented examples of success. A study has been carried out to establish whether controlled dehydration could be used to improve the anisotropy of crystals of the core protein of the human proteoglycan glypican-1. Crystals were subjected to controlled dehydration using the HC1 device. The optimal protocol for dehydration was developed by careful investigation of the following parameters: dehydration rate, final relative humidity and total incubation time T{sub inc}. Of these, the most important was shown to be T{sub inc}. After dehydration using the optimal protocol the crystals showed significantly reduced anisotropy and improved electron density, allowing the building of previously disordered parts of the structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Predictive Model of Charge Mobilities in Organic Semiconductor Small Molecules with Force-Matched Potentials

Charge mobility of crystalline organic semiconductors (OSC) is limited by local dynamic disorder. Recently, the charge mobility for several high mobility OSCs, including TIPS-pentacene, were accurately predicted from a density functional theory (DFT) simulation constrained by the crystal structure and the inelastic neutron scattering spectrum, which provide direct measures of the structure and the dynamic disorder in the length scale and energy range of interest. However, the computational expense required for calculating all of the atomic and molecular forces is prohibitive. In this work, we demonstrate the use of density functional tight binding (DFTB), a semiempirical quantum mechanical method that is 2 to 3 orders of magnitude more efficient than DFT. We show that force matching a many-body interaction potential to DFT derived forces yields highly accurate DFTB models capable of reproducing the low-frequency intricacies of experimental inelastic neutron scattering (INS) spectra and accurately predicting charge mobility. We subsequently predicted charge mobilities from our DFTB model of a number of previously unstudied structural analogues to TIPS-pentacene using dynamic disorder from DFTB and transient localization theory. The approach we establish here could provide a truly rapid simulation pathway for accurate materials properties prediction, in our vision applied to new OSCs with tailored properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR

Highlights: Black-Right-Pointing-Pointer CFTR mutations produce cystic fibrosis. Black-Right-Pointing-Pointer Chloride transport depends on the regulatory domain phosphorylation. Black-Right-Pointing-Pointer Regulatory domain is intrinsically disordered. Black-Right-Pointing-Pointer Secondary structure and protein stability change upon phosphorylation. -- Abstract: The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may be important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and {beta}-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of {alpha}-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 Degree-Sign C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states.

60 APPLIED LIFE SCIENCES↗