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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Revealing the hidden structure of disordered materials by parameterizing their local structural manifold

Abstract Durable interest in developing a framework for the detailed structure of glassy materials has produced numerous structural descriptors that trade off between general applicability and interpretability. However, none approach the combination of simplicity and wide-ranging predictive power of the lattice-grain-defect framework for crystalline materials. Working from the hypothesis that the local atomic environments of a glassy material are constrained by enthalpy minimization to a low-dimensional manifold in atomic coordinate space, we develop a generalized distance function, the Gaussian Integral Inner Product (GIIP) distance, in connection with agglomerative clustering and diffusion maps, to parameterize that manifold. Applying this approach to a two-dimensional model crystal and a three-dimensional binary model metallic glass results in parameters interpretable as coordination number, composition, volumetric strain, and local symmetry. In particular, we show that a more slowly quenched glass has a higher degree of local tetrahedral symmetry at the expense of cyclic symmetry. While these descriptors require post-hoc interpretation, they minimize bias rooted in crystalline materials science and illuminate a range of structural trends that might otherwise be missed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp

The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the subångström- resolution structure of a protofibril formed by a wild-type segment from the β2–α2 loop of the bank vole prion protein. In this work, the structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named ‘polar clasps’.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The 2.1 Å structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex

The poxvirus F9 protein is a component of the vaccinia virus entry fusion complex (EFC) which consists of 11 proteins. The EFC forms a unique apparatus among viral fusion proteins and complexes. We solved the atomic structure of the F9 ectodomain at 2.10Å. A structural comparison to the ectodomain of the EFC protein L1 indicated a similar fold and organization, in which a bundle of fve α-helices is packed against two pairs of β-strands. However, instead of the L1 myristoylation site and hydrophobic cavity, F9 possesses a protruding loop between α-helices α3 and α4 starting at Gly90. Gly90 is conserved in all poxviruses except Salmon gill poxvirus (SGPV) and Diachasmimorpha longicaudata entomopoxvirus. Phylogenetic sequence analysis of all Poxviridae F9 and L1 orthologs revealed the SGPV genome to contain the most distantly related F9 and L1 sequences compared to the vaccinia proteins studied here. The structural diferences between F9 and L1 suggest functional adaptations during evolution from a common precursor that underlie the present requirement for each protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Average structure and local configuration of excess oxygen in UO2+x

Determination of the local configuration of interacting defects in a crystalline, periodic solid is problematic because defects typically do not have a long-range periodicity. Uranium dioxide, the primary fuel for fission reactors, exists in hyperstoichiometric form, UO2+x. Those excess oxygen atoms occur as interstitial defects, and these defects are not random but rather partially ordered. The widely-accepted model to date, the Willis cluster based on neutron diffraction, cannot be reconciled with the first-principles molecular dynamics simulations present here. We demonstrate that the Willis cluster is a fair representation of the numerical ratio of different interstitial O atoms; however, the model does not represent the actual local configuration. The simulations show that the average structure of UO2+x involves a combination of defect structures including split di-interstitial, di-interstitial, mono-interstitial, and the Willis cluster, and the latter is a transition state that provides for the fast diffusion of the defect cluster. The results provide new insights in differentiating the average structure from the local configuration of defects in a solid and the transport properties of UO2+x.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structural elucidation of a mononuclear titanium methylidene

The first example of a structurally characterized titanium methylidene, (PN) 2 Ti=CH 2 , has been prepared via one-electron oxidation of (PN) 2 Ti(CH 3 ) followed by deprotonation or by H-atom abstraction using an aryloxyl radical. The Ti=C distance was found to be 1.939(3) Å, and variable temperature, multinuclear, and multidimensional NMR spectroscopic experiments revealed the methylidene to engage in long range interactions with protons on the ligand framework. Here, computational studies showed that the Ti=C bond, which until now has eluded structural studies, displays all the hallmarks of a prototypical Schrock-carbene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Nanoporous poly(3-hexylthiophene) thin film structures from self-organization of a tunable molecular bottlebrush scaffold

The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(D,L-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach. P3HT side chains induce a physical aggregation of the bottlebrush copolymers upon solvent removal by vacuum drying, primarily driven by attractive π–π interactions; however, the amount of aggregation can be controlled by adjusting side chain composition or by adding linear P3HT chains to the bottlebrush copolymers. Coarse-grained molecular dynamics simulations reveal that linear P3HT chains preferentially associate with P3HT side chains of bottlebrush copolymers, which tends to reduce the aggregation. The nanoscale morphology of microphase segregated thin films created by casting P3HT–PLA random bottlebrush copolymers is highly dependent on the composition of P3HT and PLA side chains, while domain spacing of nanostructures is mainly determined by the length of the side chains. The selective removal of PLA side chains under alkaline conditions generates nanoporous P3HT structures that can be tuned by manipulating molecular design of the bottlebrush scaffold, which is affected by molecular weight and grafting density of the side chains, and their sequence. Furthermore, the ability to exploit the unusual architecture of bottlebrushes to fabricate tunable nanoporous P3HT thin film structures may be a useful way to design templates for optoelectronic applications or membranes for separations.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Early stage structural development of prototypical zeolitic imidazolate framework (ZIF) in solution

Given the wide-ranging potential applications of metal organic frameworks (MOFs), an emerging imperative is to understand their formation with atomic scale precision. This will aid in designing syntheses for next-generation MOFs with enhanced properties and functionalities. Major challenges are to characterize the early-stage seeds, and the pathways to framework growth, which require synthesis coupled with in situ structural characterization sensitive to nanoscale structures in solution. Here we report measurements of an in situ synthesis of a prototypical MOF, ZIF-8, utilizing synchrotron X-ray atomic pair distribution function (PDF) analysis optimized for sensitivity to dilute species, complemented by mass spectrometry, electron microscopy, and density functional theory calculations. We observe that despite rapid formation of the crystalline product, a high concentration of Zn(2-MeIm) 4 (2-MeIm=2-methylimidazolate) initially forms and persists as stable clusters over long times. A secondary, amorphous phase also pervades during the synthesis, which has a structural similarity to the final ZIF-8 and may act as an intermediate to the final product.

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

Structure and proton conduction in sulfonated poly(ether ether ketone) semi-permeable membranes: a multi-scale computational approach.

The design of polymeric membranes for proton or ionic exchange highly depends on the fundamental understanding of the physical and molecular mechanisms that control the formation of the conduction channels. There is an inherent relation between the dynamical structure of the polymeric membrane and the electrostatic forces that drive membrane segregation and proton transport. Here, we used a multi-scale computational approach to analyze the morphology of sulfonated poly(ether ether ketone) membranes at the mesoscale. A self-consistent description of the electrostatic phenomenon was adopted, where discrete polymer chains and a continuum proton field were embedded in a continuum fluid. Brownian dynamics was used for the evolution of the suspended polymer molecules, while a convection-diffusion transport equation, including the Nernst-Planck diffusion mechanism, accounted for the dynamics of the proton concentration field. We varied the polymer concentration, the degree of sulfonation and the level of confinement to find relationships between membrane structure and proton conduction. Our results indicate that the reduced mobility of polymer chains, at concentrations above overlap, and a moderate degree of sulfonation -i.e., 30% - are essential elements for membrane segregation and proton domain connectivity. These conditions also ensure that the membrane structure is not affected by size or by potential gradients. Importantly, our analysis shows that membrane conductivity and current are linearly dependent on polymer concentration and quadratically dependent on the degree of sulfonation. We found that the optimal polymeric membrane design requires a polymer concentration above overlap and a degree of sulfonation around 50%. These conditions promote a dynamical membrane morphology with a constant density of proton channels. Our results and measurements agree with previous experimental works, thereby validating our model and observations.

Molina, Jarol↗
DOE OSTI2020

Photoelectron spectroscopy and computational investigations of the electronic structures and noncovalent interactions of cyclodextrin-closo-dodecaborate anion complexes x-CD·B12X122- (x = a, ß, y; X = H, F)

We report a joint negative ion photoelectron spectroscopy (NIPES) and computational study on the electronic structures and noncovalent interactions of a series of cyclodextrin-closo-dodecaborate dianion complexes, ?-CD·B12X122- (? = a, ß, ?; X = H, F). The measured vertical / adiabatic detachment energies (VDEs / ADEs) are 1.15/0.93, 3.55/3.20, 3.90/3.60, and 3.85/3.60 eV for B12H122- and its a-, ß-, ?-CD complexes, respectively; while the corresponding values are 1.90/1.70, 4.00/3.60, 4.33/3.95, and 4.30/3.85 eV for the X = F case. These results show that the inclusion of B12X122- into the CD cavities greatly increase the electronic stability of the dianions. The effect of electronic stabilization for ß-CD is roughly the same as for ?-CD, both being considerably stronger than that for a-CD. Density functional theory (DFT) based geometry optimization reveals that B12X122- are inserted into CDs increasingly deeper from a-CD to ?-CD. The calculated VDEs and ADEs agree with the experiments well, particularly, reproducing the electron binding energy (EBE) trends. The molecular orbital analyses indicate that the most loosely bound photodetached electrons origin from the guest B12X122- moieties. In addition to a shift of all signals to larger EBE, significant changes in the signal patterns are observed. At low EBE, this is due to the splitting of highly degenerate B12X122- orbitals, while at high EBE, photodetachment from CD oxygens contributes to the new bands. The guest B12X122- and host CD nocovalent, size-specific interaction based on the independent gradient model (IGM) and energy decomposition analysis (EDA), is dominated by electrostatic interactions. The analysis further unravels unambiguiously the existence of dihydrogen bonding and how it affects the total energy that stabilizes the host-guest complexes of CDs·B12H122- compared to the general hydrogen bonding interaction in CDs·B12F122-. This work clearly exhibits strong influences on the electronic structures of dodecaborates upon clustering with CDs, with both size (a-, ß-, ?-) and molecular (X = H or F) specificities, thus providing critical molecular-level information on the cyclodextrin-closo-dodecaborate interactions of interest to medical applications, e.g. Boron neutron capature therapy. The NIPES experiments done at PNNL were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Bioscience (X.-B.W.) and was performed at the EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. H.S. and Z.S. acknowledge the funding support of National Natural Science Foundation of China (Nos.11727810, 61720106009 and 21603074), the Science and Technology Commission of Shanghai Municipality (Nos. 19JC1412200), and the Program of Introducing Talents of Discipline to Universities 111 project (B12024). Z. L. thanks the China Scholarship Council (CSC) for financial support. We acknowledge the ECNU Multifunctional Platform for Innovation (001) and HPC Research Computing Team for providing computational and storage resources. J.W. acknowledges support from the Alexander von Humboldt foundation (Feodor Lynen Fellowship and Rückkehrerstipendium), a Freigeist fellowship of the Volkswagenfoundation and Prof. Vladimir A. Azov for helpful discussions.

Li, Zhipeng↗
DOE OSTI2022

Temperature-dependent behavior in the local structure of BaTiO 3 nanocrystals

Here, we use pair distribution function analysis of synchrotron X-ray total scattering data to inspect the local structure of BaTiO 3 nanocrystals from 253 K < T < 413 K. The local structure consists of ca. r = 35 Å domains in which Ti 4+ displacements have the same coherence length as the overall perovskite structure.

36 MATERIALS SCIENCE↗