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Arc GIS files of coal maps, traces and structural features for the Alabama Coalfields Project, Southern Appalachian Basin.
Vitrification is a widely accepted method to immobilize nuclear waste. Detailed structural information is critical to understand the physical and chemical behaviors, including the long-term chemical durability of these glasses that are to be stored in geological storage sites. High-energy X-ray diffraction studies are used to obtain accurate structural information of the International Simple Glass (ISG), a six-component borosilicate model nuclear waste glass with a composition (mol%) of 60.2SiO 2 -16.0B 2 O 3 -12.6Na 2 O-3.8Al 2 O 3 -5.7CaO-1.7ZrO 2 . Classical molecular dynamics (MD) simulations with recently developed effective potentials are utilized to generate structural models of the ISG glasses to provide interpretation of the high-energy X-ray structural data and additional short and medium range structural details. The atomic structure model generated from MD simulations shows an excellent agreement with high-energy X-ray diffraction, measured for the first time for ISG, with an R x value of 5.5%. Systematic investigations of the medium-range structural features of ISG are performed, built upon recent study of the short-range structure. In particular, the glass former cation oxygen polyhedral analysis show that [SiO 4 ]-[SiO 4 ] and [BO 4 ]-[SiO 4 ] connections are the most abundant while [ZrO 6 ] octohedra having higher probability to connect to another [SiO 4 ], [BO 4 ] and [BO 3 ]. Moreover, we have studied the ISG surface structure using MD simulations. Noticeable differences in terms of both chemical compositions and structural features between the bulk and surface are observed. There exist increased small-sized rings, under coordinated Si species, high 3-coordinated boron content (86.5%) on the surface. Very importantly, sodium ions are found to be enriched on the glass surface, consistent with recent experimental results. Furthermore, both bulk and surface structural information are discussed in terms of the dissolution and corrosion mechanisms of ISG and related nuclear waste glasses.
Predicting chemical durability of glass materials is important for various applications from daily life such as drink glass and kitchen ware to advanced technologies such as nuclear waste disposal and biomedicine. In this work, we explored prediction of initial dissolution rate through structural features from molecular dynamics (MD) simulations for a wide range of glass compositions (total 28) including borosilicate and aluminosilicate glasses, ZrO 2 -containing and V 2 O 5 -containing boroaluminosilicate glasses. The initial dissolution rates (r 0 ) measured experimentally at 90 °C with varying solution conditions were correlated with structural features (e.g., polyhedral linkages and non-bridging oxygen species) obtained from MD simulations, either from this study or from literature. Since hydrolysis of the glass network through breaking of the network former linkages (e.g., Si-O-Si, Si-O-Al, etc.) is a critical step of network glass dissolution, the statistics of these linkages obtained from MD were correlated to r0 through linear regression, where the coefficient of determination (R 2 ) and root mean square error are found to be 0.949 and 0.681, respectively. This model was compared and discussed with existing models developed by various approaches including machine learning, the kinetic rate equation, topological constraint theory, and other descriptors from MD simulations. The discussion provides insights on future model improvements to predict glass dissolution. In addition, the impact of V 2 O 5 on the glass dissolution was examined in detail, implicating that the impact is not the same across all glass compositions and test conditions.
Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.
ERTS-1 imagery of geological and structural features of sedimentary basin in France
The reactions of b- and f-face cyclohexene-annulated 3a,6a-diaza-1,4-diphosphapentalene (CADDP) with elemental sulfur and selenium result in the addition of two chalcogen atoms to one phosphorus atom of CADDP. A specific feature of these structures is that the diazadiphosphapentalene skeleton retains planar geometry, with a significant elongation of the N—P bond. These compounds are zwitterions, as evidenced by their electronic structures, with considerable delocalization of the negative charge in the PS{sub 2} (PSe{sub 2}) moieties and of the positive charge in the diazaphosphole ring. The reaction of CADDP with carbon disulfide is a more complicated process accompanied by the decomposition of the CS{sub 2} molecule to form a molecule containing three structurally different CADDP moieties, one of which is a stabilized carbene complex.
E1 enzymes for ubiquitin (Ub) and Ub-like modifiers (Ubls) harbor two catalytic activities that are required for Ub/Ubl activation: adenylation and thioester bond formation. Structural studies of the E1 for the Ubl small ubiquitin-like modifier (SUMO) revealed a single active site that is transformed by a conformational switch that toggles its competency for catalysis of these two distinct chemical reactions. Although the mechanisms of adenylation and thioester bond formation revealed by SUMO E1 structures are thought to be conserved in Ub E1, there is currently a lack of structural data supporting this hypothesis. Here, we present a structure of Schizosaccharomyces pombe Uba1 in which the second catalytic cysteine half-domain (SCCH domain) harboring the catalytic cysteine has undergone a 106° rotation that results in a completely different network of intramolecular interactions between the SCCH and adenylation domains and translocation of the catalytic cysteine 12 Å closer to the Ub C terminus compared with previous Uba1 structures. SCCH domain alternation is accompanied by conformational changes within the Uba1 adenylation domains that effectively disassemble the adenylation active site. Importantly, the structural and biochemical data suggest that domain alternation and remodeling of the adenylation active site are interconnected and are intrinsic structural features of Uba1 and that the overall structural basis for adenylation and thioester bond formation exhibited by SUMO E1 is indeed conserved in Ub E1. Finally, the mechanistic insights provided by the novel conformational snapshot of Uba1 presented in this study may guide efforts to develop small molecule inhibitors of this critically important enzyme that is an active target for anticancer therapeutics.
This paper introduces a new approach toward characterizing local structural features of two-dimensional particle systems. The approach can accurately identify and characterize defects in high-temperature crystals, distinguish a wide range of nominally disordered systems, and robustly describe complex structures such as grain boundaries. This paper also introduces two-dimensional functionality into the open-source software program VoroTop which automates this analysis. This software package is built on a recently-introduced multithreaded version of V ORO ++, enabling the analysis of systems with billions of particles on high-performance computer architectures.
The physical properties of quasi-one-dimensional conductors are profoundly influenced by slight changes in structure. The unusual structural features of this class of materials include only short range order of the anions and structure modulation. The nature of disorder and structure modulation can affect the character of the metal-to-insulator transition at low temperature, and may allow us to make some predictions of low temperature behavior based on room temperature structural properties.
X-ray computed tomography (CT) images of rock specimens often contain artifacts which must be corrected before scientific analyses are performed. Here, we present a new workflow of automated image processing to utilize poor-quality X-ray CT scan images. The workflow runs on the open-source image analysis software and efficiently separates desired features from low-contrast scanned images. The new workflow is a two-step technique using contrast enhancement and automated feature segmentation to generate noise-free binary images. The results of binary images using the proposed workflow and using a conventional thresholding technique are analyzed to show the quality of the proposed method. The paper also presents a workflow of estimating the structural geometries of features in two and three dimensions. The results of the structural feature analyses and computational time were compared between the open-source (ImageJ) and commercial image analysis software (Bruker Computed Tomography Analyzer). The commercial software was more computationally efficient, but the task-specific macros in open-source software enabled the user-desired automation in image processing and data extraction of desired structural features of comparable quality.
Presentation for the 2024 FECM/NETL Carbon Management Project Review Meeting describing the method and contents of the Basin-Scale Structural Features Database developed under the EDX4CCS portfolio.
Atomistic computer simulations can offer insights into silicate glass-environment interactions with the recent development of reactive potentials. Yet, the accuracy of generated glass structures with these potential was usually not fully examined. In this paper, the capability of the reactive force field (ReaxFF) to describe the short and medium range structure features of sodium silicate glasses in molecular dynamics simulations is investigated by comparing a widely used partial charge pairwise potential and available experimental data. Glass structure information such as pair distribution function (PDF), coordination number, Qn species, neutron broadened structure factor, and X-ray broadened structure factor of the glass structures from ReaxFF simulations were calculated and compared to evaluate the generated glass structure. Advantages and limitations of the potentials and glass forming procedures, as well as areas of further improvement, were discussed. The results show that the recently refined ReaxFF parameters through the proposed procedure enable the simulations of sodium silicate glass structures with minimal defects, which paves the way to investigate water-glass interaction mechanisms with the reactive enabled potentials.
We report the mechanisms behind lignin dissolution with protic ionic liquids (PILs) and their influence over lignin properties remain not fully explored. In this work, physicochemical and structural features of lignins extracted from sugarcane bagasse after pretreatment with a series of PILs (length of the cation chain combined with different anions) were assessed using analytical techniques. It was found that the lignin extracted with shorter chain length cations PILs showed the highest β-O-4 content. Opposite, the increase of the PILs cation chain length resulted in enhanced depolymerization. All lignins presented high polydispersity (>3.7), while the weight average molecular ranged from 1921 to 13,539 g/mol. The recovered [Eti][Mal] lignin presented the higher β-O-4 content and was possibly the most preserved lignin obtained. Opposite, lignin isolated from [Hex][Ac] and [Hex][For] treatments had less β-O-4 linkages attributed to the depolymerization of lignin via rupture of ether linkages generating intermediates that further repolymerized and/or depolymerized. These results suggest that the ionicity of the PIL is a crucial factor for lignin dissolution. Furthermore, these results illustrate that the proposed pretreatment using different PILs is useful to obtain high-quality lignins with distinct features and opens a new perspective for materials to match various applications.
Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.
Thin polycrystalline Sm{sub 1–x}Eu{sub x}S films (x = 0.1, 0.167, 0.2, 0.25, 0.33, 0.5) were prepared by evaporation of SmS and EuS powders. Structural features of the films were investigated. The influence of Eu concentration and temperature of film deposition on the value of lattice parameter and sizes of X-гау coherent scattering regions was studied. It is shown that formation of Sm{sub 1–x}Eu{sub x}S films comes about according to the theory that was previously suggested for SmS films and that the deviation of lattice parameter is explained by the variable valence of samarium ions.
As part of a program to develop the fundamental science of synthetic bacteriochlorins — analogues of Nature’s light-harvesting pigments in anoxygenic photosynthesis — 11 synthetic free base bacteriochlorins have been examined by single-crystal X-ray diffraction analysis. In each bacteriochlorin, each pyrroline ring contains a gem-dimethyl group to block adventitious (aerobic) dehydrogenation. The structural features of the bacteriochlorins (tetrahydroporphyrins) are compared with the less saturated counterparts, chlorins (dihydroporphyrins) and porphyrins. Only slight structural perturbation accrues due to the presence of the gem-dimethyl groups. Furthermore, the results presented herein may aid in understanding metal chelation processes and underpin the development of functional solid-state molecular assemblies.
The composition of C{sub 4}B{sub 25}Mg{sub 1.42} crystal obtained by self-propagating high-temperature synthesis was determined using X-ray diffraction. This is the first crystalline structure where all boron atoms in the B{sub 12} icosahedron occupy crystallographically independent positions; this circumstance allowed us to analyze the effect of substituents on bond lengths in the icosahedron. The crystal structure features, including the channels filled with disordered Mg atoms and the spread of B—B endo- and exo-bond lengths in the icosahedra, are described. A crystallochemical analysis of pair bonds has been performed for the first time.
We present molecular-frame measurements of the recombination dipole matrix element (RDME) in CO 2 , N 2 O, and carbonyl sulfide (OCS) molecules using high-harmonic spectroscopy. Both the amplitudes and phases of the RDMEs exhibit clear imprints of a two-center interference minimum, which moves in energy with the molecular alignment angle relative to the laser polarization. Here, we find that whereas the angle dependence of this minimum is consistent with the molecular geometry in CO 2 and N 2 O, it behaves very differently in OCS; in particular, the phase shift which accompanies the two-center minimum changes sign for different alignment angles. Our results suggest that two interfering structural features contribute to the OCS RDME, namely, (i) the geometrical two-center minimum and (ii) a Cooper-like, electronic-structure minimum associated with the sulfur end of the molecule. We compare our results to ab initio calculations using time-dependent density functional theory and present an empirical model that captures both the two-center and the Cooper-like interferences. We also show that the yield from unaligned samples of two-center molecules is, in general, reduced at high photon energies compared to aligned samples, due to the destructive interference between molecules with different alignments.