X-ray Radial Distribution Function Research Articles

Combining graph deep learning and London dispersion interatomic potentials: A case study on pnictogen chalcohalides.

Machine-learning interatomic potential models based on graph neural network architectures have the potential to make atomistic materials modeling widely accessible due to their computational efficiency, scalability, and broad applicability. The training datasets for many such models are derived from density-functional theory calculations, typically using a semilocal exchange-correlation functional. As a result, long-range interactions such as London dispersion are often missing in these models. We investigate whether this missing component can be addressed by combining a graph deep learning potential with semiempirical dispersion models. We assess this combination by deriving the equations of state for layered pnictogen chalcohalides BiTeBr and BiTeI and performing crystal structure optimizations for a broader set of V-VI-VII compounds with various stoichiometries, many of which possess van der Waals gaps. We characterize the optimized crystal structures by calculating their x-ray diffraction patterns and radial distribution function histograms, which are also used to compute Earth mover's distances to quantify the dissimilarity between the optimized and corresponding experimental structures. We find that dispersion-corrected graph deep learning potentials generally (though not universally) provide a more realistic description of these compounds due to the inclusion of van der Waals attractions. In particular, their use results in systematic improvements in predicting not only the van der Waals gap but also the layer thickness in layered V-VI-VII compounds. Our results demonstrate that the combined potentials studied here, derived from a straightforward approach that neither requires fine-tuning the training nor refitting the potential parameters, can significantly improve the description of layered polar crystals.

Understanding SiOC atomic structures via synchrotron X-ray and reactive force field potential studies

Silicon oxycarbide (SiOC) is a unique system that can generate various compositions and microstructures via different polymeric precursors and pyrolysis conditions. However, understanding of the atomic structure evolution, such as cluster formation, phase evolution, and atomic coordination, is lacking. In this study, cluster evolution and atomic coordination for different SiOC ceramics pyrolyzed at 1200 °C and 1500 °C were investigated by high energy X-ray diffraction (HE-XRD) and radial distribution function (RDF) analysis. A new Reactive Force Field (ReaxFF) molecular dynamics modeling approach was developed to understand nanocluster separation and early-stage atomic radial coordination. For the first time, we demonstrate that orthorhombic SiO2 forms and converts to growth resistant amorphous SiO2. Cubic β-SiC also forms at lower temperatures than reported, along with a minor amount of hexagonal SiC that has never been reported. The RDF data support such phase evolution understanding. ReaxFF simulation provides direct data on atomic mixing, elemental separation, and effects of precursor molecular structures and compositions, especially in the early stage of the pyrolysis. The simulated RDF data complement the experimental data, revealing the significant presence of C–H bonds along with Si–O and C–C bonds.

Structure and reactivity of sodium aluminate complexes in alkaline solutions

The underlying mechanism by which tetrahedrally-coordinated aluminate solution species react to precipitate octahedrally-coordinated Al3+ in gibbsite is unknown. Sodium aluminate solutions provide the opportunity to investigate the role of ion speciation and local structure in the reaction, as the solution metastability can be controlled by varying ratio of excess NaOD to Al3+. Here, capitalizing on this tunable precipitation behavior, aluminate speciation was investigated through a combination of Raman, infrared, and NMR spectroscopies, together with geometrical fitting of neutron and X-ray radial distribution functions. These techniques reveal a mixture of monomeric Al(OD)4− and dimeric Al2O(OD)62− in all compositions, but solutions avoiding precipitation for extended timescales (i.e. months to years) show an increased dimeric Al2O(OD)62− population formed at the expense of the Al(OD)4− monomer. Conversion between these species, as well the potential for further oligomerization and formation of larger pre-nucleation species is driven by the hydrogen/deuterium bonding (H/D-bonding) and proton/deuteron transfer reactions. Changes within the local environment around the aluminate anions, including solvation and the presence of solvent-shared ion pairs or contact ion pairs, will consequently govern the reactivity of these aluminate species to either promote or inhibit precipitation.

Probing the Operating Voltage and Structural Transitions in Li-Mn-O Layered-Spinel Composite Nanoarchitectures during the Discharge Process.

Li-Mn-O layered-spinel (LS) composite is one of the utmost promising cathode materials for advancing lithium-ion batteries, which are lacking in comparison to technological advancements. The currently used cathode materials are one of the limiting factors in realising the envisaged affordable, durable, and safe rechargeable lithium-ion batteries. Their limitations include capacity fading transpiring during cycling, inherent low operational capacities, safety issues due to thermal instabilities, and high cost which inhibit their full utilisation in large scale systems. The LS composite demonstrates enhanced electrochemical properties owing to the synergism of the layered and spinel components. In particular, the 0.7Li2MnO3.0.3Li4Mn5O12 composite, which has demonstrated a higher specific capacity, >250 mAh/g. Recent studies have focused mainly on enhancing the specific capacity of LS composites. However, there is limited knowledge of the structural changes that take place during the discharge process and how they affect the working voltage of the LS composite cathode material. Li-Mn-O LS composites indicating different stages of the discharge process have been generated using the molecular dynamics simulated amorphisation and recrystallisation method, which utilises empirical interatomic potentials. Different structural features of the LS composites in all significant stages of the discharge process were visualised and captured. X-ray diffraction patterns (XRDs) and radial distribution functions were used to characterise the formed layered and spinel components of the LS blend nanoparticles. Moreover, their average voltages were also computed using the linear scaling density functional theory code.

Comparative investigation of microjetting from tin surface subjected to laser and plane impact loadings via molecular dynamics simulations

The microjetting processes of single-crystal tin with sinusoidal surface defects under laser loading and plane impact loading are investigated by using molecular dynamics simulations via the second nearest-neighbor modified embedded atom method potential. Simulation results exhibit that the jetting factors for laser loading and plane impact loading first increase with the increment of shock breakout pressure and then reach their own saturation values, in agreement with previous experimental observations. However, the jetting factor under laser loading saturates at relatively lower shock breakout pressure than its counterpart under plane impact loading. Structure analysis via x-ray diffraction and radial distribution function techniques indicates that the laser loading leads to higher melting degree, which further facilitates the ejection process. The spike velocity linearly depends on the shock breakout pressure for both loading methods, but the bubble velocity varies with the loading method. In addition, void nucleation and growth within the sample are observed for laser loading due to the interaction of release waves. The simulation results reveal the underlying mechanisms of ejection process under plane impact loading and laser loading, helping enhance the understanding of microjetting phenomena.

Resolving local configurational contributions to X-ray and neutron radial distribution functions within solutions of concentrated electrolytes - a case study of concentrated NaOH.

Extreme conditions of complex materials often lead to a manifold of local environments that challenge characterization and require new advances at the intersection of modern experimental and theoretical techniques. In this contribution, highly caustic and viscous aqueous NaOD solutions were characterized with a combination of X-ray and neutron radial distribution function (RDF) analyses, molecular dynamics simulations and sub-ensemble analysis. While this system has been the topic of some study, the current work expands upon the state of knowledge regarding the extent to which water is perturbed within this chemically extreme solution. Further, we introduce analyses that goes beyond merely identifying the different local environments (ion solvation and coordination environments) that are present, but toward understanding their relative contributions to the ensemble solution RDF. This integrated approach yields unique insight into the experimental sensitivity of RDFs to changes in local geometries, the composition of solvation environments about ions, and the challenge of experimentally differentiating the ensemble of all superimposed local environments-a feature of increasing importance within the extreme condition of high ionic strength.

Electron tomography and fractal aspects of MoS2 and MoS2/Co spheres

A study was made by a combination of 3D electron tomography reconstruction methods and N2 adsorption for determining the fractal dimension for nanometric MoS2 and MoS2/Co catalyst particles. DFT methods including Neimarke-Kiselev’s method allowed to determine the particle porosity and fractal arrays at the atomic scale for the S-Mo-S(Co) 2D- layers that conform the spherically shaped catalyst particles. A structural and textural correlation was sought by further characterization performed by x-ray Rietveld refinement and Radial Distribution Function (RDF) methods, electron density maps, computational density functional theory methods and nitrogen adsorption methods altogether, for studying the structural and textural features of spherical MoS2 and MoS2/Co particles. Neimark-Kiselev’s equations afforded the evaluation of a pore volume variation from 10 to 110 cm3/g by cobalt insertion in the MoS2 crystallographic lattice, which induces the formation of cavities and throats in between of less than 29 nm, with a curvature radius rk < 14.4 nm; typical large needle-like arrays having 20 2D layers units correspond to a model consisting of smooth surfaces within these cavities. Decreasing DP, DB, DI and DM values occur when Co atoms are present in the MoS2 laminates, which promote the formation of smoother edges and denser surfaces that have an influence on the catalytic properties of the S-Mo-S(Co) system.

Microscopic Structure of Solvated Poly(benzyl methacrylate) in an Imidazolium-Based Ionic Liquid: High-Energy X-ray Total Scattering and All-Atom MD Simulation Study

We report a new approach for investigating polymer structures in solution systems, including polymer–solvent interactions at the molecular level. The solvation structure of poly(benzyl methacrylate) (PBnMA) in an imidazolium-based ionic liquid (IL) has been investigated at the molecular level using high-energy X-ray total scattering (HEXTS) with the aid of all-atom molecular dynamics (MD) simulations. The X-ray radial distribution functions derived from both experimental HEXTS and theoretical MD (Gexp(r) and GMD(r), respectively) were in good agreement in the present PBnMA/IL system. The G(r) functions were successfully separated into two components for the inter- and intramolecular contributions. Here, the former corresponds to polymer solvation (or polymer–solvent interactions) and the latter to polymer structure, such as conformation and interactions between side chains (benzyl groups) in PBnMA. The intermolecular GMDinter(r) revealed that the side chains are preferentially solvated by imidazolium cati...

Molecular dynamics simulation study of deformation mechanisms in 3C–SiC during nanometric cutting at elevated temperatures

Molecular dynamics (MD) simulation was employed in this study to elucidate the dislocation/amorphization-based plasticity mechanisms in single crystal 3C–SiC during nanometric cutting on different crystallographic orientations across a range of cutting temperatures, 300K to 3000K, using two sorts of interatomic potentials namely analytical bond order potential (ABOP) and Tersoff potential. Of particular interesting finding while cutting the (110)<001̅> was the formation and subsequent annihilation of stacking fault-couple and Lomer–Cottrell (L–C) lock at high temperatures, i.e. 2000K and 3000K, and generation of the cross-junctions between pairs of counter stacking faults meditated by the gliding of Shockley partials at 3000K. Another point of interest was the directional dependency of the mode of nanoscale plasticity, i.e. while dislocation nucleation and stacking fault formation were observed to be dominant during cutting the (110)<001̅>, low defect activity was witnessed for the (010)<100> and (111)<1̅10> crystal setups. Nonetheless, the initial response of 3C–SiC substrate was found to be solid-state amorphization for all the studied cases. Further analysis through virtual X-ray diffraction (XRD) and radial distribution function (RDF) showed the crystal quality and structural changes of the substrate during nanometric cutting. A key observation was that the von Mises stress to cause yielding was reduced by 49% on the (110) crystal plane at 3000K compared to what it took to cut at 300K. The simulation results were supplemented by additional calculations of mechanical properties, generalized stacking faults energy (GSFE) surfaces and ideal shear stresses for the two main slip systems of 3C–SiC given by the employed interatomic potentials.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Thermal properties and hydration structure of poly-l-lysine, polyglycine, and lysozyme

Differential scanning calorimetry (DSC) and X-ray diffraction (XRD) measurements of hydrated poly-l-lysine, polyglycine and lysozyme at hydration levels (mass of water/mass of peptide and protein)=0.30–0.82, 0.27–0.49, and 0.30–0.81, respectively, were performed in the temperature range of 180–298K. The DSC data showed that the interfacial hydration water of the polypeptides and the protein is not frozen even at 180K. The X-ray radial distribution functions revealed that with decreasing temperature the interactions of the polypeptides and the protein with hydration water molecules gradually become remarkable, resulting in the development of the structure of their hydration water. The structure change of the hydration water with lowering temperature is monotonous and could not be the origin of dynamic transition (glass transition and fragile-to-strong crossover) for hydrated proteins as previously observed by neutron scattering.

Removal of methyl green dye molecule from aqueous system using reduced graphene oxide as an efficient adsorbent: Kinetics, isotherm and thermodynamic parameters

Dyes released from different industries are one of the major pollutants in the water system. So removal of dye before disposal to the main water stream is necessary. In this study, adsorption technique was adopted for removal of the cationic dye from aqueous system using reduced graphene oxide (rGO) as adsorbent material. The kinetic study of adsorption shows that the present system follows pseudo second order kinetic (linear) model. Adsorption isotherm investigation indicates that the adsorption of methyl green onto rGO nanosheets follows the isotherm models in the order Toth>Sips>Dubinin–Radushkevich (D–R)>Scatchard>Langmuir>Temkin>Freundlich model in the pH range 4–6. However, the order changes to D–R>Scatchard>Toth>Sips>Langmuir>Temkin>Freundlich model at pH 7 and 9. The adsorption capacity of methyl green onto the rGO nanosheets increases with increasing pH of the medium due to the change in the surface properties. Presence of other ions like Na+, Ca2+, Mg2+ and SO42− also influenced on adsorption due to the change in the surface properties. The magnitude of ΔG° values are found to be in the characteristic range of physisorption nature of adsorption. Further, the mechanism of the adsorption process was investigated by FTIR spectroscopy and it indicates that the adsorption is due to electrostatic interaction between methyl green dye molecule and rGO nanosheets. X-ray radial distribution function (RDF) analysis revealed the formation regular molecular packets of graphene. X-ray diffraction (XRD) analysis of the rGO nanosheets before and after adsorption of the dye molecule indicates that some textural changes occur in the rGO nanosheets upon adsorption of the methyl green dye molecule.

Study of nanostructure characterizations and gas separation properties of poly(urethane–urea)s membranes by molecular dynamics simulation

Molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) have been employed for understanding the effect of urethane and urea contents on gas separation properties of poly(urethane–urea)s (PUUs) membranes. Five membranes considered in this study are based on polytetramethylene-glycol (PTMG), isophorone diisocyanate (IPDI), and designed ratios of 1,4-butanediamine (BDA) to 1,4-butanediol (BDO) as chain extenders. The glass transition temperature (Tg), density, fractional free volume (FFV), X-ray diffraction (XRD) pattern and radial distribution function (RDF) were calculated to examine the nanostructure characterizations of the membranes. The permeations of five gas molecules (O2, N2, CO2, CH4, and H2S) through the membranes were investigated. It was found that d-spacing, fractional free volume and phase separation of hard and soft segments increase with increasing urea contents in the membranes. The results indicated that the permeability of the membranes increases with increasing urea linkage in the polymer configuration.

Thermal Behavior and Structure of Low-temperature Water Confined in Sephadex G15 Gel by Differential Scanning Calorimetry and X-ray Diffraction Method

The thermal behavior and structure of water confined in Sephadex G15 gel were investigated over a temperature range of 298-173 K at hydration levels, h (= mass of water/mass of dry G15 gel), of 0.24-1.38 by differential scanning calorimetry (DSC) and an X-ray diffraction (XRD) method, respectively. The ice-melting peaks on the DSC curves were deconvoluted to estimate the amounts of three states of water in G15 with h: free water, freezable bound water, and unfrozen water. The X-ray radial distribution functions of unfrozen water at h = 0.24 revealed that the hydrogen-bonded structure of water is largely distorted, due to hydrogen bonding with the surface hydroxyl groups of gel substrates, compared with those of freezable bound water at h = 0.47 and bulk water. A plausible separation mechanism of solutes in gel chromatography was considered from a structural point of view of confined water.

Study on the Local Structure of PAN-Based Carbon Fiber Using Radial Distribution Function Based on XRD

The local structure evolution of polyacrylonitrile (PAN) fibers during pre-oxidation and carbonization was studied using X-ray diffraction (XRD) and radial distribution function (RDF). The nearest inter-chains distance of PAN is 6.88 Å, which is close to the diameter of the “rigid rod” model proposed by Warner. The third neighbor distances of carbon fibers are greater than that of graphite, indicating the planar six-member rings are absent in the carbon fibers from 500 to 1250°C. The structure of fibers transforms from long-range order to long-range disorder during the pre-oxidation process, then transforms from short-range order to long-range order during the carbonization process.

Thermal behavior, structure, and dynamics of low-temperature water confined in mesoporous organosilica by differential scanning calorimetry, X-ray diffraction, and quasi-elastic neutron scattering

Differential scanning calorimetry (DSC), X-ray diffraction (XRD), and quasi-elastic neutron scattering (QENS) measurements have been made at 200~330 K for capillary-condensed water confined in periodic mesoporous organosilica (PMO) materials with the phenyl groups embedded in silica matrix (Ph-PMO; pore diameter 30 Å). The DSC data showed that the capillary-condensed water in Ph-PMO freezes at 228 K. X-ray radial distribution functions (RDFs) showed that the tetrahedral-like hydrogen-bonded structure of water is distorted in Ph-PMO pores, compared with bulk water; however, with lowering temperature the tetrahedral moiety of water is gradually recovered in the pores. Below the freezing point, cubic ice I c was formed in the Ph-PMO pores. The QENS data showed that the translational diffusion constant and the residence time and the rotational relaxation time of water molecule in Ph-PMO are comparable with those in bulk. The corresponding activation energies suggested that the more hydrophobic the nature of the wall is, the smaller the activation energy of diffusion and rotation of a water molecule; this implies that water molecules confined in the hydrophobic pores are present in the core of the pores, whereas those in the hydrophilic pores strongly interact with the silanol groups.

The Interpretation of Diffraction Patterns of Two Prototypical Protic Ionic Liquids: a Challenging Task for Classical Molecular Dynamics Simulations

In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body potential energy term instead of changing the two-body potential parameters, in order to optimize the agreement with experimental data. This three-body term turns out to be naturally able to describe the complex polarization effects due to hydrogen bonding without requiring a quanto-mechanical treatment or a polarizable force field. In addition the present model turns out to be able to account for the presence of a low-Q peak in the scattering patterns of EAN, which has been commonly interpreted as a manifestation of the amphiphilic nature of this compound.

Liquid Structure and the Ion-Ion Interactions of Ethylammonium Nitrate Ionic Liquid Studied by Large Angle X-Ray Scattering and Molecular Dynamics Simulations

Room temperature ionic liquids (RTILs) are useful as new solvents or materials owing to their favorable properties such as negligible vapor pressure, non-flammability, and wide electrochemical window. For further development of new RTILs, it is indispensable to understand macroscopic properties as solvent and/or liquids of RTILs at a molecular or atomistic level. Here, liquid structure and the ion-ion interactions of room temperature ionic liquid ethylammonium nitrate (EAN) were studied by means of large angle X-ray scattering (LAXS) experiment and molecular dynamics simulations. X-ray interference function for EAN shows a small peak of 0.62 A–1 indicating nano-scale segregation in the ionic liquid. X-ray radial distribution function as the form of D(r) – 4πr2ρ0 evidently shows a peak of 3.4 and broad ones of 4.7, 8 and 12 A, suggesting that EAN has long range ordering in the liquid state. The intra-molecular X-ray interference function was estimated on the basis of molecular geometries found in crystals to yield the inter-molecular X-ray pair correlation functionG_mathrm{inter}mathrm{LAXS}(r). In G_mathrm{inter}mathrm{LAXS}(r), peaks of 3.0, 3.4, and 4.7 A were found as the atom-atom correlation. The peak of 3.0 A can be assigned to the atom-atom correlation of N (C2H5NH3+)mO (NO3–) in the NHmO hydrogen bonding. In addition, the peak of 3.4 A is also ascribable to C (C2H5NH3+)mO (NO3–) correlations in the CHmO interactions. Molecular dynamics simulations based on newly developed force fields to describe a series of primary ammonium cation were performed to ascribe the peaks found in G_mathrm{inter}mathrm{LAXS}(r). The X-ray interference function imathrm{MD}(s) and the pair correlation function Gmathrm{MD}(r) derived from simulations were reasonably in agreement with the experimental ones. According to the partial atom-atom correlation functions derived from the simulations, the experimentally observed peaks of 3.0 and 3.4 A can be ascribable to the NHmO and the CHmO correlations in the closest ethylammonium and nitrate interaction, respectively. The CHmO interactions may play an important role in macroscopic properties of this kind of ionic liquids.

The structure of densified As 2O 3 glasses

In situ high energy X-ray diffraction and Raman experiments have been carried out to probe the structure changes of vitreous As 2O 3 under pressure. The first sharp diffraction peak reduces in intensity up to 10 GPa, indicating a breakdown of intermediate range order with pressure. All features in the Raman spectra broaden with increasing pressure up to 11.6 GPa. The mode at 378 cm −1 associated with As 4O 6 molecule-like vibrations increases in intensity up to 6.2 GPa and decreases at higher pressures. In addition, X-ray and neutron structure factors have been measured for normal density and permanently densified As 2O 3 glasses recovered from 10 and 23 GPa. The results show the local AsO 3 pyramids and 3-membered rings essentially remain intact after compression. The increase in density is mainly associated with an inward shift of the third nearest neighbor peak in the X-ray radial distribution function, which indicates an increased packing of 3-membered AsO 3 rings.

Structural study of lithium phosphate glasses by X-ray RDF and computer simulations

The structures of xLi2O–(1−x)P2O5 glasses with x=0.10, 0.20 and 0.30 have been examined using X-ray radial distribution functions. The composition range x=0.10–0.75 also has been studied by molecular dynamics simulations. MD configurations were analyzed using graph theory techniques. The experimental glass transition temperature reaches a minimum at 20mol% of Li2O and the simulated glass has a minimum Tg at 23mol% of Li2O. This minimum in Tg has been explained by studying the changes in the environment of Li, P and O with Li2O composition and connectivities among the PO4 groups mediated by lithium existing in the network. X-ray RDF studies agree with the MD simulation results. Dynamic parameters of interest to structure-transport studies, namely mean square displacement and velocity autocorrelation function obtained from the MD simulations, identify Li+ as the mobile ion contributing to ionic conductivity.