Reverse Monte Carlo Simulation Research Articles

Structural and Dynamical Effects of the CaO/SrO Substitution in Bioactive Glasses.

Silicate glasses containing silicon, sodium, phosphorous, and calcium have the ability to promote bone regeneration and biodegrade as new tissue is generated. Recently, it has been suggested that adding SrO can benefit tissue growth and silicate glass dissolution. Motivated by these recent developments, the effect of SrO/CaO-CaO/SrO substitution on the local structure and dynamics of Si-Na-P-Ca-O oxide glasses has been studied in this work. Differential thermal analysis has been performed to determine the thermal stability of the glasses after the addition of strontium. The local structure has been studied by neutron diffraction augmented by Reverse Monte Carlo simulation, and the local dynamics by neutron Compton scattering and Raman spectroscopy. Differential thermal analysis has shown that SrO-containing glasses have lower glass transition, melting, and crystallisation temperatures. Moreover, the addition of the Sr2+ ions decreased the thermal stability of the glass structure. The total neutron diffraction augmented by the RMC simulation revealed that Sr played a similar role as Ca in the glass structure when substituted on a molar basis. The bond length and the coordination number distributions of the network modifiers and network formers did not change when SrO (x = 0.125, 0.25) was substituted for CaO (25-x). However, the network connectivity increased in glass with 12.5 mol% CaO due to the increased length of the Si-O-Si interconnected chain. The analysis of Raman spectra revealed that substituting CaO with SrO in the glass structure dramatically enhances the intensity of the high-frequency band of 1110-2000 cm-1. For all glasses under investigation, the changes in the relative intensities of Raman bands and the distributions of the bond lengths and coordination numbers upon the SrO substitution were correlated with the values of the widths of nuclear momentum distributions of Si, Na, P, Ca, O, and Sr. The widths of nuclear momentum distributions were observed to soften compared to the values observed and simulated in their parent metal-oxide crystals. The widths of nuclear momentum distributions, obtained from fitting the experimental data to neutron Compton spectra, were related to the amount of disorder of effective force constants acting on individual atomic species in the glasses.

Structure of Polaronic Centers in Proton-Intercalated AWO4 Scheelite-Type Tungstates.

The studies of polaronic centers in a homologous series of scheelite-type compounds AWO4 (A = Ca, Sr, Ba) were performed using the W L3-edge and Sr K-edge X-ray absorption spectroscopy combined with the reverse Monte Carlo simulations, X-ray photoelectron spectroscopy (XPS), and first-principles calculations. Protonated scheelites HxAWO4 were produced using acid electrolytes in a one-step route at ambient conditions. The underlying mechanism behind this phenomenon can be ascribed to the intercalation of H+ into the crystal structure of tungstate, effectively resulting in the reduction of W6+ to W5+, i.e., the formation of polaronic centers, and giving rise to a characteristic dark blue-purple color. The emergence of the W5+ was confirmed by XPS experiments. The relaxation of the local atomic structure around the W5+ polaronic center was determined from the analysis of the extended X-ray absorption fine structures using the reverse Monte Carlo method. The results obtained suggest the displacement of the W5+ ions from the center of [W5+O4] tetrahedra in the structure of AWO4 scheelite-type tungstates. This finding was also supported by the results of the first-principles calculations.

Enhancing the reliability of Reverse Monte Carlo simulations of metallic glass structure by imposing strict constraints from partial pair correlation functions

Reverse Monte Carlo (RMC) simulations are widely used to reconstruct 3-dimensional (3D) metallic glass (MG) structure from neutron/X-ray diffraction data, but their reliability is debated. Here, we employ RMC to simulate a Zr50Cu50 MG’s structure using two types of “experimental” inputs as constraints, one with a total pair correlation function (TPCF) and the other with 3 partial PCFs (PPCFs), all of which were generated from a 3D glass structure obtained from molecular dynamics (MD) simulations of the same alloy. This MD-generated structure is then used as a benchmark to evaluate RMC’s accuracy. Notably, both methods can replicate the MG’s TPCFs, and total bond-angle/bond-length distributions. However, only the PPCFs-constrained RMC is able to re-produce the local structure, as manifested by nearly replicated partial bond-length/bond-angle distributions, partial coordination numbers, atomic volume, etc. This work demonstrates that PPCFs can impose stricter constraints than a TPCF does, significantly improving the reliability of RMC simulations.

Local structural modelling and local pair distribution function analysis for Zr–Pt metallic glass

In disordered glass structures, the structural modelling and analyses based on local experimental data are not yet established. Here we investigate the icosahedral short-range order (SRO) in a Zr–Pt metallic glass using local structural modelling, which is a reverse Monte Carlo simulation dedicated to two-dimensional angstrom-beam electron diffraction (ABED) patterns, and local pair distribution function (PDF) analysis. The local structural modelling invariably leads to the icosahedral SRO atomic configurations that are similarly distorted by starting from some different initial configurations. Furthermore, the SRO configurations with 11–13 coordination numbers reproduce almost identical ABED patterns, indicating that these SRO structures are similar to each other. Further local PDF analysis explicitly indicates the presence of the wide distribution of atomic bond distances, which is comparable to the global PDF profile, even at the SRO level. The SRO models based on the conventional MD simulation can be strengthened by comparison with those obtained by the present local structural modelling and local PDF analysis based on the ABED data.

Decoding Active Sites for Highly Efficient Semihydrogenation of Acetylene in Palladium-Copper Nanoalloys.

Accurately decoding the three-dimensional atomic structure of surface active sites is essential yet challenging for a rational catalyst design. Here, we used comprehensive techniques combining the pair distribution function and reverse Monte Carlo simulation to reveal the surficial distribution of Pd active sites and adjacent coordination environment in palladium-copper nanoalloys. After the fine-tuning of the atomic arrangement, excellent catalytic performance with 98% ethylene selectivity at complete acetylene conversion was obtained in the Pd34Cu66 nanocatalysts, outperforming most of the reported advanced catalysts. The quantitative deciphering shows a large number of active sites with a Pd-Pd coordination number of 3 distributed on the surface of Pd34Cu66 nanoalloys, which play a decisive role in highly efficient semihydrogenation. This finding not only opens the way for guiding the precise design of bimetal nanocatalysts from atomic-level insight but also provides a method to resolve the spatial structure of active sites.

Structure of TeO2 Glass and Melt by Reverse Monte Carlo Simulations of High-Energy X-Ray Diffraction Data Sets.

The short-range and medium-range structures of TeO2 glass and melt are elucidated by Reverse Monte Carlo (RMC) simulations of High-Energy X-ray Diffraction data sets published in an earlier study by Alderman et al. (J. Phys. Chem. Lett.11(1) (2020)427-431). The RMC analysis reveals that there exists a wide range of Te-O bond lengths in both TeO2 glass and melt short-range structures. The Te-O pair distribution function (PDF) of the melt has peaks centered at 1.87, 2.06, 2.35, 2.65, and 3.00 (±0.01) Å, whereas the corresponding peaks in the glass are at 1.91, 2.07, 2.28, 2.54, 2.77, and 3.00 (±0.01) Å. The Te-O partial PDF of the melt shows a peak at 2.35 Å, which is not present in the glass structure; therefore, the same co-ordination sphere radius of 2.36 Å cannot be used for calculating the Te-O co-ordination numbers in the TeO2 melt and glass, as done in the earlier study by Alderman et al. Using a more appropriate radius of 2.41 Å for glass and 2.22 Å for the melt, the corresponding Te-O co-ordination numbers are found to be 3.99 and 3.33, respectively. The RMC analysis successfully determined the O-O pair distributions, which show the first peaks at 2.31-2.33 (±0.01) Å. Finally, Te-Te pair distributions show peaks at slightly longer distances in the melt compared to those in glass, and the melt is found to have greater medium-range disorder.

Influence of Zr element on the atomic structure of Al-Cu alloy liquid

The relationship among chemical composition, structure and glass-forming ability in multicomponent alloys is a long-standing puzzle due to the complexity of compositions. In this work, Al77.8Cu22.2 and Al70Cu20Zr10 amorphous alloy liquids were investigated by combining high-energy X-ray diffraction at a synchrotron facility, ab-initio molecular dynamics and reverse Monte Carlo simulations. The analysis of short- and medium-range order structures of two liquid alloys show that the addition of Zr element increases the number of cluster types and makes the distribution of cluster content more uniform, and enhances the structural heterogeneity and correlation of clusters with high five-fold symmetry. These findings reveal the influence of Zr element on the atomic structure of the Al-Cu liquid alloy and deepen the understanding of Al-based metallic glasses formation.

Temperature-dependent local structure and lattice dynamics of 1T-TiSe[formula omitted] and 1T-VSe[formula omitted] probed by X-ray absorption spectroscopy

The local atomic structure and lattice dynamics of two isostructural layered transition metal dichalcogenides (TMDs), 1T-TiSe2 and 1T-VSe2, were studied using temperature-dependent X-ray absorption spectroscopy at the Ti, V, and Se K-edges. Analysis of the extended X-ray absorption fine structure (EXAFS) spectra, employing reverse Monte Carlo (RMC) simulations, enabled tracking of the temperature evolution of the local environment in the range of 10–300 K. The atomic coordinates derived from the final atomic configurations obtained using the RMC method were used to calculate the partial radial distribution functions (RDFs) and the mean-square relative displacement (MSRD) factors for the first ten coordination shells around the absorbing atoms. Characteristic Einstein frequencies and effective force constants were determined for TiSe, TiTi, VSe, VV, and SeSe atom pairs from the temperature dependencies of MSRDs. The obtained results reveal differences in the temperature evolution of lattice dynamics and the strengths of intralayer and interlayer interactions in TiSe2 and VSe2.

Evidence of local structural distortions and subtle thermal disorder in transparent photochromic yttrium oxyhydride

The structural properties of photochromic yttrium oxyhydride powder in its transparent state were examined using x-ray diffraction and temperature-dependent extended x-ray absorption fine structure spectroscopy (EXAFS) combined with reverse Monte Carlo (RMC) simulations. The refinement of the x-ray powder diffraction pattern, employing the Rietveld method, indicates that yttrium oxyhydride crystallizes in the nanocrystalline phase with the cubic space group Fm-3m (225), at room temperature. The lattice parameter was determined as a = 5.404(3) Å, and the nanocrystallite size was estimated at d = 16(2) nm. The partial radial distribution functions (RDFs) g(r) for Y–O, O–O, and Y–Y atom pairs were obtained from the results of the RMC simulations of the Y K-edge EXAFS spectra measured at three temperatures (10, 150, and 300 K). The analysis of the RDFs reveals a subtle impact of the thermal disorder and splitting of the second coordination shell of yttrium atoms (the Y–Y RDF), remaining at all temperatures. This observation, also supported by our density functional theory calculations, suggests the presence of local structural distortions associated with yttrium sites, which do not affect the long-range crystal order.

Anomalies in the short-range local environment and atomic diffusion in single crystalline equiatomic CrMnFeCoNi high-entropy alloy

Multi-edge extended X-ray absorption fine structure (EXAFS) spectroscopy combined with reverse Monte Carlo (RMC) simulations was used to probe the details of element-specific local coordinations and component-dependent structure relaxations in single crystalline equiatomic CrMnFeCoNi high-entropy alloy as a function of the annealing temperature. Two representative states, namely a high-temperature state, created by annealing at 1373 K, and a low-temperature state, produced by long-term annealing at 993 K, were compared in detail. Specific features identified in atomic configurations of particular principal components indicate variations in the local environment distortions connected to different degrees of compositional disorder at the chosen representative temperatures. The detected changes provide new atomistic insights and correlate with the existence of kinks previously observed in the Arrhenius dependencies of component diffusion rates in the CrMnFeCoNi high-entropy alloy.

Highly efficient semi-hydrogenation in strained ultrathin PdCu shell and the atomic deciphering for the unlocking of activity-selectivity.

Excellent ethylene selectivity in acetylene semi-hydrogenation is often obtained at the expense of activity. To break the activity-selectivity trade-off, precise control and in-depth understanding of the three-dimensional atomic structure of surfacial active sites are crucial. Here, we designed a novel Au@PdCu core-shell nanocatalyst featuring diluted and stretched Pd sites on the ultrathin shell (1.6 nm), which showed excellent reactivity and selectivity, with 100% acetylene conversion and 92.4% ethylene selectivity at 122 °C, and the corresponding activity was 3.3 times higher than that of the PdCu alloy. The atomic three-dimensional decoding for the activity-selectivity balance was revealed by combining pair distribution function (PDF) and reverse Monte Carlo simulation (RMC). The results demonstrate that a large number of active sites with a low coordination number of Pd-Pd pairs and an average 3.25% tensile strain are distributed on the surface of the nanocatalyst, which perform a pivotal function in the simultaneous improvement of hydrogenation activity and ethylene selectivity. Our work not only develops a novel strategy for unlocking the linear scaling relation in heterogeneous catalysis but also provides a paradigm for atomic 3D understanding of lattice strain in core-shell nanocatalysts.

Atomic Three-Dimensional Investigations of Pd Nanocatalysts for Acetylene Semi-hydrogenation.

Deciphering the three-dimensional (3D) insight into nanocatalyst surfaces at the atomic level is crucial to understanding catalytic reaction mechanisms and developing high-performance catalysts. Nevertheless, better understanding the inherent insufficiency of a long-range ordered lattice in nanocatalysts is a big challenge. In this work, we report the local structure of Pd nanocatalysts, which is beneficial for demonstrating the shape-structure-adsorption relationship in acetylene hydrogenation. The 5.27 nm spherical Pd catalyst (Pdsph) shows an ethylene selectivity of 88% at complete acetylene conversion, which is much higher than those of the Pd octahedron and Pd cube and superior to other reported monometallic Pd nanocatalysts so far. By virtue of the local structure revelation combined with the atomic pair distribution function (PDF) and reverse Monte Carlo (RMC) simulation, the atomic surface distribution of the unique compressed strain of Pd-Pd pairs in Pdsph was revealed. Density functional theory calculations verified the obvious weakening of the ethylene adsorption energy on account of the surface strain of Pdsph. It is the main factor to avoid the over-hydrogenation of acetylene. The present work, entailing shape-induced surface strain manipulation and atomic 3D insight, opens a new path to understand and optimize chemical activity and selectivity in the heterogeneous catalysis process.

Effect of preparation conditions on the structure of As-Se glasses: Reverse Monte Carlo simulation

As an extension to part I, Dongol and Elhady (2020), the method of Reverse Monte Carlo simulation has been used to examine the effect of quenching rate on the structure of glassy AsxSe100−x (x=20, 30, 40, 50 at%). Results of the partial structure factors indicate that the correlations responsible for medium range order depend strongly on As-content, and distortion occurs in this structure range with increasing quenching rate. This distortion is more predominant in case of As50Se50 glass. Results of partial pair distribution function show that, most of short range order is mainly governed by the chemically ordered network model, and the random covalent network model plays a relatively small role. Also, it was clarified that the percentage of homopolar bonds increases with increasing quenching rate. In case of x=50at.%, the tendency of As segregation and formation of As–As bonds is demonstrated. Some Deviation from “8-N” rule was observed in the structure of the investigated glasses.

Evolution of Ni coordination configuration during one-pot pyrolysis synthesis of Ni-g-C3N4 single atom catalyst

In this paper, the unclear Ni atom coordination structure evolution in one-pot pyrolysis method synthesizing Ni single atom catalyst using graphitic carbon nitride as support (Ni-g-C3N4) was deeply discussed. In-situ X-ray absorption fine structure spectra and other assisted methods were used to characterize the structural evolution. The results demonstrate that the pyrolysis process can be divided into three stages. In the first stage from room temperature to 183 °C (Stage I), the NiCl2⋅6H2O was mixed with the supporting material (dicyandiamide) to form the precursor with Ni-(H2O)6 octahedral coordination configuration. In the second stage from 183 to 350 °C (Stage II), the H2O molecules have been removed and the supporting material was converted to melamine. The melamine molecules were polycondensed to melem during 308–350 °C. The intermediates labeled Ni-melamine and Ni-melem was formed with Ni-N4 planar quadrilateral coordination configuration. In the third stage from 350 to 600 °C (Stage III), the supporting material (melem) was gradually converted to g-C3N4, and the Ni-N4 coordination configurations were replaced by Ni-N6 planar hexagon coordination configuration one by one. The three Ni coordination configurations were further confirmed by Reverse Monte Carlo simulations and ab initio calculations.

Formation of the Short‐Range Order in Liquid Al−Ni−Sn Alloys

AbstractShort‐range order (SRO) in the liquid Al−Ni−Sn alloys has been investigated using the X‐ray diffraction method and Reverse Monte Carlo simulations. Obtained results point out a micro‐inhomogeneous structure of Al−Sn−Ni melts with Sn content between 10 and 65 at.% due to the presence of atomic clusters with the structure of liquid Sn and atomic clusters with Ni−Sn coordination. The influence of the atomic size ratio (size factor) and pair atomic interactions (energy factor) on the short‐range order of the investigated ternary melts are discussed. There is a competition between Al and Sn atoms in the formation of the SRO around Ni atoms due to the difference in bond energy in Ni−Al and Ni−Sn pairs. This competition, as well as a bigger radius of Sn atoms, results in the formation of atomic clusters with liquid Sn‐like local atomic structure.

Deuterium occupation of interatomic hole sites in Ni67Zr33 amorphous alloy

The occupation of interatomic hole sites by deuterium in a deuterated Ni67Zr33 amorphous alloy was investigated using diffraction measurements and a combination of reverse Monte Carlo and molecular dynamics simulation techniques. The results show that deuterium atoms occupy various types of polyhedral hole sites, as well as tetrahedral ones. The occupation by a deuterium atom of a tetrahedral hole site causes volume expansion, but that of a larger polyhedral hole site does not cause a substantial change in the volume. Each deuterium atom is chemically bonded with 4–6 metal atoms, even for a larger polyhedral hole formed by seven or more metal atoms.

Short range order of glassy KSb5S8 by diffraction, EXAFS, vibrational spectroscopy and DFT calculations

We report on a detailed experimental and simulation study of the short- and medium-range order of a potential phase change material – glassy KSb5S8. On the experimental side, diffraction techniques and EXAFS have been employed to record accurate structural data. Structural models have been generated by fitting multiple datasets simultaneously with the reverse Monte Carlo simulation technique. In addition, density functional theory was employed to study the structure and vibrational modes of selected clusters, representative of the glass structure. Unconstrained RMC simulation runs revealed that the average Sb-S coordination number is 3.18 ± 0.2, thus Sb is mostly threefold coordinated in the glassy state. The fraction of edge and corner sharing SbSn polyhedra and distribution of bridging S atoms (Qn distribution) have also been obtained. Distribution of bridging S atoms around Sb is similar in the crystalline and glassy states. DFT calculations assisted in the identification of a Raman mode at ∼468 cm−1, assigned to hypervalent bonding (quasi-tetrahedral units) in the glass structure.

Unraveling the interlayer and intralayer coupling in two-dimensional layered MoS[formula omitted] by X-ray absorption spectroscopy and ab initio molecular dynamics simulations

Understanding interlayer and intralayer coupling in two-dimensional layered materials (2DLMs) has fundamental and technological importance for their large-scale production, engineering heterostructures, and development of flexible and transparent electronics. At the same time, the quantification of weak interlayer interactions in 2DMLs is a challenging task, especially, from the experimental point of view. Herein, we demonstrate that the use of X-ray absorption spectroscopy in combination with reverse Monte Carlo (RMC) and ab initio molecular dynamics (AIMD) simulations can provide useful information on both interlayer and intralayer coupling in 2DLM 2Hc-MoS2. The analysis of the low-temperature (10–300 K) Mo K-edge extended X-ray absorption fine structure (EXAFS) using RMC simulations allows for obtaining information on the means-squared relative displacements σ2 for nearest and distant Mo–S and Mo–Mo atom pairs. This information allowed us further to determine the strength of the interlayer and intralayer interactions in terms of the characteristic Einstein frequencies ωE and the effective force constants κ for the nearest ten coordination shells around molybdenum. The studied temperature range was extended up to 1200 K employing AIMD simulations which were validated at 300 K using the EXAFS data. Both RMC and AIMD results provide evidence of the reduction of correlation in thermal motion between distant atoms and suggest strong anisotropy of atom thermal vibrations within the plane of the layers and in the orthogonal direction.

On the absence of structure factors in concentrated colloidal suspensions and nanocomposites.

Small-angle scattering is a commonly used tool to analyze the dispersion of nanoparticles in all kinds of matrices. Besides some obvious cases, the associated structure factor is often complex and cannot be reduced to a simple interparticle interaction, like excluded volume only. In recent experiments, we have encountered a surprising absence of structure factors (S(q) = 1) in scattering from rather concentrated polymer nanocomposites (Genix et al. in ACS Appl Mater Interfaces 11(19):17863-17872, 2019). In this case, quite pure form factor scattering is observed. This somewhat "ideal" structure is further investigated here making use of reverse Monte Carlo simulations in order to shed light on the corresponding nanoparticle structure in space. By fixing the target "experimental" apparent structure factor to one over a given q-range in these simulations, we show that it is possible to find dispersions with this property. The influence of nanoparticle volume fraction and polydispersity has been investigated, and it was found that for high concentrations only a high polydispersity allows reaching a state of S = 1. The underlying structure in real space is discussed in terms of the pair-correlation function, which evidences the importance of attractive interactions between polydisperse nanoparticles. The calculation of partial structure factors shows that there is no specific ordering of large or small particles, but that the presence of attractive interactions together with polydispersity allows reaching an almost "structureless" state.

Metal-Carbodithioate-Based 3D Semiconducting Metal-Organic Framework: Porous Optoelectronic Material for Energy Conversion.

Solar energy conversion requires the working compositions to generate photoinduced charges with high potential and the ability to deliver charges to the catalytic sites and/or external electrode. These two properties are typically at odds with each other and call for new molecular materials with sufficient conjugation to improve charge conductivity but not as much conjugation as to overly compromise the optical band gap. In this work, we developed a semiconducting metal-organic framework (MOF) prepared explicitly through metal-carbodithioate "(-CS2)nM" linkage chemistry, entailing augmented metal-linker electronic communication. The stronger ligand field and higher covalent character of metal-carbodithioate linkages─when combined with spirofluorene-derived organic struts and nickel(II) ion-based nodes─provided a stable, semiconducting 3D-porous MOF, Spiro-CS2Ni. This MOF lacks long-range ordering and is defined by a flexible structure with non-aggregated building units, as suggested by reverse Monte Carlo simulations of the pair distribution function obtained from total scattering experiments. The solvent-removed "closed pore" material recorded a Brunauer-Emmett-Teller area of ∼400 m2/g, where the "open pore" form possesses 90 wt % solvent-accessible porosity. Electrochemical measurements suggest that Spiro-CS2Ni possesses a band gap of 1.57 eV (σ = 10-7 S/cm at -1.3 V bias potential), which can be further improved by manipulating the d-electron configuration through an axial coordination (ligand/substrate), the latter of which indicates usefulness as an electrocatalyst and/or a photoelectrocatalyst (upon substrate binding). Transient-absorption spectroscopy reveals a long-lived photo-generated charge-transfer state (τCR = 6.5 μs) capable of chemical transformation under a biased voltage. Spiro-CS2Ni can endure a compelling range of pH (1-12 for weeks) and hours of electrochemical and photoelectrochemical conditions in the presence of water and organic acids. We believe this work provides crucial design principles for low-density, porous, light-energy-conversion materials.