Simulated X-ray Diffraction Patterns Research Articles

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debye formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.

Modeling Powder X-ray Diffraction Patterns of the Clay Minerals Society Kaolinite Standards: KGa-1, KGa-1b, and KGa-2

AbstractThree kaolinite reference samples identified as KGa-1, KGa-1b, and KGa-2 from the Source Clays Repository of The Clay Mineral Society (CMS) are used widely in diverse fields, but the defect structures have still not been determined with certainty. To solve this problem, powder diffraction patterns of the KGa-1, KGa-1b, and KGa-2 samples were modeled. In a kaolinite layer among three symmetrically independent octahedral sites named as A, B, and C and separated from each other by b/3 along the b parameter, the A and B sites are occupied by Al cations, whereas, the C sites located along the long diagonal of the oblique kaolinite unit cell are vacant. The layer displacement vectors t1 and t2 are related by a pseudo-mirror plane from defect-free 1Tc kaolinite enantiomorphs, whereas, the random interstratification within individual kaolinite crystallites creates right-hand and left-hand layer sub-sequences producing structural disorder. A third layer displacement vector, t0, located along the long diagonal of the oblique layer unit cell that contains the vacant octahedral site and coincides with the layer pseudo-mirror plane may exist. Thus, a structural model should be defined by the probability of t1, t2, and t0 layer displacement translations Wt1, Wt2, and Wt0, respectively, determined by simulated experimental X-ray diffraction (XRD) patterns. X-ray diffraction patterns were calculated for structures with a given content of randomly interstratified displacement vectors, and other XRD patterns were calculated for a physical mixture of crystallites having contrasting structural order with only C-vacant layers. The samples differ from each other by the content of high- and low-ordered phases referred to as HOK and LOK. The HOK phase has an almost defect-free structure in which 97% of the layer pairs are related by just the layer displacement vector t1 and only 3% of the layer pairs form the enantiomorphic fragments. In contrast, the LOK phases in the KGa-1, KGa-1b, and KGa-2 samples differ from HOK phases by the occurrence probabilities for the t1, t2, and t0 layer displacements. In addition, the LOK phases contain stacking faults that displace adjacent layers in arbitrary lengths and directions. Low XRD profile factors (Rp = 8-11%) support the defect structure models. Additional structural defects and previously published models are discussed.

Body-Centered Orthorhombic C_{16}: A Novel Topological Node-Line Semimetal.

We identify by abinitio calculations a novel topological semimetal carbon phase in all-sp^{2} bonding networks with a 16-atom body-centered orthorhombic unit cell, termed bco-C_{16}. Total-energy calculations show that bco-C_{16} is comparable to solid fcc-C_{60} in energetic stability, and phonon and molecular dynamics simulations confirm its dynamical stability. This all-sp^{2} carbon allotrope can be regarded as a three-dimensional modification of graphite, and its simulated x-ray diffraction (XRD) pattern matches well a previously unexplained diffraction peak in measured XRD spectra of detonation and chimney soot, indicating its presence in the specimen. Electronic band structure calculations reveal that bco-C_{16} is a topological node-line semimetal with a single nodal ring. These findings establish a novel carbon phase with intriguing structural and electronic properties of fundamental significance and practical interest.

Study on four polymorphs of bifendate based on X-ray crystallography

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C–C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

A new high-pressure silica phase obtained by molecular dynamics

A molecular dynamics study with analytical and ab initio interatomic potentials revealed the possibility of a new silica phase with Pnc2 structure, which is more stable than stishovite and its CaCl2-like modification at pressures above approximately 120 GPa over a wide range of temperature. Our analysis of simulated X-ray diffraction patterns of various hypothetical post-stishovite phases shows that this new phase should be considered in the treatment of high-pressure experiments involving silica. The new phase might be responsible for the seismic discontinuity at 2728 km depth and should be treated as potentially stable at the pressures and temperatures of the lowermost mantle.

Structures and stability of novel transition-metal(M=Co,Rh,CoandIr)borides

Recent progress of high-pressure technology enables the synthesis of novel metal borides with diverse compositions and interesting properties. A precise characterization of these borides, however, is sometimes hindered by multiphase intergrowth and grain-size limitation in the synthesis process. Here, we theoretically explored new transition-metal borides $(M\phantom{\rule{0.16em}{0ex}}=\phantom{\rule{0.16em}{0ex}}\mathrm{Co}$, Rh, and Ir) using a global structure searching method and discovered a series of stable compounds in this family. The predicted phases display a rich variety of stoichiometries and distinct boron networks resulting from the electron-deficient environments. Significantly, we identified a new $\mathrm{Ir}{\mathrm{B}}_{1.25}$ structure as the long-sought structure of the first synthesized Ir-B compound. The simulated x-ray diffraction pattern of the proposed $\mathrm{Ir}{\mathrm{B}}_{1.25}$ structure matches well with the experiment, and the convex hull calculation establishes its thermodynamic stability. Results of the present paper should advance the understanding of transition-metal borides and stimulate experimental explorations of these new and promising materials.

Structure and morphology evolution of silica-modified pseudoboehmite aerogels during heat treatment

Silica-modified pseudoboehmite aerogels (0, 10, 20at% of Si) were prepared by sol–gel method followed by supercritical drying. The phase transformations, changes in structure and morphology upon calcination were thoroughly investigated by advanced X-Ray diffraction (XRD) techniques and high-resolution transmission electron microscopy (HRTEM). Obtained pseudoboehmite samples had specific nanostructure: ultrathin two-dimensional (2D) crystallites were loosely packed. The silica dopant drastically enhanced the crystallite anisotropy. Thus, the aerogel with Al:Si atomic ratio of 9:1 consisted of the pseudoboehmite nanosheets with thickness of one unit cell (average dimensions of 14.0×1.2×14.5nm). The specific nanostructure caused remarkable features of experimental XRD patterns, including anisotropic peak broadening and appearance of forbidden reflection. Direct simulation of XRD patterns with using the Debye Scattering Equation allowed the size and morphology of pseudoboehmite crystallites to be determined. The silica addition strongly delayed formation of γ-alumina and further phase transformations upon calcinaton. Thermal stability of alumina was suggested to be affected by the particle morphology inherited from the pseudoboehmite precursor.

Highly Formed Luminescent Oxygen Trap States in Thermochemically Prepared CdS Nanocrystals and Improvement of the Luminescence Property

CdS nanocrystals were prepared through a thermally activated (thermochemical) method. The synthesis was performed in two different oxygen-saturated and Ar purged atmospheres. Na2S2O3 was used as a heat-sensitive source of S in the experiments. Thioglycerol was also applied as the capping agent to restrain the growth. The growth was activated by heating and controlled by solution pH. The results demonstrated a considerably higher luminescence intensity for the synthesis in oxygen-saturated atmosphere. This could show the role of luminescent oxygen trap states created inside the CdS nanocrystals. The improved luminescence was observed for the synthesis at different solution pHs. Nevertheless, the growth rate was slower and luminescence intensity was higher for the synthesis at higher pHs. This trend was followed for the solution pHs in the range of 4.0–7.0. For the synthesis at solution pH of 8.0 the growth rate was unexpectedly increased. This could be attributed to the epitaxial growth of CdS nanocrystals in this pH. The best photoluminescence intensity was achieved for the CdS nanocrystals prepared in oxygen-saturated atmosphere at solution pH of 8.0. The crystalline structure of these NCs was composed of 70% of the cubic and 30% of the hexagonal crystalline phases of the CdS material. This was calculated by simulation of X-ray diffraction pattern of the CdS nanocrystals.

Ab initio structure determination of n-diamond.

A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.

Segal crystallinity index revisited by the simulation of X-ray diffraction patterns of cotton cellulose Iβ and cellulose II

The Segal method estimates the amorphous fraction of cellulose Iβ materials simply based on intensity at 18° 2θ in an X-ray diffraction pattern and was extended to cellulose II using 16° 2θ intensity. To address the dependency of Segal amorphous intensity on crystal size, cellulose polymorph, and the degree of polymorphic conversion, we simulated the diffraction patterns of cotton celluloses (Iβ and II) and compared the simulated amorphous fractions with the Segal values. The diffraction patterns of control and mercerized cottons, respectively, were simulated with perfect crystals of cellulose Iβ (1.54° FWHM) and cellulose II (2.30° FWHM) as well as 10% and 35% amorphous celluloses. Their Segal amorphous fractions were 15% and 31%, respectively. The higher Segal amorphous fraction for control cotton was attributed to the peak overlap. Although the amorphous fraction was set in the simulation, the peak overlap induced by the increase of FWHM further enhanced the Segal amorphous intensity of cellulose Iβ. For cellulose II, the effect of peak overlap was smaller; however the lower reflection of the amorphous cellulose scattering in its Segal amorphous location resulted in smaller Segal amorphous fractions. Despite this underestimation, the relatively good agreement of the Segal method with the simulation for mercerized cotton was attributed to the incomplete conversion to cellulose II. The (1−10) and (110) peaks of cellulose Iβ remained near the Segal amorphous location of cellulose II for blends of control and mercerized cotton fibers.

Simulations of in situ x-ray diffraction from uniaxially compressed highly textured polycrystalline targets

A growing number of shock compression experiments, especially those involving laser compression, are taking advantage of in situ x-ray diffraction as a tool to interrogate structure and microstructure evolution. Although these experiments are becoming increasingly sophisticated, there has been little work on exploiting the textured nature of polycrystalline targets to gain information on sample response. Here, we describe how to generate simulated x-ray diffraction patterns from materials with an arbitrary texture function subject to a general deformation gradient. We will present simulations of Debye-Scherrer x-ray diffraction from highly textured polycrystalline targets that have been subjected to uniaxial compression, as may occur under planar shock conditions. In particular, we study samples with a fibre texture, and find that the azimuthal dependence of the diffraction patterns contains information that, in principle, affords discrimination between a number of similar shock-deformation mechanisms. For certain cases, we compare our method with results obtained by taking the Fourier transform of the atomic positions calculated by classical molecular dynamics simulations. Illustrative results are presented for the shock-induced α–ϵ phase transition in iron, the α–ω transition in titanium and deformation due to twinning in tantalum that is initially preferentially textured along [001] and [011]. The simulations are relevant to experiments that can now be performed using 4th generation light sources, where single-shot x-ray diffraction patterns from crystals compressed via laser-ablation can be obtained on timescales shorter than a phonon period.

Computational prediction of body-centered cubic carbon in an all-sp3six-member ring configuration

Recent shock compression experiments produced clear evidence of a new carbon phase, but a full structural identification has remained elusive. Here we establish by ab initio calculations a body-centered cubic carbon phase in Ia3¯d(O10h) symmetry, which contains twelve atoms in its primitive cell, thus termed BC12, and comprises all-sp3 six-membered rings. This structural configuration places BC12 carbon in the same bonding type as cubic diamond, and its stability is verified by phonon mode analysis. Simulated x-ray diffraction patterns provide an excellent match to the previously unexplained distinct diffraction peak found in shock compression experiments. Electronic band and density of states calculations reveal that BC12 is a semiconductor with a direct band gap of ~2.97eV. Lastly, these results provide a solid foundation for further exploration of this new carbon allotrope.

Effect of Annealing on Crystal and Local Structures of Doped Zirconia Using Experimental and Computational Methods

The effects of the annealing process on the crystal and local structures of doped zirconia were investigated by Rietveld refinements of synchrotron X-ray and neutron diffraction, the maximum entropy method (MEM), X-ray absorption spectroscopy (XAS), and first-principles calculations (FPCs). This study reveals that the crystal structures of sintered and annealed (Zr0.85Y0.15)O2−δ (8YSZ) and (Zr0.81Sc0.18Ce0.01)O2−δ (10SSZ) are cubic with the space group Fm3m and have large atomic displacement parameters (Uiso). The amounts of tetragonal and other phases are less than 0.2 mol % as estimated by comparison of the observed and simulated X-ray diffraction patterns in the annealed zirconia. For annealed 8YSZ, the Uiso values are reduced, and the electrons around the Zr and oxide ion sites gather at the center of each site. On the other hand, annealed 10SSZ shows the opposite tendency as annealed 8YSZ. From the combined XAS and FPC results, the distortion of the ZrO8 polyhedra in zirconia is related to the weake...

Ab initio models for polycrystalline diamond constructed from cold-compressed disordered graphite

A general scheme is proposed to construct systematically a family of superhard sp3 carbon phases of cold-compressed graphite by combining hexagonal to cubic diamond (named as X-Carbon). Based on calculations employing density functional theory (DFT), we find that our currently proposed X-carbon can occur by compressing disordered graphite, and the X-carbon is more stable in energy than the previously proposed M, Z, W, bct-C4, P allotropes. Thus, the X-carbon is predicted to be the transition of cold-compressed graphite. The results show that the simulated x-ray diffraction pattern, Vickers hardness and bulk modulus of X-Carbon match well with the experimental data (Mao et al Science 302, 425 (2003)). These new phases are transparent superhard materials with a large hardness and wide electronic band gaps comparable to cubic diamond.

Structure of oxides prepared by decomposition of layered double Mg–Al and Ni–Al hydroxides

Abstracts Thermal decomposition of Mg–Al and Ni–Al layered double hydroxides LDH at temperatures lower than 800 °C leads to the formation of oxides with different structures. Mg–Al oxide has a very defective structure and consists of octahedral layers as in periclase MgO and mixed octahedral–tetrahedral layers as in spinel MgAl 2 O 4 . Mixed Ni–Al oxide has a sandwich-like structure, consisting of a core with Al-doped NiO-like structure and some surface layers with spinel NiAl 2 O 4 structure epitaxial connected with the core. Suggested models were verified by simulation of X-ray diffraction patterns using DIFFaX code, as well as HRTEM, IR-, UV-spectroscopies, and XPS.

Deformation of Austenitic CrMnNi TRIP/TWIP Steels: Nature and Role of the ɛ−martensite

High-alloy CrMnNi TRIP/TWIP steels show a martensitic phase transformation, which is frequently described by the transformation sequence from ϒ-austenite (fcc) via ɛ−martensite (hcp) to α−martensite (bcc). During the plastic deformation, deformation bands in austenite are formed, which contain a high density of stacking faults on the lattice planes {111}. The formation of the stacking faults is enabled by the dissociation of perfect dislocations into the partial dislocations. In ɛ−martensite, the stacking faults are highly ordered. Diffraction experiments recognize the periodic arrangement of the stacking faults as a hexagonal phase. In this contribution, the structure of ɛ−martensite was described with the aid of the analysis and the DIFFaX simulation of X-ray diffraction patterns, electron back-scatter diffraction and high-resolution transmission electron microscopy. The faulting of austenite enhances the formation of α−martensite during deformation, thus the work hardening capability is significantly increased.

Molecular dynamics simulations of clusters and thin film growth in the context of plasma sputtering deposition

Carrying out molecular dynamics (MD) simulations is a relevant way to understand growth phenomena at the atomic scale. Initial conditions are defined for reproducing deposition conditions of plasma sputtering experiments. Two case studies are developed to highlight the implementation of MD simulations in the context of plasma sputtering deposition: ZrxCu1−x metallic glass and AlCoCrCuFeNi high entropy alloy thin films deposited onto silicon. Effects of depositing atom kinetic energies and atomic composition are studied in order to predict the evolution of morphologies and atomic structure of MD grown thin films. Experimental and simulated x-ray diffraction patterns are compared.

A New Carbon Allotrope with Six-Fold Helical Chains in all-sp2 Bonding Networks

Using a recently developed approach to constructing covalent network structures from linear carbyne, we identify by ab initio calculations a new carbon allotrope in () symmetry that comprises six-fold helical chains with alternating sp2-type single and double bonds along the chains that are connected via zigzag benzene rings. This 6-fold carbene is characterized as a three-dimensional three-connected chiral crystalline modification of graphite. Phonon and electronic band calculations indicate that this new structure is dynamically stable and is a semiconductor with a band gap of 0.47 eV, in contrast to the semimetallic nature of graphite. Simulated x-ray diffraction patterns of the 6-fold carbene provide an excellent match to the previously unexplained distinct diffraction peak of a new carbon allotrope found in recent detonation experiments. These results establish a new carbon phase and offer insights into its outstanding structural and electronic properties.

Molecular dynamics simulations of lanthanum oxide surfaces

Classical molecular dynamics was used to investigate the equilibrium state of the surface region of as-grown La2O3. It is currently thought that bulk and epitaxial thin film La2O3 surfaces exhibit amorphous structures in the as-prepared state that yield bulk crystal states upon postdeposition annealing. The focus of the study is to determine if the as-prepared surface region of La2O3 is purely amorphous as indicated from prior experimental results. Using simulation cells sufficiently large to accommodate the formation of defects, phase segregation, compositional migration, and site defects, our results show that crystalline phases are evident from simulated X-ray diffraction patterns. Although the phase of these crystallites is unresolved, we suggest that combinations of distorted hexagonal, cubic, and nonstoichiometric phases are formed in the as-prepared state prior to annealing. These crystallites likely serve as nucleation site for long-range ordered crystal growth upon annealing.

Anomalously Enhanced Hydration of Aqueous Electrolyte Solution in Hydrophobic Carbon Nanotubes to Maintain Stability

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment.