Atomic Radial Distribution Functions Research Articles

Application of fragmentary model to analysis of the atomic structure of amorphous materials

Experimental atomic radial distribution functions, obtained from diffraction amorphous materials, are proposed to be interpreted using the model curves built upon the complete structural data of crystal analogues or upon the separate fragments of their structure. This modelling technique is called a fragmentary model. A model atomic radial distribution function is a radial cross section of the spherically symmetric function of interatomic distances. It characterises a nanodispersed diffraction amorphous polycrystal as uniquely as the values of interplanar spacings and intensities characterise a regular polycrystal. Comparing the model and experimental atomic radial distribution functions by the maxima positions we can perform the “identification” and “phase analysis” of nanodispersed diffraction amorphous polycrystals and define the crystalline compounds whose fragments form the structure of glass.

The study of structure and interactions of glucose-based natural deep eutectic solvents by molecular dynamics simulation

In the current study, molecular dynamics simulations were conducted to investigate the structural and dynamical properties of glucose-based Deep Eutectic Solvents (DESs) at different molar ratios (the mixture of glucose and choline chloride with the molar ratios of 1:3, 1:1 and 3:1). Accordingly, the interaction energies of different species and structural properties such as atom–atom radial distribution functions (RDFs), the hydrogen-bonding network between species, and spatial distribution functions (SDFs) were computed to understand effective interactions in the eutectic mixture formation. It was found that the insertion of glucose molecules reduced the accumulation of chloride anions around choline cations, eventually decreasing the interaction between the choline chloride ion pairs. Moreover, the possible explanations for the thermos-physical properties of DESs, such as the shear viscosity and density, have been provided. Dynamical properties of DES were evaluated by calculating the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of the mass of the ions and glucose molecules. MSD analysis results were then used to calculate the self-diffusion parameter by applying the Einstein relation. The simulation results indicated that increasing the temperature led to easing the migration of the molecules and decreasing the dependence of the movement of the molecules on each other. This growing trend of migration may lead to an increase in the self-diffusion coefficient of molecules. Structural analysis revealed that a ratio of 1:1 of glucose: choline chloride could provide the best condition to maintain the low melting point of the mixture due to the strong hydrogen-bonded network between the two species.

Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes.

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10–20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10 cm/s for the cholesterol-free and cholesterol-rich setups.

Molecular Dynamics Simulation of Polyacrylamide Adsorption on Cellulose Nanocrystals.

Classical molecular dynamics simulations of polyacrylamide (PAM) adsorption on cellulose nanocrystals (CNC) in a vacuum and a water environment are carried out to interpret the mechanism of the polymer interactions with CNC. The structural behavior of PAM is studied in terms of the radius of gyration, atom–atom radial distribution functions, and number of hydrogen bonds. The structural and dynamical characteristics of the polymer adsorption are investigated. It is established that in water the polymer macromolecules are mainly adsorbed in the form of a coil onto the CNC facets. It is found out that water and PAM sorption on CNC is a competitive process, and water weakens the interaction between the polymer and CNC.

Calculations of Sodium Borate Systems Na2O-B2O3 Using Quantum Molecular Dynamics

The electronic structure and complexation in sodium borate network of the 80%B2O3–20%Na2O melt doped by 1% of Nd atoms at T = 1273 K was studied by quantum molecular dynamics using the SIESTA package. The obtained density of states allowed explaining some electronic transitions established previously in experimental studies of spectral characteristics of the xNa2O-(100-x)B2O3 system doped by Nd. The calculated atomic radial distribution functions show characteristic distances which are in a good agreement with those predicted earlier for the systems containing boron and oxygen complexes.

Submicrostructure and Characteristics of the Short-Range Atomic Order in an Amorphous Ti–Ni–Ta–Zr-Based Surface Alloy Formed on a TiNi Substrate by the Electron-Beam Method

This study presents the results of studying the microstructure and topological short-range atomic order in an amorphous Ti−Ni−Тa−Zr-based surface alloy formed by the additive method through pulsed electron-beam liquid-phase mixing of the “Ti70Ta30 film (50 nm)/Zr film (100 nm)/TiNi substrate” system. It is shown that an amorphous structure with a thickness of 2 μm is formed in the cross-section of the surface alloy and is characterized by the gradient chemical composition. It is found that the transition sublayer adjacent to the TiNi substrate has a nanocomposite crystalline structure based on the Ti2Ni intermetallic compound. By means of the atomic radial distribution function method, using electron nanobeam diffraction data, a study of the topological short-range atomic order in the amorphous layer is performed. It is shown that the atomic structure in the amorphous surface Ti−Ni−Тa−Zr alloy has a cluster structure which can be described by the superposition of coordination polyhedra interconnected with each other by common faces corresponding to the different crystalline devitrification phases.

X-ray diffraction study of structure of CaO-Al2O3-SiO2 ternary compounds in molten and crystalline states

Anorthite and gehlenite crystalline structure and short-range order of anorthite melt have been studied by X-ray diffraction in the temperature range from room temperature up to ~ 1923 K. The corresponding anorthite and gehlenite phases were identified as well as amorphous component for anorthite samples having identical shape to XRD pattern of the anorthite melt. The structure factor and the radial distribution function of atoms of the anorthite melt were calculated from the X-ray high-temperature experimental data. The partial structural parameters of the short-range order of the melt were reconstructed using Reverse Monte Carlo simulations.

The structure of clusters in liquid alloys of pseudo-binary PbTe-Bi2Te3 system

Purpose: of this paper is to study the structure of melts of quasi-binary system Bi2Te3-PbTe by means of X-ray diffraction method. The aim of the research was to investigate the short range order in melts comparing it with the structure in solid state. Design/methodology/approach: Analysis of the structural factors, radial distribution functions of atoms and basic structural parameters showed that the structure of melts at temperatures near the liquidus shows microheterogeneity. Findings: On the basis of the analysis of structural factors, functions of the radial distribution of atoms and basic structural parameters, it is shown that in the given concentration the short range order structure of liquid alloys of pseudo-binary PbTe-Bi2Te3 system is microinhomogeneous and is characterized by the presence of associates, whose atomic arrangement is like to the structure of solid compounds, existing in this concentration range. Research limitations/implications: To complete the understanding of short-range order effect on the formation of the physical properties of Pb-Bi-Te alloys, further studies of the thermoelectric properties of these alloys in the liquid state are needed. Practical implications: The promise of the considered direction requires an experimental and theoretical study of the processes of bulk, thin film and nanostructured material. In this case, it is necessary to develop a technology for the synthesis of compounds of Pb-Bi-Te system, obtaining thin films and nanostructures using the vapour phase methods with studying the mechanisms of thermoelectric properties of the material formation and optimization of technological regimes for obtaining effective thermoelectric materials based on compounds of Pb-Te-Bi system. Originality/value: The processes of structure formation of nanosystems with given characteristics are investigated, because among numerous thermoelectric materials, bismuth telluride (Bi2Te3) and its alloys are the most important thermoelectric materials used in state-of-the-art devices near room temperature, and lead telluride (PbTe)-based alloys are extensively used in power supplies for space exploration and generators for use at medium to high temperatures.

Molecular Dynamics Simulation of the Cu/Au Nanoparticle Alloying Process

Sintering is an important approach for the alloying of different metals, which is affected by factors such as temperature, grain size, and material properties. And it represents a complex thermodynamic process. This paper had adopted the molecular dynamics methods to investigate the evolution process of nanostructure during the sintering of Cu and Au nanoparticles. The changes in crystalline during the nanosintering process were observed, and the radial distribution function of atoms, the shrinkage ratio, and the sintering neck of the systems were discussed. The initial sintering temperature and melting temperature of the system were obtained; at the same time, the characteristics of the sintering neck with changes in temperature during the nanosintering process were revealed.

Effects of Temperature and Alloy Composition on Nanomechanical Properties of ZrCu Metallic Glass under Tension

Background: The nanomechanical properties of Zr50Cu50 metallic glass under tension are studied. The effects of temperature and alloy composition are investigated in terms of atomic trajectories, slip vectors, stress-strain curve, and radial distribution function. Methods: The molecular dynamics simulations based on the many-body tight-binding potential are applied to analyze the nanomechanical properties of metallic glass under tension. Results: The mechanical properties of the metallic glass are sensitive to temperature and alloy composition. Under tensile deformation, the stress increases with increasing temperature and Zr content in the alloys. At higher temperatures, the alloy atoms have high slip vectors, and plasticity becomes more homogeneous due to a better flow ability of atoms. Conclusion: The alloys with higher Zr content have larger mechanical strengths. The alloys with higher Cu content have more stable structures.

Water Effects on Molecular Adsorption of Poly(N-vinyl-2-pyrrolidone) on Cellulose Nanocrystals Surfaces: Molecular Dynamics Simulations.

Models of interaction between a poly(N-vinyl-2-pyrrolidone) macromolecule and a fragment of Iβ-cellulose were built in a vacuum and water environment. The models were made to interpret the mechanism of interaction of the polymer and cellulose nanocrystals by the classical molecular dynamics method. The structural behavior of a poly(N-vinyl-2-pyrrolidone) macromolecule in water has been studied in terms of the radius of gyration, atom–atom radial distribution functions and number of hydrogen bonds. It was found that the polymer has a high affinity with the solvent and each monomer unit has on average 0.5 hydrogen bonds. The structural and energy characteristics of the polymer adsorption were investigated at different initial positions of the poly(N-vinyl-2-pyrrolidone) macromolecule relative to the cellulose fragment. It was observed that the polymer macromolecule was mainly adsorbed on the cellulose fragment in the globular form. Moreover, in the solvent the interaction of poly(N-vinyl-2-pyrrolidone) with the cellulose hydrophobic surface was stronger than that with the hydrophilic one. This study will show that the presence of water makes the interaction between the polymer and cellulose weaker than in a vacuum, and the polymer and cellulose mainly interact through their solvation shells.

Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations.

The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.

Analysis of the atomic structure of the amorphous metal alloy Al84Ni6La10

The paper presents an analysis of the atomic radial distribution function of the amorphous metal alloy Al84Ni6La10 based on the fragmentary model. A comparative analysis of the most probable interatomic distances in the alloy and its compounds demonstrated the presence of crystalline nuclei of the following phases: Al3La, AlNi3, Al4La and Al. The crystalline nuclei of the Al4La compound are the smallest (~7-8 Å), while the minimal size of the most nuclei of the other phases is 1-1.5 nm. The following phases were observed in the crystallised alloy: Al11La3, Al3Ni, and Al.

X-Ray Diffraction and Differential Scanning Calorimetry Studies of Crystalline and Amorphous Regions in Composite Porous Films

A comparative analysis of the structural evolution of MGA-95 and ESPA1 polymer composite porous films is performed by plotting the radial distribution functions of atoms using empirical X-ray scattering intensity curves and the thermophysical parameters of melting are calculated using data from differential scanning calorimetry (DSC). In the case of the water-saturated MGA-95 sample, the atomic density in the first coordination sphere of the cellulose acetate macromolecule is shown to decrease due to the breaking of intramolecular hydrogen bonds. The atomic density of coordination spheres with radii corresponding to the lattice parameters decreased suggesting spatial disorder of the macromolecules. The DSC data for the MGA-95 film (the enthalpies of melting of the dry and water saturated samples are ΔH = 8.57 and 6.55 J/g, respectively) suggests that sorption of water molecules leads to a decrease in the degree of crystallinity due to a change in the crystalline fractions in the polycrystals. In the case of the ESPA1 composite film, a decrease in the radius and an increase in the atomic density of the first coordination sphere are indicative of the orientational disorder of amorphous phase molecules upon the sorption of water. The appearance of additional coordination spheres with R2 = 3.88 and R3 = 5.26 A in the swollen ESPA1 sample suggests the quantitative redistribution of crystal phases in the substrate material. A detailed analysis of endothermic peaks on the DSC curve shows that the ratio of low- and high-temperature phases varies from 64% : 36% in the dry sample up to 51% : 49% in the water saturated sample at almost identical enthalpies of melting of ΔH = 12.18 and 11.66 J/g, respectively.

Retraction Note to: MD simulations on the melting and compression of C, SiC and Si nanotubes

By the Tersoff potential based molecular dynamics (MD) method, the melting and axial compression of the (5,5) C, SiC, and Si nanotubes are simulated, and their molecular configurations, atomic radial distribution functions (RDF) and energy changes during heating-up, as well as their compressive force–strain curves, are obtained. According to the computed results, the differences of the melting and compressive mechanical properties of the three nanotubes are discussed. It is found that the melting C, SiC, and Si nanotubes have netlike, loose spherical and compact spherical configurations respectively, and that the C nanotube has the highest melting point, specific heat, melting heat and load support capability, whereas the Si nanotube has the lowest ones.

Chemical Ordering in Ni66.7 In33.3 Liquid Alloy

Short range order structure of liquid Ni66,7In33,3 alloy has been studied by means of X-ray diffraction method at temperatures 1235; 1260 and 1335 K. Experimental structure factors and radial atomic distribution function are analyzed. It is shown that structure of Ni66,7In33,3 in liquid state reveals chemical ordering, like to Ni2In type structure

Study of Three-Dimensional, Surface, and Linear Structures of Allotropic Carbon: Diffraction Spectra of Auger Electron Energy Losses

A theoretical approach is developed for determining the parameters of nanoscale crystal structures using diffraction spectra of Auger electron energy losses. The approach is based on modeling the radial distribution functions of atoms while allowing for the sizes of atomic structures, and on the geometry of surfaces of three-dimensional, surface, and linear objects intersecting with a sphere. Using the example of allotropic carbon phases, it is shown that the proposed technique allows assessment of a studied object’s thickness and the depth of the analyzed signal output with an accuracy of one atom’s diameter.

Atomic Structure of the Amorphous Metallic Alloy Al83.5Ni9.5Si1.4La5.6

The atomic structure of the amorphous metallic alloy Al83.5Ni9.5Si1.4La5.6 is investigated based on the analysis of the experimental atomic radial distribution function (ARDF) in the fragmentary model. A comparative analysis of the most probable interatomic distances in the alloy and possible compounds based on it has demonstrated the presence of crystalline nuclei of the following phases: Al3La, Al3Ni, Al2.12La0.88, Al3Ni5, and Al. The largest ones (1–2 nm) are nuclei of the Al3Ni and Al compound, while the majority nuclei of all the other phases had sizes of about 7 A. Al and Al3Ni, as well as Al11La3 and Al5.56LaNi1.44 are observed in the crystallized alloy.

The influence of moisture content on methane adsorption in lignite: A molecular simulation study

As a high-efficiency clean energy and chemical raw material, coal-bed methane (CBM) has received wide attention in recent decades. At the present stage, new strategy to achieve a breakthrough in the CBM exploration and development is regarded as the primary goal for China’s lignite region. Usually, lignite contains a high moisture content in our country. Therefore, it is of great practical significance to understand the effect of moisture content on methane adsorption in lignite. Herein, molecular simulations of Monte Carlo and molecular dynamics methods are employed to elucidate this effect on methane adsorption with three moisture contents of 0%, 1.6% and 3.2%, and three temperatures of 298 K, 313 K and 373 K and the pressure range of 0–10 MPa are considered in the work. The lignite substrate model is composed of an aromatic skeleton amorphous structure with 88 atoms, including carbon, hydrogen, oxygen, nitrogen and sulfur. The adsorption amount, adsorption heat, and atomic radial distribution function along N, O, and S atoms are investigated in turns. The results show that the adsorption amount of methane decreases with the increase of moisture content in lignite, because the water molecules would be superior to methane to occupy the adsorption sites in lignite at the initial stage. The adsorption amount of methane decreases with the increase of temperature due to the molecules thermaldynamic property. The adsorption heat of methane decreases with the increase of moisture content in lignite. In addition, the N and S atoms exhibit the stronger interactions with methane than the O atom in lignite. This molecular simulation results are not only helpful to understand the adsorption mechanism of methane in lignite, but also provide theoretical prediction and scientific evidence for the exploration of CBM.

Using the Ab Initio Molecular Dynamics Method for Simulating the Peculiarities in the Temperature Dependence of Liquid Bismuth Properties

The specific features pertinent to the temperature dependence of the electronic and atomic properties of liquid bismuth that have been observed in experiments are investigated according to the ab initio molecular dynamics method using the SIESTA open software package. The density of electronic states, the radial distribution function of atoms, and the self-diffusion coefficient are calculated for the temperature range from the melting point equal to 545 K to 1500 K. The calculated data are in good agreement with the experimental data. It is found that the position of the first peak in the radial distribution function of atoms and the self-diffusion coefficient are characterized by a nonmonotonic dependence under the conditions of superheating by approximately 150 K above the melting temperature. In the authors’ opinion, this dependence feature is attributed to a change in the liquid short-range order structure.