Atomic Radial Distribution Research Articles

Molecular Dynamics Simulation of Phosphorus Trichloride (PCl3) and Phosphorus Triiodide (PI3) Liquids by Using the Force-fields Derived from a Quantum Chemical Approach

In this study, phosphorus trichloride (PCl3) and phosphorus triiodide (PI3) as the condensed inorganic materials were investigated based on the molecular dynamics simulation. To this purpose, molecular dynamics simulations were performed by applying force field parameters derived from the quantum chemistry approach. The potential energy data were computed at the B3LYP/6-31+G (d) and B3LYP/dgdzvpd levels of theory for different configurations of PCl3 and PI3, respectively. To determine force field parameters, a four-site all-atom force field model was used to correlate the potential energy data. Therefore, the force field parameters were applied to perform the molecular dynamics simulations. The MD simulations were performed to obtain the atomic number density, enthalpy, heat capacity, and radial distribution function in the NPT and NVT ensembles for PCl3 and PI3 dimers. There is a good consistency between the experimental data and simulation results over a wide range of experimental conditions.

Analysis of Interface Fusion Effect between Old and New Asphalt under Plant Mixing and Cold Recycling Mode Based on Molecular Dynamics Simulation.

Road construction consumes a lot of resources and produces a lot of waste and other pollutants. With the emergence of a resource and energy crisis, how to make efficient use of rap has become the research focus of scientific researchers. The interface fusion effect of old and new asphalt in plant mixing and cooling recycling mode is analyzed in order to improve the utilization rate of old asphalt in reclaimed asphalt pavement. In this paper, Materials Studio software was used to establish a bitumen model using the method of four components of bitumen, and then the rationality of the model was verified by density, solubility number and atomic radial distribution function, and the diffusion coefficient obtained from the mean square displacement (MSD) was taken as its evaluation index. The results showed that the diffusion model tends to be stable after 20 ps, and the degree of diffusion increases with the increase in temperature. The degree of diffusion of new asphalt to old asphalt and the degree of diffusion of old asphalt to new asphalt are basically very similar; however, there are some differences at different temperatures. Only a small part of the surface contact between old and new asphalt has been fused, which accords with the partial fusion theory. Compared with Panjin 90# asphalt, the diffusion coefficient of Zhonghaiyou asphalt increases faster with the increase in temperature. The diffusion coefficient increases by 64.3% with the increase of the content of rejuvenators after adding different rejuvenators into the new asphalt. Clarifying the interface fusion effect will be helpful to guide the optimization design of cold-mixing recycled asphalt mixture more scientifically and reasonably. Future research should focus on increasing the fusion effect of old and new asphalt, and explore its influence on the conventional road performance of asphalt mixture.

Mechanism for anisotropic diffusion of liquid-like Cu atoms in hexagonal β−Cu2S

${\mathrm{Cu}}_{2}\mathrm{S}$ in its high-temperature phases is a promising candidate for thermoelectric materials with the combination of a solid S lattice and liquidlike Cu atoms in the context of the so-called phonon-liquid electron-crystal (PLEC) mechanism. The atomic dynamics associated with the high Cu mobility is a critical component in our understanding of the low thermal conductivity in these materials. Among various possible PLEC compounds that have been studied experimentally, hexagonal $\ensuremath{\beta}\ensuremath{-}{\mathrm{Cu}}_{2}\mathrm{S}$ is a unique case that exhibits anisotropic diffusion channels for Cu atoms in the presence of crystalline S layers. To unveil the diffusion mechanism for such liquidlike Cu atoms, we present first-principles molecular dynamics simulations over 50 ps for hexagonal ${\mathrm{Cu}}_{2}\mathrm{S}$ at 450 K. Quantitative analysis of the atomic radial distributions, mean-square displacements, velocity autocorrelations, and atomic trajectories is reported and confirms the liquid-solid hybrid features. Our simulations reveal the preference of threefold triangular sites by Cu atoms in the S lattice. The triangular sites in the interlayer region do not bind Cu atoms strongly, allowing them to diffuse in the horizontal direction between S layers like a mobile liquid with a calculated diffusion coefficient $\ensuremath{\sim}5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}6}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{2}$/s. The corresponding atomic trajectories have a wide spread and cannot be described by the Chudley-Elliott jump diffusion model. In contrast, Cu atoms are more strongly confined at the triangular sites within the S planes, and Cu diffusion takes place only when the atom hops out of the S layer and enters the interlayer region. This yields a 50% smaller diffusion coefficient in the vertical direction. The anisotropic diffusion channels for liquidlike Cu atoms in hexagonal $\ensuremath{\beta}\ensuremath{-}{\mathrm{Cu}}_{2}\mathrm{S}$ may provide an additional degree of freedom in designing promising systems for future energy applications.

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.

Improvement of Electrochemical Property of VS<sub>4</sub> Electrode Material by Amorphization via Mechanical Milling Process

Amorphous VS4 (a-VS4) electrode material was synthesized by mechanical milling of crystalline VS4 (c-VS4). The columbic efficiency of the a-VS4 cell was significantly improved (ca. 86 %) at the first cycle as compared with the c-VS4 cell (ca. 77 %), resulting in the improved capacity retention for prolonged cycling. Pair distribution function (PDF) analysis obtained from X-ray total scattering data, revealed that the radial atomic distribution of a-VS4 at initial stage was similar to that of the low-crystalline VS4 appeared after the first cycle of c-VS4. This is suggestive that the amorphization via mechanical milling process gave rise to the preparation of “first cycled VS4” which would contribute to the improved columbic efficiency at the first cycle and the resulting improved capacity retention for prolonged cycling. The structure of a-VS4 could be visualized by first-principles molecular dynamic calculation of “first-cycled VS4”.

Amorphous Alloys Atomic Structure Investigation by Means of Electron Microscopy and Diffraction

In the paper, the atomic structure of amorphous and nanocrystalline alloys of the electrolytically obtained CoP, NiP, CoNiP, CoW, and CoNiW systems has been studied. The structure was investigated by electron microscopy and diffraction using a Libra 200 HR FE transmission electron microscope at an accelerating voltage of 200 kV within a temperature range of 50-35 °C. The obtained radial atom distribution function and the coordination sphere radii are in good agreement with the data for the cobalt structure in the cubic and hexagonal modifications. The high coordination numbers of the third and fourth coordination spheres allow suggesting a predominantly cubic structure of the local atom environment in CoP samples but somewhat lower, which is explained by the presence of free volume and phosphorus atoms distorting the local structure. When heating, the near atomic order also corresponds to the cubic phase of cobalt, and the ordering occurs in the second, third, and fourth coordination spheres. The data obtained for CoNiP alloys indicate that by configuration, the local atomic environment is closer to the hexagonal structure of nickel. In general, the structure of the CoP-CoNiP system alloy films obtained by electrolytic deposition is already in one of the local minima of the total system energy, which is confirmed by the near atomic order similar to the cubic phase of cobalt or hexagonal phase of nickel. This determines the good stability of the structure and properties during thermal exposure.

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.

Specific Features of the Structure of Various Coal Ranks at the Nano Level

Structural factors and functions of radial distribution of atoms of different coal ranks have been calculated by X-ray diffraction analysis. This made it possible to establish that the main structural component is the clusters with graphite-like packing of atoms. The predominant size of these clusters (calculated from the peaks of small-angle X-ray scattering at 5° in CoKα-radiation) for coals with a carbon content of 83--95 % is within 2--3 nm. Fossil coal is an amorphous carbonaceous substance consisting of polymorphic modifications in the sp2- and sp3-states. According to the results obtained using Raman scattering spectroscopy, the physical properties of amorphous natural coals are strongly dependent on the ratio of sp2- and sp3-hybridization of atomic orbitals. Moreover, studies have shown that the carbon atoms of the coal matrix in the sp2-state are represented by both aromatic and aliphatic conjugated chain fragments. It was found that the degree of ordering in rank LF coals is higher than in coals of a higher stage of metamorphism. This is possible if the hydrocarbon matrix in rank LF coals can be represented as a polymer consisting of conjugated chains with periodicity. With an increase in the stage of coal metamorphism, starting with coal rank G, the transformation of the coal structure occurs with a violation of the periodicity of the conjugated fragments of the polymer matrix connecting graphite-like clusters, a decrease in their length, and an increase in randomness in their arrangement

Structural relationship between crystalline and amorphous states in Cu–(Zr, Ti) binary systems

This paper focuses on the revelation of structural relationship of the ordered and disordered states in Cu–(Zr, Ti) binary systems. The atomic radial distributions in real space and the electron scattering behavior in reciprocal space between crystalline and amorphous phases are compared. The spherical-periodic order, characteristic of disordered structures, is clearly present in the crystalline phases, suggesting the structural homology of crystalline and the corresponding amorphous states. Furthermore, the diameters of Brillouin- or Jones-zones at the Fermi level in the crystalline and amorphous states are also similar and they fall close to those of the calculated Fermi spheres, verifying the resonance between the static atomic structure and the electron wave.

Structural heritage of metallic glasses and relevant crystals understood via the principal cluster

ABSTRACT Structural heritage between bulk metallic glasses (BMGs) and their relevant crystals has already been acknowledged. But how this kind of heritage is represented is still unclear. In the present paper, firstly, two important characters are considered to determine the principal cluster of crystal, i.e. the atomic-packing efficiency which is evaluated by atomic density radial distribution method and cluster isolation degree which is obtained by the cluster-size reduction rate because of overlapping of clusters in crystal. Then according to these two criteria principal clusters of BMGs Cu-Zr, (Pt,Pd)-Zr and Pd-Si systems are analysed. And the results show that the principal cluster dominates the short-range-order structure of its parent phase as well as the relevant BMG. It is exactly the principal cluster that enters the cluster-plus-glue-atoms units to formulate BMG as [principal cluster](glue atom)1,3. It proves that the structural heritage between glassy state and relevant crystal is actually reflected by cluster formula which contains the principal cluster. Furthermore, via study structural similarity of metallic glass and relevant crystal, elaborated steps towards quantitatively composition design for BMGs are established.

Augmenting machine learning of energy landscapes with local structural information

We present a machine learning approach for accurately predicting formation energies of binary compounds in the context of crystal structure predictions. The success of any machine learning model depends significantly on the choice of representation used to encode the relevant physical information into machine-learnable data. We test different representation schemes based on partial radial and angular distribution functions (RDF+ADF) on Al–Ni and Cd–Te structures generated using our genetic algorithm for structure prediction. We observe a remarkable improvement in predictive accuracy upon transitioning from global to atom-centered representations, resulting in a threefold decrease in prediction errors. We show that a support vector regression model using a combination of atomic radial and angular distribution functions performs best at the formation energy prediction task, providing small root mean squared errors of 3.9 meV/atom and 10.9 meV/atom for Al–Ni and Cd–Te, respectively. We test the performance of our models against common traditional descriptors and find that RDF- and ADF-based representations significantly outperform many of those in the prediction of formation energies. The high accuracy of predictions makes our machine learning models great candidates for the exploration of energy landscapes.

Liquidlike Cu atom diffusion in weakly ionic compounds Cu2S and Cu2Se

Copper sulphide (${\mathrm{Cu}}_{2}\mathrm{S}$) and copper selenide (${\mathrm{Cu}}_{2}\mathrm{Se}$) are known to exist in solid (S/Se)-liquid (Cu) hybrid phases which exhibit favorable thermoelectrics properties. The diffusion characteristics and its mechanism in these systems are therefore of significant interest. In this paper, we analyze these properties through examining the atomic radial distributions, mean-square displacements, and velocity autocorrelations obtained from ab initio molecular dynamics simulations. Exceptionally high Cu diffusion coefficients with values over ${10}^{\ensuremath{-}5}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{2}$/s are obtained, indicating the unexpected liquidlike behavior of Cu in these weakly ionic compounds. The diffusion mechanism obtained through analysis of the Cu atomic trajectories is found to be at variance with the previously proposed Chudley-Elliott jump diffusion model. In addition, tunability of these diffusion coefficients via small changes in the stoichiometry, namely, Cu deficiencies, is demonstrated. The higher number of low-frequency acoustic phonon modes associated with Se sublattices, compared to those with S sublattices, correlates well with the experimentally observed thermal conductivity difference between ${\mathrm{Cu}}_{2}\mathrm{S}$ and ${\mathrm{Cu}}_{2}\mathrm{Se}$.

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.

Short-Range Ordering Structure of the Cu2In Intermetallic Compound in the Precrystallization Temperature Range

The structure of Cu2In melts is investigated by the X-ray diffraction method within a temperature range close to the temperature of onset of crystallization. We analyze the structural factors and functions of the radial distribution of atoms computed by the method of Fourier transforms. The results of structural investigations are compared with the literature data on the enthalpy of mixing and thermodynamic activity. It is shown that the short-range ordering structure is microinhomogeneous and has a heterocoordinated distribution of atoms.

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.

The Prospects of Applying the Mechanical Activation Method to the Manufacturing of Powder Steel Blades

Pure carbon phases formed in samples of soot-alloyed powder steel produced by mechanical activation were investigated using transmission electron microscopy and Auger-electron energy loss fine spectroscopy. A theoretical approach was proposed that considers the escape depth of the signal under analysis when modelling the functions of the radial distribution of atoms in the crystal lattice. The approach proposed allowed for the identification of the nano-crystalline pure carbon phase as a structure similar to natural diamond. The presence of nanosized diamond particles will allow for noticeable enhancement of the consumer qualities of powder steel used to manufacture blades.

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.

Dynamic behavior in lithium ion/graphene/propylene carbonate electrolyte systems through molecular dynamics simulation

The dynamic behavior of lithium ions in Li+/graphene/propylene carbonate (PC) electrolyte system was investigated by molecular dynamics (MD) simulation. The simulated system is composed of Li+, PC and graphene sheets (Gr). The radial distribution function and distribution of carboxyl oxygen atoms around Li+ indicate Li+ and PC can form coordination complexes, and the coordination number can be up to 5, which accords well with the experimental and density functional theory calculation results from literatures. The interaction energies and conductivity were obtained from the trajectories of MD simulation. The graphites were exfoliated into few-layer graphene and the dispersed graphene flakes system can keep stable because of the strong interaction between PC and Gr. The conductivity of the Li+/PC system increases with addition of Gr, which agrees well with the experimental observations. The results obtained in the current work are useful for the future design of PC-based electrolyte systems.

Conformations of poly(propylene imine) dendrimers in an ionic liquid at different pH.

The conformational behavior of poly(propylene imine) (PPI) dendrimers at three different solution pH is studied in an ionic liquid (IL) solvent, 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), through molecular dynamics (MD) simulations. The size, shape, density distribution, structure factor, and the scattering intensity are evaluated to probe the conformational transition of dendrimers as a function of pH. The results of the radial atomic and terminal amine group density distribution at low pH indicate a shift in the density towards the periphery of the dendrimers due to the electrostatic repulsion between the charged tertiary amine groups within the dendrimers. The [BMIM] cations are not encapsulated within dendrimers and predominantly reside near the periphery. The extensive back-folding of the outer branches due to the electrostatic repulsion between the solvent cations and the peripheral charged amine groups at neutral and low pH results in a dense compact structure in [BMIM]Cl as compared to that in water, as evident from the results of the structure factor and scattering intensity. The structural analysis in terms of the fractal dimension reveals that the lower generation dendrimers exhibit conformational transition as a function of pH, while the higher generations exhibit a highly compact structure at all solution pH. However, PPI dendrimers at low pH exhibit more free volume as compared to that at high pH, which may be utilized to accommodate specific guest molecules.