Atom Cluster Model Research Articles

EPR parameters and spectrum of the solid-state L-α-alanine: cluster or periodic, static or dynamic

L-α-alanine (LαA) is a non-essential α-amino acid in the human body. Free radicals formations in LαA induced by solid-state radiation have been the subject of investigations by electron paramagnetic resonance (EPR) spectroscopy. The Density Functional Theory (DFT) formalism has been used to calculate the EPR parameters of the radiation-induced radicals in the solid-state LαA in this article. Here, the effects of various factors such as the kind of hydrogen bonding (short and long-range) and the temperature have considered to calculate the EPR parameters. An atomic static cluster model has been used to evaluate the short-range hydrogen bonding effects, and Molecular Dynamic (MD) cluster model has been used simultaneously to study the influence of the short-range hydrogen bonding and temperature. A static periodic technique has been used to consider hydrogen bonds (short and long-range) effect. Finally, the MD periodic calculations have been used simultaneously to study the influence of the hydrogen bonds and temperature. These MD periodic calculations are more consistent with experiments than static periodic calculations and clusters. The EPR spectrums of LαA powder and crystal have been simulated and compared with the experimental EPR spectrums. The results show that they are in good agreement with the experimental results.

Carbon Nanotube-on-Graphene Heterostructures

This paper presents a brief review of experimental and theoretical studies on a three-dimensional heterostructure consisting of vertical carbon nanotubes (CNTs) connected perpendicularly to a graphene layer. This structure can serve as a potential building block for an all-carbon network in energy storage devices and on-chip interconnects. The review highlights reported works on the fabrication and characterization of such a heterostructure, with focus on the effect of the CNT-graphene interface on electrical conduction. While a direct comparison between experiment and theory is not possible at this time, a brief survey of theoretical efforts based on atomic cluster models nonetheless reveals important knowledge about the electronic transport properties of this all-carbon heterostructure.

Electronic structure investigation of GdNi using x-ray absorption, magnetic circular dichroism, and hard x-ray photoemission spectroscopy

GdNi is a ferrimagnetic material with a Curie temperature Tc = 69 K which exhibits a large magnetocaloric effect, making it useful for magnetic refrigerator applications. We investigate the electronic structure of GdNi by carrying out x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD) at T = 25 K in the ferrimagnetic phase. We analyze the Gd M$_{4,5}$-edge ($3d$ - $4f$) and Ni L$_{2,3}$-edge ($2p$ - $3d$) spectra using atomic multiplet and cluster model calculations, respectively. The atomic multiplet calculation for Gd M$_{4,5}$-edge XAS indicates that Gd is trivalent in GdNi, consistent with localized $4f$ states. On the other hand, a model cluster calculation for Ni L$_{2,3}$-edge XAS shows that Ni is effectively divalent in GdNi and strongly hybridized with nearest neighbour Gd states, resulting in a $d$-electron count of 8.57. The Gd M$_{4,5}$-edge XMCD spectrum is consistent with a ground state configuration of S = 7/2 and L=0. The Ni L$_{2,3}$-edge XMCD results indicate that the antiferromagnetically aligned Ni moments exhibit a small but finite magnetic moment ( $m_{tot}$ $\sim$ 0.12 $\mu_B$ ) with the ratio $m_{o}/m_{s}$ $\sim$ 0.11. Valence band hard x-ray photoemission spectroscopy shows Ni $3d$ features at the Fermi level, confirming a partially filled $3d$ band, while the Gd $4f$ states are at high binding energies away from the Fermi level. The results indicate that the Ni $3d$ band is not fully occupied and contradicts the charge-transfer model for rare-earth based alloys. The obtained electronic parameters indicate that GdNi is a strongly correlated charge transfer metal with the Ni on-site Coulomb energy being much larger than the effective charge-transfer energy between the Ni $3d$ and Gd $4f$ states.

Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies.

Protein kinases are an important class of enzymes that play an essential role in virtually all major disease areas. In addition, they account for approximately 50% of the current targets pursued in drug discovery research. In this work, we explore the generation of structure-based quantum mechanical (QM) quantitative structure-activity relationship models (QSAR) as a means to facilitate structure-guided optimization of protein kinase inhibitors. We explore whether more accurate, interpretable QSAR models can be generated for a series of 76 N-phenylquinazolin-4-amine inhibitors of epidermal growth factor receptor (EGFR) kinase by comparing and contrasting them to other standard QSAR methodologies. The QM-based method involved molecular docking of inhibitors followed by their QM optimization within a ~ 300 atom cluster model of the EGFR active site at the M062X/6-31G(d,p) level. Pairwise computations of the interaction energies with each active site residue were performed. QSAR models were generated by splitting the datasets 75:25 into a training and test set followed by modelling using partial least squares (PLS). Additional QSAR models were generated using alignment dependent CoMFA and CoMSIA methods as well as alignment independent physicochemical, e-state indices and fingerprint descriptors. The structure-based QM-QSAR model displayed good performance on the training and test sets (r2 ~ 0.7) and was demonstrably more predictive than the QSAR models built using other methods. The descriptor coefficients from the QM-QSAR models allowed for a detailed rationalization of the active site SAR, which has implications for subsequent design iterations.

The dissection of atomic clusters with local structure in Ga-Sn alloy melts

The statistic short-range order (SRO) structure parameters of the Ga-Sn alloy melt are obtained with the X-ray diffractometer. The local atomic and electronic structures around the absorption atoms of Ga and Sn elements are detected by X-ray absorption fine structure spectrum. Centered on the absorption atom, the atom cluster structure was dissected and the atom cluster model was established. Unlike the ordinary liquid metal structure, the local atomic structure demonstrates that the liquid Ga-Sn alloy is not characterized by a dominant icosahedral short-range order. Specially, Sn atoms aggregate in Ga91.6Sn8.4 alloy, giving rise to a phase separation that exhibits compositional disorder.

Effect of Thermal Treatment on the Atomic Structure and Electrochemical Characteristics of Bimetallic PtCu Core–Shell Nanoparticles in PtCu/C Electrocatalysts

Supported PtCu/C electrocatalysts containing core–shell bimetallic PtCu nanoparticles were synthesized by sequential chemical reduction of Cu2+ and Pt(IV) in a carbon suspension, prepared on the basis of ethylene glycol–water solvent, and then treated at different temperatures in the range from 250 to 350 °C. The structural characterization of “as-prepared” PtCu nanoparticles and of those obtained after the thermal treatments was performed by transmission electron microscopy, X-ray diffraction, and Pt L3- and Cu K-edge extended X-ray absorption fine structure spectroscopy. The atomic cluster models of PtCu nanoparticles before and after the thermal treatment, reflecting the character of the components’ distribution, were generated. The electrochemical performance of the obtained PtCu/C electrocatalysts in oxygen reduction reaction was studied by cycling and linear voltammetry.

Face Centered Cubic Co81.8Si9.1B9.1 With High Magnetocrystalline Anisotropy

By using the atomic cluster model, face centered cubic (FCC) Co81.8Si9.1B9.1 compound is designed and synthesized as ductile single‐phase ribbons successfully. These ribbons show strong orientation along (111) and high magnetocrystalline anisotropy with a coercivity of 430 Oe and squareness of 0.82 at room temperature. The large spin–orbit coupling also contributes to the delocalization of Co 3d band and increased character of itinerant electrons which account for the structural stability and magnetic behaviors. The experimental electronic structure indicates that the magnetic performance can be improved further. This work not only develops a low‐cost Co‐based material for hard magnetic applications, but also extends the atomic cluster model into the design of new crystalline materials.

The influence of structure on the azo dye decolourization ability of ternary Fe-rich amorphous alloy

Fe66.3B16.6Y17.1 amorphous structures designed based on a competitive atomic cluster model shows excellent catalytic ability due to the competition between two different Fe-rich clusters Fe11Y3 and Fe8B2. In this work, it was demonstrated that the minor elements play a key role in the catalytic behaviors by changing the local structure around Fe. Fe66.3B16.6Y17.1 based on Fe11Y3 and Fe8B2 clusters achieves the decolourization efficiency up to 99.2% on the azo dye Orange G (OG). The replacement of Fe11Y3 cluster by Fe11Zr3 or Fe11Nb3 leads to significantly deteriorated efficiencies of 13.2% for Fe66.3B16.6Zr17.1 and 10.4% for Fe66.3B16.6Nb17.1 at identical testing conditions. The analysis on their local structures and the bonding states of Fe revealed that the weak interactions between atoms in these structures are related to the decolourization ability and catalytic effect directly. X-ray photoelectron spectra show that the jj coupling in the Fe 2p53d7 final state is a good predictor for the decolourization ability and catalytic effect of these Fe-rich amorphous structures.

Tracking the insulator-to-metal phase transition in VO2 with few-femtosecond extreme UV transient absorption spectroscopy

Coulomb correlations can manifest in exotic properties in solids, but how these properties can be accessed and ultimately manipulated in real time is not well understood. The insulator-to-metal phase transition in vanadium dioxide (VO2) is a canonical example of such correlations. Here, few-femtosecond extreme UV transient absorption spectroscopy (FXTAS) at the vanadium M2,3 edge is used to track the insulator-to-metal phase transition in VO2 This technique allows observation of the bulk material in real time, follows the photoexcitation process in both the insulating and metallic phases, probes the subsequent relaxation in the metallic phase, and measures the phase-transition dynamics in the insulating phase. An understanding of the VO2 absorption spectrum in the extreme UV is developed using atomic cluster model calculations, revealing V3+/d2 character of the vanadium center. We find that the insulator-to-metal phase transition occurs on a timescale of 26 ± 6 fs and leaves the system in a long-lived excited state of the metallic phase, driven by a change in orbital occupation. Potential interpretations based on electronic screening effects and lattice dynamics are discussed. A Mott-Hubbard-type mechanism is favored, as the observed timescales and d2 nature of the vanadium metal centers are inconsistent with a Peierls driving force. The findings provide a combined experimental and theoretical roadmap for using time-resolved extreme UV spectroscopy to investigate nonequilibrium dynamics in strongly correlated materials.

Five-fold local symmetries in metallic liquids and glasses

In this article, we review the experimental, theoretical and simulation studies on five-fold local symmetries in metallic liquids and glasses. In the early study on simple liquid structure, it has been realized that five-fold local symmetry plays a key role in irregular structures, supercooling and crystallization of simple liquids. In particular, icosahedral short-range order, representative of five-fold local symmetry, has attracted much attention. In addition, researches proposed a dense random packing model for simple liquid structure in 1959, and found a wide variety of polyhedra and absolute predominance of pentagonal faces in simple liquids, and also pointed out that pentagonal arrangements can only occur in very complex structures such as some of the alloy structures. Based on the Frank's hypothesis of icosahedral short-range order as blocking unit in a simple liquid, a lot of theoretical and experimental efforts have been made to confirm its existence in simple liquids, metallic liquids and glasses. So far, several theoretical methods have been developed for characterizing local atomic structures in simple liquids, such as bond-orientational order parameter, Honeycutt-Andersen index, and Voronoi tessellation. Although the local atomic symmetries in atomic structures in metallic liquids and glasses can be characterized by these methods and the geometries of the atomic structures in liquids and glasses have received much more attention, an atomic cluster model has been developed for establishing the structure-property relationship in metallic liquid and glass. Due to the diversity of the atomic clusters in both type and population of different metallic liquids and glasses, the atomic cluster model could not present a simple description of structure-property relationship. Based on the fundamental characteristics of metallic liquids and glasses, five-fold local symmetry, the structure-property relationship in metallic liquids and glasses, such as dynamic crossover, glass transition, liquid-liquid phase transition, and deformation can be well described in simple, quantitative and unified ways, and therefore a clear physical picture can be provided. All these studies indicate that five-fold local symmetry as a structural parameter is simple, general and effective.

Synthesis of an Fe Rich Amorphous Structure with a Catalytic Effect To Rapidly Decolorize Azo Dye at Room Temperature

In this article, an amorphous Fe rich amorphous structure designed based on a competitive atomic cluster model was synthesized and characterized successfully. The constituent zero-valent iron (ZVI) has excellent activity and efficiency for decolorization of Orange G (OG) solution at room temperature. The decolorization is characterized by UV-vis spectrum and pseudo-first-order kinetics. The X-ray Micro fluorescence spectrometer, Inductively Coupled Plasma Optical Emission Spectrometry, and Scanning Electron Microscope were employed to trace the ZVI. The consumption of ZVI destabilizes the local atomic arrangement and yields the phase separation of Fe at the surface and responds to the high activity and the catalysis for decolorization. This observation is in accordance with the change of k1 0.011 min(-1) to k2 0.047 min(-1), which is supported by the cyclic decolorization test. This work provides a new strategy to design multifunctional metal materials and indicates their brilliant future in practical applications.

Study on glass-forming ability and hydrogen storage properties of amorphous Mg60Ni30La10 − xCox (x = 0, 4) alloys

Mg60Ni30La10−xCox (x=0, 4) amorphous alloys were prepared by rapid solidification, using a melt-spinning technique. X-ray diffraction and differential scanning calorimetry analysis were employed to measure their microstructure, thermal stability and glass-forming ability, and hydrogen storage properties were studied by means of PCTPro2000. Based on differential scanning calorimetry results, their glass-forming ability and thermal stability were investigated by Kissinger method, Lasocka curves and atomic cluster model, respectively. The results indicate that glass-forming ability, thermal properties and hydrogen storage properties in the Mg-rich corner of Mg–Ni–La–Co system alloys were enhanced by Co substitution for La. It can be found that the smaller activation energy (ΔΕ) and frequency factor (υ0), the bigger value of B (glass transition point in Lasocka curves), and higher glass-forming ability of Mg–Ni–La–Co alloys would be followed. In addition, atomic structure parameter (λ), deduced from atomic cluster model is valuable in the design of Mg–Ni–La–Co system alloys with good glass-forming ability. With an increase of Co content from 0 to 4, the hydrogen desorption capacity within 4000s rises from 2.25 to 2.85wt.% at 573K.

Ni-Hf非晶合金及其团簇式成分解析

Ni-Hf binary alloys are merely known as a category of marginal glass formers. In this system, the assessment of glass-forming abilities has not been made and the optimal glass-forming composition remains unclear. In the present work, Ni-Hf glass-forming compositions are explored using the atomic cluster plus glue atom model. Ni-Hf phase diagram shows a deep eutectic point at Ni65Hf35 which is associated two intermetallic phases, namely, Ni7Hf3 and Ni10Hf7. A predominant atomic cluster was first derived from the crystalline structures of the deep eutectic related phases, and several glass-forming compositions were determined considering the one or three glue atoms constraint condition. Rapid quenching results show that Ni71.43Hf28.57 and Ni68.75Hf31.25 metallic glasses can be made fully glassy. The latter can be well described with the model composition formula as [Ni-Ni7Hf5]Ni3. Among the melt-spun alloys, the Ni68.75Hf31.25 glass which locates in between the deep eutectic point and the Ni7Hf3 phase in the phase diagram, exhibited a highest crystallization temperature of 877 K and a lowest liquidus of 1482 K, and hence is suggested to be the optimal Ni-Hf glass former by the high reduced glass temperature criterion.

In Situ X-ray Absorption Spectroscopic Study of the Adsorption of Ni2+on Fe3O4Nanoparticles in Supercritical Aqueous Fluids

In situ X-ray absorption spectroscopy (XAS) measurements were made on Fe3O4 nanoparticles in supercritical aqueous fluids to study their reactivity with Ni2+ ions and to investigate the structural properties of the reacted nanoparticles. XAS spectra were measured from Ni2+ added to an aqueous solution containing Fe3O4 nanoparticles at temperatures up to 500 °C. The XANES and the EXAFS data indicate that reactivity of Fe3O4 nanoparticles with Ni2+ ions is negligible to 300 °C but becomes significant in the 400–500 °C temperature range. Analysis of Ni K-edge extended X-ray absorption fine structure (EXAFS) using an atomic cluster model based on the spinel structure shows that Ni2+ adsorbs predominantly on octahedral sites of the surface of nanoparticles in aqueous fluids at 400–500 °C. The EXAFS structural results are consistent with diffusion of Ni into the near-surface region of the Fe3O4 nanoparticles in the aqueous fluid at 400 and 500 °C.

High temperature oxidation mechanism of Nb-Al alloys

The atomic cluster model of the interface between aluminum oxide film and the niobium matrix has been set up with our self-programmed software. By using recursion method, the atom embedding energy, the atomic binding energy and other electronic parameters have been calculated. The high temperature oxidation mechanism of niobium alloys is analysis from the electron levels. Our study shows that， aluminum segregates on the alloy surface through the grain boundary diffusion and combines with oxygen to form dense Al2O3 oxide film which blocks oxygen to diffuse into the niobium matrix. Grain boundary and rare earth elements can increase binding energy between the oxide film and the matrix and increase the bonding strength of the interface to enhance the adhesion between the oxide film and the niobium matrix. Thus, by adding rare earth elements in the alloy or refining the alloy grains, the performance of high temperature oxidation resistance of niobium alloys can be improved.

Electronic theory study of interface characteristic of magnesium/carbon nanotube with nickel

The atomic cluster models of Mg/CNT（carbon nanotube or nickel carbon nanotube） interface have been built in magnesium composite reinforced by （nickel） carbon nanotube. The interface electronic structures have been calculated by recursion method. The calculated results show that nickel enhances the stability of nanotube/matrix interface, improves the interface bond strength, since nickel makes the structure energy and atomic binding energy of nanotube/matrix interface lowered. The positive interaction energy of magnesium atoms in nickel film of interface causes the magnesium atoms in nickel film to repel each other and can not form magnesium atomic cluster, so they prefer to form ordering phase which consolidate the interface. The carbon and magnesium atoms have higher energy of position, which causes interface instability and flimsiness at carbon nanotube without nickel plating and magnesium interface. But when the carbon nanotubes have been plated by nickel, the energy of position of carbon and magnesium atoms are made lower and the interface gets more stable and tough.

The electronic theory of the mechanism of the role of Sc in Al-Zn-Mg-Cu ultra high strength aluminium alloys

The atomic cluster models of α-Al, Al3Sc,η phase in Al-Zn-Mg-Cu ultra high strength aluminum alloys have been constructed by cell translation and the atomic cluster models of the interfaces α-Al /liquid Al and α-Al /Al3Sc have been set up by self-programmed software. The electronic structure parameters such as the density of states, the bonding energy of atom, the Fermi energy of the microscopic structure in alloys, the interaction energy between Sc and vacancy, have been calculated by recursion method. The physical nature of grain refinement and corrosion behavior of Al-Zn-Mg-Cu alloys has been explained according to the calculated electronic structure parameter. The results show that the energy given off by Al3Sc precipitating from liquid Al is less than that by α-Al and Al3Sc can precipitate from liquid Al prior to α-Al. Because of the lower interface energy of α-Al /Al3Sc compared with α-Al /liquid Al, the Al3Sc phase may offer the condition for the nucleation and growth of α-Al, which increases the nucleation rate of α-Al and refines the grain. The calculated results also indicate that Sc can attract the vacancy, decreasing the diffusion ability of vacancy and solute atoms, which makes the precipitate free zone along grain boundaries become narrower, and decreases the potential difference between grain and grain boundary, leading to the improvement of the corrosion resistance.

The ignition-proof effect of Ca and Be in Mg alloys

The atomic cluster models of α-Mg，liquid Mg and the interface between liquid/solid have been founded. The environment-sensitive embedding energy of Ca and Be in α-Mg，liquid Mg，liquid/solid interface has been calculated by recursion method. The atomic affinity energy between Mg，Ca，Be with O has been defined and calculated. The calculated results show that the solid solubility of Ca and Be is very small in α-Mg，because of their higher environment-sensitive embedding energy leads to instability in α-Mg crystal. The Ca and Be diffuse in to the liquid Mg, which has lower environment-sensitive embedding energy than the solid，and congregate on the surface of liquid Mg as the alloys solidify. Because the atomic affinity energy of Ca-O and Be-O is lower than Mg-O，The Ca and Be aggregating on the surface of liquid Mg will priorly combined with O，forming compact oxides of Ca，Be and alloys of elements，which prevent Mg alloys from burning.

Computational Nanomechanics of Materials

We present a review of computational methods and their applications for nanoscale mechanics of materials. Brief introductory overviews of first-principles calculations and molecular dynamics simulations are first provided, followed by various applications such as fracture mechanics and plasticity at the nanoscale. Next, recent advancement of multiscale materials modeling is reviewed, spanning from electronic scale to continuum scale. Among many multiscale methods, two newly proposed methods, the multiscale continuum theory and the virtual atom cluster model, are introduced with more details.

Energetics of mixing in Bi–Pb and Sb–Sn liquid alloys

We have analysed the energetics of mixing of Bi–Pb and Sb–Sn liquid alloys at respective temperatures 700 and 905 K through the study of their thermodynamic functions and surface properties using four atom cluster model and quasichemical approximation (QCA) approach, respectively. Our study reveals that the two systems exhibit chemical order or heterocoordination, with the degree of chemical order in Sb–Sn being more than that of Bi–Pb. We also observed that while Bi-atoms segregate to the surface of Bi–Pb alloy, Sb-atoms segregate to the surface of Sb–Sn alloys. The degree of segregation of Sb-atoms being more than that of Bi-atoms.