Pair Of Interacting Atoms Research Articles

Electronic Structure Simulations of the Platinum/Support/Ionomer Interface in Proton Exchange Membrane Fuel Cells

ABSTRACTIn this work, we present electronic structure calculations to quantify and rationalize the interactions between catalyst, support, ionomer, and active molecular species in proton exchange membrane fuel cells. Quantifying interaction energies and their scaling with size allows us to rationalize and compare the fundamental driving forces behind structure formation and material properties. Our basic approach involves simplifying the most important interactions between different components using smaller model systems, such as limited‐size platinum nanoparticles, polyaromatic hydrocarbons (graphene flakes), and fragments of various functional units of the Nafion ionomer while applying unbiased first‐principles (density functional theory) simulation methods. To guide this quantification, we propose an analysis based on the linear dependence of interaction energy on the number of interacting atom pairs in the interface. This enables us to compare and categorize interactions between catalyst, ionomer, and support with interactions like catalyst–reactant and catalyst–catalyst poison.

Hirshfeld Surface Analysis and Density Functional Theory Calculations of 2-Benzyloxy-1,2,4-triazolo[1,5-a] quinazolin-5(4H)-one: A Comprehensive Study on Crystal Structure, Intermolecular Interactions, and Electronic Properties

This study employs a comprehensive computational analysis of the 2-benzyloxy-1,2,4-triazolo[1,5-a] quinazolin-5(4H)-one (ID code: CCDC 834498) to explore its intermolecular interactions, surface characteristics, and crystal structure. Utilizing the Hirshfeld surface technique and Crystal Explorer 17.5, the study maps the Hirshfeld surfaces for a detailed understanding of atom pair close contacts and interaction types. The study also investigates the compound’s electronic and optical characteristics using Frontier Molecular Orbital (FMO) analysis and Global Reactivity Parameters (GRPs). The compound is identified as electron-rich with strong electron-donating and accepting potential, indicating its reactivity and stability. Its band gap suggests Nonlinear Optical (NLO) attributes. The Molecular Electrostatic Potential (MEP) map reveals charge distribution across the compound’s surface. The computational methods’ reliability is validated by the low Mean Absolute Error (MAE) and Mean Squared Error (MSE) in the comparison of experimental and theoretical bond lengths and angles.

Superradiance decoherence caused by long-range Rydberg-atom pair interactions

This work reports on the real-time detection of internal-state dynamics of cold Rb$^{87}$ atoms being excited to the $30D_{5/2}$ Rydberg state via two-photon excitation. A mesoscopic cloud of atoms is overlapped with the mode volume of a confocal optical cavity and optically pumped by two laser beams transverse to the cavity axis. The excitation to Rydberg states changes the collective atom-cavity coupling, which is detected by monitoring the light transmitted through the cavity while being weakly driven. In addition to the damped coherent excitation dynamics and the decay back to the ground state, the data show a superradiant enhancement of the black-body radiation induced transitions from the $30D_{5/2}$ state to neighboring Rydberg states. Furthermore, they show a density dependent mitigation of the superradiant decay which is attributed to long range dipole-dipole interactions between atoms in the involved Rydberg states. These results contribute to solving a recent controversy on the interplay between BBR-induced superradiance and Rydberg atom interactions.

Oxide Formation in a Melt Spun Alloy in the Zr-Ni-Cu System

The microstructure of a melt-spun Zr28Ni44Cu28 (at. %) alloy was characterized in order to determine the structures and compositions of the crystalline phases that compete with glass formation during rapid solidification. Two crystalline phases were identified, namely, a face centered cubic (FCC) zirconium oxide phase and a primitive cubic version of the big-cube oxide phase, using a combination of scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, and transmission electron microscopy techniques. Our results indicate that the Zr-O atomic pair interaction is preferential compared to the other atomic pair possibilities, supporting the formation of Zr-based oxides over the equilibrium phases in the ternary Zr-Ni-Cu system. Further, the results provide insight into the mechanisms of oxygen-induced crystallization in Zr-based BMGs and the corresponding decrease in glass forming ability (GFA) with increasing oxygen concentrations.

Half-metallic ferromagnetism induced by TM-TM atom pair co-doping in 2D hexagonal boron nitride monolayer: A first principle study

The wide band gap of graphitic 2D hexagonal boron nitride nanosheets (h-BNNS) has recently been extensively studied to engineer for next generation electronic devices. Here, we report a systematic theoretical investigation of the structural, electronics and magnetic properties for the vacancy defected and transition metal (TM) pair co-doped h-BNNSs. All of our calculations have been performed based on spin polarized first-principles calculation using density functional theory. We have investigated the structural stability of h-BNNSs monolayer due to TM-TM pair co-doping and describe their interesting magneto-electronic properties as evident from the spin polarized projected density of state. Although, pristine h-BNNS is a nonmagnetic insulator, our investigation shows that the addition of transition metal pair induced interesting magnetic ground state. The interaction of selective TM atom pairs transferred the h-BNNS from a spin non-polarized to spin polarized half-metal and semiconductor demonstrating an effective strategy to tune magneto-electronic properties of h-BNNS.

All-atom molecular dynamics study of impact fracture of glassy polymers. II: Microscopic origins of stresses in elasticity, yielding, and strain hardening

Polycarbonate (PC) is a typical ductile polymer which first undergoes shear yielding followed by plastic deformation when subjected to stress. Although numerous theoretical models have been proposed to explain the yielding, its microscopic origin remains unclear. Therefore, we analyzed herein our previous all-atomistic molecular dynamic (MD) trajectories to investigate the microscopic origins of the yielding stress as well as the entire fracture process via rigorous stress decomposition, which considered the contributions of the system alignment and the bond, angle, and van der Waals (vdW) interactions. The affine deformation in the elastic region occurs due to bond stretching, angle bending, and separation of the vdW interacting atom pairs. Plastic deformation, which initiates upon yielding, reduces the growth rate of the bond, angle stresses and vdW stresses via the interchain collisions; meanwhile, the system alignment also contributes to an increased stress. Finally, the main chain bonds and angles are further stretched after strain softening, thereby causing strain hardening.

Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations

We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time step specific to each atom-atom pair (two-body) interactions. We start by introducing the formalism of the new velocity jump molecular dynamics, ergodic with respect to the canonical measure. We then introduce the new BOUNCE integrator that allows for long-range forces to be evaluated at random and optimal time steps, leading to strong savings in direct space. The accuracy and computational performances of a first BOUNCE implementation dedicated to classical (non-polarizable) force fields are tested in the cases of pure direct-space droplet-like simulations and of periodic boundary conditions (PBC) simulations using Smooth Particle Mesh Ewald method. An analysis of the capability of BOUNCE to reproduce several condensed-phase properties is provided. Since electrostatics and van der Waals two-body contributions are evaluated much less often than with standard integrators using a 1 fs time step, up to a 400% direct-space acceleration is observed. Applying the reversible reference system propagator algorithms [RESPA(1)] to reciprocal-space (many-body) interactions allows BOUNCE-RESPA(1) to maintain large speedups in PBC while maintaining precision. Overall, we show that replacing the BAOAB standard Langevin integrator by the BOUNCE adaptive framework preserves a similar accuracy and leads to significant computational savings.

Formation of argon cluster with proton seeding

ABSTRACT We employ force-field molecular dynamics simulations to investigate the kinetics of nucleation to new liquid or solid phases in a dense gas of particles, seeded with ions. We use precise atomic pair interactions, with physically correct long-range behaviour, between argon atoms and protons. Time dependence of molecular cluster formation is analysed at different proton concentration, temperature and argon gas density. The modified phase transitions with proton seeding of the argon gas are identified and analysed. The seeding of the gas enhances the formation of nano-size atomic clusters and their aggregation. The strong attraction between protons and bath gas atoms stabilises large nano-clusters and the critical temperature for evaporation. An analytical model is proposed to describe the stability of argon-proton droplets and is compared with the molecular dynamics simulations.

Atomic and Effective Pair Interactions in FeC Alloy with Point Defects: A Cluster Expansion Study

Atomic and Effective Pair Interactions in FeC Alloy with Point Defects: A Cluster Expansion Study

Density functional theory analysis of the effect of structural configurations on the stability of GaAsBi compounds

The aggregation of Bi atoms exhibits significant influence on the stability and electronic properties of GaAsBi compounds. Here, density functional theory calculations are used to probe stabilities of different configurations of Bi atoms substituted for As at concentrations below 4% of available As sites. The configurations examined include ensembles of four or eight Bi atoms with large Bi-Bi distances (dispersed configuration) or Bi atoms occupying contiguous As sites (aggregated configurations) in periodic supercells of different sizes. The stabilities of GaAsBi compounds decrease with increasing Bi concentration. This decrease in stability is more significant for dispersed than aggregated configurations, which leads to increased favorability for the aggregation of Bi atoms at higher concentration. Among the aggregated arrangements, the linear and planar ones are much more stable than the three-dimensional arrangements at all concentrations. The stabilities also depend significantly on ensemble sizes of Bi atoms, with enhanced stability for linear [1 0 1] and planar (1 1 1) configurations in eight atom ensembles than in four atom ensembles of similar concentration. These results demonstrate distinct effects of concentration and ensemble size on the preferred configuration and suggest that accurate large-scale simulations of doped GaAs compounds require models that incorporate not only atom-pair interactions but also long-range interactions among aggregates.

Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations.

Predicting and controlling the properties of amphiphile aggregate mixtures require understanding the arrangements and dynamics of the constituent molecules. To explore these topics, we study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms to describe the dynamics. NMR relaxation rates, which depend on relative motions of interacting atom pairs, are influenced by wide distributions of dynamic time scales. We find that relative motions of neighboring atom pairs are rapid and liquidlike but are subject to structural constraints imposed by micelle morphology. Relative motions of distant atom pairs are slower than nearby atom pairs because changes in distances and angles are smaller when the moving atoms are further apart. Large numbers of atom pairs undergoing these slow relative motions contribute to predominantly negative cross-relaxation rates. For spherical micelles, but not for cylindrical micelles, cross-relaxation rates are positive only for surfactant tail atoms connected to the hydrophilic headgroup. This effect is related to the lower packing density of these atoms at the hydrophilic-hydrophobic boundary in spherical vs cylindrical arrangements, with correspondingly rapid and less constrained motion of atoms at the boundary.

Dynamic and structural heterogeneity in undercooled miscible and immiscible metallic liquid

Molecular dynamics computer simulations are performed to study the structure and dynamic relaxation of the metallic alloys Cu50Ag50 and Cu50Zr50 with and without miscibility gap, respectively. The interactions between the particles are modeled by an effective potential of the modified embedded atom method (MEAM). Cu50Zr50 undercooled liquid shows negative mixing enthalpy; the stronger interaction of heterogeneous atom pairs than that of homogeneous atom pairs, the longer the α-relaxation time and the lower the diffusion coefficient than that of the Cu50Ag50 liquid. Dynamic relaxation is related to the structural heterogeneity: the amount of five-fold symmetry (icosahedron-like) clusters is predominant in Cu50Zr50 melts, which hinders the movement of atoms and increases the dynamic relaxation time. The amount of non-five-fold symmetry (crystal-like) clusters is more pronounced in Cu50Ag50 melts, which leads to shorter dynamic relaxation time and enhanced crystallization of the Cu50Ag50 melt. The quantitative relationship between the five-fold symmetry parameter W and the diffusion coefficient D, as well as the α-relaxation time τα, is obtained in the two distinct undercooled liquids. The present work provides an understanding of the atomic-scale structure and the dynamic properties in the miscible and immiscible liquid mixtures.

Comparison of the structural and physical properties of nitrocellulose plasticized by N-butyl-N-(2-nitroxy-ethyl) nitramine and nitroglycerin: Computational simulation and experimental studies.

We performed experimental studies on the effects of N-butyl-N-(2-nitroxy-ethyl) nitramine (Bu-NENA) and nitroglycerin (NG) on the plasticization of nitrocellulose (NC). The tensile strength and elongation at break of NC/Bu-NENA measured at -40 °C show increments of about 23% and 33% respectively, compared with those of NC/NG, suggesting that Bu-NENA has a higher plasticizing efficiency than NG. Scanning electron microscope (SEM) observation reveals that NC shows better miscibility with Bu-NENA than NG, which was further evidenced by the mesoscopic morphologies derived from mesodynamics simulations. Furthermore, molecular dynamic simulations were conducted to explore the mechanical strengthening mechanism of plasticizers. The simulation results such as free volume (Vfree), binding energy (Ebind) and radial distribution function (RDF) were obtained. NC/Bu-NENA shows a 28% improvement in Vfree compared to NC/NG, suggesting that Bu-NENA molecules demonstrate higher mobility in NC matrix. The larger Ebind of NC/Bu-NENA than NC/NG indicates the stronger interaction between NC and Bu-NENA. Furthermore, g(r) values correlated to the atom pair interaction determined from RDF curves reveal that NC/Bu-NENA shows higher intensities of both hydrogen bond and van der waal force than those of NC/NG blend. These computational and experimental studies reveal great potential in design and fabricating low vulnerable insensitive propellants.

DFT and TD-DFT study of isomeric 5-(pyridyl)-1,3,4-oxadiazol-2-thiones and 2-methylthio-5-(pyridyl)-1,3,4-oxadiazoles

Internal rotations of pyridine fragment around single bond of isomeric 5-(2′, 3′ and 4′-pyridyl)-1,3,4-oxadiazol-2-thiones and 2-methylthio-5-(2′, 3′ and 4′-pyridyl)-1,3,4-oxadiazoles have been performed by DFT (B3LYP) and MP2 methods with RHF/6-31G(d,p) basis set. It was found that the MP2 barrier height lies a few below than DFT barrier heights for all studied compounds. In the molecule of 2-methylthio-5-(2′-pyridyl)-1,3,4-oxadiazole an anomeric effect detected due to a lone pair-lone pair interaction of pyridine and N4 oxadiazole nitrogen atoms. But it not found in the molecule of 5-(2′-pyridyl)-1,3,4-oxadiazol-2-thione. Furthermore, theoretical UV spectra of the compounds were studied using TD-DFT/6-31G(d,p) method. Theoretical transitions located about 10nm in the long-wavelength region relatively to the experimental bands field. Whereas, the theoretical transitions of 2-methylthio-5-(2′, 3′ and 4′-pyridyl)-1,3,4-oxadiazoles have very good agreement with the position of experimental bands. The longest wavelength band in both of experimental and theoretical spectra of the investigated compounds have been observed for 5-(4′-pyridyl)-1,3,4-oxadiazole-2-thione and 2-methylthio-5-(2′-pyridyl)-1,3,4-oxadiazole. Furthermore, the longest-wavelength experimental band's position are in good agreement with (r2=0.95) the HOMO-LUMO energetic gaps of studied compounds.

Phase separation and structure transition of undercooled Fe75Cu25 melts

ABSTRACTThe rapid quenching processes of Fe75Cu25 melt at different cooling rate are investigated by molecular dynamics simulation based on embedded atom method. Fe75Cu25 alloy ribbons are prepared by single roller rapid quenching. Liquid–liquid phase separation (LLPS) happens and the Cu-rich droplets embedded in the Fe-rich matrix can be observed both in simulation and experiments. Stronger interaction of homogeneous atom pairs than that of heterogeneous atom pairs leads to LLPS, controlled by nucleation growth mechanism in Fe75Cu25 melt, and quite different from that in Fe50Cu50 melt, which is controlled by spinodal decomposition mechanism. During the crystallisation process after LLPS, the new nuclei form only in Fe-rich regions; various multiply twinning boundaries are formed due to the minimisation of interfacial energy and only the homogeneous atomic stacking shows mirror symmetry along twinning boundary. The results provide atomic-scale understanding of phase separation mechanism and structure transition of Fe75Cu25 melt during rapid cooling processes.

Alloy Gene Sequence Project and System Science Philosophy

System Science Philosophy is a knowledge system constructed of universal principle and law sequences. Alloy gene is a characteristic atom existing in the center of coordination cluster and occupying the lattice point of a lattice cell, and carries holographic information about valence electron structure, physical and thermodynamic properties obtained by alloy gene theory. Alloy gene potential energy curve function has developed traditional atom pair interaction potential functions into many atoms’ interaction function associated with valence electron structure, bond length, bond energy, which makes alloy gene Gibbs energy function can be established. Alloy gene Gibbs energy transmissive function has developed traditional partition function. Its equilibrium and sub-equilibrium transmissive modes produce alloy holographic network positioning bank, which is operable platform to achieve transformation from “trial and error” method to the “whole obtained from a few part” law for getting advanced alloys. It has become possible to launch alloy gene sequence project.

Optimisation of data locality in energy calculations for large-scale molecular dynamics simulations

The main bottleneck of molecular dynamic simulations is the estimation of nonbonded pairwise interaction, which often employs neighbour search algorithms to find out interacting atom pairs. These methods have some drawbacks in fulfilling data locality principle, which is unable to take full advantage of modern computer architecture. In this article, we developed a new method by introducing a temporary list to reduce the sparsity in data access. This list permits to obtain a compact and sequential data structure which benefits to efficiently fulfil the data locality principle. We tested and compared the performance of the new method with that of the extensively used reordering method. The new method based on linked cell list is shown to increase 13% of computation speed and have better parallelism in comparison with reordering method. The increase in parallel efficiency makes the new method a promising option for large-scale molecular simulations.

Role of multilevel Rydberg interactions in electric-field-tuned Förster resonances

In this work, we investigate the dc electric-field dependence of two F\"orster resonant processes in ultracold $^{85}\mathrm{Rb}$, $37{D}_{5/2}+37{D}_{5/2}\ensuremath{\rightarrow}35L(L=O,Q)+39{P}_{3/2}$, as a function of the atomic density. At low densities, the $39{P}_{3/2}$ yield as a function of electric field exhibits resonances. With increasing density, the linewidths increase until the peaks merge. Even under these extreme conditions, where the F\"orster resonance processes show little electric-field dependence, the $39{P}_{3/2}$ population depends quadratically on the total Rydberg atom population, suggesting that a two-body interaction is the dominant process. In order to explain our results, we implement a theoretical model which takes into account the multilevel character of the interactions and Rydberg atom blockade process using only atom pair interactions. The comparison between the experimental data and the model is very good, suggesting that the F\"orster resonant processes are dominated by two-body interactions up to atomic densities of $3.0\ifmmode\times\else\texttimes\fi{}{10}^{12}\phantom{\rule{0.16em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$.

A method for diffraction-based identification of amorphous sp2 carbon materials

A method is suggested for estimation of structural properties of amorphous sp2 carbon and applied to amorphous fullerene and its derivatives produced by vacuum annealing. The method is based on the fitting of the neutron or x-ray powder diffraction patterns for scattering wave vector's modulus in the range from few units to several tens of inverse nanometers. The respective inverse problem assumes that the nanostructure of a sample is representable by a limited number, Nstr, of candidate structures (e.g. fullerenes, carbon flakes with graphene-like atom arrangement) of a limited number of atoms, Natom. These structures are packed heterogeneously, in the domains with various average densities of atoms and various total potential energy, using the rigid body molecular dynamics with variable parameter of pair interaction of atoms in the neighboring nanostructures. The method is applied to interpreting the data of neutron diffraction by an amorphous C60 fullerene annealed at 600, 800, 850, 900 and 1000°C. The results for Nstr=36 and Natom=14÷285 enabled us to quantify structural properties of the samples in terms of the average size and curvature of the sp2 carbon structures, and analyze sensitivity of results to the layout of these structures in the domains.

Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.

The DOcking decoy-based Optimized Potential (DOOP) energy function for protein structure prediction is based on empirical distance-dependent atom-pair interactions. To optimize the atom-pair interactions, native protein structures are decomposed into polypeptide chain segments that correspond to structural motives involving complete secondary structure elements. They constitute near native ligand-receptor systems (or just pairs). Thus, a total of 8609 ligand-receptor systems were prepared from 954 selected proteins. For each of these hypothetical ligand-receptor systems, 1000 evenly sampled docking decoys with 0-10 Å interface root-mean-square-deviation (iRMSD) were generated with a method used before for protein-protein docking. A neural network-based optimization method was applied to derive the optimized energy parameters using these decoys so that the energy function mimics the funnel-like energy landscape for the interaction between these hypothetical ligand-receptor systems. Thus, our method hierarchically models the overall funnel-like energy landscape of native protein structures. The resulting energy function was tested on several commonly used decoy sets for native protein structure recognition and compared with other statistical potentials. In combination with a torsion potential term which describes the local conformational preference, the atom-pair-based potential outperforms other reported statistical energy functions in correct ranking of native protein structures for a variety of decoy sets. This is especially the case for the most challenging ROSETTA decoy set, although it does not take into account side chain orientation-dependence explicitly. The DOOP energy function for protein structure prediction, the underlying database of protein structures with hypothetical ligand-receptor systems and their decoys are freely available at http://agknapp.chemie.fu-berlin.de/doop/.