Atomic Potentials Research Articles

ECCPA: Calculation of classical and quantum cross sections for elastic collisions of charged particles with atoms

ECCPA: Calculation of classical and quantum cross sections for elastic collisions of charged particles with atoms

Soft parameters in Coulomb potential of noble atoms for nonsequential double ionization: Classical ensemble model and simulations

We propose a procedure based on the classical ensemble model to determine the soft parameter in the Coulomb potential of noble atoms, the important parameters used in the simulations of nonsequential double ionizations (NSDI). These parameters are determined based on two conditions: ensuring the positive kinetic energy of two electrons and preventing the atom from autoionization. The optimal values of the soft parameters for He, Ne, Ar, Kr, and Xe atoms are around 0.85, 1.1, 1.5, 1.8, and 2.0 a.u., respectively. The classically allowed initial position of electrons is analytically derived from soft parameters. A simulation of NSDI using 2,000,000 particles has been done using the obtained parameters to achieve the probability distribution of the single and double ionizations. The procedure is comprehensively illustrated for Ar and He atoms and the result in this study is validated by comparing the ratio of double to single ionization yield and correlated two-electron momentum distributions with that in recent experiments.

Microscopical Justification of Solid-State Wetting and Dewetting

The continuum model related to the Winterbottom problem, i.e., the problem of determining the equilibrium shape of crystalline drops resting on a substrate, is derived in dimension two by means of a rigorous discrete-to-continuum passage by Gamma -convergence of atomistic models taking into consideration the atomic interactions of the drop particles both among themselves and with the fixed substrate atoms. As a byproduct of the analysis, effective expressions for the drop surface anisotropy and the drop/substrate adhesion parameter appearing in the continuum model are characterized in terms of the atomistic potentials, which are chosen of Heitmann–Radin sticky-disk type. Furthermore, a threshold condition only depending on such potentials is determined distinguishing the wetting regime, where discrete minimizers are explicitly characterized as configurations contained in an infinitesimally thick layer, i.e., the wetting layer, on the substrate, from the dewetting regime. In the latter regime, also in view of a proven conservation of mass in the limit as the number of atoms tends to infinity, proper scalings of the minimizers of the atomistic models converge (up to extracting a subsequence and performing translations on the substrate surface) to a bounded minimizer of the Winterbottom continuum model satisfying the volume constraint.

Measurements and calculations of Xe-broadening and shift parameters of water vapour transitions in a wide spectral region

The water vapour line broadening (γ) and shifting (δ) coefficients for 687 lines of 14 vibrational bands ν1, ν3, 2ν2, ν1 + ν2, ν2 + ν3, 3ν2, 2ν2 + ν3, ν1 + 2ν2, ν1 + ν3, 2ν1, 2ν3, 4ν2, 6ν2, and 3ν2 + ν3 induced by xenon pressure were measured with Bruker IFS 125 FTIR spectrometer. The measurements were performed at room temperature, at the spectral resolution of 0.01 cm−1 and in a wide pressure range of Xe. The broadening and shift coefficients were calculated using a semi-classical method. The intermolecular potential was taken as the sum of the anisotropic atom–atom potential and vibrationally and rotationally dependent isotropic Lennard-Jones potential. The optimal sets of potential parameters that gave the best agreements with measured coefficients γ and δ for each vibrational band were found. The measured coefficients γ were combined with the data found earlier for the ν1 + ν2 + ν3 bands as well as with those reported in literature for the ν2, ν1, ν3, 2ν1 + 2ν3, 2ν1 + 2ν2 + ν3 and 3ν1 + ν3 bands and N = 820 coefficients γ of19 vibrational bands of H2O perturbed by Xe were fitted to the empirical functions. The computed coefficients γ and δ derived from the semi-classical method as well as from the fitted parameters were compared statistically to measurements.

Layered Pt-Co alloys: Bulk, surface and nanoparticle analysis, based on DFT

Pt-based catalysts are commonly used as cathode materials in various types of fuel cells. In this work we apply DFT calculations combined with cluster expansion method to elucidate the most stable structures of Pt-Co bulk alloy across the full range of Pt (or Co) concentrations. Our calculations reveal high stability of alloy configurations with alternating layers in (001) crystallographic planes of face centered cubic (fcc) structure exclusively occupied either by Pt or Co atoms. In particular, we find that Pt1Co1, Pt2Co1 and Pt3Co1 layered structures (periodically repeated 1–3 Pt layers, separated by single Co layers) have exceptionally high stability with Pt2Co1 possessing the lowest energy of formation among all analysed alloy configurations. Employing ab initio thermodynamics approach, we discuss stability of three types of surface terminations (Miller indices (100), (110) and (111)) for these three layered structures and also for highly symmetric fcc Pt3Co1 configuration, previously identified experimentally. Applying the Wulff construction, we obtain the nanoparticle shapes as functions of chemical potentials of constituent atoms (Pt or Co), allowing for design of computational models of Pt-Co nanoparticles and subsequent analysis of their chemical properties.

Computational screening of single transition metal atom embedded in nitrogen doped graphene for CH4 detection

Sensitive and selective detection of methane (CH4) is crucial for human activities, but is severely challenging due its volatility and nonpolar nature. Herein, with the aid of first-principles calculations, we explore the potential of single transition metal atoms (Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt and Au) embedded in graphene with four pyridine nitrogen atoms doped (TMN4 @G) as efficient sensor materials towards CH4. It is found that AgN4 @G enables outstanding sensitivity, selectivity and recovery ability for CH4 detection in ambient condition. Further calculations in the presence of O2 or H2O revealed that the sensitivity of the system is remarkably improved, indicating its applicability and robustness for CH4 sensing in ambient or humid conditions.

Trapping effects in quantum atomic arrays

Quantum emitters, particularly atomic arrays with subwavelength lattice constant, have been proposed to be an ideal platform for studying the interplay between photons and electric dipoles. In this work, motivated by the recent experiment [1], we develop a microscopic quantum treatment using annihilation and creation operator of atoms in deep optical lattices. Using a diagrammatic approach on the Keldysh contour, we derive the cooperative scattering of the light and obtain the general formula for the S matrix. We apply our method to study the trapping effect, which is beyond previous treatment with spin operators. If the optical lattices are formed by light fields with magical wavelength, the result matches previous results using spin operators. When there is a mismatch between the trapping potentials for atoms in the ground state and the excited state, atomic mirrors become imperfect, with multiple resonances in the optical response. We further study the effect of recoil for large but finite trapping frequency. Our results are consistent with existing experiments.

Near-exact non-relativistic ionization energies for many-electron atoms.

Electron–electron interactions and correlations form the basis of difficulties encountered in the theoretical solution of problems dealing with multi-electron systems. Accurate treatment of the electron–electron problem is likely to unravel some nice physical properties of matter embedded in the interaction. In an effort to tackle this many-body problem, a symmetry-dependent all-electron potential generalized for an n-electron atom is suggested in this study. The symmetry dependence in the proposed potential hinges on an empirically determined angular momentum-dependent partitioning fraction for the electron–electron interaction. With the potential, all atoms are treated in the same way regardless of whether they are open or closed shell using their system specific information. The non-relativistic ground-state ionization potentials for atoms with up to 103 electrons generated using the all-electron potential are in reasonable agreement with the existing experimental and theoretical data. The effects of higher-order non-relativistic interactions as well as the finite nuclear mass of the atoms are also analysed.

Benchmarking ANO-R basis set for multiconfigurational calculations

The selection of basis sets is very important for multiconfigurational wave function calculation, due to a balance between a desired accuracy and computational costs. Recently, the atomic natural orbital-relativistic (ANO-R) basis set was published as a suggested replacement for the ANO-RCC basis set for scalar-relativistic correlated calculations Zobel et al (2021 J. Chem. Theory Comput. 16 278–294). Benchmarking ANO-R basis set against ANO-RCC for atoms (from H to Rn) and their compounds is the goal of this study. Many of these compounds (for instance, diatomic molecules containing transition metals) have open shells, for which reason a multiconfigurational approach is necessary and was primarily used throughout this project. Performance of the ANO-R basis set in multiconfigurational calculations is similar to the ANO-RCC basis set for the ionisation potential of atoms, and the bond distance in diatomic molecules. Deficiencies are noted for atomic electron affinities and dissociation energies of fluoride diatomic molecules. ANO-R basis sets are more compact in comparison to the corresponding ANO-RCC basis sets leading to smaller computational costs, which was demonstrated by chloroiron corrole molecule as an example.

Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I.

Simple SummaryMany biological systems contain iron–sulfur clusters, which are typically found as components of electron transport proteins. Continuum electrostatic calculations were used to investigate the effect of protein environment on the redox properties of the three iron–sulfur clusters in the cyanobacterial photosystem I. Our results show a good correlation between the estimated and the measured reduction potential. Moreover, the results indicate that the low potential of FX is shown to be due to the interactions with the surrounding residues and ligating sulfurs. Our results will help in understanding the electron transfer reaction in photosystem I.Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster FX, which is followed by two terminal iron–sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.

Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA.

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.

Off-axis electron holography: Materials analysis at atomic resolution

Abstract In high-resolution off-axis electron holography, the correction of coherent aberrations allows the quantitative interpretation of the amplitude and phase of the object wave up to the information limit of the electron microscope. Since the measured object phase is directly related to the projected atomic potential for sufficiently thin samples, off-axis electron holography is expected to allow distinguishing of different elements in the reconstructed phase image (“holographic materials analysis”). This has already been verified with the example of Ga and As. However, simulations of the atomic phase shift reveal that the interpretation of the measured phase shift in terms of atomic species is generally rather complex. The findings suggest that, in some cases, the requirements as to lateral resolution and phase detection limit will be met only by electron microscopes of the next generation.

Synthesis and Computational Investigations of Ruthenium(II) Complexes Containing Hydrazine Schiff Base Ligands

Three new heteroleptic ruthenium(II) complexes containing hydrazine schiff base as ligands were synthesized and characterized by using elemental analysis, FT-IR, 1H, 13C NMR, and mass spectroscopic techniques. FT-IR study showed that the substituted phenylhydrazine ligands behave as a monoanionic bidentate O and N donors (L) coordinate to ruthenium via the deprotonated phenolic oxygen and the azomethine nitrogen. They possess excellent thermal stabilities, evident from the thermal decomposition temperatures. Absorption, emission and electrochemical measurements were carried out and the structures of the synthesized complex were optimized using density functional theory (DFT). The molecular geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies, Mulliken atomic charges and molecular electrostatic potential (MEP) of the molecules are determined using B3LYP method and standard 6-311++G (d, p) basis set.

Nanotrappy: An open-source versatile package for cold-atom trapping close to nanostructures

Trapping cold neutral atoms in close proximity to nanostructures has raised a large interest in recent years, pushing the frontiers of cavity-QED and boosting the emergence of the waveguide-QED field of research. The design of efficient dipole trapping schemes in evanescent fields is a crucial requirement and a difficult task. Here we present an open-source Python package for calculating optical trapping potentials for neutral atoms, especially in the vicinity of nanostructures. Given field distributions and for a variety of trap configurations, nanotrappy computes the three-dimensional trapping potentials as well as the trap properties, ranging from trap positions to trap frequencies and state-dependent light shifts. We demonstrate the versatility for various seminal structures in the field, e.g., optical nanofiber, alligator slow-mode photonic-crystal waveguide, and microtoroid. This versatile package facilitates the systematic design of structures and provides a full characterization of trapping potentials with applications to the coherent manipulation of atoms and quantum information science.

Machine-learning-guided descriptor selection for predicting corrosion resistance in multi-principal element alloys

More than $270 billion is spent on combatting corrosion annually in the USA alone. As such, we present a machine-learning (ML) approach to down select corrosion-resistant alloys. Our focus is on a non-traditional class of alloys called multi-principal element alloys (MPEAs). Given the vast search space due to the variety of compositions and descriptors to be considered, and based upon existing corrosion data for MPEAs, we demonstrate descriptor optimization to predict corrosion resistance of any given MPEA. Our ML model with descriptor optimization predicts the corrosion resistance of a given MPEA in the presence of an aqueous environment by down selecting two environmental descriptors (pH of the medium and halide concentration), one chemical composition descriptor (atomic % of element with minimum reduction potential), and two atomic descriptors (difference in lattice constant (Delta {{{mathrm{a}}}}) and average reduction potential). Our findings show that, while it is possible to down select corrosion-resistant MPEAs by using ML from a large search space, a larger dataset and higher quality data are needed to accurately predict the corrosion rate of MPEAs. This study shows both the promise and the perils of ML when applied to a complex chemical phenomenon like corrosion of alloys.

Molecular dynamics simulation of nonisothermal crystallization of a single polyethylene chain and short polyethylene chains based on OPLS force field

Abstract Molecular dynamics simulations on the nonisothermal crystallization of a single polyethylene chain and short polyethylene chains based on the all-atom model and optimized potentials for liquid simulations-all atom (OPLS-AA) force field are conducted in this article. Four all-atom single chain models with different chain lengths (C1000, C2000, C3000, and C4000) and four all-atom short chain models with the same chain length and different number of chains (2C500, 4C500, 6C500, and 8C500) are constructed. The collapse process at a high temperature of 600 K and the nonisothermal crystallization process with different cooling rates at the temperature range of 600–300 K are simulated. Roles of chain length, number of chains, cooling rate on the potential energy, van der Waals (V dw) energy, radius of gyration, root mean square deviation, and crystallinity are explored. By comparing with the existing results obtained by the united atom model, the validity and accuracy of this study are proved. Results show that in the collapse process, the chain length is the major factor, whereas the cooling rate has the greatest influence during the nonisothermal crystallization process. As the cooling rate decreases, a “platform” appeared in the V dw energy curve, which has a profound impact on the crystallization.

Understanding of the Dual Roles of Phosphorus in Atomically Distributed Fe/Co-N4P2 over Carbon Nitride for Photocatalytic Debromination from Tetrabromobisphenol A.

Atomically dispersed Fe and Co on carbon nitride under an external phosphine (PH3) atmosphere (P-Fe1Co1/CN) are prepared. Combined with the results of calculations and experiments, the formed P-induced bimetallic single atoms of Fe/Co-N4P2 can provide more reactive sites to enhance optical performance. Meanwhile, the introduced P can coordinate with Fe and Co and change the sole nitrogen coordination environment via the bridging effect. Herein, on the one hand, the structure of Fe-P-Co enhances interactions of single atoms in heterogeneous metals, and, on the other hand, the formed Fe/Co-N4P2 effectively changes the electron configuration in coordination centers. All of the abovementioned findings can enhance the photocatalytic performance of P-Fe1Co1/CN, achieving 96% removal and 51% debromination rates from tetrabromobisphenol A under visible light irradiation. The two efficiencies can be further improved under UV-vis light irradiation. The findings of this work reveal the dual roles of P in bimetallic single-atom catalysts, provide a facile method to synthesize P-assisted bimetal single-atom photocatalysts, and highlight the great potential of carbon nitride-based single atoms as photocatalysts.

Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials.

Protein-protein interactions are crucial in many biological processes. Therefore, determining the structure of a protein-protein complex is valuable for understanding its molecular mechanisms and developing drugs. Molecular docking is a powerful computational tool in the prediction of protein-protein complex structures, in which a scoring function with good performance is very important. In this study, we have proposed a hybrid scoring function of atomic contact-based desolvation energies and distance-dependent interatomic potentials for protein-protein interactions, named HITScorePP, where the atomic contact desolvation energies were derived using an iterative method and the distance-dependent potentials were directly taken from our ITScorePP scoring function. Integrating the hybrid scoring function into our fast Fourier transform (FFT) based HDOCK docking scheme, the updated docking program, named HDOCK2.0, significantly improved the docking performance on the 55 newly added complexes in the protein docking benchmark 5.0 and a data set of 19 antibacterial protein complexes. HDOCK2.0 was also compared with four other state-of-the-art docking programs including Rosetta, ZDOCK3.0.2, FRODOCK3.0, ATTRACT, and PatchDock and obtained the overall best performance in binding mode predictions. These results demonstrated the accuracy of our hybrid scoring function and the necessity of included desolvation effects in protein-protein docking.

The study of channeling parameters of protons along axial and planar directions of Si

In this work, the channeling parameters, the ratio of channeling to random stopping power, and the mean channeling distance, of protons along the 〈100〉, 〈110〉, {100} and {110} directions of Si were studied in terms of the atomic potential of channels. The channeling parameters were deduced using the simulation of the channeling Rutherford backscattering spectra based on the exponential dechanneling function. The best simulation parameters were set using the Levenberg- Marquardt algorithm. The RBS/C spectra were taken in energy interval 1400–2200 keV, using a Si wafer. Considering the deduced parameters along the 〈100〉, 〈110〉, {100} and {110} directions in terms of the atomic potential of channels and using the data along the 〈111〉 and {111} channels reported in the literature, the channeling behavior of protons along the 〈111〉 and {111} direction was explained concerning the shallow and deep potentials. Finally, the mean channeling distance along the {111} channel was estimated.

Dislocation emission and propagation under a nano-indenter in a model high entropy alloy

The nanoindentation response of a FeNiCrCoCu high-entropy alloy is explored by means of atomistic simulations. In order to study the role of compositional complexity, we compare the behavior of the quinary FeNiCrCoCu alloy with that of an average atom potential fitted to the same overall properties of the alloy. In this way, we reveal the influence of compositional randomness of the multicomponent alloys on the onset of plasticity, deformation mechanisms and residual microstructure. Plasticity is dominated by dislocation activity, with twinning appearing as a complementary deformation mechanism in both models. While the HEA alloy substrate yields for a similar indenter penetration, indentation hardness is higher in the HEA alloy. After mitigation of strain rate effects, major differences are observed, influenced by the more difficult movement of dislocations in the compositionally complex HEA alloy. The results are in agreement with previous studies of plasticity in high entropy alloys and highlight the importance of using average atom models over comparison with single element studies for understanding complex multi principal element alloys.