Atomic Geometry Research Articles

Probing van der Waals magnetic surface and interface via circularly polarized X-rays

Advances in research of magnetic two-dimensional van der Waals (2D vdW) materials have opened up new opportunities in miniaturization of spintronic devices at the atomically thin limit. One major research thrust, which is the subject of this review, is that the magnetism of 2D vdW materials and their derived hetero-interface may be significantly affected by the local atomic geometry and environment. As a result, there is a pressing need for powerful advanced technique to characterize magnetic vdW surface and interface. Circularly polarized X-rays from synchrotron radiation light sources are key to this endeavor, as they can probe the microscopic magnetism of a specific element, for their atomic sensitivity, element-specificity, core-level excitation as well as capability of separation for the spin and orbit moments. We review a series of representative experimental achievements, exploiting circularly polarized X-rays, in (1) 2D vdW magnet, (2) magnetic metal/vdW interface, (3) molecule/vdW interface as well as (4) vdW/2D interface. On the basis of the review, advantages of probing magnetic vdW surface and interface by circularly polarized X-rays are presented, and challenges and opportunities are also discussed.

Towards structural optimization of gold nanoclusters with quantum Monte Carlo.

We study the prospects of using quantum Monte Carlo techniques (QMC) to optimize the electronic wavefunctions and atomic geometries of gold compounds. Complex gold nanoclusters are widely studied for diverse biochemical applications, but the dynamic correlation and relativistic effects in gold set the bar high for reliable, predictive simulation methods. Here we study selected ground state properties of few-atom gold clusters by using density functional theory (DFT) and various implementations of the variational Monte Carlo (VMC) and diffusion Monte Carlo. We show that the QMC methods mitigate the exchange-correlation (XC) approximation made in the DFT approach: the average QMC results are more accurate and significantly more consistent than corresponding DFT results based on different XC functionals. Furthermore, we use demonstrate structural optimization of selected thiolated gold clusters with between 1 and 3 gold atoms using VMC forces. The optimization workflow is demonstrably consistent, robust, and its computational cost scales with nb, where b < 3 and n is the system size. We discuss the implications of these results while laying out steps for further developments.

Atomic structure of the Se-passivated GaAs(001) surface revisited

We present a combined experimental and theoretical study of the Se-treated GaAs(001)-(2times 1) surface. The (2times 1) structure with the two-fold coordinated Se atom at the outermost layer and the three-fold coordinated Se atom at the third layer was found to be energetically stable and agrees well with the experimental data from scanning tunneling microscopy, low energy electron diffraction, and x-ray photoelectron spectroscopy. This atomic geometry accounts for the improved stability of the Se-treated surface against the oxidation. The present result allows us to address a long-standing question on the structure of the Se-passivated GaAs surface, and will leads us to a more complete understanding of the physical origin of the electrical and chemical passivation of Se-treated GaAs surface.

Interpolating Nonadiabatic Molecular Dynamics Hamiltonian with Bidirectional Long Short-Term Memory Networks.

Essential for understanding far-from-equilibrium processes, nonadiabatic (NA) molecular dynamics (MD) requires expensive calculations of the excitation energies and NA couplings. Machine learning (ML) can simplify computation; however, the NA Hamiltonian requires complex ML models due to its intricate relationship to atomic geometry. Working directly in the time domain, we employ bidirectional long short-term memory networks (Bi-LSTM) to interpolate the Hamiltonian. Applying this multiscale approach to three metal-halide perovskite systems, we achieve two orders of magnitude computational savings compared to direct ab initio calculation. Reasonable charge trapping and recombination times are obtained with NA Hamiltonian sampling every half a picosecond. The Bi-LSTM-NAMD method outperforms earlier models and captures both slow and fast time scales. In combination with ML force fields, the methodology extends NAMD simulation times from picoseconds to nanoseconds, comparable to charge carrier lifetimes in many materials. Nanosecond sampling is particularly important in systems containing defects, boundaries, interfaces, etc. that can undergo slow rearrangements.

Nitrogen flow rate dependent atomic coordination, phonon vibration and surface analysis of DC magnetron sputtered nitrogen rich-AlN thin films

In this work, the effect on crystallite orientation, surface morphology, fractal geometry, structural coordination and electronic environment of DC magnetron sputtered AlN films were investigated. X-ray diffraction results disclosed that the c-axis orientation of AlN films increased with the preferred wurtzite hexagonal structure above 17% N2 flow. X-ray reflectivity data confirmed AlN film density increased with increasing N2 flow and was found to be 3.18 g/cm3 for 40% N2. The transition of electrons from N 1s to 2p states hybridized with Al 3p states because of π* resonance was obtained from X-ray absorption spectroscopy of the N K-edge. The semi-empirical coordination geometry of nitrogen atoms has been studied by deconvolution of N K-edge. The surface composition of AlN films at 40% N2 consists of 32.08, 51.94 and 15.97 at.% Al, N and O respectively. Blue-shifting of A1(LO) and E1(LO) modes in the Raman spectra at phonon energies 800 and 1051 cm−1 respectively was most likely due to the presence of oxygen bonds in the AlN films.

Overall protein structure quality assessment using hydrogen-bonding parameters.

Atomic model refinement at low resolution is often a challenging task. This ismostly because the experimental data are not sufficiently detailed to be described by atomic models. To make refinement practical and ensure that a refined atomic model is geometrically meaningful, additional information needs to be used such as restraints on Ramachandran plot distributions or residue side-chain rotameric states. However, using Ramachandran plots or rotameric states as refinement targets diminishes the validating power of these tools. Therefore, finding additional model-validation criteria that are not used or are difficult to use as refinement goals is desirable. Hydrogen bonds are one of the important noncovalent interactions that shape and maintain protein structure. These interactions can be characterized by a specific geometry of hydrogen donor and acceptor atoms. Systematic analysis of these geometries performed for quality-filtered high-resolution models of proteins from the Protein Data Bank shows that they have a distinct and a conserved distribution. Here, it is demonstrated how this information can be used for atomic model validation.

Nitrogen as a probable problematic factor of computational chemistry: A benchmarking study

In the present study, theoretical IR frequencies and geometric parameters of triamterene, furosemide, and triamterene-furosemide salt were investigated. ORCA software was handled for commonly used BLYP, B3LYP, and HF (combined with various basis sets including 6-31G**, def2-SVP, cc-pVDZ, and pcseg-1 basis sets) calculations. Theoretical IR frequencies and geometric parameters of triamterene and furosemide were compared with the corresponding experimental data. In addition, theoretical geometric parameters of triamterene-furosemide salt were, as well, compared with the corresponding experimental data. Based on these comparisons, the performances of computational methods/basis sets were measured. As a result of this study, it was discovered that the studied computational approaches were generally successful in the prediction of molecular geometries and IR frequencies of the target molecules. When IR and geometry data were more deeply investigated, it was observed that there were problems specific to nitrogen atoms. The computed geometry and IR of amine and sulphonamide nitrogen atoms’ bonds strongly disagreed with the experimental data. Similar disagreements were also observed for sulphur, oxygen, and cyclic hydrogen atoms but the level of disagreements was lower.

Mdapy: A flexible and efficient analysis software for molecular dynamics simulations

The mdapy is a library for pre- and postprocessing molecular dynamics simulation data. Benefitting from the just-in-time compile technology of TaiChi mdapy can be written in pure Python while possessing similar speed to those written in C++. mdapy is designed with highly paralleled and makes full advantages of modern computer resources on both multicore CPU and GPU architecture. The package implements a fast module to find the neighbors of particles in both free and periodic boundaries, based on which it offers a wide variety of methods to analyze atomic environments, such as standard centrosymmetry parameters, radial distribution function and newer methods, such as atomic entropy fingerprint. In addition, mdapy can be used to create the geometric structure of polycrystals with metallic or graphene grain boundaries by Voronoi diagram. mdapy can directly read the DUMP and DATA format defined in LAMMPS code, and, in practice, it accepts any other format by converting it into NumPy ndarray format. This design philosophy enables seamless integration with abundant scientific ecosystems in the Python community and easy cooperation with other analysis codes like OVITO or freud. Program summaryProgram Title: mdapyCPC Library link to program files:https://doi.org/10.17632/dtdkxvcsc9.1Developer's repository link:https://github.com/mushroomfire/mdapyCode Ocean capsule:https://codeocean.com/capsule/5271472Licensing provisions: BSD 3-clauseProgramming language: Python, C++Nature of problem: Atomic environment analysis and generation of the initial structure are important in molecular dynamics simulations. Many analysis methods relying on particle neighbors, such as radial distribution functions and atomic entropy, are computationally intensive and need to be carefully implemented to scale to large systems. Traditional code is often written in C++ or Fortran to guarantee performance while causing difficulty in installation and secondary development due to the complexity of the programming language.Solution method: mdapy is written in parallel to quickly perform neighbor finding, provides a set of analysis methods and creates an atomic geometry structure on multicore CPU and GPU. Over 95 percent of mdapy is written in Python with a uniform API to call. All data are stored in NumPy ndarray, making users easy to install, use and secondary develop.Additional comments including restrictions and unusual features:1. mdapy provides fast parallel implementations of neighbor finding in periodic and free boundary system.2. mdapy can generate a polycrystalline model with graphene grain boundaries.3. mdapy is helpful for analyzing the melting process by the mean squared displacement and Lindemann index at the atomic level.4. mdapy is very easy to install via pip install mdapy without any compile steps and can be run on Windows, Linux and Mac OS with Python 3.7-3.10.5. mdapy has detailed documentation to make it easier to use.

Synthesis and Structure of Tetraphenylstibonium Organosulfonates Ph4SbOSO2R, R = C10H15O, C10H4(OH-1)(NO2)2-2,4, C10H7-1, C6H4(COOH-2)

The reaction of equimolar amounts of pentaphenylantimony with camphor-10-sulfonic, 2,4-dinitro-1-naphthol-7-sulfonic (flavianic), 1-naphthalenesulfonic, and 2-sulfobenzoic acids in benzene resulted in the synthesis of tetraphenylstibonium organosulfonates Ph4SbOSO2C10H15O∙H2O (I), Ph4SbOSO2C10H4(OH-1)(NO2)2-2,4∙PhH (II), Ph4SbOSO2(C10H7-1)∙H2O (III), and Ph4SbOSO2C6H4(COOH-2) (IV). According to X-ray diffraction data (CCDC no. 2119791 (I), 2121381 (II), 2116582 (III), and 2123516 (IV), the crystal of I contains trigonal-bipyramidal sulfonate molecules (the axial Sb−C and Sb−O bond lengths are 2.130(3) and 2.565(2) Å, respectively) and hydration water molecules, which form a centrosymmetric eight-membered ring (the S=O∙∙∙H−O−H∙∙∙O=S distances are 2.06 and 2.21 Å). In the molecules of II, the metal atom geometry is a distorted trigonal bipyramid (the axial Sb−C and Sb−O bonds are 2.133(2) and 2.643(3) Å, respectively). The Sb−O distance (2.842(3) Å) is longer in III than in I or II; the hydration water molecules form centrosymmetric twelve-membered rings with the anions (the S=O∙∙∙H−O−H∙∙∙O=S distances are 2.02 and 2.05 Å). Meanwhile, the crystal of compound IV consists of tetrahedral tetraphenylstibonium cations and (2-carboxy)benzenesulfonate anions with the intramolecular O−H∙∙∙O=S hydrogen bond (1.75 Å).

Dissociation-energy calculations of C-multivacancies in diamond: the density-functional-theory study

This work presents a study of the configurational stabilities and atomic geometries of supercell diamond (216 atomic sites) through density functional theory calculations. We build eight C-vacancies configurations consisting of mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, and octavacancies. The atomic geometries of perfect and C-multivacancies diamond are further investigated. The formation and dissociation energies are calculated to analyze the configurational stabilities. The result shows that hexavacancy is the most stable configuration of the diamond C-multivacancies which is mainly caused by the minimum number of the dangling bond.

The electrical and photophysical performances of axially-substituted naphthalene diimide-based small molecules as interface layer

To date, the number of publications on NDI-based small molecules is almost identical to the number of publications on NDI-based polymers. As opposed to the polymer examples, the design of NDI-based small molecules can be easily sub-categorized into axial (a) and core (c) substituted geometries, and have a practical use. For this purpose, in this study, initially, the symmetric and asymmetric axially-substituted-NDI-based small organic ligands (aNDIs 1A-1G) were synthesized as novel interface layers, and the values of atomic charges, geometry, dipole moment, and thermodynamical properties were calculated with DFT methods. Thus, initially, the theoric and experimental band gap values were calculated with DFT/TD-DFT and UV–Vis measurements, respectively. The theoretical band gap was found to be between 3.5 eV and 3.6 eV and the experimental band gap was found to be between 3.15 eV and 3.17 eV. Following synthesis and theoretical studies, the electrical and photophysical performances of naphthalene diimide-appended diode and photodiode devices (D1-D7) have been discussed with an analytical overview. For this, initially, the aNDIs, organic photodiodes, were fabricated with a thermal evaporation system, and the surface morphologies were examined with AFM for each interface layer. Due to the very small roughness values, about 1.8–2.1 nm, it was concluded that the thermal evaporation method is a suitable method for growing these structures. Following the fabrication of devices, the diode and photodiode parameters were investigated with current–voltage measurements at dark and different illumination conditions. The temperature-dependent performances of the fabricated devices were investigated at 100 K, 200 K, and 320 K. Additionally, the capacitance characteristics were investigated with the impedance spectroscopy method. As a result of all these studies, in addition to the literature for effective synthesis of symmetric and asymmetric aNDIs as simple structured photodiode candidates, besides the effective synthetic touches, the wide-range behavioral differences of these photodiode candidates of different natures have been investigated comparatively.

From Symbolic Representation to Submicroscopic One: Preservice Science Teachers’ Struggle with Chemical Representation Levels in Chemistry

Being able to move between different representations levels (macroscopic, sub-microscopic, and symbolic) is important to understand a chemical phenomenon meaningfully. The current study investigated how pre-service science teachers moved from symbolic representation to sub-microscopic representation. A total of 205 pre-service science teachers, first, balanced the three chemical reactions and then drew the reactions’ sub-microscopic views if they were able to observe them. The findings revealed that pre-service science teachers are most successful at the symbolic level. Yet, this is not a valid conclusion for the sub-microscopic representation level. The drawings were analyzed concerning atomic size and molecular geometry and found that pre-service science teachers have common alternative concepts. Furthermore, they mostly have a superficial knowledge of the molecular geometry of chemical compounds. In conclusion, because pre-service science teachers will teach in their future careers, it is important to encourage them to comprehend chemical phenomena at each representation level and shift between them to prevent alternative concepts they may have.

Complex ligand adsorption on 3D atomic surfaces of synthesized nanoparticles investigated by machine-learning accelerated ab initio calculation.

Nanoparticle surfaces are passivated by surface-bound ligands, and their adsorption on synthesized nanoparticles is complicated because of the intricate and low-symmetry surface structures. Thus, it is challenging to precisely investigate ligand adsorption on synthesized nanoparticles. Here, we applied machine-learning-accelerated ab initio calculation to experimentally resolved 3D atomic structures of Pt nanoparticles to analyze the complex adsorption behavior of polyvinylpyrrolidone (PVP) ligands on synthesized nanoparticles. Different angular configurations of large-sized ligands are thoroughly investigated to understand the adsorption behavior on various surface-exposed atoms with intrinsic low-symmetry. It is revealed that the ligand binding energy (Eads) of the large-sized ligand shows a weak positive relationship with the generalized coordination number . This is because the strong positive relationship of short-range direct bonding (Ebind) is attenuated by the negative relationship of long-range van der Waals interaction (EvdW). In addition, it is demonstrated that the PVP ligands prefer to adsorb where the long-range vdW interaction with the surrounding surface structure is maximized. Our results highlight the significant contribution of vdW interactions and the importance of the local geometry of surface atoms to the adsorption behavior of large-sized ligands on synthesized nanoparticle surfaces.

Boosting the Activity of Pd Single Atoms by Tuning Their Local Environment on Ceria for Methane Combustion

AbstractSupported Pd single atom catalysts (SACs) have triggered great research interest in methane combustion yet with contradicting views on their activity and stability. Here, we show that the Pd SAs can take different electronic structure and atomic geometry on ceria support, resulting in different catalytic properties. By a simple thermal pretreatment to ceria prior to Pd deposition, a unique anchoring site is created. The Pd SA, taking this site, can be activated to Pdδ+ (0&lt;δ&lt;2) that has greatly enhanced activity for methane oxidation: T50 lowered by up to 130 °C and almost 10 times higher turnover frequency compared to the untreated catalyst. The enhanced activity of Pdδ+ site is related to its oxygen‐deficient local structure and elongated interacting distance with ceria, leading to enhanced capability in delivering reactive oxygen species and decomposing reaction intermediates. This work provides insights into designing highly efficient Pd SACs for oxidation reactions.

Boosting the Activity of Pd Single Atoms by Tuning Their Local Environment on Ceria for Methane Combustion.

Supported Pd single atom catalysts (SACs) have triggered great research interest in methane combustion yet with contradicting views on their activity and stability. Here, we show that the Pd SAs can take different electronic structure and atomic geometry on ceria support, resulting in different catalytic properties. By a simple thermal pretreatment to ceria prior to Pd deposition, a unique anchoring site is created. The Pd SA, taking this site, can be activated to Pdδ+ (0<δ<2) that has greatly enhanced activity for methane oxidation: T50 lowered by up to 130 °C and almost 10 times higher turnover frequency compared to the untreated catalyst. The enhanced activity of Pdδ+ site is related to its oxygen-deficient local structure and elongated interacting distance with ceria, leading to enhanced capability in delivering reactive oxygen species and decomposing reaction intermediates. This work provides insights into designing highly efficient Pd SACs for oxidation reactions.

Electronic structures and optical properties of uniform ordered hexagonal Ge0.5Si0.5 alloys from first principles

The electronic structures and optical properties of uniform ordered hexagonal Ge0.5Si0.5 alloys were investigated by the first-principle calculations. We first validated our approach for hexagonal Ge and Si, obtaining atomic geometries and band structures in excellent agreement with available experimental data. Then, the same approach was applied to predict electronic and optical properties of uniform ordered hexagonal Ge0.5Si0.5 alloys. The hex-Ge0.5Si0.5 alloy is a direct bandgap semiconductor. The dipole-forbidden or dipole-allowed transitions from the three highest valence bands (Γ9v+, Γ7v++, Γ7v-+) to the first (Γ8c-) or second (Γ7c-) lowest conduction band at Γ point are obtained. The maximum absorption coefficient is close to 2 × 106 cm−1. The three small absorption peaks probably originates from the transition from the Γ9v+, Γ7v++ or Γ7v-+ to Γ7c- band around the Γ point, respectively.

Electron localization in recrystallized models of the Ge2Sb2Te5 phase-change memory material

Understanding the relation between the structural disorder in the atomic geometry of the recrystallized state of phase-change memory materials and the localized states in the electronic structure is necessary not only for technological advances, but also essential to achieve a fundamental understanding of these materials. In this computational study, hybrid density-functional theory simulations are employed to ascertain the impact of antisite defects on the spatial localization of the electronic states in the bottom of the conduction band in recrystallized models of the prototypical phase-change material ${\mathrm{Ge}}_{2}{\mathrm{Sb}}_{2}{\mathrm{Te}}_{5}$. $\mathrm{Te}\text{\ensuremath{-}}\mathrm{Te}$ homopolar bonds are the local defective atomic environments mainly responsible for the electron localization of the conduction-band-edge states in the simulated structures, while $\mathrm{Sb}\text{\ensuremath{-}}\mathrm{Te}$ chains can also induce spatial localization. Unoccupied defect-related electronic states can emerge in the band gap during a crystallization event, while $\mathrm{Sb}\text{\ensuremath{-}}\mathrm{Sb}$ homopolar bonds have been identified in the defect environment of a deep localized state.

Directing the Surface Atomic Geometry on Copper Sulfide for Enhanced Electrochemical Nitrogen Reduction

Directing the Surface Atomic Geometry on Copper Sulfide for Enhanced Electrochemical Nitrogen Reduction

First-principles simulation of light-ion microscopy of graphene

The extreme sensitivity of 2D materials to defects and nanostructure requires precise imaging techniques to verify presence of desirable and absence of undesirable features in the atomic geometry. Helium-ion beams have emerged as a promising materials imaging tool, achieving up to 20 times higher resolution and 10 times larger depth-of-field than conventional or environmental scanning electron microscopes. Here, we offer first-principles theoretical insights to advance ion-beam imaging of atomically thin materials by performing real-time time-dependent density functional theory simulations of single impacts of 10–200 keV light ions in free-standing graphene. We predict that detecting electrons emitted from the back of the material (the side from which the ion exits) would result in up to three times higher signal and up to five times higher contrast images, making 2D materials especially compelling targets for ion-beam microscopy. This predicted superiority of exit-side emission likely arises from anisotropic kinetic emission. The charge induced in the graphene equilibrates on a sub-fs time scale, leading to only slight disturbances in the carbon lattice that are unlikely to damage the atomic structure for any of the beam parameters investigated here.

Microwave spectra of two conformers of the (1R)-(–)-nopol monomer

The rotational spectrum of the (1R)-(-)-nopol monomer has been observed in the 6–18 GHz region using CP-FTMW spectroscopy. Transitions of two distinct conformers of the parent isotopologue have been observed and assigned. Density Functional Theory (DFT) calculations performed on the monomer predict nine distinct low-energy heavy atom geometries. The differences between these structures are attributed to changes in the orientation of two dihedral angles in the heavy atom R-CH2CH2OH functionalization, where R refers to the fixed bicyclic cage component of the molecule. Further optimization of these geometries found 27 distinct conformers associated with the hydroxyl hydrogen orientation. The rotational constants of the two lowest energy conformers were found to be in good agreement with the experimental constants of the two observed conformers and the predicted dipole moment components agree with the relative intensities of the observed transitions.