Atomic Positions Research Articles

Data science shows that entropy correlates with accelerated zeolite crystallization in Monte Carlo simulations.

We have performed a data science study of Monte Carlo (MC) simulation trajectories to understand factors that can accelerate the formation of zeolite nanoporous crystals, a process that can take days or even weeks. In previous work, MC simulations predicted and experiments confirmed that using a secondary organic structure-directing agent (OSDA) accelerates the crystallization of all-silica LTA zeolite, with experiments finding a three-fold speedup [Bores et al., Phys. Chem. Chem. Phys. 24, 142-148 (2022)]. However, it remains unclear what physical factors cause the speed-up. Here, we apply data science to analyze the simulation trajectories to discover what drives accelerated zeolite crystallization in MC simulations going from a one-OSDA synthesis (1OSDA) to a two-OSDA version (2OSDA). We encoded simulation snapshots using the smooth overlap of atomic positions approach, which represents all two- and three-body correlations within a given cutoff distance. Principal component analyses failed to discriminate datasets of structures from 1OSDA and 2OSDA simulations, while the Support Vector Machine (SVM) approach succeeded at classifying such structures with an area-under-curve (AUC) score of 0.99 (where AUC = 1 is a perfect classification) with all three-body correlations and as high as 0.94 with only two-body correlations. SVM decision functions reveal relatively broad/narrow histograms for 1OSDA/2OSDA datasets, suggesting that the two simulations differ strongly in information heterogeneity. Informed by these results, we performed pair (2-body) entropy calculations during crystallization, resulting in entropy differences that semi-quantitatively account for the speedup observed in the previous MC simulations. We conclude that altering synthesis conditions in ways that substantially change the entropy of labile silica networks may accelerate zeolite crystallization, and we discuss possible approaches for achieving such acceleration.

Antimicrobial Activity of Naphthyridine Derivatives

To combat the problem of the increasing drug resistance of microorganisms, it is necessary to constantly search for new medicinal substances that will demonstrate more effective mechanisms of action with a limited number of side effects. Naphthyridines are N-heterocyclic compounds containing a fused system of two pyridine rings, occurring in the form of six structural isomers with different positions of nitrogen atoms, which exhibit a wide spectrum of pharmacological activity, in particular antimicrobial properties. This review presents most of the literature data about the synthetic and natural naphthyridine derivatives that have been reported to possess antimicrobial activity.

Water Encapsulated [(Fe4Se4)Se4]6- Clusters in [Na6(H2O)18][Fe4Se8

[Na6(H2O)18][Fe4Se8] was synthesized using hydrothermal methods and characterized by single-crystal X-ray diffraction, 57Fe Mössbauer spectroscopy, magnetization, and muon spin resonance (μSR) measurements. The cubic crystal structure (space group I23, a = 11.785 Å, Z = 2) contains heterocubane-type clusters with Td symmetry. Four additional selenium atoms complete the tetrahedral coordination around the iron atoms, forming units. Notably, the selenide ligands do not interact with the sodium cations, as the Fe4Se86- cluster in [Na6(H2O)18][Fe4Se8] is exclusively surrounded by water molecules via weak Se···H-O hydrogen bonds. This is particularly remarkable given that [Fe4Q4] clusters are typically unstable in water. Quantum chemical calculations (DFT) confirm the crystal structure and improve the positions of the hydrogen atoms. 57Fe Mössbauer spectroscopy reveals that the spin ordering of the mixed-valence [Fe42.5+Se4]2+ cluster core mirrors the antiparallel spin arrangement found in analogous iron-sulfur clusters, such as , in protein-bound systems. An increase of the quadrupole splitting at low temperatures indicates changes of the orbital occupations. μSR Experiments show a reduction of the spin fluctuation frequency until the system becomes static at low temperatures, but no evidence of a S = 0 state above 2 K.

PolyPal: A parallel microscale virtual specimen generator

We present an open source program, PolyPal, that can generate a polycrystalline virtual specimen in the micrometer scale for atomistic calculations and visualization. Unlike regular meshes or perfect lattices, atomic positions in polycrystalline materials need to be defined before calculations, and the capability of an atom-generation code is evaluated by the maximum size of the virtual specimen it can generate as well as by the efficiency of the necessary input-output process. Present atom-generation codes are implemented in a serial fashion, and the maximum size of the virtual specimen is limited by the on-board memory. Furthermore, it is difficult to handle a single position file with billions of atoms not only because it takes a long time to read in a row but also full domain decomposition takes hours. PolyPal addresses these challenges with a fully parallelized MPI input-output scheme that supports multiple export options on a Linux cluster. It has no limit in the system size with virtually perfect scalability. Additionally by controlling the size distribution and homogeneity of grains, the program can simulate different microstructures, as typically found in the bulk system or in thin-film samples, prepared with different fabrication processes. PolyPal will harness molecular dynamics codes in the coming age of the exascale computing. Program summaryProgram Title: PolyPalCPC Library link to program files:https://doi.org/10.17632/5cpbmrtzbr.1Developer's repository link:https://gitlab.com/GeonbuShin/polypal.gitLicensing provisions: GPLv3Programming language: C++Nature of problem: There is no open source code capable of generating massive polycyrstalline microstructures that contain billions of atoms. Existing codes run in a single thread, and hence, have a system size limited by the memory resources. Also, a single input/output filestream is not appropriate for a system with a large amount of atoms as file reading and writing would take a prohibitively long time, working as a bottleneck.Solution method: PolyPal not only creates atomic structures in parallel but also writes positions to multiple files in parallel within the Message Passing Interface (MPI). The parallel computing feature not only enables access to micrometer-scale atomic systems but also accelerates the entire process from atomic generation to file generation. In this code, each subdomain is filled with atoms simultaneously according to the prescribed domain topology with inherent load balancing. The atomic structure is written out to multiple files in parallel; one structure file is generated for each domain assigned to the corresponding node of a computing cluster via MPI-IO, which drastically reduces the input-output time, and makes it possible to handle a large virtual specimen.Additional comments including restrictions and unusual features: PolyPal can generate a layered polycrystalline structure to mimic a thin-film specimen prepared by deposition. The code utilizes MPI-IO to accelerate file output.

Залежність дисторсії ґраток від температури в сплаві CrCoNiFeMn

The dependence of the average lattice distortion on temperature in the multicomponent alloy CrCoNiFeMn was investigated by computer simulation. The features of this dependence are related to the temperature dependences of interatomic distances and elastic moduli. These dependences are resulted from the anharmonicity of the interaction between atoms, i.e. the asymmetry of the interatomic potential function relative to its minimum. There are such dependences of interatomic distances and elastic moduli for the atoms of the components inside the alloy CrCoNiFeMn on temperature, each of which lies between the corresponding dependencies for the pure component and the alloy and is similar to them, while corresponding atomic size misfit and elastic modulus misfit result in lattice distortion which increases with temperature and can compensate for shear modulus decrease. Thus, it can explain the compensation of shear modulus decrease with increasing temperature, which is actually observed in experiments, where there is a “plateau” of the temperature dependence of the yield strength. This confirms the hypothesis that such compensation can depend only on the atom displacement as a result of thermal vibrations, which leads to a shift in the equilibrium position of atoms and thermal expansion of the material when the temperature rises. Keywords: lattice distorsion, solid solution, temperature, multicomponent alloy.

Unravelling the intricacies of fluorescence enhancement in heptamethine cyanine dyes induced by heavy halogen atoms

The classic heavy-atom effect refers to the photophysical phenomenon observed in fluorophores, where the interaction with heavy atoms quenches fluorescence emission. Many fluorophores containing heavy halogen atoms, such as xanthenes, BODIPYs, porphyrins, and anthracenes, adhere to this effect, while the photophysical behavior of others, e.g. halogenated heptamethine cyanine dyes, is poorly studied having contradicting results. In this study, we explored for the first time unexpected fluorescence enhancement induced by heavy halogen atoms in heptamethine dyes, contrasting the classic heavy-atom effect. To this end, a series of novel heptamethine cyanine dyes were synthesized and their photophysical properties were experimentally and theoretically investigated. Heavy halogen atoms were found to significantly affect the fluorescence behaviour of heptamethine dyes depending on the number and position of the attached halogens. Thus, the introduction of bromine and iodine atoms at the non-conjugated positions to the chromophore moieties led to an increase in the fluorescence quantum yields, which contradicts the classic principle and could be explained by heavy halogen-induced vibration restrictions. The value of halogen atom-promoted singlet oxygen generation quantum yield ΦΔ is also not straightforward and depends on the number, position and weight of the halogen atom. The breaking of the classic heavy-atom effect in halogenated heptamethine dyes provides an effective strategy to substantially increase the fluorescence intensity of long-wavelength cyanine dyes, providing new functional advantages for fluorescence imaging, diagnostics, and photodynamic therapy, among other applications.

The effect of the oxygen dangling on the thermoelectric properties of organic Thienoisoindigo single-molecule junction.

Theoretical investigation for thermoelectric characteristics of organic Thienoisoindigo single-molecule is carried out using the first-principles calculations based on the density functional theory. It reveals that modifying the position or removing oxygen atoms significantly alters the thermoelectric properties. Transmission coefficient calculations show that the lowest unoccupied molecular orbital (LUMO) dominates across all molecular configurations. Repositioning oxygen atoms increases the bandgap from 1.14 to 1.53 eV, while the complete removal of oxygen further increases to 1.8 eV. This change leads to the disruption of constructive quantum interference, which is replaced by destructive one. The electrical conductance is similarly affected by changes in oxygen atom positioning, with values shifting from 1.06 to 1.63. Molecules without oxygen atoms exhibit lower conductance compared to those with dangling oxygen, resulting in reduced semiconductor-like behavior and enhanced insulating properties. The Seebeck coefficient remains stable at 2.99 V/K when oxygen atoms are repositioned. However, the removal of one oxygen atom changes the coefficient to a positive value (290.14 V/K), causing the molecule to transition from n-type to p-type behavior. The complete absence of oxygen atoms returns the Seebeck coefficient to a negative value ( 256.08 V/K), switching the molecule back to n-type conduction. This investigation was achieved by applying the SIESTA software through density functional theory (DFT) computations. To account for exchange and correlation effects, we use a double-zeta polarized (DZP) basis set in conjunction with the generalized gradient approximation (GGA-PBE) to determine the ideal ground-state atomic locations. By combining the Hamiltonian of each system with the quantum transport code GOLLUM, we can calculate the transmission coefficient, projected density of states, electrical conductance, and Seebeck coefficient to examine the thermoelectric characteristics of the molecular junction.

Interlayer and interfacial Dzyaloshinskii-Moriya interaction in magnetic trilayers: First-principles calculations

We determine the Dzyaloshinskii-Moriya interaction within and between two magnetic cobalt layers separated by a nonmagnetic spacer through calculations. We investigate different materials for the nonmagnetic layer, focusing on the experimentally realized Co/Ag/Co system. We laterally shift the atoms in the nonmagnetic layer to achieve the symmetry breaking required for the interlayer Dzyaloshinskii-Moriya interaction. We compare the resulting interactions with the Levy-Fert model and observe a good overall agreement between the model and the calculations for the dependence on the atomic positions. Additionally, we derive a formula for the strength of the interlayer isotropic exchange interaction depending on the position of the atoms in the nonmagnetic layer and compare it to the first-principles results. We investigate the limitations of the Levy-Fert model by turning off the spin-orbit coupling separately on the nonmagnetic and magnetic atoms and by studying the effect of band filling. Our work advances the understanding of the microscopic mechanisms of the interlayer Dzyaloshinskii-Moriya interaction and gives insight into possible new material combinations with strong interlayer Dzyaloshinskii-Moriya interaction. Published by the American Physical Society 2024

Chemical disorder effects on Gilbert damping of FeCo alloys

The impact of the local chemical environment on the Gilbert damping in the binary alloy Fe100−xCox is investigated, using computations based on density functional theory. By varying the alloy composition x as well as Fe-Co atom positions we reveal that the effective damping of the alloy is highly sensitive to the nearest-neighbor environment, especially to the amount of Co and the average distance between Co-Co atoms at nearest-neighbor sites. Both lead to a significant local increase (up to an order of magnitude) of the effective Gilbert damping, originating mainly from variations of the density of states at the Fermi energy. In a global perspective (i.e., making a configuration average for a real material), those differences in damping are masked by statistical averages. When low-temperature explicit atomistic dynamics simulations are performed, the impact of short-range disorder on local dynamics is observed to also alter the overall relaxation rate. Our results illustrate the possibility of local chemical engineering of the Gilbert damping, which may stimulate the study of new ways to tune and control materials aiming for spintronics applications. Published by the American Physical Society 2024

Exploring electron-beam induced modifications of materials with machine-learning assisted high temporal resolution electron microscopy

Directed atomic fabrication using an aberration-corrected scanning transmission electron microscope (STEM) opens new pathways for atomic engineering of functional materials. In this approach, the electron beam is used to actively alter the atomic structure through electron beam induced irradiation processes. One of the impediments that has limited widespread use thus far has been the ability to understand the fundamental mechanisms of atomic transformation pathways at high spatiotemporal resolution. Here, we develop a workflow for obtaining and analyzing high-speed spiral scan STEM data, up to 100 fps, to track the atomic fabrication process during nanopore milling in monolayer MoS2. An automated feedback-controlled electron beam positioning system combined with deep convolution neural network (DCNN) was used to decipher fast but low signal-to-noise datasets and classify time-resolved atom positions and nature of their evolving atomic defect configurations. Through this automated decoding, the initial atomic disordering and reordering processes leading to nanopore formation was able to be studied across various timescales. Using these experimental workflows a greater degree of speed and information can be extracted from small datasets without compromising spatial resolution. This approach can be adapted to other 2D materials systems to gain further insights into the defect formation necessary to inform future automated fabrication techniques utilizing the STEM electron beam.

DeepBBQ: A Deep Learning Approach to the Protein Backbone Reconstruction.

Coarse-grained models have provided researchers with greatly improved computational efficiency in modeling structures and dynamics of biomacromolecules, but, to be practically useful, they need fast and accurate conversion methods back to the all-atom representation. Reconstruction of atomic details may also be required in the case of some experimental methods, like electron microscopy, which may provide Cα-only structures. In this contribution, we present a new method for recovery of all backbone atom positions from just the Cα coordinates. Our approach, called deepBBQ, uses a deep convolutional neural network to predict a single internal coordinate per peptide plate, based on Cα trace geometric features, and then proceeds to recalculate the cartesian coordinates based on the assumption that the peptide plate atoms lie in the same plane. Extensive comparison with similar programs shows that our solution is accurate and cost-efficient. The deepBBQ program is available as part of the open-source bioinformatics toolkit Bioshell and is free for download and the documentation is available online.

Hirshfeld Atom Refinement (HAR) and Complementary Bonding Analysis of Lithium m-Terphenylhydridoborates Containing B-H⋅⋅⋅Li Linkages.

The synthesis and characterization of the lithium m-terphenylhydridoborates [Li(2,6-Mes2C6H3)BH3]2 (1), Li(2,6-Mes2C6H3)2BH2 (2) and Li(OEt2)(2,6-Mes2C6H3)2BH2 (3) are reported. Hirshfeld Atom Refinement (HAR) of the experimentally obtained molecular structures by single-crystal X-ray crystallography allowed the determination of the exact positions of the hydrogen atoms. The bond situations of the various B-H⋅⋅⋅Li linkages were investigated by a complementary bonding analysis using various methods including atoms in molecules (AIM), electron localizability indicator (ELI-D), non-covalent interaction (NCI) index and the compliance matrix.

Revealing significant changes in electronic energy configurations via cation atom positions in Co(Gaₓ,Al1-x)₂O₄ spinel oxides

Revealing significant changes in electronic energy configurations via cation atom positions in Co(Gaₓ,Al1-x)₂O₄ spinel oxides

Different Magnitudes of Second-Order Jahn-Teller Effect in Isostructural NaMO2F2 (M = Nb5+, Ta5+) Oxyfluorides

The structures of the ordered and isotype oxyfluorides NaMO2F2 (M = Nb, Ta) were thoroughly investigated by combining powder X-Ray Diffraction (PXRD), 19F and high-field 23Na and 93Nb solid-state NMR, and DFT calculations. The structures, derived from Rietveld refinement of the PXRD data, exclusively consist of cis-[MO4F2]5– octahedra, in which cations are displaced from their ideal centered positions toward an oxide face. The NMR parameters were calculated for both the experimental (ES) and the atomic positions optimized (APO) structures, the latter exhibiting, as is often the case, the best agreement with the experimental data. Nb5+ and Ta5+ cations having the same size, niobium and tantalum isotypes have usually very close cell parameters. However, those of NaNbO2F2 and NaTaO2F2, particularly c, differ in unusual proportions. This difference in c parameters is due to stronger second-order Jahn-Teller effect (SOJTE) for the cis-[NbO4F2]5– than for the cis-[TaO4F2]5– octahedra, further confirmed by band structure and projected density of states calculations. Furthermore, by optimizing the synthesis conditions of these compounds using thermal analysis, a very low amplitude endothermic event, upon heating, was observed only for NaNbO2F2. An extensive analysis of the variable temperature (VT) PXRD data revealed that this event is related to a deviation from linearity of the cell parameters evolution and that structural features of these two isotypes evolve differently with temperature.

Modulating Built‐In Electronic Configuration via Variable Al Doping for Robust Oxygen Evolution Reaction

Transition metal‐based electrocatalysts play a crucial role in the oxygen evolution reaction (OER). However, their heavy reliance on free electrons at the <i>d</i>‐band significantly limits the screening of potentially efficient, earth‐abundant alternatives. Despite extensive exploration of catalyst engineering through multi‐metal cooperation to modulate electron configuration by introducing additional transition metals, practical success remains elusive. Here, we present a straightforward electrodeposition method for preparing amorphous FeCoAl hydroxide catalysts. The introduction of Al contributes external free electrons, enabling a well‐defined electron configuration for intermediate adsorption. Al doping also adjusts the <i>d</i>‐band position of adjacent Co atoms, bringing them closer to the Fermi level and significantly enhancing intrinsic activity at the active sites. Furthermore, Al dopants facilitate rapid mass and charge transfer near the catalyst layer, promoting faster reaction kinetics. Leveraging these properties, the FeCoAl hydroxide catalyst achieves a large current density of 100 mA cm <sup>‐2</sup> at an overpotential of 340 mV, with a small Tafel slope of 29.1 mV dec <sup>‐1</sup>. Our work provides valuable insights for designing efficient electrocatalysts by leveraging free electron‐rich metal doping and expanding the parameter space for catalyst engineering.

Acoustic Drift: Generating Helicity and Transferring Energy

This article studies the general properties of the Stokes drift field. This name is commonly used for the correction addedto the mean Eulerian velocity for describing the averaged transport of the material particles by the oscillating fluid flows. Stokes drift is widely known mainly in connection with another feature of oscillating flows known as steady streaming, which has been and remains the focus of a multitude of studies. However, almost nothing is known about Stokes drift in general, e.g., about its energy or helicity (Hopf’s invariant). We address these quantities for acoustic drift driven by simple sound waves with finite discrete Fourier spectra. The results discover that the mean drift energy is partly localized on a certain resonant set, which we have described explicitly. Moreover, the mean drift helicity turns out to be completely localized on the same set. We also present several simple examples to reveal the effect of the power spectrum and positioning of the spectral atoms. It is revealed that tuning them can drastically change both resonant and non-resonant energies, zero the helicity, or even increase it unboundedly.

Role of co-doping (Sm3+ and Nb5+) and Sintering Conditions on the Dielectric Properties of CaCu3Ti4O12 Ceramics

This research delves into the impact of Sm3+ and Nb5+ co–doping and the effect of sintering temperature on the grain size and the dielectric properties of CaCu3Ti4O12 (CCTO) ceramics synthesized via the sol–gel process. The Rietveld refinement provided detailed structural parameters, including atomic positions, bond lengths, bond angles, and R–factors, with a goodness of fit below 2% with no secondary phases. The expected core levels for Ca 2p, Sm 3d, Cu 2p, Ti 2p, Nb 3d, and O 1s were verified by XPS analysis, suggesting that these materials were present in their expected oxidation states. As the sintering temperature is increased, the average grain size grew from 0.61 ± 0.08 μm to 2.38 ± 0.32 μm. Notably, the sample sintered at 1050 °C exhibited huge dielectric permittivity (ε' ≈ 105) with good stability in the wide frequency range (102–105 Hz) with significantly low dielectric loss. The complex impedance analysis was studied to separate the contributions of grain and grain boundary resistances while the Nyquist plot revealed that the Rgb ranged from 4.26 × 103 to 4.95 × 106 Ω. The AC conductivities of all the ceramics displayed semiconducting characteristics, exhibiting a frequency dependence that conforms to Jonscher's power law. The observed performance of the dielectric of the ceramic can be ascribed to the Internal Barrier Layer Capacitance (IBLC) model.

Cyclic and helical symmetry-informed machine learned force fields: Application to lattice vibrations in carbon nanotubes

We present a formalism for developing cyclic and helical symmetry-informed machine learned force fields (MLFFs). In particular, employing the smooth overlap of atomic positions descriptors with the polynomial kernel method, we derive cyclic and helical symmetry-adapted expressions for the energy, atomic forces, and phonons, i.e., lattice vibration frequencies and modes. We use this formulation to construct a symmetry-informed MLFF for carbon nanotubes (CNTs), where the model is trained through Bayesian linear regression, with the data generated from ab initio density functional theory (DFT) calculations performed during on-the-fly symmetry-informed MLFF molecular dynamics simulations of representative CNTs. We demonstrate the accuracy of the MLFF model by comparisons with DFT calculations for the energies and forces, and density functional perturbation theory calculations for the phonons, while considering CNTs not used in the training. In particular, we obtain a root mean square error of 1.4×10−4 Ha/atom, 4.7×10−4 Ha/Bohr, and 4.8 cm−1 in the energy, forces, and phonon frequencies, respectively, which are well within the accuracy targeted in ab initio calculations. We apply this framework to study phonons in CNTs of various diameters and chiralities, where we identify the torsional rigid body mode that is unique to cylindrical structures and establish laws for variation of the phonon frequencies associated with the ring modes and radial breathing modes. Overall, the proposed formalism provides an avenue for studying nanostructures with cyclic and helical symmetry at ab initio accuracy, while providing orders-of-magnitude speedup relative to such methods.

What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations.

X-ray crystallography is an important technique to determine the positions of atoms in a protein crystal. However, because the native environment in which proteins function, is not a crystal, but a solution, it is not a priori clear if the crystal structure represents the functional form of the protein. Because the protein structure and function often depend critically on the pH, the question arises whether proton affinities are affected by crystallization. X-ray diffraction usually does not reveal protons, which makes it difficult to experimentally measure pKa shifts in crystals. Here, we investigate whether this challenge can be addressed by performing in silico titration with constant pH molecular dynamics (MD) simulations. We compare the computed pKa values of proteins between solution and crystal environment and analyze these differences in the context of molecular interactions. For the proteins considered in this work, pKa shifts were mostly found for residues at the crystal interfaces, where the environment is more apolar in the crystal than in water. Although convergence was an obstacle, our simulations suggest that in principle it is possible to apply constant pH MD to protein crystals routinely and assess the effect of crystallization on protein function more systematically than with standard MD simulations. We also highlight technical challenges that need to be addressed to make MD simulations of crystals more reliable.

Enhancing X-ray generation from twisted multilayer van der Waals materials by shaping electron wavepackets

We study twisted bilayer van der Waals (vdW) materials as a platform to generate versatile bremsstrahlung X-rays, and show that the twist angle in bilayer vdW materials provides an unprecedented degree of controllability over various properties of bremsstrahlung radiation from these materials. Specifically, we combine the waveshaping of the free electron’s quantum wavepacket with the unique crystalline atomic positioning of twisted bilayers to realize shaped bremsstrahlung X-rays, which feature enhancements in directionality and intensity. In the process, we present a theoretical model for bremsstrahlung radiation that is applicable to twisted multilayer vdW materials in general. We also investigate the dependence of our X-ray emission mechanism on physical parameters, including the interlayer spacing and number of layers. Our findings pave the way for the use of twisted multilayer van der Waals materials in the generation of tailored X-ray spectra for applications like X-ray imaging, X-ray fluorescence, and X-ray treatment.