Location Of Atoms Research Articles

STRUCTURAL INVESTIGATION AND HIRSHFELD SURFACE ANALYSIS OF N-(3-CHLORO-4-METHYLPHENYL)-2-(3-NITROBENZAMIDO)BENZAMIDE

A new synthesis of N-(3-chloro-4-methylphenyl)-2-(3-nitrobenzamido)benzamide was developed in acetic acid as a solvent using the reaction of 3-choloro-4-methylaniline, and 2-(3-nitrophenyl)-4H-benzo-[1,3]oxazin-4-one. This method proved to be efficient in the synthesis of the bis amide compound in good yields and purity. The compound, C21H16ClN3O4, was characterized by single-crystal XRD, IR, 1H NMR, and 13C NMR spectroscopic studies. In the crystal, the molecules are linked by N–H···O and C–H···O hydrogen bonds. There are also weak π···π interactions in the compound form a layer structure parallel to the bc plane. In addition, Hirshfeld surface analysis was carried out to investigate the location of atoms with the potential to form hydrogen bonds and the numerical ratio of these interactions of the compound.

Theoretical analysis of polarization-angle-dependent magic-wavelength optical dipole trap of Cs atoms

Laser cooling and trapping of neutral atoms is of great significance for studying the physical and chemical properties of atoms. To further realize the spatial localization of atoms, optical dipole trap (ODT) was proposed to manipulate individual atoms, ions or molecules and has become an increasingly important technique in the field of cold atomic physics and quantum optics. To eliminate the differential light shift of transitions between atomic states, ODT can be turned off during excitation/radiation. However, it will shorten the trap lifetime of the atom and reduce the repetition rate of the single photon. The AC stark shift can be eliminated experimentally by constructing blue-detuned dark ODT, but the micron-level dark ODT usually requires more complex experimental equipment and is not easy to operate. Therefore, magic-wavelength ODT was constructed to realize that the transition frequency of photons between atomic states is the same as in free space. When the trapping laser makes the differential light shift of the transition between the two atomic states zero, the laser wavelength is called the magic wavelength. The magic-wavelength ODT can eliminate the differential light shift of the transition between atoms, improve the repetition rate of the experimental sequence and weaken the atomic decoherence. In recent years, it has become a powerful tool for manipulating cold atoms, especially for coherently manipulating the atomic inner states. In the present work, with the theory of multi-level model, we calculate the dynamic electric polarizability of the 6S<sub>1/2</sub> ground state and the 6P<sub>3/2</sub> excited state connecting the D2 line of cesium atom in a range of 800–1000 nm, and obtain the magic wavelength of the optical trapping laser to trap the ground state and the excited state. Since the polarizability of atomic states with angular momentum greater than 0.5 is very sensitive to the polarization angle, the polarization-angle-dependent magic wavelength and the corresponding magic polarizability are analyzed by taking the linearly-polarized trapping laser for example. The magic polarization angle is 54.7° and the magic wavelength at this angle are 886.4315 and 934.0641 nm, respectively. The robustness of the magic conditions and the feasibility of the experimental operation are further analyzed.

INVESTIGATING THE STRUCTURAL AND SURFACE PROPERTIES OF COPPER AND NICKEL COMPLEXES FLUORINE-BASED SALEN TYPE SCHIFF BASES

Two new transition metal complexes, NiL1 (1) and CuL2 (2), with formulations C18H12F6N2NiO4 and C18H12CuF6N2O4, respectively, were synthesized through the slow evaporation method in ethanol. The synthesized complexes were extensively characterized using X-ray diffraction, Fourier transform infrared spectroscopy, and UV-Vis spectroscopy techniques. X-ray crystallographic analysis revealed that the Ni(II) and Cu(II) salen complexes consist of double deprotonated tetrafunctional chelating ligands, namely L1 for NiL1 and L2 for CuL2, along with the corresponding metal cations, Ni+2 and Cu+2. The asymmetric unit of NiL1 comprises half of the molecule, while the asymmetric unit of CuL2 consists of a single molecule. In the crystal lattice, the molecules of both complexes are interconnected through C–H···O and C–H···F hydrogen bonds. Additionally, weak π···π interactions contribute to the formation of a layered structure in both complexes. To gain further insight into the intermolecular interactions, Hirshfeld surface analysis was employed, enabling the identification of atom locations with potential for hydrogen bonding and providing a quantitative assessment of these interactions in the complexes. The analysis revealed that the dominant contributions to the Hirshfeld surface originated from F···H, H···H, and O···H contacts in both NiL1 and CuL2 complexes.

Investigations of the Mn–Ni–Sm ternary system by means of anomalous X-ray diffraction, X-ray absorption and DFT calculations

Various applications benefit from the use of compounds combining lanthanides and 3d metals because of their fundamental physicochemical properties. To tune compositions for dedicated applications and to overcome the criticality of raw materials or geopolitical tension, a better understanding of the binary, ternary and even quaternary systems is needed. The present work focuses on the ternary Mn-Ni-Sm system, which is particularly interesting for energy storage applications as it forms hydrogen absorbing intermetallic compounds. The fruitful combination of standard X-ray diffraction, anomalous X-ray diffraction close to the Mn 3d edge, X-ray absorption near edge structure, electron probe micro-analysis and first-principles calculations provides a better understanding of the physicochemical properties and phase equilibrium of this ternary system. In particular, the atomic substitution of Mn atoms in the Ni sites has been investigated for the stacking AB2/AB5 Sm2MnyNi7-y system. The Mn atoms substitute preferentially in the AB5 sub-units, whereas Sm vacancies are observed in the AB2 sub-units inducing an antagonist variation in cell volume units. In the SmMnyNi12-y system, the preferential localization of Mn atoms has been highlighted in site 8i for the SmMn4Ni8 compound.

Benchmark Tests of Atom Segmentation Deep Learning Models with a Consistent Dataset.

The information content of atomic-resolution scanning transmission electron microscopy (STEM) images can often be reduced to a handful of parameters describing each atomic column, chief among which is the column position. Neural networks (NNs) are high performance, computationally efficient methods to automatically locate atomic columns in images, which has led to a profusion of NN models and associated training datasets. We have developed a benchmark dataset of simulated and experimental STEM images and used it to evaluate the performance of two sets of recent NN models for atom location in STEM images. Both models exhibit high performance for images of varying quality from several different crystal lattices. However, there are important differences in performance as a function of image quality, and both models perform poorly for images outside the training data, such as interfaces with large difference in background intensity. Both the benchmark dataset and the models are available using the Foundry service for dissemination, discovery, and reuse of machine learning models.

The model of austenite structure state taking into account fluctuations of magnetic nature

The results of magnetic state simulation of carbon steel austenite are presented in this work. Quantitative parameters of the areas of short-range magnetic order, which are presented in paramagnetic austenite matrix and are observed as potential places of α-phase nucleation, are examined. This austenite heterogeneity in steels and clean iron is confirmed by the experimental data; however, detailed quantitative study meets technical complication of such experiments. It is suggested to use the Ising model for realization of the calculation experiment. The obtained spin configurations were analyzed for determination of geometric parameters of magnetic inhomogeneities and period of their sustainable existence. Calculations were conducted within the temperature range of austenite phase existence in steel, as well as without and with taking into account presence of external magnetic field, which strengthens existing austenite heterogeneity and has the effect on conduction of phase transformations in steel. The results of simulation confirm presence of the areas of short-range magnetic order in austenite, their size is close to the existing theoretical assessments and experimental data. It is shown that temperature rise leads to decrease of dimensions, number and life period of clusters, but these parameters are still important at the temperature of martensite transformation in steel. Overlapping of external magnetic field creates the conditions for existence of large-size ferromagnetic clusters also at more high temperatures, as well as increases time of their sustainable existence. The external magnetic field provides the conditions for more intensive and multiplicative nucleation of ferromagnetic phase, similar to short-range magnetic order fluctuations in location of atoms during liquid metal cooling. 

Elucidation of the Local Structure of the Topological Insulator β-PdBi2 by X-ray Fluorescence Holography

The local structures around the Bi and Pd atoms in β-PdBi2 were determined from Bi Lα and Pd Kα X-ray fluorescence holography (XFH) images measured with synchrotron radiation at room temperature, demonstrating clear atomically resolved images along the c-axis (z-axis). More precisely, the location of atoms in the atomic layer at z = 0 Å was unambiguously determined from each hologram; that is, the location of Bi atoms at z = 0 Å was determined from Bi Lα XFH, whereas the location of Pd atoms at z = 0 Å was unambiguously determined from Pd Kα XFH. Moreover, the Bi atoms in the atomic plane at z = 3.6 Å were clearly reconstructed from Bi Lα XFH with Barton’s algorithm. However, clear atomic images of the planes at z = 1.8 Å and z = 2.9 Å were not obtained from the Bi Lα holograms, nor were they observed at z = 1.8 Å in the case of the Pd Kα holograms; some weak atomic images of Bi at z = 4.7 Å were observed from Pd Kα holograms. Thus, two different patterns can be distinguished for the atomic images in the plane at z ≠ 0 Å: a clear atomic image and an ambiguous atomic image, owing to the order or disorder between the atomic layers. The small fluctuation or the small disorder between the atomic layers formed through the attractive interaction of Bi––Pd2+–Bi– provides clear atomic images, whereas the atomic layers formed via weak van der Waals interactions lead to ambiguous atomic images. Thus, the atomic images of β-PdBi2 obtained by XFH clearly reproduce not only the crystal structure determined by single-crystal X-ray diffraction but also provide information on thermal fluctuation and static disorder between the atomic layers.

Reduced Thermal Conductivity in Nanostructured AgSbTe2 Thermoelectric Material, Obtained by Arc-Melting.

AgSbTe2 intermetallic compound is a promising thermoelectric material. It has also been described as necessary to obtain LAST and TAGS alloys, some of the best performing thermoelectrics of the last decades. Due to the random location of Ag and Sb atoms in the crystal structure, the electronic structure is highly influenced by the atomic ordering of these atoms and makes the accurate determination of the Ag/Sb occupancy of paramount importance. We report on the synthesis of polycrystalline AgSbTe2 by arc-melting, yielding nanostructured dense pellets. SEM images show a conspicuous layered nanostructuration, with a layer thickness of 25-30 nm. Neutron powder diffraction data show that AgSbTe2 crystalizes in the cubic Pm-3m space group, with a slight deficiency of Te, probably due to volatilization during the arc-melting process. The transport properties show some anomalies at ~600 K, which can be related to the onset temperature for atomic ordering. The average thermoelectric figure of merit remains around ~0.6 from ~550 up to ~680 K.

First principles study structural and magnetic properties of Mn doped MgO

The structure, electronic and magnetic properties of the MgO bulk of (1x2x2) and (1x1x1) atoms for the B4 wurtzite phase, doped by Manganese Mn have been studied. Accordingly, the Mn atom location in the far and near spots was taken into account, as well as recognizing the magnetic interaction between both spots. Such initiative was provided thanks to the use of the density function theorem (DFT). As for the energy gap of the semiconductor MgO, it was calculated by the linearly increasing planar method, and by the local density approximation (LDA), not to mention the generalized gradient approximation (CGA).It is found that the calculated results agree well with other theoretical and experimental findings. Whereas, the energy gap and the total magnetic torque have been recorded for the Mn doped MgO in the (1x2x2) super Celle. Therefore, our given results have shown that the use of the classification-generalized approximation could enable us to provide more precise results of the d orbital composites, and they also added new properties to the new compound.

Bichromatic state-dependent disordered potential for Anderson localization of ultracold atoms

The ability to load ultracold atoms at a well-defined energy in a disordered potential is a crucial tool to study quantum transport, and in particular Anderson localization. In this paper, we present a new method for achieving that goal by rf transfer of atoms in an atomic Bose-Einstein condensate from a disorder-insensitive state to a disorder-sensitive state. It is based on a bichromatic laser speckle pattern, produced by two lasers whose frequencies are chosen so that their light-shifts cancel each other in the first state and add up in the second state. Moreover, the spontaneous scattering rate in the disorder-sensitive state is low enough to allow for long observation times of quantum transport in that state. We theoretically and experimentally study the characteristics of the resulting potential.Graphic abstract

Structural and electrical properties of Mg–Cu- and Mg–Cu–Li-doped bismuth niobate semiconductors with the pyrochlore structure

This work studies a series of synthesized Bi1.6Mg0.8-xCuxNb1.6O7-δ (x = 0.2, 0.4) semiconductors and their Li-doped compositions. A detailed structure investigation combining high-resolution neutron-, synchrotron-, and X-ray diffraction methods, as well as DFT calculations, revealed the preferential location of Cu and Li atoms at the Bi sites and Mg atoms at the Nb ones. According to high-temperature X-ray diffraction data, a structural modification caused by the activation of oxygen transport occurs at 200 °C. The linear thermal expansion coefficient was found to be 3.6–4.6·10−6 K−1 (50–400 °C). Magnetic susceptibility measurements allowed us to determine weak antiferromagnetic exchange interactions. The direct band gap was predicted using the DFT-HSE03 hybrid functional calculation, and the optical direct band gap was estimated at 2.3–2.4 eV. Impedance spectroscopy and a dc four-probe technique were also employed to examine the samples' electrical properties. The high mixed electronic-ionic conductivity of the pyrochlores was detected, while the vacancies created by Li-doping in Bi1.5-yLiyMg0.375Cu0.375Nb1.5O7-δ have been found not to affect the conductivity. Besides, the pyrochlores are chemically compatible with the La0.7Sr0.3MnO3 perovskite (up to 800 °C). These make us believe that the studied Mg–Cu- and Mg–Cu–Li-doped bismuth niobate semiconductors can become the basis for composite electrodes to boost their oxygen conductivity.

A Red-Emitting Fluorescence Sensor for Detecting Boronic Acid-Containing Agents in Cells.

The amount and localization of boron-10 atoms delivered into tumor cells determines the therapeutic effect of boron neutron capture therapy (BNCT) and, consequently, efforts have been directed to develop fluorescence sensors to detect intracellular boronic acid compounds. Currently, these sensors are blue-emitting and hence are impracticable for co-staining with nucleus staining reagents, such as DAPI and Hoechst 33342. Here, we designed and synthesized a novel fluorescence boron sensor, BS-631, that emits fluorescence with a maximum emission wavelength of 631 nm after reaction with the clinically available boronic acid agent, 4-borono-l-phenylalanine (BPA). BS-631 quantitatively detected BPA with sufficiently high sensitivity (detection limit = 19.6 µM) for evaluating BNCT agents. Furthermore, BS-631 did not emit fluorescence after incubation with metal cations. Notably, red-emitting BS-631 could easily and clearly visualize the localization of BPA within cells with nuclei co-stained using Hoechst 33342. This study highlights the promising properties of BS-631 as a versatile boron sensor for evaluating and analyzing boronic acid agents in cancer therapy.

Fe Atom—Mixed Edges Fractal Graphene via DFT Calculation

The stability of small fractal graphene models with two different symmetries and Fe atoms at their mixed edges is addressed by density functional theory (DFT) calculations. Four kinds of edge configurations and Fe atom localizations are determined depending on the model. The edges have mixed configuration, the zig-zag and “intra-zig-zag” in symmetrical structures and armchair and zig-zag type in the architectures with rotational symmetry. The rotational symmetry graphene exhibits slightly higher stability per carbon atom compared to the symmetrical model, while the localization of Fe atoms is more favorable at armchair and “inversed zigzag” than at zigzag type carbon termination. Larger graphene structures with rotational symmetry were observed previously via experimental cutting of graphene with Fe nanoparticles (NPs).

A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images.

A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.

Neural representations of cryo-EM maps and a graph-based interpretation

BackgroundAdvances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Producing a protein structure from the discrete voxel grid data of cryo-EM maps involves interpolation into the continuous spatial domain. We present a novel data format called the neural cryo-EM map, which is formed from a set of neural networks that accurately parameterize cryo-EM maps and provide native, spatially continuous data for density and gradient. As a case study of this data format, we create graph-based interpretations of high resolution experimental cryo-EM maps.ResultsNormalized cryo-EM map values interpolated using the non-linear neural cryo-EM format are more accurate, consistently scoring less than 0.01 mean absolute error, than a conventional tri-linear interpolation, which scores up to 0.12 mean absolute error. Our graph-based interpretations of 115 experimental cryo-EM maps from 1.15 to 4.0 Å resolution provide high coverage of the underlying amino acid residue locations, while accuracy of nodes is correlated with resolution. The nodes of graphs created from atomic resolution maps (higher than 1.6 Å) provide greater than 99% residue coverage as well as 85% full atomic coverage with a mean of 0.19 Å root mean squared deviation. Other graphs have a mean 84% residue coverage with less specificity of the nodes due to experimental noise and differences of density context at lower resolutions.ConclusionsThe fully continuous and differentiable nature of the neural cryo-EM map enables the adaptation of the voxel data to alternative data formats, such as a graph that characterizes the atomic locations of the underlying protein or macromolecular structure. Graphs created from atomic resolution maps are superior in finding atom locations and may serve as input to predictive residue classification and structure segmentation methods. This work may be generalized to transform any 3D grid-based data format into non-linear, continuous, and differentiable format for downstream geometric deep learning applications.

Evaluation of the Causes of Interest Decline in the Subject of Chemistry amongst Secondary and Higher Secondary School Students in Karachi Pakistan

This study aim to determine why high secondary and higher secondary school students are losing their interest in Chemistry. This comparative study polled 450 secondary and higher secondary school students from a private institute of Karachi East. Descriptive analysis was done Using SPSS, result showed that secondary school (grade 10) and higher secondary school (grade 11) students are less interested in chemistry but grade 12 students acted inconsistently. Most students of grade 12 were delighted with grade 11 chemistry's numerical-based themes, while others struggled with equations and IUPAC names in second year. The study began with interviews of first-year students (grade 11), only 10 out of 450 interviewees named chemistry as their favorite subject. Students find chemistry to be a tough subject and not career-related. Personal trait and choice decreased pupils' interest in Chemistry. Students believe that atomic structure, electron location, reaction mechanism, and orbital forms are hypothetical, making it harder to understand. They find experimental chemistry more intriguing because they can see what they are doing. The board syllabus experiments have distinct subjects from the theory syllabus. Audio-visual tools for conceptual learning, trained chemistry teachers, and seminars on "the professional scope of Chemistry courses" might assist improve students' interest in chemistry.

Quasicrystal stability in complex aluminum alloys: Insights from first principles models on structural motifs in crystalline approximants

Al81Cu7Fe4Cr8 is an alloy that readily forms quasicrystalline phases but understanding the complex atomic arrangements in the structure of such quasicrystals is challenging. For the Al-Cu-Fe-Cr system, the structures of crystalline approximants have been identified. These exhibit atomic motifs similar to those for the quasicrystalline configurations. We employ here a comprehensive methodology to analyze statistically generated ground states of orthorhombic approximants using density functional theory to shed light on the role of elemental variations of such complex alloys. Our findings show that the stability of QC approximants has a strong dependence on the specific locations of Cu and Cr atoms. The geometry of the atomic motifs from structural optimization suggests that the icosahedral phase is more favorable than the decagonal phase. The formation energy difference between these is small which indicates that the two quasicrystalline phases may coexist.

Atom Location by Channeling-Enhanced Microanalysis (ALCHEMI) Study of Structure of Complex Concentrated Alloys Derived From FeAl Iron Aluminide

Atom Location by Channeling-Enhanced Microanalysis (ALCHEMI) Study of Structure of Complex Concentrated Alloys Derived From FeAl Iron Aluminide

Shared Hydrogen Atom Location and Chemical Composition in Picolinic Acid and Pyridoxal Hydrochloride Derivatives Determined by X-ray Crystallography.

Three new single-crystal structures were isolated for picolinic acid (2), the trifluoroacetate salt of picolinic acid (1), and pyridoxal hydrochloride (3). These compounds displayed unconventional crystallographic features that must be considered when structural refinements are carried out. Thus, the generated Fourier differences map obtained with the diffraction data collected at 100 K was crucial to visualize electron densities, which were balanced by either one hydrogen atom or a hydrogen atom with an occupancy factor of 1/2 located between either two carboxylate moieties, two phenolic oxygen atoms, or two pyridinic nitrogen atoms. Moreover, NMR studies were conducted to analyze the bulk chemical composition of single crystals of 2-pyridinecarboxylic acid obtained from the gem-diol/hemiacetal forms and the polymerization products after the treatment of 2-pyridinecarboxaldehyde with TFA:H2O (1) or a diluted Cu(NO3)2 solution (2). The quantitative yield of the pyridoxal hydrochloride crystalline material (3) obtained from a diluted CuCl2 solution was exhaustively characterized by solid-state NMR methods. These methods allowed the resolution of the signals corresponding to the protons of the hydroxyl moiety of the intramolecular hemiacetal group and the phenolic hydrogen. Theoretical calculations using DFT methods were done to complement the atomic location of the hydrogen atoms obtained from the X-ray analysis.

Investigation of electric field effect on defects in GaAsN by admittance spectroscopy

• Electric-field dependent properties of defects in GaAsN. • Temperature dependent properties of defects in GaAsN. • Extraction of defect properties without the Arrhenius plot. We use the Arrhenius transformation and matching (ATM) method to extract activation energy and attempt-to-escape frequency of the nitrogen-related defect (E1) in GaAsN from admittance spectroscopy measurements taken at various temperature and electric field. The ATM method is equivalent to the conventional Arrhenius plot and line-fitting (APL) method for Arrhenius processes with temperature-independent E a and ν 0 (e.g., E1 in a low electric field and at high temperatures) and advantageous for non–Arrhenius processes with temperature-dependent E a and ν 0 , (e.g., E1 in a high electric field and at low temperatures), where the APL method is not reliable. The ATM method enables a detailed account on how E a evolves with the temperature and the electric field in a continuously varying experimental space, which is not possible with the APL method. The evolution of carrier emission behaviors from the E1 defect and a neighboring E2 defect provides experimental evidence of field-induced metastability possibly due to the interaction of two defects with close atomic origins or spatial locations.