Characterization Of Local Structures Research Articles

Mapping and Characterization of Local Structures of CsPbBr3.

Inorganic perovskite CsPbBr3 is a promising material for optoelectronic applications and high-energy radiation detection due to its excellent photophysical properties, high carrier mobility, large carrier diffusion length, and higher stability than organic perovskite materials. Understanding phase transitions at the atomic level is crucial for optimizing its applications. Here, we employ experimental characterizations and molecular dynamics simulations to study the phase transitions in CsPbBr3 as a function of temperature. The simulation results are compared with the experimental results, which include X-ray diffraction (XRD). Our simulations provide new insights into the electronic structure and dynamic behavior of the Cs, Pb, and Br atoms as a function of temperature. We observe distinct phase transitions from monoclinic to cubic and analyze the associated changes in the local environment through atomic density contour maps. Our analysis of the atomic density distributions of the Pb, Br, and Cs atoms provides information about the crystal symmetry as a function of temperature. The tilt and rotation angles of [PbBr6] octahedra are increasing with the temperature increase and are found nonzero above 410 K when the structure is cubic, exhibiting the presence of dynamic tilting. Overall, our findings shed light on the thermal stability and structural dynamics of CsPbBr3, contribute to the fundamental understanding of its phase behavior, and provide a crucial pivot for guiding the design of next-generation optoelectronic and radiation detection devices.

Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: A Symmetry-Based Perspective.

We report on a new method for the characterization of local structures in proteins based on extensive molecular dynamics (MD) simulations, here, 1 μs in length. The N-H bond of the Rho GTPase binding domain of plexin-B1 (RBD) serves as a probe and the potential, u(MD), which restricts its internal motion, as a qualifier of the local dynamic structure. u(MD) is derived from the MD trajectory as a function of the polar angles, (θ, φ), which specify the N-H orientation in the protein. u(MD) is statistical in character yielding empirical descriptions. To establish more insightful methodical descriptions, we develop a comprehensive method which approximates u(MD) by combinations of analytical Wigner functions that belong to the D2h point group. These combinations, called u(simulated), make it possible to gain a new perspective of local dynamic structures in proteins based on explicit potentials/free energy surfaces and associated probability densities, entropy, and ordering. A simpler method was developed previously using 100 ns MD simulations. In that case, the traditional "perpendicular N-H ordering" setting centered at Cα-Cα with (θ, φ) = (90, 90) and generally, featuring positive φ, prevailed. u(MD) derived from 1 μs MD simulations is considerably more complex requiring substantial model enhancement. The enhanced method applies to the well-structured sections of the RBD. It only applies partly to its loops where u(MD) extends into the negative-φ region where we detect nonperpendicular N-H ordering. This arrangement requires devising new reference structures and making substantial algorithmic changes, to be performed in future work. Here, we focus on developing the comprehensive method and using it to investigate perpendicular ordering settings. We find that secondary structures (loops) exhibit varying (virtually invariant) potentials with Ag, B2u, and B1u (Ag and B2u) D2h symmetry. Application to RBD dimerization and RBD binding to the GTPase Rac1 is described in the subsequent article. Applications to other probes, proteins, and biological functions, based on explicit local potentials, probability densities, entropy, and ordering, are possible.

Direct imaging of local atomic structures in zeolite using optimum bright-field scanning transmission electron microscopy.

Zeolites are used in industries as catalysts, ion exchangers, and molecular sieves because of their unique porous atomic structures. However, direct observation of zeolitic local atomic structures via electron microscopy is difficult owing to low electron irradiation resistance. Subsequently, their fundamental structure-property relationships remain unclear. A low-electron-dose imaging technique, optimum bright-field scanning transmission electron microscopy (OBF STEM), has recently been developed. It reconstructs images with a high signal-to-noise ratio and a dose efficiency approximately two orders of magnitude higher than that of conventional methods. Here, we performed low-dose atomic-resolution OBF STEM observations of two types of zeolite, effectively visualizing all atomic sites in their frameworks. In addition, we visualized the complex local atomic structure of the twin boundaries in a faujasite (FAU)-type zeolite and Na+ ions with low occupancy in eight-membered rings in a Na-Linde Type A (LTA) zeolite. The results of this study facilitate the characterization of local atomic structures in many electron beam-sensitive materials.

Effects of Grain Refinement and Thermal Aging on Atomic Scale Local Structures of Ultra-Fine Explosives by X-ray Total Scattering.

The atomic scale local structures affect the initiation performance of ultra-fine explosives according to the stimulation results of hot spot formation. However, the experimental characterization of local structures in ultra-fine explosives has been rarely reported, due to the difficulty in application of characterization methods having both high resolution in and small damage to unstable organic explosive materials. In this work, X-ray total scattering was explored to investigate the atomic scale local distortion of two widely applicable ultra-fine explosives, LLM-105 and HNS. The experimental spectra of atomic pair distribution function (PDF) derived from scattering results were fitted by assuming rigid ring structures in molecules. The effects of grain refinement and thermal aging on the atomic scale local structure were investigated, and the changes in both the length of covalent bonds have been identified. Results indicate that by decreasing the particle size of LLM-105 and HNS from hundreds of microns to hundreds of nanometers, the crystal structures remain, whereas the molecular configuration slightly changes and the degree of structural disorder increases. For example, the average length of covalent bonds in LLM-105 reduces from 1.25 Å to 1.15 Å, whereas that in HNS increases from 1.25 Å to 1.30 Å, which is possibly related to the incomplete crystallization process and internal stress. After thermal aging of ultra-fine LLM-105 and HNS, the degree of structural disorder decreases, and the distortion in molecules formed in the synthesis process gradually healed. The average length of covalent bonds in LLM-105 increases from 1.15 Å to 1.27 Å, whereas that in HNS reduces from 1.30 Å to 1.20 Å. The possible reason is that the atomic vibration in the molecule intensifies during the heat aging treatment, and the internal stress was released through changes in molecular configuration, and thus the atomic scale distortion gradually heals. The characterization method and findings in local structures obtained in this work may pave the path to deeply understand the relationship between the defects and performance of ultra-fine explosives.

A two-stage sparse algorithm for localization and characterization of local nonlinear structures

This paper considers the localization and characterization of nonlinear components in local nonlinear structures with noisy measurements, and a novel two-stage sparse identification method is proposed. In this algorithm, one set of candidate nonlinear basis functions are leveraged to characterize system nonlinearities. To effectively localize and characterize nonlinear components, the algorithm introduces two sparse stages. At the first sparse stage, the adaptive group Lasso is adopted to localize nonlinear components in structures. At the second sparse stage, the adaptive Lasso is used to further characterize the contributing nonlinear basis functions in the identified nonlinear positions. Since the first sparse stage can greatly decrease the number of candidate nonlinear basis functions, the contributing functions can be effectively selected and characterized at the second sparse stage. Compared with the one-stage sparse algorithms, the proposed algorithm is more robust to noise, i.e., the new method can correctly identify the local nonlinear structures with a lower Signal to Noise Ratio (SNR). In addition, many existed nonlinear identification methods, simultaneously require the synchronous data of vibration displacements, velocities and accelerations. If only vibration displacements are measured, the first and second order derivatives of displacement are conducted to estimate velocities and accelerations, respectively. Nevertheless, the noise mixed into the displacement measurement will be severely amplified in the process of derivative calculation, which will make the estimation of velocities and accelerations deviating from the actual value and reduce the identification accuracy. To avoid performing the second order derivative, the Duhamel's integral is adopted to rewrite the dynamic relationship between the system input and output. In addition, a non-parametric de-noising method based on reproducing kernel Hilbert space (RKHS) is further developed to reduce the effect of noise in vibration displacements and obtain vibration velocities, which can effectively reduce the effect of noise and improve the identification accuracy. The numerical and experimental studies verify the potential and effectiveness of the proposed algorithm in localizing and characterizing nonlinear components in local nonlinear structures.

Point defect induced incommensurate dipole moments in the KCa2Nb3O10 Dion-Jacobson layered perovskite

Local structural distortions due to isolated atomic defects and defect complexes strongly affect the macroscopic properties of oxide ceramics. While the characterization of local defect structures is more common in simple $\mathrm{AB}{\mathrm{O}}_{3}$ perovskites, unambiguous determination of the same in layered perovskites is more difficult due to their complex crystal structures. Here, we combined x-ray pair distribution function and density functional theory calculations to characterize the structure of cation-oxygen divacancy pairs in a Dion-Jacobson (D-J) layered perovskite. Our results indicate that local incommensurate dipole moments with polarization density in the range of $\ensuremath{\sim}0.1--17\phantom{\rule{0.16em}{0ex}}\ensuremath{\mu}\mathrm{C}/\mathrm{c}{\mathrm{m}}^{2}$ are created due to divacancy-induced structural distortions in the D-J phase $\mathrm{K}{\mathrm{Ca}}_{2}{\mathrm{Nb}}_{3}{\mathrm{O}}_{10}$. This is comparable with defect dipole moments observed in well-known perovskite ferroelectrics. The current results imply that controlling the atomic defects can potentially lead to significant control of dielectric properties in D-J layered perovskites.

Characterization of Local Structures of Confined Imidazolium Ionic Liquids in PVdF-co-HFP Matrices by High Pressure Infrared Spectroscopy

The nanoscale ion ordering of ionic liquids at confined interfaces under high pressures was investigated in this study. 1-Hexyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([HMIM][NTf2])/poly(vinylidene fluoride-co-hexafluoropropylene) (PVdF-co-HFP) and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][NTf2])/PVdF-co-HFP were prepared and characterized by using high-pressure infrared spectroscopy. Under ambient pressure, imidazolium C2–H and C4,5–H absorptions were blue-shifted in frequency due to the presence of PVdF-co-HFP. However, the absorption of anionic νa SO2 did not reveal any significant shifts in frequency upon dilution by PVdF-co-HFP. The experimental results suggest that PVdF-co-HFP disturbs the local structures of the imidazolium C–H groups instead of the anionic SO2 groups. The frequency shifts of C4,5–H became dramatic for the mixtures at high pressures. These results suggest that pressure-enhanced ionic liquid–polymer interactions may play an appreciable role in IL-PVdF-co-HFP systems under high pressures. The pressure-induced blue-shifts due to the PVdF-co-HFP additions were more obvious for the [HMIM][NTf2] mixtures than for [EMIM][NTf2] mixtures.

Anisotropic-Scale Junction Detection and Matching for Indoor Images.

Junctions play an important role in characterizing local geometrical structures of images, and the detection of which is a longstanding but challenging task. Existing junction detectors usually focus on identifying the location and orientations of junction branches while ignoring their scales, which, however, contain rich geometries of images. This paper presents a novel approach for junction detection and characterization, which especially exploits the locally anisotropic geometries of a junction and estimates its scales by relying on an a-contrario model. The output junctions are with anisotropic scales, saying that a scale parameter is associated with each branch of a junction and are thus named as anisotropic-scale junctions (ASJs). We then apply the new detected ASJs for matching indoor images, where there are dramatic changes of viewpoints and the detected local visual features, e.g., key-points, are usually insufficient and lack distinctive ability. We propose to use the anisotropic geometries of our junctions to improve the matching precision of indoor images. The matching results on sets of indoor images demonstrate that our approach achieves the state-of-the-art performance on indoor image matching.Junctions play an important role in characterizing local geometrical structures of images, and the detection of which is a longstanding but challenging task. Existing junction detectors usually focus on identifying the location and orientations of junction branches while ignoring their scales, which, however, contain rich geometries of images. This paper presents a novel approach for junction detection and characterization, which especially exploits the locally anisotropic geometries of a junction and estimates its scales by relying on an a-contrario model. The output junctions are with anisotropic scales, saying that a scale parameter is associated with each branch of a junction and are thus named as anisotropic-scale junctions (ASJs). We then apply the new detected ASJs for matching indoor images, where there are dramatic changes of viewpoints and the detected local visual features, e.g., key-points, are usually insufficient and lack distinctive ability. We propose to use the anisotropic geometries of our junctions to improve the matching precision of indoor images. The matching results on sets of indoor images demonstrate that our approach achieves the state-of-the-art performance on indoor image matching.

Giant Optical Second Harmonic Generation in Two-Dimensional Multiferroics.

Nonlinear optical properties of materials such as second and higher order harmonic generation and electro-optic effect play pivotal roles in lasers, frequency conversion, electro-optic modulators, switches, and so forth. The strength of nonlinear optical responses highly depends on intrinsic crystal symmetry, transition dipole moments, specific optical excitation, and local environment. Using first-principles electronic structure theory, here we predict giant second harmonic generation (SHG) in recently discovered two-dimensional (2D) ferroelectric-ferroelastic multiferroics-group IV monochalcogenides (i.e., GeSe, GeS, SnSe, and SnS). Remarkably, the strength of SHG susceptibility in GeSe and SnSe monolayers is more than 1 order of magnitude higher than that in monolayer MoS2, and 2 orders of magnitude higher than that in monolayer hexagonal BN. Their extraordinary SHG is dominated by the large residual of two opposite intraband contributions in the SHG susceptibility. More importantly, the SHG polarization anisotropy is strongly correlated with the intrinsic ferroelastic and ferroelectric orders in group IV monochalcogenide monolayers. Our present findings provide a microscopic understanding of the large SHG susceptibility in 2D group IV monochalcogenide multiferroics from first-principles theory and open up a variety of new avenues for 2D ferroelectrics, multiferroics, and nonlinear optoelectronics, for example, realizing active electrical/optical/mechanical switching of ferroic orders in 2D multiferroics and in situ ultrafast optical characterization of local atomistic and electronic structures using noncontact noninvasive optical SHG techniques.

A comparative study on local atomic configurations characterized by cluster-type-index method and Voronoi polyhedron method

To assess strengths and weaknesses of cluster-type-index method (CTIM) and Voronoi polyhedron method (VPM) in the characterization of local structures, the similarity and difference between CTIM clusters and Voronoi polyhedrons (VPs) in under-cooled liquids and rapidly solidified solids of silvers are analyzed from the configurational view of point. By tracking identification numbers of atoms, it is found that one kind of VPs usually corresponds to several kinds of CTIM clusters with same or higher coordination number of central atoms, and the local structures of fcc lattices and hcp lattices can hardly be distinguished from each other merely based on their Voronoi polyhedron indexes 〈0, 12, 0, 0〉. In CTIM, the fcc and hcp basic clusters can be characterized by (12, 12/1421) and (12, 6/1421, 6/1422), respectively, but their total are less than the population of 〈0, 12, 0, 0〉 VPs in the same simulated system. A careful analysis of VPs with and without refinement reveals that the diminishment of shell atoms associated with tiny Voronoi polygons should be responsible for low coordination numbers of central atoms in VPs relative to their counterparts of CTIM clusters. The CTIM based on Honeycutt-Andersen (H-A) pair analysis can identify more kinds of atomic clusters, but its multi-indexes nature makes the feature extraction from various local atomic configurations more difficult.

Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy.

For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties.

High spectral specificity of local chemical components characterization with multichannel shift-excitation Raman spectroscopy

Raman spectroscopy has emerged as a promising tool for its noninvasive and nondestructive characterization of local chemical structures. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances, because of limitations in the spectral resolving power. The challenge is to find a way of preserving scattered photons and retrieving hidden/buried Raman signatures to take full advantage of its chemical specificity. Here, we demonstrate a multichannel acquisition framework based on shift-excitation and slit-modulation, followed by mathematical post-processing, which enables a significant improvement in the spectral specificity of Raman characterization. The present technique, termed shift-excitation blind super-resolution Raman spectroscopy (SEBSR), uses multiple degraded spectra to beat the dispersion-loss trade-off and facilitate high-resolution applications. It overcomes a fundamental problem that has previously plagued high-resolution Raman spectroscopy: fine spectral resolution requires large dispersion, which is accompanied by extreme optical loss. Applicability is demonstrated by the perfect recovery of fine structure of the C-Cl bending mode as well as the clear discrimination of different polymorphs of mannitol. Due to its enhanced discrimination capability, this method offers a feasible route at encouraging a broader range of applications in analytical chemistry, materials and biomedicine.

G-Losa: An Efficient Computational Tool for Local Structure-Centric Biological Studies

Molecular recognition such as ligand binding and protein-protein interaction (PPI) is a fundamental way for biological molecules to play their functional roles. These specific interactions are involved in the local regions of the molecules, rather than global structures. Therefore, accurate characterization of local structures in protein is needed to better understand biological mechanisms and to rationally design effective drugs. G-LoSA, a recently developed local structure alignment tool, has the advantages of not only predicting the ligand binding sites with high accuracy, but also identifying a single template ligand that is highly similar to the target ligand. Here, we present an improved version of G-LoSA aiming at extending its applicability to broad local structure-centric biological studies. The method generates all possible alignments between two local structures by iterative maximum clique search and fragment superposition and then determines the final optimal alignment by a G-LoSA alignment scoring function, GA-score. GA-score is a length-independent and physicochemical property-based scoring function to measure structural similarity between two local structures. G-LoSA outperforms its previous version in identifying ligand templates and also shows robust performance in detecting similar ligand binding pockets and PPI interfaces from the benchmark sets. Finally, we introduce its application to in silico fragment-based drug design. As demonstrated by this work, G-LoSA is a promising computational tool that can be universally applied to diverse local structure-centric biological studies.

Characterization of local structures with bond-order parameters and graphs of the nearest neighbors, a comparison

We compare two methods for the characterization of local order in samples undergoing crystal nucleation and growth. Particles with a crystal-like surrounding need to be identified to follow the nucleation process. Both methods are based on the knowledge of the particle positions in a small volume of the sample. (i) Local bond-order parameters are used to quantify the orientation of the nearest neighbors of a particle, while (ii) the graph method determines the topological arrangement of the nearest neighbors and the bonds between them. Both methods are used to detect crystal-like particles and crystal nuclei in a supercooled fluid surrounding and to determine the structure of small crystal nuclei. The properties of these nuclei are of great interest for a deeper understanding of crystal nucleation, and they can be studied in detail in colloidal model systems that allow to follow the evolution of the nuclei with single particle resolution.

Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis

Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

Characterization of Local Strain Structures in Heteroepitaxial Ge1−x Sn x /Ge Microstructures by using Microdiffraction Method

not Available.

A Solid‐Solution Approach to Mixed‐Metal Metal–Organic Frameworks – Detailed Characterization of Local Structures, Defects and Breathing Behaviour of Al/V Frameworks (Eur. J. Inorg. Chem. 26/2013)

A Solid‐Solution Approach to Mixed‐Metal Metal–Organic Frameworks – Detailed Characterization of Local Structures, Defects and Breathing Behaviour of Al/V Frameworks (Eur. J. Inorg. Chem. 26/2013)

A Solid‐Solution Approach to Mixed‐Metal Metal–Organic Frameworks – Detailed Characterization of Local Structures, Defects and Breathing Behaviour of Al/V Frameworks

AbstractInvited for the cover of this issue is the group of Roland Fischer at Ruhr University Bochum. The cover image shows that the structure/properties of materials vary as the complexity of the framework is increased and different metals are combined in single‐phased MOFs.

Characterization of Local Strain Structures in Heteroepitaxial Ge1−x Sn x /Ge Microstructures by Using Microdiffraction Method

In this study, we have examined the local growth of Ge1 − x Sn x heteroepitaxial layers on micrometer-scale-patterned Ge substrates with molecular beam epitaxy method. We have investigated the strain relaxation behavior and microscopic local strain structure in both Ge and Ge1 − x Sn x by using x-ray microdiffraction and finite element method calculation. We found that the anisotropic strain relaxation of embedded Ge1 − x Sn x layers preferentially occurs along the direction which is perpendicular to the stripe line. Microdiffraction method revealed that the elastic strain relaxation of the embedded Ge1 − x Sn x layer occurs near the edge region. We demonstrated that the uniaxial compressive strain of 0.2% is locally induced in Ge with Ge1 − x Sn x stressors.

A Solid‐Solution Approach to Mixed‐Metal Metal–Organic Frameworks – Detailed Characterization of Local Structures, Defects and Breathing Behaviour of Al/V Frameworks

AbstractThe doping of [Al(OH)L]n [L = 1,4‐benzenedicarboxylate (bdc) or 1,4‐naphthalenedicarboxylate (ndc)] with vanadium ions yields crystalline porous mixed‐metal solid‐solution metal–organic frameworks (MOFs) of general formula [(AlOH)1–x(VO)xL]n (x can be varied in the whole range from 0 to 1). Several characterization methods, including powder X‐ray diffraction (PXRD), electron paramagnetic resonance (EPR), solid‐state NMR and FTIR spectroscopy, strongly support the effective incorporation of vanadium cations. The Al/V‐doped MOFs are isostructural to the parent monometallic MOFs and show a characteristic uniform dependence of the cell parameters on the metal ratios. Detailed spectroscopic investigation provided evidence that the introduced species are fairly well ordered. Interestingly, for low amounts of doped vanadium for both activated and as‐synthesized Al/V phases, the EPR results revealed the presence of vanadyl units as local defects in pseudo‐octahedral or square‐pyramidal environments, which are different from those in the parent MIL‐47(V). This observation matches the nonlinear response of the adsorption properties on variation of the composition. Remarkably, the presence of such mixed Al/V chains strongly affects the breathing behaviour of the materials. Both CO2 sorption and in situ PXRD studies validated a gradual change from highly flexible (with easily induced phase transitions) to totally rigid structures upon increasing vanadium content.