Three-dimensional Atomic Arrangement Research Articles

Single-Molecule Identification of the Isomers of a Lipidic Antibody Activator.

Molecular structural elucidation can be accomplished by different techniques, such as nuclear magnetic resonance or X-ray diffraction. However, the former does not give information about the three-dimensional atomic arrangement, and the latter needs crystallizable solid samples. An alternative is direct, real-space visualization of the molecules by cryogenic scanning tunneling microscopy (STM). This technique is usually limited to thermally robust molecules because an annealing step is required for sample deposition. A landmark development has been the coupling of STM with electrospray deposition (ESD), which smooths the process and widens the scope of the visualization technique. In this work, we present the on-surface characterization of air-, light-, and temperature-sensitive rhamnopolyene with relevance in molecular biology. Supported by theoretical calculations, we characterize two isomers of this flexible molecule, confirming the potential of the technique to inspect labile, non-crystallizable compounds.

Revealing the three-dimensional arrangement of polar topology in nanoparticles

In the early 2000s, low dimensional ferroelectric systems were predicted to have topologically nontrivial polar structures, such as vortices or skyrmions, depending on mechanical or electrical boundary conditions. A few variants of these structures have been experimentally observed in thin film model systems, where they are engineered by balancing electrostatic charge and elastic distortion energies. However, the measurement and classification of topological textures for general ferroelectric nanostructures have remained elusive, as it requires mapping the local polarization at the atomic scale in three dimensions. Here we unveil topological polar structures in ferroelectric BaTiO3 nanoparticles via atomic electron tomography, which enables us to reconstruct the full three-dimensional arrangement of cation atoms at an individual atom level. Our three-dimensional polarization maps reveal clear topological orderings, along with evidence of size-dependent topological transitions from a single vortex structure to multiple vortices, consistent with theoretical predictions. The discovery of the predicted topological polar ordering in nanoscale ferroelectrics, independent of epitaxial strain, widens the research perspective and offers potential for practical applications utilizing contact-free switchable toroidal moments.

"Holographic" Autostereoscopic Displays: A Perspective on Their Technology and Potential Impact in Chemistry.

The three-dimensional arrangement of atoms in molecules is essential for understanding their properties and behavior. Traditional 2D representations and digital 3D models presented on 2D media often fall short in conveying the complexity of molecular structures. Autostereoscopic displays, often marketed as "holographic" displays, pose a potential solution to this challenge. These displays, with their multi-view and single-view configurations, promise to advance chemistry education and research by offering accurate 3D representations with depth and parallax. In this perspective, I delve into the possibilities and limitations of autostereoscopic displays in chemistry, discussing the underlying technology and potential applications, from research to teaching and science communication. Multi-view autostereoscopic displays excel in facilitating collaborative work by enabling multiple viewers to simultaneously perceive the same 3D structure from different angles. However, they currently suffer from low resolution and high cost, which could limit their immediate widespread adoption. Conversely, single-view autostereoscopic displays with eye-tracking, while limited to one viewer at a time, provide higher resolution at a lower cost, thus suggesting that they might become the technology of the future given the balance of price to performance. Despite current limitations, autostereoscopic displays possess undeniable potential for shaping the future of chemistry education and research.

Direct Observation of Locally Modified Excitonic Effects within a Moiré Unit Cell in Twisted Bilayer Graphene.

Bilayer graphene, which forms moiré superlattices, possesses distinct electronic and optical properties owing to its hybridized energy band and the emergence of van Hove singularities depending on its twist angle. Extensive research has been conducted on the global characteristics of moiré superlattices induced by their long-range periodicity. However, the local properties, which differ owing to the variations in the three-dimensional atomic arrangement, within a moiré unit cell have been rarely explored. In this study, we demonstrate the highly localized excitation of carbon 1s electrons to unoccupied van Hove singularities in twisted bilayer graphene by electron energy loss spectroscopy using a monochromated transmission electron microscope. The core-level excitations associated with the van Hove singularities exhibit a systematic twist-angle dependence analogous to optical excitations. Furthermore, local variations in the core-level van Hove singularity peaks, which can originate from the core-exciton lifetimes and band modifications corresponding to the local stacking geometry within a moiré unit cell, are unambiguously corroborated.

Physio-chemical properties of HCP ( U ) and HEX ( U ) crystal structure lattice via eccentricity dependent chemical invariants

A crystal lattice is the three-dimensional structural arrangement of atoms or molecules inside a crystalline solid as points. Each crystal lattice consists of repeating unit cells in different directions. From earlier scientific research, it was recognised that the physio-chemical properties of any crystal structure lattice are highly reliant on the molecular structure of the network. This study led us to investigate complex structures through a mathematical perspective using a chemical invariant (topological index) by a chemical graph theory that correlates a chemical graph structure and physio-chemical properties, where atoms represent the nodes and a bond between atoms is considered as an edge. In this research, we have given explicit expressions for eccentricity-based chemical invariants, namely, eccentric connectivity (EC), total eccentricity (TE), eccentricity-based Zagreb (EZ) and connective eccentric (CE) for inorganic symmetrical Hexagonal Close-Packed and Hexagonal ( crystal structure lattices.

Modulation of chiral spectral deflection by van der Waals force-induced molecular electropolarization in catenane oligomers.

The striking chiral optical properties of carbon nanostructures are closely related to the precise three-dimensional spatial arrangement (interaction) of carbon atoms. This work investigated the chiral optical properties of three different structures of all-benzene catenane and trefoil knot regulated by van der Waals (vdW) forces using density functional theory (DFT) calculations and wave function analysis. We systematically illustrate how molecular electrical polarization modulates the chiral optical deflection of alkane oligomers under the induction of van der Waals forces. In this work, the UV-vis spectra, transition density matrices (TDM), and electron-hole density diagrams of three molecules have been studied. Combined with a visualization method to represent the effect of molecular polarization on transition electric/magnetic dipole moments (TEDMs\TMDMs), the results show that vdW interactions can induce chirality deflection in polymers. This mechanism provides a clear direction for designing polymers with specific chirality: by modifying the structure, vdW interactions can be generated in specific regions, and then the chirality of the molecule can be precisely regulated. This will help us to establish a strategy for precisely-oriented design of chiral optical materials, and provide guidance for the application and development of optoelectronic materials in specific fields.

Imaging Atomic Structure, Strain, and Disorder By Atomic Electron Tomography

Knowledge of the atomic structure of materials is critical to understanding their functionality in many fields such as biology, microelectronics, condensed matter, and nanotechnology. Traditionally, x-ray crystallography has been the main method used to solve structures of all types. New techniques such as micro electron diffraction and single particle cryo electron microscopy are now utilizing electrons to study crystals that cannot be crystallized at the scales necessary for x-ray experiments. However, these techniques require ensembles of identical unit cells (like molecules or proteins) to solve the structure from a series of images or diffraction patterns. The need to average over many unit cells means that important material properties such as defects, dopants, and disorder are not captured. Investigations of unique arrangements of atoms requires a direct imaging method that does not rely on structural averaging or the assumption of crystallinity.Transmission electron microscopy (TEM) provides the ability to directly image atomic structure, and the development of powerful, stable aberration correctors in the last decade now routinely provide sub-Angstrom imaging resolution. Scanning TEM (STEM) has also become an effective method for measuring the atomic structure of inorganic materials based on so-called Z-contrast where the image intensities are proportional to the atomic number of the material being imaged. However, by their nature TEMs are limited to producing only two-dimensional projections of a structure. Electron tomography is a technique that can reconstruct the three-dimensional structure of unique nanoscale objects from a series of two-dimensional images acquired at different viewing angles. Tomography was traditionally limited to nanoscale resolution due to experimental difficulties and a lack of high-quality reconstruction algorithms.We have developed atomic electron tomography (AET) by utilizing the sub-Angstrom real-space resolution of STEM with advanced tomographic reconstruction algorithms to solve the structure of materials at the single atom level without averaging or the assumption of crystallinity. This talk will present recent progress and capabilities in the field of AET for reconstructing order and disorder in materials with 20 picometer precision. Our success in resolving chemical order/disorder in metallic FePt nanoparticles was extended to include the time domain by capturing nucleation and growth or ordered phases in the same nanoparticle. Also, the ability to reconstruct atomic structure without the need for averaging or crystallinity led to the achievement of directly imaging three-dimensional atomic arrangements in amorphous solids. We determined the chemical and structural disorder of an eight-element metallic glass to quantitatively characterize short- and medium-range order, and we determined the disordered atomic packing of monatomic amorphous materials.The field of electron microscopy is rapidly changing with the advent of improved detectors, aberration correctors, and monochromators. We are exploring the use of these new hardware to implement new imaging algorithms such as ptychography to allow AET to explore all new classes of materials especially lightly scattering materials like oxygen. We have also established the Materials Databank to share experimentally determined 3D atomic structures with other scientists. As more structures and classes of materials are solved, we expect AET to become an important technique in the field of atomic structural characterization.

Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule-Solvent Interface.

A DNA molecule is highly electrically charged in solution. The electrical potential at the molecular surface is known to vary strongly with the local geometry of the double helix and plays a pivotal role in DNA–protein interactions. Further out from the molecular surface, the electrical field propagating into the surrounding electrolyte bears fingerprints of the three-dimensional arrangement of the charged atoms in the molecule. However, precise extraction of the structural information encoded in the electrostatic “far field” has remained experimentally challenging. Here, we report an optical microscopy-based approach that detects the field distribution surrounding a charged molecule in solution, revealing geometric features such as the radius and the average rise per basepair of the double helix with up to sub-Angstrom precision, comparable with traditional molecular structure determination techniques like X-ray crystallography and nuclear magnetic resonance. Moreover, measurement of the helical radius furnishes an unprecedented view of both hydration and the arrangement of cations at the molecule–solvent interface. We demonstrate that a probe in the electrostatic far field delivers structural and chemical information on macromolecules, opening up a new dimension in the study of charged molecules and interfaces in solution.

Three-dimensional Atomic Image of FeSe High-temperature Superconductor by X-ray Fluorescence Holography

Fe Kα X-ray fluorescence holography measurements were carried out at room temperature on an FeSe high-temperature superconductor to clarify the relationship between the local structures around the Fe atoms and the superconducting nature. The obtained three-dimensional atomic arrangements strongly reveal a formation of strong FeSe4 clusters. On the other hand, the Se—Fe—Se bond angle largely spreads, causing a large ambiguity in the chalcogen height and large displacements of the Fe sublattice. Thus, it is reasonable that the tetragonal-to-orthorhombic structural (nematic) transition does not affect the magnetic ordering in the Fe layer.

Investigation of Two-Dimensional Geometric Patterns of Knot Arangements and other Cryptographic Methods on the Surfaces of Ancient Tiles (Kashis) and its Adaptation to Three-Dimensional Arrangement of Atoms in Crystalline Solids

Investigation of Two-Dimensional Geometric Patterns of Knot Arangements and other Cryptographic Methods on the Surfaces of Ancient Tiles (Kashis) and its Adaptation to Three-Dimensional Arrangement of Atoms in Crystalline Solids

Extended x-ray emission times of clusters in intense x-ray pulses

Recently, intensity correlation of x-ray fluorescence, based on the principle introduced by Hanbury Brown and Twiss [R. Hanbury Brown and R. Q. Twiss, Nature (London) 177, 27 (1956)], has been proposed for high-resolution imaging of a three-dimensional arrangement of atoms. To explore the applicability of this fluorescence approach, we theoretically investigate fluorescence dynamics of nonperiodic systems subject to x-ray free electron laser (XFEL) pulses over a range of fluences from the linear to nonlinear x-ray absorption regimes as a function of system size, from a single atom to a cluster of 149 171 atoms. Fluorescence dynamics in the nonlinear x-ray regime differs from that in the weak x-ray field in that intense x-ray pulses interrupt the fluorescence dynamics by multiphoton absorption creating a dense electron environment within the sample on a femtosecond timescale. In large systems, the presence of both recombination and photoionization pathways gives rise to an enhanced $K\ensuremath{\alpha}$ and $K{\ensuremath{\alpha}}^{h}$ emission yield and an extended emission time beyond the lifetime of the core-excited states. Our analysis suggests that, in an intense x-ray pulse, the $K{\ensuremath{\alpha}}^{h}$ emission line can be a good candidate for fluorescence imaging as it has a higher yield and an emission time that is short relative to the x-ray-induced lattice distortion time.

Visualization of the three-dimensional atomic arrangement of dopants in semiconductors by photoelectron holography

Visualization of the three-dimensional atomic arrangement of dopants in semiconductors by photoelectron holography

Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to re...

Three-dimensional atomic arrangement around active/inactive dopant sites in boron-doped diamond

Boron-doped diamond has received significant attention as an advanced material for power devices owing to its high breakdown characteristics. To control the characteristics of diamond related to band conduction, it is essential to determine the atomic structure around dopants and to develop a method of controlling the atomic arrangement around dopants. We measured the photoelectron diffraction of a boron-doped diamond using a display-type ellipsoidal mesh analyzer to examine the dopant sites in heavily boron-doped diamond. The B 1s photoelectron spectrum shows two peaks for different chemical bonding sites. These two dopant sites were identified as the substitutional and interstitial sites in diamond.

Entropic Comparison of Atomic-Resolution Electron Tomography of Crystals and Amorphous Materials.

Electron tomography bears promise for widespread determination of the three-dimensional arrangement of atoms in solids. However, it remains unclear whether methods successful for crystals are optimal for amorphous solids. Here, we explore the relative difficulty encountered in atomic-resolution tomography of crystalline and amorphous nanoparticles. We define an informational entropy to reveal the inherent importance of low-entropy zone-axis projections in the reconstruction of crystals. In turn, we propose considerations for optimal sampling for tomography of ordered and disordered materials.

Deep Eutectic Solvents as Convenient Media for Synthesis of Novel Coumarinyl Schiff Bases and Their QSAR Studies.

Deep eutectic solvents, as green and environmentally friendly media, were utilized in the synthesis of novel coumarinyl Schiff bases. Novel derivatives were synthesized from 2-((4-methyl-2-oxo-2H-chromen-7-yl)oxy)acetohydrazide and corresponding aldehyde in choline chloride:malonic acid (1:1) based deep eutectic solvent. In these reactions, deep eutectic solvent acted as a solvent and catalyst as well. Novel Schiff bases were synthesized in high yields (65–75%) with no need for further purification, and their structures were confirmed by mass spectra, 1H and 13C NMR. Furthermore, their antioxidant activity was determined and compared to antioxidant activity of previously synthesized derivatives, thus investigating their structure–activity relationship utilizing quantitative structure-activity relationship QSAR studies. Calculation of molecular descriptors has been performed by DRAGON software. The best QSAR model (Rtr = 0.636; Rext = 0.709) obtained with three descriptors (MATS3m, Mor22u, Hy) implies that the pairs of atoms higher mass at the path length 3, three-dimensional arrangement of atoms at scattering parameter s = 21 Å−1, and higher number of hydrophilic groups (-OH, -NH) enhanced antioxidant activity. Electrostatic potential surface of the most active compounds showed possible regions for donation of electrons to 1,1-diphenyl-2-picryhydrazyl (DPPH) radicals.

Quantum optical rotatory dispersion.

The phenomenon of molecular optical activity manifests itself as the rotation of the plane of linear polarization when light passes through chiral media. Measurements of optical activity and its wavelength dependence, that is, optical rotatory dispersion, can reveal information about intricate properties of molecules, such as the three-dimensional arrangement of atoms comprising a molecule. Given a limited probe power, quantum metrology offers the possibility of outperforming classical measurements. This has particular appeal when samples may be damaged by high power, which is a potential concern for chiroptical studies. We present the first experiment in which multiwavelength polarization-entangled photon pairs are used to measure the optical activity and optical rotatory dispersion exhibited by a solution of chiral molecules. Our work paves the way for quantum-enhanced measurements of chirality, with potential applications in chemistry, biology, materials science, and the pharmaceutical industry. The scheme that we use for probing wavelength dependence not only allows one to surpass the information extracted per photon in a classical measurement but also can be used for more general differential measurements.

Molecular structure of vapor-deposited amorphous selenium

The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

Soft Computing Techniques for the Protein Folding Problem on High Performance Computing Architectures.

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.

Local distortions revealed by neutron holography inSnCd0.0026alloy

Local distortions of the ideal periodic structure in crystals around impurity atoms play an important role in various physical properties of materials. The aim of this study was to investigate the static distortions around cadmium impurity atoms in a ${\text{SnCd}}_{0.0026}$ single crystal using atomic resolution neutron holography technique. The cadmium nucleus was used as an inside detector to measure the holographic interference pattern from which the three-dimensional (3D) atomic arrangement of tin nuclei around the cadmium impurities was reconstructed. Detailed analysis of the reconstructed image revealed the 3D static displacements of Sn atoms around the impurity. It was found that the crystal structure contracts around the cadmium impurity atom and the displacements tend to transform the crystal to the $\ensuremath{\alpha}$ phase. The local contraction of the lattice was used to explain the slower phase transformation to $\ensuremath{\alpha}$-Sn phase when Cd impurity atoms are present. The study shows the ability of neutron holography to measure 3D displacements around impurities which can be used, e.g., to understand the mechanisms that block the phase transformations in the presence of impurities.