Coordinates Of Individual Atoms Research Articles

Molecular arrangement and fringe identification and analysis from molecular dynamics (MAFIA-MD): A tool for analyzing the molecular structures formed during reactive molecular dynamics simulation of hydrocarbons

Reactive molecular dynamics (RMD) simulations are becoming popular, with the recent developments in high-performance and efficient computing architecture, for investigating fundamental physico-chemical behaviors of reacting species. Due to the complexity of hydrocarbon systems, characterization of molecules formed during RMD simulations of hydrocarbons can be very challenging for simulations involving a large number of molecules. The novel post-processing utility “MAFIA-MD” – an acronym for “Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics” – presented in this manuscript can analyze and perform molecular characterization of a large number of RMD trajectory files (.XYZ files) simultaneously. The utility will be useful for analysis and chemical characterization of trajectories without the large bond information files. A graphical user interface (GUI) is developed for easy operation. The utility analyzes the existing cyclic structures in the domain and generates statistics of alicyclic and aromatic hydrocarbons based on the number of carbon atoms. Alongside the statistical analysis, the program also separates the constituent molecules and extracts their chemical information in terms of Simplified Molecular-Input Line-Entry System (SMILES) and Spatial Data File (.SDF)”. A methodology for calculating fringe spacing is also implemented in the code for validation of RMD simulation with High-Resolution Transmission Electron Microscopy (HRTEM) images. Program summaryProgram title:MAFIA-MDCPC Library link to program files:https://doi.org/10.17632/s7dsk553fh.1Developer's repository link:https://github.com/kmmukut/MAFIA-MD.gitLicensing provisions: MITProgramming language:Python 3.7Supplementary material: Bash script for splitting long continuous trajectory files with multiple timestep into trajectory files for individual timestep and some example input trajectory files for testing.Nature of problem: Reactive molecular dynamics (RMD) simulations of hydrocarbons allow chemical reactions between different hydrocarbon molecules through bond breaking and new bond formation. The information about the chemical changes is stored in the bond information files and trajectory of individual atoms are stored in trajectory files. While the bond files can become very large for large simulations, trajectory files remain quite small. MAFIA-MD will be useful for practitioners interested in analyzing the chemical structures of emerging molecular clusters from small individual trajectory files without requiring the large, memory-intensive bond information files. Identification of chemical characteristics, particularly aromatic and alicyclic ring structures and molecular fringes, are important for gaining insights from RMD simulations of hydrocarbons, especially in exploration of soot formation during combustion. The capability of isolating the cyclic and non-cyclic molecules from trajectory files is the novel part of MAFIA-MD.Solution method: The coordinates of individual atoms are taken as the input for the program. The coordinates are then analyzed to create an adjacency matrix [1] based on the bond distance between carbon atoms. This adjacency matrix is then converted into a directed graph and the cyclic structures are extracted from the graph by implementing an efficient depth-first-search algorithm [2] developed by Johnson [3]. Apart from the ability to isolate cyclic and non-cyclic components by chemical structural analysis, a methodology to calculate fringe spacing is also implemented by calculating the distances between cyclic structures. The utility uses a Python interface for easy management of the input and output parameters. The detailed solution methodology has been discussed in the manuscript.Additional comments including restrictions and unusual features: In the current version, the utility can analyze only carbon and hydrogen atoms. The future versions will implement the addition of other common atoms found in aromatic molecules, e.g. nitrogen, oxygen, sulfur, etc. MAFIA-MD can be run on Linux, macOS, and Windows operating systems.

Three-Dimensional Atomic Structure of Grain Boundaries Resolved by Atomic-Resolution Electron Tomography

Summary Grain boundaries (GBs) determine the properties of polycrystals, and tailoring the GB structure offers a promising method for the discovery and engineering of new materials. However, GB structures are far from well understood because of their structural complexity and limitations of conventional projection imaging methods. Here, we decipher three-dimensional atomic structure and crystallography of GBs in nanometals using atomic-resolution electron tomography. Unlike conventional descriptions, whereby they are either straight or curved planar planes with one-dimensional translational symmetry, we show that the high-angle GBs completely lose translational symmetry due to undulated curvature related to configurations of structural units. Moreover, we directly visualize kinks and jogs at the single-atom scale in dislocation-type GBs and investigate their mobilities. Our findings bring new insights to the conventional wisdom of GBs and show the importance of developing methods to include the non-planar nature of GBs to statistically evaluate the behavior of GBs in modeling studies.

Structure determination and crystal chemistry of large repeat mixed-layer hexaferrites.

Hexaferrites are an important class of magnetic oxides with applications in data storage and electronics. Their crystal structures are highly modular, consisting of Fe- or Ba-rich close-packed blocks that can be stacked in different sequences to form a multitude of unique structures, producing large anisotropic unit cells with lattice parameters typically >100 Å along the stacking axis. This has limited atomic-resolution structure solutions to relatively simple examples such as Ba2Zn2Fe12O22, whilst longer stacking sequences have been modelled only in terms of block sequences, with no refinement of individual atomic coordinates or occupancies. This paper describes the growth of a series of complex hexaferrite crystals, their atomic-level structure solution by high-resolution synchrotron X-ray diffraction, electron diffraction and imaging methods, and their physical characterization by magnetometry. The structures include a new hexaferrite stacking sequence, with the longest lattice parameter of any hexaferrite with a fully determined structure.

Reconstructing APT Datasets: Challenging the Limits of the Possible

Atom probe tomography (APT) has been successfully used in materials science for several decades for probing local compositional variations. In metals, the capacity to measure reliable composition at the nanoscale in 3D was successfully demonstrated in the early nineties [I, 2]. By using a few geometric ingredients, a reconstruction recipe was proposed at this time that surprisingly produced on selected materials, 3D images with an atomic scale precision of the distribution of atoms with elemental identification [3). The ability to localize precisely the 3-D coordinates of individual atoms in direct space of materials is expected to find important applications in materials science and engineering, nanoscience, physics and chemistry. It is particularly crucial in semiconductor industry, to design optical devices or electronic devices, such as light-emitting diodes (LEDs), or transistors. This ideal picture of near-perfect 3D microscope however faces two issues. First, the precision of images may vary strongly from one material to another. Compared to an optical or an electron microscope, the spatial resolution loss is not diffraction limited, since image is produced from the inverse projection of ion trajectories, ions been produced by field evaporation of surface atoms. Precision is perturbed by slight deviations of the trajectories of ions from their initial positions at the specimen surace to the ion detector. A real understanding of this trajectory taking into account first the quantum interaction of atoms/ions with the specimen surface under the presence of the strong electric field existing on the surface is mandatory. The interplay between quantum processes, and more classical deviations induced by the distribution of the electric field close to the surface is extremely complex. In metals, most of the deviations thought to be induced by the field, as it was recently demonstrated experimentally by field ion microscopy in tungsten (fig. I). In oxides, quantum effects such as in-flight dissociation of molecules may degrade significantly the spatial precision (fig. 2) [4]. The second issue concerns the global distortions induced by the presence in the sample of phases very different in term of the critical fields required to extract surface atoms. This is a current case when analyzing devices composed of complex structures of metals, oxides and semiconductors materials. The surface of the sample ideally modelled with a constant curvature radius evolves dynamically under the process of field evaporation in a complex 3D surface. The direct consequence is the presence of distortions in the projected image. After the evaporation of each atom, the field distribution around the sample must be evaluated, to understand the projection law that should necessary be taken into account to generate an accurate reconstruction [5, 6). To overcome this cumbersome calculation, an alternative model, much simpler, was developed to reproduce the imaging process in simple configurations. In multilayers systems, it was demonstrated that most of the distortions could be reduced using a fast and efficient reconstruction algorithm that predicts the analytical shape of the emitting surface all along the evaporation process [7]. If a complementary technique can be used on the same sample to verify the morphology or provide complementary information before APT analysis, then this can also greatly…

Atomic electron tomography: 3D structures without crystals

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity. Here we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences.

Three-Dimensional Determination of the Coordinates of Individual Atoms in Materials

Three-Dimensional Determination of the Coordinates of Individual Atoms in Materials

B21-O-09Determination of Three-Dimensional Coordinates of Individual Atoms in Nano-Materials by Electron Tomography

Richard Feynman pointed out in his 1959 speech, “It would be very easy to make an analysis of any complicated chemical substance; all one would have to do would be to look at it and see where the atoms are… I put this out as a challenge: Is there no way to make the electron microscope more powerful?” Over more than 50 years, with significant achievements in electron microscope and the developments of aberration-corrected electron optics, scanning transmission electron microscopy (STEM) has reached spatial resolution of 0.5 Å. Recently, in combination of the state-of-the-art scanning transmission electron microscope (STEM) and a tomographic reconstruction technique known as equally sloped tomography (EST), we have achieved electron tomography at 2.4 angstrom resolution [ 1 ]. This general method has been applied to reveal almost all atoms inside a Pt nanoparticle with unprecedented details [ 2 ]. Most recently, Feynman's 1959 challenge has been tackled by successfully determining 3D coordinates of 3,769 individual atoms at the tip of a tungsten needle with a precision of ~19 picometers [ 3 ]. In this talk, I will present the achievements of this novel technique.

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography

Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. Here, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ∼19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field and the full strain tensor with a 3D resolution of ∼1 nm(3) and a precision of ∼10(-3), which are further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.

Mode Analysis of the High Temperature Behaviour of some Ferroic Perovskites

The advent of user-friendly on-line software (such as ISODISTORT [1] and AMPLIMODES [2]) to analyse crystal structures in terms of `distortion modes' rather than the conventional approach of refining individual atomic coordinates, has opened up new possibilities in the understanding of structure-property relationships in functional materials. The perovskite family is ideally suited to this approach, with many different variants on the basic cubic structure-type being brought about by simple symmetry-lowering modes such as tilting or distortion of almost rigid metal-ligand octahedral groups. In this talk I will illustrate the use of distortion mode analysis in understanding the sometimes complex, unusual and surprising structural behavior of several functional perovskites, particularly ferroelectrics and multiferroics. Examples chosen will exploit the use of powder neutron diffraction as the primary experimental technique, and will include sodium niobate, NaNbO3, which has the most complex high-temperature phase diagram of any simple perovskite, and derivatives of BiFeO3 (such as La or Mn-doped) which display unusual magnetostrictive behaviour.

Symmetry mode analysis of the phase transitions in Rb2ZnBr4

Abstract Crystal structures of low temperature phases III, IV and V of Rubidium Zinc Bromide have been determined by single crystal X-ray diffraction at 90 K, 85 K, and 30 K, respectively. The analysis of the structures in terms of symmetry-adapted modes of the high temperature prototype phase permits the identification of the modes responsible for each phase and to assess its thermal evolution. The primary mode responsible for the incommensurate and lock-in phases remains dominant throughout the whole transition sequence, maintaining its structure and slightly increasing its amplitude as temperature decreases. The two monoclinic phases IV and V are presumably due to the instability of a second mode associated with a single active irreducible representation. However, the presence with similar weights of several symmetry-adapted distortions of different symmetry indicates a strong hybridization in phase III of the softer normal modes. A symmetry-mode description of the structures of phase IV and V fully consistent with a simple Landau model, can then only be obtained if phase III is taken as effective parent phase. Besides the insight on the microscopic origin of the different phases, the symmetry modes were used as crystallographic coordinates in the refinement of the structure of phase V. The result shows the advantages of using these non-conventional collective structural parameters instead of individual atomic coordinates. The refinable parameters can be reduced to the amplitudes of those symmetry modes with significant weight in the distortions.

Higher-Order Level-Set Method and Its Application in Biomolecular Surfaces Construction

We present a general framework for a higher-order spline level-set (HLS) method and apply this to bio-molecule surfaces construction. Starting from a first order energy functional, we obtain a general level set formulation of geometric partial differential equation, and provide an efficient approach to solve this partial differential equation using a C(2) spline basis. We also present a fast cubic spline interpolation algorithm based on convolution and the Z-transform, which exploits the local relationship of interpolatory cubic spline coefficients with respect to given function data values. One example of our HLS method is demonstrated, which is the construction of bio-molecule surfaces (an implicit solvation interface) with their individual atomic coordinates and solvated radii as prerequisite.

Pressure-induced melting of charge order inEu4As3 without structural change

We have carried out high-pressure x-ray diffraction experiments onEu4As3 at room temperature, and individual atomic coordinates as well as lattice parameters werederived precisely from the diffraction data. We have confirmed that a trigonal structure with theR3c space group does not change up to 19 GPa. The results show that the volume of theEuAs6 octahedron and the valence state of the Eu ion are closely correlated, and puretrivalent and divalent Eu ions occupy two nonequivalent Eu sites, respectively,in the charge-ordered state at ambient pressure. We present clear evidence onthe basis of the pressure dependence of these volumes at two nonequivalent Eusites that a melting of the static charge order occurs at about 10 GPa andEu4As3 is in a mixed-valence state above 10 GPa.

Effect of Pressure on the Vibrational Structure of Insensitive Energetic Material 5-Nitro-2,4-dihydro-1,2,4-triazole-3-one

The Raman spectra of alpha form 5-nitro-2,4-dihydro-1,2,4-triazole-3-one (alpha-NTO, space group P) were measured in a high-pressure vessel diamond anvil cell (DAC). The pressure was increased to 27.6 GPa. In general, Raman bands show a blue shift because of the nature of the molecule packing as a high-pressure effect, but some particular bands exhibited a red shift, disappearance, split, or slight shifting in our experiments. Those red-shifting bands concerning hydrogen bonds, i.e., carbonyl and amino groups, are likely to work as a stabilizer against stimuli to the molecule or crystal. This stabilizing nature might characterize the insensitivity of NTO. Molecular dynamic (MD) calculations were performed to reveal the high-pressure effect of the alpha-NTO crystal. The coordinates of individual atoms in the crystal structure were obtained using X-ray diffraction analysis. The pressure dependence of the power spectra of the correlation functions of the C=O bond length in NTO was calculated. A unique high-pressure effect of the alpha-NTO crystal was found on the power spectra. The peak frequency in the power spectrum of the C=O stretching vibration exhibited a red shift with an increase in pressure to 10.0 GPa, while the peak intensity considerably decreased under the same pressure process, because this bond length increased with an increase in pressure to 10.0 GPa. At a pressure of >20.0 GPa, a blue shift appeared. These results of the MD calculations are in good agreement with our experimental data.

A computer-generated supercoiled model of the pUC19 plasmid.

DNA models have become a powerful tool in the simulation of radiation-induced molecular damage. Here, a computer code was developed which calculates the coordinates of individual atoms in supercoiled plasmid DNA. In this prototype study, the known base-pair sequence of the pUC19 plasmid has been utilized. The model was built in a three-step process. Firstly, a Monte Carlo simulation was performed to shape a segment chain skeleton. Checks on elastic energy, distance and unknotting were applied. The temperature was considered in two different ways: (1) it was kept constant at 293 K and (2) it was gradually reduced from 350 K to less than 10 K. Secondly, a special smoothing procedure was introduced here to remove the edges from the segment chain without changing the total curve length while avoiding the production of overshooting arcs. Finally, the base pair sequence was placed along the smoothed segment chain and the positions of all the atoms were calculated. As a first result, a few examples of the supercoiled plasmid models will be presented, demonstrating the strong influence of appropriate control of the system temperature.

Neural Nets for the Simulation of Molecular Recognition within MS-Windows Environment

A neural method for the comparison of the molecule series, using a self-organizing map (SOM) procedure, is presented. The coordinates of individual atoms within the most active molecule mimicking the geometry of the receptor are trained with SOM algorithms to form a template which provides a basis for recognizing the similarity within the compounds series. Therefore the SOM matrices produced for individual molecules, if analyzed further by neural procedures or by the calculation of the matrix determinants, provide reasonable classifications according to the molecule's structure or actual activity observed, provided that this is limited by shape factors. All computational operations are performed within MS-WINDOWS environment, using commercial programs of HYPERCHEM and MATLAB.

Extension of molecular replacement: a new search strategy based on Patterson correlation refinement

A new search strategy is presented to obtain initial phases for single-crystal diffraction data by molecular replacement. It consists of carrying out 'Patterson refinements' of a large number of the highest peaks of a rotation function. The target function for Patterson refinement is proportional to the negative correlation coefficient between the squared amplitudes of the observed and the calculated normalized structure factors. If the root-mean-square difference between the search model and the crystal structure is within the radius of convergence of the minimization procedure employed, the correct orientation can be identified by having the lowest value of the target function after refinement. Similar to conventional crystallographic R-factor refinement, the target function for Patterson refinement may be combined with an empirical energy function describing geometric and non-bonded interactions. Patterson refinement of individual atomic coordinates or of rigid-group parameters may be carried out. Search models of crambin and of myoglobin with 1.6-2.0 Å backbone atomic r.m.s, differences from the target crystal structures show that the Patterson refinement strategy can solve crystal structures that cannot be solved by conventional molecular replacement or even by full six-dimensional searches.

Atomic geometry of Si(111) 7×7 by dynamical low-energy electron diffraction

A complete determination of individual atomic coordinates for the Si(111) 7×7 surface has been carried out by dynamical low-energy electron diffraction. The dimer-adatom-stacking fault (DAS) model, after large vertical and lateral relaxations, was found to produce calculated spectra in remarkably good agreement with the data. Atoms in the faulted half of the unit cell are raised from those of the unfaulted half. Adatoms at corner sites are higher than those at center sites.

Low-energy electron diffraction analysis of the Si(111)7×7 structure

We have used the dynamical theory of low-energy electron diffraction to analyze data of the Si(111)7×7 surface and determined the atomic structure. The method includes the use of symmetrized wave functions in real and reciprocal spaces. Individual atomic coordinates for the first five atomic planes (containing 200 atoms) are determined. The low-energy electron diffraction optimized structure shows an oscillatory relaxation: atomic planes with stretched bonds followed by planes with compressed bonds. Geometric displacements from the bulk dimer–adatom–stacking fault model are presented.