scholarly journals Simulation of bonding effects in HRTEM images of light element materials

2011 ◽  
Vol 2 ◽  
pp. 394-404 ◽  
Author(s):  
Simon Kurasch ◽  
Jannik C Meyer ◽  
Daniela Künzel ◽  
Axel Groß ◽  
Ute Kaiser
Keyword(s):  
Density Functional ◽  
Structural Information ◽  
Hexagonal Boron Nitride ◽  
Light Element ◽  
Model Systems ◽  
Single Atom ◽  
Transmission Electron ◽  
Relative Contrast ◽  
Oxygen Substitution ◽  
Simulation Scheme

The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) Gemming, T.; Möbus, G.; Exner, M.; Ernst, F.; Rühle, M. J. Microsc. 1998, 190, 89–98. doi:10.1046/j.1365-2818.1998.3110863.xDeng, B.; Marks, L. D. Acta Crystallogr., Sect. A 2006, 62, 208–216. doi:10.1107/S010876730601004X. This approach accounts for the fact that electrons in the specimen are redistributed according to their local chemical environment. This influences the scattering process and alters the absolute and relative contrast in the final image. For light element materials with well defined geometry, such as graphene and hexagonal boron nitride monolayers, the DFT based simulation scheme turned out to be necessary to prevent misinterpretation of weak signals, such as the identification of nitrogen substitutions in a graphene network. Furthermore, this implies that the HRTEM image does not only contain structural information (atom positions and atomic numbers). Instead, information on the electron charge distribution can be gained in addition. In order to produce meaningful results, the new input parameters need to be chosen carefully. Here we present details of the simulation process and discuss the influence of the main parameters on the final result. Furthermore we apply the simulation scheme to three model systems: A single atom boron and a single atom oxygen substitution in graphene and an oxygen adatom on graphene.

scholarly journals The abTEM code: transmission electron microscopy from first principles

2021 ◽  
Vol 1 ◽  
pp. 24
Author(s):  
Jacob Madsen ◽  
Toma Susi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Open Source ◽  
Density Functional ◽  
Hexagonal Boron Nitride ◽  
Phase Reconstruction ◽  
Simulation Code ◽  
Atomic Simulation ◽  
Transmission Electron ◽  
Scattering Potential

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document.  This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fast implementation of the PRISM algorithm for a decahedral 20000-atom gold nanoparticle.

scholarly journals Direct imaging of light-element impurities in graphene reveals triple-coordinated oxygen

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Christoph Hofer ◽  
Viera Skákalová ◽  
Tobias Görlich ◽  
Mukesh Tripathi ◽  
Andreas Mittelberger ◽  
...  
Keyword(s):  
Scanning Transmission Electron Microscopy ◽  
Light Element ◽  
Single Atom ◽  
Nitrogen Forms ◽  
Rich Variety ◽  
Transmission Electron ◽  
Graphene Lattice ◽  
Scanning Transmission ◽  
Electron Energy Loss ◽  
Aberration Corrected

Abstract Along with hydrogen, carbon, nitrogen and oxygen are the arguably most important elements for organic chemistry. Due to their rich variety of possible bonding configurations, they can form a staggering number of compounds. Here, we present a detailed analysis of nitrogen and oxygen bonding configurations in a defective carbon (graphene) lattice. Using aberration-corrected scanning transmission electron microscopy and single-atom electron energy loss spectroscopy, we directly imaged oxygen atoms in graphene oxide, as well as nitrogen atoms implanted into graphene. The collected data allows us to compare nitrogen and oxygen bonding configurations, showing clear differences between the two elements. As expected, nitrogen forms either two or three bonds with neighboring carbon atoms, with three bonds being the preferred configuration. Oxygen, by contrast, tends to bind with only two carbon atoms. Remarkably, however, triple-coordinated oxygen with three carbon neighbors is also observed, a configuration that is exceedingly rare in organic compounds.

scholarly journals One-step synthesis of single-site vanadium substitution in 1T-WS2 monolayers for enhanced hydrogen evolution catalysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ali Han ◽  
Xiaofeng Zhou ◽  
Xijun Wang ◽  
Sheng Liu ◽  
Qihua Xiong ◽  
...  
Keyword(s):  
Hydrogen Evolution ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Vapor ◽  
Single Atom ◽  
High Concentration ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Vanadium Substitution ◽  
One Step

AbstractMetallic tungsten disulfide (WS2) monolayers have been demonstrated as promising electrocatalysts for hydrogen evolution reaction (HER) induced by the high intrinsic conductivity, however, the key challenges to maximize the catalytic activity are achieving the metallic WS2 with high concentration and increasing the density of the active sites. In this work, single-atom-V catalysts (V SACs) substitutions in 1T-WS2 monolayers (91% phase purity) are fabricated to significantly enhance the HER performance via a one-step chemical vapor deposition strategy. Atomic-resolution scanning transmission electron microscopy (STEM) imaging together with Raman spectroscopy confirm the atomic dispersion of V species on the 1T-WS2 monolayers instead of energetically favorable 2H-WS2 monolayers. The growth mechanism of V SACs@1T-WS2 monolayers is experimentally and theoretically demonstrated. Density functional theory (DFT) calculations demonstrate that the activated V-atom sites play vital important role in enhancing the HER activity. In this work, it opens a novel path to directly synthesize atomically dispersed single-metal catalysts on metastable materials as efficient and robust electrocatalysts.

scholarly journals Single-atom doping of MoS2 with manganese enables ultrasensitive detection of dopamine: Experimental and computational approach

2020 ◽  
Vol 6 (32) ◽  
pp. eabc4250 ◽  
Author(s):  
Yu Lei ◽  
Derrick Butler ◽  
Michael C. Lucking ◽  
Fu Zhang ◽  
Tunan Xia ◽  
...  
Keyword(s):  
Density Functional ◽  
Transition Metal Dichalcogenides ◽  
Density Functional Theory Calculations ◽  
Single Atom ◽  
Buffer Solution ◽  
Dopamine Detection ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Metal Dichalcogenides ◽  
Metal Doped

Two-dimensional transition metal dichalcogenides (TMDs) emerged as a promising platform to construct sensitive biosensors. We report an ultrasensitive electrochemical dopamine sensor based on manganese-doped MoS2 synthesized via a scalable two-step approach (with Mn ~2.15 atomic %). Selective dopamine detection is achieved with a detection limit of 50 pM in buffer solution, 5 nM in 10% serum, and 50 nM in artificial sweat. Density functional theory calculations and scanning transmission electron microscopy show that two types of Mn defects are dominant: Mn on top of a Mo atom (MntopMo) and Mn substituting a Mo atom (MnMo). At low dopamine concentrations, physisorption on MnMo dominates. At higher concentrations, dopamine chemisorbs on MntopMo, which is consistent with calculations of the dopamine binding energy (2.91 eV for MntopMo versus 0.65 eV for MnMo). Our results demonstrate that metal-doped layered materials, such as TMDs, constitute an emergent platform to construct ultrasensitive and tunable biosensors.

scholarly journals High-resolution imaging of biotite using focal series exit wavefunction restoration and the graphene mechanical exfoliation method

2015 ◽  
Vol 79 (2) ◽  
pp. 337-344 ◽  
Author(s):  
W. Bower ◽  
W. Head ◽  
G. T. R. Droop ◽  
R. Zan ◽  
R. A. D. Pattrick ◽  
...  
Keyword(s):  
High Resolution ◽  
Structural Information ◽  
Ion Beam ◽  
Single Atom ◽  
Specimen Preparation ◽  
Specimen Thickness ◽  
Mechanical Exfoliation ◽  
Transmission Electron ◽  
Sheet Silicate ◽  
Combination Of Methods

AbstractWe have applied mechanical exfoliation for the preparation of ultra-thin samples of the phyllosilicate mineral biotite. We demonstrate that the 'scotch tape' approach, which was made famous as an early method for production of single-atom-thick graphene, can be used for production of sheet-silicate specimens that are sufficiently thin to allow high-resolution transmission electron microscope (HRTEM) imaging to be achieved successfully while also being free from the specimen preparation artefacts that are often caused by ion-beam milling techniques. Exfoliation of the biotite parallel to the (001) planes has produced layers as thin as two structural TOT units thick (∼2 nm). The minimal specimen thickness enabled not only HRTEM imaging but also the application of subsequent exit wavefunction restoration to reveal the pristine biotite lattice. Exit wavefunction restoration recovers the full complex electron wave from a focal series of HRTEM images, removing the effects of coherent lens aberrations. This combination of methods therefore produces images in which the observed features are readily interpreted to obtain atomic resolution structural information.

scholarly journals The abTEM code: transmission electron microscopy from first principles

2021 ◽  
Vol 1 ◽  
pp. 24
Author(s):  
Jacob Madsen ◽  
Toma Susi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Open Source ◽  
Density Functional ◽  
Hexagonal Boron Nitride ◽  
Phase Reconstruction ◽  
Simulation Code ◽  
Atomic Simulation ◽  
Transmission Electron ◽  
Scattering Potential

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document.  This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fast implementation of the PRISM algorithm for a decahedral 20000-atom gold nanoparticle.

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

Structural studies of small amorphous volumes by electron diffraction

1990 ◽  
Vol 48 (4) ◽  
pp. 122-123
Author(s):  
Pierre Moine
Keyword(s):  
Electron Diffraction ◽  
Born Approximation ◽  
Structural Information ◽  
Fundamental Relation ◽  
X Rays ◽  
Structural Studies ◽  
Diffraction Experiment ◽  
Transmission Electron ◽  
Amorphous Structures ◽  
Diffraction Patterns

Qualitatively, amorphous structures can be easily revealed and differentiated from crystalline phases by their Transmission Electron Microscopy (TEM) images and their diffraction patterns (fig.1 and 2) but, for quantitative structural information, electron diffraction pattern intensity analyses are necessary. The parameters describing the structure of an amorphous specimen have been introduced in the context of scattering experiments which have been, so far, the most used techniques to obtain structural information in the form of statistical averages. When only small amorphous volumes (< 1/μm in size or thickness) are available, the much higher scattering of electrons (compared to neutrons or x rays) makes, despite its drawbacks, electron diffraction extremely valuable and often the only feasible technique.In a diffraction experiment, the intensity IN (Q) of a radiation, elastically scattered by N atoms of a sample, is measured and related to the atomic structure, using the fundamental relation (Born approximation) : IN(Q) = |FT[U(r)]|.

scholarly journals Shedding Light on the Chemistry and the Properties of Münchnone Functionalized Graphene

Nanomaterials ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1629
Author(s):  
Giulia Neri ◽  
Enza Fazio ◽  
Antonia Nostro ◽  
Placido Giuseppe Mineo ◽  
Angela Scala ◽  
...  
Keyword(s):  
Density Functional ◽  
Antimicrobial Properties ◽  
Biological Properties ◽  
Azomethine Ylide ◽  
Functionalized Graphene ◽  
Functional Theory ◽  
Pyrrole Derivatives ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Direct Functionalization

Münchnones are mesoionic oxazolium 5-oxides with azomethine ylide characteristics that provide pyrrole derivatives by a 1,3-dipolar cycloaddition (1,3-DC) reaction with acetylenic dipolarophiles. Their reactivity was widely exploited for the synthesis of small molecules, but it was not yet investigated for the functionalization of graphene-based materials. Herein, we report our results on the preparation of münchnone functionalized graphene via cycloaddition reactions, followed by the spontaneous loss of carbon dioxide and its further chemical modification to silver/nisin nanocomposites to confer biological properties. A direct functionalization of graphite flakes into few-layers graphene decorated with pyrrole rings on the layer edge was achieved. The success of functionalization was confirmed by micro-Raman and X-ray photoelectron spectroscopies, scanning transmission electron microscopy, and thermogravimetric analysis. The 1,3-DC reactions of münchnone dipole with graphene have been investigated using density functional theory to model graphene. Finally, we explored the reactivity and the processability of münchnone functionalized graphene to produce enriched nano biomaterials endowed with antimicrobial properties.

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