scholarly journals Direct observation and catalytic role of mediator atom in 2D materials

2020 ◽  
Vol 6 (24) ◽  
pp. eaba4942
Author(s):  
Gun-Do Lee ◽  
Alex W. Robertson ◽  
Sungwoo Lee ◽  
Yung-Chang Lin ◽  
Jeong-Wook Oh ◽  
...  
Keyword(s):  
Direct Observation ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Tight Binding ◽  
Structural Evolution ◽  
Dark Field ◽  
Bond Rotation ◽  
Annular Dark Field ◽  
Catalytic Role ◽  
Type Bond

The structural transformations of graphene defects have been extensively researched through aberration-corrected transmission electron microscopy (AC-TEM) and theoretical calculations. For a long time, a core concept in understanding the structural evolution of graphene defects has been the Stone-Thrower-Wales (STW)–type bond rotation. In this study, we show that undercoordinated atoms induce bond formation and breaking, with much lower energy barriers than the STW-type bond rotation. We refer to them as mediator atoms due to their mediating role in the breaking and forming of bonds. Here, we report the direct observation of mediator atoms in graphene defect structures using AC-TEM and annular dark-field scanning TEM (ADF-STEM) and explain their catalytic role by tight-binding molecular dynamics (TBMD) simulations and image simulations based on density functional theory (DFT) calculations. The study of mediator atoms will pave a new way for understanding not only defect transformation but also the growth mechanisms in two-dimensional materials.

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculations

2009 ◽  
Vol 65 (5) ◽  
pp. 639-646 ◽  
Author(s):  
Edward E. Ávila ◽  
Asiloé J. Mora ◽  
Gerzon E. Delgado ◽  
Ricardo R. Contreras ◽  
Luis Rincón ◽  
...  
Keyword(s):  
Solid State ◽  
Diffraction Data ◽  
Density Functional ◽  
Simulated Annealing Algorithm ◽  
Theoretical Calculations ◽  
Tight Binding ◽  
Van Der Waals Interactions ◽  
Am1 Calculations ◽  
X Ray Diffraction ◽  
X Ray

The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

scholarly journals Two-Dimensional Frank-Kasper Z Phase with One Unit-Cell Thickness

2020 ◽  
Author(s):  
Xie Hongbo ◽  
Junyuan Bai ◽  
Haiyan Ren ◽  
Shanshan Li ◽  
Hucheng Pan ◽  
...  
Keyword(s):  
Density Functional ◽  
Three Dimensional ◽  
Volume Ratio ◽  
Dark Field ◽  
Unit Cell ◽  
Two Dimensional ◽  
Cell Height ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Annular Dark Field

Abstract Z phase is one of the three basic units by which the Frank-Kasper phases are generally assembled. Compared to the other two basic units, i.e., A15 and C15 structures, the Z phase structure is rarely experimentally observed because of a relatively large volume ratio among the constituents to inhibit its formation. Moreover, the discovered Z structures are generally the three-dimensional (3D) ordered Gibbs bulk phases to conform to their thermodynamic stability. Herein, we confirmed the existence of a metastable two-dimensional (2D) Frank-Kasper Z phase with one unit-cell height in the crystallography in a model Mg-Sm-Zn system, by using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) combined with density functional theory (DFT) calculations. This finding is important for understanding the relationship between the traditional crystal structures and the quasicrystals, and it is also expected to provide a new insight to understand the clustering and stacking behavior of atoms in condensed matters.

Simulation of Structural Evolution Using Time-Dependent Density-Functional Based Tight-Binding Method

2020 ◽  
Vol 20 (11) ◽  
pp. 7206-7209
Author(s):  
Seung Mi Lee ◽  
Thomas A. Niehaus
Keyword(s):  
Density Functional ◽  
High Efficiency ◽  
Tight Binding ◽  
Computational Cost ◽  
Structural Evolution ◽  
Simulation Method ◽  
Time Dependent ◽  
Excitation Energies ◽  
Carbon Chains ◽  
Experimental Values

A faster and more efficient quantum mechanical simulation method for application to complicated issues of real systems beyond model cases has long been sought after. The density-functional based tight-binding (DFTB) method has successfully explained the atomistic and electronic properties of semiconductors, surfaces, and nanostructures. In addition, the time-dependent formalism implemented in DFTB showed high efficiency in terms of computational cost. In this study, we demonstrated the structural and electronic evolution of small molecules induced by a laser pulse using the time-dependent DFTB (TD-DFTB) method. We identified the critical fluence of the input laser for structural dissociations in carbon chains and fullerenes, which related to the structural stability. The excitation energies of several molecules calculated by TD-DFTB agreed with the experimental values.

scholarly journals Self-adapted clustering of solute atoms into a confined two-dimensional prismatic platelet with an ellipse-like quasi-unit cell

IUCrJ ◽  
2018 ◽  
Vol 5 (6) ◽  
pp. 823-829 ◽  
Author(s):  
Hongbo Xie ◽  
Junyuan Bai ◽  
Hucheng Pan ◽  
Xueyong Pang ◽  
Yuping Ren ◽  
...  
Keyword(s):  
Density Functional ◽  
High Strength ◽  
Dark Field ◽  
Unit Cell ◽  
Ternary Alloys ◽  
Two Dimensional ◽  
Future Design ◽  
Scanning Transmission ◽  
Annular Dark Field ◽  
Solute Atoms

This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg–In–Yb and Mg–In–Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈11{\overline 2}0〉α directions formed a two-dimensional planar structure, which has three variants with a {10{\overline 1}0}α habit plane and full coherence with the α-Mg matrix. This finding is important for understanding the clustering and stacking behaviors of solute atoms in condensed matter, and is expected to guide the future design of novel high-strength Mg alloys strengthened by such high-density prismatic platelets.

scholarly journals Ultra-small rhenium clusters supported on graphene

2015 ◽  
Vol 17 (12) ◽  
pp. 7898-7906 ◽  
Author(s):  
Orlando Miramontes ◽  
Franco Bonafé ◽  
Ulises Santiago ◽  
Eduardo Larios-Rodriguez ◽  
Jesús J. Velázquez-Salazar ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Transmission Electron Microscopy ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Dark Field ◽  
High Angle ◽  
Functional Theory ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Annular Dark Field

In this work, the adsorption of very small rhenium clusters (2–13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM) in combination with density functional theory calculations.

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