scholarly journals Interaction Region Indicator: A Simple Real Space Function Clearly Revealing Both Chemical Bonds and Weak Interactions**

2021 ◽  
Vol 1 (5) ◽  
pp. 231-239
Author(s):  
Tian Lu ◽  
Qinxue Chen
Keyword(s):  
Weak Interactions ◽  
Real Space ◽  
Interaction Region ◽  
Chemical Bonds ◽  
Space Function

scholarly journals Interaction Region Indicator (IRI): A Very Simple Real Space Function Clearly Revealing Both Chemical Bonds and Weak Interactions

2021 ◽  
Author(s):  
Tian Lu ◽  
qinxue chen
Keyword(s):  
Weak Interaction ◽  
Chemical Bonding ◽  
Computational Cost ◽  
Interaction Strength ◽  
Real Space ◽  
Interaction Region ◽  
Chemical System ◽  
Chemical Bonds ◽  
Space Function ◽  
Interaction Regions

Graphically revealing interaction regions in a chemical system enables chemists to notice the areas at a glance where significant interactions have formed, it is very helpful in studying chemical bonds, intermolecular and intramolecular interactions. Reduced density gradient (RDG) has already been widely employed in literatures to visually exhibit weak interaction regions, in fact it also has the ability of revealing chemical bonding regions. Unfortunately, RDG cannot clearly show both types of the interactions at the same time. In this paper, we propose a new real space function named interaction region indicator (IRI), which is a slight modification on RDG. We found IRI can reveal chemical bonding and weak interaction regions equally well, this brings great convenience in the study of various chemical systems as well as chemical reactions. It is noteworthy that IRI has simpler definition, lower computational cost and better graphical effect than the density overlap regions indicator (DORI), which has similar purpose to IRI. In this article IRI is also compared with atom-in-molecules (AIM) topology analysis of electron density, we demonstrated that IRI has the ability to reveal additional interactions to provide chemists a more complete picture. In addition, we put forward a variant of IRI named IRI-pi, which is dedicated to reveal interactions of pi electrons. It is found that IRI-pi can not only distinguish type of pi interactions but can also exhibit pi-interaction strength. IRI and IRI-pi have been efficiently implemented in our freely available Multiwfn wavefunction analysis code, it is expected that they will become new useful members of computational chemists' toolbox in studying chemical problems.

scholarly journals Interaction Region Indicator (IRI): A Very Simple Real Space Function Clearly Revealing Both Chemical Bonds and Weak Interactions

2021 ◽  
Author(s):  
Tian Lu ◽  
qinxue chen
Keyword(s):  
Weak Interaction ◽  
Chemical Bonding ◽  
Computational Cost ◽  
Interaction Strength ◽  
Real Space ◽  
Interaction Region ◽  
Chemical System ◽  
Chemical Bonds ◽  
Space Function ◽  
Interaction Regions

Graphically revealing interaction regions in a chemical system enables chemists to notice the areas at a glance where significant interactions have formed, it is very helpful in studying chemical bonds, intermolecular and intramolecular interactions. Reduced density gradient (RDG) has already been widely employed in literatures to visually exhibit weak interaction regions, in fact it also has the ability of revealing chemical bonding regions. Unfortunately, RDG cannot clearly show both types of the interactions at the same time. In this paper, we propose a new real space function named interaction region indicator (IRI), which is a slight modification on RDG. We found IRI can reveal chemical bonding and weak interaction regions equally well, this brings great convenience in the study of various chemical systems as well as chemical reactions. It is noteworthy that IRI has simpler definition, lower computational cost and better graphical effect than the density overlap regions indicator (DORI), which has similar purpose to IRI. In this article IRI is also compared with atom-in-molecules (AIM) topology analysis of electron density, we demonstrated that IRI has the ability to reveal additional interactions to provide chemists a more complete picture. In addition, we put forward a variant of IRI named IRI-pi, which is dedicated to reveal interactions of pi electrons. It is found that IRI-pi can not only distinguish type of pi interactions but can also exhibit pi-interaction strength. IRI and IRI-pi have been efficiently implemented in our freely available Multiwfn wavefunction analysis code, it is expected that they will become new useful members of computational chemists' toolbox in studying chemical problems.

scholarly journals Beyond the molecular movie: Dynamics of bands and bonds during a photoinduced phase transition

Science ◽  
2018 ◽  
Vol 362 (6416) ◽  
pp. 821-825 ◽  
Author(s):  
C. W. Nicholson ◽  
A. Lücke ◽  
W. G. Schmidt ◽  
M. Puppin ◽  
L. Rettig ◽  
...  
Keyword(s):  
Reaction Pathway ◽  
Energy Landscape ◽  
Real Space ◽  
Nonequilibrium Dynamics ◽  
Test Case ◽  
Chemical Bonds ◽  
Ab Initio Simulations ◽  
Potential Energy Landscape ◽  
Microscopic Interactions ◽  
Space Description

Ultrafast nonequilibrium dynamics offer a route to study the microscopic interactions that govern macroscopic behavior. In particular, photoinduced phase transitions (PIPTs) in solids provide a test case for how forces, and the resulting atomic motion along a reaction coordinate, originate from a nonequilibrium population of excited electronic states. Using femtosecond photoemission, we obtain access to the transient electronic structure during an ultrafast PIPT in a model system: indium nanowires on a silicon(111) surface. We uncover a detailed reaction pathway, allowing a direct comparison with the dynamics predicted by ab initio simulations. This further reveals the crucial role played by localized photoholes in shaping the potential energy landscape and enables a combined momentum- and real-space description of PIPTs, including the ultrafast formation of chemical bonds.

An electron number distribution view of chemical bonds in real space

2007 ◽  
Vol 9 (9) ◽  
pp. 1087-1092 ◽  
Author(s):  
A. Martín Pendás ◽  
E. Francisco ◽  
M. A. Blanco
Keyword(s):  
Real Space ◽  
Chemical Bonds ◽  
Electron Number ◽  
Number Distribution

Xe Precipitates in Aluminum

2003 ◽  
Vol 792 ◽  
Author(s):  
Robert C. Birtcher ◽  
Stephen E. Donnelly ◽  
Ian Morrison ◽  
Charles W. Allen ◽  
Kazuo Furuya ◽  
...  
Keyword(s):  
Surface Energy ◽  
Room Temperature ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Real Space ◽  
Cubic Phase ◽  
Equilibrium Pressure ◽  
Yield Information ◽  
The Matrix ◽  
Dynamics Simulations

ABSTRACTReal space, high-resolution transmission electron microscopy observations of Xe confined in nanometer size faceted cavities in Al yield information on both the inert gas and the matrix in which it is confined. At room temperature, Xe in such cavities can be liquid or an fcc solid. In larger cavities, Xe within can undergo melting and recrystallization. The Al surface energy can be deduced from the largest Xe nanocrystal at 300 K by setting the corresponding calculated Laplace pressure equal to the equilibrium pressure for melting of Xe, obtained from empirical bulk compression data. These surface energy values are 1.05 J m-2 for {111} facets and 1.10 Jm-2 for {200} facets. Because of the weak interactions, these values correspond to the surface tensions for Al at 300 K.At room temperature, fluid Xe confined in small faceted cavities in aluminum has up to three ordered layers of Xe atoms at the Al interface. Conceptually in a three-dimensionally confined system of sufficiently small size, complete three-dimensional ordering of the fluid may occur. Molecular dynamics simulations have revealed that such ordering would result in fluid Xe confined to a small tetragonal volume solidifying as a body-centered cubic phase on compression.

High-resolution structure determination by ALCHEMI

1983 ◽  
Vol 41 ◽  
pp. 178-181 ◽  
Author(s):  
Peter G. Self ◽  
Peter R. Buseck
Keyword(s):  
Site Occupancy ◽  
Real Space ◽  
Unit Cell ◽  
Bragg Angle ◽  
Electron Current ◽  
High Resolution Structure ◽  
Beam Incident ◽  
Crystallographic Planes ◽  
Electron Beam Incident ◽  
Resolution Structure

ALCHEMI (Atom Location by CHanneling Enhanced Microanalysis) enables the site occupancy of atoms in single crystals to be determined. In this article the fundamentals of the method for both EDS and EELS will be discussed. Unlike HRTEM, ALCHEMI does not place stringent resolution requirements on the microscope and, because EDS clearly distinguishes between elements of similar atomic number, it can offer some advantages over HRTEM. It does however, place certain constraints on the crystal. These constraints are: a) the sites of interest must lie on alternate crystallographic planes, b) the projected charge density on the alternate planes must be significantly different, and c) there must be at least one atomic species that lies solely on one of the planes.An electron beam incident on a crystal undergoes elastic scattering; in reciprocal space this is seen as a diffraction pattern and in real space this is a modulation of the electron current across the unit cell. When diffraction is strong (i.e., when the crystal is oriented near to the Bragg angle of a low-order reflection) the electron current at one point in the unit cell will differ significantly from that at another point.

Chemical Species Identification in an SEM by Changes in Emitted X-Ray Energies

1974 ◽  
Vol 32 ◽  
pp. 570-571
Author(s):  
R. H. Duff
Keyword(s):  
Species Identification ◽  
Valence Electron ◽  
Chemical Species ◽  
X Rays ◽  
Chemical Bonds ◽  
Small Shift ◽  
X Ray ◽  
Electron Transitions ◽  
Peak Energy ◽  
Chemical Combination

A material irradiated with electrons emits x-rays having energies characteristic of the elements present. Chemical combination between elements results in a small shift of the peak energies of these characteristic x-rays because chemical bonds between different elements have different energies. The energy differences of the characteristic x-rays resulting from valence electron transitions can be used to identify the chemical species present and to obtain information about the chemical bond itself. Although these peak-energy shifts have been well known for a number of years, their use for chemical-species identification in small volumes of material was not realized until the development of the electron microprobe.

An Image Reconstruction System Applied to High Voltage Microscopy

1975 ◽  
Vol 33 ◽  
pp. 292-293
Author(s):  
D. E. Johnson
Keyword(s):  
High Voltage ◽  
Prior Information ◽  
Block Diagram ◽  
Three Dimensional ◽  
Real Space ◽  
Two Dimensional ◽  
Efficient Manner ◽  
Fourier Methods ◽  
Tilt Series ◽  
Methods Of Reconstruction

Increased specimen penetration; the principle advantage of high voltage microscopy, is accompanied by an increased need to utilize information on three dimensional specimen structure available in the form of two dimensional projections (i.e. micrographs). We are engaged in a program to develop methods which allow the maximum use of information contained in a through tilt series of micrographs to determine three dimensional speciman structure.In general, we are dealing with structures lacking in symmetry and with projections available from only a limited span of angles (±60°). For these reasons, we must make maximum use of any prior information available about the specimen. To do this in the most efficient manner, we have concentrated on iterative, real space methods rather than Fourier methods of reconstruction. The particular iterative algorithm we have developed is given in detail in ref. 3. A block diagram of the complete reconstruction system is shown in fig. 1.

Correlation averaging of two-dimensional crystals: basic strategy and refinements

1986 ◽  
Vol 44 ◽  
pp. 136-139
Author(s):  
W. Baumeister ◽  
R. Rachel ◽  
R. Guckenberger ◽  
R. Hegerl
Keyword(s):  
Low Dose ◽  
Signal To Noise Ratio ◽  
Real Space ◽  
Fourier Domain ◽  
Two Dimensional ◽  
Signal To Noise ◽  
Unit Cells ◽  
Lateral Displacements ◽  
Established Technique ◽  
Crystalline Array

IntroductionCorrelation averaging (CAV) is meanwhile an established technique in image processing of two-dimensional crystals /1,2/. The basic idea is to detect the real positions of unit cells in a crystalline array by means of correlation functions and to average them by real space superposition of the aligned motifs. The signal-to-noise ratio improves in proportion to the number of motifs included in the average. Unlike filtering in the Fourier domain, CAV corrects for lateral displacements of the unit cells; thus it avoids the loss of resolution entailed by these distortions in the conventional approach. Here we report on some variants of the method, aimed at retrieving a maximum of information from images with very low signal-to-noise ratios (low dose microscopy of unstained or lightly stained specimens) while keeping the procedure economical.

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