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Visualization For Electronic Structural Analysis)

VESTA is software that visualizes and analyzes 3D crystal structures and volumetric data derived from techniques like X-ray diffraction. It can display structural models and analyze properties like bonding distances and angles. The document describes using VESTA to model the crystal structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6, including drawing bonds, measuring distances and angles, transforming to a supercell, and analyzing the XRD pattern to determine d-spacings and planes of highest intensity.

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189 views

Visualization For Electronic Structural Analysis)

VESTA is software that visualizes and analyzes 3D crystal structures and volumetric data derived from techniques like X-ray diffraction. It can display structural models and analyze properties like bonding distances and angles. The document describes using VESTA to model the crystal structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6, including drawing bonds, measuring distances and angles, transforming to a supercell, and analyzing the XRD pattern to determine d-spacings and planes of highest intensity.

Uploaded by

Rosni hasan
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Introduction:

VESTA (Visualization for Electronic Structural Analysis) is a software for visualizing and
analyzing three-dimensional crystal structures and volumetric (voxel) data, such as electron
and coherent scattering length (nuclear) densities derived by X-ray and neutron diffraction,
respectively. Additionally, it is used to visualize volumetric data, such as electron densities,
wavefunctions, and electrostatic potentials derived from electronic state computations. Thus,
VESTA aids in the comprehension of crystal structures and a range of three-dimensional
physical variables.

Ball-and-stick, space-filling, polyhedral, wireframe, stick, and displacement ellipsoid models


are used to illustrate structural models. When atoms and bonds are selected, a variety of
crystallographic information is produced in the text area underneath the graphic area. A (4×4)
transformation matrix may be used to change general equivalent locations in a standard lattice
setting into those in a nonstandard setting. It can also be used to produce a superlattice and a
sublattice.

Volumetric data, such as electron and nuclear densities, Patterson functions, and
wavefunctions, are shown using isosurfaces, bird's-eye views, and contoured two-dimensional
maps. VESTA has a surface coloring capability that allows for the visualization of another
physical quantity at each point on the isosurfaces, generally isosurfaces of electron densities
colored in reaction to electrostatic potentials. Electron densities may be used to calculate three
different types of electronic energy densities. Laplacians may also be computed for other types
of data.

This experiment mainly worked with structural models and powder diffraction patterns of
several crystal structures. Different structural models, bonding distance, angle, and peak
analysis of powder diffraction patterns were performed.

The given Crystal structure:

Title: (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6

Lattice type: F

Space group Name: Fm-3m

Space Group number:225

Setting Number: 1
Lattice Parameters:

a b c alpha beta gamma


10.26000 10.26000 10.26000 90.0000 90.0000 90.0000

Unit Cell Volume = 1080.045648 Å3

Structural Parameter:

x y z Occ. B Site
1 Cs Cs 0.25000 0.25000 0.25000 0.450 1.000 8c
2 K K 0.25000 0.25000 0.25000 0.550 1.000 8c
3 Se Se 0.00000 0.00000 0.00000 0.500 1.000 4a
4 Bi Bi 0.00000 0.00000 0.00000 0.500 1.000 4a
5 Cl Cl 0.23500 0.00000 0.00000 1.000 1.000 24e

Procedure:
1. Building Crystal Structure:
• To create new structure: File > New Structure = “(Cs0.45K0.55)2(Se0.5Bi0.5)Cl6”
• Unit cell and Symmetry: System= “Cubic” > Space group = “Fm-3m” > Lattice
Parameter = “a=b=c=10.26000 and alpha=beta=gamma= 90.000”
• Structure Parameters: New > Symbol> Label> x > y >z > OCC > Isotropic=“B”
> B =1 >Ok.

Fig.1: Crystal structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6


2. Labeling each atom:
Objects > L> each box was selected.

Fig.2: Crystal structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6 (With Label).

3. Bond Setting:
Edit> Bonds>New>A1= “Cs/K” > A2= Cl” >Max length= “5”
New>A1= “Se/Bi” > A2= Cl” >Max length= “3”> Apply.

Fig.3: Bonds Between atoms


4. Polyhedral Shape:
• Style> Polyhedral.

Fig.4: Polyhedral structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6

• Polyhedral structure (A site):


Edit>Bonds>Unselect Bond of Se/Bi-Cl.

Fig.5: Polyhedral structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6 (A site)

• Polyhedral structure (B site):


Edit>Bonds>Unselect Bond of Cs/K-Cl.
Fig.6: Polyhedral structure of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6 (B site)

5. One Polyhedral:
Objects > Boundary > x(max) = “0.5” >y(max) = “0”> z(max) = “0” >Apply.

Fig.7: One Polyhedral

6. Measuring Bonding Distance and Angles:


• Bonding Distance:
Style > Distance >Select Two atoms (Anion and Cation)
(a) (b)

Fig.8: Bond Length (a) Cs/K –Cl (b) Se/Bi -Cl

• Bonding Angle:
Style> Angle(a) >Select Cs/K-Cl-Se/Bi

Fig.9: Bond Angle of Cs/K -Cl- Se/Bi.


7. Visualization of the structure from different orientations:

(a) (b)

(c)

Fig.10: Visualization of the structure from different orientation (a) ab–plane (b) bc-plane (c)
ac-plane

8. Making 2×2×2 Supercell:


2 0 0
Edit> Edit Data> Unit Cell> Transform> Rotation matrix > 0 2 0
>Ok>Apply. 0 0 2
Fig.11: 2×2×2 Supercell of (Cs0.45K0.55)2(Se0.5Bi0.5)Cl6

9. Drawing Lattice plane:


Edit> Lattice planes> New> Miller indices (hkl) = “(101), (010), (001), (111), (221),
(131)”> Ok

(a) (b)

(c) (d)
(e) (f)

Fig.12.Lattice plane (a)101 (b) 010(c) 001(d)111 (e)221 (f) 131 in each unit cell

• Lattice plane without Atoms:


Objects>Unselect Atoms> Edit> Lattice planes> New> Miller indices (hkl) = “(101),
(010), (001), (111), (221), (131)”> Ok

(a) (b)
(c) (d)

(e)
(f)

Fig.13: Lattice plane (a)101 (b) 010(c) 001(d)111 (e)221 (f) 131(without atoms)

10. XRD Pattern Analysis:


Utilities>Powder Diffraction Pattern>Calculate.

Fig.13: XRD pattern of the crystal structure


• Plane and d spacing Analysis:
Utilities>Powder Diffraction Pattern>Calculate>Reflections.

d- spacing:5.92
(222)
d- spacing: 3.627
(440)
d- spacing:2.565
(800)

Fig.14: XRD pattern of the crystal structure with d spacing and plane of highest three peaks.

Conclusion:

This experiment employs VESTA software to visualize the crystal structure of


(Cs0.45K0.55)2(Se0.5Bi0.5)Cl6. The crystal structure was modeled and labeled using the relevant
lattice and structural parameters. Following the formation of the cation-anion bond, a
polyhedral shape was created. The cation-anion bonding distance and angle were evaluated.
The unit cell was made transformed into a 2×2×2 supercell and several lattice planes were
drawn. Calculation and analysis of the XRD pattern revealed significant crystal structure
parameters (d-spacing and plane).

Reference:
[1] K. Momma and F. Izumi. VESTA 3 for three-dimensional visualization of crystal,
volumetric and morphology data. J. Appl. Cryst. (2011). 44, 1272-1276.
[2] K. Momma and F. Izumi. VESTA: a three-dimensional visualization system for electronic
and structural analysis. J. Appl. Cryst. (2008). 41, 653-658.

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