Using Vesta, Mercury, and Platon programs for

the analysis and visualization of crystalline and

molecular structures.
Parra Altamirano Carla,1 Achig Merino Vivian,1 Pico Perez Alejandro,1 and Cusangua Vargas Jordy1
1
Laboratory of Structure of Materials , School of Chemistry and Engineering, YachayTech, Urcuquı́. Ecuador.
(Dated: May/19/2021)

I. INTRODUCTION • The atomic positions of the atoms are shown and

the results of the measurements of the distances
In this laboratory practice, the basic functioning of and the angles between atoms.
VESTA and MERCURY programs are used by Chem-
istry students with the objective of projecting, visu-
alizing, identifying, and characterize the main differ-
ences in the crystalline systems of coordinated inorganic
(CORUNDUM), organic (BITJOD), and polymer (Com-
pound 1) compounds. To achieve this, a series of ac-
tivities in increasing order of complexity are proposed,
which will allow us to understand the operation of the
program and the fundamentals of the projection of crys-
talline structures in three dimensions; in order to under-
stand and interpret the different parts of a crystalline
structure to understand their physical behaviour.

II. OBJETIVES

FIG. 1. Vesta uses methodology

• Use VESTA and Mercury programs to identify the
symmetry elements of the molecules.
• Visualize and Identify the main differences between B. MERCURY
the crystalline systems (coordinated organic, inor-
ganic and polymers compounds) Once the structure of the 3 different compounds has
been projected, the MERCURY program allows
III. EXPERIMENTAL DETAILS • Project the structure along of different axes

A. VESTA • Show the symmetry elements of each molecule (

Once the structure of the 3 different compounds has
been projected, the VESTA program allows:
• Projects the structure along one of the axes
1. with coordinates 100
2. with coordinates 010
3. with 001 coordinates
4. a, b, c with coordinates 111
• Change the color and size of atoms
axes, planes)
• Allows you to change the style of the projected
molecule ( Ball and Stick, Wireframe, etc)
• Change the color of each atom to identify which
element is.
• Allow us to know about the information of the
molecule (structure, diagram, bonds, angles )
• Packing the molecule
• Identify the asymmetric unit
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associated with each lattice point.

Due to this molecule corresponding to coordinal poly-
mere (Fig 4), it was identified by the central atoms like
the first hint. In this case, Fe and Cu are identified; tak-
ing the atoms coordinated to these elements.
For Corundum (Figure 5), is a material with a lot of glide
plane. The motif for this material is composed by an Al
atom and an O atom.
For BITJOD (Figure 6) constituted of one sulfur atom,
one nitrogen atom, twelve hydrogen atoms and thirteen
carbon atoms.

FIG. 2. Mercury uses methodology

IV. RESULTS AND DISCUSSION

Before beginning to describe the elements of symmetry,

unit cell and other elements corresponding to crystalline
structures, it was necessary to observe the structure ob-
tained in the Mercury program (Figure 3). The 3D mod-
eling helps us to notice the elements already studied with
the naked eye; However, the application of the different
tools within the program allowed us to consolidate this
knowledge. Below we can observe different characteris-
tics that have been obtained in the Vesta and Mercury
program, according to the needs that were generated.
Thus fulfilling the main objective of this Laboratory sec- FIG. 4. Motif of Compound 1
tion.

FIG. 3. Compound 1 (C24 H16 CuF eN2 O4, 1.12(H2 O),0.38(O))

A. Identify the motifs

For the visualization of the symmetry elements in this

case the motif, it was used MERCURY, due to its facility
to localize the asymmetric unit, and motif which is inside
of the asymmetric unit. The motif is a list of the atoms FIG. 5. Motif of Corondum

FIG. 6. Motif of BITJOD
B. Identify the Unit Cell
The unit cell (UC) is the minimum portion of a crys-
talline unit necessary to repeat the whole crystal; it could
be defined as a spatial arrangement of atoms that repeat
themselves in a three-dimensional space to define the en-
tire crystal. Identifying the unit cell is a basic, but very
necessary step to recognize elements of symmetry. Gen-
erally, a reference point is taken and traversed until the
same point is found again, repeating this step in the all
direction of axes, we obtain the unit cell. In this labora-
tory section, the Mercury and Vesta programs has been
used to identify UC (Figure 7, Figure 8 and Figure 9).
FIG. 7. Unit cell of Compound 1
FIG. 8. Unit cell of Corundum
3
FIG. 9. Unit cell of BITJOD
C. Visualize and symmetry elements in 3D
dimensional.
As we know search for symmetric element in a struc-
ture with lots of atoms can be almost impossible. To
comprehend and visualize symmetry element in a 3D,
we use Mercury because it provides a tool to give all
symmetric elements. Then we must understand the data
provided by the program as follow:
• Put the molecule in the different planes
• Analyze the molecule to find any rotation.
1. Inversion element
To visualize the inversion element of the molecule,
the first step was to show the molecule on the (100)
axis. The inversion is when the molecule moves along
a straight line, passing through the center of inversion
until it reaches the same distance as the first molecule.
In Figure 10 and Figure 11 the inversion is represented by
orange points. In Figure 12 the inversion is represented
by blue points.
FIG. 10. Inversion of Compound 1
 4

FIG. 13. Symmetry elements of Compound 1

FIG. 11. Inversion of Corundum

FIG. 14. 2-fold screw axis for corundum

FIG. 12. Inversion of BITJOD

2. Axis

In the process of visualizing symmetry elements in the

polymer coordinated compound (Figure 13), only one
axis was found corresponding to 2-fold (180 o ).
For corundum, we found 2-fold and 3-fold axis (Figure
14) and (Figure 15).
For BITJOD, we found 2-fold axis (Figure 16). FIG. 15. 3-fold screw axis of of Corundum
 5

FIG. 18. 010 Flat of Compound 1

FIG. 16. 2-fold screw axis for BITJOD

D. Draw crystallographic planes (100), (010),

FIG. 19. 010 Flat of of BITJOD
(001), and (111).

For this activity, the program used was VESTA due to

its facilities to visualize the different planes. This tool is 2. 100 Flat
necessary to identify any features that require visualiza-
tion. It is showed the different flats. The crystallographic
planes (100) in (Figures 20, 21, 22); (010) in (Figures 17,
18, 19), and (001) in (Figures 23, 24, 25) are represented
according to the spatial arrangements of the unit cell de-
scribed above in the figure. In Crystallographic Plane
(111) in (Figures 26, 27, 28) is represented by the same
spatial arrangements, but turn slightly to the right to
appreciate this plane. The first three planes intersect
the axes a, b and c respectively while plane (111) crosses
them all.

FIG. 20. 100 Flat of Compound 1

1. 010 Flat

FIG. 17. 010 Flat of Corundum FIG. 21. 100 Flat of Corundum

FIG. 22. 100 Flat of of BITJOD
3. 001 Flat
FIG. 23. 001 Flat of Compound 1
FIG. 24. 001 Flat of Corundum
FIG. 25. 001 Flat of of BITJOD
6
4. 111 Flat
FIG. 26. 111 Flat of Compound 1
FIG. 27. 111 Flat of Corundum
FIG. 28. 111 Flat of BITJOD
V. CONCLUSIONS
The visualization of structures in 2D dimensions in-
crease its complexity when we go to 3D. Also, when the
structure contains more atoms, the analysis of the sym-
metry elements turns to be really hard. Then, we use
Vesta and Mercury to visualize this type of crystalline
structure and its symmetry elements. In addition, the
use of this king of tools guarantees that we analyse and
visualize of crystalline and molecular structure without
any error.
Moreover, this programs provides more information
about the crystalline structure, this is the case of Vesta
which provide the space group of the molecular struc-
tures. Compound 1, P 21/c; Corundum, R-3c; and
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BITJOD, P/21c. so we complement it with Mercury. Through the data

However, Vesta do not provide the symmetry elements retrieved from these tools, we can identify chemical and
physical behaviour of the molecular structures.

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