UNIVERSIDAD DE INVESTIGACIÓN DE
TECNOLOGÍA EXPERIMENTAL “YACHAY TECH”
Using Vesta, Mercury, and Platon programs for the analysis and visualization of
crystalline and molecular structures.
Sara Cobo, Karol Maza, Christian Muso, Esteban Vallejo.
School of Chemical Sciences and Engineering, Yachay Tech University, 100119 Urcuquí, Ecuador
Despite programs visualization of molecular and crystalline structures is a significant tool in the structural analysis; this lab
report has been developed by using VESTA and Mercury programs to identify the motifs, asymmetric units and symmetry
operations of one inorganic, organo-metallic and coordination polymer structure. In fact, it provides structure information
and visualization of 3D dimensional graphs; the symmetry operations and planes are shown in graphs that provide important
information in order to understand physical and chemical properties of each analyzed molecule.
Keywords: Crystallographic structure; 3D visualization; crystalline materials.
1. Introduction
During the last 21 years affordable commercial
software has been developed for teaching and research in
crystallography. Nowadays, visualization programs for
crystalline structures are a fundamental tool for the study
of them. Allowing the performance of complicated tasks,
such as: determining molecular geometry, point and
spatial symmetry, the position of functional groups,
angles, and even the arrangement of each atom. In this
way, these programs provide us with the necessary
information to complement scientific investigations in
different areas that include characterization or synthesis
of crystalline materials. According to the purposes of this
practice, exist several useful programs that enable the
analysis of structures of crystals and molecules. On this
opportunity, Mercury and VESTA will be used. Next, a brief
description of them1,5,6.
Vesta.
Vesta, a successor of two 3D visualization
programs, VICS and VEND, allows us to represent
crystalline structures by means of different models,
among them we have space-filling, polyhedral, thermal
ellipsoid, and so on. Among the information that this
software can provide us are the fractional coordinates,
occupancies and oxidation states of the sites; from this
information we can infer quite a lot of chemical
information of the crystalline compounds1,3,5.
Mercury
Mercury is a visualization program produced by
the Cambridge Crystallographic Data Centre (CCDC) that
offers a wide range of tools for 3D structure visualization,
crystal packing exploration and statistical analysis of CSD
search data. This requires good visualization and the
ability to display the key intermolecular interactions that
hold a crystal structure together. Among the visualization
options are the display of molecules in a variety of styles
and color schemes; and the ability to turn on or off the
display of individual atoms or molecules, and display the
contents of any number of unit cells. Besides, elements
such as atom labels and unit cell axes can be displayed.
The image provided by Mercury has the option to be
rotated, translated and scaled. Crystal structures can be
displayed along direct or reciprocal cell axes, or
perpendicular to any specified plane or bond. Finally, in
addition to the above, distances, angles and torsions can
be measured1,4.
2. Objectives
a. Identify the motifs and asymmetric unit
b. Draw of contents of unit cell.
c. Visualize and symmetry elements in 3D dimensional
d. Draw crystallographic planes (100), (010), (001), and
(111).
3. Experimental Details
3.1. Crystalline structure analyze with Mercury and
VESTA
The programs Mercury and VESTA are excellent for
visualizing the crystals and examine the arrangement of
atoms through the structure. In order to achieve the
purpose of this report, those programs were used. Both of
them allow us to observe some elements like asymmetric
units or the unit cell and provide a 3D interactive image in
which the arrangement of structures is simple to see .
However, Mercury had some well developed tools such as
the drawings of the symmetry elements, the crystalline
structure, or the structure information which were plenty
useful. Furthermore, it is very simple to use. For that
reason, on this practice to achieve the objectives we
mainly used Mercury.
Chemistry Laboratory of CrystallographyProf. Edward E. Ávila |1
