MSN 1527: Computational Materials Lab Department of Materials Science, CUTN

Expt.9:Crystal Structure Analysis Procedure

Procedure:

Mercury Software Instructions:

(1) Double Click on the Mercury 4.0.0 icon on the Desktop. It will open a new window showing
the different modules of the Mercury software.

A. Organic Molecule(s) Crystal Structure:

(2) Click 'CSD-Community' tab of the software and select ‘Open Teaching Database’ option to
load any of the crystal structures from default database of the software.

(3) Choose any one of the ‘molecules’ from the ‘Structure Navigator’ panel. Note down the
Crystal Structure name and Spacegroup of the selected molecule and report to your instructor.

(4) Go to ‘Display’ option and choose ‘Ball and Stick’ representation of the molecule under
‘Style’ category.

(5) Go to ‘Display’ option and choose ‘Label All’ view of the molecule under ‘Labels’ category.
This assigns labels for all the atoms of the molecule.

(6) Go to the ‘Edit’ option and choose ‘Copy Image to the Clip Board’ option to copy the
chemical structure of molecule.

Crystal structure (with and without packing)

(7) Choose ‘Show cell axes’ option to display the ‘unit cell’ crystal structure of the selected
molecule.

(8) You can translate or rotate the molecule by playing with the tabs x+, y- …., x-90, y+90….,
arrows, zoom options of the software or using scroll option of mouse.

(9) Go to the ‘Edit’ option and choose ‘Copy Image to the Clip Board’ option of crystal
structure of molecule in standard representation (b along x-axis direction, c along y-axis
direction and a along z-axis direction) to copy and paste the figure in a word file.

Note: Sometimes the figure is not legible under the above settings. So, align the figure in proper
direction for the best view and do the copy and paste of the crystal structure.

(10) Choose the ‘Packing’ option to notice the motifs and lattice points of the crystal structure.
Repeat the steps 8 and 9 by selecting the ‘packing’ option so as to observe the motifs and lattice
points of the crystal structure. (Additional molecule (s) adds up to the crystal structure under this
option. Choose ‘color’ by ‘symmetry operation’ to visualize the symmetry operation).

Crystal structure (with short contact and/or H-bond)

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MSN 1527: Computational Materials Lab Department of Materials Science, CUTN

(11). Select short contact (< sum of vdW radii) and H-bond (Default definition) buttons
separately for viewing the interacting atoms. Choose show hydrogens, and label atoms to find
out the interacting (short contact or H-bonds) of the crystal structure via dotted lines (red or
blue).

(12) With ‘no packing’ option, save or copy paste two images (Short Contact, and H-bond) of the
crystal structure. Make sure that the atom labeling is legible in the images that you copy.

(13) Choose packing option, select the show cell axis and deselect the label atoms. Choose
‘Short Contacts’ option to view the red dotted lines. Click contacts tab, and then under the ‘Build
network’ option, click ‘Expand All’ once or twice to observe sufficient number of structures and
contacts between atoms. Click ‘Delete Hanging Atoms’ to see only the short contacts (blue
dotted lines) within the visible crystal structures. Save the image in appropriate orientation with
all the short contacts and atoms visible.

(14) Repeat the step 13 with ‘H-Bond’ as option. Choose ‘H-Bond’ option to view the red dotted
lines. Click contacts tab, and then under the ‘Build network’ option, click ‘Expand All’ once or
twice to observe sufficient number of structures and contacts between atoms. Click ‘Delete
Hanging Atoms’ to see only the H-Bonds (blue dotted lines) within the visible crystal structures.
Save the image in appropriate orientation with all the H-Bonds and atoms visible.

Calculation (Powder XRD spectrum, Miller Planes, centroids)

(15) Click ‘calculate’ tab and choose ‘powder pattern’ to obtain the powder XRD spectrum of
the molecule. The Miller indices (hkl) for each peak are displayed at the bottom left corner of the
spectrum, by placing the cursor on to the peak maximum. Click on ‘save image’ option to save
the XRD spectrum as image file or copy and paste in your observation/lab record. Ultimately,
you have to assign and label the (hkl) values for at least 3 major peaks of the XRD plot. Note
down the three (hkl) values of the three maximum intense peaks.

(16) To view the Miller planes, click on the ‘calculate’ tab and choose ‘planes’ option and
choose ‘New Plane’ tab. You will see a new window with ‘Plane Properties’ title. Click the ‘hkl’
tab and enter the Miller Indices of the maximum peak (already noted from the powder XRD
spectrum). Choose ‘Show’, ‘Label’ and change the color and press ‘OK’ button. Miller plane
corresponding to this selection is displayed on the screen. Repeat the above procedure for other
two ‘Miller planes’ with different colors. Copy and paste the crystal structure figure showing all
the three Miller Planes.

Crystal Structural Information

(17) Click the ‘More Info’ drop down menu tab and choose ‘Structural Information’ option. This
will display crystal structural information (Chemical Formula, Space Group, Cell lengths (a, b,
c), Cell angles (, , γ), Cell Volume, etc) of the selected structure. Copy and paste the structural
information in your observation/lab record.

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MSN 1527: Computational Materials Lab Department of Materials Science, CUTN

(18) Save all the relevant information (atoms, bonds, contacts, centroids, planes, symmetry,
distances, angles, torsions, etc) in tabular format and attach to your observation/lab record.

B. Inorganic Molecule Crystal Structure:

Repeat steps from 1 to 18 with an’ inorganic molecule from the ‘CIF’ folder.

Observation: The file name and chemical formula of selected (a) organic molecule is
…………… and, (b) inorganic molecule is ………….

Results:

In this lab experiment, analysis of crystal structure of two molecules (a) ……, and (b) ……….
were performed using Mercury 4.00 software tool.

Discuss about the following results for each the molecules:

(a) Crystal structure with and with our packing (with diagrams)

……

(b) Crystal structure with short contact/H-bond (with diagrams)

…..

(c) Powder XRD spectrum, Miller Indices, Centroids (with diagrams)

……

(d) Crystal Structure Information (with tabular data)

…….

Conclusion:

The Crystal structures of ………. and ……….. were analyzed using Mercury 4.00 software.
Useful information about …….., ………, ………, the structures have been obtained. XRD
spectra for the molecules were predicted using available data base and cif files