Multi-scale Modelling and Simulation: Molecular and DEM Modelling Assignment

Part A  use the Cambridge Crystallographic Data Centre’s Materials Mercury software
and its extension Visual Habit. The learning objectives are:
 To gain practical experience of applying molecular modelling approaches.
 To develop an understanding of the types of materials and processes for which molecular modelling
provides useful insights as part of a multi-scale modelling approach.
 Through practice, to develop an improved understanding of the science underpinning the molecular
modelling of crystalline solids.
The reference codes of the two crystal structures you will be investigating are AMBNAC07 and AMBNAC08.
These crystal structures are two polymorphs of the same material. If you are unable to find these structures
within the CCDC Mercury Software, you can search for them at and
download the structure files.
Assignment tasks in outline
1. Examine the molecular packing in the crystal structures and identify key intermolecular interactions.
2. Compare and contrast the nature of the intermolecular interactions in the two polymorphs.
3. Identify the most likely crystal surfaces to appear in the morphology of the crystals.
4. Apply the BFDH model to predict the shape of crystals of the allocated structures.
5. Apply the Attachment Energy model to predict the shape of crystals of the allocated structures.
6. Calculate the surface energies of the surfaces identified in the morphology predictions.
For Part A the assignment report should have the structure described below. The percentages in square
brackets indicate the distribution of available marks for this part of the assignment. Please do not exceed the
word counts indicated, a tolerance of 10% is allowed but otherwise marks will be subtracted. Remember to
provide a cover sheet for your assignment report and to include a declaration of academic integrity, plagiarism
will not be tolerated.
Abstract – summarise the main findings of the molecular modelling study and specify details of the molecular
compound allocated to you. (Maximum 200 words) [10%]
Materials and Computational Methods – (Maximum 800 words) [20%]
1. Include a figure showing the molecular structures of the materials allocated to you. Give the name of
the molecule. Specify whether the molecular structures have one or more asymmetric centres (for
example a carbon atom bonded to four different groups).
2. Provide a table summarising the crystallographic details of the two crystal structures. This should
include the cell parameters, unit cell volume, material density, crystal system, space group and
number of molecules per unit cell.
3. Specify which atoms in the molecular structure can donate and which can accept hydrogen bonds;
where appropriate also specify the type of functional group to which the atom(s) belong(s).
4. Briefly explain:
(i) what the BFDH approach is for calculating the likely surfaces of crystals and the crystal shape,
(ii) how a lattice energy is calculated for a molecular crystal,
(iii) what the attachment energy approach is for calculating crystal shape.
Dr Robert B. Hammond & Dr Joseph Antony
Results of Analysis of Crystal Structures – (Maximum 1500 words) [65%]
In this section present the results of your molecular modelling investigation for the allocated crystal structures.
1. Use the Contacts facility in the CCDC Materials Mercury software to identify and describe hydrogen
bonding interactions in your crystal structures. Your summary should include details such as the
atoms that are participating, in each case which is the acceptor and which is the donor atom and a
table of the distances and angles between the atoms which describe the hydrogen bonding.
2. Explain the main differences and the main similarities between the hydrogen bonding interactions
observed between molecules in the two polymorphs.
3. For both polymorphs predict the expected crystal surfaces for your structures using the BFDH
approach. Create separate tables for the two polymorphs listing the four most important forms
(families of surfaces on the crystal), the Miller indices of the family of crystal surfaces within each of
those forms and the interplanar spacing of the forms (units Angstroms), dhkl. Include figures showing
the BFDH morphology and underlying molecular packing (see CCDC Tutorial 2: Rationalising Crystal
4. Now using the VisualHabit module and employing a radial cut-off distance of 30 Angstroms calculate
and report the lattice energy for your two crystal structures using the Dreiding Mod potential. When
reporting the lattice energy at a radial cut-off distance of 30 Angstroms, give a breakdown into the
component parts e.g. van der Waals attraction energy, van der Waals repulsion energy etc.
5. Include a figure showing the change in the calculated lattice energy with radial cut-off distance and
comment on whether the trend is what you would expect and why.
6. Consider the crystal shapes for the two polymorphs calculated using the Dreiding Mod potential for
the attachment energy model. In a table report which four forms have the smallest, absolute values
of attachment energy. Provide a breakdown of the attachment energies into the component parts
e.g. van der Waals attraction energy, van der Waals repulsion energy and comment on the results you
have found. Include figures showing the attachment energy model morphology (crystal shape) and
underlying molecular packing.
7. In a table for the two polymorphs report the relative surface areas, as a percentage of the total surface
area, of the four forms with the greatest relative surface area based on the attachment energy model.
8. By taking the absolute value of the attachment energies and employing the relevant equation given
in the course notes, calculate the surface energies of the four forms (surfaces) from part 7 for both
polymorphs. Show your working for the calculations in the report and place the calculated surface
energy values in the table referred to above. Comment on the surface energy values you have

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