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Assessment brief
Module code & title CAPE5320 Multi-scale Modelling and Simulation
Assignment title Molecular Modelling Assignment
Assignment type Coursework
Learning outcomes
assessed
On completion of this assignment, students should be able to:
1. Gain practical experience of applying molecular modelling approaches
using suitable tools
2. Develop an understanding of the types of materials and processes for
which molecular modelling provides useful insights within the multi-scale
modelling environment
3. Improve understanding of the science underpinning the molecular
modelling of crystalline solids
Rationale Molecular modelling is part of the multi-scale modelling advances that help to
understand the molecular properties of materials. This assessment is designed
for you to get a hands-on experience of using molecular modelling software of
various modules, and by doing so, acquire skills to simulate your molecular
structure, analyse bulk and surface properties, and interpret findings based on
underpinning science.
Word limit and guidance Your submission will be a one-page poster consisting of four sections which are
introduction, methodology, result-discussion and conclusion. There is no specific
word limit for the poster (suggested limit as guidance). The result and discussion
should be coherent and concise to represent your findings. See below for further
details.
A penalty for going over the page limit will apply as – 10% of the total mark
available for the assessment.
Use of GenAI in this
assessment
AMBER: AI tools can be used in an assistive role.
You are permitted to use AI tools for specific defined processes within the
assessment. See below for further details.
Weighting 20% of the overall module mark
Deadline of assessment 9
th May 2025
Submission method Electronic copy, via Module Minerva page/Assessment and Feedback/Submit
My work/
Feedback provision Students can obtain feedback on their work before submission (typically 1 week
before the deadline) by meeting Dr Siti Fatimah in-person and showing their
work.
Feedback on the summative submission will be provided on Minerva
Module manager Dr Siti Fatimah Ibrahim
Use of GenAI
Since Gen AI is a new and rapidly changing field, it is impossible to list every possible way it could be used.
Below are some anticipated ways you may and must not use Gen AI in this assessment. For anything involving
Gen AI not covered in this statement, please contact Dr Fatimah and assume that it is not permitted until you
have an answer.
Within this assessment, you may use Gen AI to:
generate ideas or inspiration for your poster presentation
understand more complex ideas by providing accessible summaries
recommend relevant sources, provided you also verify them yourself
You must not use Gen AI to:
produce written or poster content, which you then submit as your work, regardless of whether you
make major or minor changes to it
rewrite sentences or make substantive changes to your original work
provide feedback on accuracy or validity of content in your original work
You must include a GenAI Declaration at the beginning of your report/presentation if you have used GenAI.
The minimum requirement to include in the declaration is the name and version of the generative AI system
used (e.g., ChatGPT-4.0), the publisher (company that made the AI system) (e.g., OpenAI), the URL of the AI
system and a brief description (single sentence) of the context in which you used the tool.
Example declaration: I acknowledge using ChatGPT-3.5 (Open AI, https://chat.openai.com/) to recommend
papers published on the simulation of acetaminophen.
Assignment guidance
Molecular modelling is a useful tool for designing materials fit for purpose. It can be used in most chemical
engineering processes such as specialty chemicals, foods, polymers and others. You are required to do a
literature search on an organic system of interest to investigate. Use Conquest to search for the structure file.
You can also find the structure within the CCDC Mercury Software.

Refer to Lecture 1- Chemical Engineering at molecular scale to get general ideas of molecular systems to
work with and other lectures for simulation work.

This assignment will use the Cambridge Crystallographic Data Centre’s Materials Mercury software.
Assignment tasks in outline
1. Examine the molecular packing in the crystal structures and identify key intermolecular and
interatomic interactions.
2. Describe the nature of the intermolecular interactions.
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. Investigate the surface chemistry of the surfaces identified in the morphology predictions.
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.
Poster structure
Section (mark) Guidance Suggested limit
Title Provide suitable title to represent content of your poster. 10-15 words
Introduction (10%) Provide the context/ background for your selected topic.
List the objectives and scopes for your study.
100-150 words
Methodology (10%) Provide summary of computational approach used.
Include important correlations.
If possible, include related table and figures
150-200 words
(include captions)
Results (30%) &
Discussions (35%)
Present key findings with visuals (figures, charts, images).
Use the Contacts facility in the CCDC Materials Mercury software to identify and
describe bonds 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 bonds.
Predict the expected crystal surfaces for your structure using the BFDH approach.
Create separate tables for 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 Morphology).
Now using the VisualHabit module and employing a radial cut-off distance of 30
Angstroms calculate and report the lattice energy for your crystal structure using the
suitable 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.
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.
300-500 words
(include captions)
Consider the crystal shape for the crystal calculated using the VisualHabit or 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.
Compare both morphology prediction approaches findings.
Evaluate the surface chemistry of the four morphological importance forms by cleaving
the surfaces. Comment on the interactions available at the surface.
Conclusion (5%) Summarise the main findings and their significance. Be specific with key values/data.
Do not introduce new findings.
Suggest future work.
50-75 words
General presentation (10%) Use a clean layout with consistent fonts and colors.
Ensure text is readable from a distance; use bullet points for clarity.
Check for spelling and grammatical errors.
Design your poster creatively.
References At the end of your presentation, you must display the list of references detailing the
literature you used as sources of information for your presentation. References must
clearly identify the source material. At the appropriate location in the text, identify the
cited reference by its number in the list of references. Be sure to follow the guidance
you have received on avoiding plagiarism!
*Refer to the sample of the poster for guidance on the structure.
General guidance
1. You must make submissions by uploading the correct document to Minerva by the deadline. A standard
penalty for late submission will apply. 5% of the total mark available for the assessment will be lost, for
each 24 hours or part thereof that the assessment is overdue.
2. Extensions to coursework deadlines may be granted in exceptional circumstances. The request needs
to be made ahead of the deadline to the Student Service Office (SCAPEStudentAdvice@leeds.ac.uk)
Assessment criteria
The assessment rubric that will inform the marking of the report/presentation is provided below. The submitted
work must meet the minimum English Competency level. For the general presentation of the
report/presentation, the following points will be assessed:
Suitable title.
Poster content is free of grammatical/spelling errors.
Structure of the poster follows guidelines.
Titles and legends of figures are given and appropriately positioned.
References are well balanced (between websites, textbooks and journal articles) and appropriately
expressed.
Communication style is suitable for an academic poster.
Academic misconduct and plagiarism
All work will be assessed for plagiarism using plagiarism checking software, when applicable. The University
has issued guidelines on plagiarism. The procedure will be followed if there is suspicion of it taking place.
(https://ses.leeds.ac.uk/info/22165/coursework/635/cheating_plagiarism_fraudulent_or_fabricated_coursewor
k_and_malpractice_in_university_assessments_taught_students
Assessment criteria grid
Sections Level of Achievement
Fail
(0-39)
III
(40-49)
II/2
(50-59)
II/1
(60-69)
I
(70+)
Introduction Missing introduction
section or largely
incomplete
introduction and
missing objectives
and scopes.
Introduction section
contains the required
information but
presented with major
inconsistencies
suggesting knowledge
gaps; Incomplete
objectives and scopes.
Introduction section presented
with few inaccuracies.
objectives and scopes are
completed and appropriately
described.
Well-written/presented
introduction providing the
required background
information on the study
and coherently describing
the objectives of the
investigation along with an
appropriately defined
scope.
Exceptional orderly
presentation of introduction
content and background
information is collated from
diverse references. Scope
of the investigation is
described with sound
statements and clear
objectives. Presentation is
of a very high academic
standard.
Methodology Methodology is
unclear and poorly
organised, difficult
to follow. Methods
are inappropriate or
do not address the
objectives.
Provides minimal details,
many key procedures,
materials, or techniques
are missing.
Methodology is somewhat
clear but has several
organisational issues.
Provides some details, but
several key procedures,
materials, or techniques are
missing. Methods are
somewhat appropriate, but
some may not fully address
the objectives.
Methodology is mostly
clear and organised, minor
issues in flow. Provides
adequate details on most
procedures, materials, and
techniques used. Methods
are appropriate for the
objectives.
Methodology is clearly and
logically organised, easy to
follow. Provides
comprehensive details on
all procedures, materials,
and techniques used.
Methods are highly
appropriate for the
research question and
objectives. Excellent use of
visuals (e.g., flowcharts,
diagrams) to illustrate
methods.
Results &
Discussions
Results and
discussion have
many major errors
and represents poor
understanding;
Figure(s)/ Table(s)
missing or largely
incorrect.
Results are unclear and
poorly organised, difficult
to follow.
Discussion of findings
and accompanying
figure(s)/table(s) are
mostly superficial and
only meets the basic
requirements
representing limited
understanding.
Provides some details, but
several key findings are
missing.
Some use of visuals, but they
are not very effective or clear.
Reasonable attempt at
discussing experimental
findings but the discussion
fails to address some points of
importance/ demonstrates
some gaps in understanding
of underpinning concepts;
Provides adequate details
on most key findings.
Results are interpreted and
linked to research
questions/objectives.
Well-written/presented
discussion of the
experimental findings with
a strong understanding of
underpinning concepts and
completed with appropriate
figure(s)/tables(s)
Provides comprehensive
details on all key findings.
Excellent use of visuals
(e.g., graphs, charts,
images) to illustrate
results.
Discussion of the
experimental findings is
presented at a very high
academic standard
demonstrating
comprehensive and
nuanced understanding of
underpinning concepts;
Conclusion Fails to provide a
clear summary of
the findings.
Provides a partial
summary of the findings,
with several key points
missing.
Provides a summary of the
main findings but lacks some
clarity or detail.
Provides a clear and
concise summary of the
main findings.
Provides a clear, concise,
and comprehensive
summary of the main
findings.
General
presentation
Extremely messy
poster lacking in
basic structure with
an inarticulate
writing/verbal style,
several missing
sections or sections
of very
inappropriate
lengths, Missing or
inappropriate title.
Poster style that has a
basic structure but many
errors.
Poster sections are not
of appropriate lengths,
only few references are
expressed or references
expressed with
inconsistencies.
Poster style of a reasonable
academic standard and minor
grammatical/spelling errors.
Poster sections of acceptable
lengths.
Title reflects the study and
references are appropriately
expressed.
Poster style of a good
academic standard.
Poster sections of
appropriate length.
Title reflects the study and
references are
appropriately expressed.
Poster style of a very high
academic standard
demonstrating professional
communication skills.
Poster sections of
appropriate length.
Title reflects the study, and
references are well balanced and appropriately
expressed.