The CCDC Sponsored PhD Programme – Advancing Chemistry and Crystallography for the Public Benefit
August 4, 2023
One of the many ways we advance chemistry and crystallography for the public benefit is through our sponsored PhD programme.
As a partner institute of the University of Cambridge, we are able to supervise PhD students together with partner universities and collaborating institutions including companies.
At our annual Science Day held in Cambridge in July, some of the CCDC sponsored PhD students presented their work.
Analysing the Pharmaceutical World
Julia Gasol is a final year CCDC-sponsored PhD student within the CMAC Future Manufacturing Research Hub at the University of Strathclyde. Her research investigates the effect of pressure on the crystal structures of pharmaceuticals in order to study the pressure-induced changes upon tabletting.
“My PhD project ‘From crystal to tablet – linking structure to function through compression studies’ looks at understanding the relationship between what we see at the atomic level within the crystal, to the properties that we see in the final tablet product, aiming to begin to link both of them together.
I have used the CSD-Particle tools in my research to help understand the effect of pressure through slip planes. It has been really helpful to be able to calculate the slip planes, look at their topologies and begin to relate on the observed microscopic behaviour. This has provided a fundamental insight for my project that guided more in depth experimental studies.”
Julia Gasol, final year CCDC-sponsored PhD student.
Exploring Bioactive Conformers
Benoit Baillif is a PhD student working with the CCDC in collaboration with the University of Cambridge. Benoit’s project looks at identifying bioactive-like conformers of small molecules towards atomistic neural networks (AtNNs), important for binding pose identification in virtual screening.
“I have been using the visualization tools of the CCDC, but mostly CSD Python API, to perform GOLD docking and to check the validity of the 3D structures that I use, either from the CSD or from the PDB.“
“I am lucky because I have access to the well developed tools of the CCDC, alongside its scientists who have helped me with challenges and questions. This is not only a good association to develop a research project, but it also fits perfectly with the vision of the CCDC, which aims to help researchers with its data and tools.”
Benoit Baillif, CCDC-sponsored PhD student.
Investigating Metal Organic Frameworks (MOFs)
Lawson Glasby from the University of Sheffield and in collaboration with the University College London (UCL), is developing new computational tools for large-scale characterization of the Cambridge Structural Database (CSD) subset of metal-organic frameworks (MOFs). His research as a CCDC-sponsored PhD student aims to implement a tool for the MOFs subset that is reliable, accurate, reproducible, and accessible via CSD Python API.
“The CCDC tools have a considerable impact on my PhD work. I use ConQuest and Mercury almost every day, I use the CSD MOF subset and the 2D and 3D MOF subsets that are part of that group of structures. We also use the CSD Python API to scrape DOIs and create a web scraping tool to search for different properties of structures that are known MOFs, alongside with other customized Python scripts that the CCDC provides or that I have written to add hydrogen atoms to the structures, for example. I don’t think I would have been able to do my work without the CCDC tools!”
Lawson Glasby, CCDC-sponsored PhD student.
Investigating Crystal Sponges
A second project on MOFs involves our 1st year PhD student Aaron Horner, who is working on developing a framework for assessing and describing the quality of Crystal Sponges (CS) in collaboration with the University of Southampton. Crystal sponges are porous MOFs that have the capability to incorporate and orient poorly crystallizable compounds or very sparsely available compounds e.g. oils, gases or highly dilute solutions, as guests within their pores, enabling their structure determination.
“In my research I mainly use the CSD to investigate the crystal sponges that are available, and the CSD Python API to write code. The amount of data that I am able to collect by accessing the CSD has been fundamental for my research. Without it, my project would have been completely different and probably not possible. I would be working with our in-house material, which is a reasonable amount, but it isn’t comparable to the vast amount of curated knowledge that I can easily access in the CSD, all in one place.”
Aaron Horner, CCDC-sponsored PhD student.
The Versatility of Computational Tools
Computational chemistry is essential in investigating properties of both known and new compounds. Our PhD students Cameron Wilson from the University of Edinburgh, Harry Nash from the University of Sheffield, and Daniel Widdowson from the University of Liverpool, apply these tools to different research areas.
Cameron is a third year PhD student who is investigating the role of entropy in the C-F…H bond. His research focuses on assessing the entropies of fluorobenzene compounds via both Γ-point and full phonon density of states calculations.
Harry is undertaking a project that explores the landscape of σ-hole interactions. His PhD investigates the geometric preferences and directionality of σ-hole interactions with searches on the CSD, and maps the size of σ-holes with electrostatic surface potentials (ESPs) calculations.
Daniel’s project “Continuous invariant-based maps of the crystal universe” looks at crystallography in a mathematical way, though an approach that can be used in the detection of geometrical identities within the CSD, to generate inputs for AI, and for finite point clouds, e.g., single molecules.
“The CSD is completely integral to my research. There are other open databases of crystal structures, but not ones that are so well curated and expansive. We’ve also used a lot the CSD Python API and Mercury, because we work on similarities and comparisons. For the most part, these tools are very easy to use, and worked very well for me. I think they are excellent, and I can’t think of any other suite of tools like it.”
Daniel Widdowson, CCDC-sponsored PhD student.
Study of Properties and Behaviours
Nathan Hennessy from the University of Leeds is doing a PhD with the CCDC on nucleation and crystal growth of L-histidine. The goal of Nathan’s project is to understand whether it is possible to predict anti-solvent nucleation rates based on the cooling crystallization nucleation rates in solvent mixtures, aiming to control product properties such as polymorphism and size distribution.
“I use the CCDC tools to model and predict the full interaction maps and the hydrogen bond propensities of my systems, both when they are being solvated and when they are crystallizing. This is a unique and important suite of tools that helps to predict what is going to happen when I try new systems.”
Nathan Hennessy, CCDC-sponsored PhD student.
Investigating the Correlation Between Crystal Structures and Particle Surface Properties
Finally, our first year PhD student Emilia Prandini from the Politecnico di Torino seeks to investigate, using both computational and experimental techniques, the correlation between crystal structures and particle surface properties of small organic molecular crystals.
“It was a pleasure to be here today at the Science Day. It is my first time at the CCDC, and it is nice to meet the CSD-Particle team, and work together with them. It’s a vibrant, professional environment with a team that helped me a lot in discovering new points of view that are very interesting for my research.”
Emilia Prandini, CCDC-sponsored PhD student.
Find out more about our sponsored PhD programme.
Computational Chemistry (9)
CSD Python API (16)
Functional Materials (4)