High Throughput Modelling of Molecular Crystals Out of Equilibrium (ht-MATTER)
Lead Research Organisation:
UNIVERSITY COLLEGE LONDON
Department Name: Chemical Engineering
Abstract
Molecular crystals (MCs) are found in many everyday products, from food to pharmaceuticals, hiding in plain sight characteristics that make them ideal materials for cutting-edge technological applications. Like construction bricks, MCs' building blocks can reversibly self-assemble into a plurality of structures, thus distinguishing the chemical properties of building blocks from the physical and mechanical material properties. These characteristics open up endless possibilities in material design, with applications in pharmaceutical manufacturing, separations, catalysis, and organic electronics. Tailoring the composition of the liquid phase in which MCs assemble holds the key to designing processes able to yield materials with desired properties. However, current approaches at MCs computational design are centred on predicting the thermodynamic stability of bulk phases. This paradigm had remained essentially unchanged since its inception more than two decades ago, leaving material and process design practices to empiricism. By neglecting the role of assembly kinetics, current computational crystal structure prediction methods cannot identify attainable MC structures and the ideal conditions (i.e. solvent, composition, temperature) to obtain them.
With ht-MATTER, I will bridge this gap by developing an open, transparent and flexible molecular simulation platform that will deploy state-of-the advanced molecular simulation methods necessary to model the out-of-equilibrium processes that govern crystal precipitation from solution at the atomistic scale. ht-MATTER will catalyse a paradigm shift in computational materials design by providing the high-throughput framework necessary to identify: a) MC structures attainable at finite-temperature; b) kinetic bottlenecks associated with crystal nucleation and growth from solution; and c) their dependence on solvent choice and solute concentration.
With ht-MATTER, I will bridge this gap by developing an open, transparent and flexible molecular simulation platform that will deploy state-of-the advanced molecular simulation methods necessary to model the out-of-equilibrium processes that govern crystal precipitation from solution at the atomistic scale. ht-MATTER will catalyse a paradigm shift in computational materials design by providing the high-throughput framework necessary to identify: a) MC structures attainable at finite-temperature; b) kinetic bottlenecks associated with crystal nucleation and growth from solution; and c) their dependence on solvent choice and solute concentration.
Organisations
Publications
Advincula X
(2024)
Dynamics and nano-rheology of interfacial water: general discussion
in Faraday Discussions
Bachtiger F
(2025)
Solution Thermodynamics of l -Glutamic Acid Polymorphs from Finite-Sized Molecular Dynamics Simulations
in Industrial & Engineering Chemistry Research
Bjola A
(2024)
Estimating Free-Energy Surfaces and Their Convergence from Multiple, Independent Static and History-Dependent Biased Molecular-Dynamics Simulations with Mean Force Integration.
in Journal of chemical theory and computation
Burcham C
(2024)
Pharmaceutical Digital Design: From Chemical Structure through Crystal Polymorph to Conceptual Crystallization Process
in Crystal Growth & Design
Cai X
(2024)
Understanding the effect of moderate concentration SDS on CO2 hydrates growth in the presence of THF.
in Journal of colloid and interface science
| Description | During the second year of this award we have obtained substantial progress on three fronts: 1. We have demonstrated the applicability of machine learning techniques combined with statistical mechanics approaches to efficiently estimate the stability of polymorphs of molecular crystals. This result, represents a substantial step forward in increasing the efficiency and scalability of computational approaches for the design of novel crystalline materials, with applications in pharmaceutical manufacturing and functional materials design. 2. We have developed and tested an approach to obtain information on the stability of crystalline nuclei within a solution from equilibrium molecular dynamics simulations. This work has enabled us to make a substantial step towards developing polymorph ranking methods that include information on the kinetics on nucleation, rather than relying solely on thermodynamic information. 3. We have further developed our ability to compute the free energy landscape associated with physical-chemical transformations with multiple, independent simulations, improving the computational efficiency of enhanced sampling methods. Moreover we have gained a deeper understanding of the impact of machine-learned reaction coordinates on the interpretation of free energy landscapes. These are technical results that form the basis for substantially increasing our ability to obtain information on nucleation mechanisms from data. 4. We have developed a systematic assessment of what a fully digital workflow for the development of pharmaceutical crystallization processes would entail. As a part of an international team of scientists and engineers, and in collaboration with the Pharmaceutical industry, we have laid out the key steps to obtain a conceptual design of a crystallizer starting only from the molecular structure of an Active Pharmaceutical Ingredient. This exercise, has enabled to identify key strengths and weaknesses of current computational methods, highlighting priority areas that are strongly aligned with this award. |
| Exploitation Route | This year' outcomes provide some key methodological advances for a systematic adoption of digital technologies in the development of molecular crystalline materials. The advances on the estimate of thermodynamic stability both based on machine learning methods, and on classical thermodynamics is general and accompanied by open research code, that can be used by others in the field and that, within the context of this award, will form the basis to develop a high throughput platform for the simulation of molecular crystals. |
| Sectors | Chemicals Digital/Communication/Information Technologies (including Software) Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| URL | https://pubs.acs.org/doi/full/10.1021/acs.cgd.3c01390 |
| Description | International Scholar Award for Doctoral Training (ISAD) |
| Amount | £80,000 (GBP) |
| Organisation | University College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 10/2027 |
| Title | CmuMD for PLUMED2 |
| Description | This repository hosts the implementation for PLUMED 2 of the CmuMD method. This method allows for mimicking open boundary conditions in NVT molecular simulations involving solid/fluid interfaces and enables the simulation of concentration-driven fluxes through porous membranes. The method, with an application to crystal growth, is described in the paper: [1] Molecular dynamics simulations of solutions at constant chemical potential. C Perego, M Salvalaglio, M Parrinello, J Chem Phys (14), 144113, 2015. The adaptation of CmuMD to model concentration-driven membrane fluxes is described in the paper: [2] Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation A Ozcan, C Perego, M Salvalaglio, M Parrinello, O Yazaydin Chem Sci 8 (5), 3858-3865, 2017 The method is described and discussed in the review work: Non-Equilibrium Modelling of Concentration-Driven Processes with Constant Chemical Potential Molecular Dynamics Simulations T Karmakar, A Finney, M Salvalaglio, AO Yazaydin, C Perego, Accounts of Chemical Research, 2023. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Reproducing the published work and enabling the adoption of methods in independently run research projects. |
| URL | https://github.com/mme-ucl/CmuMD |
| Title | Mean Force Integration - code |
| Description | Repository that contains the codebase used to implement Mean Force Integration (MFI), a method for postprocessing free energy calculations that enables the calculation of free energy surface from metadynamics and their associated convergence. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Enable to reproduction of results in published papers and dissemination of the methods developed in Bjola and Salvalaglio (10.26434/chemrxiv-2024-83h5q 2023). |
| URL | https://github.com/mme-ucl/MFI |
| Title | NNucleate - Machine Learning of Nucleation Collective Variables |
| Description | This is the release version of NNucleate. NNucleate is a Python package developed for the training of GNN-based models approximating computationally expensive collective variables (CV). The primary intended application is enhanced sampling simulations of nucleation events. These types of simulations are typically limited by the computational cost of their CVs, since they require a computationally expensive, differentiable degree of order in the system to be calculated on the fly. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Enables the reproducibility of the published results and the dissemination and adoption of the methods developed. |
| URL | https://github.com/mme-ucl/NNucleate |
| Title | NaCl (aq) nucleation rates: computational results and experimental measurements |
| Description | A repository that hosts the data used to map computational predictions and experimental measurements of nucleation rates of NaCl(aq) as discussed in "Molecular simulation approaches to study crystal nucleation from solutions: Theoretical considerations and computational challenges, A. Finney, M. Salvalaglio, WIREs Computational Molecular Science, 2024." ( https://doi.org/10.1002/wcms.1697) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Enable a critical comparison between computational methods for the estimate of nucleation rates and their comparison with experiments. Will be periodically updated with data from new papers. |
| URL | https://github.com/mme-ucl/NaCl_water_Nucleation_Rates |
| Description | Crystallisation Day 2024 Industry-Academia panel |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participated in a panel discussion on Industry and academia open questions and challenges in the field of crystallization processes. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presenter and Panelist at the 2025 University of Oklahoma Sustainability Forum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I have presented my work on the digitalisation of materials research in Pharma, in the context of the University of Oklahoma sustainability forum. I was representing academic research in a panel composed of industrialists and social scientists that discussed several aspects of sustainable practices within the Pharmaceutical industry. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.ou.edu/coe/events/sustainability |
| Description | Talk at 15th CFC meeting - CCDC Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Delivered a research talk to an audience of industry professionals during the 15th CFC meeting organised by the CCDC (Cambridge). |
| Year(s) Of Engagement Activity | 2024 |
