Electrostatic Catalysis
Lead Research Organisation:
University of Oxford
Department Name: Oxford Chemistry
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Andrews KG
(2024)
Enzyme-like Acyl Transfer Catalysis in a Bifunctional Organic Cage.
in Journal of the American Chemical Society
Boaler PJ
(2024)
Origins of High-Activity Cage-Catalyzed Michael Addition.
in Journal of the American Chemical Society
DiNardi R
(2024)
Photoswitchable catalysis by a self-assembled molecular cage
DiNardi R
(2024)
Photoswitchable catalysis by a self-assembled molecular cage
DiNardi R
(2024)
Photoswitchable catalysis by a self-assembled molecular cage
DiNardi R
(2024)
Photoswitchable catalysis by a self-assembled molecular cage
DiNardi R
(2024)
Photoswitchable catalysis by a self-assembled molecular cage
DiNardi RG
(2024)
Photoswitchable Catalysis by a Self-Assembled Molecular Cage.
in Journal of the American Chemical Society
MartÃ-Centelles V
(2024)
CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages.
in Journal of chemical information and modeling
MartÃ-Centelles V
(2024)
CageCavityCalc (C3): A computational tool for calculating and visualizing cavities in Molecular Cages
| Description | What were the most significant achievements from the awards? Scientific: a) We have elucidated and fully characterised the Micheal addition reaction inside the [Pd2L4]2+ cage. We showed computationally that catalysis arises due to entropy contribution, i.e., dual biding of the reactants instead of enthalpic stabilisation. b) We have developed an automated method for parametrisation of the metal centre needed for workflow in studying the reaction in supramolecular cages. The publication is ready and will be submitted soon. c) We developed a semi-automated approach for finding ground and transition states inside the cages for the C-C forming reaction bonds. This workflow will be extremely useful to speed up future work on the project. d) We identified ground state stabilisation as a new strategy for optimising the catalytic activity of supramolecular cages. We are working closely with experimental colleagues to validate these findings experimentally. The work done in the award has been presented in several meetings by both the PI and the PDRA PDRA: a) 2023 December: Macrocyclic and Supramolecular Chemistry Meeting, Birmingham, UK (poster: "metallicious: Automated force-field parametrisation of covalently bound metals for supramolecular structures") b) 2023 May, AI for enzyme instructed catalysts, Amsterdam, the Netherlands (poster: "Catalysis in [Fe4L6]8+ supramolecular cage") c) 2022 December, Macrocyclic and Supramolecular Chemistry Meeting, Nottingham, UK (poster: "Dynamics and catalysis in [Fe4L6]8+ supramolecular cage") d) 2022 September, Confinement-Controlled Chemistry Symposium (talk: "Exploring chemical reactions through automation and machine learning") PDRA: a) 2023 December: Macrocyclic and Supramolecular Chemistry Meeting, Birmingham, UK (poster: "metallicious: Automated force-field parametrisation of covalently bound metals for supramolecular structures") b) 2023 May, AI for enzyme instructed catalysts, Amsterdam, the Netherlands (poster: "Catalysis in [Fe4L6]8+ supramolecular cage") c) 2022 December, Macrocyclic and Supramolecular Chemistry Meeting, Nottingham, UK (poster: "Dynamics and catalysis in [Fe4L6]8+ supramolecular cage") d) 2022 September, Confinement-Controlled Chemistry Symposium (talk: "Exploring chemical reactions through automation and machine learning") PI a) (To come) May 2024, Keynote speaker at Girona Seminar 2024 dedicated to Supramolecular Chemistry b) June 2023, Invited speaker at Physical Organic Gordon Research Conference. Holderness, USA c) May 2-23, RSC Prize Tour at the Universities of Liverpool, Manchester and Edinburgh, UK May d) May 2023, Invited speaker at AI4 Enzyme Instructed Catalysis Workshop. Amsterdam, NL e) Dec 2022, Invited speaker at RSC Macrocyclic and Supramolecular Chemistry Meeting. Nottingham, UK |
| Exploitation Route | We have open-source software that has significantly sped up the modelling process of systems containing metals. While our primary aim was an application for supramolecular cages, the developed tool can be used for a broad spectrum of systems, such as proteins, metalorganic frameworks and supramolecular knots. This work is completed, and the manuscript is in preparation. We expect this tool to be relevant for computational chemists across different fields. |
| Sectors | Chemicals Environment |
| Title | Metallicious |
| Description | Metallicious is an automated tool for creating force fields for metal-containing systems with a covalent model of the metal. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The group members have directly benefited, accelerating what was once a time-consuming manual task. Furthermore, various groups have reached out to use this tool, seeking to incorporate it into their workflow. |
| URL | https://github.com/duartegroup/metallicious |
| Title | cgbind |
| Description | This Python tool enables the automatic generation of metallocages. The software was created before this project started, but during this period it has been updated and new functionalities added |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | This tool has enabled us to automate our daily work and bring computation closer to the experimental supramolecular community. New collaborations have been initiated thanks to this. |
| URL | http://cgbind.chem.ox.ac.uk/ |
| Title | CCDC 2295132: Experimental Crystal Structure Determination |
| Description | Related Article: Keith G. Andrews, Tomasz K. Piskorz, Peter N. Horton, Simon J. Coles|2024|J.Am.Chem.Soc.|||doi:10.1021/jacs.4c03560 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | part of characterisation of compounds |
| URL | http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc2h18jc&sid=DataCite |
| Title | CCDC 2343886: Experimental Crystal Structure Determination |
| Description | Related Article: Ray G. DiNardi, Samina Rasheed, Simona S. Capomolla, Man Him Chak, Isis A. Middleton, Lauren K. Macreadie, Jake P. Violi, William A. Donald, Paul J. Lusby, Jonathon E. Beves|2024|J.Am.Chem.Soc.|||doi:10.1021/jacs.4c04846 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | part of characterisation of compounds |
| URL | http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc2jp07h&sid=DataCite |
| Title | CCDC 2343887: Experimental Crystal Structure Determination |
| Description | Related Article: Ray G. DiNardi, Samina Rasheed, Simona S. Capomolla, Man Him Chak, Isis A. Middleton, Lauren K. Macreadie, Jake P. Violi, William A. Donald, Paul J. Lusby, Jonathon E. Beves|2024|J.Am.Chem.Soc.|||doi:10.1021/jacs.4c04846 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | part of characterisation of compounds |
| URL | http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc2jp08j&sid=DataCite |
| Description | Collaboration with the Martí Centelles grpoup in Spain |
| Organisation | Polytechnic University of Valencia |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | We have worked together in the development of the computational tool, CageCavityCalc (C3), which enable calculating and visualizing cavities in molecular cages. |
| Collaborator Contribution | Dr Marti-VCentelles developed the idea and we contributed with testing, feedback, etc. We are working together to implement this tool as part of cgbind. |
| Impact | Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/65c9f0bf9138d23161ecc7b7 |
| Start Year | 2022 |
| Title | CageCavityCalc (C3) |
| Description | CageCavityCalc is a Python-based tool for calculating the cavity size of molecular cages available for Windows, MAC, and Linux. CageCavityCalc is designed for the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. CageCavityCalc has a PyMol plugin making very easy to compute and visualize the cavity through an automated graphical user interface. Additionally, CageCavityCalc can also be used by the command line and as a Python module. In addition to computing the cavity size, the hydrophobic and electrostatic potentials of the cavity are computed, providing insights into potential host-guest interactions. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Although C3 was published only six months ago, it has already made a significant impact on research. To date, it has been cited by 13 researchers across various groups and used by researchers from Poland, Spain, the UK, the USA, South Korea, and China. |
| Title | metallicious |
| Description | Metallicious is an automated tool for creating force fields for metal-containing systems with a covalent model of the metal. By utilizing a library of templates, metallicious identifies the template that matches the metal site in the structure. It copies the bonded parameters from the template and performs charge redistribution to account for charge transfer. In cases where no suitable template is found, metallicious automatically performs parameterization. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | While it is too early to assess broader applications, the number of users is steadily growing. This tool has proven indispensable for our own research, and we anticipate it will have similar value for other research groups. |