Periodic Reporting for period 5 - 3DMOSHBOND (Three-Dimensional Mapping Of a Single Hydrogen Bond)
Okres sprawozdawczy: 2024-01-01 do 2025-06-30
The nature of inter-atomic and inter-molecular interactions are key to a “bottom up” understanding of most aspects of matter, from solid state to biological systems. Traditionally these interactions can only be indirectly inferred from bulk (ensemble) measurements, or via modelling of samples of interest. High resolution scanning probe microscopy (SPM) offers one of the few routes available to directly access the local properties of matter at the single atom level, but until recently has been hampered by uncertainties related to the nature of the probing interaction – governed by the atomic scale properties of the end of the scanning probe tip.
In the last decade, significant progress has been made to solve these issues via the concept of functionalising probe tips with well defined molecular species and in-situ characterisation of the resultant tips. This has arisen in combination with technological developments allowing the measurement of not only electrical properties (as is common in scanning tunnelling microscopy (STM)), but also forces at the single bond level via low temperature non-contact atomic force microscopy (NC-AFM).
This project aims to explore the mapping of complex intermolecular interactions in three dimensions with sub-angstrom precision, and to use these outputs as calibration for high quality ab-initio modelling. Key to this program of work is an unprecedented level of control of the intermolecular junction formed by a functionalised probe tip and the molecular sample.
The outcome of this project will involve a step change in our ability to control and characterise matter at the single bond level, but more importantly will provide a hitherto unavailable source of fundamental information on the strength and shape of intermolecular potentials, which will provide a new method for parametrising computational models of intermolecular interactions, which are key drivers in understanding biological and pharmaceutical systems.
In the last decade, significant progress has been made to solve these issues via the concept of functionalising probe tips with well defined molecular species and in-situ characterisation of the resultant tips. This has arisen in combination with technological developments allowing the measurement of not only electrical properties (as is common in scanning tunnelling microscopy (STM)), but also forces at the single bond level via low temperature non-contact atomic force microscopy (NC-AFM).
This project aims to explore the mapping of complex intermolecular interactions in three dimensions with sub-angstrom precision, and to use these outputs as calibration for high quality ab-initio modelling. Key to this program of work is an unprecedented level of control of the intermolecular junction formed by a functionalised probe tip and the molecular sample.
The outcome of this project will involve a step change in our ability to control and characterise matter at the single bond level, but more importantly will provide a hitherto unavailable source of fundamental information on the strength and shape of intermolecular potentials, which will provide a new method for parametrising computational models of intermolecular interactions, which are key drivers in understanding biological and pharmaceutical systems.
A summary of work performed to date includes;
• Recruitment and training of complete experimental and computational project team
• Commissioning of laboratory space
• Completing the design, tender/purchase, and installation of low temperature combined STM/AFM (awaiting performance sign off)
• Design and completion of scripting framework for automated data collection, including testing in real-world environment
• Design and construction of experimental molecular deposition systems
• Design of computational framework for handling experimental data
• Design and synthesis of custom organic molecule and test deposition
• Design of computational framework for theoretical components (including installation of DFT packages, design of custom scripting software, analysis tools etc.)
Main results achieved so far include:
• Preliminary measurements on prototypical systems (atomic manipulation, force measurement on single molecules, deposition tests of molecular candidates)
• Recruitment and training of complete experimental and computational project team
• Commissioning of laboratory space
• Completing the design, tender/purchase, and installation of low temperature combined STM/AFM (awaiting performance sign off)
• Design and completion of scripting framework for automated data collection, including testing in real-world environment
• Design and construction of experimental molecular deposition systems
• Design of computational framework for handling experimental data
• Design and synthesis of custom organic molecule and test deposition
• Design of computational framework for theoretical components (including installation of DFT packages, design of custom scripting software, analysis tools etc.)
Main results achieved so far include:
• Preliminary measurements on prototypical systems (atomic manipulation, force measurement on single molecules, deposition tests of molecular candidates)
Progress beyond the state of the art has included synthesis and deposition of a novel organic molecule, and measurement of the variation of intermolecular and interatomic force induced due to substrate induced charge transfer. Expected key results by the end of the project will include new protocols for the characterisation of interatomic and intermolecular forces at the single bond level, and protocols for their implementation into molecular based simulation, to be achieved by the 3D force mapping of several novel intermolecular junctions and their complimentary simulation via ab-initio techniques.