Triggering, Controlling and Imaging Chemical Reactions at the Single-Molecule Level by Electron Beam
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Chemistry
Abstract
How do we know that molecules react in one way rather than another? In a given experiment, we study the reactions of large ensembles of molecules (billions of billions or more) that exist in different states and possess different kinetic energies, colliding with each other in a chaotic manner. Even in an ideal case, a reaction observed in a laboratory experiment by ensemble-averaging analytical techniques, such as spectroscopy or diffraction, can only support rather than confirm a proposed mechanism, as these macroscopic measurements are unable to rule out that an alternative atomistic mechanism may also exist that results in the same macroscale observation. In practice, definitive information about the mechanisms of intermolecular reactions can be provided only by a direct observation at the single-molecule level of the reactants transforming into products over time. In this context, scanning probe microscopy (SPM) methods have recently shed important light on the atomic structures of both the intermediates and products of chemical reactions; however, SPM critically lacks time resolution due to the scanning nature of AFM/STM and the fact that the molecules must be 'activated' by a stimulus, such as heat, during which the molecules remain unobserved, thus introducing the need for averaging information over an ensemble of species (albeit much smaller than in the bulk measurement).
Transmission electron microscopy (TEM) offers unique opportunities for intermolecular reactions, very different, yet highly complementary, to SPM and gas-phase molecular spectroscopy. Using the three principles of ChemTEM: (i) physical entrapment and confinement of individual molecules in nano test tubes; (ii) direct momentum transfer from the incident electron beam to atoms; (iii) stop-frame filming of chemical bond dissociation and formation in direct space at the single-molecule level, this EPSRC project will address the challenge of simultaneous triggering and imaging of reaction pathways - from reactants via intermediates to products. The molecules constrained in two dimensions, for example in a nanotube, while having the third dimension free for chemistry, will be manipulated by the electron beam and imaged as they react with each other. In this way, the chemist has the individual molecules on an 'operating table' as it were, ready to be dissected and studied with atomic-level precision.
The principles and methodology of ChemTEM developed in this project have the potential to become an imaging and analytical tool for molecular reactions, complementing and bolstering current spectroscopy, diffraction and SPM methods. ChemTEM will image reaction pathways in direct space at the single-molecule level and will enable the elucidation of reaction mechanisms of important chemical processes, such as C-C bond formation and dissociation, dehydrogenation and polycondensation reactions, leading to the improved preparative synthesis of high-value materials and the design of alternative catalysts. In addition, ChemTEM has great potential for the discovery of entirely new types of chemical reactions that can transform not only the way we study molecules but also launch a new wave of research in synthetic chemistry, which currently relies on a relatively small number of reaction types.
Transmission electron microscopy (TEM) offers unique opportunities for intermolecular reactions, very different, yet highly complementary, to SPM and gas-phase molecular spectroscopy. Using the three principles of ChemTEM: (i) physical entrapment and confinement of individual molecules in nano test tubes; (ii) direct momentum transfer from the incident electron beam to atoms; (iii) stop-frame filming of chemical bond dissociation and formation in direct space at the single-molecule level, this EPSRC project will address the challenge of simultaneous triggering and imaging of reaction pathways - from reactants via intermediates to products. The molecules constrained in two dimensions, for example in a nanotube, while having the third dimension free for chemistry, will be manipulated by the electron beam and imaged as they react with each other. In this way, the chemist has the individual molecules on an 'operating table' as it were, ready to be dissected and studied with atomic-level precision.
The principles and methodology of ChemTEM developed in this project have the potential to become an imaging and analytical tool for molecular reactions, complementing and bolstering current spectroscopy, diffraction and SPM methods. ChemTEM will image reaction pathways in direct space at the single-molecule level and will enable the elucidation of reaction mechanisms of important chemical processes, such as C-C bond formation and dissociation, dehydrogenation and polycondensation reactions, leading to the improved preparative synthesis of high-value materials and the design of alternative catalysts. In addition, ChemTEM has great potential for the discovery of entirely new types of chemical reactions that can transform not only the way we study molecules but also launch a new wave of research in synthetic chemistry, which currently relies on a relatively small number of reaction types.
Planned Impact
The ChemTEM project will enable the making and breaking of the bonds of an individual molecule and will transform the use of the electron beam in chemistry, making it an indispensable analytical tool to directly study intermolecular chemical reactions including: (i) the stop-frame filming of chemical reactions at the single-molecule level; (ii) the discovery of new chemical reactions, and (iii) the synthesis of bespoke molecular materials by harnessing the power of the e-beam.
While the main outputs of ChemTEM are aimed at delivering fundamental knowledge for the research communities (see Academic Beneficiaries section), the unique experimental skills and expertise developed in the ChemTEM project will be propagated through research staff development within this project and by transferring the skills to the next generation of researchers through the EPSRC Doctoral Training Programme in Low-Dimensional Materials and Interfaces. The new methodology for ChemTEM analysis of chemical reactions taken up by electron microscope manufacturers will shape the landscape for future TEM development, towards non-destructive analysis of molecular materials, and transforming the TEM into an analytical tool for intermolecular reactions. The ChemTEM methodology applied for the analysis of challenging molecular materials of industrial importance (polymers, lubricants, hydrogels etc.) via the ongoing business engagement programme of the Nanoscale and Microscale Research Centre (nmRC) will benefit more than 30 companies currently accessing the nmRC. Public outreach activities will create excitement for science and technology in the wider society, and advocacy for EPSRC and science in the UK will be achieved at high-profile public events.
The ChemTEM International Advisory Board composed of internationally leading experts in electron microscopy and synthetic chemistry (including Prof. F. Banhart, Strasbourg; Prof. J. Sloan, Warwick; Prof. J. Warner, Oxford, who have already given their agreement), as well as representatives of key industrial stakeholders, will oversee and advise on impact actions, as described in the Pathways to Impact document.
While the main outputs of ChemTEM are aimed at delivering fundamental knowledge for the research communities (see Academic Beneficiaries section), the unique experimental skills and expertise developed in the ChemTEM project will be propagated through research staff development within this project and by transferring the skills to the next generation of researchers through the EPSRC Doctoral Training Programme in Low-Dimensional Materials and Interfaces. The new methodology for ChemTEM analysis of chemical reactions taken up by electron microscope manufacturers will shape the landscape for future TEM development, towards non-destructive analysis of molecular materials, and transforming the TEM into an analytical tool for intermolecular reactions. The ChemTEM methodology applied for the analysis of challenging molecular materials of industrial importance (polymers, lubricants, hydrogels etc.) via the ongoing business engagement programme of the Nanoscale and Microscale Research Centre (nmRC) will benefit more than 30 companies currently accessing the nmRC. Public outreach activities will create excitement for science and technology in the wider society, and advocacy for EPSRC and science in the UK will be achieved at high-profile public events.
The ChemTEM International Advisory Board composed of internationally leading experts in electron microscopy and synthetic chemistry (including Prof. F. Banhart, Strasbourg; Prof. J. Sloan, Warwick; Prof. J. Warner, Oxford, who have already given their agreement), as well as representatives of key industrial stakeholders, will oversee and advise on impact actions, as described in the Pathways to Impact document.
Organisations
Publications
Agasti N
(2020)
Cerium Oxide Nanoparticles Inside Carbon Nanoreactors for Selective Allylic Oxidation of Cyclohexene.
in Nano letters
Astle M
(2019)
Molybdenum Dioxide in Carbon Nanoreactors as a Catalytic Nanosponge for the Efficient Desulfurization of Liquid Fuels
in Advanced Functional Materials
Astle MA
(2022)
Defect Etching in Carbon Nanotube Walls for Porous Carbon Nanoreactors: Implications for CO2 Sorption and the Hydrosilylation of Phenylacetylene.
in ACS applied nano materials
Aygün M
(2018)
Magnetically Recyclable Catalytic Carbon Nanoreactors
in Advanced Functional Materials
Cao K
(2020)
Direct Imaging of Atomic Permeation Through a Vacancy Defect in the Carbon Lattice
in Angewandte Chemie
Cao K
(2020)
Direct Imaging of Atomic Permeation Through a Vacancy Defect in the Carbon Lattice.
in Angewandte Chemie (International ed. in English)
Cao K
(2020)
Innentitelbild: Direct Imaging of Atomic Permeation Through a Vacancy Defect in the Carbon Lattice (Angew. Chem. 51/2020)
in Angewandte Chemie
Cao K
(2020)
Inside Cover: Direct Imaging of Atomic Permeation Through a Vacancy Defect in the Carbon Lattice (Angew. Chem. Int. Ed. 51/2020)
in Angewandte Chemie International Edition
Description | Transmission electron microscopy (TEM) is one of the most powerful methods to study chemistry of individual molecules as the electron beam enables near-atomic imaging of the molecules and simultaneously provides energy for the reaction. This approach, termed ChemTEM, is based on (i) entrapment of individual molecules in carbon nanotubes that allow control of positions and orientations of the molecules in the e-beam; (ii) direct momentum transfer from fast incident electrons (20-100 keV) to atoms; (iii) stop-frame filming of chemical bond dissociation and formation with spatiotemporal continuity at the single molecule level. Previously, we demonstrated that kinetic energy transferred directly from the e-beam to atoms of the molecule, displacing them from equilibrium positions, triggers bond dissociation (C-H, C-D, C-C, C-Cl, C-S) and promotes various chemical reactions (halogen elimination, cycloaddition, polycondensation) which can be imaged concurrently with their activation by the e-beam and presented as stop-frame movies. Now we applied ChemTEM to individual metal atoms and small nanoclusters to unveil a number of fascinating phenomena at the atomic scale, including metal-carbon and intermetallic bond dynamics, key for fundamental understanding of atomistic mechanisms underpinning nanocatalysis and crystal formation. |
Exploitation Route | We had tremendous response from the scientific community and the media when we reported the first chemical bond breaking recorded in real time with atomic resolution (link above). Our story was reported by popular science magazines and media outlets in 32 countries (some other examples are given below): https://www.newscientist.com/article/2230547-watch-the-first-ever-video-of-a-chemical-bond-breaking-and-forming/ https://www.dailymail.co.uk/video/sciencetech/video-2092338/Video-Chemical-bonds-form-break-molecule-microscope-video.html https://news.livedoor.com/article/detail/17692075/ https://news.sky.com/story/researchers-capture-footage-of-atoms-bonding-and-separating-for-the-first-time-11914919 https://www.sciencedaily.com/releases/2020/01/200117162705.htm https://uk.news.yahoo.com/scientists-capture-first-ever-video-104058305.html |
Sectors | Chemicals Energy |
URL | https://www.newscientist.com/article/2230547-watch-the-first-ever-video-of-a-chemical-bond-breaking-and-forming/ |
Description | The new approach to studying molecules and their chemical reaction is beginning to make impact on the chemistry community. |
Sector | Chemicals,Energy |
Title | ChemTEM |
Description | How do we know that molecules react in one way rather than another? Even in an ideal case, a reaction observed in a laboratory experiment by ensemble-averaging analytical techniques, such as spectroscopy or diffraction, can only support rather than confirm a proposed mechanism, as these macroscopic measurements are unable to rule out that an alternative atomistic mechanism may also exist that results in the same macroscale observation. In practice, definitive information about the mechanisms of intermolecular reactions can be provided only by a direct observation at the single-molecule level of the reactants transforming into products over time. Transmission electron microscopy (TEM) is one of the most powerful methods to study chemistry of individual molecules as the electron beam enables near-atomic imaging of the molecules and simultaneously provides energy for the reaction. This approach, termed ChemTEM, is based on (i) entrapment of individual molecules in carbon nanotubes that allow control of positions and orientations of the molecules in the e-beam; (ii) direct momentum transfer from fast incident electrons (20-100 keV) to atoms; (iii) stop-frame filming of chemical bond dissociation and formation with spatiotemporal continuity at the single molecule level. Previously, we demonstrated that kinetic energy transferred directly from the e-beam to atoms of the molecule, displacing them from equilibrium positions, triggers bond dissociation (C-H, C-D, C-C, C-Cl, C-S) and promotes various chemical reactions (halogen elimination, cycloaddition, polycondensation) which can be imaged concurrently with their activation by the e-beam and presented as stop-frame movies. Now we applied ChemTEM to individual metal atoms and small nanoclusters to unveil a number of fascinating phenomena at the atomic scale, including metal-carbon and intermetallic bond dynamics, key for fundamental understanding of atomistic mechanisms underpinning nanocatalysis and crystal formation. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Clear trends in bonding and reactivity between different metals and carbon demonstrated by ChemTEM open doors for studying organometallic reactions with atomic resolution and spatiotemporal continuity, from reactants through intermediates to products. New mechanistic understanding can help to optimise industrial processes involving transition metals, such as chemical vapour deposition, syngas conversion, enabled by ChemTEM which also is becoming a tool for discovery reactions leading to unprecedented products. |
Description | Jeremy Sloan, Warwick University |
Organisation | University of Warwick |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Synthesis of carbon nanomaterials |
Collaborator Contribution | Advanced TEM image simulation and analysis |
Impact | Joint publication in Journal of American Chemical Society in 2016 |
Start Year | 2015 |
Description | Kazu Suenaga, Tsukuba, Japan |
Organisation | National Institute of Advanced Industrial Science and Technology |
Country | Japan |
Sector | Public |
PI Contribution | Synthesis and advanced characterization of carbon nanomaterials |
Collaborator Contribution | Advanced TEM and STEM low-voltage analysis |
Impact | Joint publication in Journal American Chemical Society in 2016 |
Start Year | 2015 |
Description | Professor Angus Kirkland |
Organisation | Diamond Light Source |
Country | United Kingdom |
Sector | Private |
PI Contribution | Material systems for Time-resolved imaging of electron beam induced chemical reactions at the single-molecule level |
Collaborator Contribution | Access to state of the art ePSIC electron microscopy facilities and allied expertise of Dr Chris Allen. |
Impact | currently wringing a joint manuscript for publication in a peer-reviewed journal |
Start Year | 2019 |
Description | Professor Quentin Ramasse |
Organisation | Daresbury Laboratory |
Country | United Kingdom |
Sector | Private |
PI Contribution | Synthesis of materials and sample preparation for vibrational electron energy loss spectroscopy (EELS) measurements |
Collaborator Contribution | Access to the state of the art SuperSTEM facility with a unique vibrational EELS |
Impact | currently writing a joint paper for publication |
Start Year | 2019 |
Description | University of Ulm - Prof. Ute Kaiser |
Organisation | University of Ulm |
Country | Germany |
Sector | Academic/University |
PI Contribution | I provide nanomaterials for advanced electron microscopy experiments in Ulm. |
Collaborator Contribution | Collaborators in Ulm University (Germany) enable access to cutting-edge electron microscopy facilities essential for my work. |
Impact | Several high-profile publications (including 3 Nature group articles), co-supervision of PhD students. |
Start Year | 2007 |
Description | Equipment Event and launch of 3D OrbiSIMS |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | A symposium to educate researchers in academia and industry about the new facility 3D OrbiSIMS launched at the nmRC (funded by the EPSRC equipment grant). This new powerful analytical tool is first of it's kind in the academic setting in the UK. |
Year(s) Of Engagement Activity | 2019 |
URL | https://twitter.com/hashtag/OrbiSIMSLaunch?src=hash |
Description | Science & Innovation 2018, conference and exhibition, QEII Centre, Westminster, London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | A talk about nmRC research model and NanoPrime scheme for a broad audience of UK HEIs representatives responsible for research policy and business engagement, and several UK companies. Sharing good practice with other UK universities in managing collaborative cross-disciplinary research centers such as nmnRC. |
Year(s) Of Engagement Activity | 2018 |
URL | https://science-innovation.co.uk/ |
Description | Understanding Your XPS Instrument workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Two workshops have been supported by NanoPrime to improve knowledge of XPS in the research community. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.nottingham.ac.uk/nmrc |