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.

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.

Publications

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Ayg├╝n M (2018) Magnetically Recyclable Catalytic Carbon Nanoreactors in Advanced Functional Materials

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Skowron ST (2019) The effects of encapsulation on damage to molecules by electron radiation. in Micron (Oxford, England : 1993)

 
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