Atomic Force Microscopy for Molecular Structure Elucidation

Project Information

AMSEL

Grant agreement ID: 682144

DOI

10.3030/682144

Project closed

EC signature date 25 February 2016

Start date 1 June 2016

End date 31 May 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

IBM RESEARCH GMBH
Switzerland

Periodic Reporting for period 4 - AMSEL (Atomic Force Microscopy for Molecular Structure Elucidation)

Reporting period: 2020-12-01 to 2021-05-31

Summary of the context and overall objectives of the project

Identifying molecular structures is of great importance in synthetic chemistry, pharmacy, life sciences and environmental sciences. Atomic Force Microscopy (AFM) with functionalized tips, pioneered in our group, evolved as a novel tool for molecular structure elucidation, complementing conventional techniques such as nuclear magnetic resonance and mass spectrometry. In contrast to other techniques, AFM offers two unique advantages: AFM can identify the structure of an individual molecule and it can be combined with atom manipulation for on-surface synthesis. In addition to identification of molecules, AFM can elucidate properties of individual adsorbed molecules, such as conformation, adsorption geometry, adsorption site, bond-order relationships, charge state and charge distribution. This is further complemented using scanning tunneling microscopy (STM) for electronic characterization of the adsorbed molecules. For a recent review of the technique see: Atomic Force Microscopy for Molecular Structure Elucidation, L. Gross et al. Angew. Chem. Int. Ed. 2018, 57, 3888.

The three main objectives of the project AMSEL are:

1. Further improve AFM for molecular structure elucidation, increasing its applicability, sensitivity, and expanding the molecular properties that can be measured.

2. Apply AFM for molecular structure elucidation of novel and a priori unknown samples of increasing fragility, complexity, size, and three-dimensionality. We focus on samples that are challenging to characterize with conventional methods. Complex molecular mixtures with different applications are investigated molecule-by-molecule taking advantage of the single-molecule sensitivity. Unstable and highly reactive molecules that can be stabilized in our AFM, at low temperature on inert substrates, are investigated. The absolute stereochemistry of molecules is determined.

3. Employ atom manipulation for the creation of novel, elusive, custom-designed molecules and investigate them by AFM. We create radicals, diradicals, reaction intermediates, antiaromatic molecules, molecular wires, and switches and study their properties by AFM and STM. We explore novel reaction schemes induced by atom manipulation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

1. Improving AFM for molecular structure elucidation
- With atomic resolution we characterized molecules in different, controlled charge states. We obtained insights into charge-function relationships, vital in nature and with possible applications in future technologies in computing and energy harvesting. [Science. 365, 142 (2019)].
- We measured for individual molecules the reorganization energy, a fundamental parameter for the description of electron transfer rates in molecular systems. [Nat. Nano. 13, 376 (2018)]. See video: https://www.youtube.com/watch?v=R2JslFl1Syw
- By charge detachment and attachment, we put molecules in triplet and singlet excited states and measured the singlet and triplet excitation energies [Phys. Rev. Lett. 126, 176801 (2021)].
- We combined AFM with light emission scanning tunneling microscopy and used it to study a single molecule reaction. [ACS Nano. 13, 6947 (2019)].

2. Complex molecular mixtures
- We characterized molecules found in the early stages of soot formation. Our data shed light on one of the most complex and still debated aspects of soot formation, i.e. the nucleation process [Combustion and Flame 205, 154–164 (2019); Proc. Comb. Inst. 37, 885 (2019)].
- We studied heavy oil related samples of different origin and after different processing steps applied and obtained a basis for modelling geochemical oil formation processes with implications for upstream and downstream oil recovery [Energy & Fuels 31, 6856 (2017)].
- We investigated fuel pyrolysis products and developed a new method that integrates AFM with other state-of-the-art analytical tools. This approach enables the detection, identification, and quantification of novel polycyclic aromatic hydrocarbons in molecular mixtures [J. Am. Chem. Soc. 140, 8156 (2018)].
- We characterized analogs of the atmosphere of Saturn’s largest Moon Titan, interesting also in the context of the development of the atmosphere of the early Earth [Astrophys. J. 908, L13 (2021)].
- We studied marine dissolved organic carbon from different depth. The results indicate that structural recalcitrance is the reason for the old age of deep ocean dissolved organic carbon [Geophys. Res. Lett. 45, 5590 (2018)].

3. Molecules generated by atom manipulation
We generated several molecules that were long-standing goals of the community and studied their properties with AFM.
- By atom manipulation we generated the elusive carbon allotrope cyclo[18]carbon and revealed its (polyynic) structure [Science. 365, 1299 (2019) and J. Am. Chem. Soc. 142, 12921 (2020)]. See video: https://www.youtube.com/watch?v=m4T8YAL0TEA [Science. 365, 1299 (2019)].
- We generated and characterized polyynes, which constitute single-atom wide molecular wires [Nat. Chem. 10, 853 (2018)]. See video: https://www.youtube.com/watch?v=PQtCSO5rOLQ
- We generated unsubstituted triangulene, an elusive molecule with possible applications in molecular spintronics. We demonstrated the open-shell character of triangulene on Xenon [Nat. Nano. 12, 308 (2017)].
- We created and studied antiaromatic indenofluorene molecules [Nat. Commun. 9, 1198 (2018)].
- We generated a meta-aryne by atom manipulation and we confirmed its diradical structure [ACS Nano, 11, 10768 (2017)].
- We triggered reversible molecular reactions on insulators attaching/detaching single electrons and accessing multiple charge states. This marks an important step, aiming to fabricate by atom manipulation custom-designed covalently bound nanostructures on insulators with applications as single-electron devices. [Phys. Rev. Lett. 121, 226101 (2018)].
- We demonstrated by atom manipulation Glaser-like coupling [Angew. Chem. Int. Ed. 59, 22989 (2020)].

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Highlights of our work that showcase the progress beyond state-of-the-art were

1. Our charge manipulation experiments on molecules on think insulating films [Nat. Nano. 13, 376 (2018)] opening the way to study charge transitions from out-of-equilibrium initial states, revealing the structures of charged molecules [Science. 365, 142–145 (2019)] and quantifying excitation energies on the single molecule level [Phys. Rev. Lett. 126, 176801 (2021)].

2. Big impact of our research in the fields of combustion and in the field of petroleum chemistry. In both cases we could tackle most important questions of the fields, i.e. the soot nucleation pathway in combustion [Proc. Comb. Inst. 37, 885–892 (2019)] and the structure of asphaltenes and heavy oil fractions in the petroleum chemistry [Energy & Fuels 31, 6856-6861 (2017)].

3. Synthesizing by atom manipulation elusive molecules that were long-standing goals on chemistry. On the one hand triangulene [Nat. Nano. 12, 308 (2017)], which fueled the field of magnetic all carbon molecules by on-surface synthesis. On the Other hand the carbon allotrope cyclo[18]carbon, revealing its polyynic structure [Science. 365, 1299–1301 (2019)].

Nature Reviews Chemistry Cover, Nat. Rev. Chem. 1, 5 (2017)

On-surface synthesis of triyne by atom manipulation, Nat. Chem. 10, 853–858 (2018)

Nature Nanotechnology Cover, Triangulene, Nat. Nano. 12, 308–311 (2017)

Science Cover, Synthesis of cyclocarbon, 365, 1299–1301 (2019)

Structure elucidation with charge control, Science. 365, 142–145 (2019)