AMSEL is an H2020 ERC Consolidator Grant project under Grant Agreement Number 682144.

The principal investigator is Leo Gross, and the host institution is IBM Research GmbH, which is an industrial research laboratory located in Rüschlikon, Switzerland.

AMSEL started in June 2016, and will run through May 2021.

ERC logo


Identifying molecular structures is of great importance, for example in synthetic chemistry, pharmacy, life sciences and environmental sciences. Atomic force microscopy (AFM) with functionalized tips, a technology pioneered in our group, has evolved into a novel tool for molecular structure elucidation, complementing conventional techniques such as nuclear magnetic resonance and mass spectrometry. In contrast to other techniques for molecular structure elucidation, 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 identifying 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 tunnelling microscopy (STM) for electronic characterization of the adsorbed molecules [Ref].

Atomic Force Microscopy for Molecular Structure Elucidation,”
L. Gross et al.,
Angew. Chem. Int. Ed. 57, 3888, 2018.

Our experiments exploit the extreme versatility and sensitivity of a low-temperature scanning tunneling microscope/atomic force microscope (STM/AFM). Such a machine is not only a nano-analytical instrument to perform imaging and spectroscopy on the atomic scale, but can also be used as a tool to assemble atomic structures, manipulate and switch molecules, and induce chemical reactions including the synthesis of individual molecules.

Charge control

Schematic of AFM with CO functionalization (colored in center: AFM data)


1 Improve AFM
for molecular structure elucidation by enhancing its applicability, sensitivity, speed, ease-of-use, 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. We investigate unstable and highly reactive molecules that can be stabilized in our AFM at low temperature on inert substrates. The absolute stereochemistry of molecules is determined.


3 Employ atom manipulation
to create 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 and the operation of single molecular machines.


Improving AFM

Molecular structure elucidation

We measured for individual molecules the reorganization energy, a fundamental parameter for the description of electron transfer rates in molecular systems. For the first time, we determined the reorganization energy for an individual molecule and, for the first time, on an insulator. To this end, we used the AFM for tunneling spectroscopy, detecting currents on the order of zeptoamperes [Ref].

To improve chemical sensitivity by AFM, we studied several model compounds in experiment and theory, facilitating their identification in complex molecular mixtures containing a priori unknown structures [Ref].

We also studied chiral molecules and resolved the chirality of a single molecule by AFM. Furthermore, we demonstrated reversible switching of its chirality by atom manipulation [Ref].

Characterizing aliphatic moieties in hydrocarbons with atomic force microscopy,”
B. Schuler, et al.,
Chem. Sci. 8, 2315, 2017.

We are setting up a combined system of electrospray ionization deposition combined with a low-temperature atomic force/­scanning tunneling microscope for molecular structure elucidation. With this tool in ultraclean conditions, we expect to prepare and to resolve atomically by AFM large and complex molecules of sizes up to several thousand atomic units.

Schematic of detecting and manipulating single charges by AFM

Schematic of detecting and manipulating single charges by AFM

Model compound for archipelago molecules

Model compound for archipelago molecules

Applying AFM

Complex molecular mixtures

We apply AFM for molecular structure elucidation to help solve ecological and economic problems. We work on resolving the structures initially formed in fuel combustion and elucidating the pathways for the formation of soot with an impact on climate, the environment and human health. We also investigate marine-dissolved ocean carbon, which is one of the biggest exchangeable carbon reservoirs on Earth. In addition, we investigate fuel pyrolysis products and heavy oil-related products.

We have characterized molecules found in the early stages of soot formation. Our findings demonstrate the large complexity and variety of the aromatic compounds, which are the building blocks of the initial soot particles. Fundamental and specific characteristics have been ascertained by AFM. Our data sheds light on one of the most complex and controversial aspects of soot formation, namely the nucleation process [Ref].

Insights into incipient soot formation by atomic force microscopy,”
F. Schultz et al.,
Proc. Comb. Inst., covered as a Nature Research Highlight, 2018.

We have investigated fuel pyrolysis products and developed a new method that integrates AFM with analytical tools such as high-performance liquid chromatography with diode array ultraviolet−visible absorbance, and mass spectrometry along with synthetic chemistry. This highly interdisciplinary approach enables the detection, identification, and quantification of novel polycyclic aromatic hydrocarbons in complex molecular mixtures [Ref].

We have studied heavy oil-related samples of different origins and, after different processing steps, applied and obtained a basis for modelling geochemical oil formation processes [Ref].

Heavy oil based mixtures of different origins and treatments studied by AFM,”
B. Schuler et al.,
Energy & Fuels 31, 6856, 2017.

We have studied marine-dissolved organic carbon, which is the largest pool of exchangeable organic carbon in the ocean. We have analysed samples from the surface and the depths (2500 m) of the north-central Pacific Ocean using AFM. The results indicate that structural recalcitrance is the reason for the old age of deep ocean-dissolved organic carbon [Ref].


Soot formation

Molecules found in early soot formation

Interdisciplinary method for identifying and quantifying novel molecules
Interdisciplinary method for identifying and quantifying novel molecules

Different heavy oil-related samples have been investigated

Different heavy oil-related samples have been investigated

Employing atom manipulation

Generating molecules

We have generated unsubstituted triangulene, an elusive and highly reactive molecule with possible applications for molecular spintronics. In addition, we have demonstrated the open-shell character of triangulene on Xe in agreement with its triplet ground state [Ref].

Synthesis and characterization of triangulene,”
N. Pavliček et al.,
Nat. Nano. 12, 308, 2017.

triangulene Nature cover

We have generated a meta-aryne on bilayer NaCl on Cu(111) by atom manipulation. We confirmed the diradical structure of the meta-aryne by AFM [Ref].

Generation and Characterization of a Meta-Aryne on Cu and NaCl Surfaces,”
N. Pavliček et al.,
ACS Nano 11, 10768, 2017.

We created and studied an antiaromatic molecule on different surfaces, highlighting the importance of molecule–surface interactions on the π-electron distribution and aromaticity [Ref].

Studying an antiaromatic polycyclic hydrocarbon adsorbed on different surfaces
Z. Majzik et al.,
Nat. Comm. 109, 1198, 2018.

On the surface we generated and characterized polyynes, which constitute single-atom-wide molecular wires. We demonstrated that it is possible to trigger skeletal rearrangements by atom manipulation. Based on this, we succeeded in generating linear atomic wires ranging from six to sixteen carbon atoms in length, which we characterized electronically by measuring their transport gaps. [Ref].

Polyyne formation via skeletal rearrangement induced by atomic manipulation,”
N. Pavliček et al.,
Nat. Chem. 10, 853, 2018.

We triggered molecular reactions on insulators attaching/detaching single electrons and accessing multiple charge states. This marks an important step for the project, aiming to fabricate by atom manipulation custom-designed covalently bound nanostructures with applications as single-electron devices on insulators. We demonstrated a reversible dissociation upon the attachment of two electrons [Ref].

triangulene Nature cover

Triangulene on the cover of Nature Nanotechnology

Project team

Leo Gross

Leo Gross
IBM Research scientist
Principal investigator

Florian Albrecht

Florian Albrecht
Post-doctoral researcher

Shadi Fatayer

Shadi Fatayer
Post-doctoral researcher

Katharina Kaiser

Katharina Kaiser
PhD student

Fabian Schulz

Fabian Schulz
Post-doctoral researcher




Selected publications

[1] “Controlled Fragmentation of Single Molecules with Atomic Force Microscopy by Employing Doubly Charged States
S. Fatayer, N. Moll, S. Collazos, D. Pérez, E. Guitián, D. Peña, L. Gross, G. Meyer,
Phys. Rev. Lett. 121, 226101, 2018.

[2] “Polyyne formation via skeletal rearrangement induced by atomic manipulation
N. Pavliček, P. Gawel, D.R. Kohn, Z. Majzik, Y. Xiong, G. Meyer, H.L. Anderson, L. Gross,
Nat. Chem. 10, 853, 2018.

[3] “Insights into incipient soot formation by atomic force microscopy
F. Schulz, M. Commodo, K. Kaiser, G. De Falco, P. Minutolo, G. Meyer, D. Andrea, L. Gross,
Proc. Comb. Inst., 2018.

[4] “Direct visualization of individual aromatic compound structures in low molecular weight marine dissolved organic carbon
S. Fatayer, A.I. Coppola, F. Schulz, B.D. Walker, T.A. Broek, G. Meyer, E.R. Druffel, M. McCarthy, L. Gross,
Geophys. Res. Lett., 2018.

[5] “Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy
S. Fatayer, B. Schuler, W. Steurer, I. Scivetti, J. Repp, L. Gross, M. Persson, G. Meyer,
Nat. Nano. 13, 376–380, 2018.

[6] “Atomic Force Microscopy for Molecular Structure Elucidation
L. Gross, B. Schuler, N. Pavliček, S. Fatayer, Z. Majzik, N. Moll, D. Peña, G. Meyer,
Angew. Chem Int. Ed. 57, 3888, 2018.

[7] “Studying an antiaromatic polycyclic hydrocarbon adsorbed on different surfaces
Z. Majzik, N. Pavliček, M. Vilas-Varela, D. Pérez, N. Moll, E. Guitián, G. Meyer, D. Peña, L. Gross,
Nat. Comm. 9, 1198, 2018.

[8] “Damping by sequentially tunneling electrons
W. Steurer, J. Repp, L. Gross, G. Meyer,
Surf. Sci. 678, 112, 2018.

[9] “Atomic force microscopy identifying fuel pyrolysis products and directing the synthesis of analytical standards
S. Fatayer, N. Poddar, S. Quiroga, F. Schulz, B. Schuler, S.V. Kalpathy, G. Meyer, D. Pérez, E. Guitian, D. Peña, M.J. Wornat, L. Gross,
J. Am. Chem. Soc. 140, 8156–8161, 2018.

[10] “Atomic and electronic structure of Si dangling bonds in quasi-free-standing monolayer graphene
Y. Murata, T. Cavallucci, V. Tozzini, N. Pavliček, L. Gross, G. Meyer, M. Takamura, H. Hibino, F. Beltram, S. Heun,
Nano Res. 11, 864, 2018.

[11] “Understanding the Effects of Sample Preparation on the Chemical Structures of Petroleum Imaged with Non-contact Atomic Force Microscopy
Y. Zhang, B. Schuler, S. Fatayer, L. Gross, M.R. Harper, J.D. Kushnerick,
Industrial & Engineering Chemistry Research 57, 15935, 2018.

[12] “[19]Dendriphene: A 19-Ring Dendritic Nanographene
M. Vilas-Varela, S. Fatayer, Z. Majzik, D. Perez, E. Guitian, L. Gross, D. Peña,
Chemistry - A European Journal, 2018.

[13] “Addressing Long-Standing Chemical Challenges by AFM with Functionalized Tips
D. Peña, N. Pavlicek, B. Schuler, N. Moll, D. Pérez, E. Guitián, G. Meyer, L. Gross,
On-Surface Synthesis II, 209–227, Springer, 2018.

[14] “Synthesis and characterization of triangulene
N. Pavliček, A. Mistry, Z. Majzik, N. Moll, G. Meyer, D.J. Fox, L. Gross,
Nat. Nano. 12, 308, 2017.

[15] “Generation and Characterization of a Meta-Aryne on Cu and NaCl Surfaces
N. Pavliček, Z. Majzik, S. Collazos, G. Meyer, D. Pérez, E. Guitian, D. Peña, L. Gross,
ACS nano 11, 10768–10773, 2017.

[16] “Tip-induced passivation of dangling bonds on hydrogenated Si(100)-2×1
N. Pavliček, Z. Majzik, G. Meyer, L. Gross,
Appl. Phys. Lett. 111, 053104, 2017.

[17] “Generation, manipulation and characterization of molecules by atomic force microscopy
N. Pavliček, L. Gross,
Nat. Rev. Chem. 1, 0005, 2017. (Journal Cover)

[18] “Heavy oil based mixtures of different origins and treatments studied by AFM
B. Schuler, S. Fatayer, G. Meyer, E. Rogel, M. Moir, Y. Zhang, M.R. Harper, A.E. Pomerantz, K.D. Bake, M. Witt, D. Peña, J.D. Kushnerick, O.C. Mullins, C. Ovalles, F.G.A. van den Berg, L. Gross,
Energy & Fuels 31, 6856, 2017.

[19] “Characterizing aliphatic moieties in hydrocarbons with atomic force microscopy
B. Schuler, Y. Zhang, S. Collazos, S. Fatayer, G. Meyer, D. Pérez, E. Guitián, M.R. Harper, J.D. Kushnerick, D. Peña, L. Gross,
Chem. Sci. 8, 2315, 2017.