Opendata, web and dolomites


Atomic Force Microscopy for Molecular Structure Elucidation

Total Cost €


EC-Contrib. €






Project "AMSEL" data sheet

The following table provides information about the project.


Organization address
postcode: 8803

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Switzerland [CH]
 Project website
 Total cost 2˙000˙000 €
 EC max contribution 2˙000˙000 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-CoG
 Funding Scheme ERC-COG
 Starting year 2016
 Duration (year-month-day) from 2016-06-01   to  2021-05-31


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    IBM RESEARCH GMBH CH (RUESCHLIKON) coordinator 2˙000˙000.00


 Project objective

Molecular structure elucidation is of great importance in synthetic chemistry, pharmacy, life sciences, energy and environmental sciences, and technology applications. To date structure elucidation by atomic force microscopy (AFM) has been demonstrated for a few, small and mainly planar molecules. In this project high-risk, high-impact scientific questions will be solved using structure elucidation with the AFM employing a novel tool and novel methodologies.

A combined low-temperature scanning tunneling microscope/atomic force microscope (LT-STM/AFM) with high throughput and in situ electrospray deposition method will be developed. Chemical resolution will be achieved by novel measurement techniques, in particular the usage of different and novel tip functionalizations and combination with Kelvin probe force microscopy. Elements will be identified using substructure recognition provided by a database that will be erected and by refined theory and simulations.

The developed tools and techniques will be applied to molecules of increasing fragility, complexity, size, and three-dimensionality. In particular samples that are challenging to characterize with conventional methods will be studied. Complex molecular mixtures will be investigated molecule-by-molecule taking advantage of the single-molecule sensitivity. The absolute stereochemistry of molecules will be determined, resolving molecules with multiple stereocenters. The operation of single molecular machines as nanocars and molecular gears will be investigated. Reactive intermediates generated with atomic manipulation will be characterized and their on-surface reactivity will be studied by AFM.


year authors and title journal last update
List of publications.
2019 Fatayer, Shadi; Albrecht, Florian; Zhang, Yunlong; Urbonas, Darius; Peña, Diego; Moll, Nikolaj; Gross, Leo
Molecular structure elucidation with charge-state control
published pages: 142-145, ISSN: 1095-9203, DOI:
Science 1 2020-03-05
2019 Katharina Kaiser, Lorel M. Scriven, Fabian Schulz, Przemyslaw Gawel, Leo Gross, Harry L. Anderson
An sp-hybridized molecular carbon allotrope, cyclo[18]carbon
published pages: 1299-1301, ISSN: 0036-8075, DOI: 10.1126/science.aay1914
Science 365/6459 2020-02-06
2019 Fabian Schulz, Fátima García, Katharina Kaiser, Dolores Pérez, Enrique Guitián, Leo Gross, Diego Peña
Exploring a Route to Cyclic Acenes by On‐Surface Synthesis
published pages: , ISSN: 0044-8249, DOI: 10.1002/ange.201902784
Angewandte Chemie 2019-07-25
2019 Katharina Kaiser, Leo Gross, Fabian Schulz
A Single-Molecule Chemical Reaction Studied by High-Resolution Atomic Force Microscopy and Scanning Tunneling Microscopy Induced Light Emission
published pages: 6947-6954, ISSN: 1936-0851, DOI: 10.1021/acsnano.9b01852
ACS Nano 13/6 2019-09-04
2019 Yunlong Zhang, Fabian Schulz, B. McKay Rytting, Clifford C Walters, Katharina Kaiser, Jordan N. Metz, Michael R. Harper, Shamel S Merchant, Anthony S Mennito, Kuangnan Qian, J. Douglas Kushnerick, Peter K. Kilpatrick, Leo Gross
Elucidating the Geometric Substitution of Petroporphyrins by Spectroscopic Analysis and AFM Molecular Imaging
published pages: , ISSN: 0887-0624, DOI: 10.1021/acs.energyfuels.9b00816
Energy & Fuels 2019-08-05
2017 Yuya Murata, Tommaso Cavallucci, Valentina Tozzini, Niko Pavliček, Leo Gross, Gerhard Meyer, Makoto Takamura, Hiroki Hibino, Fabio Beltram, Stefan Heun
Atomic and electronic structure of Si dangling bonds in quasi-free-standing monolayer graphene
published pages: , ISSN: 1998-0124, DOI: 10.1007/s12274-017-1697-x
Nano Research 2019-06-18
2017 Niko Pavliček, Anish Mistry, Zsolt Majzik, Nikolaj Moll, Gerhard Meyer, David J. Fox, Leo Gross
Synthesis and characterization of triangulene
published pages: 308-311, ISSN: 1748-3387, DOI: 10.1038/nnano.2016.305
Nature Nanotechnology 12/4 2019-06-18
2017 Niko Pavliček, Leo Gross
Generation, manipulation and characterization of molecules by atomic force microscopy
published pages: 5, ISSN: 2397-3358, DOI: 10.1038/s41570-016-0005
Nature Reviews Chemistry 1/1 2019-06-18
2017 Bruno Schuler, Shadi Fatayer, Gerhard Meyer, Estrella Rogel, Michael Moir, Yunlong Zhang, Michael R. Harper, Andrew E. Pomerantz, Kyle D. Bake, Matthias Witt, Diego Peña, J. Douglas Kushnerick, Oliver C. Mullins, Cesar Ovalles, Frans G. A. van den Berg, Leo Gross
Heavy Oil Based Mixtures of Different Origins and Treatments Studied by Atomic Force Microscopy
published pages: 6856-6861, ISSN: 0887-0624, DOI: 10.1021/acs.energyfuels.7b00805
Energy & Fuels 31/7 2019-06-18
2017 Niko Pavliček, Zsolt Majzik, Gerhard Meyer, Leo Gross
Tip-induced passivation of dangling bonds on hydrogenated Si(100)-2 × 1
published pages: 53104, ISSN: 0003-6951, DOI: 10.1063/1.4989749
Applied Physics Letters 111/5 2019-06-18
2017 Bruno Schuler, Yunlong Zhang, Sara Collazos, Shadi Fatayer, Gerhard Meyer, Dolores Pérez, Enrique Guitián, Michael R. Harper, J. Douglas Kushnerick, Diego Peña, Leo Gross
Characterizing aliphatic moieties in hydrocarbons with atomic force microscopy
published pages: 2315-2320, ISSN: 2041-6520, DOI: 10.1039/c6sc04698c
Chem. Sci. 8/3 2019-06-18
2017 Niko Pavliček, Zsolt Majzik, Sara Collazos, Gerhard Meyer, Dolores Pérez, Enrique Guitián, Diego Peña, Leo Gross
Generation and Characterization of a meta -Aryne on Cu and NaCl Surfaces
published pages: 10768-10773, ISSN: 1936-0851, DOI: 10.1021/acsnano.7b06137
ACS Nano 11/11 2019-06-18
2018 Fabian Schulz, Mario Commodo, Katharina Kaiser, Gianluigi De Falco, Patrizia Minutolo, Gerhard Meyer, Andrea D`Anna, Leo Gross
Insights into incipient soot formation by atomic force microscopy
published pages: , ISSN: 1540-7489, DOI: 10.1016/j.proci.2018.06.100
Proceedings of the Combustion Institute 2019-05-23
2018 Shadi Fatayer, Bruno Schuler, Wolfram Steurer, Ivan Scivetti, Jascha Repp, Leo Gross, Mats Persson, Gerhard Meyer
Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy
published pages: 376-380, ISSN: 1748-3387, DOI: 10.1038/s41565-018-0087-1
Nature Nanotechnology 13/5 2019-05-23
2018 Leo Gross, Bruno Schuler, Niko Pavliček, Shadi Fatayer, Zsolt Majzik, Nikolaj Moll, Diego Peña, Gerhard Meyer
Atomic Force Microscopy for Molecular Structure Elucidation
published pages: 3888-3908, ISSN: 1433-7851, DOI: 10.1002/anie.201703509
Angewandte Chemie International Edition 57/15 2019-04-20
2018 Niko Pavliček, Przemyslaw Gawel, Daniel R. Kohn, Zsolt Majzik, Yaoyao Xiong, Gerhard Meyer, Harry L. Anderson, Leo Gross
Polyyne formation via skeletal rearrangement induced by atomic manipulation
published pages: 853-858, ISSN: 1755-4330, DOI: 10.1038/s41557-018-0067-y
Nature Chemistry 10/8 2019-04-20
2018 Shadi Fatayer, Nimesh B. Poddar, Sabela Quiroga, Fabian Schulz, Bruno Schuler, Subramanian V. Kalpathy, Gerhard Meyer, Dolores Pérez, Enrique Guitián, Diego Peña, Mary J. Wornat, Leo Gross
Atomic Force Microscopy Identifying Fuel Pyrolysis Products and Directing the Synthesis of Analytical Standards
published pages: 8156-8161, ISSN: 0002-7863, DOI: 10.1021/jacs.8b02525
Journal of the American Chemical Society 140/26 2019-04-20
2018 Manuel Vilas-Varela, Shadi Fatayer, Zsolt Majzik, Dolores Pérez, Enrique Guitián, Leo Gross, Diego Peña
[19]Dendriphene: A 19-Ring Dendritic Nanographene
published pages: 17697-17700, ISSN: 0947-6539, DOI: 10.1002/chem.201805140
Chemistry - A European Journal 24/67 2019-04-20
2018 Zsolt Majzik, Niko Pavliček, Manuel Vilas-Varela, Dolores Pérez, Nikolaj Moll, Enrique Guitián, Gerhard Meyer, Diego Peña, Leo Gross
Studying an antiaromatic polycyclic hydrocarbon adsorbed on different surfaces
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-03368-9
Nature Communications 9/1 2019-04-20
2018 Shadi Fatayer, Alysha I. Coppola, Fabian Schulz, Brett D. Walker, Taylor A. Broek, Gerhard Meyer, Ellen R. M. Druffel, Matthew McCarthy, Leo Gross
Direct Visualization of Individual Aromatic Compound Structures in Low Molecular Weight Marine Dissolved Organic Carbon
published pages: 5590-5598, ISSN: 0094-8276, DOI: 10.1029/2018GL077457
Geophysical Research Letters 45/11 2019-04-20
2018 Wolfram Steurer, Jascha Repp, Leo Gross, Gerhard Meyer
Damping by sequentially tunneling electrons
published pages: 112-117, ISSN: 0039-6028, DOI: 10.1016/j.susc.2018.02.011
Surface Science 678 2019-04-20
2018 Yunlong Zhang, Bruno Schuler, Shadi Fatayer, Leo Gross, Michael R. Harper, J. Douglas Kushnerick
Understanding the Effects of Sample Preparation on the Chemical Structures of Petroleum Imaged with Noncontact Atomic Force Microscopy
published pages: 15935-15941, ISSN: 0888-5885, DOI: 10.1021/acs.iecr.8b03962
Industrial & Engineering Chemistry Research 57/46 2019-04-20
2019 Mario Commodo, Katharina Kaiser, Gianluigi De Falco, Patrizia Minutolo, Fabian Schulz, Andrea D\'Anna, Leo Gross
On the early stages of soot formation: Molecular structure elucidation by high-resolution atomic force microscopy
published pages: 154-164, ISSN: 0010-2180, DOI: 10.1016/j.combustflame.2019.03.042
Combustion and Flame 205 2019-07-25

Are you the coordinator (or a participant) of this project? Plaese send me more information about the "AMSEL" project.

For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an  email ( and I put them in your project's page as son as possible.

Thanks. And then put a link of this page into your project's website.

The information about "AMSEL" are provided by the European Opendata Portal: CORDIS opendata.

More projects from the same programme (H2020-EU.1.1.)

SuperH (2019)

Discovery and Characterization of Hydrogen-Based High-Temperature Superconductors

Read More  


The Enemy of the Good: Towards a Theory of Moral Progress

Read More  

HOLI (2019)

Deep Learning for Holistic Inference

Read More