Single Molecule Holography Realized

I am very grateful that I could join, maybe one of the most exciting experimental efforts recently. It goes back to Denis Gabor, the inventor of holography, who really proposed an idea to improve electron microscopy (D. Gabor, A New Microscopic Principle, Nature 161, 777-778 (1948)).

Above is shown what Gabor suggested. A coherent point emitter shines electrons onto a suspended object and the a screen record the pattern that is formed by the unscattered wave interfering with the scattered part of the beam. The pattern is called the hologram. In it each point of the object creates an image that looks like a Fresnel lens. This kind of lens illuminated with light bundles it into one point again, by diffraction not refraction. And this is how the holographic image can be reconstructed, a hologram is illuminated with again coherent light and the object reappears.

Gabors idea was realized with light once the laser was invented (image below). For a holographic electron microscope there was no source and no sample holder at the time. These problems have now been solved and I had to chance to take part in the endeavor and deposit folded proteins onto the sample holder of freestanding graphene to be imaged in the holographic microscopy, with the images nowadays reconstructed in-silico.

Scheme of the holographic microscope. Below, a hologram and the reconstructed image of the protein BSA (scalebar 2nm).

Hans-Werner Finks group at the University of Zuerich built the holographic microscope for electrons. The emitter is a very sharp metal tip, the sample holder is ultrapure, freestanding graphene. And the molecule is placed on the surface with preparative mass spectrometry, hence with my ion beam deposition instrument.

Just now we published this in PNAS:

J.-N. Longchamp, S. Rauschenbach, S. Abb, C. Escher, T. Latychevskaia, K. Kern & H.-W. Fink: Imaging Proteins at the Single Molecule Level. Proc. Natl. Acad. Sci. U.S.A. doi:10.1073/pnas.1614519114 (2017)

and there was a nice accompanying article, nicely explaining the implications:

F. Forneris & A. Mattevi: Expanding the structural biology toolbox with single-molecule holography. Proc. Natl. Acad. Sci. U.S.A. (2017)

And also a few other outlets reported

NZZ article

MPG press release



STM for MS-people

Recently I published the first review article in Annual Reviews of Analytical Chemistry: “Mass Spectrometry as a Preparative Tool for the Surface Science of Large Molecules” (


In this article I make the case for analyzing molecules on surfaces with STM, especially when they are very big. I can recommend looking at this work if you are interested in molecular ion beam deposition and STM. Especially, since we have learned a lot since out first works which gives us a new perspective and thus reviewing the old data leads to some new insights. The paper is written with the analytical chemistry community in mind, specifically mass spectrometry. You may say it is STM for MS people. But not only. Surface scientist might know the surface science methods well, but may learn what is possible with big molecules now.


Sequence Controlled Self-Assembly

Look at this molecular network. It is so nice. And it is quite large too. The pores are more than 2nm wide. Each hexagon is build from 6 dimers of Angiotensin II. Please look in our latest publication for the precise structure (

The idea to build these networks and tailor their structure and ultimately their properties is around for a while. However, when you only have the molecule, it is next to impossible to predict the structure or the properties you will get. This gets even worse, of the molecules are large and functional. And then, in addition, the synthesis get more and more complicated, if for instance one would want to include a small modification.


Not so with peptides. Here you can order a sequence online and because the synthesis is universal and done by robots, they are quite cheap. In our paper we saw that we can do a similar trick as nature: We change the sequence and get a different structure. Not too surprising, true, but we can now work a lot of different sequences and maybe finally learn how to design molecular networks.

see also:

New Paper: Highly Reactive Molecule Deposition

Electrospray ionization is know to be a soft ionization method and it even works well for highly reactive molecules like oligoyns, polymers containing several triple C-C bonds. In this recent paper we demonstrate that our ion beam deposition is just as gentle and we can build structures from these reactive molecules.


Soft-landing electrospray ion beam deposition of sensitive oligoynes on surfaces in vacuum.
G. Rinke, S. Rauschenbach, S. Schrettl, T. N. Hoheisel, J. Blohm, R. Gutzler, F. Rosei, H. Frauenrath and K. Kern

NEW PAPER: 100% transmission nano-electrospray ion source

For electrospray ion beam deposition a large amount of molecules is needed to get a reasonable coverage onto the surface. For instance: 1000 ions would make a nice peak in a mass spectrum. The same 1000 molecular ions would barely be found as adsorbates on a surface by scanning probe microscopy.

The biggest losses in an ES-IBD system occur at the vacuum interface. At this place ions are generated from charged droplets. They move, influences by external electric fields, space charge fields, diffusion and hydrodynamic drag. We constructed our own interface with the idea in mind to leverage the hydrodynamic drag: indeed this is the only force that points towards the axis of the capillary.

funnel forces

We were quite surprised to find that with our specially shaped capillary interfaces we achieve magnificent performance of up to 100% transmission for up to 40 nA. With this magnitude of ion current we reach up to 6nA in high vacuum deposition and hence can make a monolayer coverage of a 5 mm diameter sample in approximately 10 minutes. This makes IBD comparable with thermal evaporation and opens the way for commercial applications, if the full intensity of electrosprays, which can be up to mikroamps, can be used.

 funnel figure

In our paper in ‘Analyst’ we show the measured transmission characteristics, deposition performance and purity and simulations, which rationalize how our capillary is working.

A hydrodynamically optimized nano-electrospray ionization source and vacuum interface

M Pauly, M Sroka, J Reiss, G Rinke, A Albarghash, R Vogelgesang, H Hahne, B Kuster, J Sesterhenn, K Kern, S Rauschenbach

Analyst, 2014,139, 1856-1867

New Paper on Dye Adsorption

If two people (groups) have the same idea, it cannot be entirely wrong. The other group which has an STM connect with an electrospray ion beam deposition system (R. Berndts group, Univ. Kiel) worked in parallel on a very similar project. The adsorption of dyes on surfaces for the purpose of energy conversion seems important enough to immediately trigger the idea to look at it with STM. But: you need an ES-IBD system to do it. Initially also James O’Shea in Nottingham built his simple electrospray deposition (ESD) source for that purpose.
We looked at the Ruthenium dye N3 on anatase, which is important for dye sensitized solar cells. This work was really tough, because the anatase surface is not easy to prepare, but Christopher made it. And then we used a vacuum suitcase (more about those at another time), which can be intense too. Anyhow, we made nice surfaces with N3 on (tested with DINeC mass spectrometry. very cool!) and the guys at the LT STM measured the electronic structure. Recently our paper came out:

Christopher S Kley, Christian Dette, Gordon Rinke, Christopher E Patrick, Jan Čechal, Soon Jung Jung, Markus Baur, Michael Dürr, Stephan Rauschenbach, Feliciano Giustino, Sebastian Stepanow, Klaus Kern

DOI: 10.1021/nl403717d

Abstract Image

Nice to compare: the works of the Kiel group and of James O’Shea (not necessarily complete)


New Paper on Photocurrent Microscopy

I supported the work of my colleague Ulrich Stuetzel for a while now and a nice paper came out of his thesis. He really prepared very good graphene nanoribbons. Even after ambient processing in acid (and what not) we were able to image the graphite ridges with atomic resolution on top. Never published that, but below is how the photocurrent images look like in the paper. Nice work of Ulrich.

image of FIG. 3.

see in peer reviewed publications

Spatially resolved photocurrents in graphene nanoribbon devices
Eberhard Ulrich Stützel, Thomas Dufaux, Adarsh Sagar, Stephan Rauschenbach, Kannan Balasubramanian, Marko Burghard and Klaus Kern
Applied Physics Letters 102 (2013) 043106

MBE and Proteins

Two new works out this week. Both key works for our lab. In the first we show that the deposition of charged particle beams can in fact be equivalent to conventional molecular beam epitaxy.

see entry [13] on the publications page:
Crystalline Inverted Membrane Growth by Electrospray Ion Beam Deposition in Vacuum.
S. Rauschenbach, R. T. Weitz, N. Malinowski, N. Thontasen, Z. Deng, G. Rinke, G. Costantini, T. Lutz, P. Martins de Almeida Rollo, L. Harnau, K. Kern
Adv. Mater. 24 (2012), pg. 2761-2767

inverted membrane deposition


The second one is even nicer: We deposited proteins a while a ago and found so many things you can do with them in vacuum: deposit them folded and unfolded and refold them and in the end look at the single amino acid. Now we only need to find a way to know which amino acid you see.

see [14] on the publications page:
A Close Look at Proteins: Submolecular Resolution of Two- and Three-Dimensionally Folded Cytochrome c at Surfaces
Zhitao Deng, Nicha Thontasen, Nikola Malinowski, Gordon Rinke, Ludger Harnau, Stephan Rauschenbach, Klaus Kern
Nano Lett. 12 (2012) 2452–2458

Proteins on surfaces in UHV

single molecular magnets probed individually

Electrospray ion beam deposition is also known under term soft landing. The softness of this approach was actually crucial in our work with molecular magnets:

S. Kahle, Z. Deng, N. Malinowski, C. Tonnoir, A. Forment-Aliaga, N. Thontasen, G. Rinke, D. Le, V. Turkowski, T. S. Rahman, S. Rauschenbach, M. Ternes, and K. Kern, “The Quantum Magnetism of Individual Manganese-12-Acetate Molecular Magnets Anchored at Surfaces.” Nano Lett. 12, 518-521 (2012),

The project was really tough: the molecule is fragile, only charged negatively, so we build a new TOF. Then we needed a UHV suitcase, we had a really crazy malfunction in the beginning. It took us several attempts to get the sample to the 1K STM. And then we saw much less features then we thought we would. Today we know that it has to be like this…

… and, there are two great things about this work:

First great thing: it worked! That was not straight forward. Manganese-12-Acetate is a notoriously unstable molecule. Even gold reacts with it, reducing the acetate ligands, which eventually causes the loss of the magnetic properties. With ES-IBD we could softly bring it to a surface and identify the individual molecules. You see the individual molecule in the first STM image (Fig. 1). Also films could be prepared nicely (Fig. 2).

Second great thing: A single Manganese12 moelcule is really a magnet. The guys at the 1K STM could actually find the signature of a high spin single entity. In the next image (Fig. 3) you see a typical tunneling spectrum. The two features – four, since its symmetric – correspond to a spin flip from S=10 to S=9 and an excitation of the spin angular momentum.

One more nice thing. The project was very ambitious and needed a lot of real experts, who in this case happen to be real nice people too and it was a real pleasure to work with them. Starting with synthetic chemists who can make such a molecule, we were able to deposit it intactly, our 1K STM guys could measure the spectra at such low energy and finally we got theory support from Florida.

… in the end this one was even featured by Nature Materials.

Abstract: The high intrinsic spin and long spin relaxation time of manganese-12-acetate (Mn12) makes it an archetypical single molecular magnet. While these characteristics have been measured on bulk samples, questions remain whether the magnetic properties replicate themselves in surface supported isolated molecules, a prerequisite for any application. Here we demonstrate that electrospray ion beam deposition facilitates grafting of intact Mn12 molecules on metal as well as ultrathin insulating surfaces enabling submolecular resolution imaging by scanning tunneling microscopy. Using scanning tunneling spectroscopy we detect spin excitations from the magnetic ground state of the molecule at an ultrathin boron nitride decoupling layer. Our results are supported by density functional theory based calculations and establish that individual Mn12 molecules retain their intrinsic spin on a well chosen solid support.

Keywords: Electrospray mass spectrometry; ion beam deposition; molecular magnetism; scanning tunneling microscopy; inelastic tunneling spectroscopy