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When additional energy (in the form of a radio wave) is added to the magnetic field, the magnetic vector is deflected. The radio wave frequency (RF) that causes the hydrogen nuclei to resonate is dependent on the element sought (hydrogen in this case) and the strength of the magnetic field.



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When the radiofrequency source is switched off the magnetic vector returns to its resting state, and this causes a signal (also a radio wave) to be emitted. It is this signal which is used to create the MR images. Receiver coils are used around the body part in question to act as aerials to improve the detection of the emitted signal. The intensity of the received signal is then plotted on a grey scale and cross sectional images are built up.


Most diseases manifest themselves by an increase in water content, so MRI is a sensitive test for the detection of disease. The exact nature of the pathology can be more difficult to ascertain: for example, infection and tumour can in some cases look similar. A careful analysis of the images by a radiologist will often yield the correct answer.


The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.


Since the pioneering work of Gross et al.1, many studies have reported submolecular resolution atomic force microscopy (AFM) images of different molecules and molecular assemblies revealing a chemical bond contrast2,3,4,5,6,7,8,9,10. Observing such contrast usually requires the use of a qPlus sensor11 at liquid helium temperature to achieve: (i) high stability and low signal to noise, (ii) small tip-sample distances and (iii) the controlled functionalization of the tip apex, usually with a CO molecule. Although very recently, a few studies showed liquid nitrogen12 and room temperature13,14 submolecular resolution.


Despite these experimental achievements and related theoretical studies, the origin and predominant factors to obtain such contrast are still a hot topic of debate in the AFM community15,16,17. The chemical bond contrast observed is usually interpreted as either the intramolecular structure of molecules or intermolecular bonds. Initially, it was suggested that this contrast arises from the Pauli repulsive force that becomes dominant at small tip-sample distances1,18. Later, based on a classical force field model9,19, the flexibility of the tip was claimed to be the dominant effect leading to the chemical bond contrast in AFM images. Also, a controversy arose following the claimed intermolecular hydrogen bond imaging by Zhong et al.20 that some subsequent studies ascribed to an artifact due to the CO tip flexibility and not necessarily hydrogen bonds9,10,21. Recently, Guo et al.22 showed that bond-like features can appear between bonded and non-bonded atoms due to the overlapping of the outermost electrons. Their density functional theory (DFT)-based approach which does not account for Pauli repulsion from electron density overlapping between the tip and sample, showed that the contrast in the NC-AFM images originates from the short-range electrostatic force22,23. Moreover, the CO tip flexibility was shown to enhance the bond-like contrast but is not necessary to observe it. This was confirmed in a more recent study by Monig et al.17 where a bond-like contrast could be seen experimentally and reproduced theoretically using a rigid Cu tip with an oxygen apex.


One remaining challenge for NC-AFM experiments on semiconductors in general is preparing and identifying a stable tip capable of producing chemical bond contrast. Here we show that following ex situ cleaning with ebeam and field ion microscopy (FIM), a qPlus senor with a tungsten tip can be prepared in situ with the hydrogen-terminated silicon surface to obtain either a reactive or a passivated tip, both identified from the typical force curves they generate. Using a hydrogen-passivated tip, we study the evolution of the frequency shift maps contrast as a function of tip-sample distance. We show that for small tip-sample distances, the AFM images change from atom-like to chemical bond-like contrast.






We used a density functional tight-binding (DFTB)-based approach to efficiently simulate AFM images at precisions on par with DFT. We discuss the observed contrast at different tip-elevations as well as the role of the tip flexibility in the imaging mechanism.


Thanks to the ex situ tip cleaning procedure using ebeam and FIM (see experimental methods section for details), we always get scanning tunnelling microscopy (STM) atomic resolution of the surface right after the approach. However, images often exhibit artifacts, such as a double/multiple tip as seen in Fig. 1a, that renders data interpretation inaccurate. Therefore, it is necessary to further process the tip by in situ techniques to obtain a single atom tip apex. When studying metal surfaces, this is usually done by applying large voltage pulses and harsh indentation of the tip into the surface, followed by functionalizing the tip using a molecule such as CO1. Unfortunately, intentional functionalization of tips when studying semiconductor surfaces has not been achieved so far. Hence, one must rely on repeating controlled crashes and voltage pulses until the tip yields STM images of the surface with no artifacts, which reflects a single atom tip. Since the tip in our experiments was already cleaned from its oxide layer in the FIM, there is no need for us to apply high-voltage pulses and harsh-controlled crashes as previously described in AFM studies of silicon surfaces25,26. Instead, we use a more gentle procedure that gives stable tips without ravaging the studied surface area.


While the above associations of image features with known structure appear compelling, we must be cautious and acknowledge that tip and substrate geometries are substantially altered during imaging, especially at very small tip heights. To determine the unperturbed substrate structure, it is necessary to create a candidate structure and subject that to a simulated imaging process at a range of tip heights. Simulations done in this way capture force-induced alterations of structure and thereby result in modelled images that can be compared with experiment. We describe the modelling process and discuss the origin of image features in the following discussion.


To simulate AFM images, it is important to choose a correct level of theory to properly consider the necessary undergoing physics and chemistry while keeping the calculations tractable. In addition, the atomistic definition of tip and substrate is a requirement in many cases. Among first-principle frameworks, DFT is the first obvious choice, especially when dispersion correction has been considered to include the small long-range forces at large tip-sample separations. Unfortunately, DFT is computationally expensive for many systems, especially those where imaging must be done for a bulk structure, not only a molecule. Here we use DFTB, which at a lower computational cost can provide results comparable with DFT using traditional semi-local functionals for the silicon-based systems36.


Partial side view of the frozen slabs (upper panel) along with their simulated force maps (lower panel). In a, the dimer hydrogens are fixed in their relaxed positions, while in b they are slightly bent and fixed to obtain reverse distances between dimer and inter-dimer hydrogens with respect to a.


How to cite this article: Labidi, H. et al. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface. Nat. Commun. 8, 14222 doi: 10.1038/ncomms14222 (2017).


The image shows sunlight that has been scattered by atomic hydrogen, and is shown as blue in this false-color representation. Comets are surrounded by a huge cloud of atomic hydrogen because water (H2O) vaporizes from the icy nucleus, and solar ultraviolet light breaks it apart into hydrogen and oxygen. Hydrogen atoms scatter solar ultraviolet light, and it was this light that was imaged by the IUVS. Two observations were combined to create this image, after removing the foreground signal that results from sunlight being scattered from hydrogen surrounding Mars.


Enhancing the imaging power of microscopy to identify all chemical types of atom, from low- to high-atomic-number elements,would significantly contribute for a direct determination of material structures. Electron microscopes have successfully provided images of heavy-atom positions, particularly by the annular dark-field method, but detection of light atoms was difficult owing to their weak scattering power. Recent developments of aberration-correction electron optics have significantly advanced the microscope performance, enabling identification of individual light atoms such as oxygen, nitrogen, carbon, boron and lithium. However, the lightest hydrogen atom has not yet been observed directly, except in the specific condition of hydrogen adatoms on a graphene membrane. Here we show the first direct imaging of the hydrogen atom in a crystalline solid YH(2), based on a classic 'hollow-cone' illumination theory combined with state-of-the-art scanning transmission electronmicroscopy. The optimized hollow-cone condition derived from the aberration-corrected microscope parameters confirms that the information transfer can be extended to 22.5 nm(-1), which corresponds to a spatial resolution of about 44.4 pm. These experimental conditions can be readily realized with the annular bright-field imaging in scanning transmission electron microscopy according to reciprocity, revealing successfully the hydrogen-atom columns as dark dots, as anticipated from phase contrast of a weak-phase object.

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