Martin Ondráček

Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.

Chemical identification of single atoms in heterogeneous III-IV chains on Si(100) surface by means of nc-AFM and DFT calculations.

Chemical identification of individual atoms in mixed In-Sn chains grown on a Si(100)-(2 × 1) surface was investigated by means of room temperature dynamic noncontact AFM measurements and DFT calculations. We demonstrate that the chemical nature of each atom in the chain can be identified by means of measurements of the short-range forces acting between an AFM tip and the atom. On the basis of this method, we revealed incorporation of silicon atoms from the substrate into the metal chains. Analysis of the measured and calculated short-range forces indicates that even different chemical states of a single atom can be distinguished.

Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy.

The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7 × 7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems.

Electronic and Chemical Properties of Donor, Acceptor Centers in Graphene

Chemical doping is one of the most suitable ways of tuning the electronic properties of graphene and a promising candidate for a band gap opening. In this work we report a reliable and tunable method for preparation of high-quality boron and nitrogen co-doped graphene on silicon carbide substrate. We combine experimental (dAFM, STM, XPS, NEXAFS) and theoretical (total energy DFT and simulated STM) studies to analyze the structural, chemical, and electronic properties of the single-atom substitutional dopants in graphene. We show that chemical identification of boron and nitrogen substitutional defects can be achieved in the STM channel due to the quantum interference effect, arising due to the specific electronic structure of nitrogen dopant sites. Chemical reactivity of single boron and nitrogen dopants is analyzed using force-distance spectroscopy by means of dAFM.

Reversal of atomic contrast in scanning probe microscopy on (111) metal surfaces

We study the origin of atomic contrast on Cu(111) and Pt(111) surfaces probed by a non-contact atomic force microscope and scanning tunnelling microscope. First-principles simulations of the interaction between the atoms of the scanning tip and those of the probed surface show a dependence of the resulting contrast on the tip-sample distance and reveal a close relation between contrast changes and relaxation of atomic positions in both the tip and the sample. Contrast reversion around the distance where the short-range attractive atomic force reaches its maximum is predicted for both types of microscopies. We also demonstrate a relation between the maximal attractive force in a F-z atomic force spectroscopy and the chemical identity of the apex atom on the imaging tip.

Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy

Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.Scanning probe microscopy has been extensively applied to probe interfacial water but the probes tend to disturb the structure of water easily. Here, the authors report submolecular-resolution imaging of water clusters within the nearly non-invasive region by qPlus noncontact atomic force microscopy.

Electronegativity determination of individual surface atoms by atomic force microscopy

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Paulings equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.

Charge Redistribution and Transport in Molecular Contacts

The forces between two single molecules brought into contact, and their connection with charge transport through the molecular junction, are studied here using non contact AFM, STM, and density functional theory simulations. A carbon monoxide molecule approaching an acetylene molecule (C_{2}H_{2}) initially feels weak attractive electrostatic forces, partly arising from charge reorganization in the presence of molecular . We find that the molecular contact is chemically passive, and protects the electron tunneling barrier from collapsing, even in the limit of repulsive forces. However, we find subtle conductance and force variations at different contacting sites along the C_{2}H_{2} molecule attributed to a weak overlap of their respective frontier orbitals.

Relation between the chemical force and the tunnelling current in atomic point contacts: a simple model

The relation between the tunnelling current I(t) and the interaction energy/force E in an atomic-scale contact is discussed in the framework of a theoretical model established here. According to our model, we predict the existence of two characteristic scaling regimes, where the tunnelling current is either proportional to the interaction energy, I(t) ~ E, or to the square of the interaction energy, I(t) ~ E(2). We show that the existence of a given regime is basically controlled by two parameters: (i) the energy degeneracy Δ and (ii) the hopping t between electronic levels involved in the interaction process. In addition, we discuss the validity of the Bardeen method to determine the tunnelling current in the short tip-sample distances.