Ab initio macromolecular phasing has been so far limited to small proteins diffracting at atomic resolution (beyond 1.2 A) unless heavy atoms are present. We describe a general ab initio phasing method for 2 A data, based on combination of localizing model fragments such as small á-helices with Phaser and density modification with SHELXE. We implemented this approach in the program Arcimboldo to solve a 222-amino-acid structure at 1.95 A.

The coupling between two atomically sharp nanocontacts provides tunable access to a fundamental underlying interaction: the formation of the bond between two atoms as they are brought into contact. Here we report a detailed experimental and theoretical analysis of the relation between the chemical force and the tunneling current during bond formation in atom-scale metallic junctions and their dependence on distance, junction structure, and material. We found that the short-range force as well as the conductance in two prototypical metal junctions depend exponentially on the distance and that they have essentially the same exponents. In the transition regime between tunneling and point contact, large short-range forces generate structural relaxations which are concomitant with modifications of the surface electronic structure and the collapse of the tunneling barrier. DOI: 10.1103/PhysRevLett.106.016802 PACS numbers: 73.22.Àf, 73.63.Rt, 74.55.+v While the first simultaneous measurements of the distance dependency of force and conductance were already performed a decade ago [1][2][3], the question of how the short-range forces relate to the tunneling conductance is still in theoretical and experimental debate [4][5][6]. Recently, these quantities have been precisely determined in a single measurement by using a combined scanning tunneling (STM) and atomic force microscope [7,8]. Such an instrument allows one to measure simultaneously the conductance and the short-range force between an atomically sharp tip and well characterized adsorbates on surfaces.In this Letter, we present measurements and simulations of prototypical atomic junctions between an individual metal adsorbate on a metal substrate and a metallic tip [ Fig. 1(a)]. All experiments where performed in ultrahigh vacuum (p < 10 À8 Pa) and at a temperature of about 5 K [9]. To discriminate between the short-range force which originates from the direct interaction of the adsorbate and the tip apex and all long-range forces between the macroscopic sample and tip, we measure directly on top of the adsorbate and again at a lateral distance of % 1:5 nm. At this distance the force is no longer influenced by the adsorbate and only long-range forces contribute to the frequency shift Áf of the force-sensing cantilever which oscillates normal to the surface (for details of the setup, see [9]). In Fig. 1(b) we show the Áf data measured on top and off a single Pt atom adsorbed on a clean Pt(111) surface at different tip-sample distances d and the corresponding time-averaged conductance G av (the conductance averaged over the oscillation of the cantilever) and dissipation D. We used the Áf data to calculate the short-range force normal to the surface F z ¼ F on À F off using the Sader-Jarvis formalism [10] [ Fig. 1(c)] and the G av data to calculate the instantaneous conductance G by removing the smearing induced by the tip oscillation [11] [ Fig. 1(d)].We observe at d % 0 the minimum of F z ¼ À1:9 nN concomitant with a conductance of G % G 0 . For smaller tip-sam...

The operation of the STM on metallic surfaces from the tunneling to the contact regime has been explored with a combination of first-principles total energy methods and a calculation of the electronic currents based on nonequilibrium Keldish-Green's function techniques. Our calculations for the behavior of the total energy, forces, atomic relaxations, and currents for an Al tip on an Al(111) surface as a function of the tip-sample distance indicate that atomic relaxations and saturation effects become relevant in a similar distance range where the onset of a short-range chemical interaction between the tip apex and the surface atoms is taking place. These two factors, that have an opposite influence in the current, lead to corrugations of the order of 0.2 Å, similar to the ones found experimentally in other (111) metal surfaces, for the closer distances (around 4.25 Å) where stable operation can be achieved.

Different S and Mo vacancies as well as their corresponding antisite defects in a free-standing MoS2 monolayer are analysed by means of scanning tunnelling microscopy (STM) simulations. Our theoretical methodology, based on the Keldysh nonequilibrium Green function formalism within the density functional theory (DFT) approach, is applied to simulate STM images for different voltages and tip heights. Combining the geometrical and electronic effects, all features of the different STM images can be explained, providing a valuable guide for future experiments. Our results confirm previous reports on S atom imaging, but also reveal a strong dependence on the applied bias for vacancies and antisite defects that include extra S atoms. By contrast, when additional Mo atoms cover the S vacancies, the MoS2 gap vanishes and a bias-independent bright protrusion is obtained in the STM image. Finally, we show that the inclusion of these point defects promotes the emergence of reactive dangling bonds that may act as efficient adsorption sites for external adsorbates.

First-principles calculations show that the rich variety of image patterns found in carbon nanostructures with the atomic force and scanning tunneling microscopes can be rationalized in terms of the chemical reactivity of the tip and the distance range explored in the experiments. For weakly reactive tips, the Pauli repulsion dominates the atomic contrast and force maxima are expected on low electronic density positions as the hollow site. With reactive tips, the interaction is strong enough to change locally the hybridization of the carbon atoms, making it possible to observe atomic resolution in both the attractive and the repulsive regime although with inverted contrast. Regarding STM images, we show that in the near-contact regime, due to current saturation, bright spots correspond to hollow positions instead of atomic sites, providing an explanation for the most common hexagonal pattern found in the experiments. Fullerenes, nanotubes, graphene, and carbon nanoribbons are among the most promising materials for nanotechnological applications due to their unique mechanical and electronic properties [1,2]. Turning these expectations into real-world devices requires tools like the STM and the atomic force microscope (AFM) with true atomic resolution (FM-AFM) [3] to visualize, characterize, and manipulate these materials at the atomic scale. However, in spite of the apparent simplicity of the common honeycomb structure and the long-standing experimental research effort, we do not know yet something as fundamental as whether the maxima in the scanning probe microscopy images correspond to atoms or to the hollow sites [4][5][6][7]. Here, we use first-principles calculations to show that the rich variety of AFM and STM image patterns found in carbon nanostructures can be rationalized in terms of the chemical reactivity of the tip and the distance range explored in the experiments.The first STM images of the graphite(0001) surface did not display the expected honeycomb pattern but a hexagonal arrangement of bright spots (topographic maxima; see Fig. 1 in [8]) [9][10][11]. The accepted interpretation relies on a subtle electronic effect [12]. The Bernal stacking makes the two surface atoms inequivalent. C atoms, with a nearest neighbor right below in the second layer, do not contribute significantly to the density of states close to the Fermi level, and only the C atoms are imaged as bright spots at low bias voltages. Although a honeycomb pattern should be recovered for larger biases, the experimental evidence accumulated over the past 25 years [9][10][11][12][13] shows that STM images with a hexagonal pattern are overwhelmingly recorded over a broad range of bias voltages and distance operation conditions. Nevertheless, several groups have reported honeycomb patterns even for small bias voltage [13][14][15][16][17].The FM-AFM, relying on the forces between the tip and surface, is expected not to be so sensitive to electronic effects and to reflect the real atomic structure of the surface. However, the first reported ...

We have studied large areas of (√3×√3)R30° graphene commensurate with a Pt(111) substrate. A combination of experimental techniques with ab initio density functional theory indicates that this structure is related to a reconstruction at the Pt surface, consisting of an ordered vacancy network formed in the outermost Pt layer and a graphene layer covalently bound to the Pt substrate. The formation of this reconstruction is enhanced if low temperatures and polycyclic aromatic hydrocarbons are used as molecular precursors for epitaxial growth of the graphene layers.

Non-contact atomic force microscopy (NC-AFM) at true atomic resolution is used to investigate the (110) surface of rutile TiO 2. We are able to simultaneously resolve both bridging oxygen and titanium atoms of this prototypical oxide surface. Furthermore, the characteristic defect species, i.e. bridging oxygen vacancies, single and double hydroxyls as well as subsurface defects, are identified in the very same frame. We employ density functional theory (DFT) calculations to obtain a comprehensive understanding of the relation between the tip apex structure and the observed image contrast. Our results provide insight into the physical mechanisms behind atomic-scale contrast, indicating that electrostatic interaction can lead to a far more complex contrast than commonly assumed.

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