Intrusive STM imaging

Abstract

An interactive scanning tunneling microscopy (STM) simulator has been designed to efficiently compute the effects of chemical and structural modifications of adsorbed species on resulting STM images. Our general approach is based on first-order perturbation theory that takes into account different tip geometries. In our intrusive STM imaging strategy, we consider small variations such as substitutions, vacancies, functionalizations, and molecular reorganizations from a reference system. First, we show that our perturbation theory approach can provide STM images that are qualitatively similar to those of a more rigorous electron scattering technique based on the Landauer-Büttiker formalism for the case of adsorbed tetracyanoethylene on a Cu(100) single crystal. Second, we demonstrate that the efficiency of Bardeen and Tersoff-Hamann approaches to generate STM images can be substantially improved by exploiting different algorithms to evaluate the tunnel current and to deal with large-scale eigenvalue problems. Following our general intrusive strategy, we have reduced the computing time to generate an STM image of a modified system by about an order of magnitude with respect to the reference image. The shape and position of the contrasts of the STM image evaluated in the context of intrusion are virtually identical to an image computed without intrusive features but within a considerably smaller computing time.

Assessment of Scanning Tunneling Spectroscopy Modes Inspecting Electron Confinement in Surface-Confined Supramolecular Networks

“…The exact contrast mechanisms for molecules being imaged in STM is currently still widely discussed424344454647. Molecules often markedly appear in STM topographs at bias voltages in the gap between the lowest unoccupied and highest occupied molecular orbitals where the orbital-related contributions to the tunnel current should be irrelevant.…”

Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time

“…Tersoff-Hamann technique remains an approximation of the Bardeen theory where the tip is more explicitly considered. 58,63,65 Although we can also produce STM images at the Bardeen theory level with our computational framework, 23 we are focusing on the TH approximation here because it generally reveals the most important features of STM images, especially for two-dimensional molecular systems, and it is coherent with our real-time STM simulation objective. In this special context, a strategy implying the parallelization of the pixels computation becomes even more highly suitable.…”

“…We also consider the possibility of a local structural or chemical modification of surface species called intrusion in the following. Such an intrusion on an adsorbed system could be induced by an external user, 23 by a STM tip through a mechanical action, 1 by a local electric field generated at the tip apex 24,25 or by using inelastic-electron tunneling induced manipulation processes. 26 A general approach in STM simulation that includes intrusion within the limits of Tersoff-Hamann and Bardeen theories was already developed by our group over the last years.…”

“…26 A general approach in STM simulation that includes intrusion within the limits of Tersoff-Hamann and Bardeen theories was already developed by our group over the last years. 23 However, despite considering an explicit intrusion followed by a very rapid calculation of the STM image, this approach does not consider any molecular relaxation after the intrusion, and this essentially leads to a static STM imaging mode. The objective of the present computational development is to produce a numerical toolm that can rapidly and accurately provide a reasonable adsorbate geometry and more importantly, a STM image that can be compared directly to experimental results.…”

Influence of Halogen Bonds on the Compactness of Supramolecular Assemblies on Si(111)-B

“…STM calculations were carried out using a modified version of Flex-STM, a code that considers extended Hückel Hamiltonian in conjunction with Tersoff–Hamann (TH) or Bardeen theory in which chemical and physical modifications can be introduced, while subsequent STM images are produced nearly in real-time. The modified code, dyFlex-STM, now considers molecular relaxation after intrusion (structural, chemical) and prior to the STM calculation. We used the Atom-Superposition and Electon-Delocalization (ASED) scheme that is based on the extended Hückel theory to evaluate the energy of the systems for the conformational relaxation procedure.…”