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The mechanism of Kondo screening in strongly correlated molecules with several unpaired electrons on a metal surface is still under debate. Here, we provide a theoretical framework that rationalizes the emergence of Kondo screening involving several extended molecular orbitals with unpaired electrons. We introduce a perturbative model, which provides simple rules to identify the presence of antiferromagnetic spin-flip channels involving charged molecular multiplets responsible for Kondo screening. The Kondo regime is confirmed by numerical renormalization group calculations. In addition, we introduce the concept of Kondo orbitals as molecular orbitals associated with the Kondo screening process, which provide a direct interpretation of experimental $dI/dV$ maps of Kondo resonances. We demonstrate that this theoretical framework can be applied to different strongly correlated open-shell molecules on metal surfaces, obtaining good agreement with previously published experimental data., Comment: 13 pages, 16 figures

Ultraviolet (UV) processing in the insterstellar medium (ISM) induces the dehydrogenation of hydrocarbons. Aliphatics, including alkanes, are present in different interstellar environments, being prevalently formed in evolved stars; thus, the dehydrogenation by UV photoprocessing of alkanes plays an important role in the chemistry of the ISM, leading to the formation of unsaturated hydrocarbons and eventually to aromatics, the latter ubiquitously detected in the ISM. Here, through combined experimental results and \textit{ab-initio} calculations, we show that UV absorption (mainly at the Ly-$\alpha$ emission line of hydrogen at 121.6 nm) promotes an alkane to an excited Rydberg state from where it evolves towards fragmentation inducing the formation of olefinic C=C bonds, which are necessary precursors of aromatic hydrocarbons. We show that photochemistry of aliphatics in the ISM does not primarily produce direct hydrogen elimination but preferential C-C photocleavage. Our results provide an efficient synthetic route for the formation of unsaturated aliphatics, including propene and dienes, and suggest that aromatics could be formed in dark clouds by a bottom-up mechanism involving molecular fragments produced by UV photoprocessing of aliphatics.

This study delves into the intriguing properties of 1H/1T-TaS$_2$ van der Waals heterostructure, focusing on the transparency of the 1H layer to the Charge Density Wave of the underlying 1T layer. Despite the sizable interlayer separation and metallic nature of the 1H layer, positive bias voltages result in a pronounced superposition of the 1T charge density wave structure on the 1H layer. The conventional explanation relying on tunneling effects proves insufficient. Through a comprehensive investigation combining lowtemperature scanning tunneling microscopy, scanning tunneling spectroscopy, non-contact atomic force microscopy, and firstprinciples calculations, we propose an alternative interpretation. The transparency effect arises from a weak yet substantial electronic coupling between the 1H and 1T layers, challenging prior understanding of the system. Our results highlight the critical role played by interlayer electronic interactions in van der Waals heterostructures to determine the final ground states of the systems.

We discuss coexistence of Kondo and spin excitation signals in tunneling spectroscopy in strongly correlated polyradical $\pi$-magnetic nanographenes on a metal surface. The Kondo signal is rationalized by a multi-orbital Kondo screening of the unpaired electrons. The fundamental processes are spin-flips of antiferromagnetic (AFM) order involving charged molecular multiplets. We introduce a~perturbative model, which provides simple rules to identify the presence of AFM channels responsible for Kondo screening. The Kondo regime is confirmed by numerical renormalization group calculations. This framework can be applied to similar strongly correlated open-shell systems., Comment: 43 pages (14 in main, 29 in SM), 20 figures (3 in main, 17 in SM)

We report an example that demonstrates the clear interdependence between surface-supported reactions and molecular adsorption configurations. Two biphenyl-based molecules with two and four bromine substituents, i.e. 2,2-dibromo-biphenyl (DBBP) and 2,2,6,6-tetrabromo-1,1-biphenyl (TBBP), show completely different reaction pathways on a Ag(111) surface, leading to the selective formation of dibenzo[e,l]pyrene and biphenylene dimer, respectively. By combining low-temperature scanning tunneling microscopy, synchrotron radiation photoemission spectroscopy, and density functional theory calculations, we unravel the underlying reaction mechanism. After debromination, a bi-radical biphenyl can be stabilized by surface Ag adatoms, while a four-radical biphenyl undergoes spontaneous intramolecular annulation due to its extreme instability on Ag(111). Such different chemisorption-induced precursor states between DBBP and TBBP consequently lead to different reaction pathways after further annealing. In addition, using bond-resolving scanning tunneling microscopy and scanning tunneling spectroscopy, we determine the bond length alternation of biphenylene dimer product with atomic precision, which contains four-, six-, and eight-membered rings. The four-membered ring units turn out to be radialene structures.

Selective activation and controlled functionalization of C-H bonds in organic molecules is one of the most desirable processes in synthetic chemistry. Despite progress in heterogeneous catalysis using metal surfaces, this goal remains challenging due to the stability of C-H bonds and their ubiquity in precursor molecules, hampering regioselectivity. Here, we examine the interaction between 9,10-dicyanoanthracene (DCA) molecules and Au adatoms on a Ag(111) surface at room temperature (RT). Characterization via low-temperature scanning tunneling microscopy, spectroscopy, and noncontact atomic force microscopy, supported by theoretical calculations, revealed the formation of organometallic DCA-Au-DCA dimers, where C atoms at the ends of the anthracene moieties are bonded covalently to single Au atoms. The formation of this organometallic compound is initiated by a regioselective cleaving of C-H bonds at RT. Hybrid quantum mechanics/molecular mechanics calculations show that this regioselective C-H bond cleaving is enabled by an intermediate metal-organic complex which significantly reduces the dissociation barrier of a specific C-H bond. Harnessing the catalytic activity of single metal atoms, this regioselective on-surface C-H activation reaction at RT offers promising routes for future synthesis of functional organic and organometallic materials., Comment: Main: 28 pages, 5 figures, 1 TOC figure and SI: 32 pages, 16 figures

Open-shell benzenoid polycyclic aromatic hydrocarbons, known as magnetic nanographenes, exhibit unconventional p-magnetism arising from topological frustration or strong electronic-electron (e-e) interaction. Imprinting multiple strongly entangled spins into polyradical nanographenes creates a major paradigm shift in realizing non-trivial collective quantum behaviors and exotic quantum phases in organic quantum materials. However, conventional design approaches are limited by a single magnetic origin, which can restrict the number of correlated spins or the type of magnetic ordering in open-shell nanographenes. Here, we present a novel design strategy combing topological frustration and e-e interactions to fabricate the largest fully-fused open-shell nanographene reported to date, a 'butterfly'-shaped tetraradical on Au(111). We employed bond-resolved scanning tunneling microscopy and spin excitation spectroscopy to unambiguously resolve the molecular backbone and reveal the strongly correlated open-shell character, respectively. This nanographene contains four unpaired electrons with both ferromagnetic and anti-ferromagnetic interactions, harboring a many-body singlet ground state and strong multi-spin entanglement, which can be well described by many-body calculations. Furthermore, we demonstrate that the nickelocene magnetic probe can sense highly-correlated spin states in nanographene. The ability to imprint and characterize many-body strongly correlated spins in polyradical nanographenes not only presents exciting opportunities for realizing non-trivial quantum magnetism and phases in organic materials but also paves the way toward high-density ultrafast spintronic devices and quantum information technologies., Comment: 17 pages, 4 figures

The interplay of magnetism and topology lies at the heart of condensed matter physics, which offers great opportunities to design intrinsic magnetic topological materials hosting a variety of exotic topological quantum states including the quantum anomalous Hall effect (QAHE), axion insulator state, and Majorana bound states. Extending this concept to one-dimension (1D) systems offers additional rich quantum spin physics with great promise for molecular-scale spintronics. Despite recent progress in the discovery of symmetry-protected topological quantum phases in 1D graphene nanoribbons (GNRs), the rational design and realization of magnetic topological GNRs (MT-GNRs) represents a grand challenge, as one must tackle multiple dimensions of complexity including time-reversal symmetry (TRS), spatial symmetry (width, edge, end geometry) and many-electron correlations. Here, we devised a new route involving the real- and reciprocal-space descriptions by unifying the chemists and physicists perspectives, for the design of such MT-GNRs with non-trivial electronic topology and robust magnetic terminal. Classic Clar's rule offers a conceptually qualitative real-space picture to predict the transition from closed-shell to open-shell with terminal magnetism, and band gap reopening with possible non-trivial electronic topology in a series of wave-like GNRs, which are further verified by first principle calculations of band-structure topology in a momentum-space. With the advance of on-surface synthesis and careful design of molecular precursors, we have fabricated these MT-GNRs with observation of topological edge bands, whose terminal pi-magnetism can be directly captured using a single-nickelocene spin sensor. Moreover, the transition from strong anti-ferromagnetic to weak coupling (paramagnetism-like) between terminal spins can be controlled by tuning the length of MT-GNRs., Comment: 29 pages, 11 figures

An ideal one-dimensional electronic system is formed along atomic chains on Au-decorated vicinal silicon surfaces but the nature of its low temperature phases has been puzzled for last two decades. Here, we unambiguously identify the low temperature structural distortion of this surface using high resolution atomic force microscopy and scanning tunneling microscopy. The most important structural ingredient of this surface, the step-edge Si chains are found to be strongly buckled, every third atoms down, forming trimer unitcells. This observation is consistent with the recent model of rehybridized dangling bonds and rules out the antiferromagnetic spin ordering proposed earlier. The spectroscopy and electronic structure calculation indicate a charge density wave insulator with a Z3 topology making it possible to exploit topological phases and excitations. Tunneling current was found to substantially lower the energy barrier between three degenerate CDW states, which induces a dynamically fluctuating CDW at very low temperature.

One-dimensional metal-organic chains often possess a complex magnetic structure susceptible to be modified by a alteration of their chemical composition. The possibility to tune their magnetic properties provides an interesting playground to explore quasiparticle interactions in low-dimensional systems. Despite the great effort invested so far, a detailed understanding of the interactions governing the electronic and magnetic properties of the low-dimensional systems is still incomplete. One of the reasons is the limited ability to characterize their magnetic properties at the atomic scale. Here, we provide a comprehensive study of the magnetic properties of metal-organic one-dimensional (1D) coordination polymers consisting of 2,5-diamino-1,4-benzoquinonediimine ligands coordinated with Co or Cr atoms synthesized in ultra-high vacuum conditions on a Au(111) surface. A combination of an integral X-ray spectroscopy with local-probe inelastic electron tunneling spectroscopy corroborated by multiplet analysis, density functional theory, and inelastic electron tunneling simulations enable us to obtain essential information about their magnetic structure, including the spin magnitude and orientation at the magnetic atoms, as well as the magnetic anisotropy., Comment: 35 pages, 8 Figures, 3 tables

Localized modes in one dimensional topological systems, such as Majonara modes in topological superconductors, are promising platforms for robust information processing. In one dimensional topological insulators, mobile topological solitons are expected but have not been fully realized yet. We discover fractionalized phase defects moving along trimer silicon atomic chains formed along step edges of a vicinal silicon surface. Tunneling microscopy identifies local defects with phase shifts of 2{\pi}/3 and 4{\pi}/3 with their electronic states within the band gap and with their motions activated above 100 K. Theoretical calculations reveal the topological soliton origin of the phase defects with fractional charges of {\pm}2e/3 and {\pm}4e/3. An individual soliton can be created and annihilated at a desired location by current pulse from the probe tip. Mobile and manipulatable topological solitons discovered here provide a new platform of robustly-protected informatics with extraordinary functionalities., Comment: 18 pages, 4 figures

Non-invasive imaging of the atomic arrangement in two-dimensional (2D) Ruddlesden-Popper hybrid Perovskites (RPPs), as well as understanding the related effects is challenging, due to the insulating nature and softness of the organic layers which also obscure the underlying inorganic lattice. Here, we demonstrate a sub-angstrom resolution imaging of both soft organic layers and inorganic framework in a prototypical 2D lead-halide RPP crystal via combined tip-functionalized Scanning Tunneling Microscopy (STM) and non-contact Atomic Force Microscope (ncAFM) corroborated by theoretical simulations. STM measurements unveil the atomic reconstruction of the inorganic lead-halide lattice and overall twin-domain composition of the RPP crystal, while ncAFM measurements with a CO-tip enable non-perturbative visualization of the cooperative reordering of surface organic cations driven by their hydrogen bonding interactions with the inorganic lattice. Moreover, such a joint technique also allows for the atomic-scale imaging of the electrostatic potential variation across the twin-domain walls, revealing alternating quasi-one-dimensional (1D) electron and hole-channels at neighboring twin-boundaries, which may influence in-plane exciton transport and dissociation.

We provide a critical overview of the theory of the chirality-induced spin selectivity (CISS) effect, i.e., phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes. Based on discussions in a recently held workshop, and further work published since, we review the status of CISS effects - in electron transmission, electron transport, and chemical reactions. For each, we provide a detailed discussion of the state-of-the-art in theoretical understanding and identify remaining challenges and research opportunities.

Carbon nanostructures with zigzag edges exhibit unique properties with exciting potential applications. Such nanostructures are generally synthesized under vacuum because their zigzag edges are unstable under ambient conditions: a barrier that must be surmounted to achieve their scalable exploitation. Here, we prove the viability of chemical protection/deprotection strategies for this aim, demonstrated on labile chiral graphene nanoribbons (chGNRs). Upon hydrogenation, the chGNRs survive an exposure to air, after which they are easily converted back to their original structure via annealing. We also approach the problem from another angle by synthesizing a chemically stable oxidized form of the chGNRs that can be converted to the pristine hydrocarbon form via hydrogenation and annealing. These findings may represent an important step toward the integration of zigzag-edged nanostructures in devices.

We report that mono-elemental black phosphorus presents a new electronic self-passivation scheme of single vacancy (SV). By means of low-temperature scanning tunneling microscopy and bond-resolved non-contact atomic force microscopy, we demonstrate that the local reconstruction and ionization of SV into negatively charged $\mathrm{SV}^-$ leads to the passivation of dangling bonds and thus the quenching of in-gap states, which can be achieved by mild thermal annealing or STM tip manipulation. SV exhibits a strong and symmetric Friedel oscillation (FO) pattern, while $\mathrm{SV}^-$ shows an asymmetric FO pattern with local perturbation amplitude reduced by one order of magnitude and a faster decay rate. The enhanced passivation by forming $\mathrm{SV}^-$ can be attributed to its weak dipole-like perturbation, consistent with density-functional theory and numerical calculations. Therefore, self-passivated $\mathrm{SV}^-$ is electronically benign and acts as a much weaker scattering center, which may hold the key to further enhance the charge mobility of BP and its analogs.

Quantum phase transitions, which are driven by quantum fluctuations, mark a frontier between distinct quantum phases of matter. However, our understanding and control of such phenomena is still limited. Here we report an atomic scale control of quantum phase transition between two different topological quantum classes of a well-defined {\pi}-conjugated polymer controlled by their length. We reveal that a pseudo Jahn-Teller effect is the driving mechanism of the phase transition, being activated above a certain polymer chain length. In addition, our theoretical calculations indicate the presence of long-time coherent fluctuations at finite temperature between the two quantum phases of the polymer near the phase transition. This work may pave new ways to achieve atomic scale control of quantum phase transitions, in particular in organic matter.

In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of {\pi}-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to new electronic in-gap states localized at the ends. These findings demonstrate the identification of a new class of isomeric hydrogen bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. We anticipate that this work will open new research directions towards the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling.

We report a multi-step on-surface synthesis strategy. The first step consists in the surface-supported synthesis of metal-organic complexes, which are subsequently used as catalysts to steer on-surface alkyne coupling reactions. In addition, we analyze and compare the electronic properties of the different coupling motifs obtained.

The development of synthetic strategies to engineer \pi-conjugated polymers is of paramount importance in modern chemistry and materials science. Here we introduce a theoretical and experimental synthetic paradigm based on the search for specific vibrational modes through an appropriate tailoring of the \pi-conjugation of the precursors, in order to increase the attempt frequency of a chemical reaction. First, we on-surface design a 1D \pi-conjugated polymer with specific \pi-topology, which is based on bisanthene monomers linked by cumulene bridges that tune specific vibrational modes. In a second step, upon further annealing, such vibrational modes steer the two-fold cyclization reaction between adjacent bisanthene moieties, which gives rise to a long and free-defect pentalene-bridged conjugated ladder polymer featuring a low band gap. In addition, high resolution atomic force microscopy allows us to identify by atomistic insights the resonant form of the polymer, thus confirming the validity of the Glidewell and Lloyd's rules for aromaticity. This on-surface synthetic strategy may stimulate exploiting previously precluded reactions towards novel pi-conjugated polymers with specific structures and properties.

Organosulfur compounds at the interface to noble metals have proved over the last decades to be extremely versatile systems for both fundamental and applied research. However, the anchoring of thiols to gold remained an object of controversy for long times. The RS-Au-SR linkage, in particular, is a robust bonding configuration that displays interesting properties. It is generated spontaneously at room temperature and can be used for the production of extended molecular nanostructures. In this work we explore the behavior of 1,4-Bis(4-mercaptophenyl)benzene (BMB) on the Au(111) surface, which results in the formation of 2D crystalline metal-organic assemblies stabilized by this type of Au-thiolate bonds. We show how to control the thiolates stereospecific bonding motif and thereby choose whether to form ordered arrays of Au3BMB3 units with embedded triangular nanopores, or linearly stacked metal-organic chains. The former turn out to be the thermodynamically favored structures and display confinement of the underneath Au(111) surface state. The electronic properties of single molecules as well as of the 2D crystalline self-assemblies have been characterized both on the metal-organic backbone and inside the associated pores.

Iron oxides are among the most abundant compounds on Earth and have consequently been studied and used extensively in industrial processes. Despite these efforts, concrete understanding of some of their surface phase structures has remained elusive, in particular the oxidized ${\alpha}-Fe_2O_3(0001)$ hematite surface. We detail an optimized recipe to produce this phase over the entire hematite surface and study the geometrical parameters and composition of its complex structure by means of atomically resolved microscopy, electron diffraction and surface-sensitive spectroscopies. We conclude that the oxidized ${\alpha}-Fe_2O_3(0001)$ surface is terminated by a two-dimensional iron oxide with structure, lattice parameters, and orientation different from the bulk substrate. Using total-energy density functional theory for simulation of a large-scale atomic model, we identify the structure of the surface layer as antiferromagnetic, conductive $1T-FeO_2$ attached on half-metal terminated bulk. The model succeeds in reproducing the characteristic modulations observed in the atomically resolved images and electron diffraction patterns.

Determination of the molecular Kondo temperature $T_K$ poses a challenge in most cases when the experimental temperature cannot be tuned to a sufficient extent. We show how this ambiguity can be resolved if additional control parameters are present, such as magnetic field and mechanical gating. We record the evolution of the differential conductance by lifting an individual molecule from the metal surface with the tip of a scanning tunneling microscope. By fitting the measured conductance spectra with the single impurity Anderson model we are able to demonstrate that the lifting tunes the junction continuously from the strongly correlated Kondo-singlet to the free spin $1/2$ ground state. In the crossover regime, where $T_K$ is similar to the temperature of experiment, the fitting yields ambiguous estimates of $T_K$ varying by an order of magnitude. We show that analysis of the conductance measured in two distinct external magnetic fields can be used to resolve this problem., Comment: Main text: 10 pages, 6 figures; Supplementary Information: 11 pages, 5 figures

The single molecule magnet (SMM) bis(phthalocyaninato)terbium (III) (TbPc$_2$) has attracted steady research attention as an exemplar system for realizing molecule-based spin electronics. In this paper, we report on the spontaneous formation of Tb$_2$Pc$_3$ species from TbPc$_2$ precursors via sublimation in ultrahigh vacuum (UHV) onto an Ag(111) surface. The molecules on the surface are inspected using combined scanning tunneling (STM) and non-contact atomic force microscopies (nc-AFM) at 5 Kelvin. Submolecular resolution and height dependent measurements supported by density functional theory (DFT) calculations unambiguously show the presence of both TbPc$_2$ and Tb$_2$Pc$_3$ species. The synthesis of Tb$_2$Pc$_3$ species under UHV conditions is independently confirmed by chemical analysis. The high-resolution AFM imaging allows us to register the orientation of the topmost Pc ligand in both Tb$_2$Pc$_3$ and TbPc$_2$ relative to the underlying Ag(111) surface. Measurements of the electronic structure reveal the selective appearance of a Kondo signature with temperature $\sim$ 30K in the Tb$_2$Pc$_3$ species, localized to the Pc ligand lobes. We attribute the presence of the Kondo resonance on select Tb$_2$Pc$_3$ molecules to the orientation of internal molecular ligands. High-resolution AFM imaging identifies geometric distortions between Tb$_2$Pc$_3$ molecules with and without the Kondo effect, the result of the complex interplay between structural and electronic differences., Comment: 29 pages, 8 figures; additional supplementary information in /anc directory

Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes - consisting of organic ligands binding to clusters of several metal atoms are of particular interest, owing to their electronic/magnetic properties and potential for functional reactivity pathways. However, their synthesis remains challenging; only a limited number of geometries and configurations have been achieved. Here, we synthesise - via supramolecular chemistry on a noble metal surface - one-dimensional metal-organic nanostructures composed of terpyridine (tpy)-based molecules coordinated with well-defined polynuclear iron clusters. By a combination of low-temperature scanning probe microscopy techniques and density functional theory, we demonstrate that the coordination motif consists of coplanar tpy's linked via a linear tri-iron node in a mixed (positive) valence, metal-metal bond configuration. This unusual linkage is stabilized by a local accumulation of electrons at the interface between cations, ligand and surface. The latter, enabled by the bottom-up on-surface synthesis, hints at a chemically active metal centre, and opens the door to the engineering of nanomaterials with novel catalytic and magnetic functionalities., Comment: 7 pages, 4 figures, 14 pages supporting information

Here we show scanning tunnelling microscopy (STM), non-contact atomic force microscopy (AFM) and inelastic electron tunnelling spectroscopy (IETS) measurements on organic molecule with a CO- terminated tip at 5K. The high-resolution contrast observed simultaneously in all channels unam- biguously demonstrates the common imaging mechanism in STM/AFM/IETS, related to the lateral bending of the CO-functionalized tip. The IETS spectroscopy reveals that the submolecular con- trast at 5K consists of both renormalization of vibrational frequency and variation of the amplitude of IETS signal. This finding is also corroborated by first principles simulations. We extend accord- ingly the probe-particle AFM/STM/IETS model to include these two main ingredients necessary to reproduce the high-resolution IETS contrast. We also employ the first principles simulations to get more insight into different response of frustrated translation and rotational modes of CO-tip during imaging.

Scanning probe microscopy (SPM) 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 non-invasive 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 without inducing any disturbance. This work may open up new possibility of studying the intrinsic structure and electrostatics of ice or water on bulk insulating surfaces, ion hydration and biological water with atomic precision., Comment: Main text (4 figures) followed by supplementary information (11 figures)

We present a numerical model which allows us to study the Kelvin force probe microscopy response to the charge switching in quantum dots at various time scales. The model provides more insight into the behavior of frequency shift and dissipated energy under different scanning conditions measuring a temporarily charged quantum dot on surface. Namely, we analyze the dependence of the frequency shift, its fluctuation and of the dissipated energy, on the resonance frequency of tip and electron tunneling rates between tip - quantum dot and quantum dot - sample. We discuss two complementary approaches to simulating the charge dynamics, a stochastic and a deterministic one. In addition, we derive analytic formulas valid for small amplitudes, describing relations between the frequency shift, dissipated energy, and the characteristic rates driving the charging and discharging processes., Comment: 15 pages, 4 figures

Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complimented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbonmonoxide (CO) molecule positioned at the apex of a scanning tunnelling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending the model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of the CO frustrated translation in response to the change of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM and IETS-STM images can deliver information about intramolecular charge transfer for molecules deposited on a~surface. To demonstrate this, we extended our numerical model by taking into the account the electrostatic force acting between the decorated tip and surface Hartree potential., Comment: 5 pages, 4 figures

The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code Fireball, suitable for the computational study of these problems. Our methodology enables simulating photo-induced reaction mechanisms over hundreds of trajectories; therefore, large statistically significant ensembles can be calculated to accurately represent a reaction profile. As an example of the application of this approach, we report results on the [2+2] cycloaddition of ethylene with maleic anhydride and on the [2+2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

High resolution Atomic Force Microscopy (AFM) and Scanning Tunnelling Microscopy (STM) imaging with functionalized tips is well established, but a detailed understanding of the imaging mechanism is still missing. We present a numerical STM/AFM model, which takes into account the relaxation of the probe due to the tip-sample interaction. We demonstrate that the model is able to reproduce very well not only the experimental intra- and intermolecular contrasts, but also their evolution upon tip approach. At close distances, the simulations unveil a significant probe particle relaxation towards local minima of the interaction potential. This effect is responsible for the sharp sub-molecular resolution observed in AFM/STM experiments. In addition, we demonstrate that sharp apparent intermolecular bonds should not be interpreted as true hydrogen bonds, in the sense of representing areas of increased electron density. Instead they represent the ridge between two minima of the potential energy landscape due to neighbouring atoms.

We discuss the possibility of a 2D ordered structure formed upon deposition of Si on metal surfaces. We investigate the atomic and electronic structure of the Si-$(\sqrt{19}\times\sqrt{19})R23.4^{\circ}$/Pt(111) surface reconstruction by means of a set of experimental surface-science techniques supported by theoretical calculations. The theory achieves a very good agreement with the experimental results and corroborate beyond any doubt that this phase is a surface alloy consisting of Si$_3$Pt tetramers that resembles a twisted Kagome lattice. These findings render unlikely any formation of silicene or germanene on Pt(111) and other transition metal surfaces., Comment: 5 pages, 4 figures