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A class of important semiconductors, such as Si, Ge, or C, has an indirect band gap, which critically limits their optical properties. Lack of efficient emission is especially unfortunate for silicon, where Si light sources could enable realization of the long-awaited on-chip-integrated Si laser for an integrated optical computing CPU architecture. Hence, methods toward the improvement of optical properties of Si-based materials are in high demand. Unlike most of the applied light-emitting semiconductor nanocrystals (NCs) with a direct band gap, the radiative rate in covalent silicon NCs (SiNCs) is size-dependent but remains low even for the smallest SiNCs. Additionally, the radiative rate is also ligand-sensitive, and the covalent bond with ligands is very rigid and static and could be, in principle, used for straining via steric hindrance, further influencing the radiative rates. In this work, we use the self-consistent density functional theory (DFT) simulation together with a "fuzzy"band-structure concept to show the effect of covalently bonded ligands on the electronic structure of NCs and their k - -space projection. For instance, in 2 nm large SiNCs with C-linked organic ligands, we demonstrate that radiative rates can be manipulated by ligands to a considerable extent through an intricate interplay between charge transfer from the core to the ligand, orbital delocalization, and strain by steric hindrance. We propose that the tunability of electronic properties achieved via ligands in covalent systems offers a possible direction toward the design of an ideal Si light-emitting system.

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., 7 pages, 4 figures, 14 pages supporting information

Ion hydration and transport at interfaces are relevant to a wide range of applied fields and natural processes1–5. Interfacial effects are particularly profound in confined geometries such as nanometre-sized channels6–8, where the mechanisms of ion transport in bulk solutions may not apply9,10. To correlate atomic structure with the transport properties of hydrated ions, both the interfacial inhomogeneity and the complex competing interactions among ions, water and surfaces require detailed molecular-level characterization. Here we constructed individual sodium ion (Na+) hydrates on a NaCl(001) surface by progressively attaching single water molecules (one to five) to the Na+ ion using a combined scanning tunnelling microscopy and noncontact atomic force microscopy system. We found that the Na+ ion hydrated with three water molecules diffuses orders of magnitude more quickly than other ion hydrates. Ab initio calculations revealed that such high ion mobility arises from the existence of a metastable state, in which the three water molecules around the Na+ ion can rotate collectively with a rather small energy barrier. This scenario would apply even at room temperature according to our classical molecular dynamics simulations. Our work suggests that anomalously high diffusion rates for specific hydration numbers of ions are generally determined by the degree of symmetry match between the hydrates and the surface lattice. A sodium ion hydrated with three (rather than one, two, four or five) water molecules diffuses orders of magnitude more quickly than the other ion hydrates owing to the interfacial symmetry mismatch.

Ferrocene-based molecules are extremely appealing as they offer a prospect of having built-in spin or charge functionality. However, there are only limited number of studies of structural and electronic properties on surfaces so far. We investigated the self-assembly processes of 1,1′-ferrocene dicarboxylic acid molecules (C12H10FeO4) on both metallic (Ag(111), Au(111), and Cu(110)) and insulating (Cu3N/Cu(110)) surfaces with high-resolution ncAFM/STM, XPS, and NEXAFS. The experimental evidence is corroborated with total energy DFT calculations and ncAFM simulations. The combined experimental and theoretical analysis allows detailed understanding of the unique arrangement and adsorption geometries of the molecules on different substrates, as well as the different chemical stability of the carboxylic (COOH) groups. The molecules on noble (Ag, Au) surfaces show only a weak interaction with the substrate forming a complex self-assembled pattern, driven by weak intermolecular interactions. In contrast, the an...

Single-molecule junctions are elementary building blocks in novel electronics devices, and therefore, it is essential to understand the charge transport mechanisms at the single-molecular level. According to recent studies, the linker atoms connecting the organic molecule with the electrodes play a crucial role in optimizing the transport properties as well as thermodynamical stability of a molecular junction. We address this issue by considering N, O, S, and Se atoms as prospective linkers anchoring the benzene molecule to the Au(1 0 0) electrodes. Calculations based on non-equilibrium Green's function approach are performed within the framework of the density functional theory. Electron transport is studied in detail by analyzing the transmission spectra, density-of-states distributions, and current–voltage characteristics. Results show that the choice of linkers strongly affects the conductance of the junctions under study: at low bias regime, the current through N-linked molecules is remarkably higher as compared to the case of S and Se linkers, whereas the thermodynamical stability is similar. This offers an additional means of modifying the current–voltage characteristics of benzene-based molecular junctions by an appropriate selection of linkers.

In this Letter, the links to Supplementary Videos 5, 7, 9 and 10 were incorrect, and there were some formatting errors in the Supplementary Video legends. These errors have been corrected online.

Nitrogen doping of graphene significantly affects its chemical properties, which is particularly important in molecular sensing and electrocatalysis applications. However, detailed insight into interaction between N-dopant and molecules at the atomic scale is currently lacking. Here we demonstrate control over the spin state of a single iron(II) phthalocyanine molecule by its positioning on N-doped graphene. The spin transition was driven by weak intermixing between orbitals with z-component of N-dopant (pz of N-dopant) and molecule (dxz, dyz, dz2) with subsequent reordering of the Fe d-orbitals. The transition was accompanied by an electron density redistribution within the molecule, sensed by atomic force microscopy with CO-functionalized tip. This demonstrates the unique capability of the high-resolution imaging technique to discriminate between different spin states of single molecules. Moreover, we present a method for triggering spin state transitions and tuning the electronic properties of molecules through weak non-covalent interaction with suitably functionalized graphene., Molecules can change their electronic properties when they are adsorbed on substrates, which can be useful for sensing and catalysis. Here, the authors use atomic force microscopy to show that the spin state of an iron complex can be changed upon displacing the molecule to different sites of a nitrogen-doped 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.

We report a straightforward method to produce high-quality nitrogen-doped graphene on SiC(0001) using direct nitrogen ion implantation and subsequent stabilization at temperatures above 1300 K. We demonstrate that double defects, which comprise two nitrogen defects in a second-nearest-neighbor (meta) configuration, can be formed in a controlled way by adjusting the duration of bombardment. Two types of atomic contrast of single N defects are identified in scanning tunneling microscopy. We attribute the origin of these two contrasts to different tip structures by means of STM simulations. The characteristic dip observed over N defects is explained in terms of the destructive quantum interference.

Electron donor–acceptor molecules are of outstanding interest in molecular electronics and organic solar cells for their intramolecular charge transfer controlled via electrical or optical excitation. The preservation of their electronic character in the ground state upon adsorption on a surface is cardinal for their implementation in such single-molecule devices. Here, we investigate by atomic force microscopy and scanning tunneling microscopy a prototypical system consisting of a π-conjugated tetrathiafulvalene-fused dipyridophenazine molecule adsorbed on thin NaCl films on Cu(111). Depending on the adsorption site, the molecule is found either in a nearly undisturbed free state or in a bound state. In the latter case, the molecule adopts a specific adsorption site, leading to the formation of a chelate complex with a single Na+ alkali cation pulled out from the insulating film. Although expected to be electronically decoupled, the charge distribution of the complex is drastically modified, leading to t...

We report on our systematic investigation of Au nanoparticles highly dispersed in the mesopores of (s)-(–)-2-pyrrolidinone-5-carboxylic acid (Py)-modified SBA-15 (Au/SBA-15-Py) by using a series of modern techniques. 13C NMR and IR spectroscopies indicate that Py species are successfully grafted on the surface of mesopores in SBA-15; XRD patterns and N2 adsorption isotherms show that the sample mesostructures are well preserved; TEM images clearly confirm the uniform Au nanoparticles in the mesopores; and XPS suggests an interaction between Au nanoparticles with Py species. Interestingly, Au/SBA-15-Py catalysts always exhibit superior catalytic properties in the oxidation of cyclohexene and styrene by molecular oxygen at atmospheric pressure, compared with the pyrrolidone-free SBA-15 supported Au catalyst (Au/SBA-15-N). This phenomenon is reasonably related to the interaction between Au nanoparticles with Py species, which is consistent with results analyzed from our density-functional theory (DFT) calculations.

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., Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface, usually at low temperatures. Here, the authors demonstrate that the chemical structure of a single molecule strongly adsorbed onto a silicon surface can be determined at room temperature.

Under the terms of the Creative Commons Attribution License 3.0 (CC-BY).-- et al., 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 (C2H2) 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 C2H2 molecule attributed to a weak overlap of their respective frontier orbitals., The research was supported by DFG (Grant No. Sfb 658), the Czech Science Foundation (GAČR) Project No. 14-02079S, GAAV Grant No. M100101207, and the Spanish MINECO (Grant No. MAT2013-46593-C6-01). M. C. acknowledges support from the Alexander von Humboldt Foundation.

We discuss the possibility of a two-dimensional ordered structure formed upon deposition of Si on metal surfaces. We investigate the atomic and electronic structure of the Si-$(\sqrt{19}\ifmmode\times\else\texttimes\fi{}\sqrt{19})R23.{4}^{\ensuremath{\circ}}$/Pt(111) surface reconstruction by means of a set of experimental surface-science techniques supported by theoretical calculations. The theory achieves very good agreement with the experimental results and is corroborating beyond any doubt that this phase is a surface alloy consisting of ${\mathrm{Si}}_{3}$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.

The following article appeared in Journal of Chemical Physics 138.15 (2013): 154106 and may be found at http://scitation.aip.org/content/aip/journal/jcp/138/15/10.1063/1.4801511, Most of today's molecular-dynamics simulations of materials are based on the Born-Oppenheimer approximation. There are many cases, however, in which the coupling of the electrons and nuclei is important and it is necessary to go beyond the Born-Oppenheimer approximation. In these methods, the non-adiabatic coupling vectors are fundamental since they represent the link between the classical atomic motion of the nuclei and the time evolution of the quantum electronic state. In this paper we analyze the calculation of non-adiabatic coupling vectors in a basis set of local orbitals and derive an expression to calculate them in a practical and computationally efficient way. Some examples of the application of this expression using a local-orbital density functional theory approach are presented for a few simple molecules: H3, formaldimine, and azobenzene. These results show that the approach presented here, using the Slater transition-state density, is a very promising way for the practical calculation of non-adiabatic coupling vectors for large systems., This work was partially supported by Spanish Ministerio de Economía y Competitividad (Contract No.FIS2010-16046), the Comunidad de Madrid (Contract No.S2009/MAT-1467), the Office of Science, Basic Energy Sciences in the US Department of Energy (Grant No. DEFG02-10ER16164), the Czech Science Foundation (GAČR)(Project No. 204/10/0952), the Grant of the MŠMT of the Czech Republic (Grant No. ME 09048), and COST-CMTS Action CM1002 (CODECS). J.O. gratefully acknowledges support from the Spanish Ministerio de Ciencia e Innovación (PR2008-0027). E.A. gratefully acknowledges financial support by the Consejería de Educación de la Comunidad de Madrid and Fondo Social Europeo.

Silicon, a semiconductor underpinning the vast majority of microelectronics, is an indirect-gap material and consequently is an inefficient light emitter. This hampers the ongoing worldwide effort towards the integration of optoelectronics on silicon wafers. Even though silicon nanocrystals are much better light emitters, they retain the indirect-gap nature. Here, we propose a solution to this long-standing problem: silicon nanocrystals can be transformed into a material with fundamental direct bandgap via a concerted action of quantum confinement and tensile strain. We document this transformation by DFT calculations mapping the E(k) band-structure of Si nanocrystals. The experimental proofs are then given firstly by a 10 000× increase in the photon emission rate of strained silicon nanocrystals together with their altered absorbance spectra, both of which point to direct dipole-allowed transitions, secondly by single nanocrystal spectroscopy, confirming reduced phonon energies and thus the presence of tensile strain, and lastly by photoluminescence studies under external hydrostatic pressure.