Self-assembly of s-indacene-tetrone on Cu(111): molecular trapping and patterning of Cu adatoms.

The supramolecular self-assembly of s-indacene-1,3,5,7(2H,6H)-tetrone on the Cu(111) surface was investigated under ultrahigh vacuum by room-temperature scanning tunneling microscopy supported by theoretical modelling based on density functional theory. In total, six different phases were found, driven by hydrogen bonding, metal ligand coordination or covalent coupling. Host-guest interactions allowed for the accommodation of molecular or metal clusters inside the open nanoporous patterns. In one phase, molecular trapping was stochastically observed inside the large periodic nanopores created inside the supramolecular network. The three metal-organic networks observed resulted in the creation of different kinds of regular arrays of isolated metal adatoms or adatom clusters with a lattice period larger than 1 nm.

Switching the Spin on a Ni Trimer within a Metal-Organic Motif by Controlling the On-Top Bromine Atom.

Controlling the spin of metal atoms embedded in molecular systems is a key step toward the realization of molecular electronics and spintronics. Many efforts have been devoted to explore the influencing factors dictating the survival or quenching of a magnetic moment in a metal-organic molecule, and among others, the spin control by axial ligand attachments is the most promising. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and scanning tunneling spectroscopy measurements together with density functional theory calculations, we successfully demonstrate that a Ni trimer within a metal-organic motif acquires a net spin promoted by the adsorption of an on-top Br atom. The spin localization in the trimetal centers bonded to Br was monitored via the Kondo effect. The removal of the Br ligand resulted in the switch from a Kondo ON to a Kondo OFF state. The magnetic state induced by the Br ligand is theoretically attributed to the enhanced Br 4pz and Ni 3dz2 states due to the charge redistribution. The manipulation strategy reported here provides the possibility to explore potential applications of spin-tunable structures in spintronic devices.

Unraveling the molecular conformations of a single ruthenium complex adsorbed on the Ag(111) surface by calculations.

The tris(dibenzoylmethanato)ruthenium (Ru(dbm)3) molecule has recently been characterized by scanning tunneling microscopy (STM) experiments upon adsorption on Ag(111). The adsorbed Ru(dbm)3 molecule shows two conformations with respect to the [11[combining macron]0] direction of the substrate, one with a three-lobed feature and the other one with a bi-lobed structure. For each of these structures, the molecule can take two geometries (states). Molecular mechanics calculations in a semi-empirical framework and STM calculated images reveal that these states on the substrate originate from the enantiomer of the Ru(dbm)3 molecule in the case of three-lobed structure and from the rotation of the two phenyls in the top dbm moities for the bi-lobed form.

Three-dimensional hydrogen bonding between Landers and planar molecules facilitated by electrostatic interactions with Ni adatoms.

Using a combination of UHV-STM and molecular mechanics calculations, we investigate the surface self-assembly of a complex multi-component metal-molecule system with synergistic non-covalent interactions. Hydrogen bonding between three-dimensional Lander-DAT molecules and planar PTCDI molecules, adsorbed closer to the surface, is found to be facilitated by electrostatic interactions between co-adsorbed Ni adatoms and the flexible molecular DAT groups.

Nonisotropic Self-Assembly of Nanoparticles: From Compact Packing to Functional Aggregates.

Quantum strongly correlated systems that exhibit interesting features in condensed matter physics often need an unachievable temperature or pressure range in classical materials. One solution is to introduce a scaling factor, namely, the lattice parameter. Synthetic heterostructures named superlattices or supracrystals are synthesized by the assembling of colloidal atoms. These include semiconductors, metals, and insulators for the exploitation of their unique properties. Most of them are currently limited to dense packing. However, some of desired properties need to adjust the colloidal atoms neighboring number. Here, the current state of research in nondense packing is summarized, discussing the benefits, outlining possible scenarios and methodologies, describing examples reported in the literature, briefly discussing the challenges, and offering preliminary conclusions. Penetrating such new and intriguing research fields demands a multidisciplinary approach accounting for the coupling of statistic physics, solid state and quantum physics, chemistry, computational science, and mathematics. Standard interactions between colloidal atoms and emerging fields, such as the use of Casimir forces, are reported. In particular, the focus is on the novelty of patchy colloidal atoms to meet this challenge.

Conformation Manipulation and Motion of a Double Paddle Molecule on an Au(111) Surface.

The molecular conformation of a bisbinaphthyldurene (BBD) molecule is manipulated using a low-temperature ultrahigh-vacuum scanning tunneling microscope (LT-UHV STM) on an Au(111) surface. BBD has two binaphthyl groups at both ends connected to a central durene leading to anti/syn/flat conformers. In solution, dynamic nuclear magnetic resonance indicated the fast interexchange between the anti and syn conformers as confirmed by density functional theory calculations. After deposition in a submonolayer on an Au(111) surface, only the syn conformers were observed forming small islands of self-assembled syn dimers. The syn dimers can be separated into syn monomers by STM molecular manipulations. A flat conformer can also be prepared by using a peculiar mechanical unfolding of a syn monomer by STM manipulations. The experimental STM dI/dV and theoretical elastic scattering quantum chemistry maps of the low-lying tunneling resonances confirmed the flat conformer BBD molecule STM production. The key BBD electronic states for a step-by-step STM inelastic excitation lateral motion on the Au(111) are presented requiring no mechanical interactions between the STM tip apex and the BBD. On the BBD molecular board, selected STM tip apex positions for this inelastic tunneling excitation enable the flat BBD to move controllably on Au(111) by a step of 0.29 nm per bias voltage ramp.

Bicomponent Supramolecular Architectures at the Vacuum-Solid Interface.

This review aims at giving the readers the basic concepts needed to understand two-dimensional bimolecular organizations at the vacuum-solid interface. The first part describes and analyzes molecules-molecules and molecules-substrates interactions. The current limitations and needs in the understanding of these forces are also detailed. Then, a critical analysis of the past and recent advances in the field is presented by discussing most of the key papers describing bicomponents self-assembly on solid surface in an ultrahigh vacuum environment. These sections are organized by considering decreasing molecule-molecule interaction strengths (i.e. starting from strong directional multiple H bonds up to weaker nondirectional bonds taking into account the increasing fundamental role played by the surface). Finally, we conclude with some research directions (predicting self-assembly, multi-components systems, and nonmetallic surfaces) and potential applications (porous networks and organic surfaces).

Adsorption of single 1,8-octanedithiol molecules on Cu(100).

Single 1,8-octanedithiol (ODT) molecules adsorbed onto the Cu(100) surface have been characterized by using scanning tunneling microscopy (STM) and studied by semi-empirical calculations. STM images have revealed two types of chiral molecules on the surface upon adsorption and both types of molecules showed two bright spots at the extremities of a small rod due to the enhanced electronic density contrast of the chemisorbed sulfur atoms. In sub-monolayer regime deposition, ODT molecules exhibit preferential adsorption directions and the relaxation mechanism is driven by the chemisorption of the two sulfur atoms in a hollow site of the surface. By means of calculations several conformations of the molecule according to the energetically favorable alkane body stretching constraint have been studied. The comparison between relaxed conformations and between calculated and experimental STM images, followed by an analysis of different orientations, has allowed determining unambiguously the most favorable position of the ODT molecule on Cu(100).

Observation and manipulation of hexa-adamantyl-hexa-benzocoronene molecules by low temperature scanning tunneling microscopy.

Large molecules made of a central hexa-adamantyl-hexa-benzocoronene plateau surrounded by six adamantyl groups have been investigated by low temperature scanning tunneling microscopy and scanning tunneling spectroscopy coupled with image calculations and molecular mechanics. The structure of large self-assembled domains reveals that the intermolecular interactions between adamantyl peripheral groups dominate film growth. At very low coverage, the molecules can exhibit a certain instability for negative bias voltages which induces a partial rotation. Manipulations of single objects using the STM tip are used to create small clusters of two or three molecules. The formed structures can be obtained and manipulated provided that the flexible adamantyl moieties of neighbouring molecules are brought in close contact promoting a robust mechanical anchoring.

Directional molecular sliding at room temperature on a silicon runway.

The design of working nanovehicles is a key challenge for the development of new devices. In this context, 1D controlled sliding of molecules on a silicon-based surface is successfully achieved by using an optimized molecule-substrate pair. Even though the molecule and surface are compatible, the molecule-substrate interaction provides a 1D template effect to guide molecular sliding along a preferential surface orientation. Molecular motion is monitored by STM experiments under ultra-high vacuum at room temperature. Molecule-surface interactions are elucidated by semi-empirical calculations.

Graphite, graphene on SiC, and graphene nanoribbons: Calculated images with a numerical FM-AFM.

BACKGROUND: Characterization at the atomic scale is becoming an achievable task for FM-AFM users equipped, for example, with a qPlus sensor. Nevertheless, calculations are necessary to fully interpret experimental images in some specific cases. In this context, we developed a numerical AFM (n-AFM) able to be used in different modes and under different usage conditions. RESULTS: Here, we tackled FM-AFM image calculations of three types of graphitic structures, namely a graphite surface, a graphene sheet on a silicon carbide substrate with a Si-terminated surface, and finally, a graphene nanoribbon. We compared static structures, meaning that all the tip and sample atoms are kept frozen in their equilibrium position, with dynamic systems, obtained with a molecular dynamics module allowing all the atoms to move freely during the probe oscillations. CONCLUSION: We found a very good agreement with experimental graphite and graphene images. The imaging process for the deposited nanoribbon demonstrates the stability of our n-AFM to image a non-perfectly planar substrate exhibiting a geometrical step as well as a material step.

Self-assembly of hydrogen-bonded chains of molecular landers.

One-dimensional chains of a specially designed lander molecule with di-carboxyl imide functional moieties, enabling complementary intermolecular hydrogen bonding, have been self-assembled under ultra high vacuum conditions on a Au(111) surface and characterized by scanning tunneling microscopy.

Supramolecular architectures on surfaces formed through hydrogen bonding optimized in three dimensions.

Supramolecular self-assembly on surfaces, guided by hydrogen bonding interactions, has been widely studied, most often involving planar compounds confined directly onto surfaces in a planar two-dimensional (2-D) geometry and equipped with structurally rigid chemical functionalities to direct the self-assembly. In contrast, so-called molecular Landers are a class of compounds that exhibit a pronounced three-dimensional (3-D) structure once adsorbed on surfaces, arising from a molecular backboard equipped with bulky groups which act as spacer legs. Here we demonstrate the first examples of extended, hydrogen-bonded surface architectures formed from molecular Landers. Using high-resolution scanning tunnelling microscopy (STM) under well controlled ultrahigh vacuum conditions we characterize both one-dimensional (1-D) chains as well as five distinct long-range ordered 2-D supramolecular networks formed on a Au(111) surface from a specially designed Lander molecule equipped with dual diamino-triazine (DAT) functional moieties, enabling complementary NH...N hydrogen bonding. Most interestingly, comparison of experimental results to STM image calculations and molecular mechanics structural modeling demonstrates that the observed molecular Lander-DAT structures can be rationalized through characteristic intermolecular hydrogen bonding coupling motifs which would not have been possible in purely planar 2-D surface assembly because they involve pronounced 3-D optimization of the bonding configurations. The described 1-D and 2-D patterns of Lander-DAT molecules may potentially be used as extended molecular molds for the nucleation and growth of complex metallic nanostructures.

Self-assembly of fivefold-symmetric molecules on a threefold-symmetric surface.

Buckybowls: The adsorption of penta-tert-butylcorannulene, a molecule with fivefold symmetry, on Cu(111), a surface with threefold symmetry, is investigated by scanning tunneling microscopy complemented by structure calculations. The symmetry mismatch is resolved by the formation of threefold-symmetric subunits consisting of three molecules, which combine with single molecules to form a nearly perfect filling of the plane (see picture).

Room-temperature electronic template effect of the SmSi(111)-8x2 interface for self-alignment of organic molecules.

This work describes an innovative concept for the development of organized molecular systems based on the template effect of the pre-structured semi-conductive SmSi(111) interface. This substrate is selected because Sm deposition in the submonolayer range leads to a 8x2-reconstruction, which is a well-defined one-dimensional semi-metallic structure. Adsorption of aromatic molecules [1,4-di-(9-ethynyltriptycenyl)-benzene] on SmSi(111)- 8x2 and Si(111)-7x7 interfaces is investigated by scanning tunneling microscopy (STM) at room temperature. Density functional theory (DFT) and semi-empirical (ASED+) calculations define the nature of the molecular adsorption sites of the target molecule on SmSi as well as their self-alignment on this interface. Experimental data and theoretical results are in good agreement.