Influence of the solvent on the stability of bis(terpyridine) structures on graphite.

The effect of solvation on the adsorption of organic molecules on graphite at room temperature has been addressed with force-field molecular dynamics simulations. As a model system, the solvation of a bis(terpyridine) isomer in water and 1,2,4-trichlorobenzene was studied with an explicit solvation model. The inclusion of solvation has a noticeable effect on adsorption energies. Although the results of the various considered force fields differ quite significantly, they all agree that the adsorption of BTP from the TCB solvent is almost thermoneutral. The substrate simply acts as a template to allow a planar arrangement of the network, which is stabilized by the intermolecular interaction. Using an atomic thermodynamics approach, the order of the stability of various network structures as a function of the chemical potential is derived yielding a sequence in agreement with the experiment.

Oxidation of an organic adlayer: a bird's eye view.

The reaction of O(2) with an adlayer of the oligopyridine 2-phenyl-4,6-bis(6-(pyridine-2-yl)-4-(pyridine-4-yl)-pyridine-2-yl)pyrimidine (2,4'-BTP), adsorbed on the (111) surfaces of silver and gold and on HOPG--which can be considered as a model system for inorganic|organic contacts--was investigated by fast scanning tunneling microscopy (video STM) and dispersion corrected density functional theory (DFT-D) calculations. Only on Ag(111), oxidation of the 2,4'-BTP adlayer was observed, which is related to the fact that under the experimental conditions O(2) adsorbs dissociatively on this surface leading to reactive O adatoms, but not on Au(111) or HOPG . There is a distinct regiospecifity of the oxidation reaction caused by intermolecular interactions. In addition, the oxidation leads to a chiral ordering. The relevance of these findings for reactions involving organic monolayers is discussed.

Intermolecular vs molecule-substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001).

The competition between intermolecular interactions and long-range lateral variations in the substrate-adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results.

Simulation of bonding effects in HRTEM images of light element materials.

The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) [1-2]. This approach accounts for the fact that electrons in the specimen are redistributed according to their local chemical environment. This influences the scattering process and alters the absolute and relative contrast in the final image. For light element materials with well defined geometry, such as graphene and hexagonal boron nitride monolayers, the DFT based simulation scheme turned out to be necessary to prevent misinterpretation of weak signals, such as the identification of nitrogen substitutions in a graphene network. Furthermore, this implies that the HRTEM image does not only contain structural information (atom positions and atomic numbers). Instead, information on the electron charge distribution can be gained in addition.In order to produce meaningful results, the new input parameters need to be chosen carefully. Here we present details of the simulation process and discuss the influence of the main parameters on the final result. Furthermore we apply the simulation scheme to three model systems: A single atom boron and a single atom oxygen substitution in graphene and an oxygen adatom on graphene.

Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly.

The position of the peripheral nitrogen atoms in bis(terpyridine)-derived oligopyridines (BTPs) has a strong impact on their self-assembly behavior at the liquid/HOPG (highly oriented pyrolytic graphite) interface. The intermolecular hydrogen bonding interactions in these peripheral pyridine units show specific 2D structures for each BTP isomer. From nine possible constitutional isomers only four have been described in the literature. The synthesis and self-assembling behavior of an additional isomer is presented here, but the remaining four members of the series are synthetically inaccessible. The self-assembling properties of three of the missing four BTP isomers can be mimicked by making use of the energetically preferred N-C-C-N transoid conformation between 2,2'-bipyridine subunits in a new class of so-called septipyridines. The structures are investigated by scanning tunneling microscopy (STM) and a combination of force-field and first-principles electronic structure calculations.

Hierarchical interactions and their influence upon the adsorption of organic molecules on a graphene film.

The competition between intermolecular interactions and lateral variations in the molecule-substrate interactions has been studied by scanning tunneling microscopy (STM), comparing the phase formation of (sub)monolayers of the organic molecule 2,4'-BTP on buckled graphene/Ru(0001) and Ag(111) oriented thin films on Ru(0001). On the Ag films, the molecules form a densely packed 2D structure, while on graphene/Ru(0001), only the areas between the maxima are populated. The findings are rationalized by a high corrugation in the adsorption potential for 2,4'-BTP molecules on graphene/Ru(0001). These findings are supported by temperature programmed desorption (TPD) experiments and theoretical results.

Experimental analysis of charge redistribution due to chemical bonding by high-resolution transmission electron microscopy.

The electronic charge density distribution or the electrostatic atomic potential of a solid or molecule contains information not only on the atomic structure, but also on the electronic properties, such as the nature of the chemical bonds or the degree of ionization of atoms. However, the redistribution of charge due to chemical bonding is small compared with the total charge density, and therefore difficult to measure. Here, we demonstrate an experimental analysis of charge redistribution due to chemical bonding by means of high-resolution transmission electron microscopy (HRTEM). We analyse charge transfer on the single-atom level for nitrogen-substitution point defects in graphene, and confirm the ionicity of single-layer hexagonal boron nitride. Our combination of HRTEM experiments and first-principles electronic structure calculations opens a new way to investigate electronic configurations of point defects, other non-periodic arrangements or nanoscale objects that cannot be studied by an electron or X-ray diffraction analysis.

Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study.

Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations.