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1.  Influence of the solvent on the stability of bis(terpyridine) structures on graphite 
Summary
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.
doi:10.3762/bjnano.4.29
PMCID: PMC3678400  PMID: 23766949
computer simulations; energy related; force-field calculations; nanomaterials; solvation
2.  Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly 
Summary
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.
doi:10.3762/bjnano.2.46
PMCID: PMC3190612  PMID: 22003448
oligopyridines; self-assembled monolayer; STM
3.  Simulation of bonding effects in HRTEM images of light element materials 
Summary
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.
doi:10.3762/bjnano.2.45
PMCID: PMC3190611  PMID: 22003447
chemical bonding; DFT; graphene; HRTEM
4.  Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001) 
Summary
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.
doi:10.3762/bjnano.2.42
PMCID: PMC3190608  PMID: 22003444
graphene film; intermolecular interaction; large organic molecules; substrate–adsorbate interaction; supramolecular structure

Results 1-4 (4)