Selection of conformational states in surface self-assembly for a molecule with eight possible pairs of surface enantiomers.

Self-assembly of a molecule with many distinct conformational states, resulting in eight possible pairs of surface enantiomers, is investigated on a Au(111) surface under UHV conditions. The complex molecule is equipped with alkyl and carboxyl moieties to promote controlled self-assembly of lamellae structures. From statistical analysis of Scanning Tunnelling Microscopy (STM) data we observe a clear selection of specific conformational states after self-assembly. Using Density Functional Theory (DFT) calculations we rationalise how this selection is correlated to the orientation of the alkyl moieties in mirror-image domains of the lamellae structures, leading to selection of three out of the eight possible enantiomeric pairs.

Structure and role of metal clusters in a metal-organic coordination network determined by density functional theory.

We present a comprehensive theoretical investigation of the structures formed by self-assembly of tetrahydroxybenzene (THB)-derivatives on Cu(111). The THB molecule is known to dehydrogenate completely during annealing, forming a reactive radical which assembles into a close-packed structure or a porous metal-coordinated network depending on the coverage of the system. Here, we present details on how the structures are determined by density functional theory calculations, using scanning tunneling microscopy-derived information on the periodicity. The porous network is based on adatom trimers. By analysing the charge distribution of the structure, it is found that this unusual coordination motif is preferred because it simultaneously provides a good coordination of all oxygen atoms and allows for the formation of a two-dimensional network on the surface.

Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch.

Supra-molecular self-assembly on surfaces often involves molecular conformational flexibility which may act to enrich the variation and complexity of the structures formed. However, systematic and explicit investigations of how molecular conformational states are selected in surface self-assembly processes are relatively scarce. Here, we use a combination of high-resolution scanning tunneling microscopy and Density Functional Theory (DFT) calculations to investigate self-assembly for a custom-designed molecule capable of assuming eight distinct surface conformations (four enantiomeric pairs). The conformations result from binary positions of n = 3 naphtalene units on a linear oligo(naphthylene-ethynylene) backbone. On Au(111), inter-molecular interactions involving carboxyl and bulky tert-butyl-phenyl functional groups induce the molecules to form two ordered phases with brick-wall and lamella structure, respectively. These structures each involve molecules in two conformational states, and there is a clear separation between the conformers involved in the two types of structures. On Cu(111), individual molecules isolated by carboxylate-substrate binding show a distribution involving all possible conformational states. Together these observations imply selection and adaptation of conformational states upon molecular self-assembly. From DFT modeling and statistical analysis of the molecular conformations, the observed selection of conformational states is attributed to steric interaction between the naphthalene units. The present study enhances our understanding of how ordering and selection of molecular conformations is controlled by intermolecular interactions in a complex situation with many distinct conformational states for the participating molecules.

Bicomponent hydrogen-bonded nanostructures formed by two complementary molecular Landers on Au(111).

The co-adsorption of two molecular Landers equipped with functional groups capable of forming a complementary triple hydrogen-bonding motif is investigated with scanning tunneling microscopy and molecular mechanics calculations. Surprisingly, the anticipated complementary motif is not realised in 2-D terrace structures, but is observed in 1-D structures at step edges where molecular conformational flexibility is confined.

Growth of unidirectional molecular rows of cysteine on Au(110)-(1 x 2) driven by adsorbate-induced surface rearrangements.

Using scanning tunneling microscopy we have studied the nucleation and growth of unidirectional molecular rows upon adsorption of the amino acid cysteine onto the anisotropic Au(110)-(1 x 2) surface under ultrahigh vacuum conditions. By modeling a large variety of possible molecular adsorption geometries using density-functional theory calculations, we find that in the optimum, lowest energy configuration, no significant intermolecular interactions exist along the growth direction. Instead the driving force for formation of the unidirectional molecular rows is an adsorbate-induced surface rearrangement, providing favorable adsorption sites for the molecules.

Long jumps in the surface diffusion of large molecules.

We have studied the diffusion of the two organic molecules DC and HtBDC on the Cu(110) surface by scanning tunneling microscopy. Surprisingly, we find that long jumps, spanning multiple lattice spacings, play a dominating role in the diffusion of these molecules--the root-mean-square jump lengths are as large as 3.9 and 6.8 lattice spacings, respectively. The presence of long jumps is revealed by a new and simple method of analysis, which is tested by kinetic Monte Carlo simulations.