B. Hammer

Chiral recognition in dimerization of adsorbed cysteine observed by scanning tunnelling microscopy

Stereochemistry plays a central role in controlling molecular recognition and interaction: the chemical and biological properties of molecules depend not only on the nature of their constituent atoms but also on how these atoms are positioned in space. Chiral specificity is consequently fundamental in chemical biology and pharmacology and has accordingly been widely studied. Advances in scanning probe microscopies now make it possible to probe chiral phenomena at surfaces at the molecular level. These methods have been used to determine the chirality of adsorbed molecules, and to provide direct evidence for chiral discrimination in molecular interactions and the spontaneous resolution of adsorbates into extended enantiomerically pure overlayers. Here we report scanning tunnelling microscopy studies of cysteine adsorbed to a (110) gold surface, which show that molecular pairs formed from a racemic mixture of this naturally occurring amino acid are exclusively homochiral, and that their binding to the gold surface is associated with local surface restructuring. Density-functional theory calculations indicate that the chiral specificity of the dimer formation process is driven by the optimization of three bonds on each cysteine molecule. These findings thus provide a clear molecular-level illustration of the well known three-point contact model for chiral recognition in a simple bimolecular system.

Adsorption of O2 and oxidation of CO at Au nanoparticles supported by TiO2(110)

Density functional theory calculations are performed for the adsorption of O2, coadsorption of CO, and the CO+O2 reaction at the interfacial perimeter of nanoparticles supported by rutile TiO2(110). Both stoichiometric and reduced TiO2 surfaces are considered, with various relative arrangements of the supported Au particles with respect to the substrate vacancies. Rather stable binding configurations are found for the O2 adsorbed either at the trough Ti atoms or leaning against the Au particles. The presence of a supported Au particle strongly stabilizes the adsorption of O2. A sizable electronic charge transfer from the Au to the O2 is found together with a concomitant electronic polarization of the support meaning that the substrate is mediating the charge transfer. The O2 attains two different charge states, with either one or two surplus electrons depending on the precise O2 adsorption site at or in front of the Au particle. From the least charged state, the O2 can react with CO adsorbed at the edge sites of the Au particles leading to the formation of CO2 with very low (approximately 0.15 eV) energy barriers.

Adsorption, diffusion, and dissociation of molecular oxygen at defected TiO2(110): A density functional theory study

The properties of reduced rutile TiO2(110) surfaces, as well as the adsorption, diffusion, and dissociation of molecular oxygen are investigated by means of density functional theory. The O2 molecule is found to bind strongly to bridging oxygen vacancies, attaining a molecular state with an expanded O-O bond of 1.44 A. The molecular oxygen also binds (with somewhat shortened bond lengths) to the fivefold coordinated Ti atoms in the troughs between the bridging oxygen rows, but only when vacancies are present somewhere in the surface. In all cases, the magnetic moment of O2 is lost upon adsorption. The expanded bond lengths reveal together with inspection of electron density and electronic density of state plots that charging of the adsorbed molecular oxygen is of key importance in forming the adsorption bond. The processes of O2 diffusion from a vacancy to a trough and O2 dissociation at a vacancy are both hindered by relative large barriers. However, we find that the presence of neighboring vacancies can strongly affect the ability of O2 to dissociate. The implications of this in connection with diffusion of the bridging oxygen vacancies are discussed.

Adsorption properties versus oxidation states of rutile TiO2(110)

Using density functional theory we have studied the adsorption properties of different atoms and molecules deposited on a stoichiometric, reduced, and oxidized rutile TiO(2)(110) surface. Depending on the oxidation state of the surface, electrons can flow from or to the substrate and, therefore, negatively or positively charged species are expected. In particular, we have found that a charge transfer process from or to the surface always occurs for highly electronegative or highly electropositive species, respectively. For atoms or molecules with intermediate electron affinity, the direction of the charge flow depends on the oxidation state of the rutile surface and on the adsorption site. Generally, the charging effect leads to more stable complexes. However, the increase in the binding energy of the adsorbates is highly dependent on the electronic states of the surface prior to the adsorption event. In this work we have analyzed in details these mechanisms and we have also established a direct correlation between the enhanced binding energy of the adsorbates and the induced gap states.

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.

Accelerating atomic structure search with cluster regularization

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

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.