Effects of non-local exchange on core level shifts for gas-phase and adsorbed molecules

Density functional theory calculations are often used to interpret experimental shifts in core level binding energies. Calculations based on gradient-corrected (GC) exchange-correlation functionals are known to reproduce measured core level shifts (CLS) of isolated molecules and metal surfaces with reasonable accuracy. In the present study, we discuss a series of examples where the shifts calculated within a GC-functional significantly deviate from the experimental values, namely the CLS of C 1s in ethyl trifluoroacetate, Pd 3d in PdO and the O 1s shift for CO adsorbed on PdO(101). The deviations are traced to effects of the electronic self-interaction error with GC-functionals and substantially better agreements between calculated and measured CLS are obtained when a fraction of exact exchange is used in the exchange-correlation functional

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

Kühnle A, Linderoth TR, Hammer B, Besenbacher F. Chiral recognition in dimerization of adsorbed cysteine observed by scanning tunnelling microscopy. Nature. 2002;415(6874):891-893.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(1,2) 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(3-5), and to provide direct evidence for chiral discrimination in molecular interactions(6) and the spontaneous resolution of adsorbates into extended enantiomerically pure overlayers(3,7-9). 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(10) 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(11,12) for chiral recognition in a simple bimolecular system

Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on Au(111)

© 2014 American Chemical Society. The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS•Au(0)S•R or involves direct binding of RS• to face-centered-cubic or hexagonal-close-packed sites. Binding as RS• produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS• also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs

Theoretical Characterization of Cyclic Thiolated Copper, Silver, and Gold Clusters

Density functional theory calculations are used to study structural, electronic, and vibrational properties of cyclic (MeSM)(x) clusters where MeS is methylthiolate and M is copper, silver, or gold. The clusters show a flexible bond motif where monocyclic rings, catenanes, and helix structures compete in energy. In the investigated series, the copper-sulfur bond is found to be the strongest metal-sulfur bond, followed by gold-sulfur and silver-sulfur. Analysis of the bond character reveals that Cu-S is the most polar bond, whereas Au-S is mainly of covalent type. Vibrational analysis shows characteristic metal-sulfur stretch vibrations for each noble metal

Charging of atoms, clusters, and molecules on metal-supported oxides: A general and long-ranged phenomenon

The density-functional theory is used to investigate the adsorption of Au atoms, Au clusters, and NO2 molecules on transition-metal-supported oxides. As compared to unsupported oxides, the adsorbates on supported oxide films are charged and experience a higher adsorption energy. The origin of the effect is explored by considering two different oxides (MgO and Al2O3) and a range of supporting metals. Moreover, the limits of the enhancement are probed by explicit calculations for thick MgO films and low coverage. The long-range character of the phenomenon is attributed to electrostatic polarization. The absolute strength depends on several contributions and their relative importance changes with system composition

Z. Phys. D 40, 469–471 (1997) Hydrogen induced melting of Palladium clusters

Abstract. To investigate the effect of adsorbates on structural transitions in small palladium aggregates, we have performed molecular dynamics simulations of cluster “melting” in presence of atomic hydrogen. Intriguing questions are how the exposure to hydrogen modifies the metal-metal interaction, and whether hydrogen could lower the onset of melting. Various structural and caloric methods were used to capture signatures of melting. We present results for the bare icosahedral Pd55 cluster and also Pd55 exposed to different amounts of hydrogen. Our results indicate that the melting transition is significantly lowered as hydrogen adsorbs on the cluster, and that the decrease in melting temperature depends sensitively on the hydrogen loading. PACS: 36.40.+Ei During the last few years, considerable theoretical effort ha

Assessing the validity of theoretical results

We present recent theoretical results for the V3 and Au4 clusters. Calculations of the V3 doublet system indicate that the 6-311+G(d) basis set is sufficiently flexible to provide reliable minimum energy structures and vibrational frequencies, that these structures and frequencies are insensitive to spin contamination of the wave function when the BPW91 functional is used, and that changing to the B3LYP functional may result in very different structures and frequencies. A computationally less expensive scalar relativistic treatment of Au4 clusters gives structural properties that are in good agreement with those obtained using a four-component method