Thiolate versus Selenolate: Structure, Stability, and Charge Transfer Properties.

Selenolate is considered as an alternative to thiolate to serve as a headgroup mediating the formation of self-assembled monolayers (SAMs) on coinage metal substrates. There are, however, ongoing vivid discussions regarding the advantages and disadvantages of these anchor groups, regarding, in particular, the energetics of the headgroup-substrate interface and their efficiency in terms of charge transport/transfer. Here we introduce a well-defined model system of 6-cyanonaphthalene-2-thiolate and -selenolate SAMs on Au(111) to resolve these controversies. The exact structural arrangements in both types of SAMs are somewhat different, suggesting a better SAM-building ability in the case of selenolates. At the same time, both types of SAMs have similar packing densities and molecular orientations. This permitted reliable competitive exchange and ion-beam-induced desorption experiments which provided unequivocal evidence for a stronger bonding of selenolates to the substrate as compared to the thiolates. Regardless of this difference, the dynamic charge transfer properties of the thiolate- and selenolate-based adsorbates were found to be nearly identical, as determined by the core-hole-clock approach, which is explained by a redistribution of electron density along the molecular framework, compensating the difference in the substrate-headgroup bond strength.

How surface bonding and repulsive interactions cause phase transformations: ordering of a prototype macrocyclic compound on Ag(111).

We investigated the surface bonding and ordering of free-base porphine (2H-P), the parent compound of all porphyrins, on a smooth noble metal support. Our multitechnique investigation reveals a surprisingly rich and complex behavior, including intramolecular proton switching, repulsive intermolecular interactions, and density-driven phase transformations. For small concentrations, molecular-level observations using low-temperature scanning tunneling microscopy clearly show the operation of repulsive interactions between 2H-P molecules in direct contact with the employed Ag(111) surface, preventing the formation of islands. An increase of the molecular coverage results in a continuous decrease of the average intermolecular distance, correlated with multiple phase transformations: the system evolves from an isotropic, gas-like configuration via a fluid-like phase to a crystalline structure, which finally gives way to a disordered layer. Herein, considerable site-specific molecule-substrate interactions, favoring an exclusive adsorption on bridge positions of the Ag(111) lattice, play an important role. Accordingly, the 2D assembly of 2H-P/Ag(111) layers is dictated by the balance between adsorption energy maximization while retaining a single adsorption site counteracted by the repulsive molecule-molecule interactions. The long-range repulsion is associated with a charge redistribution at the 2H-P/Ag(111) interface comprising a partial filling of the lowest unoccupied molecular orbital, resulting in long-range electrostatic interactions between the adsorbates. Indeed, 2H-P molecules in the second layer that are electronically only weakly coupled to the Ag substrate show no repulsive behavior, but form dense-packed islands.

Chemical transformations drive complex self-assembly of uracil on close-packed coinage metal surfaces.

We address the interplay of adsorption, chemical nature, and self-assembly of uracil on the Ag(111) and Cu(111) surfaces as a function of molecular coverage (0.3 to 1 monolayer) and temperature. We find that both metal surfaces act as templates and the Cu(111) surface acts additionally as a catalyst for the resulting self-assembled structures. With a combination of STM, synchrotron XPS, and NEXAFS studies, we unravel a distinct polymorphism on Cu(111), in stark contrast to what is observed for the case of uracil on the more inert Ag(111) surface. On Ag(111) uracil adsorbs flat and intact and forms close-packed two-dimensional islands. The self-assembly is driven by stable hydrogen-bonded dimers with poor two-dimensional order. On Cu(111) complex structures are observed exhibiting, in addition, a strong annealing temperature dependence. We determine the corresponding structural transformations to be driven by gradual deprotonation of the uracil molecules. Our XPS study reveals unambiguously the tautomeric signature of uracil in the contact layer and on Cu(111) the molecule's deprotonation sites. The metal-mediated deprotonation of uracil and the subsequent electron localization in the molecule determine important biological reactions. Our data show a dependence between molecular coverage and molecule-metal interaction on Cu(111), as the molecules tilt at higher coverages in order to accommodate a higher packing density. After deprotonation of both uracil N atoms, we observe an adsorption geometry that can be understood as coordinative anchoring with a significant charge redistribution in the molecule. DFT calculations are employed to analyze the surface bonding and accurately describe the pertaining electronic structure.

Orbital-Symmetry-Dependent Electron Transfer through Molecules Assembled on Metal Substrates.

Femtosecond charge-transfer dynamics in self-assembled monolayers of cyano-terminated ethane-thiolate on gold substrates was investigated with the core hole clock method. By exploiting symmetry selection rules rather than energetic selection, electrons from the nitrogen K-shell are state-selectively excited into the two symmetry-split π* orbitals of the cyano end group with X-ray photons of well-defined polarization. The charge-transfer times from these temporarily occupied orbitals to the metal substrate differ significantly. Theoretical calculations show that these two π* orbitals extend differently onto the alkane backbone and the anchoring sulfur atom, thus causing the observed dependence of the electron-transfer dynamics on the symmetry of the orbital.

PNA-PEG modified silicon platforms as functional bio-interfaces for applications in DNA microarrays and biosensors.

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). The long PEG(45) spacer was used to distance the PNA probe from the surface and to minimize undesirable nonspecific adsorption of DNA analyte. The short PEG(12) "back-filler" was used to provide additional passivation of the surface against nonspecific DNA adsorption. X-ray photoelectron spectroscopic (XPS) analysis near the C 1s and N 1s ionization edges was done to characterize chemical groups formed in the near-surface region, which confirmed binding of PEG and PNA to the phosphonate and silane films. XPS also indicated that additional PEG chains were tethered to the surface during the back-filling process. Fluorescence hybridization experiments were carried out with complementary and noncDNA strands; both phosphonate and siloxane biofunctional surfaces were effective for hybridization of cDNA strands and significantly reduced nonspecific adsorption of the analyte. Spatial patterns were prepared by polydimethylsiloxane (PDMS) micromolding on the PNA-functionalized surfaces; selective hybridization of fluorescently labeled DNA was shown at the PNA functionalized regions, and physisorption at the probe-less PEG-functionalized regions was dramatically reduced. These results show that PNA-PEG derivatized phosphonate monolayers hold promise for the smooth integration of device surface chemistry with semiconductor technology for the fabrication of DNA biosensors. In addition, our results confirm that PNA-PEG derivatized self-assembled carboxyalkylsiloxane films are promising substrates for DNA microarray applications.