A. Morgante

X-ray Diffraction and Computation Yield the Structure of Alkanethiols on Gold(111)

The structure of self-assembled monolayers (SAMs) of long-chain alkyl sulfides on gold(111) has been resolved by density functional theory–based molecular dynamics simulations and grazing incidence x-ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur-gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies (which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.

Zwitterionic self-assembly of l-methionine nanogratings on the Ag(111) surface

The engineering of complex architectures from functional molecules on surfaces provides new pathways to control matter at the nanoscale. In this article, we present a combined study addressing the self-assembly of the amino acid l-methionine on Ag(111). Scanning tunneling microscopy data reveal spontaneous ordering in extended molecular chains oriented along high-symmetry substrate directions. At intermediate coverages, regular biomolecular gratings evolve whose periodicity can be tuned at the nanometer scale by varying the methionine surface concentration. Their characteristics and stability were confirmed by helium atomic scattering. X-ray photoemission spectroscopy and high-resolution scanning tunneling microscopy data reveal that the l-methionine chaining is mediated by zwitterionic coupling, accounting for both lateral links and molecular dimerization. This methionine molecular recognition scheme is reminiscent of sheet structures in amino acid crystals and was corroborated by molecular mechanics calculations. Our findings suggest that zwitterionic assembly of amino acids represents a general construction motif to achieve biomolecular nanoarchitectures on surfaces.

Relating Energy Level Alignment and Amine-Linked Single Molecule Junction Conductance

Using photoemission spectroscopy, we determine the relationship between electronic energy level alignment at a metal-molecule interface and single-molecule junction transport data. We measure the position of the highest occupied molecular orbital (HOMO) relative to the Au metal Fermi level for three 1,4-benzenediamine derivatives on Au(111) and Au(110) with ultraviolet and resonant X-ray photoemission spectroscopy. We compare these results to scanning tunnelling microscope-based break-junction measurements of single molecule conductance and to first-principles calculations. We find that the energy difference between the HOMO and Fermi level for the three molecules adsorbed on Au(111) correlate well with changes in conductance and agree well with quasiparticle energies computed from first-principles calculations incorporating self-energy corrections. On the Au(110) that presents Au atoms with lower-coordination, critical in break-junction conductance measurements, we see that the HOMO level shifts further from the Fermi level. These results provide the first direct comparison of spectroscopic energy level alignment measurements with single molecule junction transport data.

High resolution X-ray photoelectron spectroscopy of L-cysteine self-assembled films

The increasing demand for heterogeneous materials prompts the interest for the physics and chemistry of organic–inorganic interfaces. Within this field of interest we have investigated the electronic states of L-cysteine (Cys) adsorbed on Au(111) from aqueous solution with synchrotron-based, high resolution X-ray photoemission spectroscopy. The analysis of the S 2p core level region in pristine samples prepared with purified Cys indicates that Cys adsorbs on gold as a thiolate. The absence of a signal related to physisorbed sulfur indicates that Cys forms a monomolecular layer. The high resolution allowed us to resolve two components in the C 1s spectral region related to carboxyl. The comparative analysis of C 1s, N 1s and O 1s core level regions indicates the presence of the neutral and ionic form for both the carboxyl and the amine groups. From the quantitative analysis of the C 1s and N 1s data we can infer that the zwitterionic form is the prevalent one, with a ratio of zwitterionic to neutral molecules of 3∶1. This value is quite different from that in the deposition solution. Prolonged exposure to the X-ray beam and thermal annealing induce the formation of atomic sulfur through S–C bond breaking and molecular fragment desorption. This response to X-ray irradiation differs from the results recently reported on long chain alkanethiols.

Spectromicroscopy of single and multilayer graphene supported by a weakly interacting substrate

We report measurements of the electronic structure and surface morphology of exfoliated graphene on an insulating substrate using angle-resolved photoemission and low-energy electron diffraction. Our results show that, although exfoliated graphene is microscopically corrugated, the valence band retains a massless fermionic dispersion with a Fermi velocity of

Corrugation in Exfoliated Graphene: An Electron Microscopy and Diffraction Study

\ensuremath{\sim}{10}^{6}\text{ }\text{m}/\text{s}

A new model for atom–atom potentials

. We observe a close relationship between the morphology and electronic structure, which suggests that controlling the interaction between graphene and the supporting substrate is essential for graphene device applications.

Probing the mechanism for graphene nanoribbon formation on gold surfaces through X-ray spectroscopy

Low-energy electron microscopy and microprobe diffraction are used to image and characterize corrugation in SiO(2)-supported and suspended exfoliated graphene at nanometer length scales. Diffraction line-shape analysis reveals quantitative differences in surface roughness on length scales below 20 nm which depend on film thickness and interaction with the substrate. Corrugation decreases with increasing film thickness, reflecting the increased stiffness of multilayer films. Specifically, single-layer graphene shows a markedly larger short-range roughness than multilayer graphene. Due to the absence of interactions with the substrate, suspended graphene displays a smoother morphology and texture than supported graphene. A specific feature of suspended single-layer films is the dependence of corrugation on both adsorbate load and temperature, which is manifested by variations in the diffraction line shape. The effects of both intrinsic and extrinsic corrugation factors are discussed.

Quantifying through-space charge transfer dynamics in π-coupled molecular systems

A new model potential for van der Waals atomic pairs is proposed and shown to be in excellent agreement with ab initio calculations and experimental potentials. The model allows the potential energy of a given pair to be estimated with good accuracy from ab initio density functional calculations of the free‐atom electron densities.

High resolution XPS of the S?2p core level region of the L-cysteine/gold interface

We studied the formation of graphene nanoribbons (GNRs) via the self-assembly of 10,10′-dibromo-9,9′-bianthryl precursor molecules on gold surfaces with different synchrotron spectroscopies. Through X-ray photoemission spectroscopy core-level shifts, we followed each step of the synthetic process, and could show that the Br–C bonds of the precursors cleave at temperatures as low as 100 °C on both Au(111) and Au(110). We established that the resulting radicals bind to Au, forming Au–C and Au–Br bonds. We show that the polymerization of the precursors follows Br desorption from Au, suggesting that the presence of halogens is the limiting factor in this step. Finally, with angle-resolved ultraviolet photoemission spectroscopy and density functional theory we show that the GNR/Au interaction results in an upshift of the Shockley surface state of Au(111) by ∼0.14 eV, together with an increased electron effective mass.