Energetics and Kinetics of the Physisorption of Hydrocarbons on Au(111)

Towards supramolecular engineering of functional nanomaterials: pre-programming multi-component 2D self-assembly at solid-liquid interfaces

Materials with a pre-programmed order at the supramolecular level can be engineered with a sub-nanometer precision making use of reversible non- covalent interactions. The intrinsic ability of supramolecular materials to recognize and exchange their constituents makes them constitutionally dynamic materials. The tailoring of the materials properties relies on the full control over the self-assembly behavior of molecular modules exposing recognition sites and incorporating functional units. In this review we focus on three classes of weak-interactions to form complex 2D architectures starting from properly designed molecular modules: van der Waals, metallo-ligand and hydrogen bonding. Scanning tunneling microscopy studies will provide evidence with a sub-nanometer resolution, on the formation of responsive multicomponent architectures with controlled geometries and properties. Such endeavor enriches the scientist capability of generating more and more complex smart materials featuring controlled functions and unprecedented properties.

On the thermodynamic stability of alpha,omega-alkanedithiols self-assembled monolayers on unreconstructed and reconstructed Au(111)

A comparative study on the thermodynamic stability of the lying down (LD) and standing up (SU) phases of alpha,omega-butanedithiol (BDT) on unreconstructed (U) and on reconstructed (R) Au(111) surfaces is presented. The R surface is made of dithiol-Au adatom units. Density functional calculations (DFT) allow the estimation of the adsorption energy of the LD and SU BDT phases on both substrates. Surface free energies based on the DFT calculations show the coverage of the clean Au(111) surface by the LD phase, and the LD to SU phase transition as the chemical potential of the BDT molecule is increased. The LD and SU phases are more stable on R than on U substrates, suggesting that the Au(111) surface should reconstruct upon BDT adsorption. The stability analysis is extended to longer alpha,omega-dithiols. Results reveal that the LD to SU phase transition is favored as the hydrocarbon chain length of the dithiol molecule is increased. Changes in the hydrogen pressure affect the formation of the LD phase, while they have only minor effects on the LD to SU phase transitions. Our calculations explain the influence of the number of carbon atoms in the hydrocarbon chains, hydrogen pressure and dithiol pressure (or concentration) on dithiol adsorption, and phase transitions. This information is relevant to control the coverage, reactivity, and surface chemistry of the alpha,omega-dithiol self-assembled monolayers on Au surfaces.

A density functional for sparse matter

Sparse matter is abundant and has both strong local bonds and weak nonbonding forces, in particular nonlocal van der Waals (vdW) forces between atoms separated by empty space. It encompasses a broad spectrum of systems, like soft matter, adsorption systems and biostructures. Density-functional theory (DFT), long since proven successful for dense matter, seems now to have come to a point, where useful extensions to sparse matter are available. In particular, a functional form, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401; Thonhauser et al 2007 Phys. Rev. B 76 125112), has been proposed for the nonlocal correlations between electrons and applied to various relevant molecules and materials, including to those layered systems like graphite, boron nitride and molybdenum sulfide, to dimers of benzene, polycyclic aromatic hydrocarbons (PAHs), doped benzene, cytosine and DNA base pairs, to nonbonding forces in molecules, to adsorbed molecules, like benzene, naphthalene, phenol and adenine on graphite, alumina and metals, to polymer and carbon nanotube (CNT) crystals, and hydrogen storage in graphite and metal-organic frameworks (MOFs), and to the structure of DNA and of DNA with intercalators. Comparison with results from wavefunction calculations for the smaller systems and with experimental data for the extended ones show the vdW-DF path to be promising. This could have great ramifications.

Accelerated molecular dynamics of temperature-programed desorption

We use accelerated molecular dynamics to simulate temperature-programed desorption (TPD) of n-pentane from the basal plane of graphite in the first atomistic simulations to probe TPD over laboratory time scales. Although the simulated TPD spectra agree with experiment, a detailed analysis reveals underlying kinetic phenomena that contrast the standard experimental interpretation and opens new possibilities for understanding molecular kinetics at solid surfaces.

High resolution radially symmetric nanostructures from simultaneous electron beam induced etching and deposition

Electron beam induced etching (EBIE) and deposition (EBID) are promising fabrication techniques in which an electron beam is used to dissociate surface-adsorbed precursor molecules to achieve etching or deposition. Spatial resolution is normally limited by the electron flux distribution at the substrate surface. Here we present simultaneous EBIE and EBID (EBIED) as a method for surpassing this resolution limit by using adsorbate depletion to induce etching and deposition in adjacent regions within the electron flux profile. Our simulation results indicate the possibility of growth control of radially symmetric nanostructures at the sub-1 nm length scale on bulk substrates. The technique is well suited to the fabrication of ring-shaped nanostructures such as those employed in plasmonics, sensing devices, magneto-optics and magnetoelectronics.

Competition and coadsorption of di-acids and carboxylic acid solvents on HOPG

The self-assemblies of di-acids HOOC-(CH(2))(n)-COOH (n = 20, 18, 16, 14, 12, 10) in three solvents hexanoic acid, octanoic acid, and decanoic acid on highly oriented pyrolytic graphite (HOPG) were studied with scanning tunneling microscopy (STM). In the solvent hexanoic acid, solvent molecules coadsorb with HOOC-(CH(2))(n)-COOH (n = 20, 18, 16) via formation of hydrogen bonds. The solvent octanoic acid coadsorbs with HOOC-(CH(2))(n)-COOH (n = 20, 18). Decanoic acid only coadsorbs with HOOC-(CH(2))(20)-COOH. In each solvent, the trend of coadsorption between solvent molecules and di-acid molecules decreases with decreasing chain-length of di-acid molecules. These systematic investigations suggest that coadsorption of solvent molecules with di-acid solute molecules is mainly dependent on the relative hydrogen-bond densities in the formed monolayer. This is consistent with the maximization of adsorption heat of the self-assembled monolayers of di-acids dissolved in solvents of carboxylic acids.

Structures of 17,19-hexatriacontadiyne monolayers on Au(111) studied by infrared reflection absorption spectroscopy and scanning tunneling microscopy

The aggregation and reaction of 17,19-hexatriacontadiyne molecules are studied on a Au(111) surface. The molecular orientation and arrangement are elucidated by infrared reflection absorption spectroscopy (IRAS) and scanning tunneling microscopy (STM). A vapor-deposited monolayer and a multilayered film formed by adsorption from the solution provide IRA spectra with bands due to the antisymmetric and symmetric stretching of methylenes in the gauche conformation. After the adsorbed film is rinsed with the solvent, however, the spectrum loses the gauche bands and is characterized by the enhanced C-H(distal) and C-H(proximal) stretching bands, which means that all-trans molecules are laid flat. Only STM images for the rinsed film display columnar structures on the herringbones of the reconstructed Au(111) surface; the alkyl chain direction is found to be parallel to the Au atom row. The results indicate that an ordered monolayer is formed first at the liquid-solid interface, and then, disordered overlayers with the gauche conformation are grown but removed by a rinse. Upon exposure to UV light, thus obtained monomer columns are converted into oligomers with flexible backbones and an increased gauche population in the alkyl chains, which resemble red phase polydiacetylenes in LB films.

n-alkanes on Pt(111) and on C(0001)∕Pt(111): Chain length dependence of kinetic desorption parameters

We have measured the desorption of seven small n-alkanes (C(N)H(2N+2), N=1-4,6,8,10) from the Pt(111) and C(0001) surfaces by temperature programed desorption. We compare these results to our recent study of the desorption kinetics of these molecules on MgO(100) [J. Chem. Phys. 122, 164708 (2005)]. There we showed an increase in the desorption preexponential factor by several orders of magnitude with increasing n-alkane chain length and a linear desorption energy scaling with a small y-intercept value. We suggest that the significant increase in desorption prefactor with chain length is not particular to the MgO(100) surface, but is a general effect for desorption of the small n-alkanes. This argument is supported by statistical mechanical arguments for the increase in the entropy gain of the molecules upon desorption. In this work, we demonstrate that this hypothesis holds true on both a metal surface and a graphite surface. We observe an increase in prefactor by five orders of magnitude over the range of n-alkane chain lengths studied here. On each surface, the desorption energies of the n-alkanes are found to increase linearly with the molecule chain length and have a small y-intercept value. Prior results of other groups have yielded a linear desorption energy scaling with chain length that has unphysically large y-intercept values. We demonstrate that by allowing the prefactor to increase according to our model, a reanalysis of their data resolves this y-intercept problem to some degree.

Accelerated molecular dynamics simulation of the thermal desorption of n-alkanes from the basal plane of graphite

We utilize accelerated molecular dynamics to simulate alkane desorption from the basal plane of graphite. Eight different molecules, ranging from n-pentane to n-hexadecane, are studied in the low coverage limit. Acceleration of the molecular dynamics simulations is achieved using two different methods: temperature acceleration and a compensating potential scheme. We find that the activation energy for desorption increases with increasing chain length. The desorption prefactor increases with chain length for molecules ranging from pentane to decane. This increase subsides and the value of the preexponential factor fluctuates about an apparently constant value for decane, dodecane, tetradecane, and hexadecane. These trends are consistent with data obtained in experimental temperature-programed desorption (TPD) studies. We explain the dependence of the preexponential factor on alkane chain length by examining conformational changes within the alkane molecules. For the shorter molecules, torsional motion is not activated over experimental temperature ranges. These molecules can be treated as rigid rods and their partial loss in translational and rotational entropies upon adsorption increases as chain length increases, leading to an increasing preexponential factor. At their typical TPD peak temperatures, torsions are activated in the longer adsorbed chain molecules to a significant extent which increases with increasing chain length, increasing the entropy of the adsorbed molecule. This increase counteracts the decrease in entropy due to a loss of translation and rotation, leading to a virtually constant prefactor.

The Nature of the Adsorption of Nucleobases on the Gold [111] Surface

Biochip technology is based on the immobilization of biological macromolecules on the surface of electronic devices. The biochemical properties of the immobilized molecules can be influenced to a large extent by the interaction with the inorganic surface. The interaction of DNA with the surface of gold, a metal commonly used in biochip technologies, is sequence dependent as the four nucleobases, adenine, thymine, cytosine, and guanine, interact to a different extent with the gold surface. The nature of nucleobase adsorption on the gold [111] surface has been investigated by performing density functional theory and post-Hartree-Fock calculations. It turns out that the interaction is dominated by dispersion forces and an appreciable degree of chemisorption is observed for adenine only. A set of Lennard-Jones parameters that describe the interaction was derived from the post-Hartree-Fock calculations. Classical molecular dynamics simulations of nucleobase monolayers based on these parameters are in remarkable agreement with the experiment and show that the interaction of the nucleobases with the gold surface is strongly modulated by base-base interactions and reaches a maximum when a full monolayer is formed.

Impact of molecular structure on the lubricant squeeze-out between curved surfaces with long range elasticity

The properties of butane (C4H10) lubricants confined between two approaching solids are investigated by a model that accounts for the curvature and elastic properties of the solid surfaces. We consider the linear n-butane and the branched isobutane. For the linear molecule, well defined molecular layers develop in the lubricant film when the width is of the order of a few atomic diameters. The branched isobutane forms more disordered structures which permit it to stay liquidlike at smaller surface separations. During squeezing the solvation forces show oscillations corresponding to the width of a molecule. At low speeds (<0.1 ms) the last layers of isobutane are squeezed out before those of n-butane. Since the (interfacial) squeezing velocity in most practical applications is very low when the lubricant layer has molecular thickness, one expects n-butane to be a better boundary lubricant than isobutane. With n-butane possessing a slightly lower viscosity at high pressures, our result refutes the view that squeeze-out should be harder for higher viscosities; on the other hand our results are consistent with wear experiments in which n-butane were shown to protect steel surfaces better than isobutane.

n-alkanes on MgO(100). I. Coverage-dependent desorption kinetics of n-butane

High-quality temperature-programmed desorption (TPD) measurements of n-butane from MgO(100) have been made for a large number of initial butane coverages (0-3.70 ML, ML-monolayers) and a wide range of heating ramp rates (0.3-10 K/s). We present a TPD analysis technique which allows the coverage-dependent desorption energy to be accurately determined by mathematical inversion of a TPD spectrum, assuming only that the preexponential factor (prefactor) is coverage independent. A variational method is used to determine the prefactor that minimizes the difference between a set of simulated TPD spectra and corresponding experimental data. The best fit for butane desorption from MgO is obtained with a prefactor of 10(15.7+/-1.6) s(-1). The desorption energy is 34.9+/-3.4 kJ/mol at 0.5-ML coverage, and varies with coverage approximately as Ed(theta)=34.5+0.566theta+8.37 exp(-theta/0.101). Simulations based on these results can accurately reproduce TPD experiments for submonolayer initial coverages over a wide range of heating ramp rates (0.3-10 K/s). Advantages and limitations of this method are discussed.

Interaction Model for the Adsorption of Organic Molecules on the Silver Surface

Adsorption of organics on a silver surface is simulated. An Embedded Atom Model is used for the metal, a standard force field for the organics, and a combination of the charge equilibration model and the Morse potential for their electrostatic and nonbonding interactions. The only adjustable parameters of this approach appear in the Morse potential. They are tuned to reproduce experimental and high level quantum chemical data. The adsorption energies of 13 molecules on the Ag(111) surface are obtained with an average error of less than 1 kcal mol(-1). The model should be transferable to molecules with the same chemical groups used in regressing the potential parameters when physisorption or weak chemisorption, i.e., no bond breaking, occur, and also to other Ag surfaces. When used to simulate perylene tetracarboxylic acid dianhydride (PTCDA) on Ag(111), correct geometry of mono- and multilayers are observed in molecular dynamics simulations at room temperature.

Preparation and structure of a low-density, flat-lying decanethiol monolayer from the densely packed, upright monolayer on gold

This study investigates the formation of low-density, flat-lying decanethiol chemisorbed on Au prepared by heating the surface covered with a densely packed, upright monolayer to a surface temperature above that of the onset of desorption. We determined conditions for preparing the low-density phase by observing the evolution of the photoemission spectrum as a function of the surface temperature using polarized ultraviolet light and by utilizing scanning tunneling microscopy. The preparation conditions were similar for single- and polycrystalline gold surfaces. Once the low-density decanethiol phase was formed, reflection absorption infrared spectroscopy was employed to determine the orientation of the carbon chain backbone with respect to the Au surface. The nature of the valance electronic structure for flat-lying decanethiol is described.

Direct observation of thiolate displacement reactions on Au(111): the role of physisorbed disulfides

Line-of-sight mass spectroscopy (LOSMS) has been used to study the displacement reaction of ( radical3x radical3)R30 degrees methylthiolate on Au(111) by butylthiolate. The reaction was carried out at room temperature and constant saturation coverage, by exposing the methylthiolate-covered surface to dibutyl disulfide gas. The adsorbed methylthiolate was desorbed as dimethyl disulfide and the cross product methylbutyl disulfide, both identified by LOSMS. This shows that reaction occurs between adsorbed thiolates of different chain length at room temperature, while the kinetics indicate that a rapid equilibrium is established between immobile, chemisorbed thiolates, and highly mobile, physisorbed disulfides.

n-alkanes on MgO(100). II. Chain length dependence of kinetic desorption parameters for small n-alkanes

Coverage-dependent desorption-kinetics parameters are obtained from high-quality temperature-programmed desorption data for seven small n-alkane molecules on MgO(100). The molecules, CNH2N+2 (N=1-4,6,8,10), were each studied for a set of 29 initial coverages at a heating ramp rate of 0.6 K/s as well as at a set of nine ramp rates in the range of 0.3-10.0 K/s. The inversion analysis method with its least-squares preexponential factor (prefactor) optimization discussed in the accompanying article is applied to these data. This method allows for accurate determination of prefactors and coverage-dependent desorption energies. The prefactor for desorption increases dramatically with chain length from 10(13.1) to 10(19.1) s(-1) over the range of N=1-10. We show that this increase can be physically justified by considering the increase in rotational entropy available to the molecules in the gaslike transition state for desorption. The desorption energy increases with chain length as Ed(N)=6.5+7.1N, which implies an incremental increase of 7.1+/-0.2 kJ/mol per CH2.

Binding of propene on small gold clusters and on Au(111): Simple rules for binding sites and relative binding energies

We use density functional theory (DFT) to investigate the bonding of propene to small gas-phase gold clusters and to a Au(111) surface. The desorption energy trends and the geometry of the binding sites are consistent with the following set of rules. (1) The bond of propene to gold is formed by donation of electron density from the highest occupied molecular orbital (HOMO) of propene to one of the low-lying empty orbitals [denoted by LUMO1, LUMO2, em leader (LUMO-lowest unoccupied molecular orbital)] of the gold cluster. (2) Propene binds to a site on the Au cluster where one of the low-lying LUMOs protrudes in the vacuum. Different isomers (same cluster, but different binding sites for propene) correspond to sites where different low-lying LUMOs protrude in space. (3) The desorption energy of the lowest energy isomer correlates with the energy of the lowest empty orbital of the cluster; the lower the energy of that LUMO, the higher the desorption energy. (4) If the lowest-lying LUMO protrudes into space at two nonequivalent sites at the edge of a cluster, propene binds more strongly to the site with the lowest coordination. These rules are consistent with the calculated bond energies and geometries for [Au(n)(C(3)H(6))](q), for n=1-5 and n=8 and q=-1, 0, +1. Based on them we have made a number of predictions that have been confirmed by DFT calculations. The bond of propene to gold is strengthened as the net charge of the cluster varies from -1, to zero, to +1. Compared to a gas-phase cluster, a cluster on a support binds propene more strongly if the support takes electron density from the cluster (e.g., a Au cluster on a gold surface) and more weakly if the support donates electron density to the cluster (e.g., a Au cluster on an oxygen vacancy on an oxide surface).

Adsorption and Reactions of C6 Hydrocarbons at High Pressures on Pt(111) Single-Crystal Surfaces Studied by Sum Frequency Generation Vibrational Spectroscopy: Mechanisms of Isomerization and Dehydrocyclization of n-Hexane

The adsorption geometries and surface reactions of various C(6) hydrocarbons (n-hexane, 2-methylpentane, 3-methylpentane, and 1-hexene) adsorbed on Pt(111) were investigated using sum frequency generation (SFG) surface vibrational spectroscopy. The adsorptions and reactions were carried out in 1.5 Torr of C(6) hydrocarbons in the absence and presence of excess hydrogen (15 Torr) and in the temperature range 296-453 K. At 296 K and in the presence of excess hydrogen, n-hexane and 3-methylpentane adsorbed molecularly on Pt(111) mostly in "flat-lying" geometries. Upon heating the sample up to 453 K, the molecules underwent dehydrogenation to form new surface species in "standing-up" geometries, such as hexylidyne and metallacyclic species. However, 2-methylpentane and 1-hexene were dehydrogenated to metallacyclobutane and hexylidyne, respectively, at 296 K in the presence of excess hydrogen. The dehydrogenated species remained unreacted on the surface upon heating the sample up to 453 K. The absence of excess hydrogen enhanced dehydrogenation of n-hexane and 3-methylpentane to form pi-allyl c-C(6)H(9) and metallacyclohexane, respectively, at 296 K. Upon heating to 453 K, the pi-allyl c-C(6)H(9) species underwent irreversible dehydrogenation, while hexylidyne and metallacyclic species remained unreacted. On the basis of these results, the mechanisms for catalytic isomerization and dehydrocyclization of n-hexane, which are the important "reforming" reactions to produce high-octane fuels over platinum, were discussed.

Surface vibrations in alkanethiol self-assembled monolayers of varying chain length

The effect of chain length on the low-energy vibrations of alkanethiol striped phase self-assembled monolayers on Au(111) was studied. We have examined the low-energy vibrational structure of well-ordered, low-density 1-decanethiol (C10), 1-octanethiol (C8), and 1-hexanethiol (C6) to further understand the interaction between adsorbate and substrate. Dispersionless Einstein mode phonons, polarized perpendicularly to the surface, were observed for the striped phases of C10, C8, and C6 at 8.0, 7.3, and 7.3 meV, respectively. An overtone at 12.3 meV was also observed for C6/Au(111). These results, in concert with molecular dynamics simulations, indicate that the forces between the adsorbate and substrate can be described using simple van der Waals forces between the hydrocarbon chains and the Au substrate with the sulfur chemisorbed in the threefold hollow site.

Thermal desorption of large molecules from solid surfaces

We use molecular-dynamics simulations and importance sampling to obtain transition-state-theory rate constants for thermal desorption of an n-alkane series from Au(111). We find that the binding of a large molecule to a solid surface involves different types of local minima. The preexponential factors increase with increasing chain length and can be substantially larger than typical estimates for small molecules. Our results match recent experimental studies and indicate that a proper treatment of conformational isomerism and entropy, heretofore not found in coarse-grained models, is essential to quantitatively describe the thermal desorption of large molecules from solid surfaces.

Kinetics and energetics of oligomer desorption from surfaces

The dynamics of oligomer desorption from surfaces has been studied by measuring the desorption kinetics of a set of straight chain alkanes [ H(CH2)(n)H, with n = 5 to 60] from the surface of single crystalline graphite. Desorption is observed to be a first-order process and the preexponent of the desorption rate constant has a value nu = 10(19.6+/-0.5) sec(-1) and is independent of the oligomer chain length. More interestingly, we find that the barrier to desorption has a nonlinear dependence on chain length and takes the form DeltaE(double dagger)(des) = A+Bn(alpha), with the exponent alpha = 0.50+/-0.01.