Electron transport across the alkanethiol self-assembled monolayer/Au(111) interface: role of the chemical anchor

Alkanethiol self-assembled monolayers (SAMs) on Au(111) are model systems for molecular electronics. We probe the role of the chemisorption bond on electron dynamics at the SAM/Au interface using time-resolved two-photon photoemission. Formation of the Au-S bond is evidenced by a localized sigma resonance, which broadens and shifts upward in energy when the lying-down chemisorbed molecules stand up. The localized chemisorption bond does not affect the electronic coupling between delocalized image resonances and the metal substrate. Instead, lifetimes of image resonances are decreased due to scattering with S atoms within the thiol or thiolate monolayer.     

Adsorption modes of cysteine on Au(111): thiolate, amino-thiolate, disulfide

The adsorption of cysteine on the (111) surface of gold has been studied by means of periodic supercell density-functional theory calculations. A number of different adsorption modes are examined, including adsorption through the thiol group in either thiolate or disulfide form, and adsorption through both the thiol and amino functional groups. We find that at intermediate coverage densities the latter mode of adsorption is favored, followed by thiolate adsorption at the bridge (slightly displace toward fcc) site. The N-Au and S-Au bond strengths in the amino-thiolate adsorption are estimated to be of the order of 6 and 47 kcal/mol, respectively. The electronic structure of the different systems is analyzed, with focus on the total and projected density of states, as well as on the detailed character of the electronic states at the interface. States near the Fermi energy are found to have a metal-molecule antibonding character, whereas metal-molecule bonding states mostly occur near the lower edge of the Au-d band.     

Surface dipoles and work functions of alkylthiolates and fluorinated alkylthiolates on Au(111)

We study the dipole formation at the surface formed by -CH(3) and -CF(3) terminated short-chain alkylthiolate monolayers on Au(111). In particular, we monitor the change in work function upon chemisorption using density functional theory calculations. We separate the surface dipole into two contributions, resulting from the gold-adsorbate interaction and the intrinsic dipole of the adsorbate layer, respectively. The two contributions turn out to be approximately additive. Adsorbate dipoles are defined by calculating dipole densities of free-standing molecular monolayers. The gold-adsorbate interaction is, to a good degree, determined by the Au-S bond only. This bond is nearly apolar and its contribution to the surface dipole is relatively small. The surface dipole of the self-assembled monolayer is then dominated by the intrinsic dipole of the thiolate molecules. Alkylthiolates increase the work function of Au(111), whereas fluorinated alkylthiolates decrease it.     

Formation of gold-methanethiyl self-assembled monolayers

The energetics of formation of thiyl-gold self-assembled monolayers is investigated using density-functional theory simulations. It is found that the chemisorption of dimethyl disulfide on the reconstructed Au(111) (22 x radical3) surface is most favored at the fcc reconstruction stripe, with initial physisorption leading to disulfide dissociation, adatom/vacancy-pair formation, and then, at a coverage of 7.8% sulfur atoms per gold atom, surface reconstruction lifting. At higher coverages, monolayer formation proceeds similarly on the unreconstructed surface, leading to surface pitting. Formation of the analogous adatom/vacancy-pair bound dissociated adsorbate complex on exposure of the clean unreconstructed surface to methanethiol is shown to be endothermic, however.     

Interaction of benzene thiol and thiolate with small gold clusters

We studied the interaction between benzene thiol and thiolate molecules, and gold clusters made of 1 to 3 atoms, by means of ab initio density functional theory in the local density approximation. We find that the thiolate is energetically more stable than the thiol, however the process of detachment of H from the thiol appears to be possibly mediated by the intermediate step of H chemisorption on Au. Cleavage of the S-H bond is accompanied by a 90 degrees rotation of the molecule around the S-Au bond, showing a strong steric specificity. Such a rotation is induced by the relative energy shift of the S atom p orbitals with respect to the benzene pi ring and the Au d orbitals. By analyzing the correlation of the bond energy, bond lengths, and HOMO-LUMO gap with the number of S-Au bonds, we find that the thiolate S atom appears to prefer a low-coordination condition on Au clusters.     

Effect of coverage and defects on the adsorption of propanethiol on Au(111) surface: a theoretical study

Periodic density functional calculations have been carried out to investigate both the thiol adsorption on Au(111) surface and the reaction mechanism for the formation of the self-assembled monolayers, taking propanethiol as a representative example. The effect of coverage and surface defects (adatoms and vacancies) has been analyzed. It is found that the most stable physisorption (undissociated) site is an adatom site, whereas the chemisorption site for the thiol is a vacancy site or protrusion consisting of a pair of adatoms, followed by one adatom site. The results point out that the thiolate self-assembled monolayer adsorption process occurs preferentially on step edges.     

Thiol and thiolate bond formation of ferrocene-1,1-dithiol to a Ag(111) surface

Using density functional calculations, we show that the adsorption of ferrocene dithiol on the Ag(111) surface is remarkably flexible, i.e., a large number of different configurations have binding energies that differ by less than 0.1 eV per molecule. The thiolate bond is slightly favored over the thiol bond (by less than 0.1 eV) but may not be formed due to considerable activation barriers. Electronically, we found that the thiolate bound molecule is conducting, whereas thiol bonds turn it into semiconducting.     

Density functional theory study of the adsorption of alkanethiols on Cu(111), Ag(111), and Au(111) in the low and high coverage regimes

The structure, the surface bonding, and the energetics of alkanethiols adsorbed on Cu(111), Ag(111), and Au(111) surfaces were studied under low and high coverages. The potential energy surfaces (PES) for the thiol/metal interaction were investigated in the absence and presence of externally applied electric fields in order to simulate the effect of the electrode potential on the surface bonding. The electric field affects the corrugation of the PES which decreases for negative fields and increases for positive fields. In the structural investigation, we considered the relaxation of the adsorbate and the surface. The highest relaxation in a direction perpendicular to the surface was observed for gold atoms, whereas silver atoms presented the highest relaxation in a plane parallel to the surface. The surface relaxation is more important in the low coverage limit. The surface bonding was investigated by means of the total and projected density of states analysis. The highest ionic character was observed on the copper surface whereas the highest covalent character occurs on gold. This leads to a strong dependence of the PES with the tilt angle of the adsorbate on Au(111) whereas this dependence is less pronounced on the other metals. Thus, the adsorbate-relaxation and the metal-relaxation contributions to the binding energy are more important on gold. The adsorption of thiols on gold was investigated on the 111 surface as well as on a surface with gold adatoms in order to elucidate the effect of thiols on the surface diffusion of gold. The CH(3)CH(2)S radical adsorbs ontop of the gold adatom. The diffusional barrier of the CH(3)CH(2)SAu species is lower than that for a bare gold adatom and is also lower than that for the bare thiol radical. The adsorption of the molecular species CH(3)SH and CH(3)CH(2)SH was also investigated on Au(111). They adsorb via the sulfur atom ontop of a gold atom. On the other hand, the adsorption of the alkanethiol radicals on the perfect 111 surfaces occurs on the face centered cubic (fcc)-bridge site in the low coverage limit for all metals and shifts toward the fcc site at high coverage on copper and silver.     

Thiol with an unusual adsorption-desorption behavior: 6-mercaptopurine on Au(111)

A multitechnique study of 6-mercaptopurine (6MP) adsorption on Au(111) is presented. The molecule adsorbs on Au(111), originating short-range ordered domains and irregular nanosized aggregates with a total surface coverage by chemisorbed species smaller than those found for alkanethiol SAMs, as derived from scanning tunneling microscopy (STM) and electrochemical results. X-ray photoelectron spectroscopy (XPS) results show the presence of a thiolate bond, whereas density functional theory (DFT) data indicate strong chemisorption via a S-Au bond and additional binding to the surface via a N-Au bond. From DFT data, the positive charge on the Au topmost surface atoms is markedly smaller than that found for Au atoms in alkanethiolate SAMs. The adsorption of 6MP originates Au atom removal from step edges but no vacancy island formation at (111) terraces. The small coverage of Au islands after 6MP desorption strongly suggests the presence of only a small population of Au adatom-thiolate complexes. We propose that the absence of the Au-S interface reconstruction results from the lack of significant repulsive forces acting at the Au surface atoms.     

Cluster and periodic DFT calculations: the adsorption of atomic nitrogen on M(111) (M = Cu, Ag, Au) surfaces

First-principle density functional calculations with cluster and slab models have been performed to investigate adsorption and thermally activated atomic nitrogen on M(111) (M = Cu, Ag, Au) surfaces. Optimized results indicate that the basis set of the N atom has a distinct effect on the adsorption energy but an indistinct one on the equilibrium distance. For the N/M(111) adsorption systems studied here, the threefold face centered cubic (fcc) hollow site is found to be the most stable adsorption site. The reason for the fcc site is that the perfected adsorption site has been explained by the density of states (DOS) analysis, that is, that N(2p) has the smallest DOS population near the Fermi level on the fcc site as compared with other adsorption sites. The variations of the adsorption energy as a function of adsorption site are similar and in the following order of N-M(111) binding strengths on a given site: Cu(111) > Ag(111) > Au(111). It is found that the N atom forms essentially an ionic bond for the most stable site. Large contributions between the M(ns) and N(2p) orbitals (n = 4, 5, and 6 for Cu, Ag, and Au, respectively) are found for the cluster model at the B3LYP/LANL2DZ-6-31G(d,p) level and also found in the slab DFT-GGA calculation results, which are the main characteristics of M-N bonds. At last, the dissociation of N2 on Cu(111) and Au(111) has also been obtained in this work, and the results showed that the dissociation of N2 on Cu(111) is more active than that on the Au(111) surface.     

Experimental and theoretical study of the interaction of CO2 with alpha-Al2O3

Density functional molecular cluster calculations are combined with X-ray photoelectron spectroscopy (XPS), quadrupolar mass spectrometry (QMS), and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy to investigate the interaction of CO2 with alpha-Al2O3 and partially reduced alpha-Al2O3. The electronic structure of the stoichiometric and partially reduced substrate, adsorbate geometries, chemisorption enthalpies, and adsorbate vibrational parameters are computed and discussed. Theoretical results agree quite well with experimental data and previous theoretical investigations. As far as the adsorbate-substrate interaction is concerned, the results of our calculations indicate that CO2 forms bidentate-chelating carbonate species. The bonding scheme of this surface complex implies a significant substrate-->adsorbate transfer of charge (from the occupied dangling bond of a surface Lewis base site into one component of the CO2 2 pi u LUMO) assisted by a definitely weaker adsorbate-->substrate donation (from one component of the CO2 1 pi g HOMO into an empty dangling bond of a surface Lewis acid site). Our estimate of the chemisorption enthalpy (-15 kcal/mol) agrees quantitatively with calorimetric data reported for CO2 adsorbed on high surface area alpha-alumina (-16.0 kcal/mol). [Mao, C.-F.; Vannice, M. A. Appl. Catal. A 1994, 111, 151.] According to XPS and QMS outcomes, theoretical results predict that the interaction of CO2 with partially reduced alpha-Al2O3 gives rise to the reduction of the adsorbate to CO and to the concomitant substrate reoxidation.     

Self-assembled monolayers of aromatic selenolates on noble metal substrates

Self-assembled monolayers (SAMs) formed from bis(biphenyl-4-yl) diselenide (BBPDSe) on Au(111) and Ag(111) substrates have been characterized by high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, infrared reflection absorption spectroscopy, water contact angle measurements, and scanning tunneling microscopy (STM). BBPDSe was found to form contamination-free, densely packed, and well-ordered biphenyl selenolate (BPSe) SAMs on both Au and Ag. Spectroscopic data suggest very similar packing density, orientational order, and molecular inclination in BPSe/Au and BPSe/Ag. STM data give a similar intermolecular spacing of 5.3 +/- 0.4 A on both Au and Ag but exhibit differences in the exact arrangement of the BPSe molecules on these two substrates, with the (2 square root[3] x square root[3])R30 degrees and (square root[3] x square root[3])R30 degrees unit cells on Au and Ag, respectively. There is strong evidence for adsorbate-mediated substrate restructuring in the case of Au, whereas no clear statement on this issue can be made in the case of Ag. The film quality of the BPSe SAMs is superior to their thiol analogues, which is presumably related to a better ability of the selenolates to adjust the surface lattice of the substrate to the most favorable 2D arrangement of the adsorbate molecules. This suggests that aromatic selenolates represent an attractive alternative to the respective thiols.     

A spectroscopic study of self-assembled monolayer of porphyrin-functionalized oligo(phenyleneethynylene)s on gold: the influence of the anchor moiety

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules () with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH(3) (), an acetyl protected thiol with methylene linker, -CH(2)-S-COCH(3) (), and a trimethylsilylethynyl group, -C[triple bond, length as m-dash]C-Si(CH(3))(3) () have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared. The integrity and structural properties of these films were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The results suggest that the films formed from have a high orientational order with an almost upright orientation and dense packing of the molecular constituents, i.e. represent a high quality SAM. In contrast, molecule formed disordered molecular layers on Au, even though the molecule-surface bonding (thiolate) is the same as in the case of molecule . This suggests that the methylene linker in molecule has a strong impact on the quality of the resulting film, so that a well-ordered SAM cannot be formed. The silane system, , is also able to bind to the gold surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised of strongly inclined molecules. The above results suggest that the nature of the anchor group along with a possible linker is an important parameter which, to a high extent, predetermines the entire quality of OPE-based molecular layers.     

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.     

Surface bonding and dynamical behavior of the CH3SH molecule on Au(111)

The chemisorption of the undissociated CH3SH molecule on the Au(111) surface has been studied at 5 K using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The molecule was found to adsorb on atop Au sites on the defect-free surface. CH3SH undergoes hindered rotation about the Au-S bond on the defect-free surface which is seen in STM as a time-averaged 6-fold pattern. The pattern suggests that the potential minima directions occur for the rotating molecule at the six hollow sites surrounding the atop adsorption site. The barrier for rotation, obtained by DFT calculations, is approximately 0.1 kcal.mol(-1). At low coverages, preferential adsorption occurs at defect sites in the surface, namely, the herringbone "elbows" and random atomic step sites. Molecules adsorbed on these sites do not exhibit rotational freedom.     

Conformation and dynamics of arylthiol self-assembled monolayers on Au(111)

We report a computational investigation of the conformation and the dynamics of self-assembled monolayers (SAMs) of a set of aromatic thiols arranged in the ( radical3 x radical3)-R30 degrees packing ratio on a Au(111) surface using molecular dynamics (MD) simulations. It was found that the molecular conformations were better defined for the arylthiol with two phenyl groups as compared to those with a single phenyl group and that the chemical structure of the head and tail groups had a considerable influence on the system geometry. In line with the density functional theory (DFT) calculations of small thiol molecules, we found for the SAMs that the face-centered cubic (fcc) site on the Au(111) surface was the most preferred, followed by the hexagonal close-packed (hcp) site, while the bridge position showed the characteristics of a local energy maximum. The dynamics of thiol head groups on these three Au sites was found to govern the overall dynamics of SAMs as measured by the mean square displacement. We also report that both the conformation and the dynamics on the studied time scale were driven by the SAM formation energy.     

Theoretical study of ethynylbenzene adsorption on Au(111) and implications for a new class of self-assembled monolayer

Density functional calculations of the adsorption of ethynylbenzene on the Au(111) surface show that, after cleavage of the C-H bond, the terminal carbon makes a strong covalent bond to the surface. The bond energy is shown to be about 70 kcal.mol(-1) with the fcc hollow site being most stable and the molecule oriented perpendicular to the surface. Adsorption without elimination of hydrogen is also possible via a hydrogen 1,2 shift to form a vinylidene surface-bound species, or opening of the C-C triple bond and adsorption through the two carbon atoms in a flat conformation. The reaction energy for formation of the surface-bound vinylidene is estimated to be 5 kcal.mol(-1) exothermic relative to the isolated ethynylbenzene and gold substrate.     

Chemisorption of (CHx and C2Hy) hydrocarbons on Pt(111) clusters and surfaces from DFT studies

We used the B3LYP flavor of density functional theory (DFT) to study the chemisorption of all CH(x) and C(2)H(y) intermediates on the Pt(111) surface. The surface was modeled with the 35 atom Pt(14.13.8) cluster, which was found to be reliable for describing all adsorption sites. We find that these hydrocarbons all bind covalently (sigma-bonds) to the surface, in agreement with the studies by Kua and Goddard on small Pt clusters. In nearly every case the structure of the adsorbed hydrocarbon achieves a saturated configuration in which each C is almost tetrahedral with the missing H atoms replaced by covalent bonds to the surface Pt atoms. Thus, (Pt(3))CH prefers a mu(3) hollow site (fcc), (Pt(2))CH(2) prefers a mu(2) bridge site, and PtCH(3) prefers mu(1) on-top sites. Vinyl leads to (Pt(2))CH-CH(2)(Pt), which prefers a mu(3) hollow site (fcc). The only exceptions to this model are ethynyl (CCH), which binds as (Pt(2))C=CH(Pt), retaining a CC pi-bond while binding at a mu(3) hollow site (fcc), and HCCH, which binds as (Pt)HC=CH(Pt), retaining a pi bond that coordinates to a third atom of a mu(3) hollow site (fcc) to form an off center structure. These structures are in good agreement with available experimental data. For all species we calculated heats of formation (DeltaH(f)) to be used for considering various reaction pathways on Pt(111). For conditions of low coverage, the most strongly bound CH(x) species is methylidyne (CH, BE = 146.61 kcal/mol), and ethylidyne (CCH(3), BE = 134.83 kcal/mol) among the C(2)H(y) molecules. We find that the net bond energy is nearly proportional to the number of C-Pt bonds (48.80 kcal/mol per bond) with the average bond energy decreasing slightly with the number of C ligands.     

Static investigation of adsorption and hetero‐diffusion of copper,silver, and gold adatoms on the (111) surface

In this work, we have used the static molecular simulations combined with an interatomic potential derived from the embedded‐atom method to study the adsorption and hetero‐diffusion on the (111) surface of Cu, Ag, and Au adatoms by using LAMMPS code. The investigation is performed for six heterogeneous systems such as Ag/Au(111), Ag/Cu(111), Au/Ag(111), Au/Cu(111), Cu/Ag(111), and Cu/Au(111). First, we have investigated the relaxation trends and the bond lengths of the atoms in the systems. The calculation results show that, the top layer spacing between the first and second layers of the Au(111), Ag(111), and Cu(111) substrates is contracted. This contraction is found to be more important in the Au(111) substrate. On the other hand, the strong reduction of the binding length is found in Au/Cu(111) for the different adsorption sites. In addition, the binding, adsorption, and static activation energies for all studied systems were examined. The results indicated that the binding and adsorption energies reached their maximum values in the Au/Cu(111) and Au/Ag(111) systems, respectively. Moreover, the static activation barriers for hopping diffusion on the (111) surfaces are found to be low compared with those found in the (100) and (110) surfaces. Therefore, our calculations showed that the difference in energy between the hcp and fcc sites on the (111) surfaces is very small. Copyright © 2017 John Wiley & Sons, Ltd.     

Theoretical Investigations of the Activation of CO_2 on the Transition Metal-doped Cu(100) and Cu(111) Surfaces

Periodic density functional theory calculations have been performed to investigate the chemisorption behavior of CO_2 molecule on a series of surface alloys that are built by dispersing individual middle-late transition metal(TM) atoms(TM = Fe, Co, Ni, Ru, Rh, Pd, Ag, Os, Ir, Pt, Au) on the Cu(100) and Cu(111) surfaces. The most stable configurations of CO_2 chemisorbed on different TM/Cu surfaces are determined, and the results show that among the late transition metals, Co, Ru, and Os are potentially good dopants to enhance the chemisorption and activation of CO_2 on copper surfaces. To obtain a deep understanding of the adsorption property, the bonding characteristics of the adsorption bonds are carefully examined by the crystal orbital Hamilton population technique, which reveals that the TM atom primarily provides d orbitals with z-component, namely d_z~2, d_(xz), and d_(yz) orbitals to interact with the adsorbate.