Density Functional Theory with Modified Dispersion Correction for Metals Applied to Self-Assembled Monolayers of Thiols on Au(111) (original) (raw)
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Theoretical Chemistry Accounts, 2015
predicted by density functionals taking into account the vdW corrections, with values increasing in the order GGA-PBE-D2 < GGA-PBE-TS < optB86b-vdW. Furthermore, the functionals considering dispersion interactions favor much more tilted orientations of the SAMs over the surface with respect to those found using the standard GGA functional (the SAMs' tilt angles increase from 17°-24° to 37°-46°), being the former in closer agreement with available experimental data. In contrast, the SAMs' precession angle and monolayer thickness are less affected by the type of DFT exchange-correlation functional employed. In the case of low surface coverage, the chains of the thiols adopt more tilted configurations and tend to lay side-down onto the surface. Keywords Gold (111) surface • Thiols • Periodic density functional theory • van der Waals effects Published as part of the special collection of articles derived from the 9th Congress on Electronic Structure: Principles and Applications (ESPA 2014).
Thiophene thiol on the Au(111) surface: Size-dependent adsorption study
The Journal of Chemical Physics, 2003
The adsorption of the thiophene-2-thiolate and thiophen-2-yl-methanethiolate radicals has been investigated on the Au͑111͒ surface using density functional theory under the framework of the generalized gradient approximation for the exchange-correlation functionals. In order to underscore the quantum size effects on the adsorption geometry, the Au͑111͒ surface was modeled using a finite-sized cluster (Au 3 and Au 24 ) truncated from the surface as well as a periodic slab consisting of 100 atoms. The results reveal that the preferential adsorption site differs for the cluster models and slab approaches. The directional nature of the Au-S bond and the influence of the back bond of the terminal sulfur atom are found to play key roles in the adsorption geometry. The adsorption energies suggest that the binding energies for the cluster models are stronger than the slab. Inclusion of an alkyl group in between the thiophene ring and the thiol group enhances the interaction energies of the gold-sulfur bonds.
Background: The adsorption of organic molecules on metal surfaces has a broad array of applications, from device engineering to medical diagnosis. The most extensively investigated class of metal-molecule complexes is the adsorption of thiols on gold. Results: In the present manuscript, we investigate the dependence of methylthiol adsorption structures and energies on the degree of unsaturation at the metal binding site. We designed an Au 20 cluster with a broad range of metal site coordination numbers, from 3 to 9, and examined the binding conditions of methylthiol at the various sites. Conclusion: We found that despite the small molecular size, the dispersive interactions of the backbone are a determining factor in the molecular affinity for various sites. Kink sites were preferred binding locations due to the availability of multiple surface atoms for dispersive interactions with the methyl groups, whereas tip sites experienced low affinity, despite having low coordination numbers.
Solvent Effects in the Adsorption of Alkyl Thiols on Gold Structures: A Molecular Simulation Study
Journal of Physical Chemistry C, 2007
We carried out Monte Carlo simulations of gold nanocrystals (NCs) and (111) slabs covered with alkyl thiols, with and without explicit solvent (n-hexane), at T ) 300 K. Adsorption isotherms for propane-and octanethiol showed a phase behavior measured previously in experiments. Comparison of the adsorption isotherm of octanethiol in hexane on a (111) slab with experimental data suggests that, in this system, no thiolate bond was formed. The geometry of a gold surface strongly influences the formation and structure of the capping monolayer. On a (111) surface, attractive interactions between carbon chains are more pronounced than on a NC. This leads to a stronger penetration of the capping layer by the solvent. Adsorption selectivity for binary alkyl thiol mixtures is stronger in vacuum than in solution. The convex shape of the NCs also reduces the adsorption selectivity of binary thiol mixtures. This result shows that the solvent cannot be ignored in simulations.
Physical Chemistry Chemical Physics, 2011
Here we present DFT calculations based on a periodic mixed gaussians/plane waves approach to study the energetics, structure, bonding of SAMs of simple thiols on Au(111). Several open issues such as structure, bonding and the nature of adsorbate are taken into account. We started with methyl thiols (MeSH) on Au(111) to establish the nature of the adsorbate. We have considered several structural models embracing the reconstructed surface scenario along with the MeS-Au ad-MeS type motif put forward in recent years. Our calculations suggest a clear preference for the homolytic cleavage of the S-H bond leading to a stable MeS on a gold surface. In agreement with the recent literature studies, the reconstructed models of the MeS species are found to be energetically preferred over unreconstructed models. Besides, our calculations reveal that the model with 1 : 2 Au ad /thiols ratio, i.e. MeS-Au ad-MeS , is energetically preferred compared to the clean and 1 : 1 ratio models, in agreement with the experimental and theoretical evidences. We have also performed Molecular Orbital/Natural Bond Orbital, MO/NBO, analysis to understand the electronic structure and bonding in different structural motifs and many useful insights have been gained. Finally, the studies have then been extended to alkyl thiols of the RSR 0 (R, R 0 = Me, Et and Ph) type and here our calculations again reveal a preference for the RS type species adsorption for clean as well as for reconstructed 1 : 2 Au ad /thiols ratio models.
Theoretical Chemistry Accounts, 2012
Abounding potential technological applications is one of the many reasons why adsorption of aliphatic thiols on gold surface is a subject of intense research by many research groups. Understanding and exploring the nature of adsorbed species, the site of adsorption and the nature of interaction between adsorbed species and the gold surface using experimental and theoretical investigations is an active area of pursuit. However, despite a large number of investigations to understand the atomistic structures of thiols on Au(111), some of the basic issues are still unaddressed. For instance, there is still no clear information about the mechanism of adsorption of alkylthiol on gold surface. Furthermore, the reactivity and mechanism of adsorption of alkylthiol is likely to differ when gold adatoms and/or vacancies in the gold layers are considered. In this work, we have tackled these issues by computing the stationary states involved in the thiols adsorption in order to shed light on the kinetics aspects of adsorption process. In this respect, we have considered a variety of thiols into consideration such as methylthiol, dimethylsulfide, dimethyldisulfide, thioacetates, and thiocyanates. We have also considered the cleavage mechanism in the clean and the reconstructed surface scenario and the structure, energetics and spin densities have been computed using electronic structure calculations. For all the studied cases, an homolytic cleavage of CH 3 S-X (X = H, CH 3 , SCH 3 , CN, and COCH 3 ) bond has been found to occur upon adsorption on the gold surface.
Theoretical study of thiol-induced reconstructions on the Au(111) surface
Chemical Physics Letters, 2002
A new suggestion for the structure of the Au substrate underlying self-assembled monolayers (SAM) made of thiols is presented on the basis of density functional theory results for methylthiolate (-SCH 3 Þ adsorption on Au(1 1 1). It is found that by introducing vacancy defects on the substrate, the adsorption of SCH 3 is stabilized by about 0.8 eV with respect to the perfect Au(1 1 1) surface. As this overcomes the vacancy formation energy (%0.6 eV), a net driving force exists leading to an adsorbate-induced reconstruction, that enhances adsorption at defected Au(1 1 1). A comparison of results at high and low SCH 3 coverage provides further insight into which specific gold vacancy sites enhance the adsorption energy of the SCH 3 molecule. Ó
Physical Review B, 2007
A long-standing controversy related to the dimer pattern formed by S atoms in methanethiol (CH3SH) on the Au(111) surface has been resolved using density functional theory. For the first time, dimerization of methanethiol adsorbates on the Au(111) surface is established by computational modeling. For methylthiolate (CH3S), it is shown that the S atoms do not dimerize at high coverage but reveal a dimer pattern at intermediate coverage. Molecular dynamics simulation at high coverage demonstrates that the observed dialkyl disulfide species are formed during the desorption process, and thus are not attached to the surface.
Thiol Adsorption on the Au(100)-hex and Au(100)-(1 × 1) Surfaces
The Journal of Physical Chemistry C, 2015
Alkanethiol adsorption on the Au(100) surfaces is studied by using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and electrochemical techniques. Adsorption of hexanethiol (HT) on the Au(100)-hex surface results in the formation of elongated Au islands following the typical stripes of the reconstruction. Ordered molecular arrays forming hexagonally distorted square patterns cover the stripes with surface coverage ≈0.33. On the other hand, HT adsorption on the Au(100)-(1 × 1) surface shows the absence of the elongated island and the formation of square molecular patterns with a surface coverage ≈0.44. The core level shift of thiolates adsorbed on the Au(100)-(1 × 1) and Au(111) is only 0.15 eV, suggesting that chemistry rather than surface sites determines the binding energy of the S 2p core level. These results are also important to complete our knowledge of the chemistry and surface structure for small thiolated AuNPs where the Au(100) together with the Au(111) are the dominant faces.
The Journal of Chemical Physics, 2005
The adsorption of phenylthiol on the Au͑111͒ surface is modeled using Perdew and Wang density-functional calculations. Both direct molecular physisorption and dissociative chemisorption via S-H bond cleavage are considered as well as dimerization to form disulfides. For the major observed product, the chemisorbed thiol, an extensive potential-energy surface is produced as a function of both the azimuthal orientation of the adsorbate and the linear translation of the adsorbate through the key fcc, hcp, bridge, and top binding sites. Key structures are characterized, the lowest-energy one being a broad minimum of tilted orientation ranging from the bridge structure halfway towards the fcc one. The vertically oriented threefold binding sites, often assumed to dominate molecular electronics measurements, are identified as transition states at low coverage but become favored in dense monolayers. A similar surface is also produced for chemisorption of phenylthiol on Ag͑111͒; this displays significant qualitative differences, consistent with the qualitatively different observed structures for thiol chemisorption on Ag and Au. Full contours of the minimum potential energy as a function of sulfur translation over the crystal face are described, from which the barrier to diffusion is deduced to be 5.8 kcal mol −1 , indicating that the potential-energy surface has low corrugation. The calculated bond lengths, adsorbate charge and spin density, and the density of electronic states all indicate that, at all sulfur locations, the adsorbate can be regarded as a thiyl species that forms a net single covalent bond to the surface of strength 31 kcal mol −1 . No detectable thiolate character is predicted, however, contrary to experimental results for alkyl thiols that indicate up to 20%-30% thiolate involvement. This effect is attributed to the asymptotic-potential error of all modern density functionals that becomes manifest through a 3 -4 eV error in the lineup of the adsorbate and substrate bands. Significant implications are described for density-functional calculations of through-molecule electron transport in molecular electronics.