Adsorption of Methanethiolate and Atomic Sulfur at the Cu (111

Subscriber access provided by UNIV OF ARIZONA

Article

Adsorption of Methanethiolate and Atomic Sulfur at the Cu(111) Surface: A Computational Study Porntip Seema, Joerg Behler, and Dominik Marx J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/jp309728w • Publication Date (Web): 14 Dec 2012 Downloaded from http://pubs.acs.org on December 15, 2012

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry C is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

Adsorption of Methanethiolate and Atomic Sulfur at the Cu(111) Surface: A Computational Study Porntip Seema, Jörg Behler,∗ and Dominik Marx Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany E-mail: [email protected]

∗ To

whom correspondence should be addressed

1 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Abstract Density-functional theory calculations have been carried out to study the adsorption of methanethiolate and atomic sulfur as a non-molecular reference at the Cu(111) surface. A large number of surface models has been investigated considering a variety of binding sites and coverages at the ideal and reconstructed surface. For methanethiolate we find that the  5 0 proposed   supercell commonly used to approximate the experimentally observed non1 3 commensurate pseudo(100) reconstruction yields the lowest surface energy, but several similar local minima exist differing in the positions of the copper atoms. None of these structures shows the regular nearly square coordination of the thiolate species observed in STM. Modifying the chemical composition of the relaxed layer, e.g. by adding  copper atom, yields  another 5 0 structures of comparable stability. It is thus very likely that the   supercell is not a good 1 3 approximation to the true pseudo(100) phase and that larger unit cells are needed to allow for

a realistic relaxation of the reconstructed layer. For atomic sulfur it is well established that √ √ the most stable phase at Cu(111) is a ( 7 × 7)R19.1◦ reconstruction. Its structure, however, has been discussed controversially in the literature for many years. While there is consensus that the unit cell contains three sulfur atoms, there are still several competing models differing in the number of copper adatoms in the reconstructed layer. We find that three models have a very similar stability, and a three copper adatom model is only marginally preferred. These results will be of importance for many fields from heterogeneous catalysis to covalent mechanochemistry and molecular nanomechanics. Keywords: self-assembled monolayers, thiolates, catalysis, surface reconstruction, densityfunctional theory


Page 2 of 39

Page 3 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Introduction Self-assembled monolayers (SAMs) of organic molecules at metal surfaces attract a lot of attention because they offer to synthesize functionalized surfaces with a wide range of properties in an easy and controlled way. In particular SAMs formed by thiolates at the surfaces of the coinage metals copper, silver, and most importantly gold have become prototype systems for these studies. 1–7 They are usually well-ordered, can be synthesized either from the gas phase or in solution, and are technically relevant for many applications. For instance, sulfur-containing molecules act as catalyst poisons in the petrochemical industry, 8,9 they are interesting for applications in molecular electronics, 10 they can protect metal surfaces from corrosion, 11,12 they stabilize reactive metal clusters by surface coating, 13 and they can be used in chemical sensing. 14 In general thiolate SAMs can be formed either by the deprotonation of thiols or by cleaving the sulfur-sulfur bond of dialkyl disulfides. In both cases chemically identical adsorbate phases are obtained. Here we use the notation Cn for n–alkyl thiols of chemical composition CH3 (CH2 )n−1 SH and for the respective thiolates. SAMs of alkylthiols at copper surfaces have been studied significantly less than SAMs at gold surfaces, partially because their experimental preparation is more challenging due to the sensitivity of copper to oxidation. 15 Further, thiols bind stronger to Cu than to Ag and Au surfaces and it often takes a long time to reach equilibrium. 16 Still, a number of experimental studies have been carried out for thiols of different chain lengths at copper surfaces, like C1 , 17–24 C2 , 22,25 C4 , 26 C5 , 27 C6 , 28,29 C8 , 26,30–32 C10 , 27 C12 , 29,33 C16 , 26,31 C18 , 11,15,27 and C22 . 11 In particular, molecule/metal junctions and SAMs obtained after adsorption of short-chain thiols on copper have been shown to feature most interesting nanomechanical properties including mechanochemical transformations. 34–39 Among all n–alkyl thiols the most basic n = 1 molecule, methanethiol, has received most attention. At Cu(111) methanethiol shows four different phases as a function of temperature. 22,23 At very low temperatures the undissociated molecule is adsorbed. Above about 140 K significant deprotonation occurs and two different thiolate phases are formed. The low-temperature (LT) “honeycomb phase” 19,23 has been suggested to be metastable and probably corresponds to the unrecon3 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

structed surface with thiolate adsorption in bridge and hollow sites. 23 Already at these temperatures also a second thiolate phase is reported, which becomes dominant at room temperature. In this high temperature (HT) phase, whose formation is kinetically hindered at low temperatures, the copper atoms undergo a major reconstruction, which in early papers has been described as adsorption in a “deep threefold hollow site”, 18 but it has now been recognized as a pseudo(100) reconstruction of the first metal layer. 17,19,20,30 In the pseudo(100) reconstruction the thiolate molecules are arranged in a c(2×2) structure with respect to the reconstructed topmost (100)-like metal layer, which has a reduced density of metal atoms of 2/3 of the Cu(111) layers below. The structure is probably non-commensurate with the underlying Cu(111) surface, and structural models based on sulfur atoms in distorted fourfold coordination sites have been suggested in experimental studies. 19,20 Also longer chain thiols like C6 , 29 C8 , 30,32 and C12 29 show a similar reconstruction of Cu(111) and in general a similar phase diagram. Apart from the LT and HT thiolate phases also a third thiolate phase has been observed in STM experiments, 19 which is a hexagonal phase and has been suggested to be the stable structure at very high coverages. The atomic structure of this phase is unknown. Upon heating to about 400 K thermal decomposition of the thiolate species sets in resulting in the formation of atomic sulfur at the surface. 40 Consequently, atomic sulfur can be present under catalytic conditions and adsorbate structures formed by sulfur atoms are important reference systems for understanding the chemical behavior of sulfur-containing molecules at metal surfaces. Theoretical studies on the adsorption of thiols at copper surfaces using first principles methods like density-functional theory (DFT) are still surprisingly rare. 31,34–37,39,41–43 A first stimulus to study such systems, starting in 2004, came from molecular nanomechanics of SAMs, where copper-based systems have been contrasted to thiolates on gold. 34–39 In 2005, Cometto et al. studied C1 adsorption at low and high coverages employing cluster and periodic slab calculations, respectively, identifying the bridge site as the most stable site in the high-coverage regime. 42 In the same year, adsorption at the unreconstructed surface was also investigated by Akinaga, Nakajima, and Hirao, who suggested adsorption of C1 in a threefold hollow site. 41 To date, the most compre-


Page 4 of 39

Page 5 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


hensive study of the adsorbate structures of C1 at Cu(111) has been carried out by Grönbeck only in 2010. 43 Several structures have been considered including the ideal surface, at which a distorted bridge site has been found to be most stable, a structure including metal adatoms, a structure with a vacancy and an adatom as well as the experimentally suggested pseudo(100) reconstruction, which has been found to be energetically most stable of all investigated models. However, the optimized pseudo(100) structure shows significant deviations from the initial (100)-like arrangement as the copper atoms of the reconstructed layer relax to close-by threefold hollow sites of the underlying Cu(111) surface. This results in large distortions of the fourfold coordination of the sulfur atoms. To date, no calculations have been reported for the LT honeycomb structure and the hexagonal high-coverage phase. The adsorption of atomic sulfur at Cu(111) has first been studied experimentally by Domange and Oudar in 1968 44 as an important reference system for organic sulfur compounds. Three differ√ √ ent phases have been observed, a ( 3 × 3)R30◦ structure, a “complex intermediate phase”, and √ √ √ √ the ( 7 × 7)R19◦ structure. While the existence of the ( 3 × 3)R30◦ structure could not be 8 confirmed by later studies with the exception  of astudy at elevated temperatures, the intermediate

 4 1 structure has now been identified as a   supercell 45 in the matrix notation of Park and −1 4 √ √ Madden. 46 It transforms to the ( 7 × 7)R19◦ structure at higher sulfur coverages. The phases of sulfur at Cu(111) are most commonly studied by dissociatively adsorbing H2 S molecules at the surface. Most of the obtained phases have very large unit cells with to date unresolved structures. It is now commonly agreed that in general these phases do not correspond to simple superstructures of sulfur atoms adsorbed at the ideal Cu(111) surface, but complex mixed layers of copper and sulfur atoms as well as small clusters of these species are formed requiring a significant mass transport along the surface. This mass transport of copper atoms originating from step edges occurs via mobile clusters containing copper as well as sulfur atoms. 47 Based on DFT calculations it has been suggested that Cu3 S3 clusters are the most important species in this process. 48



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Several experimental studies for low sulfur coverages in the range between about 0.1 and 0.3 monolayers (MLs) exist with interesting results. 49–51 At room temperature it has been found that disordered layers contain S atoms and Cu3 S3 units. By decreasing the temperature to about √ 170 K several ordered structures can be observed. At lowest coverages a honeycomb-like ( 43 × √ 43)R7.5◦ structure is formed, which covers the full surface if the coverage is increased to 0.25 MLs. At further increasing coverage three more phases have been identified, which are stable even  

 4 0 up to temperatures of about 250 K. Their supercells are very large and correspond to a  , −3 6      5 −1  3 3 a , and a   supercell, respectively. At room temperature these phases are not −3 8 −9 16 stable and decompose to very mobile species that are invisible in STM. If, however, the   sulfur  4 1 coverage is further increased, at a coverage of about 0.35 MLs an intermediate   phase −1 4 forms, which is also called “zig-zag” phase due to its characteristic appearance in STM. 45,52 Its structure is unknown but it has been speculated that it contains similar structural motifs as the very √ √ stable ( 7 × 7)R19◦ structure forming at a saturation coverage of 0.43 MLs. 8,44 In spite of its comparably small supercell and many experimental studies, 8,44,45,52–58 the atomic √ √ structure of the ( 7 × 7)R19◦ phase has been discussed controversially for many years and numerous structural models have been published. It is now commonly accepted that it contains three sulfur atoms per unit cell corresponding to a coverage of 3/7 MLs in a mixed layer with copper atoms. In the model suggested by Prince in 1990, 54 which is based on the early work of Domange and Oudar, 44 the three sulfur atoms occupy top, fcc and hcp sites and each sulfur atom is coordinated by three copper adatoms. Consequently, there are also three copper adatoms per unit cell in the reconstructed layer. In the model suggested by Saidy and Mitchell in 1999 58 two sulfur atoms are adsorbed in fcc and hcp hollow sites while a third sulfur atom replaces a copper atom in the first Cu(111) layer. On top of this sulfur atom a cluster consisting of three copper atoms is adsorbed. Contrarily, in the model proposed by Foss et al. in 1997 56 the reconstructed layer contains in total four copper atoms, which form a nearly square Cu4 cluster with a sulfur 6 ACS Paragon Plus Environment

Page 6 of 39

Page 7 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


atom on top of its fourfold hollow site, and two more sulfur atoms are located in between the clusters. Many other models have been suggested in the literature, and the analysis of the available experimental data does not yet allow for an unambiguous identification of the atomic structure of √ √ the ( 7 × 7)R19◦ phase. Apart from the dissociative adsorption of H2 S, another way to obtain sulfur adlayers at Cu(111) is the thermal decomposition of self-assembled monolayers of alkylthiols. 23,26 Further, in 2001 it has been demonstrated by Driver and Woodruff that a pseudo(100) reconstruction with fourfold coordinated sulfur atoms in a c(2 × 2) overlayer can be obtained by the decomposition of a methylthiolate SAM using an electron beam. 59 The obtained structure is metastable and converts √ √ slowly to the ( 7 × 7)R19◦ phase. Nevertheless, some domains have been found to exist even up to a few days. A detailed analysis of this structure has shown that the reconstructed layer shows a significant corrugation and differs also in registry from the pseudo(100) reconstructed phase of alkylthiolates. DFT calculations addressing the sulfur adsorption at Cu(111) are very rare and most of these studies only focus on the adsorption at high-symmetry fcc, hcp, top, and bridge sites at the unreconstructed Cu(111) surface. 60–63 The fcc site has been identified as the most stable adsorption site, but in all these studies the experimentally found reconstructed phases have not been investigated. Only a single theoretical study addressing the three most prominent structural models of √ √ the ( 7 × 7)R19◦ phase has been reported recently 64 finding very similar energies for the models proposed by Foss 56 and Prince, 54 while the energy of the structure suggested by Saidy and Mitchell 58 has been found to be too high to be competitive. In spite of a large number of experimental and a few theoretical studies, many questions on the stable and metastable phases formed by thiolates and atomic sulfur at the Cu(111) surface remain unanswered. Understanding the structural details of these phases at the atomic level is of fundamental importance for a deeper insight into the formation and stabilization principles of SAMs and their technological applications. Furthermore, they are the key to understanding their nanomechanical properties such as the response of these SAMs upon tensile stress, shear forces,



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 39

or nanoindentation. Here, we report detailed DFT calculations for a variety of adsorbate phases of methanethiolate and of sulfur atoms at the Cu(111) surface. Ideal as well as reconstructed surface models of different stoichiometry are considered covering a large number of structures proposed in experimental studies.

Computational Details The structural and energetic properties of thiolates and atomic sulfur at Cu(111) have been studied by DFT as implemented in the pseudopotential plane wave code PWSCF, which is part of the Quantum ESPRESSO package. 65 The PBE functional has been used to describe electronic exchange and correlation. 66,67 Ultrasoft pseudopotentials have been employed 68 in combination with an energy cutoff of 25 Ry to expand the Kohn-Sham orbitals. k-point meshes with a density corresponding to a 12 × 12 × 12 grid for the four-atom fcc unit cell of bulk copper have been used, yielding a convergence of energy differences to about 1 meV per atom. For all structures except for the free sulfur atom closed-shell calculations have been carried out. For the calculation of the binding energy of methanethiolate, the dimethyl disulfide molecule has been used as reference. The metal surface has been described by slab models consisting of five Cu(111) layers, which provide binding energies converged to about ten meV per adsorbate. Sulfur atoms and thiolate molecules have been adsorbed on one side of the slab. In the structural optimizations the positions of all atoms except for the two bottom metal layers have been fully relaxed. A vacuum of at least 15 Å has been used in all calculations to avoid interactions between the slabs. The binding energy Eb per adsorbate, and the energy per surface area γ , 43 which allows to compare structures with different coverages, have been calculated according to

Eb =

1 n Eads/Cu(111) − ECu(111) + (X −Y )ECu − Eads n m


(1)

Page 9 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


and

γ =

n 1 Eads/Cu(111) − ECu(111) + (X −Y )ECu − Eads . A m

(2)

Here, Eads/Cu(111) is the total energy of the adsorbate structure at Cu(111) containing n sulfur species (S atoms or thiolates) as well as X vacancies and Y adatoms. ECu(111) is the total energy of the clean unreconstructed Cu(111) surface, and ECu is the total energy of a copper atom in the bulk metal. Eads is the total energy of the free adsorbate in the gas phase with m = 1 for the adsorption of atomic sulfur and m = 2 for the adsorption of methanethiolate due to the dimethyl disulfide reference molecule. A is the surface area of the supercell. A fundamental requirement for studying the adsorption of sulfur species at the Cu(111) surface is a reliable description of copper. In Table 1 various properties of bulk copper like the cohesive energy, the equilibrium lattice constant and the bulk modulus are listed. As expected, we find that the PBE functional provides an excellent description of copper using our general setup. The lattice parameter of 3.63 Å for the cubic fcc unit cell is in very good agreement with experiment. The resulting DFT-PBE lattice constant of the (1 × 1) (111) surface unit cell is 2.567 Å. Also the energetic properties like the cohesive energy and the bulk modulus are well represented by the PBE functional.

Results and Discussion Methanethiolate Self-Assembled Monolayers at Cu(111) In order to investigate the structural and energetic properties of methanethiolate SAMs at Cu(111), a wide range of structural models shown in Figure 1 has been considered taking into account a large number of phases proposed in the literature. The obtained binding and surface energies are listed in Table 2. In general, as a reference, we have studied the adsorption of C1 in each unit cell also for the ideal, unreconstructed Cu(111) surface. Further, a thiolate coverage θ = 1/3 MLs and



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

copper vacancy concentration of 1/3 MLs similar to the composition of the adsorbate layer in the pseudo(100) reconstruction has been tested where applicable. In structure T1, a defect-free (2 × 2) cell with coverage θ = 1/4 MLs, methanethiolate is adsorbed in an fcc site shifted towards a bridge site and has a binding energy of about -0.85 eV, which is nearly the same as the binding energy of -0.86 eV for θ = 1/9 MLs in a defect-free (3× 3) cell (not shown). However, due to the larger surface area of the (3 × 3) cell, the surface energies differ substantially. It is about -37 meV/Å2 for the (2 × 2) cell, but only -17 meV/Å2 for the (3 × 3) cell. Increasing the coverage in the (3 × 3) cell to θ = 1/3 MLs by adsorbing in total three molecules (structure T2) reduces the surface energy roughly to the value of the (2 × 2) cell. In the next step, we have then introduced three copper vacancies in the topmost Cu(111) layer (structure T3), which corresponds to the proposed vacancy concentration in the pseudo(100) reconstruction. The initial structure before optimization is shown in Figure 2. All atoms have been arranged to ensure an initial fourfold coordination of the sulfur atoms, which is the dominant structural motif in the pseudo(100) reconstruction and thus should be energetically preferable. Still, we note that the arrangement of the atoms is very different from the pseudo(100) structure. In the relaxed structure T3 in Figure 1 this fourfold coordination is strongly distorted and the binding energy is even marginally higher than at the vacancy-free surface. √ √ Another possibility to realize a coverage of θ = 1/3 MLs is the ( 3 × 3)R30◦ cell, which has been reported in experiments by Domange and Oudar in 1968 44 but could not be reproduced √ √ by other groups. The ideal Cu(111) surface with a ( 3 × 3)R30◦ cell is structure T4. The sulfur headgroup atom is adsorbed in a shifted fcc site and the surface energy is significantly lower than the surface energy of structure T2 with the same coverage. The most important structural difference between these models is that the thiolates are arranged in a regular hexagonal pattern in T4, while they adopt a honeycomb-like lattice in the (3 × 3) structure T2.

√ √ The introduction of a vacancy in the topmost Cu(111) layer of the ( 3 × 3)R30◦ cell in

structure T5 increases the surface energy, although also in T5 the stoichiometric composition of the “adsorbate phase” formed by the thiol and the two remaining copper atoms in the topmost layer


Page 10 of 39

Page 11 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


corresponds to that of the pseudo(100) phase. 19 Based on STM experiments it has been proposed by  Driver  and Woodruff that the pseudo(100)

5 0 reconstruction can be described approximately by a   supercell. 70 In this cell, which con1 3 tains 15 copper atoms per Cu(111) layer, there are five adsorbed thiolate For reference,  molecules. 

5 0 we have first determined the stability of a SAM in the defect-free   cell T6. The binding 1 3 energy as well as the surface energy show that this structure is less stable than the defect-free √ √ ( 3 × 3)R30◦ cell T4.

In the next step, we have introduced five vacancies in the top copper layer corresponding to the experimentally determined vacancy concentration of the pseudo(100) phase. The remaining copper atoms have been arranged initially following the experimentally suggested structure to obtain fourfold coordinated sulfur atoms, as shown in the top left panel of Figure 3. The optimization of this structure yields structure T7a shown in the same figure, which contains strongly distorted fourfold and threefold coordinated thiolate molecules. Comparing this result with the minimum structure obtained in DFT calculations by Grönbeck 43 we find that there are slight differences in the positions of the reconstructed copper atoms. Recalculating the structure using the copper atom positions of Grönbeck yields structure T7c. A third copper configuration we tried (T7b) relaxed to structure T7a for C1 adsorption but remained stable for longer alkyl chains like C2 . In general, the binding energies of all these local minima are extremely similar and differ only by a few meV per thiolate, which is well below the intrinsic error of the PBE functional. The low surface energies of about -48 meV/Å2 show that these structures are more stable  than  all structures discussed

5 0 above. Analyzing these structures in more detail it seems that the   cell may not be the op1 3 timum choice for the pseudo(100) phase since only strongly distorted copper squares are obtained

in apparent contradiction to very regular features in STM images. We find that the copper atoms generally tend to relax to threefold hollow sites of the underlying Cu(111) layer. This in principle does not allow for the square arrangement of the copper atoms. Still, there are several local min-



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 12 of 39

 5 0 imum structures with comparable energy and it should be kept in mind that the   cell just 1 3 represents an approximation to the pseudo(100) reconstruction, which is most probably incom

mensurate with the Cu(111) surface. Therefore, the available surface area per thiolate molecule is not the same as in the true phase, and the resulting stress may distort the structure sufficiently to enable a relaxation of the copper atoms into the threefold hollow sites. At this point, we can only speculate that dynamical averaging effects might play an overriding role, such as those that have been shown recently to be necessary for explaining STM images of water monolayers on ZnO or F-centers on TiO2 , thus going beyond static total energy calculations as enabled by ab initio molecular dynamics. 71,72 This endeavor, however, would be clearly beyond the scope of the present investigation given that these effects, if present, are expected to be much more complex in nature than those seen earlier.



 5 0 Encouraged by the high stability of the   cell containing five copper vacancies, we have 1 3 also explored higher and lower vacancy concentrations. In structure T8 there are just four vacancies, and we find that this structure has basically the same binding energy as the different minima of T7 with the “correct” copper atom density in the reconstructed layer. Also in T8 most of the thiolates are fourfold coordinated, but the squares are strongly distorted as well and it should be noted that the stoichiometry of the surface reconstruction is not compatible with the experimentally determined ratio of copper to sulfur, which is only  correct  in models T7. The easy incorporation

5 0 of an additional atom further supports that the   cell may not be the optimum choice to 1 3 represent the pseudo(100) reconstruction. In structure T9 there is one copper atom less in the reconstructed layer than in structure T7, and the resulting binding energy is slightly higher than for T7 and T8. As a consequence of the missing copper atom, one thiolate is only twofold coordinated. Due to the lower density of copper atoms in the reconstructed layer, like for T7 also for T9 there are certainly several other energetically comparable local minimum structures, but we did not investigate this in more detail.


Page 13 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


 5 0 Since the shape of the   cell is maybe not the optimum one, we have explored another 1 3    4 3 cell with the matrix notation   shown in Figure 1 having the same surface area and cov−1 3 erage. Initially we have investigated the binding energy at the unreconstructed defect-free surface 

in structure T10. It is less stable than structures T4 and T6, which have the same coverage. In the next step, we have introduced five copper vacancies (structure T11) such that the chemical composition of the reconstructed layer is the same as in the pseudo(100) phase. Further, we have arranged the copper atoms initially to obtain fourfold coordinated sulfur atoms (cf. Figure 2). The relaxed structure T11 in Figure 1 still shows somewhat distorted fourfold coordinations, but it is energetically not competitive. Structure T12 represents a (5 × 5) supercell of the ideal unreconstructed Cu(111) surface, which has been suggested in experiment as a model for the honeycomb phase forming initially before the kinetically hindered reconstruction towards the pseudo(100) phase sets in. 19 The thiolate coverage of this phase is not known. Therefore, we have varied the number of thiolate molecules from six to nine corresponding to coverages between 6/25 and 9/25 MLs. Due to the size of the supercell, only a four-layer slab has been used in this case. We find the lowest binding and surface energies for the adsorption of seven molecules, which form a honeycomb lattice of thiolate molecules adsorbed in threefold hollow sites, in which an additional thiolate is adsorbed in every third thiolate hexagon. This model has also been proposed by Driver and Woodruff based on STM data. 19 Remarkably, the surface energy of this structure is only slightly higher than the surface energy of the pseudo(100) structures T7. √ √ Finally, we have investigated the stability of a fictitious ( 7 × 7)R19.1◦ phase, because this supercell is the most stable structure of atomic sulfur at Cu(111) (cf. Section ). We have chosen two different initial arrangements for the copper atoms of the topmost vacancy-free layer, the ideal Cu(111) surface and a reconstruction providing a fourfold coordination for all sulfur atoms as shown in Figure 2. Upon relaxing both models we find the same optimized structure T13 shown in



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Figure 1. It corresponds to the ideal Cu(111) surface and is energetically very unfavorable. In summary, many structural models have been tested to investigate the stable phase of C1 at Cu(111). Many of these structures (T3, T5, T7, and T11) have a thiolate coverage and copper vacancy concentration corresponding to the experimentally found pseudo(100) reconstruction.   The

5 0 most stable structures we find are several basically degenerate local minima in a   cell, 1 3

which has been suggested as a good approximation to the true non-commensurate phase. 19 One

of these structures has been identified in previous theoretical work by Grönbeck. 43 Still, the local coordination of the sulfur atoms does not correspond to the almost ideal square features observed in STM, and it is likely that larger unit cells can provide better structural models. For the honeycomb structure formed in experiment before the reconstruction to the pseudo(100) phase sets in we find a (5 × 5) cell with seven thiolate species to be most stable in agreement with experiment, but also here other competitive local minimum structures cannot be excluded.

Sulfur Adsorption at Cu(111) The rich phase diagram for sulfur adsorption at the Cu(111) surface represents a challenge for theoretical investigations since many of the experimentally observed structures, in particular in the low-coverage regime, have very large supercells. Further, for these structures the available experimental data is very limited and their low thermal stability indicates that weak interactions are responsible for their stabilization. The situation is different for the high-coverage regime, and √ √ in particular the very stable ( 7 × 7)R19.1◦ structure has been subject of many experimental studies. Still, its atomic structure has not yet been identified unambiguously, and experiments have led to contradictory conclusions. √ √ Here, we focus on DFT calculations for a variety of models for the ( 7 × 7)R19.1◦ structure including a wide range of structures discussed in the literature. In addition, for comparison calculations for the metastable pseudo(100) reconstruction of sulfur at Cu(111), and for basic models √ √ of the unreconstructed surface were carried out employing ( 3 × 3)R30◦ , (2 × 2), and (3 × 3) 14 ACS Paragon Plus Environment

Page 14 of 39

Page 15 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


supercells. The structural models considered are shown in Figure 4 along with the labels used in the present work. The corresponding sulfur binding energies and surface energies are given in Table 3. √ √ Structures S1 and S2 represent ( 3 × 3)R30◦ supercells with a sulfur coverage of θ = 1/3 MLs. At the ideal (111) surface in structure S1 the sulfur atoms are adsorbed in the energetically preferred fcc hollow sites with a binding energy of -4.28 eV per atom and a Cu-S bond length of 2.22 Å. Structure S2 contains a copper vacancy resulting in the formation of copper hexagons at the surface. In this structure, the sulfur atoms are adsorbed at the vacancy only about 0.79 Å above the first metal layer, while in S1 the sulfur layer is 1.61 Å above the surface. The sulfur coordination in the copper vacancy of S2 does not correspond to an ideal hexagon, but the sulfur atom binds closer to two of the metal atoms, resulting in two Cu-S bonds of about 2.23 Å, while the copper atoms at the opposite side of the hexagon have a distance of 3.31 Å. The copper vacancy results in a weaker sulfur binding energy in comparison to structure S1. Despite the low binding energy √ √ of about -4.28 eV in structure S1, the ( 3 × 3)R30◦ is energetically not competitive, because the surface energy is comparably small due to the low coverage. This is in agreement with the √ √ experimental finding that the ( 3 × 3)R30◦ is not observed at room temperature. √ √ Structures S3 to S10 represent models for the ( 7 × 7)R19.1◦ reconstruction differing in the number of copper adatoms and vacancies. In all structures there are three adsorbed sulfur atoms resulting in a coverage of θ = 3/7 MLs as has been found in experiment. An even distribution of the sulfur atoms can be achieved by occupying three different sites, the fcc, hcp and top sites. The optimization of this initial arrangement at the ideal vacancy-free Cu(111) surface yields structure S3, in which a copper atom is lifted by about 1.06 Å to form a CuS3 complex at the surface. The positions of the three S atoms adjust to bridge sites around the lifted atom, and the obtained sulfur pattern corresponds to a distorted hexagonal sulfur layer. Structure S4 has been obtained by optimizing the ideal Cu(111) surface with the three sulfur atoms initially adsorbed in bridge sites corresponding to a pattern of empty hexagons as shown in the left panel of Figure 5. During the optimization we found a remarkable reordering of the copper



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

atoms in the first layer resulting in fourfold coordinated sulfur atoms with a Cu-S bond length of about 2.3 Å. The squares formed by the copper atoms are somewhat distorted, and the topmost copper layer is slightly corrugated, which might be an indication for surface stress. In spite of the fourfold coordinated sulfur atoms, structure S4 has a clearly higher energy than structure S3. Both structural models, S3 and S4, have been proposed in experiment, 55 but they are among the √ √ least stable models for the ( 7 × 7)R19.1◦ structure we found. We have also tested a modified version of structure S4, in which the copper atom not participating in the copper squares is removed to reduce possible surface stress (not shown). In the resulting structure the fourfold coordination of the sulfur atoms is maintained, but the binding energy increases by about 0.09 eV to -3.67 eV per atom, rendering this structure even less competitive than S4, its surface energy is -276 meV/Å2 . Further, we have investigated model S5, which has been suggested by Kitajima et al. 55 In this structure there is one vacancy, and optimizing an initial structure with sulfur atoms in fcc, hcp and top sites and the copper vacancy below the top site sulfur atom we find that the structure hardly changes except for a large corrugation in the heights of the sulfur atoms. The sulfur atom at the vacancy is about 1.7 Å lower than the sulfur atoms at the hcp and fcc sites. In contrast to the vacancy in structure S2 here the sulfur atom occupies approximately the center of the copper hexagon with a Cu-S distance of about 2.5 to 2.6 Å. The sulfur atom at the vacancy is about 0.1 Å below the topmost copper layer. In structure S6 there are two copper vacancies and the obtained structure is very similar to √ √ the ( 7 × 7)R19.1◦ structure formed by methylthiolate at the Ag(111) surface. 73 Also for sulfur atoms at Cu(111) this structure is surprisingly stable, and only three other structures in our set have a lower surface energy. The sulfur atoms are located in the two vacancies and after relaxation they are approximately fivefold coordinated by the copper atoms in the first layer. The shortest Cu-S distance in this distorted pentagon is 2.26 Å, the longest Cu-S distance is 2.96 Å. All copper atoms have about the same height, and the sulfur atoms are located about 0.8 Å above the copper layer. Alternatively to distorted pentagons, the structure can also be viewed as one Cu3 S3 cluster per unit cell and a honeycomb lattice formed by two more copper atoms per cell to fill the gaps in between


Page 16 of 39

Page 17 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


the clusters. The Cu3 S3 clusters are rotated about 10◦ with respect to the [101] direction of the surface. In structures S7 and S8 there are four copper vacancies or alternatively three copper adatoms. Both structures have very low surface energies, and S7 is the most stable of all structures we investigated within the accuracy our DFT calculations. It consists of two nested hexagonal lattices of three sulfur atoms and three copper atoms in the first layer. The Cu-S bonds have a length of 2.36 (for S at fcc), 2.27 (for S at hcp) and 2.22 (for S at top) Å. This structure has first been suggested in experimental work by Prince et al. 54 We can confirm that the sulfur atom at the top site of the underlying full metal layer is located slightly, i.e. about 0.42 Å, above the topmost incomplete copper layer, while the sulfur atoms in the fcc and hcp sites are about 0.25 and 0.08 Å below the topmost copper atoms. Another similar structure suggested by Ruan et al. 45 with all sulfur atoms above the topmost copper layer has not been found to be stable. In structure S8 there are Cu3 S3 clusters at the surface with the sulfur atoms adsorbed in distorted bridge sites around the Cu3 core, which has an increased Cu-Cu distance of about 2.78 Å compared to 2.57 Å in the bulk. This distortion can be explained by a slight counterclockwise rotation of about 10◦ of the cluster with respect to the [101] direction to allow for a shorter distance between the sulfur atoms of one cluster and the copper atoms of another neighboring cluster, which is about 2.70 Å as compared to 2.22 Å within a Cu3 S3 cluster. In fact, structure S7 could be viewed as structure S8 with drastically expanded Cu-Cu distances in the Cu3 S3 clusters, and indeed also ◦

the copper adatoms in S7 form rows, which are tilted by an angle of about 10 with respect to the copper rows in the ideal (111) surface below. Alternatively, structure S8 can be derived from structure S6 by removing the two copper atoms in between the Cu3 S3 clusters. Structure S9, which has been suggested by Foss et al., 56 contains four copper adatoms, which form distorted square clusters at the surface. Two sulfur atoms occupy fcc and hcp hollow sites of the underlying (111) layer in between the clusters, while a third sulfur atom is located above the fourfold hollow side of the Cu4 cluster. This structure, in which at least one of the three sulfur atoms is fourfold coordinated, has been discussed as the most stable structure in recent years by



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

several groups 51,56 but in our calculations it is slightly less stable than the model suggested by Prince et al. 54 This is in agreement with the only published theoretical study of these models by Alfonso, 64 but we find a binding energy difference per sulfur atom of only about 30 meV, which is too small to make a conclusive statement based on the present calculations. √ √ The last model for the ( 7 × 7)R19.1◦ phase we studied is structure S10, which has been suggested by Saidy and Mitchell. 58 It is similar to structure S7 proposed by Prince et al., 54 but in the Saidy and Mitchell model the copper atom below the sulfur at the top site is removed. In the calculations by Alfonso 64 this structure has been found to have a binding energy approximately 0.4 eV higher than for the models by Prince and by Foss. In our calculations this difference is much smaller and only about 0.1 eV per sulfur atom. A reason for this difference might be that during the geometry relaxation in our calculations we find that the sulfur atom originally located in the energetically unfavorable copper vacancy moved upwards on top of the Cu3 cluster yielding a more stable structure. In many structural models discussed above, Cu3 S3 clusters are important components, and it has also been proposed that they are crucial for the transport of copper atoms along the surface during the formation of sulfur adsorbate phases. 48 To further investigate the stability of Cu3 S3 clusters at the Cu(111) surface we have also studied the larger (3 × 3) supercell S11. Its binding energy is very low, but nevertheless the structure is not very stable in terms of the surface energy due to the large surface area of the (3 × 3) cell. It should be noted that in principle there are four possibilities to adsorb the Cu3 S3 clusters at the surface. The copper atoms can be adsorbed in fcc or hcp hollow sites and for both cases there are two possibilities to form microfacets with the underlying Cu(111) surface as shown in Figure 7. The resulting sulfur binding energies for these structures vary by about 0.11 eV (cf. Table 4) and in Table 3 only the most stable configuration is listed. A similar set of Cu3 S3 cluster arrangements is also possible for structure S8. In this case, however, we have not been able to obtain all four possible configurations after structural relaxations, and instead in two cases structures very similar to S7 have been obtained. In contrast to the more open structure S11, in the remaining two configurations the clusters are slightly rotated


Page 18 of 39

Page 19 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


√ √ because of the more densely packed ( 7 × 7)R19.1◦ phase. The corresponding binding energies are also listed in Table 4. The metastable pseudo(100) structure found by Driver and Woodruff is more complicated than the corresponding reconstructed phase of thiolate SAMs 59 in that the mixed Cu-S layer is corrugated and there is a modulation in the distortion  ofthe Cu4 clusters coordinating the sulfur 5 0 atoms. For reference we have first calculated the   supercell structure S12 corresponding to 1 3 the pseudo(100) reconstruction observed for thiols at the Cu(111) surface. The atomic rearrangements obtained in the optimization of the initial ideal structure shown in Figure 5b are significantly smaller resulting in an almost ideal c(2 × 2) superlattice of the sulfur atoms, which are located in distorted fourfold sites. In contrast to the thiolate structure, the copper atoms do not relax to threefold hollow sites, probably due to the much stronger interaction with sulfur atoms. A more realistic structural model for the pseudo(100) phase of sulfur has been suggested by Driver and Woodruff. 59 This structure has a very large supercell, which we have approximated by a (2 × 11) cell (S13 in Figure 6) containing eight sulfur atoms resulting in a coverage of 4/11 MLs, which is the same coverage as the coverage of 0.36 MLs by Driver and Woodruff, 59 but slightly larger than  as mentioned 

5 0 the coverage of 1/3 MLs in the   supercell of structure S12. In the relaxed structure S13 all 1 3 sulfur atoms are still fourfold coordinated, while the copper squares are only slightly distorted. In comparison with structure S12, the surface energy of S13 is clearly lower showing that larger unit cells than in structure S12 are needed to accommodate the pseudo(100) phase of sulfur at Cu(111). More realistic models employing larger unit cells are likely to provide structures with even lower surface energies. Still, in contrast to the structures formed by thiolates at the Cu(111) surface, this model for the pseudo(100) reconstruction of sulfur atoms is energetically not competitive with the √ √ ( 7 × 7)R19.1◦ phase. Finally, for reference, we have also calculated the energies of sulfur atoms adsorbed in regular (2 × 2) (S14, not shown, θ = 1/4 MLs) and (3 × 3) (S15, not shown, θ = 1/9 MLs) supercells. Although the binding energy in the (3 × 3) cell is the lowest of all obtained binding energies, the 19 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

surface energies of the (2 × 2) and (3 × 3) structures show that these structures are not competitive in agreement with experiment. √ √ In conclusion, the ( 7 × 7)R19.1◦ phase has been confirmed by our DFT calculations as the most stable structure in the high coverage regime in agreement with experiment. However, several structural models including the models proposed by Foss et al. 56 and by Prince et al. 54 are too close in energy to make a conclusive statement. In agreement with previous theoretical work 64 the model suggested by Saidy and Mitchell 58 has a too high binding energy to be competitive. It should be noted that in order to identify the most stable structure, suitable structural models are required, and it may well be that there are other even more stable structures not considered in this work. Ideally, systematic searches of the configuration space should be carried out to identify further interesting candidates, but the related computational costs are very high. Also the chemical composition of the mixed copper-sulfur reconstructed layer should be included in this search as no consensus has yet been reached on the number of copper adatoms, which is three in the model by Prince and four in the model by Foss. Last but not least, entropy and temperature effects might be decisive factors in addition to just total energies, which would require converged free energy calculations for an enormous set of configurations, which appears to us outside reach. Several other questions on the phase diagram of sulfur at Cu(111) remain to be answered, and in particular the   low-coverage phases observed at low temperatures, but also the intermediate “zig 4 1 zag”   phase reported by Ruan et al., 45 represent a challenge for theory due to the large −1 4 supercells and small amount of available experimental data on these structures.

Conclusions and Outlook In summary, a comprehensive study on the adsorbate phases of methanethiolate and of sulfur atoms formed at the Cu(111) surface has been carried out by density-functional calculations. For   5 0 methanethiolate it has been confirmed that the   cell represents to date the best approxi1 3 20 ACS Paragon Plus Environment

Page 20 of 39

Page 21 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


mation to the experimentally observed pseudo(100) reconstruction. Still, the strong distortions in the fourfold coordination of the thiolate molecules, the existence of several local minima differing in the positions of the reconstructed copper atoms as well as that an additional copper atom yields an equally favorable structure suggest that this supercell is not the optimum choice for the pseudo(100) reconstruction. Larger supercells may provide a more realistic model for this proba√ √ bly non-commensurate structure. For atomic sulfur we can confirm that a ( 7 × 7)R19.1◦ cell yields the most stable structure, but several models differing even in the number of copper atoms in the reconstructed layer have similar binding energies. Taking into account the intrinsic error of the PBE exchange correlation functional, it is not possible to make a conclusive statement on the most stable structure, and there may be further structures with a comparable stability. Last but not least, thermodynamics, dynamics and particle exchange might be required to provide the final answer in view of both small total energy differences of various structures, possibly of slightly different compositions, as well as putative averaging effects involving quasi-degenerate superstructures with shallow interconnecting barriers. Yet, our current results provide a solid basis for carrying out follow-up studies of the mechanical stability of thiolate/copper SAMs and monatomic junctions in the realm of molecular nanomechanics and covalent mechanochemistry of molecule/metal hybrid interfaces.

Acknowledgement We thank the NRW Research School “Research with Synchrotron Radiation”, the DFG (Emmy Noether program, Reinhart Koselleck program), the Research Department “ Interfacial Systems Chemistry”, and the FCI for partial financial support.

References (1) Woodruff, D. P. Phys. Chem. Chem. Phys. 2008, 10, 7211-7221. (2) Ulman, A. Chem. Rev. 1996, 96, 1533-1554.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(3) Schreiber, F. Prog. Surf. Sci. 2000, 65, 151-256. (4) Vericat, C.; Vela, M. E.; Salvarezza, R. C. Phys. Chem. Chem. Phys. 2005, 7, 3258-3268. (5) Vericat, C.; Vela, M. E.; Benitez, G. A.; Gago, J. A. M.; Torrelles, X.; Salvarezza, R. C. J. Phys.: Condens. Matter 2006, 18, R867-R900. (6) Schreiber, F. J. Phys.: Condens. Matter 2004, 16, R881-R900. (7) Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M. Chem. Rev. 2005, 105, 1103-1169. (8) Campbell, C. T.; Koel, B. E. Surf. Sci. 1987, 183, 100-112. (9) Wiegand, B. C.; Friend, C. M. Chem. Rev. 1992, 92, 491-504. (10) Mirkin, C. A.; Ratner, M. A. Annu. Rev. Phys. Chem. 1992, 43, 719-754. (11) Jennings, G. K.; Laibinis, P. E. Colloid Surf. A 1996, 116, 105-114. (12) Laibinis, P. E.; Whitesides, G. M. J. Am. Chem. Soc. 1992, 114, 9022-9028. (13) Jadzinsky, P. D.; Calero, G.; Ackerson, C. J.; Bushnell, D. A.; Kornberg, R. D. Science 2007, 318, 430-433. (14) Saha, K.; Agasti, S. S.; Kim, C.; Li, X.; Rotello, V. M. Chem. Rev. 2012, 112, 2739-2779. (15) Laibinis, P. E.; Whitesides, G. M.; Allara, D. L.; Tao, Y. T.; Parikh, A. N.; Nuzzo, R. G. J. Am. Chem. Soc. 1991, 113, 7152-7167. (16) Kondoh, H.; Saito, N.; Matsui, F.; Yokoyama, T.; Ohta, T.; Kuroda, H. J. Phys. Chem. B 2001, 105, 12870-12878. (17) Parkinson, G. S.; Muñoz-Márquez, M. A.; Quinn, P. D.; Gladys, M. J.; Woodruff, D. P.; Bailey, P.; Noakes, T. C. Q. Surf. Sci. 2005, 598, 209-217.


Page 22 of 39

Page 23 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(18) Prince, N. P.; Seymour, D. L.; Woodruff, D. P.; Jones, R. G.; Walter, W. Surf. Sci. 1989, 215, 566-576. (19) Driver, S. M.; Woodruff, D. P. Surf. Sci. 2000, 457, 11-23. (20) Woodruff, D. P. Nucl. Instrum. Methods Phys. Res. Sect. B: Beam Int. Mat. Atoms 2007, 256, 293-299. (21) Furlong, O. J.; Miller, B. P.; Li, Z.; Walker, J.; Burkholder, L.; Tysoe, W. T. Langmuir 2010, 26, 16375-16380. (22) Kariapper, M. S.; Grom, G. F.; Jackson, G. J.; McConville, C. F.; Woodruff, D. P. J. Phys.: Condens. Matter 1998, 10, 8661-8670. (23) Jackson, G. J.; Woodruff, D. P.; Jones, R. G.; Singh, N. K.; Chan, A. S. Y.; Cowie, B. C. C.; Formoso, V. Phys. Rev. Lett. 2000, 84, 119-122. (24) Prince, N. P.; Ashwin, M. J.; Woodruff, D. P.; Singh, N. K.; Walter, W.; Jones, R. G. Faraday Discuss. Chem. Soc. 1990, 89, 301-310. (25) Paterson, S.; Allison, W.; Hedgeland, H.; Ellis, J.; Jardine, A. P. Phys. Rev. Lett. 2011, 106, 256101-1(4). (26) Sung, M. M.; Sung, K.; Kim, C. G.; Lee, S. S.; Kim, Y. J. Phys. Chem. B 2000, 104, 22732277. (27) Floriano, P. N.; Schlieben, O.; Doomes, E. E.; Klein, I.; Janssen, J.; Hormes, J.; Poliakoff, E. D.; McCarley, R. L. Chem. Phys. Lett. 2000, 321, 175-181. (28) Laurin, M.; Shao, X.; Fujimori, Y.; Nojima, A.; Sako, E. O.; Miyawaki, J.; Shimojo, M.; Iwasawa, Y.; Ohta, T.; Kondoh, H. J. Electr. Spectr. Rel. Phen. 2009, 1 72, 88-94. (29) Imanishi, A.; Isawa, K.; Matsui, F.; Tsuduki, T.; Yokoyama, T.; Kondoh, H.; Kitajima, Y.; Ohta, T. Surf. Sci. 1998, 407, 282-292. 23 ACS Paragon Plus Environment


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(30) Driver, S. M.; Woodruff, D. P. Langmuir 2000, 16, 6693-6700. (31) Calderón, C. A.; Ojeda, C.; Macagno, V. A.; Paredes-Olivera, P.; Patrito, E. M. J. Phys. Chem. C 2010, 114, 3945-3957. (32) Rieley, H.; Kendall, G. K.; Chan, A.; Jones, R. G.; Lüdecke, J.; Woodruff, D. P.; Cowie, B. C. C. Surf. Sci. 1997, 392, 143-152. (33) Dilimon, V. S.; Fonder, G.; Delhalle, J.; Mekhalif, Z. J. Phys. Chem. C 2011, 115, 1820218207. (34) Konôpka, M.; Rousseau, R.; Štich, I.; Marx, D. J. Am. Chem. Soc. 2004, 126, 12103-12111. (35) Konôpka, M.; Rousseau, R.; Štich, I.; Marx, D. Phys. Rev. Lett. 2005, 95, 096102-1(4). (36) Konôpka, M.; Turanský, R.; Reichert, J.; Fuchs, H.; Marx, D.; and Štich, I. Phys. Rev. Lett. 2008, 100, 115503-1(4). (37) Konôpka, M.; Turanský, R.; Dubecký, M.; Marx, D.; Štich, I. J. Phys. Chem. C 2009, 113, 8878-8887. (38) Konôpka, M.; Turanský, R.; Doltsinis, N. L.; Marx, D.; Štich, I. Adv. Solid State Phys. 2009, 48, 219-235. (39) Ribas-Arino, J.; Marx, D. Chem. Rev. (online at http://pubs.acs.org/doi/abs/10.1021/cr200399q). (40) Lai, Y.-H.; Yeh, C.-T.; Cheng, S.-H.; Liao, P.; Hung, W.-H. J. Phys. Chem. B 2002, 106, 5438-5446. (41) Akinaga, Y.; Nakajima, T.; Hirao, K. J. Chem. Phys. 2001, 114, 8555-8564. (42) Cometto, F. P.; Paredes-Olivera, P.; Macagno, V. A.; Patrito, E. M. J. Phys. Chem. B 2005, 109, 21737-21748.


Page 24 of 39

Page 25 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(43) Grönbeck, H. J. Phys. Chem. C 2010, 114, 15973-15978. (44) Domange, J. L.; Ouder, J. Surf. Sci. 1968, 11, 124-142. (45) Ruan, L.; Stensgaard, I.; Besenbacher, F.; Laegsgaard, E. Ultramicroscopy 1992, 42-44, 498504. (46) Park, R. L.; Madden, H. H. Jr. Surf. Sci. 1968, 11, 188-202. (47) Ling, W. L.; Bartelt, N. C.; Pohl, K.; de la Figuera, J.; Hwang, R. Q.; McCarty, K. F. Phys. Rev. Lett. 2004, 93, 166101-1(4). (48) Feibelman, P. J. Phys. Rev. Lett. 2000, 85, 606-609. (49) Rousseau, G. B. D.; Mulligan, A.; Bovet, N.; Adams, M.; Dhanak, V.; Kadodwala, M. Surf. Sci. 2006, 600, 897-903. (50) Wahlström, E.; Ekvall, I.; Olin, H.; Lindgren, S.; Walldén, L. Phys. Rev. B 1999, 60, 1069910702. (51) Wahlström, E.; Ekvall, I.; Kihlgren, T.; Olin, H.; Lindgren, S.; Walldén, L. Phys. Rev. B 2001, 64, 155406-1(7). (52) Jackson, G. J.; Driver, S. M.; Woodruff, D. P.; Cowie, B. C. C.; Jones, R. G. Surf. Sci. 2000, 453, 183-190. (53) Wang, D.; Xu, Q. M.; Wan, L.; Wang, C.; Bai, C. Surf. Sci. 2002, 499, L159-L163. (54) Prince, N. P.; Seymour, D. L.; Ashwin, M. J.; McConville, C. F.; Woodruff, D. P.; Jones, R. G. Surf. Sci. 1990, 230, 13-26. (55) Kitajima, Y.; Yokoyama, T.; Takata, Y.; Yoshiki, M.; Ohta, T.; Funabashi, M.; Kuroda, H. Physica Scripta. 1990, 41, 958-961.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(56) Foss, M.; Feidenhans’l, R.; Nielsen, M.; Findeisen, E.; Buslaps, T.; Johnson, R. L.; Besenbacher, F. Surf. Sci. 1997, 388, 5-14. (57) Moison, J. M.; Domange, J. L. Surf. Sci. 1977, 69, 336-348. (58) Saidy, M.; Mitchell, K. A. R. Surf. Sci. 1999, 441, 425-435. (59) Driver, S. M.; Woodruff, D. P. Surf. Sci. 2001, 479, 1-10. (60) Alfonso, D. R.; Cugini, A. V.; Sholl, D. S. Surf. Sci. 2003, 546, 12-26. (61) Alfonso, D. R. Surf. Sci. 2008, 602, 2758-2768. (62) May, M.; Gonzalez, S.; Illas, F. Surf. Sci. 2008, 602, 906-913. (63) Pang, X.-Y.; Xue, L-Q.; Wang, G.-C. Langmuir 2007, 23, 4910-4917. (64) Alfonso, D. R. J. Phys. Chem. C 2011, 115, 17077-17091. (65) Baroni, S.; Dal Corso, A.; de Gironcoli, S.; Giannozzi, P.; Cavazzoni, C.; Ballabio, G.; Scandolo, S.; Chiarotti, G.; Focher, P.; Pasquarello, A. et al., http://www.pwscf.org. (66) Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868. (67) Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1997, 78, 1396(E). (68) Vanderbilt, D. Phys. Rev. B 1990, 41, 7892-7895. (69) Kittel, C. Introduction to solid state physics; 7th ed.; New York: Wiley, 1996.   5 0 (70) Depending on the choice of lattice vectors in some publications the   cell 19,43 is also 1 3    4 3 described as a   cell. 1,20 −1 3 (71) Dulub, O.; Meyer, B.; Diebold, U. Phys. Rev. Lett. 2005, 95, 136101-1(4).


Page 26 of 39

Page 27 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(72) Kowalski, P. M.; Farnesi Camellone, M.; Nair, N. N.; Meyer, B.; Marx, D. Phys. Rev. Lett. 2010, 105, 146405-1(4). (73) Yu, M.; Woodruff, D. P.; Bovet, N.; Satterley, C. J.; Lovelock, K.; Jones, R. G.; Dhanak, V. J. Phys. Chem. B 2006, 110, 2164-2170.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Table 1: Selected properties (equilibrium lattice constant a0 , bulk modulus B0 and cohesive energy Ecoh ) of bulk Cu obtained with the PBE functional. property a0 (Å) B0 (GPa) Ecoh (eV)

DFT-PBE experiment 69 3.63 3.61 138 137 3.58 3.49


Page 28 of 39

Page 29 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table 2: Binding energies Eb and surface energies γ for the investigated models for methanethiolate at the Cu(111) surface for different thiolate coverages θ (see Figure 1 and Figure 3 for the corresponding structural models). label

supercell

(2 × 2) (3 × 3) (3 √× 3)√ (√3 × √3)R30◦ ( 3 × 3)R30◦ 5 0 T6 1 3 5 0 T7a 1 3 5 0 T7b 1 3 5 0 T7c 1 3 5 0 T8 1 3 5 0 T9 1 3 4 3 T10 −1 3 4 3 T11 −1 3 T12 (5 × 5) T12 (5 × 5) T12 (5 × 5) T12 (5 √× 5)√ T13a (√7 × √7)R19.1◦ T13b ( 7 × 7)R19.1◦

T1 T2 T3 T4 T5

number of molecules 1 3 3 1 1

θ number of Eb γ (MLs) vacancies (eV/adsorbate) (meV/Å2 ) 1/4 0 -0.85 -37 1/3 0 -0.63 -37 1/3 3 -0.62 -36 1/3 0 -0.79 -46 1/3 1 -0.70 -41

5

1/3

0

-0.71

-41

5

1/3

5

-0.81

-48

5

1/3

5

5

1/3

5

-0.81

-48

5

1/3

4

-0.82

-48

5

1/3

6

-0.79

-46

5

1/3

0

-0.68

-39

5

1/3

5

-0.71

-41

6 7 8 9 3 3

6/25 7/25 8/25 9/25 3/7 3/7

0 0 0 0 0 0


same minimum as T7a

-0.85 -36 -0.96 -47 -0.81 -45 -0.74 -42 -0.49 -37 same minimum as T13a


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 30 of 39

Table 3: Binding energies Eb of atomic sulfur adsorbed on the Cu(111) surface and surface energies γ of the resulting phases for different sulfur coverages θS (see Figure 4 and Figure 6 for the corresponding structural models). label S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15

supercell √ √ (√3 × √3)R30◦ (√3 × √3)R30◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ (√7 × √7)R19.1◦ ( 7 × 7)R19.1◦ (3 × 3) 5 0 1 3 (2 × 11) (2 × 2) (3 × 3)

number of S atoms 1 1 3 3 3 3 3 3 3 3 3

number of Cu θS Eb adatoms / vacancies (MLs) (eV/S atom) 0/0 1/3 -4.28 0/1 1/3 -3.66 0/0 3/7 -3.91 0/0 3/7 -3.76 0/1 3/7 -3.95 0/2 3/7 -4.07 0/4 3/7 -4.20 0/4 3/7 -4.12 0/3 3/7 -4.17 3/1 3/7 -3.83 3/0 1/3 -4.18

γ (meV/Å2 ) -250 -214 -294 -283 -296 -306 -315 -309 -313 -287 -244

5

0/5

1/3

-4.15

-242

8 1 1

0/6 0/0 0/0

4/11 1/4 1/9

-4.17 -4.36 -4.38

-265 -191 -85


Page 31 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table 4: Dependence of the sulfur binding energies on the rotation of the Cu3 S3 clusters in structures S8 and S11 (cf. Figure 7). structure S8 S8 S8 S8 S11 S11 S11 S11

site for Cu adatoms microfacet fcc 100 fcc 111 hcp 100 hcp 111 fcc 100 fcc 111 hcp 100 hcp 111

Eb (eV/S) -4.108 -4.169* -4.117 -4.164* -4.180 -4.073 -4.072 -4.068

* The initial S8-fcc111 and S8-hcp111 structures relax to atomic positions very similar to structure S7.



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 32 of 39

T1

T2

T3

T4

T5

T6

T8

T9

T10

T11

T12 6C1

T12 7C1

T12 8C1

T12 9C1

T13

Figure 1: Structural models for self-assembled monolayers of methylthiolate at the Cu(111) surface (see text).


Page 33 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


T3 initial

T11 initial

T13a initial

T13b initial

Figure 2: Initial models for methanethiolate self-assembled monolayers at Cu(111) before relaxation (see text).



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

T7 initial

T7a

T7b

T7c

Figure 3: Structural models for the pseudo(100) reconstruction induced by alkylthiolate adsorption at Cu(111). In the top left panel, the initial structure suggested by experiment 19 is shown, which has a Cu atomic density of 2/3 MLs in the reconstructed (100)-like layer. The sulfur atoms form a c(2×2) superstructure with respect to the reconstructed metal layer. In the other panels, several obtained local minimum structures are shown differing in the positions of the Cu atoms in the reconstructed layer. Structure T7b is not a minimum for methanethiolate, but for ethanethiolate.


Page 34 of 39

Page 35 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


S1

S2

S3

S4

S5

S6

S7

S8

S9

S10

S11

S12

Figure 4: Relaxed structures and labels of the investigated sulfur phases at Cu(111).



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

S4 initial

S12 initial

Figure 5: Initial sulfur atom positions for structural models S4 and S12 before the relaxation.


Page 36 of 39

Page 37 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


S13 initial

S13 final

Figure 6: Initial and relaxed structural model S13 for the pseudo(100) reconstruction of atomic sulfur at Cu(111).



1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

(a)

fcc−{100}

(b)

fcc−{111}

(c)

hcp−{100}

(d)

hcp−{111}

Figure 7: Top view of the optimized structures for Cu3 S3 clusters at (3×3) Cu(111) surfaces with four configurations: fcc-{100}, fcc-{111}, hcp-{100} and hcp-{111} when fcc and hcp refer to the adsorption sites of Cu adatoms, as well as {100} and {111} refer to the microfacets of the edge Cu atoms. The dashed black lines indicate the microfacets.


Page 38 of 39

Page 39 of 39

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table of Contents Image


Adsorption of Methanethiolate and Atomic Sulfur at the Cu (111

Recommend Documents