Article pubs.acs.org/Langmuir

Characterization of Two-Dimensional Chiral Self-Assemblies L- and D‑Methionine on Au(111) Vincent Humblot,* Frederik Tielens,* Noelia B. Luque, Harout Hampartsoumian, Christophe Méthivier, and Claire-Marie Pradier Sorbonnes Universités, UPMC Univ Paris 06, UMR CNRS 7197, Laboratoire de Réactivité de Surface, 4 place jussieu, F-75005 Paris, France S Supporting Information *

ABSTRACT: A combination of XPS, in situ RAIRS, LEED, and STM experiments together with ab initio DFT calculations were used to elucidate the self-assembly properties at the atomic level, and enabled the interpretation of the expression of surface chirality upon adsorption of both enantiomers of methionine on a clean Au(111) surface under UHV conditions. The combination of experimental results, in particular, LEED and STM data with quantum chemical calculations is shown to be a successful setup strategy for addressing this challenge. It was found that the methionine molecular self-assembly consists of the first molecule lying parallel to the gold surface and the second interacting with the first methionine through a 2D Hbond network. The interaction with the gold surface is weak. The stability of the assembly is mainly due to the presence of intermolecular H bonds, resulting in the formation of ziplike dimer rows on the Au(111) surface. The methionine molecules interact with each other via their amino acid functional groups. The assembly shows an asymmetric pattern due to a slightly different orientation of the methionine molecules with respect to the surface. Simulations of the STM image of methionine assemblies were consistent with the experimental STM image. The present study shows another example of Au(111) stabilizing a self-assembled biological layer, which is not chemically perturbed by the surface.

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INTRODUCTION The adsorption of biomolecules (amino acids, peptides, and proteins) on metal or oxidized surfaces is of the utmost importance in understanding biointerface phenomena in the fields of biomaterials, biocompatibility, and chiral recognition.1 Since the late 1990s, the adsorption of small biomolecules such as amino acids on metal surfaces has been extensively studied by means of surface science techniques in combination with quantum chemical calculations to identify the molecular orientation, adsorption mode, and 2D surface organization and assign the molecular interactions at the biointerface.2−8 The interest in self-assembling organic molecules at metal and oxide surfaces has been continuously growing. This is due to the large variety of possible applications foreseen, ranging from nanoelectronics9 to the preparation of hybrid organic− inorganic nano-objects,10 biosensors,11 and biomaterials.12 Bio-organic molecules such as amino acids are expected to play a primary role in these fields for several reasons. Amino acids are ideal model systems for the study of the adsorption behavior of biofunctional and bioactive molecules. They are the basic units of peptides and proteins and provide models for elucidating the interaction of these complex molecules with surfaces and thus for clarifying issues of biocompatibility. Because of the complexity of these systems, a careful combination of several techniques is indeed mandatory to provide a detailed characterization of the molecule−surface and © 2013 American Chemical Society

intermolecular interactions. Investigations have concentrated mainly on the adsorption of the most common amino acids (glycine, alanine, lysine) on various crystal faces of metals, especially on the coinage metals (Cu, Ag, and Au).2,9,13,14 Several studies of S-containing amino acids (mainly cysteine and methionine) at poorly reactive substrates such as Au15−20 and Ag9,21 or at chiral surfaces22 are reported in the literature. On the less reactive Au(111) surface, the adsorption of cysteine is governed by the creation of an S−Au bond with the S headgroup sitting preferentially at bridge sites.16 Methionine (met) is an important amino acid molecule participating in molecular biosynthesis in the human body. Its antioxidant properties have been shown to prevent cell damage resulting from chemotherapy and radiation during cancer treatment but without delaying antitumor activity.23 The study of mechanisms governing the adsorption of these molecules on metal surfaces is of great interest for the fundamental understanding of molecular self-assembly,24 and it represents, among other examples, a promising approach to the design of drug delivery carriers and bioarchitectures with controlled structure. Although the self-assembly of several amino acids on metal surfaces, such as Au(110)18,19 and Au(111),16,25,26 has Received: November 5, 2013 Revised: December 9, 2013 Published: December 10, 2013 203

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XPS Analysis. XPS analysis was performed using a SPECS (Phoibos 100-5 MCD) X-ray photoelectron spectrometer (SPECS, Germany) equipped with a monochromatized aluminum (Al Kα) Xray source (hν = 1486.6 eV) powered at 10 mA and 15 kV and a Phoibos 100 hemispherical energy analyzer. A pass energy of 50 eV was used for the survey scan, and 10 eV was used for high-resolution scans. The pressure in the analysis chamber during measurement was around 10−10 Torr or less. The photoelectron collection angle between the normal to the sample surface and the analyzer axis was 0°. The binding energy scale was set by fixing the C 1s component due to carbon bound only to carbon and hydrogen at 284.8 eV or the Au 4f peak at a binding energy of 84.0 eV. Data treatment was performed with the Casa XPS software (Casa Software Ltd., U.K.). Unless stated otherwise, the peaks were decomposed using a linear baseline and a component shape defined by the product of a Gauss and Lorentz function in a 70:30 ratio, respectively. Molar concentration ratios were calculated using peak areas normalized according to Scofield factors.33 STM Analysis. STM experiments were conducted in an Omicron Vakuumphysik XA VT-STM chamber with facilities for STM, LEED, and sample cleaning and a base pressure of 5 × 10−11 Torr. The Au(111) crystal was cleaned by cycles of Ar+ sputtering (PAr = 7 × 10−5 Torr, 600 V, duration 15 min), flashing, and annealing to 850 K for 30 min. Dosing of met was performed as described previously with the sample held at room temperature, all STM experiments were carried out with the sample at room temperature, and the images were acquired in constant current mode. The STM scanner was calibrated using the interspaced rows of the Au(110)-(1 × 2) reconstructed surface (interspacing distance = 8.15 Å) and the Cu(110)-O-(2 × 1) missing/added rows (interspacing distance = 5.1 Å).

attracted considerable attention, only a few studies have been dedicated to met, despite the aforementioned potential applications.9,27,28 Extended 2D molecularly ordered structures have been observed by Schiffrin et al.9 upon adsorption of Lmet on Ag(111); the silver surface was held at 320 K during the deposition in order to promote the formation of regular gratings. Even though chirality plays a key role in the assembly and ordering of molecules on metal substrates29 and also offers a promising tool for molecular recognition,18,30 the possible chiral arrangement of adsorbed met on various materials has never been characterized in detail by means of complementary surface science techniques and theoretical calculations. In these studies, theoretical calculations, aimed at describing self-assemblies on surfaces, are crucial and very powerful for the precise determination of the adsorption geometry on the molecular level, especially when combined with STM experiments.15,16,31,32 In this study, we investigated the self-assembly of both enantiomers of methionine on the less reactive Au(111) surface under UHV conditions by means of experimental techniques, reflection absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and low energy electron diffraction (LEED), together with the use of periodic density functional theory (DFT) calculations. Our study highlights the formation of highly ordered and extended 2D chiral arrays and strongly suggests that the molecular chirality of the met adsorbed layer, on the achiral Au(111) surface, proceeds via the creation of intramolecular and intermolecular H-bond networks.

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COMPUTATIONAL METHOD Calculations were performed in the framework of periodic DFT by means of the Vienna ab initio simulation package (VASP).34,35 The electron−ion interactions were described by the projector augmented wave (PAW)36,37 method, representing the valence electrons, as provided in the code libraries. The convergence of the plane-wave expansion was obtained with a cutoff of 500 eV. The generalized gradient approximation (GGA) was used with the functional of Perdew−Burke− Ernzerhof (PBE).38 Sampling in the Brillouin zone was performed on 3 × 2 × 1 and 6 × 3 × 1 grids. Because our system involves interacting organic molecules, we investigated the influence of introducing dispersion forces by using the Grimme D2 method39 as implemented in VASP 5.2.11. DFT-D2 Grimme (G, D2) describes the van der Waals interactions between a particle and its neighbors for a given radius via a simple pairwise force field. This force field is optimized for several popular DFT functionals. In this case, this operator takes one atom as a reference and calculates the interactions of this atom with those around until a given distance or radius is attained and is the same for all atoms in the system. Finally, the dispersion energy is summed to the pure DFT energy:

EXPERIMENTAL METHODS

Materials. L- and D-methionine (met, purity >99%) from Fluka Sigma−Aldrich Inc. were used as received; they were deposited in a small glass tube heated with a system of electrodes placed in a steel evaporator and can be placed in both UHV chambers very close to the surface using a translational system. The evaporator is initially separated from the main chamber by a gate valve and differentially pumped by a turbomolecular pump. Before sublimation, the methionine powder was gently outgassed at 410 K. It was then continuously heated to 400 K and introduced into the chamber where the glass tube was placed in front of the gold crystal. The dosing pressure was maintained around 2 × 10−9 Torr during the deposition of the adlayer The gold crystal was provided by Surface Preparation Laboratory (The Netherlands) with a purity of 99.99% (4N) and an alignment accuracy of 0.1°. In Situ PM-RAIRS Characterizations. PM-RAIR spectra were recorded using a Nicolet 5700 spectrometer equipped with a nitrogencooled MCT wide-band detector. A ZnSe grid polarizer and a ZnSe photoelastic modulator to modulate the incident beam between p and s polarization (HINDS Instruments, PEM 90, modulation frequency = 50 kHz) were placed prior to the sample. The spectrometer was interfaced to an ultrahigh vacuum (UHV) chamber with ZnSe windows. The reflected light is focused onto the detector at an optimal incident angle of 85°. The RAIR spectra were recorded in situ throughout a continuous dosing regime, and their ratio against a reference single-beam spectrum was recorded on the clean Au(111) crystal. All spectra were obtained at 8 cm−1 resolution by the coaddition of 512 scans. The Au(111) single crystal was first mounted in a multitechnique UHV chamber (base pressure 1 × 10−10 Torr) with PM-RAIRS, low energy electron diffraction (LEED), and X-ray photoemission spectroscopy (XPS) facilities. The gold crystal was cleaned with cycles of Ar+ sputtering (PAr = 5 × 10−5 Torr, 3 kV, duration 5 min), flashing, and annealing to 850 K for 30 min. The surface structure and cleanliness were monitored by LEED and XPS before and after adsorption experiments.

E = E DFT + E D2

(1)

The adsorption energy of the self-assembled monolayer can be separated in the binding or interaction energy (ΔEbind) and the cohesion energy (ΔEcoh). The adsorption energy (ΔEads) is calculated using the formula ΔEads =

⌊E(metads) − nE(met) − E(Ausurf )⌋ n

(2)

where E(met) and E(Ausurf) are, respectively, the total electronic energy of methionine (neutral) and of the Au surface obtained after separate geometry optimization; 204

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Figure 1. (a) PM-RAIRS spectra of L-methionine adsorbed on Au(111) as a function of continuous dosing regime in minutes; from low coverage up to monolayer saturation (1−13 mn) and the multilayer regime (29−50 mn). (b) Schematic representation of the orientation of one met molecule with respect to the gold surface for the low coverage (9 or 13 min) proposed from PM-RAIR data. This representation does not take the data from the further theoretical investigation into account. (See the geometry optimization later.)

of zwitterionic glycine/Cu(110),43 they can be assigned, respectively, to the asymmetric deformation of NH3+ groups and to the asymmetric stretching of the deprotonated carboxylic acid groups, COO−. The presence of these two specific groups, NH3+ and COO−, together with the absence of the CO IR feature at around 1720 cm−1, suggests the zwitterionic character of the methionine adlayer. A careful analysis of the remaining IR bands gives hints as to the molecular orientation of the admolecules with respect to the surface. At very low coverage (after 5 or 9 min), the symmetric COO− stretching band is detected at ca. 1410 cm−1, whereas no asymmetric signal is observed; this suggests that the molecules first interact with the gold surface via their two oxygen atoms. At intermediate coverage (9 or 13 min), the adsorption band at 1562 cm−1, appearing as a shoulder on the IR large feature at 1600 cm−1, and the weak symmetric COO− band, at ca. 1400− 1420 cm−1, imply that the met molecules are now adsorbed, with the two oxygen atoms of the COO− groups no longer being equidistant from the surface; the O−C−O plane is likely tilted with respect to the gold surface. At higher coverage (13 min), a weak signal at 1410 cm−1 appears, suggesting that the COO− groups of the incoming molecules are slightly tilted and not all perfectly normal to the surface. In addition, the very strong intensity of the asymmetric deformation of the ammonium group at 1623 cm−1 and the absence of the corresponding symmetric vibration (expected at around 1510 cm−1) suggest that the NH3+ group is held close to the surface, with the umbrella axis of the tetrahedral ammonium being parallel to the surface; this orientation would imply that the C− N bond is parallel to the surface, in agreement with the absence of any absorption below 1400 cm−1, a region where νCN is expected. Consequently, methionine molecules are positioned parallel to the surface, and because of the fact that molecules are chiral and interact with each other via their amino acid groups, the geometries are constrained to two backbone orientations: one pointing outward and the other pointing toward the surface. Therefore, the adsorption geometry for a single met molecule

E(metads) is the energy of the optimized (met + Au surface); and n is the number of methionine molecules in the unit cell. To analyze further the adsorption mode of methionine on the Au surface, the cohesion energy within the methionine layer (ΔEcoh) and the binding energy with the Au surface (ΔEbind) were calculated with ΔEcoh =

⌊E(metlayer) − nE(met)⌋ n

(3)

and ΔE bind = ΔEads − ΔEcoh

(4)

where E(metlayer) is the energy of the layer of methionine molecules in a unit cell in the absence of the Au substrate Electronic properties such as the density of states (DOS) and theoretical STM images are calculated by performing a singlepoint calculation at higher precision than for the geometry optimization calculations. The STM images are drawn using visualization software Hive.40

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RESULTS AND DISCUSSION For clarity in this section, only results obtained for the Lmethionine adsorption are reported because no differences were observed between the two enantiomers in the RAIRS or XPS data.14,41 Chemical Analysis: PM-RAIRS and XPS. PM-RAIRS characterizations were carried out at several coverage values from the submonolayer regime up to the monolayer saturation (ML) (Figure 1a). The exposure time, needed to obtain a full monolayer, was determined by monitoring the continuous adsorption by PM-RAIRS (Figure S1 in the Supporting Information section) and was estimated to be reached after a continuous dose of approximately 25 min. Figure 1a presents the PM-RAIR spectra obtained from a sub-ML low coverage (1 min) up to a high coverage near ML saturation (13 min). One can isolate two main IR peaks at 1623 and 1562 cm−1. From previous data obtained for methionine on a gold surface adsorbed in the liquid phase42 and the adsorption 205

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Ca/Cb/Cc/Cd in a 1:1:2:1 ratio, from higher to lower binding energy) in very good agreement with the stoichiometric composition and chemical state of the molecule, H3Cc−S− CcH2−CdH2−CbH(NH3+)(CaOO−). Finally, the S 2p region (Figure 2d) displays a single doublet (due to the sulfur 2p orbital spin−orbit coupling) at a rather high binding energy (BE), 2p3/2 and 2p1/2 at 164.0 ± 0.1 and 165.1 ± 0.1 eV assigned to sulfur atoms that are not bound to the metal surface,45 thus confirming the anchoring mode of the molecules deduced from the RAIRS data (Figure 1b). XPS data recorded at various surface exposures were used to calculate the thickness and hence the surface coverage of methionine molecules. A model with a homogeneous layer of molecules was used to calculate the thickness by using the ratio IC/IAu as described elsewhere.46 Using the thickness results obtained for different met exposures, we calculated the surface coverage by incorporating the density of the methionine molecules, and the results are presented in Figure 3.

can be proposed in Figure 1b, and this model will be implemented thanks to the DFT calculations carried out in the following section. XPS measurements were then carried out after recording RAIRS data, at the chosen exposures shown in Figure 1a, to elucidate the chemical states of the adsorbed methionine molecules. Several sets of data were obtained depending on the coverage and, except for an increase in intensity of the XPS peaks (Figure S2 in the Supporting Information section), no qualitative differences were noticed from very low coverage up to a saturated monolayer. Figure 2 presents the high-resolution

Figure 3. Methionine surface coverage as a function of exposure time, calculated using XPS intensity data of the C 1s and Au 4f regions. Figure 2. XPS high-resolution spectra of the core-level (a) N 1s and (b) O 1s showing single peaks at EN 1s = 401.6 eV and EO 1s= 531.5 eV, respectively, assigned to the NH3+ and COO− groups of the zwitterionic methionine adsorbed on Au(111). (c, d) C 1s and S 2p regions; the latter shows the presence of unbound sulfur atoms only with a doublet with a maximum BE at 164.0 eV for the principal 2p3/2 component.

The saturated monolayer regime is obtained for an exposure higher than 25 min, as shown before by PM-RAIRS, and in Figure 3, one can see the formation of a plateau for the same exposure time. The calculations give ∼4.5 × 1014 methionine molecules per cm2, and considering the fcc-Au(111) surface density (1.4 × 1015 atoms/cm2), we can estimate that 1 molecule of methionine occupies slightly more than 3 Au atoms. STM data presented in the following section will enhance the 2D adsorption model and, more specifically, the space occupied by a single methionine molecule. Two-Dimensional and Structural Analysis: LEED and STM. Diffraction patterns obtained for a low dose of Lmethionine, and Figure 4a shows a whole set of extra diffraction spots with respect to the clean surface pattern, which is a clear indication of an ordered met structure on the surface. A precise analysis of these images allowed us to identify the presence of three equivalent rotational domains, obviously due to the C3 symmetry of the (111) face of the gold fcc surface. Figure 4b presents the calculated LEED pattern deduced from the experimental one (LEEDpat v3.0, http://www.fhi-berlin.mpg. de/KHsoftware/LEEDpat/), where the three equivalent rotational domains are depicted by different colors; Figure 4c shows only one isolated single domain.

core-level regions for N 1s, O 1s, C 1s, and S 2p, respectively from a to d, obtained for a low coverage (1 min) of methionine molecules on the Au(111) surface. Both nitrogen and oxygen XPS spectra show a single contribution at 401.6 ± 0.1 eV for the N 1s peak and at 531.5 ± 0.1 eV for the O 1s peak. The presence of these two single peaks is a good indicator of the chemical state of the molecule, with all nitrogen atoms in a protonated form, NH3+, and all oxygen atoms in deprotonated carboxylate moieties.17,44 Therefore, in this case, methionine molecules are adsorbed in their zwitterionic chemical state. Similar data were obtained in the case of methionine deposited on Ag(111), leading to the same conclusion, with two peaks at 401.15 and 531.2 eV, respectively, for the N 1s and O 1s regions.9 In addition, the C 1s region, shown in Figure 2c, presents four different contributions with an atomic ratio (carbon atoms 206

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arrangement forms at room temperature without annealing after the adsorption of the met molecules. Although three domains are observed in Figure 5a,b, one orientation is predominant (domain α, Figure 5b) and corresponds to the most favorable geometry with respect to the substrate structure (i.e., on top of the fcc part of the reconstructed (23 × √3)Au(111) surface. However, this effect is coverage-dependent because it governs the orientation of molecules only at low coverage (Figure 5a), and as the coverage is increased close to monolayer saturation, the whole surface is covered with met molecules under the three different domains (Figure 5b). The orientation of the molecules at low coverage of adsorption and hence the anchoring mode are both directly linked to the subsurface structure. The organization is also related to the lack, in met molecules, of a functional group with a strong affinity for gold such as cysteine on Au(111),16 where the molecule is adsorbed via a thiolate−Au bond. Therefore, in the early stage of growth, nucleation occurs only on the lowcoordination face-centered-cubic (fcc) regions of Au(111); see the arrows in Figure 5a, where the herringbone reconstruction is still visible below the domains of adsorbed molecules. Such a mechanism is evidenced by the arrangement of molecules located only on the fcc areas and separated by disordered or unstable molecular domains located on the hexagonal-closepacked (hcp) area, symbolized by plain lines in Figure 5a. The electronic structure of the gold surface is affected by the herringbone reconstruction that results in a slightly higher concentration of Au atoms in the hcp areas, which in turn induces a weaker attractive electronic potential compared to that for the fcc areas.47 As a consequence, the interactions between the highly localized electronic states of the gold surface and the molecular orbitals of the adsorbed molecules must be weak, resulting in a poor stability of the met molecules on the hcp areas compared to that on the fcc areas. Therefore, the adsorption mechanism is more likely due to molecule− molecule interactions that appear to be stronger than the molecule−substrate interaction (discussed in detail in the theoretical part). In addition, the molecule−substrate interactions are rather weak, allowing significant mobility and rearrangement of the molecules; a mild annealing of the surface to 365 K ends up with the complete desorption of the molecules and the total recovery of the original herringbone structure of the Au(111) surface (data not shown). As a consequence, when the coverage is increased, there is a prevalence of molecule−molecule over molecule−substrate interactions, with the hcp sites being covered with rows of met molecules bridging the alreadycovered fcc domains (Figure 5b). Therefore, the 2D ordering of met on Au(111) is more likely the result of intermolecular interactions within the adlayer rather than a substrate-induced arrangement. Nevertheless, we believe that the early stages of adsorption (low-coverage phase as in Figure 5a) are induced and thus governed by the subsurface herringbone reconstruction, showing a predominant domain, named α, but still showing the presence of the two other geometrically equivalent domains, β and γ. When isolating a given domain of L-methionine at high coverage (Figure 6a), one can see the molecular arrangement in rows of dimers following an orientation perpendicular to the ⟨1−21⟩ crystallographic axis. The L-met chiral array (2 0, 5 8) is formed from chains of molecules, themselves arranged in dimers. In the STM data of Figure 6a, each molecule is imaged as two brighter points, one corresponding to the amino acid

Figure 4. (a) Snapshots of the diffraction LEED pattern on the Au(111) surface covered with a small amount of L-methionine, with the pattern recorded at 17 eV. (b) Schematic representation of the diffraction pattern in (a), where each color represents a rotational domain and the diagram is scaled to fit the LEED screen. (c) Diagram of an isolated domain in reciprocal space and (d) its equivalent in real space (2 0, 5 8), together with the projection of a molecule of Lmethionine on the corresponding real scale.

The analysis of this isolated domain allows us to determine the unit cell of the 2D domain reported on a clean gold surface (real space, Figure 4d); it can be depicted as a chiral (2 0, 5 8) arrangement. Indeed, it has no mirror image by any type of rotation or symmetry along the crystallographic As1 or As2 axis. For better clarity, Figure 4d also shows a scheme of the methionine molecule on the correct scale. STM experiments performed under identical exposure conditions as for PM-RAIRS and XPS experiments also show the presence of three equivalent rotational chiral domains on the surface (Figure 5b).

Figure 5. STM images of L-methionine adsorbed on Au(111) at low and high coverages. (a) 2 and (b) 15 min. (a) The hcp areas where no met molecules are absorbed are brighter. (b) The three equivalent rotational domains are named α, β, and γ, with α being the predominant domain.

The growth of methionine molecules occurs through the formation of parallel molecular rows into three well-ordered domains, appearing in Figure 5 as single bright lines rotated from each other by 120°, as seen previously with the LEED data. In Figure 5b, the resolution within the lines shows the presence of dimers that were not resolved in Figure 5a, hence appearing only as lines. It is important to note that this 207

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COMPUTATIONAL RESULTS: BUILDING THE METHIONINE/AU(111) SUPERCELL The surfaces are modeled as a slab, where a unit cell is periodically reproduced in the 3D space. In this approach, the surface is infinite in two dimensions, with a vacuum space in the z-axis direction. This vacuum space between the subsequent Au slabs should be large enough to enable methionine adsorption and disable its interaction with the consecutive repetition of the system. The vacuum layer is about 15 Å. In the present case, a slab representing a (111) surface was cut out of the bulk facecentered cubic cell of gold. The optimized cell parameter, a, at the PBE level was found to be equal to 4.177 Å, in good agreement with experiment (4.0782 Å).48 The Au(111) surface model consists of five Au layers where the two bottom layers are frozen to the optimized bulk positions and the three upper layers are free to relax. The theoretical unit cell parameters in closest agreement with the experimentally observed parameters described by vectors (2 0, 5 8) obtained from the LEED and high-resolution STM data have the following calculated parameters: a = 5.8935 Å, b1 = 2.9468 Å, b2 = 20.4158 Å, c = 26.4663 Å, α = β = 90°, and γ = 81.7868°. Following the experiment, two methionine molecules are present in this unit cell. The difficulty at this stage is to find the most energetically favorable conformation of both methionine molecules out of thousands of possibilities. This problem has been tackled by scanning the potential energy surface using an ab initio molecular dynamics procedure within the microcanonical ensemble (NVE) approach at T = 350 K. Several intuitive starting configurations were used as inputs, and the trajectories were scanned for possible conformations of the system for sampling times of t ≥ 2 ps. The local minima found from MD results were systematically reoptimized at 0 K in order to achieve the absolute electronic minimum energy for each configuration. Geometry and Energetics. The choice of starting geometries for the geometry optimizations has been made as systematically as possible. All main functional groups of methionine have been considered to be in direct interaction with the gold surface as well as in interaction with the neighboring methionine forming the adsorbed dimer. To help select pertinent candidates for stable methionine assemblies and understand the nature of the interaction with the surface and between the methionine molecules, a single isolated methionine molecule and an isolated dimer of methionine were also studied on the surface. From the experiments, it is found that the methionine molecules are present on the surface in their zwitterionic form (vide infra). Each methionine molecule can adopt various relative orientations and different intermolecular distances. A selection of the geometries is made on the basis of their total energy after optimization. Finally, the geometries were corrected for their dispersion interactions. Four almost all-isoenergetic structures with comparable geometries were obtained. Some geometrical parameters of these structures are tabulated in Table 1. The S− S and N−N distances describe the position in the xy plane, whereas the methionine−Au distance describes the position along the z direction. A distance of 8.64 Å between the sulfur atoms is found, with 4.173 Å between the nitrogen atoms (structure 3). The met−Au distance is about 3 Å. Therefore, the methionine molecules on the surface prefer to interact with

Figure 6. STM images of (a) L-methionine and (b) D-methionine dimers showing channels oriented perpendicularly to the main ⟨1−21⟩ crystallographic axis of the Au(111) surface. The two chiral unit cells (2 0, 5 8) and (−5 8, 2 0) are shown by plain lines. (c) Schematic adsorption model for L-methionine molecules creating a chiral (2 0, 5 8) unit cell. The distances are measured on the high-resolution STM images in part a.

moiety of the head of the molecule (−C−(NH3+) (COO−)), and the second corresponds to the tail of the molecule (−S− CH3). The dissymmetry in the two brightest points of each molecular dimer within the rows suggests slightly different relative orientations and z positions of the two met molecules in the given dimers with respect to the plane of the surface. By measuring intermolecular distances and distances between two dimers or two rows, one is able to propose a schematic molecular model of adsorption for L-methionine molecules within the chiral unit cell (2 0, 5 8) (Figure 6c), where each cell is composed of two molecules. This information is crucial in the construction of the unit cell model used in the DFT calculations. Indeed this unit cell serves as a starting structure in the molecular dynamics run. The adsorption of the opposite enantiomer, D-methionine, also leads to a truly chiral surface, where the D-met molecules arrange themselves under a (−5 8, 2 0) chiral unit cell, which happens to be the mirror image of that created by the L-enantiomer (Figure 6b). In addition, the spacing between two rows of dimers is probably governed by the crystallography of the underlying gold surface and possibly by electrostatic repulsion that may exist between the sideways CH3 groups. The two-dimensional chiral arrangement is essentially dictated by the chemical form of the methionine molecule, mode, and adsorption geometry of the molecules but also by their ability to create intermolecular H-bonds due to the presence of the zwitterionic form of the molecule. 208

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Table 1. Selected Geometric Parameters, Relative Energies, and Dispersion-Corrected Adsorption Energies for the Four Most Stable Methionines on Au(111) Surface Structuresa

structure

S−S distance

N−N distance

1 2 3 4

7.884 8.416 8.638 8.902

4.571 4.019 4.173 4.741

a

closest distance between methionine and the Au(111) surface 3.286 3.009 2.809 3.007

(H −Au) (H −Au) (S −Au) (S −Au)

relative energy

adsorption energy (ΔEads)

0.02 0.06 0.00 0.04

−1.36 −1.32 −1.38 −1.34

Distances are in angstroms, and energies are in electronvolts.

each other via their amino acid head rather than via their methylthiol tail. Structure 3 was found to be the most stable onl the basis of its total electronic energy (Table 1). The van der Waals (VDW), here mainly dispersion, correction has only a small effect on the geometry. The stability trend was not altered. The adsorption energy of methionine on Au(111) varies between −0.69 and −1.38 eV and between −1.92 and −2.02 eV (including VDW interactions), showing the importance of the presence of H bonds between two molecules (Table 2).

Figure 7. (a) Most stable configuration found for the met monolayer on Au(111). (b) Unit cell containing two met molecules.

adsorption, which might indicate that primary and secondary thiols containing molecules interact similarly with a gold surface (i.e., no interaction or almost none). From the geometry optimizations for the large collection of conformations, it is found that within a dimer one methionine molecule is parallel to the Au surface and the other slightly tilted. From the experimental STM images, it was also concluded that the two methionine molecules do not have the same orientation toward the Au surface. In this conformation, one thiol group is oriented upward and the other horizontal. The molecules are positioned one in front of the other in a ziplike order (Figure 7), with different z-positions for each part of both molecules, thus explaining the difference in brightness observed in the STM images (Figure 6a,b). By summarizing the geometrical data obtained from experiments and calculations, one can conclude that two NH3+ groups interact with two COO− oxygen atoms, forming a dense 2D H-bond network contributing two-thirds of the interaction energy. The sulfur atom of one of the two methionine molecules interacts very weakly with the surface, contributing one-third of the total adsorption energy (Table 2). Electronic Properties. Density of States (DOS). In solidstate and condensed matter physics, the density of states (DOS) of a system describes the number of states per interval of energy at each energy level that is available to be occupied by electrons. Unlike isolated systems, such as atoms and molecules in the gas phase, the density distributions are not discrete, like a spectral density, but continuous. A high DOS at a specific energy level means that there are many states available for occupation. A DOS of zero means that no states can be occupied at that energy level. In general, a DOS is an average over the space and time domains occupied by the system. The goal of calculating the DOS is to assign the spots in the STM images to specific orbitals/bands located on the atoms in the molecular assembly, thus helping to interpret the STM images. The tunneling energies corresponding to the experimental bias voltages will fill up or empty the conduction and valence bands, respectively. Localizing these bands in the system enables us to assign the associated molecular structure to the STM image. Subsequently, the experimental STM image can be compared to the theoretical image.

Table 2. Adsorption Energy, Cohesion Energy, and Interaction Energies as Defined in Equations 2−4 for the Most Stable Isomeric Systema structure name

adsorption energy (ΔEads)

interaction Au-meth energy (ΔEbind)

cohesion energy (ΔEcoh)

3 3 VDW

−1.38 −2.02

−1.28 −0.68

−0.10 −1.34

a

The energies are calculated per methionine molecule. (Values are in electronvolts.).

The adsorption energy per methionine molecule on the defect-free Au(111) surface is finally calculated to be equal to −2.02 eV for VDW dispersion correction. The VDW contribution is 0.60 eV, thus accounting for about 30% of the total adsorption energy. The VDW correction also reverses the contribution of the energy of interaction with the surface compared to the intermolecular cohesion energy. One methionine molecule is thus preferentially in direct interaction with the Au surface, and the other one is interacting with the first methionine (Figure 7). The cohesion energy contributes one-third of the total adsorption energy. The second methionine molecule is stabilized by hydrogen bonds between carboxylate and ammonium groups (Figure 7) with a cohesion energy reaching −1.28 eV as a result of the 2D H-bond network. It is interesting that the interaction with the surface is mainly due to dispersion forces. The shortest Au−S distance (2.8 Å) between one of the molecules shows a situation comparable to weakly physisorbed alkyl thiol/Au self-assemblies.49 This comparison helps us to understand better the adsorption of thiol group containing molecules. Indeed, here we have studied an example of a secondary thiol group whereas alkyl thiols are primary thiols. Comparing the results of met and alkyl thiols, one can answer the question, does the interaction energy change when there is a leaving group (−H vs −CH3) present on the thiol S atom to form a covalent S−Au bond? From Table 2, it can be seen that the Au−S distance and energy for met are similar to those for low-coverage alkyl thiol 209

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methionine on a clean Au(111) surface under UHV conditions. We have shown that met molecules are adsorbed intact on a Au(111) surface in their zwitterionic chemical form. Each enantiomer gives rise to a single 2D chiral domain, with the mirror image obtained with the other enantiomer. These chiral domains are composed of chains of met molecules, themselves arranged in dimers within a given chain. The 2D chiral arrangement is essentially dictated by the chemical form of the met molecule, the mode and adsorption geometry of the molecules, and their ability to create intermolecular H bonds as a result of the presence of the zwitterionic form of the molecule. Indeed, we performed the same experiments on Cu(110) in which methionine is adsorbed as anionic molecules (COO−/NH2) anchored to the surface by two oxygen atoms with no possibility to create H bonds, resulting in the total absence of the 2D array. Because of the strong H-bond intramolecular network involved in the creation of the 2D chiral array, a very weak interaction between met molecules and the surface was concluded. The higher intermolecular interaction forces compared to the molecule substrate interaction forces explain the high mobility of the rearrangement of the molecules on the surface. The combination of experiment and theoretical calculations was shown to answer some questions such as why only one domain is predominant, domain α, on the symmetrical Au(111) surface. A possible explanation lies in the fact that in the early stages of adsorption the molecule−substrate interactions prevailed (adsorption only on fcc sites) whereas at higher coverage the 2D arrays are mainly driven by intermolecular interactions. What is the exact orientation of the molecules within a dimer and with respect to the gold surface? Thus, theoretical calculations and a systematic investigation of the molecular self-assembly of methionine on the defect-free Au(111) surface were performed. After defining the surface unit cell in combination with experimental LEED and STM data, the relative positions of both methionine molecules of the unit cell were determined. Molecular dynamics runs, followed by geometry optimization, led to the proposal of possible molecular structures selected on the basis of their stability. Subsequently, electronic properties, in particular, those from the DOS and STM images, were calculated. The experimental STM images were recovered and interpreted. These results show the competition between intramolecular and molecule−surface interactions. The balance of forces results in the unique pattern observed on the surface. For methionine, it is shown that the molecules are not forming a symmetric assembly and that the interactions between the carboxylic and ammonium groups via a 2D H-bond network account for two-thirds of the total adsorption energy. An S−Au distance of 2.809 Å in the met, which is comparable to the S− Au distance found for the physisorption of primary alkyl thiols, indicated a very weak interaction with the gold surface. Finally, it is concluded that dispersion forces play an important role in the adsorption energy but a less important one in the equilibrium geometry of the assembly.

Figure S3 represents the total DOS and the projected DOS on the different atoms (Au, C, H, O, N, and S) present in the system over the interval from −5.0 to 5.0 eV. The DOS revealed a strong bias dependence of the STM images, as can be seen from the different behavior of the positive- and negative-energy DOS. Remembering that the STM images are indeed a 2D map of the integrated density of states (DOS) of the surface, we find that the observed bias dependence is thus indicative of a strong modulation of the DOS. From the experimental STM images, we may infer that the bright features are due to tunneling through the carboxylic groups and that for V = −1.0 V such a channel is inhibited or strongly reduced while tunneling through another functional group of methionine. Indeed, the sulfur projected DOS shows bands around the Fermi level. An inspection of the DOS in the −0.3 to 0.3 eV range reveals the presence of a band for sulfur and small contributions for carbon and hydrogen. Around −1.0 eV, a band from oxygen and carbon with a lower density originates. In the conduction band up to 3.5 eV, no band is observed. STM Simulations. STM images can be reproduced by plotting the electron density of the system of energy in the 0 to −1.5 eV range. This corresponds to the emptying of the bands of the oxygen, sulfur, and some contributions of carbon atoms present at −1.5 eV, in perfect agreement with the deductive conclusion from the STM experimental data, as seen from the calculated STM image in Figure 8.

Figure 8. (Left) Calculated STM image for an energy of −1.5 eV and (right) experimental STM image for D-methionine on the Au(111) surface at −1.0 V bias voltage.

The asymmetric feature of the image is revealed and can now be clearly associated with the fact that one methionine molecule is closer to the surface than the other (Figure 7a). One spot originating from the sulfur moiety is less bright on one side than on the other as a result of the fact that one sulfur atom is pointing toward the Au surface and the other pointing up, away from the surface (Figure 7a). The two middle spots originate from the carboxylic oxygen atoms, which also have different orientations depending on the methionine to which it belongs. In summary, the present study illustrates the convergence of energetic and electronic calculations to reproduce and explain the unique structure observed experimentally by STM, thus confirming the strength of the combination of STM with theory.

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CONCLUSIONS The combination of XPS, in situ RAIRS, LEED, and STM experiments and ab initio DFT calculations gives a unique set of data that enables the interpretation of the expression of surface chirality upon adsorption of both enantiomers of

ASSOCIATED CONTENT

S Supporting Information *

Kinetics of adsorption of L-methionine on Au(111) as a function of the continuous dosing regime. XPS high-resolution spectra of core-level N 1s. Projected density of states of C, H, 210

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O, N, and S around the Fermi level. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was performed using HPC resources from GENCI[CCRT/CINES/IDRIS] (grants 2012-[x2012082022] and 2013-[x2013082022]) and the CCRE of Université Pierre et Marie Curie. Dr. B. Diawara from ENS Paris is kindly acknowledged for providing us with ModelView used in the visualization of the structures.

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