Accommodation of Lattice Mismatch in a Thiol Self-Assembled

Article pubs.acs.org/JPCC

Accommodation of Lattice Mismatch in a Thiol Self-Assembled Monolayer Zhe She,† Dorothée Lahaye,‡ Neil R. Champness,‡ Michael Bühl,† Hicham Hamoudi,§,∥ Michael Zharnikov,§ and Manfred Buck*,† †

EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, U.K. School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K. § Angewandte Physikalische Chemie, University of Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany ‡

ABSTRACT: The structure of self-assembled monolayers (SAMs) of 3-(4′-(methylthio)-[1,1′-biphenyl]-4-yl)propane-1thiol (CH3S(C6H4)2(CH2)3SH) formed on Au(111)/mica has been investigated by scanning tunneling microscopy (STM), high-resolution X-ray photoemission spectroscopy (HRXPS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and density functional theory (DFT) calculations. A highly crystalline monolayer terminated by thioether moieties is formed, which adopts a structure that differs from the previously studied CH3 terminated analogue with its 2√3 × √3 unit cell. An oblique 2√3 × √61 chiral unit cell containing 8 molecules is proposed. Accommodation of the substantial mismatch between the lattices of the SAM and substrate is explained by molecular design. Serving as a buffer layer, the alkane spacer decouples the SAM lattice, defined by the functionalized aromatic moieties, from the substrate.

■

INTRODUCTION Thiol self-assembled monolayers (SAMs) combining aromatic moieties with short aliphatic linker units, typically between one to six CH2 groups in length, have been studied in quite some detail over the years1−31 and are now being investigated for the control of interfacial chemistry, in particular metal coordination and deposition.32−36 What makes this class of thiols interesting for nanoscience is the excellent crystallinity and low defect density of the SAMs, which is a problem to achieve in SAMs where the aromatic moiety is directly attached to the thiol group.37−41 The aliphatic spacer chain affects a SAM structure in two ways, one being that misfits between the lattices of the rigid aromatic moieties and the substrate can be accommodated via a flexible linker. The other one is the odd−even effect, which is a striking dependence of the SAM structure and properties on whether the number of methylene units is even or odd and is understood to arise from the directive effect of the C−S−substrate bonding configuration and stiffness of the associated bending potential.2,7,8,42 The structural studies on chemically inert biphenyl and terphenyl based thiols suggest that this aromatic−aliphatic architecture represents a suitable platform to be extended for chemistry on well-defined SAMs. A few derivatives have been studied to date, namely, CN, NH2, SH terminated biphenyl, and terphenyl thiols,4,11,22,43 as well as analogues where the terminating benzene ring is substituted by pyridine.15,16,18,20,44−46 Spectroscopic characterization suggests that the high order of these layers is maintained, and in the very few cases where microscopic characterization of substituted aromatic−aliphatic SAMs has been performed,15,20 © 2013 American Chemical Society

the modification does not seem to affect the crystalline packing of the molecules in the SAM, which makes these systems interesting due to their modularity. Motivated by the need to tune chemistry and interfacial energy on the nanoscale, in particular, for SAM controlled deposition of metals and metallic nanoparticles,35,47−49 the present study of 3-(4′-(methylthio)[1,1′-biphenyl]-4-yl)propane-1-thiol (CH3S(C6H4)2(CH2)3SH, MeSBP3) reports a further step in the exploration of aromatic− aliphatic SAMs. In comparison with the small tail groups studied so far, the methyl thioether investigated here introduces a sterically different, nonlinear geometry. Its effect can be compared to the well studied system of ω-(4′-methyl-biphenyl4-yl)-propanethiol (CH3(C6H4)2(CH2)3SH, MeBP3).2,3,7,9,23

■

EXPERIMENTAL SECTION

Synthesis. All reactions were carried out under an atmosphere of nitrogen or argon. Column chromatography was performed on silica gel (Merck silica gel 60, 0.2−0.5 mm, 50−130 mesh). 1H nuclear magnetic resonance (NMR) and 13 C NMR spectra were obtained on either a 300 or 400 MHz Bruker spectrometer. Microanalyses were performed by Stephen Boyer, London Metropolitan University. MS Spectra (ESI-MS) were determined on a Micromass LCT mass spectrometer. Received: December 4, 2012 Revised: January 31, 2013 Published: February 4, 2013 4647

dx.doi.org/10.1021/jp311927z | J. Phys. Chem. C 2013, 117, 4647−4656

The Journal of Physical Chemistry C

Article

Synthesis of MeSBP3. In a round-bottom flask placed under nitrogen, a previously sonicated mixture of compound D (91 mg, 0.29 mmol) in MeOH (6 mL) was treated with a 0.2 M solution of NaOH (4 mL). The reaction mixture was then stirred at 80 °C for 3 h. MeOH was removed under reduced pressure and the resulting residue was neutralized with diluted HCl and extracted with CH2Cl2. The organic extracts were washed with water, dried (MgSO4), filtered, and concentrated. The crude mixture was purified by column chromatography [silica, hexane to hexane/CH2Cl2 (3:1)] to yield MeSBP3 (480 mg, 60%). 1H NMR (CDCl3) (400 MHz) δ 1.39 (t, J = 8 Hz, 1H), 1.98 (quin, J = 8 Hz, 2H), 2.53 (s, 3H), 2.58 (q, J = 8 Hz, 2H), 2.78 (t, J = 8 Hz, 2H), 7.26 (m, 2H), 7.33 (m, 2H), 7.52 (m, 4H); 13C NMR (CDCl3) (75 MHz) δ 15.95, 23.99, 33.96, 35.40, 126.83, 126.99, 127.30, 128.94, 137.29, 137.84, 138.26, 140.35; ESI-MS obsvd 274.0852, calcd 274.0850 (M+) with M = C16H18S2. Monolayer Preparation. Flame annealed Au/mica substrates (Georg Albert PVD) were immersed in 100−250 μM solutions of MeSBP3 or MeBP3 in ethanol for about 15 h at temperatures between 340 and 373 K. For temperatures above the boiling point of the solvent, a glass vial containing the immersed substrate was placed in a pressure-tight stainless steel container under nitrogen atmosphere. After immersion, samples were thoroughly rinsed with ethanol and blown dry with a stream of N2. Characterization of SAMs. Layers were characterized by scanning tunneling microscopy (STM), synchrotron based Xray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. All experiments were performed at room temperature. STM. A Pico SPM (Molecular Imaging) in ambient atmosphere was used with tips cut from Pt/Ir wire (80:20, Advent). Typical tunneling parameters were in the range of ±200−600 mV and 10−50 pA. XPS. Measurements were carried out at the bending magnet HE-SGM beamline of the synchrotron storage ring BESSY II in Berlin, Germany, using a Scienta R3000 spectrometer. The spectra were collected in normal emission geometry with an energy resolution of 0.3 eV at an excitation energy of 350 eV and somewhat lower resolution at 580 eV. The binding energy (BE) scale was referenced to the Au4f7/2 peak at a BE of 84.0 eV.50 Spectra were fitted by symmetric Voigt functions and a Shirley-type background. Sulfur doublets were fitted by fixed ratios of peak area (2:1) and fwhm (1:1) and a 1.2 eV separation. Film thickness was determined from the intensity ratios of C1s and Au4f emission peaks, using a general formalism51 and the attenuation length reported in ref 52. NEXAFS. The NEXAFS measurements were performed at the same beamline using a partial electron yield detector. The spectra were collected at the carbon K-edge with a retarding voltage of 150 V. Linearly polarized X-ray light with a polarization factor of 91% was used. The energy resolution was 0.30 eV. The incidence angle of the light was varied from 90° (E-vector in the surface plane) to 20° (E-vector nearly normal to the surface) in steps of 10−20° to monitor the orientational order of the biphenyl moieties in the films. This approach is based on the linear dichroism in X-ray absorption, i.e., the strong dependence of the cross-section of the resonant photoexcitation process on the orientation of the electric field vector of the linearly polarized light with respect to the molecular orbital of interest.53 The raw NEXAFS spectra were normalized to the incident photon flux by division by a

Synthesis of Compound B: 4′-Hydroxyethyl-4-methylthiobiphenyl. To a flame-dried round-bottom flask placed under argon were added allyl alcohol (520 μL, 8 mmol) and predegassed tetrahydrofuran (THF) (7.4mL). 9-BBN, 9borabicyclononane (47.3 mL, 0.02 mmol, 0.5M in THF), was then added over 30 min at 0°C. The mixture was allowed to warm to room temperature and stirred for 12 h. The resulting solution of B-propyloxy-9-BBN was then transferred to a round-bottom flask placed under argon containing A (2.00 g, 7.16 mmol), Pd(PPh3)4 (827 mg, 10 mol %, 0.72 mmol), K2CO3 (4.11 g, 29.79 mmol), H2O (3.34 mL), and N,N′dimethylformamide (17.2 mL). The mixture was heated at 70 °C for 36−40 h then cooled to room temperature. The solvent was removed under reduced pressure. CH2Cl2 and water were added, and the organic layer was washed twice with water, dried (MgSO4), filtered, and concentrated. The resulting solid was recrystallized in heptane/iPrOH (3/1) to yield B as a pale yellow solid (1.03 g, 55.7%). 1H NMR (CDCl3) (300 MHz) δ 1.32 (br, 1H), 1.95 (m, 2H), 2.76 (t, J = 8 Hz, 2H), 3.73 (t, J = 6 Hz, 2H), 3.73 (t, J = 6 Hz, 2H), 7.30 (m, 4H), 7.51 (m, 4H); 13 C NMR (CDCl3) (75 MHz) δ 15.93, 31.66, 34.15, 62.25, 126.80, 126.96, 127.28, 128.88, 137.22, 137.86, 138.13, 140.89; ESI-MS obsvd 281.0965, calcd 281.0971 [(M + Na+), M = C16H18OS]. Synthesis of Compound C: 4′-Methylthio-4-mesyloxyethylbiphenyl. To a stirred mixture of compound B (1 g, 3.87 mmol) and Et3N (1.55 mL, 11.09 mmol) in THF (15.5 mL) cooled to −30 °C was added dropwise a solution of mesyl chloride (0.6 mL, 7.74 mmol) in THF (7.8 mL) over 20 min. After an additional 30 min stirring, aqueous NH4Cl was added to render the solution acidic. The phases were separated and the aqueous phase was further extracted three times with EtOAc. The combined organic extracts were washed with water and brine, dried (MgSO4), filtered, and concentrated generating C as a yellow residue (1.18 g, 91 %). 1H NMR (CDCl3) (400 MHz) δ 2.12 (m, 2H), 2.53 (s, 3H), 2.80 (t, J = 10 Hz, 2H), 3.02 (s, 3H), 4.27 (t, J = 8 Hz, 2H), 7.26 (m, 2H), 7.34 (m, 2H), 7.52 (m, 4H); 13C NMR (CDCl3) (75 MHz) δ 15.91, 30.62, 31.16, 37.39, 69.06, 126.96, 126.98, 127.30, 128.92, 137.45, 137.66, 138.60, 139.32; ESI-MS obsvd 354.1192 (M + NH4+), 359.0746 (M + Na+), calcd 359.0752 [(M + Na+), M = C17H20O3S2]. Synthesis of Compound D: 4′-Methylthio-4-thioacetoxyethylbiphenyl. To a stirred solution of cesium thioacetate (3.6 mmol, prepared by mixing 1.18 g of Cs2CO3 and 262 μL of thioacetic acid in 17.5 mL DMF) was added, at room temperature, compound C (1.1 g, 3.27 mmol) in DMF (7.5 mL). After overnight stirring at room temperature, water was added. The mixture was extracted with EtOAc, and the combined organic extracts were washed with water and brine, dried (MgSO4), filtered, and concentrated. The resulting residue was purified by column chromatography [silica, hexane/EtOAc (8:1)] to generate D as a white solid (846 mg, 82%). 1H NMR (CDCl3) (400 MHz) δ 1.94 (m, 2H), 2.35 (s, 3H), 2.53 (s, 3H), 2.74 (t, J = 8 Hz, 2H), 2.99 (t, J = 7 Hz, 2H), 7.25 (m, 2H), 7.33 (m, 2H), 7.50 (m, 4H); 13C NMR (CDCl3) (75 MHz) δ 15.94, 28.58, 30.66, 31.06, 34.44, 126.83, 126.98, 127.31, 128.91, 137.26, 137.85, 138.29, 140.22, 195.86; ESI-MS obsvd 334.1315, 339.0869, 655.1830, calcd 334.1299 (M + NH4+), 339.0848 (M + Na+), 655.1809 (2M + Na+) with M = C18H20OS2; EA obsvd C, 68.27; H, 6.27; calcd C, 68.31; H, 6.37. 4648



Article

Scheme 1. Synthetic Pathway to MeSBP3

separated from the target compound. Deprotection of the thioacetyl group gave MeSBP3 in 60% yield. Spectroscopic Characterization of SAMs. Since MeSBP3 is a structural analogue of MeBP3 (labeled BP3 in previous work, the notation MeBP3 is used here for clarity and to illustrate the analogy between both SAMs) of which SAMs have been studied in detail before,2,3,9 the interpretation of the spectroscopic data of MeSBP3 SAMs are facilitated by comparison with MeBP3. XPS. Figure 1 compiles XPS spectra acquired in the S2p and C1s regions. As seen from Figure 1a, the spectrum of MeBP3 is characterized by a single sulfur signal (S2p3/2 at 162.034 eV) characteristic for a thiolate,69 whereas the MeSBP3 monolayer exhibits two signals, a small thiolate signal at essentially the same binding energy (162.068 eV) as MeBP3 and another much larger one at 163.283 eV from the thioether. Comparison of the intensities of the thiolate signals suggests that the packing density of the molecules is similar in both SAMs. The pronounced deviation of the thiolate and thioether signal from the stoichiometric 1:1 ratio is due to the small probing depth at the photon energy of 350 eV and strongly suggests that thioether and thiolate species are located at the SAM surface and SAM/Au interface, respectively. This is confirmed by the dependence of the signals on the photon energy (Figure 1b). The increase of the probing depth with higher photon energy decreases the thioether to thiolate signal ratio from 8.6 at 350 eV to 3.1 at 580 eV. A similar packing density of the two SAMs is also concluded from the thiolate to Au signal ratio measured at 350 eV. Calculating the film thickness from the C1s and Au4f signals following the general formalism,51 essentially identical values of 1.66 and 1.72 nm are obtained for MeSBP3 and MeBP3, respectively. Considering these values and taking into account one more atom in the case of MeSBP3, we can conclude that the effective packing density of MeSBP3 is lower than that of MeBP3 by ∼9%. The C1s spectra of both SAMs are dominated by a strong emission at 284.1 eV, which is accompanied by a weaker feature

spectrum of a clean, freshly sputtered gold sample. Afterward, the spectra were reduced to the standard form by subtracting a linear pre-edge background and normalizing to the unity edge jump in the far postedge range. The energy scale of the C Kedge spectra was referenced to the most intense π* resonance of highly oriented pyrolytic graphite at 285.38 eV.54 Calculations. Starting from the molecular crystal structure of biphenyl at room temperature,55 a dimeric model was extracted and one H atom in the para position of each biphenyl monomer was replaced with an SMe group. Periodic slabs were constructed using a supercell approach, using a, b, and γ values from experiment, and setting c to 25 Å to have enough vacuum between the slabs. Atomic coordinates were optimized in the fixed cells at the PBE-D level56 including empirical dispersion corrections.57,58 Calculations were performed with the CASTEP program,59 using the default pseudopotentials,60 a planewave cutoff of 400 eV, and a Monkhorst-Pack grid61 with 2, 3, and 1 k-points along the reciprocal a, b, and c-axes, respectively. No constraints were necessary to avoid slippage of the aromatic moieties past each other during optimization. Rotational barriers were calculated for isolated molecules at the PBE/631G* level (which for biphenyl affords very similar results as B3LYP/6-31G*62,63) using the Gaussian03 suite of programs.64

■

RESULTS

Synthesis. MeSBP3 was synthesized following the route shown in Scheme 1. Compound A, 4′-bromo-4-methylthiobiphenyl, was prepared by the literature method65 and then converted to B, 4′-hydroxyethyl-4-methylthiobiphenyl, through an adaptation of a method reported by Iglesias et al.66 Mesylation of this compound67 gave C, which was in turn converted to D through reaction with cesium thioacetate, which was prepared in situ.67,68 Initial attempts at the synthesis of D were attempted directly from B via a Mitsunobu reaction. However, this method resulted in the formation of a large amount of triphenylphosphine oxide, which could not be 4649



Article

Figure 2. C K-edge NEXAFS spectra of MeSBP3 (left) and MeBP3 (right) on Au(111). Top panels: Series of spectra measured at different angles of incidence of the X-ray radiation. Bottom panels: Difference between spectra acquired at angles of 90° and 20°. Angle of incidence is defined by beam propagation direction and surface plane. Figure 1. HRXPS spectra of MeSBP3 and MeBP3 on Au(111). (a) Comparison of MeSBP3 and MeBP3 in the S2p region. Photon energy = 350 eV. (b) S2p spectra of MeSBP3 using different photon energies. The spectrum at 350 eV is identical to the one shown in panel a. (c,d) Comparison of MeSBP3 and MeBP3 in the C1s region for different photon energies. Black squares are experimental data; solid lines are fits. For details, see text.

not revealed in the STM images, we cannot differentiate between mirror domains, and therefore, the number of differently orientated domains observed in the experiments is reduced to three. Looking at the large scale image of a MeSBP3 SAM (Figure 3a,) mostly triangular shaped gold terraces are seen with steps running along the ⟨11̅0⟩ directions. Occasionally, as marked by the arrows, steps meeting at an angle of 90° are observed. The

at ∼285 eV (Figure 1c,d). The former emission can be assigned to the aromatic rings (CAr), while the latter feature, which is also observed for nonsubstituted oligophenyl thiolate SAMs,70 can be assigned to the carbon atom bound to sulfur or/and a low-energy shake up excitation in the aromatic matrix.14,70 This is evidenced by Figure 1d, which shows that the intensity ratio of the peaks at 284.1 and 285 eV is clearly different for both SAMs. The increased intensity of the CS peak relative to CAr for MeSBP3 compared to MeBP3 must originate from the additional thioether carbon. NEXAFS. The most prominent feature in the C K-edge spectra of both SAMs (Figure 2) is the π* resonance of the phenyl rings at 284.9 eV (π*ph). From the difference between the spectra acquired at 90° and 20°, it is already obvious that the orientation of the biphenyl moieties in the MeSBP3 and MeBP3 SAMs is very similar. Neglecting molecular twist, average molecular tilt angles of 12° and 10.5° were found for MeSBP3 and MeBP3, respectively. Assuming a reasonable value for the twist angle, based on the data for bulk biphenyl71 and biphenyl-based SAMs,72 we get average molecular tilt angles of 14.5° and 12.5°. Together with the film thickness determined by XPS, one has to conclude that the biphenyl moiety adopts a rather upright orientation in both SAMs. Note also that the average tilt angles in both SAMs are quite similar but slightly higher in the case of MeSBP3, in good agreement with slightly lower effective packing density in this film given by HRXPS. STM. Since SAMs of MeBP3 on Au(111) have been studied before, we refer to the literature for details2,3,7,9 and only mention here that the film structure is described by a 2√3 × √3R30° unit cell, i.e., the unit cell vectors are parallel to the ⟨112̅⟩ directions. With the molecules being uniaxially aligned, six equivalent domains exist. However, since the alignment is

Figure 3. STM images of MeSBP3 on Au(111). (a) Large-scale image with arrows indicating corners where orthogonal step edges of the substrate meet. (b) Higher magnification image with square marking the area shown in panel c. (c) Unit cells of the molecular lattice of two adjacent domains. Small image shows Fourier transform of the area marked by the dotted square in panel c. Arrows mark spots along the ⟨11̅0⟩ direction. Scale bars = 50 nm (a), 10 nm (b), and 5 nm (c). 4650



Article

unit cells are parallel. For molecular rows running parallel to b and b′, a periodicity comprising two protrusions is discernible. This suggests that the structure is commensurate with the underlying substrate along the ⟨112̅⟩ direction with, as for MeBP3, a periodicity of 2√3 for the Au−Au distance (10 Å). The Fourier transform (Figure 4b) exhibits the same features as the one shown in Figure 3c with the singular spots (1) corresponding to molecular rows running along ⟨112̅⟩. This is identical to the domain boundary marked by the dashed line (1) in Figure 4a. The other spots arise from the molecular rows indicated by the correspondingly labeled lines in the STM image. While a and a′ are along a high symmetry axis of the substrate, b and b′, which are parallel to lines 3 and 3′, are not. They run at an angle of α = 54 ± 3° relative to the ⟨112̅⟩ direction (dashed line 1). Correspondingly, the angle between lines 2/2′ and 1 is around 65°. The deviation from the 60° angle of the substrate symmetry is also obvious from the angle between the dotted (3′) and dash−dotted lines (2), which is 9−10°. Obviously, compared to the reference system MeBP3 with its 2√3 × √3 structure, the methyl thioether moiety gives rise to a change in lattice, which is expressed by a reorientation of one unit cell vector along a direction off the symmetry axis of the substrate. The intermolecular distance along b/b′, 5.7 Å, is 13% larger than along a/a′. On the basis of these results, the smallest unit cell of the SAM commensurate with the Au substrate is described by a ⎛ 2 −4 ⎞ ⎜ ⎟ matrix, corresponding to an oblique 2√3 × √61 unit ⎝2 9 ⎠ cell containing 8 molecules. Using a Au−Au distance of 2.89 Å, the lattice parameters are aS = 10.01 Å, bS = 22.57 Å, and α = 56.33°, and the corresponding intermolecular distances along the unit cell vectors are 5.05 and 5.64 Å. The area/molecule amounts to 23.51 Å2, which is 8.3% larger than for MeBP3 with its 2√3 × √3 structure. Comparing the different domains of Figure 4 substantial variations in the imaging contrast are seen. Similar to terphenyl thiol SAMs,77 the imaging contrast depends on the orientation of the domains relative to the scan direction. This results in a 2√3 double row structure, which is more pronounced for domains II and IV than for I and III and is a manifestation of a tip shape, which deviates from a point-like geometry. An interesting aspect, which we come back to below, is the fact that even domains whose unit cells seem to adopt the same orientation, i.e., domains I/IV and II/III, appear different. In addition to the domain dependent contrast, there are also variations within a domain. Some molecules appear up to 0.1 nm deeper, which, in analogy to similar systems,7,9 is thought to arise from a locally different adsorption geometry. This can result in either a real height difference or an apparent one caused by a change in tunneling resistance. These defects are different from other ones observed, which are up to 0.2 nm deep and where no molecular features can be resolved. They appear at low concentration and are thought to arise from impurities and/or variations in the substrate quality and cleanliness. This is concluded from sample to sample variations in their density. Since they do not affect the SAM structure, no particular attempts were made to eliminate them. While in the majority of images like the ones displayed in Figure 3 and 4 the protrusions lack any particular shape, in a number of experiments, the molecular features exhibit a pronounced anisotropy, which we ascribe to a particular (but unknown) tip geometry. Thus revealing additional molecular

well-known vacancy islands (VIs) are clearly seen as roundshaped depressions. These monatomic deep defects in the substrate, which are well-known to occur in thiol SAMs where the sulfur is bound to an aliphatic chain,7,73 originate from the restructuring of the substrate surface upon thiol SAM formation. Au atoms from the topmost gold layer are expelled to form adatoms involved in the binding of the thiols.73−76 At higher magnification, the molecular features of the SAM become visible and Figure 3b exemplifies the excellent crystallinity of the layer. Also seen in the image are the thiolcovered VIs both on terraces and at steps. The size of domains is in the range of 102 to 103 nm2. Figure 3c, which is an enlarged section of Figure 3b, displays two domains. They are mirror images as highlighted by the oblique unit cells whose long sides are aligned with the ⟨112⟩̅ direction. For clarity, we note that this unit cell describes only the packing of the molecules. It is one-fourth of the unit cell discussed below, which takes into account the registry with the substrate. An interesting structural feature is revealed by looking at the Fourier transform of the area covering the two domains. Whereas single spots are seen along the ⟨11̅0⟩ direction, i.e., both domains have molecular rows running parallel to ⟨112̅⟩, pairs of spots appear in other directions. This already indicates that the angle between the unit cell vectors is different from the 60° given by the C3v symmetry of the substrate. The situation is analyzed quantitatively by looking at the molecularly resolved STM image of Figure 4, which exhibits four domains, two of which (I, IV) are mirror images of the other two (II, III). As in Figure 3c, the long axes (a, a′) of the

Figure 4. (a) High-resolution STM image of MeSBP3 SAM on Au(111) showing four domains. Boundaries are marked by dashed lines. Domains I and IV are mirror images of II and III. Corresponding unit cells of the SAM shown in domains III and IV. Scale bar = 3 nm. (b) Fourier transform of panel a with schematic illustration of diffraction spots. Molecular rows parallel to lines in panel a give rise to diffraction spots labeled correspondingly in panel b. 4651



Article

pattern is not only chiral but also lacks inversion symmetry. As a consequence of the C1 symmetry, inversion of the pattern can alter the STM contrast, and the different appearance of domains aligned along the same directions as mentioned above (Figure 4) is consistent with this interpretation. As a last point in the STM analysis of the SAM, we address structural features seen in Figure 5c,d. Rows of molecules appearing higher (brighter) by up to 0.3 Å run pronouncedly parallel to the ⟨112⟩̅ direction, in particular on samples whose crystallinity, i.e., domain size, has been improved by preparation at temperatures around 373 K. Similar to the MeBPn series9 where contrast variations beyond the unit cell have been observed, this is ascribed to stress originating from a mismatch between the lattices of SAM and substrate. The alignment of the lines and the variation in their separation, which ranges between 20 and 40 Å, indicates that, in line with the discussion of the unit cell (Figure 4), the SAM matches the substrate lattice along the ⟨112̅⟩ direction but deviates from simple commensurability along the direction of the other unit cell vector. Calculations. Assuming that the molecular packing in the MeSBP3 SAM is essentially determined by the aromatic moieties and the tail group, a model based on a truncated MeSBP3 molecule was used in the calculations. Consisting of the biphenyl fragment with the tail group but not taking the aliphatic linker and the molecule−substrate bonding into account, this simplified model of the SAM is computationally significantly less expensive compared to the full SAM−substrate system not only because of the reduced number of atoms but also due to reduction of the rather large 2√3 × √61 unit cell with 8 molecules (dashed red line in Figure 6a) to 1/4 of its original size. For comparison with the structure of biphenyl and MeBP3, the unit cell is conveniently defined as indicated by the orange rectangle. With dimensions of a = 8.33 Å, b = 5.64 Å, and γ = 89.36°, it contains two molecules. Another aspect of this model is that any uncertainties are eliminated regarding details of the structure74,75,78 and energetics of the SAM substrate interface, which for the biphenyl based species are unknown at present. The structure resulting from the DFT calculations is represented by the space filling model displayed in Figure 6a. Qualitatively analogous to the bulk structure of oligophenylenes,55,79,80 the biphenyl molecules adopt a herringbone packing with the 4,4′-axis of the biphenyl moiety being tilted toward the next nearest neighbor (NNN) by ϕ = 20° (for definition of angles and coordinates, see Figure 6b). However, in contrast to the unsubstituted oligophenylenes where the two molecules are symmetrically rotated out of the zNNN plane around the 4,4′-axis, there is no glide plane for MeSBP3, and thus, the domains are chiral. Furthermore, since the benzene rings are differently rotated against each other in the biphenyl units I and II, four values (ϑm,i with m = I, II and i = 1,2) are required to characterize the twist of all benzene rings. From the values of ϑI,i (65°, 45° for i = 1,2) and ϑII,i (−59°, −42°), the orientation of the transition dipole moments (TDMs) orthogonal to the ring planes are calculated according to

features, this provides further insight into the structure of the MeSBP3 SAM. An example is presented in Figure 5, and already in the unfiltered image (Figure 5a) it is seen that molecular features appear elongated and aligned along two essentially orthogonal directions.

Figure 5. (a) Unfiltered high-resolution STM image of a MeSBP3 SAM on Au(111). Height profiles A and B shown below are along the respective lines. (b) Fourier transform of image shown in panel a and enlarged section of the Fourier filtered image with illustration of the unit cell. In the structural model shown, the protrusions are identified with the thioether moiety. Large yellow and small gray circles represent sulfur and CH3, respectively. (c,d) STM images of MeSBP3 SAM showing contrast features beyond the molecule. Arrows mark lines appearing higher and running parallel to ⟨112̅⟩. Scale bars = 3 nm (a), 2 nm (b), 20 nm (c), and 3 nm (d). Height scale bar in line profiles A and B: 0.05 nm.

Parallel to the unit cell vector a, i.e., along the ⟨112̅⟩ direction, the orientation of the protrusions alternates, whereas the protrusions along the unit cell vector b are parallel. This is reflected in the corresponding height profiles A and B shown in Figure 5. Contrasting profile B, an alternating appearance of the protrusions is seen in profile A with those marked by the gray shaded bars being wider and less symmetric than the ones in between. Frequently even two maxima less than 3 Å apart are resolved. The overall structure is described by a herringbone pattern as clearly seen from the enlarged section of the Fourier filtered image, which is displayed in Figure 5b. The sub 3 Å separation of the twinned protrusions suggests an intramolecular feature, and the most obvious interpretation is that they represent the methyl thioether tail groups, i.e., in these STM images, the methyl group and the sulfur are resolved. Marking of the protrusions accordingly as illustrated in Figure 5b yields a herringbone pattern where the methyl groups point toward the sulfur atom of the next nearest neighbor. Such a 2D

(

ρm , i = arccos sin ϕ cos(90° − ϑm , i)

)

where ϑm,i = 0°, if the planes of the benzene rings are in the zNNN plane. The average value of ρ = 74.2° compares well with the corresponding experimental value of 78° obtained from 4652



Article

which is 8.3% larger than in the MeBP3 SAM, a value for the angle α between the unit cell vectors aS and bS (see Figure 6b) a few degrees smaller than 60°, and an intermolecular distance along bS, which is 13% larger than the 5 Å along aS. Therefore, while the molecules are in registry with the substrate lattice along the ⟨112̅⟩ direction, there is a mismatch along bS. The arrangement of molecules in a herringbone pattern as concluded from Figure 5a and corroborated by the calculated structure depicted in Figure 6a explains the 2√3 double row periodicity along aS. We stress at this point that, first, the structure of the SAM−substrate interface is not known at present and information about the exact adsorption sites of the molecules is lacking. Thus, the underlying lattice shown in Figure 6c merely serves as reference to illustrate dimensions. Second, the suggested structure is the smallest commensurate unit cell consistent with our data. Keeping the limited precision of STM data in mind, we cannot exclude incommensurability along the b-axis, that is, small deviations from √61. In fact, the varying distance between lines of bright contrast as those shown in Figure 5 is indicative that the suggested unit cell might only be an approximation. However, this caveat does not affect the general conclusion that the biphenyl moieties in a unit cell are not in simple registry with the underlying Au lattice, i.e., the thiol head groups should occupy different adsorption sites. In general, this mismatch of lattices results in stress and thus poor film quality, but in the present case, the flexibility of the alkane spacer seems to compensate this mismatch, which allows formation of highly crystalline SAMs. The fact that SAMs of MeBP3 and MeSBP3 exhibit different unit cells but are both highly ordered suggests that the molecular architecture comprising a rigid aromatic moiety and a flexible alkane linker, which largely decouples SAM and substrate lattices, affords substantial flexibility in the choice of the tail group without compromising the crystallinity of the SAM. This is in contrast to SAMs where the headgroup is directly attached to the aromatic ring.37−41 However, this does not mean that the influence of the substrate is negligible. The extent to which the substrate affects the packing of the SAM molecules depends on a proper choice of the length of the alkane spacer. The SAM−substrate interface, namely, the directive force of the C−S−substrate bending potential, can exert a crucial influence on the SAM structure as evidenced by the odd−even effects reported for biphenyl and terphenyl based thiols with alkane spacers2−4,8,31 where pronounced differences in SAM structure are observed, with more than 20% variation in coverage between odd and even numbers of methylene units. An influence of the substrate for an odd number of CH2 units in the linker can be concluded from the comparison of the packing of the biphenyl units in MeBP3 SAMs compared to bulk biphenyl (BP). As seen from Figure 6c, which shows a comparison of the different unit cells and the compilation of the respective dimensions in Table 1, it is seen that the 2√3 × √3 structure of MeBP3 deviates significantly from the molecular arrangement in BP with an expansion and contraction along a and b, respectively, and ∼5% contraction of area per molecule. This is contrasted by MeSBP3 for which the unit cell geometry is very close to BP as illustrated by Figure 6c with an area per molecule only about 3% larger. It is tempting to conclude from the 8% difference in molecular area between MeSBP3 and MeBP3 that the thioether introduces a repulsive force. However, calculations based on the truncated MeSBP3 model do not corroborate this conclusion as there are essentially no significant energy differences between this molecule in the 2√3

Figure 6. (a) Calculated arrangement of MeSBP3 molecules in a 2√3 × √61 unit cell (red dotted line). Red circles illustrate the experimentally observed distribution of molecules in the oblique unit cell. The experimentally observed pattern as presented in Figure 5a,b is also shown with black arrows representing the alignment of the double protrusion features. (b) Angles defining orientation of biphenyl moiety and transition dipole moments μm,i orientated normal to the planes of benzene rings 1 and 2. Direction of next nearest neighbor (NNN) indicated in panel a. (c) Comparison of 2√3 × √61 unit cell of MeSBP3 (red, circles and dotted line) with the 2√3 × √3 structure of MeBP3 (brown circles) and molecular packing in bulk biphenyl (BP, blue ellipses). Origin of all unit cells is the molecule at the bottom left.

NEXAFS experiments taking into account the simplifying assumptions of the model and the fact that the calculations are at T = 0 K, whereas the experiments were performed at room temperature. The thioether groups are also arranged in a herringbone pattern as the C−S bonds are essentially parallel to the upper benzene rings. The excellent agreement with experimental results is highlighted in Figure 6a where the model is overlaid with the STM pattern presented in Figure 5a (short black arrows). This corroborates the interpretation that the pairs of protrusions seen in the STM image represent the thioether moieties. Note that experiment and model match even with regard to the small shift in the position of the sulfur atoms of the thioether group in adjacent rows of molecules parallel to the unit cell vector b.

■

DISCUSSION Summarizing the main experimental results, MeSBP3 forms highly crystalline SAMs on Au(111), which are terminated by the thioether moiety. The thioether tail group induces a change in the molecular packing known from analogous aliphatic− aromatic SAMs, such as MeBP3, studied so far.3,7,31 The suggested commensurate 2√3 × √61 unit cell containing 8 molecules deviates significantly from the 2√3 × √3 structure found for MeBP3 with two molecules per unit cell. This is graphically illustrated in Figure 6c where the unit cell of the MeSBP3 SAM and the distribution of the molecules are shown (red dotted line and red circles) in comparison with the structure of the MeBP3 SAM (brown circles). The differences are reflected by an area per molecule of 23.5 Å2 for MeSBP3, 4653



■

Table 1. Comparison of Unit Cell Dimensions for MeBP3, MeSBP3, and the a−b Plane of Bulk Biphenyl (BP);55 the Unit Cell Parameters Are Defined in Figure 6a a (Å) difference (%) b (Å) difference (%) γ (deg) area/molecule (Å2) difference (%)

MeBP3

MeSBP3

BP

8.67 6.7 5.01 −12.7 90.0 21.68 −5.3

8.33 2.5 5.643 0.14 89.4 23.51 +2.7

8.12

REFERENCES

(1) Tao, Y. T.; Wu, C. C.; Eu, J. Y.; Lin, W. L. Structure Evolution of Aromatic-Derivatized Thiol Monolayers on Evaporated Gold. Langmuir 1997, 13, 4018−4023. (2) Rong, H. T.; Frey, S.; Yang, Y. J.; Zharnikov, M.; Buck, M.; Wühn, M.; Wöll, C.; Helmchen, G. On the Importance of the Headgroup Substrate Bond in Thiol Monolayers: A Study of BiphenylBased Thiols on Gold and Silver. Langmuir 2001, 17, 1582−1593. (3) Azzam, W.; Cyganik, P.; Witte, G.; Buck, M.; Wöll, C. Pronounced Odd−Even Changes in the Molecular Arrangement and Packing Density of Biphenyl-Based Thiol Sams: A Combined STM and Leed Study. Langmuir 2003, 19, 8262−8270. (4) Ballav, N.; Schüpbach, B.; Neppl, S.; Feulner, P.; Terfort, A.; Zharnikov, M. Biphenylnitrile-Based Self-Assembled Monolayers on Au(111): Spectroscopic Characterization and Resonant Excitation of the Nitrile Tail Group. J. Phys. Chem. C 2010, 114, 12719−12727. (5) Chang, S.-C.; Chao, I.; Tao, Y.-T. Structure of Self-Assembled Monolayers of Aromatic-Derivatized Thiols on Evaporated Gold and Silver Surfaces: Implication on Packing Mechanism. J. Am. Chem. Soc. 1994, 116, 6792−6805. (6) Chesneau, F.; Schüpbach, B.; Szelagowska-Kunstman, K.; Ballav, N.; Cyganik, P.; Terfort, A.; Zharnikov, M. Self-Assembled Monolayers of Perfluoroterphenyl-Substituted Alkanethiols: Specific Characteristics and Odd−Even Effects. Phys. Chem. Chem. Phys. 2010, 12, 12123−12137. (7) Cyganik, P.; Buck, M.; Azzam, W.; Wöll, C. Self-Assembled Monolayers of Ω-Biphenyl-Alkane Thiols on Au(111): Influence of Spacer Chain on Molecular Packing. J. Phys. Chem. B 2004, 108, 4989−4996. (8) Cyganik, P.; Buck, M.; Strunskus, T.; Shaporenko, A.; Wilton-Ely, J. D. E. T.; Zharnikov, M.; Wöll, C. Competition As a Design Concept: Polymorphism in Self-Assembled Monolayers of Biphenyl-Based Thiols. J. Am. Chem. Soc. 2006, 128, 13868−13878. (9) Cyganik, P.; Buck, M.; Wilton-Ely, J. D. E. T.; Wöll, C. Stress in Self-Assembled Monolayers: The Case of Ω-Biphenyl-Alkane Thiols on Au(111). J. Phys. Chem. B 2005, 109, 10902−10908. (10) Dauselt, J.; Zhao, J.; Kind, M.; Binder, R.; Bashir, A.; Terfort, A.; Zharnikov, M. Compensation of the Odd−Even Effects in Araliphatic Self-Assembled Monolayers by Nonsymmetric Attachment of the Aromatic Part. J. Phys. Chem. C 2011, 115, 2841−2854. (11) Dietrich, P. M.; Graf, N.; Gross, T.; Lippitz, A.; Schüpbach, B.; Bashir, A.; Wöll, C.; Terfort, A.; Unger, W. E. S. Self-Assembled Monolayers of Aromatic Omega-Aminothiols on Gold: Surface Chemistry and Reactivity. Langmuir 2010, 26, 3949−3954. (12) Felgenhauer, T.; Rong, H. T.; Buck, M. Electrochemical and Exchange Studies of Self-Assembled Monolayers of Biphenyl Based Thiols on Gold. J. Electroanal. Chem. 2003, 550, 309−319. (13) Feng, D. Q.; Wisbey, D.; Losovyj, Y. B.; Tai, Y.; Zharnikov, M.; Dowben, P. A. Electronic Structure and Polymerization of a SelfAssembled Monolayer with Multiple Arene Rings. Phys. Rev. B 2006, 74, 165425. (14) Heister, K.; Rong, H. T.; Buck, M.; Zharnikov, M.; Grunze, M.; Johansson, L. S. O. Odd−Even Effects at the S−Metal Interface and in the Aromatic Matrix of Biphenyl-Substituted Alkanethiol SelfAssembled Monolayers. J. Phys. Chem. B 2001, 105, 6888−6894. (15) Liu, J. X.; Schüpbach, B.; Bashir, A.; Shekhah, O.; Nefedov, A.; Kind, M.; Terfort, A.; Wöll, C. Structural Characterization of SelfAssembled Monolayers of Pyridine-Terminated Thiolates on Gold. Phys. Chem. Chem. Phys. 2010, 12, 4459−4472. (16) Liu, J.; Stratmann, L.; Krakert, S.; Kind, M.; Olbrich, F.; Terfort, A.; Wöll, C. IR Spectroscopic Characterization of SAMs Made from a Homologous Series of Pyridine Disulfides. J. Electron Spectrosc. Relat. Phenom. 2009, 172, 120−127. (17) McCarthy, F. J.; Buck, M.; Hähner, G. Friction and Adhesion on Different Phases of a Biphenyl-Alkanethiol Self-Assembled Monolayer on Gold Studied with Scanning Force Microscopy. J. Phys. Chem. C 2008, 112, 19465−19469. (18) Muglali, M. I.; Bashir, A.; Terfort, A.; Rohwerder, M. Electrochemical Investigations on Stability and Protonation Behavior

5.635 90.0 22.89

× √3 and the 2√3 × √61 structures. Using the cell dimensions of the MeSBP3 structure, the energy per molecule is even marginally higher (by about 4 kJ/mol) compared to the same model in the MeBP3 cell. Considering the 150−200 kJ/ mol per S−Au bond,81,82 it is enthalpically even less favorable for the system to adopt the lower coverage. Another possible reason, a change in the twist angle of the biphenyl rings caused by substitution of CH3 by SCH3, is also not supported by the calculations that yield a marginal decrease of the rotational barrier by 0.4 kJ/mol in agreement with the tendency of electron donating groups to slightly lower the barrier.83 While reasoning based on enthalpic factors does not explain the preference of the MeSBP3 SAM for the larger lattice, one has to keep in mind that these are static calculations, i.e., T = 0 K. In the range of about 300−400 K where the system has been prepared and characterized, entropic factors might play a role. The introduction of low frequency torsional modes upon change from the CH3 aligned with the 4,4′-axis of biphenyl to the bent geometry of the CH3S moiety and lattice phonons arising from its intermolecular interactions could give rise to thermally activated molecular dynamics.84,85 While a more thorough test of this interpretation is beyond the scope of the work presented here, we hope that this suggestion will trigger computational activities along this direction.

■

Article

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: +44(0)1334 467232. Fax: +44(0)1334 463808. Present Address ∥

International Center for Materials Nanoarchitectonics, Institute for Materials Science, Namiki 1−1, Tsukuba, Ibaraki, Japan. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS This work has been supported by EPSRC (EP/E061303/1, EP/D048761/1) and DFG (ZH 63/14-1). N.R.C. gratefully acknowledges receipt of a Royal Society Wolfson Merit Award. Mi.B. wishes to thank the School of Chemistry and EaStCHEM for support and H. Frü c htl for technical assistance. Computations were performed on a local Opteron PC cluster at the University of St. Andrews. H.H. and M.Z. thank Ch. Wöll and A. Nefedov (KIT) for the technical cooperation at BESSY II and BESSY II staff for the assistance during the synchrotronrelated experiments. 4654



Article

of Pyridine-Terminated Aromatic Self-Assembled Monolayers. Phys. Chem. Chem. Phys. 2011, 13, 15530−15538. (19) Shaporenko, A.; Brunnbauer, M.; Terfort, A.; Johansson, L. S. O.; Grunze, M.; Zharnikov, M. Odd−Even Effects in Photoemission from Terphenyl-Substituted Alkanethiolate Self-Assembled Monolayers. Langmuir 2005, 21, 4370−4375. (20) Silien, C.; Buck, M.; Goretzki, G.; Lahaye, D.; Champness, N. R.; Weidner, T.; Zharnikov, M. Self-Assembly of a PyridineTerminated Thiol Monolayer on Au(111). Langmuir 2009, 25, 959−967. (21) Tai, Y.; Shaporenko, A.; Grunze, M.; Zharnikov, M. Effect of Irradiation Dose in Making an Insulator from a Self-Assembled Monolayer. J. Phys. Chem. B 2005, 109, 19411−19415. (22) Tai, Y.; Shaporenko, A.; Rong, H. T.; Buck, M.; Eck, W.; Grunze, M.; Zharnikov, M. Fabrication of Thiol-Terminated Surfaces Using Aromatic Self-Assembled Monolayers. J. Phys. Chem. B 2004, 108, 16806−16810. (23) Thom, I.; Buck, M. Electrochemical Stability of Self-Assembled Monolayers of Biphenyl Based Thiols Studied by Cyclic Voltammetry and Second Harmonic Generation. Surf. Sci. 2005, 581, 33−46. (24) Aguilar-Sanchez, R.; Su, G. J.; Homberger, M.; Simon, U.; Wandlowski, T. H. Structure and Electrochemical Characterization of 4-Methyl-4′-(N-Mercaptoalkyl)Biphenyls on Au(111)-(1 × 1). J. Phys. Chem. C 2007, 111, 17409−17419. (25) Su, G. J. J.; Aguilar-Sanchez, R.; Li, Z. H.; Pobelov, I.; Homberger, M.; Simon, U.; Wandlowski, T. Scanning Tunneling Microscopy and Spectroscopy Studies of 4-Methyl-4′-(NMercaptoalkyl)Biphenyls on Au(111)-(1 × 1). ChemPhysChem 2007, 8, 1037−1048. (26) Heimel, G.; Romaner, L.; Bredas, J. L.; Zojer, E. Odd−Even Effects in Self-Assembled Monolayers of Omega-(Biphenyl-4-yl)Alkanethiols: A First-Principles Study. Langmuir 2008, 24, 474−482. (27) Vervaecke, F.; Wyczawska, S.; Cyganik, P.; Postawa, Z.; Buck, M.; Silverans, R. E.; Lievens, P.; Vandeweert, E. Phase-Dependent Desorption from Biphenyl-Substituted Alkanethiol Self-Assembled Monolayers Induced by Ion Irradiation. J. Phys. Chem. C 2008, 112, 2248−2251. (28) Vervaecke, F.; Wyczawska, S.; Cyganik, P.; Bastiaansen, J.; Postawa, Z.; Silverans, R. E.; Vandeweert, E.; Lievens, P. Odd−Even Effects in Ion-Beam-Induced Desorption of Biphenyl-Substituted Alkanethiol Self-Assembled Monolayers. ChemPhysChem 2011, 12, 140−144. (29) Lüssem, B.; Müller-Meskamp, L.; Karthäuser, S.; Homberger, M.; Simon, U.; Waser, R. Electrical and Structural Characterization of Biphenylethanethiol SAMs. J. Phys. Chem. C 2007, 111, 6392−6397. (30) Sharif, A. M.; Buckley, D. N.; Buck, M.; Silien, C. Bonding Asymmetry and Adatoms in Low-Density Self-Assembled Monolayers of Dithiols on Au(111). J. Phys. Chem. C 2011, 115, 21800−21803. (31) Azzam, W.; Bashir, A.; Terfort, A.; Strunskus, T.; Wöll, C. Combined STM and FTIR Characterization of Terphenylalkanethiol Monolayers on Au(111): Effect of Alkyl Chain Length and Deposition Temperature. Langmuir 2006, 22, 3647−3655. (32) Noda, H.; Tai, Y.; Shaporenko, A.; Grunze, M.; Zharnikov, M. Electrochemical Characterizations of Nickel Deposition on Aromatic Dithiol Monolayers on Gold Electrodes. J. Phys. Chem. B 2005, 109, 22371−22376. (33) Rajalingam, K.; Strunskus, T.; Terfort, A.; Fischer Roland, A.; Wöll, C. Metallization of a Thiol-Terminated Organic Surface Using Chemical Vapor Deposition. Langmuir 2008, 24, 7986−94. (34) Silien, C.; Lahaye, D.; Caffio, M.; Schaub, R.; Champness, N. R.; Buck, M. Electrodeposition of Palladium onto a Pyridine-Terminated Self-Assembled Monolayer. Langmuir 2011, 27, 2567−2574. (35) Thom, I.; Hähner, G.; Buck, M. Replicative Generation of Metal Microstructures by Template Directed Electrometallization. Appl. Phys. Lett. 2005, 87, 024101. (36) Felgenhauer, T.; Yan, C.; Geyer, W.; Rong, H. T.; Gölzhäuser, A.; Buck, M. Electrode Modification by Electron-Induced Patterning of Aromatic Self-Assembled Monolayers. Appl. Phys. Lett. 2001, 79, 3323−3325.

(37) Kang, J. F.; Ulman, A.; Liao, S.; Jordan, R.; Yang, G. H.; Liu, G. Y. Self-Assembled Rigid Monolayers of 4′-Substituted-4-Mercaptobiphenyls on Gold and Silver Surfaces. Langmuir 2001, 17, 95−106. (38) Duan, L.; Garrett, S. J. An Investigation of Rigid pMethylterphenyl Thiol Self-Assembled Monolayers on Au(111) Using Reflection-Absorption Infrared Spectroscopy and Scanning Tunneling Microscopy. J. Phys. Chem. B 2001, 105, 9812−9816. (39) Azzam, W.; Fuxen, C.; Birkner, A.; Rong, H. T.; Buck, M.; Wöll, C. Coexistence of Different Structural Phases in Thioaromatic Monolayers on Au(111). Langmuir 2003, 19, 4958−4968. (40) Käfer, D.; Witte, G.; Cyganik, P.; Terfort, A.; Wöll, C. A Comprehensive Study of Self-Assembled Monolayers of Anthracenethiol on Gold: Solvent Effects, Structure, and Stability. J. Am. Chem. Soc. 2006, 128, 1723−1732. (41) Dhirani, A. A.; Zehner, R. W.; Hsung, R. P.; Guyot-Sionnest, P.; Sita, L. R. Self-Assembly of Conjugated Molecular Rods: A HighResolution STM Study. J. Am. Chem. Soc. 1996, 118, 3319−3320. (42) Zharnikov, M.; Frey, S.; Rong, H.; Yang, Y. J.; Heister, K.; Buck, M.; Grunze, M. The Effect of Sulfur-Metal Bonding on the Structure of Self-Assembled Monolayers. Phys. Chem. Chem. Phys. 2000, 2, 3359−3362. (43) Azzam, W.; Wehner, B. I.; Fischer, R. A.; Terfort, A.; Wöll, C. Bonding and Orientation in Self-Assembled Monolayers of Oligophenyldithiols on Au Substrates. Langmuir 2002, 18, 7766−7769. (44) Poppenberg, J.; Richter, S.; Darlatt, E.; Traulsen, C. H. H.; Min, H.; Unger, W. E. S.; Schalley, C. A. Successive Coordination of Palladium(II)-Ions and Terpyridine-Ligands to a Pyridyl-Terminated Self-Assembled Monolayer on Gold. Surf. Sci. 2012, 606, 367−377. (45) Muglali, M. I.; Bashir, A.; Rohwerder, M. A Study on Oxygen Reduction Inhibition at Pyridine-Terminated Self Assembled Monolayer Modified Au(111) Electrodes. Phys. Status Solidi A 2010, 207, 793−800. (46) Richter, S.; Poppenberg, J.; Traulsen, C. H. H.; Darlatt, E.; Sokolowski, A.; Sattler, D.; Unger, W. E. S.; Schalley, C. A. Deposition of Ordered Layers of Tetralactam Macrocycles and Ether Rotaxanes on Pyridine-Terminated Self-Assembled Monolayers on Gold. J. Am. Chem. Soc. 2012, 134, 16289−16297. (47) She, Z.; DiFalco, A.; Hähner, G.; Buck, M. Electron-Beam Patterned Self-Assembled Monolayers as Templates for Cu Electrodeposition and Lift-Off. Beilst. J. Nanotechnol. 2012, 3, 101−113. (48) Boyen, H. G.; Ziemann, P.; Wiedwald, U.; Ivanova, V.; Kolb, D. M.; Sakong, S.; Gross, A.; Romanyuk, A.; Buttner, M.; Oelhafen, P. Local Density of States Effects at the Metal−Molecule Interfaces in a Molecular Device. Nat. Mater. 2006, 5, 394−399. (49) Qu, D.; Uosaki, K. Electrochemical Metal Deposition on Top of an Organic Monolayer. J. Phys. Chem. B 2006, 110, 17570−17577. (50) Moulder, J. F.; Stickle, W. E.; Sobol, P. E.; Bomben, K. D. Handbook of X-Ray Photoelectron Spectroscopy; Perkin-Elmer Corp.: Eden Prairie, MN, 1992. (51) Thome, J.; Himmelhaus, M.; Zharnikov, M.; Grunze, M. Increased Lateral Density in Alkanethiolate Films on Gold by Mercury Adsorption. Langmuir 1998, 14, 7435−7449. (52) Lamont, C. L. A.; Wilkes, J. Attenuation Length of Electrons in Self-Assembled Monolayers of n-Alkanethiols on Gold. Langmuir 1999, 15, 2037−2042. (53) Stöhr, J. NEXAFS Spectroscopy; Springer: Berlin, Germany, 1992. (54) Batson, P. E. Carbon 1s Near-Edge-Absorption Fine Structure in Graphite. Phys. Rev. B 1993, 48, 2608−2610. (55) Hargreaves, A.; Rizvi, S. H. The Crystal and Molecular Structure of Biphenyl. Acta Crystallogr. 1962, 15, 365−373. (56) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865−3868. (57) Grimme, S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. J. Comput. Chem. 2006, 27, 1787−1799. (58) McNellis, E. R.; Meyer, J.; Reuter, K. Azobenzene at Coinage Metal Surfaces: Role of Dispersive van der Waals Interactions. Phys. Rev. B 2009, 80, 205414. 4655



Article

(82) Schreiber, F. Self-Assembled Monolayers: From ’Simple’ Model Systems to Biofunctionalized Interfaces. J. Phys.: Condens. Matter 2004, 16, R881−R900. (83) Gomez-Gallego, M.; Martin-Ortiz, M.; Sierra, M. A. Concerning the Electronic Control of Torsion Angles in Biphenyls. Eur. J. Org. Chem. 2011, 6502−6506. (84) Upadhya, P. C.; Nguyen, K. L.; Shen, Y. C.; Obradovic, J.; Fukushige, K.; Griffiths, R.; Gladden, L. F.; Davies, A. G.; Linfield, E. H. Characterization of Crystalline Phase-Transformations in Theophylline by Time-Domain Terahertz Spectroscopy. Spectrosc. Lett. 2006, 39, 215−224. (85) Wojcik, G.; Holband, J. Variable-Temperature Studies of the 4Isopropylphenol Crystal Structure from X-Ray Diffraction. Comparison of Thermal Expansion and Molecular Dynamics with Spectroscopic Results. Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 2002, 58, 684−689.

(59) Clark, S. J.; Segall, M. D.; Pickard, C. J.; Hasnip, P. J.; Probert, M. J.; Refson, K.; Payne, M. C. First Principles Methods Using Castep. Z. Kristallogr. 2005, 220, 567−570. (60) Yates, J. R.; Pickard, C. J.; Mauri, F. Calculation of NMR Chemical Shifts for Extended Systems Using Ultrasoft Pseudopotentials. Phys. Rev. B 2007, 76, 024401. (61) Monkhorst, H. J.; Pack, J. D. Special Points for Brillouin-Zone Integrations. Phys. Rev. B 1976, 13, 5188−5192. (62) Lee, C.; Yang, W.; Parr, R. G. Development of the Colle− Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37, 785−789. (63) Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648−5652. (64) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; et al. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004. (65) Hiremath, R.; Basile, J. A.; Varney, S. W.; Swift, J. A. Controlling Molecular Crystal Polymorphism with Self-Assembled Monolayer Templates. J. Am. Chem. Soc. 2005, 127, 18321−18327. (66) Iglesias, B.; Alvarez, R.; de Lera, A. R. A General Synthesis of Alkylpyridines. Tetrahedron 2001, 57, 3125−3130. (67) Crich, D.; Hao, X. Generation and Cyclization of Acyl Radicals from Thiol Esters under Nonreducing, Tin-Free Conditions. J. Org. Chem. 1997, 62, 5982−5988. (68) Marinzi, C.; Bark, S. J.; Offer, J.; Dawson, P. E. A New Scaffold for Amide Ligation. Bioorg. Med. Chem. 2001, 9, 2323−2328. (69) Nuzzo, R. G.; Zegarski, B. R.; Dubois, L. H. Fundamental Studies of the Chemisorption of Organosulfur Compounds on Gold(111). Implications for Molecular Self-Assembly on Gold Surfaces. J. Am. Chem. Soc. 1987, 109, 733−740. (70) Shaporenko, A.; Terfort, A.; Grunze, M.; Zharnikov, M. A Detailed Analysis of the Photoemission Spectra of Basic Thioaromatic Monolayers on Noble Metal Substrates. J. Electron Spectrosc. Relat. Phenom. 2006, 151, 45−51. (71) Trotter, J. The Crystal and Molecular Structure of Biphenyl. Acta Crystallogr. 1961, 14, 1135−1140. (72) Ballav, N.; Schüpbach, B.; Dethloff, O.; Feulner, P.; Terfort, A.; Zharnikov, M. Direct Probing Molecular Twist and Tilt in Aromatic Self-Assembled Monolayers. J. Am. Chem. Soc. 2007, 129, 15416− 15417. (73) Poirier, G. E. Mechanism of Formation of Au Vacancy Islands in Alkanethiol Monolayers on Au(111). Langmuir 1997, 13, 2019−2026. (74) Woodruff, D. P. The Interface Structure of N-Alkylthiolate SelfAssembled Monolayers on Coinage Metal Surfaces. Phys. Chem. Chem. Phys. 2008, 10, 7211−7221. (75) Hakkinen, H. The Gold-Sulfur Interface at the Nanoscale. Nat. Chem. 2012, 4, 443−455. (76) Maksymovych, P.; Sorescu, D. C.; Yates, J. T. Gold-AdatomMediated Bonding in Self-Assembled Short-Chain Alkanethiolate Species on the Au(111) Surface. Phys. Rev. Lett. 2006, 97, 146103/ 1−4. (77) Korolkov, V. V.; Allen, S.; Roberts, C. J.; Tendler, S. J. B. HighTemperature Adsorption of p-Terphenylthiol on Au(111) Surfaces. J. Phys. Chem. C 2011, 115, 14899−14906. (78) Mazzarello, R.; Cossaro, A.; Verdini, A.; Rousseau, R.; Casalis, L.; Danisman, M. F.; Floreano, L.; Scandolo, S.; Morgante, A.; Scoles, G. Structure of a CH3S Monolayer on Au(111) Solved by the Interplay between Molecular Dynamics Calculations and Diffraction Measurements. Phys. Rev. Lett. 2007, 98, 016102. (79) Bacon, G. E.; Curry, N. A.; Wilson, S. A. A Crystallographic Study of Solid Benzene by Neutron Diffraction. Proc. R. Soc. London, Ser. A 1964, 279, 98−110. (80) Rietveld, H. M.; Maslen, E. N.; Clews, C. J. B. An X-Ray and Neutron Diffraction Refinement of Structure of para-Terphenyl. Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. 1970, 26, 693−706. (81) Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M. Self-Assembled Monolayers of Thiolates on Metals as a Form of Nanotechnology. Chem. Rev. 2005, 105, 1103−1170. 4656


Accommodation of Lattice Mismatch in a Thiol Self-Assembled

Recommend Documents