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C: Surfaces, Interfaces, Porous Materials, and Catalysis

Assignment of NEXAFS Resonances in Alkanethiols and Their Implication on the Determination of Molecular Orientation of Aliphatic SAMs Johannes Völkner, Michael Klues, and Gregor Witte J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b04342 • Publication Date (Web): 02 Jul 2018 Downloaded from http://pubs.acs.org on July 12, 2018

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The Journal of Physical Chemistry

Assignment of NEXAFS Resonances in Alkanethiols and Their Implication on the Determination of Molecular Orientation of Aliphatic SAMs Johannes Völkner, Michael Klues*, and Gregor Witte* Molekulare Festkörperphysik, Philipps-Universität Marburg, 35032 Marburg, Germany ABSTRACT Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has become a widely used technique to analyze the molecular orientation of functional adlayers by analyzing the dichroism of NEXAFS resonances. In contrast to π-conjugated systems, which exhibit distinct π-resonances whose transition dipole moments are oriented perpendicular to the aromatic planes, the analysis of purely aliphatic systems is not as straightforward and requires a precise identification of the underlying resonances and their polarization. Here we analyze the carbon K-edge NEXAFS signature and its dichroism of a self-assembling monolayer (SAM) formed by octadecanethiol (ODT) on gold representing the widely studied class of alkanethiol-SAMs. Employing density functional theory calculations and using the transition potential method, the polarizations of all NEXAFS resonances at excitation energies around and below the ionization threshold are precisely determined. This information is then used to simulate expected dichroism curves for various adlayer arrangements which are compared with our experimental findings for ODT-SAMs on singlecrystalline Au(111) and polycrystalline gold surfaces. This analysis demonstrates a novel strategy to precisely deduce the molecular orientation from the experimental NEXAFS data of aliphatic SAMs.

1. INTRODUCTION Self-assembling monolayers (SAMs) have become a subject of intense research in surface science due to their useful capability to tailor surface properties such as e.g. wettability, adhesion, lubrication, and work function. 1-3 The vast majority of related studies have been carried out for organothiol-based SAMs with aliphatic backbones such as alkanethiols on gold surfaces because of their ease of preparation by immersion, hence serving as prototypical and extensively characterized model system. 1,2 Despite intense research, the exact binding geometry and adsorbate coupling of such supposed model systems are, however, still controversially debated. 2,4 One important parameter of such films is the orientation of the backbones with respect to the substrate surface. While densely packed SAMs with saturated hydrocarbon backbones generally reveal an upright molecular orientation on gold, a tilting of the alkyl chains occurs as a consequence of the structural optimization of the intermolecular van der Waals forces with the boundary condition of specific adsorption sites at the metal substrate. 1,3 For this tilt angle, α, with respect to the surface normal, very different values are reported in the literature, ranging from 20° - 40° 3,5-14, which on the one hand depends on the applied technique, while on the other hand might be attributed to the different crystallinity of the used substrates, as it will be discussed later. A very elegant method to determine the molecular orientation is based on C 1s near-edge X-ray absorption fine structure (NEXAFS) measurements. Since corresponding transitions from core levels into unoccupied molecular orbitals are governed by dipole selection rules, they allow to determine the molecular orientation by analyzing the linear dichroism which occurs when the incidence angle and polarization of the linearly polarized synchrotron light is varied. 15 For π-conjugated molecules with extended π-systems distinct π*resonances can be identified at energies well below the ionization threshold and thus without overlapping background due to σ*resonances forming a quasi-continuum. Since the transition dipole moments (TDM) of these resonances are all collinear and oriented perpendicular to the aromatic plane, this enables an evaluation of the molecular orientation without detailed identification of the individual resonances. When deriving the molecular tilt angle with respect to the surface normal also the molecular twist and the packing motif within the unit cell need to be taken into account. 16-18 In contrast, such simple analyses are hampered for aliphatic systems

because they possess only σ*-resonances which are located close to the ionization threshold which requires a detailed analysis of the spectra. In addition, also the nature of the final orbital states as well as the corresponding TDMs of the transitions are not so easy to predict. Early NEXAFS studies assumed that the electronic transitions of σ*-resonances for saturated hydrocarbon chains can be described by isolated σ*(C-C) and σ*(C-H) orbitals. 5 Later works, however, have disproved the validity of this “building block” scheme and pointed out that instead a consideration of final states delocalized over the entire molecule is required. 6,19-21 Consequently, the TDM of the σ*(C-C) resonances are not oriented along the C-C bond but along the chain axis direction. The most intense resonance within the C 1s NEXAFS signature of saturated hydrocarbons occurs at about 288 eV (denoted as R*), which has been ascribed to mixed Rydberg/σ*(C-H) character (based on the size and nodal structure of the final state orbitals). 20,22 Although its energetic position below the ionization threshold allows straightforward determination of the intensity, the corresponding symmetry character and orientation of the associated TDM remained unclear for a long time. Later on, high-resolution NEXAFS measurements have shown that the signal around 288 eV actually consists of various sub-resonances of different symmetry character. 19-24 Therefore, Kondoh et al. solely considered the first σ*(C-C) peak intensity (~292.5 eV) for a dichroism analysis to circumvent the complication. 25 Other strategies to determine the average molecular orientation from dichroism measurements involve evaluation of peak height or area of R* and/or σ*(C-C) 5-7,21,27, often using a plane orbital approximation while assuming a four-fold symmetric orbital shape. 15 Alternatively, difference spectra are utilized to eliminate angular independent background, however, requiring a well-known reference value. 5,6,8,27 Based on a theoretical analysis for the case of n-octane adsorbed on copper Weiss et al. have shown that the main NEXAFS resonance (R*) is dominated by two transitions with corresponding TDMs oriented perpendicular to the molecular long axis, but also perpendicular to each other. 22 To avoid additional electronic substrate interactions due to chemisorption on metal surfaces, similar studies were later also performed for alkanes on graphite or graphene coated metal substrates. 25,26 Such an orientation of the corresponding TDMs was been taken into account for the orientation analysis of ordered alkane films 21,22 but was not yet done for aliphatic organothiol SAMs. In case of

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SAMs, also the packing motif of the alkyl chains must be considered. The combination of results of STM and LEED measurements clearly shows, that alkanethiols do not form a primitive unit cell, but instead adopt a herringbone-type arrangement of the CCCplanes of the alkyl chains. 1,28 These findings make a straightforward estimation of the molecular tilt angle obsolete, so that the quantitative evaluation of the linear dichroism for self-assembled monolayers of alkanethiols has to be rethought. It indicates in particular that the intensity of σ*(C-H) resonances is not only determined by the tilt of the alkyl chain but also by the twist and pairing arrangement of the CCC-planes. To shed more light on these aspects we analyzed in the present study the dichroism of octadecanethiol (ODT) SAMs on gold, which is known to form well-ordered films on Au(111). 1,7,13 In a first step, we have calculated the C 1s NEXAFS signature in the frame of density functional theory (DFT) by using the Slater transition potential method, and then used the orientation of the TDMs of all calculated resonances to simulate dichroism curves for various molecular geometries and arrangements. These results are finally compared with our dichroism measurements of ODT-SAMs on Au(111) as well as on polycrystalline gold substrates. 2. METHODS 2.1 Experimental Details. For the present study, substrates of different crystalline quality were used comprising atomically flat Au(111) as well as polycrystalline gold samples. The polycrystalline gold substrates were prepared by sputter deposition of 15 nm Au onto polished Si(100) wafers (Siegert Wafer GmbH) covered with a native oxide layer. Before the sputter deposition under an argon atmosphere (POLARON sputter coater), the wafers are cleaned in an acetone ultrasonic bath and rinsed thoroughly with 2propanol. The Au(111) samples consist of 100 - 200 nm metal films that were epitaxially grown by vapor deposition under high vacuum conditions onto freshly cleaved and carefully degassed mica substrates, as described elsewhere. 17 They were additionally prepared under UHV conditions by several cycles of Ar-ion sputtering (800 eV) and annealing (730 K) until a sharp (1x1) LEED pattern was observed which confirms the excellent surface ordering. Self-assembled monolayers were prepared by immersing the gold samples in a 3 mM ethanolic solution of 1-octadecanethiol (ODT, Sigma-Aldrich, purity: 98%) for about 24 h at room temperature. After removal from the solution the samples were carefully rinsed with ethanol and subsequently dried under a nitrogen stream. The carbon K-edge NEXAFS measurements were performed at the HE-SGM dipole beamline of the synchrotron storage ring BESSY II of the Helmholtz Center Berlin (Germany). It provides linearly polarized light (polarization factor: 0.91) and an energy resolution of about 300 meV at the C K-edge. Spectra were acquired in a partial electron yield (PEY) mode using a channel plate detector with a retarding field of -150 V. To determine the average molecular orientation relative to the sample surface, NEXAFS spectra were recorded at different angles of incidence (θ = 30°, 55° and 90°, cf. inset of Fig. 1a). To compare the intensity of the angular dependent NEXAFS resonances, the acquired spectra were normalized following a procedure introduced by Calvin 29, which is described in detail in the Supporting Information (Fig. S1). Further details on the experimental setup and the energy calibration are provided in the literature. 16 2.2 Computational Approach. To identify the NEXAFS signature of ODT SAMs and the polarization of the various resonances, density functional theory (DFT) based single-molecule NEXAFS

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calculations are performed using the StoBe code. 30 Previous work has shown that the C 1s NEXAFS signature for pentacene is very similar for gas phase and solid state 31, hence indicating that matrix effects in van der Waals bound molecular solids have a negligible influence on the X-ray absorption. By contrast, for alkanes notable differences are found in the NEXAFS signature in both phases, showing up as an additional fine structure in the gas phase spectrum. These excitations are attributed to vibronic effects, which are not taken into account in the present calculations, while electronic excitations are very similar and reveal only a slight energetic shift in both phases. 24,26 They are thus not expected to significantly affect our analysis since we are essentially aiming at identifying the character and polarization of the NEXAFS resonances. Moreover, the C 1s NEXAFS signature of densely packed alkanethiol SAMs and alkane multilayers are nearly identical. 23 This indicates that the electronic structure of the aliphatic chain within the SAMs is hardly affected by the covalent thiolate bonding to the gold substrate, and therefore justifies the single-molecule approach, as long as the backbone is not in close contact to the metal surface (i.e. uprightly oriented). The various steps of the used computational approach have been described in detail previously. 32 The first step comprises a structural optimization of the free ODT molecule using the gradient-corrected revised Perdew-BurkeErnzerhof (RPBE) functional 33,34 and all-electron Gaussian basis sets of valence triple-ξ plus polarization quality. 35 Here we consider only an all-trans configuration of the molecule as it is the most stable conformation and also found in alkane solid as well as dense packed SAMs. To describe the localized excitation and enable a distinction from the electrons of the other atoms, the 1s electrons of the core hole center are represented by a basis set of IGLO-III quality 36, whereas the 1s electrons of all other C atoms are described by a [3s3d1d] valence basis set to prevent mixing of 1s core orbitals. 37,38 Since the ODT molecule has no inversion or mirror symmetry due to two different terminating (-SH and -CH3) groups, all 18 carbon atoms (Ci) are symmetry non-equivalent. Ionization potentials are calculated for each excitation center as total energy difference of ground and ionized states and subsequently shifted by 0.4 eV to higher energies to account for relativistic effects. 39 The actual transition probability of the individual X-ray absorption transitions are calculated using the transition potential approximation. 40,41 Therefore, the basis set of the excitation center, described above, is augmented by a [19s19p19d] set of diffuse functions within a double basis set technique to allow proper representation of diffuse molecular states 42,43, such as Rydberg levels. Visualization of the orbitals is performed with the MacMolPlt program. 44 To account for the natural peak width due to finite lifetime of the excited molecular final states and enable a comparison with the experimental NEXAFS spectra, the calculated transition energies are convoluted by Gaussian functions. Here one has to consider that the lifetime of final states above the ionization potential (IP) is distinctly shorter than for states below the IP. The carbon K-edge NEXAFS signatures are best described by using full width at halfmaximum (FWHM) values of 0.5 eV and 4.5 eV for resonances below and above IP, linearly increasing in a window of 10 eV above the IP. Without consideration of any angular effects, the calculated spectra are comparable to experimental data of an amorphous sample (with isotropic molecular orientation) or a spectrum acquired under the so-called magic angle (θ = 55°), where the resonance intensities are independent of the actual molecular orientation. 16 In addition also orientation effects can be computed by considering the transition dipole vectors Tj of the individual molecular excitations. The comparison with experimental data requires consideration of the molecular arrangement inside the SAM, usually described by a tilt (α) and twist angle (β), and corresponding transformation of Tj into the


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Cartesian coordinate system of the sample. By that, the relative angle of the Tj vectors with respect to the surface normal can be determined and thus the dichroism for every Tj. Appropriately weighed by the individual oscillator strength the sum over all excitations then delivers the total dichroism curves for a single molecule. If necessary, summation over all molecules in the unit cell further yields the effective dichroism of the monolayer. 16,45 3. RESULTS AND DISCUSSION 3.1 Experimental C 1s NEXAFS Spectra. The experimental carbon K-edge NEXAFS data of ODT-SAMs on gold substrates are summarized in Fig. 1, where the intensity is given in units of edge jump, i.e. all spectra are normalized to the intensity of the postedge region (E > 315 eV). Characteristic signatures are a sharp and intense resonance (labeled R*) at about 288 eV and a substantially broader resonance around 293 eV (σ*). In Fig. 1a also the X-ray absorption K-edge of carbon is depicted (dashed green line), which is represented by a modified step function as described elsewhere 15,46 using the calculated average C 1s ionization potential of ODT (cf. Fig. 2). The sharp resonance R* appears well below the ionization threshold and has been attributed to orbitals of mixed Rydberg and valance character associated with σ*(C-H) bonds. 20,22 By contrast the broad resonance is above the ionization threshold where excited final states have very short life times and are attributed to σ*-type transitions associated with σ*(C-C) bonds. 5,6,19-22 This C 1s NEXAFS signature is very similar to that of unsubstituted alkanes. 19-22 In addition, a weak signal is observed at about 285 eV, a typical energy for π*-type transitions in molecules containing conjugated subunits. 16 While ODT is an aliphatic molecule which does not actually possess such π* states, similar low energetic resonances have been observed for alkanethiols also in previous works and were attributed to formation of C=C-bonds upon hydrogen abstraction and crosslinking due to extensive X-ray exposure (or secondary electrons from the substrate). 21,47,48 Although special care was taken to minimize radiation damage throughout the experiment they are not fully excluded. Notably, our DFT calculations presented below suggest an alternative origin of such resonance. NEXAFS spectra that are recorded at the so-called magic angle (θ ≈ 55° for substrates of 3-fold or higher symmetry) remain invariant to the molecular orientation and can therefore be used as spectral fingerprint of a molecule. By contrast, a distinct variation of the NEXAFS resonance intensities is observed at other angles of incidence, θ. In turn, this linear dichroism can be used to analyze the orientational order of the molecules. In the present case the leading resonance, R*, shows a distinct linear dichroism with largest intensity at normal incidence which indicates an upright orientation of the alkyl chains expected for a dense packed SAM. 1 By contrast, the σ* resonance at higher energy exhibits a reverse dichroism and the energetic position of the peak maximum appears to shift for different angles of incidence. For a quantitative analysis of the molecular tilt angle the first resonance R* is analyzed in more detail and also its dichroism is compared for ODT-SAMs adsorbed on gold substrates of different crystallinity. The magnified view of the leading resonance (cf. Fig. 1b and c) shows a shoulder revealing the presence of at least two sub-resonances (denoted R1*, R2*). Such a splitting has also been observed for alkanes and was clearly resolved in previous highresolution studies. 21-24 Moreover, our comparison clearly shows a larger dichroism for ODT-SAMs prepared on Au(111) than on polycrystalline gold (cf. Fig. 1b,c). A quantitative analysis of the molecular orientation is possible since the intensity of NEXAFS resonances upon excitation with linearly polarized light scales according to ~| ∙ | . Here, E denotes the electric field vector and T is the transition dipole moment (TDM) of the involved molecular excitation. For alkanes and

alkanethiols, the leading NEXAFS resonance, R*, has been attributed to excitations into σ*(C-H) orbitals, with corresponding TDMs oriented perpendicular to the molecular backbone (denoted as TR in the inset in Fig. 1a). Assuming two or more vectors with higher than 2-fold sym-

Figure 1: C 1s NEXAFS data of ODT-SAMs on gold: (a) overview scan for a ODT monolayer on Au(111) recorded at different angles of incidence (blue: θ = 30°, black: 55°, red: 90°). The dashed green curve represents the K-edge and the inset depicts a sketch of the experimental geometry. The bottom row shows magnified spectra of the main resonance R* for ODT-SAMs (b) on Au(111) and (c) on polycrystalline gold substrates. To visualize the different dichroism on both substrates the intensity of the black curves (θ = 55°) are levelled. metry forming a plane mathematically described by its normal the appropriate azimuthal averaging for a substrate of 3-fold or higher symmetry yields the expression for the NEXAFS resonance intensities of such plane orbitals , ~ ∙ cos 1 3 cos cos 1 with the polarization factor and γ defining the angle between the plane normal and surface normal. 15 In the present case γ equals the molecular tilt α as the normal of the plane points along the molecular axis (equaling the orientation of transitions along the chain, TC). Using this expression and the integral intensity of the R* resonance enables a first analysis of the observed dichroism and yields tilt angles of α = 37° for ODT on Au(111) and α = 46.5° on the polycrystalline gold substrate, respectively. We note, however, that this analysis does neither consider the splitting of the R* resonance, nor account for the exact orientation of the TDMs within the molecule (which might be different for the various sub-resonances R1* and R2*) or a potential twist of the molecules. To shed more light on the plurality of such contributions to the resulting dichroism a theoretical characterization of such


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NEXAFS resonances was performed that will be presented in the next section. 3.2 Theoretical Analysis of the NEXAFS Signature. To identify the underlying NEXAFS resonances and determine the orientation of the corresponding transition dipole moments (i.e. their polarization), precise DFT calculations of the C 1s transitions into unoccupied molecular states were performed for a free ODT molecule. Since all carbon atoms within the molecule are symmetry non-equivalent, excitations at each carbon atom are treated individually. Fig. 2 summarizes the results of our theoretical analysis in terms of polarization-resolved NEXAFS spectra together with the energy and oscillator strength of the involved transitions for each carbon atom. The energetic position of the ionization potential for each carbon atom is shown in green. The summed spectrum of all polarizations (black curve in Fig. 2a) resembles the main features found in the experimental spectra recorded at the magic angle (where the NEXAFS signature is not sensitive to the molecular orientation). Note that no absorption edge is added to the calculated spectra. The main resonance (R*) is reproduced at ~288.2 eV as well as the dominant contribution (σ*) above the ionization threshold around 293 eV. Compared to the experimental data the computed energy of the distinct resonances appears slightly blue shifted by only 0.2 eV. Such a close agreement has been also found in previous C 1s NEXAFS calculations of π* resonances of aromatic molecules 32 and demonstrates the accuracy of the Slater transition potential method for computing NEXAFS resonances with final states below the ionization potential. By contrast, this DFT-based approach becomes increasingly inaccurate for higher-lying final states, especially those with energies above the ionization potential. 45 However, the character and sequence of resonances in the energetic window of interest (cf. Fig. 2b,c, excitation energy < 292 eV) delivers a valuable source for analyzing and understanding the experimental findings. Next, the TDMs of the various NEXAFS resonances have been analyzed in more detail. It was found that their orientation can be grouped according to the molecular axis, with x describing the molecular long axis, together with the y-axis defining the CCCplane, while the z-axis is orthogonal to this plane (cf. inset of Fig. 2a). The polarization resolved calculated NEXAFS spectra represent all resonances whose TDMs are aligned to the principle axes within an acceptance angle of ±5°. Notably, there is only one additional class of resonances left, which reveal a non-negligible portion of both, x- and y-components of their TDMs. They correspond to excitations into orbitals of mixed σ*(C-C) and σ*(C-H) character and provide a large contribution to resonances above the ionization potential. At first glance one may be tempted to assign these transitions to σ* orbitals associated to C-C bonds of the alkyl chain. However, a closer inspection reveals a rather uniform angular distribution of these TDMs without any accumulation for directions along the C-C bonds (cf. Fig. S2, Supp. Inf.) which provides another evidence for the non-validity of a “building block” model. Notably, an intermixing of orbitals showing TDM components within the xy-plane and along the z-axis does not occur. The computational results reveal a distinct splitting of the dominant resonance into sub-resonances with corresponding final states of yand z-symmetry and are therefore denoted as Ry* and Rz*. A closer inspection shows that each of these resonances is actually composed of several sub-resonances due to the individual excitation centers. Fig. 2b,c summarizes the energy and corresponding oscillator strength of the excitations associated to the individual excitation centers (i.e. carbon atoms). Despite the multitude of sub-resonances one can identify rather isolated groups for Ry* and Rz* with reso-

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nances energetically located in a narrow window for the central excitation centers (regions labeled ‘A’ and ‘B’ in Fig. 2c). While the energetic variation of the individual resonances is well below the experimental resolution, the weighted group average (cf. black curve in Fig. 2b) can be measured. Our calculation yields an energetic separation of the sub-resonances of about 0.5 eV and an intensity ratio of

Figure 2: (a) Calculated C 1s NEXAFS spectra for a free ODT molecule, decomposed into contributions with TDM oriented along the molecular x-, y- and z-directions (magenta, blue, orange) as defined in the inset and with TDM oriented within the molecular xy-plane (gray). The calculated ionization potentials are shown in green. Note that the individual curves are shifted vertically for clarity. (b) Visualization of the individual contributing resonances in a magnified energy window with corresponding oscillator strength, and ionization potentials. Panel (c) shows the energy of all transitions with an oscillator strength above the dashed black line in (b) for each carbon excitation center of the ODT molecule. The color code denotes the polarization of the resonances and the ionization potentials.


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I(Ry*)/I(Rz*)≈0.88 which is in close accordance with the experimental data (~0.5 eV and 0.87, respectively). We note further that such a splitting has also been observed before for the NEXAFS signatures of alkanes 21-26 and differs only slightly from values obtained from calculations for e.g. n-octane (0.65 eV; 0.8). 22 Sub-resonances with noticeable different excitation energy occur only at carbon centers close to the terminating groups of the molecule, i.e. thiol (with carbon center C1) and methyl unit (C18). This nicely visualizes the influence of the chemical environment, known as chemical shift, with an effect observable over four to five methylene units of the saturated hydrocarbon chain. Consequently, only the inner part of the chain, containing carbon atoms C6 to C14, resemble an alkane of infinite length. This may explain the deviations of our results to descriptions of alkanes and alkanethiols of shorter length, such as n-octane 22, n-hexane(thiol) 23, neopentane 24 or propane. 20 Interestingly, our calculations reveal also low energetic resonances with mixed xy-polarization (gray bars in Fig. 2b) that are related to excitations at the terminal C atoms (C1 and C18). To model the covalent bonding of ODT to the substrate, further explorative calculations were performed where a small Au cluster was attached to the thiol anchoring unit. It was found, that C1 related transitions with xy-polarization are quenched while new resonances arise around 286 eV, which implies an origin of the low inevitable contribution observed in recorded data (cf. Fig. 1a) alternative to beam damage. With increasing excitation energy, the density of unoccupied final states drastically increases and forms a quasi-continuum. As respective transitions with final states above the ionization threshold have a rather short lifetime they appear as fairly broad resonances in the NEXAFS spectrum, thus making it impossible to resolve individual contributions from the spectral shape. Although precise calculation of such high energetic unoccupied final states are hardly possible by DFT, our calculations allow to identify groups of transitions around 292-293 eV with different character and various TDM orientation. As shown in the Supporting Information (Fig. S3) such groups of differently polarized transitions reveal various dichroic behavior which explains the supposed energetic shift of the resonance maximum (σ*) for different θ, as observed in the experimental data (cf. Fig. 1a). This situation demonstrates in particular that evaluation strategies using the intensity of an apparent peak observed at different angles of the incident X-ray light (i.e. representing the continuum of states by a hypothetic resonance) as performed in several previous works 5-7,27, is physically rather questionable.

of the electron density contour lines (red, blue) in the yellow slices the wave functions of the final state reveal a node at the C-H bonds thus representing the antibonding σ*C-H character and allow a clear correlation to the direction of the TDM (indicated by the arrows). Based on the size and nodal structure of the orbitals, the resonances Ry* and Rz* thus represent final states of mixed Rydberg/valencecharacter, confirming previous interpretations. 20,22,49,50 Although discussed over a period of time it was shown, that despite their spatial extension such Rydberg-type orbitals are not entirely suppressed in the condensed phase and, hence, are also not expected to vanish within

3.3 Orbital Character of NEXAFS Resonances. Our assignment of the various NEXAFS resonances becomes intriguingly plausible when inspecting the corresponding molecular orbitals of the corresponding final states. Fig. 3 illustrates final state orbitals representing the two main resonances (Ry* and Rz*) as well as the intense σ* resonance feature occurring in the continuum above the ionization threshold. Here, final state orbitals are depicted for core hole excitations at atom C10, which is located in the center of the aliphatic chain, where the influence of the terminal groups (CH3 or thiolate) is negligible. The shown orbitals correspond to transitions from the C 1s level into the lowest and second lowest unoccupied molecular orbitals (LUMO at 287.75 eV, LUMO+1 at 288.2 eV) and a highly excited state (at 292.5 eV), respectively. The first two presented orbitals are characteristic for K-shell excitations of hydrocarbon. As can be seen from cutting planes through the excitation center (yellow slices in Fig. 3), the electron density is located around the ionization center and exhibits a nearly spherical distribution which exceeds the radial extension of the molecule, characteristic for Rydberg-type orbitals. As indicated by the color

Figure 3: Visualization of (a) LUMO and (b) LUMO+1 of ODT representing final states of the Ry* and Rz* resonances, as well as (c) a highly excited state exhibiting the characteristic of a σ*(C-C) resonance. All orbitals are calculated for excitations at carbon atom C10 (indicated by the green torus). The 2D electron density is shown for various cutting planes: the plane spanned by opposing hydrogens (turquoise), the xy-plane (green) and a plane parallel to yzplane running through the excitation center (yellow). For each 3Dplot the latter is shown in detail in the upper left corner while the arrows indicate the direction of the associated TDM. the densely packed SAM. Some variation in their character is described, from Rydberg to more valence-like, however, without providing a distinct definition of the orbital character, e.g. by means of a band structure and its polarization. 21,22,24 Above the ionization threshold, excitations with TDM oriented along the molecular x-axis gain spectral relevance (cf. magenta curve in Fig. 2a). Fig. 3c shows a typical σ*-type final state orbital


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which exhibits characteristic nodes in C-C bonds hence reflecting the antibonding σ*C-C character. Note, that these orbital expands over the entire molecule length and thus demonstrates impressively that a “building block” model of molecular subunits does not provide a valid description here. Cutting the electron density along the yz-plane (yellow circle in Fig. 3c) and plotting at same scaling as the R* orbitals reveals a substantially smaller radial extension than for the Rydberg/valence type orbitals which is rather comparable to the size of typical π* states found in π-conjugated molecules. 16,32

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clockwise twist, while the direction of tilt α matters. 1,28 The example given in Fig. 4c,d shows dichroism curves simulated for a typical tilt angle of α = 30° and a twist of β = 55°. As in the top row, the sum spectra for both regions, A and B, are composed of partial dichroism curves of somewhat different curve progression while the general behavior remains similar to the case of non-tilted molecules discussed above. Again applying the plane orbital analysis to the total resonance intensity (Σtot) yields tilt angles of α = 36° and 37° for the energy regions A and B, respectively.

3.4 Modeling the NEXAFS Dichroism. Next, the calculated TDM vectors are used to model the variation of NEXAFS resonance intensities with varying angle of light incidence. Thereby, effects of various molecular geometries on the resulting linear dichroism can be simulated. Here, we concentrate only on the first two resonances (Ry* and Rz*) of the C 1s NEXAFS signature, because they are experimentally accessible with a low level of overlapping background signal and show reasonable sharpness as they are located below the ionization threshold. For this analysis, transitions from all different excitation centers contributing to resonances in the considered energy range (marked as ‘A’ and ‘B’ in Fig. 2c) as well as the corresponding TDM orientation and oscillator strength are evaluated. Therefore, the plane-orbital representation is not applicable here. Instead, the individual transitions are described by vector-type orbitals which yields for substrates with 3fold or higher symmetry the expression

, ~ ∙ cos² ∙ cos² sin ²

with α defining the orientation of the transition dipole vector Tj with respect to the surface normal. 15 The resulting total dichroism curves (black curve labeled as Σtot in Fig. 4) are obtained by summation over all excitation centers and polarizations. In case of perfectly upright standing molecules, the substrate normal is identical to the x-axis of the molecule and the TDMs of the Ry*- and Rz*-resonances are oriented parallel to the surface plane, yielding an invariance with regard to the twist angle. Consequently, transitions polarized along the x-axis are excited maximally at grazing incidence, whereas normal incidence (i.e. θ = 90°) yields maximum intensity for transition dipole moments oriented along the molecular y- or z-axis, as depicted in Fig. 4a,b. The analysis shows further that the polarization resolved partial dichroism curves for some excitation centers behave differently. In particular, contributions from carbon atoms of the terminal groups (C1 and C18) exhibit an opposite dichroism (dashed and solid gray lines in Fig. 4). This means, that the true tilt angle is systematically underestimated when considering the total dichroism curve (Σtot), which equals a quantitative evaluation of the measured total peak intensity as it was performed in section 3.1. This effect is clarified, if one uses the simulated dichroism curves of uprightly oriented ODT (α = 0°) and applying the plane orbital approximation for the orientation analysis. This yields tilt angles of α = 37° and 28° when considering total resonance intensity (Σtot) for the energetic regions A and B, respectively, while a consideration of only the partial intensities Σy (for A) or Σz (for B) would yield indeed a tilt angles of α = 0°. This demonstrates that the presence of resonances with mixed xypolarization drastically reduce the total dichroism which is different for both spectral regions. The situation changes as soon as the molecules are tilted. As a consequence the symmetry for rotations around the x-axis (twist) vanishes and the projections of the y- and z-polarized resonances onto the surface normal contribute differently, yielding notably different dichroism curves. Due to the mirror symmetry of alkanethiols with respect to the CCC-plane, the outcome is invariant for clockwise or counter-

Figure 4: Simulated dichroism curves for the first two C 1s NEXAFS resonances of ODT located at energy regions A (left column) and B (right column, as defined in Fig. 2c) for different molecular orientations. (a,b) Upright standing (tilt α = 0°), (c,d) slightly tilted (α = 30°) and twisted (β = 55°), as well as flat lying molecules with the CCC-plane oriented (e,f) parallel and (g,h) perpendicular to the substrate surface. The color code of the different polarizations with respect to the molecular axis is defined in Fig. 2a. Since alkanethiols can also adopt a lying orientation at low coverage (so-called striped phase 51,52), we also simulated the expected dichroism curves for flat-lying ODT molecules. In addition, we note that alkanes which feature C 1s NEXAFS signatures very similar to alkanethiols likewise adopt a lying adsorption geometry on metals 53,54 as well as on graphite. 55,56 Here, we consider lying molecules with their CCC-plane oriented parallel to the surface, as observed for adsorption of n-alkanes on metals 22,57, as well as a perpendicular CCC-plane, as reported for some n-alkane molecules upon formation of an incommensurate crystalline phase on graphite. 23 For both CCC-plane orientations the simulated dichroism curves reveal an opposite behavior for the resonances Ry* and Rz* in the considered energy regions A and B (cf. Fig. 4e,f and g,h). We note that the different dichroic behavior of the more intense Rz* resonance for the various orientations of the CCC-plane allows a


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clear identification of the adsorption geometry. This characteristic is in accordance with C 1s NEXAFS data obtained for n-alkanes on metals 21,22, which confirms the validity of our considerations and demonstrates their transferability to other systems, although alkyl chain - metal substrate interaction 22,54 is not included here. 3.5 Determination of Molecular Orientation. Finally, we have refined the analysis of the molecular orientation based on the experimentally observed dichroism by taking the results presented in the previous section into account. In particular, we make use of the calculated relative portion of NEXAFS resonances polarized along the three molecular axes defined in Fig. 2a. Thereby, resonances with xy-polarization are considered through projections of their TDMs onto the cardinal axes. In principle this allows to determine the resulting total dichroism and thus a calculation of the theoretically expected NEXAFS intensity for each excitation energy value and angle of incidence, as a function of the angles α and β. A comparison of the simulated intensity with the experimental data then delivers presumable values for tilt and twist. For the sake of simplicity and comparability to previous works we chose three characteristic spectral features as representative for each acquired experimental spectrum. Here, we use the intensity of the NEXAFS spectra at the energies 287.5 eV, 288.0 eV and 292.4 eV to represent the resonances Ry*, Rz* and σ*c-c. Note that the dichroism of some of these features was also considered in earlier works. 6,7 These resonances are dominated by TDMs oriented mainly along the y, z and x-axis, respectively, but also contain considerable fraction of other orientations, as discussed above. To generalize our approach one may estimate these portions based on our computations for ODT as a function of the chain length due to the strong influence of the terminal groups. For our analysis, we also considered two different molecular arrangements for the SAM, namely a primitive unit cell and a unit cell containing at least a pair of molecules adopting a 90°herringbone motif. These structural models are currently discussed and are referred to as single-chain and two-chain model in the literature. 1 The comparison of the experimentally observed and simulated dichroisms for the various NEXAFS resonances is depicted in Fig. 5, where on the lhs (rhs) the outcome of the single (two)-chain model is presented. For modeling the SAM by a single molecule on the surface, a vector-type dichroism curve for each cardinal axis was fitted such that their superposition matches the experimental data and their intensity portions at the magic angle reflect their contributions to the total spectrum (Fig. 2a). This was performed for each of the three considered energies in a multi-fit procedure in order to find the best values of tilt and twist. In case of the two-chain model, curves for y- and z-oriented transitions are represented as one plane-type function with summed up intensity. This assumption is valid as the TDMs span a four-fold symmetric plane when molecules appear pairwise with orthogonally twisted alkyl chains whereby the dependency on the twist angle is canceled out. In the single-chain model the experimental data points are best represented by the simulated dichroism curves for molecular tilt of α = 25° ± 2° and twist of β = 56° ± 3°. Both values agree well with literature data obtained from IR measurements 3,11, however, are smaller than e.g. concluded from GIXD and the typically mentioned 30°. 1,2,10 This difference is more pronounced when considering a non-primitive unit cell and applying the two-chain model, which yields a tilt angle of α ≈ 22°. We attribute these findings to a better-defined substrate crystallinity as compared to commonly used polycrystalline surfaces. Applying the same evaluation route to data acquired for ODT SAMs formed on the latter surface, we obtained a remarkably larger tilt of about 41° and a twist of β ≈ 47°

for the single-chain model and α ≈ 40° in case of two chain model for an orthogonal herringbone arrangement of the CCC-planes. These numbers are comparable to other NEXAFS studies 7-9 and reflect the lower level of molecular order in SAMs on polycrystalline substrates due to large density of defects such as steps and grain boundaries as emphasized in earlier work. 1 We note that the reduced film quality may not only be attributed to structural defects of the metal substrate, but also be caused by surface contaminations since the polycrystalline gold samples were not subject of additional cleaning (by ion sputtering) prior to the immersion. This procedure was chosen deliberately to mimic

Figure 5: Refined analysis of the tilt (α) and twist angle (β) for an ODT-SAM on Au(111) on the basis of simulated C 1s NEXAFS dichroism curves. Contributions from resonances with TDMs oriented along the different molecular axes (x, y and z) are considered and their total intensity (black curve) is compared with the experimental data (filled squares) for different energetic positions associated to the various resonances Ry* (top), Rz* (middle) and σc-c* (bottom row, step height subtracted). The left (right) column shows the data for the single (two)-chain model, of which geometry is sketched in the inset in the top row. the process conditions that are typically used to modify metal electrodes in electronic devices by means of SAMs. 58 In order to account for the limited resolution of the presently used beamline and its influence on the accuracy of determination of the molecular tilt angle we estimate an error for α of ±5°. Nevertheless, our analysis clearly shows that the derived tilt angle is strongly dependent on the adsorption geometry (packing motif and twist), that must be taken into account. To derive a particular accurate tilt angle for such SAMs, we suggest performing dichroism measurements at a high-resolution beamline (cf. refs. [21,24]) on long-range ordered Au(111) substrates and acquiring NEXAFS data for many different angles of incidence (cf. ref. [16]) to minimize statistical errors. 4. CONCLUSIONS We investigated the carbon K-edge NEXAFS signature of SAMs formed by ODT on gold surfaces. A clear dichroism was observed in the angular resolved NEXAFS data for Au(111) and polycrystal-


7


line gold substrates, while to lower extent for the latter. However, the quantitative evaluation of the dichroism is not straightforward for such aliphatic systems since the σ*-resonances generally appear less separated and might partially overlap with the ionization edge. In comparison, the orientation analysis of planar π-conjugated molecules is simpler because, despite the multitude of π*resonances, all the associated TDMs are collinear and oriented perpendicular to the molecular plane. Moreover, the excitation energy of such π*-resonances is well below the ionization potential so that their intensity can be used without overlapping background signal for the dichroism analysis even without the exact knowledge of the final states of the excitations. 16 In the case of aliphatic systems these simplifications are not fulfilled, instead they require a detailed characterization of the various resonances. To determine the average molecular tilt our present analysis focusses on features slightly below the ionization edge. Using the transition potential method our DFT based calculations of the NEXAFS signature show that the leading resonance actually consists of two sub-resonances. While both exhibit σ*(C-H) character, their TDMs are oriented radially to the aliphatic chain either parallel or perpendicular to the CCC-plane of the alkyl chain. The corresponding final state orbitals have a distinct spatial extension that is characteristic for Rydberg-states. Our analysis shows further that the common description of the NEXAFS signatures by a few σ*-resonances is an oversimplification since they occur actually for each excitation center (i.e. carbon atom) leading to a continuum of resonances rather than individual ones. Below the ionization potential the energetic variation of the individual excitations due to the chemical shift of the initial states is small, so that they can be combined to few resonance groups. On base of the character and polarization of all resonances within the energetic window of interest, including the ones appearing due to terminating group effects, we developed an alternative strategy for a quantitative analysis of the dichroism in order to determine the molecular orientation on the substrate. For Au(111)-substrates, as representative of a well-defined singlecrystalline surface and thus standard for comparison with theoretical models, we obtain a molecular tilting of the alkyl chain with respect to the surface normal of 22° - 25° (depending on the structural model used for the analysis). This marks a notable difference to the tilt angle usually referred to 1,2,10, but shows consistency with results obtained from infrared spectroscopy. 3,11 Remarkably, on polycrystalline gold ODT forms SAMs with more inclined molecular backbones represented by an effective tilt of about 41°. We emphasize that such structural differences have to be taken into account when comparing the structure of SAMs on technically relevant substrates, such as e.g. gold electrodes of organic electronic devices 59, and a theoretical modelling of SAMs which considers single-crystalline substrates. 60 Since the C 1s NEXAFS signature of alkanethiols and alkanes is very similar, our analysis is also applicable to aliphatic molecules different from ODT. Based on the detailed characterization of the polarization of the various NEXAFS resonances we introduced a refined evaluation scheme for the analysis of the molecular tilt which might be useful for future structural analyses of functional molecular adlayers.

Associated Content Supporting Information The Supporting Information is available free of charge on the ACS Publication website at DOI: […] . Exemplary presentation of applied normalization route for NEXAFS data; analysis of computed resonances and simulated

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dichroism curves of the σ* resonances around 293 eV; angular distribution of the computed NEXAFS resonances.

Author Information Corresponding Authors *(M.K.) E-Mail: [email protected] Telephone: +49 6421 28-24133 *(G.W.) E-Mail: [email protected] Telephone: +49 6421 28-21384 ORCID: Gregor Witte: 0000-0003-2237-0953

Notes The authors declare no competing financial interest. Acknowledgments We acknowledge financial support provided by the German Science Foundation (DFG) through the Research Training Group RTG 1782 "Functionalization of Semiconductors” and thank the Helmholtz-Zentrum Berlin (electron storage ring BESSY II) for provision of synchrotron radiation at the beamline HE-SGM.

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