Computational Study of Amino Mediated Molecular Interaction

Dec 29, 2014 - Department of Physics, University of Trieste, Trieste, Italy. ⊥. Department of Applied Physics and Applied Mathematics, Columbia Univ...
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Computational Study of Amino Mediated Molecular Interaction Evidenced in N 1s NEXAFS: 1,4-Diaminobenzene on Au (111) Gabriele Balducci,† Michele Romeo,† Mauro Stener,† Giovanna Fronzoni,*,† Dean Cvetko,*,‡,§ Albano Cossaro,‡ Martina Dell’Angela,‡ Gregor Kladnik,§,‡,∥ Latha Venkataraman, ⊥ and Alberto Morgante‡,∥ †

Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy CNR-IOM Laboratorio Nazionale TASC, Basovizza SS-14, km 163.5, I-34012 Trieste, Italy § Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia ∥ Department of Physics, University of Trieste, Trieste, Italy ⊥ Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, United States ‡

S Supporting Information *

ABSTRACT: Primary amines can interact with neighbor molecules or with a metal substrate via weak bonds involving the electron lone pair of their amino functional group. Near edge X-ray absorption spectra (NEXAFS) on the N 1s edge show that the structure of the empty molecular orbitals localized on the nitrogen atom is very sensitive to these interactions. Here we investigate the origin of these changes by means of theoretical calculations. NEXAFS spectra are simulated for the 1,4-benzenediamine (BDA) molecule in its free, crystalline, and monolayer on Au(111) forms. We identify the electronic states which are affected by these amino-based interactions. In the case of the molecular layer grown on the gold substrate, we show how the results of the calculations can be used to identify intermolecular interactions influencing adsorption geometries in molecular monolayers.

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INTRODUCTION Primary amines have a preeminent role in many biological processes like the condensation of the peptides, the folding of the proteins, and the metabolism of living cells. In all these cases, the chemistry of the amines is crucial. In particular, the nitrogen lone pair enables the formation of weak bonds with less electronegative terminations of other molecules or with inorganic compounds. In recent years an effort has been made in surface science to exploit the chemical properties of amines to control the growth of ordered organic structures on surfaces. It has been shown that in the assembly of biotemplates of amino acids on metal surfaces, the affinity between amino- and carboxylic-groups leads to the formation of hydrogen bonds between adjacent molecules and drives the growth of longrange ordered 2D systems.1,2 The same interaction has been adopted to form complex hetero-organic architectures both in solution and in vacuum, based on the recognition between the two terminations.3−5 More recently, the chemistry of the amino group has been investigated in single molecule conductance experiments with the amino-terminated molecules in contact with gold electrodes.6 Interestingly, despite the weaker donor/ acceptor bond in the amine-Au junction, these measurements provide well-defined and uniform values of molecular conductance contrary to the case of thiol terminated molecules. Such a uniform bonding scheme has been attributed to the © 2014 American Chemical Society

donor−acceptor coupling between nitrogen lone pair of the molecule and under coordinated Au atoms on the tip/substrate. A deeper understanding of how the electronic properties of the amines change when involved in a lone-pair interaction becomes therefore important for characterizing the electronic coupling between the functional group and the surrounding environment. We have recently studied the amino−gold interaction for the prototype case of the 1,4-benzenediamine (BDA) on Au(111) surface, by means of X-ray spectroscopies. A coverage dependent geometry was observed7 with strong impact on the molecular transport properties.8 Whereas for low molecular coverages a flat molecular geometry was found, at increasing coverages, a tilted molecular adsorption geometry was reported with average tilt angles values up to 48°.8 This finding alone indicates that at higher coverages intermolecular interactions may play a crucial role in the geometry of the molecular assembly. In fact when symmetrical molecules such as BDA with two amine end-groups weakly coupled to the Au substrate tilt off the surface at increasing molecular coverage, the effective strength of the intermolecular coupling competes with that of the amine−Au bond.9 Theoretical studies of BDA molecule adsorption at Au adatom sites have reported a Received: December 5, 2014 Published: December 29, 2014 1988

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

The Journal of Physical Chemistry C possible inclined geometry for the molecule,9 whereas almost flat adsorption geometry was found on flat Au(111) with the inclusion of van der Waals dispersion forces. Recently, the role of van der Waals forces in stabilizing nonflat molecular adsorption was also addressed10 where similarly small tilt angles (5°−9°) have been found, but adsorption angles as high as 21° have been obtained with the inclusion of intermolecular interactions. Experimentally, nonflat geometry of BDA/Au can be identified as nonequivalency of the two amine molecular end-groups, one close to and coupled to the Au(111), and one far from the surface and effectively decoupled from the Au, but coupled to the adjacent molecules. Here we address the spectroscopic fingerprints of such intermolecular couplings between BDA molecules in the tilted/flat monolayer phase, as measured by the NEXAFS experiments. Whereas C 1s NEXAFS results are found to be mostly unaffected by both molecule−molecule and molecule−substrate interactions, the N 1s NEXAFS spectra are an extremely sensitive spectroscopic fingerprint of the amine coupling, as it is observed from the comparison with the gas phase spectrum. The resonances in the edge region are quenched upon the formation of the aminogold bond, and the quenching is different for the different features of the absorption edge, i.e. for the different unoccupied electronic states corresponding to the NEXAFS peaks. Moreover, a similar behavior was notably observed in the case of the self-assembly of the amino-terminated alkanethiol cysteamine, where only intermolecular interactions can be considered to affect the amine chemistry.11 In order to understand the role of environmental changes around the amino groups, we investigate the nature of the N K-edge resonances in the case of BDA on Au(111) system by means of DFT calculations. We compare the experimental N 1s NEXAFS spectra with the calculated core excitation energies and oscillator strengths, obtained by a molecular density functional methodology based on the transition potential (TP) scheme.12 The agreement between theory and experiments is first verified on the gas-phase spectra of the BDA molecule where the nature of the different resonances can be properly assigned. Then different on-surface configurations are explored and the role of both the molecule−substrate and the molecule−molecule interaction is investigated. In the calculations of the crystalline form of BDA, the intermolecular forces are shown to cause a redistribution of the intensities of the resonances, which is consistent with the experimentally observed smoothing of the features present in the NEXAFS spectra with respect to the gas phase case. At the monolayer stage we identify new electronic states in the low photon energy range, which can be assigned to the Au−N interaction and that involve the lone pair electrons of the amino group in contact with the substrate. Moreover, the NEXAFS resonance corresponding to the σ*(NH) transition is identified as a fingerprint of the interacting state of the amine with adjacent molecules in the tilted phase. To confirm our assignments, we also examine experimentally the case of a similar molecule, the p-toluidine, which has just one amine termination. When compared to BDA, the toluidine molecule adsorbs on Au(111) with similar geometries and with the same interaction with the substrate, but the resonance attributed to the amino−amino intermolecular forces is indeed missing, as the amino groups are involved only in the anchoring process with the substrate.

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THEORETICAL METHODS

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EXPERIMENTAL METHODS

The approach to the calculations of NEXAFS spectra of the BDA on Au(111) is characterized by two main steps. In the first step a periodic slab methodology is used for the optimization of the BDA molecules adsorbed on the Au(111) surface. DFT calculations are performed with the Kohn−Sham orbitals expanded in plane waves and the effects of atomic core regions accounted for by pseudopotentials. The Quantum-Espresso suite of code13 was used for the implementation of this methodology. In the second step, suitable finite clusters are cut out from the periodic relaxed structures and used for the calculation of core excitation energies and oscillator strengths, employing the molecular quantum chemistry Amsterdam density functional (ADF) code.14,15 This methodology has been previously tested on organic molecules adsorbed on the Si(100) surface16,17 showing its reliability for describing the polarized K-shell spectra of the adsorbed molecules. More details on the theoretical approach are reported in the Supporting Information.

The experiments were conducted at the ALOISA beamline of the Elettra Synchrotron in Trieste, Italy in an ultrahigh vacuum end-station.18 All films were prepared and characterized in situ on Au(111) monocrystalline substrates. The Au substrate was first cleaned using 1 keV beam of Ar+ from a sputtering source, followed by an anneal to 900 K. BDA and p-toluidine molecules were purchased from Sigma-Aldrich (purity >98%) and dosed in the chamber from a valved pyrex cell. The evaporation rates were checked a posteriori by measuring the thickness of the layer grown on the Au substrate by monitoring the attenuation of the Au 4f signal. During the deposition the pressure in the preparation chamber was kept in the 10−8 mbar range, whereas a base pressure of ∼10−10 mbar was maintained during measurements. Multilayer BDA (p-toluidine) films were formed with the substrate kept at 200 K and a deposition flux of 3−5 Å/min. Typical multilayers were grown to 2−3 nm thickness. Molecular deposition of BDA (and p-toluidine) with the sample at 300 K resulted in a flat monolayer phase. Flat monolayer phases could also be obtained from the multi phase and subsequent flash heating to 300 K, followed by rapid cooling. The tilted phase was obtained either by dosing BDA (p-toluidine) molecules with the sample at 245 K ± 3 K or by flash heating the multi phase to 245 K followed by rapid cooling. For XPS measurements, X-rays with electric field perpendicular to the sample (p-pol) of energy 500 eV were used at grazing-incidence (4°) to the sample. Photoelectrons were collected normal to the sample using a hemispherical electron analyzer with an acceptance angle of 1°. The energy scale for XPS spectra was calibrated by aligning the Au 4f7/2 peak to a binding energy of 84.0 eV. NEXAFS measurements were conducted on the C (N) Kedge, with incident photon energy between 280 and 315 eV (395−425 eV), and incidence angle of 6°. Spectra were acquired in partial electron yield mode, with a high pass filter set to 250 eV (370 eV), and normalized to the beam current measured on the last aperture of the beam path. Carbon K-edge NEXAFS on clean Au was also measured for the intensity normalization. The spectra were collected with electric field polarization parallel (s-pol) and perpendicular (p-pol) to the 1989

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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The Journal of Physical Chemistry C sample. Extended NEXAFS and XPS measurements were performed by continuously moving the illumination area of incident X-rays (estimated as 250 μm) over the surface to avoid any beam induced desorption and/or chemical modification of the films. Spectral indications of the damage are the slight changes in the N 1s and C 1s XPS profiles and, more clearly, the appearance of new features in the N K-edge NEXAFS in the energy region between 395 and 400 eV.

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RESULTS AND DISCUSSION The BDA adsorbs on Au(111) in two different phases in the monolayer range, characterized by different tilt of the molecules with respect to the surface,8 namely the flat phase and the tilted phase. The two phases can be prepared by changing the molecular coverage on the surface, with the tilted phase forming at almost 3 times higher density of molecules with respect to the flat phase, as we have determined from the XPS N 1s and C 1s relative intensities (see the Supporting Information). In the flat phase the symmetric BDA molecule adopts a symmetrical geometry, with nearly flat lying aromatic ring. At higher coverages the tilted phase appears, with the molecules in a standing-up geometry and coupled to the Au substrate via one of the two amine terminations. This suggests that the intermolecular forces are responsible for the symmetry breaking of the adsorption geometry. To enlighten in detail their role, both monolayer phases and the bulk phase have been considered for the calculations. We focus our attention here on the tilted phase and on the bulk phase, where the contribution of the intermolecular forces plays an important role. The results and the discussion for the flat phase are reported in the Supporting Information. In order to have a reference for the condensed phases spectra, we first simulated the N 1s NEXAFS spectrum of the free BDA. Figure 1 reports the experimental gas phase spectrum and the simulated one (upper panel). To facilitate the comparison between experiment and theory, the theoretical spectrum has been shifted on the experimental energy scale (by about 1.4 eV). The calculated spectrum of the free BDA shows a lower energy two peaked feature which compares well with the first asymmetric peak of the experiment; this structure is attributed to transitions to the π*(CC) orbitals of the benzene ring (LUMO+1 and LUMO+2); the rather large intensity of the line calculated at 400.9 eV is due to a valence σ*(N−H) contribution while the second line (at 401.4 eV) to a small N lone pair participation to the final MO. The next band (at 402.1 eV) derives from a single transition toward a final state of Rydberg nature mixed with σ*(N−H) valence contribution which is responsible for its large intensity. The next peaks below the N 1s threshold correspond to transitions to Rydberg orbitals of mainly nitrogen np and nd character. Few states have rather large intensity because of mixed Rydberg-valence character (σ*(N−H)) of the transitions. The Rydberg orbitals are split into a number of components in the nonspherical symmetry of the molecule; the symmetry lowering (to Cs) due to the localization of the N 1s core hole further splits the Rydberg orbitals, giving rise to the multiple lines observed in the calculated spectrum. The overall comparison with the experimental spectrum is satisfactory, confirming the reliability of the DFT-TP computational approach. We explored the effects of the intermolecular forces on the BDA electronic structures by studying the bulk phase of the molecule, where the amines are involved in a hydrogenbonding scheme. The environmental conditions of thick film

Figure 1. Upper panel: experimental and theoretical N K-edge spectra of the free BDA. Calculated lines are convoluted with Gaussian functions of 0.5 eV width (fwhm) and shifted by −1.4 eV. Lower panel: experimental and theoretical N K-edge spectra of bulk BDA. Calculated lines are convoluted with Gaussian functions of fwhm = 0.8 eV and shifted by 1.38 eV. Vertical dashed lines: Δ Kohn−Sham (ΔKS) N 1s ionization thresholds (free BDA: 403.93 eV; model cluster for bulk BDA: 403.46 eV).

adsorption have been simulated assuming that the structure of the adsorbed thick film may be approximated by the bulk crystalline structure of the BDA. The experimentally determined X-ray geometry of bulk BDA19 has been thus taken as a starting point for a geometrical relaxation. The final relaxed geometry was nearly equal to the starting experimental one, thus validating our general computational methodology. From the obtained relaxed structure a cluster of five BDA molecules has been isolated (see Figure 1, inset in lower panel). The main aim was to capture any possible effect due to intermolecular H-bonding: for this reason, the cluster consisted of a central molecule surrounded by four molecules involved in H-bonds with the two amino groups of the former. The two N atoms of the central molecule interact with two H atoms of two of the peripheral molecules at 2.11 Å; moreover, one H atom on each of the two amino groups of the central molecule interacts with a N atom on each of the remaining two peripheral molecules, at a longer distance of 2.41 Å. The N 1s spectrum has been calculated for the central BDA molecule (labeled A), whose amino groups can form H-bonds with the four surrounding molecules (B and C), and it has been compared with that of the free BDA molecule in Figure 1. The first two main transitions have a nature similar to those present in the free BDA spectrum; the main difference is the energy decrease (of about 0.4 eV) of the second transition, which has a 1990

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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The Journal of Physical Chemistry C contribution from the nitrogen lone-pair. This energy shift could be ascribed to a stabilization of the structure due to the interaction of the N atoms of the central BDA with the H atoms of the peripheral molecules (B and C in lower panel of Figure 1) and the concomitant increasing of its coordination number. The third major transition has a mixed Rydberg and σ*(NH) valence character as in the free BDA. A significant quenching of this component can be observed when compared with the gas phase spectrum. The cluster considered is too simple for representing the thick film phase; in particular a very large cluster should have been cut out from the bulk structure in order to include the contribution to the spectra of the several nonequivalent N atoms of the BDAs surrounding the A molecule. However, the cluster allows us to point out the quite significant change of the spectral shape and the intensity redistribution induced by the intermolecular interactions. A more reliable and detailed study has been done on the monolayer phases, for which several adsorption models have been built to simulate the flat and tilted binding geometry of BDA on Au surface and reliable clusters have been cut out from the optimized periodic structures. The results for the flat phase are reported in the Supporting Information. Here we focus on the tilted phase, tackling the issue of the interplay between the amino−gold and the amino−amino interactions the two amino functional groups are involved in. We investigated two different possible configurations to describe the local molecular arrangement. First, a (2 × 2) surface unit cell with a single BDA N-bonded to an Au atom has been optimized (see panel a of SI, Figure S1). The relaxed values of the Au−N distance and the dihedral angle between the phenyl ring and the surface are 2.92 Å and 46.3°, respectively. These values are both higher than the corresponding values (2.66 Å and 22°) recently reported in the literature.10 The difference can be rationalized with the much higher coverage of the surface simulated in the present study: assuming that every Au atom at the surface is a possible adsorption site, our coverage is 1/4, i.e., three times larger than the coverage in the quoted paper. The larger tilt angle can thus be explained with the need to accommodate more molecules per unit surface area and the adsorbed molecules tend to move outward in response to the increased lateral interactions. The second configuration setup for the tilted phase aims at exploring the possible influence of H−bond formation between adsorbed molecules. Two BDA molecules have been placed in a (3 × 3) surface unit cell, facing each other in a roof-like scheme, such that an H−bond interaction could be established between the two amino groups pointing away from the surface (“tilted-facing” mode, see panel a of Figure 3). In line with an increased intermolecular interaction, after relaxation the tilt angles of the two molecules are 71.6° and 76.8° and the Au−N distances increase to 3.12 Å (N1R) and 3.20 Å (N1L), respectively. An H−bond interaction between the two facing molecules is suggested by the intermolecular N− H distance of 2.51 Å, slightly longer than the experimental Xray diffraction value of 2.37 Å found for the BDA crystalline form.19 The calculated N 1s spectra of the two configurations are reported in Figures 2 and 3 respectively. The p-pol and s-pol spectra have been calculated considering the two light polarizations used for the acquisition of the experimental spectra: the polarization with the electric field vector E normal to the surface (p-pol) and with E parallel to the surface (s-pol). In the reference system used for the calculations, the Au surface lies in the xy plane and z is the normal direction. The s-pol

Figure 2. Molecular adsorption scheme and N K-edge polarized spectra of BDA in the tilted adsorption phase. All the spectral profiles have been convoluted with Gaussian functions of fwhm = 0.5 eV and shifted by −1.65 eV to facilitate the comparison. Vertical dashed lines: ΔKS N 1s ionization thresholds (N1:403.59 eV; N2:404.15 eV).

spectra have been obtained as an average of the x and y components of the dipole transition moments. For the simpler tilted mode a cut cluster containing seven BDA molecules has been adopted (see Figure S3 in Supporting Information), which allows us to consider only the central BDA molecule for the spectral simulations because in this position it feels the presence of the neighbor BDA molecules on the surface and is virtually free from border effects of the cluster. The N 1s experimental and theoretical p-pol and s-pol spectra are reported in Figure 2; there are two nonequivalent N sites in the adsorbed BDA labeled N1 and N2 in the sketch of 1991

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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The Journal of Physical Chemistry C

atoms. Small N 2p components of the N1 atom pointing toward the surface are present and are probed by the p-pol spectrum where two weak features are present (around 398.3 and 399.3 eV) while they disappear in the s-pol spectrum. Only one weak structure is present in the s-pol spectrum at 400.1 eV, and its intensity mainly derives from the N1 excitations due to the presence of a small σ*(N−H) component, which almost lies in the xy plane, in an orbital mostly localized on the Au surface. The comparison with the experimental spectra in the low energy region has to be performed carefully because of the radiation induced damaging observed during the measurements. In fact, the residual intensity in the s polarization observed in the experimental data cannot be explained by the theoretical results. However, the presence of electronic states in the pristine amino-gold interfaces has been suggested not only for this system but also in other similar cases.11 Many transitions starting from both N1 and N2 1s orbitals give rise to an intense double peaked feature in the 400.5−402 eV energy region. The p-polarization enhances the lower energy side of the feature for the contributions from the N1 2pz atomic component around 401 eV, which is involved in antibonding interactions with the π*(CC) ring orbitals, and from the z component of the N2 lone pair; also the small components along the z direction of the σ*(N2−H) bond can contribute to the p-pol intensity. The higher energy side of the double peaked feature increases the intensity in the s-pol spectrum due to the σ*(N−H) character of the final MOs: the σ*(N−H) bonds of both N1 and N2 atoms have major components in the xy plane. The transitions in the 402−404 eV energy range are due to strong Rydberg-valence final states involving the σ*(N−H) unoccupied MOs; the enhanced intensity in the s polarization with respect to the p-polarization probes the major components of these MO in the xy plane. The theoretical spectra reproduce quite well the shape of the corresponding experimental spectra supporting the hypothesis of a tilted binding of the molecules to the Au surface in the higher coverage experimental conditions. A more complex arrangement of the molecules has been considered with the “tilted-facing” binding mode, where more effective intermolecular interactions take place. The corresponding results are reported in Figure 3. The tilted-facing cluster adopted for the NEXAFS calculations, shown in panel d of SI, Figure S3, includes eight adsorbed BDA molecules; the central pair of “facing” BDA molecules feels the electronic environment generated by neighbor molecules and is virtually free from border effects, therefore it has been considered for the spectra calculation of each of the four nonequivalent nitrogen sites indicated by the labels reported in the panel a of Figure 3. A moderate modification in the spectral shape is apparent with respect to the simpler tilted model which improves the comparison with the experiment. The lower energy structures (below 400 eV) derive from transitions toward orbitals largely localized on the surface, as in the tilted model; the N1R spectrum gives the main contribution in this energy region. In particular, the p-pol polarization probes the interaction of the N1R atom with the surface which has a significant component along the z direction. The N 2p contribution of the N1L atom to these final orbitals is lower, due to the larger distance of the left BDA molecule from the surface. Accordingly with the model geometry and as in the tilted case, very low intensity is found in the s-pol spectrum, which does not account for the bump observed in the experiment around 400 eV. The next energy region up to the ionization thresholds is essentially

Figure 3. Molecular adsorption scheme and N K-edge polarized spectra of BDA in the tilted-facing adsorption mode. All the spectral profiles have been convoluted with Gaussian functions of fwhm = 0.5 eV and shifted by −1.65 eV to facilitate the comparison. Contributions of the four nonequivalent N atoms are reported. Vertical dashed lines: ΔKS N 1s ionization thresholds (N1L: 403.31 eV; N2L: 404.29 eV; N1R: 403.16 eV; N2R: 403.57 eV).

the cluster: the N1 atom refers to the nitrogen of the amino group pointing toward the Au surface while N2 refers to the nitrogen of the free amino group. The total calculated N 1s NEXAFS spectrum is obtained by summing up the contributions of the nonequivalent N atoms. The calculated spectral structures in the lower energy region (up to 400 eV) have low intensity, the final orbitals being largely localized on the surface with strong contributions from the Au surface 1992

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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The Journal of Physical Chemistry C characterized by transitions due to strong Rydberg-valence states involving σ*(NH2) unoccupied MOs. All the spectra of the four nonequivalent N atoms contribute and the resulting high number of transitions makes the analysis of the spectral features very complex. We focus therefore only on the most salient features in the p- and s polarization spectra. In particular, the intense and well-defined peak around 401 eV which dominates the p-pol spectrum mainly derives from a N2L transition to a final MO of very diffuse nature involving the two hydrogen atoms of the N2L amino group. This orbital of σ*(N2L-H) character is the only one having a significant component along the z direction, and thus it is probed by the polarization normal to the surface. Around 401.5 eV the s-pol spectrum acquires intensity for the N1R and N2R transitions toward orbitals with σ*(N−H) character which mainly extend in the xy plane. It is interesting to note that none of the main structures in this energy region can be specifically related to the H−bond formation between the two N2L and N2R amino groups. Only the small peak at 400.7 in the s-pol spectrum generated by the N2R spectrum is assigned to a final state localized on the H atoms of the N2R amino group which points toward the N2L atom and extends mainly in the xy plane. The H-bond formation can account for the lower energy of this transition with respect to the others with σ*(N−H) character. The energy region around and above 402 eV is still associated with σ*(NH2) transitions from all the four N atoms; depending on the shape of the final MO these components can be enhanced more or less in one of the two polarizations, although the overall intensity is higher in the s-pol spectrum because of the major components in the xy plane of the various σ*(N−H) bonds. The comparison of the theoretical p- and spol spectra with the experimental ones is overall satisfactory and improved with respect to the simpler tilted model. The results support the hypothesis that in the experimental conditions of high coverage the molecules interact with the surface with a large tilt angle as well as that the intermolecular interactions can play an important role in determining the adsorption geometry. The contribution of the two N moieties to the calculated spectra of each BDA molecule can be more easily discussed by looking at the detail of the four N 1s spectra contributing to the total spectrum of the tilted-facing model. We restrict our analysis to the calculated p-pol spectra and compare these to the experimental p-pol spectrum. The two N sites pointing toward the Au surface (N1L and N1R, following the sketch in Figure 3) do not interact with each other and give similar contributions to the lower energy features (below 400 eV), which are assigned to the N−Au orbital interaction. Transitions starting from the two N sites far from the Au surface (N2L and N2R) do not contribute to this energy region. Transitions from N2L and N2R sites start beyond 400 eV and are the most responsible for the strongest peak around 401 eV, which has a σ*(NH2) character. The main contribution comes from a N2L transition to a final MO of very diffuse nature involving the two hydrogen atoms of the N2L amino group. The intermolecular interaction through H-bond between the two NH2 groups can be associated with the spectral contribution deriving from the N2R site, again in this energy region (at 400.7 eV). A picture of the relative virtual MO (N2R-A667) involved in this p-pol transition is reported in Figure 4 and shows that this orbital is mainly localized on the H atom of the N2R amino group and points toward the N2L nitrogen site.

Figure 4. 3D plot of the N2R-A667 unoccupied MO of the tiltedfacing cluster from the DFT-TP relaxed calculation on N2R site. Displayed isosurface corresponds to ±0.035 e1/2a0−3/2 value. Atoms of the two central BDA molecules involved in the DFT-TP calculations are depicted in orange; C atoms of the surrounding BDA molecules are depicted in gray and the N atoms in blue.

To provide further evidence on the different contributions of the amino groups interacting with gold (N1L and N1R) and those involved in the intermolecular interaction (N2L and N2R), the individual spectra are reported in the right panel of Figure 5. We can see that the first part of the spectrum provides a fingerprint for the amino−gold interaction, while the structure at 401 eV monitors the intermolecular coupling. We have experimentally tested this MO assignment by measuring the N 1s NEXAFS of a similar system, a monolayer of ptoluidine on Au(111). p-toluidine differs from BDA in that one of the amine groups is changed to a −CH3 group. However, it adsorbs on Au(111) with a similar tilted geometry and with the same N−Au bonding chemistry (see the Supporting Information), anchoring its amino termination to the gold surface. This gives therefore the opportunity to evidence just the contribution of the amino group interacting with the gold in the NEXAFS measurements. The left panel of Figure 5 shows the comparison of N 1s NEXAFS of BDA and p-toluidine monolayers. In particular, for the p-polarization, it shows that the strong resonance at 401 eV is missing for p-toluidine and that s- and p-pol spectra differ mainly in the dichroism at the low energies, i.e., in correspondence to the transitions related to the amino−gold interactions. In conclusion, we have calculated the N 1s NEXAFS spectra for the BDA molecule in different environmental conditions, with the amino-group involved in weak interaction with the substrate and/or the neighboring molecules. For the crystalline phase, a redistribution of the empty electronic states localized on the N atoms is observed and shown to be responsible for the smoothing of the measured NEXAFS spectrum. For the monolayer stage, we first of all evidenced the presence of electronic states at low photon energies, which are not present in the gas phase and can be attributed to the Au−N interaction. For higher photon energies, we showed that the intermolecular interaction strongly affects the spectra profile. The amino− amino interaction between adjacent molecules is responsible for the better agreement of the simulated p-pol spectrum of the tilted-facing model with the experiment, with respect to the simpler tilted model where the H-bond interaction is absent. 1993

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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The Journal of Physical Chemistry C

Figure 5. Left panel: Nitrogen NEXAFS in p-pol and s-pol photon polarization for BDA (red color) and p-toluidine (blue color) tilted monolayer phase on Au(111). Right panel: Site decomposition of calculated nitrogen NEXAFS of tilted BDA monolayer on Au(111), with NAu and NN−H denoting respectively the N atom coupled to Au and that on the far end of the tilted BDA molecule.

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Our calculations confirm therefore the occurrence of BDA intermolecular coupling in the tilted phase, which involves the amino molecular groups not coupled to Au substrate. This finding may be related to the fast charge delocalization over these amino terminations, previously reported in ref 8.

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ASSOCIATED CONTENT

S Supporting Information *

(i) Further details on the theoretical methods; (ii) the theoretical results for the flat phase of BDA; (iii) the determination of the coverage and of the molecular orientation, based on the photoemission spectroscopy and NEXAFS analysis respectively; (iv) the XPS and C K edge NEXAFS of p-toluidine on Au(111). This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Authors

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

The authors declare no competing financial interest.

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REFERENCES

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ACKNOWLEDGMENTS

Calculations have been supported by grants from MIUR (PRIN 2010BNZ3F2) of Italy. Generous CINECA ISCRA grants for computer time on the FERMI Blue Gene of CINECA (Bologna, Italy) are gratefully acknowledged. The synchrotron experiments were performed at the ALOISA/Elettra beamline of the IOM-CNR laboratory, supported by the Italian government. The authors thank the staff of the ALOISA and GAPH beamlines. This work is supported in part by Packard Foundation. D.C. and G.K. acknowledge partial support by Slovenian Ministry of Science (Program No.P1-0112). Support from MIUR (PRIN 20105ZZTSE, FIRB RBFR10FQBL) and MAE (US14GR12) is acknowledged. 1994

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995

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1995

DOI: 10.1021/jp512146t J. Phys. Chem. C 2015, 119, 1988−1995