On the Importance of Long-Term Storage for Fluorine-Substituted

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

On the Importance of Long-Term Storage for FluorineSubstituted Aromatic Self-Assembled Monolayers by the Example of 4-Fluorobenzene-1-Thiolate Films on Au(111) Waleed Azzam, Eric Sauter, Awad A. Alrashdi, Najd AlRefaie, Michael Rohwerder, Asif Bashir, and Michael Zharnikov J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b12030 • Publication Date (Web): 28 Jan 2019 Downloaded from http://pubs.acs.org on February 3, 2019

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The Journal of Physical Chemistry

On the Importance of Long-Term Storage for Fluorine-Substituted Aromatic SelfAssembled Monolayers by the Example of 4-Fluorobenzene-1-Thiolate Films on Au(111) Waleed Azzam†,‡,*, Eric Sauter#, Awad A. Alrashdi‡, Najd Al-Refaie‡, Michael Rohwerder§, Asif Bashir§, ,*, and Michael Zharnikov#,*

†

Department of Chemistry, Tafila Technical University, P.O. Box 179, Tafila 66110, Jordan ‡

Department of Chemistry, University College in Al-Qunfudah, Umm Al-Qura University, 1109 Makkah Al-Mukarramah, Saudi Arabia

#

Applied Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 253, D-69120 Heidelberg, Germany

§ Max-Planck-Institut

für Eisenforschung GmbH, Max-Planck-Str. 1, 40237 Düsseldorf, Germany

 Current

address: Thyssenkrupp Bilstein GmbH, Herner Str. 299, 44809 Bochum, Germany

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

Abstract By the example of 4-fluorobenzene-1-thiolate (p-FTP) films on Au(111), we show that a long-term post-preparation storage can improve significantly the quality of fluorinated aromatic self-assembled monolayers (SAMs). Whereas the freshly prepared p-FTP films exhibit a polymorphism, with a dominance of a disordered phase, the post-preparation storage triggers a gradual phase transition to a single phase SAM of exceptional quality. This phase is characterized by the commensurate (16  3) structure, a molecular footprint of 23.1 Å2, high orientational order, and hardly perceptible borders between individual domains, with sizes exceeding 80 nm. Significantly, the phase transition is accompanied by morphological transformation of the substrate: whereas the freshly prepared films exhibit comparably large Au adatom islands, typical of aromatic SAMs, the long-storage samples rather reveal etchpits, typical of alkanethiolate SAMs on Au(111), which generally have a high structural order immediately after the preparation. The above results suggest a deep interrelation between the structural order in the SAMs and surface morphology. A further implication is the importance of both thermodynamic and kinetic factors, a delicate interplay of which is presumably responsible for the observed evolution of p-FTP/Au in the present case.


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1. Introduction Self-assembled monolayers (SAMs) prepared from aromatic thiols have attracted significant attention over the last 20 years,1-11 in particular in view of their potential applications in molecular electronics,12-15 interface engineering in organic electronics,16-21 and nanofabrication22. Among different kinds of such SAMs, fluorine-decorated and fluorinesubstituted aryl thiols23-27 are especially interesting because of their relevance for optoelectronic devices,27-28 organic field-effect transistors (OFETs),29 molecular diodes,25, 30 etc., where these SAMs were mainly used for work function adjustment at the metal electrodes. Significantly, as far as the modified electrodes were used as substrates for the growth of organic semiconductors, both growth mode of thereof and performance of the resulting devices were found to be strongly influenced by the structure and morphology of the SAMs.31-33 Therefore, the fabrication of highly ordered and oriented fluorinated aromatic SAMs is of great importance for optimization and performance enhancement of molecular electronic devices. Accordingly, over the last few years, several studies have specifically dealt with the preparation and characterization of fluorinated aromatic thiols/selenols SAMs on coinage metal substrates in order to find the optimal conditions for the fabrication of highly ordered and defect-free monolayers. It has been found that the structural order of the fluorinated aromatic SAMs, formed usually by the standard immersion procedure,1, 23-27, 30, 3437

depends strongly on the preparation conditions, including such parameters as temperature

of the thiol/selenol solution,23-24,

26, 37

immersion time (IT),23 and storage time after the

preparation38 Interesting examples of such systems are SAMs of perfluoroterphenyl- and perfluoroanthracene-substituted alkanethiols (C6F5–C6F4–C6F4–(CH2)n–SH and C14F9–NH– (CH2)n–SH, respectively) with variable length of the aliphatic part (n = 2 and 3), which have been reported just recently.24,

39

Another representative example is SAMs of pentafluoro-

benzenethiol (PFBT) on Au(111), the quality of which depends strongly on the IT. In case of the standard immersion time (12-24 h) and room temperature (RT) preparation, these SAMs contain a plenty of structural defects, such as dislocation of rows, disordered domains, and molecular rows with different apparent heights.23, 26 In contrast, an increase of the IT to 190 h resulted in high quality and defect-free monolayers.23 Further interesting example are SAMs generated from 3,5-bis(trifluoromethyl)benzenethiolate (TFBT) molecules on Au(111), the structure and morphology of which were found to depend strongly on the IT, post-preparation storage time, and post-preparation treatment.38 The standard preparation conditions (i.e., an IT of 24 h and RT) resulted in formation of poorly ordered films, having a large defect density and only a small portion of the surface covered by ordered molecular domains. Well-ordered 3 ACS Paragon Plus Environment


monolayers, with extraordinary length of the ordered domains, could only be prepared at a short IT (5 min) and an additional re-immersion of the sample into pure ethanol at high temperature.38 Interestingly, these monolayers exhibited the formation of etch-pits rather than gold islands, which are usually formed after the adsorption of purely aromatic thiols3, 5, 23, 40-42 and selenols1, 43 on Au(111). Alternatively to two trifluoromethyl groups in TFBT, just one fluorine atom can be used for the substitution of benzenethiolate, resulting in para-fluorothiophenol (p-FTP), monolayers of which have been previously used to improve hole injection in photonic devices.30 The performance of these devices was found to be significantly influenced by the structural order of the p-FTP SAMs, implying the necessity of their improvement.30 In this context, Jiang et al. tried the preparation of these SAMs on Au(111) substrate from ntetradecane solution at RT, resulting in the formation of a (16  3) R30o structure with six molecules per unit cell.25 However, the respective SAM surface were found to have a high density of defects, such as small etch-pits, disordered regions, small elevated islands on and around the domains, disordered domain boundaries, and rows of the p-FTP molecules within the ordered domains appearing dark in the STM images. In this context, in the present study, we deal again with the p-FTP SAMs on Au(111), performing an in-depth study of this system using several complementary techniques, with an emphasis on scanning tunneling microscopy (STM). The goals are to improve the quality of the p-FTP SAMs and find an optimal procedure for the preparation of thereof. As the major parameter, which turned out to have a tremendous impact on the structure and quality of these monolayers, we used the post-preparation storage time. 2. Experimental Section 2.1 Preparation of Gold Substrates. STM measurements were carried out on substrates that were prepared by evaporating 140 nm of Au onto freshly cleaved mica, which was preliminary kept at ~600 K for 3 days in the evaporation chamber. After evaporation of Au, the substrates were cooled and the chamber was backfilled with nitrogen. The substrates were stored under argon and flame-annealed in a butane/oxygen flame immediately before the SAM preparation. This procedure yields Au substrates with large terraces (several hundreds of nanometres, as evidenced by STM) exhibiting a (111) orientation. The Au substrates for the spectroscopic experiments were prepared by subsequent evaporating 5 nm of titanium and 140 nm of gold onto Si(100) wafers under a pressure of 10-7 mbar. 4 ACS Paragon Plus Environment

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2.2 Chemicals. p-FTP, ethanol, and acetone were purchased from Sigma-Aldrich and used as received. 2.3 Preparation of SAMs. The formation of the p-FTP monolayers was carried out by immersing the substrates into 0.1 mM ethanolic solution of p-FTP for 24 h at RT and, optionally, at an elevated temperature (70 °C). The samples were either characterized immediately after the preparation or subjected to a post-preparation storage before the characterization. 2.4 Characterization of SAMs - General Comments. The SAMs were characterized by STM, synchrotron-based X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. In all cases, the characterization was performed at room temperature. XPS and NEXAFS spectroscopy experiments were conducted under UHV conditions at a base pressure better than 1×10-9 mbar. A special care was taken to minimize potential modification of the SAMs induced by the primary X-rays.44,45 2.5 Scanning Tunnelling Microscopy (STM). All STM measurements were carried out under ambient conditions, using an Agilent STM setup, which had been cross-calibrated by imaging HOPG with atomic resolution. The tips were prepared mechanically by cutting a 0.25 mm Pt0.8Ir0.2 wire (Goodfellow). All data were collected in a constant-current mode with typical tunnelling currents of 0.15 – 0.5 nA and a sample bias of 0.5-1.0 V. 2.6 Spectroscopic Characterization. The XPS and NEXAFS spectroscopy experiments were performed several days after the sample preparation, due to the time necessary for their delivery to the synchrotron. The approximate post-preparation storage time could be estimated as 144 h. The samples were stored in containers filled with nitrogen, where they were placed immediately after the preparation. The experiments were carried out at the HESGM beamline (bending magnet) of the synchrotron storage ring BESSY II (Helmholtz Zentrum Berlin, HZB). A custom-designed experimental station was used.46 The XP spectra were acquired in normal emission geometry at a primary photon energy (PE) varied between 350 or 750 eV, depending on the particular binding energy (BE) range. The energy resolution was ∼0.3 eV at a PE of 350 eV and progressively lower at higher PEs. The BE scale was referenced to the Au 4f7/2 peak of the Au substrate at 84.0 eV.47 The spectra were fitted using Voigt peak profiles and either a linear or Shirley background. The S 2p signal, which represents a doublet (2p3/2/2p1/2), was fitted by two peaks with the same full width at half-maximum (fwhm), a spin-orbit splitting of ~1.18 eV (verified by fit),47 and a standard branching ratio of 2:1. 5 ACS Paragon Plus Environment


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The NEXAFS spectroscopy measurements were performed at the C K-edge in the partial electron yield mode with a retarding voltage of –150 V. Linear polarized synchrotron light with a polarization factor of % was used and the energy resolution was 0.3 eV. The incidence angle of the primary X-rays was varied from 90° (E-vector in surface plane) to 20° (E-vector near surface normal) in steps of 10-20°, to monitor the orientational order in the SAMs. This approach is based on the dependence of the cross section of the resonant photoexcitation process on the orientation of the electric field vector of the synchrotron light with respect to the molecular orbital of interest (so-called linear dichroism in X-ray absorption).48 The raw NEXAFS spectra were normalized to the incident photon flux by division through a spectrum of a clean, freshly sputtered gold sample and subsequently shaped in a standard fashion

48

setting the intensity in the pre-edge and far post-edge regions

to zero and one, respectively. The PE scale was referenced to the pronounced * resonance of highly oriented pyrolytic graphite at 285.38 eV.49 3. Results 3.1. STM Experiments Figures 1 and 2 present large-scale STM images (with a higher magnification in Figure 2) obtained for the freshly prepared p-FTP SAM (RT; an IT of 24 h) as well as for the SAMs stored for a certain time after the preparation. This time was varied from 24 to 288 h. The images of the freshly prepared SAM in Figures 1a and 2a exhibit pronounced gold islands, which are typical of purely aromatic thiols3,

5, 23, 40-42

and selenols1,

43

on Au(111). These

islands have lateral dimensions of 10-60 nm and mostly rounded or oval shape. Significantly, these island do not remain stable in the course of the post-preparation storage but exhibit a gradual size reduction and disappear completely, as follows from the images of the respective samples in Figures 1b-f and 2b-f, in particular, after the 24 h storage, a significant increase in the density of the gold islands on the expense of their size was observed, so that the lateral dimensions of these islands decreased to 2-10 nm (see Figures 1b and 2b). A further increase of the storage time to 48 h caused a sharp drop in the density of the gold islands while retaining their sizes. Subsequently, for the 72 h and longer storage, the islands disappeared completely from the sample surface (see Figures 1d-f and 2d-f). At the same time, after 48 h and especially 72 h storage, the STM data showed the formation of cracks within the monolayer, as documented by the images in Figures 1c,d and 2c,d. These cracks appear in the images as dark regions with an apparent height decrease of 1.0-1.5 Å, which is smaller than 6 ACS Paragon Plus Environment

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the usual depth of the vacancy islands on the Au(111) surface (2.4 Å). Interestingly, upon further increase of the storage time to 144 h and longer, the cracks mostly disappear and a number of etch-pits appear in the plateau areas of the surface terraces. These pits have a depth corresponding to that of a single atomic step on the Au(111) surface and are randomly distributed within the monolayer.

Figure 1. Large-scale STM images of the p-FTP SAMs measured either immediately after the preparation (a) or after the post-preparation storage for 24 h (b), 48 h (c), 72 h (d), 144 h (e), and 288 h (f). The dashed black triangles mark the < 110 > directions of the substrate. Following this quick description of the morphology transformation of p-FTP/Au observed during the post-preparation storage, we turn now to the molecular structure of the pFTP monolayers. As seen in Figure 2a, the freshly prepared p-FTP SAMs exhibit a polymorphism, viz. a coexistence of two phases, which we will denote as α and β. These phases can be better recognized and analyzed on the basis of high-resolution STM images of the freshly prepared p-FTP SAMs shown in Figure 3a,b,d. In these images, well-ordered stripe-like domains of the p-FTP molecules, representing the α phase, coexist with disordered regions, representing the β phase. The α phase domains are aligned along the < 110 > substrate directions mimicking the threefold symmetry of the Au(111) surface. The length of 7 ACS Paragon Plus Environment


the domains varies from 25 to 60 nm. The structure of the α phase can be described by an oblique unit cell, indicated in Figure 3b,d and containing twelve molecules. The dimensions of this unit cell can be estimated using the height profiles across the STM images, such as shown in Figure 3c. The analysis carried out on several STM images revealed average values of a   ±  Å, b= 10.5 ± 0.8 Å, and an angle between the unit cell vectors of 60 ± 2°. Accordingly, the structure of the α phase can be described as the (8 3  2 3) R 30o lattice and the molecular footprint can be estimated at 28.9 Å2. Considering the van der Waals dimensions of the molecule (a cross-sectional area of 21.1 Å2 for the phenyl ring) and the area per molecule, one can expect a tilt angle of about 43°, given by arccos(21.1/28.87), with respect to the surface normal.

Figure 2. Higher magnification STM images of the p-FTP SAMs measured either immediately after the preparation (a) or after the post-preparation storage for 24 h (b), 48 h (c), 72 h (d), 144 h (e), and 288 h (f). The image in (a) shows the α and β phases, while the γ phase is shown in the images (b-f); see text for details. The dashed black and white triangles mark the < 110 > and < 112 > directions of the substrate, respectively.


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Figure 3. (a, b, d) High-resolution STM images of the p-FTP SAM measured immediately after the preparation. The image displayed in panel a shows the coexisting α and β phases. The images displayed in panels b and d show the α phase only. The oblique boxes depicted in panels b and d mark the (8 3  2 3) R 30o unit cell of the α phase. Its dimensions were calculated from the cross-sectional height profiles, such as displayed in panel c along the lines labeled A and B in panel b. The dashed white triangles mark the < 112 > directions of the substrate.

Figure 4. High-magnification STM images of the p-FTP SAMs measured immediately after the preparation. The images displayed in panels a-c show the  and  phases. The red dotted circles in panel c indicate bright features. The dashed white triangles mark the < 112 > directions of the substrate. 9 ACS Paragon Plus Environment


The second phase, denoted as β phase, is present in areas between the rotational domains of the α phase. The β phase exhibits no molecular order as can also be recognized in several additional STM images of the freshly prepared p-FTP SAMs shown in Figure 4. According to these images, the β phase contains dense bright features with an apparent height corresponding to that of a single atomic step on Au(111) surface (i.e., 2.4 Å) (see the red dotted circles in Figure 4c). Such features have been previously observed in SAMs of different thiols on Au(111) and attributed to the thiolate-Au adatom(s) complexes23, 40 As seen in Figure 2, the morphology transformations of p-FTP/Au in the course of the post-preparation storage are accompanied by the phase transition within the p-FTP SAMs, with a gradual transformation of the α and β phases into a new phase, which we will denote as the γ phase. This process evolves slowly and passes through several stages, as additionally illustrated by the STM data presented in Figures 5. The STM image corresponding to 24 h storage in Figure 5a shows a single terrace of the gold substrate, with clearly visible ordered domains between the gold islands. The length of these domains is fairly small, with values ranging from 5 to 15 nm. Also, the molecular stripes within these domains do not run straight but are curved to some extent. The stripes are aligned along the directions, reflecting the threefold symmetry of the substrate, and have an inter-row spacing of 45 ± 2.0 Å. Since this value is distinctly different from the spacing between the molecular rows of the  phase, we can indeed assume the appearance of a new phase, on the expense of the  and  phases. A further increase of the storage time to 48 h (see Figure 5b) resulted in a significant improvement in the molecular order of the γ phase. The ordered rows of the rotational domains became straight without curving and had a length of about 20-50 nm. The image also shows the cracks residing at the domain boundaries (marked by white dotted loops in Figure 5b,c) which, however, become significantly reduced upon the 72 h storage, as documented by the STM image displayed in Figure 5c. The surface became free of the gold islands but still exhibited the cracks, accompanied by deeper depressions (etch-pits), which emerged initially with a very low density, looking as small dark spots in the STM image (see the features marked by black dotted circles in Figure 5c). As mentioned above and illustrated by the height profile in Figure 5d, their depth amounts to the height of a step on the Au(111) surface. The above morphology changes were accompanied by an improvement of the structural order of the γ phase and an increase in the size of the ordered domains up to 75 nm. These transformations progressed upon the further storage. In particular, after 144 h, a pronounced increase in the size and density of the depressions was observed, as illustrated by the STM image displayed in Figure 5e. This dramatic change in the surface morphology is 10 ACS Paragon Plus Environment

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accompanied by a complete disappearance of the cracks, which were observed in the SAMs stored for a shorter time. Moreover, a noticeable improvement in the molecular order of the pFTP SAMs was observed. The ordered domains increased in size by several tens of nanometers and distinct domain boundaries were formed.

Figure 5. STM images of the p-FTP SAM stored for 24 hours (a), 48 h (b), 72 h (c), 144 h (e), and 288 h (f) after the preparation, along with a height profile along the blue line labeled A in panel c (d). The height profile shows that both topographical height of the bright features and the depth of the etch-pits are ~2.4 Å. The STM images show the evolution of the  phase upon the storage. The white dotted loops in panels b and c indicate representative cracks. The dotted black circles in panel c indicate representative etch-pits. The dashed white triangles mark the < 112 > directions of the substrate. The white arrows in panels b and c mark bright spots, assigned to thiolate-Au adatom(s) complexes. For a more prolonged storage, such as 288 h, an even larger improvement in the molecular order of the p-FTP SAMs was observed, as illustrated by the STM image displayed in Figure 5f. The resulting SAMs are characterized by an extraordinary degree of structural order with no disordered regions, domain sizes exceeding 80 nm, and even the boundary regions between the rotational domains being well-ordered and hardly perceptible. The size and density of the vacancy island did not change noticeably from those observed for the 144 h storage. 11 ACS Paragon Plus Environment


A detailed analysis of the p-FTP adlayer structures observed in the STM images displayed in Figure 5a-c,e,f clearly indicates that all the structures are closely identical in nature. This suggests that upon a storage time of 24-288 h only a single phase (i.e., the γ phase) is present in the p-FTP SAMs. The ordered domains of this phase are composed of rows, whose orientations reflect the threefold symmetry of the underling Au(111) substrate (see the image displayed in Figure 5f).

Figure 6. (a-c) STM images of the p-FTP SAM stored for 288 h after the preparation. The images displayed in panels a and b show a superposition of different rotational domains of the γ phase. The image displayed in panel c shows a single rotational domain of the  phase. The rectangular box depicted in panel c marks the unit cell of the α phase. The dashed white triangles mark the < 112 > directions of the substrate. The molecular structure of the γ phase is reflected by the high-resolution STM images and height profiles measured for the p-FTP SAMs after 288 h storage and presented in Figures 6 and 7. The images displayed in Figures 6a and 6b show a superposition of several rotational domains of the γ phase, whereas the image in Figure 6c presents a single rotational domain. Within this domain there are rows of the p-FTP molecules that appear noticeably brighter and are separated by darker regions. These features are even more distinct in the images displayed in Figures 7a and 7c, where also molecular rows within the darker regions can be recognized. The cross-sectional profiles in Figure 7b taken along the lines A and B labeled in Figure 7a, show that the distances between the protrusions along and perpendicular to the "bright" molecular rows amount to 5.0 ± 0.5 Å and 46 ± 1.0 Å, respectively. Accordingly, the γ phase can be described as the commensurate (16  3) structure. The rectangular unit cell of this phase contains ten molecules, and consequently, the molecular footprint can be evaluated as 23.1 Å2. Accordingly, the angle between the surface normal and the molecular axis is coarsely estimated as ca. 24°. The smaller molecular footprint of the γ phase as compared to 12 ACS Paragon Plus Environment

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the  one suggests a higher packing density, which can only be achieved as far as the additional molecules are provided by the  phase, Consequently, this phase should be densely packed, even though disordered.

Figure 7. (a, c) High-resolution STM images of the p-FTP SAM stored for 288 h after the preparation along with (b) cross-sectional height profiles along the lines labeled A and B in panel a. The images in panels a and c show the adlayer structure of the γ phase. The dotted blue rectangular boxes depicted in these panels mark the (16  3) unit cell of the γ phase. The dashed white triangle in panel c marks the < 112 > directions of the substrate. It is worthwhile to mention that the STM images of the p-FTP SAMs stored for longer than 288 h did not exhibit any further morphological or structural changes as compared to the SAMs stored for 288 h. Moreover, the preparation of the p-SAMs at the elevated temperature did not improve the structural order, resulting in a coexistence of the α and ß phases, remaining stable also upon a prolonged storage. Interestingly, neither removal of the gold islands nor emergence of the vacancy islands was observed. 3.2. Spectroscopy Experiments As mention in section 2, the samples characterized by the spectroscopic technique corresponded to a storage time of ca. 144 h, i.e., according to the STM data presented in



section 3.1, represented the  phase with well defined domains (see Figure 5e). The XPS and NEXAFS spectroscopy data for these samples are compiled in Figures 8 and 9. The S 2p XP spectrum of the p-FTP SAM in Figure 8a is dominated by a S 2p3/2,1/2 doublet at 162.0 eV (S 2p3/2), characteristic of the thiolate-gold bond (1).44 This suggests that nearly all molecules in the p-FTP film are anchored to the substrate in a proper fashion, typical for a well-defined SAM. The only additional feature is a low intense (14% of the entire intensity) doublet at 161.0 eV (S 2p3/2), exhibited as a weak shoulder of the thiolate signal. This doublet (2), frequently observed in the high-resolution XP spectra of thiolate SAMs, is usually ascribed to atomic sulfur, appearing presumably after the cleavage of the Au-thiolate bond (see discussion in ref 46). An alternative assignment is a distinctly different bonding configuration of the S atom as compared to thiolate,24 but the atomic sulfur description appears to be more realistic to us.

XPS: S 2p

a

1

h = 350 eV

2

168

Intensity (arb. units)

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

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166

164

162

C 1s

160

1

h = 580 eV

2

b

3

296 294 292 290 288 286 284 282

F1s

h = 750 eV

c

692 690 688 686 684 682

Binding energy (eV)

Figure 8. S 2p (a), C 1s (b), and F 1s (c) XP spectra of the p-FTP SAM stored for ca. 144 h after the preparation. The C 1s and S 2p spectra are decomposed into individual peaks (C 1s) and doublets (S 2p) marked by numbers; see text for the assignments. 14 ACS Paragon Plus Environment

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The C 1s XP spectrum of the p-FTP SAM in Figure 8b exhibits a superposition of two peaks at 284.15 eV (1) and 286.25 eV (2) assigned to the non-substituted carbon atoms of the phenyl ring and the carbon atom bonded to the fluorine substituent, respectively,50 and an additional weak peak at 285.1 eV (3). The intensity relation between the peaks 2 and 1 is ca. 1:3, which differs from the stoichiometric 1:5 ratio due to the progressing attenuation of the photoelectron signal for the carbon atoms located further away from the SAM-ambient interface, as can be expected for an upright molecular orientation. The minor peak 3 can be tentatively assigned to shake-up processes in the aromatic matrix (see discussion in ref

51);

this feature is typical for aromatic SAMs. The F 1s XP spectrum of the p-FTP SAM in Figure 8c exhibits a single peak at 686.7 eV assigned to the terminal fluorine atom. The binding energy position of this peak agrees well with the previous results obtained for SAMs of fluorine-substituted 4-mercaptobihenyls on Au(111) and Ag(111).50 Along with the qualitative analysis of the XP spectra, we performed their numerical evaluation to estimate the molecular footprint of the p-FTP SAM. The latter value was calculated on the basis of the S 2p/Au 4f intensity ratio, following the approach of ref 24, with the literature values for the attenuation lengths52 and a SAM with a well defined molecular footprint (hexadecanethiolate/Au(111); 21.6 Å2)53 as a reference. The estimated value of 22.2  1.5 Å2 correlates well with the analogous value for the  phase obtained from the STM experiments (23.1 Å2; see section 3.1). The NEXAFS spectroscopy data for the p-FTP SAMs in Figure 9 are represented by the spectrum acquired at an X-ray incidence angle of 55° and the difference between the spectra collected at X-ray incidence angles of 90° and 20°. The 55° spectrum is exclusively representative of the electronic structure of the sample and is not affected by any effects related to molecular orientation.48 In contrast, the 90°-20° difference curve is a fingerprint of molecular orientation in the monolayers, relying on the linear dichroism effects (see section 2.6). The 55° spectrum is dominated by a pronounced absorption resonance at ~285.1 eV (1a*; 1) assigned to the phenyl ring of the p-FTP moieties.48, 54 This feature is accompanied by another * resonance at 287.35 eV (1b*; 2), typical of the fluorine substitution of the phenyl ring.48,

50, 55

Further prominent features, typical of non-substituted and substituted

phenyls,13, 38, 48, 54 are 2* resonance of the phenyl ring at 288.5 eV (3) and a variety of * resonances at ~290.2 eV, ~294.0 eV, and 303.5 eV. 15 ACS Paragon Plus Environment


1

NEXAFS: C K-edge 3 4 5 2

intensity (arb. units)

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

6

55°

90°-20°

280

290

300

310

Photon energy (eV)

Figure 9. C K-edge NEXAFS spectra of the p-FTP SAM stored for ca. 144 h after the preparation. The top curve represents the spectrum acquired at an X-ray incidence angle of 55°; the bottom curve represent the difference between the spectra acquired at X-ray incidence angles of 90° and 20°. The most prominent absorption resonances are marked by numbers; see text for the assignments. The horizontal dashed line corresponds to zero. Along with the above analysis of the 55° spectra, supporting the identity of the p-FTP SAMs, the linear dichroism effects in these monolayers were considered. These effects are quite strong in the given case as followed from the occurrence of the pronounced peaks at the positions of the characteristic absorption resonances in the difference spectrum. This suggests a high orientational order in the p-FTP SAMs. Significantly, the signs of the observed difference peaks, viz. the positive sign for the *-like resonances and the negative sign for the *-like ones, suggest an upright molecular orientation in these monolayers, in view of the specific orientations of the above molecular orbital with respect to the molecular framework. A quantitative evaluation of the entire set of the NEXAFS data according to the procedure described in our previous publications38, 50 resulted in an average tilt angle of the 1a* orbital of ~703°. This gives an average molecular tilt angle of ~203° as far as the molecules are not significantly twisted (see ref

56

for a discussion regarding the molecular

twist), which, in our opinion, is a realistic assumption. The latter value correlates well with the tilt angle estimated for the  phase of the p-FTP SAMs on the basis of the STM data.


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Generally, both XPS and NEXAFS spectroscopy data suggest a well-defined character and high quality of the p-FTP SAMs after a prolonged storage, in full agreement with the STM results presented in section 3.1. Note that along with the p-FTP SAM prepared at RT, a monolayer assembled at the elevated temperature was characterized as well. The quality of this monolayer was found to be inferior to that of the SAM prepared at RT, in full agreement with the STM results (see section 3.1). In particular, all characteristic peaks in the XP spectra (not shown) turned out to be broader, contribution of the atomic sulfur was much stronger, and the fluorine signal was much weaker. In the NEXAFS spectra (not shown), the resonances associated with p-FTP turned out to be much weaker, a pronounced signal of C=O/COOH (contamination) was observed, and the linear dichroism was hardly perceptible. 4. Discussion In this section, we will mainly focus on two important issues, namely the disappearance of the gold islands upon the post-preparation storage and the phase transition within the pFTP SAMs, occurring at the same time. As mentioned in section 3.1, the freshly prepared SAMs revealed the formation of the gold islands, which were nearly identical in shape, size, and density to those previously observed for SAMs of purely aromatic thiols3, selenoles43, others,5,

5, 42, 57

and

58-59

on Au(111). As demonstrated by previous STM studies by our group and

42-43, 57

the formation of the gold islands, which are generally stable after the

preparation, is a specific feature of such monolayers regardless of the preparation conditions. This phenomenon was attributed to a restructuring of the gold atoms in the topmost layer of the substrate, which become highly mobile because of the strong binding to the anchoring groups of the SAM constituents, either thiolates23, 42 or selenolates.43 In contrast, for the pFTP SAMs, we found that these islands are not stable upon even a short-term storage (24 h) and disappear completely upon a prolonged storage (72 h and longer). As an alternative, one gold atom deep vacancy islands, which are typically associated with the adsorption of nalkanethiols60-63/selenols64-65 and hybrid aromatic-aliphatic thiols/selenols2,

66

on Au(111),

were formed. Such a behavior makes the p-FTP system quite different from most aromatic thiol and selenol SAMs studied so far. The only system with similar behavior is, to the best of our knowledge, TFMB SAMs on Au(111), for which the gold islands were found to be not stable as well; they disappeared already after the 24 h storage, accompanied by the transformation of the initially disordered SAM into ordered molecular arrangements, once 17 ACS Paragon Plus Environment


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again similar to the p-FTP system of the present study.38 Such a similar behavior for the two different, fluorine-substituted aromatic SAMs suggests an intrinsic correlation between the surface morphology and structural perfection of these monolayers. For the p-FTP SAMs of the present study, the dramatic change in the surface morphology was accompanied by the phase transition from a mixture of the loosely packed () and disordered () phases into a new high-density structure (γ phase) that is characterized by exceptional structural quality. This phase should then be thermodynamically favorable and more stable but needs a prolonged time for its formation. Based on the above observations, the major reasons for the formation of the gold islands in purely aromatic SAMs and not directly the vacancy islands as in the case of n-alkanethiols/selenols and hybrid aromatic-aliphatic thiols/selenols systems on Au(111) are most likely (i) a slow diffusion rate of the SAM constituents on this surface and (ii) an occurrence of certain energetic barriers along the morphology transformation and SAM crystallization pathway. Such a low mobility was also reported previously for PFBT23, benzenethiol (BT)27,

35,

26,

and TFBT38 molecules and attributed to their insufficient dipole

character. Concerning the structure of the freshly prepared p-FTP SAMs, two distinct, coexisting phases, α and β, were observed. Both these phases were found to be stable within few hours after the preparation, necessary for the STM measurements. Interestingly, the disordered β phase was a predominant one, covering about 60% of the total substrate area (note that the areas of the monolayer presented in the images of Figure 4(a-c) were intentionally selected with high density of the α phase). These are unexpected results since the standard, one-day immersion of Au(111) surface into a purely aromatic thiol3-5 or selenol1, 67 solution usually yields ordered films, even though with varying quality depending on different parameters such as the docking group (S vs. Se), number of benzene rings in the molecular backbone, terminal group, and preparation conditions such as the temperature of deposition. Therefore, the presence and dominance of the β phase in the p-FTP SAMs in the present study indicates that these monolayers did not reach the fully maturity stage, even though a certain 2D crystallization, represented by the coexisting α phase, occurred. This phase, which is characterized by the (8 3  2 3) R 30o structure, a molecular footprint of 28.87 Å2, and an average domain size of ca. 50 nm, is comparable to that previously observed for the hybrid aromatic-aliphatic thiols2, 6 on gold surface. With increasing storage time, phase transition from the mixture of the α and β phases to the closely packed and well-ordered γ phase took place. At the initial stage of this transition, the ordered domains of the γ phase were observed to be incoherent, with fairly small and 18 ACS Paragon Plus Environment

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bended molecular rows. Moreover, there were still considerable surface areas covered by the disordered β phase, as documented by Figure 5a,b. The structural quality of the γ phase, i.e., domain size, gradually improved with disappearance of the gold islands and appearance of the vacancy islands. At the same time, the fraction of the surface area covered by the a and β phases was reduced continuously for the benefit of the γ phase, so that, finally, after the longterm storage, the latter arrangement becomes the only one present on the SAM surface. The STM images of the p-FTP SAMs stored for 144 and 288 h (Figure 5e,f) show that these samples closely resemble SAMs of n-alkanethiols on Au(111), with probably even better structural quality. Interestingly, the boundaries between the adjacent ordered domains, which are frequently found as defective region in a variety of thiol2-3, 5 and selenol1, 67 SAMs, were hardly perceptible in the p-FTP SAMs after the long-term storage (see Figure 5f). Further increase in the storage duration did not result in structural changes or any modification regarding the quality of the SAMs (the data are not shown). The formation and stabilization of defect-free ordered domains of the γ phase (with the exception of the vacancy islands) is presumably driven by an optimization of intermolecular π-π interactions. Obviously, this phase and the respective morphology of the surface are energetically more favorable than the coexisting α and β phases. The γ phase has a commensurate (16  3) structure with 10 molecules in the unit cell, corresponding to a molecular footprint of 23.1 Å2. The high quality of the γ phase SAMs was additionally supported by the XPS and NEXAFS spectroscopy data, which suggest a thiolate-type bonding of all p-FTP molecules to the substrate and an upright molecular orientation, associated with a dense molecular packing. Interestingly, as indicated by both STM and spectroscopy data, the deposition and selfassembly of the p-FTP molecules from a hot solution has not a positive but rather a negative effect on the quality of the SAMs, resulting in particular in luck of the orientational order and a high density of defects, like disordered regions and small bright islands, which seem to hamper significantly the formation and growth of highly ordered phases. Consequently, it looks that the adjustment of temperature alone is not sufficient to get high structural quality of the SAM. It is presumable a gentle interplay of both kinetic and thermodynamic factors, which allows the formation of the extremely well-ordered γ phase SAMs. The morphology of the substrate plays a certain role as well, since there is a distinct correlation between the structural perfection of the SAMs and surface morphology (compare Figures 5a and 5f).



The structures discussed above can be compared with the literature data for the p-FTP SAMs. In particular, upon the drop-cast, RT assembly of these SAMs on Au(111) covered by n-tetradecane solvent, the (16  3) structure, similar to the  phase of the present study, was resolved, which, however, had not ten but six molecules per unit cell, corresponding to a larger molecular footprint (38.3 Å2).25 The disappearance of the large gold islands was observed as well but, in contrast to the  phase samples of the present study, the ordered domains were found to coexist with disordered regions accompanied by a variety of structural defects, such as a dense network of small etch-pits and randomly distributed small islands on and around the domains. It seems therefore likely that these SAMs did not reach the fullgrowth stage and a long-term arrangement is required to finally get rid of the defects as took place in the p-FTP monolayers described in the present work. 4. Conclusions By the example of the p-FTP SAMs on Au(111), we demonstrate that a long-term postpreparation storage can significantly improve the structural and morphological quality of fluorine-substituted aromatic monolayers. The freshly prepared p-FTP SAMs, fabricated under standard conditions, exhibited a superposition of a loosely-packed ordered phase and a densely-packed disordered phase, accompanied by comparable large, elevated gold island, typical of the purely aromatic SAMs. In contrast, upon a prolonged post-preparation storage, progressing transformation of the above coexisting phases into a single, densely packed and highly ordered phase occurred, accompanied by the change in the sample morphology from adatom gold islands to etch-pits, typical of alkanethiolate SAMs on Au(111). The resulting pFTP SAMs, characterized by the commensurate (16  3) structure and a molecular footprint of 23.1 Å2, exhibit an exceptional structural quality, with hardly perceptible borders between the individual domains, with sizes exceeding 80 nm. The nearly all molecules in these SAMs are bound to the substrate by the thiolate anchor and are oriented uprightly. The average tilt angle could be estimated as 20-24°. The above results have several important implications. First, they show a high potential of aromatic SAMs in terms of structural quality, even without insertion of an aliphatic linker between the phenyl/oligophenyl moiety and the thiol/selenol headgroup or other essential changes in the molecular structure. Second, they imply a certain correlation between the structural perfection and substrate morphology for these systems. Third, the low quality of the SAMs prepared at the elevated temperature suggests that not only a thermodynamic but also 20 ACS Paragon Plus Environment

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kinetic factors are of importance. Whereas the resulting, high-ordered structure is certainly preferred energetically, it is a sequence of specific kinetic processes, governed by the thermodynamic variables, which makes the formation of the highly ordered p-FTP SAMs, along with the morphology transformation of the substrate, possible. It is a good question to what extent the fluorine substitution contributes to the ability of the p-FTP SAMs to the structural and morphological transformation in the course of the long term storage. The presence of fluorine should certainly affect intermolecular interactions and steric constraints in the SAM, which probably makes possible the observed commensurate adaptation of the molecular lattice to the structural template provided by the substrate. Corresponding Authors *E-mail: [email protected] *E-mail: [email protected] *E-mail: [email protected] ORCID Michael Zharnikov: 0000-0002-3708-7571 Waleed Azzam: 0000-0001-5461-0398 Notes The authors declare no competing financial interest.  Current

address: Thyssenkrupp Bilstein GmbH, Herner Str. 299, 44809 Bochum, Germany.

Acknowledgements E.S. and M.Z thank the Helmholtz Zentrum Berlin for the allocation of synchrotron radiation beamtime at BESSY II and A. Nefedov and Ch. Wöll for the technical cooperation during the experiments there. We also thank the German Research Foundation (Deutsche Forschungsgemeinschaft; DFG) for the financial support.



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On the Importance of Long-Term Storage for Fluorine-Substituted

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