Molecular Passivation of Substrate Step Edges as Origin of Unusual

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Molecular Passivation of Substrate Step Edges as Origin of Unusual Growth Behavior of 4,4’ Biphenyl Dicarboxylic Acid on Cu(001) Lukáš Kormoš, Pavel Procházka, Tomas Sikola, and Jan #echal J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b11436 • Publication Date (Web): 17 Jan 2018 Downloaded from http://pubs.acs.org on January 17, 2018

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The Journal of Physical Chemistry C is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

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The Journal of Physical Chemistry

Molecular Passivation of Substrate Step Edges as Origin of Unusual Growth Behavior of 4,4’ Biphenyl Dicarboxylic Acid on Cu(001) Lukáš Kormoš,† Pavel Procházka, †‡ Tomáš Šikola,†‡Jan Čechal†‡* †

CEITEC - Central European Institute of Technology, Brno University of Technology,

Purkyňova 123, 612 00 Brno, Czech Republic ‡

Institute of Physical Engineering, Brno University of Technology, Technická 2896/2, 616 69

Brno, Czech Republic.

ACS Paragon Plus Environment

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ABSTRACT

The structure and morphology of organic thin films on solid substrates influences their functional properties. Therefore, the knowledge on molecular structure, orientation, diffusion, and involved interactions on particular surfaces is required to gain control over the growth process and prepare layers with the required functionality. However, the resulting morphology is dictated by the delicate interplay of several interactions, which in many cases results in novel and unexpected behavior. Here, we show that strong interaction of 4,4’ biphenyl dicarboxylic acid (BDA) with the step edges on Cu(001) results in the formation of densely packed molecular row, which causes the step edge passivation. The step edge passivation limits the BDA diffusion over the step edges and inhibits the attachment of additional BDA molecules preventing nucleation and growth of molecular islands on the step edges. Our results thus provide fundamental insight into the anomalous growth behavior exhibited by certain organic/inorganic systems, which allows the development of models enabling the control of the growth of organic heterointerfaces.


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Introduction Organic layers and multilayers with engineered properties lay in the heart of the recent development of advanced materials with prospective electronic, optical and spintronic properties.1–7 Detailed quantitative understanding of thin film nucleation and growth is a key prerequisite for fabrication of layers and thin films possessing well-defined properties. In this respect, theoretical models developed for homoepitaxial and later extended for heteroepitaxial systems8,9 are being adapted to describe organic thin film growth.10–15 Despite many similarities, some systems show unusual and unexpected behavior. This can be exemplified by low energy electron microscopy (LEEM) observation of anomalies during the growth of 4,4’ biphenyl dicarboxylic acid (BDA, Scheme 1) islands on Cu(001).16 The most striking is the observation that any preference for nucleation at steps is absent.16,17 This unexpected growth behavior was ascribed to the strong non-wetting of the step edges by BDA.16 However, the physical origin of the non-wetting and consequently the peculiar growth behavior was not yet identified despite extensive local probe studies of systems comprising BDA,18,19 terephthalic acid (TPA),20–23 and related dicarboxylic acids24 on Cu substrates. These studies were focused mainly on the structure at the molecular scale but largely neglected the mesoscopic view on the growth of the submonolayer phases.

Here, on the basis on local probe measurements we show that the peculiar growth behavior is the result of the strong interaction of BDA molecules with the step edges and consequent step edge passivation by densely packed row of BDA molecules. The BDA passivated step edge prevents the attachment of additional BDA molecules and hinders their diffusion across the step edges.


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Scheme 1. Chemical structure of 4,4’ biphenyl dicarboxylic acid (BDA).

The existence of molecular self-passivation of step edges preventing molecular island nucleation contradicts the typical appearance of island nucleation: as the step edges represent natural defects, the island nucleation typically takes place there and an extended decoration of the step edges is observed for the vast majority of inorganic systems15 and many organic systems.15,25–30 In general, the nucleation and growth of molecular films differs from inorganic systems, where monomers are single atoms displaying an isotropic behavior. In contrast, the organic molecules are one-, two- or three dimensional objects that can display anisotropy in respect to the shape of the molecule, surface/interlayer diffusion, interaction with other molecules/substrate, and of their functionality.31 These anisotropies and additional energy barriers introduced to the system can potentially lead to different nucleation regimes and thin film growth modes.12,31,32

In particular, the necessary reorientation of diffusing molecules for their attachment to existing islands induces an energy barrier for the attachment of molecules to the islands resulting in the transition from diffusion-limited to attachment-limited aggregation.32–34 Next, the Ehrlich– Schwoebel (step edge) barriers play a decisive role in interlayer diffusion and, consequently, change the thin film growth, leading, e.g., to mold formation and rapid roughening.31 The several examples given above stress the importance of knowledge on the relevant fundamental physical processes for the understanding of the molecular thin film growth on a mesoscopic level. In this


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respect, our description of BDA step edge decoration at molecular scale explains the unusual growth where the nucleation takes place on plain terraces.

Methods All experiments were carried out in a complex ultrahigh vacuum (UHV) system installed at the CEITEC Nano Research Infrastructure. Samples were prepared and analyzed in separate chambers between which each as transferred through a transfer line under UHV conditions (base pressure 2×10-10 mbar). During the transfer (60 – 150 s), the pressure slowly increased up to 2×10-9 mbar and quickly restored to base level when the movement had ceased.

Sample Preparation. Single crystal Cu(001) substrate (Mateck) was cleaned by repeated cycles of Ar+ sputtering and annealing at 550 °C followed by a slow cooling to the room temperature in the preparation chamber with a base pressure of 2×10-10 mbar. BDA molecules were deposited in the neighboring chamber (deposition) by the near ambient effusion cell (Createc) from an oil heated crucible held at 185°C on the sample held at room temperature. Submonolayer coverages (~ 40 % of the surface) were obtained by BDA deposition for 5 min at a pressure lower than 8×10-10 mbar. BDA was purchased from Sigma−Aldrich (97% purity) and used after thorough degassing in UHV.

Scanning Tunneling Microscopy. Scanning tunneling microscopy images were recorded with a commercial system Aarhus 150 (SPECS) equipped with KolibriSensor featuring a tungsten tip. Images presented in this work were measured at room temperature in the constant current mode;


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sample bias voltage was set between -150 mV and -300 mV and tunneling current to 60 – 100 pA. During the STM measurement the KolibriSensor oscillator was turned on without the activation of the AFM feedback. This provided additional high frequency (~1 MHz) oscillation of the tip and in our experience allowed for more stable long term STM measurements.

Distortion in the STM images (except for the image in Figure 1b) was corrected assuming linear thermal drift of the sample derived from a series of consecutive images. To increase the contrast over multiple atomic terraces, the STM image in Figure 1b was additionally processed by adaptive filtering implemented in Gwyddion software35 as local contrast function (kernel size 3px, blending depth 4, and weight 0.5); details on the processing and the unfiltered image are given in Supporting Information (Figure S1).

Low Energy Electron Microscopy. LEEM experiments were carried out in a SPECS FE-LEEM P90 instrument with a base pressure of 2×10-10 mbar. Electrons with an energy of 15 keV that had passed through the electron optics and objective lens were decelerated in a strong electric field (5 kV/mm) to low energy in the range of 0 – 80 eV by applying a tunable voltage to the sample. A bright field image was formed by the detection of electrons with an energy of 3 eV from the (0,0) diffracted beam. All other electrons were blocked by a contrast aperture placed in the backfocal plane of the objective lens. An electron energy of 3 eV was chosen in order to get the best contrast between the substrate and the BDA molecules. The diffraction pattern was collected from the area of 15×10 µm2 using 30 eV. Microdiffraction with a 185 nm e-beam spot size on the sample showed qualitatively the same results.


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Results and discussion At the submonolayer coverage, BDA molecules form separated islands as imaged by low energy electron microscopy (LEEM) and shown in Figure 1a. Here, the areas of dark contrast represent molecular islands and the thin and thick dark lines depict the step edges and narrow terraces, respectively. Interestingly, no preference for the growth starting from the step edges is observed. This is confirmed by the wide-field STM image shown in Figure 1b where the large molecular islands touch the step edges only in a few points of contact.

Figure 1. (a) Overview image taken by LEEM after room temperature deposition of BDA on Cu(001). (b) Overview STM image on the same sample showing molecular islands. The overall contrast of image was increased by adaptive filtering (see methods), unfiltered image is given in Supporting Information. Scale bar is 30 nm.

The low energy electron diffraction (LEED) pattern taken over a large number of DBA islands shown in Figure 2a can be associated with 4√2 4√2R45°, or equivalently, c(8×8) molecular superstructure (p4g wallpaper group). The single BDA molecule on the Cu surface is visualized as a symmetric rod-like protrusion with the apparent length of (1.08 ± 0.03) nm (measured at 10% of the apparent height) as displayed in the high resolution STM image of the self-assembled


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BDA islands in Figure 2b. This length is comparable with the theoretical length of 1.14 nm obtained by gas-phase geometry calculation using Arguslab and considered in recent studies.18,36 Consistently with the BDA structure, this protrusion displays a slight narrowing in its center. The molecular assembly displays a long range ordered structure with the molecules oriented in 〈110〉 directions. Within the molecular domain, the adjacent BDA molecules are oriented perpendicular to each other; the carboxylate moiety of each pointing to the center of the neighboring BDA. These observations are consistent with earlier studies on the BDA/Cu(001).17,19,22

Figure 2. (a) LEED pattern taken on BDA layer deposited on Cu(001) at room temperature; the substrate spots are marked by red rectangles and arrows are the reciprocal vectors of the 4√2 4√2R45° superstructure. Missing spots are the result of extinction due to the glide symmetry of molecular superstructure along 〈110〉 directions.17 (b) Detailed STM image of self-assembled BDA phase overlapped with molecular structural models. (c) Tentative model of Cu(001)c(8×8)-BDA phase (C: black, O: red, H: white). The principal lattice directions are marked by black arrows, primitive vectors of 4√2 4√2R45° superstructure by blue arrows, and unit vectors of equivalent c(8×8) superstructure by green arrows. Scale bar in (b) is 2 nm.


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The tentative model for this structure shown in Figure 2c is consistent with both LEED and STM data. The relative positions of BDA on Cu(001) are determined in accordance with recent studies on relevant systems:18,20 two carboxylate oxygen atoms point to two distinct substrate atoms and phenyl rings are localized near substrate hollow sites. The mutual interaction of the adjacent molecules in both BDA and related TPA/Cu systems was tentatively ascribed to ionic hydrogen bonding in the original studies.19,21,22 However, if we take the length of the BDA molecule of 1.14 nm into consideration, the obtained C–H…O distance of 0.34 nm is too long for typical hydrogen bonds occurring both in 3D systems37 and at surfaces38. In these studies, the hydrogen bonds of a shorter length of 0.30 nm were already identified as weak38 with the estimated bond energy at around 0.03 eV37. The reported interaction energy of 0.175 eV for two adjacent BDA molecules on Cu(001)16 is much higher than expected from two hydrogen bonds of this length. Moreover, the absence of any distortion in C–H modes in the electron energy loss spectra39 casts doubt upon the presence of intermolecular hydrogen bonds in related TPA/Cu(001) system, suggesting a different origin of intermolecular interactions.39

Indeed, recent studies employing tetracyanoquinodimethane (TCNQ) on Cu(001) substrates reveal that two adjacent TCNQ molecules are bound via substrate mediated interaction.40 Here, the strong bonding of cyano groups with the substrate atoms causes significant lifting of these substrate atoms from the equilibrium positions, which is associated with an increase of elastic energy of the system. However, the overall elastic energy is lowered if two neighboring substrate atoms are lifted, which is expressed as an intermolecular interaction. In parallel with a recent study employing TCNQ on Cu(001) substrate,40 the substrate mediated interactions were also suggested to be the origin of the binding of two neighboring deprotonated TPA molecules20 as


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carboxylates also display strong carboxylate oxygen binding to substrate, charge transfer, and lifting of substrate atoms. Based on the fact that there is a significant charge transfer from the BDA carboxylate group to the substrate41 and lifting of substrate atoms20, we assume that a single substrate atom cannot accommodate the binding of two and more carboxylate oxygen atoms (site exclusion). Nevertheless, we obtain qualitatively the same interpretation of the measured data if we consider the mutual repulsion of partially negatively charged carboxylate moieties. As was already discussed, two carboxylate oxygen atoms point to two distinct substrate atoms. In the molecular model (Figure 2c) we have marked all interacting substrate atoms in a darker color. Taking the site exclusion into account, it can be predicted that only a limited number of mutual molecular orientations is allowed in addition to the equilibrium structure. Careful inspection of obtained images reveals the presence of distinct structural defect motives observed in the periodic structure (described below) that are in agreement with the presented “site exclusion” model. There is one type of point defect within the network structure and two types of dislocation lines dividing two long range ordered domains. In the series of subsequent images showing the same area given in Figure 2b for a prolonged period of time we have observed the formation of the metastable point defect shown in Figure 3a and modelled in Figure 3c. In several consecutive images we have observed the transition of the BDA molecule back to the regular position after a few intermediate jumps. Next, Figure 3b shows a part of the molecular island where two distinct close-by line defects (or dislocation lines) are observed within the molecular islands. The molecular models of these two dislocation types are presented in Figure 3 d and e. The molecular arrangement within all types of defects is consistent with the site exclusion model based on the assumption that a single Cu atom cannot provide more than one bond with carboxylate oxygen


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(or simply that the highlighted substrate positions cannot overlap). A direct consequence of the site exclusion is the limited diffusion of BDA molecules along the side of the molecular islands, which would inherently involve the restriction of mutual molecular positions where the substrate atoms would be bound to the same substrate atom. Hence, the movement along the island edges should involve detachment, diffusion in the vicinity of the edge, and reattachment at an appropriate position as already suggested by Schwartz et al.16

Figure 3. (a, b) Detailed STM images of point (a) and line (b) defects in self-assembled BDA phase. (c, d, e) Tentative models of molecular structures associated with these defects. Green and blue arrows in (b), (d), and (e) mark the position of dislocation lines. Scale bars are 2 nm.


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The strong interaction of carboxylate moieties with substrate copper atoms is even more pronounced at the step edges.18,20 The detailed look at the step edges presented in Figure 4a,b reveals a densely decorated step edge where BDA molecules possess several orientations. Their orientation is not entirely random: as schematically depicted in Figure 4a, BDA molecules are preferentially oriented in 〈110〉 and 〈100〉 directions on Cu(001) surface, i.e., parallel to the orientation of BDA molecules in the molecular island or rotated by 45° to this direction, respectively. The statistical analysis of more than 200 individual molecules decorating the step edges shows that the 〈100〉 direction is slightly favoured over the 〈110〉 with the ratio 1.6:1 (see Supporting Information for a detailed analysis). The tentative models in Figure 4c,d show that these two configurations match the substrate structure, however their precise positions cannot be established from our data. Importantly, the BDA molecules form a denser packing than is observed in the BDA islands. If we consider the dense arrangement of Cu atoms interacting with the carboxylate moieties and recall the site exclusion model, we immediately see that the dense packing of DBA molecules at a step edge prevents the attachment of additional molecules and formation of extended molecular islands there. Only a few points of contact of molecular islands with the step edges are observed, as demonstrated in Figure 4a. Another possible aspect of the BDA passivated step edge is the formation of a barrier against the diffusion of BDA molecules across the step edges (a type of Ehrlich–Schwoebel barrier).


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Figure 4. (a, b) STM images of BDA step edge decoration on Cu(001) surface. Two prevalent orientations of BDA on step edges are marked by green and red arrows and encircled molecular model; red: molecular orientation is the same as within the islands, green: 45 ° tilt in respect to BDA direction within the islands. (c, d) Tentative models of BDA molecules attached to the step edges. The restricted hopping directions are demonstrated for a free molecule residing on the substrate. The crossed arrows denote the restricted diffusion directions. Scale bars are 2 nm.

In the seminal works based exclusively on LEEM real-time imaging, the unusual growth, i.e., the preference for nucleation on flat terraces instead on the step edges, was explained by a weak interaction of BDA molecules with the step edges, which was ascribed to a strong non-wetting of the step edges by BDA.16 However, it would be surprising if the strong carboxylic-substrate interaction would coexist alongside the negligible interaction with the step edge atoms. Indeed,


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the growth starts at the step edges, but once the first row of molecules is completed, the step edge is passivated, preventing any further growth of molecular islands there.

Comparing of the presented results on BDA/Cu(001) substrate with relevant systems comprising BDA/Cu(111)18 and BDA/Ag(001) we infer, that there is a pronounced role of the substrate in step edge passivation. Concerning the BDA/Ag(001), we have not observed the discussed passivation for both fully protonated (intact) and fully deprotonated BDA molecules as documented in the STM images given in Supporting Information. On Cu(111), the DBA step edge decoration is also visible in STM images given by Schmitt et al.18 In this system, the step edge decoration alters the deprotonation of DBA molecules and induces the growth of specific molecular phases. The step edge passivation is therefore caused primarily by the strong binding of carboxylate groups to the substrate. However, the substrate symmetry also plays its role in defining the possible molecular orientations.

Conclusion Here, we have shown that the growth of 4,4’ biphenyl dicarboxylic acid starts at the step edges of Cu(001) substrate, but once the first row is completed, the step edge is passivated preventing any further growth of molecular islands there. The perfect decoration of step edges will result in a compact line of substrate Cu atoms bonding to oxygen atoms of BDA carboxylate end-groups. In this configuration, the attachment of any additional BDA is prevented as depicted in Figure 4c,d. As a consequence, the strong non-wetting of the step edges is observed at mesoscopic level.


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Contrary to the other systems where the molecular decoration of step edges either presents the nucleation centers for molecular island growth15,25–30 or even mediate a continuous growth of a molecular layer over the step edge,42–44 we introduce a system in which the step decoration inhibits further molecular growth. The BDA/Cu(001) system thus presents an important model system for understanding the role of the substrate in self-assembly and development of nucleation and growth theory beyond the standard model. This understanding is important for fabrication of functional molecular devices.


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ASSOCIATED CONTENT Supporting Information contains a more detailed discussion on (1) statistical analysis of molecular step edge decoration, (2) interaction of BDA with Ag(001) step edges, and (3) adaptive filtering of Figure 1b. This material is available free of charge via the Internet at http://pubs.acs.org.” AUTHOR INFORMATION Corresponding Author * E-mail: [email protected] Author Contributions All authors have given approval to the final version of the manuscript. ACKNOWLEDGMENT This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) under the National Sustainability Programme II, project CEITEC Nano+ (CZ.02.1.01/0.0/0.0/16_ 013/0001728) under programme OPVVV, and project TC17021 under the programme Inter-Excellence. The research was carried out using the CEITEC Nano Research Infrastructure (MEYS, 2016–2019). ABBREVIATIONS BDA, 4,4’ biphenyl dicarboxylic acid; TPA, terephalic acid; XPS, STM, Scanning Tunneling Microscopy; LEEM, low-energy electron microscopy; LEED, low energy electron diffraction; X-ray Photoelectron Spectroscopy; UHV, Ultra-High Vacuum.


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TOC graphics:


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Chemical structure of 4,4’ biphenyl dicarboxylic acid (BDA). 13x3mm (300 x 300 DPI)



(a) Overview image taken by LEEM after room temperature deposition of BDA on Cu(001). (b) Overview STM image on the same sample showing molecular islands. The overall contrast of image was increased by adaptive filtering (see methods), unfiltered image is given in Supporting Information. Scale bar is 30 nm. 159x47mm (300 x 300 DPI)


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(a) LEED pattern taken on BDA layer deposited on Cu(001) at room temperature; the substrate spots are marked by red rectangles and arrows are the reciprocal vectors of the (4√2×4√2)R45° superstructure. Missing spots are the result of extinction due to the glide symmetry of molecular superstructure along 〈110〉 directions.17 (b) Detailed STM image of self-assembled BDA phase overlapped with molecular structural models. (c) Tentative model of Cu(001)-c(8×8)-BDA phase (C: black, O: red, H: white). The principal lattice directions are marked by black arrows, primitive vectors of (4√2×4√2)R45° superstructure by blue arrows, and unit vectors of equivalent c(8×8) superstructure by green arrows. Scale bar in (b) is 2 nm. 170x59mm (300 x 300 DPI)



(a, b) Detailed STM images of point (a) and line (b) defects in self-assembled BDA phase. (c, d, e) Tentative models of molecular structures associated with these defects. Green and blue arrows in (b), (d), and (e) mark the position of dislocation lines. Scale bars are 2 nm. 82x98mm (300 x 300 DPI)


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(a, b) STM images of BDA step edge decoration on Cu(001) surface. Two prevalent orientations of BDA on step edges are marked by green and red arrows and encircled molecular model; red: molecular orientation is the same as within the islands, green: 45 ° tilt in respect to BDA direction within the islands. (c, d) Tentative models of BDA molecules attached to the step edges. The restricted hopping directions are demonstrated for a free molecule residing on the substrate. The crossed arrows denote the restricted diffusion directions. Scale bars are 2 nm. 82x95mm (300 x 300 DPI)



47x28mm (300 x 300 DPI)


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Molecular Passivation of Substrate Step Edges as Origin of Unusual

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