How Does Chemisorption Impacts Physisorption? A Molecular View of

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

How Does Chemisorption Impacts Physisorption? A Molecular View of Defect Incorporation and Perturbation of 2D Self-Assembly Ana M. Bragança, Brandon E. Hirsch, Ana Sanz Matias, Yi Hu, Peter Walke, Kazukuni Tahara, Jeremy N. Harvey, Yoshito Tobe, and Steven De Feyter J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b05667 • Publication Date (Web): 27 Sep 2018 Downloaded from http://pubs.acs.org on September 27, 2018

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The Journal of Physical Chemistry

How Does Chemisorption Impact Physisorption? A Molecular View of Defect Incorporation and Perturbation of 2D Self-Assembly Ana M. Bragança1, Brandon Hirsch1*, Ana Sanz-Matias2, Yi Hu1, Peter Walke1, Kazukuni Tahara3,4,5, Jeremy N. Harvey2, Yoshito Tobe3,6*, and Steven De Feyter1* 1

Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium 2

Division of Quantum Chemistry and Computational Chemistry, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium 3

Division of Frontier Materials Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.

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Department of Applied Chemistry, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan. 5

PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan

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The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan

ABSTRACT Chemical and structural defects in otherwise pristine materials can result in either improved or degraded material performance. Unfortunately, little is known about the role of these defects on complex hierarchical processes such as self-assembly. Here, the influence of defective surfaces on physisorbed self-assembly occurring at liquid/solid interfaces is investigated. Covalently bound defects on graphite surfaces are generated by electrochemically activating diazonium cations. After creating the defective substrates, a solution containing self-assembling molecules was deposited on the surface. Subsequent scanning probe investigations expose how the chemisorbed molecular units can either be incorporated within a porous hexagonal network, or generate local perturbations in the form of partial or full desorption of the physisorbed molecules. Overall, the chemisorbed molecules alter the local energy landscape for self-assembly to isolate new molecular packing arrangements. With a single-molecule perspective, this work outlines how chemical defects contribute to the formation of metastable assemblies and their evolutionary pathways toward higher-symmetry networks.

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Introduction Chemical and structural abnormalities in materials, i.e., defects, can have either detrimental or beneficial effects on functionality depending on the location, size, and type.1,2 Catalytic,3,4 electronic,5 and sensing platforms6–8 commonly display defect dependent performance. The emerging field of defect engineering seeks to manipulate the type, concentration, and spatial distribution of defects within a material to optimize performance.9 For example, topological defects in liquid crystals have been shown to direct the assembly of metallic nanoparticles and act as a template to promote the formation of molecular amphiphilic assemblies.10 In bulk metal-oxide semiconductors, point defects can alter electronic carrier concentrations and mobility, while extended defects can impact the physical strength of the material.2,8 For two-dimensional (2D) materials such as graphene and transition metal dichalcogenides, defects give rise to significant redistributions of the local density of states to modulate electronic, magnetic, and chemical properties.7,11 The role of defects on complex hierarchical processes such as self-assembly and surface mediated reactions is poorly understood.12 To mitigate the unfavorable effects and possibly leverage beneficial outcomes, it is necessary to develop a fundamental understanding regarding the influence that defects have on fabrication and processing of multifaceted self-assembled materials.13,14 The impact of defects on 2D self-assembly are often visualized directly with scanning tunneling microscopy (STM). Defects in alkanethiol self-assembled monolayers on gold were used as a tool to isolate single molecules and measure switching rates15 and photoisomerization behavior.16 On silicon surfaces, chemical defects terminate self-directed chemical growth of styrene nanowires.17 In previous work, we probed the impact of purposely defective surfaces on the 2D self-assembly of a densely packed hydrogen bonded system.18 Chemisorbed molecular

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units were observed to locally disrupt 2D crystallization events and slow down domain growth and ripening. This fundamental study revealed how physisorbed molecular assemblies can be controlled by chemisorbed molecular units. Many fundamental questions, which have been previously interrogated on pristine surfaces, i.e., phase transitions,19 chirality,20–22 threedimensional stacking,23–25 switching effects,26–28 and reactions12,29 have yet been addressed on defective substrates. In this work, we investigate how defective substrates impact the phase behavior between linear and porous structures of dehydrobenzo[12]annulene (DBA) derivative30 on graphite surfaces (Figure 1). Defects on the substrates were generated by electrochemical (EC) reduction of 3,4,5-trimethoxybenzenediazonium (3,4,5-TMeOD)31, as shown in Figure 1a to produce a covalently modified highly oriented pyrolytic graphite surface (CM-HOPG). After covalent modification, the molecular self-assembly of DBA molecules bearing six tridecyloxy chains (DBA-OC13) was interrogated at the 1-phenyloctane-graphite interface using STM. The selfassembly of DBA molecules has been extensively studied on pristine HOPG surfaces with wellestablished chirality32,33 phase transitions,30,34 and host-guest binding effects.35–37 Here, we demonstrate how defective substrates create confinement effects that alter the local energy landscape for the self-assembly and affect molecular dynamics.

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Covalent Modification O

(a)

O

O

EC reduction

O O

O

N2

(3,4,5-TMeOD)

Pristine HOPG

CM-HOPG RO

OR

(b)

(c)

RO

Unperturbed self-assembly

RO

(d)

(+) type dimer

(–) type dimer

C6 CCW

C6 CW

OR

DBA

Perturbed self-assembly

OR

Hot Deposition at 80ºC

R= −C13H27

(e) Pentagon

C1

C2

C3

Incorporated self-assembly

Figure 1. Schematic illustrations of (a) covalent modification of HOPG surface using EC reduction of in situ generated 3,4,5-trimethoxybenzenediazonium (3,4,5-TMeOD) cations. (b) Molecular self-assembly of DBA-OC13 on pristine HOPG in the linear phase (black) and in the hexagonal porous phase (blue). (c) Perturbed molecular self-assembly occurring on CM-HOPG. (d) Space filling models of (+) and (–) type alkyl interdigitation patterns, shown in black, to generate counter-clockwise (CCW) and clockwise (CW) nanoporous assemblies with C6-symmetry, shown in blue. The presence of localized defects in the surface induces the formation of lower symmetry pores with perturbed interdigitation patterns. (C3 in pink, C2 in green, C1 in yellow, and pentagons shown in red). (e) Hot solution deposition at 80 ºC provided the DBA network sufficient thermal energy to assemble around the chemisorbed defects and incorporate them within the porous structure, while also generating more high-symmetry C6 pores.

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Results and Discussion DBA-OC13 Self-Assembly on pristine HOPG Early work involving the self-assembly of DBA molecules on HOPG revealed a phase transition from a dense, non-porous packing arrangement at high concentration to a porous lower-density structure at low concentration.30 Both networks are stabilized by van der Waals interactions that exist between interdigitating alkoxy chains of adjacent molecules.38 Typically, only four or five chains adsorb in the dense non-porous structure, while all six chains are adsorbed in the porous low-density structure. In the porous structure, the relationship between the chains within a DBA dimer pair can be categorized as either “+” or “–” type interdigitation (Figure 1d, black schematic). High-symmetry (C6) hexagonal pores containing exclusively “+” or “–” type dimer interdigitation are classified as counterclockwise (CCW) and clockwise (CW) pores, respectively (Figure 1d, blue schematic).32 Linear combinations of the dimer interdigitation patterns give rise to distorted hexagonal pores of lower symmetry, i.e., C2 and C3, (Figure 1d, green and pink schematics, respectively). This symmetry breaking effect is strongest for DBA systems containing an odd number of carbon atoms in the alkyl chain.39 In this work, DBA-OC13 was thus chosen for assembly on chemically defective surfaces to expose symmetry breaking and alternative packing effects that arise from the defects. As a point of reference, DBA-OC13 self-assembly was initially characterized on the pristine graphite substrate (Figure S1-S2). A concentration of 2.7 × 10–6 M was chosen as STM imaging revealed a porous structure with a surface coverage of approximately 76.4 ± 4.7%, while avoiding the contamination that shows up at lower concentrations.36 A representative STM image of the assembly is shown in Figure 2a (top). Small regions of non-porous assembly can be easily identified at the domain boundaries of the porous structure in the analyzed image.

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Covalent Modification of HOPG Individual chemisorbed molecular defects were deliberately created on the pristine graphite surface using electrochemical covalent modification. This process involves the generation of aryl radicals by the EC reduction of 3,4,5-trimethoxybenzenediazonium (3,4,5TMeOD) cations. A subsequent radical attack reaction with the surface results in chemisorption of 3,4,5-trimethoxyphenyl molecular units, abbreviated TMeOP (Figure 1a). Control over the density of chemisorbed molecular defects was achieved using chronoamperometry.40 During this procedure, a fixed potential (+0.15, +0.02, and –0.02 V) is applied to the surface for 10 seconds to promote diazonium reduction. In general, negative EC potentials yield a higher density of molecular defects (Figure S7 and S8). The degree of covalent functionalization was established by analysis of the ratio between the D- and G-bands in the Raman spectrum (Figure S9).41,42 Additional details regarding the grafting procedure, the choice of the aryl species, Raman and data analysis are available in supporting information (Section S1, S3-S7).

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Figure 2. Representative STM images of DBA-OC13 (2.7 × 10–6 M) assemblies on (a) pristine HOPG and CM-HOPG with (b) low, (c) intermediate and (d) high density of chemisorbed TMeOP species. The DBA porous network and the chemisorbed TMeOP molecular units are highlighted by superimposing schematic illustrations on the STM images below. Histograms overlaid inside the STM images reveal the DBA-OC13 porous (light gray) and non-porous (dark gray) network surface coverage for each defect density category. Regions of monolayer disorder are indicated in black. As a result of a gradual increase in the amount of chemisorbed TMeOP units on the surface, a more compact, non-porous self-assembled DBA-OC13 structure is observed. Imaging parameters: (a) Vs = –0.20 V, It = 200 pA; (b), (d) Vs = –0.82 V, It = 70 pA and (c) Vs = –0.80 V, It = 70 pA.

DBA-OC13 Self-Assembly on CM-HOPG The impact of the chemisorbed TMeOP defects on the self-assembly of DBA-OC13 at room temperature was investigated using three different categories of defect density. The number of TMeOP units in a scan area of 100 nm × 100 nm was used to define these categories: low (60 - 110 TMeOP), intermediate (200 - 300 TMeOP) and high (360 - 555 TMeOP) (Figure S8). In the STM images, the TMeOP defects appear with bright contrast, while the DBA-OC13 triangular cores are characterized by an intermediate contrast. The darker regions between the triangular cores are filled by alkyl chains from the DBA molecules. On low defect density surfaces, perturbations to the DBA-OC13 assembly were clearly observed in the STM images (Figure 2b) when compared to the pristine surface (Figure 2a). The size of the porous domains decreases, and their total porous surface coverage is reduced from 75% to approximately 50% (Figure 2b, gray histogram). The small porous domains are broken up by non-porous assembly. For medium and high defect density surfaces, the non-porous assembly becomes more prominent than the porous structure (Figure 2c-d). A network analysis of the STM images appears below the unmodified STM image. Isolated pores can easily be identified in these analyzed images

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(Figure 2d, bottom row of images). As a result of this structural shift, a slightly larger number of DBA molecules were observed on defective substrates (~1260 molecules per 100 × 100 nm) when compared to pristine graphite (~1190 molecules) (Table S1). The relatively small aerial footprint of a TMeOP unit (0.94 ± 0.36 nm2) accounts for less than 5% of the surface area even for the highly defective surfaces. Despite the small area occupied on the surface, the presence of the defects has a dramatic influence on the nature of the self-assembly. The shift from the porous structure to the dense non-porous assembly at room temperature is believed to result from the reduction in extended open terrace space on surface for network assembly. This is supported by a nearest neighbor distance analysis between TMeOP defects for the three different categories (Figure S11 and S12). The average nearest-neighbor distance changes from 4.95 nm for the low defect density surfaces to 2.20 nm for high defect density samples. Though there is a tendency to cluster, even in the low defect density samples, these averages are comparable to the unit cell distance (4.7 nm) for the porous structure. These matching length scales suggest that confinement-based perturbation due to the defects is likely to occur.

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Figure 3. (a) STM image showing covalently bound TMeOP molecular units at an intermediate defect density, which appear with bright contrast, and physisorbed self-assembly of DBA-OC13. Colored schematic illustrations of porous structures obtained on the CM-HOPG surface are added for clarity. (b)(g): High-resolution STM images and tentative models of C6 symmetry pores: (b) CW and (c) CCW; and lower symmetry pores: (d) C3, (e) C2, (f) C1 and (g) pentagon. The appearance of C3 and C2 pores has been previously reported.39 The high symmetry axis of graphite is represented by black arrows. Imaging parameters: (a) Vs = –0.80 V, It = 60 pA; (b-f) Vs = –0.20 V, It = 200 pA and (g) Vs = –0.80 V, It = 90 pA.

High-resolution STM imaging of the intermediate TMeOP defect density provides a submolecular view of the adaptations the DBA-OC13 self-assembly must make in order to accommodate the chemisorbed molecular units (Figure 3a). The porous self-assembled structures are highlighted with a colored network overlay, which corresponds to the pore symmetry. Pores of C6 symmetry are labeled in blue, while lower symmetry pores, C3 and C2, are labelled pink and green, respectively. It is important to note that the domains of hexagonal pores on the defective surfaces follow the same packing arrangement and are similarly aligned with respect to

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the main symmetry axis as on the pristine HOPG surface. Two previously unobserved porous structures are also found. A pore with C1 symmetry (yellow) is generated by an asymmetric interdigitation pattern of (+) and (–) type dimer pairs. This situation results in the forced desorption of four alkyl chains, two from each neighboring DBA molecule. The second new pore, a pentagon shown in red, is observed when five DBA-OC13 molecules assemble in regions that are dimensionally confined by chemisorbed defects. High-resolution STM images of these pore variations are shown beside tentative molecular models in Figure 3b-g. The results of a statistical analysis of each pore occurrence on pristine and covalently modified surfaces were examined. This statistical sampling of each category was based on more than fifteen STM images obtained during several experimental sessions, covering an area of at least 150000 nm2. A histogram shown in Figure 4 concisely reveals the outcome of this analysis. Surfaces with more chemisorbed TMeOP units show fewer high-symmetry C6 hexagonal pores. Coincident with the loss of C6 symmetric pores, the non-porous structure, shown in gray, is more commonly observed. The non-porous assembly consists of densely packed DBA-OC13 cores that are organized in a linear phase or in a host-guest phase where the pores of the nanoporous phase contain a DBA-OC13 guest molecule. Upon increasing the density of TMeOP defects, the high-density phase appears to become more disordered.

The imaging quality on TMeOP

modified surfaces often hinders a more detailed assessment of the high-density phase (Figure S4). The relative number of low-symmetry pores also increases abruptly with the introduction of TMeOP defects and remains fairly consistent across the defective surface categories sampled. The full statistical data set can be found in Table S2. This analysis demonstrates that the DBAOC13 porous structures are locally disturbed by the presence of TMeOP defects; however, the DBA porous network can potentially avoid disruption by encircling the defective surface sites.

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Figure 4. Histogram representation of the statistical analysis performed on the DBA-OC13 assembly structure (non-porous, porous, and symmetry relationships) on pristine and defective surfaces with low, intermediate, and high defect density.

Defect Incorporation versus Perturbation When the DBA-OC13 solution is added to the defective substrates, the DBA-OC13 molecular assembly has three options to alleviate the impact of the chemisorbed defect on the total energy of the system. The defect can either 1) be incorporated into the network, 2) induce a perturbation within the assembly or 3) experience a combination of both. Defect incorporation involves the DBA nanoporous assembly encircling the TMeOP defects within the 2.8 nm supramolecular pore. Incorporation of as many as five TMeOP defects was observed within a single supramolecular pore (Figure 5).

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Figure 5. High resolution STM images showing (a) an empty C6 pore and the incorporation of (b) one (c) two (d) thee (e) four, and (f) five chemisorbed TMeOP molecular defects inside a single nanopore. Illustrative models are shown below. Imaging parameters: (a) Vs = –0.20 V, It = 200 pA; (b)-(d) Vs = – 0.80 V, It = 90 pA and (e)-(f) Vs = –0.80 V, It = 60 pA.

Local perturbations to the molecular assembly occur when the defect directly induces a change in the DBA self-assembly. Partial or full molecular desorption, alternative interdigitation patterns, and shifts in the surface adsorption site are common examples of local perturbations to the DBA assembly (Figure 6a, red dots). Alternatively, through-space perturbations do not occur via immediate interactions with DBA network. Rather, these perturbations occur when two or more TMeOP defects impose geometric confinement limitations on the DBA network as a result of the spatial relationships between the defects (distance and angles). When this inter-defect relationship between TMeOP units conflict with the DBA network periodicity (≈ 4.7 nm), the self-assembly must adapt to the defect by locally altering the structure to best mitigate the presence of the chemisorbed TMeOP unit. As the density of TMeOP defects increases, the average nearest neighbor defect distance approaches that of the DBA network periodicity and through-space perturbations become more common. Defect categorization concerning incorporation and perturbation is not mutually exclusive though. Examples of TMeOP defects

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that are incorporated within the DBA network yet produce through-space perturbations are highlighted with green dots in Figure 6.

Figure 6. High-resolution STM image showing TMeOP defects creating local perturbations (red) where partial or complete desorption of a DBA molecule is observed, as well as incorporated defects that produce through space perturbations (green) to the porous network. One defect marked in yellow is able to be fully incorporated and clearly not produce any through-space perturbations. (b) A zoom-in STM image and corresponding schematic analysis of the through-space perturbative behavior. Imaging parameters: Vs = –0.80 V, It = 100 pA.

It is remarkable how well the DBA-OC13 unit, whose only intermolecular interactions are van der Waals based and who shows porous pattern formation, is able to cope with the presence of the chemisorbed defects. More rigid densely packed systems are subject to a larger degree of perturbative character from the presence of the chemisorbed units. When the lamellar

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assembly formed by 5-octadecyloxyisophthalic acid was investigated on defective substrates, the network responded in a dramatically different fashion.18 Frequently, regions defined by no assembly, domain breaks, and stacking faults were observed on the defective surfaces. The 5octadecyloxyisophthalic acid lamellar network is largely stabilized by directional hydrogen bonding interactions and interdigitated alkyl groups. As a result, this densely packed network displayed much less flexibility and therefore had much weaker adaptability when compared to the DBA network investigated here.

Kinetic Trapping Revealed by Hot Deposition Protocol Early fundamental work established that the sticking probability of gases on metals is greater on rough surfaces (e.g., stepped surfaces) than smooth surfaces.43,44 Based on these insights, which are difficult to quantify at the liquid-solid interface, we hypothesize that the sticking probability is higher on CM-HOPG than on pristine HOPG. Along the same lines, molecular diffusion on pristine HOPG should be greater when compared to CM-HOPG, as the chemisorbed TMeOP defects impose a diffusion barrier. The presence of the defects is expected to limit surface translational and rotational motion of DBA molecules and possibly affect desorption dynamics as well. Overall, we anticipate reduced dynamics, which might hamper any temperature driven pattern reorganization. To examine the role of kinetic trapping present in the assembly on the defective surfaces a DBA solution was dropcast onto a hot HOPG surface held at 80 ºC. After this “hot deposition” protocol the HOPG substrate was left on the thermal plate for three to nine minutes in a saturated atmosphere of 1-phenyloctane solvent. This was accomplished by covering the surface with a small petri dish cover after placing a few drops of solvent around the sample. This procedure ensured minimal evaporation of the solvent, so the concentration of the DBA solution on the

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surface remained virtually constant. After hot deposition, samples were allowed to cool to room temperature prior to STM imaging.

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Figure 7. Representative STM images of DBA-OC13 (2.7 × 10 M) assemblies on (a) pristine HOPG and (b)-(d) CM-HOPG with an intermediate density of defects, after following different hot deposition experiments. Duration of time for hot deposition cycle: a-b) 3 min., c) 6 min., and d) 9 min. Histograms show the total amount of porous phase (grey) and the relative ratio of each pore type. Unlike on pristine HOPG, lower symmetry pores remain on the CM-HOPG irrespective of the time. Increasing the time of the thermal treatment results in a gradual increase on the amount of higher symmetry hexagonal pores (C6) at the expense of the dense non-porous network. Imaging parameters: (a) Vs=–0.20 V, It=200 pA, (b)(c) Vs=–0.80 V, It=70 pA, (d) Vs=–0.80 V, It=80 pA.

STM imaging after a three-minute hot deposition treatment on the pristine HOPG surface resulted in complete surface coverage of the C6 symmetric porous structure (Figure 7a). The lower symmetry pores (C1, C2; C3 and pentagons), which represented ~20% of the surface after room temperature deposition (Figure 4) are no longer observed after the hot deposition treatment. Few differences were observed after three-minutes at 80 ºC when compared to room temperature 15



deposition for the intermediate defect density substrates (Figure 7b & S14, respectively). The relative amount of each pore type and the total amount of porous phase remained comparable. The samples exposed to a hot deposition treatment for longer times showed an increase in the surface coverage of the C6 symmetric pores at the expense of the non-porous structure (Figure 7c-d). Across all the samples, the relative ratio of lower symmetry pores remained fairly constant (see Table S3). The rise in C6-symmetric porous population upon heat treatment provides strong evidence that the TMeOP defects impose kinetic constraints that trap the system in the nonporous structure. The onset transitionary phase progression observed between the three- and sixminute hot deposition treatments is symptomatic of a tempering process required for the DBA network to adjust its assembly on defective substrates. The origin of this behavior can be twofold. The expansion of the C6 network over time can be justified by an increased growth rate during the initial stages of crystal formation or, alternatively, due to the coalescence of preformed domains via Ostwald ripening. Both processes are thermally activated.45,46 Introduction of TMeOP defects complicates the DBA self-assembly energy landscape by presenting the possibility of new intermolecular interactions between the chemisorbed defects and the physisorbed molecules. Depending on the strength of these interactions, they may be capable of providing sufficient stability to trap previously metastable arrangements. In an attempt to address the nature and strengths of possible stabilizing interactions between the chemisorbed defects, the DBA-OC13 molecules and their supramolecular structures, we have carried out molecular mechanics geometry optimizations (RMSG=0.05 kcal/mol/Å) with the MM3 force field. Be aware that we ignore any solvent effects which is a major simplification, and that we restrict these calculations to C6-symmetric pores. For more details see

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section S13 of the supporting information. The lowest energy system occurs when the TMeOP defect (colored in blue) is positioned at the edge of the pore directly neighboring interdigitated alkyl chains (Figure 8). A stabilization of –12 kJ/mol results from the additional van der Waals interactions between the defect and the alkyl group. When the TMeOP unit is positioned at a vertex of the pore, the system also experienced slight stabilization (–7 kJ/mol). The two conformations with the TMeOP defect positioned between the alkyl chains are destabilized by ~30 kJ/mol. When the TMeOP defect is located at a center of the hexagonal pore, no stabilization was found. By comparison, the stabilization arising from the molecule-molecule interactions within a DBA pore is, at the same level of theory, -108 kJ/mol per molecule. Thus, the interaction of the physisorbed DBA with the vertically oriented chemisorbed TMeOP defect at the edge of the pore is nearly 10% that of the DBA pairing between molecules. Although these calculations must be interpreted with caution, they support our view that the new interactions between the defects and the physisorbed DBA molecules can generate both local stabilizing and destabilizing forces. Furthermore, entropic effects, not considered in these calculations, may play a role in decreasing the destabilization caused by the defects. When these interactions are combined with geometrically controlled confinement effects, they are likely to produce significant complications to the self-assembly free energy landscape to result in previously unobserved kinetically trapped states.

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Figure 8. Schematic representation of the simulated porous structures and their relative energetic differences. Molecular mechanics simulations were performed at the MM3 level of theory on bilayer graphene for the porous DBA-OC13 structure (RMS=0.05 kcal/mol). The pristine unmodified surface is set to the relative energy of 0.0 kJ/mol. TMeOP defects were simulated at various positions: center, edge, vertex, between parallel alkyls, and between zig-zag alkyl groups.

As a result of these additional forces, the overall stability of both the porous and nonporous DBA assembly on the defective substrates is believed to be enhanced when compared to the pristine graphite surface, going hand in hand with reduced dynamics. Heat treatments on the defective substrates allowed the system to escape its local minimum to generate more C6 symmetric pores. Alongside the increased C6 porous population, these structures also appear to become more extended by forming well-connected domains. Second to the C6 pores, the C2-symmetric pores are consistently observed to form larger domains when compared to the other low-symmetry pores (Figure 7d). For a detailed analysis, see Section S14. 18


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The prominence of C6- and C2-symmetric pores over the other low-symmetry pores can be rationalized by two simple crystallographic relationships - chiral and rotational symmetry matching. C6 pores benefit from high rotational symmetry, which supports the growth of homochiral CW or CCW domains. The two chiral handed domains are rotationally displaced by 26° (Figure S18). This chiral displacement results in domains of opposite handedness that can only be connected by lower symmetry pores (Figure S19). Alternatively, C2-symmetric domains can be formed by either homochiral or heterochiral domains. Simple tessellation without rotation or the tiling of a racemate mixture can support 2D propagation (Figure S20). The third largest population, C1-symmetric pores, experience limited rotational and chiral symmetry matching characteristics and thus results in small aperiodic homochiral or heterochiral structures (Figure S21). The remaining porous symmetries (C3 and pentagons) are commonly found isolated within the DBA-OC13 self-assembled network. Under severe confinement conditions created by TMeOP defects, occasional transmission of these structures is observed (Figure S22-S23). The combination of the reduced open terrace space alongside simple crystallographic tiling relationships dictates the final population and the extent of porous connectivity. Considering the concentration-dependent phase behavior of DBA-OC13 on pristine surfaces, there is a possibility that the presence of defect-induced structures is also dependent on the concentration. Future studies aiming to extend this method and investigate the effect of solute concentration in the appearance of lower symmetry structures are planned.

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Conclusions This work demonstrates how chemisorbed molecules alter the local energy landscape for self-assembly to perturb the phase behavior of a conformationally flexible molecule that forms porous and non-porous structures. The molecule’s structural flexibility and symmetry matching with the surface allows the stabilization of a variety of new supramolecular arrangements. New interactions between the defects and physisorbed molecules assist in stabilizing kinetically trapped structures. We attribute this to the chemisorbed aryl units that alter the sticking probability of the DBA molecules and act as barriers to hinder lateral surface diffusion. Confinement effects generated by these defective substrates present new possibilities to form molecular glass structures.47,48 Nanostructured chemically defective surfaces may be designed to harness kinetic controls and slow self-assembly processes allowing a controlled approach to metastable materials and novel polymorphic assemblies.49

ASSOCIATED CONTENT Supporting Information The Supporting Information is available free of charge on the ACS Publications website. Experimental details regarding sample preparation, STM measurements, data analysis and molecular mechanics calculations can be found in supporting information. Additional data on the self-assembly of DBA-OC13 on covalently modified HOPG at room temperature and after following a thermal treatment are also available.

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AUTHOR INFORMATION Corresponding Authors * [email protected] * [email protected] * [email protected]

ORCID iD Ana M. Braganca: 0000-0001-6853-1025 Brandon Hirsch: 0000-0002-3452-0990 Ana Sanz-Matias: 0000-0002-4662-5140 Yi Hu: 0000-0003-1073-7009 Kazukuni Tahara: 0000-0002-3634-541X Jeremy Harvey: 0000-0002-1728-1596 Yoshito Tobe: 0000-0002-1795-5829 Steven De Feyter: 0000-0002-0909-9292

Notes The authors declare no competing financial interest.

ACKNOWLEDGEMENTS The authors gratefully acknowledge financial support from the Fund of Scientific Research Flanders (FWO), KU Leuven - Internal Funds, Belgian Federal Science Policy Office (IAP7/05). The research leading to these results has also received funding from the European Research Council under the European Union's Seventh Frame- work Programme (FP7/20072013)/ERC Grant Agreement No. 340324 to S.D.F. This work is supported by JST-PRESTO

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“Molecular technology and creation of new functions” and JSPS KAKENHI (15H02164). B.E.H. thanks FWO for a postdoctoral fellowship and the Belgian-American Educational Foundation.

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Table of contents figure:

Pristine Surface Assembly

Defective Surface Assembly

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Pristine Surface Assembly


Defective Surface Assembly


How Does Chemisorption Impacts Physisorption? A Molecular View of

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