This may be the author’s version of a work that was submitted/acceptedfor publication in the following source:

Abyazisani, Maryam, Bradford, Jonathan, Motta, Nunzio, Lipton-Duffin,Josh, & MacLeod, Jennifer(2019)Adsorption, deprotonation, and decarboxylation of isophthalic acid onCu(111).Langmuir, 35(22), pp. 7112-7120.

This file was downloaded from: https://eprints.qut.edu.au/130008/

c© Consult author(s) regarding copyright matters

This work is covered by copyright. Unless the document is being made available under aCreative Commons Licence, you must assume that re-use is limited to personal use andthat permission from the copyright owner must be obtained for all other uses. If the docu-ment is available under a Creative Commons License (or other specified license) then referto the Licence for details of permitted re-use. It is a condition of access that users recog-nise and abide by the legal requirements associated with these rights. If you believe thatthis work infringes copyright please provide details by email to qut.copyright@qut.edu.au

Notice: Please note that this document may not be the Version of Record(i.e. published version) of the work. Author manuscript versions (as Sub-mitted for peer review or as Accepted for publication after peer review) canbe identified by an absence of publisher branding and/or typeset appear-ance. If there is any doubt, please refer to the published source.

https://doi.org/10.1021/acs.langmuir.8b04233

https://eprints.qut.edu.au/view/person/Abyazisani,_Maryam.htmlhttps://eprints.qut.edu.au/view/person/Bradford,_Jonathan.htmlhttps://eprints.qut.edu.au/view/person/Motta,_Nunzio.htmlhttps://eprints.qut.edu.au/view/person/Lipton-Duffin,_Josh.htmlhttps://eprints.qut.edu.au/view/person/Lipton-Duffin,_Josh.htmlhttps://eprints.qut.edu.au/view/person/MacLeod,_Jennifer.htmlhttps://eprints.qut.edu.au/130008/https://doi.org/10.1021/acs.langmuir.8b04233

1

Adsorption, deprotonation and decarboxylation of

isophthalic acid on Cu(111)

Maryam Abyazisania, Jonathan Bradforda, Nunzio Mottaa,b, Josh Lipton-Duffina,b and Jennifer

MacLeoda,b*

a School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology

(QUT), 2 George Street, Brisbane QLD 4000, Australia.

b Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street,

Brisbane QLD 4000, Australia.

2

Abstract:

The surface-assisted reaction of rationally designed organic precursors is an emerging approach towards

fabricating atomically precise nanostructures. Recently, on-surface decarboxylation has attracted attention due

to its volatile by-products which tend to leave the surface during the reaction, which means that only the desired

products are retained on the surface. However, in addition to acting as the reactive site, the carboxylic acid

groups play a vital role in the adsorption configuration of small-molecule molecular precursors and therefore in

the reaction pathways. Here, scanning tunnelling microscopy (STM), synchrotron radiation photoelectron

spectroscopy (SRPES) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy have been employed

to characterize the mono-deprotonated, fully deprotonated and decarboxylated products of isophthalic acid

(IPA) on Cu(111). IPA is partially reacted (mono-deprotonated) upon adsorption on Cu(111) at room

temperature. Angular dependent x-ray photoelectron spectroscopy reveals that IPA initially anchors to the

surface via the carboxylate group. After annealing, the molecule fully deprotonates and reorients so that it

anchors to the surface via both carboxylate groups in a bipodal configuration. NEXAFS confirms that molecule is

tilted upon adsorption as well as after full deprotonation. Following decarboxylation, the flat-lying molecule

forms into oligomeric motifs on the surface. This work demonstrates the importance of molecular adsorption

geometry for on-surface reactions.

3

Introduction

The fabrication of surface-confined covalent polymers from molecular precursors has drawn attention in the

past decade due to potential relevance to nanoscale electronic and optical devices.1-2 Different on-surface

reactions and precursors are being explored with the goal of optimizing the resultant nanostructures. In this

regard, precursors functionalized with carboxylic acid3-5 have recently attracted attention as they present a route

to surface-confined polymer formation that may offer advantages over Ullmann coupling, a reaction that has

been widely used to grow 1D and 2D polymers.6 The Ullmann reaction produces halogen by-products, which can

remain chemisorbed on the surface and might have a negative effect on the diffusion of surface-stabilized

radicals and the spatial extension of the polymers. In contrast, the by-products resulting from decarboxylation,

H2 and CO2 leave the surface.7-10

Gao et al. reported that the polymerization of 2,6-naphthalenedicarboxylic acid via decarboxylative coupling

proceeds in a three-step process: deprotonation to convert the carboxylic groups to carboxylate, followed by

cleavage of the carboxylate groups and finally diffusion of the activated moieties to allow the formation of C-C

coupling. Each of these processes can be triggered through thermal activation.3 On reactive surfaces, the

presence of carboxylic acid can affect the adsorption geometry of small molecules, since the molecule can

deprotonate on deposition and the molecular plane can be oriented upright or tilt with respect to the substrate.9,

11-13 Benzoic acid, a simple monocarboxylic acid, deprotonates upon adsorption on copper surfaces and assumes

an upright configuration with respect to the surface, i.e., the molecules are oriented with their phenyl rings

perpendicular to the substrate.14-21 This adsorption geometry arises from the strong carboxylate-copper

interaction.19 The addition of more than one carboxylic group to a molecule introduces some complication to

this scenario owing to competition between substrate-molecule (copper-carboxylate) and molecule-molecule

interactions.9, 22-23 For example, the copper-carboxylate interaction suppresses hydrogen bonding between

molecules in terephthalic acid (TPA), a dicarboxylated phenyl, since TPA adsorbs in a perpendicular orientation

with respect to the Cu(110) surface.9 In the TPA study, one of the carboxyl groups of molecule deprotonates

upon adsorption and forms a carboxylate group which anchors to the copper surface and leaves the other acid

group intact and oriented away from the surface.

A central theme in these studies of aromatic carboxylic acid-functionalized molecules has been the importance

their adsorption configuration on the surface. Systematic investigations of the adsorption of the various

aromatic carboxylate acid precursors will ultimately result in recipes for a deliberate design of precursors with a

rational number of carboxylate acid groups in a specific geometry to fabricate ordered polymers via

decarboxylative coupling. Understanding of molecule-substrate interactions is a key step towards controlling

the growth of polymer films at surfaces.24

Here, we present a study of the adsorption, deprotonation and decarboxylation of 1,3-benzenedicarboxylic acid

(isophthalic acid, IPA) on Cu(111). Photoemission spectroscopy (PES) was used to monitor the chemistry of the

IPA molecules. Measurements collected at different angles with respect to the surface provide insight into the

4

orientation of the different parts of the molecule during the reactions. We obtained additional insight into the

adsorption geometry using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy, and by imaging

the molecular films using scanning tunnelling microscopy (STM). Together, these investigations provide a

complete picture of the adsorption, deprotonation, decarboxylation, and subsequent C-C coupling of IPA on

Cu(111).

Experimental Section

The ultrahigh vacuum (UHV) system at Queensland University of Technology has a base pressure better than 2

× 10−10 mbar and comprises two chambers: the first is equipped with a dual-anode x-ray lamp (ScientaOmicron

GmbH DAR 400) and a hemispherical electron energy analyzer (iSphera), as well as standard facilities for sample

preparation, and the second chamber houses a scanning tunnelling microscope (ScientaOmicron GmbH VT-

AFM/XA). All STM images for this study were recorded in constant current mode and at room temperature with

an electrochemically etched tungsten tip. Bias voltages are measured with respect to the tip. For every STM data

set, corresponding XP spectra were measured with the Al Kα x-ray laboratory source to check the chemistry of

the surface before STM scanning.

Synchrotron radiation photoelectron spectroscopy (SRPES) experiments were performed on the soft x-ray (SXR)

beamline of the Australian Synchrotron. Survey spectra were recorded using a beam energy of 1487 eV with a

pass energy of 100 eV. Core level spectra of the C 1s and O 1s regions were acquired using photon energies of

486 and 980 eV, respectively. The pass energy was set at 20 eV during high resolution scans for an overall energy

resolution of 0.29 eV. CasaXPS software was used to analyze the PES spectra 25 and all spectra were energy-

calibrated by rigidly shifting to set the Fermi level to zero binding energy. Shirley and linear backgrounds were

used for the C 1s and O 1s regions, respectively. The PE spectra of C 1s core level were acquired with the surface

normal at different angles with respect to the analyzer to elucidate the carboxyl/carboxylate group location with

respect to phenyl group. PE spectra of the C 1s core level were also collected with different beam energies

between 380 eV and 908 eV.

NEXAFS spectra were collected using linearly polarized light at glancing incidence (Ө = 20°), magic angle (Ө = 55°)

and normal incidence (Ө = 90°) with respect to the surface plane. The QANT software package was used to

analyze all spectra.26

Sample Preparation: a Cu(111) crystal was cleaned by repeated cycles of Ar+ ion sputtering (1 keV) at room

temperature and flash annealing to 780 K. Low-energy electron diffraction (LEED) and PES of C 1s and O 1s

verified the sample cleanliness. Commercially purchased isophthalic acid (IPA) (98%, Sigma Aldrich Corp.) was

thoroughly degassed at 383 K in UHV and was deposited by organic molecular beam epitaxy (OMBE) from a

Knudsen cell held at 393 K onto a room temperature (RT) substrate for 10 minutes. The sample was subsequently

heated stepwise until the molecule fully decarboxylated.

Results

5

The polymerization of IPA via decarboxylative coupling is shown in Figure 1a. In the decarboxylative reaction,

bonds are successively cleaved at the carboxylic group: deprotonation as a result of O-H bond scission and then

decarboxylation through cleavage of –COO– from the ring. Following decarboxylation, the activated moieties can

form an organometallic through participation of surface atoms/adatoms. Scission of the C-Cu bond and coupling

of the resultant activated moieties results in formation of polymeric structures. The carboxylate groups in the

IPA are in the meta positions, thus three well-defined products are possible: zig-zag chains, crinkled chains and

rosette macrocycles (see Figure 1b).

Figure 1 (a) Decarboxylation reaction schematic for IPA molecule in the presence of copper and (b) three possible structural products of polymerization of IPA, from left to right: zig-zag, crinkled and rosette macrocycles respectively.

XPS

The C 1s and O 1s photoemission spectra of IPA on Cu(111) are compiled in Figure 2. The experimental data

points are shown as black circles and the corresponding fit with a gray line. The main feature consists of two

peaks 284.9 eV and 285.3 eV, which are assigned to the carbon atoms of phenyl rings in the first and second

layers respectively. Peaks at 288.0 and 289.4 eV originate from the carboxylate and carboxylic groups,

respectively, of molecules in the first layer.27-28 Additional spectral intensity mandates the use of a second

feature at 289.4 eV to account for carboxylic groups of intact molecules in the second layer, which forms due to

deposition of slightly more than 1 ML of molecules. The small peak at 291.5 eV is assigned to the π−π* shake-up

transition of the aromatic system.27. It is well-known that carboxylic acids either fully or partially deprotonate

upon adsorption on copper surfaces.4, 27, 29 Here, both intact (–COOH) and deprotonated (–COO–) groups are

evident in the spectrum originating from the first layer, with the deprotonation contribution 40% larger than the

intact contribution. After annealing to 373 K the phenyl and carboxylic acid peaks originating from molecules in

the second layer disappear, consistent with desorption of intact molecules from the second layer, and the –

COOH and –COO– peaks become equal in magnitude (See Figure S1). The presence of equal COO– and COOH in

the first monolayer could arise from two different scenarios: (a) fully deprotonated and intact IPA molecules

coexisting on the surface, (b) mono-deprotonated molecules. We believe that scenario (b) is more likely and the

first monolayer of IPA mono-deprotonates upon adsorption on Cu(111) at room temperature. The adsorption

geometry of the mono-deprotonated molecule will be further discussed later, based on angular and energy

6

dependent PES, which illustrates the location of carboxyl (–COOH) and carboxylate groups (–COO–) respect to

the surface and phenyl ring.

The O 1s spectrum confirms the coexistence of chemical states for carboxylate and carboxylic groups for the as-

deposited sample: a peak at 531.6 eV is assigned to the carboxylate group,28 while the hydroxyl (533.8 eV) and

carbonyl (532.4 eV) peaks, locked to a 1:1 ratio, are attributed to the two chemical state of oxygen in a carboxylic

group. This is in accordance with the results from the C 1s core level. Furthermore, a pair of extra peaks at 532.9

and 534.4 eV is attributed to the carboxylic groups of molecules in the second layer.

Figure 2 (a) C 1s and (b) O 1s spectra for IPA deposited onto Cu(111) at 300 K, followed by two annealing steps at 453 K and 488 K. The black markers represent the acquired data, and the coloured peaks show synthetic fits.

Before discussing the structural model of molecule in different stages, we turn to spectroscopic data that can

provide insight into the adsorption geometry of the molecules. Comparing PE spectra collected at different

angles with respect to the surface normal provides information about the relative geometry of –COOH, –COO–

and phenyl with respect to the surface. All spectra were fitted with the same peak set determined from normal-

incidence data collected at 380 eV. The intensity ratios of –COOH, –COO– and phenyl normalized to the total C

1s region for the as-deposited sample are plotted in Figure 3. The change in the ratio between the phenyl and

the functional groups depends on the escape depth of the electrons.30-31 The distance that a photoelectron has

to travel to escape the surface is shorter when the optical axis of the detector lies along the surface normal and

increases when the emission angle is off-normal, meaning that the chemical species closest to the substrate will

decrease in intensity with increased angle.

7

The comparison of the intensities of different signals reveals that –COOH intensity increases with off-normal

measurements, while the intensities of both phenyl and –COO– decrease. This indicates that the molecule is not

adsorbed planar, and that the carboxylate group is buried beneath the aromatic ring. On the other hand, both

the –COOH and phenyl intensity are reduced at off-normal angles, suggesting that the carboxyl group is in the

outer-most plane surface of as-deposited sample. This is consistent with the molecule being anchored to the

copper via the –COO– group in a monopodal configuration while the phenyl ring is perpendicular/tilted with

respect to the surface and –COOH pointing out of the surface.

A variation in intensity for spectra collected at different angles can arise from photoelectron diffraction effects.32-

33 To verify that the observed variation was due to the adsorption geometry of the molecules and not

photoelectron diffraction, we confirmed our findings by varying the photon energy of the probe beam, which

provides similar information to the angle-resolved measurements, but without the possibility for photoelectron

diffraction effects (see Figure S2). This measurement agrees with our angle-dependent results, supporting that

the observed variation in the angle-resolved measurements arises from the adsorption geometry of the

molecules. This interpretation is further supported by STM and NEXAFS measurements, which will be discussed

later. The same adsorption geometry has been reported for mono-deprotonated IPA on Au(111) molecules on

Au(111).34-35

Figure 3 Angular dependence of the apparent stoichiometry of IPA deposited at room temperature collected at hυ=380 eV using four different angles with respect to the surface normal. The intensity of carboxylate, carboxyl and phenyl components have been normalized with repect to the total C 1s. Inset shows a schematic of the adsorption geometry.

Annealing the sample at 453 K results in the disappearance of the carboxyl peak in C 1s (c.f. Figure 2),

demonstrating that the molecule is fully deprotonated at this stage. This agrees well with the O 1s spectrum

shown in the same figure, which confirms that the hydroxyl and carbonyl peaks have vanished. We also note

that the C 1s peak shifts towards lower binding energy. The shift is attributed to desorption of second-layer

molecules after the first annealing step, which enhances core-hole screening for the surface monolayer.36

PE spectra of the fully deprotonated sample acquired at different angles and the corresponding normalized

intensities of –COO– and phenyl are shown in Figure 4. Comparison of the two trends reveals that the relative

8

intensity of –COO– signal is highest at angles close to surface normal and in contrast the phenyl signal is stronger

for the off-normal measurements. This implies that both –COO– groups are beneath the phenyl ring suggesting

that the molecule has re-oriented so that both –COO– groups coordinate to the surface. This implies a bipodal

configuration where two –COO– are facing the surface while the phenyl ring is tilted/perpendicular to the

surface.

Figure 4 Angular dependence of the apparent stoichiometry of fully deprotonated IPA collected at hυ=380 eV using four different angles with respect to the surface normal The intensity of carboxylate, carboxyl and phenyl peak has been normalized with respect to the total C 1s. Inset shows a schematic of the adsorption geometry.

Annealing up to 488 K induces decarboxylation of the molecule. Both the C 1s and O 1s spectra shown in Figure

2 confirm that the majority of molecules have lost their carboxylate groups.

NEXAFS

The adsorption geometry of the molecule on the surface was further studied using NEXAFS spectroscopy. Figure

5 shows the carbon K-edge and oxygen K-edge NEXAFS spectra for surfaces with partially and fully deprotonated

IPA, and for a surface with decarboxylated IPA. Comparing the spectra obtained with s-polarized (normal

incidence), p-polarized (glancing incidence at 20°) and magic-angle (55°) incidence light reveals the dichroism of

the π* resonance of aromatic ring and carboxylate/carboxylic acid groups, as shown in Figure 5. Consistent with

previous work on similar systems, we assign the two sharp peaks at 285 and 288 eV in the carbon spectra to the

π* resonance of the aromatic ring and carboxylate/carboxylic acid group in the molecule, respectively, and the

peaks at 532.7 and 535.3 eV in the oxygen spectrum to the π* resonance of the carboxylic/carboxylate groups.30-

31, 37 The wide peaks at 293 and 300 eV in the carbon spectrum originate from the * resonance of the aromatic

ring and carboxylic acid group, respectively, with the * resonance of the carboxylic/carboxylate group also

responsible for the broad feature starting at ~540 eV in the oxygen spectrum.

9

Figure 5 NEXAFS spectra collected (a) at the carbon K-edge for half-deprotonated, fully-deprotonated, and decarboxylated IPA on Cu(111) with s-polarized (normal incidence), magic angle (55° incidence) and p-polarized (glancing incidence, 20°), and (b) at the oxygen K-edge for the half- and fully-deprotonated samples using the same incident beam geometries.

10

We are able to characterize the adsorption geometry of the partially and fully deprotonated molecules by

creating synthetic (Gaussian) fits to the NEXAFS spectra obtained at different incident radiation angles,

considering the selection rules for the electric dipole transitions associated with photon absorption, and applying

the formalism laid out in the book by Stöhr for π* resonances.38 Plotted intensities are provided in the Figure

S3. This analysis reveals that the half-deprotonated molecules adsorb with their π* orbitals at 52°±3° with

respect to the surface normal, whereas the fully deprotonated molecules assume a less upright geometry ( =

46°±3°). In the half-deprotonated molecules the carboxyl/carboxylic group tilt matches the phenyl ring tilt ( =

51°±3°), but in the fully-deprotonated molecules the carboxylates are less upright than the ring ( = 33°±7°). The

oxygen K-edge provides redundant information for the carboxylic/carboxylate groups, and corroborates these

findings. For the decarboxylated molecule, the π* resonance at 289 eV has disappeared, and the average

inclination calculated from the phenyl-derived π* resonance is = 40°±3°. The oxygen K-edge data shown in

Figure 5b are similar to the carboxyl/carboxylic orientations obtained from the carbon K-edge data. The

extracted tilt angles are shown in Table 1.

Table 1: NEXAFS-derived tilt angles for the phenyl and carboxylic/carboxylate of IPA in different states of reaction. Angles

are averages, and specify the angle of the π* orbital with respect to the surface normal.

Reacted state of molecule

Carbon K-edge Oxygen K-edge

Phenyl ring (°) Carboxylic/carboxylate (°) Carboxylic/carboxylate (°)

Half-deprotonated 52±3 51±3 46±1

Deprotonated 46±3 33±7 40±1

Decarboxylated 40±3 - -

STM

Figure 6 shows STM images of IPA deposited on Cu(111) at RT. The as-deposited self-assembled IPA is hard to

scan, lacks lateral order, and the molecules cannot be imaged individually. The corresponding XP spectrum

reveals that 39% of the carboxylate groups are deprotonated at this stage (see Figure S1), which we speculate

as being due to a small amount of unreacted molecules in a second layer, on top of a layer of singly-deprotonated

molecules.

11

Figure 6 STM image of an IPA layer deposited onto Cu(111) at room temperature. Image parameters: U=-360 mV, I=0.3 nA, 72 nm × 72 nm.

After annealing the sample to 373 K for 5 minutes the molecules rearrange into small domains of chain-like lines

aligned with their long axes along , and ˂-1 -1 2˃, shown in Figure 7. XPS reveals that 48% of

the carboxylate groups are deprotonated, which we take as an indication that the second layer has been

desorbed and that the layer comprises only singly-deprotonated molecules in contact with the copper surface.

Angle-resolved PES (see previous) indicated that these mono-deprotonated molecules adsorb in an upright

orientation with the carboxylate group facing into the Cu(111) and the carboxyl group pointing up, i.e. molecules

anchor to Cu in a monopodal adsorption geometry via the carboxylate group. The intact carboxyl groups are free

to engage in hydrogen bonding with adjacent molecules, however, if present, this interaction may not be highly

stabilizing since scanning with the STM tip easily perturbs the structure (see Figure S4). Previously, a disturbance

caused by a tunnelling current of more than 30 pA has also been reported for IPA in a monodentate configuration

on Au(111).34 Although additional stabilization of the structure is provided via stacking of the tilted phenyl

rings, the structure of monopodal IPA on the surface is fragile, as the intact carboxyl group hinders molecule

from optimal adsorption on the surface.34

12

Figure 7 STM image of the IPA layer after annealing to 373 K, U=-470 mV, I=0.01 nA. The inset shows the tentative adsorption configuration of mono-deprotonated IPA superimposed on the high resolution STM of chains, 19.7 nm × 19.7 nm, inset: U=-760 mV, I=0.01 nA, 3.7×1.9 nm2.

A tentative model for the adsorption structure IPA at 373 K on Cu(111) is shown Figure 7. The carboxylate group

anchors to the surface via an adatom while the intact carboxylic group orients out of the surface and towards

neighboring molecules.

Annealing the sample to 433 K gives rise to a distinctly different pattern of striped structures. In Figure 8, the

STM image illustrates single-feature rows that are aligned in three domains, reflecting the symmetry of the

substrate. At domain boundaries between these striped regions, both amorphous and locally ordered structures

can be seen. Under different tip conditions (bias and/or tip termination), the single-row structure appears as a

double-stacked row. The periodicity measured perpendicular to the row direction is 0.93 ± 0.20 nm and

measurement along the row is 0.48 ± 0.10 nm. These values are in agreement with value of row and

intermolecular distances for IPA solution-deposited onto Cu/Au(111).39 In the proposed model for the

IPA/Cu/Au(111) system, IPA is anchored to the substrate via two carboxylate groups, leading to the formation

of a highly crystalline stripe-like arrangements of molecules. This is consistent with what we observed for

deprotonated IPA on Cu(111).

13

Figure 8 STM image of the fully-deprotonated IPA layer after annealing to 433 K. Image parameters: U=-1100 mV, I=0.2 nA, 49 nm × 49 nm. Inset: U=-1100 mV, I=0.1 nA. The inset is a tentative model.

After annealing at 513 K for 160 minutes, XPS showed that the molecule was fully decarboxylated (see Figure

S1). Figure 9 shows the overview and detailed STM images of the corresponding structures, which are disordered

and scattered on the surface. Small fragments of both zig zag and crinkled polymers, as well as the macrocycle

product, are observable in the STM image Figure 9. The diameter (distance between diametrically opposed

phenyl rings) of the macrocycle is found to be 0.75 ± 0.16 nm, which is consistent with the formation of a

covalent bond between phenyls and is in agreement with previous reported values4, 40 and with molecular

mechanics calculations of the pore diameter (see Figure S5). Inspection of the bonding geometries of the

macrocycles suggests that the molecule may have experienced some C-H bond scission, as threefold bonding

geometries are apparent in the images; activation at only the meta-sites would lead to isolated macrocycles, but

the observed macrocycles appear as substituents of extended oligomeric structures.

14

Figure 9 STM images showing the polymer resulting from IPA annealed at 513 K at different magnification, (a) U=-1100 mV, I=0.1 nA, 80.9×80.9 nm2, (b) U=-140 mV, I=0.2 nA, 22.6×22.6 nm2.

Discussion

PES reveals that IPA adsorbs partially deprotonated following deposition onto Cu(111) at RT. Carboxylated

molecules are known to partially/fully deprotonate on different facets of copper at RT,23, 27-28, 41 and our result is

consistent with these previous findings. From the angular and beam energy dependence of the C 1s core level

components we find that IPA adopts a monopodal upright adsorption geometry, wherein the molecule is bound

to the surface via the carboxylate group. This is in agreement with our expectations that the

deprotonation/decarboxylation reactions are metal-catalyzed, and consistent with a previous study that

revealed that proximity of the copper surface is required for the deprotonation of carboxylic acid.4 The carboxylic

groups in the molecules present in a second layer appear to be intact, as expected for -COOH not in contact with

the metal surface. Following desorption of the multilayer with annealing at 373 K, the ratio of the carboxyl and

carboxylate intensities becomes 1:1, and is accompanied by a 59% decrease of the phenyl intensity. The

integrated intensity of phenyl is only negligibly reduced following annealing to 488 K. This corroborates that the

multilayer desorbs after annealing at 373 K, leaving the monolayer IPA on the surface and suggests that only a

negligible amount of molecules desorb after annealing the surface-bound layer at higher temperatures.

At the monolayer molecular coverage presented here, the deprotonation of IPA’s two carboxylic groups occurs

in two steps: the first carboxyl group deprotonates upon adsorption of the IPA on the surface, whereas the

second group deprotonates only after annealing at 453 K, suggesting that the lack of proximity between the

second carboxylic group and the surface, which arises due to the molecular adsorption geometry, increases the

activation barrier for the second deprotonation. This second deprotonation event is associated with a change in

the adsorption configuration from monopodal to bipodal geometry. The NEXAFS spectra demonstrate that this

reorientation of the molecule does not significantly change the inclination of the molecule with respect to the

surface. As has been observed previously,30 the carboxylate groups maintain a slightly different orientation angle

15

with respect to the surface, likely to accommodate coordination to surface atoms. It should be noted that the

molecular coverage also has influence on the adsorption geometry, i.e., a flat adsorption geometry is generally

favorable at low coverages while more upright standing geometries are reported for high coverages.42-43 This

adsorption geometry in turn affects the deprotonation reactions - our PES data collected from a low-coverage

surface show that the molecule is fully deprotonated at 300 K (see Figure S7).

We attribute the chain-like structure of the monodeprotonated molecules to a motif in which one Cu adatom

sits between the carboxylate groups of four IPA molecules in each unit cell. A somewhat similar cloverleaf

structure has been observed for flat-laying 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA) on Cu(110), with

a bright protrusion at the center indicative of formation of coordinative bonds between four carboxylate ligands

and one Cu adatom [Cu(TMA)4]n-.41 Important differences arise in our study, since the molecules are oriented

upright with respect to the surface. The second deprotonation of the molecule creates a well-ordered, metal-

coordinated linear structure consistent with one observed previously.39

Decarboxylation of the IPA leads to covalent coupling of the molecules, but the resulting oligomeric structures

suffer from poor crystallinity and limited spatial expansion. NEXAFS spectra acquired on the decarboxylated

product indicate that the phenyl rings may be inclined with respect to the surface; since we expect the oligomer

product to adsorb relatively flat on the surface, we attribute this apparent non-planar adsorption to molecules

trapped at defects and step edges, which may account for a significant proportion of the retained molecular

product after high-temperature annealing and the accompanying desorption (c.f. the low signal to noise for the

NEXAFS scan of the decarboxylated sample in Figure 5a, which is consistent with low molecular coverage relative

to the previous annealing step.) Further optimization of the experimental conditions may lead to increased

spatial extent of the structures, but is unlikely to improve the crystallinity due to the number of polymorphs

allowed by the precursor molecule, and by the possibility for additional activation via dehydrogenation at C-H

bonds.44

Conclusions

We found that isophthalic acid mono-deprotonates upon adsorption on Cu(111) at room temperature. By

collecting PE spectra at different angles and also at different beam energies, we reveal the relative geometry of

carboxyl group, carboxylate group and the phenyl ring, and find that the molecule stands up via the surface-

bound carboxylate group upon adsorption. Annealing at 453 K causes full deprotonation of the molecule, which

re-orientates and anchors to the surface via both carboxylate groups. NEXAFS confirms that the molecule is

inclined from the surface in both mono-deprotonated and fully-deprotonated forms, and that the inclination

angle with respect to surface is larger for the monopodal configuration compared to the bipodal configuration.

STM demonstrates the structure of molecules at different steps of deprotonation. The tentative structural model

for mono-deprotonated molecules consists of four mono-deprotonated molecules anchor to the surface via

carboxylate group with one copper adatom siting between them.

16

Following annealing at 513 K, the molecule fully decarboxylates and forms C-C bonds that define oligomeric

structures on the surface. The results presented in this work add to our understanding of the important balance

between adsorbate-adsorbate and substrate-adsorbate interactions as a key factor in the defining the pathway

through which molecular reactions proceed on a surface. In this case, we find successive deprotonation steps

for the meta-configured carboxylic groups. This suggests that the number and relative geometry of the

carboxylic acid groups in a molecule will affect both adsorption and reactivity on surfaces, and should be

carefully considered in selecting molecules for on-surface materials design and synthesis.

Supporting Information

Beam energy dependence PES, additional XPS data, additional STM images and measurement of macrocycle

diameter.

Corresponding Author

*jennifer.macleod@qut.edu.au

Acknowledgment

This research was undertaken on the SXR beamline at the Australian Synchrotron, part of ANSTO. We

acknowledge the Australian Synchrotron for travel support and gratefully thank Bruce Cowie and Anton Tadich

for their assistance during experiments and useful discussions on NEXAFS measurements. Some data to support

this study were collected at the Central Analytical Research Facility (CARF) operated by the Institute for Future

Environments IFE at Queensland University of Technology (QUT). JMM acknowledges support from the

Australian Research Council (ARC) through DE170101170. JL-D acknowledges support from the ARC through

DP160103116.

References

1. Held, P. A.; Fuchs, H.; Studer, A., Covalent‐Bond Formation via On‐Surface Chemistry. Chem. Eur. J. 2017, 23 (25), 5874-5892. 2. Shen, Q.; Gao, H.-Y.; Fuchs, H., Frontiers of on-surface synthesis: From principles to applications. Nano Today 2017, 13, 77-96. 3. Gao, H.-Y.; Held, P. A.; Knor, M.; Mück-Lichtenfeld, C.; Neugebauer, J.; Studer, A.; Fuchs, H., Decarboxylative Polymerization of 2,6-Naphthalenedicarboxylic Acid at Surfaces. J. Am. Chem. Soc. 2014, 136 (27), 9658-9663. 4. Morchutt, C.; Björk, J.; Straßer, C.; Starke, U.; Gutzler, R.; Kern, K., Interplay of Chemical and Electronic Structure on the Single-Molecule Level in 2D Polymerization. ACS Nano 2016, 10 (12), 11511-11518. 5. Abyazisani, M.; Bradford, J.; Motta, N.; Lipton-Duffin, J.; MacLeod, J., Adsorption and Reactivity of Pyridine Dicarboxylic Acid on Cu (111). J. Phys. Chem. C 2018, 122 (31), 17836-17845. 6. Lackinger, M., Surface-Assisted Ullmann coupling. Chem. Commun. 2017, 53 (56), 7872-7885.

mailto:*jennifer.macleod@qut.edu.au

17

7. Schmitt, T.; Hammer, L.; Schneider, M. A., Evidence for On-Site Carboxylation in the Self-Assembly of 4, 4′-Biphenyl Dicarboxylic Acid on Cu (111). J. Phys. Chem. C 2016, 120 (2), 1043-1048. 8. Franke, M.; Marchini, F.; Zhang, L.; Tariq, Q.; Tsud, N.; Vorokhta, M.; Vondráček, M.; Prince, K.; Röckert, M.; Williams, F. J., Temperature-Dependent Reactions of Phthalic Acid on Ag (100). J. Phys. Chem. C 2015, 119 (41), 23580-23585. 9. Martin, D.; Cole, R.; Haq, S., Creating a functionalized surface: The adsorption of terephthalic acid onto Cu (110). Phys. Rev. B 2002, 66 (15), 155427. 10. Lee, J.; Dougherty, D. B.; Yates, J. T., Phenyl species formation and preferential hydrogen abstraction in the decomposition of chemisorbed benzoate on Cu (110). J. Phys. Chem. B 2006, 110 (20), 9939-9946. 11. Wühn, M.; Weckesser, J.; Wöll, C., Bonding and Orientational Ordering of Long-Chain Carboxylic Acids on Cu(111):  Investigations Using X-ray Absorption Spectroscopy. Langmuir 2001, 17 (24), 7605-7612. 12. Tait, S. L.; Lim, H.; Theertham, A.; Seidel, P., First layer compression and transition to standing second layer of terephthalic acid on Cu (100). Phys. Chem. Chem. Phys. 2012, 14 (22), 8217-8223. 13. Tekiel, A.; Prauzner-Bechcicki, J. S.; Godlewski, S.; Budzioch, J.; Szymonski, M., Self-assembly of terephthalic acid on rutile TiO2 (110): Toward chemically functionalized metal oxide surfaces. J. Phys. Chem. C 2008, 112 (33), 12606-12609. 14. Frederick, B.; Ashton, M.; Richardson, N.; Jones, T., Orientation and bonding of benzoic acid, phthalic anhydride and pyromellitic dianhydride on Cu (110). Surf. Sci. 1993, 292 (1-2), 33-46. 15. Pascal, M.; Lamont, C. L.; Kittel, M.; Hoeft, J. T.; Terborg, R.; Polcik, M.; Kang, J.; Toomes, R.; Woodruff, D. P., Quantitative structural determination of the high coverage phase of the benzoate species on Cu (1 1 0). Surf. Sci. 2001, 492 (3), 285-293. 16. Woodruff, D.; McConville, C.; Kilcoyne, A.; Lindner, T.; Somers, J.; Surman, M.; Paolucci, G.; Bradshaw, A., The structure of the formate species on copper surfaces: new photoelectron diffraction results and sexafs data reassessed. Surf. Sci. 1988, 201 (1-2), 228-244. 17. Frederick, B.; Leibsle, F.; Haq, S.; Richardson, N., Evolution of lateral order and molecular reorientation in the benzoate/Cu (110) system. Surf. Rev. Lett. 1996, 3 (04), 1523-1546. 18. Frederick, B.; Chen, Q.; Leibsle, F.; Lee, M.; Kitching, K.; Richardson, N., Long-range periodicity in c (8× 2) benzoate/Cu (110): a combined STM, LEED and HREELS study. Surf. Sci. 1997, 394 (1-3), 1-25. 19. Perry, C.; Haq, S.; Frederick, B.; Richardson, N., Face specificity and the role of metal adatoms in molecular reorientation at surfaces. Surf. Sci. 1998, 409 (3), 512-520. 20. Chen, Q.; Perry, C. C.; Frederick, B. G.; Murray, P. W.; Haq, S.; Richardson, N. V., Structural aspects of the low-temperature deprotonation of benzoic acid on Cu(110) surfaces. Surf. Sci. 2000, 446 (1), 63-75. 21. Lennartz, M. C.; Atodiresei, N.; Müller-Meskamp, L.; Karthäuser, S.; Waser, R.; Blügel, S., Cu-adatom-mediated bonding in close-packed benzoate/Cu (110)-systems. Langmuir 2008, 25 (2), 856-864. 22. Dmitriev, A.; Spillmann, H.; Stepanow, S.; Strunskus, T.; Wöll, C.; Seitsonen, A. P.; Lingenfelder, M.; Lin, N.; Barth, J. V.; Kern, K., Asymmetry Induction by Cooperative Intermolecular Hydrogen Bonds in Surface‐Anchored Layers of Achiral Molecules. ChemPhysChem 2006, 7 (10), 2197-2204. 23. Dmitriev, A.; Lin, N.; Weckesser, J.; Barth, J. V.; Kern, K., Supramolecular Assemblies of Trimesic Acid on a Cu(100) Surface. J. Phys. Chem. B 2002, 106 (27), 6907-6912. 24. Sandoval, T. E.; Bent, S. F., Adsorption of Multifunctional Organic Molecules at a Surface: First Step in Molecular Layer Deposition. 2013. 25. Fairley, N., CasaXPS Manual 2.3. 15: Introduction to XPS and AES. Casa Software: 2009.

18

26. Gann, E.; McNeill, C. R.; Tadich, A.; Cowie, B. C.; Thomsen, L., Quick AS NEXAFS Tool (QANT): a program for NEXAFS loading and analysis developed at the Australian Synchrotron. J. Synchrotron Radiat. 2016, 23 (1), 374-380. 27. Stepanow, S.; Strunskus, T.; Lingenfelder, M.; Dmitriev, A.; Spillmann, H.; Lin, N.; Barth, J. V.; Wöll, C.; Kern, K., Deprotonation-Driven Phase Transformations in Terephthalic Acid Self-Assembly on Cu(100). J. Phys. Chem. B 2004, 108 (50), 19392-19397. 28. Classen, T.; Lingenfelder, M.; Wang, Y.; Chopra, R.; Virojanadara, C.; Starke, U.; Costantini, G.; Fratesi, G.; Fabris, S.; de Gironcoli, S.; Baroni, S.; Haq, S.; Raval, R.; Kern, K., Hydrogen and Coordination Bonding Supramolecular Structures of Trimesic Acid on Cu(110). J. Phys. Chem. A 2007, 111 (49), 12589-12603. 29. Payer, D.; Comisso, A.; Dmitriev, A.; Strunskus, T.; Lin, N.; Wöll, C.; DeVita, A.; Barth, J. V.; Kern, K., Ionic Hydrogen Bonds Controlling Two‐Dimensional Supramolecular Systems at a Metal Surface. Chem. Eur. J. 2007, 13 (14), 3900-3906. 30. Shen, C.; Cebula, I.; Brown, C.; Zhao, J.; Zharnikov, M.; Buck, M., Structure of isophthalic acid based monolayers and its relation to the initial stages of growth of metal–organic coordination layers. Chem. Sci. 2012, 3 (6), 1858-1865. 31. Cebula, I.; Lu, H.; Zharnikov, M.; Buck, M., Monolayers of trimesic and isophthalic acid on Cu and Ag: the influence of coordination strength on adsorption geometry. Chem. Sci. 2013, 4 (12), 4455-4464. 32. Poon, H.; Tong, S., Focusing and diffraction effects in angle-resolved x-ray photoelectron spectroscopy. Phys. Rev. B 1984, 30 (10), 6211. 33. Smith, N.; Farrell, H.; Traum, M.; Woodruff, D.; Norman, D.; Woolfson, M.; Holland, B., Photoelectron diffraction effects in core-level photoemission from Na and Te atoms adsorbed on Ni (001). Phys. Rev. B 1980, 21 (8), 3119. 34. Li, Z.; Wandlowski, T., Structure Formation and Annealing of Isophthalic Acid at the Electrochemical Au (111)− Electrolyte Interface. J. Phys. Chem. C 2009, 113 (18), 7821-7825. 35. Han, B.; Li, Z.; Wandlowski, T., Adsorption and self-assembly of aromatic carboxylic acids on Au/electrolyte interfaces. Anal. Bioanal. Che 2007, 388 (1), 121-129. 36. Tait, S. L.; Wang, Y.; Costantini, G.; Lin, N.; Baraldi, A.; Esch, F.; Petaccia, L.; Lizzit, S.; Kern, K., Metal− organic coordination interactions in Fe− terephthalic acid networks on Cu (100). J. Am. Chem. Soc. 2008, 130 (6), 2108-2113. 37. Zhang, W.; Nefedov, A.; Naboka, M.; Cao, L.; Wöll, C., Molecular orientation of terephthalic acid assembly on epitaxial graphene: NEXAFS and XPS study. Phys. Chem. Chem. Phys. 2012, 14 (29), 10125-10131. 38. Stöhr, J., NEXAFS spectroscopy. Springer Science & Business Media: 2013; Vol. 25. 39. Cebula, I.; Shen, C.; Buck, M., Isophthalic acid: a basis for highly ordered monolayers. Angew. Chem. 2010, 49 (35), 6220-6223. 40. Bieri, M.; Treier, M.; Cai, J.; Aït-Mansour, K.; Ruffieux, P.; Gröning, O.; Gröning, P.; Kastler, M.; Rieger, R.; Feng, X., Porous graphenes: two-dimensional polymer synthesis with atomic precision. Chem. Commun. 2009, (45), 6919-6921. 41. Lin, N.; Dmitriev, A.; Weckesser, J.; Barth, J. V.; Kern, K., Real-Time Single-Molecule Imaging of the Formation and Dynamics of Coordination Compounds. Angew. Chem. 2002, 41 (24), 4779-4783. 42. Lee, A. F.; Wilson, K.; Lambert, R. M.; Goldoni, A.; Baraldi, A.; Paolucci, G., On the coverage-dependent adsorption geometry of benzene adsorbed on Pd {111}: a study by fast XPS and NEXAFS. J. Phys. Chem. B 2000, 104 (49), 11729-11733. 43. Bader, M.; Haase, J.; Frank, K.-H.; Puschmann, A.; Otto, A., Orientational phase transition in the system pyridine/Ag (111): A near-edge x-ray-absorption fine-structure study. Phys. Rev. Lett. 1986, 56 (18), 1921.

19

44. Li, Q.; Yang, B.; Björk, J.; Zhong, Q.; Ju, H.; Zhang, J.; Cao, N.; Shi, Z.; Zhang, H.; Ebeling, D.; Schirmeisen, A.; Zhu, J.; Chi, L., Hierarchical Dehydrogenation Reactions on a Copper Surface. J. Am. Chem. Soc. 2018, 140 (19), 6076-6082.