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Coverage Induced Conformational Selectivity Konrad Boom, Friederike Stein, Steffen Ernst, and Karina Morgenstern J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b04986 • Publication Date (Web): 04 Aug 2017 Downloaded from http://pubs.acs.org on August 7, 2017

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The Journal of Physical Chemistry

Coverage Induced Conformational Selectivity Konrad Boom, b Friederike Stein, b Steffen Ernst, c and Karina Morgenstern*a [a] Lehrstuhl für physikalische Chemie, Ruhr-Universität Bochum, Universitätsstr. 150, D-44801 Bochum, Germany [b] ATMOS, Leibniz Universität Hannover, Appelstr. 2, D-30167 Hannover, Germany [c] Ortsteil Wolfen, FEW Chemicals GmbH, Technikumstr. 1, D-06766 Bitterfeld-Wolfen, Germany

Supporting Information Placeholder ABSTRACT: Different conformations of organic molecules are often almost isoenergetic, giving rise to their coexistence at finite temperature. In the gas phase, pressure was used to shift the equilibrium towards desired conformers. Here we use lateral pressure, enforced by increased coverage, to change the relative abundance of conformers of astraphloxin, an industrial dye, on Ag(100). We show in a variable temperature scanning tunnelling microscopy study that higher coverages enforce the predominance of one conformer, only, leading to a homo-conformational superstructure. The necessary conformational changes are possible at temperatures as low as 120 K.

I. Introduction Molecular conformation is an important property in chemistry, in particular of the organic solid state. When conformers differ by only small energy differences, separation by purely energetic means (e.g. by a change in temperature) is often arduous.1 Under such circumstances, pressure provided an elegant and efficient means for stabilizing high-energy conformers. Generally, pressure affects the chemical equilibrium. Le Châtelier's principle predicts that the application of pressure shifts a chemical equilibrium towards the side that occupies a smaller volume than the ground state. In particular, stereoisomers are such energetically (almost) degenerate and coexisting conformers. For instance, organic molecules with flexible torsion are discussed extensively with respect to formation and stability of polymorphism they cause in organic crystals.2 As the conformers exhibit different physico-chemical properties, homo-conformational aggregates with defined properties are desirable. Conventionally, molecular conformation is determined in single-crystal X-ray crystallography or NMR spectroscopy, which both average over a large number of molecules. The determination of local molecular conformation in smaller two-dimensional molecular aggregates is possible by scanning tunneling microscopy (STM),3-8 and is often related to a change in apparent height.9-11 While tip-enforced conformational changes have been reported frequently,4,12 only a few direct STM observations of natural conformational changes exist so far. At room temperature, individual phenylene ethynylene oligomers within self-assembled monolayers showed stochastic conformational changes, whose frequency was influenced by the density of the surrounding matrix.13 In a STM study at ambient conditions, the collective con-

formational change of dendritic wedge functionalized ligands within small domains was triggered by exposure to HCl.8 What remains to be explored is the influence of lateral pressure on the conformation of adsorbed molecules. Previous work suggests that conformational changes should be possible on metal surfaces at room temperature and below. The chirality of a linear molecule functionalized at its end by an aldehyde, a hydroxyl and a bulky t-butyl group changed thermally between its enantiomers at room temperature, despite the high energy usually needed to lift part of a molecule from the surface.14 An molecule bond was rotated15 as well as the chirality changed16,17 in a controlled manner at cryogenic temperature using the manipulation capabilities of STM.12 However, this approach is neither directed nor scalable to larger numbers of molecules. In this article, we use lateral pressure as built up by molecule density to tune the relative abundance of two conformers for a rather flexible molecule, astrophloxin, a cyanine dye. We investigate adsorption of this molecule on Ag(100) at two temperatures. At the lower adsorption temperature of 180 K diffusion is largely suppressed allowing to image individual molecules. At low coverage, such individual molecules represent one of the conformers. Molecules of this conformation repel each other. At intermediate coverage, dimers, trimers, and predominately tetramers form. The molecules within these oligomers are of the other conformation. At the higher adsorption temperature of 240 K, single molecules are mobile facilitating the formation of a highly ordered superstructure. While at coverages slightly below one monolayer coverage some molecules of the repulsive conformer still exist, the closure of the layer leads to a selection of the attractive conformer, only. We thus demonstrate that the relative abundance of the conformers depends on coverage. II. Experimental Section STM measurements are performed with a variable-temperature scanning tunneling microscope (STM) under ultra-high vacuum (UHV) conditions (base pressure below 4 ⋅ 10-10 mbar). The Ag(100) surface is cleaned by repeated cycles of Ar+-sputtering (6 µA, 1.3 keV) and annealing at 935 K. The annealing times are 45 min and 4 min in the first and second cycle, respectively, for the sputtering and 30 min and 2 min, respectively. After sample cleaning, the sample is cooled to the deposition temperature of either 180 K or 240 K.

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Astraphloxin is a crystalline salt with a melting temperature of (553 ± 5) K and a phase transition at (480 ± 5) K. A purity of 99.9 % is determined by high performance liquid chromatography. The pink powder is filled into a glass tube, which is connected via a leak valve to the UHV chamber. An aluminum foil protects the molecule from light. The glass tube is annealed by means of a heating band wrapped around it. For cleaning, the vapor above the molecules is pumped for some days, while keeping the tube at 433 K, i.e. well below their transition temperature. The cleanliness of the deposit is monitored during cleaning by quadrupole mass spectrometry of the vapor above the salt. The largest impurity is water. Consequently, we aim for a reduction of the water peak at mass 18 as compared to the molecule fragment at mass 50 during the cleaning procedure. Note that the molecule dissociation occurs at the hot filament of the mass spectrometer, only, which is switched off during deposition. Ex-situ NMR spectroscopy of the remaining powder confirms that the molecules in the powder did not degenerate during this cleaning procedure or the deposition procedure described below.

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Cyanine dyes consist of two hydrocarbon end groups. The nitrogen atoms within the end groups are connected via a methine chain.18 Today, cyanine dyes are used on an industrial level, e.g. on DVD master disks. The cyanine dye used, 2-[3-(1,3-dihydro1,3,3-trimethyl-2H-indol-2-ylidene)-propenyl]-1,3,3-trimethyl3H-indolium chloride, is commonly named astraphloxin (Fig. 1). It consists of two indole groups that are connected via a methine chain of three carbon atoms (Fig. 1a). Because of steric repulsion between the di-methyl groups, all conformations of the all-transisomer (Fig. 1b) are energetically unfavorable with respect to the 10-cis-isomer as revealed in semi-empirical gas phase calculations.11 There exist three different conformers of the 10-cis-isomer in gas phase (Fig. 1c-e). Recently, we investigated astraphloxin on Au(111) and Ag(111) at low coverage. 11 The stereoisomers were named in dependence of the relative orientations of the indole groups; 'll', 'dl', or 'dd' for the two di-methyl groups on the same (ll or dd) or opposite sides (dl or ld) of the methine chain, respectively. 11 High-resolution imaging at 5 K revealed the existence of only two conformers, dd and dl, on Au(111) and Ag(111) (Fig. 1d,e). Both isomers are imaged as an ellipsoidal protrusion by a metallic STM tip.

For deposition, the glass tube temperature is adjusted to achieve a vapor pressure of (2.4 ± 0.2) ⋅ 10-7 mbar in a separately pumped chamber, which is connected to the main chamber via a gatethrough valve. Note that this pressure is measured close to the powder. Because of the large distance of the source to the sample, the pressure is considerably lower at the sample. Precise final coverages are thus deduced from STM images. Molecules are deposited at a deposition rate of (5.5 ± 0.5) ⋅ 10-2 ML/s for up to 20 min. The substrate is quenched to approx. 110 K immediately after deposition. Measurements are performed between this temperature and 140 K, as given in the Figure captions. Tunneling parameters are between -1 and -3.5 V and between 0.3 and 0.6 nA. III. Results and Discussion

Figure 2. Astraphloxin on Ag(100) adsorbed at 180 K (a-e) at terraces with increasing coverage; numbers in (b) mark number of molecules in cluster (f) clusters: upper image: rhomboidal tetramer; lower image: pentamer (g,h) line scans as indicated in (b,c) (i,j) at step edges; measurement temperature: (a) 127 K (b) 131 K (c) -2.41 V, 0.28 nA, 115 K (d) 123 K (e) 120 K (f) upper image: 128 K; lower image: 125 K (i) 105 K (j) 120 K. In order to identify different conformers and their interaction, we first deposit the molecules at a temperature, at which isolated molecules exist. This is the case at 180 K. The protrusions on the terraces are of similar shape as on Ag(111) and Au(111) (Fig. 2a) and are thus attributed to single molecules. These molecules agglomerate to small clusters at slightly higher coverage (Fig. 2b,c). Eventually, the layer closes, but no long range order is observed (Fig. 2d,e). Usually, such a growth behavior is interpreted as resulting from the hit-and-stick mechanism, where the particles stay at or close to their point of impact to the surface.20 However, even at the smallest coverage, step edges are decorated by a row of molecules (Fig. 2i,j). Thus, the molecules are mobile at 180 K. The existence of isolated molecules on terraces (Fig. 2j) thus implies that the molecules do not show an attractive interac-

Figure 1. Astraphloxin: (a) Molecule model (b) Side view of trans-isomer calculated semi-empirically in gas phase;19 C in black, H in white, N in blue (c-e) Side view of stereoisomers of 10-cis-astrophloxin; for naming on bottom side see text.

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tion, neither between each other on the terrace nor with the molecules that decorate the step edges.

remain in the layer (Fig. 3c,d). These holes are surrounded by individual protrusions of similar size as the individual molecules at lower coverage (cf. Fig. 2).

On the other hand, we observe small clusters of molecules largely before the layer closes (Fig. 2b and c). In particular, rhombical tetramers are preferred, though all clusters up to pentamers are regularly observed (Fig. 2f) pointing to an attractive interaction between the molecules. These two observations would contradict each other, unless there were two different species present on the surface. Indeed, the apparent height of molecules within the clusters are smaller than the one of isolated molecules (Fig. 2g,h). The apparent height difference in the case shown is at -2.4 V approximately 70 pm. Note that the apparent heights differ in the voltage range probed, but for all voltages there is clearly observable apparent height difference between approx. 50 pm at -1.8 V and approx. 100 pm at 3 V. On Au(111) and Ag(111), we showed that astraphloxin molecules of different apparent heights represent different conformers.11 As one of the indole groups adsorbs parallel to the surface, the different apparent heights reflect the different geometrical heights of the two conformers (cf. Fig. 1d to e). Thus, protrusions of larger apparent height are dl-isomers and those of smaller apparent height are dd-isomer. The observation here thus suggests that less high dd-isomers cluster, but the higher dd-isomers do not. For agglomeration of oligomers consisting of more than two molecules, we suggest an edge-to-face interaction, which has been found to be the true ground state for a benzene dimer through π-interaction in gas phase.21 Thus, both the tetramer and the pentamer in Fig. 2f should be considered as ring-like structures. Further support for this information results from a structural model for a closed monolayer (see below).

Figure 4: Agglomerations of dl-isomers (brighter protrusions) within dd-superstructure after adsorption of astraphloxin on Ag(100) at 240 K; tunneling parameters: (a,b) 3.37 V, 0.21 nA, 119 K (c) 3.37 V, 0.13 nA, 119 K (d) 2.84 V, 0.48 nA, 118 K (e) 2.84 V, 0.48 nA, 118 K (f,g) 2.1 V, 0.25 nA, 123 K. Fig. 4a to g demonstrate the large variety of forms and sizes of the structures. Extended holes as those in Fig. 3c,d of around 2 nm in diameter allow determining the apparent height of the molecule layer as 230 pm at around -2 V. This value corresponds to the height of the clusters of molecules observed after low temperature adsorption (cf. Fig. 2g,h). The height of the protrusions directly surrounding the hole is by 50 to 80 pm larger (Fig. 3e,f). The difference in apparent height is comparable to the difference between the isomers of different height identified after low temperature adsorption.11 We conclude that the terraces are covered by a closed-packed layer of the less high dd-isomer and that higher dl-isomers form the border of the hole, by this avoiding contact to other molecules as far as possible at the crowded situation. The large abundance of the less high dd-isomer suggests a conformational change upon layer formation at 240 K. Even at 120 K such a conformational change can be observed (Fig. 3g-j). Not only does the shape of the holes change on the timescale of tens of seconds, but also the number of higher dl-isomers. In Fig. 3g, the dl-isomers form a rectangle. The number of dl-isomers has changed by one after 15 s at 117 K (Fig. 3h); accompanied by a change in position and shape of the hole. In Fig. 3i, the higher dlisomers surround an irregular hole. This structure has changed to a more regular arrangement after 43 s in Fig. 3j, thereby reducing the number of dl-isomers. These observations confirm that isomerization between the two isomers is possible during layer formation.

Figure 3. Astraphloxin on Ag(100) adsorbed at 240 K at a coverage of 0.95 ML: (a-d) STM images (e,f) line scans along lines shown in panels (c,d). (g,h) same region imaged 15 s apart (i,j) same region imaged 43 s apart; (a) 125 K (b) 136 K (c) 128 K (d) 119 K (g) 117 K (h) 117 K (i) 119 K (j) 119 K. After having identified the two conformers, we now explore qualitatively, whether lateral pressure shifts the equilibrium between the two. For observing a pressure effect, the molecules should fill the first layer before occupying the second one. This is the case at 240 K. At the higher deposition temperature, the step edges are likewise decorated by molecules, but the terraces seem to be bare (Fig. 3a). However, a closer look reveals a depression next to the molecules at the step edges (Fig. 3b), indicating mobile molecules on the terrace.22

Figure 5. Complete monolayer of astraphloxin on Ag(100) adsorbed at 240 K in molecular resolution: (a) 129 K, inset: fastFourier transform of superstructure (b) 132 K, single and double defect are marked by an arrow each; inset: triple defect, 3.59 V, 0.32 nA, 130 K.

At higher coverage, unperturbed imaging of a seemingly flat surface is impossible. On each image stripes are visible (e.g. Fig. 3c,d), interpreted as mobile molecules on top of an almost closed monolayer. Despite this availability of molecules some holes

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At the same temperature of 240 K at which holes are observed, the higher dl-isomer disappears completely at full monolayer coverage (Fig. 5a). We prove that the closed-packed layer consists of a regular arrangement of molecules by imaging at reduced tipsample distance (higher voltages and lower current). The structure of the monolayer is crystalline with an oblique superstructure with an angle of (76 ± 3)° and a unit cell of (0.86 ± 0.05) nm by (1.00 ± 0.03) nm (Fig. 5a). The structure is thus not commensurate with the surface, suggesting a predominance of intermolecular interaction in structure formation.

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above for clusters upon low temperature adsorption. The largest extent of the dd-confomer in parallel to the surface in is 0.92 nm; the methyl groups perpendicular to this direction have a distance of 0.6 nm in gas phase. The dd-isomer thus fits nicely into the determined unit cell (Fig. 6d). IV. Conclusion In conclusion, we show that the abundance of different astraphloxin conformers depends on coverage and relate this observation qualitatively to local pressures. The lateral pressure forces isomerisation to the dd-isomer even below room temperature. Our study opens up the possibility to produce homo-conformational superstructures, not only of the investigated dye. Transferability to other surfaces is likely as the superstructure is not commensurate and thus the effect should not depend on the specific surface investigated. AUTHOR INFORMATION

Corresponding Author K. Morgenstern Physical Chemistry I Ruhr-Universität Bochum Universitätsstr. 150 D-44803 Bochum Germany phone: +49-234-322552 karina.morgenstern @rub.de

Figure 6. Superstructure of dd-isomers of astraphloxin on Ag(100) after adsorption at 240 K imaged with different tips (a) imaged with metallic tip, 0.33 nA, -3.02 V, 127 K (b,c) Tip change of superstructure by transient voltage increase at indicated row: (b) 0.32 nA, -3.02 V, 130 K (c) 0.31 nA, -2.84 V, 118 K (d) zoom-in into structure as after such a tip change in (b) with two ball-and-stick models superimposed, 0.35 nA, -2.84 V, 117 K (e) zoom-in into structure as after tip change in (c) 0.35 nA, -2.84 V, 119 K.

Notes The authors declare no competing financial interests. ACKNOWLEDGMENT This research has been supported by the German Science Foundation (DFG) via the Cluster of Excellence RESOLV (EXC 1069).

The superstructure consists of slightly ellipsoidal protrusions, if imaged by a metallic tip, consistent with regular imaging of single molecules at low coverage (cf. Fig. 6a). Occasional tip changes give further information about the bonding within the superstructure. The enhancement of STM resolution using a so-called modified tip for imaging is well-established.23,24 Such a tip enhances the resolution due to molecules transferred to the tip. Here, the tip change is induced by an increase in voltage while scanning the line marked in Fig. 6b,c. Such an increase in voltage corresponds to a physical approach of the tip to the sample. By this procedure we pick up one of the molecules that are mobile on top of the superstructure. Different changes to the image are induced by this process (compare Fig. 6b to c). Sometimes, we observe a chess board pattern (Fig. 6e). This simply corresponds to a contrast inversion. However, most often, the modified image leads to a row pattern (Fig. 6b). The lines from a zig-zag pattern (Fig. 6d). The zig-zag pattern follows the rows of protrusions (Fig. 6b) and its continuation allows identifying the position of single molecules (Fig. 6b).

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Defects of the size of one (Fig. 5b), two (Fig. 5b), and three (Fig. 5b, inset) protrusions suggest that each protrusion in the superstructure corresponds to a single molecule (Fig. 5b). The similarity to earlier imaging of the same molecule by a modified tip11 allows us to propose the model as shown in Fig. 6d consistent with the edge-to-face interaction of the aromatic system suggested

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Coverage-Induced Conformational Selectivity - The Journal of

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