Ag(111): a

Subscriber access provided by UNIVERSITY OF TOLEDO LIBRARIES

Article

Adsorption of Terarylenes on Ag(111) and NaCl(001)/Ag(111): a Scanning Tunneling Microscopy and Density Functional Theory Study Jan Patrick Dela Cruz Calupitan, Olivier Guillermet, Olivier Galangau, Mayssa Yengui, Jorge Echeverría, Xavier Bouju, Takuya Nakashima, Gwénaël Rapenne, Roland Coratger, and Tsuyoshi Kawai J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b11122 • Publication Date (Web): 05 Feb 2018 Downloaded from http://pubs.acs.org on February 6, 2018

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

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

Page 1 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

Adsorption of Terarylenes on Ag(111) and NaCl(001)/Ag(111): a Scanning Tunneling Microscopy and Density Functional Theory Study Jan Patrick Dela Cruz Calupitan,†,‡,§ Olivier Guillermet,§ Olivier Galangau, †,‡ Mayssa Yengui, § Jorge Echeverría,# Xavier Bouju,§ Takuya Nakashima,‡ Gwénaël Rapenne,*,†,§ Roland Coratger,*§ and Tsuyoshi Kawai*,†,‡ †

NAIST-CEMES International Collaborative Laboratory, 29 rue Jeanne Marvig, 31055

Toulouse, France #

Departament de Química Inorgànica i Orgànica & Institut de Química Teòrica i Computacional

IQTC-UB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain ‡

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5

Takayama, Ikoma, Nara, Japan §

CEMES, Université de Toulouse, CNRS, Toulouse, France

ABSTRACT

Photoswitching materials are building blocks of next generation optoelectronic devices which may require molecule deposition on a solid substrate. However, molecule properties change upon

ACS Paragon Plus Environment

1

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

Page 2 of 61

adsorption due to surface-molecule interactions and symmetry considerations. Scanning tunneling microscopy (STM) and density functional theory (DFT) offer techniques to address interactions of functional molecules down to the single-molecular level on solid substrates. In this paper, we present a combined STM and DFT study of a tert-butyl functionalized terarylene molecule on Ag(111) and NaCl(001)/Ag(111) at ~5 K. Tert-butyl groups aided in identifying three conformations of the compound upon adsorption on the surface. DFT calculations showed that two of these conformations refer to different adsorption geometries of the trans conformation in the gas phase. The other was assigned to the non-reactive cis conformation. For the first time, this conformation was isolated and imaged at the single-molecular level. Calculations further showed that aside from the electronic structure of the molecule, methyl groups sticking out of the surface are the origin of bright spots observed on the STM. On NaCl(001)/Ag(111), only the trans conformation was found and the mapping of occupied and unoccupied states of terarylenes was accomplished for the first time.

Introduction Photo-responsive molecular materials are at the forefront of the search for next-generation molecular opto-electronic devices.1-2 The power of these devices which require immobilization on a solid surface are due to miniaturization down to the molecular level.3-5 Even if many candidate molecules are well-understood in bulk 3D phases (i.e. in crystalline/amorphous solids or when dissolved in a liquid solution), excellent performance and reliability will require an accurate control and elucidation of molecular properties on a solid 2D-surface.6-7 Indeed,


2

Page 3 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


adsorption may lead to new phenomena such as induction of chirality due to the suppression of some symmetry elements.7-9 Due to this promise in molecular electronics applications, photo-responsive materials have been the subject of scanning tunneling microscopy (STM) studies in recent years.10-12 STM is based on vacuum tunneling of electrons13 that has the capability not only to probe surfaces in real space14 but also to manipulate molecules15 and atoms16 at the nanoscale. The high resolution makes it possible to study the electronic properties of species at the atomic scale. Further, the STM tip can also provide an additional stimulus for changing the molecular state by using tunneling electrons or the electric field between tip and surface. Such a controlled manipulation allows, for example, to reversibly isomerize, change the bonds/charges/dipoles, flip the chirality, or switch the conductance of these photoactive molecules.10-12 For example, azobenzene has been well-studied not only as a photoswitch in the solid state or in solution but on 2D surfaces by STM as well. It has been shown that these molecules can be switched by light, tunneling electrons, or localized electric field when deposited on a solid surface so that from a fundamental point of view, these studies also provided insights on the well-known cis-trans isomerization of the compound.10-12, 17-20 However, the thermal instability at room temperature of the cis isomer of azobenzene makes it less than ideal for the given applications.19-20 The simple geometric flipping of phenyl rings around the N=N bond upon cistrans isomerization generates two conformations different enough to make their identification under the STM17-20 rather trivial. The high degree of symmetry around the N=N bond and the small difference in electronic structure of the two isomers also makes these model systems rather simple.


3


Page 4 of 61

Diarylethenes may present alternatives for these applications because of the stability of their two isomers having immensely different electronic structures. These molecules switch between their open and closed isomers referring to the open hexatriene and closed cyclohexadiene moieties in the center of the molecule upon exposure to appropriate wavelengths of light with high sensitivities and excellent fatigue resitance.21-22 In fact, fluorescence switching at the singlemolecular level of a diarylethene derivative was first observed by fluorescence microscopy.23 The huge difference in π-conjugation connection between open and closed forms has motivated conductance switching experiments using these molecules.24-25 These studies cemented their promise for next generation molecular electronics and memories as it was shown that they could be addressed, i.e. “written” and “read”, at the single-molecular level. Modification of central ethenyl units of diarylethene to become part of an aromatic ring, so that there are three aromatics contributing one double bond each to the hexatriene moiety (dubbed as terarylenes), could further expand the variety of these molecules in terms of symmetry breaking, fine-tuning of properties, and incorporation of more advanced functions.26-34 Due to this extra aromatic ring, terarylenes that display photon-quantitative reactions,27 oxidative chain cycloreversion,28-29 fluorescence and luminescence switching,30-31 control of electron delocalization,32 and photorelease of organic fragments33-34 have been developed. These new phenomena promise access to new advanced functions which could be incorporated to nextgeneration molecular electronics whilst preserving the well-known open-closed isomerization of diarylethenes. Even if significant advances were made with STM studies on diarylethenes containing perfluorocyclopentene or perhydrocyclopentene in their central hexatriene structure35-47, it is imperative that the effect of the extra aromatic ring in terarylenes once deposited on a surface be


4

Page 5 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


observed by STM as well. In fact, most studies in the solid-liquid interface that elucidated their molecule-molecule and surface-molecule interactions utilized the non-functional perfluoro head on top of the photochromic core which usually do not interact with the surface in a way that would show contrast in the STM images.35-42 Additionally, a terarylene derivative having 2phenylthiophene moieties instead of perfluorocyclopentene was able to develop switching involving four states beyond the usual photochromic switching of the compound.48 Under ultrahigh vacuum (UHV), the strong dipole of the perfluorocyclopentene group was shown to promote assembly formation43-46 but the electronic switching remained mainly dependent on the rearrangement around the aromatic rings. Self-assembled monolayers of terarylene under ambient conditions have already been studied by STM49-50 and we recently reported on assemblies of a terarylene derivative formed by alignment of molecules along the electric field between the tip and the surface.51 The central aromatic rings certainly played a role in contributing to (1) the dipole moment that allowed for the alignment along the field and (2) the π-π stacking that were the main intermolecular forces that stabilized the assemblies.51 Nevertheless, as the 2D solid surface could induce new phenomena previously unobserved in solution or in the solid state,6-12 breakthroughs were uncovered such as chiral resolution of the closed forms,37 inelastic electron induced switching that goes through thermal routes,44 and reversal of stabilities of open and closed isomers on the metallic surface.47 Even then, the complexity afforded by diarylethenes over azobenzene due to the former’s larger and dissymmetric molecular structure and the higher number of degrees of freedom makes these systems challenging; the small difference between the geometry of the open and closed forms4344

also makes their identification by STM under UHV difficult.


5


Page 6 of 61

In this study, we report on a combined STM and DFT study of 2,3-bis[2-(3,5-di-tertbutylphenyl)-5-methylthiazol-4-yl]benzothiophene, a specifically designed terarylene having a benzothiophene and two thiazole moieties in its central switching unit and four peripheral tertbutyl groups (tBDTB hereafter, Scheme 1). The benzothiophene moiety is known to present a sulfur heteroatom and an aryl hydrogen atom against the side thiazole rings for effective S-N and N-H bonding interactions that lock the molecule in its reactive conformation leading to photonquantitative yields upon photoreaction.27 (Scheme 1) The benzothiophene ring is also expected to break the symmetry that is present in diarylethenes with perfluorocyclopentene rings. Meanwhile, the tert-butyl moieties play the role of contrast enhancers for the STM identification of the molecule, prevent aggregation, and raise the switching backbone from the metallic surface.52-54 For the first time, the molecule was studied on Ag(111) to elucidate its surface conformation and on an insulating NaCl(001) bilayer deposited on Ag(111) that allowed for the mapping of occupied and unoccupied states. In order to check for the effect of tert-butyl groups, we

compared

with

an

analogous

compound,

2,3-bis(5-methyl-2-phenylthiazol-4-

yl)benzothiophene, (DTB hereafter, Scheme 1) that does not display such groups.

Scheme 1. Photon-quantitative isomerization reactions of DTB and its derivative tBDTB.


6

Page 7 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


STM imaging showed that the tert-butyl groups did improve the contrast of the molecule. This allowed for identifying three conformations of the compound on the surface. Two of such conformations were assigned to adsorption geometries of tBDTB with the aid of DFT and Elastic Scattering Quantum Chemistry (ESQC) calculations. The other remaining conformation was assigned to a non-reactive rotational isomer of tBDTB. This showed that despite the strong intramolecular forces of attraction that keep the molecule in one conformation, the relatively high temperature of deposition conditions (typically 200 oC) allowed the molecule to adopt other rotational conformers. This was the first isolation and single imaging of this rotational conformer under ultra-high vacuum conditions. These results were important as the rotational equilibrium between these conformers influences photoswitching properties in solution.21-22 With these calculations we also rationalize the origin of the bright contrast as due to the methyl groups of the tert-butyl moiety that stick out of the surface. Imaging on the NaCl(001)/Ag(111) also allowed mapping of occupied and unoccupied states of the compound.

Methods DTB and tBDTB were synthesized as previously reported and all characterizations agreed well with literature.55 STM imaging was performed with an Omicron Low-Temperature Ultra-High Vacuum System working with a base pressure of 1.5 × 10-11 mbar. The Ag(111) crystal was prepared by repeating cycles of sputtering with Ar+ ions and subsequent annealing at 750 K. For imaging experiments on insulating bilayers of NaCl(001), NaCl (Sigma Aldrich, reagent grade) was evaporated onto the metallic substrate held at room temperature until a 20 % monolayer coverage was achieved as monitored by a quartz crystal microbalance. This value corresponds to


7


Page 8 of 61

an average over the whole silver surface. The local coverage on typical areas of a few tens of square nanometers can be slightly different. These bilayers have a perfect crystallographic structure and the STM images with atomic resolution show the well-known squared lattice of Cl atoms.56 In addition, the I(V) spectra on the NaCl layer present the characteristic interface state about 90 meV above the Fermi level.57 The tips were prepared by electrochemical etching of a W wire 0.2 mm in diameter. The tip was then cleaned by direct current heating on a clean Ag(111) surface until the surface state of Ag(111) was observed and images showed molecular resolution without any multiple tip effect. The molecules were then evaporated from a Knudsen cell directly onto the substrate held at liquid helium temperature. All images were taken at 4.5 K at constant current mode. STS were performed by pointing the STM tip on top of the molecule center, turning off the feedback-loop system, recording the tunneling current while scanning over the bias interval at typically 0.1 V/s. All bias voltages reported refer to the surface relative to the tip. DFT calculations for the optimal geometry of the molecules in the gas phase were first accomplished using Gaussian 0958 with the method B3LYP and basis set 6-31G(d,p). Optimized geometries were characterized as true minima of the corresponding potential energy surfaces by frequency analysis; calculation of IR spectra showed no negative vibrations. The reactive antiparallel conformation was used as input structure. Then, time-dependent DFT calculations were carried out and the HOMO and LUMO maps in the gas phase were generated. Periodic DFT calculations were then performed using numeric atom-centered basis sets allelectron software FHI-aims.59-60 We used the PBE exchange-correlation functional with inclusion of van der Waals interactions via the Tkatchenko-Scheer procedure.61

Geometry


8

Page 9 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


optimizations were carried out until forces were smaller than 10-4 eV Å-1. A set of radial functions was used to describe atoms. Each basis set consists of the core and valence radial functions of a spherical free atom extended with extra groups of functions (Ag = [Kr]+5s4d+pfsdg+fhpds; C = [He]+2s2p+psd+fpsgd; N = [He]+2s2p+pds+fpsgd; S = [Ne]+3s3p+dpfs+dgpfs; H = 1s+sp+spsd).62 The close-packed Ag(111) surface was modeled by periodic (10 x 10) unit cells containing three atomic layers, separated by 20 Å to avoid undesired interactions of the molecule with the upper metal slab. Both the molecule and the upper layer were relaxed during geometry optimizations while the other two layers were kept frozen. The adsorption energies of the different molecules on the Ag(111) surface were calculated as Eads = Em-s – Em – Es, where Em-s is the total electronic energy of the molecule-surface system and Em and Es are the energies of the relaxed silver slab and of the relaxed gas-phase molecule (both in the same unit cell), respectively. STM images of relaxed adsorbates were then calculated by using the ESQC technique63-64 (ESQC). Here, the complete STM junction, comprising the surface, the molecular adsorbate, the tip apex and the tip body, is described by a set of molecular orbitals for each atom of this junction at the semi empirically extended Hückel level. The scattering matrix of electrons crossing the tip-surface junction is calculated and the tunneling current is estimated by the Landauer formula.65 This method provides reliable theoretical STM images for small66-67 and large68-69 adsorbed molecules. We used Vesta70 for the visualization of surface conformation.

Results


9


Page 10 of 61

The full chemical characterization of DTB27 and tBDTB55 were reported elsewhere. Figure 1a,b shows the DFT-optimized geometry of the compounds DTB (trans) and tBDTB (trans) in the gas phase. The trans assignment refers to the methyl groups (dashed gray circles) pointing to anti-parallel directions relative to the benzothiophene ring. This is the reactive conformation that results to photon-quantitative reaction as drawn in Scheme 1. S-N and N-H atomic distances are both less than the sum of van der Waals radii. For DTB, these interactions were experimentally shown by NMR, DFT calculations, and crystallography.27 In our previous report, we showed that despite the big tert-butyl groups, tBDTB maintains these interactions by demonstrating that the photon-quantitative photocyclization is preserved, by performing DFT calculations, and by measuring NMR data.55 These peripheral groups do not have considerable effect on the electronic properties of the molecule. To illustrate, calculations show that these groups do not contribute to the molecular orbitals HOMO-2 to LUMO+2 (Figure S1,S2).

Figure 1. DFT-optimized structures of different rotational conformers of DTB (a) and tBDTB (b) and their respective torsion angle scans (c,d) in vacuum. The reactive conformation, the most


10

Page 11 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


stable one as shown on Scheme 1, are labelled as trans conformers referring to the opposite directions to which methyl groups are pointing (gray hashed circles). The S-N and N-H interaction distances responsible for locking the molecule in such conformation are shown. The sizes are end-to-end distance between the protons. The tert-butyl groups extend the size of the molecule from 1.7 nm to 2.0 nm while the distance between the top proton of the benzothiophene moiety and the methyl protons are 0.9 nm for both molecules. Torsion angle scans revealed two other stable conformers for both molecules. These are designated as cis conformers referring to the parallel direction of the methyl groups (gray hashed circles) relative to the benzothiophene ring. Each of these conformers maintain either S-N or N-H interactions, as labelled by the subscript on the cis label.

Essentially, these interactions keep both compounds in a conformation in which the thiazole rings are slightly skewed from the plane of the benzothiophene ring with dihedral angle between 45-55o. This could present another difficulty in interpreting STM images as the aromatic rings are not in an entirely planar configuration. The bulky tert-butyl groups do not seem to affect this arrangement of the aromatic rings in 3D space because of their peripheral placement. To probe the strength of these interactions, we calculated the torsion energy with respect to the relevant dihedral angles and showed that the loss of each one of these interactions leads to two other metastable conformers having either one of the N-H or S-N interactions.51,55 (Figure 1c,d) In both conformers, the methyl groups (Figure 1a,b gray hashed circles) are pointing to parallel directions with respect to the benzothiophene moiety so we label these as cis conformers. In DTB, the loss of S-N interaction leading to a conformation with only N-H interaction causes a


11


Page 12 of 61

destabilization of 9 kJ/mol in conformer DTB (cisNH) (Figure 1a) while the reverse leads to a destabilization of 13 kJ/mol in DTB (cisSN) (Figure 1a). Meanwhile, for tBDTB, the cisNH and cisSN conformers are destabilized by 7 kJ/mol and 9 kJ/mol relative to the trans isomer respectively. In solution, the equilibrium between these cis and trans conformations has a big influence on the photocyclization quantum yield of diarylethenes/terarylenes.21-22 The N-H and S-N interactions are therefore expected to be strong enough so that 94-96 % of the molecules in solution phase at room temperature are in the reactive trans conformation as evidenced by photocyclization quantum yields close to these values.27,55 However, the deposition procedure implies warming the sample up to ~473 K which, by Boltzmann distribution, lowers the population of the trans isomers to 81 %.51,55 Although majority of the population are still in the trans conformation, those in the cis conformation could be significant enough in number to show on the surface. In both compounds, the benzothiophene and the two thiazole rings are arranged in a triangular configuration typical of terarylenes.26 End-to-end distance between the phenyl rings was 1.7 nm while the “height” between the benzothiophene and methyl moieties was 0.9 nm. The tert-butyl groups extend the end-to-end distance by 2.0 nm. Since these bulky groups are only in the periphery, they do not affect the overall configuration of the central benzothiophene moiety so that the distance between it and the methyl groups is the same as in DTB. Distances between neighboring tert-butyl groups are also 0.9 nm. (Figure 1a DTB trans, Figure 1b DTB trans)

Experimental Results on Ag(111)


12

Page 13 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Large scale images of Ag(111) with deposited DTB show identical bright circular spots (Figure 2a). The images did not show any voltage dependence. Zooming in on the spots, their perfect symmetry did not reveal any feature that could be assigned to the expected triangular configuration of the aromatic rings (Figure 2b). The observed diameter of the circular spot was 1.2 nm, which is lower than the geometry of the molecule in the gas phase.

Figure 2. (a) Large scale images upon deposition of DTB on Ag(111). Scale bar = 5 nm. (b) Zoom in on one of the spots. Scale bar = 1 nm. Imaging conditions: -1.0 V, 1pA, T = 4.5 K.

Figure 3 shows tBDTB single molecules adsorbed on Ag(111) with 20 % coverage of a bilayer of NaCl(001). The NaCl bilayer may be identified by the presence of the characteristic islands close to the Ag steps and by their 90° corners due to the square lattice of the NaCl(001) face (Figure 3, dark arrows). Three shapes of tBDTB single molecules could be identified; these are labelled as Forms 1, 2, and 3 on Figure 3. This could be due to the presence of different surface absorption structures as predicted by an increase in the population of cis conformers upon heating by DFT calculations.


13


Page 14 of 61

Figure 3. Sample of a large scale image (1.4 V, 1pA, T = 4.5 K) of Ag(111) with 2 monolayers of NaCl followed by subsequent deposition of tBDTB. Dark arrows point to 90o corners characteristic of NaCl(001) crystal structure; dark rectangles on aggregates of molecules; white arrows point to different forms of the compound with their corresponding label. Scale bar = 12 nm.

In the ~200 single molecules we observed, (Figure 3, see S3-4 for more sample images) Forms 1, 2, and 3 displayed a distribution of 60%, 26%, and 14% respectively. Some molecules looked like they started to aggregate (dark circle, Figure 3) but upon zooming in on them, they could still be discriminated as different forms (Figure S3) sticking to each other. It must be noted that majority of molecules observed (>95 %) are found on the metallic surface rather than on the NaCl. Due to the non-polar nature of the tert-butyl groups, the interactions with NaCl are expected to be weaker than with the metallic surface.


14

Page 15 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


We focus first on the results on Ag(111). Due to the bulky tert-butyl groups that interact with the surface mainly by weak van der Waals forces, no preferred direction or conformation could be observed for all forms. Another consequence is that some of our images show fuzzy objects that move on the surface (Figure 3 dark rectangles) and made imaging under some conditions difficult. For large-scale images, relatively high voltages (typically 1.4 V), corresponding to higher tip-surface distances, were necessary to minimize molecule displacement. On the other hand, it was possible to obtain images at low voltages when smaller areas were imaged. Figure 4 shows a series of STM images of a single isolated molecule and two other molecules (seemingly interacting with each other) having Form 1. Form 1 displays four lobes surrounding a bright central lobe. At bias voltages 1.2 to 2.2 V (Figure 4c-h), the four peripheral lobes are easier to discriminate. However, at 0.8-1.0 V, two lobes on the same are indistinguishable (Figure 4a,b). At higher bias voltages starting from 1.8V, the bright central structure becomes more prominent than the surrounding lobes (Figure 4f-h).


15


Page 16 of 61

Figure 4. Zoom in on Form 1 at differing bias voltages a) 0.8 V b) 1.0 V c) 1.2 V d) 1.4 V e) 1.6 V f) 1.8 V g) 2.0 V h) 2.2 V. All images taken with 1pA at T=4.5 K. Scale bar = 1.2 nm.

The four small lobes are arranged in an almost rectangular manner similar to the arrangement of tert-butyl groups of trans tBDTB in Figure 1b. These arrangements and shapes are reminiscent of STM images of trans-azobenzene functionalized with 4 tert-butyl groups reported by L. Grill et al.17-18 The length of the molecule, i.e. the distance between ends of two lobes, is 2.2 nm apart


16

Page 17 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


while the width between two side lobes is 1.2 nm. (See Figure S4 for details of size measurements dimensions.) These correspond well with the interatomic distances shown for tBDTB (trans) in Figure 1b. The central bright spot could be due to the central part of the molecule. It has a width of about 1 nm, similar to the 0.9 nm distance between the methyl and benzothiophene moieties of tBDTB. We therefore ascribe the four bright peripheral lobes to the bulky tert-butyl groups while the spot between them to the central aromatic rings. Form 2 on the other hand seems to have the four lobes and a central part skewed out of the rectangular arrangement of Form 1 (Figure 5a-c). One side roughly maintains a 2.2 nm length and another a 1.2 nm width previously seen. The other side appears to be lifted from the surface so that the central part is brighter. These are reminiscent of cis-azobenzene studied by L. Grill et al.17-18 We therefore postulate that this form is one of the stable cis conformers of tBDTB. At higher voltages, (Figure 5d-f) the molecule seems to shift its contrast to a different part, similar to the behavior of Form 1. Due to the dissymmetry of Form 2, it is notable that chirality is expected on the surface. In the gaseous state, tBDTB is not chiral per se but the dissymmetry due to the benzothiophene moiety may render it chiral once adsorbed. However, because of low contrast in the images, it is rather difficult to show. (Figure S5)


17


Page 18 of 61

Figure 5. Zoom in on Form 2 and imaging at a) -1.5 V b) -0.5 V c) 1.0 V d) 2.0 V e) 2.5 V f) 3.0 V. All images taken at 1pA, T=4.5 K. Scale bar = 1 nm.

STM images of Form 3 as a function of bias voltage are shown in Figure 6. This form has almost similar measurements as those of Forms 1 and 2 (Figure S4). The main difference is that the lobes on each of the two sides are slightly skewed from the rectangular arrangement and are less intense than the central spot even at the same imaging conditions. This form displays similar behavior as Forms 1 and 2 at higher voltages. Up to 1.5 V, no remarkable difference could be observed (Figure 6a-d) but starting at 2.0 V, the surrounding lobes decrease in contrast while the central spot gets brighter (Figure 6e-f).


18

Page 19 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 6. Zoom in on Form 3 and bias-dependent images at a) -0.2 V b) 0.3 V c) 1.0 V d) 1.5 V e) 2.0 V f) 2.5 V Images were taken at constant current (1pA, T=4.5 K). Scale bar = 1 nm.

For all forms, the presence of tert-butyl groups clearly helped identify the tBDTB molecules on the surface. This is a great improvement compared to DTB giving only bright symmetric spots (Figure 2). Further, the observed decrease in contrast of tert-butyl groups as the imaging potential increases means that unoccupied states are being probed. (In our system, the bias is applied to the sample so that a positive voltage generates a tunneling current from the tip to the surface.) This is consistent with the location of the unoccupied states near the center of the


19


Page 20 of 61

molecule and not on the tert-butyl groups, as shown in the maps of LUMO and LUMO+1 of tBDTB (Figure S1). We therefore performed scanning tunneling spectroscopy (STS) measurements. The original I(V) spectra are then numerically derived and are presented in Figure 7. They all display strong resonance peaks at -1.3 and 2.1 V which have resonance onset at -0.4 and 1.5 V respectively, resulting to an estimated gap of 1.9 V. All STS spectra measured on all forms showed the same peaks, indicating that they are almost chemically identical, differing only as surface conformational isomers.

Figure 7. Typical STS spectrum of tBDTB. All forms displayed similar peaks at -1.5 and 2.1 V relative to the Fermi level.


20

Page 21 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Calculation results on Ag(111) We postulate the existence of different conformers of tBDTB on the surface due to the variety of forms observed. In order to understand these experimental STM images vis-à-vis such plurality of conformations, we performed a comprehensive computational study to obtain adsorption energies, adsorption geometry, and predicted STM images of different conformers. Table 1 summarizes the adsorption energies calculated for these forms while Figure 8 shows the calculated adsorption geometries.

Table 1. Adsorption Energies of DTB and tBDTB Conformations on Ag(111) Eads (eV)* Conformer DTB tBDTB open (trans1) -3.476 -4.572 open (cis) -3.390 -4.321 closed (trans) -3.070 -4.620 open (cis) -3.705 -4.187 † open (trans2) -5.836 * Eads on the Ag(111) surface calculated as Eads = Em-s – Em – Es, where Em-s is the total electronic energy of the molecule-surface system and Em and Es are the energies of the relaxed silver slab and of the relaxed gas-phase molecule (both in the same unit cell), respectively. † This conformation refers to the trans conformation of tBDTB in which the benzothiophene is sticking out of the surface and a strong bond was found between a sulfur atom from a thiazole and a silver atom (Figure 8d,e).


21


Page 22 of 61

Figure 8. DFT-optimized surface geometry of three possible conformations of the tBDTB. (a), (d), and (g) show views from the top while (b), (e), and (h) show views from the side. ESQC calculated images taken at 0.10 V above the Fermi level are shown in (c), (f) , and (i). (a), (b), and (c) refer to a trans conformation (Figure 1b) in which all the aromatic rings except one thiazole ring are protruding from the surface (trans1). (d), (e), (f) is the trans2 conformation (Figure 1b) in which the benzothiophene moiety is the one protruding from the surface. Lastly, (g), (h), and (i) refers to that of tBDTB cisSN deposited on the surface. The optimized conformation of tBDTB viewed perpendicular to and from the side of Ag(111) are shown in Figures 8a and 8b respectively. This calculated surface conformation is labelled as


22

Page 23 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


trans1. All aromatic rings bar one thiazole lie on almost the same plane, maximizing the surface area parallel to the Ag(111). The dihedral angle between the benzothiophene moiety and the flat thiazole ring is only 9o (in contrast to 45-55o in the gas phase). Focusing on the tert-butyl groups, two of the three methyl groups are on almost the same plane as the aromatic rings. Between these methyl groups and the quaternary carbon of the tert-butyl group, angles between 108.2-108.7o were calculated, indicating a slight distortion in order to maximize surface contact. These methyl groups present eight hydrogen atoms close to the Ag(111) surface which raise the aromatic plane from the surface by only ~3.0 Å. This is comparable to the calculated distance of flat benzene rings and other methyl-substituted aromatic systems when adsorbed on Ag(111) surface.71 Due to this planarity, the N-H and S-N bonds which lock the molecule in its reactive conformation in the gaseous and solution state increased in strength as evidenced by lower interatomic distances (Figure S6). Optimization also results in the formation of a strong bond between the silver atom and the sulfur atom of the benzothiophene moiety of typical lengths.72-73 These interactions add up to an adsorption energy of -4.572 eV (Table 1), which is five to eight times stronger than that calculated for single aromatic rings with different substitutions.71 The molecule presents five protrusions on top of the aromatic ring: four methyl groups and one thiazole ring with a methyl group (Figure S6) pointing upwards. Aside from the electronic structure of the molecule, these topographical features could also contribute to the STM image calculated on Figure 8c which shows one slightly brighter central spot surrounded by four lobes. The arrangement, distances, and size of these lobes correspond well to those observed for Form 1. We then checked a different surface conformation in which it is the benzothiophene moiety, rather than the thiazole ring, which protrudes from the surface (Figure 8d and 8e). This surface conformation is labelled as trans2 from here on. Optimization found the two phenyl rings parallel


23


Page 24 of 61

to the surface and the methyl groups of the tert-butyl arranged as in trans1. Further, the thiazole rings are slightly twisted towards the surface so that a bond was found between the sulfur atom of one thiazole group and a silver atom on the surface (with 2.6 Å interatomic distance). The thiazole rings are no longer parallel with the surface, but instead seem to mimic their gas-phase optimized structures skewing around the benzothiophene moiety to avoid direct steric repulsion between the methyl groups. The S-N distance between the benzothiophene sulfur atom and the dihedral angle between these two planes are 3.22 nm and 58o respectively, which are in agreement with the values obtained in the gas phase. (Figure S6) The benzothiophene moiety is virtually unhindered by the silver surface. It feels attractive forces towards the surface plane, however, due to strong N-H bonding as evidenced by the short N-H distance between the benzothiophene group and the side thiazolyl moiety (2.18 nm) (Figure S6). This conformation has an adsorption energy of -5.836 eV. The shorter silver-sulfur bond in trans2 than in trans1 correlates to this stronger adsorption energy. The aromatic and highly-protruding benzothiophene rings could contribute to the bright STM contrasts relative to the low methyl groups, in accordance with ESQC calculation of the STM image (Figure 8f). This calculated image is in good agreement with the geometry of Form 3 in Figure 6. Finally, we also calculated the surface adsorption of tBDTB (cisSN) on Ag(111). Optimized geometry again shows benzothiophene and phenyl rings on almost the same plane about 3.2 Å away from the surface. (Figure S7) The methyl groups of the tert-butyl moieties protrude from the surface plane, similar to trans1 and trans2. Meanwhile, the thiazole rings are angled so that the methyl groups are protruding from the surface. This conformation has a slightly lower adsorption energy of -4.321 eV. The high features of the two methyl groups from thiazole rings and the four methyl groups from the tert-butyl functionalities could contribute to the contrast of


24

Page 25 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


the calculated STM image on Figure 8i. We could not resolve the lobes experimentally but the size and shape of the calculated image corresponds well with that of Form 2. Although we performed the deposition of native open forms carefully under dark conditions, the photon-quantitative sensitivity of tBDTB55 may cause unwanted formation of the closed form due to any incident photon that leaks into the sublimation pathway. (Scheme 1) This closed form has two isomers, a trans isomer in which the methyl groups are pointing in opposite directions from the plane of the photoswitching backbone and a cis isomer in which the methyl groups are on the same side of the plane. (See Figure S8-9 for the DFT-optimized geometries of these closed isomers.) The former is the product of photo-induced processes in solution22, and probably in the gas phase, while the latter is the result of thermal processes on surfaces.44,47 We therefore expanded the theoretical studies to a full calculation of both cis and trans isomers of the closed form. (Figure 9) In both of these isomers, all the rings are locked on the same rigid plane which attempts to approach the surface to maximize adsorption energies despite the steric hindrance due to CH3 groups. In the close trans isomer, the methyl group on the reactive carbon raises the molecule 3.6 Å from the surface (Figure 9a,b, S10). This distance is quite far so a low adsorption energy of -4.19 eV was calculated. This surface conformation has five protrusions: one methyl group on the thiazole ring that contributes to a bright spot at the center of the calculated ESQC image and four methyl groups that contribute to a weaker contrast around it (Figure 9c). Meanwhile, the conformation of the close cis isomer also exhibits all rings on the same plane with sulfur atoms attempting to approach the Ag(111) surface so that one formed a bond with a silver atom (Figure 9d,e, S10). Along with van der Waals interactions, these add up to an adsorption energy of -4.620 eV. The ESQC calculated image of close cis form is therefore rather similar to that of the close trans form except for the brighter central spot due to the


25


Page 26 of 61

additional methyl group protruding at the center of the molecule (Figure 9f). These ESQCcalculated images (Figure 9c,f) however do not fit with the experimental images as well as those on Figure 8c,f,i. As a consequence, we discount the possibility of the images in Figures 3-6 corresponding with any of the closed forms.

Figure 9. DFT-optimized surface geometries of tBDTB close cis and trans isomers. (a) and (d) show views from the top and (b) and (e) show views from the side. ESQC predicted images taken at 0.10 V above the Fermi level are shown on (c) and (f), (a), (b), and (c) refer to a trans isomer while (d),(e), and (f) refer to a cis isomer in which the methyl groups point up to the surface.


26

Page 27 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


We further discuss the STS spectrum of tBDTB on Ag(111) based on the calculations. For the open form, we obtained a gap of 2.4 eV between occupied and unoccupied states (Figure 10a). The calculated STS for the closed form on the other hand resulted to a gap difference of only 1 V (Figure 10b).55 This lower gap is due to the increased conjugation in the closed form which is well-documented in the literature and is the basis of many of its switching properties1,21-23 and applications1,21-23,26-34.

Figure 10. Calculated STS spectra of tBDTB (a) open form and (b) closed form.

Experimental Results on NaCl(001)/Ag(111) Finally, we look at the mapping of electronic states of tBDTB on the surface. Two monolayers of NaCl were shown to be effective in decoupling the molecular states of the compound from those of the metallic surface to gain access to occupied and unoccupied states.74-77 The STM of single tBDTB molecules on NaCl(001)/Ag(111) showed similar images adopting a structure similar to Form 1/tBDTB trans1. At low voltage, the molecules exhibit the same shape as observed on the metallic surface. No noticeable differences in shape nor contrast were observed from 1.0 to 2.2 V


27


Page 28 of 61

until the voltage was ramped up to 2.4 V (Figure 11a). Meanwhile, at negative voltage, no change was seen from -1.8 to -2.4 V until -2.6 V (Figure 11b). Above 2.4 V and below -2.6 V, the tert-butyl groups lose their influence on the STM image while the central part of the molecule increases in contrast.

Figure 11. Images of tBDTB on NaCl(001)/Ag(111) at (a) increasing positive voltage (image sizes 6 nm x 6 nm) and at (b) increasing negative voltage (image sizes 7 nm x 7 nm). Images were taken at constant current (1 pA).

Scanning at positive bias voltage means accessing unoccupied states while a negative bias probes occupied states. The loss of contribution from the large tert-butyl groups on STM images at very positive and very negative voltages leads us to believe that the measured current at these conditions is mainly due to the unoccupied and occupied states of the compound respectively. Indeed, maps of molecular orbitals (Figure S2-3) clearly show that the tert-butyl groups do not


28

Page 29 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


have a contribution to the MOs in the gas phase. MO maps from HOMO-2 to LUMO+2 are mainly dominated by the aromatic rings.

DISCUSSION Comparing the experimental images (Figure 4) and ESQC calculations (Figure 8c), we assign the observed Form 1 to tBDTB (trans1) (Figure 8a,b). Figure 8a, however, shows only one of four possible adsorption geometries of this trans conformation. Whereas in solution at ambient conditions, with a high thermal energy and with unhindered rotational movements, the difference between molecular conformations may be considered trivial, on a two dimensional surface at a single-molecular level, different conformations of the molecule are expected due to interactions with the substrate.7 Because of the dissymmetry of the central benzothiophene ring, another possible unique surface conformation may come up from exchanging which thiazole ring lies flat on the surface and which one protrudes from it. Whereas Figure 8a shows the thiazole ring attached at the 3-position of benzothiophene protruding from the surface, another possibility is that the thiazole ring at the 2-position of benzothiophene is the one protruding from the surface. Further, the reduction of symmetry elements in two dimensions may induce chirality8-9, so that the enantiomers of these two conformations are also expected resulting to four possible surface adsorption geometries. The lack of STM contrast on the central part of the isomer, however, renders calculations to find the adsorption sites of other enantiomeric confirmers unnecessarily costly so that it must be nuanced that the observed Form 1 may correspond to one of four possible conformations. Figure 8d is similarly one of four possible surface conformations of tBDTB trans2. Another possibility is that the sulfur atom from the other side of the thiazole


29


Page 30 of 61

group could be interacting with a silver atom. These two possibilities could have enantiomeric forms, bringing the total number of surface configurations to four. Meanwhile, Figure 8g corresponds to tBDTB (cisSN) deposited on Ag(111). The STM contrast in the ESQC calculated image seems to be mainly due to six methyl groups: two from the thiazole rings and four from the tert-butyls. The case would be similar if tBDTB (cisNH) were instead adsorbed on the surface. Aside from these two, their respective enantiomers would also be possible surface conformers. We are careful, therefore, to say that Form 2 also corresponds to a conformation of the tBDTB cis adsorbed on the surface. It is worth noting that, Forms 1 and 3 which have the trans conformation contribute to 86 % of the molecules observed while the rest are in the cis conformation. Assuming a Boltzmann distribution and using the relative energy differences of the trans and cis conformations (Figure 1d), this corresponds well to the expected population of the molecules at 473 K. This implies that when the molecule is heated, the thermal energy was instrumental not only for sublimation but also for allowing the molecule to adapt the other metastable rotational conformers (Figure 1b, cisNH, cisSN). Upon landing on the substrate at liquid helium temperature, molecules in the metastable cis conformation are frozen and are hindered from rotation by the surface. Matsuda and co-workers reported the observation of assemblies of this cis conformation of diarylethenes on the solid-liquid interface,41 but to the best of our knowledge, this is the first isolation and imaging of the unreactive cis isomer at the single-molecular level under ultra-high vacuum conditions. The central part of the molecule is the main source of dissymmetry of tBDTB. Given the low resolution obtained for the central bright part, it is unnecessary to find conformations of other enantiomeric forms by DFT. The optimizations performed precisely provided these


30

Page 31 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


conformations as minima so we focused on these conformers. For our purposes, these calculations are precise enough to guide us in interpreting the STM images and finding the surface conformation. Finding other adsorption sites could also be costly so we prioritized in our calculations the question of the possibility that these forms may correspond to cyclization products (closed form, Scheme 1) which have cis and trans isomers as well (Figure S8-9). Although we performed deposition carefully under dark conditions, the high photosensitivity of the molecule may cause a response from any photon that may leak to the aluminum foil-covered windows of the UHV chamber. In addition to this, Kim and co-workers reported that charge transfer between the metallic surface and classical diarylethenes may reverse the relative stabilities of the open and closed forms so that closed forms may appear when induced thermally.47 Franke and co-workers on the other hand showed that thermal processes induced by the STM tip result to the formation of the cis close isomer.44 In our system, we discount these possibilities for two main reasons. First, the experimental STM images and STS spectra correspond much better to those calculated for the open than the closed isomers. Further, the partial induction of closed forms by thermal processes were accomplished at room temperature and complete conversion were reported by Kim’s group after heating of the substrate at 80 oC.47 All our measurements were performed at 4.5 K so that no thermal reaction was expected once the molecule is adsorbed on the cold substrate. Franke’s group44 performed switching using tunneling electrons from the STM tip. We attempted several ways to induce the switching such as bias pulses, electric-field induction, or consecutive scanning at high potentials but no such switching was observed. This may be due to strong hybridization of the molecular orbitals to the metallic state as sulfur atoms may interact strongly with silver atoms. Particularly, Forms 1 and 3 maintain the reactive trans conformation but they


31


Page 32 of 61

have strong silver-sulfur interactions. These may have drastically modified the MOs of tBDTB especially that Ag-S bonds were previously shown to have a strong electrostatic character.72 We also attempted such switching for the molecules found on the NaCl bilayer. Tunneling electrons however caused translation of the molecules due to the weak interactions on the surface. The small amount of molecules on NaCl proves this, as the molecules seem to prefer adsorption on the Ag(111) surface. To find out the influence of the tert-butyl groups on the adsorption energy (Eads), we also performed calculations for the derivative without tert-butyl groups. (Table 1, Figure S10-11) For the open forms, the aromatic rings both lie at almost the same distance (about 3.0 Å) from the surface (Figure S10). The distance between different peripheral tert-butyl groups seems large enough to allow some flexibility for the central photochromic core of tBDTB to approach the surface with similar distance as that of DTB (about 3.1 Å). In comparison, the tert-butyl groups in azobenzene are separated only by two phenyl rings connected by a N=N bond which do not have the same flexibility to approach the surface so that switching was observed.17-18 The tert-butyl groups also prefer a conformation in which two out of three methyl moieties are in contact with the surface favoring van der Waals interactions so that the adsorption energy increases by almost 1 eV in all forms. For tBDTB, (Figure 8b, e, h) the tert-butyl groups seem to rotate and have enough flexibility to present two methyl groups on the surface implying that their carbon atoms are almost on the same plane as the aromatic rings. These methyl groups could contribute to the stronger van der Waals interactions with the surface. These strong interactions undoubtedly cause hybridization of the molecular orbitals with the metallic substrate, preventing the switching of the molecule.


32

Page 33 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The remaining methyl group on the other hand protrudes from the surface and seems to be the main topographical feature that gives tert-butyl groups strong contrasts under STM. So that despite the stronger adsorption energy for these compounds, the tip could easily cause translational motion at low voltages due to its proximity to these groups. Meanwhile, high voltages could cause electric-field-induced “jumping” of the molecule either to the tip or on the surface. For the closed trans form, the steric hindrance induced by the methyl group directly on the face of the solid substrate lifts the central part of the ring 3.6 Å from the surface. This seems to be the appropriate conformation in order to lift the molecule from the surface. It is interesting to note that the calculated Eads for the unsubstituted terarylenes with five aromatic rings are almost five times higher than that calculated for benzene and its derivatives.71 This could point to possible additive nature of adsorption energies of aromatic rings for future computational studies. Barring synergistic effects, the 1 eV increase in Eads may also be a measure of the attractive forces due to the eight methyl groups from the tert-butyl functionalities in contact with the surface. Lastly, considering that tert-butyl groups started to lose their influence on the images at 2.4 V and at -2.6 V on the NaCl surface, we could estimate the gap to be around 5 V which is higher than that observed by STS on Ag(111), predicted by TD-DFT in the gas phase, and observe when the molecule is dissolved in solution55. This could be due to the imaging of transient states due to the increased lifetime of electrons/holes on the NaCl layer74-77 or an uncontrolled voltage drop between the tip and molecule, molecule/NaCl, or NaCl/Ag interfaces.


33


Page 34 of 61

CONCLUSION In this study, we compared the adsorption of non-functionalized (DTB) and tert-butyl functionalized (tBDTB) terarylene on Ag(111) by a combination of STM and DFT studies. STM images reveal three different forms of the terarylene on Ag(111) thanks to the contrast afforded by the tert-butyl groups. Such information was not available in the STM imaging of DTB on the same substrate. Analysis of adsorption geometries reveals that dissymmetry of the central benzothiophene moiety could lead to two pairs of enantiomeric forms of tBDTB. The low STM contrast on the central ring, however, renders calculation for all twelve forms unnecessarily costly. The first single-molecule images of the unreactive cis conformation was also reported. We show by DFT that despite the size of tert-butyl groups, they are not enough to prevent hybridization of the molecular orbitals from the surface, as the distance between the surface and the aromatic rings of the molecule remained almost similar for tBDTB to that of DTB. The angle between two methyl groups seem to bend towards the surface, contributing to molecule-surface interaction via van der Waals interactions. Meanwhile, the remaining methyl groups protrude from the surface so that these contribute to bright topographical features when scanned at low bias voltages. We consider therefore that when methyl groups are oriented in the right direction, they could be enough to show the contrast expected of tert-butyl groups. The contrast is not by itself due to the tert-butyl group but due to the orienting effect brought by the other methyl groups so that one methyl group protrudes from the surface, as closed forms also have bright contrast due to the central methyl groups not attached to tert-butyl groups. STM images are a combination of topographical and electronic states. At higher bias potentials, (either above 2.0 V or below -2.0 V) the tip-surface distance is high so that the topographical


34

Page 35 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


features due to methyl groups start to lose their influence on the STM images, similar to how they do not contribute to the MOs in the gas phase. The tert-butyl group therefore could serve another purpose of disentangling topographical states and ensuring that at some bias voltages, only electronic states could be imaged. Further, STM experiments are also currently underway for a DTB derivative functionalized with chlorine groups, which could be valuable in forming assemblies on an NaCl surface, which could decouple the MOs from the surface and could at the same time orient the molecules to form 1D/2D assemblies. Given the two-dimensional solid substrate may bring about new surface-molecule interactions, this study contributes a significant insight to how a functional group may behave on 2D surfaces. We detailed the origin of bright contrasts due to tert-butyl groups while showing their potential to ensure that only electronic states are imaged. This study provides a molecular principle to guide the design of new molecules for next generation surface-based electronic devices.

SUPPORTING INFORMATIONS Supplementary information on calculation methods, HOMO-LUMO maps, conformations, image comparisons, STS data, supplementary images, and ESQC calculated images at various bias voltages are available. The following files are available free of charge.

AUTHOR INFORMATION Corresponding Authors *E:mail: [email protected]. Phone +33 562 257 841 *E:mail: [email protected]. Phone +33 562 257 899 *E:mail: [email protected]. Phone + 81 743 72 6170


35


Page 36 of 61

Present addresses ‡

T.K.: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5

Takayama, Ikoma, Nara 630-0192, Japan §

G.R. and R.C.: CEMES, Université de Toulouse, 29 rue Jeanne Marvig, BP 94347, 31055

Toulouse Cedex 4, France * (T. K.) Address: 8916-5 Takayama, Ikoma, Nara, Japan; Telephone: 630 0192 ; E-mail: [email protected] Notes The authors declare no competing financial interest. ACKNOWLEDGMENT This work was supported by the MEXT Program for Promoting the Enhancement of Research Universities in NAIST, the CNRS and the University Paul Sabatier (Toulouse). This research was also partly supported by the JSPS KAKENHI Grant Number JP26107006 in Scientific Research on Innovative Areas “Photosynergetics” and the Programme Investissements d’Avenir ANR-11-IDEX-0002-02, reference ANR-10-LABX-0037-NEX. JE thaks the Spanish MINECO for financial support (IJC-2014-20097 and CTQ2015-64579-C3-1-P) and CSUC for the allocation of computational resources. We would like to thank Dr Sébastien Gauthier for fruitful discussions. We also warmly acknowledge Dr. Colin Martin for his careful reading of the final version of the manuscript.

REFERENCES 1. Photon-Working Switches; Yokoyama, Y.; Nakatani, K., Eds.; Springer: Tokyo, 2017.


36

Page 37 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


2. Molecular switches; Feringa, B. L.l Wiley-VCH: Weinheim, 2001. 3. Dresselhaus, M. A revolution of nanoscale dimensions. Nat. Rev. Mater. 2016, 1, 1-2 4. Marqués-González, S.; Low, P. J. Molecular Electronics: History and Fundamentals. Aust. J. Chem. 2016, 69, 244-253. 5. van Ruitenbeek, J. M. Molecular Electronics: A Brief Overview of the Status of the Field. In Single-Molecule Electronics: An Introduction to Synthesis, Measurement and Theory. Kiguchi, M. Ed.; Springer: Singapore, 2016, 1-23. 6. Bouju, X.; Mattioli, C.; Franc, G.; Pujol, A.; Gourdon, A. Bicomponent supramolecular architectures at the vacuum-solid Interface. Chem. Rev.2017, 117, 1407-1444. 7. Mali, K.S.; Pearce, N.; De Feyter, S.; Champness, N.R. Frontiers of supramolecular chemistry at solid surfaces. Chem. Soc. Rev. 2017, 46, 2520-2542. 8. De Feyter, S.; Iavicoli, P.; Xu, H. Expression of chirality in physisorbed monolayers observed by scanning tunneling microscopy. In Chirality at the Nanoscale. Amabilino, D. Ed.; Wiley-VCH: Weinheim, 2009. 9. Ernst, K.-H. Supramolecular surface chirality. In Supramolecular Chirality. CregoCalama, M.; Reinhoudt, D.N. Eds.; Springer: Heidelberg, 2006; pp 209-252. 10. Morgenstern, K. Switching individual molecules by light and electrons: From isomerization to chirality flip. Prog. Surf. Sci. 2011,86, 115-161. 11. Pathem, B. K.; Claridge, S. A.; Zheng, Y. B.; Weiss, P. S. Molecular switches and motors on surfaces. Annu. Rev. Phys. Chem. 2013, 64, 605-630.


37


Page 38 of 61

12. Zhang, J. L.; Zhong, J. Q.; Lin, J. D.; Hu, W. P.; Wu, K.; Xu, G.Q.; Wee, A. T. S.; Chen, W. Towards single molecule switches. Chem. Soc. Rev. 2015, 44, 2998-3022. 13. Binnig, G.; Rohrer, H.; Gerber, Ch.; Weibel, E. Tunneling through a controllable vacuum gap. Appl. Phys. Lett. 1982, 40, 178-180. 14. Binnig, G.; Rohrer, H.; Gerber, Ch.; Weibel, E. 7 x 7 Reconstruction on Si(111) resolved in real space. Phys. Rev. Lett. 1983, 50, 120-123. 15. Foster, J. S.; Frommer, J. E.; Arnett, P. C. Molecular manipulation using a scanning tunneling microscope. Nature, 1988, 331, 324-326. 16. Eigler, D. M.; Schweizer, E. K. Positioning single atoms with a scanning tunneling microscope. Nature, 1990, 344, 524-526. 17. Alemani, M.; Peters, M.V.; Hecht, S.; Rieder, K.H.; Moresco, F.; Grill, L. Electric fieldinduced isomerization of azobenzene by STM. J. Am. Chem. Soc. 2006, 128, 1444614447. 18. Alemani, M.; Selvanathan, S.; Ample, F.; Peters, M.V.; Rieder, K.-H.; Moresco, F.; Joachim, C.; Hecht, S.; Grill. L. Adsorption and switching properties of azobenzene derivatives on different noble metal surfaces: Au(111), Cu(111), and Au(100). J. Phys. Chem. C 2008, 112, 10509-10514. 19. Comstock, M. J.; Strubbe, D. A.; Berbil-Bautista, L.; Levy, N; Cho, J.; Poulsen, D.; Fréchet, J. M. J.; Louie, S. G.; Crommie, M. F. Determination of photoswitching dynamics through chiral mapping of single molecules using a scanning tunneling microscope. Phys. Rev. Lett. 2010, 104, 178301.


38

Page 39 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


20. Kazuma, E.; Han, M.; Jung, J.; Oh, J.; Seki, T.; Kim, Y. Elucidation of isomerization pathways of a single azobenzene derivative using an STM. J. Phys. Chem. Lett. 2015, 6, 4239-4243. 21. New Frontiers in Photochromism; M. Irie, M., Yokoyama, Y., Seki, T., Eds.; Springer: Tokyo, 2013. 22. Irie, M.; Fukaminato, T.; Matsuda, K.; Kobatake, S. Photochromism of diarylethene molecules and crystals: memories, switches, and actuators. Chem. Rev. 2014, 114, 1217412277. 23. Irie, M.; Fukaminato, T.; Sasaki, T.; Tamai, N.; Kawai, T. Organic chemistry: a digital fluorescent molecular photoswitch. Nature 2002, 420, 759-760. 24. Uchida, K.; Yamanoi, Y.; Yonezawa, T.; Nishihara, H. Reversible on/off conductance switching of single diarylethene immobilized on a silicon surface. J. Am. Chem. Soc. 2011, 133, 9239-9241. 25. Arramel, T. C. P.; Kudernac, T.; Katsonis, N.; van der Maas, M.; Feringa, B.L.; van Wees, B.J. Reversible light induced conductance switching of asymmetric diarylethenes on gold: surface and electronic studies. Nanoscale 2013, 5, 9277-9282. 26. Nakashima,

T.;

Kawai,

T.

Photochromic terarylenes.

In

New

Frontiers

in

Photochromism; Irie, M.; Yokoyama, Y.; Seki, T.s Eds.; Springer: Japan, 2013; pp 183204. 27. Fukumoto, S.; Nakashima, T.; Kawai, T. Photon-quantitative reaction of a dithiazolylarylene in solution. Angew. Chem. Int. Ed. 2011, 50, 1565-1568.


39


Page 40 of 61

28. Nakashima, T.; Kajiki, Y.; Fukumoto, S.; Taguchi, M.; Nagao, S.; Hirota, S.; Kawai, T. Efficient oxidative cycloreversion reaction of photochromic dithiazolythiazole. J. Am. Chem. Soc. 2012, 134, 19877-19883. 29. Calupitan, J. P.; Nakashima, T.; Hashimoto, Y.; Kawai. T. Fast and efficient oxidative cycloreversion reaction of a π-extended photochromic terarylene. Chem. Eur. J. 2016, 22, 10002-10008. 30. Kanazawa, R.; Taguchi, M.; Nakashima, T.; Kawai, T. Experimental and theoretical investigation of tetra-oxidized terarylenes with high-contrast fluorescence switching. New J. Chem. 2015, 39, 7397-7402. 31. Nakagawa, T.; Hasegawa, Y.; Kawai, T. Photoresponsive Europium(III) complex based on photochromic reaction. J. Phys. Chem. A 2008, 112, 5096-5103. 32. Kawai, T.; Iseda, T.; Irie, M. Photochromism of triangle terthiophene derivatives as molecular re-router. Chem. Commun. 2004, 72-73 33. Nakashima, T.; Tsuchie, K.; Kanazawa, R.; Li, R.; Iijima, S.; Galangau, O.; Nakagawa, H.; Mutoh, K.; Kobayashi, Y.; Abe, J.; et al. Self-contained photoacid generator triggered by photocyclization of triangle terarylene backbone. J. Am. Chem. Soc. 2015, 137, 70237026. 34. Galangau, O.; Delbaere, S.; Ratel-Ramond, N.; Rapenne, G.; Li, R.; Calupitan, J. P. D. C.; Nakashima, T.; Kawai, T. Photon-quantitative 6π-electrocyclization of a diarylbenzo[b]thiophene in polar medium. J. Org. Chem. 2016, 81, 11282-11290.


40

Page 41 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


35. Arai, R.; Uemura, S.; Irie, M.; Matsuda, K. Reversible photoinduced change in molecular ordering of diarylethene derivatives at a solution-HOPG interface. J. Am. Chem. Soc. 2008, 130, 9371-9379. 36. Maeda, N.; Hirose, T.; Yokoyama, S.; Matsuda, K. Rational design of highly photoresponsive surface-confined self-assembly of diarylethenes: reversible three-state photoswitching at the liquid/solid interface. J. Phys. Chem. C 2016, 120, 9317-9325. 37. Maeda, N. Hirose, T. Matsuda, K. Discrimination between conglomerates and pseudoracemates using surface coverage plots in 2-D self-assemblies at the liquid/graphite interface. Angew. Chem. Int. Ed. 2017, 56, 2371-2375. 38. Bonacchi, S.; El Garah, M.; Ciesielski, A.; Herder, M.; Conti, S.; Cecchini, M.; Hecht, S.; Samori, P. Surface-induced selection during in situ photoswitching at the solid/liquid interface. Angew. Chem. Int. Ed. 2015, 54, 4865-4869. 39. Frath, D.; Sakano, T.; Imaizumi, Y.; Yokoyama, S.; Hirose, T.; Matsuda, K. Diarylethene self-assembled

monolayers:

cocrystallization

and

mixing-induced

cooperativity

highlighted by scanning tunnelling microscopy at the liquid/solid interface. Chem. Eur. J. 2015, 21, 11350-11358. 40. Yokoyama, S.; Hirose, T.; Matsuda, K. Effects of alkyl chain length and hydrogen bonds on the cooperative self-assembly of 2-thienyl-type diarylethenes at a liquid/highly oriented pyrolytic graphite interface. Chem. Eur. J. 2015, 21, 13569-13576.


41


Page 42 of 61

41. Yokoyama, S.; Hirose, T.; Matsuda, K. Phototriggered formation and disappearance of surface-confined self-assembly composed of photochromic 2-thienyl-type diarylethene: a cooperative model at the liquid/solid interface. Chem. Commun. 2014, 5964-5966. 42. Sakano, T.; Imaizumi, Y.; Hirose, T.; Matsuda, K. Formation of two-dimensionally ordered diarylethene annulated isomer at the liquid/HOPG interface upon in situ UV irradiation. Chem. Lett. 2013, 42, 1537-1539. 43. Shimizu, T.K.; Jung, J.; Imada, H.; Kim, Y. Supramolecular assembly through interactions between molecular dipoles and alkali metal ions. Angew. Chem. Int. Ed. 2014, 53, 13729-13733. 44. Wirth, J.; Hatter, N.; Drost, R.; Umbach, T.R.; Barja, S.; Zastrow, M.; Rück-Braun, K.; Pascual, J.I.; Saalfrank, P.; Franke, K.J. Diarylethene molecules on a Ag(111) surface: stability and electron-induced switching. J. Phys. Chem. C 2015, 119, 4874-4883. 45. Reecht, G.; Lotze, C.; Sysoiev, D.; Huhn, T.; Franke, K. Visualizing the role of molecular orbitals in charge transport through individual diarylethene isomers. ACS Nano, 2016, 10, 10555-10562. 46. Reecht, G.; Lotze, C.; Sysoiev, D.; Huhn, T.; Franke, K.J. Disentangling electron- and electric field-induced ring-closing reactions in a diarylethene derivative on Ag(111). J. Phys. Condens. Matter 2017, 29, 294001. 47. Shimizu, T. K.; Jung, J.; Imada, H.; Kim, Y. Adsorption-induced stability reversal of photochromic diarylethene on metal surfaces. Chem. Commun. 2013, 8710-8712.


42

Page 43 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


48. Yokoyama, S.; Hirose, T.; Matsuda, K. Photoinduced four-state three-step ordering transformation of photochromic terthiophene at a liquid/solid interface based on two principles: photochromism and polymorphism. Langmuir 2015, 31, 6404-6414. 49. Snegir, S. V.; Marchenko, A.; Yu, P.; Maurel, F.; Kapitanchuk, O.; Mazerat, S.; Lepeltier, M; Léaustic, A.; Lacaze, E. STM observation of open- and closed-ring forms of functionalized diarylethene molecules self-assembled on a Au(111) surface. J. Phys. Chem. Lett. 2011, 2, 2433-2436. 50. Snegir, S. V.; Yu, P.; Maurel, F.; Kapitanchuk, O.; Marchenko, A.; Lacaze, E. Switching at the nanoscale : light- and STM-tip-induced switch of a thiolated diarylethene selfassembly on Au(111). Langmuir 2014, 30, 13556-13563. 51. Calupitan, J. P. D. C.; Galangau, O.; Guillerment, O.; Coratger, R.; Nakashima, T.; Rapenne, G.; Kawai, T. Scanning tunneling microscope tip-induced formation of a supramolecular network of terarylene molecules on Cu(111). J. Phys. Chem. C 2017, 121, 25384–25389. 52. Gimzewski, J. K.; Joachim, C.; Schlittler, R. R.; Langlais, V.; Tang, H.; Johannsen, I. Rotation of a single molecule within a supramolecular bearing. Science 1998, 281, 531533. 53. Chiaravalloti, F.; Gross, L.; Rieder, K. H.; Stojkovic, S.; Gourdon, A.; Joachim, C.; Moresco, F. A rack-and-pinion device at the molecular scale. Nat. Mater. 2007, 6, 30-33.


43


Page 44 of 61

54. Jacquot de Rouville, H. P.; Garbage, R.; Cook, R. E.; Pujol, A. R.; Sirven, A. M.; Rapenne, G. Synthesis of polycyclic aromatic hydrocarbon-based nanovehicles equipped with triptycene wheels. Chem. Eur. J. 2012, 18, 3023-3031. 55. Calupitan, J. P. D. C.; Galangau, O.; Guillermet, O.; Coratger, R.; Nakashima, T.; Rapenne, G.; Kawai, T. Synthesis and photochromism of chloro- and tert-butyl functionalized terarylene derivatives for surface deposition. Eur. J. Org. Chem. 2017, 17, 2451-2461. 56. Hebenstreit, W.; Redinger, J.; Horozova, Z.; Schmid, M.; Podloucky, R.; Varga, P. Atomic resolution by STM on ultra-thin films of alkali halides: Experiment and local density calculations. Surf. Sci. 1999, 2-3, L321-L328. 57. Heidorn, S.; Bertram, C.; Koch, J.; Boom, K.; Matthaei, F.; Safie, A.; Morgenstern, K. Influence of Substrate Surface-Induced Defects on the Interface State between NaCl(100) and Ag(111). J Phys. Chem C. 2013, 31 16095-16103. 58. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian 09, revision E.01; Gaussian, Inc.: Wallingford, CT, 2009. 59. Blum, V.; Gehrke, R.; Hanke, F.; Havu, P.; Ren, X.; Reuter, K.; Scheffler, M. Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun. 2009, 180, 2175-2196.


44

Page 45 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


60. Havu, V.; Blum, V.; Havu, P.; Scheffler, M. Efficient O(N) integration for all-electron electronic structure calculation using numeric basis functions. J. Comput. Phys. 2009, 228, 8367-8379. 61. Tkatchenko, A.; Scheffler, M. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett. 2009, 102, 073005. 62. van Lenthea, J. H.; Faasa, S.; Snijdersb, J. G. Gradients in the ab initio scalar zerothorder regular approximation (ZORA) approach. 2000. Chem. Phys. Lett. 1-2, 107-112. 63. Sautet, P.; Joachim, C. Calculation of the benzene on rhodium STM images. Chem. Phys. Lett. 1991, 185, 23−30. 64. Sautet, P.; Joachim, C. Electronic transmission coefficient for the single-impurity problem in the scattering-matrix approach. Phys. Rev. B: Condens. Matter Matter. Phys. 1988, 38, 12238-12247. 65. Landauer, R. Electrical resistance of disordered one-dimensional lattices. Philos. Mag. 1970, 21, 863-867. 66. Yu, M.; Kalashnyk, N.; Barattin, R.; Benjalal, Y.; Hliwa, M.; Bouju, X.; Gourdon, A.; Joachim, C.; Lægsgaard, E.; Besenbacher, F.; et al. Self-assembly of hydrogen-bonded chains of molecular landers. Chem. Commun. 2010, 5545–5547. 67. Villagomez, C. J.; Castanié, F.; Moblona, C.; Gauthier, S.; Zambelli, T.; Bouju, X. Adsorption of single 1,8-octanedithiol molecules on Cu(100). Phys. Chem. Chem. Phys. 2016, 18, 27521-27528.


45


Page 46 of 61

68. Yu, M.; Xu, W.; Kalashnyk, N.; Benjalal, Y.; Nagarajan, S.; Masini, F.; Lægsgaard, E.; Hliwa, M.; Bouju, X.; Gourdon, A.; et al. From zero to two-dimensions: supramolecular nanostrucutres formed from perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and Ni on the Au(111) surface through the interplay between hydrogen-bonding and electrostatic metal-organic interactions, Nano Res. 2012, 5, 903–916. 69. Saywell, A.; Greń, W.; Franc, G.; Gourdon, A.; Bouju, X.; Grill, L. Manipulating the conformation of single organometallic chains on Au(111). J. Phys. Chem. C 2014, 118, 1719–1728. 70. Momma, K.; Izumi, F. VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. J. Appl. Crystallogr. 2011, 44, 1272-1276. 71. Miller, M.; Simpson, S.; Tymińska, N.; Zurek, E. Benzene derivatives adsorbed to the Ag(111) surface: binding sites and electronic structures. J. Chem. Phys. 2015, 142, 101924. 72. Pakiari, A. H.; Jamshidi, Z. Nature and strength of M−S bonds (M = Au, Ag, and Cu) in binary alloy gold clusters. J. Phys. Chem. A 2010, 114, 9212-9221. 73. Yang, H.; Wang, Y.; Huang, H.; Gell, L.; Lehtovaara, L.; Malola, S.; Häkkinen, H.; Zheng, N. All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures. Nat. Commun. 2013, 4, 2422. 74. Guo, J.; Meng, X.; Chen, J.; Peng, J.; Sheng, J.; Li, X.-Z.; Xu, L.; Shi, J.-R.; Wang, E.; Jiang, Y. Real-space imaging of interfacial water with submolecular resolution. Nature Mater. 2014, 13 184-189.


46

Page 47 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


75. Gross, L. Recent advances in submolecular resolution with scanning probe microscopy. Nature Chem. 2011, 3. 273-278. 76. Repp, J.; Meyer, G.; Stojković, S. M.; Gourdon, A.; Joachim, C. Molecules on insulating films: scanning-tunneling microscopy imaging of individual molecular orbitals. Phys. Rev. Lett. 2005, 94, 026803. 77. Villagomez, C. J.; Zambelli, T.; Gauthier, S.; Gourdon, A.; Stojkovic, S.; Joachim, C. STM images of a large organic molecule adsorbed on a bare metal substrate or on a thin insulating layer: visualization of HOMO and LUMO. Surf. Sci. 2009, 603, 1526-1532.


47


TOC GRAPHIC:

S

N S

S N H

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

Page 48 of 61


48

Page 49 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Scheme 1. Photon-quantitative isomerization reactions of DTB and its derivative tBDTB. 496x175mm (144 x 144 DPI)



Figure 1. DFT-optimized structures of different rotational conformers of DTB (a) and tBDTB (b) and their respective torsion angle scans (c,d) in vacuum. The reactive conformation, the most stable one as shown on Scheme 1, are labelled as trans conformers referring to the opposite directions to which methyl groups are pointing (gray hashed circles). The S-N and N-H interaction distances responsible for locking the molecule in such conformation are shown. The sizes are end-to-end distance between the protons. The tert-butyl groups extend the size of the molecule from 1.7 nm to 2.0 nm while the distance between the top proton of the benzothiophene moiety and the methyl protons are 0.9 nm for both molecules. Torsion angle scans revealed two other stable conformers for both molecules. These are designated as cis conformers referring to the parallel direction of the methyl groups (gray hashed circles) relative to the benzothiophene ring. Each of these conformers maintain either S-N or N-H interactions, as labelled by the subscript on the cis label. 273x129mm (150 x 150 DPI)


Page 50 of 61

Page 51 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 2. (a) Large scale images upon deposition of DTB on Ag(111). Scale bar = 5 nm. (b) Zoom in on one of the spots. Imaging conditions: -1.0 V, 1pA, T = 4.5 K. Scale bar = 1 nm. 81x40mm (150 x 150 DPI)



Figure 3. Sample of a large scale image (1.4 V, 1pA, T = 4.5 K) of Ag(111) with 2 monolayers of NaCl followed by subsequent deposition of tBDTB. Dark arrows point to 90o corners characteristic of NaCl(001) crystal structure; dark rectangles on aggregates of molecules; white arrows point to different forms of the compound with their corresponding label. Scale bar = 12 nm. 133x88mm (150 x 150 DPI)


Page 52 of 61

Page 53 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 4. Zoom in on Form 1 at differing bias voltages a) 0.8 V b) 1.0 V c) 1.2 V d) 1.4 V e) 1.6 V f) 1.8 V g) 2.0 V h) 2.2 V. All images taken with 1pA at T=4.5 K. Scale bar = 1.2 nm. 147x144mm (150 x 150 DPI)



Figure 5. Zoom in on Form 2 and imaging at a) -1.5 V b) -0.5 V c) 1.0 V d) 2.0 V e) 2.5 V f) 3.0 V. All images taken at 1pA, T=4.5 K. Scale bar = 1 nm. 112x74mm (150 x 150 DPI)


Page 54 of 61

Page 55 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 6. Zoom in on Form 3 and bias-dependent images at a) -0.2 V b) 0.3 V c) 1.0 V d) 1.5 V e) 2.0 V f) 2.5 V Images were taken at constant current (1pA, T=4.5 K). Scale bar = 1 nm. 218x144mm (150 x 150 DPI)



Figure 7. Typical STS spectrum of tBDTB. All forms displayed similar peaks at -1.3 and 2.1 V relative to the Fermi level. 236x258mm (144 x 144 DPI)


Page 56 of 61

Page 57 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 8. DFT-optimized surface geometry of 3 possible conformations of the tBDTB. (a), (d), and (b) show views from the top and (b), (e), (f) show views from the side. ESQC calculated images taken at 0.10 V above the Fermi level are shown on (c), (f), (i). (a), (b), and (c) refer to a trans conformation (Figure 1c) in which all the aromatic rings but a thiazole ring are protruding from the surface (trans1). (d), (e), (f) is the trans conformation (Figure 1c) in which the benzothiophene moiety is the one protruding from the surface (trans2). Lastly, (g), (h), (i) refers to that of tBDTB cisSN on the surface. 287x256mm (144 x 144 DPI)



Figure 9. DFT-optimized surface geometry of 2 possible conformations of the tBDTB closed forms. (a) and (d) show views from the top and (b) and (e) show views from the side. ESQC predicted images taken at 0.10 V above the Fermi level are shown on (c) and (d), (a), (b), and (c) refer to a trans-conformation while (d),(e), and (f) refer to a cis-conformation in which the methyl groups point up to the surface. 408x225mm (144 x 144 DPI)


Page 58 of 61

Page 59 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 10. Calculated STS spectra of tBDTB (a) open form and (b) closed form. 414x214mm (144 x 144 DPI)



Figure 11. Images of tBDTB on NaCl(2)/Ag(111) at (a) increasing positive voltage (image sizes 6 nm x 6 nm) and at (b) increasing negative voltage (image sizes 7 nm x 7 nm). Images were taken at constant current (1 pA). 255x103mm (150 x 150 DPI)


Page 60 of 61

Page 61 of 61 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Table of content 82x40mm (150 x 150 DPI)


Ag(111): a

Recommend Documents