Molecular Graph Paper

Article abstract of DOI:10.1002/anie.201703586

We present a self-assembled template that consists of tetraphenylmethane derivatives and adopts a periodic lateral arrangement on a Au(111) surface with acetyl groups sticking out of the molecular film. By using the tip of a scanning tunneling microscope, these acetyl groups can be removed in a spatially controlled way without significantly affecting the remaining molecular assembly. The chemically modified molecules can be readily distinguished from the original ones such that information can be engraved in the molecular film. Both the modified nature of an individual molecule and the order of the molecular film are shown to persist at room temperature. The mesh size of this molecular graph paper can be tuned by varying the length of the molecular spacer so that writing and reading information on the nanoscale with variable letter sizes becomes possible.

Full text of DOI:10.1002/anie.201703586

A Journal of the Gesellschaft Deutscher Chemiker
Angewandte
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Accepted Article
Title: Molecular Graph Paper
Authors: Marcin Lindner, Michal Valášek, Marcel Mayor, Timo
Frauhammer, Wulf Wulfhekel, and Lukas Gerhard
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To be cited as: Angew. Chem. Int. Ed. 10.1002/anie.201703586
Angew. Chem. 10.1002/ange.201703586
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http://dx.doi.org/10.1002/ange.201703586

10.1002/anie.201703586
Angewandte Chemie International Edition
Molecular Graph Paper**
Marcin Lindner[a], Michal Valášek[a], Marcel Mayor[a,b,c]*, Timo Frauhammer[a,d], Wulf Wulfhekel[a,d] and
Lukas Gerhard[a]*
Dedicated to Professor Dieter Fenske on the occasion of his 75th birthday
[a]
M. Lindner, Dr. M. Valášek , Prof. Dr. M. Mayor, T. Frauhammer, Prof. Dr. W. Wulfhekel, Dr. L. Gerhard
Institute of Nanotechnology (INT)
Karlsruhe Institute of Technology (KIT)
P. O. Box 3640
76021 Karlsruhe, Germany
E-mail: lukas.gerhard@kit.edu
[b]
Department of Chemistry
University of Basel
St. Johanns-Ring 19
4056 Basel, Switzerland
E-mail: marcel.mayor@unibas.ch
[c]
Lehn Institute of Functional Materials (LIFM)
Sun Yat-Sen University (SYSU)
Guangzhou (P. R. China)
[d]
Physikalisches Institut
Karlsruhe Institute of Technology (KIT)
Wolfgang-Gaede-Str. 1
76131 Karlsruhe (Germany)
[**]
The authors acknowledge financial support by the Research Network »Functional Nanostructures« of the Baden-
Württemberg Stiftung and by the Helmholtz Research Program STN (Science and Technology of Nanosystems).
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10.1002/anie.201703586
Angewandte Chemie International Edition
Abstract: We present a self-assembled template of tetraphenylmethane-based variants on a Au(111)
surface which feature a periodic lateral arrangement of acetyl groups sticking out of the molecular film.
Using the tip of a scanning tunneling microscope, this acetyl group can be removed in a spatially controlled
way without a significant effect on the remaining molecular assembly. The chemically modified molecule
can readily be distinguished from the original ones such that information can be engraved in the molecular
film. Both the modified nature of an individual molecule and the order of the molecular film are shown to
persist at room temperature. We show that the mesh size of this molecular graph paper can be tuned by
varying the length of the molecular spacer group so that writing and reading information on the nanoscale
with variable letter size becomes possible.
TOC Graphic:
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10.1002/anie.201703586
Angewandte Chemie International Edition
Words of human language have been stored and transmitted in written form on paper since its invention in
ancient China about 2000 years ago. Over the time, printing, micro-photography and electron beam writing
pushed the smallest possible size of individual letters to the nanoscale. Feynman's challenge of writing the
entire Encyclopædia Britannica on the head of a pin [1] is long achieved, and writing letters with atoms
arranged by the tip of a scanning tunneling microscope (STM), as first was shown by Eigler et al. [2,3], has
become common practice [4] and even kilobyte atomic memories have been realized [5]. However, atomic
manipulation is an intrinsically slow technique and truly nanoscale writing with tunable mesh sizes is still
demanding. Typically, single atoms arranged at low temperatures start to diffuse well below room
temperature and any predefined order like e.g. arranged characters will vanish. Therefore, bistable atomic
switches at room temperature are rare [6]. Supramolecular self-assembly in two dimensions on metal
surfaces is meanwhile a reasonably well understood process providing laterally ordered structures with
nanoscale precision which can be stable at room temperature [7-12]. In order that such self-assembled
patterned structures can serve as a writable template, a suitable, modifiable marker must be implemented
such that it can be addressed in a spatially controlled manner by an external stimulus. While the self-
assembly of molecules has been used to organize reactants for subsequent intermolecular reactions [13],
as markers only locally resolved molecular events triggered by the STM tip like e.g. single molecule switches
[14, 15] or even single molecule reactions [16-20] are suited.
Here we present a new approach of molecularly defined graph paper which can be written on with the STM
tip. The graph paper consists of tailor-made tetraphenylmethane-based molecules deposited on a Au (111)
surface. As the molecules were initially designed to study the dimensionality of the molecular rod arranged
perpendicular to the surface mounted on tripodal foot structures [21], the here presented study is first of
all another example of the limited comprehension we have about molecular behavior at interfaces.
However, the unexpected molecular arrangement upon the applied deposition method enabled the
observation of the phenomenon enabling the here reported molecular graph paper. The molecular
structures arrange in regular patterns in which the mesh size is controlled by the length of the molecular
spacer group consisting of a para-oligophenyl rod with a terminal nitrile group. The terminal nitrile groups
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10.1002/anie.201703586
Angewandte Chemie International Edition
ensure a strong enough interaction with the gold surface that upon deposition on the substrate and
subsequent annealing, only two of the three thiol groups decorating the tetraphenylmethane subunit
interact with the gold surface and are deprotected, while the third one is exposed in its acetyl protected
form. Furthermore, the interaction in the densely packed self-assembled pattern with the substrate is
strong enough to prevent thermally activated diffusion at room temperature. The surface pattern results in
a periodic lateral arrangement of exposed acetyl protected thiophenol groups reminding the periodic
squares of graph paper. However, acetyl protected thiophenol rods have been reported to be cleavable by
voltage pulses in STM experiments from single molecules [22]. We here present molecular graph paper by
demonstrating that the acetyl groups sticking out from the surface can be selectively cleaved by application
of voltage pulses with the STM tip positioned above the acetyl group. The molecules without the acetyl
protecting groups typically appear darker in STM, which allows an easy identification and opens the
possibility of writing and retrieving information on the nanoscale with a predefined spacing of the mesh.
The contrast of this molecular graph paper is based on the cleavage of chemical bonds and the applicability
of this mechanism at room temperature is demonstrated for the case of an individual molecule.
In Scheme 1, the syntheses of the four members of the tetraphenylmethane family 1-4 are displayed. While
the synthesis of the shortest derivative 1, as well as of the triflate 12 and the pinacol boronate 13
derivatives of tetraphenylmethane as common precursors of the entire family were already reported [23],
all longer derivatives 2-4 were assembled by Pd catalyzed Suzuki coupling between 12, 13 respectively and
the corresponding bromo-aryl 11 or aryl pinacol boronate derivatives 8, 10 [24], from which 10 was itself
assembled by sequence of Suzuki coupling and Miyaura borylation [25] protocols and 11 was assembled via
Suzuki cross-coupling reaction. Final transprotection of the 2-(trimethylsilyl)ethyl protected thiols 5-7 has
been successfully performed using silver tetrafluoroborate and acetyl chloride to afford the desired
thioacetates 2-4. Detailed synthetic protocols of all new compounds are provided in the supporting
information and the identity of all new compounds was corroborated by their full characterization.
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10.1002/anie.201703586
Angewandte Chemie International Edition
Scheme 1: The members of the tetraphenylmethane family 1-4 and the syntheses of the longer derivatives 2-4.
Reagents and conditions: a) [Pd(PPh3)4], K2CO3, dioxane (THF)/H2O (5/1, v/v), reflux, 16 h; b) AgBF4, AcCl, CH2Cl2, 0°C-
RT.
The molecules 1-4, 15 were deposited from a dichloromethane solution that was sprayed onto clean
Au(111) surfaces as described previously [23,26]. In order to promote proper arrangement in regular
pattern, the samples were mildly annealed to 165 °C in ultra-high vacuum (UHV) and transferred in situ into
the STM working at 5.3 K if not indicated otherwise.
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Figure 1: Adsorption configuration of the tetraphenylmethane variants 1-4 with different spacer groups: row a) phenyl
1 (tunnelling conditions: 0.8 V, 5 pA), row b) biphenyl 2 (1.3 V, 4 pA), row c) terphenyl 3 (1.3 V, 6 pA), row d)
quarterphenyl 4 (1.4 V, 21 pA). Column 1 shows large scale overview images, column 2 shows images of 7 nm in width
with the motifs of individual acetyl groups of the corresponding variant, columns 3 and 4 show STM images of 5 nm in
width with the molecular models superimposed to scale and the corresponding model of the Au(111). The size of the
experimentally determined unit cell is given in column 4.
All four tetraphenylmethane derivatives 1-4 arrange in regular islands with almost square-like unit cells (see
Fig. 1). The appearance of one bright feature can take three different basic motifs while all four variants
show the very same three motifs (column 2 in Fig. 1). The size of the unit cell varies with the length of the
p-oligophenylene spacer and is indicated by a black rhomboid in the columns 3,4 in Fig. 1. We propose the
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10.1002/anie.201703586
Angewandte Chemie International Edition
following adsorption model which is supported by superposition of our STM measurement with the
molecular models and which assumes a molecular film that is commensurate with the Au(111) lattice (see
Fig. 1, column 4). All molecules 1-4 are arranged in a close-packed pairwise fashion. The brightest spot
within the unit cell is formed by the acetyl groups of two adjacent tetraphenylmethanes (see Fig. 1,
columns 3, 4). The presence of different motifs within one island is explained by different conformations of
the paired acetyl groups (see Figure SI-24). Thus, we obtain a density of protruding acetyl pairs of between
0.21 and 0.55 per square nm.
Figure 2: a) Modification of the molecular motif (variant 2) by application of a voltage of 3 V across the tunneling
junction. The molecular motif is reduced to a single blob of drastically lower intensity. b) Tunneling current as a
function of the applied voltage recorded for six individual experiments analogous to a) with the tip positioned above a
molecular motif. The modification is reflected by a small increase in the current followed by a sudden drop to a
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10.1002/anie.201703586
Angewandte Chemie International Edition
drastically lower value. The voltage sweep from 2 to 3 V is shown in black, the sweep back to 2 V is shown in red. c)
The proposed mechanism of acetyl groups cleavage by applying a voltage pulse from the STM tip.
As the acetyl groups point away from the surface and are arranged in laterally separated pairs, they can be
freely addressed with the STM tip. Because this part of the molecule is decoupled from the metal surface
by the central sp3-hybridized carbon atom of the tetraphenylmethane center, it is particularly suited for
electron-induced single molecule chemistry. It is known that in thiol-based molecules which adsorb flat on
a metal substrate, voltage pulses from the STM tip can dissociate the end group by selective breaking of the
sulfur-acetyl (S-Ac) bond [22]. We show that also freestanding acetyl groups can be removed by selective
bond dissociation using tunneling electrons from the STM tip at precisely defined locations above the
molecules. As is shown in Fig. 2a, voltage pulses of about +3 V applied across the tunneling junction lead to
a clear modification of the molecular motif and a drastic reduction of the intensity in the STM image. Pulses
of opposite polarity were less successful and required higher voltages. The threshold voltage for this
process can be determined more precisely by ramping the voltage and simultaneously recording the
tunneling current. The modification of the molecule under the STM tip is then accompanied by a drop in
the tunneling current (see Fig. 2b) which can be associated with the sulfur-acetyl (S-Ac) dissociation event.
In such I-V curves, we found critical values of the voltage in the range of 2.55 to 2.73 V for a ramp speed of
1 V/s. The observed modification of the protruding motif was irreversible in all cases. Also, the application
of voltages of opposite polarity did not allow to reverse the process. In the view of these high energies and
the irreversibility of the process, conformational changes seem to be very unlikely. Furthermore,
application of even harsher conditions, that is higher voltages of 3 V or more and reduced distance
between tip and sample, leads to further reduction of the apparent height which might be attributed to the
additional sulfur atom abstraction (see Figure SI-25). We did, however, not look into the details of this
second modification process, because at these conditions it is very likely to modify the tip as well, which
makes systematic experiments difficult.
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10.1002/anie.201703586
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Although the cleavage mechanism of individual acetyl groups is not fully understood and a number of
mechanisms can play a role in the same molecule [27], our currently favored hypothesis is based on a
radical mechanism which seems most likely considering the UHV surrounding of the reaction (see Fig. 2c).
The STM tip induced cleavage of thioacetate may involve a homolytic cleavage of the S-Ac bond with the
injected electrons forming thiyl (phenylsulfanyl) radicals (RS·). Due to their proximity in the self-assembled
molecular arrangements we further assume that the two neighboring thiyl radicals (RS·) immediately form
the corresponding disulfide (RS-SR). As side product of the homolytic cleavage labile acyl anions (-COCH3)
are formed. Whether these anions are immediately adsorbed by the positively charged substrate or they
undergo rapid decarbonylation providing methyl anions, which subsequently are attracted by the substrate
is beyond the scope of the present study. After deacetylation at low temperatures, we neither observe a
change of the tip nor find isolated acetyl groups in the vicinity of the writing position. As additional
experimental indication for the formation of disulfide bonds (RS-SR) stabilizing the structure we rate our
unsuccessful attempts to separate an isolated dimer with the STM tip. Instead of separating, the whole
isolated dimer simply rotates (see Figures SI-27b,c).
The described cleavage process is highly reproducible and selective to the acetyl groups in the tunneling
junction such that the self-assembled molecular layers can be modified molecule by molecule. Fig. 3a
shows a sequence of four images of the same area of a self-assembled monolayer of 2. Step by step, acetyl
groups are removed in order to engrave the letter “K” and finally writing “KIT” (see Fig. 3b). The self-
assembled template functions as a molecular graph paper that allows us to write information on the
nanoscale in a well-controlled manner as is also shown in Fig. 3c by writing “MGP”. In order to proof our
concept of deacetylation, we performed controlled writing on the fully thiol-terminated
tetraphenylmethane 15 which is similar to 1 (see Figure SI-23 b). We successfully wrote the letter “S” on a
molecular array with a density as high as 0.59 pixels per nm² (see Figure SI-26c), which clearly shows that
the effect is highly localized. The grid spacing of the molecular graph paper depends on the length of the
spacer group. Figures SI-26a,b show the letters “KIT”, written on self-assembled monolayers of derivative 4
(grid spacing is 2.01 x 2.30 nm², see Fig. SI-26a) and derivative 2 (grid spacing of 1.46 x 1.77 nm² see Fig SI-
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10.1002/anie.201703586
Angewandte Chemie International Edition
26b). In principle, the writing process works in the same way for all variants presented, however a larger
intermolecular spacing allows to address single molecule even with a blunt but stable STM tip.
Figure 3: Writing experiments at 5.3 K. a) Writing the capital letter “K” on a 12x12 nm area of a monolayer of 2 by
sequential removing the acetyl groups. b) “KIT” written on a monolayer of 2 (Constant height mode, 1.5 V). c) “MGP”
as acronym for molecular graph paper, written on a monolayer of 4 (1.5 V, 6 pA). All acetyl groups are cleaved off,
except for those forming the letters “MGP”.
A particularly interesting feature is the thermal stability of the molecular graph paper. The practical
applicability requires that the mechanisms of writing and reading remain functional at room temperature
and a written bit remains stable, i.e. does not diffuse. Therefore, in order to test for room temperature
performance of the proposed writing concept, we directly performed room temperature STM on a layer of
derivative 3 deposited as described above. The ordered islands can clearly be imaged with sub-molecular
resolution revealing the same motif as at low-temperature (see Fig. 4a), which shows the room
temperature stability of the self-assembly (see also Figure SI-27). Furthermore, we show that modification
of a single molecule by a voltage pulse (+2.5 V applied to the sample) and readout is possible at room
temperature (see Fig. 4b-d). Furthermore, we did not observe that the written information diffuses in the
molecular layer (see Fig. 4d). However, writing clearly works better at low temperature. At room
temperature the application of voltage pulses is very likely to lead to modifications of the STM tip (see
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10.1002/anie.201703586
Angewandte Chemie International Edition
slight changes of the molecular motif from Fig. 4b to Fig. 4c), which hampered the creation of more
complex structures.
Figure 4: STM at room temperature: a) Ordered islands of tetraphenylmethane-derivative 3 imaged at room
temperature. The size of the image is 100 x 30 nm². Array of 3 before (b) and after (c) application of a voltage pulse
(+2.5 V applied to the sample) at the position indicated with a red arrow. d) An image acquired 2 min later still shows
the same structure. The width of the images is 9 nm. Tunneling parameters are 1.5 V, 5 pA for all panels.
In conclusion, we have realized a novel type of nanostructurization with room temperature stability. The
key to making this molecular graph paper work lies in the combination of the self-assembled molecular
layer and the possibility to manipulate individual molecular groups with voltage pulses in the STM junction.
The clear separation of the molecular spacer and the marker group allows us to engrave information by
chemically modifying single molecular groups without interfering with the well-ordered mesh. The idea of
conceptual separation of the substrate-molecule interaction and the manipulatable marker is likely to be
transferable to similar molecular structures and allows to explore a huge variety of molecular groups.
Finally, this method allows chemical functionalization on the nano-scale such that in a second step, other
molecules may selectively react with the molecular graph paper only at positions that were engraved.
Keywords
nanostructures, scanning probe microscopy, self-assembly, surface chemistry, tetraphenylmethane
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10.1002/anie.201703586
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References
[1] R. P. Feynman, Engineering and Science 1960, 22-36.
[2] D. M. Eigler, E. K. Schweizer, Nature 1990, 344, 524-526.
[3] J. A. Stroscio, D. M. Eigler, Science 1991, 254, 1319-1326.
[4] K. Morgenstern, N. Lorente, K.-H. Rieder, Phys. Status Solidi B 2013, 250(9), 1671-1751.
[5] F. E. Kalff, M. P. Rebergen, E. Fahrenfort, J. Girovsky, R. Toskovic, J. L. Lado, J. Fernández-Rossier, A. F.
Otte, Nat. Nanotech. 2016, 11, 926-929.
[6] U. J. Quaade, K. Stokbro, C. Thirstrup, F. Grey, Surface Science 1998, 415(3), L1037-L1045.
[7] J. Teyssandier, S. De Feyter, K. S. Mali, Chem. Commun., 2016, 52, 11465-11487.
[8] J. C. Love, L. A. Estroff, J. K. Kriebel, R. G. Nuzzo, G. M. Whitesides, Chem. Rev. 2005, 105, 1103-1169.
[9] C. Vericat, M. E. Vela, G. Benitez, P. Carro, R. C. Salvarezza, Chem. Soc. Rev. 2010, 39, 1805-1834.
[10] F. Klappenberger, Prog. Surf. Sci. 2014, 89, 1-55.
[11] W. Auwärter, D. Écija, F. Klappenberger, J. V. Barth, Nat. Chem. 2015, 7, 105–120.
[12] X. Bouju, C. Mattioli, G. Franc, A. Pujol, A. Gourdon, Chem. Rev. 2017, 117, 1407–1444.
[13] J. A. W. Münninghoff, J. A. A. W. Elemans, Chem. Commun. 2017, 53, 1769-1788.
[14] J. L. Zhang, J. Q. Zhong, J. D. Lin, W. P. Hu, K. Wu, G. Q. Xu, A. T. S. Wee, W. Chen, Chem. Soc. Rev.
2015, 44, 2998-3022.
[15] L. Gerhard, K. Edelmann, J. Homberg, M. Valášek, S. G. Bahoosh, M. Lukas, F. Pauly, M. Mayor, W.
Wulfhekel, Nat. Commun. 2017, 8, 14672.
[16] S.-W. Hla, L. Bartels, G. Meyer, K.-H. Rieder, Phys. Rev. Lett. 2000, 85, 2777-2780.
[17] A. Zhao, S. Tan , B. Li , B. Wang, J. Yang, J. G. Hou, Phys. Chem. Chem. Phys. 2013, 15, 12428-12441.
[18] L. Grill, M. Dyer, L. Lafferentz, M. Persson, M. V. Peters, S. Hecht, Nat. Nanotechnol. 2007, 2, 687-691.
[19] J. Cai, P. Ruffieux, R. Jaafar, M. Bieri, T. Braun, S. Blankenburg, M. Muoth, A. P. Seitsonen, M. Saleh, X.
Feng, K. Müllen, R. Fasel, Nature 2010, 466, 470-473.
[20] D. Zhong, J. –H. Franke, S. K. Podiyanachari, T. Blömker, H. Zhang, G. Kehr, G. Erker, H. Fuchs, L. Chi,
Science 2011, 334, 213–216.
12
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10.1002/anie.201703586
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[21] M. Valášek, M. Lindner, M. Mayor, Beilstein J. Nanotechnol. 2016, 7, 374–405.
[22] Y. Jiang, Q. Huan, L. Fabris, G. C. Bazan, W. Ho, Nat. Chem. 2013, 5, 36–41.
[23] M. Lindner, M. Valášek, J. Homberg, K. Edelmann, L. Gerhard, W. Wulfhekel, O. Fuhr, T. Wächter, M.
Zharnikov, V. Kolivoška, L. Pospíšil, G. Mészáros, M. Hromadová, M. Mayor, Chem. Eur. J. 2016, 22,
13218-13235.
[24] A. Suzuki, Angew. Chem. Int. Ed. 2011, 50, 6723-6737; Angew. Chem. 2011, 123, 6854-6869.
[25] T. Ishiyama, M. Murata, N. Miyamura, J. Org. Chem. 1995, 60, 7508-7510.
[26] M. Valášek, K. Edelmann, L. Gerhard, O. Fuhr, M. Lukas, M. Mayor, J. Org. Chem. 2014, 79, 7342-7357.
[27] S.-W. Hla, K.-H. Rieder, Annu. Rev. Phys. Chem. 2003, 54, 307–330.
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