A rigid sublimable naphthalenediimide cyclophane as model compound for UHV STM experiments

Article abstract of DOI:10.1039/b719796a

The design, synthesis and characterization of a rigid naphthalenediimide cyclophane as a model compound for ultrahigh vacuum (UHV) STM experiments are described together with first self-assembly investigations on an Au(111) substrate displaying the format

Full text of DOI:10.1039/b719796a

View Article Online / Journal Homepage / Table of Contents for this issue
COMMUNICATION
www.rsc.org/chemcomm | ChemComm
A rigid sublimable naphthalenediimide cyclophane as model compound
for UHV STM experimentsw
Sandro Gabutti,a Marco Knutzen,b Markus Neuburger,a Guillaume Schull,b
Richard Berndt*b and Marcel Mayor*ac
Received (in Cambridge, UK) 2nd January 2008, Accepted 14th March 2008
First published as an Advance Article on the web 11th April 2008
DOI: 10.1039/b719796a
The design, synthesis and characterization of a rigid naphthale-
nediimide cyclophane as a model compound for ultrahigh va-
cuum (UHV) STM experiments are described together with first
self-assembly investigations on an Au(111) substrate displaying
the formation of densely packed parallel rows of molecules.
partially decoupled from the surface’s electronic states. A first
important step towards the investigation of this concept would
be the design and synthesis of rigid, stable and sublimable
cyclophanes comprising two chromophores. Naphthalene
diimides (NDIs) have already been used successfully as build-
ing blocks for cyclophanes with interesting host/guest proper-
ties7 and as subunits of mechanically interlinked
supermolecules.8 Furthermore, NDIs display physical proper-
ties ideally suited for the envisaged experiments like the tune-
ability of the electronic properties by its core-substituents15 and
a rather low molecular weight, providing the sublimability of
NDI derivatives required for UHV surface experiments.
Here we report the synthesis, characterization and first UHV-
STM investigations on an Au(111) surface of the cyclophane 1
(Scheme 1). To fix both NDI chromophores as tight as possible,
a rigid meta-methylenebenzene spacer has been chosen.
Since Pellegrin synthesized [2.2]metacyclophane in 1899,1
cyclophanes have attracted considerable attention due to both
their structural beauty and their intrinsic physical proper-
ties.2,3 While the synthetic challenge, the extent of aromaticity
of strained cyclic compounds4 and the electronic interactions
of interlinked aromatic systems5 were initially the driving force
for cyclophane chemistry, their supramolecular host proper-
ties have been investigated more recently.6,7 The considerable
stability of the resulting supramolecular complexes even made
mechanically interlinked supermolecules, like catenanes and
rotaxanes, synthetically accessible.8
To meet both requirements, solubility for chemical proces-
sing and sublimability for UHV-investigations, the spacer has
been functionalized with an additional bulky tert-butyl group.
The assembly of the cyclophane 1 is displayed in Scheme 1.w
Starting from commercially available 1-tert-butyl-3,5-dimethyl-
benzene (2), bromination followed by a Gabriel synthesis provided
the rather labile diamine 5 after cleavage with hydrazine. A variety
of reaction conditions, including microwave irradiation,16 have
been investigated to obtain the cyclophane 1 in a single reaction
step by condensing 5 and 6. However, the isolated yields of 1 did
not exceed 4%. Interestingly, the best isolated yield of 3.4% for
the cyclophane assembly in a single step was obtained from a
reaction mixture comprising a large excess of the dianhydride 6 (36
mM) in a mixture of dimethylformamide and acetic acid at 120 1C
to which the dissolved diamine 5 had been added over a period of
1 h. In a typical 1 : 1 entry, a 36 mM solution of both 5 and 6 in
iso-propanol, containing triethylamine as a base, was refluxed for
3 days. After column chromatography, the desired cyclophane 1
was isolated as a white solid in only 1.2% yield. To further
improve the yield of the desired cyclophane, a sequential assembly
strategy was investigated. Thus, one of the two amine functions of
5 was protected with a tert-butoxycarbonyl group (BOC) to
provide the amine 7. Condensation of 2 equiv. of 7 with the
dianhydride 6 gave the doubly BOC protected naphthyldiimide 8
in a yield of 44%, which was deprotected to the diamine 9
quantitatively. Subsequent condensation of the diamine 9 with
the dianhydride 6 provided the desired cyclophane 1 in 40% yield
after column chromatography.
Our interest in cyclophanes results from scanning probe
investigations of p-systems on metallic substrates. While cyclo-
phanes have already been investigated by STM either at the
solid/liquid interface9,10 or after deposition from solution,11
high resolution ultrahigh vacuum (UHV) investigations are
missing so far due to the poor sublimability of the macro-
molecular cyclophanes under investigation.11 As displayed by
UHV-STM investigations, delocalized planar p-systems usual-
ly form well ordered surface patterns on flat substrates.12
However, optical properties of these immobilized chromo-
phores are affected by the electronic states of the underlying
substrate. To decouple the chromophore from the substrate
either multilayers of molecules13 or thin insulating salt layers
have been investigated.14 In cyclophanes, which consist of two
parallel p-systems, adsorption with only one p-system appears
likely, while the second chromophore would be lifted and hence
a University of Basel, Department of Chemistry, St. Johannsring 19,
CH-4056 Basel, Switzerland. E-mail: marcel.mayor@unibas.ch;
Fax: þ41 61 267 1016; Tel: þ41 61 267 1006
b Christian-Albrechts-Universitat zu Kiel, Institut fur Experimentelle
¨
¨
und Angewandte Physik, D-24098 Kiel, Germany. E-mail:
berndt@physik.uni-kiel.de; Fax: þ49 431 880 2510; Tel: þ49 431
880 3850
c Forschungszentrum Karlsruhe GmbH, Institute for Nanotechnology,
P. O. Box 3640, D-76021 Karlsruhe, Germany
w Electronic supplementary information (ESI) available: Synthetic
protocols, analytical data and NMR spectra of the compounds 1,
3–5, 7–9 and 11; X-ray structures of cyclophane 1 with different
solvent molecules; UHV STM pictures of monolayers of 1 and 11
on Au(111). Crystallographic data in CIF format: CCDC
673653–673654. See DOI: 10.1039/b719796a
Compound 1 and its precursors have been fully character-
1
ized by H- and 13C-NMR spectroscopy, mass spectrometry
ꢀc
This journal is The Royal Society of Chemistry 2008
2370 | Chem. Commun., 2008, 2370–2372

View Article Online
Fig. 2 (a) Large scale STM image of a cluster of self-assembled
cyclophanes 1 on Au(111) and (b) enlarged stripe-region with the structure
of 1 overlaid. Arrows in (a) represent unit cell vectors of the 2D molecular
organisation. Dotted lines in (b) indicate stabilizing hydrogen bonds.
structure, a CH2Cl2 solvent molecule is partially penetrating the
cavity of 1. A very comparable solid state structure has been
obtained from technical grade xylene with a para-xylene molecule
partially penetrating the cavity of 1.17
Scheme 1 Synthesis of the macrocycle 1 and its precursors.w Molecular
structures of the compounds 10 and 11. (a) NBS, AIBN, CHOOCH3, hn,
4.5 h, 48%; (b) C6H4(CO)2NK, K2CO3, CH3CN, reflux, 5 h, 86%; (c)
N2H4, MeOH, reflux, 2 h, 82%; (d) Et3N, i-PrOH, reflux, 3 d, 2–3%; (e)
BOC2O, CHCl3, 0 1C, 5 h, 47%; (f) Et3N, i-PrOH, reflux, 3 d, 44%; (g)
CF3COOH, CH2Cl2, rt, 2 h, 100%; (h) Et3N, i-PrOH, reflux, 3 d, 40%.
Due to the short rigid spacers of 1, the tiny cavity between
the two NDIs should not allow for complexation of electron
rich aromatic systems. The cyclophane 1 was still to some
extent able to quench the fluorescence of the electron rich
guest 1,5-dimethoxynaphthalene 10. Assuming a 1 : 1 com-
plex 10 C 1, a moderate binding constant of 81 Mꢁ1 has been
determined. As a control experiment, the model compound 11
displayed comparable quenching properties with an associa-
tion constant of the same order, 106 Mꢁ1, pointing to associa-
tion of 10 to the outer surface as a quenching mechanism.18
Of particular interest was the suitability of 1 for UHV experi-
ments and its self-assembly properties on metal surfaces. Thus, the
cyclophane 1 was deposited on Au(111) samples in a UHV
chamber by sublimation.19a Subsequent investigation of the sam-
ple surface by STM at 6 K revealed large islands consisting of
parallel stripes with a regular periodicity of about 2.7 ꢂ 0.2 nm
(Fig. 2a). The high resolution of the STM pictures of the mono-
layers formed by 1 together with the comparison with monolayers
obtained from the NDI model compound 11,19b made it possible
to identify individual cyclophanes as the building blocks of the
stripes (Fig. 2b)19c and demonstrated the sublimation of cyclo-
phane molecules without degradation. The bent crescent-like
shape of the immobile cyclophane 1 corresponds to its solid state
structure. As illustrated by the added model, the stripes consist of
two rows of intercalated cyclophane molecules which are rotated
by about 1201 with respect to each other. Each row is stabilized by
a pair of intermolecular hydrogen bonds, formed between the
carbonyl oxygens and the naphthalene hydrogens of the surface
immobilized NDI chromophores (dotted lines in Fig. 2b). Similar
hydrogen bonds have been found to stabilize the formation of
supramolecular nanotubes of amino acid functionalized NDIs.20
and elemental analysis.w Furthermore, single crystals suitable
for X-ray analysis have been obtained by slow evaporation of
solutions of 1 in CH2Cl2 or xylene.z
In spite of the molecule’s symmetry, the cyclophane 1 does not
crystallize with an inversion centre, but opens a minute cavity by
tilting both NDI planes with respect to each other (Fig. 1). The
inter NDI C–C distances are with 0.71 nm between C20 and C40
doubled at the front rim compared with the values of 0.36 nm
observed in the back (C14–C46). Furthermore, the interlinking
tert-butylphenyl spacers both point towards the open side with a
distance between C1 and C33 of 1.59 nm. In the solid state
Fig. 1 Solid state structure of the cyclophane 1 obtained by evapora-
tion of a CH2Cl2 solution. The partially penetrating CH2Cl2 molecule
is omitted for clarity. ORTEP representation; thermal ellipsoids are set
at the 50% probability level.
ꢀc
This journal is The Royal Society of Chemistry 2008
Chem. Commun., 2008, 2370–2372 | 2371

View Article Online
ORTEP3. 1-xylene formula C68.60H61.20N4O8, M ¼ 1069.66, F(000) ¼
2259.200, colourless block, size 0.32 ꢃ 0.34 ꢃ 0.44 mm3, monoclinic, space
group P21/c, Z ¼ 4, a ¼ 17.7349(2) A, b ¼ 16.9022(2) A, c ¼ 19.1495(2) A, a
¼ 901, b ¼ 92.6081(6)1, g ¼ 901, V ¼ 5734.29(11) A3, Dcalc. ¼ 1.239 Mg
The intercalation of both rows as well as the densely packed
arrangement of the parallel stripes seems to be driven by max-
imisation of the surface coverage. The two vectors defining the 2D
unit cell have lengths of 3.5 ꢂ 0.2 and 0.9 ꢂ 0.1 nm, respectively
and open an angle of 50 ꢂ 31.
m
ꢁ3. Minimal/maximal transmission 0.97/0.97, m ¼ 0.081 mmꢁ1. The
COLLECT suite has been used for data collection and integration. From
a total of 50 388 reflections (Ymax ¼ 27.8581), 13 631 were independent
(merging r ¼ 0.033). From these, 9239 were considered as observed (I 4
3.0s(I)) and were used to refine 802 parameters. The structure was solved by
direct methods using the program SIR92. Least-squares refinement against
F was carried out on all non-hydrogen atoms using the program CRYS-
TALS. R ¼ 0.0839 (observed data), wR ¼ 0.0867 (all data), GOF ¼ 1.0531.
Minimal/maximal residual electron density ¼ ꢁ0.46/1.12 e Aꢁ3. Chebychev
polynomial weights were used to complete the refinement. Restraints have
been used to control the refinement of the disordered solvent molecules and
one tert-butyl group in the case of the single crystal obtained from technical
xylene. Plots were produced using ORTEP3.
The reconstruction of the underlying Au surface can still be
observed (see contents entry image) which is indicative of a
weak interaction between molecule and substrate.21 More
importantly, this image shows that the molecules are attached
to the Au with one chromophore, while the other remains
separated from the substrate. The structural analogy of im-
mobilized 1 with its solid state structure suggests a comparable
spacing of approximately 0.7 nm from the surface for the
upper chromophore. While the conservation of the spatial
separation of both chromophores in these surface immobilized
cyclophanes and the predominant interaction of the metal
surface with only one of the two p-systems are promising
results on the way towards surface decoupled chromophores,
the parallel arrangement of the main axis of both NDI
1 M. M. Pellegrin, Recl. Trav. Chim. Pays-Bas, 1899, 18, 457.
2 F. Vogtle, Cyclophane-Chemistry, Teubner, Stuttgart, 1990.
¨
3 Modern Cyclophane Chemistry, ed. R. Gleiter and H. Henning,
Wiley-VCH, Weinheim, 2004.
4 D. J. Cram and J. M. Cram, Acc. Chem. Res., 1971, 4, 204.
5 T. Kawashima, T. Otsubo, Y. Sakata and S. Misumi, Tetrahedron
Lett., 1978, 51, 5115.
6 (a) S. I. Pascu, T. Jarrosson, C. Naumann, S. Otto, G. Kaiser and J. K.
M. Sanders, New J. Chem., 2005, 29, 80; (b) K. D. Johnstone, K.
Yamaguchi and M. J. Gunter, Org. Biomol. Chem., 2005, 3, 3008.
7 A. J. Blacker, J. Jazwinski, J.-M. Lehn, M. Cesario, J. Guilhem
and C. Pascard, Tetrahedron Lett., 1987, 28, 6057.
8 (a) G. D. Fallon, M. A.-P. Lee, S. J. Langford and P. J. Nichols,
Org. Lett., 2004, 6, 655; (b) J. G. Hansen, N. Feeder, D. G.
Hailton, M. J. Gunter, J. Becher and J. K. M. Sanders, Org. Lett.,
2000, 2, 449; (c) T. Iijima, S. A. Vignon, H. R. Tseng, T. Jarrosson,
J. K. M. Sanders, F. Marchioni, M. Venturi, E. Apostoli, V.
Balzani and J. F. Stoddart, Chem.–Eur. J., 2004, 10, 6375.
subunits may be less favourable considering Forster energy
¨
transfer as a potential quenching mechanism for the decoupled
chromophore.22 However, the synthesis described here is
ideally suited for the assembly of cyclophanes consisting of
two differently functionalized NDI subunits. Through steri-
cally demanding core substituents the intramolecular spatial
arrangement of both chromophores of the cyclophane may
become tuneable. Furthermore, the optical properties of both
NDIs can be tailored by these substituents.15
9 F. Jackel, M. D. Watson, K. Mullen and J. P. Rabe, Phys. Rev. B:
¨
Condens. Matter Mater. Phys., 2006, 73, 045423.
¨
In conclusion, the design, synthesis and characterization of
a new rigid NDI cyclophane are reported. Its immobilization
and self-assembly on Au(111) are discussed. The cyclophane is
perfectly sublimable and self-assembles to ordered patterns
driven by hydrogen bonds. Moreover the molecules adopt a
staged configuration on the surface with one chromophore
over the other. This system may be regarded as a model for the
design of separated platforms. Related cyclophane structures
are currently under investigation. Such systems are of great
interest for single molecule fluorescence studies using STM.
The authors from Basel acknowledge the support of the
Swiss National Center of Competence in Research ‘‘Nanoscale
Science’’ and of the Swiss National Science Foundation. The
authors from Kiel acknowledge support through SFB 677.
10 M. D. Watson, F. Jackel, N. Severin, J. P. Rabe and K. Mullen, J.
¨
¨
Am. Chem. Soc., 2004, 126, 1402.
11 R. E. Palmer and Q. Guo, Phys. Chem. Chem. Phys., 2002, 4, 4275.
12 J. V. Barth, Annu. Rev. Phys. Chem., 2007, 58, 375.
13 (a) H. Kuhn, Pure Appl. Chem., 1965, 11, 345; (b) K. H. Drexhage, M.
Fleck, F. P. Schafer and W. Sperling, Ber. Bunsen-Ges. Phys. Chem.,
¨
1966, 72, 1179; (c) X. H. Qiu, G. V. Nazin and W. Ho, Science, 2003,
299, 542; (d) Z.-C. Dong, X.-L. Guo, A. S. Trifonov, P. S. Dorozhkin,
K. Miki, K. Kimura, S. Yokoyama and S. Mashiko, Phys. Rev. Lett.,
´
2004, 92, 086801; (e) E. Cavar, M.-C. Blum, M. Pivetta, F. Patthey, M.
¨
Chergui and W.-D. Schneider, Phys. Rev. Lett., 2005, 95, 196102.
14 (a) R. Berndt, R. Gaisch, J. K. Gimzewski, B. Reihl, R. R.
Schlittler, W.-D. Schneider and M. Tschudy, Science, 1993, 262,
1425; (b) G. Hoffmann, L. Libioulle and R. Berndt, Phys. Rev. B:
Condens. Matter Mater. Phys., 2002, 65, 212107.
15 (a) F. Wurthner, S. Ahmed, C. Thalacker and T. Debaerdemaeker,
¨
Chem.–Eur. J., 2002, 8, 4742; (b) A. B"aszczyk, M. Fischer, C. von
Hanisch and M. Mayor, Helv. Chim. Acta, 2006, 89, 1986.
¨
16 P. Pengo, G. D. Pantos, S. Otto and J. K. Sanders, J. Org. Chem.,
2006, 71, 7063.
17 Further details concerning both X-ray structures of 1 are available
in the electronic supporting information.
18 (a) J. J. Reczek, K. R. Villazor, V. Lynch, T. M. Swager and B. L.
Iverson, J. Am. Chem. Soc., 2006, 128, 7995; (b) G. Kaiser, T.
Jarrosson, S. Otto, Y.-F. Ng, A. D. Bond and J. K. M. Sanders,
Angew. Chem., Int. Ed., 2004, 43, 1959; (c) S. Bhosale, A. L. Sisson,
Notes and references
z Crystal data and structure refinement for 1-CH2Cl2 and 1-xylene: The
crystals were measured on a Nonius KappaCCD diffractometer at 173 K
using graphite-monochromated Mo Ka-radiation with l ¼ 0.71073 A. 1-
CH2Cl2 formula C53H42Cl2N4O8, M ¼ 933.84, F(000) ¼ 972, colourless
3
ꢀ
plate, size 0.09 ꢃ 0.14 ꢃ 0.30 mm , triclinic, space group P1, Z ¼ 2, a ¼
P. Talukdar, A. Furstenberg, N. Banerji, E. Vauthey, G. Bollot, J.
¨
¨
Mareda, C. Roger, F. Wurthner, N. Sakai and S. Matile, Science,
2006, 313, 84.
11.2478(2) A, b ¼ 13.9007(2) A, c ¼ 14.9298(3) A, a ¼ 90.3583(11)1, b ¼
¨
110.9346(11)1, g ¼ 90.1421(12)1, V ¼ 2180.15(7) A3, Dcalc. ¼ 1.422 Mg mꢁ3
.
Minimal/maximal transmission 0.97/0.98, m ¼ 0.214 mmꢁ1. The COLLECT
suite has been used for data collection and integration. From a total of
20 283 reflections (Ymax ¼ 27.8711), 10 386 were independent (merging r ¼
0.041). From these, 6267 were considered as observed (I 4 1.0s(I)) and were
used to refine 622 parameters. The structure was solved by direct methods
using the program SIR92. Least-squares refinement against F was carried
out on all non-hydrogen atoms using the program CRYSTALS. R ¼ 0.0662
(observed data), wR ¼ 0.1089 (all data), GOF ¼ 1.1417. Minimal/maximal
residual electron density ¼ ꢁ1.09/0.43 e Aꢁ3. Chebychev polynomial
weights were used to complete the refinement. Plots were produced using
19 Further details concerning the UHV STM experiment together with
additional pictures are displayed in the supporting information: (a)
Experimental set-up and sublimation procedure; (b) STM pictures of
11; (c) Details of STM pictures of 1; (d) Au(111) reconstruction.
20 G. Dan Pantos, P. Pengo and J. K. M. Sanders, Angew. Chem., Int.
Ed., 2007, 46, 194.
21 F. Vonau, D. Aubel, L. Bouteiller, G. Reiter and L. Simon, Phys.
Rev. Lett., 2007, 99, 086103.
22 Principles of Fluorescence Spectroscopy, ed. J. R. Lakowicz,
Springer, New York, 2006, ch. 13, p. 443.
ꢀc
This journal is The Royal Society of Chemistry 2008
2372 | Chem. Commun., 2008, 2370–2372