Monitoring conformational diversity in self-organised monolayers with scanning tunnelling microscopy at near atomic resolution

Article abstract of DOI:10.1039/b401710b

The evaporation of solutions of dendron-functionalised 2,2′- bipyridines on a graphite surface gives highly ordered monolayers; near atomic resolution STM imaging has allowed a detailed conformational analysis to be made.

Full text of DOI:10.1039/b401710b

Monitoring conformational diversity in self-organised monolayers with
scanning tunnelling microscopy at near atomic resolution
Edwin C. Constable,*a Bianca A. Hermann,*b Catherine E. Housecroft,a Leo Merzc and Lukas J.
Scherera
a Department of Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland.
E-mail: edwin.constable@unibas.ch; Fax: +41 61 267 1018; Tel: +41 61 267 1001
b WMI/CeNS, LMU Munich, Walther-Meissner-Str. 8, 85748 Garching, Germany.
E-mail: b.hermann@cens.de; Fax: +49 89 289 14258; Tel: +49 89 289 14206
c
Institute of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
Received (in Cambridge, UK) 5th February 2004, Accepted 24th February 2004
First published as an Advance Article on the web 11th March 2004
The evaporation of solutions of dendron-functionalised 2,2A-
bipyridines on a graphite surface gives highly ordered mono-
layers; near atomic resolution STM imaging has allowed a
detailed conformational analysis to be made.
dendritic wedge was coupled with 1 under phase-transfer condi-
tions to give 4 in 74% yield.† A related ligand with a spacer
between the bipy unit and the wedge has been reported by
Vögtle.12
Compound 4 contains two peripheral first-generation dendritic
wedges. One drop of a 0.2 mM CH2Cl2 or hexane solution of 4 was
allowed to evaporate on a freshly cleaved highly-oriented pyrolytic
graphite (HOPG) surface. The formation of monolayers was
immediately detected (Fig. 1) by low-current STM measurements‡
under ambient conditions. The results were fully reproducible.
When measured with a negative bias voltage, the HOMOs of the
molecule are visualised in the STM image.13 Semi-empirical
calculations at the PM3 level§ confirmed the expected ordering of
orbitals with a cluster of filled orbitals of the benzyl substituents
close to the HOMO–LUMO gap, and filled bipy orbitals lying at
lower energy. The images were obtained at submolecular resolution
showing the extension of the HOMO over the oxygen atoms of the
octyloxy chains, allowing us to interpret them in terms of molecular
structure. Conformational analysis was made by measuring the
distances between the two peripheral benzyl groups which
appeared on the STM image as regions of highest intensity.
Multiple domains were observed in the monolayers; those from
hexane were typically larger than those from CH2Cl2 (Fig. 1),
The direct imaging of chemical species at molecular and sub-
molecular levels using tunnelling and force microscopy has
revolutionised the visualisation and control of nanostructures.1 It is
now possible to probe self-assembled structures using scanning
tunnelling microscopy (STM),2 and interest in nano-assemblies has
grown.3 Although static and dynamic systems have been investi-
gated, there is scope for addressing structural questions. Conven-
tional 3D-methods (single-crystal X-ray crystallography or NMR
spectroscopy) of determining molecular conformation give struc-
tures averaged over some 1015 molecules. Analysis of the surface
molecular conformation of 2D-arrays averaged over hundreds of
molecules can be performed by analysing submolecular resolved
STM images. Here, we report a system that exhibits multiple
conformations on a graphite surface. We have chosen a bipy-based
ligand because the coordination chemistry of such ligands is well
understood,4 and the coordination to a metal centre results in a loss
of conformational freedom, locking the ligand in a cis conforma-
tion. This contrasts with a time-averaged trans conformation in the
free ligand.5,6
consistent with a slower rate of evaporation of hexane (DHv°ap
=
Aromatic-rich Fréchet-type dendrimers7 are ideally suited to
visualisation by tunnelling methods.8 In addition, these dendrimers
provide a significant mechanical barrier to rotation about the bipy
interannular C–C bond when the conjugate is in a conformationally
restricted environment, e.g. a lattice or on a surface. In this paper,
we discuss the consequences of forming monolayers of such
conjugate structures on surfaces and show that not only the global
minimum, but a range of conformations, can be found in surface-
bound domains.
31.56 kJ mol21) than of CH2Cl2 (DH° = 28.82 kJ mol21). We
normally observed two sets of threevadpomains, with an angular
relationship between the sets of 6.5°. Within each set, three
domains reflect the 3-fold symmetry of the graphite surface.14 The
two sets of domains arise from different conformations of 4. In
most images, domains corresponding to two conformers were
observed. Although previously documented,15 this is unusual
because one would expect only the lowest energy conformer to be
present in a thermodynamically stable self-assembled monolayer
(Scheme 2). The domains were very stable; no bleeding or
migration was observed in response to the STM tip.
Compound 4 was synthesised by the reaction of 1 9 with an
electrophilic dendritic wedge (Scheme 1). The first-generation
mesylate wedge 3 10 was prepared from benzylic alcohol 2.7,11 This
Compound 4 possesses many degrees of conformational freedom
(cis–trans at bipy; syn–anti at ArOCH2Ar). We assumed (and
subsequently confirmed) that the bipy-unit would always adopt the
Fig. 1 STM image of a monolayer formed from (a) CH2Cl2 (Ut = 2700
mV, It = 0.8 pA), and (b) hexane (Ut = 2700 mV, It = 1 pA). Left:
different small domains are seen. Right: the image shows part of a domain
extending over > 500 nm 3 500 nm.
Scheme 1 Reagents and conditions: (a) methanesulfonyl chloride, NEt3,
CH2Cl2, 215 °C, 1 h; (b) nBu4NI, EtOAc/H2O, 60 °C, 16 h.
928
C h e m . C o m m u n . , 2 0 0 4 , 9 2 8 – 9 2 9
T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 4

lowest energy trans-conformation.16 As the octyl chains are not
expected to be imaged at high resolution, we limit the discussion to
the syn- or anti-conformation between bipy and the wedge. Co-
planar bipy and benzyl groups were assumed based on p-stacking
interactions with the graphite and the known conformation of
structurally characterised Fréchet dendrimers. In the two domains
in Fig. 2(b), the difference in conformation can be shown by
comparing the relative positions of the benzyl groups of two
neighbouring molecules. Manual fitting of all possible conformers
constrained to co-planar arrangements of the aromatic groups gave
unique fits of the conformations to the STM images [Fig. 2(c) and
2(d)]. Conformer trans-2 (Scheme 2) occurred in two different
packing arrangements [Fig. 2(a) and 2(c)]. These packing arrange-
ments differ in the orientation of the molecules with respect to the
surface, and in the inter- and intra-lamellar spacings. The 2D
packing densities are similar for both arrangements.
The near atomic resolution allows us to assign two conformers
which spontaneously and rapidly form molecular domains under
ambient conditions. Within a molecular domain, only one con-
former is present and domains of different conformers are observed
side by side. No preference for one conformer was observed. We
aim to attach higher-generation dendrons to bipy and investigate
self-assembly properties.
This work was supported by the Swiss National Science
Foundation (program NRP 47) and the University of Basel. We
thank Professor Dr H.-J. Güntherodt for continuous support.
Notes and references
† MeSO2Cl (1.04 mL, 13.5 mmol) was added over 15 min at 215 °C to 2
(1.23 g, 3.38 mmol) and NEt3 (2.08 mL, 16.9 mmol) in dry CH2Cl2 (20 mL).
After 1 h, the mixture was poured into crushed ice/conc. HCl (10 mL). The
CH2Cl2 layer was separated, washed with saturated NaHCO3 solution, dried
(Na2SO4) and evaporated to give 3 (1.80 g, 3.20 mmol) as an oil. Crude 3
(41.5 mg, ca. 75.0 mmol), 1 (6.90 mg, 35.0 mmol), K2CO3 (50.0 mg, 362
mmol) and nBu4NI (2 mg) were stirred in EtOAc (400 mL) and H2O (400 mL)
(60 °C, 16 h). Water (20 mL) was added; the mixture was extracted with
EtOAc (3 3 20 mL). The combined organic layers were dried (MgSO4) and
evaporated. Preparative chromatography (SiO2; CH2Cl2:MeOH 10:1) gave
4 as a white powder (23.1 mg, 74%). For 4: mp 61 °C; dH (250 MHz,
CDCl3): 8.49 [d, J = 6.0 Hz, 2H, H6(bipy)], 8.11 [d, J = 2.3 Hz, 2H, H3(bipy)],
6.91 [dd, J = 5.7, 2.7 Hz, 2H, H5(bipy)], 6.58 [d, J = 2.2 Hz, 4H, H2(Ar)],
We have shown that deposition of a dendritic wedge-function-
alised ligand on HOPG results in the formation of well-defined
monolayers exhibiting different conformations of the molecule.
6.42 [t, J = 2.3 Hz, 2H, H4(Ar)], 5.15 [s, 4H, HOCH Ar], 3.94 [t, J = 6.6 Hz,
2
OCH2CH2
8H, HOCH CH ], 1.80–1.72 [tt, J = 6.8, 6.5 Hz, 8H, H
], 1.49–1.21
2
2
CH3
[m, 48H, Hoctyl-(CH ) ], 0.92–0.84 [t, J 7.8 Hz, 12H, H ]. MS (ESI+): m/z
903.5 ([M + Na]+), 881.6 ([M + H]+). Found: C, 76.10; H, 9.80; N, 2.78.
C56H84N2O6 requires: C, 76.32; H, 9.61; N, 3.18%.
2
5
‡ Experiments were carried out in constant-current mode using a Nano-
scopeIII and data were processed with SXM software (JUni Basel). STM
tips were mechanically formed from Pt/Ir (90%:10%) wire. The 10 nm 3 10
nm images were processed by correlation averaging.
§ PM3 implementation, Spartan’04, JWavefunction Inc., 2003.
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Scheme 2 The two conformations of 4 observed in the STM study.
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Fig. 2 (a) STM image of a monolayer from hexane (10 nm 3 10 nm,
Ut = 2900 mV, It = 4 pA). The benzyl groups have the highest intensity.
(b) STM images of two domains; the angle between them is 6.5° (50 nm 3
50 nm, Ut = 21111 mV, It = 1.5 pA). (c) and (d) Expanded images (10 nm
3 10 nm) of the left and right domains, respectively, of (b). Angle a in (c)
and (d) is 55 and 38°, respectively. Overlaying the molecular structures
confirms that (c) corresponds to conformation trans-2 and (d) to trans-1.
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C h e m . C o m m u n . , 2 0 0 4 , 9 2 8 – 9 2 9
929