Nanopatterning the surface with ordered supramolecular architectures of N9-alkylated guanines: STM reveals

Article abstract of DOI:10.1039/c0cc00443j

STM study of the self-assembly at the solid-liquid interface of substituted guanines exposing in the N⁹-position alkyl side chains with different lengths revealed the formation of distinct crystalline nanopatterns.

Full text of DOI:10.1039/c0cc00443j

View Article Online / Journal Homepage / Table of Contents for this issue
COMMUNICATION
www.rsc.org/chemcomm | ChemComm
Nanopatterning the surface with ordered supramolecular architectures
of N9-alkylated guanines: STM revealsw
Artur Ciesielski,a Rosaria Perone,b Silvia Pieraccini,b Gian Piero Spada*b and
Paolo Samorı*a
Received 17th March 2010, Accepted 29th April 2010
First published as an Advance Article on the web 19th May 2010
DOI: 10.1039/c0cc00443j
STM study of the self-assembly at the solid–liquid interface of
substituted guanines exposing in the N9-position alkyl side
chains with different lengths revealed the formation of distinct
crystalline nanopatterns.
the effort was mainly addressed towards the study of lipophilic
guanosine monolayers.9a,14 We decided to extend our studies
at the solid–liquid interface to physisorbed monolayers of
N9-alkylguanines because the absence of the sugar when
compared to the previously studied guanosines and the presence
of an aliphatic side-group can be foreseen to favor the
molecular adsorption on graphite.1d In general, the formation
of ordered motifs stabilized by hydrogen bonds on a solid
surface requires the fine tuning of the interplay between the
interactions among adjacent molecules and the adsorbate–
substrate interactions.15 To achieve a full understanding of
the self-assembly of guanine at the solid–liquid interface, here
we performed a sub-molecularly resolved STM study of
physisorbed monolayers on graphite of a series of N9-alkyl-
guanines with linear alkyl side-chains from –C2H5 up to
–C18H37 (Fig. 1).16 This comparative study was carried out
by applying a drop of a 1.0 Æ 0.1 mM solution of the chosen
guanine molecule in 1,2,4-trichlorobenzene (TCB) on freshly
cleaved highly oriented pyrolytic graphite (HOPG).
The self-assembly of small molecular modules into non-covalently
linked polymeric nanostructures is a subject of continuous
interest.1 In particular, supramolecular structures with a high
degree of order can be obtained through the self-association of
organic molecules on flat solid surfaces.2 Such structures can
be used as scaffolds to position electrically/optically active
groups in pre-determined locations in 2D,3 thereby paving the
way towards a wide range of applications, e.g. in electronic
and optical devices.4 Among weak interactions, H-bonding
offers high control over the process of molecular self-assembly
because it combines reversibility, directionality, specificity
and cooperativity. Such a unique character is the basis of
sophisticated programs for self-assembly such as those based
on the Watson–Crick base pairing5 which directs the formation
of the helical structure of DNA. Among nucleobases, guanine
is very versatile:6 depending on the experimental conditions it
can undergo different self-assembly pathways. In the presence
of certain metal ions, guanines can form G-quartet based
architectures (Fig. 1b) such as octamers or columnar polymeric
aggregates.6b–c,7 In the absence of metal templates, guanines
without a C(8) sterically demanding substituent8 can self-assemble,
both in solution and in the solid state, into ribbonlike
architectures.6c,9 For guanosine derivatives physisorbed at
surfaces the thermodynamically stable ribbons were found to
be characterized by cyclic NH(2)–O(6) and NH(1)–N(7)
hydrogen bonds (Fig. 1c). In the solid state, the ribbons, by
bridging gold electrodes, were found to be photoconductive.10
More interestingly, these ribbons also exhibit rectifying
properties.11 A field-effect transistor based on these supra-
molecular structures was described.12 Hitherto guanine based
H-bonded supramolecular architectures were self-assembled
on surfaces into highly ordered motifs and studied with
scanning tunneling microscopy (STM) under ultra-high
vacuum (UHV).13 Conversely at the solid–liquid interface
For the crystalline pattern obtained from each guanine self-
assembled on HOPG the unit cell parameters, i.e. length of
vectors a and b, a (angle between the vectors), unit cell area
(A), number of molecules in the unit cell (Nmol), area occupied
by a single molecule in the unit cell (Amol, with Amol = A/Nmol
)
and estimated projection of the molecular van der Waals
volume onto surface (AvdW) are given in Table 1. All proposed
packing motifs for molecules 1–9 have been compared with
theoretical models (see Supplementary Informationw).
Fig. 2a shows an STM image of the monolayer obtained
from molecule 1: it reveals a crystalline ribbon-like architecture.
In this 2D crystal the ethyl side chains are most likely
a
´
´
ISIS/UMR CNRS 7006, Universite de Strasbourg, 8 allee Gaspard
Monge, 67000 Strasbourg, France. E-mail: samori@unistra.fr
b Dipartimento di Chimica Organica ‘‘A. Mangini’’, Alma Mater
`
Studiorum, Universita di Bologna, Via S. Giacomo 11,
Fig. 1 (a) Chemical formulae of the different investigated guanines;
H-bonded motifs of self-assembled guanines; (b) quartet based
(involved pairing: NH(2)–N(7) and NH(1)–O(6)) and (c) ribbon based
(involved pairing: NH(2)–O(6) and NH(1)–N(7)) architectures.
40126 Bologna, Italy. E-mail: gianpiero.spada@unibo.it
w Electronic supplementary information (ESI) available: Synthesis of
guanine derivatives; investigation in solution; experimental details for
STM investigation. See DOI: 10.1039/c0cc00443j
ꢀc
This journal is The Royal Society of Chemistry 2010
Chem. Commun., 2010, 46, 4493–4495 | 4493

View Article Online
Table 1 Unit cell parameters of all guanine derivatives at the solid–liquid interface
Unit cell parametersa
a/nm
b/nm
a
A/nm2
Nmol
Amol/nm2
AvdW/nm2
Guanine derivative
Side chain
1
2
3
4
5
6
7
8
9
C2H5
1.00 Æ 0.2
0.98 Æ 0.2
0.97 Æ 0.2
1.27 Æ 0.2
1.19 Æ 0.2
1.00 Æ 0.2
1.00 Æ 0.2
1.00 Æ 0.2
1.00 Æ 0.2
1.51 Æ 0.2
1.63 Æ 0.2
1.85 Æ 0.2
2.01 Æ 0.2
1.46 Æ 0.2
4.19 Æ 0.2
4.73 Æ 0.2
5.27 Æ 0.2
5.81 Æ 0.2
(92 Æ 3)1
(84 Æ 3)1
(81 Æ 3)1
(58 Æ 3)1
(96 Æ 3)1
(68 Æ 3)1
(68 Æ 3)1
(68 Æ 3)1
(68 Æ 3)1
1.51 Æ 0.21
1.58 Æ 0.20
1.77 Æ 0.19
2.15 Æ 0.22
1.72 Æ 0.21
3.76 Æ 0.21
4.25 Æ 0.21
4.73 Æ 0.21
5.22 Æ 0.21
2
1
2
2
1
4
4
4
4
0.75 Æ 0.1
1.58 Æ 0.2
0.88 Æ 0.1
1.07 Æ 0.1
1.72 Æ 0.2
0.94 Æ 0.1
1.06 Æ 0.1
1.18 Æ 0.1
1.31 Æ 0.1
0.55 Æ 0.02
0.75 Æ 0.02
0.80 Æ 0.02
0.85 Æ 0.02
0.90 Æ 0.02
1.00 Æ 0.02
1.10 Æ 0.02
1.20 Æ 0.02
1.30 Æ 0.02
C6H13
C7H15
C8H17
C10H21
C12H25
C14H29
C16H33
C18H37
a
a and b are the vector lengths and a the angle between those vectors; A is the unit cell area, Nmol the number of molecules in the unit cell and
Amol (=A/Nmol) is the area occupied by single molecules within the unit cell; AvdW is the estimated van der Waals area.
physisorbed flat on the surface, although due to their high
conformational dynamics they could not be resolved. The area
occupied by a single molecule 1 corresponds to 0.75 Æ 0.1 nm2,
being in good agreement with the van der Waals area of 1.
The supramolecular motif can be well described by the
formation of a one-dimensional H-bonded ribbon involving
the following pairing: NH(2)–O(6) and NH(1)–N(7) (model in
Fig. 1c), in good accordance with previous observations on
N9-octadecylguanine 91d and guanosine9a derivatives.
Self-assembled structures of molecule 2 exhibit a 2D crystal
with the hexyl side-chains physisorbed flat on the surface
(Fig. 2b). Differently from the monolayer of 1, self-assembly
of 2 is not dictated by the formation of H-bonding between
adjacent molecules, but rather unspecific van der Waals
interactions between molecules and the substrate rule the
generation of an ordered monolayer. A similar motif was
observed in a monolayer of 5 (Fig. 2c). The packing is very
loose as proved by the large discrepancy between Amol and
AvdW. Despite such large voids which could host a second
ad-molecule, we observed only one molecule per unit cell as
probably ruled by the registry with the substrate.
Fig. 3 STM images of monolayers of (a) 3 and (b) 4 forming dimers.
Tunneling parameters: It = 17 pA, Vt = 360 mV.
NH(1)–O(6). The octyl side chains are supposedly physisorbed
on the graphite surface. However, differently from the case of the
pattern formed through self-assembly of 3, within the dimers
only one alkyl chain is physisorbed on the HOPG surface.
Subsequently, we have focused our attention on the
self-assembly of guanines exposing longer alkyl side chains.
Interestingly, regardless of the length of the side chain (C12H25
for 6, C14H29 for 7, C16H33 for 8 and C18H37 for 9) the
observed monolayers exhibit a similar motif consisting of
H-bonded ribbons, involving the pairing NH(2)–O(6) and
NH(1)–N(7) (Fig. 4). In the 2D crystals the long side chains
are clearly visible: they are physisorbed flat on the surface and
are interdigitated between adjacent supramolecular ribbons,
thereby stabilizing the entire monolayer. Further, the comparison
of the unit cell parameters of monolayers of 6–9 self-assembled at
the HOPG–solution interface (Table 1) reveals that the only
difference between those structures is the value of the b vector,
thus affecting also the area occupied by a single guanine molecule
(Amol). Interestingly, the difference between Amol6 and Amol7
matches the difference between Amol7 and Amol8, i.e. 0.11 nm2,
being in good agreement with the area occupied by an ethylene
group, i.e. 0.12 Æ 0.01 nm2. The difference between Amol8 and
Amol9 amounts to 0.13 Æ 0.01 nm2. For monolayers of 6–9 the
packing is extremely tight as revealed by the very similar values
of Amol and AvdW for each system.
Fig. 3a portrays the STM image recorded for a monolayer of
molecule 3. It reveals large ordered lamellae featuring a dimer
packing motif involving the following pairing: NH(2)–N(7) and
NH(1)–O(6). The comparison of the area occupied by a single
molecule, i.e. 0.88 Æ 0.1 nm2, with the van der Waals molecule’s
size of 0.80 Æ 0.02 nm2 suggests that the heptyl side chains
are physisorbed at the surface, though due to their high
conformational dynamics they could not be resolved.
Fig. 3b shows a monolayer of 4 at the HOPG–solution
interface. As in the case of 3, the packing can be described by
the formation of a dimer involving the pairing NH(2)–(7) and
The thermodynamic characteristics of guanine association,
obtained from the gas phase experiments,17 revealed that the
energy of supramolecular polymerization in motifs like those
visualized by STM amounts to 32–36 kcal molÀ1 per molecule.
In comparison the adsorption energy of alkyl chains on
the HOPG surface, determined by temperature-programmed
desorption experiments,18 increases linearly with the chain
Fig. 2 STM images of monolayers of 1, 2 and 5. Ribbon-like
structure of 1 (a) and crystalline structures of 2 (b) and 5 (c). Tunneling
parameters: average tunneling current (It) = 15 pA, bias voltage
(Vt) = 350 mV.
ꢀc
This journal is The Royal Society of Chemistry 2010
4494 | Chem. Commun., 2010, 46, 4493–4495

View Article Online
2009, 1192; (d) A. Ciesielski, S. Lena, S. Masiero, G. P. Spada and
P. Samorı, Angew. Chem., Int. Ed., 2010, 49, 1963.
2 (a) J. A. Theobald, N. S. Oxtoby, M. A. Phillips, N. R. Champness
and P. H. Beton, Nature, 2003, 424, 1029; (b) J. V. Barth,
G. Costantini and K. Kern, Nature, 2005, 437, 671; (c) M. Surin
and P. Samorı, Small, 2007, 3, 190; (d) T. Kudernac, S. B. Lei,
J. A. A. W. Elemans and S. De Feyter, Chem. Soc. Rev., 2009, 38,
402.
3 (a) G. P. Spada, S. Lena, S. Masiero, S. Pieraccini, M. Surin and
P. Samorı, Adv. Mater., 2008, 20, 2433; (b) A. Ciesielski, L. Piot,
P. Samorı, A. Jouaiti and M. W. Hosseini, Adv. Mater., 2009, 21,
1131.
4 A. P. H. J. Schenning and E. W. Meijer, Chem. Commun., 2005,
3245.
5 J. D. Watson and F. H. C. Crick, Nature, 1953, 171, 737.
6 (a) S. Sivakova and S. J. Rowan, Chem. Soc. Rev., 2005, 34, 9;
(b) J. T. Davis and G. P. Spada, Chem. Soc. Rev., 2007, 36, 296;
(c) S. Lena, S. Masiero, S. Pieraccini and G. P. Spada, Chem.–Eur. J.,
2009, 15, 7792.
7 (a) J. T. Davis, Angew. Chem., Int. Ed., 2004, 43, 668;
(b) S. Pieraccini, S. Masiero, O. Pandoli, P. Samorı and
G. P. Spada, Org. Lett., 2006, 8, 3125; (c) L. Ma, M. Melegari,
M. Colombini and J. T. Davis, J. Am. Chem. Soc., 2008, 130, 2938;
(d) S. Martic, X. Y. Liu, S. N. Wang and G. Wu, Chem.–Eur. J.,
2008, 14, 1196; (e) M. Nikan and J. C. Sherman, Angew. Chem.,
Int. Ed., 2008, 47, 4900; (f) D. Gonzalez-Rodriguez, J. L. J. van
Dongen, M. Lutz, A. L. Spek, A. P. H. J. Schenning and
E. W. Meijer, Nat. Chem., 2009, 1, 151; (g) M. D. Rivera-Sanchez,
I. Andujar-de-Sanctis, M. Garcia-Arriaga, V. Gubala, G. Hobley
and J. M. Rivera, J. Am. Chem. Soc., 2009, 131, 10403.
8 J. L. Sessler, M. Sathiosatham, K. Doerr, V. Lynch and
K. A. Abboud, Angew. Chem., Int. Ed., 2000, 39, 1300.
9 (a) G. Gottarelli, S. Masiero, E. Mezzina, S. Pieraccini, J. P. Rabe,
P. Samorı and G. P. Spada, Chem.–Eur. J., 2000, 6, 3242;
(b) I. Yoshikawa, S. Yanagi, Y. Yamaji and K. Araki, Tetrahedron,
2007, 63, 7474; (c) H. Liddar, J. Li, A. Neogi, P. B. Neogi,
A. Sarkar, S. Cho and H. Morkoc, Appl. Phys. Lett., 2008, 92,
013309; (d) A. M. S. Kumar, J. D. Fox, L. E. Buerkle,
R. E. Marchant and S. J. Rowan, Langmuir, 2009, 25, 653;
(e) S. Mihai, A. Cazacu, C. Arnal-Herault, G. Nasr, A. Meffre,
A. van der Lee and M. Barboiu, New J. Chem., 2009, 33, 2335;
(f) W. M. Heckl, D. P. E. Smith, G. Binning, H. Klagges,
T. W. Hansch and J. Maddocks, Proc. Natl. Acad. Sci. U. S. A.,
1991, 88, 8003; (g) W. Mamdouh, R. E. A. Kelly, M. Dong,
L. N. Kantorovich and F. Besenbacher, J. Am. Chem. Soc.,
2008, 130, 695.
Fig. 4 STM images of hydrogen bonded ribbons obtained from (a) 6,
(b) 7, (c) 8, and (d) 9. Tunneling parameters: It = 17 pA, Vt = 360 mV.
length and is in the same energy range (see Table S1 in
Supplementary Informationw).
In summary, we have performed a comparative STM study
on the self-assembly at the HOPG–solution interface of
substituted guanines exposing in the N9-position alkyl side
chains with different length. Molecules 1–9 were found to form
monomorphic 2D crystals, which are stable on the several tens
of min time scale and exceed various hundreds of nm2. Subtle
changes in the length of the alkyl side-chains dramatically
influenced the 2D patterns on graphite. Derivatives with alkyl
tails longer than C12 (6–9) self-assembled into linear H-bonded
ribbons through the NH(2)–O(6) and NH(1)–N(7) pairing
with 4 molecules in the unit cell. The same H-bonding pattern
was observed for N9-ethylguanine 1, but the packing shows
only 2 molecules in the unit cell (the adjacent H-bonded non-
centrosymmetric ribbons run indeed in a parallel way while for
6–9 they are antiparallel). For derivatives with tails of inter-
mediate length (from C6 to C10) no H-bonded supramolecular
polymers were formed at the surface: ordered monolayers of
single (non-H-bonded) molecules (2 and 5) or H-bonded
dimers (3 and 4) were observed. In light of the dynamic
self-assembly characteristics of guanines, our results may be
of interest for the generation of responsive nanopatterned
surfaces featuring pre-programmed structural motifs at the
supramolecular level.
10 R. Rinaldi, E. Branca, R. Cingolani, S. Masiero, G. P. Spada and
G. Gottarelli, Appl. Phys. Lett., 2001, 78, 3541.
11 R. Rinaldi, G. Maruccio, A. Biasco, V. Arima, R. Cingolani,
T. Giorgi, S. Masiero, G. P. Spada and G. Gottarelli, Nano-
technology, 2002, 13, 398.
12 G. Maruccio, P. Visconti, V. Arima, S. D’Amico, A. Blasco,
E. D’Amone, R. Cingolani, R. Rinaldi, S. Masiero, T. Giorgi
and G. Gottarelli, Nano Lett., 2003, 3, 479.
13 (a) R. Otero, M. Schock, L. M. Molina, E. Laegsgaard,
I. Stensgaard, B. Hammer and F. Besenbacher, Angew. Chem.,
Int. Ed., 2005, 44, 2270.
14 (a) T. Giorgi, S. Lena, P. Mariani, M. A. Cremonini, S. Masiero,
S. Pieraccini, J. P. Rabe, P. Samorı, G. P. Spada and G. Gottarelli,
J. Am. Chem. Soc., 2003, 125, 14741; (b) S. Lena, G. Brancolini,
G. Gottarelli, P. Mariani, S. Masiero, A. Venturini, V. Palermo,
O. Pandoli, S. Pieraccini, P. Samorı and G. P. Spada, Chem.–Eur. J.,
2007, 13, 3757.
We thank Dr Luc Piot for performing preliminary experi-
ments on molecule 1. This work was supported by the COST
Network G4-NET (MPNS Action MP0802), the EC Marie
Curie ITN-SUPERIOR (PITN-GA-2009-238177), the EC
FP7 ONE-P large-scale project no. 212311, the International
Center for Frontier Research in Chemistry (FRC, Strasbourg)
and the University of Bologna.
15 S. De Feyter and F. C. De Schryver, Chem. Soc. Rev., 2003, 32,
139.
16 Preliminary 1H-NMR experiments (see ESI) showed that the
various alkylguanines exhibit a very similar behaviour in solution
and form hydrogen-bonded ribbonlike structures1d,9a
.
17 J. Sponer, J. Leszczynski and P. Hobza, J. Phys. Chem., 1996, 100,
1965.
Notes and references
18 (a) K. Paserba and A. J. Gellman, Phys. Rev. Lett., 2001, 86, 4338;
(b) A. J. Gellman and K. P. Paserba, J. Phys. Chem. B, 2002, 106,
13231; (c) T. Muller, G. W. Flynn, A. T. Mathauser and
A. Teplyakov, Langmuir, 2003, 19, 2812.
1 (a) J. M. Lehn, Science, 2002, 295, 2400; (b) T. F. A. de Greef and
E. W. Meijer, Nature, 2008, 453, 171; (c) O. Ivasenko, J. M. MacLeod,
K. Y. Chernichenko, E. S. Balenkova, R. V. Shpanchenko,
V. G. Nenajdenko, F. Rosei and D. F. Perepichka, Chem. Commun.,
ꢀc
This journal is The Royal Society of Chemistry 2010
Chem. Commun., 2010, 46, 4493–4495 | 4495