Design and STM investigation of intramolecular folding in self-assembled monolayers on the surface

Article abstract of DOI:10.1021/ja046124j

The rational design of catechol bis-amides rendered molecular structures that fold into β-turn mimics at the interface of HOPG and 1-octanol as demonstrated by STM. These self-assembled monolayers provide a prototypical model for linear sequences containing more turn mimics, which will allow for true synthetic surface confined foldamers. Copyright

Full text of DOI:10.1021/ja046124j

Published on Web 10/07/2004
Design and STM Investigation of Intramolecular Folding in Self-Assembled
Monolayers on the Surface
Norbert Schuurmans,† Hiroshi Uji-i,‡ Wael Mamdouh,†,‡ Frans C. De Schryver,‡ Ben L. Feringa,†
Jan van Esch,*,† and Steven De Feyter*,‡
Laboratory of Organic and Inorganic Molecular Chemistry, Material Science Center, Stratingh Institute,
UniVersity of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands, and Department of Chemistry,
Laboratory of Photochemistry and Spectroscopy, UniVersity of LeuVen (KULeuVen), Celestijnenlaan 200-F,
B-3001 LeuVen, Belgium
Received June 30, 2004; E-mail: esch@chem.rug.nl
The patterning of surfaces by lithography1 techniques and
µ-contact printing2 has now reached the 50 nm regime, but the two-
dimensional (2D) spatial positioning of functional groups at
0.2-20 nm length scales is still a major challenge in nanotechnol-
ogy and surface science.3 A powerful approach is the decoration
of interfaces with organic molecules that form regular 2D patterns
by self-assembly, and recently this strategy has been exploited to
organize discrete molecular features.4 It remains however a chal-
lenge to design systems which combine flexibility in the imple-
mentation of chemical functionalities, size, and symmetry.
In proteins, exact positioning of functionality (in 3D) is achieved
from linear sequences of monomers that adopt very specific folded
conformations.5 The observation that linear alkyl fragments featur-
ing amide or urea groups form lamellar structures reminiscent of
the â-sheets found in nature upon adsorption at the solid-liquid
interface of HOPG6 prompted us to introduce a â-turn mimic in
these systems as a next logic step. A 2D turn mimic should obey
the requirements that (i) the entire structure is flat, (ii) the alkyl
groups are spaced by approximately 5.0 Å, that is the optimal
distance for H-bonding,7 and (iii) the amide moieties are kept in
registry, with respect to position as well as orientation.
Here we report on the design of such a 2D turn mimic, which
fulfills all the requirements. The general structure is depicted in
Figure 1a. We envisage that connection of multiple units will render
true minimal foldamers8, which, in principle, will give ultimate
control over the position of integrated functionality in a 2D
crystalline lattice.
Figure 1. (a) Chemical structure of the turn mimics. Optimized conforma-
tions of (b) 1 (n ) m ) 10), (c) 2 (m ) 10, n ) 11), and (d) 3 (m ) 3, n
) 6). (e) Demonstration of the concept showing extended and folded
conformations.
the zigzag plane of both alkyl groups is almost parallel to the surface
of graphite. This is also reflected in the energy differences between
folded and extended conformations for these derivatives. The
relative energy-difference for 2 is 4.7 kcal/mol larger than for 1,
indicating a higher propensity to fold for the former. In both cases
the folded conformation is more favorable then the extended one.
To test the predictions of our model, self-assembled monolayers
at the liquid-HOPG interface were investigated by scanning
tunneling microscopy (STM). STM images of the monolayers of
these compounds are shown in Figure 2a,d. The bright spots
correspond to the catechol groups and the darker rods to the alkyl
chains. The H-bonding sites, via the amide groups appear as bright
spots in the middle of the alkyl chains in the monolayers of 1 and
2 (blue dotted lines). The apparent molecular lengths are in
agreement with the models. The distance between adjacent alkyl
chains was measured to be 0.47 ( 0.01 nm.
The confinement in 2D space greatly reduces conformational
degrees of freedom, which facilitates rational design by means of
molecular modeling.9 The catechol moiety (Figure 1a) is flat,
bifunctional, and derivatives are synthetically accessible; the ortho-
substitution pattern endowes the structure with the necessary
geometry for making turns. A systematic conformational search
identified the conformation most likely to fold in a plane involving
the formation of an intramolecular hydrogen bond (Figure 1b,c).
Modeling showed that folding is facilitated by a dissymmetry with
respect to the spacers. Best results are obtained for combinations n
) m + 1 or n ) m + 3. The longer spacer is bending away from
the catechol moiety. Comparison between a symmetric (1, n ) m
) 10, Figure 1b) and a nonsymmetric (2, n ) m + 1; m ) 10,
Figure 1c) derivative shows that 1 adopts a twisted conformation
when folding in the constrained environment defined by the
graphite, while 2 can adopt the favorable all-trans conformation.
This renders 2 the more likely candidate for our purposes because
this conformation allows for efficient adsorption onto graphite, as
Compound 1 gives rise to head-to-head, tail-to-tail as well as
head-to-tail lamella structures. On the basis of the line profile
analysis as shown in Figure 2b, it indeed does not adopt a folded
conformation in the plane of the graphite (one alkyl chain per
catechol group): possibly only one alkyl chain is adsorbed on the
† University of Groningen.
‡ University of Leuven (KULeuven).
9
13884
J. AM. CHEM. SOC. 2004, 126, 13884-13885
10.1021/ja046124j CCC: $27.50 © 2004 American Chemical Society

C O M M U N I C A T I O N S
Modeling indicated that the minimum-energy conformation for 3
obeyed all the criteria (vide supra). As can be seen in Figure 1d,
the all-trans conformation is similar to that of compound 2.
Although this is a smaller molecule (less methylene groups), and
can therefore not a priori be compared to compounds 1 and 2,
folding of 3 is again favorable with respect to extended conforma-
tions. This compound formed much more stable and well-ordered
monolayers with a head-to-head type interaction (Figure 2g). Here
the amide groups appear dark, which suggests that the in-plane
orientation of the H-bonding site is different from the other
derivatives. The line profile analysis clearly indicates that every
molecule adopts the folded conformation on the surface as illustrated
with a model (superimposed on the image in Figure 2g; two alkyl
chains per catechol group).
In conclusion, we successfully designed a 2D turn element for
oligo-amide sequences. The length of the spacers between the
catechol and amide moieties plays an important role in the folding
process. As forecasted by the calculations, derivatives obeying the
rule n ) m + 1 or n ) m + 3 give folded structures upon adsorption
at the liquid/solid interface. These results constitute a promising
approach toward surface patterning and extension of the concept
toward derivatives incorporating multiple turns is underway.
Acknowledgment. The authors thank the Federal Science
Policy, through IUAP-V-03. H.U. thanks the KU Leuven for a grant
in the framework of an Interdisciplinary Research Program. S.D.F.
is a postdoctoral fellow of the Fund for Scientific Research-Flanders.
Supporting Information Available: Schemes showing the reactions
and text giving details on synthesis and characterization of 1-3,
molecular modeling, and STM. This material is available free of charge
via the Internet at http://pubs.acs.org.
References
(1) Wang, X. J.; Hu, W. C.; Ramasubramaniam, R.; Bernstein, G. H.; Snider,
G.; Lieberman, M. Langmuir 2003, 19, 9748-9758.
Figure 2. (a) STM image of monolayer from 1. Iset ) 0.6 nA. Vbias
)
(2) Xia, Y. N.; Whitesides, G. M. Annu. ReV. Mater. Sci. 1998, 28, 153-
-0.90 V. (b) Line profiles along the dashed lines in part a. (c) Packing
model of 1 at the interface. (d) STM image of monolayer from 2. Iset ) 1.0
nA. Vbias ) -0.82 V. (e) Line profiles along the lines in part d. (f) Packing
model of 2 according to the information derived from part e. Only one
alkyl tail is visible for the molecule in green. (g) STM image of monolayer
from 3. Iset ) 0.8 nA. Vbias ) -0.93 V. Insets: line profiles and a tentative
model of packing.
184.
(3) (a) Kim, J; Swager, T. M. Nature 2001, 411, 1030-1034. (b) Joachim,
C.; Gimzewski, J. K.; Aviram, A. Nature 2000, 408, 541-548. (c) Watson,
M. D.; Ja¨ckel, E.; Severin, N.; Rabe, J. P.; Mu¨llen, K. J. Am. Chem. Soc.
2004, 126, 1402-1407. (d) Miura, A.; Chen, Z. J.; Uji-i, H.; De Feyter,
S.; Zdanowska, M.; Jonkheijm, P.; Schenning, A. P. H. J.; Meijer, E. W.;
Wurthner, F.; De Schryver, F. C. J. Am. Chem. Soc. 2003, 125, 14968-
14969. (e) Hla, S. W.; Rieder, K. H. Annu. ReV. Phys. Chem. 2003, 54,
307-330. (f) Lewis, P. A.; Donhauser, Z. J.; Mantooth, B. A.; Smith, R.
K.; Bumm, L. A.; Kelly, K. F.; Weiss, P. S. Nanotechnology 2001, 12,
231-237. (g) Maoz, R.; Frydman, E.; Cohen, S. R.; Sagiv, J. AdV. Mater.
2000, 12, 725-731.
surface while the other one is pointing into the solution (Figure
2c). This may seem counterintuitive, but it has been observed
previously.10 The extended conformation was not observed. In
contrast, the catechol groups appear more isolated in monolayers
of 2 (Figure 2d). Folded as well as unfolded conformations are
observed in coexistence on the surface: both the alkyl chains of
molecules i, iii, and iv (Figure 2e,f) are adsorbed on the surface,
while one of the alkyl chains of molecule ii points into the solution
(Figure 2e,f). Since the amide groups are located in the middle of
the aliphatic part of the molecule, there is no preference for the
catechol groups to be aligned at the same side, as intermolecular
hydrogen bonding is still possible.
To corroborate the initial results and test the n ) m + 3 case,
derivative (3, n ) m + 3; m ) 3) was synthesized. The shorter
spacers were chosen to remove the symmetry in the aliphatic part
by placing the amide groups off-center. The choice of spacers also
dictates the directionality of the H-bonding array (Figure 1d).
(4) (a) Yokoyama, T.; Yokoyama, S.; Kamikado, T.; Okuno, Y.; Mashiko,
S. Nature 2001, 413, 619-621. (b) Theobald, J. A.; Oxtoby, N. S.; Phillips,
M. A.; Champness, N. R.; Beton, P. H. Nature 2003, 424, 1029-1031.
(c) Hoeppener, S.; Wonnemann, J.; Chi, L.; Erker, G.; Fuchs, H.
ChemPhysChem 2003, 4, 490-494. (d) Barth, J. V.; Weckesser, J.;
Trimarchi, G.; Vladimirova, M.; De Vita, A.; Cai, C.; Brune, H.; Gu¨nter,
P; Kern, K. J. Am. Chem. Soc. 2002, 124, 7991-8000. (e) De Feyter, S.;
Larsson, M.; Schuurmans, N.; Verkuijl, B.; Zoriniants, G.; Gesquiere, A.;
Abdel-Mottaleb, M. M.; van Esch, J.; Feringa, B. L, van Stam, J.; De
Schryver, F. C. Chem.sEur. J, 2003, 9, 5, 119-1206.
(5) (a) Saven, J. G, Chem. ReV. 2001, 101, 3113-3130. (b) Koonin, E. V.;
Wolf, Y. I.; Karev, G. P. Nature 2002, 420, 218-223.
(6) van Esch, J.; De Feyter, S.; Kellogg, R. M.; De Schryver, F. C.; Feringa,
B. L. Chem.sEur. J. 1997, 1238-1243.
(7) Jeffrey, G. A. Distance between two carbonyl carbons in the respective
chains. Hydrogen bonding in biological structures; 1991.
(8) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem.
ReV. 2001, 101, 3893-4011.
(9) Materials Studio package has been used. See www.accelrys.com.
(10) Gorman, C. B.; Touzov, I.; Miller, R. Langmuir 1998, 14, 3052-3061.
JA046124J
9
J. AM. CHEM. SOC. VOL. 126, NO. 43, 2004 13885