STM-based molecular detection of "catch-and-release" of protons for bipyridine bound to phenylene-ethynylene thiol

Article abstract of DOI:10.1039/b402251c

The protonation/deprotonation response of a novel bipyridine containing (phenylene-ethynylene) thiol adsorbed to a Au surface was investigated with scanning tunneling microscopy (STM), showing reversible changes in the average heights (～50 spots) and the

Full text of DOI:10.1039/b402251c

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STM-based molecular detection of “catch-and-release” of protons for
bipyridine bound to phenylene–ethynylene thiol†
Emiko Koyama,*a Takao Ishida,b Hideo Tokuhisa,a Abdelhak Belaissaoui,a Yoshinobu Nagawaa and
Masatoshi Kanesatoa
a Nanoarchitectonics Research Center (NARC), National Institute of Advanced Industrial Science and
Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan.
E-mail: e-koyama@aist.go.jp; Fax: +81 29 861 3029; Tel: +81 29 861 2443
b Institute of Mechanical Systems Engineering (IMSE), AIST, 1-2-1 Namiki, Tsukuba, Ibaraki 305-8564,
Japan. E-mail: t-ishida@aist.go.jp; Fax: +81 29 861 7844; Tel: +81 29 861 7203
Received (in Cambridge, UK) 13th February 2004, Accepted 17th May 2004
First published as an Advance Article on the web 14th June 2004
The protonation/deprotonation response of a novel bipyridine
containing (phenylene–ethynylene) thiol adsorbed to a Au
surface was investigated with scanning tunneling microscopy
(STM), showing reversible changes in the average heights ( ~ 50
spots) and the height distribution arising from protonation/
deprotonation.
proton and the two nitrogen (N1 and N2) atoms in bipyridine are
1.115 and 2.250 Å, respectively, meaning that the N1 nitrogen
binds the proton more strongly and almost dominantly, respective
to the N2 nitrogen. It is noteworthy that the N atoms in the bicyclic
rings of 3 are oriented in the cis-position, with a torsional angle
between two pyridine rings of 0.1°. This suggest that one nitrogen
binds weakly and one nitrogen binds strongly to the proton so as to
keep the coplanar structure of the bipyridine moiety.
XPS measurements10 for cast samples of compounds 2 and 3 on
Au were also performed. While, in the case of compound 2, only
one peak at 400.1 eV was observed in N (1s) region, two significant
peaks appeared with almost the same intensities at 399.6 and 401.8
eV as referenced to the Au (4f7/2) level at 84.00 eV in the case of
compound 3. Based upon the X-ray structure, these two peaks are
assigned to weakly and strongly protonated nitrogens present in the
bipyridine rings.
In order to study the protonation/deprotonation of a SAM of
compound 1 on Au by XPS and STM, we prepared three samples:
sample I was obtained by immersing a Au substrate in a 3 mM
ethanol solution of 1 for 24 h. The substrate was removed and
rinsed copiously with CH2Cl2 to remove any physisorbed 1; sample
II was prepared by subjecting sample prepared as in the case of
sample I to a 5 mM solution of TfOH in CH2Cl2 and CH3CN (9:1)
for 5 min, followed by rinsing with CH2Cl2; sample III was
prepared by the further soaking of a sample prepared as in the case
of sample II in ethanol for 30 min to deprotonate 1.
The electronic properties of p-conjugated molecules have recently
attracted much attention, based largely on their potential applica-
tions as molecular wires.1–4 For example, the electronic properties
of an oligo(p-phenylene–ethynylene)thiolate, inserted into an
alkanethiolate self-assembled monolayer (SAM) on Au has been
previously investigated using scanning tunneling microscopy
(STM), finding a higher conductivity relative to an alkanethio-
late.1
On the other hand, 2,2A-bipyridine is one of the most widely used
bidentate ligands for coordination of various metal cations5 as well
as protons.6 The coordination affects electronic states of the
conjugation system, resulting in drastic changes in color and
changes in redox potential.
Thus, incorporating 2,2A-bipyridine into a p-conjugated system
promises to provide a new single-molecule device, in which the
conductance is a function of cation coordination. In this study, we
have synthesized 1, in which a bipyridine unit is connected to a
conjugated phenylene–ethynylene system. The response of 1
inserted in an octanethiol SAM matrix on Au has been investigated
as a function of addition and removal of a proton using STM. The
protonation and deprotonation of the bipyridine moiety on the
surface was also carefully examined by X-ray photoelectron
spectroscopy (XPS) by comparison to the related compound 2 and
protonated compound 3 whose crystal structure was determined by
X-ray crystallography.
In the case of sample I, formation of a well-ordered SAM of
compound 1 was confirmed by STM11 as shown in Fig. 2A. Two
Compound 1 was synthesized in good yield, by a Sonogashira
coupling of 5,5A-dibromo-2,2A-bipyridine, which was obtained
according to reported procedures,7,8 with methylthiophenyl acet-
ylene in the presence of Pd(PPh3)4 catalyst, followed by the
oxidation using meta-chloroperbenzoic acid to give the correspond-
ing sulfoxide. The Pummerer reaction was then used to convert
from the methylsulfinyl to the thiol 1 using trifluoroacetic
anhydride.9 Model compound 2 was obtained by a Sonogashira
coupling of 5,5A-dibromo-2,2A-bipyridine with hexylthiophenyl
acetylene in the presence of Pd(PPh3)4 catalyst.
Fig. 1 X-ray crystal structure of 3. Selected interatomic distances in Å: N1–
H1 = 1.115(5), N2–H1 = 2.250(1).
In order to confirm the structure, we have made a single crystal
of monoprotonated compound 3, and performed X-ray crystallo-
graphic analysis (Fig. 1).‡ This additionally makes it easier to
assign peaks in the XPS spectra. The single crystal was prepared
from a CH2Cl2 and CH3CN (9:1) solution containing model
compound 2 and 1 equivalent of trifluoromethane sulfonic acid
(TfOH). Slow evaporation of the solvent gave a plate-like, red,
single crystal. X-ray analysis determined the distances between the
† Electronic supplementary information (ESI) available: cross sectional
profiles of the STM images before and after the addition of TfOH. See
http://www.rsc.org/suppdata/cc/b4/b402251c/
Fig. 2 STM image of SAM of 1 (A) and 1 inserted into an octanethiol SAM
(B) on Au. The image was obtained in constant current mode at a bias of 0.5
V and 1.0 V, and a current of 100 pA and 25 pA.
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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

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typical orientations were observed in this STM image, labeled a and
b in Fig. 2A. For the distinct patterns observed of domain a, the
average distances between each spot along lines A and B were
approximately 0.8 and 1.0 nm, respectively, and the angle between
lines A and B was around ~ 57°. These results suggest the
formation of a A7 3 A13 R20° structure. In the case of domain b,
the distances between each spot along both lines C and D were the
same (0.85 nm), and the angle between line C and D was around 60
°, indicating a 3 3 3 structure. Interestingly, these two domain
structures show less-packed patterns than a well ordered (2A3 3
A3) R30° structure of oligo(p-phenylene–ethynylene)thiolates on
Au that was reported previously.12 We expect this less efficient
packing will make it easier to protonate/deprotonate the adsorbed
molecule.
The spectrum of a self-assembled monolayer of compound 1 on
Au (sample I) reveals only one peak at 398.4 eV, which is assigned
to the nitrogens of the bipyridine. The protonated SAM (sample II)
consists of two peaks at 399.0 and 402.0 eV with almost identical
intensities, in good agreement with our observations of compound
3, as mentioned above. This suggests that under these conditions,
bipyridine exists solely as a monoprotonated species, even on the
surface. Interestingly, soaking the protonated SAM surface in
ethanol (sample III) leads to complete recovery of the peak arising
from a nonprotonated bipyridine at 398.7 eV. These results suggest
we can control the “catch-and-release” of a proton on the bipyridine
rings of compound 1 when present in a SAM using the
aforementioned conditions.
Scheme 1 Structures for phenylene–ethynylene thiol derivatives containing
the bipyridine studied here.
free surfaces, 0.50 and 0.56 nm (Fig. 3A and C). Furthermore, the
acid-free surfaces have a larger statistical distribution of apparent
heights, 0.180 and 0.213, relative to the protonated surface, 0.143.
It is noteworthy that the changes in the average height and the
height distribution are almost reversible through the protonation/
deprotonation process. A control experiment was performed using
a compound incorporating a biphenyl unit instead of the bipyridine
unit in compound 1, resulting in that no change in either the height
and the distribution was observed upon the addition of TfOH. This
clearly suggests that those changes we observed in the STM images
arise from the protonation/deprotonation of the bipyridine.
This work was partly supported by NEDO under the Nano-
technology Materials Program.
Notes and references
‡ Crystal data for compound 3: C25H24N2O3S2F3Br, M = 601.50, triclinic,
a = 10.50(1), b = 11.15(2), and c = 12.58(2) Å, a = 98.96(7)°, b =
¯
93.25(6)°, g = 106.31(5)°, V = 1388.1(3) Å3, T = 168 K, space group P1,
Z = 2, m = 16.84 cm21, 11 489 reflections measured, 5781 unique (Rint
=
0.110), final R indices [I > 2t(I)] R1 = 0.077, wR2 = 0.146. CCDC number
231280. See http://www.rsc.org/suppdata/cc/b4/b402251c/ for crystallo-
graphic data in .cif format.
Finally, we have investigated the molecular level response to the
protonation/deprotonation of the bipyridine in compound 1 on Au
by using STM. In this case, because of the difficulty in measuring
the absolute height changes of the uniform SAM of compound 1
before and after the addition of TfOH by STM, we utilize a matrix
of octanethiol to isolate compound 1 on Au so that apparent height
changes upon protonation/deprotonation in the STM images can be
measured as a constant. The apparent height difference is
potentially a function of physical height, conductance, or both.
Compound 1 isolated in a matrix of octanethiol was prepared by
soaking the matrix monolayer in 0.14 mM ethanolic solution of
compound 1 for 30 min. The STM image of the matrix-isolated 1 is
shown in Fig. 2. The images were acquired in constant current
mode at a bias of 1.0 V and a current of 25 pA. The bright spots
protruding through the matrix layer, which were not observed in the
octanethiol-only monolayer, are due to either an isolated molecule
or a small collection of compound 1. The substrate is then
processed as described above to effect the “catch-and-release”
process. STM images of both the protonated and deprotonated
surface were acquired. Typical bright spots from each these three
images, are summarized as histograms (n = 50) of the apparent
height in Fig. 3.
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