Chemical and constitutional influences in the self-assembly of functional supramolecular hydrogen-bonded nanoscopic fibres

Article abstract of DOI:10.1002/chem.200601089

A new series of secondary amides bearing long alkyl chains with π-electron-donor cores has been synthesized and characterised, and their self-assembly upon casting at surfaces has been studied. The different supramolecular assemblies of the materials have been visualized by using atomic force microscopy (AFM) and transmission electron microscopy (TEM). It is possible to obtain well-defined fibres of these aromatic core molecules as a result of the hydrogen bonds between the amide groups. Indeed, by altering the alkyl-chain lengths, constitutions, concentrations and solvent, it is possible to form different rodlike aggregates on graphite. Aggregate sizes with a lower limit of 6-8 nm width have been reached for different amide derivatives, while others show larger aggregates with rodlike morphologies which are several micrometers in length. For one compound that forms nanofibres, doping was 'performed by using a chemical oxidant, and the resulting layer on graphite was shown to exhibit metallic-like spectroscopy curves when probed with current-sensing AFM. This technique also revealed current maps of the surface of the molecular material. Fibre formation not only takes place on the graphite surface: nanometre scale rods have been imaged by using TEM on a grid after evaporation of solutions of the compounds in chloroform. Molecular modelling proves the importance of the hydrogen bonds in the generation of the fibres, and indicates that the constitution of the molecules is vital for the formation of the desired columnar stacks, results that are consistent with the images obtained by microscopic techniques. The results show the power of noncovalent bonds in self-assembly processes that can lead to electrically conducting nanoscale supramolecular wires.

Full text of DOI:10.1002/chem.200601089

FULL PAPER
DOI: 10.1002/chem.200601089
Chemical and Constitutional Influences in the Self-Assemblyof Functional
Supramolecular Hydrogen-Bonded Nanoscopic Fibres
Josep Puigmartí-Luis,[a] Andrea Minoia,[b] ngel PØrez del Pino,[a] Gregori Ujaque,[c]
Concepció Rovira,[a] Agustí Lledós,[c] Roberto Lazzaroni,[b] and David B. Amabilino*[a]
Abstract: A new series of secondary
amides bearing long alkyl chains with
p-electron-donor cores has been syn-
thesized and characterised,and their
self-assembly upon casting at surfaces
has been studied. The different supra-
molecular assemblies of the materials
have been visualized by using atomic
force microscopy (AFM) and transmis-
sion electron microscopy (TEM). It is
possible to obtain well-defined fibres
of these aromatic core molecules as a
result of the hydrogen bonds between
the amide groups. Indeed,by altering
the alkyl-chain lengths,constitutions,
concentrations and solvent,it is possi-
ble to form different rodlike aggregates
on graphite. Aggregate sizes with a
lower limit of 6–8 nm width have been
reached for different amide derivatives,
while others show larger aggregates
with rodlike morphologies which are
several micrometers in length. For one
compound that forms nanofibres,
al. Fibre formation not only takes place
on the graphite surface: nanometre
scale rods have been imaged by using
TEM on a grid after evaporation of
solutions of the compounds in chloro-
form. Molecular modelling proves the
importance of the hydrogen bonds in
the generation of the fibres,and indi-
cates that the constitution of the mole-
cules is vital for the formation of the
desired columnar stacks,results that
are consistent with the images obtained
by microscopic techniques. The results
show the power of noncovalent bonds
in self-assembly processes that can lead
to electrically conducting nanoscale
supramolecular wires.
doping was performed by using
chemical oxidant,and the resulting
a
layer on graphite was shown to exhibit
metallic-like spectroscopy curves when
probed with current-sensing AFM. This
technique also revealed current maps
of the surface of the molecular materi-
Keywords: hydrogen bonds · iso-
mers · pi interactions · supramolec-
ular assembly · tetrathiafulvalene
Introduction
offers many advantages over strictly covalent approaches,
but one limiting factor is control over the self-assembly pro-
cess. In this sense,a delicate balance between building block
functionality and supramolecular synthons is required.[9]
Apart from the supramolecular design built into the com-
The self-assembly of nanoscopic fibres and rods is an ap-
pealing pursuit given that they may form part of molecular
electronic devices.[1–3] This bottom-up approach[4–8] to wires
ponents of these nanometre scale objects,the importance of
[10–14]
the deposition method,the solution nature
and concen-
[a] J. Puigmartí-Luis,Dr. . PØrez del Pino,Prof. C. Rovira,
Dr. D. B. Amabilino
tration,[15–18] the chain-length dependence,[19–23] and the
nature of the surfaces[24–26] on the characteristics of aggre-
gates have been demonstrated for some molecules. To self-
assemble wires required for new challenges in molecular
electronics,in this work we report the influence of these fac-
tors as well as the molecular constitution on hydrogen-
bonded assemblies[27–31] of functional p-electron-rich com-
pounds.
The molecules we have chosen for this study are tetrathia-
fulvalene derivatives (TTFs),because of their great poten-
tial in the area of molecular electronics as switches,[32–36] con-
ductors[37,38] and their use in field-effect transistors.[39,40] Our
work aims to arrange the TTFs with a close contact in be-
Institut de Ci›ncia de Materials de Barcelona (CSIC)
Campus Universitari de Bellaterra
08193 Cerdanyola del Vall›s,Catalonia (Spain)
Fax : (+34)93-580-5729
E-mail: amabilino@icmab.es
[b] A. Minoia,Prof. R. Lazzaroni
Service de Chimie des MatØriaux Nouveaux
UniversitØ Mons-Hainaut,Place du Parc 20
7000 Mons (Belgium)
[c] Dr. G. Ujaque,Prof Dr. A. Lledós
Unitat de Química Física
Departament de Química,Edifici Cn
Universitat Autònoma de Barcelona
08193 Bellaterra,Barcelona,Catalonia (Spain)
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tween the p surfaces (so that they may be useful for the
aforementioned applications) by using hydrogen bonds,and
to form nanoscale fibres in a controlled way. In the solid
state,hydrogen bonds have been used to influence the dis-
position of TTF units with varying degrees of success,[41–47]
one example being that of amide bonds which aid the for-
mation of stacks of molecules.[48] On the other hand,fibres
have been formed in Langmuir films[49,50] and gels[51] with a
random orientation,and gels of TTFs have shown some
alignment of the fibres.[52] In two cases xerogels based on
TTF derivatives have been proven to conduct electricity.[53,54]
Here,we show how chemical constitution and composition
as well as the surface,solvent of deposition and concentra-
tion influence in hydrogen bonded assemblies that the new
compounds we report form.
portance of the TTF unit in the self-assembly process can be
evaluated. Two of them are constitutional isomers that have
an aromatic core,a naphthalene unit ( 3 and 4),which can
form p–p interactions with themselves.[56,57] The last one 5,
does not have a planar core. All of them have amide groups
in their structure just to prove the directionality of the hy-
drogen bond to self-assemble into anisotropic aggregates
just casting them from the solution. All the compounds stud-
ied include two amide groups,which permit the formation
of hydrogen bonds,[58,59] in the case of the TTF as well as
short contacts of the sulfur atoms in the residue. In addition,
the long alkyl chains can provide a “fastener” effect[60]
through dispersion interactions,and can also interact with a
graphite surface through van der Waals interactions.
A series of TTF–amide derivatives and other aromatic an-
alogues have been synthesised in order to prove the impor-
tant role that the amide group plays in forming fibres and
rods with nanometre dimensions upon casting them from so-
lution. Two isomers, cis- and trans-TTF,were targeted to
study the effect of the constitution in relation the molecular
assembly on a hydrophobic surface.[55] Six different TTF de-
rivatives were studied,three cis (1a, 1b and 1c) and three
trans (2a, 2b and 2c),in which the length of the aliphatic
Results and Discussion
Synthesis and characterisation: The TTF–amide derivatives
were synthesised starting from thione 6 (Scheme 1).[61] Re-
moval of the protecting propionitrile group with base fol-
Scheme 1. Synthesis of the TTF constitutional isomers with different
alkyl-chain lengths.
lowed by reaction with amides 7 (prepared using a method
based on that of Thorsteinsson et al. for 7a[62]) gave thiones
chains were varied. The reason for the different alkyl units
was to observe possible effect of chain length and odd–even
numbers of carbon atoms on the supramolecular structure.
On the other hand,three aliphatic amide substituted aro-
matic hydrocarbon compounds were studied so that the im-
8,which in turn were converted into the oxo compounds 9
by treatment with mercury(ii) acetate. The self-coupling of
these compounds in refluxing trimethylphosphite gave the
mixtures of isomers 1 and 2,which were separated by flash
column chromatography. The assignment of the trans consti-
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tution of the eluted compounds is in accord with previous
observations on other isomers of this type,[23,55] and on the
ease of crystallization of the two compounds—the trans
compound 2 crystallises far easier than the corresponding
cis compound. The compounds were fully characterised by
using the usual spectroscopic techniques and elemental anal-
ysis (see Experimental Section). The IR spectra of the iso-
mers show the same characteristic band at approximately
ꢀ
The AFM images of the aggregates formed from concen-
trated solutions (10ꢀ4 m) of 2a and 2b in chloroform (Fig-
ure 1A and 1B respectively) reveal rodlike objects of vary-
ing length and breadth,but with a remarkably consistent
orientation. The angle that the rodlike aggregates make
with respect to each other in both compounds is: a=59ꢁ78
and a=59ꢁ88,respectively. This angle corresponds to the
complementary axis angle of the highly oriented pyrolitic
graphite (HOPG); so both molecules have an orientation
that is determined by this surface,seen previously for com-
pletely different systems.[63]
3300 cmꢀ1,which is indicative of hydrogen-bonded N
H
ꢀ
groups,and the corresponding C =O stretching and N H
bending bands at 1645 and 1551 cmꢀ1,respectively. The
1H NMR spectra are also very
similar,with the amide NH res-
onances appearing at approxi-
mately d=6.8 ppm.
Compounds 3, 4 and 5 were
prepared from the commercial-
ly available phenols that were
treated with 7a (Scheme 2)
with potassium carbonate as the
base. The products were puri-
fied after filtering the reactant
solution and cleaning the solid
residue with dichloromethane.
Scheme 2. Synthesis of the aliphatic amides derived from dioxynaphthalenes and biphenol.
They were fully characterized
by using the usual spectroscopic
techACHTREUNGniques as well as elemental
analysis.
AFM studies of self-assembled
fibres: Solutions of the trans-
TTF isomers in chloroform
were deposited onto highly ori-
ented
pyrolytic
graphite
(HOPG) by simple casting and
the solvent was allowed to
evaporate. The topography of
the nanoscopic solids formed
were investigated by atomic
force microscope (AFM) by
using the acoustic (oscillating
tip) mode,in several regions of
the surface and in several ses-
sions with different stock solu-
tions and different tips. The
images that are presented are
the most representative ones
for each sample. The com-
pounds form fibres with varying
dimensions depending on the
concentration of the solutions
employed in the casting experi-
ment and the region of the
evaporated drop that is studied.
The centre of the drop always
contained higher concentration
of compound.
Figure 1. AFM images of A) 2a,B) 2b and C) 2c on HOPG after evaporation of the solvent from 10ꢀ4 m solu-
tions of the samples in chloroform.
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D. B. Amabilino et al.
For the trans-TTF compound 2a,the blocklike objects
have varying length,but have a quite uniform lateral dimen-
sion. The averaged width over different images is 190ꢁ
73 nm and the height is 3.3ꢁ0.6 nm. However,within these
aggregates much smaller features are observable (vide
infra). In the case of compound 2b in which the aliphatic
chains are longer by three methylene groups,the average di-
mensions from different images were around 53ꢁ17 nm in
width and 1.2ꢁ0.2 nm in height. In the fibres of this com-
pound too,it is possible to discern small fibres that do not
agglomerate as do those of 2a,and resolution of the individ-
ual fibres is more evident.
The lateral dimensions of the aggregates were measured
by using the profile from the AFM images (Figure 2). These
contours show that the larger fibres formed by 2a are quite
smooth,although very small features can be discerned. The
calculated end-to-end distance for a fully-extended molecule
of 2a is 4.7 nm,and that of the core of the TTF (between
the sulfur atoms appended to the fulvalene rings) is approxi-
mately 0.97 nm. On the other hand,the topographic analysis
of the fibres of 2b on the HOPG shows much better defined
and smaller fibres. Individual features less than 10 nm in
width and 0.5 nm height indicates that these are fibres com-
posed of single hydrogen-bonded chains of molecules. The
calculated distance between the sulfur atoms at either “end”
of the TTF unit is approximately 0.9 nm (taking into ac-
count tip broadening,an apparent width would be approxi-
mately 6 nm). The end-to-end distance for a fully extended
molecule of 2b is 5.5 nm (taking into account the tip broad-
ening,an apparent fibre width would be approximately
15 nm). The features observed therefore point to individual-
ly resolved supramolecular fibres.
The fact that the blocks have such a well-defined size and
orientation implies that the surface is certainly aiding as a
template during their formation. The different lateral di-
mensions (especially the observation that the height and
width of the aggregates of 2b are smaller than those of 2a)
could point to the different solubility in the solvent used for
deposition,which introduces a kinetic factor into the forma-
tion of the self-assembled fibres.
The trans isomer 2c was studied under the same condi-
tions as the homologues with shorter chains. A very differ-
ent topography is observed in this case. It is characterized
by a dense mesh of very fine fibres (width 48ꢁ20 nm and
height 6.3ꢁ2.6 nm) with lengths between 50 and 200 nm.
These fibres are randomly distributed over all directions of
the surface (Figure 1C). The length of the alkyl chain would
not be expected to change the preferred orientation of the
hydrogen-bonded assemblies along the principle graphite
symmetry axes. Therefore,the small dimensions of the
fibres and their random orientation indicate that these nano-
scale acicular objects precipitate in solution (rather than on
the surface). This hypothesis is supported by the TEM
images of the compound away from any surface (vide infra).
Similar casting experiments were carried out to study the
influence of the concentration on the supramolecular ar-
rangement of the compounds. Therefore,lower concentra-
tion (10ꢀ5 m) for each trans isomer were used. Identical mor-
phologies were observed except for the trans isomer 2c. At
10ꢀ5 m,this trans isomer generates small aggregates and very
long isolated fibres (Figure 3). The two types of aggregate
have virtually identical height (13.3ꢁ0.2 nm) and width
(119ꢁ2 nm) (Figure 3 right-hand image). This observation
makes us hypothesize that the organization of the molecules
in the blocks and in the fibres is similar.
Figure 2. Close-up of AFM images of A) 2a and B) 2b on HOPG after
evaporation of the solvent from 10ꢀ4 m solutions of the samples in chloro-
form,and the corresponding profiles.
Figure 3. Topographic AFM images of 2c on HOPG after evaporation of
the solvent from a 10ꢀ5 m solution of the samples in chloroform.
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The long aggregates are tens of micrometers in length and
are slightly curved on this length scale,although locally they
are apparently quite uniform (Figure 3,right-hand image).
Working with this lower concentration,it is also possible to
generate short aggregates of 2c,with equal dimensions as
described above,which are oriented following the graphite
axes (a=61ꢁ68),as shown in Figure 4. These objects were
Figure 4. An AFM image of a drop-cast solution (10ꢀ5 m in chloroform)
of compound 2c on a graphite surface with coloured lines added to show
the preferred orientation of the nanorods.
observed in a different area of the surface of the cast mate-
rial on graphite,although the alignment with the graphite
axes can also be seen in the images in Figure 3. The disper-
sion in the width of the fibres between high and low concen-
tration deposition and the lack of orientation of the fibres
for 2c implies that the ones formed from more concentrated
solutions of this compound are deposited under kinetic con-
trol rather than under a more thermodynamic influence
seen at lower concentrations in chloroform,and in the more
general sense for 2a and 2b.
Figure 5. A) An AFM image of a drop-cast solution (10ꢀ4 m in chloro-
form) of compound 2c on a mica surface,showing layer-type morpholo-
gy,and B) a closer view with the corresponding profile.
However,it is not possible to exclude the possibility that
the surface plays some role in the formation of the finer
fibres observed in the AFM images of the more concentrat-
ed cast solutions of 2c on graphite.
When the same casting experiments are performed on
freshly cleaved mica no fibres or blocks are observed. In-
stead,mono- and multilayers are observed (Figure 5) along
with amorphous chunks of material. Therefore,it appears
that the amide derivativeꢁs ability to self-assemble is distur-
bed greatly by the hydrophilic surface,possibly by interac-
tion with the amide groups of the molecule as seen for other
amide derivatives.[64]
formed for which resolution of the individual fibril struc-
tures was reached (width 5.5ꢁ0.4 nm) by using acoustic
mode AFM. The nanodomains are composed mainly of
three or four fibres of approximately equal length,indicat-
ing that there is some interaction between them,the most
likely one being between the alkyl chains by interdigitation.
There is no evident alignment of the nanofibres with the
graphite axes in these domains (Figure 6D a=109ꢁ238,Fig-
ure 6E a=104ꢁ118) and these are invariant with the con-
centration,as is appreciable in Figure 6E.
The constitution of the molecule is also of critical impor-
tance. When cis-TTF derivatives (1a–c) were cast onto
graphite from toluene or chloroform (at the same concentra-
tions as the trans isomers),no well ordered fibres or blocks
were observed. Rarely,nanofibres of the type seen for the
trans isomers (Figures 1 and 6) were observed for the cis
isomer (Figure 7),but in general the monolayer is far more
amorphous than that of the former. Very short fibres which
are in close contact were seen for 1a,while for 1b longer
and wider fibres were seen occasionally,but with no specific
orientation in either case. The cis compound with the lon-
gest alkyl chains (1c) forms nanodomains of fibres aligned
with each other,rather similar to those of the trans com-
pound cast from toluene.
Solvent has been shown to play an important role on the
aggregation of other components which are useful in molec-
[65,66]
ular electronics,for polymers
and small mole-
cules,[10–14,67] and the same is true here. When solutions of
the compounds in tetrahydrofuran were deposited on graph-
ite,films with amorphous character were formed,with no
fibril morphology evident (images not shown). When tolu-
ene was used to deposit compound 2c on graphite,no well-
defined fibres were formed (as they were in chloroform),
but in areas a monolayer was imaged by AFM in which
fibril morphology is evident (Figure 6D and E). Within the
monolayer small domains with short-range order were
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D. B. Amabilino et al.
Figure 6. Effects of concentration,solvent and surface type on the mor-
phology of surface-supported aggregates of compound 2c. The topo-
graphic AFM images were recorded for samples on mica (C and F) and
graphite (A,B,D and E) surfaces. The high concentration is 10 ꢀ4 m and
the low one 10ꢀ5 m.
These dramatic changes observed in the topography as a
result of the molecular constitution makes us hypothesize
that in the case of the cis isomers smaller fibril structures
are observed because of the stronger interaction of the TTF
derivatives with the surface. Both alkyl chains of these cis
isomers can bond with the surface through van der Waals in-
teractions,making short and small fibril-containing domains,
while for the trans isomers the contact of both chains is less
favourable because of their S shape (as seen perpendicular
to the plane of the molecule).
Figure 7. AFM images of cast layers of A) 1a,B) 1b and C) 1c from
10ꢀ4 m solutions of the samples in chloroform on HOPG.
The hypothesis described above is in total agreement with
the experimental data obtained from averaged measure-
ments of the different cis-TTF derivative AFM images.
Their aggregate dimensions never exceed those of the trans
derivatives (Figure 8). The size of the fibril structures
imaged for the cis isomers (1a and 1c) are consistent with
the molecular dimensions (width 6–7 nm and height be-
tween 0.2–0.4 nm). For the trans isomer hierarchical supra-
molecular interactions are possible because this constitution
allows one of the chains to be lifted up from the surface and
this can interact with other molecules making the surface
less influential in the aggregate formation than for the cis
isomers. The relative surface independence is exemplified
for 2c at the higher concentration studied.
A parallel study was carried out with the different amide
derivatives 3–5 that do not contain the TTF unit,but rather
aromatic hydrocarbon groups. The aim of this investigation
Figure 8. Graphs showing the average dimensions of the fibre-like objects
of the TTF derivatives 1 and 2 observed from different images and sam-
ples.
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was to evaluate the relative importance of the hydrogen
bond in the fibre formation,and the role of the planar core
(in 3 and 4) with p–p interaction ability or the nonplanar
core (5) on the supramolecular assembly. Two molecules
with a planar naphthalene core (3 and 4),and the other with
a more conformationally flexible biphenyl core (5) were de-
posited onto the graphite in the same way as for the TTF
derivatives. All them have two possible hydrogen-bond cen-
tres and dodecyl chains,and so can be compared with 1a
and 2a. The 2,7-naphthyl derivative 3 is comparable in its
constitution to the cis-TTF derivative 1a,while the 26,-
naphthyl derivative 4 is similar to the trans isomer 2a,and
this fact is reflected to some extent in the type of aggregates
that they form (vide infra).
The type of self-assembled structure observed for 3, 4 and
5 on graphite depends strongly on the amount of material
deposited on the surface (determined by the local concen-
tration during evaporation of the solvent) in the area being
imaged (Figure 9). Comparison of the AFM images of mole-
cules 3 and 4 shows the important role that constitution has
in the self-organization with respect to the surface. For com-
pound 3 (Figure 9A) a dense mesh of thin fibres,which have
no strict alignment with the graphite axes,is observed. This
kind of supramolecular assembly was also seen for the cis
isomer 1c,but the uniform areas were not as large and the
definition of the fibres was nowhere near as high as in the
present case. This type of aggregate seems characteristic of
a strong interaction between the alkyl chains of the mole-
cule and the surface,thanks to the location of these chains
on the same “side” of the aromatic rings. The small fibrils
are of molecular dimensions (width 4.8ꢁ1.1 nm and height
0.13ꢁ0.03 nm,Figure 10). There is also evidence of larger
fibres for compound 3,something not seen for compounds
1. This evidence indicates a stronger molecule–molecule in-
teraction in the naphthalene derivative than in the TTF
compound. The images of compound 4 (Figure 9B) also
reveal the formation of fibril-like structures,but with much
larger dimensions (width 152ꢁ25 nm and height 17.6ꢁ
1.7 nm,Figure 9Bi) similar,but much larger than those
formed by 2a,which has a similar molecular constitution.
Also,areas that appear to be uniform mono- and multilayers
are formed on the graphite surface. Again,then,the AFM
Figure 9. AFM images of 10ꢀ4 m solutions of compounds A) 3,B) 4 and
C) 5 in chloroform after evaporation of the solvent after casting on
graphite. All images show the topography signal except Bii and Cii,
which show the phase shift of the oscillation of the AFM tip in order to
show the fine structure more clearly.
Figure 10. Profiles from the AFM images of cast samples of compounds
A) 3 and B) 5 on HOPG.
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D. B. Amabilino et al.
evidence points to stronger molecule–molecule interactions
in the naphthalene derivative than in the TTF derivative.
Images of compound 5 on graphite (Figure 9C) show
areas of monolayer (top left in Ci) and rodlike aggregates.
As in the case of the TTF derived compounds 2,these ag-
gregates are aligned with the graphite symmetry axes. The
oblong objects also have internal fibril structure,as shown
the phase image in Figure 9Cii. Therefore,we can conclude
that a planar molecular centre is not essential to achieve the
fibrelike aggregates,although it does influence greatly their
dimensions and morphology.
Current sensing AFM Studies of self-assembled fibres:
After studying the supramolecular arrangement of the dif-
ferent amide derivatives on graphite,we chose to study the
electrical properties of a conducting film on graphite pre-
pared by doping compound 2c on the substrate. We used
compound 2c,because it is the one material which forms a
mesh of fibres,and close contacts between crystals have
been shown to be important for conductivity in films of
larger crystals of TTF salts.[68,69] The film was prepared with
a concentrated solution of neutral 2c (10ꢀ4 m) after casting it
several times onto graphite to give a film of up to 300 nm in
thickness,with the same morphology as thinner films. The
material was doped by exposure to iodine vapour for two
minutes,which generates the cation radical of the p donor
while leaving some in the neutral state. This mixed valence
material was studied with current sensing AFM,a technique
which has proven useful in the characterization of covalent
polymer systems.[70,71]
Figure 12. Current map of a doped film of compound 2c on graphite and
I/V curves taken at different locations in the current maps.
Several current images were recorded by applying a bias
voltage to the sample while scanning with a grounded con-
ducting tip. Current maps were obtained where fibre struc-
ture arising from the differences in electronic transport in
the film can be observed clearly (Figures 11 and 12). This
different slope according to the zone (Figure 12). The dis-
persion in the slope of the I/V curves and the appearance of
the current map over the whole sample is essentially negligi-
ble. A representative selection of averaged spectroscopy
curves is shown in Figure 12. The most inclined curve was
observed in areas with higher current,and is associated with
a resistance of 7.5 MW. The curve with intermediate slope,
corresponding to an area of intermediate conductivity,had a
resistance of 18.0 MW. The zones where the current is lowest
had a resistance of 33.0 MW,but still showed metallic char-
acteristic,that is,no experimental gap was observed. These
data correspond well with the resistance obtained from the
statistical calculations done on the current sensing images.
These calculations consisted of obtaining the current value
which was most probable from the current distribution,
which gave a value of 4.5 nA. This current would imply a re-
sistance of 25.0 MW (far greater than the tip resistance,of
approximately 1 kW) for the map generated at 0.1 V.
Figure 11. A) Topographic and B) current image (0.1 V bias) of an
iodine-doped sample of 2c on HOPG.
detail was not discernable in the topographic images which
were acquired simultaneously. This result implies that the
current is flowing along the stacked TTF moieties in the
supramolecular wires.
The spectroscopy (I versus V) curves obtained in different
areas of the sample show metallic character clearly,with a
TEM studies of self-assembled fibres: When the molecule–
molecule interactions are sufficiently strong,it should be
possible to obtain fibril-like aggregates of nanoscopic size
and acicular shape. To evaluate the influence of the surface
in the aggregate assembly of the compounds reported here,
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Supramolecular Chemistry
FULL PAPER
we studied the amide derivatives by using a technique which
allows observation of the aggregates away from the surface:
Transmission electron microscopy (TEM) was used,deposit-
ing the compounds from chloroform solutions onto carbon
coated copper grids. The samples were not coated with any
contrast agent,and the images were recorded at room tem-
perature.
The images confirm the tendency of trans conformers to
form fibrelike structures. Representative examples of the
anisotropic objects are shown in Figure 13. The fibres,which
Figure 14. TEM images of compound 3 after evaporation of the solvent
from a 10ꢀ4 m solution of the sample in chloroform on the holey carbon
grid.
has a profound influence on the supramolecular structures
that are formed through hydrogen bonds.
Simulation of aggregate formation—the role of interactions
in columnar stacks: To study the influence of hydrogen
bonds in self-assembly of TTF derivatives with a tractable
computational effort,the compounds 1 and 2,in which a
methyl group is the substituent at the nitrogen atom,have
been modelled with force field (FF) techniques. The most
likely conformers have been identified with Monte Carlo
(MC) conformational analysis (see Computational Methods
for details). Then stacks of eight molecules were built,their
structure optimized with molecular mechanics (MM) and
the final energy evaluated. Each structure is composed of
only one conformer of the molecule,all with the same orien-
tations in space and relative positions,because it is clear
that the high order observed experimentally in the aggre-
gates must arise from a high regularity at the molecular
level. The final structures of the aggregates are strongly in-
fluenced by the type of interaction that starts to act between
the molecules,as the stack is formed independently from
the order in the stack.
Figures 15A and 16A show two different initial structures
for the trans-TTF isomer: In the first one,the TTF parts of
the molecules are approximately 7 Š distant,while in the
second one the intermolecular distances are less than 4 Š.
When the molecules are far from each other,as in Fig-
ure 15A,the intermolecular interactions have a dipole–
dipole nature,while p–p interactions and hydrogen bonds
act only when the molecules get close to each other. The
dipole–dipole forces induce a misalignment of the molecules
and the resulting structure (Figure 15B) is quite disordered
and is not consistent with what is observed experimentally.
Instead,when molecules are close to each other,as in Fig-
ure 16A,and the intermolecular distances are comparable
to the range of action for p–p interactions,the resulting
structure (Figure 16B) maintains the initial regular packing.
Figure 16 shows the initial structure in which the molecules
of the trans-TTF derivative are closely packed (A) and the
resultant optimized structure (B). Here p–p interactions al-
ready act in the starting geometry keeping the molecules
Figure 13. TEM images of the aggregates formed by compounds A) 2a,
B) 2b,C) 2c,D) 1a,E) 1b and F) 1c after evaporation of the solvent
from 10ꢀ4 m solutions of the samples in chloroform on the carbon-coated
copper grid.
are approximately 20–40 nm wide and several hundreds of
nanometres long,have internal structure that corresponds to
the length of the molecules,5–6 nm. This study confirms the
inherent capacity of the trans molecules to form fibres from
a solution of the sample in chloroform and bears witness to
the strong molecule–molecule interactions that take place
while the solvent evaporates from the solutions. The fact
that the most well-defined fibres are seen for 2c explains
the observation of the fibres on the graphite surface without
any orientation with respect to the substrate: They presuma-
bly precipitate from solution before growth from adsorbed
molecules on the surface can take place.
In case of the cis conformers,the behaviour is different.
The compounds 1 cannot form fibril-like aggregates without
surface influence (Figure 13D,E and F).
The TEM study of the other amide derivatives (3–5)
which do not contain the TTF unit,confirms the strong in-
teraction only between molecules of 3. In Figure 14 the
TEM images of this compound are shown in which fibrous
texture can be discerned. Compounds 4 and 5 do not show
the same surface independence of fibre formation,only
amorphous material was observed in the TEM experiments
(images not shown). The molecular constitution therefore
Chem. Eur. J. 2006, 12,9161 – 9175
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9169

D. B. Amabilino et al.
ecules to each other. It is important to notice that,with re-
spect to the real case,here there is no surface to force the
molecules into a particular alignment,so we can also ob-
serve other structures such as the helical aggregate shown in
Figure 17.
Figure 15. A) Initial structure of the trans-TTF compound in which the
molecules are 6–7 Š apart. B) Optimized geometry: the disorder is due
to the dipole–dipole interactions,which act on a longer scale with respect
hydrogen-bond and p–p interactions.
Figure 17. Optimised helical structure: this is the most stable stack in ab-
sence of a surface.
Seven different structures,which show a well ordered
packing (compatible with assembly on a surface or that ob-
served in the TEM measurements),have been studied and
all are within 13 kcalmolꢀ1 in absolute energy. We have also
examined the molecular binding energy in those structures,
as defined in Equation (1),which is possibly more significant
than the absolute energy for the stacks,because it represents
the gain in energy for an isolated molecule when incorporat-
ed in the structure.
stack
abs
E
ꢀðNmol Eimsoinl Þ
ð1Þ
Ebind
¼
Nmol
stack
abs
In Equation (1), E
is the energy of the stack, Nmol is
isol
the number of molecules in the stack and E is the energy
min
Figure 16. A) Initial structure in which the molecules of the trans-TTF
derivative are closely packed and B) the resultant optimized structure.
of the most stable conformer for the isolated molecule,ob-
tained by Monte Carlo conformer search. All the binding
energies calculated for the structures analysed (Table 1) are
quite close,so it is not possible to identify a structure that is
clearly the most stable.
aligned together. The effect of the minimization is the for-
mation of the hydrogen bonds,which strongly bind the mol-
9170
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Chem. Eur. J. 2006, 12,9161 – 9175

Supramolecular Chemistry
FULL PAPER
Table 1. Binding energy (Ebind in kcal molꢀ1 per molecule) of molecular
packing.
tremely useful tool for their generation on and off surfaces
thanks to intermolecular hydrogen bonds. The formation of
these fibres is sensitive to solvent,surface,and constitution
and composition of the molecule,but it is controllable.
Graphite clearly plays a role in orienting them in some
cases and in certain conditions under which the surface–mol-
ecule interactions are able to organize the aggregates. In the
cases in which molecule–molecule interactions are strong in
the evaporating solution,the fibres are non-oriented,as in
the case of 2c and the naphthalene derivatives 3 and 4. The
different sizes of the aggregates observed on graphite are in-
fluenced by the local concentration of the molecules in the
evaporating solution. Kinetics is clearly an important factor
in this crystallization process at the surface,but the thermo-
dynamics of the interaction between the molecules and the
graphite also plays a key role in the self-assembly process.
The constitution of the molecules is very important,the
transoid have a clear advantage over cisoid forms of the
molecules,because the two hydrogen bonds that are formed
favour an additional stabilizing interaction for the aggre-
gates between the aromatic groups as shown by the theoreti-
cal studies. The cisoid-type molecules apparently interact
more favourably with the surface,and modelling indicates
that dimerisation of the molecules could act as a barrier to
growth of the chains. The length of the alkyl chains attached
to the secondary amide also influence the size of the aggre-
gates,longer alkyl chains giving rise to the formation of
longer,thinner fibres.
Configuration
Ebind
Configuration
Ebind
cis
cis
cis
cis
ꢀ22.7
ꢀ22.0
ꢀ23.9
ꢀ23.3
trans
trans
trans
ꢀ22.9
ꢀ24.0
ꢀ22.4
The calculations also show that the two amide groups in
the TTF derivatives under study,as well as the p–p interac-
tions between the conjugated cores,are needed for the for-
mation of stable aggregates. These groups are,in fact,the
active sites for the formation of the hydrogen bonds that
strongly bind the molecules to each other. Furthermore,
while stable aggregates can be obtained with both cis and
trans conformers modelled,the most ordered are those
formed by the trans derivatives,consistent with the AFM re-
sults. This can be explained in terms of stacking capabilities
of the two isomers. Two molecules arrange so as to maxi-
mize the number of intermolecular interactions,as shown by
MM optimization: cis molecules tend to form a “closed
shell” using all the amide groups to form hydrogen bonds,
as shown in Figure 18. This leads to a “building block” with
The TTFs reported here are promising components for
molecular electronics as indicated by the current sensing
AFM studies,which show metallic-type behaviour when
doped chemically on the graphite surface.
Experimental Section
General methods and materials: IR spectra were recorded on a Fourier
transform Perkin–Elmer,Spectrum One spectrometer; the samples were
dispersed in KBr pellets. 1H NMR and 13C NMR were recorded with a
Bruker Avance 250. Tetramethylsilane or residual solvent protons were
used as internal standard. Laser desorption ionization time-of-flight
(LDI-TOF) mass spectra were recorded on a Maldi2K-probe (KRATOS
ANALYTICAL) mass spectrometer. The spectra were recorded by using
pulsed extraction of positive ions and with high power (20 kV). Samples
were deposited onto the stainless steel sample plates from chloroform.
The atomic force microscopy (AFM) images were recorded on a Pi-
coSPM (Molecular Imaging). The acoustic mode was used with reso-
nance frequencies of the silicon tips (Nanosensors,FM type force con-
stant 1.2–3.5 Nmꢀ1 and diameter 5 nm) of around 60–70 kHz. All the
images were recorded under atmospheric conditions. The current images
were recorded in contact mode with a bias voltage applied to the sample,
while scanning with a grounded conducting Pt–Ir coated silicon tip (force
constant around 1.2 Nmꢀ1). The graphite used was highly oriented pyro-
lytic graphite (HOPG),ZYB quality,12”12”2 mm 3,GE Advanced Ce-
ramics. The transmission electron microscopy (TEM) was performed by
using a Hitachi 800MT microscope with a Multiscan camera from Gatan.
The grids used were carbon-coated copper grids from Monocomp. The
melting points were recorded by using a Perkin–Elmer DSC7 differential
scanning calorimeter with 25 mL aluminium pans. To check the purity of
the compounds analytical TLC (silica 60F254 (Merck) on aluminium foil)
were carried out. Flash column chromatography was carried out on silica
Figure 18. Representation of the cis–cis dimer,in which the maximum
number of hydrogen bonds is formed between the two molecules.
poor stacking capabilities,which can introduce disorder in
the supramolecular structure. In contrast,for trans mole-
cules the “building block” has better stacking capabilities,
since two amide groups on each side of the supramolecule
are still available to bind other units in a “columnar” geom-
etry,leading to a well-ordered,close-packed situation.
Conclusion
Nanometre-scale fibres containing p-electron-rich units can
be favoured by employing the amide group as a noncovalent
assemble; the use of this group has proven to be an ex-
Chem. Eur. J. 2006, 12,9161 – 9175
ꢀ 2006 Wiley-VCH Verlag GmbH & Co. KGaA,Weinheim
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9171

D. B. Amabilino et al.
(35–70 mm (from SDS)). The solvents used during the synthesis were dis-
tilled using standard methods. In particular,THF was distilled from
elemental analysis calcd (%) for C20H40ClNO: C 69.43,H 11.65,N 4.05;
found: C 69.54,H 11.55,N 3.97.
sodium benzophenone ketal under nitrogen atmosphere and PACHTRE(UNG OMe)3
4-Thioacetododecylamido-5-methylthio-1,3-dithiol-2-thione
(8a):
was distilled in vacuo from sodium metal. Dichloromethane,chloroform
and acetonitrile were distilled from phosphorous pentoxide under an
inert atmosphere. Compound 6 was synthesised according to a known
method.[61]
CsOH·H2O (0.95 g,5.66 mmol) in MeOH (8 mL) was added over a
period of 30 min to a solution of 6 (1.53 g,5.65 mmol) in CH 3CN/THF
(1:1,60 mL) under Ar and with vigorous stirring. The resulting mixture
was stirred for a further 30 min,then 7a (2.51 g,9.59 mmol) and a small
amount of NaI were added and the solution was heated at reflux for 5 h.
The organic solvent was filtered while hot to remove a white solid (which
was discarded) and the solution was evaporated to dryness in vacuo. The
resulting oily material was purified by flash column chromatography on
silica gel (CHCl3/EtOAc; 99:1) to give 8a in 98% yield (2.30 g) as a
yellow powder. M.p. 76.48C; FT-IR: n˜ =3296 (m,NH),2955 (s),2919 (s),
2849 (s),1637 (s,CONH),1545 (s,CONH),1462 (w),1401 (w),1317 (w),
Computational methods: Several aggregates (dimers,stacks) were simu-
lated using the molecular modeling package TINKER 4.2.[72] Molecular
mechanics (MM) calculations were performed with the MM3 FF avail-
able in the TINKER package. This force field was chosen because it
takes explicitly into account directional hydrogen bonds and provides a
reliable description of p-systems.
Monte Carlo (MC) simulations were used to find the most likely con-
formers for single molecules of the modelled compounds (with the long
ꢀ1
ꢀ
1264 (w,C N),1234 (w),1056 (m,C =S),1032 (w),920 (w),721 cm
(w,
NH); 1H NMR (250 MHz,CDCl 3): d=6.53 (s,1H; -SCH 2CONH-),3.56
alkyl groups replaced by methyl groups) at room temperature. Seven
(s,2H; -SC H2CO-),3.32 (q, J=7 Hz,2H; -CONHC H
(s,3H; -SC H3),1.29 (m,20H; -CONHCH 2A(CH2)10CH3),0.91 ppm (t, J=
6.2 Hz,3H; -CONHCH 2A
(CH2)10CH3; 13C NMR (62.8 MHz,CDCl 3): d=
2ACTHER(UNG CH2)10CH3),2.57
ꢀ1
conformers,both cis and trans,within 3 kcalmol
with respect the most
CTHREUNG
stable one were identified and used to model aggregates.
CTHREUNG
N-Dodecyl-2-chloroacetamide (7a): This method was similar to that de-
scribed by Thorsteinsson et al.[62] with minor modifications. Chloroacetyl
chloride (4.4 mL,55 mmol) and N-N- dimethyl-4-aminopyridine (0.1 mg)
were dissolved in dichloromethane (50 mL). This solution was cooled to
08C and dodecylamine (9.30 g,50 mmols) with triethylamine (8.4 mL) in
dichloromethane (10 mL) was added dropwise over one hour. The result-
ing solution was stirred for a further three hours at room temperature.
The solvent residue was filtered and the filtrate was treated with HCl
(1m),by extraction (3”15 mL). The resulting organic phase was dried
using MgSO4. Finally,the organic solvent was filtered and evaporated to
give 8.40 g of a white solid (65%). M.p. 61.98C; FT-IR: n˜ =3299 (m,
NH),2955 (s),2917 (s),2872 (s),2848 (s),1670 (s,CCONH),1644 (s,
209.6 (-C=S),165.9 (- CONH-),128.8 (-C =C-),39.9 (-NH CH2CH2-),39.4
(-SCH2CONH-),31.6,29.4,29.3,29.2,29.2,29.0,26.7,22.4 (-NHCH
-
2
ACHETRNU(G CH2)10CH3),19.0 (-S- CH3),13.8 ppm (-NH AHCRTE(UGN CH2)11CH3); elemental anal-
ysis calcd (%) for C18H31NOS5: C 49.38,H 7.14,N 3.20; found: C 49.13,
H 7.72,N. 3.83.
4-(Thioacetopentadecylamido)-5-methylthio-1,3-dithiol-2-thione
The procedure was the same as that described for 8a,with 6 (1.40 g,
5.27 mmol),CsOH·H 2O (0.90 g,5.35 mmol) and of 7b (2.35 g,
(8b):
7.73 mmol). The eluent for the column chromatography was CHCl3/
EtOAc 95:5. Finally 1.95 g (77%) of 8b was isolated. M.p. 84.38C; FT-
IR: n˜ =3287 (m,NH),2954 (s),2919 (s),2848 (s),1634 (s,CONH),1546
ꢀ
(s,CONH),1460 (w),1417 (w),1400 (w),1316 (w),1262 (w,C
N),1199
CONH),1549 (m,CONH),1518 (m,C
=O),1468 (m),1400 (w),1264
ꢀ1
(w),1131 (w),1057 (m,C
=S),902 (w),722 cm
(w,NH); 1H NMR
ꢀ
(w),1234 (w,C N),1071 (w),928 (w),835 (w),786 (w),721 (w,NH),
(250 MHz,CDCl 3): d=6.49 (s,1H; -SCH 2CONH-),3.54 (s,2H;
-SCH2CO-),3.29 (q, J=6.7 Hz,2H; -CONHC H2A(CH2)13CH3),2.54 (s,
3H; -SCH3),1.26 (m,26H; -CONHCH 2A(CH2)13CH3),0.88 ppm (t, J=
6.2 Hz,3H; -CONHCH 2A
(CH2)13CH3; 13C NMR (62.8 MHz,CDCl ): 209.6
1
617 cmꢀ1 (w); H NMR (250 MHz,CDCl ): d=6.61 (s,1H; -NH),4.07 (s,
3
CTHREUNG
2H; ClCH2CO-),3.32 (q, J=6.9 Hz,2H; - NHC H2-),1.5–1.2 (m,20H;
CTHREUNG
-NHCH
C
J=6.4 Hz,3H; -(CH 2)10CH3);
CTHREUNG
3
(-C=S),165.9 (- CONH-),128.8 (-C =C-),39.9 (-NH CH2CH2-),39.3
(-SCH2CONH-),31.6,29.3,29.2,29.1,29.0,26.7,22.4 (-NHCH
-
2
-
2
ACHTREUNG(CH2)10CH3),13.8 ppm (-NH CAHTRE(UNG CH2)11CH3); elemental analysis calcd (%)
for C14H28ClNO: C 64.22,H 10.78,N 5.35; found: C 64.33,H 10.66,N
5.26.
ACHETRNU(G CH2)13CH3),19.0 (-S- CH3),13.8 ppm (-NH AHCRTE(UGN CH2)14CH3); elemental anal-
ysis calcd (%) for C21H37NOS5: C 52.56,H 7.77,N 2.92; found: C 52.65,
H 7.84,N 3.02.
N-Pentadecyl-2-chloroacetamide (7b): The method used was that de-
scribed for 7a,in which chloroacetyl chloride (0.9 mL,11 mmol) and
pentadecylamine (3.12 g,13.7 mmol) were reacted together. Compound
7b was isolated as a white solid (2.25 g,54%). M.p. 68.7 8C; FT-IR: n˜ =
3307 (m,NH),2956 (s),2922 (s),2852 (s),1737 (s,CONH),1655 (s,
CONH),1548 (m,CONH),1464 (m),1452 (m),1354 (w),1317 (w),1212
4-(Thioacetooctadecylamido)-5-methylthio-1,3-dithiol-2-thione (8c): The
procedure was the same as that described for 8a,with (2.10 g,
7.91 mmol),CsOH·H 2O (1.33 g,7.92 mmol) and 7c (4.62 g,13.3 mmol).
In this case the column chromatography was done using CHCl3 as eluent
to give 2.77 g (67%) of a yellow powder characterized as 8c. M.p.
98.78C; FT-IR: n˜ =3292 (m,NH),2918 (s),2849 (s),1637 (s,CONH),
6
ꢀ1
(s,C N),1178 (w),1143 (w),786 (w),720 cm
(w,NH); 1H NMR
ꢀ
ꢀ
1544 (m,CONH),1463 (m),1418 (w),1401 (w),1315 (w),1211 (w,C
N),1160 (w),1057 (m,C =S),1031 (w),945 (w),898 (w),721 cm
ꢀ1
(250 MHz,CDCl 3): d=6.58 (s,1H; -NH),4.04 (s,2H; ClC H2CO-),3.29
(w,
NH); 1H NMR (250 MHz,CDCl 3): d=6.52 (s,1H; -SCH 2CONH-),3.56
(s,2H; -SC H2CO-),3.32 (q, J=6.9 Hz,2H; -CONHC H2A(CH2)16CH3),
2.57 (s,3H; -SC H3),1.28 (m,32H; -CONHCH 2A(CH2)16CH3),0.91 ppm (t,
J=6.2 Hz,3H; -CONHCH 2A
(CH2)16CH3; 13C NMR (62.8 MHz,CDCl3):
(q, J=7.0 Hz,2H; -NHC
H2ACHTRE(UGN CH2)13CH3),1.5–1.2 (m,26H;
-ClCH2CONHCH2(CH2)13CH3),0.89 ppm (t, J=6.4 Hz,3H; -(CH2)13CH3);
13C NMR (62.8 MHz,CDCl 3): d=165.4 (-CONH-),42.4 ( CH2Cl),39.6
(-NHCH2CH2-),31.6,29.4,29.4,29.3,29.3,29.2,29.0,29.0,28.9,26.5,22.4
(-NHCH2ACHTREUNG(CH2)13CH3),13.8 ppm (-NH CAHTREU(GN CH2)14CH3); elemental analysis
calcd (%) for C17H34ClNO: C 67.18,H 11.28,N 4.61; found: C 67.24,H
11.36,N 4.59.
CTHREUNG
CTHREUNG
CTHREUNG
d=209.5 (-C=S),165.8 (- CONH-),128.7 (-C =C-),39.9 (-NH CH2CH2-),
39.3 (-SCH2CONH-),31.6,29.4,29.3,29.2,29.2,29.1,29.0,26.7,22.4
(-NHCH2ACHTREUG(N CH2)16CH3),19.0 (-S- CH3),13.8 ppm (-NH ACHTRE(UGN CH2)17CH3); ele-
mental analysis calcd (%) for C24H43NOS5: C 55.23,H 8.30,N 2.68;
found: C 55.33,H 8.52,N 2.87.
N-Octadecyl-2-chloroacetamide (7c): The method used was that de-
scribed for 7a,in which chloroacetyl chloride (2.0 mL,25 mmol) and oc-
tadecylamine (8.12 g,30 mmol) were reacted together,giving
7c as a
4-(Thioacetododecylamido)-5-methylthio-1,3-dithiol-2-one (9a): Com-
white solid (5.31 g,51%). M.p. 76.9 8C; FT-IR: n˜ =3292 (m,NH),2954
pound 8a (2.28 g,5.21 mmol) was dissolved with Hg CAHTRE(UGN OAc)2 (7.47 g,
(s),2916 (s),2848 (s),1666 (s,CONH),1645 (s,CONH),1551 (m,
23.4 mmol) in CHCl3/HOAc (3:1,180 mL) and was stirred at room tem-
perature overnight under argon atmosphere. A Celite filter was required
to remove the excess of HgACHTRE(UNG OAc)2. The solution was extracted with a sa-
ꢀ
CONH),1468 (m),1415 (w),1375 (w),1301 (w),1264 (w,C
N),1233
(w),1161 (w),720 cm ꢀ1 (w,NH); 1H NMR (250 MHz,CDCl ): d=6.57 (s,
3
1H; -NH),4.04 (s,2H; ClC H2CO-),3.30 (q, J=6.7 Hz,2H; -NHC H2-
turated solution of NaHCO3 (3”30 mL) and water (4”25 mL) The or-
ganic layer was dried (MgSO4) and stripped of solvent and the oily resi-
due was purified by flash column chromatography on silica gel (CHCl3/
EtOAc 95:5) to give 1.83 g (83%) of 9a as a white powder. M.p. 76.08C;
FT-IR: n˜ =3291 (m,NH),2954 (s),2921 (s),2848 (s),1672 (s,CONH),
ACHTREUNG(CH2)16CH3),1.5–1.2 (m,32H; -ClCH 2CONHCH2AHCTRE(UGN CH2)16CH3),0.88 ppm
(t, J=6.2 Hz,3H; -(CH 2)16CH3); 13C NMR (62.8 MHz,CDCl 3): d=165.4
(-CONH-),42.4 ( CH2Cl),39.6 (-NH CH2CH2-),31.6,29.4,29.3,29.2,29.0,
29.0,28.9,26.5,22.4 (-NHCH
2ACHRTE(NUG CH2)16CH3),13.8 ppm (-NH AHCTRE(UGN CH2)17CH3);
9172
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Chem. Eur. J. 2006, 12,9161 – 9175

Supramolecular Chemistry
FULL PAPER
1629 (s,CONH),1547 (m,CONH),1466 (w),1425 (w),1376 (w),1265
2,7-Bis(methylthio)-3,6-bis(thioacetopentadecylamidotetrathiafulvalene)
(2b) and 2,6-bis(thioacetopentadecylamido)-3,7-bis(methylthiotetrathia-
fulvalene) (1b): The procedure for the synthesis of the two compounds
was that described for 2a and 1a. The coupling was done with 9b (0.72 g,
1,54 mmol) and to purify the orange solid the same eluent (CH2Cl2/
EtOAc (90:10)) and the same method were used to give 179 mg (13%)
of 1b and 124 mg (9%) of 2b.
ꢀ1
(w,C N),1203 (w),902 (w),885 (w),722 cm
(w,NH); 1H NMR
ꢀ
(250 MHz,CDCl 3): d=6.63 (s,1H; -SCH 2CONH-),3.53 (s,2H;
-SCH2CONH-),3.29 (q, J=6.2 Hz,2H; -CONH C H
(s,3H; -SCH ),1.26 (m,20H; -CONH CH 2A(CH2)10CH3),0.88 ppm (t, J=
(CH2)10CH3); 13C NMR (62.8 MHz,CDCl3): d=
2ACTHER(UNG CH2)10CH3),2.51
CTHREUNG
3
6.2 Hz,3H; -CONH CH 2ACHTREUNG
188.4 (-C=O),166.0 (- CONH-),120.8 (-C =C-),39.9 (-NH CH2CH2-),39.3
(-SCH2CONH-),31.6,29.3,29.3,29.2,29.1,29.0,29.0,26.7,22.4
Data for 1b: M.p. 878C; LDI-TOF/MS: m/z (%): 895 (100) [M]+; FT-IR:
(-NHCH2ACHTREUNG(CH2)10CH3),19.1 (-S- CH3),13.8 ppm (-NH ACHTRE(UGN CH2)11CH3); ele-
n˜ =3298 (s,NH),2955 (m),2915 (s),2849 (s),1644 (s,CONH),1554 (s,
ꢀ
mental analysis calcd (%) for C18H31NO2S4: C 51.27,H 7.41,N 3.32;
found: C 51.37,H 7.50,N 3.35.
CONH),1470 (w),1408 (w),1317 (w),1301 (w),1221 (w,C
(w),1080 (w),886 (w),718 cm
N),1149
ꢀ1
(w,NH); 1H NMR (250 MHz,CDCl 3):
d=6.84 (s,2H; -SCH 2CONH-),3.51 (s,4H; -SC H2CONH-),3.28 (q, J=
6.7 Hz,4H; -CONH C H2A(CH2)13CH3),2.47 (s,6H; -SCH 3),1.26 (m,
52H; -CONH CH2A(CH2)13CH3),0.88 ppm (t, J=6.2 Hz,6H; -CONH
CH2A(CH2)13CH3); elemental analysis calcd (%) for C42H74N2O2S8:
56.33,H 8.33,N 3.13; found: C 56.42,H 8.25,N 3.12.
4-(Thioacetopentadecylamido)-5-methylthio-1,3-dithiol-2-one (9b): The
method of synthesis and purification was that described for 9a,but with
CTHREUNG
CTHREUNG
8b (1.00 g,2.08 mmol) and Hg
ACHTRE(UNG OAc)2 (1.66 g,5.21 mmol),and giving
C
C
0.84 g (87%) of a white solid. M.p. 75.88C; FT-IR: n˜ =3292 (m,NH),
2956 (m),2922 (s),2848 (s),1671 (s,CONH),1627 (s,C
=O),1547 (m,
ꢀ
Data for 2b: M.p. 928C; LDI-TOF/MS: m/z (%): 895 (100) [M]+; FT-IR:
CONH),1464 (w),1425 (w),1314 (w),1265 (w,C
N),1201 (w),903 (w),
ꢀ1
886 (m),723 cm (w,NH); 1H NMR (250 MHz,CDCl 3): d=6.62 (s,1H;
n˜ =3298 (m,NH),2955 (w),2920 (s),2851 (s),1644 (s,CONH),1554 (m,
ꢀ1
ꢀ
CONH),1468 (w),1406 (w),1317 (w),1219 (w,C
N),1149 (w),720 cm
-SCH2CONH-),3.53 (s,2H; -SC H2CONH-),32,9 (q, J=6.7 Hz,2H; -
(w,NH); 1H NMR (250 MHz,CDCl 3): d=6.79 (s,2H; -SCH 2CONH-),
CONH CH (CH2)13CH3),2.51 ( s,3H; -SCH 3),1.29 (m,20H; -CONH
2ACHTREUNG
3.50 (s,4H; -SC H2CONH-),3.26 (q, J=6.7 Hz,4H; -CONH
(CH2)13CH3),2.45 s,6H; -SCH 3),1.25 (m,52H; -CONH CH
(CH2)13CH3),0.88 ppm (t, J=6.2 Hz,6H; -CONH CH 2A
C
H2-
CH2ACHTREUNG(CH2)13CH3),0.88 ppm (t, J=6.4 Hz,3H; -CONH CH 2ACHTRE(UNG CH2)13CH3);
13C NMR (62.8 MHz,CDCl3): d=188.6 (-C=O),165.9 (- CONH-),120.7
(-C=C-),39.9 (-NH CH2CH2-),39.3 (-S CH2CONH-),31.6,29.3,29.3,29.2,
G
(
-
2
G
(CH2)13CH3); ele-
mental analysis calcd (%) for C42H74N2O2S8: C 56.33,H 8.33,N 3.13;
found: C 56.26,H 8.20,N 3.17.
29.1,29.1,29.0,28.9,26.7,26.5,22.4 (-NHCH
CH3),13.8 ppm (-NH (CH2)14CH3); elemental analysis calcd (%) for
2ACHTERU(NG CH2)13CH3),19.2 (-S-
ACHTREUNG
2,7-Bis(methylthio)-3,6-bis(thioacetooctadecylamidetetrathiafulvalene)
(2c) and 2,6-bis(thioacetooctadecylamide)-3,7-bis(methylthiotetrathiaful-
valene) (1c): The method used was that reported above for 1a and 2a.
The starting compound 9c (2.08 g,4.11 mmol) was dissolved in trimethyl-
phosphite (6 mL). The purifications was done as for the other TTF deriv-
atives to give 317 mg (8%) of 1c and 156 mg (4%) of 2c.
C21H37NO2S4: C 54.38,H 8.04,N 3.02; found: C 54.45,H 8.04,N 3.12.
4-(Thioacetooctadecylamido)-5-methylthio-1,3-dithiol-2-one (9c): The
procedure was that used for 9a,but with 8c (4.00 g,1.91 mmol) and Hg-
ACHTREUNG(OAc)2 (6.11 g,19.2 mmol). After workup,the oily residue was purified
by flash column chromatography (SiO2,CHCl 3:EtOAc (90:10)),giving
2.73 g (72%) of a white powder. M.p. 88.08C; FT-IR: n˜ =3292 (m,NH),
Data for 1c: M.p. 1068C; LDI-TOF/MS: m/z (%): 978 (100) [M]+; FT-
2919 (s),2850 (s),1680 (s,CONH),1643 (s,C
=O),1555 (m,CONH),
ꢀ1
IR: n˜ =3300 (m,NH),2916 (s),2849 (s),1644 (s,CONH),1551 (m,
ꢀ
1467 (w),1424 (w),1324 (w),1217 (w,C
N),1154 (w),901 (m),720 cm
ꢀ1
(w,NH); 1H NMR
(w,NH); 1H NMR (250 MHz,CDCl 3): d=6,63 (s, 1H; -SCH2CONH-),
CONH),1471 (w),1146 (w),885 (w),717 cm
(250 MHz,CDCl 3): d=6.87 (s,2H; -SCH 2CONH-),3.53 (s,4H;
-SCH2CONH-),3.31 (q, J=6.9 Hz,4H; -CONH C H2A(CH2)16CH3),2.49
(s,6H; -SCH ),1.28 (m,64H; -CONH CH 2A(CH2)16CH3),0.91 ppm (t, J=
(CH2)16CH3); elemental analysis calcd (%) for
C48H86N2O2S8: C 58.84,H 8.85,N 2.86; found: C 58.96,H 8.76,N 3.00.
Data for 2c: M.p. 1198C; LDI-TOF/MS: m/z (%): 978 (100) [M]+; FT-
3.53 (s,2H; -SC H2CONH-),3.28 (q, J=6.7 Hz,2H; -CONH
(CH2)16CH3),2.51 (s,3H; -SCH 3),1.26 (m,32H; -CONH CH
2A
13C NMR (62.8 MHz,CDCl3): d=188.3 (-C=O),165.9 (- CONH-),120.7
(-C=C-),39.9 (-NH CH2CH2-),39.3 (-S CH2CONH-),31.6,29.4,29.3,29.3,
C
H2-
CTHREUNG
G
-
2
CTHREUNG
3
(CH2)16CH3),0.88 ppm (t, J=6.2 Hz,3H; -CONH CH
(CH2)16CH3);
6.2 Hz,6H; -CONH CH 2ACHTREUNG
29.1,29.1,29.0,26.7,22.4 (-NHCH
(-NH(CH2)17CH3); elemental analysis calcd (%) for C24H43NO2S4: C
2CATHRE(UNG CH2)16CH3),19.2 (-S- CH3),13.8 ppm
IR: n˜ =3300 (m,NH),2916 (s),2850 (s),1645 (s,CONH),1554 (m,
ACHTREUNG
ꢀ
CONH),1470 (w),1409 (w),1314 (w),1217 (w,C
(w),718 cm
N),1146 (w),1028
56.98,H 8.57,N 2.77; found: C 56.12,H 8.39,N 2.55.
ꢀ1
(w,NH); 1H NMR (250 MHz,CDCl 3): d=6.80 (s,2H;
2,7-Bis(methylthio)-3,6-bis(thioacetododecylamidotetrathiafulvalene)
(2a) and 2,6-bis(thioacetododecylamido)-3,7-bis(methylthiotetrathiaful-
valene) (1a): Compound 9a (1.83 g,4.34 mmol) was refluxed and stirred
in dry trimethylphosphite (6 mL) under inert atmosphere for 7 h. The so-
lution was cooled down and the trimethylphosphite was evaporated leav-
ing an orange powder,which was purified by flash column chromatogra-
-SCH2CONH-),3.53 (s,4H; -SC H2CONH-),3.29 (q, J=7.2 Hz,4H;
-CONH CH2A(CH2)16CH3),2.48 (s,6H; -SCH 3),1.28 (m,64H; -CONH
CH2A(CH2)16CH3),0.91 ppm (t, J=6.3 Hz,6H; -CONH CH 2A(CH2)16CH3).
2,7-Bis(acetoxydodecylamido)naphthalene (3): Naphthalene-2,7-diol
(1.00 g,62,4 mmol,from Aldrich) and 7a (3.92 g,14.97 mmol) were dis-
CTHREUNG
C
CHTREUNG
solved in CH3CN (80 mL) and potassium carbonate (5.17 g,37.41 mmol)
was added. The mixture was refluxed overnight under an inert atmos-
phere. The cooled solution was filtered and the solid residue was washed
with MeCN,then dissolved in CH 2Cl2/EtOAc (1:1) and filtered,and the
solvent evaporated leaving a white powder characterized as compound 3
(2.32 g,61%). M.p. 147 8C; LDI-TOF/MS: m/z (%): 611 (100) [M]+; FT-
IR: n˜ =3388 (m,NH),2917 (f),2849 (s),1658 (s,CONH),1549 (m,
phy (SiO2,CH Cl2/EtOAc 90:10) to collect 2a and by increasing the pro-
portion of EtOAc the cis isomer, 1a,was collected. The amount of 2a
obtained was 277 mg (8%),and for 1a is 269 mg (8%).
Data for 1a: M.p. 838C; LDI-TOF/MS: m/z (%): 811 (100) [M]+; FT-IR:
2
n˜ =3300 (s,NH),2915 (s),2849 (s),1646 (s,CONH),1550 (m,CONH),
ꢀ
1470 (w),1407 (w),1377 (w),1305 (w),1218 (w,C
N),1146 (w),965 (w),
ꢀ1
770 (w),718 cm (w,NH); 1H NMR (250 MHz,CDCl 3): d=6.75 (s,2H;
CONH),1468 (w),1392 (w),1216 (w),1168 (w),1052 (w),843 (w),720
-SCH2CONH-),3.50 (s,4H; -SC H2CONH-),3.28 (q, J=6.2 Hz,4H;
ꢀ1
(w),583 cm (w,NH); 1H NMR (250 MHz,CDCl ): d=7.73,7.69 (d, J=
3
-CONH CH
(CH2)10CH3),2.46 (s,6H; -SCH 3),1.26 (m,40H; -CONH
2A(CH2)10CH3).
9.8 Hz,2H; -HC =CH-),7.09 (s,2H; -HC =),7.08,7.05 (d, J=8,5 Hz,
2H; -HC=CH-),66, 2 (s,2H; -OCH 2CONH-),4.58 (s,4H; -OC H2CONH-
CH2A(CH2)10CH3),0.88 ppm (t, J=6.2 Hz,6H; -CONH CH CHTREUNG
N
Data for 2a: M.p. 988C; LDI-TOF/MS: m/z (%): 811 (100) [M]+; FT-IR:
),3.35 (q, J=6.7 Hz,4H; -CONH C H
-CONH CH2A(CH2)10CH3),0.87 ppm (t, J=6.3 Hz,6H; -CONH CH
AHCTREUNG
(CH2)10CH3); 13C NMR (62.8 MHz,CDCl3): d=167.5 (-CONH-),155.6
2ACHTREU(GN CH2)10CH3),1.23 (m,40H;
n˜ =3299 (s,NH),2915 (s),2850 (m),1645 (s,CONH),1551 (s,CONH),
C
-
2
ꢀ1
1470 (w),1408 (w),1146 (m),1098 (m),885 (w),770 (w),718 cm
(w,
NH); 1H NMR (250 MHz,CDCl 3): d=6.84 (s,2H; -SCH 2CONH-),3.51
(O-C aromatic),135.2 (C =C aromatic central),129.4 (C =C aromatic),
125.1 (C=C aromatic central),115.9 (C =C aromatic),106.9 (C =C aromat-
ic),67.1 (-O CH2CONH-),38.8 (-NH CH2CH2-),31.6,29.3,29.3,29.2,29.0,
(s,4H; -SC H2CONH-),3.28 (q,
(CH2)10CH3),2.47 s,6H; -SCH 3),1.26 (m,40H; -CONH CH
(CH2)10CH3),0.88 ppm (t, J=6.4 Hz,6H; -CONH CH 2A
J=6.9 Hz,4H; -CONH
C
H2-
G
(
-
2
G
(CH2)10CH3); ele-
28.9,26.6,22.4,(-NHCH
2CAHRTU(NEG CH2)10CH3),13.8 ppm (-NH HCATRE(UGN CH2)11CH3); ele-
mental analysis calcd (%) for C36H62N2O2S8: C 53.29,H 7.70,N 3.45;
found: C 53.15,H 7.80,N 3.55.
mental analysis calcd (%) for C38H62N2O4: C 74.71,H 10.23,N 4.59;
found: C 74.60,H 10.16,N 4.57.
Chem. Eur. J. 2006, 12,9161 – 9175
ꢀ 2006 Wiley-VCH Verlag GmbH & Co. KGaA,Weinheim
www.chemeurj.org
9173

D. B. Amabilino et al.
2,6-Bis(acetoxydodecylamido)naphthalene (4): Commercial naphthalene-
2,6-diol (1.00 g, 6.24 mmol) and 7a (3.92 g,14.97 mmol) were dissolved
toluene/THF (1:1,80 mL) and potassium carbonate (3.88 g,28.09 mmol)
was added. The resulting solution was refluxed overnight. The desired
compound was purified as described for 3,giving 1.58 g (42%) of an off-
white solid. M.p. 1608C; LDI-TOF/MS: m/z (%): 611 (100) [M]+; FT-IR:
n˜ =3366 (m,NH),2919 (s),2849 (s),1654 (s,CONH),1536 (m,CONH),
1470 (w),1394 (w),1231 (w),1164 (w),1064 (w),848 (w),722 (w),
584 cmꢀ1 (w,NH); 1H NMR (250 MHz,CDCl 3): d=7.71,7.68 (d, J=
8.9 Hz,2H; -HC =CH-),7.26 (s,1H; -HC =),7.21,7.18 (d, J=8.9 Hz,2H;
-HC=CH-),7.11 (s,1H; -HC =),6.61 (s,2H; -OCH 2CONH-),4.59 (s,4H;
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(m,40H; -CONH CH 2A(CH2)10CH3),0.88 ppm (t, J=6.3 Hz,6H; -CONH
CH2A
(CH2)10CH3); 13C NMR (62.8 MHz,CDCl3): d=167.7 (-CONH-),
2ACTHER(UNG CH2)10CH3),1.24
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CHTREUNG
153.8 (O-Caromatic),129.8 (C =C aromatic),128.6 (C =C aromatic),118.6
(C=C aromatic),107.5 (C =C aromatic),67.2 (-O CH2CONH-),38.8
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2
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4.61.
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(3.04 g,11.60 mmol) were reacted together by using the same procedure
described for 3. The yield of the reaction was 81% (2.50 g) of a white
solid characterized as compound 5. M.p. 1828C; LDI-TOF/MS: m/z (%):
637 (100) [M]+; FT-IR: n˜ =3299 (m,NH),2918 (s)2,849 (s),1653 (s,
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CONH),1544 (m,CONH),1501 (w),1469 (w),1286 (w),1180 (w),1063
ꢀ1
(w),821(w),720 (w),590 cm
(w,NH); 1H NMR (250 MHz,CDCl ): d=
3
7.51,7.47 (d, J=8.8 Hz,4H; -HC =CH-),7.00,6.96 (d, J=8.8 Hz,4H;
-HC=CH-),6.60 (s,2H; -OCH 2CONH-),4.51 (s,4H; -OC H2CONH-),
3.34 (q, J=6,7 Hz, 4H; -CONH CH (CH2)10CH3),1.24 (m,40H; -CONH
2ACHTREUNG
CH2ACHTREUNG(CH2)10CH3),0.87 ppm (t, J=6.3 Hz,6H; -CONH CH 2ACHTRE(NGU CH2)10CH3);
13C NMR (62.8 MHz,CDCl3): d=167.7 (-CONH-),156.3 (O- Caromatic),
134,2 (C=C aromatic),127.9 (C =C aromatic),114.7 (C =C aromatic),67.3
(-OCH2CONH-),38.8 (-NH CH2CH2-),31.6,29.3,29.3,29.2,29.1,29.0,
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8489–8498.
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This work was supported by the DGI,Spain (Project No. BQU 2003-
00760),the Belgian Federal Science Policy Office (PAI 5/3),FNRS,and
the Marie Curie Research Training Network CHEXTAN (MRTN-CT-
2004-512161). J.P. thanks the Generalitat de Catalunya for a pre-doctoral
grant,linked with the Fundació Institut Català de Nanotecnologia. A.L.
and G.U. acknowledge the Generalitat de Catalunya,(project 2005/SGR/
00896) and the Spanish MEC for Grant no. CTQ2005-09000-C02-01,and
a “Ramon y Cajal” contract to G.U. We warmly thank Amable BernabØ
for recording IR and LDI-TOF spectra. We thank Hiroshi Uji-i and
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Chem. Eur. J. 2006, 12,9161 – 9175

Supramolecular Chemistry
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Published online: November 22,2006
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