Self-assembly of alkylcatechols on HOPG investigated by scanning tunneling microscopy and molecular dynamics simulations

Article abstract of DOI:10.1039/c1ce06010d

Two alkylcatechols have been studied by means of STM at the liquid-solid interface. While for catechol 3 no molecular domains on the surface have been observed most likely due to the steric constraints imposed by the tert-butyl group, catechol 2 self-orga

Full text of DOI:10.1039/c1ce06010d

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PAPER
Self-assembly of alkylcatechols on HOPG investigated by scanning tunneling
microscopy and molecular dynamics simulations
c
c
d
a
Javier Saiz-Poseu,ab Isaac Alcon, Ramon Alibes, Felix Busque, Jordi Faraudo and Daniel Ruiz-Molina
ꢀ c
*
*
ꢀ
ꢀ
ꢀ
Received 5th August 2011, Accepted 28th September 2011
DOI: 10.1039/c1ce06010d
Two alkylcatechols have been studied by means of STM at the liquid–solid interface. While for catechol
3 no molecular domains on the surface have been observed most likely due to the steric constraints
imposed by the tert-butyl group, catechol 2 self-organizes both in nonanoic acid and TCB solvents.
Combined molecular dynamics simulations have shown the large tendency of this catechol to remain
and organize on surfaces. Moreover, by comparison with the results previously described for catechol 1,
valuable information about the energetic and thermodynamics for the adsorption process of catechols
can be extracted.
interactions.7b–g A wide range of compounds have been studied with
STM at the liquid–solid interface, including simple linear alkanes,8
long chain alcohols,9 aromatic carboxylic acids,10 amides,11
aromatic cores functionalized with alkyl chains,12 crown13 and
thiacrown ethers14 and even more complex structures like fuller-
enes15 and macrocyclic coordination compounds.16 Nevertheless,
no examples of catechols at the liquid–solid interface can be found
in the literature, and only scarce examples of these compounds on
surfaces have been studied by STM under UHV conditions.17
For this reason we have started new research focused to study
the self-assembly of catechols at the liquid–solid interface by
STM. Following this approach, very recently we described for
the first time the self-assembly of the 4-heptadecylcatechol 1
(Fig. 1) at the nonanoic acid–HOPG interface.18 Compound 1
was shown to exhibit a large tendency to adsorb on the surface as
a result of both energetic (interactions on the surface) and
entropic factors (temperature and solvent). Energetic factors
arise from the presence of attractive van der Waals (vdW)
interactions with the HOPG surface and alkyl chains of other
adsorbed molecules as well as from the formation of hydrogen
bonds between different catechol moieties. Entropic factors arise
from the relatively poor solvation of compound 1 in solvents
such as nonanoic acid. This combination of complex factors,
resulted in a rich self-assembly behaviour of 1 at the HOPG
surface (with and without coadsorption of the solvent) that
Introduction
Catechols have been found to strongly interact with surfaces in
different natural systems. One of the most well-known examples
is the aminoacid L-3,4-dihydroxyphenylalanine (DOPA), which
has been found to play a crucial role in the strong adhesive
capacity of mussels.1 In this case, interfacial adhesion to
substrates arises from interactions between the catechol form of
DOPA and a variety of substrates (e.g. minerals, metal surfaces,
and wood, among others). Catechol derivatives also play an
important role in Asian lacquers used as durable coating mate-
rials.2 All these saps present catechol compounds with alkyl and
alkenyl chains of different length, degree of saturation and
position in the benzene ring,3 that upon a cross-linked poly-
merization constitute the protective film.4
This ability of catechol derivatives to interact with surfaces has
been exploited by many scientists worldwide to prepare new
synthetic functional adhesives5 and coatings.6 However, under-
standing the basic behaviour and assembly of catechols on surfaces
still remains a challenge. For this reason, new basic studies that gain
information about the self-assembly and interaction of catechols
with surfaces are highly required. Scanning tunneling microscopy
(STM) is an excellent technique for such studies.7 STM can allow
the direct observation of the molecular self-assembly processes on
surfaces with molecular resolution, and therefore, the study and
modelization of molecule–molecule and molecule–surface
aCentro de Investigacion en Nanociencia
ICN-CSIC), Esfera UAB, Edificio CM7, Campus UAB, 08193
Cerdanyola del Valleꢀs, Spain. E-mail: druiz@cin2.es; Fax: +34935813717
ꢀ
ꢀ
y Nanotecnologıa (CIN2,
b
ꢀ
ꢀ
Fundacion Privada ASCAMM, Unidad de Nanotecnologıa
(NANOMM), Parc Tecnoloꢁgic del Valleꢁs, Av. Universitat Autoꢁnoma,
23, 08290 Cerdanyola del Valleꢁs (Barcelona), Spain
cDepartment de Quꢀımica, Universitat Autoꢁnoma de Barcelona, Edifici Cn,
Campus UAB, 08193 Cerdanyola del Valleꢀs (Barcelona), Spain
d
ꢁ
Institut de Ciencia de Materials de Barcelona, ICMAB-CSIC, Campus de
la UAB, E-08193 Bellaterra, Spain
Fig. 1 Structure of alkylcatechols 1–3.
264 | CrystEngComm, 2012, 14, 264–271
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depends on thermodynamic and kinetic aspects. Moreover, the
nontrivial implications of structural factors on the interaction
with surfaces are also relevant.
methyl sulfate in basic conditions to afford the methoxy pro-
tected derivative 5 (ref. 20) in 67% yield (Scheme 1). The Wittig
reaction of the dialdehyde 5 with hexadecyl triphenylphospho-
nium bromide and potassium tert-butoxide in dry THF afforded
in 70% yield a mixture of olefinic isomers 6 wherein the (Z,Z)-6
was the major component. Conventional hydrogenation, using
hydrogen and palladium on carbon catalyst, followed by
demethylation by treatment with boron tribromide in CH2Cl2
gave catechol 2 in 77% yield for the two steps.
These interesting results led us to continue within this research
line by studying how modifications on their chemical structure can
affect the self-assembly on surfaces. With this aim, in this work we
report the synthesis of two new alkylcatechols 2 and 3 (Fig. 1) and
the study of their self-assembly on HOPG by STM in two different
solvents. Theadditionofasecondalkylchainin2isusedtoevaluate
the contribution of the catechol unit to the energetic interplay of
thermodynamic and kinetic aspects that control the self-assembly.
Compound 3 has also been synthesized for comparison purposes,
bearing a bulky tert-butyl group that is expected to disrupt the
assembly processes. The experimental results have been rational-
ized according to theoretical calculations.
The synthesis of catechol 3 began from the commercially
available phenol 8 which was converted to 9 in a moderate 55%
yield by reaction with tBuOH in H3PO4 (Scheme 2). Oxidation of
9 and demethylation of the resulting aldehyde 10 (ref. 21)
afforded the catechol 11 which was protected as the MOM
derivative 12 (ref. 22) by standard conditions in 37% yield for the
three steps. Then, the Wittig reaction of aldehyde 12 with hexa-
decylidene(triphenyl)phosphorane gave the olefin 13 as a 10 : 1
mixture of the (Z)- and (E)-isomers in 58% combined yield.
Hydrogenation of olefins 13 using hydrogen and palladium on
carbon catalyst, followed by acid treatment in refluxing meth-
anol to cleave the MOM ethers provided the target compound 3
in 86% yield for the two steps.
Results and discussion
Synthesis of compounds 2 and 3
The synthesis of the 3,5-dialkyl-1,2-dihydroxybenzene 2 started
from the isophthalaldehyde 4 (ref. 19) which was treated with
Thermodynamics for the adsorption of 2 at the nonanoic acid–
HOPG interface
Initially, the Gibbs free energy associated to the transfer of
compound 2 from solution to the liquid–solid interface was
theoretically evaluated, putting special emphasis on its molecular
origin. Technical details of the calculations are described in the
Materials and methods section. It should be emphasized here
that theoretical predictions of this kind, involving not only
enthalpy but also free energy calculations, are rather difficult and
very time-consuming for liquid solutions. In fact, the realization
of such calculations has become possible thanks to recent new
developments in simulation techniques. This is the case for the
new MD-ABF technique employed in this work.23
First, Molecular Dynamics (MD) simulations of a liquid
solution composed of 48 molecules of 2 andꢀ400 nonanꢀoic acid
molecules at two different temperatures (20 C and 80 C) and
Scheme 1 (a) Me2SO4, K2CO3, (n-Bu)4NI, DMF, 67%; (b) 1-(hexadecyl)
triphenylphosphonium bromide, tBuOK, THF, 70%; (c) H2, Pd/C, ethyl
acetate, 80%; (d) BBr3, CH2Cl2, 96%.
Scheme 2 (a) tBuOH, H3PO4, 55%; (b) Br2, tBuOH, 62%; (c) AlCl3, pyridine, CHCl3, 85%; (d) methoxymethyl bromide, iPr2EtN, DMAP, CH2Cl2,
70%; (e) 1-(hexadecyl)triphenylphosphonium bromide, tBuOK, THF, 58%; (f) H2, Pd/C, ethyl acetate, 98%; (g) HCl (cat.), MeOH, 88%.
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1 atm were done. This molecular ratio corresponds to a concen-
tration similar to that used for the STM experiments shown later
on. Afterwards, the resulting equilibrated solution was placed in
contact with a large graphite surface of 87.81 nm2 that was
immediately covered by molecules. A second set of MD simu-
lations were then run to allow further equilibration and
adsorption/desorption events at the surface. An illustrative
snapshot of the simulation is shown in Fig. 2. A first qualitative
observation is the strong tendency to adsorb of compound 2,
which covers most of the surface after 1 ns together with a small
amount of a few nonanoic acid molecules. It is important to
mention that this situation takes place in spite of the large excess
of the nonanoic acid that has also been shown to organize under
these circumstances. However no clear self-assembly patterns
were observed on the surface, at least under simulation scales
accessible with MD simulations (more details about this issue are
given in the next section).
Afterwards, biased MD-ABF simulations were performed on
the resulting combined (solution + surface) system to obtain the
thermodynamic free energy associated with the transfer of 2 from
liquid to the graphite surface as a function of the distance. In
these MD-ABF simulations, an adsorbed molecule was selected
and pulled out from the surface in a very slow, quasi-static
process. We recall that during this pulling process, the selected
molecule interacts not only with the surface but also with the
other solute molecules and the solvent which are also moving
according to Newton motion equations during the simulation.
Also, the simulation technique maintains thermal equilibrium
during the process by employing a thermostat, as described in the
Methods section. The work performed in this process gives the
free energy associated with the transfer of compound 2 from
the bulk solution to the surface under given thermodynamic
conditions (composition, temperature, pressure). The results for
the free energy profile at 20 ꢀC and 80 ꢀC are shown in Fig. 3. The
insets show representative snapshots of the process, in which the
desorption event is highlighted.
As can be seen in Fig. 3, the adsorption minimum corresponds
to an adsorption free energy of DG ¼ ꢁ133.5 kcal molꢁ1 at 20 ꢀC.
The first thing to recall is the resulting large value for DG, indi-
cating a strong affinity of this compound for the liquid–solid
interface, as expected in general for catechols. It is important to
emphasize the fact that this value is comparable to the free energy
gain previously obtained for the adsorption of compound 1 at the
nonanoic acid–HOPG interface (DG ¼ ꢁ122 kcal molꢁ1 at
ꢀ
20 C). Therefore, the addition of a second alkyl chain induces
a small increase of the affinity for the surface, smaller than 10%.
While the second alkyl chain is expected to enhance the gain in
the adsorption free energy by promoting favourable van der
Waals interactions, the induction of stronger steric interactions
can simultaneously disrupt the formation of hydrogen bonds
Fig. 2 Molecular Dynamics (MD) simulations of a liquid solution
composed of 48 molecules of 2 and 400 nonanoic acid molecules at 20 ꢀC.
(a) Lateral view of the simulated system, solvent molecules are shown
translucent for clarity. (b) Top view showing only the molecules adsorbed
at the surface after putting the graphite surface in contact with the pre-
equilibrated solution. The rest of the molecules of the system (which
correspond to the large majority of the system) are not shown for the sake
of clarity. Coadsorption of molecules of 2 with a few nonanoic acid
molecules is also observed. The colour code follows standard crystallo-
graphical conventions: red for oxygen, cyan for carbon and white for
hydrogen (the surface is shown in blue for clarity).
Fig. 3 Free energy (DG) profile for the transfer of a molecule of 2 from
the graphite surface to the bulk solution as a function of the distance of
the centre of mass of the molecule (z) to the surface. The MD-ABF
calculations were performed at 20 ꢀC and 80 ꢀC. The snapshots are
images of a solute molecule in a desorption event. All other molecules of
the large simulated system are not shown for clarity.
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between catechol units. This fact would indicate that the catechol
moiety is responsible for a substantial part of the affinity of these
compounds for the surface.
areas were obtained with the conditions described in Fig. 4. A
representative image of the domains found for 2 is shown in
Fig. 4a. The analysis of the images evidences high-contrast bright
spots associated to dimers of catechol rings that arrange with
a hexagonal centred symmetry. This packing differs from that
found for 1 (shown in Fig. 4b for comparison purposes), being an
indication of the second chain effect on the 2-D molecular
packing.
The second remarkable result is the substantial dependence of
DG on temperature, which confirms that entropic factors also
play an important role in the affinity of compound 2 for the
surface (recall here the thermodynamic relationship between
entropy and T dependence of the free energy at a constant
pressure). The adsorption free energy decreases from DG ¼
Moreover, two different orientations of these dimers can be
observed, with a relative rotation between them of approxi-
mately 90ꢀ. This leads to the formation of two different domains,
as can be seen in Fig. 4c. To facilitate the location and imaging of
such orientations, the differently oriented dimers have been
coloured in Fig. 4d. As can be observed there, none of them
seems to be especially favoured from an energetic point of view,
since both spread spontaneously all over the surface with an
approximate half occupation. The zones between the bright spots
are expected to be occupied by the alkyl chains, though unfor-
tunately the resolution was not good enough to determine the
exact number and position of them. Nevertheless, there is room
enough in the unit cell (area z 17 nm2) to accommodate all the
alkyl chains and 4–6 nonanoic acid molecules.
ꢁ133.5 kcal molꢁ1 at 20 C to DG ¼ ꢁ89 kcal molꢁ1 at 80 C.
Such remarkable temperature dependence therefore strongly
precludes the use of total energy methods developed to study self-
assembly processes under vapour deposition techniques. These
simulations can be done only in situations in which temperature
(and entropic) factors do not play a significant role, which is not
the case.
ꢀ
ꢀ
Experimental self-assembly of 2 and 3 at the nonanoic acid–
HOPG interface
The self-assembly of 2 was initially studied at the nonanoic acid-
HOPG interface at room temperature. For this, a drop of
a nonanoic acid solution of compound 2 (2 mg mLꢁ1) was cast
onto a freshly cleaved HOPG surface at room temperature.
Considerable experimental difficulties were found when obtain-
ing images of 2 with good resolution, in spite of the numerous
experiments attempted. From all the conditions tested, the best
large-scale STM images at least over three independent surface
To gain more insight into the disposition of the alkyl chains,
additional experiments were done with trichlorobenzene instead
of nonanoic acid. For this, a drop of a TCB solution of
compound 2 (2 mg mLꢁ1) was cast onto a freshly cleaved HOPG
surface at room temperature using the experimental parameters
described in Fig. 5. Immediately after, large-scale STM images
under ambient conditions were obtained at least over three
independent surface areas. In this case, the resulting molecular
packing was obtained with high reproducibility between different
casting experiments of freshly prepared samples and its stability
assessed by taking different STM images over the same region at
Fig. 4 Self-assembly pattern of 2 at the nonanoic acid–HOPG interface.
(a) Zoom of the self-assembly pattern obtained for 2. Unit cell parameters:
a¼ 5.0ꢂ0.2 nm, b¼ 3.4ꢂ 0.2nm, g ¼95ꢂ 2ꢀ. Scanningconditions:34nm
ꢃ 34 nm, Iset ¼ 50 pA, Vbias ¼ 540 mV. (b) STM image of the self-assembly
pattern of 1. (c) Wide view for the self-assembly of 2 where the different
orientations of the dimers can already be seen. Scanning conditions:
130 nm ꢃ 130 nm, Iset ¼ 55 pA, Vbias ¼ 540 mV. (d) Code of colours to
distinguish the differently oriented dimers shown in (c).
Fig. 5 Self-assembly pattern of 2 at the TCB–HOPG interface. (a) Wide
view. Scanning conditions: 20 nm ꢃ 20 nm, Iset ¼ 63 pA, Vbias ¼ 500 mV.
(b) Zoom view. Unit cell parameters: a ¼ 3.4 ꢂ 0.2 nm, b ¼ 1.0 ꢂ 0.2 nm,
g ¼ 95 ꢂ 4ꢀ. Scanning conditions: 10 nm ꢃ 10 nm, Iset ¼ 64 pA, Vbias
¼
500 mV. (c) Profile marked as a green line in (b), coincident with the
length of 2 molecule in its most extended conformation.
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different time intervals. As can be seen in Fig. 5, a better
molecular resolution is obtained though with a different molec-
ular packing. In this case compound 2 arranges forming rows of
bright spots that can be associated to the catechol moieties, from
where the alkyl chains can be observed with better resolution
lying at both sides of the catechol ring with an angle of 180ꢀ
between them.
described. The argument is as follows. A surface covered only by
nonanoic acid considering an effective area of 1.5 nm2 per
molecule will correspond to a free energy gain of DG ¼ 45/1.5 ¼
ꢁ30 kcal molꢁ1 per nm2 of the covered surface. A surface covered
only by molecules of 2 assuming a unit cell of 17 nm2 involving 4
molecules gives an almost identical free energy gain of DG ¼ (4 ꢃ
133.5)/17 ¼ ꢁ31.4 kcal molꢁ1 per nm2 of the covered surface.
Finally, a coadsorption pattern with the same hypothetical unit
cell but with co-adsorption of 4 nonanoic acid molecules in the
remaining free space (6 nm2) gives a free energy gain of DG ¼
ꢁ(4 ꢃ 133.5 + 4 ꢃ 45)/17 ¼ ꢁ42 kcal molꢁ1 per nm2. These
theoretical estimations suggest that the free energy differences
between different possible self-assembly patterns are small,
which could justify the difficulties observed in obtaining these
self-assembly patterns both in the experiments and theoretical
calculations. For instance, we tried to obtain clear self-assembly
patterns by direct MD simulations, starting from different initial
conditions with pre-adsorbed molecules on the surface and
putting the system in contact with the liquid solution, without
success. Self-assembly patterns cannot be simulated in this case
employing popular energy minimization methods to give more
insight, due to the importance of thermal and entropic factors in
the affinity of compound 2 (neglected in these methodologies).
The profile marked as a green line in Fig. 5b is coincident with
the length of this molecule in its most extended conformation.
The orientation of the catechol moieties can also be resolved
from this image, confirming that all of them are pointing in the
same direction without establishing hydrogen bonds between
them. In fact, taking into account the profile marked in Fig. 5b
and the unit cell area (ꢄ3.3 nm2), where only one molecule of 2
per unit cell can be accommodated, it can be concluded that the
self-assembly pattern corresponds to an arrangement of mono-
mers of 2 into rows. The neighbouring rows interact between
them through van der Waals forces by clearly interdigitating the
alkyl chains, resulting in the formation of the mentioned very
compact packing.
Finally, the self-assembly of 3 was studied at the liquid–HOPG
interface at room temperature in both solvents, nonanoic acid
and TCB. For this, a drop of a nonanoic acid solution of
compound 3 (2 mg mLꢁ1) was cast onto a freshly cleaved HOPG
surface at room temperature. In this case, and even though
several different experimental conditions were used including
those described in Fig. 3 and 4, no images showing the crystal
packing of 3 were obtained. This fact has been attributed to the
presence of the bulky tert-butyl group that most likely disrupts
the formation of good molecular assemblies on surfaces.
Materials and methods
Synthesis
ꢁ
NMR experiments were performed at the Servei de Ressonancia
ꢁ
ꢁ
Magnetica Nuclear of the Universitat Autonoma de Barcelona.
1H NMR spectra were recorded on Bruker DPX250 (250 MHz)
and Bruker DPX360 (360 MHz), spectrometers. Proton chemical
shifts are reported in ppm (d) (CDCl3, d 7.26). 13C NMR spectra
were recorded on Bruker DPX250 (62.5 MHz) and Bruker
DPX360 (90 MHz) spectrometers with complete proton decou-
pling. Carbon chemical shifts are reported in ppm (d) (CDCl3,
d 77.2). NMR signals were assigned with the help of COSY and
HSQC experiments. Infrared spectra were recorded on
Conclusions
The self-assembly of compounds 2 and 3 at the liquid–solid
interface has been studied in two different solvents. While in the
case of compound 3 no self-assembly patterns have been exper-
imentally observed most likely due to the presence of the bulky
tert-butyl groups, STM images have been obtained in both
solvents for compound 2. Experimental results indicate that the
molecules arrange on the surface with both alkyl chains
extended, forming an angle of 180ꢀ for the TCB. Such disposition
leads to the observation of a compact packing with inter-
penetrated chains without coadsorbed solvent molecules. On the
contrary, coadsorption phenomena could take place when using
nonanoic acid. In this case a hexagonal centred symmetry is
observed though the poor image resolution prevents us from
observing the positions of the chains.
a Sapphire-ATR Spectrophotometer; peaks are reported in cmꢁ1
.
High resolution mass spectra (HRMS) were recorded at Micro-
mass-AutoSpec using (ESI+).
Preparation of 4,5-dimethoxyisophthaldehyde 5. Compound 4
(ref. 11) (250 mg, 1.39 mmol) was dissolved in DMF (8 mL) and
K2CO3 (576 mg, 4.17 mmol) and (n-Bu)4NI (22 mg) were added.
The mixture was stirred at room temperature for 2 h and then
Me2SO4 (0.3 mL, 2.78 mmol) was added dropwise. After 24 h,
the solvent was evaporated under vacuum, yielding a solid that
was redissolved in water and extracted with EtOAc (3 ꢃ 3 mL).
The combined organic phases were dried over MgSO4 and the
solvent evaporated under reduced pressure yielding 5 (182 mg,
67% yield). The NMR data were consistent with the values
reported in the literature.12
Theoretical calculations have confirmed the tendency of
compound 2 to adsorb on the surfaces with a free energy of DG ¼
ꢁ133.5 kcal molꢁ1 at 20 ꢀC. Though this value is high if
compared for instance with that obtained for nonanoic acid
under the same conditions (DG ¼ ꢁ45 kcal molꢁ1 at 20 ꢀC), it is
comparable to the free energy gain previously obtained for the
adsorption of compound 1 also under the same experimental
conditions (DG ¼ ꢁ122 kcal molꢁ1 at 20 ꢀC). This is a clear
indication of the importance of catechol in front of the alkyl
chains to promote their surface organization.
Preparation of 1,5-di(heptadec-1-enyl)-2,3-dimethoxybenzene 6.
Hexadecyl-triphenylphosphonium bromide (1.03 g, 1.82 mmol)
was dissolved in anhydrous THF (10 mL) under nitrogen
atmosphere and tBuOK (352 mg, 3.14 mmol) was added por-
tionwise. After stirring for 45 min, a solution of 5 (160 mg,
In fact, the gain in the free energy value obtained for 2 can now
be used to rationalize some of the experimental results previously
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0.83 mmol) in anhydrous THF (4 mL) was added and the
mixture was stirred for 2 h. The reaction was quenched with
water (10 mL) and the aqueous phase was extracted with EtOAc
(3 ꢃ 10 mL). The combined organic phases were dried over
MgSO4 and concentrated under vacuum, affording a residue that
was purified by column chromatography on silica gel with
hexane/EtOAc (6 : 1) to give a mixture of different isomers 6
(318 mg, 63% yield), where the (Z,Z)-isomer is the major
Preparation of 3-tert-butyl-4-hydroxy-5-methoxybenzaldehyde
10. Compound 9 (1.98 g, 10.2 mmol) was dissolved in tBuOH (30
mL) under nitrogen atmosphere and Br2 (1.32 mL, 25.8 mmol)
was added dropwise. The mixture was stirred for 1 h and the
reaction was quenched with water (40 mL). The aqueous phase
was separated and extracted with EtOAc (3 ꢃ 40 mL). The
combined organic layers were washed with NaHSO3 10% (2 ꢃ 50
mL), dried over MgSO4 and concentrated under vacuum to give
a reddish brown oil that was purified by column chromatography
on silica gel with hexane/EtOAc (8 : 1), affording 10 (1.33 g, 62%
yield). The NMR data were consistent with the values reported in
the literature.21
1
component. Spectroscopic data of major isomer: H NMR (250
MHz, CDCl3) d 6.80 (s, 1H), 6.68 (s, 1H), 6.50 (d, 1H, J ¼ 12.5
Hz), 6.31 (d, 1H, J ¼ 12.5 Hz), 5.69 (dt, 1H, J ¼ 12.5, 7.5 Hz),
5.59 (dt, 1H, J ¼ 12.5, 7.5 Hz), 3.81 (s, 3H), 3.73 (s, 3H), 2.22 (m,
4H), 1.46–1.08 (m, 52H), 0.84 (t, 6H, J ¼ 6.4 Hz). 13C NMR
(62.5 MHz, CDCl3) d 152.1, 145.5, 133.7, 133.0, 132.5, 131.4,
128.5, 123.9, 122.5, 111.6, 60.5, 55.6, 31.9, 30.1–29.4, 28.7, 22.7,
14.1. IR (ATR) n 2916, 2849, 1571, 1466, 1326, 1142, 1081,
1008, 721.
Preparation of 3-tert-butyl-4,5-dihydroxybenzaldehyde 11.
Compound 10 (2.00 g, 9.61 mmol) was dissolved in CHCl3 (20
ꢀ
mL) and the solution was cooled down to 0 C. AlCl3 (1.79 g,
13.5 mmol) was added and then pyridine (3.4 mL) was added
dropwise. The mixture was refluxed for 24 h, cooled down to 0 ꢀC
and acidified with HCl 10%. The filtration of the mixture gave
a dark brown solid that was washed with little portions of ether
Preparation of 1,5-diheptadecyl-2,3-dimethoxybenzene 7. A
stirred solution of a mixture of the isomeric olefins 6 (300 mg,
0.49 mmol) in EtOAc (7 mL) was hydrogenated over Pd/C (30
mg) under 1 atm of H2 for 7 h. Filtration over Celite and evap-
oration of the solvent yielded 7 as a yellow oil (241 mg, 80%
yield). 1H NMR (250 MHz, CDCl3) d 6.57 (s, 2H), 3.84 (s, 3H),
3.78 (s, 3H), 2.58 (t, 2H, J ¼ 7.5 Hz), 2.52 (t, 2H, J ¼ 7.5 Hz), 1.55
(m, 4H), 1.37–1.18 (m, 56H), 0.88 (t, 6H, J ¼ 6.5 Hz). 13C NMR
(62.5 MHz, CDCl3) d 152.3, 144.9, 138.4, 136.2, 121.5, 109.9,
60.6, 55.6, 35.9, 31.9, 31.6, 30.9, 29.9–29.4, 22.7, 14.1. IR (ATR) n
2915, 2849, 1588, 1491, 1229, 1149, 1014, 720. HRMS (ESI+)
calcd for [C42H78O2 + Na]+: 637.5894, found 637.5892.
1
(4 ꢃ 10 mL) affording 11 (1.59 g, 85% yield). H NMR (250
MHz, acetone-d6) d 9.81 (s, 1H), 7.46 (d, 1H, J ¼ 2.0 Hz,), 7.34
(d, 1H, J ¼ 2.0 Hz,), 1.48 (s, 9H). 13C NMR (62.5 MHz, acetone-
d6) 192.5, 152,4, 146.8, 138.0, 130.5, 124.6, 113.4, 36.4, 30.4. IR
(ATR) n 3381, 3203, 2959, 2868, 1642, 1591, 1296, 1248, 1167,
864, 670. HRMS (ESI+) calcd for [C11H14O3 ꢁ 1H]+: 193.0870,
found 193.0865.
Preparation of 3-tert-butyl-4,5-bis(methoxymethoxy) benzal-
dehyde 12. To a stirred solution of 11 (1.44 g, 7.42 mmol) in
CH2Cl2 (14 mL) at 0 ꢀC, iPr2EtN (7.8 mL, 44.5 mmol) and
DMAP (0.14 g) were added. Then, methoxymethyl bromide (2.7
mL, 29.7 mmol) was added dropwise, keeping the temperature at
Preparation of 3,5-diheptadecylcatechol 2. Compound 7 (210
mg, 0.34 mmol) was dissolved in CH2Cl2 (4 mL) under nitrogen
atmosphere. The mixture was cooled down to ꢁ78 ꢀC and BBr3
(2.1 mL, 2.05 mmol) was added dropwise. After stirring for 1 h,
the reaction was allowed to warm up to 0 ꢀC, and then the
reaction was quenched with water (4 mL). The organic phase was
separated, dried over MgSO4 and concentrated under reduced
pressure affording 2 (191 mg, 96% yield) as a solid. 1H NMR (250
MHz, CDCl3) d 6.54 (d, 1H, J ¼ 2 Hz), 6.50 (d, 1H, J ¼ 2 Hz),
3.72 (broad s, 2H), 2.56 (t, 2H, J ¼ 7.5 Hz), 2.46 (t, 2H, J ¼ 7.5
Hz), 1.60 (m, 4H), 1.35–1.12 (m, 6H), 0.88, 2.56 (t, 6H, J ¼ 6.3
Hz). 13C NMR (62.5 MHz, CDCl3) d 143.1, 139.6, 135.3, 129.2,
122.0, 113.0, 35.5, 32.1, 30.0, 29.9–29.5, 22.9, 14.2. IR (ATR) n
3340, 2915, 2849, 1522, 1471, 1199, 815. HRMS (ESI+) calcd for
[C40H74O2 + Na]+: 609.5587, found 609.5592.
0
ꢀC, for 1 h. Then, the mixture was allowed to reach room
temperature and was heated to reflux overnight. The reaction
mixture was allowed to cool down to room temperature and
washed with brine (15 mL). The phases were separated and the
aqueous was extracted with CHCl3 (3 ꢃ 7 mL). The combined
organic layers were then dried over MgSO4 and concentrated
under reduced pressure yielding an oil that was purified by
column chromatography on silica gel with hexane/EtOAc (20 : 1)
to give 12 (1.44 g, 70% yield). The NMR data were consistent
with the values reported in the literature.14
Preparation
of
5-(heptadec-1-enyl)-1-tert-butyl-2,3-bis
(methoxymethoxy)benzene 13. Hexadecyl-triphenylphosphonium
bromide (2.28 g, 4.02 mmol) was dissolved in anhydrous THF
(20 mL) under nitrogen atmosphere and tBuOK (0.74 g, 6.59
mmol) was added portionwise. After stirring for 30 min, a solu-
tion of 12 (1.03 g, 3.65 mmol) in anhydrous THF (10 mL) was
added and the mixture was stirred for 2 h, and then the reaction
was quenched with water (20 mL). The aqueous phase was
extracted with EtOAc (3 ꢃ 15 mL). The combined organic
phases were dried over MgSO4 and concentrated under vacuum,
affording a residue that was purified by column chromatography
on silica gel with hexane/EtOAc (8 : 1) to give a mixture of (Z)-
and (E)-13 (10 : 1) (1.05 g, 58% yield). The NMR spectroscopic
Preparation of 2-tert-butyl-6-methoxy-4-methylphenol 9.
Commercial 2-methoxy-4-methylphenol, 8 (5.00 g, 36.2 mmol),
and H3PO4 (11 mL) were mixed and heated at 75 ꢀC. Then tert-
butanol (5.16 mL, 54.3 mmol) was added and the mixture was
heated to reflux for 4 days. The reaction was quenched with
water (15 mL). The phases were separated and the aqueous phase
was extracted with EtOAc (15 mL) and CH2Cl2 (2 ꢃ 15 mL). The
combined organic layer was dried over MgSO4 and concentrated
under vacuum yielding an oil that was purified by column
chromatography on silica gel with hexane/EtOAc (10 : 1) to give
9 as a slightly yellow oil (3.85 g, 55% yield).The NMR data were
consistent with the values reported in the literature.13
1
data are referred to (Z)-13. H NMR (250 MHz, CDCl3) d 7.04
(d, 1H, J ¼ 2.0 Hz), 6.97 (d, 1H, J ¼ 2.0 Hz), 6.35 (d, 1H, J ¼ 11.6
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Hz), 5.63 (dt, 1H, J ¼ 11.6, 7.3 Hz), 5.24 (s, 2H), 5.19 (s, 2H), 3.68
(s, 3H), 3.53 (s, 3H), 2.35 (m, 2H), 1.46 (s, 9H), 1.43–1.21 (m,
26H), 0.91 (t, 3H, J ¼ 6.8 Hz,). 13C NMR (62.5 MHz, CDCl3)
d 149.7, 144.5, 142.8, 132.7, 132.4, 128.6, 121.3, 115.1, 98.9, 95.5,
57.5, 56.2, 35.1, 31.9, 30.5, 30.1, 29.7–29.4, 28.9, 22.7, 14.1. IR
(ATR) n 2921, 2852, 1571, 1466, 1391, 1155, 1078, 1037, 1015,
961, 877. HRMS (ESI+) calcd for [C31H54O4 + Na]+: 513.3914,
found 513.3920.
Methodology for the computer simulations. We performed
theoretical calculations of the thermodynamic free energy
involved in the transfer of compound 2 from liquid solution to
the graphite surface. The calculations were made employing the
Molecular Dynamics (MD) technique, which is the technique of
choice in liquid phase simulations (instead of much simpler total
energy molecular mechanics calculations). MD is based on the
numerical solution of the Newton equations of motion for all
atoms of a molecular system constrained to the thermodynamic
conditions (T, p, .). In our simulations, the equations of motion
were solved with a 2 fs time step. All MD simulations were
performed using the NAMD2 software,24 version 2.7 running in
parallel at the Finisterrae Supercomputer (CESGA Super-
computing Center). In our simulations, the temperature was
maintained constant (at 20 ꢀC or 80 ꢀC) using the Langevin
thermostat with a relaxation constant of 1 psꢁ1. In simulations at
constant pressure and temperature (NPT), we employed the
Preparation of 1-tert-butyl-5-heptadecyl-2,3-bis(methoxy-
methoxy)benzene 14. A stirred solution of a mixture of the
isomeric olefins 13 (0.92 g, 1.88 mmol) in EtOAc (15 mL) was
hydrogenated over Pd/C (92 mg) under 1 atm of H2 for 24 h.
Filtration over Celite and evaporation of the solvent yielded 14
as an oil (0.91 g, 98% yield). 1H NMR (250 MHz, CDCl3) d 6.88
(d, 1H, J ¼ 2.0 Hz,), 6.83 (d, 1H, J ¼ 2.0 Hz,), 5.21 (s, 2H), 5.19
(s, 2H), 3.67 (s, 3H), 3.53 (s, 3H), 2.56 (t, 2H, J ¼ 7.8 Hz), 1.60
(m, 2H), 1.45 (s, 9H), 1.43–1.20 (m, 14H), 0.92 (t, 3H, J ¼ 6.8
Hz,). 13C NMR (62.5 MHz, CDCl3) 149.9, 143.6, 142.9, 137.8,
120.4, 114.5, 98.9, 95.3, 57.4, 56.2, 36.0, 35.0, 31.9, 31.6, 30.6,
29.7–29.3, 22.7, 14.1. IR (ATR) n 2917, 2849, 1578, 1472, 1434,
1153, 1081, 1035, 1013, 942, 881, 728. HRMS (ESI+) calcd for
[C31H56O4 + Na]+: 515.4071, found 515.4065.
ꢀ
Nose–Hoover–Langevin piston as implemented in NAMD2 with
an oscillation period of 100 fs and a decay time of 50 fs to adjust
the solution pressure at 1 atm.
The model for the molecules was based on the CHARMM22/
CMAP force field,25 designed for biomolecular simulations. The
modular structure of this force field (constructed from quantum
chemical calculations of the interactions between model
compounds and water) allows one to easily construct the model
parameters for a given organic compound from the basic
building blocks of the force field. Within this force field, intra-
molecular interactions contained bonding, torsion and dihedral
potentials and intermolecular interactions were described by
electrostatic interactions (modelled with partial charges) plus
a Lennard-Jones interaction potential. The values of all partial
charges and other relevant details of the force field are the same
as employed in our previous work.18 We should note that in this
force field, hydrogen bonds appear in a natural way as a result of
the interaction between partial charges. Previous work (see for
example ref. 26) has shown the validity of this kind of force field
for describing the role of hydrogen bonding in self-assembly at
interfaces.
Preparation of 3-tert-butyl-5-heptadecylcatechol 3. Compound
14 (0.91 g, 1.85 mmol) was dissolved in MeOH (45 mL) and 10
drops of concentrated HCl were added. The mixture was
heated to reflux overnight. Evaporation of the solvent under
reduced pressure yielded a solid residue which was dissolved in
ether (10 mL), and washed with a NaHCO3 saturated solution
(3 ꢃ 4 mL). The organic phase was dried over MgSO4 and
concentrated under vacuum affording 3 (652 mg, 88% yield).
1H NMR (250 MHz, CDCl3) d 6.68 (d, 1H, J ¼ 2.0 Hz), 6.56
(d, 1H, J ¼ 2.0 Hz), 2.48 (t, 2H, J ¼ 7.8 Hz), 1.55 (m, 2H), 1.40
(s, 9H), 1.35–1.20 (m, 14H), 0.90 (t, 3H, J ¼ 6.6 Hz). 13C NMR
(62.5 MHz, CDCl3) 142.6, 140.9, 136.2, 133.9, 119.2, 112.9,
35.6, 34.5, 31.9, 31.7, 29.67–29.5, 22.6, 14.1. IR (ATR) n 3344,
2915, 2848, 1520, 1470, 1443, 1356, 1282, 1183, 1115, 954, 749,
717. HRMS (ESI+) calcd for [C27H48O2 ꢁ 1H]+: 403.3582,
found 403.3573.
The procedure employed in the simulations is the following.
First, we conducted a NPT simulation of a system containing 400
nonanoic acid molecules inside a cubic box with periodic
boundary conditions in all directions. The barostat was adjusted
at 1 atm and the thermostat at 20 ꢀC or 80 ꢀC. After a 2 ns
simulation run, the solution was considered equilibrated, since
all magnitudes of interest (size of simulation box, pressure,
temperature) were clearly stabilized. Then, we added 48
compound 2 molecules and the resulting solution was placed in
contact with a large graphite slab. The graphite solid has an area
of 87.81 nm2 and was made by placing 6724 carbon atoms. In
order to speed up our highly time-consuming MD simulations,
all atoms of the graphite substrate were maintained fixed in their
equilibrium positions, an approximation which is innocuous
since we do not expect any reconstruction or chemical alteration
of the graphite surface. Then, a second set of MD simulations at
constant temperature (NVT conditions) were run to allow
equilibration of the solution with the surface and adsorption/
desorption events. Periodic boundary conditions were also
Experimental STM
All experiments were performed at room temperature using
a PicoSPM (Agilent) in constant current mode. When the
heating of the sample was needed, a LakeShore 331 Temper-
ature Controller was used. Pt/Ir STM tips were prepared by
mechanical cutting of the Pt/Ir wire (80 : 20, diameter 0.25 mm,
Advent Research Materials, Ltd). The molecules were dissolved
in each solvent with a concentration of approximately 2 mg
mLꢁ1. A hot drop of the solution was applied to a freshly
cleaved graphite substrate (HOPG, grade ZYB, Momentive
Performance Materials Quartz GMBH) and the tip was
immersed in it. The STM images were then obtained at the
liquid–solid interface. It was possible to scan the underlying
graphite substrate after scanning the molecules self-assembled
monolayer. This enabled us to correct for the drift effects using
the Scanning Probe Image Processor (SPIP) software (Image
Metrology ApS).
ꢂ
employed in all directions, employing a simulation cell (in A)
with vectors (50.348,87.207,0), (50.348,ꢁ87.207,0) and (0,0,80).
This journal is ª The Royal Society of Chemistry 2012
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ꢂ
A
and the simulations were typically run for 10 ns. All
ꢁ
P. Samorı, Angew. Chem., Int. Ed., 2009, 48, 2039–2043.
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tions has required around 1.57 days running in 32 Itanium
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This work was partly funded by grants MAT 2009-13977-C03,
CTQ2007-60613/BQU, CTQ2010-15380/BQU, CONSOLIDER-
NANOSELECT-CSD2007-00041 and FIS2009-13370-C02-02.
J.S.-P. thanks the Generalitat de Catalunya for a FI predoctoral
ꢁ
Grant and the Institut Catala de Nanotecnologia for their
support. We also acknowledge the CESGA Supercomputing
Center for computational time at the Finisterrae Supercomputer
and technical assistance.
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