Synthesis and photophysics of new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based Janus tectons: Surface-confined self-assembly of their model pedestal on HOPG

Article abstract of DOI:10.1039/d0nj00110d

Surface-confined supramolecular self-assembly is currently a promising strategy to create well-organised 2D-networks on conducting surfaces. However, using such substrates tends to quench any electronic properties of the adsorbed molecules. In this context, new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based molecules were designed, along with their model compound (pedestal), with the objective of self-assembling these tectons on any substrate. The synthesis of these new molecules was not straightforward and is consequently described in detail. Once the materials were successfully isolated, their optoelectronic properties were investigated to study potential non-covalent interactions: through pH-dependent absorption and emission measurements, and infra-red spectrometry. We evidenced that both ionic bonding and coordination bonding are compatible with the molecules design. Finally, preliminary scanning tunneling microscopy (STM) studies were performed to study the supramolecular self-assembly properties of the model lower-deck (pedestal) on highly oriented pyrolytic graphite (HOPG): we observed a quasi-square lattice of self-assembled 2D-networks that appear to form independently of the underlying HOPG lattice.

Full text of DOI:10.1039/d0nj00110d

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Synthesis and photophysics of new pyridyl end-capped 3D-
dithia[3.3]paracyclophane-based Janus tectons: surface-confined
self-assembly of their model pedestal on HOPG
Received 00th January 20xx,
Accepted 00th January 20xx
a
b
a
a
a
a*
M. Auffray, F. Charra, L. Sosa Vargas, F. Mathevet, A-J. Attias and D. Kreher
DOI: 10.1039/x0xx00000x
Surface-confined supramolecular self-assembly is currently a promising strategy to create well-organised 2D-networks on
conducting surfaces. However, using such substrates tends to quench any electronic properties of the adsorbed molecules.
In this context, new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based molecules were designed, as well as its model
compound (pedestal), with the objective of self-assembling these tectons on any substrate. The synthesis of these new
molecules was not straightforward and is consequently described into detail. Once the materials were successfully isolated,
their optoelectronic properties were investigated to study potential non-covalent interactions: by pH-dependant absorption
and emission measurements, and by infra-red spectrometry. We evidenced that both ionic and coordination bonding are
compatible with the molecules’ design. Finally, preliminary scanning tunneling microscopy (STM) studies were performed
to study the supramolecular self-assembly properties of the model lower-deck (pedestal) on highly oriented pyrollitic
graphite (HOPG): we observed a quasi-square lattice of self-assembled 2D-networks which appear to form independently of
the underlying HOPG lattice.
www.rsc.org/
3
both dynamic and thermodynamic control. Several examples have
1
. Introduction
already been developed, by exploiting various supramolecular
In the field of nanotechnology, surface science plays a crucial role as
most (nano-) devices eventually need to be supported on a surface.
Therefore, controlling the adsorption on surface is utterly required,
and commonly two contrasting strategies can be cited: top-down
4
5
interactions such as van der Waals interactions, ionic bonds,
6
7
8
hydrogen bonds, halogen bonds or even coordination. But in view
of practical applications, it is still challenging to obtain functional
surfaces, in particular due to the fact that by using semi-conducting
or conducting substrates, charge-transfer and hybridisation
occurring between the molecules and the substrate might
significantly alter the electronic properties of the adsorbed
molecules. As a consequence, and to preserve the electronic
properties, the molecule has to be decoupled (or “lifted”) from the
1
and bottom-up approaches. This latter consists in creating from a
substrate a macro-scale object, starting from specifically designed
molecular building blocks (tectons), through either chemisorption or
physisorption process. In particular, the physisorption strategy is
entirely based on the spontaneous organisation of molecules into
stable and structurally well-defined networks on the surface,
occurring by reversible supramolecular bonds between molecules
and substrates, also called supramolecular self-assembly. On the one
hand, the supramolecular bond between molecule and substrate
depends on the nature of both, for example, the van der Waals
interactions between alkyl chains and highly oriented pyrolytic
9
substrate. To overcome this issue, effective ways of decoupling have
been studied by using multilayers of molecules,10 ultra-thin
insulating layers onto the conducting surface11 or by chemically
modifying the structure molecule with molecular landers.12
However, all these strategies do not allow to preserve
simultaneously both the self-assembly and the electronic properties
of the adsorbed molecules. Moreover, drastic conditions such as low
temperature and high vacuum are required. To overcome this
drawback, our group recently proposed a new molecular design
strategy that will allow us to conserve the molecular electronic
properties whilst maintaining a stable, supramolecular self-
assembled network. Our goal was to achieve a highly ordered, self-
assembly on highly oriented pyrolytic graphite (HOPG) and graphene
2
graphite (HOPG). On the other hand, it can be tuned via the main
interactions between molecules themselves. In this context, surface-
confined self-assembly at the liquid/solid interface is considered
nowadays as a promising approach for directly building low-
dimensional (2D) supramolecular nanostructures on surfaces, under
a.Sorbonne Université, UPMC Univ Paris 06, Institut Parisien de Chimie
Moléculaire, UMR CNRS 8232, 4 Place Jussieu, 75252 Paris Cedex
05, France
.
substrates at room temperature, by using the so-called Janus-like 3D-
tecton design.13 This type of molecular architecture presents doubly-
b.
Service de Physique de l’Etat Condensé, CEA CNRS Université Paris -
Saclay, CEA Saclay, F-91191 Gif-sur-Yvette Cedex, France
Electronic Supplementary Information (ESI) available:
See DOI: 10.1039/x0xx00000x
.
functionalised building blocks where two opposite faces are linked
This journal is © The Royal Society of Chemistry 20xx
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by a rigid dithia[3,3]paracyclophane bridge. One face (pedestal) is Synthesis of 1,4-Bis[(trimethylsilyl)ethynyl]-2,5-dimVeietwhyArltbicelenOzenlninee
responsible for guiding the 2D self-assembly whereas the other can 1.16 In a Schlenk tube, 2,5-dibromo-p-xyDleOnIe: 10(2.103g9, /D70.6NJm00m11o0lD),
be functionalised at will by any active moiety. The concept was PdCl (PPh ) (265 mg, 0.4 mmol), copper(I) iodide (70mg, 0.4 mmol)
2 3 2
proven successful, and the fluorescence of self-assembled molecular and triethylamine (40 mL, 300 mmol) were added and put undert an
monolayers could be measured from perylene-functionalised Janus Argon atmosphere. Trimethylsilylacetylene (3.5 mL, 24 mmol)
tectons on graphene, at ambient conditions.14 These Janus-tectons wasadded, and the Schlenk tube was sealed. The mixture was stirred
were initially developed with self-organising pedestals that were at 100°C for 8 hours. The solution was diluted with dichloromethane,
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driven by van der Waals interactions between alkylated chains.
washed with water and dried over magnesium sulfate. After
evaporation in vacuo, the residue was purified by flash
chromatography (SiO , petroleum ether) to afford 1 as a white
2
)  7.26 (s, 2H), 2.34
s, 6H), 0.25 (s, 18 H). 13C NMR (300 MHz, CDCl
)  137.66, 132.97,
2
But such a design restricted its adsorption to only sp -hybridised
carbon substrates as HOPG or graphene. Therefore, a new design of
cyclophane-based molecules is proposed using a new pedestal able
to adsorb and self-organise on any substrate, by exploiting different
supramolecular interactions. To achieve this goal, the pyridine
moiety was chosen due to its well-known ability to form ionic bonds
1
powder in 91 % yield. H NMR (300 MHz, CDCl
(
1
3
3
23.18, 104.03, 99.67, 19.97, 0.18.
Synthesis of 1,4-Diethynyl-2,5-dimethylbenzene 2.17 To a solution of
1 (415 mg, 1.4 mmol) in methanol (25 mL),potassium fluoride (350
mg, 6.0 mmol) was added. The mixture was stirred overnight at room
temperature and then evaporated in vacuo. The crude product was
via a simple protonation, halogen or hydrogen bonding or
coordination-type bonding with the corresponding additives.15
purified by flash chromatography (SiO
2
, dichloromethane) to afford
1
2
. Experimental
2 as a light yellow powder in 96 % yield. H NMR (300 MHz, CDCl
3
)


7.26 (s, 2H), 3.33 (s, 2H), 2.34 (s, 6H). 13C NMR (300 MHz, CDCl
3
)
2.1 Materials and methods
137.91, 133.40, 122.48, 82.33, 82.26, 19.94.
All solvents and reactants were purchased from commercial
suppliers. The reactants were used without further purification. Synthesis of 1,4-Bis[(pyridyl)ethynyl]-2,5-dimethylbenzene P.18 In a
When necessary, the solvents were dried by using a MBraun solvent Schlenk tube, compound 2 (200 mg, 1.3 mmol), p-bromopyridine
3 2 2
purification system (MB SPS-800). The organic compounds hydrochloride (500 mg, 2.0 mmol), Pd(PPh ) Cl (46 mg, 0.07 mmol)
purifications performed by chromatography were either carried out and CuI (13 mg, 0.07 mmol) were introduced. Then,
by gravity column chromatography using silica gel (Si 60, 40-63 μm, diisopropylamine (15 mL, 107.0 mmol) was added and the mixture
Merck) or by flash chromatography (Combiflash Companion) with was stirred at RT, under an argon atmosphere for 8 hours. The
the same type of silica. The nuclear magnetic resonance experiments resulting solution was diluted with dichloromethane, washed with
were recorded at 300 or 600 MHz (Bruker, BBFO probe for the 2D- water and dried over magnesium sulfate. After evaporation in vacuo,
experiments). The proton and carbon chemical shifts (δ) are reported the residue was purified by flash chromatography (SiO
in ppm and are referenced to the residual solvent signal: chloroform ether/ethyl acetate, 9:1) to afford P as a white powder in 85 % yield.
,7.26, 77.16). Infra-red spectra were recorded with a 1H NMR (300 MHz, CDCl
) δ 8.63 (m, 4H), 7.40 (m, 6H), 2.49 (s, 6H).
CDCl
ThermoFisher Nicolet iS10 FT-IR spectrometer. UV/Vis spectra were 13C NMR (300 MHz, CDCl
) δ 149.89, 138.03, 133.26, 131.59, 125.59,
2
, petroleum
(
3
3
3
recorded with a Varian Cary WinUV spectrophotometer. The cells 122.92, 92.75, 92.18, 20.12. HRMS: (EI) m/z (%) for C22H16N2; calcd
were in quartz with two faces (thickness: 1cm). Photoluminescence 308.1313; found 308.1315. Anal. Calcd for C22H16N2 (MW 308.13):
spectra were recorded with a Varian Cary Eclipse fluorescence C, 85.69; H, 5.23; N, 9.08. Found: C, 85.75; H, 5.29; N, 8.92.
spectrophotometer. STM images were acquired at room
Synthesis of 1,4-dibromo-2,5-bis(bromomethyl)benzene 3.19 To a
temperature with a homemade digital system. The fast scan axis was
solution of 2,5-dibromo-p-xylene (5 g, 19 mmol) in acetonitrile (75
kept perpendicular to the sample slope. Images acquired
mL) NBS (7.1 g, 40 mmol) and AIBN (160 mg, 1 mmol) were added.
simultaneously in both fast scan directions are systematically
The mixture was left stirring for 24 hours under reflux, after which
recorded and compared. All images are corrected for the drift of the
the mixture was evaporated in vacuo and washed by hot methanol
instrument by combining two successive images with downward and
upward slow-scan directions. The solvent was phenyloctane (Aldrich,
1
to afford 3 as a white powder in 60% yield. Mp = 161°C. H NMR (300
MHz, CDCl
39.14, 135.50, 123.43, 31.62.
3
) δ 7.66 (s, 2H), 4.51 (s, 4H). 13C NMR (300MHz, CDCl
3
) δ
9
8%). The substrate was HOPG (Goodfellow) and the tips were
1
mechanically formed from a 250mm Pt–Ir wire (Pt80/Ir20,
Goodfellow). The monolayers were formed by drop casting a droplet Synthesis of 1,4-dibromo-2,5-dimethoxymethylbenzene 4. In a
ca. 10 μL, in dichloromethane) of the solution immediately after Schlenk tube compound 3 (1 g, 2.4 mmol), was added to degassed
(
cleaving the substrate. The samples were heated at 80°C for 10 methanol (20 mL) and set to stir under an argon atmosphere. After
minutes before immersing the STM junction in an additional droplet stirring for 10 minutes, a freshly prepared sodium methoxide (0.14 g
of phenyloctane (ca. 10 μL) and approaching the STM tip.
of sodium in 20 mL of methanol) was added dropwise. Upon
addition, the reaction was heated to 90°C and left stirring overnight.
The resulting solution was then poured into water, extracted with
dichloromethane and dried over magnesium sulfate. The
2.2 Synthesis
2
| J. Name., 2012, 00, 1-3
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dichloromethane was removed in vacuo to afford the title compound xylene (2 g, 19 mmol) in acetonitrile (60 mL). After VsiteiwrrAinrtgiclefoOrnl1in6e
1
DOI: 10.1039/D0NJ00110D
4
as a white powder in quantitative yield. Mp = 70°C. H NMR (300 hours under reflux, the mixture was evaporated in vacuo and purified
MHz, CDCl
MHz, CDCl
3
) δ 7.63 (s, 2H), 4.47 (s, 4H), 3.47 (s, 6H). 13C NMR (300 by flash chromatography (SiO
) δ 138.50, 112.33, 121.30, 73.23, 58.89.
2
, petroleum ether: dichloromethane
1:1) to afford 8a as a white powder in 87% yield. H NMR (300 MHz,
1
3
3
CDCl ) δ 7.37 (s, 4H), 4.48 (s, 4H).
Synthesis of 1,4-bis[(trimethylsilyl)ethynyl]-2,5-dimethoxymethyl
benzene 5. In a Schlenk tube, compound 4 (1.9g, 6 mmol), Synthesis of the 4'-bromo-2,5-bis(bromomethyl)-1,1'-biphenyl 8b.
PdCl (PPh (200 mg, 0.3 mmol), CuI (0.1 mg, 0.3 mmol) and To a solution of 7 (1 g, 3.8 mmol) in acetonitrile (100 mL) NBS (1.4 g,
2
3 2
)
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triethylamine (30 mL, 225 mmol) were mixed together under an 8,0 mmol) and AIBN (60 mg, 0.4 mmol) were added. After stirring for
argon atmosphere. Trimethylsilylacetylene (2.7 mL, 19 mmol) was 14 hours at 90 °C, the mixture was evaporated in vacuo and purified
then added, the Schlenk tube was sealed and the mixture stirred at by flash chromatography (SiO
2
, Petroleum ether) to afford the title
1
1
00°C for 8 hours. The resulting solution was diluted with compound 8b as a white powder in 90% yield. H NMR (300 MHz,
3
3
3
3
dichloromethane, washed with water and dried over magnesium CDCl ) δ 7.60 (d, J = 8.5 Hz, 2H), 7.50 (d, J = 8.0 Hz, 1H), 7.41 (dd, J
sulfate. After evaporation in vacuo, the residue was purified by flash = 8.0 Hz, J = 2.0 Hz, 1H), 7.32 (d, J = 8.5 Hz, 2H), 7.24 (d, J = 2.0 Hz,
chromatography (SiO
compound 5 as a white powder in 84 % yield. Mp = 89 °C. H NMR
(300 MHz, CDCl ) δ 7.53 (s, 2H), 4.57 (s, 4H), 3.44 (s, 6H), 0.24 (s,
3
18H).. 13C NMR (300 MHz, CDCl
72.11, 58.73, 0.07.
4
3
4
2
, petroleum ether) to afford the title 1H), 4.49 (s, 2H), 4.39 (s, 2H).
1
Synthesis of the 1,4-bis(mercaptomethyl)benzene 9a.21 To a
solution of 8a (5 g, 18.9 mmol) in ethanol (75 mL) thiourea (3.6 g,
7.4 mmol) was added. The mixture was heated at 80°C for 3h and
3
) δ 139.43, 121.23, 122.01, 100.96,
4
then cool down to room temperature. After evaporation in vacuo,
Synthesis of 1,4-diethynyl-2,5-bis(bromomethyl)benzene 6.20 In a the residue was dissolved in water (20 mL). Sodium hydroxide was
Schlenk tube compound 5 (0.45g, 1.2 mmol) and dichloromethane added (2.25 g, 56.7 mmol) to the mixture, heated to 100 °C and left
(
10 mL) were introduced and placed under an argon atmosphere. overnight. The solution was then extracted with diethylether and
The mixture was then cooled to 0°C and then left to stir for 10 dried over magnesium sulfate. Evaporation in vacuo gave 9a as
minutes, after which a solution of BBr
1
3
(3.7 mL, 3.7 mmol) in colourless crystals in 79% yield. H NMR (300 MHz, CDCl
3
) δ 7.27 (s,
) δ 140.07,
dichloromethane (10 mL) was added dropwise through a dropping 2H), 3.72 (d, 4H), 1.75 (t, 2H). 13C NMR (300 MHz, CDCl
funnel. After stirring for 2 hours, the reaction mixture was poured 128.46, 28.72.
into water and extracted with dichloromethane. The solution was
dried over magnesium sulfate and evaporated in vacuo. The crude
mixture obtained was then dissolved in methanol (80 mL) and
potassium fluoride (340 mg, 6 mmol) was added. The solution was
stirred overnight at room temperature and then poured onto water,
extracted with dichloromethane and dried over magnesium sulfate.
The solution was then evaporated in vacuo to afford the title
3
Synthesis of the 4'-bromo-2,5-bis(mercaptomethyl)-1,1'-biphenyl
9
b. To a solution of 8b (900 mg, 2.15 mmol) in ethanol (50 mL)
thiourea (410 mg, 5.35 mmol) was added. The mixture was heated at
0°C in a sealed Schlenk tube under an argon atmosphere for 3h and
then cooled down to room temperature. After evaporation in vacuo,
the residue was dissolved in water (50 mL) and the solution was
degassed. Potassium hydroxide was added (1.2 g, 21.5 mmol) and
the mixture was heated at 100 °C overnight in a sealed Schlenk tube.
The solution was then extracted with diethylether and dried over
8
1
compound 6 as a light-yellow powder in 47% yield. H NMR (300 MHz,
CDCl
CDCl
3
) δ 7.58 (s, 2H), 4.60 (s, 4H), 3.51 (s, 2H). 13C NMR (300 MHz,
3
) δ 140.13, 134.50, 122.98, 85.02, 79.83, 30.15.
magnesium sulfate. The evaporation in vacuo gave the title
1
Synthesis of 4'-bromo-2,5-dimethyl-1,1'-biphenyl 7. p-bromo- compound 9b as colourless crystals in 83% yield. H NMR (300 MHz,
phenyl boronic acid (860 mg, 4.30 mmol) and Pd(PPh
3
3
3
3
)
2
Cl
2 3
(175 mg, CDCl ) δ 7.55 (d, J = 8.5 Hz, 2H), 7.37 (d, J = 8.0 Hz, 1H), 7.29 (dd, J
4
3
4
0
4
.25 mmol) were added to a solution of 2-iodo-p-xylene (0.62 mL, = 8.0 Hz, J = 2.0 Hz, 1H), 7.32 (d, J = 8.5 Hz, 2H), 7.13 (d, J = 2.0 Hz,
.30 mmol) in dioxane (20 mL) in an argon atmosphere. Then, K
3
3
3
2
CO
3
1H), 3.72 (d, J = 7.5 Hz, 2H), 3.62 (d, J = 7.5 Hz, 2H), 1.77 (d, J = 7.5
3
(
2 g, 15.00 mmol) dissolved in water (5 mL) was added, and the Hz, 1H), 1.66 (d, J = 7.5 Hz, 1H).
mixture was heated at 110°C for 12 hours. The reaction was cooled
to room temperature, and washed with water. The mixture was then
extracted with dichloromethane, dried over magnesium sulfate and
evaporated in vacuo. The crude was purified by chromatography
Synthesis of the 5,8-diethynyl-2,11-dithia[3.3]paracyclophane 10a.
To a solution of potassium hydroxide (100 mg, 1.8 mmol) in methanol
(350 mL), a mixture of 6 (400 mg, 1.3 mmol) and 9a (200 mg, 1.3
mmol) in dichloromethane (50 mL) were added dropwise using a
syringe pump (4 mL/h), simultaneously with another solution of
potassium hydroxide (200 mg, 3.6 mmol) in methanol (50 mL). At the
end of the addition, the mixture was evaporated in vacuo. The
residue was then dissolved in dichloromethane, washed with water,
dried over magnesium sulfate and evaporated again in vacuo. The
(
SiO
2
, petroleum ether) to afford the title compound 7 as a colourless
1
3
oil in 94% yield. H NMR (300 MHz, CDCl
3
) δ 7.61 (d, J = 8.5 Hz, 2H),
3
3
3
7
1
.27 (d, J = 8.5 Hz, 2H), 7.25 (d, J = 8.0 Hz, 1H), 7.18 (d, J = 8.0 Hz,
H), 7.12 (s, 1H), 2.45 (s, 3H), 2.31 (s, 3H). 13C NMR (300 MHz, CDCl
)
3
δ 141.05, 140.56, 135.40, 132.07, 131.26, 130.95, 130.49, 130.38,
28.40, 130.98, 21.01, 20.00.
1
2
crude was purified by column chromatography (SiO , petroleum
Synthesis of 1,4-bis(bromomethyl)benzene 8a. 18 NBS (7.1 g, 40 ether: dichloromethane 1:1) to afford the title compound 10a as a
mmol) and AIBN (160 mg, 1 mmol) were added to a solution of p- white powder in 43 % yield. H NMR (300 MHz, CDCl
1
3
) δ 7.14 (s, 2H),
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.06 (d, J = 8 Hz, 2H), 7.02 (d, J = 8 Hz, 2H), 4.30 (d, J = 15 Hz, 2H),
View Article Online
DOI: 10.1039/D0NJ00110D
3
3
3
.87 (d, J = 15 Hz, 2H), 3.78 (d, J = 15 Hz, 2H), 3.59 (d, J = 15 Hz,
H), 3.43 (s, 2H).
Synthesis of the 5,8-diethynyl-13-(p-bromophenyl)-2,11-dithia[3.3]
paracyclophane 10b. To a solution of potassium hydroxide (100 mg,
1
.8 mmol) in methanol (600 mL), a solution of 6 (420 mg, 0.9 mmol)
and 9b (300 mg, 0.9 mmol) in dichloromethane (50 mL) were added
dropwise using a syringe pump (3.5 mL/h), simultaneously with
another solution of potassium hydroxide (200 mg, 3.7 mmol) in
methanol (50 mL). After addition was completed, the mixture was
acidified with dilute H
with water, dried over magnesium sulfate and evaporated in vacuo.
The crude was purified by flash chromatography (SiO , petroleum
ether: dichloromethane using a gradient from 1:0 to 1:1) to afford
the title compound 10b as a white powder with a yield of 60 %. 1H
3
NMR (300 MHz, CDCl ) δ 7.63-7.00 (m, 18H), 4.45-3.46 (m, 16H+4H).
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2 4
SO , extracted with dichloromethane, washed
Scheme 1: Bis(pyridyl)acetylene-based target molecules
.1 Synthesis
The molecule P was synthesised from the 2,5-dibromo-p-xylene via
a Sonogashira cross-coupling reaction with trimethylsilylacetylene
TMSA), followed by the deprotection of the trimethylsilyl groups
with potassium fluoride and finally by a second Sonogashira coupling
with an overall yield of 70% (scheme 2).
2
3
Synthesis of the 5,8-bis[(pyridyl)ethynyl]-2,11-dithia[3.3]para
cyclophane C. In a Schlenk tube, 10a (150 mg, 0.5 mmol),
iodopyridine (480 mg, 2.4 mmol), Pd(PPh ) Cl (35 mg, 0.05 mmol)
3 2 2
and poper(I) iodide (10 mg, 0.05 mmol) were added under an argon
atmosphere. Then, diisopropylamine (1.5 mL, 10.0 mmol) was added
and the mixture was stirred for 20 hours at 20°C. The solution was
diluted with dichloromethane, washed with water and dried over
magnesium sulfate. After evaporation in vacuo, the residue was
(
purified by flash chromatography (SiO
acetate, with a gradient 9:1 to 1:1) to afford the title compound C as
a yellow powder in 44 % yield. H NMR (300 MHz, CDCl
2
, petroleum ether: ethyl
1
3
) δ 8.69 (s,
3
3
4
H), 7.49 (d, J = 5.5 Hz, 4H), 7.22 (s, 2H), 7.08 (d, J = 8 Hz, 2H), 7.05
3
3
3
(
(
d, J = 8 Hz, 2H), 4.32 (d, J = 15 Hz, 2H), 3.90 (d, J = 15 Hz, 2H), 3.85
d, J = 15 Hz, 2H), 3.72 (d, J = 15 Hz, 2H). HRMS: (EI) m/z (%) for
; calcd 474.1224; found 474.1224.
3
3
30 22 2 2
C H N S
Synthesis of the 5,8-bis[(pyridyl)ethynyl]-13-(p-bromophenyl)-
2,11-dithia[3.3]paracyclophane JT. In a Schlenk tube, 10b (170 mg,
0.36 mmol), iodopyridine (370 mg, 1.8 mmol), Pd(PPh ) Cl (30 mg,
3 2 2
0.04 mmol) and copper iodide(8 mg, 0.04 mmol) were introduced
under an argon atmosphere. Diisopropylamine (1,5 mL, 10.0 mmol)
was then added and the mixture was stirred for 24 hours at 20°C. The
solution was diluted with dichloromethane, washed with water and
dried over magnesium sulfate. After evaporation in vacuo, the
Scheme 2: Synthesis of P
The syntheses of the cyclophane derivatives C and JT were not as
simple and therefore several retrosynthetic routes were pursued in
order to finally obtain the desired compounds (scheme 3). A total of
four approaches were investigated with only route number four
resulting successful (scheme 4).
Following route 4, 1,4-dibromo-p-xylene was brominated with NBS,
following the Wohl and Ziegler radical pathway where AIBN is the
radical initiator.16 The two bromomethyl groups of 3 were then
protected by methoxy units (4) in order to perform a Sonogashira
coupling with TMSA and give intermediate 5. After deprotection of
both methoxy and trimethylsilyl groups using boron tribromide and
potassium fluoride, respectively; the resulting compound 6 and
either 1,4-bis(mercaptomethyl)benzene or 1,4-bis(mercaptomethyl)
2
residue was purified by flash chromatography (SiO , petroleum
ether: ethyl acetate, 9:1 to 1:1) to afford the title compound JT as a
yellow powder in 84 % yield. H NMR (300 MHz, CDCl
1
3
) δ 8.78-8.65
(
m, 8H), 7.61-7.06 (m, 26H), 4.45-3.46 (m, 16H). HRMS: (EI) m/z (%)
; calcd 628.0643; found 628.0642.
25 2 2
for C36H N S
3
. Results and discussion
-
2-(p-bromophenyl)-benzene were solubilised in dichloromethane
In this paper, three bis(pyridyl)acetylene derivatives were and slowly added to a highly diluted solution of potassium hydroxide
synthesized (scheme 1): the planar pedestal P (for reference), the in methanol, to afford the cyclophane derivatives.
pedestal incorporating a cyclophane C (to check the influence of the
cyclophane incorporation) and finally a functionalisable Janus tecton
JT (where any active component could potentially be grafted).
Finally, a last Sonogashira coupling with iodopyridine enabled us to
recover the final products C and JT with an overall yield of 8% and
1
0%, respectively.
4
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Scheme 3: Retrosynthetic routes attempted to reach target compound C
Scheme 4: Synthesis of C and JT
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It is important to note as well that the Janus tecton JT was obtain as The attribution of the second part of the spectrum, concerning the
a mixture of two structural isomers, staggered and eclipsed, which CH
could not be separated by chromatography.
2
protons of the cyclophane-bridge, is entirely based on second
order couplings. Four doublets with a roof-top shape can be
observed at the chemical shifts of 4.32, 3.90, 3.85 and 3.70 ppm,
integrating for 2 protons each. The protons 4’ and 5’ should thus be
3
.2 Nuclear Magnetic Resonance
All intermediates and final compounds were first studied by NMR to deshielded compared to their homologues 4 and 5. However, since
confirm their chemical structures, before confirming their purity by 4’ is closer to the alkyne than 5’, the effect would be enhanced. As a
elemental analysis or high resolution mass spectrometry. As an consequence, 5 and 5’ are respectively attributed to the pair of
1
example, the H NMR spectrum of C in deuterated chloroform is doublets located at 3.85 and 3.90 ppm, 5’ being slightly more
depicted in Figure 1.
deshielded than 5. The protons 4 are the more shielded of all, and
correspond to the doublet at 3.70 ppm. Finally 4’, the most
deshielded of all, is located at 4.32 ppm.
3
.3 Photophysics
The absorption and emission spectra of both molecules P and C were
measured in dichloromethane, as depicted in the Figure 3.
3
5
’ 5
2
6 + 6’ + 7 + 7’
1,0
1,0
0,8
0,6
0,4
0,2
0,0
a)
1
4’
4
0,8
0,6
0,4
0,2
1
Figure 1: 300 MHz H NMR of C in deuterated chloroform
The attribution of the aromatic part of this spectrum was made easy
by the previous study of P pedestal’s NMR spectrum. Thus, the
pyridine’s protons 1 and 2 respectively correspond to the wide
singlet at 8.69 ppm and to the doublet at 7.48 ppm, both integrating
for four protons. Then the protons 3 borne by the lower deck of the
cyclophane are represented by a peak at 7.22 ppm, integrating for 2.
Finally, 6, 6’, 7 and 7’ are attributed to the close pair of doublet with
a chemical shift of 7.06 ppm integrating for 4 protons. These signals
are undergoing a “roof-top effect” which indicates the second order
coupling occurring between 6 and 6’, and between 7 and 7’. This
slight coupling might occur because in each pair, one is located above
the alkyne (6 and 7’) and the other above a simple proton (6’ and 7).
As a consequence, the deshielding of the alkyne would slightly affect
one of each pair, making them lightly different. A representation of
the deshielding area of the alkyne is represented in Figure 2.
0,0
2
50
300
350
400
450
500
Wavelength (nm)
b)
1,0
1,0
0,8
0,6
0,4
0,2
0,0
0,8
0,6
0,4
0,2
0,0
3
00
350
400
450
500
550
600
Wavelength (nm)
Figure 3: Absorption and emission spectra of P (a)
and C (b) in dichloromethane
On the one hand, the absorption spectrum of P presented four
transition bands at 318, 331, 347 and 380 nm,the band at λmax = 331
nm being used to estimate the extinction coefficient (ε), which was
Figure 2: Deshielding effect of the alkyne unit in C
-1
-1
calculated at 35500 Lmol cm . The emission spectrum showed
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fluorescence in the blue region with a λmax at 362 nm, giving a Stokes 3.4 Supramolecular interactions studies on bulk
View Article Online
DOI: 10.1039/D0NJ00110D
-
1
shift value of 31 nm (1100 cm ). On the other hand, molecule C Therefore, one of the aim of this work being to create self-assemblies
presented one single absorption band at λmax = 345 nm. The based on the co-adsorption of P (respectively C, JT) with different
fluorescence was redshifted from P, emitting at λmax = 434 nm with a additives, preliminary studies on bulk materials were performed, all
new Stokes shift of 89 nm (5900 cm ), indicating a higher degree or three expected supramolecular entities being represented in Figure
reorganisation of the derivative C’s excited state in comparison with 5 along with the predicted supramolecular bonds with the pedestal
-1
that of pedestal P.
P.
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In addition, as pyridine units are commonly used as a Lewis base in
organic reactions, a pH-dependent study was therefore carried out
by successive additions of trifluoroacetic acid (TFA) to a solution of P
(
respectively C, JT) in dichloromethane, each addition corresponding
to 0.1 equivalents of TFA in the quartz cell. We will illustrate the
results with focusing on P (Figure 4), as C and JT compounds behave
in a similar way.
As reported, the addition of acid in the solution drastically increased
the absorption band intensity at 380 nm and also reduced the two
bands at 318 and 331 nm with an isobestic point located at 350 nm.
In addition, with a large excess of acid a slight blueshift of the maxima Figure 5: Expected supramolecular bonds between the pedestal P
from 380 to 360 nm was observed, this hypsochromic shift being
attributed to the second protonation.
(
respectively C, JT) and a) terephtalic acid TPA (H-bond),
b) bis(benzonitrile)PdCl Pd (coordination bond) and
2
II
c) 1,4-diiodobenzene IPhI (X-bond)
0
0
.0eq
.1eq
0.40
0.35
0.30
0.25
As evidenced by the protonation studies, the formation of ionic
bonds by P (respectively C, JT) could be monitored by changes in the
absorption and emission spectra after adding acid in the solution. But
common characterisation to measure the strength of other
supramolecular bonds such as coordination, hydrogen and halogen
bonding by NMR being unsuccessfull due to poor solubility,
additional infrared studies were performed.
a)
0.2eq
0.3eq
0.4eq
0.5eq
0.20
0.15
0.10
0.05
0.00
0.6eq
0
0
.7eq
.8eq
0.9eq
1.0eq
To do so, as an example, different supramolecular entities were
prepared in solution by simply mixing P with bis(benzonitrile)-
palladium(II) for coordination (P-Pd ), terephtalic acid for hydrogen
bond (P-TPA) and finally 1,4-diiodobenzene for halogen bond (P-
IPhI). The infra-red spectra were recorded on bulk after evaporation
or filtration of the supramolecular complexes (see Figure S29 in SI).
Note that the specific C-N stretching band within the pyridine units
is centered at 1591 cm for P (see Figure 6), this shift being known
to depend on the different supramolecular assemblies present, as
described for different coordination complexes in the literature.22
2
50 275 300 325 350 375 400 425 450
Wavelength (nm)
II
b)
0.0eq
0
0.2eq
0.3eq
0
.1eq
3
00
50
2
.4eq
.5eq
200
0
0.6eq
.7eq
0.8eq
-1
1
1
50
00
0
0
1
.9eq
.0eq
5
0
0
3
50
400
450
500
550
600
Wavelength (nm)
Figure 4: Absorption (a) and emission (b)
spectra of P acidified with TFA
P
Moreover, the addition of acid quenched the emission of the neutral
pedestal at both wavelengths 362 and 378 nm in favour of a new
redshifted band at λ = 439 nm corresponding to the molecule mono-
protonated. In this case, the isobestic point was located at λ = 419
nm. In accordance with the study on the absorption, a bis-
protonated specie with a slight blue shift of the maxima of emission
from 439 to 427 nm could be observed with a large excess of TFA. To
sum up, the protonation of the pyridine units have a strong impact
on the optical properties of P, C and JT.
P-PdII
P-TPA
P-IPhI
1
640 1630 1620 1610 1600 1590 1580 1570 1560
Wavenumber (cm-1)
Figure 6: Infra-red spectra of the different supramolecular
entities ; focus on the C-N stretching bands
-1
The stretching bond value of the C-N bond is shifted by 18 cm in the
II
-1
P-Pd (1609 cm ) compared to that of the P alone. We can thus
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conclude to the effective formation of the coordination bonds.22
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the quasi-square lattice is close to a <100> axis of VHieOwPAGrticsleuOrfnalicnee
However, considering the weak change of the stretching bond value whereas the other is close to the <110> axDisOIp:e10rp.1e0n3d9/icDu0lNarJ0t0o11t0hDe
-1
in P-IPhI (1589 cm ), the halogen bonding is only suspected. former <100> one. Notice that this relation with HOPG is preserved
-1
Unfortunately, the hydrogen bond in P-TPA (1591 cm ) could not be through a 30° (mod. 60°) rotation of the molecular lattice, which
observed. There are two possible explanations for this absence of explains the observed orientations between domains. Since the
shift: first, the procedure to prepare the supramolecular structure lattice is formed of two prochiral molecules in the same left- or right-
may not be efficient and thus the expected interactions was not handed configuration, the lattice itself is pro-chiral, and becomes
obtained. Second, the pedestal may naturally display hydrogen chiral by considering the vertical axis orientation due to the substrate
bonds between the pyridine unit and the methyl group of its p-xylene surface.24 One thus expect the existence of mirror symmetric
core. As a consequence, the pedestal alone could already present the domains forming angles of ± with HOPG <100> axis.23 From STM
signal of a hydrogen bonded pyridine. This second hypothesis would image and molecular model [figure 7 (c-d) ] it appears that  is small,
be in accordance with the negative shift for the halogen bond i.e. of the order of 2°. It nevertheless explains the small variations of
0
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(
weaker than the H-bond) and the positive shift of the coordination domain-to-domain angles with respect to the 0°, ±30°, ±60° rule. The
bond (stronger than the H-bond).
above mentionned difference in contrast between the two
molecules in the unit cell can be explained by the difference of
relations between molecule and HOPG conjugated orbitals which is
known to strongly influence the electron density of states.25 An
3.5 Self-assembly of P on HOPG
Scanning tunnelling microscopy (STM) was used to observe first the
self-assembly of the pedestal P alone at the liquid/solid interface.
Indeed, based on our previous works on Janus tectons, we expect
that the arrangement of C and JT would be similar on the same
substrate, since in all known examples the lower-deck (pedestal, P)
governs the final arrangement. This is the reason why we focused
first on this model plannar tecton, which is more easily imaged by
STM than its 3D derivatives. Experimentally, a solution of P in
influence of tip shape cannot be ruled out, and can also contribute
to this differential contrast and more specifically to the different
patterns presented by the same molecules with different
orientations.
Considering the organised system absorbed on the surface, the
network seems to be driven by hydrogen bonds between the
pyridine units and the methyl groups on the core of the molecule.
This is consistent with the principles of interactions between
adsorbed molecules with pyridyl and alkyl terminations.15 Such
pyridyl-driven assemblies has been observed for molecules bearing
two26-28 but also three29-31 and even four pyridine entities32. The
proposed scheme [figure 7 (d) ] is fully consistent with the assembly
of short bivalent pyridyl-terminated rod-shaped molecules [FC5].
Notice however, that longer molecules could lead to structures with
parallel molecules in order to improve the coverage.27 The
observation that the same molecular arrangement can align either
on a <100> or <110> direction of HOPG shows the poor influence of
the substrate on the organization. This is further substantiated by the
above cited literature which shows that the same self-assembling
principles apply for various substrates as dissimilar as Au and HOPG.
This self-assembly thus appears to be driven by intrinsic
intermolecular interactions, which doesn’t need assistance of the
substrate in contrast with alkyl-chain based assembly.
-
3
-1
dichloromethane was prepared at a concentration of 10 mol.L and
deposited on the HOPG surface. As shown in Figure 7 (a), ordered 2D
domains formed by the assembly of pedestal P were observed as
bright more or less elongated patterns in a quasi-square lattice
network with the unit cell dimensions a = 2.1±0.1 nm, b = 2.2±0.1 nm
and an angle α = 94°±2°. Figure 7 (b) shows a first set of bright
patterns that are nearly parallel to the fast-scan direction. A second
set of less contrasted patterns are elongated in the direction
perpendicular to the former (I.e. close to the slow scan direction).
These patterns can be ascribed to a quasi-square molecular lattice
with two nearly-perpendicular rod-shaped molecules per unit cell as
illustrated in upper left corner of figure 7 (b). Larger-scale STM
images show numerous domains oriented at approximately 0°, ±30°,
±
60° from each other, as illustrated in figure 7 (c). Following the
principles of molecular epitaxy on HOPG, 23 these data are consistent
with the model approximately described in figure 7 (d) : One axis of
0
°
+60°
-62°
0°
a)
b)
c)
d)
+28°
Figure 7: STM images of the self-assembled monolayer of P (a, I = 35 pA, Ubias = 630 mV, 50 x 50 nm), with overlaid
molecular models (b, 10 x 10 nm) large scale (c, 110nm) showing different domain orientations (light green) and
the molecular model on a HOPG layer (d).
8
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9, 4456–4458; J.C. Russell, M.O. Blunt, J.MD.OGI:a1r0f.i1t0t,39D/.DJ.0NScJu0r0r1,10MD.
Alexander, N.R. Champness and P.H. Beton, J. Am. Chem. Soc. 2011,
Conclusions
We designed and synthesised new molecular architectures based on
the 3D Janus tecton concept that can be suitable for surface self-
assembly by supramolecular interactions such as ionic, coordination, Wang, Y. Li, M. Wang, S. Lu, X-Q. Hao, X. Li, B. Xu and X. Li, Nat.
halogen or hydrogen bonding. These non-covalent interactions were
studied by pH-dependent absorption and emission measurements,
and by infra-red spectrometry which proved that both ionic and
coordination bonding are compatible with the molecules’ design.
Finally, the supramolecular self-assembly of the pedestal P was
studied on HOPG at the liquid/solid interface. The arrangement of
1
33, 4220–4223.
8
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Tech. Adv. Mater. 2019, 20:1, 51-95.
hydrogen bonding between the pyridine unit and the methyl groups
on the p-xylene core. The quasi-square lattice indicates strong
intermolecular interactions are present between the P molecules
leading to a supramolecular self-assembly which is independent of
the underlying HOPG structure. As perspectives, such different
10
Z.C. Dong, X.L. Zhang, H.Y. Gao, Y. Luo, C. Zhang, L.G. Chen, R.
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interactions being able to favour or modify the supramolecular self- 26803.
12
assembly of P (respectively C, JT) at the liquid/solid interface,
additional experiments will be performed in a near future to study
their different supramolecular self-assemblies with other substrates.
J.A. Mann, J. Rodríguez-López, H.D. Abruña and W.R. Dichtel, J.
Am. Chem. Soc. 2011, 133, 17614–17617.
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13
Kreher, F. Mathevet, C. Fiorini-Debuisschert, F. Charra and A-J. Attias,
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Conflicts of interest
There are no conflicts to declare.
14
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Debuisschert, L. Douillard and F. Charra, ACS Photonics 2016, 3,
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291–2296.
1
5
X. K. Li, S. Q. Zhang, J. Q. Li, Y. X. Qian, W. B. Duan and Q. D. Zeng,
Acknowledgements
This research was supported by a PhD grant overseen by the
French government (Ministry of Education and Research).
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DOI: 10.1039/D0NJ00110D
Synthesis and photophysics of new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based Janus
tectons: surface-confined self-assembly of their model pedestal on HOPG
N
Synthesis
P
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P self assembly on HOPG
NP
Once synthesized, these new tectons demonstrated both ionic and coordination bondings.
Surprisingly, P forms a quasi-square self-assembly independently of the underlying HOPG lattice.