Aromatic interaction vs. hydrogen bonding in self-assembly at the liquid-solid interface

Article abstract of DOI:10.1039/b812890a

Interfacial self-assembly of specific monolayer structures from solution on a graphite surface can be steered by tuning the interplay between solute-solute and solute-solvent interactions. The Royal Society of Chemistry 2009.

Full text of DOI:10.1039/b812890a

S1
Supporting Information
Aromatic Interaction vs. Hydrogen Bonding in Self-Assembly
at the Liquid-Solid Interface
Rico Gutzler*a, Sophie Lappea, Kingsuk Mahatab, Michael Schmittelb,
Wolfgang M. Heckla,c, and Markus Lackingera
Department of Earth and Environmental Sciences and Center for
NanoScience (CeNS), Ludwig-Maximilians-University, Theresienstraße 41,
80333 Munich, Germany; Center of Micro and Nanochemistry and
Engineering, Organische Chemie I, University Siegen, Adolf-Reichwein-
Straße 2, 57068 Siegen, Germany; Deutsches Museum, Museumsinsel 1,
80538 Munich, Germany
Contents
I.
Synthesis of Chemical Compound II
Experimental details and additional STM topographs
Additional UV/vis absorption spectroscopy data
Theoretical Calculations
II.
III.
IV.
V.
References
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S2
I. Synthesis of Chemical Compound II
4-{2-{3,5-Bis[2-(4-carboxyphenyl)-1-ethynyl]-2,4,6-trimethylphenyl}-1-ethynyl}benzoic
acid
Scheme 1
O
O
O
O
Pd(0), DMF, TEA, rt
+
I
1
A
B
2
3
O
O
O
C
O
4
5
Preparation of C: To a solution of ethyl 4-iodobenzoate (A, 1.15 g, 4.16 mmol) in
triethylamine (20 mL) and DMF (20 mL), triethynylmesitylene (B, 200 mg, 1.04 mmol) and
Pd(PPh3)4 (120 mg, 104 μmol) were added under N2. The resulting mixture was stirred at
room temperature for 20 h. The reaction mixture was dissolved in CH2Cl2 (100 mL) and
washed with water (2 × 100 mL). The organic phase was dried over MgSO4 and filtered.
After removal of the solvents the crude product was purified by column chromatography
(silica, ethylacetate:hexane, 1:4) to afford the product as a white solid (490 mg, 77%). MP:
~
162 °C. IR (KBr): = 3424 (w), 2980 (w), 2203 (w), 17186 (s), 1605 (s), 1506 (w), 1404
ν
(w), 1366 (w), 1271 (s), 1174 (m), 1105 (s), 1019 (m), 854 (m), 767 (s), 694 (w), 526 (w).
1H-NMR (400 MHz, CDCl3): δ = 1.41 (t, J = 7.1 Hz, 9H, 5-H), 2.73 (s, 9H, 1-H), 4.40 (q, J
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S3
13
= 7.1 Hz, 6H, 4-H), 7.58 (d, J = 8.3 Hz, 6H, 2-H), 8.02 (d, J = 8.3 Hz, 6H, 3-H). C-NMR
(100 MHz, CDCl3): δ = 14.4, 20.5, 61.3, 89.6, 97.1, 121.2, 128.0, 129.7, 130.0, 131.4, 143.0,
166.1. Anal calcd for C42H36O6: C, 79.22; H, 5.70; found: C, 79.81; H, 5.69.
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S4
h
t
b
p
0
-
7
p
0
r
1
o
6
t
a
o
r
C D C l
C D C l
3
3
t
n
D :
P a
o
r
c
1
6
t
*
*
*
C u
r
e
n
0
t
D a
a
a
m e
e
r
s
* * *
N A M
E
h :b
:
0
7
1
6
a
1
1
E X P N O
P R O C N O:
8 .
5
8 .
0
7 .
5
7 .
0
6 .
5
6 .
0
5 .
5
5 .
0
4 .
5
4 .
0
3 .
5
3 .
0
2 .
5
2 .
0
1 .
5
1 .
0
0 .
5
(
p p m)
1H-NMR spectrum of compound C
h
t
b
p
0
7
0
1
3
6
a
C D C l 3
-
C 1
C DC l
3
D :
o
c
1
6
*
*
*
C u
r
r
e
n
0
t
Da
a
t
a
P a
r
a
m e
t
e
r
s
* * *
N A M
E
h :b
:
0
7
1
6
E X P N O
1
0
P R O C N O:
1
1 7 0
1 6 0
1 5 0
1 4 0
1 3 0
1 2 0
1 1 0
1 0 0
9 0
8 0
7 0
6 0
5 0
4 0
3 0
2 0
1 0
0
(
p p m)
13C-NMR spectrum of compound C
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S5
Scheme 2
O
O
HO
O
LiOH, THF, H2O, rt, overnight
1
2
3
O
O
O
O
O
C
D
O
OH
OH
4
Preparation of D: Ester C (430 mg, 675 μmol) was dissolved in a mixture of THF (12 ml)
and H2O (1.8 mL). Then, LiOH monohydrate (568 mg, 13.5 mmol) was added and the
mixture was stirred at room temperature while H2O (6 mL) was added over a period of 1
hour. After the mixture had been stirred at room temperature overnight, 30 mL of THF was
added. Then 100 mL of 1 M HCl was added to this solution and the precipitate was filtered
by suction. The solid was washed with 100 mL of 1 M HCl and 100mL of acetone to afford
~
product D as a white powder (340 mg, 0.615 mmol, 91%). MP: >300 °C. IR (KBr): = 3445
ν
(w), 2850 (w), 2525 (w), 2361 (w), 2200 (w), 1686 (s), 1604 (s), 1558 (m), 1417 (s), 1311
(m), 1275 (s), 1172 (m), 1106 (w), 1015 (w), 854 (m), 768 (s), 690 (w), 551 (w), 510 (w).
1H-NMR (400 MHz, DMSO-d6): δ = 2.74 (s, 9H, 1-H), 7.72 (d, J = 8.3 Hz, 6H, 2-H), 7.99
13
(d, J = 8.3 Hz, 6H, 3-H), 13.22 (br s, 3H, 4-H). C-NMR (100 MHz, DMSO-d6): δ = 20.2,
88.6, 97.1, 120.6, 126.5, 129.6, 130.8, 131.4, 142.6, 166.7. Anal calcd for
C36H24O6*1.25H2O: C, 75.19; H, 4.64; found: C, 75.15; H, 4.40.
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S6
k
t
m- me
-
e
t
t
c
n
e
a
1
n
p
*
-
p
r
o
o
r
2
t
8
D M
Da
S
O
D:
o
c
t
1
e
w
r
5
*
*
C u
r
t
a
P a
r
a
m e
s
* * *
N A MKEM :-
E X P N O
P R O C N O:
M
E - ~ 1
:
1
1
1 3 .
0
1 2 .
0
1 1 .
0
1 0 .
0
9 .
0
8 .
0
7 .
0
6 .
0
5 .
0
4 .
0
3 .
0
2 .
0
1 .
0
0 . 0
(
p p m)
1H-NMR spectrum of compound D
k
t
m- me
-
e
(
t
c
0
e
a
p
*
-
C 1
3
1
r
h
n
o
t
u
r
s
)
t
D M
P a
S
r
O
a
D :
m e
o
r
c
s
1
w
*
5
*
*
*
C u
r
Da
a
t
e
*
N A MKEM :-
E X P N O
P R O C N O:
M
E - ~ 1
:
1
0
1
1 7 0
1 6 0
1 5 0
1 4 0
1 3 0
1 2 0
1 1 0
1 0 0
9 0
(
8 0
7 0
6 0
5 0
4 0
3 0
2 0
1 0
0
p p m)
13C-NMR spectrum of compound D
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S7
II. Experimental details and additional STM topographs
STM experiments were performed with a home-built instrument at ambient temperature (20-
25 °C). Solvents were purchased from Aldrich and used as received. STM tips were cut
mechanically from platinum/irdium wire (80% Pt / 20% Ir, diameter = 0.25 mm). Molecules
I and II were dissolved in all solvents until saturation. Prior to imaging, a drop (~2.5 µL) of
saturated solution was applied to a freshly cleaved (0001) surface of HOPG (Highly Oriented
Pyrolytic Graphite). STM experiments were carried out at the liquid-solid interface with the
tip immersed into solution in constant-current mode. Atomically resolved graphite images
were used for lateral calibration.
UV/vis absorption spectra were recorded with the USB4000 spectrometer from Ocean Optics
and a deuterium tungsten lamp as excitation source. Due to high absorbance of the solute
molecules a quartz glass cuvette with an optical path length of 1 mm was used. Absorption
spectra of pure nonanoic acid were used as a reference.
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S8
Figure S1. STM topograph of self-assembled monolayers of molecule I dissolved in NA (1.2
V; 20 pA). Interrow spacing is 1.9 nm. A high number of defects can be observed and is
typical for this self-assembled monolayer.
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S9
Figure S2. STM topograph of self-assembled monolayers of molecule I dissolved in DBB
(1.2 V; 100 pA). The lattice parameter of this hexagonal structure accounts to 4.1 nm and is
equal to the value of the hexagonal structure of compound I in TCB. This class of aromatic
nonprotic solvents interacts with the solute through aromatic interactions and is able to break
up preformed solute aggregations in solution. Consequently, monomeric adsorption results
and the H-bonded chickenwire structure can form.
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S10
Figure S3. STM topograph of self-assembled monolayers of molecule I dissolved in PBA
(1.3 V; 23 pA). The same row structure with a row spacing of 1.9 nm is observed in NA.
Although the phenyl ring of the solvent might interact with the aromatic system of the solute,
the interaction is too weak to cause monomeric dissolution and consequently precipitation of
the H-bonded chickenwire structure.
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S11
Figure S4. High resolution STM image of self-assembled monolayers of molecule I in TCB.
Within each cavity 19 bright spots can be identified as indicated by the white dots. The close
packed arrangement of the dots exhibits hexagonal symmetry and the size of one dot
corresponds to the size of a TCB molecule. This contrast can be explained by planar co-
adsorption of 19 solvent molecules within the cavity, thus each bright dot corresponds to one
TCB molecule.
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S12
Figure S5. STM topograph of self-assembled monolayer of molecule II in TCB (1.1 V; 70
pA). As in Fig. S4, the cavities of the hexagonal arrangement appear brighter than the
surrounding molecules II themselves. This can be explained by co-adsorption of solvent
molecules within the cavities of the open pore network. Molecular resolution of co-adsorbed
solvent molecules could not be achieved.
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S13
III. Additional UV/vis absorption spectroscopy data
2,0
1,5
1,0
0,5
0,0
0
20
40
60
80
100
concentration (% from saturation)
Figure S6. Lambert-Beer plot of molecule I dissolved in nonanoic acid. Black squares
correspond to the absorbance at λ = 304 nm (aggregate related peak) and red triangles to the
absorbance at λ = 323 nm (monomer related peak) (see also Fig. 3 main text). Absorbance is
plotted as measured with a 1 mm cuvette.
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S14
IV. Theoretical Calculations
The Consistent Valence Force Field (CVFF) was applied to model monolayers of adsorbed
molecules on graphite using the Cerius2 (Version 4.5, MSI) software package. The use of the
CVFF was motivated by previous works on structure optimization of organic monolayers on
graphite.1 Here, periodic boundary conditions were employed with the experimental unit
cells as a constraint. The graphite substrate was approximated by two layers and atomic
positions in the second layer were fixed. Values for the unit cell parameters were deduced
from split images, where one part of the image depicts the adsorbate layer and in the other
part the graphite substrate was atomically resolved. Molecules were arranged on the surface
without further constraints. An energy difference of < 2×10-5 kcal/mol between single steps
served as a convergence criteria.
The geometry of isolated molecules I and II was optimized using density functional theory
(DFT) implemented in the Gaussian03 software package.2 For this purpose, the B3LYP
functional was used with the 6-31G(d) basis set. Convergence RMS force criterion was set to
3×10-4 Hartree/Bohr.
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S15
Figure S7. Schematic drawing indicating the distance between two carboxylic groups
(carbon atoms were used as reference) of molecule I as calculated by DFT calculations.
Figure S8. (a) Top view and (b) side view of a dimer of molecule I in the row structure on
HOPG after geometry optimization by force-field calculation. Molecules in adjacent rows are
tilted in opposite directions. The tilting angle of the molecule with respect to the substrate is
~36°. The distance of the upper phenyl ring of a molecule to the C-C triple bond of its intra-
row neighbor accounts to ~3.7 Å which allows for aromatic interaction. Unit cell: 3.8 nm ×
0.8 nm, 84°.
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S16
Figure S9. Top view of a dimer of molecule II on HOPG after geometry optimization by
force-field calculations. Three pairs of hydrogen bonds per molecule stabilize the hexagonal
structure. Unit cell: 4.1 nm × 4.1 nm, 60°.
Figure S10. Force field calculation of a model with 19 co-adsorbed TCB solvent molecules
within the cavities of an H-bonded network of molecule I. Four unit cells (4.1 nm × 4.1 nm,
60°).
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S17
V. References
1.
2.
Yin, S. X.; Wang, C.; Xu, Q. M.; Lei, S. B.; Wan, L. J.; Bai, C. L. Chem. Phys. Lett.
2001, 348, (3-4), 321-328.
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;
Cheeseman, J. R.; Montgomery, J., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.;
Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.;
Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.;
Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao,
O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken,
V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A.
J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G.
A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.;
Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman,
J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.;
Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.;
Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.;
Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A., Gaussian 03,
Revision C.02, 2004, Gaussian, Inc., Wallingford CT, USA
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