Conformational analysis of self-organized monolayers with scanning tunneling microscopy at near-atomic resolution

Article abstract of DOI:10.1021/ja043638+

We describe the synthesis and a novel approach to the conformational analysis of 2,2′-bipyridines (bpy) bearing aromatic rich Frechet-type dendritic wedges of the first and second generation as substituents. The evaporation of solutions of these new ligan

Full text of DOI:10.1021/ja043638+

Published on Web 02/25/2005
Conformational Analysis of Self-Organized Monolayers with
Scanning Tunneling Microscopy at Near-Atomic Resolution
Lukas J. Scherer,† Leo Merz,‡ Edwin C. Constable,*,† Catherine E. Housecroft,*,†
Markus Neuburger,† and B. A. Hermann*,§
Contribution from the Departments of Chemistry and Physics, UniVersity of Basel,
Basel, Switzerland, and the Walther-Meissner-Institute (WMI) of Low Temperature Research of
the BaVarian Academy of Science and Faculty of Physics/Center for Nano Science (CeNS),
LMU Munich, Germany
Received October 20, 2004; E-mail: edwin.constable@unibas.ch; catherine.housecroft@unibas.ch; b.hermann@cens.de
Abstract: We describe the synthesis and a novel approach to the conformational analysis of 2,2′-bipyridines
(bpy) bearing aromatic rich Fre´chet-type dendritic wedges of the first and second generation as substituents.
The evaporation of solutions of these new ligands on graphite surfaces under ambient conditions results
in the formation of self-organized monolayers. Scanning tunneling microscopy (STM) investigations of the
monolayers under ambient conditions (air, 298 K) gave images at submolecular and near-atomic resolution.
The analysis of the STM images includes the following processes: (i) identification and reproduction of
potential homoconformational domains, (ii) exclusion of improper data using quality criteria for drift and
feedback artifacts, (iii) compilation of running averages and checking for averaging artifacts, (iv) analysis
of three-dimensional and contour plots, (v) calculation of the HOMO properties of the free molecules, and
(vi) final conformational assignment based on all accessible information. Following this procedure, two
different conformations could be assigned to domains observed in the monolayers of the first-generation
(G1) and second-generation (G2) dendritic compounds. Homoconformational domains are observed side-
by-side. The different conformations arise from syn or anti arrangements at the ether substituents. An
additional conformational effect is found upon treating the G1 domains with HCl gas, when a partial
rearrangement of the bpy from trans to cis occurs, concomitant with protonation.
Introduction
within the monolayer and the factors controlling the extended
two-dimensional structure that is assembled. However, there is
also considerable potential for the study of intramolecular as
well as intermolecular structural questions of chemical interest
using these new methods. Conventional methods of determining
molecular conformation and metrical parameters such as single-
crystal X-ray crystallography or NMR spectroscopic methods
give structures averaged over some 1015 molecules. Analysis
of the surface molecular conformation of molecular components
within two-dimensional arrays averaged over tens to hundreds
of molecules can now be performed by analyzing submolecular-
resolved STM images. In other words, it is now becoming
possible for the chemist to regard STM as a valid and accessible
tool to add to the more conventional methods of determining
molecular structure and spatial properties. Here, we report the
analysis by STM of a system that exhibits multiple conformers
on a graphite surface. We have chosen a 2,2′-bipyridine (bpy)
ligand functionalized with Fre´chet-type dendrimers of various
generations as our core structural unit. STM studies of the parent
2,2′-bipyridine adsorbed on a Au(111) surface have already been
reported.7 The coordination chemistry of bpy ligands is well
understood,8 and coordination to a metal center results in a loss
of conformational freedom, locking the ligand in a cis confor-
The direct imaging of species of chemical interest at the
molecular and submolecular levels using scanning tunneling and
force microscopy has revolutionized possibilities for the visu-
alization and control1,2 of self-organized systems. Self-assembly
and self-organization are increasingly finding application as
methodologies for device fabrication, display manufacture,
sensor design, and heterogeneous catalyst production.3 Scanning
tunneling microscopy (STM) is an ideal technique for probing
self-organized structures, allowing one to investigate molecular
orientation and site specificity in a single experiment, and the
analysis of a wide range of organic, coordination, and organo-
metallic compounds has been reported.4-6 Although both static
and dynamic properties of these systems have been investigated,
the emphasis has generally been upon interactions of molecules
† Department of Chemistry, University of Basel.
‡ Institute of Physics, University of Basel.
§ WMI and CeNS, LMU Munich.
(1) Binnig, G.; Rohrer, H. HelV. Phys. Acta 1982, 55, 726-735.
(2) Binnig, G.; Rohrer, H.; Gerber, C.; Weibel, E. Phys. ReV. Lett. 1982, 49,
57-61.
(3) Lehn, J.-M. Supramolecular Chemistry: Concepts and PerspectiVes;
VCH: Weinheim, Germany, 1995.
(4) De Feyter, S.; De Schryver, F. C. Chem. Soc. ReV. 2003, 32, 139-150
and references therein.
(5) De Feyter, S.; Gesquie`re, A.; Abdel-Mottaleb, M. M.; Grim, P. C. M.; De
Schryver, F. C.; Meiners, C.; Sieffert, M.; Valiyaveettil, S.; Mu¨llen, K.
Acc. Chem. Res. 2000, 33, 520-531.
(7) Pinheiro, L.S.; Temperini, M. L. A. Surf. Sci. 1999, 441, 45-52.
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(6) Giancarlo L. C.; Flynn, G. W. Acc. Chem. Res. 2000, 33, 491-501.
9
10.1021/ja043638+ CCC: $30.25 © 2005 American Chemical Society
J. AM. CHEM. SOC. 2005, 127, 4033-4041
4033

A R T I C L E S
Scherer et al.
Chart 1
mation, in contrast to the time-averaged trans conformation in
the free ligand.8,9 This will ultimately allow us to address the
conformation of a ligand within a monolayer by reaction with
metal salts.10
The aromatic-rich system of the Fre´chet-type dendrimer11 is
ideally suited for visualization by tunneling methods.12-16
Additionally, the dendritic compound provides a significant
mechanical barrier to rotation about the interannular C-C bond
when the conjugates are in a conformationally restricted
environment such as in a lattice or in a monolayer on a surface.
In this article, we analyze self-organized monolayers of such
conjugate structures on surfaces and show that not only one
global minimum, but a range of conformations, may be found
in surface-bound domains.
the averaging procedure was carried out. The process of conformational
analysis is described in the Results section. Scanning voltages were
tried from +1.5 to -1.5 V. The best resolution was obtained between
-300 and -1300 mV. We did not observe significant changes in the
contrast in this range.
Compound 3. Methanesulfonyl chloride (1.04 mL, 13.5 mmol) was
added over 15 min to a mixture of 1 (1.23 g, 3.38 mmol) and NEt3
(2.08 mL, 16.9 mmol) in dry CH2Cl2 (20 mL) at -15 °C under N2.
After being stirred for 1 h at -15 °C, the reaction mixture was poured
into a mixture of crushed ice (100 mL) and concentrated HCl (10 mL).
The CH2Cl2 layer was separated, washed with saturated NaHCO3
solution, dried (Na2SO4), and evaporated to give 2 (1.80 g, ca. 80%
pure, 3.20 mmol) as an oil. Crude 2 (41.5 mg, ca. 80% pure, 75.0
µmol), 4,4′-dihydroxy-2,2′-bipyridine (6.90 mg, 35.0 µmol), K2CO3
(50.0 mg, 362 µmol), and nBu4NI (2 mg, 6 µmol) were stirred
vigorously in ethyl acetate (400 µL) and water (400 µL) at 60 °C for
20 h. Water (20 mL) was added, and the mixture was extracted three
times with ethyl acetate (20 mL). The combined organic layers were
dried (MgSO4) and evaporated. Preparative chromatography on silica
(CH2Cl2/MeOH 10:1) yielded 3 as a white powder (23.1 mg, 26.1 µmol,
Experimental Section
General. Commercially available chemicals were reagent grade and
were used without further purification. 1H and 13C NMR spectra were
recorded on a Bruker DRX500 spectrometer; δ is relative to TMS,
internally referenced to solvent. Infrared spectra were recorded on a
Shimadzu FTIR-8400S spectrophotometer with neat samples using a
Golden Gate ATR accessory. UV/vis measurements were performed
using a Perkin-Elmer Carey 5000 spectrophotometer and were recorded
in CH2Cl2 solution. Electrospray (ES) mass spectra were recorded on
a Bruker Esquire 3000 plus instrument, FAB mass spectra on a Finnegan
MAT 312, and MALDI-TOF mass spectra on a Vestec Voyager Elite
instrument with R-cyano-4-hydroxycinnamic acid as matrix. The
microanalyses were performed with a Leco CHN-900 microanalyzer.
4,4′-Dihydroxy-2,2′-bipyridine17 and compound 718,19 were prepared by
literature methods.
1
74.1%). Chart 1 shows the structures of 1-3. H NMR (500 MHz,
CDCl3, 25 °C): δ 8.48 (d, J ) 5.7 Hz, 2H, H6A), 8.05 (d, J ) 2.7 Hz,
2H, H3A), 6.91 (dd, J ) 5.7, 2.7 Hz, 2H, H5A), 6.57 (d, J ) 2.1 Hz,
STM. The experiments were carried out in constant current mode
using a NanoscopeIII scanning tunneling microscope, equipped with a
low current converter. STM tips were mechanically formed from Pt/Ir
(9/1) wire. All images were obtained from monolayers on highly
oriented pyrolytic graphite (HOPG) substrates. All data used for the
analysis were carefully reproduced several times with different tips and
different substrate pieces. The data were analyzed using the program
SXM-shell (University of Basel, 2004). The 10 nm × 10 nm STM
images were prepared by an averaging procedure written for SXM-
shell. (Averaging procedures have been used successfully to enhance
signal:noise ratios in a wide variety of studies.)20,21 A sub-image is cut
as reference, several similar locations on the original image are found
by cross-correlation, and flawed sections are manually deselected. Sub-
images cut at the selected places are then averaged into a noise-reduced
image. Special care was taken to exclude any averaging artifacts.
Individual figure captions state the number of sub-images over which
4H, H2B), 6.42 (t, J ) 2.2 Hz, 2H, H4B), 5.15 (s, 4H, HOCH -ringB), 3.94
2
OCH CH
2
(t, J ) 6.6 Hz, 8H, HOCH CH ), 1.77 (tt, J ) 6.8, 6.5 Hz, 8H, H
),
2
2
2
1.45 (tt, J ) 7.5, 7.3 Hz, 8H, HOCH CH CH ), 1.25-1.37 (m, 32H,
2
2
2
Hoctyl(CH ) ), 0.88 (t, J ) 7.0 Hz, 12H, H ). 13C NMR (125 MHz,
CDCl3, 25 °C): δ 166.1, 160.7, 157.7, 150.4, 138.0, 111.7, 107.5, 105.9,
101.2, 70.1, 68.3, 32.0, 29.5, 29.4 (two overlapping signals), 26.2, 22.8,
14.3. IR (neat): νj (cm-1) 2924 s, 2855 m, 1582 s, 1458 s, 1296 m,
1234 m, 1173 s, 1057 s, 995 s, 833 s. MS (ESI+): m/z 903.5 [M +
Na]+, 881.6 [M + H]+; UV/vis (CH2Cl2): λ/nm (ꢀ/M-1 cm-1) 274 (22
400). Anal. Calcd for C56H84N2O6: C, 76.32; H, 9.61; N, 3.18. Found:
C, 76.10; H, 9.80; N, 2.78.
CH
2
4
3
Compound 6. Methanesulfonyl chloride (0.12 mL, 1.54 mmol) was
added over 15 min to a mixture of 4 (330 mg, 0.390 mmol) and NEt3
(0.260 mL, 2.12 mmol) in dry CH2Cl2 (5 mL) at -15 °C under N2.
After being stirred for 1 h at -15 °C, the reaction mixture was poured
into a mixture of crushed ice (50 mL) and concentrated HCl (4 mL).
The CH2Cl2 layer was separated, washed with saturated NaHCO3
solution, dried (Na2SO4), and evaporated to give mesylate 5 (390 mg,
ca. 80% pure, 0.35 mmol) as an oil. Crude 5 (170 mg, ca. 0.15 mmol),
4,4′-dihydroxy-2,2′-bipyridine (11.8 mg, 60.0 µmol), K2CO3 (50.0 mg,
362 µmol), and nBu4NI (2 mg, 6 µmol) were stirred vigorously in ethyl
acetate (500 µL) and water (500 µL) at 60 °C for 20 h. Water (20 mL)
was added, and the mixture was extracted three times with ethyl acetate
(20 mL). The combined organic layers were dried (MgSO4) and
evaporated. Preparative chromatography (silica, CH2Cl2/MeOH 10:1)
yielded 6 as a white powder (49.2 mg, 27.1 µmol, 44.0%). Chart 2
(9) Constable, E. C. Metals and Ligand ReactiVity; VCH: Weinheim, Germany,
1996; Chapter 2.
(10) Abdel-Mottaleb, M. M. S.; Schuurmans, N.; De Feyter, S.; van Esch, J.;
Feringa, B. L.; De Schryver, F. C. Chem. Commun. 2002, 1894-1895.
(11) Hawker, C. J.; Fre´chet, J. M. J. J. Am. Chem. Soc. 1990, 112, 7638-7647.
(12) Widmer, I.; Huber, U.; Sto¨hr, M.; Merz, L.; Gu¨ntherodt, H.-J.; Hermann,
B. A.; Samor´ı, P.; Rabe, J. P.; Rheiner, P. B.; Creiveldinger, G.; Murer, P.
HelV. Chim. Acta 2002, 85, 4255-4263.
(13) Wu, P.; Fan, Q.; Deng, G.; Zeng, Q.; Wang, C.; Bai, C. Langmuir 2002,
18, 4342-4344.
(14) Prokhorova, S. A.; Sheiko, S. S.; Mourran, A.; Azumi, R.; Beginn, U.;
Zipp, G.; Ahn, C. H.; Holerca, M. N.; Percec, V.; Mo¨ller, M. Langmuir
2000, 16, 6862-6867.
(15) Wu, P.; Fan, Q.; Zeng, Q.; Wang, C.; Deng, G.; Bai, C. ChemPhysChem.
2002, 633-637.
1
shows the structures of 4-6. H NMR (500 MHz, CDCl3, 25 °C): δ
(16) Constable, E. C.; Hermann, B. A.; Housecroft, C. E.; Merz, L.; Scherer,
L. J. Chem. Commun. 2004, 928-929.
8.50 (d, J ) 5.7 Hz, 2H, H6A), 8.14 (s br, 2H, H3A), 6.93 (dd, J ) 5.5,
2.1 Hz, 2H, H5A), 6.71 (d, J ) 2.1 Hz, 4H, H2B), 6.60 (t, J ) 2.2 Hz,
2H, H4B), 6.56 (d, J ) 2.2 Hz, 8H, H2C), 6.41 (t, J ) 2.2 Hz, 4H, H4C),
(17) Case, F. H. J. Org. Chem. 1962, 27, 640-641.
(18) Forier, B.; Dehaen, W. Tetrahedron 1999, 55, 9829-9846.
(19) Ichinose, K.; Ebizuka, Y.; Sankawa, U. Chem. Pharm. Bull. 2001, 49, 192-
196.
5.18 (s, 4H, HOCH -ringB), 4.97 (s, 8H, HOCH -ringC), 3.94 (t, J ) 6.6 Hz,
2
2
(20) Patrick, D. L.; Cee, V. J.; Beebe, T. P., Jr. Science 1994, 265, 231-234.
(21) Scheuring, S.; Ringler, P.; Borgnia, M.; Stahlberg, H.; Mu¨ller, D. J.; Agre,
P.; Engel, A. EMBO J. 1999, 18, 4981-4987.
16H, HOCH 2), 1.77 (tt, J ) 7.3, 6.6 Hz, 16H, HOCH CH ), 1.45 (tt, J )
CH
2
2
2
octyl(CH )
2 4
7.5, 7.3 Hz, 16H, HOCH CH CH ), 1.29-1.38 (m, 64H, H
), 0.89
2
2
2
9
4034 J. AM. CHEM. SOC. VOL. 127, NO. 11, 2005

Analysis of Self-Organized Monolayers with STM
A R T I C L E S
Chart 2
HOCH -ringB), 5.05 (s, 8H, HOCH Ph). 13C NMR (125 MHz, CDCl3, 25
°C, CHCl3): δ 165.9, 160.4, 158.0, 150.4, 138.3, 136.8, 128.8, 128.2,
127.7, 111.7, 107.3, 106.6, 102.0, 70.3, 69.9. IR (neat): νj (cm-1) 3032
w, 2901 w, 2870 w, 1967 w, 1875 w, 1736 w, 1590 s, 1443 m, 1373
m, 1296 s, 1149 s, 1027 s, 864 m, 825 s, 733 m, 694 s. MS (ESI+):
m/z 793 ([M]+). Anal. Calcd. for C52H44N2O6‚2H2O: C, 75.34; H, 5.86;
N, 3.38. Found: C, 75.56; H, 5.67; N, 3.05.
2
2
Chart 3
[Pd(3)Cl2]. Compound 3 (35 mg, 39 µmol) and K2[PdCl4] (13 mg,
40 µmol) were refluxed in ethanol (20 mL) for 16 h. The solvent was
evaporated, hexanes were added to the yellow residue, and the resultant
suspension was filtered through Celite to give a yellow filtrate. The
solvent was evaporated to give [Pd(3)Cl2] as a yellow oil (41 mg, 39
1
µmol, 98%). H NMR (500 MHz, CDCl3, 25 °C): 8.62 (d, J ) 6.7
Hz, 2H, H6A), 7.66 (d, J ) 2.6 Hz, 2H, H3A), 6.77 (dd, J ) 6.7, 2.6
Hz, 2H, H5A), 6.62 (d, J ) 2.2 Hz, 4H, H2B), 6.43 (t, J ) 2.2 Hz, 2H,
H4B), 5.32 (s, 4H, HOCH -ringB), 3.94 (t, J ) 6.6 Hz, 8H, HOCH CH ), 1.74
2
2
2
(tt, J ) 6.8, 6.5 Hz, 8H, HOCH CH ), 1.42 (tt, J ) 7.5, 7.3 Hz, 8H,
2
2
octyl(CH )
HOCH CH CH ), 1.25-1.37 (m, 32H, H
), 0.88 (t, J ) 7.0 Hz, 12H,
2
2
2
2 4
HCH ). 13C NMR (125 MHz, CDCl3, 25 °C): δ 167.2, 160.8, 157.2,
150.8, 136.4, 113.1, 110.3, 106.3, 101.6, 71.8, 68.3, 31.8, 29.4, 29.3
(two overlapping signals), 26.1, 22.7, 14.1. IR (neat): νj (cm-1) 2924
s, 2854 m, 1736 m, 1605 s, 1450 m, 1335 m, 1219 w, 1165 s, 1041 m,
841 m, 764 m. MS (FAB): m/z 985 [M - 2Cl]+; UV/vis (CH2Cl2):
λ/nm (ꢀ/M-1 cm-1) 301 (10 000), 289 (9800). Anal. Calcd for C56H84-
Cl2N2O6Pd: C, 63.54; H, 8.00; N, 2.65. Found: C, 63.90; H, 8.09; N,
2.42.
3
(t, J ) 6.9 Hz, 24H, HCH ). 13C NMR (125 MHz, CDCl3, 25 °C): δ
3
166.2, 160.7, 160.3, 157.2, 150.0, 139.0, 138.1, 112.0, 107.5, 106.6,
105.8, 102.1, 101.0, 70.3, 70.1, 68.2, 32.0, 29.5, 29.4, 29.4, 26.2, 22.8,
14.2. IR (neat): νj (cm-1) 2924 m, 2854 m, 1589 s, 1450 s, 1373 m,
1157 s, 1049 s, 825 m. MS (MALDI+): m/z 1818.7 [M]+, 1880.6 [M
+ Na + K]+. UV/vis (CH2Cl2): λ/nm (ꢀ/M-1 cm-1) 276 (37 200).
Anal. Calcd for C116H172N2O14: C, 76.61; H, 9.53; N, 1.54. Found: C,
76.07; H, 9.37; N, 1.76.
[Pd(3)2][PF6]2. [Pd(3)Cl2] (38.0 mg, 35.9 µmol), compound 3 (31.6
mg, 35.9 µmol), and TlPF6 (26.2 mg, 75 µmol) were stirred in
dichloromethane (20 mL) at room temperature for 4 h. The suspension
was filtered through Celite, and the solvent of the filtrate was
evaporated. Sonicating in MeOH (15 mL) for 2 min afforded [Pd(3)2]-
[PF6]2 as a pale yellow powder (68.0 mg, 31.5 µmol, 87.7%). 1H NMR
(500 MHz, CD2Cl2, 25 °C, CH2Cl2): 8.38 (d, J ) 6.8 Hz, 4H, H6A),
7.69 (d, J ) 2.1 Hz, 4H, H3A), 7.50 (br s, 4H, H5A), 6.58 (d, J ) 2.2
Compound 8. Crude mesylate 7 (see Chart 3, 400 mg, ca. 80%
pure, 800 µmol), 4,4′-dihydroxy-2,2′-bipyridine (60.0 mg, 305 µmol),
K2CO3 (240 mg, 1.74 mmol) and nBu4NI (10 mg, 30 µmol) were stirred
vigorously in ethyl acetate (1 mL) and water (1 mL) at room
temperature for 20 h. Water (20 mL) was added, and the mixture was
extracted three times with ethyl acetate (20 mL). The combined organic
layers were dried (Na2SO4) and evaporated. Chromatography over silica
(CH2Cl2/MeOH 15:1) yielded 8 as a white powder (82.5 mg, 104 µmol,
Hz, 8H, H2B), 6.42 (t, J ) 2.1 Hz, 4H, H4B), 5.27 (s, 8H, HOCH -ringB),
2
3.92 (t, J ) 6.5 Hz, 16H, HOCH CH ), 1.73 (tt, J ) 6.7, 6.5 Hz, 16H,
2
2
OCH CH CH
HOCH CH ), 1.42 (tt, J ) 7.5, 6.7 Hz, 16H, H
), 1.23-1.37 (m,
2
2
2
2
2
CH
64H, Hoctyl-(CH ) ), 0.87 (t, J ) 7.1 Hz, 24H, H ). 13C NMR (125
MHz, CD2Cl2, 25 °C): δ 168.7, 160.8, 157.2, 151.8, 135.9, 114.3,
111.6, 105.9, 101.5, 72.1, 68.2, 31.8, 29.3, 29.2, 29.2, 26.0, 22.6, 13.9.
IR (neat): νj (cm-1) 2924 s, 2854 m, 1605 s, 1443 m, 1335 m, 1227 w,
1165 s, 1041 m, 825 s, 687 m. MS (ESI+): m/z 2012.3 [M - PF6]+,
933.3 [M - 2PF6]2+; UV/vis (CH2Cl2) λ/nm (ꢀ/M-1 cm-1): 288
2
4
3
1
34.7%). H NMR (500 MHz, CDCl3, 25 °C, CHCl3): δ 8.48 (d, J )
5.7 Hz, 2H, H6A), 8.06 (d, J ) 2.4 Hz, 2H, H3A), 7.42 (d, J ) 7.1 Hz,
8H, H2C), 7.37 (dd, J ) 7.6 Hz, 7.6 Hz, 8H, H3D), 7.32 (dd, J ) 7.3
Hz, 7.1 Hz, 4H, H4C), 6.89 (dd, J ) 5.6, 2.5 Hz, 2H, H5A), 6.70 (d, J
) 2.1 Hz, 4H, H2B), 6.60 (t, J ) 2.2 Hz, 2H, H4B), 5.16 (s, 4H,
9
J. AM. CHEM. SOC. VOL. 127, NO. 11, 2005 4035

A R T I C L E S
Scherer et al.
(27 700), 236 (92 400). Anal. Calcd for C112H168F12N4O12P2Pd: C,
62.31; H, 7.84; N, 2.60. Found: C, 63.38; H, 7.80; N, 3.05.
Crystal Data for Compound 8. Data were collected on an Enraf
Nonius Kappa CCD instrument; for data reduction, solution, and
refinement we used the programs COLLECT,22 SIR97,23 and CRYS-
TALS (version 12).24 Crystal data: C158H134Cl6N6O18 (3C52H44N2O6.-
2CHCl3), M ) 2617.55, triclinic, space group P1h, a ) 12.7464(2),
b ) 15.0932(2), c ) 18.6957(3) Å, R ) 95.3241(7), â ) 95.2033(7),
γ ) 108.0007(7)°, U ) 3378.78(9) Å3, Z ) 1, Dc ) 1.286 Mg m-3
,
µ(Mo KR) ) 0.197 mm-1, T ) 173 K. Reflections collected ) 16 039;
refinement of 9188 reflections (883 parameters) with I >1.5σ(I)
converged at final R1 ) 0.0659, wR2 ) 0.0786.
Figure 1. Solid-state structure of the noncentrosymmetric molecule of
compound 8 present in the unit cell. For clarity, hydrogen atoms are omitted
and selected atoms only are numbered. Important bond lengths and angles:
N(1)-C(5) ) 1.342(3), N(2)-C(6) ) 1.343(3), C(5)-C(6) ) 1.491(3),
O(1)-C(3) ) 1.368(3), O(1)-C(11) ) 1.433(3), O(2)-C(14) ) 1.369(3),
Results
Compound Synthesis and Single-Crystal Structure of
Compound 8. The synthetic strategy adopted was the reaction
of a nucleophilic bpy derivative 4,4′-dihydroxy-2,2′-bipyridine17
with an electrophilic dendritic wedge. The first-generation
mesylate wedge 218,19 was prepared in 80% yield by mesylation
of the benzyl alcohol 111,25-27 under standard reaction conditions.
This first-generation dendritic wedge was coupled with 4,4′-
dihydroxy-2,2′-bipyridine under phase-transfer conditions
(nBu4NI, ethyl acetate-water) in the presence of K2CO3 to give
the first-generation (G1) ligand 3 in 74% yield. A related ligand
with a different spacer between the bpy domain and the wedge
has been reported by Vo¨gtle et al.28 Compound 3 was character-
ized by routine techniques. The major peaks in the electrospray
mass spectrum were assigned to [M + H]+ and [M + Na]+.
O(2)-C(18)
) 1.432(3), O(3)-C(16) ) 1.372(3), O(3)-C(25) )
1.440(3), O(4)-C(8) ) 1.363(3), O(4)-C(32) ) 1.440(3), O(5)-C(35) )
1.368(3), O(5)-C(39) ) 1.441(3), O(6)-C(37) ) 1.374(3), O(6)-C(46)
) 1.430(3) Å; C(3)-O(1)-C(11) ) 116.6(2), C(14)-O(2)-C(18) )
116.7(2), C(16)-O(3)-C(25) ) 117.2(2), C(8)-O(4)-C(32) ) 116.5(2),
C(35)-O(5)-C(39) ) 117.3(2), C(37)-O(6)-C(46) ) 116.7(2)°. The other
molecule in the unit cell has similar bond lengths and angles.
Chart 4. Conformations (syn and anti) of the Benzyl Groups Are
Defined (a) with Respect to the Interannular C-C Bond of the bpy
Unit or (b) with Respect to the C4-H Bond of a Phenyl Ring
1
Signals in the H NMR spectrum were assigned by COSY
methods. The solution room temperature 1H NMR spectrum was
sharp and well-resolved and indicated that rotation about the
C-C and C-O single bonds is unhindered.
The second-generation mesylate wedge, 5, was prepared from
the corresponding alcohol 425 by a strategy analogous to the
first-generation wedge. Compound 5 was coupled to 4,4′-
dihydroxy-2,2′-bipyridine to give 6 under the same phase
transfer conditions as when 2 was converted to 3. Compound 6
was obtained as a white powder in 44% yield and was
characterized by 1H (COSY) and 13C NMR and UV-vis
spectroscopies, mass spectrometry, and elemental analysis. Of
particular note was the fact that the signal assigned to the two
bipyridine protons H3A was broad, in contrast to the well-
resolved signal observed for H3A in the first-generation analogue
3. Other signals in the 1H NMR spectrum of 6 were sharp and
well-resolved. We attribute this phenomenon to hindered rotation
about the inter-ring C-C bond in the bipyridine unit arising
from the increased steric requirements of the second-generation
wedge.
yield by the same methodology as compound 6, and its structure
has been determined by single-crystal X-ray diffraction. The
triclinic unit cell contains two independent fragments: one
complete molecule is noncentrosymmetric, and the second is
located on the center of symmetry. Figure 1 shows the structure
of the noncentrosymmetric molecule. In both molecules, the
bipyridine unit adopts the expected trans conformation with the
two pyridine rings coplanar (dihedral angle between least
squares planes is 2°). Also in both molecules, the two inner
benzyl substituents adopt syn conformations with respect to the
bpy unit (see Chart 4). The outer benzyl groups adopt syn and
anti conformations with respect to the C4 proton (Chart 4). A
search of all aromatic ethers in the Cambridge Crystallographic
Database indicates a strong preference for the COCH2C residue
to lie in the plane of the attached aromatic ring. In compound
8, these torsion angles lie in the range 1.0-20.8° for the two
different molecules; the dihedral angles between the least squares
planes of adjacent pairs of pyridine-benzyl or benzyl-benzyl
rings lie in the range 4.2-88.2°. These metrical data, in
particular the angular information relating to the ether groups,
provide valuable supporting evidence for the conformational
analysis that follows.
In parallel with our studies of monolayers, we are continuing
to investigate solution- and solid-state structural properties of
related molecular systems. Compound 8 was prepared in ∼35%
(22) Collect Software; Bruker Nonius BV: Delft, The Netherlands, 1997-2001.
(23) Altomare, A.; Burla, M. C.; Camalli, M.; Cascarano, G. L.; Giacovazzo,
C.; Guagliardi, A.; Grazia, A.; Moliterni, G.; Polidori, G.; Spagna, R. J.
Appl. Crystallogr. 1999, 32, 115-119.
(24) Betteridge, P. W.; Carruthers, J. R.; Cooper, R. I.; Prout, K.; Watkin, D. J.
J. Appl. Crystallogr. 2003, 36, 1487-1487.
(25) Rheiner, P. B.; Seebach, D. Chem.-Eur. J. 1999, 5, 3221-3236.
(26) Nierengarten, J.-F.; Felder, D.; Nicoud, J.-F. Tetrahedron Lett. 1999, 40,
269-272.
Imaging the First- and Second-Generation Dendrons 3
and 6. Good quality and extensive self-organized monolayers
of 3 were obtained upon allowing solutions in volatile solvents
to evaporate under ambient conditions. Although some regions
of multilayers and apparently amorphous material are obtained,
this method of solution casting has, in our hands, proved to be
(27) Felder, D.; Nava, M. G.; Carreon, M. D. P.; Eckert, J.-F.; Luccisano, M.;
Schall, C.; Masson, P.; Gallani, J.-L.; Heinrich, B.; Guillon, D.; Nieren-
garten, J.-F. HelV. Chim. Acta 2002, 85, 288-319.
(28) Vo¨gtle, F.; Plevoets, M.; Nieger, M.; Azzelini, G. C.; Credi, A.; De Cola,
L.; De Marchis, V.; Venturi, M.; Balzani, V. J. Am. Chem. Soc. 1999,
121, 6290-6298.
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Analysis of Self-Organized Monolayers with STM
A R T I C L E S
the atomic level. With such weakly physisorbed molecules, very
low tunneling currents have to be used in order not to destroy
the self-organized monolayers. Despite this, we obtained
remarkably high-resolution images.
We regularly observed these two sets of three domains with
a reproducible small angle relationship between the sets of 6.5°
(Figure 4a). In the high-resolution image in Figure 4a, the two
peripheral benzyl groups of molecule 3 appear as regions of
highest intensity, consistent with the occupied frontier orbitals
being localized on these sites. The contrast in STM images of
organic molecules has often been successfully compared to the
frontier orbitals, either the HOMO or LUMO, according to the
polarity of the applied potential.30,31 Semiempirical calculations
at the PM3 level32 confirmed that the highest filled orbitals of
3 are located on the benzyl substituents and extend to the oxygen
atoms. The occupied orbitals localized on the central bpy unit
have a slightly lower energy. In the STM images of 3, the
bipyridine rings are harder to identify than the benzyl groups.
A detailed analysis is described later in this article and allows
a clear identification of the molecular conformation. Parts b and
c of Figure 4 were obtained by averaging a 10 nm × 10 nm
window over 121 and 104 positions for the left and right
domains shown in Figure 4a, respectively. STM image appear-
ance is dependent on different scanning parameters, tips, and
orientation relative to the scanning direction. Indeed, a com-
parison of Figures 3 and 4 shows differences in resolution. This
is due to a different tip and a difference in the orientation of
the molecules, which only becomes apparent when the images
are examined in detail. Differences between parts b and c of
Figure 4 cannot be a consequence of instrumental technique
since the two figures are enlargements of the same image. Two
differences between parts b and c of Figure 4 are apparent: (i)
the alignment of the individual molecules within the rows and
(ii) different “internal” structure of the molecules. We can
quantify these differences by measuring an angle θ that is the
internal angle between two lines defined by connecting the two
benzyl groups (i.e., seen as the bright spots) of one molecule
and connecting two benzyl groups of adjacent molecules (see
parts b and c of Figure 4). We discuss these differences in terms
of anti,syn and anti,anti conformations of molecules of 3 later
in the article.
Figure 2. STM image of a monolayer of 3 on HOPG formed (a) from
dichloromethane solution (80 nm × 80 nm, Ub ) -700 mV, It ) 8 pA)
and (b) from hexane solution (80 nm × 80 nm, Ub ) -700 mV, It ) 10
pA). In image (a), different small domains can be seen; image (b) shows
part of a domain extending over more than 500 nm × 500 nm.
Figure 3. STM image of a monolayer of 3 formed from hexane solution
on HOPG (10 nm × 10 nm, averaged over 41 positions, Ub ) -900 mV,
It ) 40 pA). The benzyl groups have the highest intensity. Molecular models
of 3 showing the best-fit conformation are also shown; this is discussed
later in the article.
a reliable and reproducible method for obtaining monolayers
with large homogeneous domains. In STM images of self-
organized monolayers of molecule 3 (Figure 2a), we observed
multiple domain formation with a lamellar arrangement. The
individual domain sizes ranged from some 50 nm × 50 nm up
to 1000 nm × 1000 nm depending on the exact preparation
conditions. While on first sight the orientations of domains in
Figure 2a appear to reflect the threefold symmetry of the frontier
orbitals of the graphite surface (the sixfold symmetry of single
graphite layer is reduced to threefold as a consequence of
A-B-A stacking of the layers in R-graphite29), a detailed
analysis reveals the additional presence of small angle domain
boundaries (see the following discussion).
Evaporation of solutions of the second-generation compound
6 also gave good quality monolayers in which multiple domains
were observed. Figure 5 depicts the STM images of two domains
showing a slightly different arrangement of the rows and
different internal structure of the molecules. For these images,
the averaging analysis of the upper and lower domains in Figure
5a was performed over 62 and 44 positions, respectively,
allowing the identification of single molecules almost without
further interpretation. In the upper domain (Figure 5b), the
molecule is stretched in an X-like configuration. However, in
the lower domain (Figure 5c), molecule 6 clearly adopts a
different conformation on the graphite surface. In contrast to 3,
the second-generation compound 6 does not form lamellar
stripes. The bipyridine rings of molecule 6 are imaged with
We prepared these multiple domains from hexane and
dichloromethane solutions. Those from hexane were typically
and reproducibly of much larger size than those from dichlo-
romethane (Figure 2). This is consistent with a slower rate of
evaporation of hexane (bp 342 K, ∆vapH° ) 31.56 kJ mol-1
)
than dichloromethane (bp 313 K, ∆vapH° ) 28.82 kJ mol-1).
Figure 3 shows an enlargement of a monolayer of 3 obtained
from hexane solution. The high-resolution images that we were
able to obtain at room temperature in air (for example, that
shown in Figure 3) display submolecular resolution approaching
(30) Miura, A.; Chen, Z.; Uji-I, H.; De Feyter, S.; Zdanowska, M.; Jonkheijm,
P.; Schenning, A. P. H. J.; Meijer, E. W.; Wu¨rthner, F.; De Schryver, F.
C. J. Am. Chem. Soc. 2003, 125, 14968-14969.
(31) Qiu, X.; Wang, C.; Yin, S.; Zeng, Q.; Xu, B.; Bai C. J. Phys. Chem. B
2000, 104, 3570-3574.
(29) Lim, R.; Li, J.; Li, S. F. Y.; Feng, Z.; Valiyaveettil, S. Langmuir 2000, 16,
7023-7030.
(32) Calculations were made using the PM3 implementation in Spartan ‘04,
Wavefunction Inc.: Irvine, CA, 2003.
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A R T I C L E S
Scherer et al.
Figure 4. (a) STM images of two domains of monolayers of 3 on HOPG. The angle difference between the two domains is 6.5°. (b) and (c) Expanded
images (10 nm × 10 nm) of the left and right domains, respectively, of (a). Panel (b) corresponds to conformation anti,anti-3 (θ ) 55°), and panel (c)
corresponds to conformation anti,syn-3 (θ ) 38°) (see Chart 4 and later discussion). Scan parameters: 50 nm × 50 nm, Ub ) -1111 mV, It ) 15 pA.
Figure 5. (a) STM images of two domains of monolayers of 6 on HOPG (50 nm × 50 nm. (b) and (c) Expanded images (10 nm × 10 nm) of the upper
and lower domains, respectively, of (a). Scan parameters: Ub ) -1111 mV, It ) 15 pA.
higher contrast than those in molecule 3, and this allows a
straightforward interpretation of the structure of monolayers of
6 since all of the aromatic rings are directly observed.
square planar PdN4 and PdN2Cl2 units, respectively, which are
expected to interact optimally with the graphite surface.
However, treatment of a graphite surface with hexane solutions
of either of these complexes did not result in the formation of
ordered monolayers. Treating the monolayers of 3 with aqueous
acidic solutions (0.1 M HCl or 0.1 M AcOH) did not influence
the structure of the monolayers, which were imaged unchanged
after this treatment. However, passing gaseous HCl over the
monolayers resulted in a conformational change of all molecules
in small domains, and the formation of a highly ordered structure
with new periodic properties (Figure 6). The molecules are no
longer stacked side by side in a trans conformation, forming
lamellar stripes as in Figure 3. In contrast, the domains in the
protonated system are built from large X-like structures. In many
hundreds of recorded images of compound 3, these X-shaped
structures have never been observed, and we are confident that
they are a result of the treatment with HCl. The smaller size of
the domains makes them less stable for imaging. Drift in the
images is frequently observed, and this makes it impossible to
record images of the protonated monolayer of the quality used
for the conformational analysis of 3.
Switching Molecular Conformation. Large dendritic sub-
stituents are expected to impose a significant mechanical barrier
to conformational change involving the bpy unit when the
molecule is constrained on a surface. In particular, the confor-
mational change from the trans arrangement of nitrogen atoms
in a free ligand to the cis conformation within a coordinated
ligand is expected to have a high activation barrier associated
with both the mechanical motion of the dendritic substituents
and the necessary involvement of nonplanar bpy which cannot
lie flat on the surface during the conformational change. Despite
this, we attempted to address the conformation of the bpy
domain of molecule 3 through interaction with metal ions or
protons, both of which result in the formation of cis species
under solution and normal solid-state conditions.33 Treating the
adsorbed monolayer of 3 with dilute aqueous solutions of metal
salts (copper(II) sulfate or palladium(II) acetate) destroyed the
ordered domains. After such treatment, no organized monolayers
were observed with STM. The complexes [Pd(3)2][PF6]2 and
[Pd(3)Cl2] were prepared from 3. These complexes contain
Although the protonation itself cannot be seen directly, the
conformational change after treatment with HCl is dramatic and
(33) Constable, E. C. AdV. Inorg. Chem. 1989, 34, 1-63.
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4038 J. AM. CHEM. SOC. VOL. 127, NO. 11, 2005

Analysis of Self-Organized Monolayers with STM
A R T I C L E S
Figure 6. STM image of a monolayer of 3 on HOPG after treatment with
gaseous HCl (80 nm × 80 nm, Ub ) -800 mV, It ) 9 pA). The ragged
line running from top to bottom of the figure is a graphite step edge.
characteristic. Qualitative modeling and the known protonation
chemistry of 2,2′-bipyridine are consistent with the molecule
adopting a cis conformation. Even after treatment with gaseous
HCl, some large domains in the monolayers retain a lamellar
structure similar to that observed for unprotonated 3. It is
proposed that the cis domains are formed in a concerted
conformational change in which a number of molecules in a
domain change simultaneously. This conclusion follows from
observations that (i) only small domains were observed and (ii)
no domains showed mixtures of both cis and trans conforma-
tions. At this stage, we cannot speculate on the stoichiometry
of the protonated species, but offer these preliminary results as
an indication of the use of the STM to monitor chemical changes
within a self-organized monolayer.
Figure 7. Process of data analysis of a measurement of a domain containing
3 after (a) flattening and (b) enlargement and averaging over 46 positions.
Panel (c) shows overlaid unit cells and (d) shows a contour plot of (b).
Scale: (a) 30 nm × 30 nm; (b)-(d) 10 nm × 10 nm.
Data Analysis and Discussion
While the analysis of pattern formation in STM images of
self-organized monolayers is at a very advanced stage,4-6 studies
including conformational analysis of flexible molecules are still
scarce.34-37 There are several factors responsible for this.
Usually, very high resolution images are necessary to identify
individual conformations, but these are often difficult to obtain
with highly flexible molecules. Additionally, molecules with
conformational freedom have to be designed carefully, if they
are to form self-organized monolayers at all. Last, but not least,
most high-resolution STM studies are still performed in ultrahigh
vacuum with sublimed molecules; this is often impossible for
large, flexible molecules. Many researchers refrain from mea-
suring in air at room temperature because there are many more
uncertainties, impurities, and thermal motion associated with
the surface molecules. Thus, it remains a challenge to obtain
high-resolution images under ambient conditions. The exclusion
of measurement artifacts, errors due to drift, and averaging
artifacts is very important. Also, reproducibility of experimental
results is essential, as measurements of single events and
molecules sometimes show noise (irregularities, etc.) and
impurities on the same scale as the measured molecules. Errors
Figure 8. (a) and (b) Images from Figure 4, parts b and c, respectively,
with their corresponding unit cells.
due to thermal drift of the apparatus can be excluded by carefully
checking follow-up scans of the opposite slow scanning
direction. Any compression or elongation due to drift is then
easily recognized. A general observation in the STM images
of our systems was that the domains were present from the first
scan lines and remained very stable over time; no bleeding or
migration was observed. Even though the monolayers were
stable over time, they were very easily disturbed by scanning
with tunneling currents above some 10 pA. In rare cases, a
growth of domains was observed at the cost of unordered phases.
Only measurements that meet the rigorous requirements listed
above could be used for a successful conformational analysis.
We next describe in detail the process of conformational
analysis for one example. Figure 7a shows the flattened (but
otherwise raw) measurement of a monolayer of 3 on HOPG.
The application of an averaging procedure (for details, see the
Experimental Section) further reduces the random noise. Figure
7b shows an enlargement from Figure 7a that has been averaged
(34) Jung, T. A.; Schlittler, R. R.; Gimzewski, J. K. Nature 1997, 386, 696-
698.
(35) Kim, K.; Plass, K. E.; Matzger, A. J. Langmuir 2003, 19, 7149-7152.
(36) Plass, K. E.; Kim, K.; Matzger, A. J. J. Am. Chem. Soc. 2004, 126, 9042-
9053.
(37) Schuurmans, N.; Uji-I, H.; Mamdouh, W.; De Schryver, F. C.; Feringa, B.
L.; van Esch, J.; De Feyter, S. J. Am. Chem. Soc. 2004, 126, 13884-
13885.
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A R T I C L E S
Scherer et al.
Figure 9. Molecular models of monolayers on graphite corresponding to the images shown in (a) Figure 4b, (b) Figure 4c, and (c) Figure 3. In the representations
in this figure, the orientation of the graphite substrate is the same. The two-dimensional packing density is the same within experimental error.
Chart 5. Two Conformations of Compound 3 Observed in the
proposed molecular arrangements. The unit cell dimensions
(defined by the cell lengths a and b and the acute angle, R, in
STM Study
the rhombus) are a ) 3.8 nm, b ) 1.1 nm, R ) 51° (Figures 8a
and 9a), a ) 3.8 nm, b ) 1.1 nm, R ) 52° (Figures 8b and 9b),
and a ) 4.1 nm, b ) 1.2 nm, R ) 38° (Figures 7c and 9c).
This gives unit cell areas of 3.2, 3.3, and 3.0 nm2, respectively.
The alkane chains were not modeled, as they are not sufficiently
resolved to be assigned with certainty. Nevertheless, the spacing
between the molecules is exactly the right width for an
arrangement in which all the octyl chains are in an extended
conformation. It is assumed that they form an interdigitated
pattern, thereby optimizing the two-dimensional crystallization
energy. Only two of the possible conformations were found,
but the anti,syn conformation at each B ring (Charts 1 and 4)
was found at each side of molecule 3 as also found in the three-
dimensional single-crystal X-ray structure of 8. It is noteworthy
that although the conformations and the molecular arrangements
in Figure 9a-c are different, the two-dimensional packing
density per molecule is roughly the same. In the domain of
over 46 positions. The unit cell of the molecular layer can be
deduced from a Fourier spectrum of an averaged image. One
possible unit cell of the above measurement is shown in Figure
7c. The averaged image is printed with different contrast
Figure 9c, the molecules are tilted much more along the row of
settings, and if needed, contour plots (Figure 7d) are printed as
molecules than for the other two domains shown.
well. Molecular models of all relevant conformations were
analyzed using computer graphics. The Cbpy-O-C and Cbenzyl
-
The STM imaging measurements for the second-generation
compound 6 proved to be more difficult than those of 3. The
monolayers of 6 are less stable than those of 3, and it is more
challenging to obtain images with a resolution as high as for
the first-generation 3. Nevertheless, most conformations could
easily be excluded, and the conformation could be assigned with
a high certainty. Figure 10 shows the observed molecular
arrangements and conformations of 6 in the two different
domains shown in Figure 5. In one domain (Figure 10a), the
bpy unit is in a trans conformation (with respect to pyridine
rings) and an anti,syn conformation (defined in Chart 4). The
outer generation of benzyl groups attached to the inner-
generation anti-benzyl group adopts an anti,syn conformation;
the outer generation of benzyl groups attached to the syn-benzyl
ring exhibits a syn,syn conformation (see Chart 4). In the other
domain (Figure 10b), the benzyl groups attached to the bpy
domain adopt an anti,anti conformation, while each pair of outer-
generation benzyl groups adopts a syn,syn arrangement (Chart
4). At present, we are unable to say that these are the only
conformations that are present in the monolayers of 6.
O-C bond angles were constrained to the values observed
crystallographically for compound 8 (117°) to reflect the
π-component in the Caromatic-O bond. The models were overlaid
on the STM images to find the best fits. Molecular orbital
calculations were run on molecule 3 in different conformations
to confirm that there was no significant change in either
composition or relative ordering of the highest filled orbitals.
Following this analysis procedure, the unit cells, the molecular
ordering, and the molecular conformation within the domains
in Figures 3 and 4b,c could be identified. As the alkyl chains
are insulating, and therefore hardly seen in STM images,38,39
the following discussion is focused on the syn and anti
conformations of the ArOCH2Ar groups. Two different con-
formations of 3 could be determined, and these are shown in
Chart 5. In addition to this, the molecules were found in different
assembly patterns. Figures 7c and 8a,b show the averaged
images with their respective unit cells, and Figure 9 shows the
(38) Rabe, J. P.; Buchholz, S. Science 1991, 253, 424-427.
(39) Cai, Y.; Bernasek, S. L. J. Am. Chem. Soc. 2004, 126, 14234-14238.
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Analysis of Self-Organized Monolayers with STM
A R T I C L E S
of the molecule. The near-atomic resolution allows us to clearly
assign two conformers. Both of them spontaneously and rapidly
form molecular domains under ambient conditions. Within a
molecular domain, only one conformer is present and domains
of different conformers were observed side by side. No
preference for one conformer was observed. Higher-generation
dendrons attached to the bpy also showed at least two different
conformers in self-organized monolayers.
Acknowledgment. This work was supported by the Swiss
National Science Foundation under program NRP 47, the
Portlandcementfabrik Laufen, and the University of Basel. We
thank Prof. Dr. H.-J. Gu¨ntherodt for his continuous support and
encouragement.
Figure 10. Expanded images (10 nm × 10 nm) of (a) the upper and (b)
the lower domains, respectively, of Figure 5a. Overlaying the molecular
structures confirms the two different conformations.
Supporting Information Available: Crystal data for com-
pound 8 (CIF). This material is available free of charge via the
Internet at http://pubs.acs.org.
Conclusions
We have shown that deposition of a dendritic wedge
functionalized ligand on a HOPG surface results in the formation
of well-defined monolayers exhibiting different conformations
JA043638+
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