Nanografting versus Solution Self-Assembly of r,ω-Alkanedithiols on
Au(111) Investigated by AFM
Jing-Jiang Yu,† Johnpeter N. Ngunjiri,‡ Algernon T. Kelley,‡ and Jayne C. Garno*,‡
Nanotechnology Measurements DiVision, Agilent Technologies, Inc. 4330 West Chandler BouleVard,
Chandler, Arizona 85226, and Chemistry Department, Louisiana State UniVersity and the Center for
Biomodular Multi-Scale Systems, 232 Choppin Hall, Baton Rouge, Louisiana 70803
ReceiVed July 13, 2008. ReVised Manuscript ReceiVed August 18, 2008
The solution self-assembly of R,ω-alkanedithiols onto Au(111) was investigated using atomic force microscopy
(AFM). A heterogeneous surface morphology is apparent for 1,8-octanedithiol and for 1,9-nonanedithiol self-assembled
monolayers (SAMs) prepared by solution immersion as compared to methyl-terminated n-alkanethiols. Local views
from AFM images reveal a layer of mixed molecular orientations for R,ω-alkanedithiols, which evidence surface
structures with heights corresponding to both lying-down and standing-up orientations. For dithiol SAMs prepared
by solution self-assembly, the majority of R,ω-alkanedithiol molecules chemisorb with both thiol end groups bound
to the Au(111) surface with the backbone of the alkane chain aligned parallel to the surface. However, AFM images
disclose that there are also islands of standing molecules scattered throughout the surface. To measure the thickness
of R,ω-alkanedithiol SAMs with angstrom sensitivity, methyl-terminated n-alkanethiols with known dimensions were
used as molecular rulers. Under conditions of spatially constrained self-assembly, nanopatterns of R,ω-alkanedithiols
written by nanografting formed monolayers with heights corresponding to an upright configuration.
Introduction
Methyl-terminated n-alkanethiols have been widely studied
and are known to reproducibly form well-ordered commensurate
monolayers for a range of experimental conditions (e.g.,
concentration, immersion intervals). On the other hand, self-
assembled monolayers (SAMs) of R,ω-alkanedithiols have not
been as extensively characterized and there is considerable debate
about whether one or both sulfur atoms of dithiols bind to gold
surfaces, and if intermolecular S-S bonds are formed to produce
multilayer films.1 For solution self-assembly, there is also a
question of whether the lying-down phases rearrange into an
upright monolayer over time for R,ω-alkanedithiols. When
preparing SAMs of R,ω-alkanedithiols, the resulting surface
morphology of the films is far less reproducible than for methyl-
terminated SAMs because alkanedithiols are more sensitive to
sample preparation conditions such as the duration of substrate
immersion, shelf life of the parent stock, nature of the solvent,
oxidation processes and solution concentration.
Monolayers of n-alkanethiols on coinage metal surfaces such
as gold have promising applications as lithographic resists2-6
and chemical/biological sensors.7-13 Upon immersion of a gold
substrate into a thiol solution, the -SH end groups of methyl-
terminated n-alkanethiol molecules bind spontaneously to metal
surfaces by chemisorption to form densely packed monolay-
ers.14-16 The solution self-assembly of n-alkanethiol SAMs on
bare gold is reported to occur in two phases. A mobile physisorbed
phase forms when n-alkanethiol molecules initially make contact
with the surface, in which the backbone of the molecules is
oriented parallel to the plane of the substrate in a lying-down
configuration. However, over time the n-alkanethiol molecules
rearrange into a standing orientation with the molecular backbone
tilted from surface normal. The mature crystalline phase forms
an enthalpy favorable, close-packed commensurate (
3 ×

3)R30° configuration with respect to the Au(111) lattice.15,17,18
Methyl-terminated n-alkanethiols form SAMs with a single thiol
end group chemisorbed to Au(111) with the all-trans carbon
chains oriented in an upright configuration. According to previous
studies, the alkyl chains of n-alkanethiol SAMs tilt approximately
30° with respect to surface normal.19-25 Thiol end groups of
SAMs are considered to bind to the triple hollow sites of the
Au(111) lattice by chemisorption. The carbon chains are capped
with a headgroup (esters, alkyls, hydroxyls, carboxylates, amides,
etc.) presented at the surface. The length of the alkane chain and
* To whom correspondence should be addressed. Phone: 225-578-8942.
Fax: 225-578 3458. E-mail: jgarno@lsu.edu.
† Agilent Technologies, Inc.
‡ Louisiana State University.
(1) Liang, J.; Rosa, L. G.; Scoles, G. J. Phys. Chem. C 2007, 111, 17275–
17284.
(2) Childs, W. R.; Nuzzo, R. G. Langmuir 2005, 21, 195–202.
(3) Weimann, T.; Geyer, W.; Hinze, P.; Stadler, V.; Eck, W.; Golzhauser, A.
Microelectron. Eng. 2001, 57-8, 903–907.
(4) Gorman, C. B.; Biebuyck, H. A.; Whitesides, G. M. Chem. Mater. 1995,
7, 252–254.
(5) Sondaghuethorst, J. A. M.; Vanhelleputte, H. R. J.; Fokkink, L. G. J. Appl.
Phys. Lett. 1994, 64, 285–287.
(6) Xia, Y.; Whitesides, G. M. Angew. Chem., Int. Ed. 1998, 37, 550–575.
(7) Schreiber, F. J. Phys.: Condens. Matter 2004, 16, R881-R900.
(8) Flink, S.; van Veggel, F.; Reinhoudt, D. N. AdV. Mater. 2000, 12, 1315–
1328.
(9) Mrksich, M.; Whitesides, G. M. Trends Biotechnol. 1995, 13, 228–235.
(10) Pena, D. J.; Raphael, M. P.; Byers, J. M. Langmuir 2003, 19, 9028–9032.
(11) Crooks, R. M.; Ricco, A. J. Acc. Chem. Res. 1998, 31, 219–227.
(12) Chaki, N. K.; Vijayamohanan, K. Biosens. Bioelectron. 2002, 17, 1–12.
(13) Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides, G. M.
Chem. ReV. 2005, 105, 1103–1169.
(14) Xu, S.; Cruchon-Dupeyrat, S.; Garno, J. C.; Liu, G.-Y. J. Chem. Phys.
1998, 108, 5002–5012.
(15) Ulman, A. Chem. ReV. 1996, 96, 1533–1554.
(16) Schreiber, F. Prog. Surf. Sci. 2000, 65, 151–257.
(17) Poirier, G. E.; Pylant, E. D. Science 1996, 272, 1145–1148.
(18) Poirier, G. E. Chem. ReV. 1997, 97, 1117–1127.
(19) Fenter, P.; Eberhardt, A.; Liang, K. S.; Eisenberger, P. J. Chem. Phys.
1997, 106, 1600–1608.
(20) Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem.
Soc. 1987, 109, 3559–3568.
(21) Nuzzo, R. G.; Allara, D. L. J. Am. Chem. Soc. 1983, 105, 4481–4483.
(22) Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109,
2358–2368.
(23) Fenter, P.; Eisenberger, P.; Liang, K. S. Phys. ReV. Lett. 1993, 70, 2447–
2450.
(24) Nuzzo, R. G.; Dubois, L. H.; Allara, D. L. J. Am. Chem. Soc. 1990, 112,
558–569.
(25) Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93,
767–773.
11661Langmuir 2008, 24, 11661-11668
10.1021/la802235c CCC: $40.75  2008 American Chemical Society
Published on Web 09/27/2008

the nature of the SAM headgroup largely determine the surface
properties such as wettability.26-28 Readers are directed to
previous reports for details regarding synthesis, preparation, and
characterization of n-alkanethiol SAMs.29 Since methyl-
terminated n-alkanethiols can be prepared reproducibly with
predictable, well-defined surface structures, nanografted patterns
of n-alkanethiols furnish a reliable height reference for nanoscale
measurements of film thickness.
In contrast to methyl-terminated SAMs, monolayers produced
from R,ω-alkanedithiols are not densely packed and are less
ordered. Approaches which most commonly have been applied
to prepareR,ω-alkanedithiol SAMs are vapor phase deposition30
and solution immersion.31,32 Previous investigations provide
conflicting reports of either a predominance of lying-down or
standing-up conformations for alkanedithiols.1 A number of
ultrahigh vacuum scanning tunneling microscopy (UHV-STM)
studies reveal that n-alkanedithiol SAMs prepared from vapor
phase deposition or from immersion in ethanolic solutions
predominantly assemble with a lying-down configuration on
gold.30,33,34
Dithiol SAMs are promising materials for molecular electronic
devices35-38 or can provide linker groups for attaching nano-
particles to surfaces.39-47 For certain applications, a standing-up
configuration of the molecules of R,ω-alkanedithiols SAMs is
compulsory to present a thiol at the surface that is available for
further chemical reactions. The upright orientation offers a route
to form stable multilayer structures with S-S bonds for interlayer
covalent linkages. For example, catalysis or oxidation reactions
with thiols will produce a sulfonate-terminated surface that can
react to form hybrid multilayer assemblies.48-50 Considerable
research effort has been invested to gain better control for
constructing thiol-terminated surfaces with the favored standing
conformation. One reported approach used alkanedithiols with
a rigid molecular backbone containing either aromatic rings or
double/triple bonds.51-53 The inflexible nature of conjugated
structures prohibits the twisting of the backbone and thus makes
it difficult for both ends of dithiol molecules to have good contact
or to simultaneously interact with the gold surface.
A second approach for preparing thiol-terminated surfaces
was to induce exchange reactions by soaking a previously formed
SAM in an alkanedithiol solution. For this strategy, a standing-
up configuration for R,ω-alkanedithiols is obtained through a
replacement reaction that occurs with a previously formed
n-alkanethiol SAM after immersion in a dithiol solution.39,54-56
Exchange reactions produce domains of upright dithiols on gold
because the matrix n-alkanethiol SAMs can sterically prevent
the incoming molecules from lying-down to form a side-on
configuration. For exchange reactions, the distribution of dithiols
occurs randomly throughout the surface. Exchange reactions
initiate preferentially at sites of surface defects, such as at step
edges and domain boundaries.54,57 Therefore, this approach does
not provide precise control of the location of dithiols in the
resulting SAM.
A third approach for generating surfaces with thiol head groups,
applies a stepwise protection/deprotection strategy to prepare
SAMs.32,35,58-61 One of the thiol groups of the molecule is
protected by thioacetyl or thioester groups. After the organ-
othiolate adlayer is formed, the protected thiolate group can be
restored under controlled conditions, such as by immersion in
a sodium hydroxide solution. This strategy requires delicate
control of acid/base deprotection chemistry and involves extra
chemical steps for sample preparation.
In these investigations, we demonstrate an AFM-based
nanofabrication strategy for writing nanopatterns of R,ω-
alkanedithiol SAMs directly in an upright orientation using
nanografting. The nanografting approach bypasses the formation
of an intermediate (lying-down) phase during spatially constrained
self-assembly to directly produce an upright molecular config-
uration.62 Precise control of the placement and nanopattern
geometry for presenting thiol head groups at surfaces can be
achieved by nanografting. With nanografting, surface assembly
(26) Ulman, A.; Evans, S. D.; Shnidman, Y.; Sharma, R.; Eilers, J. E. AdV.
Colloid Interface Sci. 1992, 39, 175–224.
(27) Bain, C. D.; Troughton, E. B.; Tao, Y. T.; Evall, J.; Whitesides, G. M.;
Nuzzo, R. G. J. Am. Chem. Soc. 1989, 111, 321–335.
(28) Laibinis, P. E.; Whitesides, G. M.; Allara, D. L.; Tao, Y. T.; Parikh, A. N.;
Nuzzo, R. G. J. Am. Chem. Soc. 1991, 113, 7152–7167.
(29) Ryu, S.; Schatz, G. J. Am. Chem. Soc. 2006, 128, 11563–11573.
(30) Leung, T. Y. B.; Gerstenberg, M. C.; Lavrich, D. J.; Scoles, G.; Schreiber,
F.; Poirier, G. E. Langmuir 2000, 16, 549–561.
(31) Esplandiu, M. J.; Carot, M. L.; Cometto, F. P.; Macagno, V. A.; Patrito,
E. M. Surf. Sci. 2006, 600, 155–172.
(32) Niklewski, A.; Azzam, W.; Strunskus, T.; Fischer, R. A.; Woll, C.Langmuir
2004, 20, 8620–8624.
(33) Kobayashi, K.; Yamada, H.; Horiuchi, T.; Matsushige, K. Appl. Surf. Sci.
1999, 145, 435–438.
(34) Kobayashi, K.; Umemura, J.; Horiuchi, T.; Yamada, H.; Matsushige, K.
Jpn J. Appl. Phys 1998, 37, L297–L299.
(35) Tour, J. M.; Jones, L.; Pearson, D. L.; Lamba, J. J. S.; Burgin, T. P.;
Whitesides, G. M.; Allara, D. L.; Parikh, A. N.; Atre, S. J. Am. Chem. Soc. 1995,
117, 9529–9534.
(36) Engelkes, V. B.; Beebe, J. M.; Frisbie, C. D. J. Am. Chem. Soc. 2004,
126, 14287–14296.
(37) Blum, A. S.; Yang, J. C.; Shashidhar, R.; Ratna, B. Appl. Phys. Lett. 2003,
82, 3322–3324.
(38) Adams, D. M.; Brus, L.; Chidsey, C. E. D.; Creager, S.; Creutz, C.;
Kagan, C. R.; Kamat, P. V.; Lieberman, M.; Lindsay, S.; Marcus, R. A.; Metzger,
R. M.; Michel-Beyerle, M. E.; Miller, J. R.; Newton, M. D.; Rolison, D. R.;
Sankey, O.; Schanze, K. S.; Yardley, J.; Zhu, X. Y. J. Phys. Chem. B 2003, 107,
6668–6697.
(39) Huang, W.; Masuda, G.; Maeda, S.; Tanaka, H.; Ogawa, T. Chem. Eur.
J. 2005, 12, 607–619.
(40) Vandamme, N.; Snauwaert, J.; Janssens, E.; Vandeweert, E.; Lievens, P.;
Van Haesendonck, C. Surf. Sci. 2004, 558, 57–64.
(41) Yang, Y. C.; Yau, S. L.; Lee, Y. L. J. Am. Chem. Soc. 2006, 128, 3677–
3682.
(42) Noda, H.; Tai, Y.; Shaporenko, A.; Grunze, M.; Zharnikov, M. J. Phys.
Chem. B 2005, 109, 22371–22376.
(43) Sugawara, T. J. Synth. Org. Chem. Jpn. 2004, 62, 447–458.
(44) Joseph, Y.; Besnard, I.; Rosenberger, M.; Guse, B.; Nothofer, H. G.;
Wessels, J. M.; Wild, U.; Knop-Gericke, A.; Su, D. S.; Schlogl, R.; Yasuda, A.;
Vossmeyer, T. J. Phys. Chem. B 2003, 107, 7406–7413.
(45) Fendler, J. H. Chem. Mater. 2001, 13, 3196–3210.
(46) Nakanishi, T.; Ohtani, B.; Uosaki, K. J. Phys. Chem. B 1998, 102, 1571–
1577.
(47) Smith, R. K.; Nanayakkara, S. U.; Woehrle, G. H.; Pearl, T. P.; Blake,
M. M.; Hutchison, J. E.; Weiss, P. S. J. Am. Chem. Soc. 2006, 128, 9266–9267.
(48) Brower, T. L.; Garno, J. C.; Ulman, A.; Liu, G.-Y.; Yan, C.; Golzhauser,
A.; Grunze, M. Langmuir 2002, 18, 6207–6216.
(49) Kohli, P.; Taylor, K. K.; Harris, J. J.; Blanchard, G. J. J. Am. Chem. Soc.
1998, 120, 11962–11968.
(50) Joo, S. W.; Han, S. W.; Kim, K. Langmuir 2000, 16, 5391–5396.
(51) Haiss, W.; vanZalinge, H.; Hobenreich, H.; Bethell, D.; Schiffrin, D. J.;
Higgins, S. J.; Nichols, R. J. Langmuir 2004, 20, 7694–7702.
(52) Jiang, W.; Zhitenev, N.; Bao, Z.; Meng, H.; Abusch-Magder, D.; Tennant,
D.; Garfunkel, E. Langmuir 2005, 21, 8751–8757.
(53) Tai, Y.; Shaporenko, A.; Rong, H. T.; Buck, M.; Eck, W.; Grunze, M.;
Zharnikov, M. J. Phys. Chem. B 2004, 108, 16806–16810.
(54) Fuchs, D. J.; Weiss, P. S. Nanotechnology 2007, 18, 1–7.
(55) Henderson, J. I.; Feng, S.; Ferrence, G. M.; Bein, T.; Kubiak, C. P. Inorg.
Chim. Acta 1996, 242, 115–124.
(56) Wakamatsu, S.; Nakada, J.; Fujii, S.; Akiba, U.; Fujihira, M. Ultrami-
croscopy 2005, 105, 26–31.
(57) Dunbar, T. D.; Cygan, M. T.; Bumm, L. A.; McCarty, G. S.; Burgin, T. P.;
Reinerth, W. A.; Jones, I., L.; Jackiw, J. J.; Tour, J. M.; Weiss, P. S.; Allara, D. L.
J. Phys. Chem. B 2000, 104, 4880–4893.
(58) Badin, M. G.; Bashir, A.; Krakert, S.; Strunskus, T.; Terfort, A.; Woll,
C. Angew. Chem., Int. Ed. 2007, 46, 3762–3764.
(59) Lau, K. H. A.; Huang, C.; Yakovlev, N.; Chen, Z. K.; O’Shea, S. J.
Langmuir 2006, 22, 2968–2971.
(60) de Boer, B.; Meng, H.; Perepichka, D. F.; Zheng, J.; Frank, M. M.; Chabal,
Y. J.; Bao, Z. Langmuir 2003, 19, 4272–4284.
(61) Walzer, K.; Marx, E.; Greenham, N. C.; Less, R. J.; Raithby, P. R.;
Stokbro, K. J. Am. Chem. Soc. 2004, 126, 1229–1234.
(62) Xu, S.; Laibinis, P. E.; Liu, G.-Y. J. Am. Chem. Soc. 1998, 120, 9356–
9361.
11662 Langmuir, Vol. 24, No. 20, 2008 Yu et al.