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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, selfassembled 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 methylterminated 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 * To whom correspondence should be addressed. Phone: 225-578-8942. Fax: 225-578 3458. E-mail:
[email protected]. † 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.
substrate into a thiol solution, the -SH end groups of methylterminated n-alkanethiol molecules bind spontaneously to metal surfaces by chemisorption to form densely packed monolayers.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 (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.
10.1021/la802235c CCC: $40.75 2008 American Chemical Society Published on Web 09/27/2008
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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 methylterminated 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 prepare R,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 nanoparticles 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 (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.
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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 standingup 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 organothiolate 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,ωalkanedithiol 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 configuration.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 (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. Ultramicroscopy 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.
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follows a different reaction pathway due to the effects of spatial confinement.62 Very small areas of freshly exposed gold are produced by scanning with a high force applied to the AFM tip. The transient reaction environment is sufficiently small to prevent the molecules from assembling in a lying-down position. The transient uncovered regions along the track of the scanning tip are spatially confined by a passivating matrix n-alkanethiol monolayer. The confined area has dimensions less than the molecular length of the thiols, therefore the ink molecules in solution do not have sufficient room to assemble in a lying-down configuration. Thus, the initial lying-down phase is bypassed during nanografting and molecules assemble directly onto gold with the favored standing-up configuration.
Methods Materials. Reagents such as decanethiol, dodecanethiol, hexanethiol, 1,8-octanedithiol, 1,9-nonanedithiol and 2-butanol were purchased from Sigma Aldrich (St. Louis, MO) and used as received. 1,16-Hexadecanedithiol was obtained from Asemblon (Redmond, WA). Ethanol (200 proof) was purchased from Aaper Alcohol and Chemical Co. (Shelbyville, KY). Two types of atomically flat gold substrates were used for experiments. Flame-annealed gold-coated mica substrates with 150 nm gold films were obtained from Agilent Technologies, Inc. (Chandler, AZ). However, Figure 5 was produced using a template-stripped gold film.63,64 Preparation of Self-Assembled Monolayers. Monolayers of R,ωalkanedithiols or n-alkanethiols were prepared by immersion of Au(111)/mica substrates in ethanol or 2-butanol solutions (0.01 mM to 1 mM) for at least 12 h. Glassware used for preparing SAMs was cleaned in piranha solution and rinsed with deionized water followed by ethanol. To minimize photooxidation of SAMs, the containers were wrapped with aluminum foil and stored in the dark at room temperature. The surfaces were rinsed with ethanol and then immersed in clean ethanol solutions within a liquid cell for AFM imaging. The shelf life of the parent stock is of consideration when preparing R,ω-alkanedithiols; to minimize oxidation the stock reagents were used within 6 months of purchase. Atomic Force Microscopy. Topography and friction images were acquired using a model 5500 AFM/SPM operated with Picoscan v5.3.3 software, from Agilent Technologies, Inc. (Chandler, AZ). Picolith beta version 0.4.5 software was used to position and control the movement of the AFM tip for nanografting. Gwyddion software was used for image processing, which is freely available on the Internet (http://gwyddion.net/). The instrument has an opticaldeflection configuration in which the tip is mounted on the piezotube scanner for imaging. Images were obtained using contact-mode AFM in ethanol. Oxide-sharpened silicon nitride probes (MSCT-AUHW) with an average force constant of 0.1 or 0.5 N/m were used for imaging and writing nanopatterns (Veeco Probe Store, Santa Barbara, CA). Image Analysis. Estimates of surface coverage were obtained using UTHSCA Image Tool.65 The AFM images were converted to 24-bit grayscale bitmaps and a threshold value was selected visually for conversion to black and white pixels. The relative percentage of colored pixels provided an estimate of surface coverage. Nanografting and Nanoshaving. Nanografting was applied to write nanopatterns of n-alkanethiol and R,ω-alkanedithiol SAMs (Figure 1).66,67 The imaging media contains fresh “ink” molecules for writing in situ. Both the AFM tip and sample are submerged in dilute ethanolic solutions containing the ink molecules selected for writing. First, the surface is characterized under low force (less than (63) Wagner, P.; Zaugg, F.; Kernen, P.; Hegner, M.; Semenza, G. J. Vac. Sci. Technol. B 1996, 14, 1466–1471. (64) Hegner, M.; Wagner, P.; Semenza, G. Surf. Sci. 1993, 291, 39–46. (65) Wilcox, D.; Dove, B.; McDavid, D.; Greer, D. UTHSCSA Image Tool for Windows Version 3.00, The University of Texas Health Science Center San Antonio, 1995-2002. (66) Xu, S.; Liu, G.-Y. Langmuir 1997, 13, 127–129. (67) Xu, S.; Miller, S.; Laibinis, P. E.; Liu, G.-Y. Langmuir 1999, 15, 7244– 7251.
Figure 1. Steps for nanografting. (A) Characterization of the SAM using low force; (B) writing step with high force applied to the AFM tip while scanning; (C) returning to low force the nanopattern can be characterized in situ.
1 nN) to identify a flat area for nanofabrication (Figure 1A). A flat area is helpful for clearly distinguishing the thickness differences for molecular height measurements. With low force the sample can be characterized without modifying the surface. To accomplish writing, the force applied to the AFM probe is increased (0.5-30 nN). Under higher force, the tip is pushed through the matrix monolayer to shave away selected areas, and ink molecules from solution immediately assemble onto the surface following the scanning track of the AFM tip (Figure 1B). The same probe can then be used for imaging the SAM nanopatterns by returning to a low force setpoint (Figure 1C). Depending on the choice of ink molecules, nanografting can generate patterns of desired thickness. Nanografting provides advantages for in situ experiments, such as high spatial resolution, flexibility to introduce multiple components of thiols on the same surface, enabling one to modify the fabricated nanostructures in situ and providing well-defined placement and geometries for constructing SAM patterns.67 Nanoshaving is accomplished by imaging in a solution of fresh solvent, without ink molecules. By sweeping an area several times with the AFM tip under high force, areas of the substrate can be uncovered to expose the underlying substrate. Small areas of the SAM can be shaved away to provide a nanoscale height measurement, referencing the uncovered areas of the substrate as a baseline. It has been established that mature SAMs of n-alkanethiols form wellordered, 2D periodic structures with a lattice constant of 0.5 nm, in which hydrocarbon chains are close-packed and are tilted ∼30°
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from surface normal.19,20,28,68 To determine the theoretical heights of n-alkanethiols on Au(111), the value for the fully extended molecular length from chemical models of energy minimized structures69 was adjusted with an estimated tilt of 30 degrees. Using this approach, the theoretical heights for reference molecules of hexanethiol, decanethiol and dodecanethiol are ∼0.9, 1.3 and 1.5 nm, respectively. The theoretical values are consistent with experimental measurements using various surface techniques, such as ellipsometry.69 The measured thickness of hexanethiol was reported as 0.8 nm using ellipsometry,70 for comparison to a calculated theoretical value of 0.85 nm. For a molecular film of decanethiol prepared from solution immersion, the thickness was determined as 1.3 ( 0.2 nm, calculated from the attenuation of the Au 4f signal measured with X-ray photoelectron spectroscopy (XPS).71 Using grazing incidence X-ray diffraction the thickness of decanethiol monolayer was measured as 1.32 ( 0.10 nm.72 The height of dodecanethiol was reported as 1.5 ( 0.1 nm using ellipsometry measurements.73
Results Several different experiments were conducted to investigate the self-assembly and surface morphology of R,ω-alkanedithiols. Solution self-assembly was evaluated using in situ nanofabrication and characterization of SAMs of 1,8-octanedithiol and 1,9nonanedithiol in a liquid cell. In addition, nanografted patterns of well-known structures of methyl-terminated n-alkanethiols were written within the dithiol SAMs as a molecular ruler. Local AFM views of nanografted patterns enable a side-by-side comparison of the morphology of SAMs with different head groups, and provide an internal height reference for measuring differences in molecular thickness. Also, patterns of 1,8octanedithiol, 1,9-nonanedithiol, and 1,16-hexadecanedithiol were written within methyl-terminated SAMs, to measure height differences for nanografted patterns. AFM Characterization of SAMs of 1,8-Octanedithiol Formed in Solution. The surface of a dithiol SAM produced after 1 week of immersion in 1,8-octanedithiol (0.02 M) is viewed in Figure 2. The AFM topograph (Figure 2A) reveals predominantly flat (lying-down) matrix areas interspersed with nanoscopic island protrusions. The underlying triangular shapes of terraces of Au(111) are apparent. The bright spots exhibit relatively uniform dimensions for the protrusions. A cursor profile (Figure 2B) corresponding to the line drawn across two of the small islands indicates that the islands are about 0.8 ( 0.2 nm taller than the surrounding matrix areas. The protrusions cover ∼7% of the surface of Figure 2A. Statistical analysis of the heights of the protrusions corresponds closely to the expected theoretical difference in thickness between a standing-up versus a lying-down orientation for 1,8-octanedithiol. An average value of 0.8 nm was measured for the protrusions using cursor profiles (n ) 102), with a standard deviation of 0.2 nm. The theoretical dimensions for the molecular diameter assumes an all-trans alkyl chain (0.4 nm) and the thickness of an upright 1,8-octanedithiol layer (1.2 nm) relies on the assumption that molecules have the same orientation as 1-octanethiol in which the hydrocarbon backbone tilts ∼30° from the surface normal. The dimensions are calculated by assuming that 1,8-octanedithiol has an all-trans configuration for the alkyl chain. (68) Dubois, L. H.; Nuzzo, R. G. Annu. ReV. Phys. Chem. 1992, 43, 437–463. (69) CS Chem3D Pro, 4.0; CambridgeSoft Corporation: Cambridge, MA. (70) Cheng, Q.; Brajter-Toth, A. Anal. Chem. 1995, 67, 2767–2775. (71) Mendoza, S. M.; Arfaoui, I.; Zanarini, S.; Paolucci, F.; Rudolf, P. Langmuir 2007, 23, 582–588. (72) Pflaum, J.; Bracco, G.; Schreiber, F.; Colorado, R.; Shmakova, O. E.; Lee, T. R.; Scoles, G.; Kahn, A. Surf. Sci. 2002, 498, 89–104. (73) Godin, M.; Williams, P. J.; Tabard-Cossa, V.; Laroche, O.; Beaulieu, L. Y.; Lennox, R. B.; Grutter, P. Langmuir 2004, 20, 7090–7096.
Figure 2. Surface morphology of 1,8-octanedithiol SAM formed in solution. (A) Topograph; (B) cursor profile for the line in A; (C) rectangular pattern (200 × 300 nm2) of decanethiol nanografted within a SAM of 1,8-octanedithiol; (D) corresponding cursor profile; (E) proposed model for the nanopattern thickness.
Nanografting was accomplished in situ to measure the thickness of the 1,8-octanedithiol SAM formed in solution. The surface of the 1,8-octanedithiol SAM was immersed in a dilute solution (0.2 µM) of decanethiol (ink molecules for writing) within the AFM liquid cell assembly. A rectangular pattern (280 × 300 nm2) of decanethiol was nanografted within the 1,8-octanedithiol SAM (Figure 2C). The surface of the pattern exhibits a smooth morphology typical of n-alkanethiol SAMs. The established dimensions of decanethiol SAMs provide a height reference. The height of the decanethiol nanopattern is 0.9 ( 0.2 nm taller than the surrounding areas of 1,8-octanedithiol as shown by the representative cursor line profile in Figure 2D. The height of the pattern is a local measurement based on several cursor profiles, chosen at selected areas to avoid step edges and defects. The local roughness of Au(111) predominates the measurement, therefore a conservative error estimate was made based on the height of a monatomic Au(111) step. The thickness typical of a decanethiol SAM is 1.3 nm and the expected height for a lying-down orientation of 1,8-octanedithiol is 0.4 nm. The difference measured by nanografting with decanethiol as a reference matches well with the expected thickness for a side-on orientation of the 1,8-octanedithiol molecule for the matrix areas, as represented in the molecular model of Figure 2E. The nanografting measurements confirm that most of the areas of the 1,8-octanedithiol SAM formed by solution immersion are composed of lying-down molecules, with the protrusions corresponding to isolated areas of standing molecules. Two distinct conformations are visible in Figure 2A, a lying-down orientation in which both sulfur atoms attach through chemisorption onto Au(111), interspersed with islands of upright molecules that attached through a single sulfur end group.
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Figure 3. Selected area of a SAM of hexanethiol before and after nanografting. (A) AFM topograph of hexanethiol/Au(111); (B) same area after writing a square pattern of 1,8-octanedithiol by nanografting; (C) corresponding frictional force trace and (D) retrace images.
The coexistence of the predominantly lying-down orientation with the small protrusions of nearly upright conformation remains evident after immersion intervals of 12 h or longer. Combining the results from AFM using both high-resolution imaging and nanolithography establishes that 1,8-octanedithiol molecules assemble predominantly with a lying-down orientation for a SAM formed by solution immersion, with a small percentage of protruding upright molecules (Figure 2). Nanografting of 1,8-Octanedithiol. A square nanopattern of 1,8-octanedithiol was written within a matrix of hexanethiol (Figure 3). A flat terrace area of the hexanethiol SAM is displayed in the topography images before (Figure 3A) and after (Figure 3B) nanografting a pattern of 1,8-octanedithiol. The characteristics typical of the morphology of an n-alkanethiol SAM are observed throughout areas of the surface for Figure 3A, where relatively broad flat terrace domains were chosen for writing. The small circular dark holes are known as etch pits or molecular vacancy islands, and are readily distinguishable for identifying a methylterminated SAM. The larger dark hole at the left of the image is a defect of the Au(111) film. As an internal reference for z calibration of the AFM, the heights at the edge of the Au(111) steps measure 0.23 nm, also the distinct outline of the squareshaped terraces provide landmarks for in situ imaging. The surrounding areas of the hexanethiol SAM exhibit a smooth surface and thus the features of the underlying substrate such as the Au(111) steps are visible. The same area is shown in Figure 3B after a square pattern was nanografted. The topography of the patterned area has a rougher morphology, and there are several higher spots of adsorbate molecules attached to the nanopattern. The brighter color of the square indicates that the pattern is taller than the surrounding hexanethiol SAM. The trace and retrace friction images acquired simultaneously with the topographic image of Figure 3B are presented in panels C and D of Figure 3,
respectively. The friction images furnish evidence that the functionality exposed on the surface of the pattern is different than the surrounding SAM. In comparison to the surrounding methyl-terminated matrix, the patterned area of dithiol SAM exhibits distinct differences in frictional contrast for the two images. This indicates greater frictional force between the head groups of the dithiols and the AFM tip while the tip is scanning in contact mode. Compared to the methyl headgroup of a hexanethiol SAM, the -SH group is more hydrophilic due to higher polarity. The silicon nitride AFM tip is also relatively hydrophilic;74,75 therefore, a higher frictional force between the -SH headgroup of dithiols and the AFM tip results from the stronger hydrophilic-hydrophilic adhesive interactions. A close-up view (500 × 500 nm2) of the same square pattern of Figure 3 is displayed in Figure 4. The fine details of the edges of the square pattern are visible for the zoom-in image. The clustered morphology of the surface of the thiol-terminated pattern is visible and distinctive changes are revealed when compared side-by-side with the surrounding methyl-terminated areas of hexanethiol matrix (Figure 4A). A representative cursor line was drawn at a flat edge of the square pattern to measure the height difference between the nanografted 1,8-octanedithiol pattern and hexanethiol SAM (Figure 4B). The pattern measures 0.4 ( 0.2 nm taller than the hexanethiol monolayer, which matches a standing orientation for 1,8-octanedithiol. The theoretical height difference between hexanethiol and 1,8-octanedithiol is 0.3 nm, assuming an orientation with an all-trans alkyl chain tilted ∼30 degrees from surface normal (Figure 4C). These results demonstrate that with nanografting, dithiol molecules are directed to assume an upright configuration. When (74) Tsukruk, V. V.; N., B. V Langmuir 1998, 14, 446–455. (75) Hamley, I. W.; Connell, S. D.; Collins, S. Macromolecules 2004, 37, 5337–5351.
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Figure 4. Close-up view of the 1,8-octanedithiol pattern. (A) Contact-mode topograph of the pattern surface; (B) selected cursor for the line in A; (C) proposed height model.
nanografting, the molecules adsorb to the surface immediately following the track of the AFM tip in a standing orientation due to an effect of spatial confinement.62 During writing, there is not sufficient substrate area exposed for dithiol molecules to assemble in a lying-down orientation; therefore, the assembly mechanism when nanografting occurs in a single step. Without a lying-down step during molecular assembly, there is no opportunity for both sulfur groups to bind to gold. One would expect that if the 1,8octanedithiol molecules had assembled in a lying-down orientation, the nanopattern would be 0.5 nm shorter than the hexanethiol matrix SAM. Thus the spatial confinement effect of nanografting can be used to engineer an upright orientation of 1,8-octanedithiol molecules. Nanoshaving of 1,9-Nonanedithiol. To corroborate the observations for 1,8-octanedithiol SAMs, similar AFM experiments were conducted for a monolayer of 1,9-nonanedithiol prepared by 3 days of immersion in a 0.02 mM ethanol solution (Figure 5). A surface composed of mixed phases is viewed in the AFM topographs of Figure 5A and B, with island protrusions scattered throughout the surface. A zoom-in view of the surface is presented in Figure 5B. As a reference, there is a dark hole (which is a defect of the gold film) in the upper corner of the frame which provides a landmark that is located at the center of the left side of Figure 5A. The height of the protrusions measures 0.9 ( 0.2 nm above the matrix areas of the SAM, and the taller features cover ∼6% of the surface (Figure 5B). Nanoshaving was used to measure the thickness of the 1,9-nonanedithiol SAM.76 A selected area of the SAM can be shaved away by applying a higher force (0.5 nN) and sweeping the tip across the region several times. A rectangular area of the substrate (300 × 340 nm2) is exposed in Figure 5C which is easily distinguished from the surrounding areas of 1,9-nonanedithiol. The clean removal of 1,9-nonanedithiol adsorbates from the nanoshaved area is confirmed in the corresponding frictional force image (Figure 5D) which evidence brighter color for the nanoshaved (76) Liu, G.-Y.; Xu, S.; Qian, Y. Acc. Chem. Res. 2000, 33, 457–466.
area of the pattern. The thickness of the SAM can be measured directly by referencing the uncovered area of the substrate as a baseline for cursor profiles. The morphology of the underlying template-stripped gold surface has small irregular terraces; therefore the placement of the representative cursor line was chosen to provide a relatively even background. Two different heights are displayed in the cursor plot (Figure 5E) measuring 1.3 ( 0.1 and 0.4 ( 0.1 nm, which correspond well with the predicted dimensions for upright and lying-down orientations of 1,9-nonanedithiol, respectively. As with the previous example of 1,8-octanedithiol SAM formed spontaneously by solution selfassembly, SAMs of 1,9-nonanedithiol formed by solution selfassembly adopt both lying-down and standing-up orientations on gold, with a predominance of lying-down molecules. A height model is proposed showing the dimensions and different orientations (Figure 5F) observed for 1,9-nonanedithiol molecules. Nanografting Dodecanethiol into a SAM of 1,9-Nonanedithiol. Nanografting was accomplished using 1,9-nonanedithiol as the matrix SAM, with a 0.02 mM ethanolic solution of dodecanethiol as ink molecules for writing patterns (Figure 6A). The morphology of the dodecanethiol nanopattern (300 × 300 nm2) appears smooth and even, furnishing a side-by-side view for comparing the surface morphology of a methyl-terminated SAM versus the less ordered matrix areas of 1,9-nonanedithiol. The cursor profile (Figure 6B) displays a thickness difference of 1.0 ( 0.2 nm, which matches well with the expected theoretical height difference between a lying-down alkane chain (0.4 nm) and upright orientation of dodecanethiol (1.5 nm) of the pattern. Nanografted Pattern of 1,16-Hexadecanedithiol in a Decanethiol Matrix. Dithiol molecules with a longer backbone chain were nanopatterned in Figure 7. 1,16-Hexadecanedithiol was nanografted (0.1 mM) into a decanethiol SAM. Figure 7A displays the surface topography of the decanethiol SAM/Au(111) before nanografting. The matrix SAM was prepared by 3 days immersion of a Au(111)/mica substrate in an ethanolic solution of decanethiol (1 mM). A detailed view of a progression of steps
AFM of R,ω-Alkanedithiols on Au(111)
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Figure 6. Nanografted pattern of dodecanethiol within a 1,9-nonanedithiol matrix. (A) Topograph of a 300 × 300 nm2 pattern; (B) height profile for the line in A. Figure 5. Nanoshaving with 1,9-nonanedithiol. (A) Topographic view before fabrication (2 × 2 µm2); (B) zoom in view of A (0.9 × 0.9 µm2); (C) after shaving a 300 × 340 nm2 pattern; (D) friction image for C; (E) corresponding profile for the line in C; (F) proposed model for a mixture of surface orientations of 1,9-nonanedithiol.
of gold terraces is apparent, with a relatively large flat plateau area in the center for writing. A single white spot is visible in the center of the image, which is a contaminant adsorbate. After writing a nanopattern of 1,16-hexadecanedithiol (Figure 7B), the contaminant was removed, and the regular geometry of the positive-height pattern is observed. There are a few white lines at the center and right edges of the pattern which are a common artifact for AFM imaging caused by tip-surface adhesion. The corresponding frictional force image (Figure 7C) distinguishes the different surface chemistries of the thiol nanopattern and the surrounding methyl-terminated areas. A cursor profile across the left edge of the nanopattern (Figure 7D) indicates a height difference of 0.9 ( 0.2 nm. The expected difference in height for an upright orientation of 1,16-hexadecanedithiol (2.1 nm) and decanethiol (1.3 nm) is ∼0.8 nm (Figure 7E), which matches well with the experimental measurement.
Discussion Solution Immersion of r,ω-Alkanedithiols. The spontaneous, unconstrained self-assembly process for R,ω-alkanedithiols from solution immersion of gold substrates begins in a similar manner as for n-alkanethiols, with molecules attaching to the surface in
a lying-down phase. However, at this initial stage both ends of the molecules of R,ω-alkanedithiols chemisorb to the Au(111) substrate and thus trap the molecules in a lying-down orientation. Over time, more molecules adsorb to the surface until there is no longer sufficient room for molecules to assemble in a fully stretched, lying-down configuration. At a later stage of selfassembly as the surface reaches saturation coverage of lyingdown molecules, the dithiol molecules attach at the pinhole sites of uncovered gold in a standing orientation. This description of solution self-assembly for R,ω-alkanedithiols fits well with the observations for Figures 2 and 5 which reveal the coexistence of both lying-down and standing-up phases. The initial adsorption step with a lying-down orientation for R,ω-alkanedithiols results in both ends of the molecules binding to gold, forming alkanedithiolates. The additional binding of an extra thiolate (20 kcal/mol) group stabilizes the lying-down phase and thus increases the activation energy barrier for transformation to a standing-up orientation. As a result, a phase transition beyond the intermediate phase is inhibited and dithiol molecules persist in a lying-down configuration for the resulting alkanedithiol monolayer. Evidence of whether alkanedithiol molecules are lying-down or standing-up can be provided by AFM topography images, however, these characterizations cannot distinguish whether the initial adsorption step results from physisorption or chemisorption. The evidence that the initial adsoption is a chemisorption process is that the molecules persist in a lyingdown configuration and do not immediately rearrange into a
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the lying-down phase to the surface, which increases the activation barrier between the two intermediate states (lying-down and standing-up). Therefore, a kinetic trap inhibits the phase transition and results in a percentage of dithiol molecules persisting in a lying-down configuration. Spatially Constrained Self-Assembly of r,ω-Alkanedithiols. Due to a different assembly mechanism, nanografting generates patterns of R,ω-alkanedithiols presenting free -SH groups at the interface. The spatially constrained self-assembly of R,ωalkanedithiols is the same as for n-alkanethiols during nanografting. The mechanical process of writing with nanografting enables the molecules to bypass the lying-down phase and assemble immediately into a standing configuration because there is insufficient space on the surface for the molecules to assemble in a lying-down orientation.62 A key element of nanografting is that n-alkanethiols chemisorb spontaneously to surfaces in an upright arrangement to form a crystalline phase, due to a mechanism of spatial confinement. A kinetic Monte Carlo model of solution and nanografted deposition of n-alkanethiols on gold surfaces was developed by Ryu and Schatz, which reproduces experimental observations for the variation of SAM heterogeneity with AFM tip writing speed.29 The speed of the AFM tip influences the composition of the monolayers formed along the writing track. Nanografting can be performed routinely in thiol solutions with concentrations as dilute as 0.01 µM. Therefore, using nanografting in liquid media, nanopatterns of R,ωalkanedithiol SAMs can be written directly on gold with a standing-up configuration.
Summary
Figure 7. Nanografted pattern of 1,16-hexadecanedithiol written within a decanethiol SAM. (A) Area of the decanethiol SAM chosen for nanofabrication; (B) after nanografting a 300 × 300 nm2 pattern of 1,16-hexadecanedithiol; (C) corresponding frictional force image; (D) cursor profile for the line in B; (E) proposed height model.
standing phase. Future ex situ AFM experiments are in progress to compare the surface coverage after extended immersion intervals, to determine if a slower kinetics takes place for rearrangement into a standing phase. In the case of self-assembly during solution growth of n-alkanethiols, monothiol molecules go though multiple steps to form a densely packed commensurate SAM.14,17 Molecules initially adsorb to the surface with the molecular axis of the hydrocarbon chains oriented parallel to the substrate. When the surface density of the lying-down phase reaches near saturation coverage, continuous collisions of thiols from solution induce a lateral pressure, which leads to a two-dimensional phase transition. The thiol molecules rearrange into a standing-up configuration with the hydrocarbon axis tilted ∼30° with respect to the surface normal. The energy barrier of the phase transition for organothiols with only one thiol end group is moderate, thus even at room temperature thiol molecules can readily convert from a lying-down to an upright monolayer. On the other hand, for R,ω-alkanedithiol molecules the formation of alkanedithiolates with both -SH groups chemisorbed to gold stabilizes and anchors
For R,ω-alkanedithiols formed from ethanol solutions, the resulting SAM is composed of lying-down dithiol molecules with isolated islands of upright molecules. The chemisorption of both -SH groups locks the lying-down phase on the surface and inhibits the transition from a lying-down to standing upright configuration. After 7 days immersion, the lying-down orientation of 1,8-octanedithiol was observed to persist and did not rearrange completely into a standing-up configuration. Even from simple R,ω-alkanedithiols without rigid backbones, patterns of upright SAMs can be written directly on gold by nanografting. Using 1,8-octanedithiol, 1,9-nonanedithiol and 1,16-hexadecanedithiol as examples, SAMs were prepared by either solution growth or an AFM-based nanofabrication approach (nanografting) with spatially confined self-assembly. High-resolution AFM characterizations demonstrate that molecules of nanografted SAM patterns of R,ω-alkanedithiols assemble with a preferred standingup conformation, which generates a surface presenting free -SH groups. Acknowledgment. This research was supported by the American Chemical Society Petroleum Research Fund PRF G43352-G5 and the Louisiana Board of Regents Research Competitiveness subprogram, LEQSF(2006-09)-RD-A-04. Algernon Kelley gratefully acknowledges Eastman Kodak Company for a graduate fellowship award. The authors thank W. K. Serem and Z. M. LeJeune for helpful discussion. LA802235C
