Two-Dimensional Assembly of Purines and Pyrimidines on Au(111

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Langmuir 1994,10, 3845-3852

Two-DimensionalAssembly of Purines and Pyrimidines on Au(ll1) Thomas Boland and Buddy D. Ratner* Department of Chemical Engineering and Center for Bioengineering, BF-10, University of Washington, Seattle, Washington 98195 Received June 23, 1994@ Purines and pyrimidines slowly self-assembled from solution on a crystalline gold surface to form a dense ordered monolayer. The adsorbed layers have been imaged with scanning tunneling microscopy and atomic force microscopyand analyzed with electron spectroscopyfor chemical analysis and static secondary ion mass spectrometry. It was found that the adsorptionprocess occurs in three stages: (1)the molecules adsorb first in random clusters, (2) then the clusters adsorb at the reconstruction sites of the Au(ll1) surface,and (3)finally a structured overlayer is assembled. The surface lattice dimensions ofthe assembled film correspond to those of the bulk lattice. The driving force for the self-assembly is discussed.

Introduction The appreciation of the ease with which many molecules spontaneously organize into ordered assemblies, and the ubiquity of such assembled structures in biology, has stimulated a significant research effort to explore systems demonstrating Such systems are challenging to investigate because they exploit geometrically specific surface bonding and flexible noncovalent interactive forcesto shift the balance from entropic dissociation to energetic stability. Molecular assembly of organic molecules a t solid surfaces to form ordered two dimensional molecular aggregates presents synthetic,theoretical, and analytical problems. For such systems, the unique properties that dominate a t the abrupt division region between phases must be ~onsidered.~ Furthermore, the mass of material is low (on the order of ng/cm2),necessitating specialized analytical methods to study the molecular organization. Still, such organized organic surface structures have been explored by research groups studying photoresists, nanoelectronics, molecular recognition, electrochemistry, and biomaterials. Furthermore, these systems provide highly ordered and well-defined organic surfaces analogous to the single crystal surfaces that have permitted much progress in the understanding ofthe reactivity of inorganic surface^.^ The majority of organic self-assembled surface structures studied to date consist, at the molecular level, of three components: an anchoring functional group, a structure-inducing region, and a head group that resides at the air-solid or liquid-solid interface.2 Those systems with silane or thiol anchoring groups and n-alkane organization regions dominate this literature with hundreds of studies on these types of systems being reported in the last five years. However, other systems, often involving still ring structures, have also been observed to self-assemble at surfaces. Scanning tunneling microscopy (STM)has been used to investigate these systems, which inlude phthalocyaniness and nucleotide However, most of those studies were conducted using highly

* Author to whom correspondence should be addressed.

Abstract published in Advance ACS Abstracts, September 1, 1994. (1)Whitesides, G.M.;Mathias, J. P.; Seto, C. T. Science 1991,254, 1312-1319. (2)Ulman, A. Ed.; An Introduction to Ultrathin Organic Films; Academic Press, Inc.: Boston, MA, 1991;442 pages. (3)Tabor, D. Gases,Liquids, and Solids: and Other StatesofMatter; Cambridge University Press: Cambridge, 1991,418 pages. (4)Somorjai, G. A. Lungmuir 1991, 7(12),3176-3182. @

oriented pyrolytic graphite (HOPG)as the substrate, which can yield artifacts that can be mistaken for biological molecules.12J3 Furthermore, the studies frequently lack corroborative surface analysis. We are interested in the STM imaging of nucleotide bases on gold because of the relevance of such studies for STM observation of DNA.14 We present here a report on the spontaneous assembly in solution at a gold (111) surface of a number of purine and pyrimidine bases, with and without explicit anchoring groups to the substrate. DNA nucleotide adsorption and assembly have been studied by STM with potential control by Tao et al.ll We describe the adsorption kinetics of slow, spontaneous molecular aggregation without an applied potential. The structure of the films produced and their monolayer nature have been confirmed by electron spectroscopyfor chemical analysis (ESCA) and by static secondary ion mass spectrometry (SSIMS).

Experimental Section Substrate Preparation. Gold substrates were prepared using the method of Clavalier16 by flame annealing a gold wire (99.9%Alfa, Ward Hill, MA) into a bead and slowly cooling it.

The resulting polycrystalline beads possess several atomically

flat facets onto which the assembly can occur and clear images

can be generated. For the ESCA analysis,epitaxially grown gold films on mica with predominant (111) surface structure were obtained by evaporationl6 in a turbomolecular pumped vacuum system. Immediately after being cleaved,the mica sampleswere inserted into the vacuum chamber and heated by electron beam to 300 "C at a final pressure of 5 x 10-8 Torr. Gold was evaporated at (5)Luttrull, D. IC;Graham, J.; De Rose, J. A,; Gust, D.; Moore, T. A.; Lindsay, S. M. Langmuir 1992,8(3),765-768. (6)Ratner, B. D.;Boland, T.; Llanos, G.; Lewis, IC B.; Castner, D. G. ACS Polym. Mater. Sci. Eng. 1992,66(1),220-221. (7)Heckl, W.M.; Smith, D. P. E.; Ginnig, g.; Klagges, H.; Hansch, T. W.; Maddocks, J.Proc. Natl. Acad. Sci. U.SA. 1991,88,8003-8005. (8) Allen, A. J.; Balooch, M.; Subbiah, S.;Tench, R. J.; Siekhaus, W. J.; Balhorn, R. Scanning Microscopy 1991,5(3),625-630. (9)Allen, M. J.; Balooch, M. Ultramicroscopy 1992,42-44, 10491053. (10)Srinivasan,R.;Murphy, J. C.; Fainchtein,R.; Pattabiraman, N. J.Electrounal. Chem. 1991,312,293-300. (11)Tao, N.J.;DeRose, J. A.; Lindsay, S. M. J.Phys. Chem. 1993, 97(4),910-919. (12)Clemmer, C. R.;Beebe, T. P., Jr. Science 1991,251,640-642. (13)Heckl. W.M.: Binnie, -. G. Ultramicroscopy _ - 1992.42-44,10731078. (14)Lindsay,S.M.;Philipp,M.Ge~~aZ.Technol. 1991,8(1),8-13. (15)Clavalier, J.;Faure, R.; Guinet, G.; Durand, R.J . Electropanal. Chem. 1980,107,205-209. (16)Chidsey, C. E. D.; Loiacono, D. N.; Sleator, T.; Nakahara, S. SUI$ Sci. 1988,200,45-66.

0743-7463/94/2410-3845$04.50l0 0 1994 American Chemical Society

3846 Langmuir, Vol. 10, No. 10,1994

Boland and Ratner

a rate of -0.9 n d s , and the sample was allowed to cool to ambient temperature and withdrawn from the chamber. Immediately after preparation, the gold substrates were immersed in 1 mM solutions of 6-mercaptopurine (6MP)(Aldrich Chemical Co., Milwaukee, WI),purine (SIGMA Chemical Co., St. Louis, MO), and the four DNA bases adenine, cytosine, thymine, and guanine (Aldrich) in absolute ethanol (Midwest Grain Products Co., Weston, MO). After times varying from 0 to 24 h, the samples were removed from solution, thoroughly rinsed with ethanol, and air-dried in a laminar flow hood. Mercaptopurine crystals were prepared by recrystallization of mercaptopurine powder in KOH from an aqueous solution accordingto the method describedby Hoogsteen.17 These crystals are used as a control for the ESCA analysis. Instrumentation. STM observations were conducted with a Nanoscope I1 (Digital Instruments, Santa Barbara, CA) equipped with a 0.5 x 0.5 pm scanner. The microscope was operated in air with platinudrhodium (87%/13%) tips (99.99% Alfa, Ward Hill, MA). The tips were mechanicallycut and cleaned with a 50% HN03 solution prior to mounting into the microscope to minimize any organic contamination. The STM was operated in the constant current mode with a tunneling current of 0.5nA, the bias voltage applied to the sample was 500 mV, and the scan rate in the x-direction was approximately 0.2p d s . For AFM measurements, a Nanoscope I1(Digital Instruments, Santa Barbara, CA) equipped with a 10 x 10 pm scanner and a fluid cell was used. Commercially available cantilevers with spring constants of about 0.12 N/m with integrated tips (r 50 nm) (Digital Instruments, Santa Barbara, CA) were used. The ESCA analysis was performed on a SSX-100X-probe surface analysis system (Surface Science Instruments,Mountain View, CA) which uses an Al Ka monochromatic X-ray source, a hemispherical analyzer, and a position-sensitivedetection system with a 30" solid angle acceptance lens. For nonconductive samples the low-energy electron flood gun was used at a 5 eV setting. The static S N Sexperiments were also performed on the SSX100 X-probe system equipped with a Leybold-Heraeus ion gun and a Balzers QMG 511 quadrupole mass analyzer with an adjustable energy filter. The xenon ions used as primary particles were accelerated with a potential of 3.5keV and formed a primary ion current of 0.5 nA/cm2. The ion beam was scanned over an area of -0.25 cm2,resulting in a primary ion particle flux density of 2 nA/cm2 and a particle dose of less than 5 x 10l2ions/cm2. Image Analysis. Particle quantification (e.g., size, area, and coverage)was performed using the NIH Image software package (v. 1.49). Fourier transform analysis was done with the software supplied with the scanning tunneling microscope.

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Results STM Observations. One STM image of a gold (111) surface exposed to pure ethanol is shown in Figure 1.As expected, the surface does not appear different from a surface without solvent exposure. No solvent-induced reconstruction is observed, and the only noticeable characteristic of ethanol-exposed gold (111)surfaces is that they are often highly stepped. Figure 1shows two monoatomic steps in the upper right hand corner. We first investigated 6-mercaptopurine, which resembles adenine with the amino group being replaced by a thiol.

I

SH

k

We used this molecule as a model nucleotide compound, expectingthat the thiol group would serve as an anchoring agent strongly binding the molecules to the gold surface. The adsorbed molecules would then be stable enough not to be swept by the STM tip during imaging. (17)Hoogsteen, K. Nature (London) 1956,178,379.

Figure 1. STM image of a gold surface soaked in ethanol. The scan area is 72 x 72 nm, and the z-scale ranges from 0 to 1 nm.

.

Two single atom steps are located in the upper right corner.

The sequence of events occurring at the Au(111)surface during adsorptionfrom a 1mMsolution of mercaptopurine in ethanol is shown in Figure 2 in four STM images (1 min, 6 h, 12 h, and 24 h). The area of the scan is 72 x 72 nm, and the elevation (2)scale ranges from 0 nm (black) to 3 nm (white). Immediately after immersion into solution, the surface shows bright islands of different sizes ranging from 0.50 to 2.00 nm in diameter with an apparent height of 0.45 f 0.15 nm (Figure 2A). The islands are randomly distributed on the surface and cover less than 10%of the total surface area. With time the number of islands increases steadily, and after 6 h exposure, about 22% of the surface is covered (Figure 2B). The islands are more regular in size with an average diameter of 2.11 f 0.40 nm and an average area of 3.44 f 1.29 nm2. After approximately 12 h exposure to the solution (Figure2C), the surface has a considerablydifferent aspect. Now, the islands are seen to be ordered as parallel rows on the surface. The average spacing between rows is measured as 6.85 f 0.40 nm with an average spacing between islands of one row of 3.43f0.25 nm. The coverage is increased to 50%,or half of a monolayer. After 24 h exposure (Figure 2D), a complete overlayer with full monolayer coverage and an ordered, twodimensional lattice is formed. The structure was analyzed by Fourier transform analysis for information about its two-dimensional periodicity. This analysis, shown in Figure 2E, results in two periodicities at r1= 3.43nm and r 2 = 6.85nm with an interior angle ofp = 101.02". These periodicitiescorrespond to the 2-D oblique lattice observed. The contiguity and coverage of the assembled monolayer is illustrated by the scan over a larger total area (Figure 2F). The highest resolution image realized exhibits a full monolayer coverage a t the molecular level. In Figure 3A, a top view of this STM image is shown. In this image, individual molecules are resolved. The dark inserted parallelogram corresponds to the bulk unit cell measured elsewhere by X-ray crystallography.18 Many different mercaptopurine samples have been imaged with STM, and the results consistently show the (18)Brown, G.M.Acta Crystallogr. 1969,B25, 1338-1353.

2 0 Assembly of Purines and Pyrimidines on Au(ll1)

Langmuir, Vol. 10,No. 10,1994 3847

Figure 2. STM images of the gold surface afier 1 min and 6,12, and 24 h exposure to the mercaptopurine solution. The scan size is 72 x 72 nm with a vertical scale ranging from 0 nm (black) to 3 nm (white). The samples were air-dried in a laminar flow hood and imaged in air. The bias is 500 mV bias, and the tunneling current is 0.5 nA. Immediately after exposure to the mercaptopurine solution, randomly distributed islands are “visible”with STM. The islands vary significantly in size (A). After exposures of -6 h, more random clusters appear (B). The white spots on the surface have a diameter of 2.10 nm and an apparent height of 0.45 nm. They are never seen on clean gold. After exposures of -12 h, the clusters assemble into long chains (0.These chains are parallel and do not seem to be influenced by the steps on the surface. After 24 h, a dense overlayer is formed (D). A Fourier transform of D (E) shows the two periodicities r1= 3.43 nm and r2 = 6.85 nm with an angle p = 101.02”. A large scan illustrates the contiguity and coverage of the assembled film (F).

described behavior. In addition, AFM images were obtained that confirm the STM results (Figure 3B). This image was obtained in the repulsive force mode under ethanol with a scan rate of 0.86 p d s in the x-direction. The image shows instabilities due to the applied force (