Adsorption and In Situ Scanning Tunneling Microscopy of Cysteine on

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Adsorption and In Situ Scanning Tunneling Microscopy of Cysteine on Au(111): Structure, Energy, and Tunneling Contrasts Renat R. Nazmutdinov,† Jingdong Zhang,‡ Tamara T. Zinkicheva,† Ibragim R. Manyurov,† and Jens Ulstrup*,‡ Kazan’ State Technological UniVersity, 420015 Kazan, Republic of Tatarstan, Russia, and Department of Chemistry, Building 207, Technical UniVersity of Denmark, DK-2800 Kgs. Lyngby, Denmark ReceiVed February 17, 2006. In Final Form: June 1, 2006 The amino acid L-cysteine (Cys) adsorbs in highly ordered (3x3 × 6) R30° lattices on Au(111) electrodes from 50 mM ammonium acetate, pH 4.6. We provide new high-resolution in situ scanning tunneling microscopy (STM) data for the L-Cys adlayer. The data substantiate previous data with higher resolution, now at the submolecular level, where each L-Cys molecule shows a bilobed feature. The high image resolution has warranted a quantum chemical computational effort. The present work offers a density functional study of the geometry optimized adsorption of four L-Cys formssthe molecule, the anion, the neutral radical, and its zwitterion adsorbed a-topsat the bridge and at the threefold hollow site of a planar Au(111) Au12 cluster. This model is crude but enables the inclusion of other effects, particularly the tungsten tip represented as a single or small cluster of W-atoms, and the solvation of the L-Cys surface cluster. The computational data are recast as constant current-height profiles as the most common in situ STM mode. The computations show that the approximately neutral radical, with the carboxyl group pointing toward and the amino group pointing away from the surface, gives the most stable adsorption, with little difference between the a-top and threefold sites. Attractive dipolar interactions screened by a dielectric medium stabilize around a cluster size of six L-Cys entities, as observed experimentally. The computed STM images are different for the different L-Cys forms. Both lateral and vertical dimensions of the radical accord with the observed dimensions, while those of the molecule and anion are significantly more extended. A-top L-Cys radical adsorption further gives a bilobed height profile resembling the observed images, with comparable contributions from sulfur and the amino group. L-Cys radical a-top adsorption therefore emerges as the best representation of L-Cys adsorption on Au(111).

1. Introduction L-Cysteine (Cys; HS-CH2-CH(NH2)-COOH) is an amino acid with a thiol side group, widely present in proteins, and with crucial roles in molecular biology, medicine, and biochemistry. Cys is an important precursor in the synthesis of glutathione, taurine, and enzyme A, as well as inorganic sulfate in nature,1 and is a strong ligand for transition metals. Important structural Cys functions are to retain protein tertiary structures by disulfide (cystine) bond formation, which are also exploited as a natural linker for the immobilization of metalloproteins in redox active states on gold surfaces.2-4 Biotechnology perspectives of Cys are associated with self-assembled monolayers (SAMs) based on sulfur-metal bonds. SAMs are essential for molecular surface architectures and have attracted broad interest due to potential application in sensor and other nanotechnology. Carboxylterminated SAMs on electrochemical Au surfaces efficiently immobilize the positively charged heme protein cytochrome c with electron-transfer function retained. Variable-length alkanethiols on single-crystal Au(111)5,6 and polycrystalline Au * Corresponding author. Fax: (+45) 4588 3136; e-mail: kemi.dtu.dk. † Kazan’ State Technological University. ‡ Technical University of Denmark.

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(1) Fasman, G. B., Ed. Prediction of Protein Structure and the Principles of Protein Conformation; ISBN 0-306-43131-9; Plenum: New York, 1989. (2) Chi, Q.; Zhang, J.; Nielsen, J. U.; Friis, E. P.; Chorkendorff, I.; Canters, G. W.; Andersen, J. E. T.; Ulstrup, J. J. Am. Chem. Soc. 2000, 122, 4047-4055. (3) Zhang, J.; Chi, Q.; Kuznetsov, A. M.; Hansen, A. G.; Wackerbarth, H.; Christensen, H. E. M.; Andersen, J. E. T.; Ulstrup, J. J. Phys. Chem. B 2002, 106, 1131-1152. (4) Chi, Q.; Zhang, J.; Friis, E. P.; Andersen, J. E. T.; Ulstrup, J. Electrochem. Commun. 1999, 1, 91-96. (5) Song, S.; Clark, R. A.; Bowden, E. F.; Tarlov, M. J. J. Phys. Chem. 1993, 97, 6564-6572.

surfaces7 are supports for the blue copper protein azurin by hydrophobic interactions.3,8 Cys SAMs with both carboxylic and amine groups have been found to support immobilization of the strongly negatively charged iron-sulfur protein ferredoxin on Au(111) surfaces and to promote electron transfer between the [3Fe-4S] redox center and the Au(111) electrode.9 Cys monolayers at both metal surfaces and metal/liquid interfaces have been broadly studied.10-16 Pioneering work addressed Cys electrochemistry on Hg surfaces.10 This was followed by studies of Cys SAMs on polycrystalline gold, silver, and copper surfaces by X-ray photoelectron spectroscopy (XPS), infrared reflection-absorption spectroscopy (IR), static secondary ion mass spectrometry (MS) and electrochemistry.11-16 Recent structure analysis of Cys monolayers has focused on singlecrystal gold surfaces, mostly Au(111), using XPS,17,18 temper(6) Avila, A.; Gregory, B. W.; Niki, K.; Cotton, T. M. J. Phys. Chem. B 2000, 104, 2759-2766. (7) Fujita, K.; Nakamura, N.; Ohno, H.; Leigh, B.; Niki, K.; Gray, H. B.; Richards, J. H. J. Am. Chem. Soc. 2004, 126, 13954-13961. (8) Chi, Q.; Zhang, J.; Andersen, J. E. T.; Ulstrup, J. J. Phys. Chem. B 2001, 105, 4669-4679. (9) Zhang, J.; Christensen, H. E. M.; Ooi, B. L.; Ulstrup, J. Langmuir 2004, 20, 10200-10207. (10) Ralph, T. R.; Hitchman, M. L.; Millington, J. P.; Walsh, F. C. J. Electroanal. Chem. 1994, 375, 1-15. (11) His, A.; Liedberg B. J. Colloid Interface Sci. 1991, 144, 282-292. (12) Uvdal, K.; Bodo¨, P.; Liedberg, B. J. Colloid Interface Sci. 1992, 149, 162-173. (13) Tu¨do¨s, A. J.; Vandeberg, P. J.; Johnson, D. C. Anal. Chem. 1995, 67, 552-556. (14) Fawcett, W. R.; Fedurco, M.; Kovacova, Z.; Borkowska, Z. J. Electroanal. Chem., 1994, 368, 275-280. (15) Leggett, G. J.; Davies, M. C.; Jackson, D. E.; Tendler, S. J. B. J. Phys. Chem. 1993, 97, 5348-5355. (16) Hager, G.; Brolo, A. G. J. Electroanal. Chem. 2003, 550, 291-301. (17) Dodero, G.; Michieli, L. D.; Cavalleri, O.; Rolandi, R.; Oliveri, L.; Dacca, A.; Parodi, R. Colloids Surf., A 2000, 175, 121-128.

10.1021/la060472c CCC: $33.50 © 2006 American Chemical Society Published on Web 07/28/2006

Adsorption and In Situ STM of Cysteine on Au(111)

ature-programmed desorption (TPD),19 electrochemistry,16,20,21 and in situ scanning tunneling microscopy (STM)22,23 in different aqueous media. As a zwitterionic molecule, both the amine and the carboxylic acid group can be protonated or deprotonated, depending on pH, to become a cation, an anion, or a zwitterion. Dakkouri and Kolb reported a (x3 × x3) R30° structure of Cys adlayers found by in situ STM in perchloric acid solution.21 A (4 × x7) R19° structure in the same reaction medium was observed by Xu et al.23 Packing, however, appears to depend strongly on the medium and other conditions. A (3x3 × 6) R30° surface structure with six Cys molecules packed by hydrogen bonds and electrostatic interactions was observed by in situ STM in aqueous acetate buffer, pH 4.6.22 Later, ultrahigh vacuum (UHV) STM studies of Cys on Au(110) showed individual molecular cluster-like structures at low temperatures.24,25 As a sensitive high-resolution surface technique, STM has impacted many areas in physics, chemistry, and biology.3,26,27 Image interpretation, however, calls for theoretical input because STM imaging rests on the tunneling current rather than physical shape. The functional groups in halides, amines, alcohols, nitriles, alkenes, alkynes, esters, and thiols thus give different STM contrasts, despite similar topographic heights.28 The location of the groups in the tunneling gap also affects the contrasts. The STM contrast is thus determined by local electronic coupling.28 Resonance tunneling enhances the contrast when the substrate or tip Fermi levels match suitable highest occupied (HOMO) or lowest unoccupied (LUMO) molecular orbitals or the redox potential of adsorbate molecules.2,29,30 The latter is strikingly illustrated by in situ STM of Fe-protoporphyrin,31 a class of Os complexes,32 and viologen-based molecules.33,34 Quantum chemistry has offered important insight in adsorbed single-molecule energetics, structure, and electronic properties, including the single-molecule conductivity35-40 of thiol-based molecules adsorbed on gold surfaces. The metal surface has (18) Cavalleri, O.; Gonella G.; Terreni, S.; Vignolo M.; Floreano, L.; Morgante, A.; Canepa, M.; Rolandi, R. Phys. Chem. Chem. Phys. 2004, 6, 4042-4046. (19) Shin, T.; Kim, K. N.; Lee, C. W.; Shin, S. K.; Kang, H. J. Phys. Chem. B 2003, 107, 11674-11681. (20) Fawcett, W. R.; Fedurco, M.; Kovacova, Z.; Borkowska, Z. Langmuir, 1994, 10, 912-919. (21) Dakkouri, A. S.; Kolb, D. M.; Edelstein-Shima, R.; Mandler, D. Langmuir 1996, 12, 2849-2852. (22) Zhang, J.; Chi, Q.; Nielsen, J. U.; Friis, E. P.; Andersen, J. E. T.; Ulstrup, J. Langmuir 2000, 16, 7229-7237. (23) Xu, Q.; Wan, L.; Wang, C.; Bai, C.; Wang, Z.; Nozawa, T. Langmuir 2001, 17, 6203-6206. (24) Ku¨hnle, A.; Linderoth, T. R.; Besenbacher, F. J. Am. Chem. Soc. 2003, 125, 14680-14681. (25) Ku¨hnle, A.; Linderoth, T. R.; Hammer, B.; Besenbacher, F. Nature 2002, 415, 891-893. (26) Gewirth, A. A.; Niece, B. K. Chem. ReV. 1997, 97, 1129-1162. (27) Itaya, K. Prog. Surf. Sci. 1998, 58, 121-248. (28) Claypool, C. L.; Faglioni, F.; Goddard, W. A., III; Gray, H. B.; Lewis, N.; Marcus, R. A. J. Phys. Chem. B 1997, 101, 5978-5995. (29) Kuznetsov, A. M.; Sommer-Larsen, P.; Ulstrup, J. Surf. Sci. 1992, 275, 52-64. (30) Kuznetsov, A. M.; Ulstrup, J. J. Phys. Chem. A 2000, 104, 11531-11540. Addition/Correction: 2001, 105, 7494. (31) Tao, N. J. Phys. ReV. Lett. 1996, 76, 4066-4070. (32) Albrecht, T.; Guckian, A.; Ulstrup, J.; Vos, J. G. IEEE Trans. Nanotechnol. 2005, 4, 430-434. (33) Li, Z.; Han, B.; Meszaros, G.; Pobelov, I.; Wandlowski, T.; Blaszcyk, A.; Mayor, M. Faraday Discuss. 2006, 131, 121-143. (34) Haiss, W.; van Zalinge, H.; Higgins, S. J.; Bethell, D.; Ho¨benreich, H.; Schiffrin, D. J.; Nichols, R. J. J. Am. Chem. Soc. 2003, 125, 15294-15295. (35) Ulman, A. Chem. ReV. 1996, 96, 1533-1554. (36) Tian, W.; Datta, S.; Hong, S.; Reifenberger, R.; Henderson, J. I.; Cubiak, C. P. J. Chem. Phys. 1998, 109, 2874-2882. (37) Joachim, C.; Ratner, M. A. Nanotechnology 2004, 15, 1065-1075. (38) Nitzan, A. Annu. ReV. Phys. Chem. 2001, 52, 681-750. (39) Hall, L. E.; Reimers, J. R.; Hush, N. S.; Silverbrook, K. J. Chem. Phys. 2000, 112, 1510-1521. (40) Zhang, J.; Bilic, A.; Reimers, J. R.; Hush, N. S.; Ulstrup, J. J. Phys. Chem. B 2005, 109, 15355-15367.

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been represented by clusters,41-44 clusters with periodic boundary conditions,45 or slabs with two-dimensional translational symmetry.40,46-49 Modeling a metal surface by slabs including the relaxation of the metal atoms presently offers the most reliable information. Most computations have been at the density functional theory (DFT) level,41,42,44-48 although other methods (many-body perturbation theory and the Carr-Parrinello scheme43) have also been employed. Modeling of solvation, which strongly complicates the computations, has only recently been reported. Solvation was found to crucially affect the surface packing of charged adlayers.40 We first report here new in situ STM data for Cys SAMs on Au(111) electrode surfaces at a higher, submolecular resolution than in our previous report.22 Prompted by the new data, a computational effort toward a better understanding of the contrast is warranted. Compared with the considerable amount of experimental data, there are only few computational studies of Cys adsorption.25,50,51 Felice and associates explored the energetics and electronic structure of Cys adsorption on Au(111) by periodic DFT calculations50,51 but did not address STM contrasts. Similar studies for Cys on Au(110) were reported by Hammer et al.,25 who considered the STM contrast by the Tersoff-Haman formalism.52 Cys was regarded as a neutral molecule in these reports, representative of UHV, while Cys is a solvated zwitterion in aqueous media. In addition to the new in situ STM data, we address the electronic properties of Cys adsorption on Au(111) by DFT with a particular view on the high-resolution submolecular STM contrasts. As in previous computational efforts, gas-phase Cys adsorption is addressed. The models used are simpler than previous models, as only a single Cys molecule and a smaller Au(111) cluster are included, but other effects can then be included. These are comparisons between the neutral cysteinyl radical, S-CH2-CH(NH2)-COOH, its zwitterionic form, S-CH2-CH(NH3+)-COO-, and the cysteinate anion, -S-CH2CH(NH2)-COOH, as well as specific representations of the tip as a tungsten atom or cluster of tungsten atoms. The computed data are subsequently recast as tunneling contrasts, that is, apparent height distributions over all the Cys atoms and orbitals in the constant current mode. The computed charge distributions enable finally estimating the effects of multiple dipolar interactions and solvation. Following the Experimental Section (section 2), the new data are presented in section 3. The cluster model and computations are described in section 4. The computational data on equilibrium geometry, charge distribution, and adsorption of different Cys forms are given in section 5. Solvation effects on the adsorption, formation of zwitterions, and analysis of lateral interactions in a Cys monolayer are discussed in section 6. The combination of the electronic structures and the tungsten tip, and computation (41) Sellers, H.; Ulman, A.; Shnidman, Y.; Eilers, J. E. J. Am. Chem. Soc. 1993, 115, 9389-9401. (42) Beardmore, K. M.; Krebs, J. D.; Bishop, A. R.; Grønbech-Jensen, N. Synth. Met. 1997, 84, 317-318. (43) Beardmore, K. M.; Krebs, J. D.; Grønbech-Jensen, N.; Bishop, A. R. Chem. Phys. Lett. 1998, 286, 40-45. (44) Kru¨ger, D.; Fuchs, H.; Rousseau, R.; Marx, D.; Parrinello, M. J. Chem. Phys. 2001, 115, 4776-4786. (45) Akinaga, Y.; Nakajima, T.; Hirao, K. J. Chem. Phys. 2001, 114, 85558564. (46) Hayashi, T.; Morikawa, Y.; Nozoye, H. J. Chem. Phys. 2001, 114, 76157621. (47) Morikawa, Y.; Hayashi, T.; Liew, C. C.; Nozoye, H. Surf. Sci. 2002, 50, 46-50. (48) Yourdshahyan, Y.; Rappe, A. M. J. Chem. Phys. 2002, 117, 825-833. (49) Molina, L. M.; Hammer, B. Chem. Phys. Lett. 2002, 360, 264-271. (50) Di Felice, R.; Selloni, A.; Molinari, E. J. Phys. Chem. B 2003, 107, 1151-1156. (51) Di Felice, R.; Selloni, A. J. Chem. Phys. 2004, 120, 4906-4914. (52) Tersoff, J.; Hamann, D. R. Phys. ReV. B 1985, 31, 805-813.

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Figure 1. Cyclic voltammograms of bare Au(111) (dotted line) and L-Cys-covered Au(111) (solid line). 50 mM NH4Ac (pH 4.6). 50 mV s-1.

of the constant current STM height are given in section 7, followed in section 8 by a discussion of the experimental data. Section 9 offers some concluding remarks. 2. Experimental Section Reagents. L-Cys (>98%) was purchased from Sigma and used without further purification. NH4Ac (50 mM, pH 4.6) was prepared from 5 M stock solution (Fluka, ultrapure grade) as a supporting electrolyte and pH adjusted by HClO4 (70%, Fluka, ultrapure). Millipore water (Milli-Q Housing, 18.2 MΩ) was used throughout. Sample Preparations. Gold single-crystal beads were prepared by melting the end of a gold wire (1.0 mm diameter, > 99.99%).2,22 The Au(111) facets were used directly for STM. The Au(111) electrode was annealed in a hydrogen flame, quenched in dihydrogensaturated Millipore water, and transferred to the cell with NH4Ac (50 mM, pH 4.6) solution. Cys monolayers were prepared in two ways, with identical results. Clean Au(111) electrodes were soaked in 0.1-1.0 mM L-Cys for 3-6 h, followed by rinsing in Millipore water. Alternatively, Cys was introduced into pure buffer solution during electrochemistry or in situ STM. Instrumentation. In situ STM was recorded using a Rasterscope 3000 STM instrument (Danish Microengineering Ltd., Copenhagen, Denmark) with independent electrochemical substrate and tip potential control. STM tips were prepared from electrochemically etched 0.38 mm tungsten wire and coated by Apiezon wax. Homemade 3.5 mL Teflon in situ STM cells were used. The STM scanner was calibrated against the Au(111) reconstruction lines under the same experimental conditions prior to each measurement. This was also a check of the quality of the Au(111) surface and experimental environment in the system. Electrochemistry measurements were carried out using an Autolab system (The Netherlands).2,4,22 All glassware and STM cells were cleaned as previously described.2,4 Potentials reported are versus the standard hydrogen electrode.

3. Voltammetry and In Situ STM Images of L-Cys on Au(111) Surfaces Figure 1 shows voltammetric properties of the Cys monolayer on Au(111). The dotted line is a voltammogram of clean Au(111) in 50 mM NH4Ac buffer, pH 4.6. A sharp anodic peak at 0.48 V is caused by the potential induced lift of the reconstruction as well as acetate adsorption. A doublet of anodic peaks at 0.720.85 V and corresponding cathodic peaks at 0.70-0.80 V are caused by adsorption and desorption of acetate. In the presence of a Cys adlayer, the anodic peak at 0.48 V disappears, and the acetate adsorption/desorption peaks are shifted positively with a lower current shown by the solid line in Figure 1. The Cys monolayer induces cathodic peaks at -0.10 to -0.30 V from reductive S-Au bond desorption and dihydrogen evolution with a featureless voltammogram in the potential range of 0.0-0.70 V and a capacitance of 4.7 µF‚cm-2. The capacitance is 5 times

Figure 2. In situ STM images of a Cys monolayer on Au(111) in 50 mM NH4Ac, pH 4.6. Scan area: 9.2 × 9.2 nm2 (A) and 5.3 × 5.3 nm2 (B). It ) 0.80 nA, Vbias ) 0.2 V, Ew ) 0.34 V. Black arrows indicate the x3 direction. The black box represents a (3x3 × 6) R30° unit cell. The green arrow in panel A shows a defect with one missing Cys molecule.

larger than that for bare Au(111) in the same buffer, which is probably caused by the hydrophilic -NH2 and -COOH groups in the Cys SAMs. A similar phenomenon is observed in SAMs with other hydrophilic end groups.53,54 The Cys adlayer is robust enough in the double-layer region that stable and highly ordered structures can be observed by in situ STM. Figure 2A,B shows two representative high-resolution in situ STM images of the L-Cys monolayer on Au(111) in 50 mM NH4Ac buffer, pH 4.6. A highly ordered lattice with a (3x3 × 6) R30° structure is indicated by a black box (Figure 2A), consistent with the network-like cluster structure in our previous report.22 In the present higher resolution images, fine features with a class of round spots are observed in each cluster. A single Cys defect is pointed out by a green arrow in Figure 2A. The area of this defect is 47 Å2, which is close to the average space of 43 Å2 occupied by each Cys in the lattice. This value is comparable to 54 Å2 estimated from a single 2.4 × 1.8 nm2 cluster, containing eight Cys molecules on Au(110) in UHVSTM at low temperature.24 We therefore conclude that a Cys molecule occupies an area of a 7-8 Å extension in the monolayer. The shape of a single Cys defect is elliptical and suggests that a similar Cys shape should be present in the SAMs. Figure 2B (53) Imabayashi, S.; Iida, M.; Hobara, D.; Feng, Z. Q.; Niki, K.; Kakiuchi, T. J. Electroanal. Chem. 1997, 428, 33-38. (54) Nishizawa, M.; Sunagawa, T.; Yoneyama, H. J. Electroanal. Chem. 1997, 436, 213-218.


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shows a high-resolution image with a substructure in each Cys cluster. Spots with different contrasts are found, implying that multiple conformations or adsorption sites are present, or they represent a submolecular feature. Analysis of spot patterns along the x3 row direction such as the [1h1h2] direction, indicated by green lines, shows that the distance between nearest neighbor spots is 5.0 ((0.2) Å, and the size of each spot is in the range of 2.1-3.2 Å. Larger spots appear with stronger contrast. The distance between nearest neighbor spots along the blue and red lines are 4.1 ((0.2) and 3.8 ((0.2) Å, respectively. If each spot would represent one Cys molecule, the Cys coverage would be 8.3 ((0.3) × 10-10 mol cm-2. This is twice as much as the value of 4.0 ((0.4) × 10-10 mol cm-2 from the voltammetric data.22 Each Cys molecule, therefore, most likely contributes two spots and gives an oblong bilobed form, resolved to the submolecular level. The quantum chemical computations offer a clue to the L-Cys fragments represented by each spot.

4. Computational Details A planar Au12 cluster was used to model three adsorption sites, that is, a-top, threefold hollow, and bridge sites on the Au(111) surface. Two-layer clusters of larger size, Au19(12+7), Au22(12+10), Au28(18+10), and Au31(19+12), were also employed in a series of test calculations. The nearest Au-Au distance was taken as that for the crystalline bulk (2.88 Å). The projection of the sulfur atom of Cys was fixed at the a-top, hollow, and bridge sites. (The projection of the S atom on the cluster plane was initially fixed for the bridge site but was allowed to relax during the calculations.) The Au-S distance was allowed to relax, together with full geometry optimization of the Cys molecule, anion, or radical at the Au12 surface. The adsorption energy (∆Eads) was computed as

∆Eads ) Etot(Aun-Cys) - Etot(Aun) - Etot(Cys)

(1)

where Etot(Aun-Cys) is the total energy of the Aun-Cys system, and Etot(Au12) and Etot(Cys) are the total energies of the cluster and a Cys species, respectively. The quantum chemical calculations were performed at the DFT level using the Gaussian 98 and Gaussian 03 program packages.55 The Becke’s three-parameter hybrid functional with the nonlocal correlation provided by the Perdew 91 expression (B3PW91)56 was used to treat the correlation effects known to be important for transition metals. The valence electrons (5d106s1) of the gold atom were described by the double-ζ (DZ) basis set.57 The effect of inner electrons was taken into account by the relativistic effective core potential (ECP) of Hay and Wadt.57 The electrons of S, O, N, C, and H atoms were described by the standard 4-31G basis set.58 The basis set for the sulfur atom was augmented by polarization d-orbitals. The inclusion (55) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Salvador, P.; Dannenberg, J. J.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.11.2; Gaussian Inc.: Pittsburgh, PA, 2001; Gaussian 03, Revision B.04; Gaussian Inc.: Pittsburgh, PA, 2003. (56) Perdew, J. P.; Burke, K.; Wang, Y. Phys. ReV. B 1996, 54, 16533-16539. (57) Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270-283. (58) Hehre, W. J.; Radom L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; J. Wiley & Sons: New York, 1986.

Figure 3. Optimized structure of the bare L-Cys molecule with numerated atoms.

of d-orbitals was found to affect significantly the adsorption energy, whereas the geometry and charge distribution do not change much. Several calculations of the Cys radical adsorbed on the Au12 cluster were also tested using the larger triple-ζ basis set augmented by diffuse and polarization functions, 6-311+G(d,p).60 The electronic structure of open-shell systems was treated in the framework of spin-polarized (unrestricted) formalism. To elucidate the influence of the basis sets and computational level on the geometry, a series of self-consistent field and DFT calculations on an L-Cys molecule as well as on the AuO and AuS59 diatomics were performed using different basis sets. The results are given in Supporting Information S1 and show that the relatively small basis set 4-31G(d) is likely to adequately describe important qualitative effects in the Aun-Cys system.

5. Adsorption of Single Cys Molecular Species from the Gas Phase 5.1. Adsorption Energies and Molecular Adsorbate Structures. As an illustration, Figure 3 shows the optimized structure of an isolated L-Cys molecule (comparison of selected bond length values obtained at different computational levels with experimental X-ray data86 can be found in Supporting Information S1). The orientations of the three different structure optimized Cys species adsorbed at the Au12 cluster are presented in Figure 4. The adsorption energies and equilibrium atomic coordinates along the normal to the cluster surface are collected in Table 1A,B. Table 2 shows a comparison of selected bond lengths and valence angles for the free and adsorbed Cys species. The COOH group is oriented toward the gold surface in positions a-g. The main contribution to the chemical bond with the metal therefore results from the S, or SH and COOH groups. The NH2 group is always remote from the metal surface and is of minor importance in this respect (Table 1A,B). A similar orientation of L-Cys on polycrystalline silver in certain potential ranges was suggested by Brolo et al.61 on the basis of in situ surface-enhanced Raman spectroscopy and second harmonic generation. Evidence of coordination of both amino and carboxyl groups to the surface, in addition to chemisorption through the thiol groups on a copper electrode, was reported in ref 12. Another possible orientation (“bridge-NS”), where the S and NH2 groups are both positioned (59) Huber, K. P.; Herzberg, G. Molecular Spectra and Molecular Structure IV. Constants of Diatomic Molecules; Van Nostrand Reinhold Company: New York, 1979. (60) Krishnan, R.; Binkley, J. S.; Seeger R.; Pople, J. A. J. Chem. Phys. 1980, 72, 650-654. (61) Brolo, A. G.; Germain, P.; Hager, G. J. Phys. Chem. B 2002, 106 59825987.

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NazmudtinoV et al. Table 1. Adsorption Energy (∆EAds) and the Distance from Specific Adsorbate Atoms to the Au12 Cluster Surface (z(Au-X)) computed for (A) the Cys Molecule and Anion in Two Different Sites (See Figure 4a-d)a, (B) the Cys Radical in Four Different Orientations (See Figure 4e-h), and (C) the Cys Zwitterion in Two Different Orientations (See Figure 6c,d) (A) Cys molecule X

a-top 25.9

S H1 C1 H2 H3 C2 H4 N H5 H6 C3 O2 O1 H7

3.958 2.947 5.144 6.136 5.124 4.898 4.972 5.906 5.903 6.068 3.502 3.211 2.737 2.309

Cys anion

hollow

a-top

hollow

-∆Eads/kcal mol-1 24.9 57.4 z(Au-X) /Å 3.870 2.971 3.992 4.714 3.032 4.542 5.342 5.073 4.377 5.853 3.435 3.155 2.812 2.344

56.1

2.585 3.254 3.553 2.464 4.472 5.265 4.966 4.300 5.887 4.146 3.166 4.706 2.924

2.496 3.527 4.209 2.882 4.397 4.981 5.308 4.826 6.051 3.492 3.295 2.969 2.514

(B) Cys radical X

a-top 16.3

Figure 4. Optimized orientations of the three Cys forms on the Au12 surface adsorbed at different sites: molecule, a-top (a) and hollow (b); anion, a-top (c) and hollow (d); radical, a-top (e), hollow (f), bridge (g), and bridge-NS (h).

toward the metal surface for the Cys radical at the bridge site, was also addressed (Figure 4h). This orientation on Au(110) and Au(111) was studied in refs 25, 48, and 49. Evidence of the coordination of both amino and carboxyl groups to the surface, in addition to chemisorption through the thiol group on a copper electrode surface, was previously reported.12 The computed adsorption energy was largest for the anion (57.4 kcal mol-1) and smallest (16.3 kcal mol-1) for the radical (the a-top site, Table 1A,B). The difference between the a-top and hollow sites is small for the Cys molecule and the anion. The corresponding difference between the four orientations explored for the Cys radical is more significant. The bridge-NS position was found to be the most favorable (Table 1B), in qualitative agreement with previous observations.25,50,51 The adsorption energies for the hollow and bridge site do not differ significantly. This observation differs from those of Felice et al.,50,51 who found that the bridge site slightly displaced toward the hollow position is the most favorable. Both models and computational levels are, however, different in the two approaches. At the same time, our test calculations on the adsorption of CH3S on the Au12 cluster at the same level (section 4) indicate that the bridge position is

S H1 C1 H2 H3 C2 H4 N H5 H6 C3 O2 O1 H7

hollow -∆Eads,/ kcal 20.7

bridge

bridge-NS

mol-1 20.2

2.626

z(Au-X) /Å 2.668 2.579

3.326 3.679 2.543 4.508 5.277 5.077 4.503 6.0591 4.073 3.160 4.491 2.902

3.573 4.267 2.845 4.402 5.064 5.204 4.679 6.032 3.466 3.355 2.846 2.619

24.2 2.409 3.283 4.131 2.610 3.764 4.187 2.662 2.462 2.704 4.879 5.942 4.862 6.648

3.574 4.297 2.923 4.389 4.906 5.365 4.963 6.177 3.458 3.180 2.992 2.471

(C) X

orientation I -∆Eads/kcal mol-1 15.4

S C1 H1 H2 C2 H3 N H4 C3 O1 O2 H5 H6

z(Au-X)/Å 2.911 3.800 4.543 3.112 4.487 5.071 5.419 5.836 3.406 3.438 2.544 4.957 6.152

orientation II 14.1 2.928 3.977 4.897 3.506 4.344 4.665 3.159 3.314 5.509 5.545 6.355 3.002 2.308

a The atoms are numbered in the same order for all the three Cys species (Figure 4).

more favorable (=2.5 kcal mol-1) than the hollow site. This accords with conclusions elsewhere.46


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Table 2. Selected Bond Lengths (Å) and Valence Angles (grad) of the Three Cys Forms Computed for the Gas Phase and for the A-Top and Hollow Adsorbed Sites Cys molecule

S-H1 S-C1 S-C1-H2 C1-C2-N C1-C2-C3 C2-C3-O2 C3-O2-H7

anion

ads. (a-top)

ads. (hollow)

gas phase

ads. (a-top)

ads. (hollow)

gas phase

ads. (a-top)

ads. (hollow)

1.375 1.889 104.32 109.80 110.70 112.74 110.4

1.347 1.834 106.65 109.56 112.02 111.57 112.52

1.345 1.831 105.27 109.9 109.24 112.59 112.33

1.886 113.34 113.43 106.40 113.07 107.08

1.823 110.72 109.99 111.11 111.29 109.74

1.847 108.40 108.30 109.28 113.43 111.59

1.829 105.38 109.97 110.63 112.92 110.42

1.816 111.44 109.37 110.93 111.05 110.17

1.836 108.74 108.07 109.60 113.11 112.26

Table 3. Adsorption Energy (-∆EAds, kcal mol-1) Computed for the Three Cys Forms Adsorbed in Hollow Site on the Au(111) Surface Modeled by Clusters of Different Size molecule radical anion

radical

gas phase

Au12

Au19(12+7)

Au22(12+10)

Au28(18+10)

Au31(19+12)

24.9 20.7 56.1

27.30 15.4 71.8

30.40 44.5 96.2

25.19 23.03 73.73

25.10 25.35

The quantum chemical calculations show that adsorption generally results in molecular structural changes. (The structural changes of the Cys radical adsorbed at the bridge and bridge-NS sites fall in the same range as that found for this species adsorbed a-top and at the hollow site (Table 1).) Adsorption is, particularly, accompanied by shortening of the S-C bond length which is, however, small for the radical. The valence angles are also changed, whereas the N-C, C-C, and C-O bond length changes are very small and do not exceed 0.01 Å. The orientation of the three Cys forms in the adsorbed state differs noticeably (Figure 4), but the structures of adsorbed Cys anion and radical also show common features. The Au-S distance is much shorter than it is for the molecule. The r(Au-S) value for the anion (2.59 Å, Table 1A) is close to those for the Cys radical (2.51 Å)49,50 and CH3S (2.45Å).46 (Test calculations using a two-layer cluster Au19(12+7) with full optimization of the Cys radical adsorbed a-top showed some shortening (∼0.18 Å) of the Au-S bond.) It is important to stress that the structure and charge distribution of the Cys anion and radical at equilibrium should be similar. The differences observed can be attributed mainly to cluster size effects. This means that starting from the initially “prepared” anion or radical forms, closely similar adsorbed species at the metal surface emerge. The S-C1 bond tilt angle with respect to the surface normal is 61° for both the radical (orientation bridge-NS) and the anion, which agrees with a previous conclusion (57°).49,50 For this orientation, we found values of 2.812 Å and 2.806 Å for the closest Au-S and Au-N distances, in accordance with estimations based on the sum of the metal radius of the Au atom and the ionic radii of S2- and N3-, but different from those reported in refs 25, 50, and 51. The test calculations based on the 6-311+G(d, p) basis set (g and h orientations of the Cys radical, Figure 4) indicate a shortening of the Au-S bond length (∼0.17 Å), while the other adsorbate degrees of freedom change only slightly. Again, the more crude 4-31G(d) basis set seems adequate at least for a comparative study of the different Cys forms. To clarify the sensitivity of the adsorption energy on the cluster size, we performed calculations of the three L-Cys forms adsorbed at different two-layer gold clusters. The adsorbate geometry optimized by using the Au12 cluster geometry was employed. The adsorption energy is seen to oscillate with an increasing number of gold atoms: slightly for the Cys molecule and more for the Cys radical and anion (Table 3). Nevertheless, the computed energies can be used for a comparative study.

Table 4. Components of the Total Dipole Moment in a Cylindrical Coordinate System (µG )

xµx2 + µy2, µ⊥) Calculated for the Cys

Molecule and Radical Adsorbed in Different Orientations at the Au(111) Surface

molecule radical zwitterion a

site

µF/D

µ⊥/D

on-top hollow on-top hollow bridge orientation I orientation II

2.95 1.52 2.86 0.86 1.18 (1.79)a 8.1 5.25

0.42 -0.39 0.25 1.00 1.01 (1.83)a 8.71 -9.1

Data are related to the orientation bridge-NS.

5.2. Dipole Moments and Charge Densities. The dipole moment of electrostatically neutral species adsorbed on a metal surface is a useful basis for discussion of their orientations. The computed dipole moment components using the optimized geometry of the molecular and radical Cys forms on the a-top and hollow sites are given in Table 4. Notably, the normal (vertical) dipole moment component (µ⊥) of a Cys molecule in the hollow site differs even in sign from that of the molecule adsorbed a-top. Another observation is that the perpendicular (lateral) component exceeds the normal projection of the dipole moment (|µ⊥| , µF) except for the radical in the hollow site, for which µ⊥ g µF. The large perpendicular dipole moment component (µF) would be important in forming the ordered SAM surface structures (section 6). On the other hand, these will be weakly affected by external fields in certain ranges of the electrode charge densities (σ). The interaction energy of adsorbed species with a homogeneous electric field thus does not exceed 3 kcal mol-1 at σ ) +10 µC cm-2 and a dielectric constant of 2 in the interfacial region. µ⊥ ≈ µF for the molecule and radical in the bridge and bridge-NS orientations (Figure 4h), and µ⊥ is here the largest among all orientations. Such a position for the adsorbed Cys radical can hardly be considered as being the most favorable (compared with adsorption of a single particle) taking into account the “repulsive” monolayer effects. This expectation is supported by other estimations (section 6). The atomic charges of the adsorbed species were computed by two different schemes, that is, the Mulliken method58 and the natural population analysis (NPA).62 The latter is considered more reliable and depends insignificantly on the basis set compared with the former. Both schemes predict small electron density transfer from an adsorbed Cys molecule to the metal (Table 5). In contrast, partial charge transfer (PCT) from the anion to the gold surface is significant (Table 5). The Mulliken method predicts complete discharge, which is, however, an overestimation. PCT for the radical by the two methods differs even in sign. The results of the NPA analysis lead to slight partial electron density transfer from metal to radical and seem to be (62) Foster, J. P.; Weinhold, F. J. Am. Chem. Soc. 1980, 102, 7211-7218.

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Table 5. Charges in the Au12 Cluster Resulting from the Adsorption of Different Cys Forms Computed by Using the Mulliken Scheme and NPA (In Parentheses) adsorption site on-top hollow bridge

a

Cys molecule

Cys anion

Cys radical

-0.23 (-0.01) -0.24 (-0.02)

-0.96 (-0.55) -0.99 (-0.48)

-0.2 (0.12) -0.23 (0.13) -0.25(0.14) -0.32 (0.17)a (-0.02 ÷ -0.05)b

NS orientation. b The zwitterion adsorbed in two orientations.

Figure 5. Averaged electronic density along the surface normal of the Au12 cluster calculated for the Cys molecule (solid line), anion (dashed line), and radical (dotted line) absorbed on the hollow site. Table 6. Solvation Free Energy Values Computed in the Framework of Two Models, COSMO and IEFPCM (In Parentheses), with Two Different Values of the Solvent Dielectric Constants (E) for Several Cys Forms and the “Desolvation” Term (δ(∆Fsolv), kcal mol-1) -∆Fsolv Cys zwitterion Cys molecule Cys anion Cys radical

) 80

)5

δ(∆Fsolv)

44.83 (44.48) 13.7 (13.6) 74.5 (75.) 12.4 (12.3)

32.9 (29.5) 10.8 (9.4) 59.7 (56.5) 9.70 (8.5)

11.9 (15.) 3.00 (4.2) 14.8 (18.5) 2.7 (3.9)

more reasonable. Both the Cys anion and radical thus bear a negative charge in the adsorbed state. The changes of charge distribution in the Cys atomic groups induced by adsorption show that adsorption in the a-g positions (Figure 4) does not lead to charge redistribution in the NH2 group for any of the Cys species, but a change in the carboxyl oxygen atom charge is noticeable. Charge transfer is in both directions for all the species, that is, from the CdO moiety of the carboxyl group to metal and from metal to the hydroxo group. Anion or radical adsorption reduces the negative charge of the S atom. This correlates with the shortest Au-S distance (Table 1). Most of the electron spin density of the Cys radical (≈ 0.71) is concentrated on the sulfur atom, in keeping with the high affinity of Cys radical sulfur to the Au surface leading to the short Au-S distance. N Analysis of the electron density (nel ) ∑i)i φi2, where φi refers to a given molecular orbital, and N is the number of electrons) of the adsorbed species is finally helpful. Figure 5 shows the electronic density of the Au12 adsorbate averaged along the cluster surface, (〈nel(z)〉), as a function of the distance from the metal nuclei. Three common groups of peaks are noted, with a distinct difference between 1 Å e z e 4 Å for all the Cys forms. Electronic density depletion for the Cys radical compared to the molecule is observed closest to the gold cluster (metal “edge”). At the same time, there is a noticeable excess 〈nel〉 at z ≈ 3 Å (Figure 5). In contrast, 〈nel〉 depletion for the anion at z ≈ 4-5 and 6.5-7 Å and a slight 〈nel〉 accumulation for the radical are observed. Such features accord with the PCT for the Cys anion and radical.

6. Solvation and Collective Monolayer Effects The computational data refer to the adsorption of Cys species from the gas phase. A recent combined molecular dynamics and DFT study of cysteamine adsorption on Au(111) showed that solvation effects are crucial for the surface packing and orientation of a charged adsorbate.40 We address here solvation in a simpler but instructive way by combining the computed data with a simple dielectric model. Solvent effects are important first by modifying the molecular structure by the formation of the zwitterion, S-CH2-CH(NH3+)-COO-, which is not stable in the gas phase. The Gaussian 98 package implemented by COSMO (conductor polarizable continuum model)63 and IEFPCM (polarizable continuum model with integral equation formalism)64 in the framework of self-consistent reactive field theory were employed. The solvation free energies (including both electrostatic and nonelectrostatic terms) are summarized in Table 6. The zwitterion geometry with solvation included was fully optimized. The gasphase equilibrium geometry was used for the other species. Calculations based on both models give about -10 kcal mol-1 for the free energy of formation of the zwitterion from the neutral molecule. A similar conclusion was reported elsewhere.65 There are two additional contributions to the adsorption energy at a metal/solvent interface compared to the metal/vacuum interface. The first one is the reduction of the solvation free energy δ(∆Gsolv) when a particle from the bulk approaches the interface. This can be described by a lower dielectric constant close to the interface. The second one is that at least one water molecule must be desorbed. Both effects lower the metaladsorbate interaction energy compared with vacuum. A microscopic approach to δ(∆Gsolv)calls for molecular dynamics (or Monte Carlo) simulations.66,67 Being designed for bulk solvation, continuum models such as COSMO and IEFPCM cannot be used directly. These models do not, for example, address the crucial feature of spatial dielectric permittivity dispersion at the interface.68 Instead, we estimate δ(∆Gsolv) as the difference between the bulk solvation free energies for media with different dielectric constants ():

δ(∆Gsolv) ≈ ∆Gsolv,)5 - ∆Gsolv,)80

(2)

The value of was taken as ) 80 for the aqueous solution bulk and as 5 in the interlayer corresponding to the vibrational solvent modes. Table 6 shows that δ(∆Gsolv) for the zwitterion is about 4 times larger than that for the Cys molecule and radical because of increased electrostatic solvation free energy. A molecular-level description of the interaction of the Cys zwitterion with the metal surface was also attempted. Four water molecules were included to model the solvation sheath. A small number of solvent molecules appears to be enough to provide stabilization on the gold surface, otherwise the zwitterion turns into the adsorbed Cys radical. Two different orientations were explored (Figure 6c,d), similar to those considered for the Cys radical (Figure 4 g,h). The adsorption energy for the zwitterion was estimated by eq 1. The solvent molecules were not included in the calculations (63) Barone, V.; Cossi, M. J. Phys. Chem. 1998, 102, 1995-2001. (64) Cance`s, E.; Mennucci, B.; Tomassi J. J. Chem. Phys. 1997, 107, 30323041. (65) Fernańdez-Ramos, A.; Cabaleiro-Lago, E.; Hermida-Ramoń, J. M.; Martıńez-Nuń˜ez, E.; Penã-Gallego, A. J. Mol. Struct. (THEOCHEM) 2000, 498, 191-200. (66) Ignaczak, A.; Gomes, J. A. N. F.; Romanowski, S. J. Electroanal. Chem. 1998, 450, 175-188. (67) Pecina, O.; Schmickler, W. Chem. Phys. 2000, 252, 349-357. (68) Kharkats, Yu. I.; Nielsen, H.; Ulstrup, J. J. Electroanal. Chem. 1984, 169, 47-57.


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Figure 6. (a) Optimized structures of bare Cys zwitterion with numbered atoms adsorbed on the bridge site of the Au12 cluster. Displayed (b) with and (c,d) without the water molecules (c orientation I, d - orientation II).

of the total energies, but the total energy of the zwitterion-metal cluster system was computed using the optimized adsorbate geometry obtained in the previous calculations. The corresponding values and the atomic coordinates along the normal to the surface are compiled in Table 1C. The zwitterion adsorption energy is smaller than that for the other Cys forms, with a negligibly small PCT to the metal cluster upon adsorption (Table 4). Since practically no difference between the ∆Eads values for two orientations of the zwitterions was found, coexistence is probable (at least for the uncharged metal surface). A Au-S bond length of =3 Å was obtained for both orientations. The carboxyl group approaches close to the metal surface in orientation I (Figure 4c), giving a Au-O bond length of 2.66 Å. The Au-N adsorption bond length is 3.23 Å in orientation II (Figure 4d). Both distances exceed those for the Cys radical in similar orientations. The resulting zwitterion adsorption energy from aqueous solution is small (Tables 1C and 6). However, the total dipole moment components (µ⊥ and µF) characterizing the orientation of the adsorbed zwitterion (Table 4) point to a key role of intermolecular interactions in the further stabilization of a monolayer. The lateral projections µF are large for both orientations, while the µ⊥ values are nearly equal but with opposite sign. Evidence of zwitterionic L-Cys in a SAM on Au(111) based on TPD, Cs+ reactive ion scattering and low-energy secondary ion MS was provided recently.19 The Cys anion was found to have the largest computed δ(∆Gsolv) (Table 6), while δ(∆Gsolv) is approximately the same for the molecule and radical. Despite a noticeable loss in adsorption energy due to partial desolvation, the anion-metal adsorption bond remains the strongest. As the number of water molecules desorbed depends insignificantly on the Cys form, the solvent effects therefore do not change the adsorption order obtained in section 4, that is, the order remains anion > molecule ≈ radical < zwitterion (Table 1A-C). The large lateral dipole moments of the adsorbed Cys molecule and radical (Table 4) hold a clue to the formation of the ordered monolayer, illustrated by the following simple model. The pair interaction (Up-p) between two molecules or radicals are treated

Figure 7. (A) Selected arrays of the Cys molecules (radicals). Arrows point in the direction of the longitudinal dipole moment component (µF). (B) total electrostatic energy of the interaction between the Cys molecules (a) and radicals (b) (referred to one particle, Ucoul/n kT) adsorbed on a Au12 cluster (hollow site) composed of the arrays in panel A, as a function of the particle number (n).

as purely electrostatic:

Up-p )

qiqj

∑ i* j r

(3) ij

where qi(j) are the atomic charges, and rij is the distance between two point charges. The atomic charges were computed in the ChelpG scheme,69 which offers the best fit to molecular electrostatic potentials. We restrict ourselves to specific arrays that mimic monolayer clusters with close-packed lattice structure (Figure 7A). A distance of 5.76 Å (twice the closest Au-Au distance) was used for the lattice constant. A similar approach has been used to study a monolayer of solvent molecules at a neutral metal surface.70 The lateral components of the dipole vector of each molecule (radical) are aligned along a given direction (Figure 7A), while all z-coordinates were taken from Table 1A-C. (Changes in the geometry of adsorbed species due to the lateral interactions are neglected.) Such an orientation is favorable.70 The results obtained by the summation of all Coulombic interactions within the monolayer fragments referred to a single particle (Ucoul/n) are shown in Figure 7B, with hollow site adsorption for both Cys forms. It is seen that Ucoul/n is negative, which points to electrostatic stabilization, and the Coulombic interactions are stronger for the Cys molecule than for the radical. Moreover, Ucoul/n increases with an increasing number of particles, most strongly for small arrays (n < 4) and more slowly for n > 4, reaching a plateau. Stabilization of Cys SAMs on the Au(69) Breneman, C. M.; Wieberg, K. B. J. Comput. Chem. 1990, 11, 361-373. (70) Parsons, R.; Reeves, R. M. J. Electroanal. Chem. 1981, 123, 141-149.

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(111) surface can therefore be understood from electrostatic interactions between dipoles in a simple lattice. The plateau for both Cys species is reached at n ≈ 6 (Figure 7B). Six-molecule Cys clusters on the Au(111) surface might thus be favored, as observed.22 Ucoul/6 ≈ -4.7 kcal mol-1 (Figure 7B) for an array of six Cys molecules (approximately -2.3 kcal mol-1 for the Cys radical). Adding this value (comparable to the energy of a H bond) to the adsorption energy of a Cys molecule in the hollow site (Table 1A), we obtain a value of ∼30 kcal mol-1. This accords with the adsorption energy of alkanethiols on Au(111) (≈ 31.5 kcal mol-1) obtained by TPD.71 Estimations based on this model do not predict “lateral” stabilization for the Cys radical adsorbed in the bridge-NS orientation (Figure 4h). In this case, Ucoul/n is positive, indicative of repulsion between the adsorbed particles.

states would open new electron transfer channels through temporarily populated and depopulated surface states in vibrationally dynamic or sequential modes.30,75 Such modes could be disclosed by in situ STM current-voltage spectroscopy, but this will not be addressed in the present report. In the framework of first-order perturbation theory, the resonance exchange factor is

7. Computation of STM Image Contrasts

where e is the electronic charge, and Ucoul is the Coulomb part of the Fock operator (electrostatic potential) used in the quantum chemical calculations (Supporting Information S2). The exchange potential can be neglected since it decays significantly faster with increasing interatomic distance. In a vacuum, Ucoul takes the form

The STM process has been addressed as a three-channel transition in the spirit of scattering theory72 and other three-level or bridge-assisted charge-transfer processes.29,30,73-75 The three channels are the electrode, the adsorbed Cys species, and the tip. The Cys forms are strongly coupled to the gold electrode. This corresponds to the strongly adiabatic limit of electron transfer between an adsorbed molecule and a metal electrode. The adsorbate-tip interaction is, however, weak, and tunneling is controlled by this contact. This holds the following implications: • The process can be viewed as a superexchange between the substrate and the tip, electronically mediated by the adsorbed Cys species. The Cys HOMO or LUMO are not directly populated.3,75 The superexchange scheme was checked in a set of computations on the three Cys forms, that is, the molecule, the radical, and the zwitterion (with an additional electron). The species geometry was fixed as obtained in the previous cluster calculations. Screening by the fast solvent modes was incorporated by a value of 1.8 for the dielectric constant in the PCM computational scheme. The HOMO energies of the charged species were found to range from -1.9 eV (the molecule) to -0.84 eV (the radical) and -0.1 eV (the zwitterion). These values are widely different from the Fermi energies of the tip and metal surface and support the superexchange view. • Superexchange is equivalent to a view of the tip states as being electronically weakly coupled to the combined, substrateadsorbate state, broadened in the Anderson-Newns scheme.76-78 This view79 is the conceptual basis for the present computations. • The tunneling probability is approximately proportional to the square of the resonance integral, |Vif|2, coupling the tip to the combined substrate-adsorbate complex. |Vif|2 is thus the direct basis for the computed electronic contour plots and STM contrasts. • The computational scheme rests on a purely electronic transition (including structurally optimized adsorbed Cys configurations). Evidence of localized, energetically low-lying Au-S surface electronic states has, however, been reported.80,81 Such (71) Lavrich, D. J.; Wetterer, S. M.; Bernasek, S. L.; Scoles, G. J. Phys. Chem. B. 1998, 102, 3456. (72) Schiff, L. I. Quantum Mechanics, 3rd ed.; McGraw-Hill: Tokyo, 1968. (73) Kuznetsov, A. M.; Ulstrup, J. Chem. Phys. 1991, 157, 25-31. (74) Schmickler, W.; Widrig, C. J. Electroanal. Chem. 1992, 336, 213-221. (75) Kuznetsov, A. M.; Ulstrup, J. Probe Microsc. 2001, 2, 187-200. (76) Anderson, P. W. Phys. ReV. 1961, 124, 41-53. (77) Newns, D. M. Phys. ReV. 1969, 178, 1123-1135. (78) Koper, M. T. H.; Mohr, J.-H.; Schmickler, W. Chem. Phys. 1997, 220, 95-114. (79) Zhang, J.; Chi, Q.; Albrecht, T.; Kuznetsov, A. M.; Grubb, M.; Hansen, A. G.; Wackerbarth, H.; Welinder, A. C.; Ulstrup, J. Electrochim. Acta 2005, 50, 3143-3159. (80) Gregory, B. W.; Clark, B. K.; Standard, J. M.; Avila, A. J. Phys. Chem. B 2001, 105, 4684-4689.

Vif )

∫ψiVˆ iψfdΩ

(4)

where ψi and ψf are the donor and acceptor one-electron molecular orbitals, respectively. Vˆ i is the perturbation that induces electron transfer between the tip (donor) and the adsorbate (acceptor):

V ˆ ) Ucoule

Zi

(5)

∑i |RB - b|r ∑j ∫

r )Ucoul(b)

+

|ψj(b r /) |2dΩ/

i

|b r / - b| r

(6)

where Zi and B Ri are the charge and radius-vector of the ith nuclear core, respectively. Equation 6 can be significantly simplified using a set of atomic charges (q/i ) calculated by the ChelpG method69 (section 6):

r ≈ Ucoul(b)

q/i

∑i |RB - b|r

(7)

i

which was used in the following. In general, Ucoul includes a contribution from the bias voltage. This is, however, small and weakly distance dependent compared with Ucoul and is therefore unimportant in the calculations. The STM images are isosurfaces built for the constant current mode. Since the resonance integral Vif is the only factor in the tunnel current,3,30,75 which depends significantly on the adsorbatetip distance, the contour |Vif|2 ) constant is qualitatively similar to the constant current surface and is isomorphic with the STM images. |Vif|2 is scaled to a value of 3 × 10-7 eV2 for |Vif|2, close to the diabatic limit of electron transfer. Computations corresponding to significantly diabatic transitions, that is, much smaller |Vif|2, are not reliable since Gaussian basis sets58 do not provide correct descriptions of the wave function tails. Solvent effects were taken into account by scaling the perturbation as Vˆ /*, where * is an effective dielectric constant. This does not affect the shape of the computed STM images. The STM tip was represented as a tungsten atom or small tungsten cluster. The valence orbitals (5s, 5p, 5d, 6s, 6p) were described by a basis set of DZ quality.57 The inner electrons were addressed by the ECP.57 A detailed description of the electronic structure of a W tip including the most important 5d electrons is thus included. The s-wave approximation in the TersoffHaman theory52 is otherwise commonly used to model the STM tip. The STM tip was also modeled by Tsukada et al.82 using (81) Avila, A.; Gregory, B. W.; Clark, B. K.; Standard, J. M.; Cotton, T. M. Langmuir 2002, 18, 4709-4719. (82) Tsukada, M.; Kobayashi, K.; Isshiki, N. Surf. Sci. 1993, 242, 12-17.


Langmuir, Vol. 22, No. 18, 2006 7565

small W clusters. Other STM tip models have included a jellium sphere83 or a single W atom on a W(110) surface.84,85 The highest occupied orbital of a W atom or cluster with the charge -1 was used as the initial-state wave function (ψi). Since 5d-electronic states of W- are degenerate, the 5dz2 dangling orbital, which provides the best overlap with the wave function ψf, was chosen to compute Vif. ψf was treated as the HOMO of the adsorbed species with charge -1. The optimized adsorbate geometry (section 5) was used. The overlap of the tip states with the electronic adsorbate states depends on the position of the tip and substrate. The influence of the metal surface on the atomic charges was disregarded because the contribution of the Au atoms to ψf was found to be small. Additional calculations using timedependent density functional theory (TD DFT) as implemented in the Gaussian 98 suite showed that the nearest electronic states of the Cys radical bearing the charge -1 × e is more than 2.3 eV higher than the HOMO. This energy gap is well above the bias voltages used, and the frontier orbital approximation is therefore adequate. Calculation of Vif using Gaussian-type atomic orbitals58 gives three-center integrals for which exact, although cumbersome, analytical expressions have been derived. Such expressions for s-orbitals are given as Supporting Information S2. Details of the contribution of the different atomic orbitals to the STM contrast can be examined using the parameter ξ:

V Rif )2 ∑ R∈ I

( ξ)

Vif2

(8)

where V Rif is the contribution to the overall Vif from the atomic orbital R of a given atomic group I. This parameter is the basis for the isosurface contour plots shown in Figures 8-10. Two computed STM images of a Cys molecule adsorbed a-top on the Au(111) surface were compared for a W atom and a small tetrahedral W cluster W4(3+1) representing the tip. Both contours were quite similar. Analysis showed that the main contribution to Vif is from the W atom 5dz2 orbital closest to the adsorbate, in accordance with ref 82. In most calculations, the tip was therefore modeled solely as a W atom.

8. Discussion and Comparison with Experimental In Situ STM Contrasts of Cys The physical mechanisms of STM and in situ STM rest on single-molecule electronic conductivity and interfacial electron transfer. Interpretation of STM images of intermediate size and large molecules remains a challenge because image recording must be combined with large-scale computations of electronic structures and electronic conductivity. Cys is adsorbed on Au(111) surfaces in a highly ordered (3x3 × 6) R30° lattice in aqueous acetate buffer, pH 4.6. The adlayer has been mapped by in situ STM to higher resolution in the present study than it had been previously, and submolecular features can be clearly distinguished. This has warranted computational efforts based on electronic structure analysis of the Cys molecule, the (neutral) radical, and the zwitterion adsorbed in different configurations on the top, hollow, and bridge sites of a variable-size Au(111) (83) Schmickler, W.; Henderson, D. J. Electroanal. Chem. 1990, 290, 283291. (84) Doyen, G.; Koether, E.; Barth, J.; Drakova, D. In Scanning Tunneling Microscopy and Related Methods; Behm, R. J., Garcia, N., Rohrer, H., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1989. (85) Sautet, P. Chem. ReV. 1997, 97, 1097-1116. (86) Go¨rbitz, C. H.; Dalhus, B. Acta Crystallogr., Sect. C 1996, 52, 1756.

Figure 8. Model STM contrasts (contour isosurfaces |Vif|2 ) const ) 3 × 10-7 eV2) built for the three neutral Cys forms adsorbed on the Au(111) surface in different orientations: molecule, a-top (a) and hollow (b); zwitterion, orientation I (c) and II (d); radical, a-top (e), hollow (f), and bridge-NS (g). Axis dimension are given in angstroms.

cluster surface. As noted in section 5.1, there is no difference in electronic structure between the adsorbed anion and radical forms going to infinitely large metal clusters. This is why the main focus was not on the Cys anion. The electronic structure computations have illuminated details of the adsorption geometry and energies of the three Cys forms. An important observation is that the Cys radical adsorption is favorable in approximately neutral form. This is in keeping with both electrochemical reductive desorption and previous electronic structure reports on Cys and other thiol-based molecules.24,25,35-43,45-51 Adsorption energy differences in the a-top, threefold hollow, and bridge sites are small and would be affected significantly by lateral interactions and solvation effects. Solvation effects were estimated by combining the computed dipole moments of the adsorbed Cys species with a computation of the lateral attractive electrostatic interactions in variable-size two-dimensional Cys clusters. These estimates are crude, but do suggest that collective lateral interactions stabilize at a cluster size of six Cys molecular entities. This size emerges as a compromise between energetically attractive forces and en-

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Figure 9. Cross-sections along the XZ plane of the model STM contrast built for the Cys radical adsorbed a-top (Figure 8e); Y ) -1.5, 2, and 4 Å.

tropically limited larger clusters and accords with the observed cluster size in both our previous and present reports. The electronic structure features were converted to electronic conductivity using concepts of bridge-group-assisted molecular electron transfer.3,75 Specific electronic properties of the tungsten tip have been introduced. The electron transport has been recast directly in the form of constant current STM height profiles as the common in situ STM mode. The models used are “generic” in the sense that only a single Cys species is included in the electronic structural frame. Combined with the high-resolution in situ STM images, the computations still illuminate important image features, distinctive of particular electronic features and Cys adsorption modes. This warrants comparison with the experimental high-resolution in situ STM data. The experimental in situ STM images disclose clear submolecular features, with a bilobed single-molecule image form. The computations show that the different computed Cys forms differ significantly in both apparent heights and lateral extension (Figure 8). The molecular and zwitterionic forms are clearly more expanded, both laterally and vertically, than the radical form, which is notably better in keeping with the data. This originates from the different structure of the acceptor orbitals of adsorbed Cys species. For example, a significant contribution to the HOMO of the radical results from the 2pz orbital of the sulfur atom, while the contributions from the S and C atoms are comparable for the molecular form. The S, C, O, and N atoms contribute noticeably to the zwitterion acceptor orbital. The HOMO of the radical should therefore be more localized compared with that for the Cys molecule and the zwitterion. Taking approximately neutral Cys radical form as best in keeping with the lateral extension of the observed molecular features, another computed feature emerges. The radical but not the anion shows submolecular features (Figure 8 and 9). The features are more pronounced and “bilobe-like” for the a-top position than they are for the hollow and bridge-NS position. The pronounced submolecular feature is seen clearly in the crosssection of the a-top adsorbed Cys radical (Figure 9). The zwitterion and the Cys molecule do not show similar submolecular STM resolution (Figure 8). The two lobes have comparable contribu-

Figure 10. Model contour isosurfaces (|Vif|2 ) const ) 3 × 10-7 eV2) built for the Cys radical adsorbed a-top and showing the contributions of specific atoms, (a) sulfur, (b) nitrogen, and (c) carbon, to the resulting three-dimensional STM image (Figure 8e). Axis dimensions are given in angstroms.

tions from the bound S end and the remote -NH2/-COOH part (cf. Figure 10). This can be compared with the pattern for cysteamine, for which in situ STM contrasts also hold contributions from the S- and -NH2 parts, but is dominated by the latter with no bilobe feature. Within the crude computational model, the Cys radical in a-top position and in tilted orientation thus accords best with the experimental high-resolution in situ STM data. This conclusion is tentative and subject to reservations regarding the model size, absence of solvent and buffer, and so forth. In these respects, they follow other reported computations of Cys adsorption. As in ref 40, the analysis, however, illustrates the degree of detail accessible when high-resolution experimental data and computations are combined.

9. Concluding Remarks In situ STM for Cys adsorption on Au(111) electrode surfaces at a new level of submolecular resolution has been achieved and compared with electronic structure computations of Aun-Cys cluster models in different electronic and molecular structural configurations. The cluster models are crude representations of the real Au-Cys interactions but offer a useful frame for important trends in the nature of the metal-adsorbate bond and the molecular electronic conductivity and STM contrasts. The computed electronic structures have been the basis for the estimation of lateral adsorbate interactions, pointing to six-molecule cluster assemblies as being particularly favorable. The models are


distinctive to the adsorption modes and electronic structures, suggesting that Cys radical adsorption is the most favorable. The models are also reflected differently in the electronic and molecular structural features of the Aun-Cys complexes in the STM contrasts. A-top Cys radical adsorption is best in keeping with the observed bilobed single-molecule in situ STM contrasts resolved to the submolecular level. There are two possible reasons why zwitterions are not assembled in an adsorbed monolayer at the Au(111) electrode surface. The most favorable structure of a layer of Cys zwitterions would require an ordered lattice with adsorbed zwitterions in two different orientations (section 6). The formation of such a layer (in part, reorientation processes) may require long time scales. Second, an ordered structure may be highly sensitive to the electrical double layer and simply may not be formed in the strong field at the interface. The computational approach holds perspectives for other related systems, such as the dimeric Cys form, cystine. High-resolution in situ STM images of Cys and cystine are indistinguishable,22

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posing dissociative adsorption as a challenge. Other challenges involve more rigorous computational schemes, larger-scale models, and comprehensive solvent representations combined with the construction of STM images and tunneling spectroscopy. Acknowledgment. It is a pleasure to thank Galina A. Tsirlina, Alexander M. Kuznetsov, and Dmitrii V. Glukhov for helpful discussions. Financial support from the EU program INTAS 99-1093, Russian Foundation of Basic Research (Project Nos. 03-03-2006 and 05-03-32381a) and the Danish Research Council for Technology and Production Sciences (Contract No. 56-000034) is acknowledged. Supporting Information Available: (S1) Optimized SCF and DFT bond lengths of an L-Cys molecule from different basis sets and (S2) analytical expression for the electron exchange factor for the electrostatic coupling between two s-like orbitals, ψi and ψf. This material is available free of charge via the Internet at http://pubs.acs.org. LA060472C

Adsorption and In Situ Scanning Tunneling Microscopy of Cysteine on

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