Photoemission Study of Thymidine Adsorbed on Au(111) and Cu(110

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J. Phys. Chem. C 2010, 114, 15036–15041

Photoemission Study of Thymidine Adsorbed on Au(111) and Cu(110) Oksana Plekan,*,† Vitaliy Feyer,† Sylwia Ptasin´ska,‡ Nataliya Tsud,§ Vladimı´r Cha´b,# Vladimı´r Matolı´n,§ and Kevin C. Prince† Sincrotrone Trieste S.C.p.A., in Area Science Park, Strada Statale 14, km 163.5, I-34012 BasoVizza, Trieste, Italy, Department of Physics and Astronomy, The Open UniVersity, Walton Hall, Milton Keynes, MK7 6AA, United Kingdom, Faculty of Mathematics and Physics, Department of Surface and Plasma Science, Charles UniVersity, V HolesˇoVie`ka´ch 2, 18000 Prague 8, Czech Republic, and Institute of Physics, Academy of Sciences of the Czech Republic, CukroVarnicka´ 10, 16253 Prague 6, Czech Republic ReceiVed: June 10, 2010; ReVised Manuscript ReceiVed: July 13, 2010

The adsorption geometry of the DNA nucleoside thymidine on Au(111) and Cu(110) surfaces has been determined from experimental results of soft X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The XPS of C, N, and O 1s as well as the absorption spectra at the N and O K-edges were measured for monolayer thymidine films, and the nature of the bonding with the two metal surfaces has been determined. The NEXAFS data at the N and O K-edge show a strong angular dependence of the π*/σ* intensity ratios. We conclude that the thymine moiety is lying nearly parallel to the Au(111) surface, while on the Cu(110) surface, it adsorbs at a steep angle. Introduction The adsorption of biomolecules on metal surfaces, analyzed by advanced surface science techniques, is an important topic nowadays and is relevant to the understanding of the interface phenomenon in nanomechanical biosensors, organic semiconductors, biochemistry, and pharmacology.1-5 The molecular systems studied in the past decade have been continuously growing in complexity. One area that has been studied extensively, both experimentally and theoretically, is selfassembled monolayers of molecules with several kinds of interacting functional groups present in nucleobases or amino acids.6-10 It is generally expected that for such molecules with multifunctional groups a hierarchical self-assembly process exists.7,8 At low surface coverage, directional bonds determine the formation of supramolecular structures of adsorbed molecules, while with increasing surface coverage, the weaker interaction such as van der Waals or hydrogen bonding become more important. Thymidine is one of the nucleosides and is a building block of DNA. Its structure consists of the pyrimidine base thymine bonded to a deoxyribose moiety via a C-N glycosidic bond (see Figure 1). Because of the complexity of thymidine’s molecular structure, most previous studies were focused on its subunits, mainly, thymine. A variety of experimental techniques such as reflection absorption infrared spectroscopy (RAIRS), photoelectron diffraction (PhD), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) together with theoretical approaches have been used to study the adsorption of thymine nucleobases on different metal surfaces.11-19 Applying dipole selection rules in the measurement of angle* To whom correspondence should be addressed. Phone: +4589423774; fax:+45 8612 0740; e-mail: [email protected]. Permanent address: Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark. † Sincrotrone Trieste S.C.p.A. ‡ The Open University. § Charles University. # Academy of Sciences of the Czech Republic.

Figure 1. Molecular structure of thymidine (C10H14N2O5) with labeled atoms in the nucleobase unit.

resolved ultraviolet photoelectron spectroscopy, Rocco et al. reported that thymine molecules in the monolayer phase adsorbed on Cu(110) in a standing-up geometry.11 Later RAIRS data also indicated that in the temperature range from 300 K up to 558 K the adsorbed thymine has its molecular plane essentially perpendicular to the Cu(110) surface.12,13 In these studies, bidentate surface interaction via deprotonated N3 and C2dO functionalities was proposed leaving the N1-H and C4dO groups free to engage in intermolecular hydrogen bonding. The upright position of thymine at low coverage was also clearly evidenced by angular-resolved NEXAFS by Furukawa et al.,14 where the chemical shifts observed in N 1s and O 1s XPS spectra implied coordination via only the deprotonated N3 atom. The qualitative controversies over the local bonding of thymine to Cu(110) were resolved by Allegretti et al. using scanned-energy mode photoelectron diffraction (PhD).15 These data showed that the molecules bond to the copper surface through both carbonyl O atoms and the deprotonated N3 atom. The molecular plane lies almost exactly in the close-packed [11j0] azimuth, but it tilts by ∼20° relative to the surface normal.15 Haiss et al. and Li et al. using infrared spectroscopy and scanning tunneling microscopy (STM) reported that thymine on Au(111) electrode surfaces adsorbed in anionic form with tridentate coordination in which the deprotonated N3 and both CdO groups participated in the bonding to the surface.16,17 This

10.1021/jp105341k  2010 American Chemical Society Published on Web 08/12/2010

Study of Thymidine Adsorbed on Au(111) and Cu(110) geometry is similar to that proposed by Allegretti et al. for thymine on Cu(110).15 In contrast, on the Au(111) surface, Xu et al. using STM recently reported that at low coverage selfassembled thymine lies essentially parallel to the surface and forms dimer filaments stabilized by hydrogen bonds, while at high coverage, dimer islands have been observed.18 These structures were previously predicted by density functional theory (DFT) and post-Hartree-Fock calculations, where the isolated bases are found to lie flat on the gold surface, but at higher coverage, base-base interaction becomes competitive with base-surface interaction.19 Recently, we have investigated coverage-dependent behavior of nucleobases, and it was shown that at low coverage the adenine molecule adsorbs on Cu(110) nearly parallel to the surface, while at high coverage, the molecular plane is strongly tilted.20 The nucleosides such as thymidine (dT) can serve as models for the understanding of the adsorption behavior of DNA. However, spectroscopy studies dedicated to the investigation of nucleosides are very limited. Using STM, Yang et al. found that deoxyribose groups of thymidine adsorbed onto Au(111) surface have remarkably enhanced intermolecular interaction.21 At low temperature, molecules form the dimer structure on the surface, while at room temperature, the thymidine molecules aggregate into well-ordered dimer islands. However, the chemical nature of the adsorbents is not usually determined from STM studies; therefore, in the present work, we have used the XPS technique to provide this information. In addition, NEXAFS spectroscopy was used since it is sensitive to the molecular adsorption geometry. The Au(111) surface was chosen as an inert substrate22 to minimize molecule-surface interaction thus allowing dominance of the self-assembly processes by intermolecular interactions. Cu(110) is another interesting metal surface because of its higher reactivity in comparison with Au(111), which may lead to stronger molecule-surface interaction.10 Experimental Section The experiments were performed at the Materials Science Beamline at the Elettra synchrotron light source in Trieste,23 and the experimental details are very similar to those described in ref 20. During the experiments, the base pressure in the main chamber was about 10-10 mbar. The C 1s and N 1s XPS spectra were recorded in normal emission (incidence/emission angles of 60°/0°) using the multichannel Specs Phoibos electron energy analyzer. The photon energy and the total resolution were 500 and 0.45 eV, respectively. The O 1s core level spectra were measured with the same analyzer using Al KR radiation as the ionization source, and the total energy resolution was 1.0 eV. This source was also used to measure C 1s and N 1s spectra in test measurements before the synchrotron radiation experiments. The binding energy (BE) scale was calibrated by measuring the Fermi edge. The NEXAFS spectra were taken at the N and O K-edge using the nitrogen and oxygen KVV Auger yield at normal (NI, 90°) and grazing (GI, 10°) incidence of the photon beam with respect to the surface. The polarization of light from the beamline has not been measured, but it is believed to be between 80 and 90% linear as the source is a bending magnet. The energy resolution in NEXAFS was estimated to be 0.8 eV. The raw NEXAFS data were normalized to the intensity of the photon beam. The Au(111) and Cu(110) single crystals were cleaned using standard procedures of cycles of Ar ion sputtering (kinetic energy 1.0 keV) followed by flashing to 870 K. The surface

J. Phys. Chem. C, Vol. 114, No. 35, 2010 15037 order and cleanliness were monitored by low-energy electron diffraction (LEED) and XPS. Contaminants (such as C, N, and O) were below the detection limit. The Cu(110) crystal was mounted with its [001] crystallographic direction in the horizontal plane, that is, perpendicular to the manipulator rotation axis. Thus, in the NEXAFS experiment, the E-vector was perpendicular to the close-packed copper rows and was along the [001]-direction at normal incidence and was nearly normal to the surface ([110]-direction) at grazing incidence. Thymidine (99.5% purity) was obtained from Sigma Aldrich and was used without further purification. The deposition was done in a separate preparation chamber with base pressure 5 × 10-9 mbar using a homemade Knudsen cell type evaporator. First, the thymidine (referred to as dT hereafter) powder was degassed in vacuum at 350 K and then was heated to 375 K and was dosed onto the metal surfaces. The deposition rate was approximately 1.0 monolayer (ML) in 300 s. The single ML of dT was prepared by adsorbing a multilayer film on the surfaces and then by flashing to 350 K to desorb the weakly adsorbed thymidine species. The desorption yields characterized by the decrease of the integrated intensities (areas of peaks) of C 1s, N 1s, and O 1s measured with Al KR excitation remained constant in the range of temperature between 325 and 375 K, and we define the coverage obtained under these conditions as 1 ML. Organic molecules have a tendency to dissociate when exposed to ionizing radiation; to check for radiation damage, valence band photoemission spectra of the multilayer and monolayer films were measured at 120 eV photon energy, where the beamline has a high photon flux and the cross section for absorption is high. No spectral changes were observed after 1 h, so we believe that dT is reasonably stable under our experimental conditions; at higher photon energies, fluxes and cross sections are generally much lower. Results and Discussion 3.1. C, N, and O 1s Core Level Spectra. The experimental C 1s, N 1s, and O 1s photoemission spectra of multilayer and monolayer coverages of thymidine on Au(111) and Cu(110) crystals are presented in Figure 2. The multilayer coverage of dT on Au(111) and Cu(110) was determined to be 1.7 and 1.5 ML, respectively. For comparison, the corresponding spectra of thymine in the gas phase24 are also shown in the same figure. The energies of the observed spectral features and proposed assignments are listed in Table 1. 3.1.1. Au(111). The gas-phase C 1s spectrum of thymine shows four distinct peaks A, B, D, and E. These peaks were assigned to urea carbon (C2), amide carbon (C4), carbon bound to nitrogen (C6), and hydrocarbons (C5 and C7), respectively.24 These assignments are also in agreement with published C 1s spectra of thymine thin films;26-28 however, the spectra for thymidine showed broader structures in comparison with the gas-phase spectrum because of the lower resolution and solidstate effects. The C 1s spectrum of one monolayer of dT resembles the corresponding spectrum of poly(dT)25 oligonucleotides self-assembled on a gold substrate.25 The C 1s spectrum was fitted with five Gaussian functions (A-E) to yield an intensity ratio for the features of 1:1:1:3.8:2.9, respectively, which is quite close to the stoichiometric ratio for 10 carbon atoms, 1:1:1:4:3. Upon bonding of thymine to the deoxyribose ring to form the nucleoside, an additional carbon peak appears in the C 1s spectra because of carbon in the deoxyribose. On the basis of the thymine C 1s peaks’ assignment and expected stoichiometric ratio in the dT C 1s spectrum, we attribute the

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Figure 2. C (a), N (b), and O (c) 1s core level spectra of thymidine adsorbed on Au(111) and Cu(110); photon energy: 500 eV. Lines: Gaussian peaks fitted to the spectra. The thymine gas phase spectrum24 has been shifted to lower values by 6.7, 6.0, and 5.5 eV for the C, N, and O 1s edges, respectively.

TABLE 1: C, N, and O 1s Binding Energies of dT Adsorbed on the Au(111) Surface C-C, C7, C5

C-N, C-OH, C6

thymidine ML on Au(111) thymine film on Au(111)27

284.25 (E) 285.58

285.55 (D) 286.73

poly(dT)25 oligonucleotides on gold substrate25

284.4

285.5

C-O-C

C4

C2

286.80 (C)

287.50(B) 288.86

288.45 (A) 289.96 401.46 288.3

286.9

additional peak C in the spectrum to the carbon atom of the glycosidic bond. The three carbon atoms bonded to oxygen (alcohol (C-OH) and cyclic ether (C-O-C)) in the deoxyribose ring contribute to the feature D, while the hydrocarbon atoms of the sugar ring contribute to peak E.25,26 The energy separation of the features in the gas-phase thymine spectrum and the corresponding peaks in dT spectra are very similar (see Figure 2a). This suggests that the carbon atoms of dT adsorbed on the Au(111) surface are not strongly involved in the molecular-surface or intermolecular interactions. The N 1s spectra of multilayer and ML coverages of dT on Au(111) are shown in Figure 2b. The full width at halfmaximum (fwhm) of the multilayer peak is about 1.6 eV and narrows to 1.25 eV for the monolayer spectrum. On the basis of this, the multilayer peak can be deconvoluted with two Gaussian functions A and B with fwhm ) 1.25 eV. The peak A at 400.40 eV is attributed to the dT species weakly bonded via van der Waals or hydrogen bond interactions. The feature B at 399.85 eV is related to the dT molecules lying closer to the surface in the first layer. The observed shift to lower BE is probably due to more efficient screening of core holes in the first layer molecules by the metal, that is, to a final state effect. The two nitrogen atoms in dT are both amines but are in different chemical environments, and so a small chemical shift is expected.24 Indeed, the N 1s XPS spectra of thick poly(dT)25 oligonucleotide films as well as thymine in the gas phase and solid state show single unresolved peaks.24,27,28 According to the surface-enhanced Raman scattering data, the dT molecule binds to gold nanoparticles via one oxygen atom and not via a nitrogen atom, as do all other nucleosides.29 In fact, for thymine chemisorbed on Au(111) via a nitrogen atom and in an upright

N1, N3

O8, O9

C-O-C,OH

399.85 400.86

531.60 (B) 532.30

532.65 (A)

401.0-400.5

531.7

533.3

position, a shift of 1.5 eV to lower BE was reported in the N 1s spectrum.30 Similar chemical shifts were also observed in the spectra of chemisorbed poly(dT)25 oligonucleotides adsorbed onto a gold substrate at low coverage.25 Our results indicate that nitrogen is not involved in strong (chemisorption) interaction with the Au(111) surface as no chemical shifts in N 1s XPS spectra are observed (see Figure 2b). The effect of adding the deoxyribose ring to the thymine nucleobase is clearly noticeable in the O 1s spectra (see Figure 2c). The spectrum was fitted with two Gaussians centered at 531.60 and 532.65 eV with full width at half-maxima (fwhm) of 0.69 and 0.75 eV, respectively, and an intensity ratio of A:B ) 3:2. The low BE peak B is assigned to the carbonyl oxygen atoms of the thymine moiety, while the feature A corresponds to the alcohol C-OH and cyclic ether C-O-C oxygen atoms of the deoxyribose. The previously reported O 1s spectrum of poly(dT)25 oligonucleotide films adsorbed on gold substrates also showed two prominent features at 531.7 and 533.3 eV of BE.25 However, for the ML of dT, the two features A and B have a significantly smaller BE difference of ∼1.05 eV, which we attribute to intermolecular hydrogen bonding involving the OH or ether groups. Recent STM studies of thymidine on Au(111) show that the deoxyribose group has a strong influence on the self-assembly behavior of dT on gold.21 In the model of Yang et al., the adsorbate-substrate interaction is laterally flat, and two dT molecules are linked together via O-H · · · O-R bonds of the sugar moiety and two pairs of N-H · · · O)R bonds via the thymine moiety. At low temperature, the lines of molecules are further connected by pairs of O-H · · · O-R bonds, which leads to a dense array.21 Thus, the adsorbed dT molecules are

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TABLE 2: C, N, and O 1s Binding Energies of Thymidine Adsorbed on Cu(110) C-C, C7, C5 C-N, C-OH, C6 thymidine on Cu(110) thymine on Cu(110)14,15

284.90 (E)

286.25 (D)

C4C-O-C

C2

287.50 (B/C) 288.40 (A)

stabilized by intermolecular hydrogen bonds between deoxyribose rings, which would shift the binding energy of the alcohol oxygen atoms toward that of the carbonyl oxygen atom of the thymine moiety. We have recently shown that hydrogen bonding can cause significant core level shifts for adenine adsorbed on Cu,20 and Nyberg et al. have shown that significant changes in the electronic structure occur because of hydrogen bonding between adsorbed glycine molecules.31 3.1.2. Cu(110). The C 1s XPS spectra of multilayer and monolayer thymidine on the Cu(110) surface are shown in Figure 2a. The features in the C 1s dT monolayer spectrum are labeled as in the above C 1s spectrum of dT adsorbed on Au(111) surface. The maxima A and B related to the urea (C2) and amide (C4) carbon atoms, respectively, have similar BE to the corresponding features in the C 1s spectrum of a dT monolayer on gold (see Figure 2), while the peaks corresponding to the other carbon atoms of thymine (C-N, C-OH, and C-O-C) and deoxyribose moieties are shifted by ∼0.75 eV toward higher BE. The energy separation between the features related to the thymine moiety of dT on Cu(110) is significantly smaller than that observed in the thymine gas phase spectrum (see Figure 2a). These differences suggest that dT is chemisorbed rather than physisorbed on Cu(110). The chemical states depend on the charges associated with the nucleobase and deoxyribose functional groups of dT, and as a result, energy shifts in the C 1s spectrum are observed. The N 1s XPS spectra of dT adsorbed on Cu(110) for multilayer and monolayer coverages are presented in Figure 2b. As noted above, thymidine contains two amino nitrogen atoms in its thymine moiety, and so their binding energies are expected to be very similar. This is so for dT adsorbed on Au(111) and for thymine in the gas phase and in the solid state,24,27,28 but the N 1s XPS spectrum of dT on Cu(110) shows two features (see Figure 2b). The relative intensities of these peaks in the multilayer and monolayer spectra are different. This difference is due to the change in the relative concentrations of weakly and strongly adsorbed species of dT samples at different coverage. The two nitrogen atoms of weakly bonded dT contribute to the feature A of the N 1s spectra. The chemical shifts of ∼1.7 eV in the N 1s spectrum (peak C) are clear evidence that one of the nitrogen atoms is bound to the surface. The lower BE peak is usually related to nitrogen with an unsaturated chemical bond, that is, imino N.32 The copper surface is more reactive compared with gold and can catalyze hydrogen loss. Therefore, we assign this peak (A) to deprotonated N3 of dT and the feature B to the N1 atom of the glycosidic bond. This assignment makes chemical sense as the N1 atom is a tertiary amine bonded to three carbon atoms, and there is steric hindrance to bond-breaking, whereas N3 is a secondary amine with a free hydrogen when the molecule is deposited. Our assignments are consistent with studies of thymine adsorbed on Cu(110), where two features in the N 1s XPS spectrum were observed.14,15 After annealing to 350 K (monolayer regime), the most weakly adsorbed dT molecules desorb, and as a result, the intensity of feature A decreases. On the basis of quantitative analysis, in the dT monolayer, 80% of the molecules are chemisorbed on the Cu(110) surface via dehydrogenated N3 nitrogen atoms, and there is a minority population of 20% of nonchemisorbed species.

N3 chemisorbed 398.80 (C) 398.70

N1

O8, O9

400.65 (B) 531.90 (B) 400.40 531.1

C-O-C,OH 533.70(A)

The O 1s XPS spectra of dT adsorbed on Cu(110) are presented in Figure 2c. They show two relatively well resolved features, and the monolayer spectrum has been fitted with two Gaussian functions (A and B) centered at 533.70 and 531.90 eV, respectively. As for the O 1s spectrum of dT adsorbed on the Au(111) surface, we assume that carbonyl atoms O8 and O9 of the thymine moiety contribute to the lower BE feature, while the higher BE peak A is related to the three oxygen atoms of deoxyribose. The intensity ratio between fitted peaks is 3:2 in agreement with the expected stoichiometric ratio. The energy separation between features A and B is 1.8 eV and is a little larger than the value of 1.6 eV in the O 1s XPS spectrum of a poly(dT)25 film.25 Also, the separation is larger than for dT on Au. On the basis of this, we believe that the carbonyl oxygen atoms contribute to the interaction with the surface, although the chemical shift is much smaller than for the N 1s core levels. Also, the BE of the feature related to carbonyl carbon atoms matches well the corresponding peak of thymine molecules chemisorbed on the same surface via two oxygen atoms.15 Overall, the most significant changes between adsorption on Cu and Au occur for the N 1s spectra with lesser changes for the C and O 1s spectra. This also supports our bonding model in which the largest chemical changes occur at the nitrogen site with weaker bonding via oxygen and with carbon being indirectly involved in the surface bond. 3.2. NEXAFS Spectra of Thymidine on Au(111) and Cu(110). We have analyzed the geometry of adsorbed dT using NEXAFS spectroscopy. Figure 3 shows the N and O K-edge NEXAFS spectra recorded at normal and grazing incidence with respect to the Au(111) and Cu(110) surfaces. The peak positions and assignments are summarized in Table 3. The nitrogen atoms in the dT molecule reside in the thymine nucleobase moiety, and so the N K-edge NEXAFS spectra can be used to selectively probe the nucleobase structure in immobilized dT. These spectra of dT adsorbed on Au(111) resemble the gas phase24 and the thin solid film thymine spectra.33-35 On the basis of our previous gas-phase results, the A, B, and C features in the spectra can be assigned to the excitation of N1 and N3 1s core electrons to the π*6 , π*7 , and π*8 unoccupied molecular orbitals, respectively.24 These peaks are shifted by ∼0.5 eV toward lower photon energy with respect to the observed features in the gas-phase thymine spectrum. However, the energies of the resonances match well with similar NEXAFS peaks of thin solid film thymine.35 The broad features D and E in the higher energy range are assigned to N 1s f σ* transitions. The similarities between the spectrum of dT adsorbed on Au(111) and those of the gas-phase and solid film thymine suggest that the nitrogen atoms of the nucleobase in dT are not strongly involved in the molecule-surface or intermolecular interactions. This is consistent with the N 1s XPS result mentioned above. In contrast, the N K-edge NEXAFS spectra of dT adsorbed on Cu(110) are drastically changed and show new peaks labeled A′ and B′. On the basis of the N 1s XPS spectra (Figure 2b), these features are related to the excitations of 1s electrons of the deprotonated chemisorbed N3 atoms to the unoccupied π* orbitals. The energy separation between the peaks A and A′ is 1.6 eV, while in the N 1s XPS spectra, the BE chemical shift is ∼1.8 eV. This indicates that the unoccupied π* orbitals shift because of the chemisorption of dT molecules

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Figure 3. N (a) and O (b) NEXAFS spectra of thymidine ML adsorbed on Au(111) and Cu(110) surfaces measured at grazing (GI) and normal incidence (NI).

TABLE 3: Peak Positions for the π* and σ* Resonances in the N and O NEXAFS Spectra present data dT on Au(111) N K-Edge π* resonance, (eV)

σ* resonance, (eV)

O K-Edge π* resonance, (eV) σ* resonance, (eV)

present data dT on Cu(110)

401.15 (A) 402.15 (B) 405.15 (C) 407.75 (D)

399.8 (A′) 401.4(A) 403.2 (B′) 404.8 (C) 408.0 (D)

416.15 (E)

416.15 (E)

531.6 (A) 532.6 (B)

531.8 (A) 532.6 (B)

537.2 (C) 541.0 (D)

537.2 (C) 541.0 (D)

thymine thin film35

on the Cu(110) surface. The N K-edge NEXAFS spectra of dT adsorbed on Cu(110) are similar to the spectra of thymine adsorbed at low coverage on the same surface.14 This suggests that the nucleobase moiety of dT and thymine adsorb similarly on Cu(110). The O K-edge NEXAFS spectra of dT adsorbed on Au(111) and Cu(110) are shown in Figure 3b. The peak positions and assignments are presented in Table 3. On the basis of the assignments of the gas-phase O K-edge NEXAFS spectra,24 the two low energy features A and B (531.57 and 532.57 eV in Figure 3b) are related to O8 1s f π*6 and O9 1s f π*7 transitions, respectively. The broad peaks C and D are attributed to excitation to σ* resonances of all oxygen atoms in dT.34,36 Both N and O NEXAFS spectra of dT adsorbed on Au(111) and Cu(110) show strong angular dependence (see Figure 3). In the case of Au(111) at GI, the π* resonances are stronger than the σ* resonances, while at NI, the π*/σ* intensity ratio reverses. The dipole moment of the 1s f π* transition is oriented perpendicular to the pyrimidine ring of the thymine moiety, and so the vanishing intensity of the π* resonances at NI indicates that the molecular plane of the nucleotide base in adsorbed dT lies parallel to the Au(111) surface. On the contrary, on Cu(110) at GI, the σ* resonances are stronger than the π* resonances and vice versa at NI (Figure 3). The angular

thymine thin film33

thymine (T) and dT thin films34

398.0-404.0

401.2 (T) 401.0 (dT)

407.0

408.0

407.0

415.0

415.0

416.0

530.5 532.0

531.0-534.0

532.0-550.0

538.0-540.0

401.1 402.0

400.7 401.5

405.0 408.0

531.2 532.8

thymine on Cu(110)14

531.8(T) 533.0 (T) 531.9(dT) ∼540.0 (T)

dependence of the π* resonance intensity varies as I ∝ cos2 θ,37 where θ is the angle between the E-vector and the orbital plane. Using this equation, we find that the nucleobase of dT adsorbs at a steep angle (∼78-83°) with respect to the Cu(110) surface, and the molecular plane of the pyrimidine ring is azimuthally oriented along the close-packed Cu[11j0] rows. 4. Conclusions Using synchrotron radiation based, high-resolution core level spectroscopies, the electronic structures and adsorption geometries of the DNA nucleoside thymidine on Au(111) and Cu(110) have been studied. The photoelectron spectra show that on Au(111), there is no evidence of chemical interaction with the surface, but instead, we find effects that are due to intermolecular hydrogen bonding. This confirms the conclusions of Yang et al.21 that the process of self-assembly of dT is stabilized mainly by intermolecular hydrogen bonds of the deoxyribose moiety. On the more reactive Cu(110) surface, the molecule-surface interaction dominates and dT chemisorbs on the surface via the deprotonated nitrogen atom of its thymine moiety. Thus, the higher reactivity permits dehydrogenation and formation of a Cu-N bond. The angular dependences of the N and O NEXAFS spectra show that on the gold substrate the thymine component of

Study of Thymidine Adsorbed on Au(111) and Cu(110) adsorbed dT is nearly parallel to the surface, while on the copper surface, it is in a nearly perpendicular configuration. Acknowledgment. We gratefully acknowledge the assistance of our colleagues at Elettra for providing good quality synchrotron light. The Materials Science Beamline is supported by the Ministry of Education of Czech Republic under Grant No. LC06058. S.P. acknowledges support from the Engineering and Physical Sciences Research Council EPSRC (EP/D067138/1), United Kingdom, and Electron Controlled Chemistry Lithography (ECCL, CM0601-05047). References and Notes (1) Wan, L. J. Acc. Chem. Res 2006, 39, 334. (2) Dimitrakopoulos, C. D.; Malenfant, P. R. L. AdV. Mater. 2002, 14, 99. (3) Shaheen, S. E.; Brabec, C. J.; Sariciftci, N. S.; Padinger, F.; Fromherz, T.; Hummelen, J. C. Appl. Phys. Lett. 2001, 78, 841. (4) Fritz, J.; Baller, M. K.; Lang, H. P.; Rothuizen, H.; Vettiger, P.; Meyer, E.; Guntherodt, H. J.; Gerber, C.; Gimzewski, J. K. Science 2000, 288, 316. (5) Kasemo, B. Surf. Sci. 2002, 500, 656. (6) Chen, Q.; Richardson, N. V. Nat. Mater. 2003, 2, 324. (7) Kuhnle, A.; Linderoth, T. R.; Hammer, B.; Besenbacher, F. Nature 2002, 415, 891. (8) Otero, R.; Scho¨ck, M.; Molina, L. M.; Lægsgaard, E.; Stensgaard, I.; Hammer, B.; Besenbacher, F. Angew. Chem. 2005,117, 231; 2005,44, 2270. (9) Xu, Q. M.; Wan, L. J.; Wang, C.; Bai, C. L.; Wang, Z. Y.; Nozawa, T. Langmuir 2001, 17, 6203. (10) Barlow, S. M.; Raval, R. Surf. Sci. Rep. 2003, 50, 201. (11) Rocco, M. L. M.; Dudde, R.; Frank, K.-H.; Koch, E.-E. Chem. Phys. Lett. 1989, 160, 366. (12) McNutt, A.; Haq, S.; Raval, R. Surf. Sci. 2002, 502-503, 185. (13) Yamada, T.; Shirasaka, K.; Takano, A.; Kawai, M. Surf. Sci. 2004, 561, 233. (14) Furukawa, M.; Fujisawa, H.; Katano, S.; Ogasawara, H.; Kim, Y.; Komeda, T.; Nilsson, A.; Kawai, M. Surf. Sci. 2003, 532-535, 261. (15) Allegretti, F.; Polcik, M.; Woodruff, D. P. Surf. Sci. 2007, 601, 3611.

J. Phys. Chem. C, Vol. 114, No. 35, 2010 15041 (16) Haiss, W.; Roelfs, B.; Port, S.; Bunge, E.; Baumga¨rtel, H.; Nichols, R. J. J. Electroanal. Chem. 1998, 454, 107. (17) Li, W.; Haiss, W.; Floate, S.; Nichols, R. J. Langmuir 1999, 15, 4875. (18) Xu, W.; Kelly, R. E. A.; Otero, R.; Scho¨ck, M.; Lœgsgaard, E.; Stensgaard, I.; Kantorovich, L. N.; Besenbacher, F. Small 2007, 3, 2011. (19) Piana, S.; Bilic, A. J. Phys. Chem. B 2006, 110, 23467. (20) Feyer, V.; Plekan, O.; Prince, K. C.; Sˇutara, F.; Ska´la, T.; Cha´b, V.; Matolı´n, V.; Stenuit, G.; Umari, P. Phys. ReV. B 2009, 79, 155432. (21) Yang, B.; Wang, Y.; Li, G.; Cun, H.; Ma, Y.; Du, S.; Xu, M.; Song, Y.; Gao, H.-J. J. Phys. Chem. C 2009, 113, 17590. (22) Hammer, B.; Nørskov, J. K. Nature 1995, 376, 238. (23) Vasˇina, R.; Kolarˇ´ık, V.; Doleeˇl, P.; Myna´rˇ, M.; Vondra´cˇek, M.; Cha´b, V.; Sleza´k, J.; Comicioli, C.; Prince, K. C. Nucl. Instrum. Methods Phys. Res., Sect. A 2001, 467-468, 561. (24) Plekan, O.; Feyer, V.; Richter, R.; Coreno, M.; de Simone, M.; Prince, K. C.; Trofimov, A. B.; Gromov, E. V.; Zaytseva, I. L.; Schirmer, J. Chem. Phys. 2008, 347, 360. (25) Petrovykh, D. Y.; Kimura-Suda, H.; Tarlov, M. J.; Whitman, L. J. Langmuir 2004, 20, 429. (26) May, C. J.; Canavan, H. E.; Castner, D. G. Anal. Chem. 2004, 76, 1114. (27) Haug, A.; Schweizer, S.; Latteyer, F.; Casu, M. B.; Peisert, H.; Ochsenfeld, C.; Chasse´, T. Chem. Phys. Chem. 2008, 9, 740. (28) Ptasin`ska, S.; Stypczyn`ska, A.; Nixon, T.; Mason, N. J.; Klychko, D. V.; Sanche, L. J. Chem. Phys. 2008, 129, 065102. (29) Jang, N. H. Bull. Korean Chem. Soc. 2002, 23, 1790. (30) Roelfs, B.; Bunge, E.; Schroter, C.; Solomon, T.; Meyer, H.; Nichols, R. J.; Baumga¨rtel, H. J. Phys. Chem. B 1997, 101, 754. (31) Nyberg, M.; Odelius, M.; Nilsson, A.; Pettersson, L. G. M. J. Phys. Chem. 2003, 119, 12577. (32) Feyer, V.; Plekan, O.; Richter, R.; Coreno, M.; Vall-llosera, G.; Prince, K. C.; Trofimov, A. B.; Zaytseva, I. L.; Moskovskaya, T. E.; Gromov, E. V.; Schirmer, J. J. Phys. Chem. A 2009, 113, 5736. (33) Fujii, K.; Akamatsu, K.; Yokoya, A. J. Phys. Chem. B 2004, 108, 8031. (34) Samuel, N. T.; Lee, C.-Y.; Gamble, L. J.; Fischer, D. A.; Castner, D. G. J. Electron Spectrosc. Relat. Phenom. 2006, 152, 134. (35) Zubavichus, Y.; Shaporenko, A.; Korolkov, V.; Grunze, M.; Zharnikov, M. J. Phys. Chem. B 2008, 112, 13711. (36) Akamatsu, K.; Yokoya, A. J. Synchrotron Radiat. 2001, 8, 1001. (37) Sto¨hr, J. NEXAFS Spectroscopy; Springer: Berlin, 1992.

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