Reactivity of Pyrimidine on Clean Ru (0001): Experimental and

Article pubs.acs.org/JPCC

Reactivity of Pyrimidine on Clean Ru(0001): Experimental and Calculated Infrared Spectra Ana R. Garcia,†,‡ Adelino M. Galvaõ ,§ and Laura M. Ilharco*,† †

Centro de Química-Física Molecular and INInstitute of Nanoscience and Nanotechnology, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal ‡ Departamento de Química e Farmácia, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal § Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal ABSTRACT: The chemical behavior of pyrimidine on the (0001) close-packed surface of a Ru single crystal was studied by reflection−absorption infrared spectroscopy (RAIRS) and by Hartree−Fock ab initio calculations. At 95 K, the spectra and theoretical simulations indicate molecular docking at fcc hollow sites, as a π-complex almost parallel to the surface. With increasing coverage, some η4 on-top docked species appear, and for a highly packed monolayer physically adsorbed pyrimidine, with some preferential orientation induced by the chemically bonded species, is also present. Subsequent physisorbed layers, randomly oriented, form as exposure increases. The behavior of adsorbed species with thermal activation is not coverage dependent: annealing a low temperature packed monolayer induces rearrangements toward a denser π-complex layer, at the expense of the other surface species, up to 130 K. At this temperature, a tilted intermediate and 2-pyrimidyl bonded to the surface by dehydrogenated C2 and one N, with loss of resonance, and oriented with the C−N bond tilted toward the surface are also proposed. 2-Pyrimidyl is stable between 130 and 180 K and starts desorbing or decomposing above this temperature. A multilayer formed at low temperature is stable up to 110 K and desorbs by annealing to 120 K. For higher temperatures, the composition of the surface layers is similar to that obtained from thermal activation of a dense monolayer. At 150 K, the surface adlayer has the same composition whether it results from an annealed low-temperature monolayer, an annealed multilayer, or a layer built above the stability limit of the multilayer. The relevance of the results obtained is based on the eventual extrapolation to the interactions of pyrimidinic ring molecules with ruthenium.

1. INTRODUCTION Ruthenium is regarded as an effective catalyst for a considerable number of reactions, either in metallic form or complexed with a wide range of ligands and in different oxidation states.1,2 In particular, the role played by ruthenium and its organometallic complexes in the reactions of biologically important molecules is of great interest, since some of those compounds are strong candidates for the therapy of specific diseases.3−6 On the other hand, nitrogen-containing molecules are interesting for their biological relevancy, since they can be used as models to predict possible DNA or RNA interactions with metals. The pyrimidine nucleus is one of the most important heterocyclic compounds. It is pharmacologically inactive but has biological importance, since it is one of the possible reasons for the activity of the nucleic acid bases thymine, cytosine, and uracil and is also present in vitamins such as folic acid and riboflavin.7 We believe that by understanding the reactivity of pyrimidine on a ruthenium metal surface, some extrapolation may be made to clarify the reaction mechanisms involving this metal and biological molecules with similar rings. Pyrimidine (1,3-diazine, C4H4N2), schematized in Figure 1, is a planar six-membered ring, polar, with C2v symmetry. Of the 24 fundamental vibrational modes, only two are infrared inactive (A2 species). Assuming the molecular plane as [σv(yz)], the infrared allowed modes belong to species A1 (nine, totally © 2014 American Chemical Society

Figure 1. Ball and stick model of the pyrimidine molecule.

symmetric), B1 (five out-of-plane), and B2 (eight).8,9 The vibrational spectrum of pyrimidine as isolated molecule and in different physical states has been thoroughly discussed.8−16 The band assignments are not straightforward because the C−H stretching region is complicated by a number of combination bands and overtones, while in the low frequency region some predicted fundamental modes appear as bands with very low intensity and are experimentally difficult to observe. Recently, some attention was given to clarify previous assignments, combining theoretical methods and experimental results.8,10,16 Received: March 3, 2014 Revised: June 17, 2014 Published: July 15, 2014 17521

dx.doi.org/10.1021/jp5021752 | J. Phys. Chem. C 2014, 118, 17521−17530

The Journal of Physical Chemistry C

Article

Figure 2. Scaling between experimental and calculated (A) infrared frequencies, ṽexp = (0.9017 ± 0.0029)ṽcalc (R2 = 0.9998), and (B) intensities, Iexp = (29.0 ± 1.7)Icalc (R2 = 0.938). Experimental values are from Breda et al.9

Table 1. Proposed Band Assignments for the RAIR Spectrum of a Pyrimidine Multilayer on Ru(0001) and for the Transmission Spectrum of a Solid Film at 100 Ka wavenumber, cm−1 literature8,9

this work modeb 2 × (4) (13) + (4) ν1 ν2 ν12 ν3 (13) + (14) (4) + (14) (4) + (5) 2 × (8) 2 × (18) ν13 ν4 ν14 ν5 (23) + (9) ν15 ν16 ν17 (22) + (24) ν6 ν18 ν7 ν8 ν20 ν10 ν21 ν22 ν23 ν9 ν19 ν11 ν24

symmetry (C2v)

A1 A1 B2 A1

assignment

7 L on Ru(0001), 100 K (RAIRS)

solid film, 100 K 3133w 3078w 3050m

ν(C5H9) ν(C2H7) νas(CH) νs(CH)

RHF 3-21G**

DFTc,d

3083 3030 3045 3034

3126 (3074) 3098 (3045) 3086 (3040) 3082 (3025)

1572 (1562) 1572 (1565) 1459 (1464) 1404 (1404)

3016vw 2976vw 2921 1982w B2 A1 B2 A1

νas(CC) + νas(NC)1 νs(NC)2 + δs(CH) + νs(CC) δ(C2H7) + δ(C5H9) + νas(NC)2 + δas(CH) δs(CH) + νs(NC)1 + νs(NC)2

B2 B2 B2 A1 B2 A1 A1 B1 A2 B1 B1 B1 A1 B2 A2 B1

1579VS

1570VS

1471m 1402VS

1467S 1399VS

1613 1614 1477 1413

δ(C2H7) + δas(CH) νas(NC)1 + δas(CH) + δ(C5H9) νas(NC)2 + νas(CC)

1365w 1230m 1165w

1367sh 1226m 1159m

1369 1228 1142

1362 (1365) 1225 (1225) 1188 (1173)

νs(NC)1 + δring1 + δs(CH) + νs(CC) δ(C5H9) + νas(NC)2 + νas(CC) νs(CC) + δring1 + δs(CH) δring1 + νs(NC)1 + νs(NC)2 + νs(CC) γ(C2H7) + γs(CH) + γ(C5H9) γas(CH) γ(C2H7) + γ(C5H9) + γs(CH) τring1 + γ(C5H9) + γs(CH) τring1 + γ(C5H9) δring2 δring3 τring2 τring3

1120vw 1095w 1053m 999w

1139m

815S

817m 720S 678m 625S

1086 1068 1059 1001 1039 1037 1022 845 731 687 623 425 384

1135 (1139) 1070 (1072) 1056 (1071) 989 (989) 989 (1006) 971 (982) 955 (962) 803 (809) 717 (723) 681 (685) 622 (623) 398 (396) 339 (340)

1071m 992m

Ar matrix, 10 K 3138.2vw 3133.4vw 3091.4vw 3057.4w 3052.1vw 3041.0vw 3019.2vw 3006.4vw 2921.0vw 1979.5 1955.6 1570.5VS 1567.3VS 1464.8w 1400.6VS 1391.0vw 1374.0vw 1223.2w 1156.8vw 1146.7vw 1138.2vw 1073.9vw 1070.7vw 989.5w

803.1w 719.2S 677.7w 620.9m

crystal, 10 K

3076.0vw 3047.0vw 3035.4vw 3018.5vw 3001.7vw 2930.2vw

1575.7VS 1566.0S 1476.2S 1403.3VS 1380.9sh 1236.5w 1160.8w 1142.5vw 1083.7w 1064.0vw 991.1m

831.7w 720.5S 675.6w 628.0S

a ν(NC)1: ν(N1C2/C2N3). ν(NC)2: ν(N3C4/N1C6). VS: very strong. S: strong. m: medium. w: weak. vw: very weak. bNumbering of modes according to Bose et al.8 and Breda et al.9 cCalculated using DFT with B3LYP functional and 6-311++G(d,p) basis set.9 dIn parentheses: calculated values taking into account Fermi resonance when applicable, using DFT with B97-1 exchange−correlation functional and a triple-ζ plus double polarization (TZ2P) basis set.8

The existence of weak C−H···N hydrogen bonding was proposed to explain the shifts observed when comparing the normal modes involving motion of the hydrogen atoms in solid and liquid phases with the isolated molecule.16

In principle, the chemical adsorption of pyrimidine on a metal surface may occur through the π-electronic system and/or through the unshared electron pairs of the nitrogen atoms, giving rise to essentially parallel or tilted orientations with respect to the 17522



Article

3. RESULTS AND DISCUSSION 3.1. Computational Results for the Free Molecule. Because of the computational limitations in the extension of the basis set and aiming at maximizing the number and dimensions of metallic slabs, in the free molecule, a full range of ab initio calculations at RHF and MP2 levels was carried out with basis sets ranging from 3-21G to 6-31G** to determine which one would provide enough structural and topological accuracy to unambiguously assign the vibrational modes observed in the experimental data. A proper scaling of calculated IR frequencies (Figure 2A) and intensities (Figure 2B) at RHF/3-21G** generated quantitative frequencies and good qualitative intensities. The resulting optimized structural parameters are slightly overbinding but do not compromise the quality of the scaled potential energy surfaces (PES) topology. The calculated value for the scaling of IR frequencies, 0.9017, lies within the range proposed at the CCCBDB (Computational Chemistry Comparison and Benchmark Database)41 (0.903 ± 0.032) for similarly sized data sets at HF level. The corrected frequencies are included in Table 1. Although most frequencies fall within 15 cm−1 of the experimental ones, the very strong vibrations ν4 and ν13 have larger deviations. This will be taken into account when assigning modes of docked molecules by comparing the spectral shift between chemisorbed and free molecules computed at the same level of theory. 3.2. Adsorption of a Multilayer on Ru(0001). The RAIR spectrum of a pyrimidine multilayer grown on clean Ru(0001) at 100 K, for a 7 L exposure, is compared to the transmission spectrum of a thick amorphous film solidified at 100 K between two KBr disks in Figure. 3.

surface, respectively. This problem has not been handled in theoretical literature to date.17 A number of studies were focused on pyrimidine adsorption from aqueous solutions to electrodes or metal colloidal particles, by surface-enhanced Raman spectroscopy (SERS).18−20 On metal single crystal surfaces, the adsorption of closely related cyclic molecules, such as pyridine and benzene, has deserved considerable attention,17,21−30 but pyrimidine has been scarcely studied. On Pd(110), it was shown, by scanning tunneling microscopy, that it adsorbs molecularly at room temperature, not building ordered superstructures, and has a strong tendency to form dimers by N··· HC hydrogen bonds, even at a low coverage.31 On Ge(100), on the contrary, STM and temperature-programmed desorption results have shown that pyrimidine is capable of forming different ordered structures, depending on coverage.32 In the present account, the adsorption of pyrimidine on the (0001) close-packed surface of a Ru single crystal is studied by reflection−absorption infrared spectroscopy (RAIRS) in order to discuss the influence of coverage and temperature on the geometry and stability of the surface species formed. The results are interpreted taking into account the vibrational analysis carried out in fully optimized pyrimidine molecules docked to a nonoptimized triple slab of ruthenium atoms at the RHF level of theory.

2. EXPERIMENTAL SECTION 2.1. Reflection Absorption Infrared Spectroscopy (RAIRS). The experiments were carried out in a stainless steel UHV chamber described in detail elsewhere,33 at a base pressure of 1 × 10−10 mbar. Standard procedures such as argon sputtering (with 2500 eV Ar+ ions) and annealing (to 1300 K) cycles were used to prepare and clean the (0001) surface of a Ru single crystal (1 mm thick and 10 mm diameter). Its cleanliness and smoothness were tested by LEED and by the RAIR spectrum of adsorbed CO at 90 K.34,35 A Mattson Research Series 1 FTIR spectrometer is coupled to the UHV chamber by differentially pumped KBr windows through purged optical boxes. An external narrow-band mercury−cadmium telluride (MCT) detector was used with a wire-grid polarizer to detect only p-polarized light. The RAIR spectra were obtained keeping the crystal at 90 K, with 4 cm−1 resolution, and were the result of 1000 coadded scans ratioed to the same number of background scans obtained for the clean surface. Pyrimidine (1,3-diazine, C4H4N2) from Alfa Aesar, 99% pure, was repeatedly distilled under vacuum (10−7 mbar) before use. By backfilling of the chamber, the crystal surface was exposed to different doses of pyrimidine at different temperatures. The exposures are quoted in units of langmuir (1 L = 1.33 × 10−6 mbar·s). 2.2. Computational Calculations. All computational calculations were carried out using GAMESS-US,36 version R3. SBKJC VDZ ECP37 basis set was used for ruthenium atoms in the docking area of the metallic surface (see details below), while a lower quality CRENBS ECP38 was used in ruthenium atoms in the remaining metallic slab. 3-21G** basis set39 was used in all the nonmetallic atoms with polarization exponents of 1.1(p) and 0.8(d). All structural optimizations were carried out at restricted Hartree−Fock (RHF) level with Hessians computed at the equilibrium geometry by coupled perturbed Hartree−Fock (CPHF) method40 (undocked molecules) or by a seminumerical approach with a frozen metallic slab.

Figure 3. (a) Solid film of pyrimidine at 100 K (transmission FTIR) multiplied by 0.02. (b) 7 L on Ru(0001) at 100 K (RAIRS).

The proposed band assignments are summarized in Table 1 and compared with published results for crystalline pyrimidine at 10 K, the isolated monomer in Ar matrix at 10 K, and DFT8,9 and RHF/3-21G** calculations (this work). The indicated symmetry species of the vibrational modes are consistent with the C2v point group. The general pattern of the multilayer spectrum is similar to that of the amorphous solid phase at 100 K, with band shifts that may be a consequence of the metal surface vicinity. The strongest 17523



Article

bands (Figure 3b) are at 1579 and 1402 cm−1, the first assigned to overlapped ν13 (B2) and ν4 (A1) modes, with large contributions of νCC and νNC, and the second to ν5 (A1), mostly δsCH. In the spectrum of the monomer in Ar matrix, the modes ν13 and ν4 appear as a doublet due to the high resolution of matrix isolation spectroscopy. For the crystal at 10 K, the shift between the two modes is larger because of the organized structure (pyrimidine crystallizes in a Pna21 structure, with four molecules per unit cell42). The out of plane B1 modes ν20, ν21, and ν22 lie within the narrow band MCT detector range, but ν20 and ν21, predicted for the monomer at 1039 and 1022 cm−1, respectively, are intrinsically weak and were not observed in Ar matrix or in the crystal at 10 K. Thus, not surprisingly, only ν22 was observed in this work, at 815 cm−1. Since all the active modes within the detector range are observed and taking into account the metal surface selection rule applicable in RAIRS,43 it is possible to conclude that the multilayer on Ru(0001) at 100 K was built without preferential orientation of the adlayers. 3.3. Coverage Effect at Low Temperature. 3.3.1. Computational Results. The Ru(0001) surface was modeled as a hexagonal triple layer slab, with crystallographic parameters a = 270.4 pm and c/a = 1.584,44 with a central docking area of seven ruthenium atoms surrounded by a hexagonal 12 atoms surface extension. The second and third layers of this slab are limited to the area underneath the docking area, arranged to provide three fcc and an equal number of hcp coordination holes (Figure 4).

unfavorable when compared with the adsorption in a flat conformation using the π-system. Several flat coordinative positions were attempted (Figure 5). Three of the optimized geometries (Table 2) have energies within a 21 kJ mol−1 interval and were subject to a full vibrational Table 2. Ab Initio Interatomic Distances (pm) for Free and Coordinated Pyrimidine N1−C2 N1−C6 C5−C6 C4−C5 N3−C4 N3−C2

fcc

top

hcp

free

exp9

143.2 129.5 143.4 142.8 129.8 142.6

140.6 140.2 137.7 146.5 146.9 126.2

135.6 137.1 136.8 147.0 146.6 126.8

131.5 131.7 138.0 138.0 131.7 131.5

134.0 134.0 139.3 139.3 134.0 134.0

analysis. The most stable docking conformation was found for the fcc hollow site (Figure 6A), with the N−C2 bonds stretched to become nearly single, because of rehybridization of C2 toward sp3 (C2 is 36 pm below the plane defined by N1, H7, and N3). The adsorbed molecule is almost flat, π-bonded to the surface, with C2 interacting at an hcp hollow site with three Ru atoms. The coordination on top to a single ruthenium atom deforms the molecule the most (Figure 6B), with the destruction of the aromatic π-bonding system. In this kind of docking, the molecule distorts into a slipped η4 moiety, bonded to the surface, and an undocked localized CN bond (Figure 6B′). Finally the docking in an hcp-hole (Figure 6C) leads to a nearly flat pyrimidine but with a localized CN double bond. The geometrical parameters of the two less stable dockings are similar (interatomic distances in Table 2) except for the tilting of the ring. The IR absorption spectrum was computed for each adsorption geometry, and the observable frequencies (threshold for observability set at the relative intensity of 10) as well as the calculated shifts from the free ligand are collected in Table 3. 3.3.2. RAIRS Results at 95 K. The RAIR spectrum obtained by exposing the surface to 0.05 L of pyrimidine at 95 K shows only a very weak band, at 1539 cm−1 (Figure 7a). Assuming in a first approach that only physical adsorption takes place without preferential orientation, and according to Table 1, all the A1, B1, and B2 modes would be allowed on symmetry grounds. However, the only band observed is

Figure 4. Top (A) and side (B) views of the triple layer metallic slab.

The simulation of pyrimidine adsorption on the Ru(0001) surface was performed for one molecule on this triple layer slab, modeling the equivalent to a very low coverage. The docking of pyrimidine to the metal surface by one of the nitrogen lone pairs, in a tilted configuration, was found to be energetically

Figure 5. Schematic representation of flat coordination modes on fcc hollow (A), hcp hollow (B), top (C), and bridge (D) sites. The highlighted examples are the most stable coordination modes. The remaining coordinative positions have relative energies between 20 and 60 kJ mol−1 higher. 17524



Article

Figure 6. Adsorption of pyrimidine on fcc (A), top (B, B′), and hcp (C) sites.

Table 3. Calculated Scaled Frequencies (in cm−1) of the Infrared Active Modes and Relative Intensities (I) for Each Adsorption Sitea

a

Within parentheses: shifts from the free molecule at RHF/3-21G** level.

considerably shifted with reference to ν13 or ν4 overlapped modes, expected at ∼1570 cm−1, as well as to the other unperturbed pyrimidine monomer modes.8,9,13,16 Thus, nonoriented physical adsorption is ruled out. If the pyrimidine molecular plane (i.e., the plane containing the ring atoms, considering a planar configuration) were parallel to the surface, then just the out-of-plane modes would be observable. The only one expected above the threshold of the detector used would be ν22 (at ∼815 cm−1), which is not compatible with spectrum 7a. Therefore, we must conclude that pyrimidine adsorbs chemically on Ru(0001) at 95 K, at such a low exposure.

By analysis of Table 3 and bearing in mind the metal surface selection rule, for the most favorable docking conformation (on fcc hollow sites) only two modes combine a good dipole component perpendicular to the surface and a strong intrinsic IR intensity: at 1561 and 809 cm−1, the latter much stronger. The shifts to lower frequencies regarding the unperturbed modes of the free ligand (within parentheses in Table 3) can be explained by the docking that involves weakening of the CN bonds and pyramidalization of C2 (as suggested by the interatomic distances in Table 2). Although by exposing the surface to 0.05 L of pyrimidine at 95 K only one band is observed (at 1539 cm−1), spectrum 7a is consistent with this almost flat π species on 17525



Article

appears that these pyrimidine molecules have a preferential tilted orientation, determined by the chemically bonded neighbors. In summary, increasing pyrimidine exposure to 0.1 L leads to the coexistence of two types of chemically bonded species, plus some physically adsorbed molecules (illustrated in Figure 8).

Figure 8. Schematic representation of the proposed pyrimidine adsorption on Ru(0001) at 95 K: (A) low submonolayer coverage; (B) high submonolayer coverage.

A comparison may be established with pyrimidine parent molecules: for benzene, increasing coverage produces physically adsorbed overlayers that change from a parallel orientation relatively to the surface (phase α1) to a highly tilted phase;26 a similar parallel π species was detected for pyridine at low coverage (θ ≈ 0.3θmax), independent of the adsorption temperature, which changes to an inclined, mainly N-bonded state at higher coverage.29 For an exposure of 0.5 L (spectrum 7c) the relative intensities of the bands at 1577 and 1400 cm−1 approach those of a multilayer, new ones appear at 1226 (ν16) and 3049 cm−1 (ν2), and the band at 1539 cm−1 from the π-complex loses importance. These changes suggest the physisorption of randomly oriented molecules. The new band that appears at 1344 cm−1 is tentatively assigned to largely shifted and enhanced ν15, suggesting that these new molecules are still affected by the orientation in the first layer. The subsequent spectra in Figure 7 show that as the exposure of the surface to pyrimidine increases, the characteristic peaks of a multilayer progressively dominate the spectrum, masking the fingerprints of the first chemisorbed layer. 3.4. Temperature Effect on Adsorbed Pyrimidine. In order to investigate if the behavior of adsorbed pyrimidine as a function of temperature is coverage dependent, several annealing experiments were performed starting from different low temperature layers. A dense monolayer deposited at 95 K, formed by a mixture of π-complex (fcc hollow sites), η4-bonded pyrimidine (on-top), and physisorbed molecules, was successively annealed up to 600 K (Figure 9). By annealing to 110 K (spectrum 9a), the bands at 1574, 1458, 1390, and 1354 cm−1 still identify physisorbed molecules, although their relative intensities decrease in comparison with the characteristic band of the fcc flat species. There is no indication of the presence of on-top molecules. By annealing to 130 K, the amount of physisorbed molecules becomes residual and the increase in the relative intensity of the band at 1539 cm−1 suggests that thermal activation induces rearrangements toward a denser π-complex layer at the expense of the other surface species; additionally, there are two new bands at 3016 and 1419 cm−1 plus a weaker one at 1304 cm−1. The band at 3016 cm−1, assigned to the νCH mode of a sp2 hybridized C, indicates the presence of a new species with one or more C−H bonds almost perpendicular to the surface. It must belong to the same highly tilted species as the small feature at 1304 cm−1, since they grow concurrently up to 180 K. Since the C2−H7 has the lowest bond order (0.92) when compared to the other CH bonds (0.97), H7 is the most acidic proton in the molecule and, because of the

Figure 7. RAIR spectra of pyrimidine adsorbed on Ru(0001) at 95 K: (a) 0.05 L; (b) 0.1 L; (c) 0.5 L; (d) 1.5 L; (e) 5 L (multiplied by 0.5).

fcc sites: the observed band, assigned to the [νs(NC)2 + δs(CH) + νs(CC)] mode, is shifted to lower wavenumbers in comparison to the equivalent mode of the unperturbed molecule in Ar matrix (Table 1), and the other predicted mode shifted to a frequency value below the detector limit. The latter is assigned to the [τring1 + γ(C5H9) + γs(CH)] mode, which for the monomer in Ar matrix is observed at 803 cm−1. The C2H7 stretching, observable taking into account that C2 is out of the N1H7N3 plane, has a very low intensity (according to the results in Table 3), so it comes as no surprise that it is not observed. Compared with parent molecules of pyrimidine on Ru(0001), both benzene (θ < 0.14 ML below 320 K)21,24,26,45 and pyridine (θ < 0.05 ML below 250 K)27,29 chemisorb by π bonding, with the molecular plane essentially parallel to the surface, with a small degree of distortion,22 in a similar conformation to pyrimidine. However, benzene adsorbs preferentially on hcp 3-fold hollow sites with C3v(σv) symmetry,22,26 whereas for pyridine the existence of preferred adsorption sites is not clear so far. The docking site for pyrimidine is therefore determined by the second nitrogen atom, which allows the C2 to bend toward the metal and interact at the center of an hcp hollow site with three Ru atoms. When the exposure is increased to 0.1 L (spectrum 7b), the band at 1539 cm−1 grows, revealing a coverage increase of the fcc docked π complex. Additional bands appear at 1574, 1456, 1392, and 883 cm−1 that are not correlated to this species. The small band at 883 cm−1 may tentatively be assigned to a few molecules docked on-top sites (corresponding essentially to a γCH mode, calculated at 931 cm−1 in Table 3), since the other modes of these species generate dynamic dipoles almost parallel to the surface. Chemical adsorption on the less stable hcp sites is ruled out because several modes would be observed by RAIRS, namely, at 2857, 1244, 1082, 852, and 829 cm−1 (Table 3). To fully interpret spectrum 7b, we must admit that most of the incoming pyrimidine molecules are just physically adsorbed, the new bands at 1574, 1456, and 1392 cm−1 corresponding to overlapped ν13/ ν4, ν14, and ν5 modes, respectively. However, by comparison of the relative intensities of the three bands with those obtained for randomly oriented pyrimidine adlayers (Figure 3b) and taking into account that the out-of-plane ν22 mode is not observed, it 17526



Article

Figure 10. Initial normal mode direction in the saddle point optimization (A). Saddle point geometry (B). 2-Pyrimidyl geometry with C−H stretching normal mode represented (C).

be different from zero. Therefore, the bonding through C2 and an N seems the most probable. Adsorbed 2-pyrimidyl is stable on Ru(0001) between 130 and 180 K and starts desorbing or decomposing above this temperature. Simultaneously, the band at 1419 cm−1 that is initially stronger loses intensity, which correlates it with an intermediate that progressively converts into 2-pyrimidyl. It could be due to a tilted species already interacting with the surface by the lone pair of one N, and the band assigned to the νCN mode of the noninteracting N. This being the case, it appears that some of the residual pyrimidine physisorbed molecules gradually convert into the more stable flat species docked on fcc sites and others react toward 2-pyrimidyl surface complex. By annealing the previous adlayer to 600 K (spectrum 9e), the band at ∼1537 cm−1 suggests the presence of some π-complex, which is only explained at such high temperature by readsorption upon recooling the crystal to 90 K, in order to scan the spectrum. A second experimental approach to the temperature behavior of adsorbed pyrimidine consisted of the thermal activation of a multilayer built at 100 K (Figure 11).

Figure 9. RAIR spectra of the pyrimidine thermal evolution on clean Ru(0001): 0.1 L adsorbed at 95 K and annealed for 60 s to 110 K (a), 130 K (b), 150 K (c), 180 K (d), and 600 K (e). All of the spectra were scanned at 90 K.

pyramidalization of C2 toward the surface, a strong candidate to be abstracted by the metal. Therefore, the formation of a 2pyrimidyl radical is most plausible. Two bonding modes are conceivable: by the dehydrogenated C2 and one N (covalent dative bond), with loss of resonance and oriented with the C−N bond tilted toward the surface, or just by C2, with the C5−H9 bond almost vertical. Both species are compatible with spectrum 9b, with the band at 1304 cm−1 being assigned to νC−N modes. The formation of a species bonded to the surface by a carbon and a nitrogen was proposed for pyridine on Ru(0001), in which a Nbonded molecule acts as an intermediate for the dehydrogenation of an α-carbon, resulting in the gradual conversion to αpyridyl with increasing temperature.28,29 On Ru nanoparticle film electrodes, it was shown by in situ surface-enhanced infrared absorption spectroscopy (SEIRAS) that pyridine molecules essentially remain intact by adopting a slightly edge-tilted configuration through bonding with its N lone pair electrons.46 Pyrimidine is a weaker base than pyridine because of the inductive effect of the second nitrogen atom,47 which could favor the bonding of 2-pyrimidyl just by the dehydrogenated C2. However, the high acidity of this metal surface plays in favor of the bonding also by the nitrogen lone pair. In order to propose the more stable solution, this problem was addressed by a computational approach: the H atom was kicked in the direction of the 2869 cm−1 normal mode (Figure 10 A); the Hessian was computed, and the negative eigenvalue was followed until a saddle point was fully optimized (Figure 10 B). From this point the adsorbed species was optimized to the nearest minimum to obtain the structure and normal modes of the bonded 2pyrimidyl. An active mode was calculated at 3026 cm−1 (Figure 10 C), which was identified as the experimental one at 3016 cm−1. The activation energy for the process was estimated to be 37 kcal/mol. The 2-pyrimidyl + H system is 30 kcal/mol more stable than the fcc-docked pyrimidine. Since the coordination exclusively by C2 is not a minimum or a saddle point, the vibrational analysis would be meaningless, as the gradients would

Figure 11. RAIR spectra of a pyrimidine multilayer on Ru(0001) (7 L at 100 K), annealed for 60 s to (a) 110 K, multiplied by 0.2, (b) 120 K, (c) 130 K, and (d) 150 K. All of the spectra were scanned at 90 K.

The multilayer is still stable at 110 K, since 7 L deposited at 100 K and annealed to this temperature produces a very strong and well-defined spectrum, with all the characteristic bands of pyrimidine (spectrum 11a). No rearrangement toward a more long-range ordered phase is suggested by the spectrum, similar to pyridine29 and contrary to benzene, whose low temperature 17527



Article

surface at the reaction temperature. Upon annealing to a higher temperature, namely, 150 K, the mixture of species obtained is independent from the starting layer: there are no differences between the corresponding spectra in Figures 9c, 11d, and 12b, irrespective of the experimental procedure followed.

amorphous phase converts to a crystalline phase with increasing temperature.23 By annealing to 120 K (spectrum 11b), most of pyrimidine adlayers desorb: the total intensity of the spectrum decreases significantly and the relative intensities of the bands change, showing that the multilayer is no longer stable at this temperature. The presence of the band at 1471 cm−1, although reduced, indicates that there is still some residual physisorbed pyrimidine coadsorbed with flat species docked on fcc sites. The new bands at 3016 and 1429 cm−1 show that some 2-pyrimidyl and the intermediate species are already present. The spectral pattern changes again by annealing this layer to 130 K (spectrum 11c): the band at 1537 cm−1 becomes dominant. Very weak bands appear at 3016 and 1306 cm−1. As observed when annealing a less dense initial layer (Figure 9), it is clear that at this temperature the surface species are mainly the flat π complex and the tilted 2-pyrimidyl, plus some residual physisorbed molecules. When this layer is annealed to 150 K (spectrum 11d), the bands at 3016 and 1306 cm−1 increase, while that at 1429 cm−1 disappears. At this temperature, the stable species are the same observed when annealing a dense monolayer. Apparently, the thermal decomposition of adsorbed pyrimidine is independent from initial coverage. The strategy for obtaining a dense layer at higher temperatures consisted of exposing the crystal to 2 L of pyrimidine at 130 K, ensuring that the multilayer would not be stable. Annealing this layer up to 200 K resulted in the spectra shown in Figure 12.

4. CONCLUSIONS The most stable pyrimidine docking to the Ru(0001) surface was obtained for the fcc hollow site, with the molecule adsorbed by the π-system, in an almost flat conformation. The RAIR spectrum for a low exposure shows that this species is the only one detected on the clean Ru(0001) surface at 95 K. With increasing coverage, a few incoming molecules dock on-top sites and others just adsorb physically. On top of the first layer it is possible to build a multilayer as the exposure to pyrimidine increases. The multilayer is stable up to 110 K. Above this temperature and independent of the initial surface layer, the predominant species is the flat π-complex. The stability of this surface complex may be due to the high tendency of Ru to participate in the extensive resonant system of the pyrimidine ring. Concurrently, for temperatures above 130 K, either by annealing a multilayer or a submonolayer deposited at low temperature or by adsorbing directly at 130 K, the radical 2pyrimidyl is formed by dehydrogenation at C2 and bonds to the surface through C2 and one N. The RAIR spectra, corroborated by the theoretical calculations, enable proposing that 2-pyrimidyl is oriented with the molecular plane almost perpendicular to the surface. It is also possible to propose a highly tilted species as the intermediate in 2-pyrimidyl formation. 2-Pyrimidyl is stable between 130 and 180 K and starts desorbing or decomposing above this temperature. The Ru−pyrimidine chemical bonding suggested by the present results may have important implications for the behavior of Ru containing drugs from two points of view: clarifying the interactions of promising antitumor drugs (Ru(III) and Ru(II) complexes) with the pyrimidine rings of purine DNA bases; optimizing the design of Ru containing drugs that involve pyrimidine rings or derivatives as the active principle (e.g., antiviral, antileukemic, or photodynamic agents).

■

AUTHOR INFORMATION

Corresponding Author

*Phone: +351-218419220. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS This work was supported by Fundaçaõ para a Ciência e a Tecnologia (FCT).

Figure 12. RAIR spectra of the pyrimidine thermal evolution on clean Ru(0001): (a) 2 L adsorbed at 130 K; (b) annealed to 150 K; (c) annealed to 200 K.

■

Spectrum 12a shows that the predominant species in this dense layer is the fcc-docked flat π-complex (band at 1539 cm−1), with some 2-pyrimidyl (bands at 3016 and 1304 cm−1), its intermediate (band at 1429 cm−1), and few unperturbed molecules (small bands at 1577, 1354, and 1456 cm−1). The difference between this surface and the one obtained by annealing a multilayer built at low temperature to 130 K (spectrum 11c) is in the relatively higher amount of physisorbed species and 2-pyrimidyl. This is not surprising, since when a multilayer is annealed by steps, favorable reorientation of the molecules may occur, which does not happen when they hit the

REFERENCES

(1) Boyer, J. L.; Rochford, J.; Tsai, M.-K.; Muckerman, J. T.; Fujita, E. Ruthenium Complexes with Non-Innocent Ligands: Electron Distribution and Implications for Catalysis. Coord. Chem. Rev. 2010, 254, 309− 330. (2) Amiens, C.; Chaudret, B.; Ciuculescu-Pradines, D.; Collière, V.; Fajerwerg, K.; Fau, P.; Kahn, M.; Maisonnat, A.; Soulantic, K.; Philippot, K. Organometallic Approach for the Synthesis of Nanostructures. New J. Chem. 2013, 37, 3374−3401. (3) Bratsos, I.; Jedner, S.; Gianferrara, T.; Alessio, E. Ruthenium Anticancer Compounds: Challenges and Expectations. Chimia 2007, 61, 692−697. 17528



Article

Metal Surfaces: Comparison to Benzene Cluster Complexes. J. Vac. Sci. Technol., A 1998, 16, 1017−1022. (26) Braun, W.; Held, G.; Steinrück, H.-P.; Stellwag, C.; Menzel, D. Coverage-Dependent Changes in the Adsorption Geometries of Ordered Benzene Layers on Ru(0001). Surf. Sci. 2001, 475, 18−36. (27) Hahn, J. R.; Kang, H. S. Role of Molecular Orientation in Vibration, Hopping, and Electronic Properties of Single Pyridine Molecules Adsorbed on Ag(110) Surface: A Combined STM and DFT Study. Surf. Sci. 2010, 604, 258−264. (28) Bridge, M. E.; Connolly, M.; Lloyd, D. R.; Somers, J.; Jakob, P.; Menzel, D. Electron Spectroscopic Studies of Pyridine on Metal Surfaces. Spectrochim. Acta, Part A 1987, 43, 1473−1478. (29) Jakob, P.; Lloyd, D. R.; Menzel, D. Pyridine on Ru(001): Thermal Evolution. Surf. Sci. 1990, 227, 325−336. (30) Mollenhauer, D.; Gaston, N.; Voloshina, E.; Paulus, B. Interaction of Pyridine Derivatives with a Gold(111) Surface as a Model for Adsorption to Large Nanoparticles. J. Phys. Chem. C 2013, 117, 4470− 4479. (31) Kim, J.-T.; Kawai, T.; Yoshinobu, J.; Kawai, M. Adsorption of Pyrimidine Molecules on Pd(110) Observed by Scanning Tunneling Microscopy. Surf. Sci. 1996, 360, 50−54. (32) Lee, J. Y.; Jung, S. J.; Hong, S.; Kim, S. Double Dative Bond Configuration: Pyrimidine on Ge(100). J. Phys. Chem. B 2005, 109, 348−351. (33) Ilharco, L. M.; Garcia, A. R.; da Silva, J. L. The Chemical Adsorption of 1-Hexene on Ru(0001) Studied by ReflectionAbsorption Infrared Spectroscopy. Surf. Sci. 1997, 371, 289−296. (34) Pfnür, H.; Menzel, D.; Hoffmann, F. M.; Ortega, A.; Bradshaw, A. M. High Resolution Vibrational Spectroscopy of CO on Ru(001): The Importance of Lateral Interactions. Surf. Sci. 1980, 93, 431−452. (35) Jacob, P.; Gsell, M.; Menzel, D. Interactions of Adsorbates with Locally Strained Substrate Lattices. J. Chem. Phys. 2001, 114, 10075− 10085. (36) Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; et al. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14, 1347−1363. (37) Stevens, W. J.; Krauss, M.; Basch, H.; Jasien, P. G. Relativistic Compact Effective Potentials and Efficient, Shared-Exponent Basis Sets for the Third-, Fourth-, and Fifth-Row Atoms. Can. J. Chem. 1992, 70, 612−630. (38) LaJohn, L. A.; Christiansen, P. A.; Ross, R. B.; Atashroo, T.; Ermler, W.C. Ab Initio Relativistic Effective Potentials with Spin−Orbit Operators. III. Rb through Xe. J. Chem. Phys. 1987, 87, 2812−2824. (39) Binkley, J. S.; Pople, J. A.; Hehre, W. J. Self-Consistent Molecular Orbital Methods. 21. Small Split-Valence Basis Sets for First-Row Elements. J. Am. Chem. Soc. 1980, 102, 939−947. (40) King, H. F.; Komornicki, A. Single Configuration SCF Second Derivatives on a Cray. In Geometrical Derivatives of Energy Surfaces and Molecular Properties; Jorgensen, P., Simons, J., Eds.; D. Reidel: Dordrecht, The Netherlands, 1986; pp 207−214. (41) NIST Computational Chemistry Comparison and Benchmark Database, NIST Standard Reference Database Number 101, release 16a; Johnson, R. D., III, Ed.; NIST: Gaithersburg, MD, Aug 2013; http:// cccbdb.nist.gov/. (42) Wheatley, P. J. The Crystal and Molecular Structure of Pyrimidine. Acta Crystallogr. 1960, 13, 80−85. (43) Trenary, M. Reflection Absorption Infrared Spectroscopy and the Structure of Molecular Adsorbates on Metal Surfaces. Annu. Rev. Phys. Chem. 2000, 51, 381−403. (44) Physics of Solid Surfaces: Electronic and Vibrational Properties; Chiarotti, G., Ed.; Landolt-Börnstein, News Series, Group III, Vol. 24, Part b; Springer-Verlag: Berlin, Germany, 1994. (45) Polta, J. A.; Thiel, P. A. Unusually Facile Dissociation of Benzene by Ruthenium Metal. J. Am. Chem. Soc. 1986, 108, 7560−7567. (46) Li, Q. X.; Xue, X. K.; Xu, Q. J.; Cai, W. B. Application of SurfaceEnhanced Infrared Absorption Spectroscopy To Investigate Pyridine Adsorption on Platinum-Group Electrodes. Appl. Spectrosc. 2007, 61, 1328−3133.

(4) Antonarakis, E. S.; Emadi, A. Ruthenium-Based Chemotherapeutics: Are They Ready for Prime Time? Cancer Chemother. Pharmacol. 2010, 66, 1−9. (5) Kljun, J.; Bytzek, A. K.; Kandioller, W.; Bartel, C.; Jakupec, M. A.; Hartinger, C. G.; Keppler, B. K.; Turel, I. Physicochemical Studies and Anticancer Potency of Ruthenium η6-p-Cymene Complexes Containing Antibacterial Quinolones. Organometallics 2011, 30, 2506−2512. (6) Hufziger, K. T.; Thowfeik, F. S.; Charboneau, D. J.; Nieto, I.; Dougherty, W. G.; Kassel, W. S.; Dudley, T. J.; Merino, E. J.; Papish, E. T.; Paul, J. J. Ruthenium Dihydroxybipyridine Complexes Are Tumor Activated Prodrugs Due to Low pH and Blue Light Induced Ligand Release. J. Inorg. Biochem. 2014, 130, 103−111. (7) Joule, J. A.; Mills, K. Heterocyclic Chemistry, 5th ed.; John Wiley & Sons Ltd.: Chichester, U.K., 2010; p 253 and following pages. (8) Boese, A. D.; Martin, J. M. L. Vibrational Spectra of the Azabenzenes Revisited: Anharmonic Force Fields. J. Phys. Chem. A 2004, 108, 3085−3096. (9) Breda, S.; Reva, I. D.; Lapinski, L.; Nowak, M. J.; Fausto, R. Infrared Spectra of Pyrazine, Pyrimidine and Pyridazine in Solid Argon. J. Mol. Struct. 2006, 786, 193−206. (10) Navarro, A.; Fernández-Gómez, M.; López-González, J. J.; Fernández-Liencres, M. P. Inelastic Neutron Scattering Spectrum and Quantum Mechanical Calculations on the Internal Vibrations of Pyrimidine. J. Phys. Chem. A 1999, 103, 5833−5840. (11) Ito, M.; Shimada, R.; Kuraishi, T.; Mizushima, W. Vibrational Spectra of Diazines. J. Chem. Phys. 1956, 25, 597−598. (12) Lord, R. C.; Marston, L. A.; Miller, F. A. Infra-Red and Raman Spectra of the Diazines. Spectrochim. Acta 1957, 9, 113−125. (13) McCarthy, W.; Smets, J.; L. Adamowicz, L.; Plokhotnichenko, A. M.; Radchenko, E. D.; Sheina, G. G.; Adamowicz, L.; Stepanian, S. G. Competition between H-Bonded and Stacked Dimers of Pyrimidine: IR and Theoretical ab-Initio Study. Mol. Phys. 1997, 91, 513−526. (14) Billes, F.; Mikosch, H.; Holly, S. A Comparative Study on the Vibrational Spectroscopy of Pyridazine, Pyrimidine and Pyrazine. J. Mol. Struct.: THEOCHEM 1998, 423, 225−234. (15) Fazli, M.; Tayyari, S. F.; Milani-nejad, F. Vibrational Assignment of C2v Deuterium Substituted Pyrimidines. Spectrochim. Acta, Part A 1999, 55, 179−188. (16) Wright, A. M.; Joe, L. V.; Howard, A. A.; Tschumper, G. S.; Hammer, N. I. Spectroscopic and Computational Insight into Weak Noncovalent Interactions in Crystalline Pyrimidine. Chem. Phys. Lett. 2011, 501, 319−323. (17) Jenkins, S. J. Aromatic Adsorption on Metals via First-Principles Density Functional Theory. Proc. R. Soc. A 2009, 465, 2949−2976. (18) Dornhaus, R.; Long, M. B.; Benner, R. E.; Chang, R. K. Time Development of SERS from Pyridine, Pyrimidine, Pyrazine, and Cyanide Adsorbed on Ag Electrodes during an Oxidation-Reduction Cycle. Surf. Sci. Lett. 1980, 93, A93−A94. (19) Muniz-Miranda, M.; Neto, N.; Sbrana, G. Surface-Enhanced Raman Spectra of Pyrazine, Pyrimidine, and Pyridazine Adsorbed on Silver Sols. J. Phys. Chem. 1988, 92, 954−959. (20) Centeno, S. P.; López-Tocón, I.; Arenas, J. F.; Soto, J.; Otero, J. C. Selection Rules of the Charge Transfer Mechanism of Surface-Enhanced Raman Scattering: The Effect of the Adsorption on the Relative Intensities of Pyrimidine Bonded to Silver Nanoclusters. J. Phys. Chem. B 2006, 110, 14916−14922. (21) Jakob, P.; Menzel, D. The Adsorption of Benzene on Ru(001). Surf. Sci. 1988, 201, 503−530. (22) Stellwag, C.; Held, G.; Menzel, D. The Geometry of Ordered Benzene Layers on Ru(001). Surf. Sci. 1995, 325, L379−L384. (23) Jakob, P.; Menzel, D. Initial Stages of Multilayer Growth and Structural Phase Transitions of Physisorbed Benzene on Ru(001). J. Chem. Phys. 1996, 105, 3838−3848. (24) Haq, S.; King, D. A. Configurational Transitions of Benzene and Pyridine Adsorbed on Pt{111} and Cu{110} Surfaces: An Infrared Study. J. Phys. Chem. 1996, 100, 16957−16965. (25) Weiss, K.; Gebert, S.; Wühn, M.; Wadepohl, H.; Wöll, Ch. Near Edge X-ray Absorption Fine Structure Study of Benzene Adsorbed on 17529



Article

(47) Joule, J. A.; Mills, K. Heterocyclic Chemistry, 5th ed.; John Wiley & Sons Ltd.: Chichester, U.K., 2010; p 253 and following pages.

17530


Reactivity of Pyrimidine on Clean Ru (0001): Experimental and

Recommend Documents