Quantitative determination of the local structure of thymine on Cu(110) using scanned-energy mode photoelectron diffraction

Allegretti, Francesco; Polčík, Martin; Woodruff, D.P.

doi:10.1016/j.susc.2007.07.006

Cited by 39 publications

(54 citation statements)

References 27 publications

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“…These weak modulations may be due to these emitter atoms being further from high-symmetry sites relative to neighbouring (strongly-scattering) Pd atoms, but this particular problem can be even more exaggerated if a planar molecule is more nearly 'standing-up' on the surface. In this geometry, however, intramolecular scattering can prove more important and orientational information can be obtained even from emitter atoms within the molecule that are far from the surface, such as in the case of thymine on Cu(110) [33]. Despite these special problems, however, bearing in mind the probable equivalence of the bonding energy of furan at fcc and hcp hollow sites on the Pd(111) surface, our structural study only reveals two possible local adsorption sites that are consistent with our data.…”

Section: General Discussion and Conclusionmentioning

confidence: 99%

The adsorption structure of furan on Pd(111)

et al. 2008

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The structure of molecular furan, C 4 H 4 O, on Pd(111) has been investigated by O K-edge near-edge X-ray absorption fine structure (NEXAFS) and C 1s scanned-energy mode photoelectron diffraction (PhD). NEXAFS shows the molecule to be adsorbed with the molecular plane close to parallel to the surface, a conclusion confirmed by the PhD analysis. Chemical-state specific C 1s PhD data were obtained for the two inequivalent C atoms in the furan, the α-C atoms adjacent to the O atom, and the β-C atoms bonded only to C atoms, but only the PhD modulations for the α-C emitters were of sufficiently large amplitude for detailed evaluation using multiple scattering calculations. This analysis shows the α-C atoms to be located approximately 0.6 Å off-atop surface Pd atoms with an associated C-Pd bondlength of 2.13±0.03 Å. Two alternative local geometries consistent with the data place the O atom in off-atop or near-hollow locations, and for each of these local structures there are two equally-possible registries relative to the fcc and hcp hollow sites. The results are in good agreement with earlier density functional theory calculations which indicate that the fcc and hcp registries are equally probable, but the PhD results fail to distinguish the two distinct local bonding geometries.

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Section: General Discussion and Conclusionmentioning

confidence: 99%

The adsorption structure of furan on Pd(111)

et al. 2008

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“…Had it been a deprotonation of the N1 site, the chemical shift would be observed in the peaks corresponding to C2 and C6 atoms. Consequently, it is the N3 atom that undergoes deprotonation, as it is also the case for uracil and the closely related species, thymine, on the Cu(110) surface 19,33 and in solution, 34 but not in the gas phase, where the N1 atom is found to be more acidic. 35 However the authors of the last study argue also that the stability of N3 − is enhanced in polar solvents, therefore tuning the deprotonation selectivity in a biological environment.…”

Section: Uracil On Cu(111)mentioning

confidence: 92%

“…This is consistent with PhD measurements, a powerful technique for accurate determination of the adsorbate geometry, of uracil and the similar DNA base, thymine, on Cu(110). 19,33 Both molecules are found to bind along the close-packed direc- Figure 6b reveals also features of different contrast in STM data; therefore it is plausible that molecules with different adsorption geometries are present. From the NEXAFS measurements we deduce the average tilt of the molecular ensemble to be ∼ 65 • ; therefore, we can conclude that this phase consists mainly of strongly inclined molecules.…”

Section: Uracil On Cu(111)mentioning

confidence: 96%

“…The PhD study of the same system revealed that thymine preserves its tridentate adsorption geometry upon annealing and creates doubly deprotonated thymine molecules.33 Moreover, PhD investigations of both uracil and thymine on Cu(110) found the O-Cu distances to be comparable with the typical O-Cu distances of acetate species on the same surface, further supporting the formation of molecular bonds between O and Cu. 19,33 Summary and Conclusions.…”

Section: Dft Modelingmentioning

confidence: 99%

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Chemical Transformations Drive Complex Self-Assembly of Uracil on Close-Packed Coinage Metal Surfaces

et al. 2012

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We address the interplay of adsorption, chemical nature, and self-assembly of uracil on the Ag(111) and Cu(111) surfaces as a function of molecular coverage (0.3 to 1 monolayer) and temperature. We find that both metal surfaces act as templates and the Cu(111) surface acts additionally as a catalyst for the resulting self-assembled structures. With a combination of STM, synchrotron XPS, and NEXAFS studies, we unravel a distinct polymorphism on Cu(111), in stark contrast to what is observed for the case of uracil on the more inert Ag(111) surface. On Ag(111) uracil adsorbs flat and intact and forms close-packed two-dimensional islands. The self-assembly is driven by stable hydrogen-bonded dimers with poor two-dimensional order. On Cu(111) complex structures are observed exhibiting, in addition, a strong annealing temperature dependence. We determine the corresponding structural transformations to be driven by gradual deprotonation of the uracil molecules. Our XPS study reveals unambiguously the tautomeric signature of uracil in the contact layer and on Cu(111) the molecule's deprotonation sites. The metal-mediated deprotonation of uracil and the subsequent electron localization in the molecule determine important biological reactions. Our data show a dependence between molecular coverage and molecule-metal interaction on Cu(111), as the molecules tilt at higher coverages in order to accommodate a higher packing density. After deprotonation of both uracil N atoms, we observe an adsorption geometry that can be understood as coordinative anchoring with a significant charge redistribution in the molecule. DFT calculations are employed to analyze the surface bonding and accurately describe the pertaining electronic structure.

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“…However, the elemental and chemical-state specificity of scanned-energy mode photoelectron diffraction (PhD) [1,2], combined with its essentially local character, make it wellsuited to investigating such systems. On the Cu(110) surface, PhD has already been used to determine the adsorption geometry of the simple amino acids glycine [3,4] and alanine [5], and two of the pyrimidine nucleobases, cytosine [6] and thymine [7 There have been rather few studies of uracil adsorption at surfaces at the solidvacuum interface although the gold/uracil system has attracted significant interest in model electrochemical studies of nucleobase/metal surface interactions. At different applied potentials both physisorbed and chemisorbed species have been proposed, but while there have been several investigations using in situ STM (scanning tunnelling microscopy), no significant information regarding the adsorption geometry at the interface has emerged from most of these studies.…”

Section: Introductionmentioning

confidence: 99%

Uracil on Cu(110): A quantitative structure determination by energy-scanned photoelectron diffraction

Duncan¹,

Unterberger²,

Kreikemeyer-Lorenzo³

et al. 2011

The Journal of Chemical Physics

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Citation: Duncan, D. A. et al. (2011). Uracil on Cu (110) AbstractThe local adsorption site of the nucleobase uracil on Cu(110) has been determined quantitatively by energy-scanned photoelectron diffraction (PhD). Qualitative inspection of the O 1s and N 1s soft X-ray photoelectron spectra, PhD modulation spectra, and O K-edge near-edge X-ray adsorption fine structure indicate that uracil bonds to the surface through its nitrogen and oxygen constituent atoms, each in near atop sites, with the molecular plane essentially perpendicular to surface and aligned along the close packed [110] azimuth. Multiple scattering simulations of the PhD spectra confirm and refine this geometry. The Cu-N bondlength is 1.96±0.04Å, while the Cu-O bondlengths of the two inequivalent O atoms are 1.93±0.04Å and 1.96±0.04Å, respectively. The molecule is twisted out of the [110] direction by 11±5• .

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Quantitative determination of the local structure of thymine on Cu(110) using scanned-energy mode photoelectron diffraction

Cited by 39 publications

References 27 publications

The adsorption structure of furan on Pd(111)

The adsorption structure of furan on Pd(111)

Chemical Transformations Drive Complex Self-Assembly of Uracil on Close-Packed Coinage Metal Surfaces

Uracil on Cu(110): A quantitative structure determination by energy-scanned photoelectron diffraction

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