Complete Experimental Structure Determination of the p(3 × 2)pg Phase of Glycine on Cu{110}

Abstract

We present a quantitative low energy electron diffraction (LEED) surface-crystallograpic study of the complete adsorption geometry of glycine adsorbed on Cu{110} in the ordered p(3 × 2) phase. The glycine molecules form bonds to the surface through the N atoms of the amino group and the two O atoms of the de-protonated carboxylate group, each with separate Cu atoms such that every Cu atom in the first layer is involved in a bond. Laterally, N atoms are nearest to the atop site (displacement 0.41 Å). The O atoms are asymmetrically displaced from the atop site by 0.54 Å and 1.18 Å with two very different O-Cu bond lengths of 1.93 Å and 2.18 Å. The atom positions of the uppermost Cu layers show small relaxations within 0.07 Å of the bulk-truncated surface geometry. The unit cell of the adsorbate layer consists of two glycine molecules, which are related by a glide-line symmetry operation. This study clearly shows that a significant coverage of adsorbate structures without this glide-line symmetry must be rejected, both on the grounds of the energy dependence of the spot intensities (LEED-IV curves) and of systematic absences in the LEED pattern.

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

“…The precise location of the O and N atoms with respect to the Cu(110) substrate was determined with high accuracy by photoelectron diffraction (PhD) and the resulting configuration is summarised in Figure 6A [66; 176]. A subsequent structural LEED study [173] substantially confirms the model. The Gly/Cu(110) overlayer was analysed from the electronic point of view by combining DFT with XES and NEXAFS [67; 102].By performing angular resolved measurements, it was possible to separate the 2p density of states into three different spatial directions for all the four atoms of interest in the molecule.…”

Surface chemistry of glycine on Pt{111} in different aqueous environments

“…1 ML corresponds to 1 atom per substrate surface atom) before the start of each experiment. Glycine (> 99% pure, from Sigma-Aldrich) was dosed via sublimation at 140 • C in vacuum from a home-build evaporation source, as described in [30,45]. Even though the temperature of the evaporator was kept constant within 1 • C the deposition rate was not constant over time, therefore the coverage was calibrated via the peak height of the N 1s XP signal.…”

Energy landscapes and dynamics of glycine on Cu(110)

“…4 According to the reported RAIRS results, glycine adopts a two point binding arrangement (µ2) at low temperature and low coverage, but converts readily to an overall more stable µ3 footprint with increasing coverage and surface temperature. 4,14 Although it is well understood that glycine (as alanine) adopts a µ3 footprint and a heterochiral (in terms of surface chirality) arrangement 15,25 in the (3 x 2) phase, there is relatively little information regarding the energy difference between the µ3 conformers (having the same footprint, but different C-C-N backbone torsional angles) and about how they interconvert. In this work we have initially compared the energetics of three µ3 glycine conformers (Figure 1) and we have performed transition state calculations to estimate the energy barriers for conversion between them.…”

“…Although glycine is not intrinsically chiral, when adsorbed on the Cu(110) surface it produces the same chiral footprint typical of alanine 11,20,21 and proline 2, 22-24 on this surface, so glycine can be used as a model to understand the assembly of more complex amino acids on Cu(110). 2,8,25 Even though the bonding, structure and long range arrangement of glycine on Cu(110) have been investigated by several groups using a wide range of experimental 8,13,14,26 and computational tools 15,17,27,28 , the energy barriers between adsorbed conformers and the dynamics of glycine surface diffusion are still largely unresolved. In this work we have investigated, using DFT calculations, the energy landscapes of glycine conformers with identical footprint chirality and possible reaction pathways that convert the footprint chirality.…”