Energy landscapes and dynamics of glycine on Cu(110)

Abstract

Amino acids adsorbed over single crystal metal surfaces have emerged as prototypical systems for exploring the properties that govern the development of long-range chirality in selfassembled monolayers (SAM) and supramolecular 2D networks. In this study, we characterise the self-assembly mechanism for glycine on the Cu (110) surface. This process occurs on a time scale that is too fast for most atomically resolved microscopic techniques, so the mechanism we propose here provides new insight for an important unexplored surface phenomenon.

Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}

“…For a coherent narrative, we present calculational details of the DFT simulations and how they form the basis of our discrete kinetic model. The DFT energy calculations were performed with CASTEP, a plane-wave, periodic boundary conditions DFT code.…”

“…Diffusion across the close-packed Cu{110} rows: paths 5 to 8, see numbers on the left, with initial geometry (R or reactant) on the left panel, the first transition state structure (TS) of the path in the center, and the first intermediate minimum as product (P) on the right. Above each configuration, the energy difference is given in eV.…”

“…Each GLY molecule diffuses along or across the Cu{110} rows from one minimum, X i , to another, X j , via a fixed set of n = 10 possible moves. The moves were identified via DFT calculations (see next section) 92 and remain the same over time, unless neighboring atoms block a move (Figure 3).…”

“…We focus on GLY adsorbed as glycinate in a µ 3 footprint, with both oxygens and nitrogen bound to the copper surface on close-packed [110] rows, which is the most stable adsorbed configuration obtained in experiments. 17,21 For a coherent narrative we present calculational details of the DFT simulations 92 108 and hybrid eigenvector-following as coded in the OPTIM program. [109][110][111] GLY, as ALA, adopts a µ 3 footprint and a heterochiral (in terms of surface chirality) arrangement 22,29 in the (3×2) phase.…”

“…We focus on GLY adsorbed as glycinate in a μ 3 footprint, with both oxygens and nitrogen bound to the copper surface on closepacked [110] rows, which is the most stable adsorbed configuration obtained in the experiments. 17,21 For a coherent narrative, we present calculational details of the DFT simulations 92 and how they form the basis of our discrete kinetic model. The DFT energy calculations were performed with CASTEP, 103 a plane-wave, periodic boundary conditions DFT code.…”