Canonical, Deprotonated, or Zwitterionic? A Computational Study on Amino Acid Interaction with the TiO₂ (101) Anatase Surface

Abstract

The interaction of 11 amino acids with the TiO2 (101) anatase surface was investigated by means of PBE-D2* periodic simulations, both from a static and dynamic points of view. Several adsorption states, with the amino acid in its canonical, zwitterionic, or deprotonated forms, were considered. The strongest interactions correspond to dative interactions between the electron pairs of N or O atoms of the amino acids and the Ti atoms of the surface. For glycine, the most stable configuration corresponds to the deprotonated (N,O) binding mode, at variance to that observed for the adsorption of glycine on rutile (110) surface, for which the dissociative (O,O) binding mode was determined to be the preferred one. For the remaining amino acids, the following general trend was identified: those amino acids with acidic or a basic lateral chain groups, except Arg, exhibit a deprotonated (N,O) binding mode as glycine, because the additional dative interactions with the side chain overcome the destabilizing effect induced by steric hindrances. However, for the remaining amino acids, with weaker side chain interactions, the zwitterionic state is the most stable conformer because the steric hindrances between the lateral chains and the surface are minimized. Overall, the present results indicate that the most stable amino acid adsorption state on the surface arises from a delicate balance between favorable interactions and steric hindrances of the amino acids with the surface, the latter ones becoming particularly relevant when lateral chains are considered.

When the Surface Matters: Prebiotic Peptide‐Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT‐D2 Simulations

“…That is, Ti atoms can accept lone pairs of donor atoms (e.g., N or O), whereas O surface atoms can become Brønsted bases by accepting protons released by acidic compounds. This is indeed the case for glycine, which on the (101) anatase surface spontaneously transfers the −COOH proton to the surface giving rise to a glycine − /surface + ion pair . In this work, kinetic and thermodynamic effects of the TiO 2 (101) anatase surface, caused by the presence of Ti Lewis and O Brønsted sites, for the peptide‐bond formation between two glycine molecules is demonstrated by periodic DFT‐D2 simulations.…”

Insights into the role of D‐A‐π‐A type pro‐aromatic organic dyes with thieno[3,4‐b]pyrazine as A acceptor group into dye‐sensitized solar‐cells. A TD‐DFT/periodic DFT study

“…In this Hessian matrix, only the dyes and the first layer of the surface were considered. This methodology confirmed that the optimized structures were minimal, and enabled the calculation of the free energy G at T = 298.15 K. For this purpose, a script was used, which calculated the quasi‐harmonic thermochemical corrections. Specifically, the entropy S was computed in terms of the vibrational (harmonic oscillator approximation) and rotational (quasi‐RRHO approach) entropies, in addition to a damping function, as it has been described by Grimme, while the enthalpy H was obtained through H = U + PV , where P was given by the total energy change in function of the volume cell optimized.…”

Toward the origin of life over feldspar surfaces: Adsorption of amino acids and catalysis of conformational interconversions

“…In addition to glycine (Gly), four amino acids with sidechains that have the distinct physiochemical properties were subject to p‐DFT calculations, as valine (Val), proline (Pro), arginine (Arg), and aspartic acid (Asp), see Scheme . Pro is the only natural amino acid with the secondary N atom and often results in the β‐turn structures in peptides and proteins.…”

“…In addition to glycine (Gly), four amino acids with sidechains that have the distinct physiochemical properties were subject to p-DFT calculations, as valine (Val), proline (Pro), arginine (Arg), and aspartic acid (Asp), see Scheme 1. [24,44] Pro is the only natural amino acid with the secondary N atom and often results in the β-turn structures in peptides and proteins. Three representative isomers of amino acids reported previously [14,18,29] become the focus of this study (Scheme 2): For all amino acids, zwitterions (A) are the principal conformations in aqueous solutions and are the active form to conduct the biological and pharmaceutical functions.…”

“…[8][9][10][11]13,14] As aforementioned, minerals play a central role during birth of life, and their interactions with amino acids have recently emerged to be a research hotspot. [17][18][19][20][21][22][23][24][25][26][27][28][29] The periodic density functional theory (p-DFT) calculations of Pantaleone et al [24] showed that the strongest interaction of anatase (101) surface with amino acids corresponds to the dative bonding between the N or O atoms of amino acids and surface-Ti atoms. As indicated by the p-DFT results of Rimola et al, [19] glycine adsorption over the silica surface with isolated hydroxyl groups is dominated by canonical isomers.…”