Single Molecule Investigation of Glycine–Chlorite Interaction by Cross-Correlated Scanning Probe Microscopy and Quantum Mechanics Simulations

Abstract

In this work, we studied the interaction of glycine with the (001) surface of chlorite mineral at a single molecule level by cross-correlating scanning probe microscopy (SPM) and ab initio quantum mechanics (QM) investigations. Chlorite mineral is particularly interesting and peculiar for the interaction with organic molecules because it presents an alternated stacking of brucite-like (hydrophobic) and talc-like (hydrophilic) layers of different polarities. Brucite-like is positive, whereas talc-like is negative. The experimental atomic force microscopy (AFM) observations show that glycine is stably and selectively adsorbed on the brucite-like layer, organized in monolayers with different patterns. The sizes of single molecules of glycine measured by AFM are in agreement with those calculated by QM. Glycine molecules were found to align both at the edges and on the terraces of the brucitic surface. QM simulations confirmed the AFM observations that glycine molecule is adsorbed with high adsorption energy preferentially with its plane parallel to the (001) brucite-like surface. QM also provided the geometry conformation of the molecule and the bonding scheme between glycine and brucite surface. This kind of data can be very helpful both to biotechnological applications of this substrate and to depict some important processes that might have been occurred in prebiotic environments.

Second‐order elastic constants of hexagonal hydroxylapatite (P63) fromab initioquantum mechanics: Comparison between DFT functionals and basis sets

“…Multielectron wave functions are described by linear combination of crystalline orbitals (CO), expanded in terms of Gaussian‐type basis sets. We employed the same all‐electron basis sets adopted in our previous work on the bulk of OHAp and different types of carbonated hydroxylapatites, and of other minerals . The calcium has been described with a 86–511G(2d), with outer shell exponents α sp = 0.453 bohr −2 , α d1 = 3.1910 and 0.8683 bohr −2 , and α d2 = 0.2891 bohr −2 .…”

“…This particular DFT method is called B3LYP‐D*. The same approach has been adopted with good results in previous works on phyllosilicates, where dispersive forces are dominant …”

“…Since the advent of modern quantum chemistry, experimental methods and theoretical simulations have obtained beneficial contributions by cross‐correlations of each other, the firsts by reaching atomic‐level understanding of physico‐chemical phenomena observed at lager scales, the seconds by including methods to correctly describe the experimental results . Furthermore, the constant increase in computation powers allows simulating very complex system in reasonable time.…”

“…The theoretical data, especially those from plan waves simulations, are in good agreement with available results in literature and further extend the knowledge of the mechanical and vibrational properties of hydroxylapatite.density functional theory, elastic constants, GTO and PW basis sets, hydroxylapatite 1 | I N TR ODU C TI ON Since the advent of modern quantum chemistry, experimental methods and theoretical simulations have obtained beneficial contributions by crosscorrelations of each other, the firsts by reaching atomic-level understanding of physico-chemical phenomena observed at lager scales, the seconds by including methods to correctly describe the experimental results. [1,2] Furthermore, the constant increase in computation powers allows simulating very complex system in reasonable time. In the last decade, many computational chemistry researches were aimed to investigate the mechanical properties of several solid phases, at both athermal [3][4][5][6][7][8] and thermal conditions.…”

“…[23,24] hydroxylapatites, [31][32][33] and of other minerals. [1,2] The calcium has been described with a 86-511G(2d), with outer shell exponents a sp 5 0.453 bohr 22 , a d1 5 3.1910 and 0.8683 bohr 22 , and a d2 5 0.2891 bohr 22 . We also considered, for a comparison with previous works on hydroxylapatite, [34] a Hay and Wadt small core pseudopotential (SCP), consisting of an effective core pseudopotential (ECP) for the first 10 electrons and the remaining ones (10 electrons in the 3sp and 4s orbitals) by three contracted Gaussian-type functions.…”