Nano‐atomic scale hydrophobic/philic confinement of peptides on mineral surfaces by cross‐correlated SPM and quantum mechanical DFT analysis

Abstract

The fundamental knowledge of the interaction between biomolecules and mineral surfaces is of utmost importance to drive new technological advancements, particularly for condensation, aggregation, catalysis and exchange of biomolecules. The mineral surface can be used in several fields and applications, for instance in biotechnology, environmental science and remediation, soil science, agro-food and related technology. This kind of knowledge may also provide several suggestions and have implications also for the prebiotic chemistry field, namely the study of the abiotic physicochemical steps that could have led to the 'creation' of the first known living organism. Nowadays, this kind of information at the micro and nanometric scale can be explored with several experimental and theoretical techniques and, among them, atomic force microscopy (AFM)-related methods and density functional theory (DFT) are particularly suited to investigate adsorption processes at single molecule level. In the present work, the specific interaction at the atomic scale between a small peptide (di-glycine) and the (001) surface of clinochlore, a mineral presenting alternately stacked talc-like layers (hydrophilic) and brucite-like sheets (hydrophobic), was characterized by means of a cross-correlated approach combining AFM and DFT simulations. The experiments evidenced the preferential adsorption of di-glycine onto the hydrophobic brucite-like sheet of the mineral, with the observed molecules organized as dot-like (single-molecules), agglomerates, filament-like and network structures by the surface, whereas only very few peptides were imaged onto the hydrophilic talc-like layer. From the theoretical analysis, the most stable conformation of the

DFT Simulation of the Water Molecule Interaction with the (00l) Surface of Montmorillonite

“…Further, the internal geometries (bond lengths and angles) of the Na-MMT and Ca-MMT models are consistent with those of the massive mineral, meaning that the surface reconstruction is almost negligible. Hence, as also stated elsewhere by Moro and co-workers [19][20][21][22], a single layer of 2:1 phyllosilicates is sufficient for the treatment and analysis of surface adsorption phenomena.…”

“…CRYSTAL employs a linear combination of crystalline orbitals, expanded as Gaussiantype functions (basis sets), to describe the multielectronic function of the system. Here, the atomic basis sets were the same as those used in previous work on both bulk and surface properties of phyllosilicates [19,20,22,38,[46][47][48][49][50][51][52][53], where they produced effective results of excellent quality. For the 2:1 layer, silicon, aluminium, oxygen, and hydrogen were described in terms of 88-31G* [54], 8-511d1G [55], 8-411d11G [56], and 3-1p1G [57], respectively.…”

“…In the last two decades, smectites and, in general, clay minerals were employed as substrates for different and various fundamental and applied research involving biomolecules. For example, clays are able to condense, organize, and concentrate biomolecules of different kinds and sizes [15][16][17][18][19][20][21], and, if the clay substrates present both Brønsted and Lewis acid sites [22,23], they may also act as catalysts. Notwithstanding the important biotechnological applications of clay minerals, these types of studies are also of utmost interest in the field of prebiotic chemistry, i.e., in all the steps (selection, concentration, synthesis, and protection) that lead from the basic building blocks of life (amino acids, nucleotides, lipids) to functional macromolecules (peptides, RNA/DNA, membranes) and, eventually, to the first cell [24,25].…”

Preface to StSPM2019EV special issue

“…10 In addition, atomic force microscopy and quantum-mechanical simulations were used together to characterise hydrophobic/philic confinement of peptides onto selected mineral surfaces, with possible application in biotechnology, environmental science and remediation, soil science, agro-food and related technology. 9…”

“…At the biological/inorganic interface, AFM was employed to study the interaction of prototypical citrated gold nanoparticles, a model system of inorganic nanoparticles, with biological membranes, the latter being multicomponent supported lipid bilayers 10 . In addition, atomic force microscopy and quantum‐mechanical simulations were used together to characterise hydrophobic/philic confinement of peptides onto selected mineral surfaces, with possible application in biotechnology, environmental science and remediation, soil science, agro‐food and related technology 9 …”