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 di-glycine peptide adsorbed on the mineral surface was calculated, and the binding energy analysis of the specific interaction of the molecule, depending on the local chemistry of the substrate, provided fundamental information to interpret end explain the experimental evidence. LAY DESCRIPTION: The present work aims at extending the knowledge of the biomolecules/minerals interaction world. The fundamental knowledge of the interaction between biomolecules and mineral surfaces is of utmost importance to drive the development of new technological advancements, particularly for condensation, aggregation, catalysis and exchange of biomolecules. The mineral surface can be used as substrate in several fields and applications, for instance in biotechnology, environmental science and remediation, soil science, agro-food and related technology. This kind of research 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 research at the micro and nanometric scale can be performed with several experimental techniques and, among them, scanning probe microscopy-related methods are particularly suited to investigate surface adsorption processes at single molecule level. In the present work, the focus is on the specific interaction at the atomic scale between a small peptide (di-glycine) and the surface of clinochlore (a diffuse clay mineral). Clinochlore is a mineral belonging to the phyllosilicate, formed by alternately stacked hydrophilic talc-like layers [chemical formula Mg3 Si4 O10 (OH)2 ] and hydrophobic brucite-like sheets [magnesium hydroxide, Mg(OH)2 ]. Since these two kind of layered structures are held together by weak (van der Waals) forces, the mineral can be easily cleaved along the [001] crystallographic direction (the stacking direction) and the resulting (001) clinochlore surface may presents at the nanoscale some remainders of one layer (brucite-like or talc-like) on the other. This means that this mineral exposes to the environment two different type of surfaces, one hydrophilic and one hydrophobic, which can selectively interact with (adsorb) different type of molecules at the nanoscale. Clinochlore is also one of the 420 mineral species that were likely present on Earth at the time of life's origins, thus it could have played a fundamental role in prebiotic chemistry. In this study, the interaction between di-glycine and clinochlore was characterized by means of both atomic force microscopy (AFM) at the nanometric scale and density functional theory (DFT) simulations, correlating the results of the two methods (cross-correlation approach). 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) structures, agglomerates, filaments and networks 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 di-glycine adsorbed on the mineral surface was calculated, and the binding energy analysis of the specific interaction of the molecule, depending on the local chemistry of the substrate, provided fundamental information to interpret end explain the experimental evidence.