Dataset on the phospholipid adsorption onto clinochlore

The data reported in this repository is related to a Density Functional Theory (DFT) investigation of the adsorption of phospholipids onto the (001) surface of clinochlore, a mineral belonging to the phyllosilicate family. Clinochlore is a chlorite, i.e., a layered silicate formed by an alternate stacking of talc-like layers [labelled as TOT, ideal chemical formula Mg3Si4O10(OH)2] and brucite-like ones [B, Mg(OH)2].

In this study, we characterised the adsorption behaviour of the simplest phospholipid, i.e., 1, 2-divaleroyl-sn-glycero-3-phosphatidic acid (DVPA), onto the two types of clinochlore layers to understand the relationship between the biomolecule and the clay mineral, and the possible mineral-mediated formation of cell membranes. Several DVPA/substrate interaction models were considered, encompassing low and high surface coverages, molecular orientations and presence of natural atomic substitutions in the clinochlore sub-units (e.g., Al3+/Mg2+ and Al3+/Si4+ substitutions in the B and TOT layers, respectively). The results provided further information on the phospholipid-mineral interactions, which could be useful in devising innovative applications in biotechnology and environmental fields.

The present dataset is organised in folders as follows:
- Initial models: this folder contains the starting DVPA molecule and the B and TOT (001) surface models, which were geometrically optimised (i.e., relaxed) at the DFT/B3LYP-D3 level of theory.
- Adsorption: this folder contains a series of sub-folders labelled as XPYY, where X = B, T indicates the type of substrate (brucite-like and talc-like layers, respectively), and YY represents a sequential number. For instance, BP01 is the first model related to the adsorption of DVPA onto the brucite-like layer. A README file was provided to briefly describe each model. Each sub-folder reports:
(1) the CRYSTAL code (see the "Steps to reproduce" section) relaxation output of the adsorption model, named as "xpyy_b3lyp-d3_relaxed.out";
(2) a structural file obtained from the cited output (labelled as "xpyy.cif", Crystallographic-Interchange Format);
(3) a "BSSE" folder containing the outputs produced by CRYSTAL, which were used to calculate the Basis Set Superposition Error. These outputs are related to the calculation of the energy of the DVPA/substrate, considering (a) ghost functions on the molecule ("xpyy_bsse_ghosts_p.out") or on the mineral layer ("xpyy_bsse_ghosts_b.out" or "xpyy_bsse_ghosts_t.out"), (b) the infinite two-dimensional repetitions (monolayers) of the biomolecule ("xpyy_bsse_monolayer_p.out") or substrate ("xpyy_bsse_monolayer_b.out" or "xpyy_bsse_monolayer_t.out"), and (c) the isolated DVPA with the adsorption conformation ("xpyy_bsse_molecule.out").

The CRYSTAL output files can be visually inspected using the Moldraw software (10.1107/S0021889887008665), whereas the CIF files can be opened with any crystallographic software, e.g., VESTA (10.1107/S0021889811038970).