Dataset on the phospholipid adsorption onto clinochlore
Description
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).
Files
Steps to reproduce
The CRYSTAL23 code (10.1021/acs.jctc.2c00958) was employed throughout the present work to perform the quantum mechanical simulations, using the well-known hybrid functional B3LYP and Gaussian-type orbitals basis sets. The DFT-D3 scheme (10.1063/1.4927476) was also implemented in the calculations to include the effects of van der Waals interactions. The total energy of the system (phospholipid, mineral surface and DVPA/substrate) was calculated using the XLGRID keyword, TOLINTEG 8 8 8 8 16 (ITOL1-5 parameters), TOLDEE (8) and shrinking factor SHRINK 6 6 (see the CRYSTAL manual for the meaning of these keywords). Unit cell parameters and atomic coordinates were optimised with a BFGS algorithm, setting the tolerances on the maximum allowed gradient (TOLDEG) and maximum atomic displacements (TOLDEX) to 0.00001 and 0.00004, respectively. The following formula was used to calculate the adsorption (binding) energy BE between the phospholipid and the (001) clinochlore surface: BE = E(SM//SM) – E(S//S) – EM(M//M), where E(SM//SM) is the energy of a fully relaxed unit cell with the molecule(s) M interacting with the slab S, E(S//S) is the energy of a fully relaxed slab, and EM(M//M) is the molecular energy of the free, optimised molecule. In Eq.(1), the symbols S, M or SM before the double slash (//) indicate the system under consideration, and the symbols after the double slash specify the geometry in which the energy was calculated. If we consider the energy required to change the conformation of the molecule and substrate after the interaction, we can write: BE = BE* + δES + δEM, δES = E(S//SM) – E(S//S), δEM = E(M//SM) – EM(M//M) = ΔEM + ΔEL, BE* = E(SM//SM) – E(S//SM) – E(M//SM), where δES represents the deformation energy of the slab surface (δES > 0), δEM is the sum of the deformation energy of the molecule (ΔEM) and the intermolecular interactions (ΔEL) occurring between the infinite 2D replicas of the phospholipid in the slab-to-molecule (SM) configuration. The purely molecular deformation energy was computed as: ΔEM = EM(M//SM) – EM(M//M), where EM(M//SM) is the molecular (non-periodic) energy of the phospholipid with the geometry occurring on the slab surface, hence it follows that ΔEM > 0. The lateral intermolecular interactions, ΔEL, were calculated as: ΔEL = E(M//SM) – EM(M//SM). where the ΔEL values can be either positive (indicating repulsion between the molecular replicas) or negative (attraction). According to Eq.(5), the BE* binding energy is then free from deformational and lateral interaction contributions, because it is the result of energy differences between periodic calculations carried out at the geometry of the SM system. Because Gaussian-type orbitals basis sets are not complete, the above BE definition must include the basis set superposition error (BSSE) correction, using the same counterpoise method adopted for intermolecular complexes (10.1080/00268977000101561).
Institutions
- Universita degli Studi di Bologna Dipartimento di Scienze Biologiche Geologiche ed Ambientali