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).

本仓库所报道的数据，与密度泛函理论（Density Functional Theory, DFT）针对磷脂在斜绿泥石（clinochlore）(001)晶面的吸附行为研究相关。斜绿泥石属于页硅酸盐矿物家族，是一类绿泥石矿物，即由类滑石层[标记为TOT，理想化学式为Mg₃Si₄O₁₀(OH)₂]与类水镁石层[标记为B，化学式为Mg(OH)₂]交替堆叠形成的层状硅酸盐。

本研究针对最简单的磷脂——1,2-二戊酰基-sn-甘油-3-磷脂酸（1,2-divaleroyl-sn-glycero-3-phosphatidic acid, DVPA）在两种斜绿泥石层上的吸附行为进行了表征，旨在阐明该生物分子与黏土矿物之间的相互作用关系，以及矿物介导的细胞膜潜在形成机制。本研究考量了多种DVPA/底物相互作用模型，涵盖低、高表面覆盖率，分子取向，以及斜绿泥石亚单元中天然原子取代的情况（例如B层中的Al³+/Mg²+取代与TOT层中的Al³+/Si⁴+取代）。研究结果为磷脂-矿物相互作用提供了更多信息，可为生物技术与环境领域的创新应用开发提供参考。

本数据集按文件夹组织如下：
- 初始模型（Initial models）：该文件夹包含初始DVPA分子与B、TOT型(001)表面模型，所有模型均在DFT/B3LYP-D3理论级别下完成了几何优化（即结构弛豫）。
- 吸附（Adsorption）：该文件夹包含一系列以XPYY命名的子文件夹，其中X取B或T，分别代表类水镁石层与类滑石层两种底物类型；YY为顺序编号。例如，BP01代表DVPA在类水镁石层上吸附的首个模型。文件夹附带README文件，用于简要说明每个模型的信息。每个子文件夹包含以下内容：
(1) 吸附模型的CRYSTAL代码弛豫输出文件（详见“复现步骤”章节），命名为“xpyy_b3lyp-d3_relaxed.out”；
(2) 从上述输出文件提取得到的结构文件，格式为晶体交换格式（Crystallographic-Interchange Format, CIF），命名为“xpyy.cif”；
(3) 名为“BSSE”的子文件夹，内含CRYSTAL生成的用于计算基组叠加误差（Basis Set Superposition Error, BSSE）的输出文件。这些输出文件对应DVPA/底物体系的能量计算场景：(a) 仅在生物分子上添加鬼基函数（ghost functions）的情况（文件名为“xpyy_bsse_ghosts_p.out”），或仅在矿物层上添加鬼基函数的情况（文件名为“xpyy_bsse_ghosts_b.out”或“xpyy_bsse_ghosts_t.out”）；(b) 仅考虑生物分子无限二维平铺（单层）的情况（“xpyy_bsse_monolayer_p.out”）或仅考虑底物无限二维平铺的情况（“xpyy_bsse_monolayer_b.out”或“xpyy_bsse_monolayer_t.out”）；(c) 吸附构象下的孤立DVPA分子（“xpyy_bsse_molecule.out”）。

CRYSTAL输出文件可通过Moldraw软件（DOI: 10.1107/S0021889887008665）进行可视化查看，而CIF文件可通过任意晶体学软件打开，例如VESTA（DOI: 10.1107/S0021889811038970）。