Abstract In the context of the origin of life, clays have been proposed as possible materials to adsorb, protect and potentially foster the formation of complex bio molecules. In the present study, the adsorption of nucleotides onto clay surfaces has been tackled through classical molecular dynamics calculations. Various parameters have been varied by modelling the deoxyguanosine mono phosphate molecule at the basal surface of two clay minerals: montmorillonite and nontronite, at pH = 3 and 7, and in a 0.5 M NaCl solution in presence or absence of Ca2+ divalent cations. It has been firstly observed that counter cations in solution adopts a three-layers structure above the mineral basal surfaces which can be modified by the mineral composition, the location of the surface charge, and results in substantial effects on nucleotide adsorption. For montmorillonite, for which the charge is located in the octahedral (inner) layer, the two closest counter cations layers above the mineral surface are less populated while the third layer comprises the largest cations density. For nontronite, for which the negative charge is located on the surface oxygen atoms of the tetrahedral layer in contact with the aqueous solution, the first two counter cations layers are the most populated. The negative charge on the surface is thus screened by the first two layers above nontronite surface, and by only the third layer for montmorillonite. As a result, the negatively charged phosphate moiety of nucleotides can approach closer to the surface of nontronite by coordinating with the first two layers cations and the nucleobase adsorb on the surface in a parallel orientation maximizing Van der Walls interactions. On montmorillonite, the phosphate coordinates the cations of the third layer and thus remains rather far from the surface, which does not allow the nucleobase parallel binding. These theoretical results explain experimental results on the effect of mineral and solution composition on the adsorption of nucleotides on the surface of swelling clays.

中文翻译：

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粘土表面上核苷酸的吸附：矿物组成、pH 值和溶液盐的影响

摘要 在生命起源的背景下，粘土已被提出作为可能的材料来吸附、保护和潜在地促进复杂生物分子的形成。在本研究中，核苷酸在粘土表面的吸附已通过经典分子动力学计算得到解决。通过对两种粘土矿物（蒙脱石和绿脱石，pH = 3 和 7）以及存在或不存在 Ca2+ 二价阳离子的 0.5 M NaCl 溶液中的脱氧鸟苷单磷酸分子进行建模，可以改变各种参数。首次观察到溶液中的抗衡阳离子在矿物基底表面上方采用三层结构，可通过矿物组成、表面电荷的位置进行修饰，并对核苷酸吸附产生实质性影响。对于电荷位于八面体（内）层的蒙脱石，矿物表面上方两个最近的抗衡阳离子层较少，而第三层包含最大的阳离子密度。对于 nontronite，其负电荷位于与水溶液接触的四面体层的表面氧原子上，前两个抗衡阳离子层最多。因此，表面上的负电荷被非脱脱石表面上方的前两层屏蔽，而蒙脱石仅被第三层屏蔽。因此，通过与前两层阳离子配位，核苷酸的带负电荷的磷酸酯部分可以更接近非脱氧核糖核酸的表面，并且核碱基以平行方向吸附在表面上，从而最大限度地发挥范德沃尔斯相互作用。在蒙脱石上，磷酸盐与第三层的阳离子配位，因此离表面很远，这不允许核碱基平行结合。这些理论结果解释了矿物和溶液组成对核苷酸在膨胀粘土表面吸附的影响的实验结果。