Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba 305-8568, Japan.
J Am Chem Soc. 2012 Sep 5;134(35):14401-7. doi: 10.1021/ja303542r. Epub 2012 Aug 22.
Molecular dynamics simulations were performed to study the self-assembly of a spherical complex through metal-ligand coordination interactions. M(6)L(8), a nanosphere with six palladium ions and eight pyridine-capped tridentate ligands, was selected as a target system. We successfully observed the spontaneous formation of spherical shaped M(6)L(8) cages over the course of our simulations, starting from random initial placement of the metals and ligands. To simulate spontaneous coordination bond formations and breaks, the cationic dummy atom method was employed to model nonbonded metal-ligand interactions. A coarse-grained solvent model was used to fill the gap between the time scale of the supramolecular self-assembly and that accessible by common molecular dynamics simulation. The simulated formation process occurred in the distinct three-stage (assembly, evolution, fixation) process that is well correlated with the experimental results. We found that the difference of the lifetime (or the ligand exchange rate) between the smaller-sized incomplete clusters and the completed M(6)L(8) nanospheres is crucially important in their supramolecular self-assembly.
采用分子动力学模拟研究了通过金属-配体配位相互作用的自组装球形配合物。选择 M(6)L(8)（具有六个钯离子和八个吡啶封端的三齿配体的纳米球）作为目标体系。我们成功地观察到了从金属和配体的随机初始位置开始，在模拟过程中自发形成的球形 M(6)L(8)笼。为了模拟自发的配位键形成和断裂，采用阳离子虚拟原子方法来模拟非键合的金属-配体相互作用。使用粗粒溶剂模型来填补超分子自组装的时间尺度和常见分子动力学模拟之间的间隙。模拟的形成过程发生在明显的三个阶段（组装、演化、固定）过程中，这与实验结果很好地相关。我们发现，较小尺寸的不完整簇和完整的 M(6)L(8)纳米球之间的寿命（或配体交换率）差异在它们的超分子自组装中至关重要。
