Faculty of Chemistry, Jagiellonian University in Kraków, Gronostajowa 2, PL-30 387 Krakow, Poland.
Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, PL-87 100 Torun, Poland.
J Chem Inf Model. 2024 Oct 28;64(20):7925-7937. doi: 10.1021/acs.jcim.4c01040. Epub 2024 Oct 11.
Superphanes are a group of organic molecules from the cyclophane family. They are characterized by the presence of two parallel benzene rings joined together by six bridges. If these bridges are sufficiently long, the superphane cavity can be large enough to trap small molecules or ions. Using ab initio (time scale of 80 ps) and classical (up to 200 ns) molecular dynamics (MD) methods, we study the behavior of five fundamental molecules (M = HO, NH, HF, HCN, MeOH) encapsulated inside the experimentally reported lantern-like superphane and its two derivatives featuring slightly modified side bridges. The main focus is studying the dynamics of hydrogen bonds between the trapped M molecule and the imino nitrogen atoms of the side chains of the host superphane. The length of the N···H hydrogen bond increases in the following order: HF < HCN < HO < MeOH < NH. The mobility of the trapped molecule and its preferred position inside the superphane cage depend not only on the type of this molecule but also largely on the in/out conformational arrangement of the imino nitrogens in the side chains of the superphane. Their inward-pointing positions allow the formation of strong N···H hydrogen bonds. For this reason, these nitrogens are the preferred sites of interaction. The mobility of the molecules and their residence times on each side of the superphane have been explained by referring to the symmetry and conformation of the given superphane cage. All force field MD simulations have shown that the encapsulated molecule remained inside the superphane cage for 200 ns without any escape event to the outside. Moreover, our simulations based on some endohedral complexes in the water box also showed no exchange event. Thus, the superphanes we study are true carcerand molecules. We attribute this property to the hydrophobic side chains and their pinwheel arrangement, which makes the side walls of the studied superphanes fairly impenetrable to small molecules.
超轮烷是环芳烷家族的一类有机分子。它们的特点是存在两个由六个桥连在一起的平行苯环。如果这些桥足够长，超轮烷的空腔可以大到足以捕获小分子或离子。我们使用从头算（80 ps 时间尺度）和经典（高达 200 ns）分子动力学（MD）方法，研究了五种基本分子（M = HO、NH、HF、HCN、MeOH）封装在实验报道的灯笼状超轮烷及其两个具有略微修饰的侧桥衍生物中的行为。主要重点是研究被捕获的 M 分子与主体超轮烷侧链亚氨基氮原子之间氢键的动力学。被捕获的 M 分子与超轮烷侧链亚氨基氮原子之间的 N···H 氢键长度按以下顺序增加：HF < HCN < HO < MeOH < NH。被捕获分子的迁移率及其在超轮烷笼内的优先位置不仅取决于该分子的类型，而且在很大程度上取决于超轮烷侧链中亚氨基氮原子的内外构象排列。它们指向内部的位置允许形成强的 N···H 氢键。出于这个原因，这些氮原子是相互作用的首选位点。通过参考给定超轮烷笼的对称性和构象，解释了分子的迁移率及其在超轮烷两侧的停留时间。所有力场 MD 模拟都表明，被捕获的分子在 200 ns 内保持在超轮烷笼内，没有任何逃逸到外部的事件。此外，我们基于水盒中一些包合物的模拟也没有显示交换事件。因此，我们研究的超轮烷是真正的笼烷分子。我们将此性质归因于疏水侧链及其风车排列，这使得所研究的超轮烷的侧壁对小分子相当不可渗透。
