Ion Binding to Cucurbit[6]uril:  Structure and Dynamics

Abstract

Molecular dynamics simulations are used to study the microscopic structure and dynamics of cations bound to cucurbit[6]uril (CB[6]) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183 M for the salts and 0.0184 M for CB[6]. The cations bind only to CB[6] carbonyl oxygens. They are never found inside the CB[6] cavity. Complexes with Na(+) and K(+) mostly involve one cation, whereas with Ca(2+) single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. When bound to CB[6], sodium and potassium cations jump mainly between nearest or second-nearest neighbors. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB[6] oxygen. A few water molecules (zero to four) can occupy the CB[6] cavity, which is limited by the CB[6] oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cation activity as "lids" over the CB[6] portal cannot, however, be identified. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells.

Improving platinum(II)-based anticancer drug delivery using cucurbit[n]urils

“…The solubility of CB[n]s in water also varies depending on the method used to synthesise and purify them; many CB[n]s precipitate from solution with co-crystallised acid molecules [26], which can be difficult to remove. Alkali earth metal salts also increase the solubility of CB[n]s, particularly saline [37][38][39][40][41][42]. In the latter case, the cations are strongly bound at the portals and can help stabilise the binding of small guests inside the cavity [37][38][39][40][41][42].…”

Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study

“…The capability of this setup has been documented in a number of publications. [11][12][13][14] Table 1 summarizes some information on the simulated samples. Each system contains atactic PVA oligomers with methyl groups at both chain ends.…”

The Interface Between Platinum(111) and Poly(vinyl Alcohol) Melt: A Molecular Dynamics Study

“…While studying the Pt(111)/isopropanol interface, we have found that the electrostatic interactions between the metal surface and isopropanol molecules had no significant effect on almost any of the structural and dynamical properties reported in our previous article (28). Mass density and separate atom distributions, order parameter as function of distance, in-plane radial distribution functions, diffusion and exchange dynamics at different distances to the Pt(111) surface seem identical.…”

“…They showed that, in order to study thermodynamic properties of interfaces between metal and organic matter, one has to parameterize each selected system carefully and separately. In our previous work we studied platinum(111)/liquid isopropanol (2-propanol) interface (28), where isopropanol molecules bind to the platinum surface through a weak chemical bond between the hydroxyl oxygen and individual platinum atoms. The purpose of the current work is to make the next step and to study the properties of the interface between the platinum(111) surface [Pt(111)] and poly(vinyl alcohol) [PVA].…”