Abstract
The basket-like geometry of cyclodextrins (CDs), with a cavity able to host hydrophobic groups, makes these molecules well suited for a large number of fundamental and industrial applications. Most of the established CD-based applications rely on trial and error studies, often ignoring key information at the atomic level that could be employed to design new products and to optimize their use. Computational simulations are well suited to fill this gap, especially in the case of CD systems due to their low number of degrees of freedom compared with typical macromolecular systems. Thus, the design and validation of solid and efficient methods to simulate and analyze CD-based systems is key to contribute to this field. The behavior of supramolecular complexes critically depends on the media where they are embedded, so the detailed characterization of the solvent is required to fully understand these systems. In the present work, we use the inclusion complex formed by two α-CDs and one sodium dodecyl sulfate molecule to test eight different parameterizations of the GROMOS and AMBER force fields, including several methods aimed to increase the conformational sampling in computational molecular dynamics simulation trajectories. The system proved to be extremely sensitive to the employed force field, as well as to the presence of a water/air interface. In agreement with previous experiments and in contrast to the results obtained with AMBER, the analysis of the simulations using GROMOS showed a quick adsorption of the complex to the interface as well as an extremely exotic behavior of the water molecules surrounding the structure both in the bulk aqueous solution and at the water surface. The chirality of the CD molecule seems to play an important role in this behavior. All together, these results are expected to be useful to better understand the behavior of CD-based supramolecular complexes such as adsorption or aggregation driving forces, as well as to introduce new methods able to speed up general MD simulations.
Highlights
The behavior of native cyclodextrins (CDs) in aqueous solution and at the air/water interface is much more complex than expected just considering their apparently simple molecular structure [1,2,3]
The complexes were much less tight in the simulations using AMBER/GAFF and, in contrast with experimental evidences and with the results obtained with GROMOS, they did not adsorb to the interface using this force field
When they reached the interface by diffusion using AMBER/GAFF, they stayed with the symmetry axis perpendicular to the surface during a few ns and they went back to the bulk solution
Summary
The behavior of native cyclodextrins (CDs) in aqueous solution and at the air/water interface is much more complex than expected just considering their apparently simple molecular structure [1,2,3]. It is not a surprise that the behavior of native and modified CDs, as well as that of the supramolecular complexes they form upon interacting with different types of molecules, is not trivial [7]. In spite of their great potential for a large number of applications, atomic level information of CD molecules, which is key to understand how structure relates to function, is really scarce. Without the ability to understand dynamic structural changes, the design, development, and optimization of applications using CDs has been traditionally based on empirical trial-and-error essays as well as a fair degree of serendipity
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