A Collective Variable for Controlling Occupation in Flexible Confined Volumes

Area of Science:

• Supramolecular Chemistry
• Computational Chemistry
• Materials Science

Background:

• Host-guest complexation is crucial but solvent effects are often overlooked in simulations.
• Existing methods struggle to dynamically control and quantify guest loading in flexible supramolecular structures.

Purpose of the Study:

• To introduce a novel collective variable (CV) for controlling supramolecular structure occupation in molecular dynamics (MD) simulations.
• To enable quantitative analysis of solvent loading and its impact on host-guest systems.
• To provide a versatile tool for studying flexible and deforming molecular cages.

Main Methods:

• Developed a collective variable (CV) using tetrahedral tessellation to approximate accessible volume.
• Employed a symmetric and smooth function for continuous loading control.
• Utilized harmonic bias and umbrella sampling to control solvent occupation and compute free energy profiles.
• Validated the method on organic porous liquids and a palladium-based metal-organic cage.

Main Results:

• Successfully controlled and quantified solvent molecule loading within flexible supramolecular structures.
• Demonstrated the method's ability to adapt to changing system shapes during simulations.
• Validated results against experimental data and prior simulation studies.
• Showcased versatility for flexible and deforming molecular cages.

Conclusions:

• The proposed CV method offers an efficient and versatile approach for controlling and quantifying guest loading in MD simulations.
• This technique is relevant for studying host-guest complexation, catalytic processes, and separation applications involving tunable molecular systems.
• The method provides a robust framework for investigating dynamic solvent-structure interactions in complex systems.