Quickstart guide to model structures and interactions of artificial molecular muscles with efficient computational...

Area of Science:

• Computational chemistry
• Molecular modeling
• Materials science

Background:

• Artificial molecular muscles (AMMs) are complex molecular machines.
• Theoretical modeling of AMMs is challenging due to their size and intricate structures.
• Experimental methods often lack detailed 3D structural information.

Purpose of the Study:

• To develop a standardized computational protocol for modeling AMMs.
• To enable efficient and reliable prediction of AMM structures and contraction free energies.
• To provide a reproducible method for theoretical studies of AMMs.

Main Methods:

• Utilized a quantum chemical protocol combining GFN-FF and GFNn-xTB methods.
• Employed dispersion-corrected density functional theory (DFT-D) for reference calculations.
• Focused on daisy-chain rotaxane AMMs.

Main Results:

• Achieved efficient computation of structures and contraction free energies (ΔGc).
• Demonstrated excellent agreement (1-2 kcal mol⁻¹) between theoretical and experimental ΔGc in one case.
• Established a reproducible modeling approach for AMMs.

Conclusions:

• The developed protocol offers a reliable method for studying AMMs.
• This approach facilitates theoretical investigations into AMM behavior and design.
• The findings support the use of GFN-FF and GFNn-xTB for AMM modeling.