Molecular Dynamics Simulations of Dynamic Combinatorial Catenanes

Raw results from molecular dynamics simulations performed for a 2014 Chemical Science paper on catenane cooperativity. The fileset contains simulation data for self-assembled tetrameric azobenzene macrocycles, cyclodextrins, and their [2]- and [3]catenane structures. Files include 40 ns trajectory files, topology/parameter files, and time-series data for distances, solvent-accessible surface area, and hydrogen bonds.

Use Cases

• Visualizing molecular trajectories based on the provided .traj files.
• Analyzing structural stability based on distance data between cyclodextrins and macrocycles.
• Studying solvent interactions based on partitioned solvent-accessible surface area (SASA) data.
• Investigating intermolecular bonding based on hydrogen bond count time-series data.

Strengths

• Includes 40 nanosecond trajectory files for detailed temporal analysis.
• Data is partitioned for specific molecular components (4AB, CD1, CD2) and properties (hydrophobicity/hydrophilicity).
• Raw results are directly linked to a peer-reviewed publication from 2014.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred from filenames and descriptions.
• Last update date is unknown; freshness unverified.

Provenance

Source

Piotr Nowak, associated with the paper 'Catenanes from Catenanes...' in Chemical Science, 2014.

Collection Method

Results of molecular dynamics simulations performed for the cited research.