DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using...

Area of Science:

• Computational Chemistry
• Materials Science
• Molecular Dynamics

Background:

• Describing atomistic interactions in molecular simulations often relies on complex visualizations.
• A need exists for a precise, yet interpretable, notation for molecular interactions.
• Existing universal atom typing schemes like DL_F Notation provide a foundation for chemical representation.

Purpose of the Study:

• To introduce the DL_ANALYSER Notation for Atomic Interactions (DANAI) as a novel syntax for describing molecular interactions.
• To demonstrate the utility of DANAI in analyzing hydrogen bond and hydrophobic contact networks within molecular dynamics simulations.
• To showcase the integration of DANAI within the DL_ANALYSER software for DL_POLY.

Main Methods:

• Developed DANAI, a notation syntax for annotating detailed atomistic interactions.
• Utilized the DL_F Notation for expressing atomic species in a chemically relevant manner within DANAI.
• Implemented DANAI within the DL_ANALYSER software for processing DL_POLY molecular dynamics simulation data.

Main Results:

• DANAI successfully annotates atomistic interactions without requiring diagrammatic illustrations, ensuring interpretability for both humans and computers.
• Molecular dynamics simulations of pure ethanoic acid liquid revealed distinct hydrogen bond and hydrophobic contact networks using DANAI.
• Analysis showed preferential 'head-to-tail' orientation of carboxylic groups, forming linear hydrogen-bonded structures intertwined with methyl clusters.

Conclusions:

• DANAI provides an effective and versatile notation for describing molecular interactions in computational simulations.
• The DL_ANALYSER software, incorporating DANAI, can accurately identify and differentiate various intermolecular interaction networks.
• The study elucidates the structural organization of ethanoic acid liquid, highlighting the interplay between hydrogen bonding and hydrophobic interactions.