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DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using Ethanoic Acid Liquid as a Test Case

Authors :
Chin W. Yong
Ilian T. Todorov
Source :
Molecules, Vol 23, Iss 1, p 36 (2017)
Publication Year :
2017
Publisher :
MDPI AG, 2017.

Abstract

The DL_ANALYSER Notation for Atomic Interactions, DANAI, is the notation syntax to describe interactions between molecules. This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic illustrations, and yet can be interpreted easily by both human users and computational means. By making use of the DL_F Notation, a universal atom typing scheme for molecular simulations, DANAI contains the expression of atomic species in a natural chemical sense. It is implemented within DL_ANALYSER, a general analysis software program for DL_POLY molecular dynamics simulation software. By making references to the molecular dynamics simulations of pure ethanoic acid liquid, it is shown that DL_ANALYSER can identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through the use of the DANAI expression. It was found that the carboxylic groups preferentially orientated in a “head-to-tail” conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters.

Details

Language :
English
ISSN :
14203049
Volume :
23
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Molecules
Publication Type :
Academic Journal
Accession number :
edsdoj.f3120615dbc74e1a899b5edb41512242
Document Type :
article
Full Text :
https://doi.org/10.3390/molecules23010036