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Molecules 2018, 23(1), 36; doi:10.3390/molecules23010036

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

1
Scientific Computing Department, Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, UK
2
Manchester Pharmacy School, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9NT, UK
*
Author to whom correspondence should be addressed.
Received: 28 November 2017 / Revised: 20 December 2017 / Accepted: 21 December 2017 / Published: 24 December 2017
(This article belongs to the Section Theoretical Chemistry)
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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. View Full-Text
Keywords: atomic interactions; hydrogen bonds; hydrophobic interactions; ethanoic acid; molecular dynamics (MD); DL_F Notation; DL_POLY; DL_FIELD; DL_ANALYSER. atomic interactions; hydrogen bonds; hydrophobic interactions; ethanoic acid; molecular dynamics (MD); DL_F Notation; DL_POLY; DL_FIELD; DL_ANALYSER.
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Yong, C.W.; Todorov, I.T. DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using Ethanoic Acid Liquid as a Test Case. Molecules 2018, 23, 36.

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