An Integrated Graph-Theoretic Approach to Understanding Solvation Using a Novel Data Mining Tool, moleculaRnetworks

Persistent Link:
http://hdl.handle.net/10150/243096
Title:
An Integrated Graph-Theoretic Approach to Understanding Solvation Using a Novel Data Mining Tool, moleculaRnetworks
Author:
Mooney, Barbara Logan
Issue Date:
2012
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Embargo:
Release after 21-Aug-2013
Abstract:
An integrated graph-theoretic and geometric approach to the analysis of aqueous solvation of atomic ions is presented. This analysis makes use of a novel data-mining tool, moleculaRnetworks, to process data from molecular dynamics simulations. The workings and structure of this tool are discussed, along with the development and testing of its PageRank algorithm-based rapid solvation polyhedra classifier. The ability to classify instantaneous solvation polyhedra enables a finely detailed understanding of shell structure-behavior relationships, as water molecules simultaneously rearrange about ions, exchange with the bulk, and rearrange their hydrogen-bond network. The application of the tool to cation systems, including lithium, sodium, potassium, magnesium, calcium, and lanthanum, yields new insight into the mechanisms of water exchange about these ions. It is shown that in order for exchange events to occur, the solvation shell must "preorganize" to admit or expel a molecule of water: this preorganization is reflected in the mechanistic preference for each ion. The application of the tool to anion systems, including fluoride, chloride, and bromide, reveals that these ions have an extended effect on the reorientation ability of water molecules beyond their first solvation shell. Finally, when both ions are present, as in the potential of mean force simulation between lanthanum and chloride, structural rearrangements can be seen as the ions break through the barrier to form the contact ion pair. Taken together, these results show the utility of the moleculaRnetworks tool in broadening our understanding of aqueous ion solvation.
Type:
text; Electronic Dissertation
Keywords:
networks; solvation; Chemistry; data mining; hydrogen bond
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Chemistry
Degree Grantor:
University of Arizona
Advisor:
Corrales, L. René

Full metadata record

DC FieldValue Language
dc.language.isoenen_US
dc.titleAn Integrated Graph-Theoretic Approach to Understanding Solvation Using a Novel Data Mining Tool, moleculaRnetworksen_US
dc.creatorMooney, Barbara Loganen_US
dc.contributor.authorMooney, Barbara Loganen_US
dc.date.issued2012-
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.releaseRelease after 21-Aug-2013en_US
dc.description.abstractAn integrated graph-theoretic and geometric approach to the analysis of aqueous solvation of atomic ions is presented. This analysis makes use of a novel data-mining tool, moleculaRnetworks, to process data from molecular dynamics simulations. The workings and structure of this tool are discussed, along with the development and testing of its PageRank algorithm-based rapid solvation polyhedra classifier. The ability to classify instantaneous solvation polyhedra enables a finely detailed understanding of shell structure-behavior relationships, as water molecules simultaneously rearrange about ions, exchange with the bulk, and rearrange their hydrogen-bond network. The application of the tool to cation systems, including lithium, sodium, potassium, magnesium, calcium, and lanthanum, yields new insight into the mechanisms of water exchange about these ions. It is shown that in order for exchange events to occur, the solvation shell must "preorganize" to admit or expel a molecule of water: this preorganization is reflected in the mechanistic preference for each ion. The application of the tool to anion systems, including fluoride, chloride, and bromide, reveals that these ions have an extended effect on the reorientation ability of water molecules beyond their first solvation shell. Finally, when both ions are present, as in the potential of mean force simulation between lanthanum and chloride, structural rearrangements can be seen as the ions break through the barrier to form the contact ion pair. Taken together, these results show the utility of the moleculaRnetworks tool in broadening our understanding of aqueous ion solvation.en_US
dc.typetexten_US
dc.typeElectronic Dissertationen_US
dc.subjectnetworksen_US
dc.subjectsolvationen_US
dc.subjectChemistryen_US
dc.subjectdata miningen_US
dc.subjecthydrogen bonden_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineChemistryen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorCorrales, L. Renéen_US
dc.contributor.committeememberClark, Aurora E.en_US
dc.contributor.committeememberJewett, Johnen_US
dc.contributor.committeememberSanov, Andreien_US
dc.contributor.committeememberCorrales, L. Renéen_US
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