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Title:Elucidating the structures of ionic clusters, from ion-water complexes to ion-biomolecule-water complexes
Author(s):Ke, Haochen
Director of Research:Lisy, James M.
Doctoral Committee Chair(s):Glumac, Nick G.
Doctoral Committee Member(s):Gruebele, Martin; McCall, Benjamin J.
Department / Program:Mechanical Sci & Engineering
Discipline:Mechanical Engineering
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Molecular Spectroscopy
Ionic Clusters
Abstract:The competition and cooperation between various noncovalent interactions in hydrated ions and hydrated ion-biomolecule systems are systematically characterized and examined using infrared spectroscopy and various theoretical approaches. The Multiple Channel InfraRed PhotoDissociation spectroscopy (MC-IRPD) method is further developed and applied to argon-tagged hydrated alkali cation systems, M+(H2O)nAr (M = Li, Na, K, Rb, Cs; n = 3-5) with simultaneous monitoring of the [Ar] and [Ar+H2O] fragmentation channels. The comparison between spectral features in the two channels and corresponding energy analyses provide definitive spectral assignments of the stable structural conformers and substantial insights of hydration mechanism of the cations. Results revealed that smaller cations (Li+ and Na+), with higher charge density, prefer to form structural configurations with extended linear networks of hydrogen bonds. Larger cations (Rb+ and Cs+), with lower charge density, prefer to generate configurations with cyclic hydrogen-bonded water subunits. It appears that K+ is somewhat unique with very simple (and predominantly) single structural conformers. This has led to the suggestion that K+ can "move" easily in or through biological systems, concealing its identity as an ion, under the "appearance" or disguise as a water molecule. Indole is used as tractable model to study the hydration structures of biomolecules as well as the interplay of non-covalent interactions within ion-biomolecule-water complexes. With three potential binding sites: above the six- or five-member ring, and the N-H group, the competition between π and hydrogen bond interactions involves multiple locations. Electrostatic interactions from monovalent cations are in direct competition with hydrogen bonding interactions, as structural configurations involving both direct cation-indole interactions and cation-water-indole bridging interactions (π-hydrogen bond) were observed. The different charge densities of Na+/K+ give rise to different structural conformers at the same level of hydration. Infrared spectra with parallel Density Function Theory (DFT) calculations and Gibbs free energy calculations revealed rich structural insights of Na+/K+(Indole)(H2O)3-6 cluster ion complexes. Isotopic (H/D) analyses were applied to decouple the spectral features originating from the OH and NH stretches. Results showed no evidence of direct interaction between water and NH group of indole (via a σ-hydrogen bond) at current levels of hydration with the incorporation of cations, however π-hydrogen bonding interactions were ubiquitous at hydration levels between two and five. Density Functional Theory based ab initio Molecular Dynamics simulations (DFT-MD) are applied to analyze the anharmonic coupling of O-H stretching modes and large amplitude intermolecular rocking modes in the water-nitrite complex system (H2O)-(NO2)-. MD simulated spectra reproduced earlier IR-IR double resonance spectra of water-nitrite remarkably well. Thorough analyses of dynamic trajectories revealed two distinct dynamic patterns, large amplitude symmetric rocking motion and asymmetric rocking motion, which yield completely different spectral features. Systematic application of autocorrelation functions, using Fourier transforms, of chosen dynamic parameters provided unambiguous assignments of both overall infrared spectra and motion-specific infrared spectra. DFT-MD simulations are proved to be a promising and powerful alternative tool in studying systems with anharmonic couplings, considering its reasonable computational cost, easy accessibility and sufficient accuracy.
Issue Date:2015-06-24
Type:Thesis
URI:http://hdl.handle.net/2142/88253
Rights Information:Copyright 2015 Haochen Ke
Date Available in IDEALS:2015-09-29
Date Deposited:August 201


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