A Multifaceted Phenomenon of Hydrophobic Effects: Insights Learned from Nucleation Algorithm Based Computer Simulation Approach
type: CreativeWork
description: We have applied our new approach, a combination of the AVUS-HR nucleation algorithm and a thermodynamic cycle, to the studies of hydrophobicity-related researches. Due to the multifaceted characteristics of hydrophobicity, it is essential to acquire knowledge in various environments where hydrophobic relevant events occur for comprehensive understanding of this process. In this regards, we have chosen two relatively unstudied hydrophobic subjects for application of our new methodology. For the first subject, hydrophobic association behaviors of a methane pair confined into a nanometer sized hydrophobic cavity have been investigated. Our new approach demonstrates that the association behavior between two methane molecules is enhanced under confined environment rather than in bulk water. This association is primarily driven by energy originating from the unique situation where small (i.e., two methane molecules) and large (i.e., boundary of the hydrophobic cavity) hydrophobic units come together. For the second subject, hydration thermodynamics for confined spaces between two infinitely parallel walls have been studied. Our simulation results demonstrate that the weak attractive interaction between water molecules and walls allows water molecules to pack more efficiently for the smallest wall separation of 3 Å considered here comparing with the hard wall case where there is no interaction between water molecules and walls. Furthermore, these weak attractive interactions lower the free energy penalty for the formation of water clusters inside a confined space, ultimately lowering the total energy of the system when compared with the hard wall. Based on the successful applications of our novel nucleation algorithm to the two different hydrophobic related researches, further, we believe that it will contribute to the various and more complex hydrophobic researches (i.e., association behaviors of nonpolar and/or polar amino acid residues in the presence of salts under con…
abstract: We have applied our new approach, a combination of the AVUS-HR nucleation algorithm and a thermodynamic cycle, to the studies of hydrophobicity-related researches. Due to the multifaceted characteristics of hydrophobicity, it is essential to acquire knowledge in various environments where hydrophobic relevant events occur for comprehensive understanding of this process. In this regards, we have chosen two relatively unstudied hydrophobic subjects for application of our new methodology. For the first subject, hydrophobic association behaviors of a methane pair confined into a nanometer sized hydrophobic cavity have been investigated. Our new approach demonstrates that the association behavior between two methane molecules is enhanced under confined environment rather than in bulk water. This association is primarily driven by energy originating from the unique situation where small (i.e., two methane molecules) and large (i.e., boundary of the hydrophobic cavity) hydrophobic units come together. For the second subject, hydration thermodynamics for confined spaces between two infinitely parallel walls have been studied. Our simulation results demonstrate that the weak attractive interaction between water molecules and walls allows water molecules to pack more efficiently for the smallest wall separation of 3 Å considered here comparing with the hard wall case where there is no interaction between water molecules and walls. Furthermore, these weak attractive interactions lower the free energy penalty for the formation of water clusters inside a confined space, ultimately lowering the total energy of the system when compared with the hard wall. Based on the successful applications of our novel nucleation algorithm to the two different hydrophobic related researches, further, we believe that it will contribute to the various and more complex hydrophobic researches (i.e., association behaviors of nonpolar and/or polar amino acid residues in the presence of salts under con…
author: Kim, Hyunmi
keywords: thermodynamic quantities of water filling process, entropy and energy contributions to the PMF
date published: 2011-01-01T08:00:00Z
date modified: 2026-07-24T02:57:00Z
provider: Lousiana State University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Chemistry

PropertyValue
property ID: DOI
value: 10.31390/gradschool_dissertations.48