Triplet correlation functions in liquid water

Dhabal, Debdas; Singh, Murari; Wikfeldt, Kjartan Thor; Chakravarty, Charusita

doi:10.1063/1.4898755

Cited by 26 publications

(28 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Preliminary results for triplet O–O–O correlations in pair-additive, rigid-body, atomistic models of water strongly resemble the mW water model. 334 …”

Section: Relation Between Dynamics and Thermodynamicsmentioning

confidence: 99%

Water: A Tale of Two Liquids

et al. 2016

Self Cite

View full text Add to dashboard Cite

Water is the most abundant liquid on earth and also the substance with the largest number of anomalies in its properties. It is a prerequisite for life and as such a most important subject of current research in chemical physics and physical chemistry. In spite of its simplicity as a liquid, it has an enormously rich phase diagram where different types of ices, amorphous phases, and anomalies disclose a path that points to unique thermodynamics of its supercooled liquid state that still hides many unraveled secrets. In this review we describe the behavior of water in the regime from ambient conditions to the deeply supercooled region. The review describes simulations and experiments on this anomalous liquid. Several scenarios have been proposed to explain the anomalous properties that become strongly enhanced in the supercooled region. Among those, the second critical-point scenario has been investigated extensively, and at present most experimental evidence point to this scenario. Starting from very low temperatures, a coexistence line between a high-density amorphous phase and a low-density amorphous phase would continue in a coexistence line between a high-density and a low-density liquid phase terminating in a liquid–liquid critical point, LLCP. On approaching this LLCP from the one-phase region, a crossover in thermodynamics and dynamics can be found. This is discussed based on a picture of a temperature-dependent balance between a high-density liquid and a low-density liquid favored by, respectively, entropy and enthalpy, leading to a consistent picture of the thermodynamics of bulk water. Ice nucleation is also discussed, since this is what severely impedes experimental investigation of the vicinity of the proposed LLCP. Experimental investigation of stretched water, i.e., water at negative pressure, gives access to a different regime of the complex water diagram. Different ways to inhibit crystallization through confinement and aqueous solutions are discussed through results from experiments and simulations using the most sophisticated and advanced techniques. These findings represent tiles of a global picture that still needs to be completed. Some of the possible experimental lines of research that are essential to complete this picture are explored.

show abstract

“…Preliminary results for triplet O–O–O correlations in pair-additive, rigid-body, atomistic models of water strongly resemble the mW water model. 334 …”

Section: Relation Between Dynamics and Thermodynamicsmentioning

confidence: 99%

Water: A Tale of Two Liquids

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Site-specific magnesium binding is a significant factor in the selection of a dominant structure. , However, for the model systems we considered there is no tight binding of magnesium and the RNA still collapses. A concern is the quality of the force field .…”

mentioning

confidence: 99%

Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix–Junction–Helix Systems

Templeton

Elber

2018

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Using computer simulations we consider the balance of thermodynamic forces that collapse RNA. A model helix-junction-helix (HJH) construct is used to investigate the transition from an extended to a collapsed conformation. Conventional Molecular Dynamics and Milestoning simulations are used to study the free energy profile of the process for two ion concentrations. We illustrate that HJH folds to a collapsed state with two types of counter ions (Mg2+ and K+). By dissecting the free energy landscape into energetic and entropic contributions we illustrate that the electrostatic forces between the RNA and the mobile ions do not drive the RNA to a collapsed state. Instead, entropy gains from water expulsion near the neighborhood of the RNA provide the stabilization free energy that tilt HJH into more compact structures. Further simulations of a three-helix hammerhead ribozyme show a similar behavior and support the idea of collapse due to increased gain in water entropy.

show abstract

“…Here, the variation of the fluid structure factor with pressure is investigated and related to a single integral over the corresponding triplet correlation function [7, 25–27]. More recently, this analysis has involved a combination of experimental and simulation based approaches [28, 29]. The triplet correlations displayed by the simulations can then be examined further to provide additional detail.…”

Section: Introductionmentioning

confidence: 99%

Experimental investigation of triplet correlation approximations for fluid water

Pallewela

Ploetz

Smith

2018

Fluid Phase Equilibria

View full text Add to dashboard Cite

Triplet correlations play a central role in our understanding of fluids and their properties. Of particular interest is the relationship between the pair and triplet correlations. Here we use a combination of Fluctuation Solution Theory and experimental pair radial distribution functions to investigate the accuracy of the Kirkwood Superposition Approximation (KSA), as given by integrals over the relevant pair and triplet correlation functions, at a series of state points for pure water using only experimental quantities. The KSA performs poorly, in agreement with a variety of other studies. Several additional approximate relationships between the pair and triplet correlations in fluids are also investigated and generally provide good agreement for the fluid thermodynamics for regions of the phase diagram where the compressibility is small. A simple power law relationship between the pair and triplet fluctuations is particularly successful for state points displaying low to moderately high compressibilities.

show abstract

Triplet correlation functions in liquid water

Cited by 26 publications

References 81 publications

Water: A Tale of Two Liquids

Water: A Tale of Two Liquids

Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix–Junction–Helix Systems

Experimental investigation of triplet correlation approximations for fluid water

Contact Info

Product

Resources

About