Structural Inhomogeneity of Water by Complex Network Analysis

Abstract

There is still an open debate regarding the structure forming capabilities of water at ambient conditions. In order to probe the presence of such inhomogeneities, we apply complex networks analysis methods to a molecular dynamics simulation at room temperature. This study provides both a structural and quantitative characterization of kinetically homogeneous substates present in bulk water. We find that the conformation-space-network is highly modular, and that structural properties of water molecules are spatially correlated over at least two solvation shells. From a kinetic point of view, the free energy surface is characterized by multiple heterogeneous metastable regions with different populations and marginal barriers separating them. The typical timescale of hopping between them is 200-400 fs. A scanning in temperature reveals that those substates can be stabilized either entropically or enthalpically. The latter resembles an ice-like domain that extends for at least two solvation shells.

Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide

“…However, processes involving barrier crossings are expected to have the same relaxation kinetics when either the whole state is selected as a target or just the most probable conformation of the state (i.e. conformations at the peak of the order parameter distribution) [19]. Consequently, the disagreement between the fpt distribution to R g < 3.4 and to a more stringent target (i.e.…”

“…Within this approach, free-energy representations are obtained in a more universal way without using arbitrarily projections on order parameters. Both thermodynamics and kinetics come from the analysis of the transition network with methods like network clusterization algorithms [15,18,20], network flow analysis [9,19,21] and spectral methods [16,17].…”

“…Even for the well-studied case of structured peptides and the folding of small proteins, there is no consensus on the best practice [19,22]. Moreover, a broad set of problems including molecular association [23,24], the analysis of intrinsically disordered proteins [25,26] and liquids [27,28] are very hard to tackle with the current methodology.…”

“…such descriptions can be highly inaccurate due to the presence of overlaps, i.e., configurations with different properties corresponding to the same value of the order parameter [10,12]. An important improvement in this respect was the introduction of configuration-spacenetworks, providing accurate and concise descriptions of the system kinetics and thermodynamics [8,9,[15][16][17][18][19]. Their application however is still limited, lacking a general way to build the transition network.…”

“…1c-d). It is worth noting that while this reduced kinetic model satisfies the Markov property [19], this is not generally the case for the starting transition network. (This property is in any case not needed when it comes to network clusterization [15,18].)…”