Molecular aggregation in liquid water: Laplace spectra and spectral clustering of H-bonded network

Bakó, Imre; Csókás, Dániel; Pothoczki, Szilvia

doi:10.1016/j.molliq.2020.114802

Cited by 6 publications

(6 citation statements)

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“…Since liquid water at 170K behaves similarly to ice, we expect that for water networks at this low temperature the bipartivity measure defined in (3.14) is close to 1 (nearly bipartite graph). At higher temperatures, when this ordered structure is perturbed by the appearance of new links (see first column of Table [6]), the (near) bipartivity of the network is lost, and we expect the bipartivity measure to decrease. This intuition is confirmed by the results reported in Table [3].…”

Section: Results Using Global Metricsmentioning

confidence: 98%

“…The LDL and HDL phases feature different structural and topological properties (see section 2) and several studies in the literature proposed a variety of chemical order parameters to investigate these two forms, [17, 20, 31, 32, 47-49, 49, 50, 56-59, 61]. We also mention works of Bakó et al, [5,6], in which the authors use a spectral clustering method, based on the analysis of the eigenvalues of the graph Laplacian, to study the global properties of an H-bonded network.…”

Section: Introductionmentioning

confidence: 99%

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Structural analysis of water networks

Benzi

Daidone

Faccio

2022

Journal of Complex Networks

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Liquid water, besides being fundamental for life on Earth, has long fascinated scientists due to several anomalies. Different hypotheses have been put forward to explain these peculiarities. The most accredited one foresees the presence in the supercooled region of two phases at different densities: the low-density liquid phase and the high-density liquid phase. In our previous work [Faccio et al. (2022), J. Mol. Liq., 355, 118922], we showed that it is possible to identify these two forms in water networks through a computational approach based on molecular dynamics simulation and on the calculation of the total communicability of the associated graph, in which the nodes correspond to water molecules and the edges represent the connections (interactions) between molecules. In this article, we present a more in-depth investigation of the application of graph-theory based approaches to the analysis of the structure of water networks. In particular, we investigate different connectivity and centrality measures and we report on the use of a variety of global metrics aimed at giving a topological and geometrical characterization of liquid water.

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Section: Results Using Global Metricsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Structural analysis of water networks

Benzi

Daidone

Faccio

2022

Journal of Complex Networks

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“…Different hydrogen bond definitions have been proposed in the literature. 64,65 In the present study, we use the CHIMERA 66 software to identify the hydrogen bond network. The CHIMERA tool applies a geometric criterion to compute a three dimensional hydrogen bond distribution, and therefore a probability of hydrogen-bond formation, for each hydrogen-bonding site.…”

Section: Impact Of Electric Fields On Ccn-water Mixturesmentioning

confidence: 99%

The Effect of Electric Fields on the Structure of Water/Acetonitrile Mixtures

Sourpis,

Forero-Martinez,

Schmid

2023

J. Electrochem. Soc.

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We study the effect of external electric fields on the structure of water/acetonitrile mixtures at high acetonitrile content by molecular dynamics simulations. We find that the linear response regime extends up to roughly 0.03 V /nm in these mixtures, then nonlinear behavior sets in. The most pronounced nonlinear effect of electric field is a change of relative orientations of neighboring acetonitrile molecules, from predominantly antiparallel to predominantly parallel. Nevertheless, the hydrogen bond network topology remains remarkably stable and conserves its overall properties in the whole range of considered applied fields up to 0.5 V /nm, which is far beyond the dielectric breakdown limit of pure water.

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“…In particular, recently, there have been interesting investigations concerning the topology and statistics of the network of hydrogen bonds in the case of water, revealing a clear topological characterization of the LLPT as well as features in the statistics of rings that correlate with the enhanced fluctuations associated with the Widom line. , In correspondence with the Widom lines, the topology of the hydrogen bond network acquires an equal number of hexagonal rings (known to promote crystallization) and pentagonal rings (known to act against crystallization). This evidence has led to the hypothesis that the maxima in the thermodynamic response functions may be linked to the condition of maximal frustration (maximum structural heterogeneity or maximum competition between ordered and disordered local structures) in the network of bonds, sparking a large number of investigations connecting the properties of water with the underlying network of bonds. ,− …”

Section: Introductionmentioning

confidence: 99%

Analysis of Structural Change across the Liquid–Liquid Transition and the Widom Line in Supercooled Stillinger-Weber Silicon

2023

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We consider the changes in the structure of supercooled Stillinger-Weber silicon at pressures at which the studied range of temperatures traverses the liquid−liquid transition or the "Widom line" (at which the isothermal compressibility or the specific heat exhibits a maximum). In addition to the conventional characterizations in terms of the pair-correlation function and bond orientational order, we analyze the statistics of rings in the bond network as well as the statistics of clusters of low density liquid (LDL)-and high density liquid (HDL)-like atoms. We investigate the nature of the change in these structural characterizations when the liquid−liquid transition line or the Widom line is crossed. We find that the isobaric temperature variation of these structural features reveals clear indications of maximal structural heterogeneity or frustration upon crossing the liquid−liquid transition or the Widom line, as in the case of water, but with some differences in detail, which we discuss.

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Molecular aggregation in liquid water: Laplace spectra and spectral clustering of H-bonded network

Cited by 6 publications

References 64 publications

Structural analysis of water networks

Structural analysis of water networks

The Effect of Electric Fields on the Structure of Water/Acetonitrile Mixtures

Analysis of Structural Change across the Liquid–Liquid Transition and the Widom Line in Supercooled Stillinger-Weber Silicon

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