Relevance of hydrogen bond definitions in liquid water

Matsumoto, Masakazu

doi:10.1063/1.2431168

Cited by 88 publications

(67 citation statements)

References 31 publications

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“…For pure water the most popular ring size of twelve atoms is in accordance with previous findings [13,36], supposedly inheriting this feature from the 6 molecule membered rings of Ice-Ih and Ice-II [37]. The occurrence of 5 and 7 molecule membered rings (10 and 14 atoms) is the characteristic of Ice-III [37].…”

Section: Ring Size Distributionssupporting

confidence: 81%

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Ring structure analysis of ethanol–water mixtures

Gereben

2015

Journal of Molecular Liquids

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Section: Ring Size Distributionssupporting

confidence: 81%

“…In our preceding publication, morphological analyses of pure ethanol were provided [12]. Matsumoto [13] investigated the network topology of water and performed ring analysis: 6-membered (6 molecules, 12 atoms) rings were found with the highest probability.…”

Section: Introductionmentioning

confidence: 99%

Ring structure analysis of ethanol–water mixtures

Gereben

2015

Journal of Molecular Liquids

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“…give different estimations of the hydrogen bonds present in water 78 . Our approach here is to establish a reasonable criterion to distinguish liquid-like from ice-like molecules in a given configuration.…”

Section: Methodsmentioning

confidence: 99%

The thickness of a liquid layer on the free surface of ice as obtained from computer simulation

Conde¹,

Vega²,

Patrykiejew³

2008

The Journal of Chemical Physics

165

216

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Molecular dynamic simulations were performed for ice I h with a free surface by using four water models, SPC/E, TIP4P, TIP4P/Ice and TIP4P/2005. The behavior of the basal plane, the primary prismatic plane and of the secondary prismatic plane when exposed to vacuum was analyzed. We observe the formation of a thin liquid layer at the ice surface at temperatures below the melting point for all models and the three planes considered. For a given plane it was found that the thickness of a liquid layer was similar for different water models, when the comparison is made at the same undercooling with respect to the melting point of the model. The liquid layer thickness is found to increase with temperature. For a fixed temperature it was found that the thickness of the liquid layer decreases in the following order: the basal plane, the primary prismatic plane, and the secondary prismatic plane. For the TIP4P/Ice model, a model reproducing the experimental value of the melting temperature of ice, the first clear indication of the formation of a liquid layer appears at about -100 Celsius for the basal plane, at about -80 Celsius for the primary prismatic plane and at about -70 Celsius for the secondary prismatic plane.

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“…The downside is that these structural definitions invariably contain a degree of arbitrariness, as they are based on the heuristic introduction of ranges of structural parameters that are deemed to represent a hydrogen bond in a given context. [45,46] Kumar et al carried out a systematic comparison of many of these structural definitions in the case of liquid water, [47] and recognized that the best way to assess whether a given definition makes physical sense is to compare the probability distribution of the structural parameters with the range of values associated with the hydrogen bond.…”

Section: The Hydrogen Bond Revisitedmentioning

confidence: 99%

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

Gasparotto

Ceriotti

2014

The Journal of Chemical Physics

103

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The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding -a central concept to our understanding of the physical chemistry of water, biological systems and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

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Relevance of hydrogen bond definitions in liquid water

Cited by 88 publications

References 31 publications

Ring structure analysis of ethanol–water mixtures

Ring structure analysis of ethanol–water mixtures

The thickness of a liquid layer on the free surface of ice as obtained from computer simulation

Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

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