The ability to form hydrogen bonds is one of the most important factors behind water’s many anomalous properties. However, there is still no consensus on the hydrogen bond structure of liquid water, including the average number of hydrogen bonds in liquid water. We use molecular dynamics simulations of the polarizable iAMOEBA water model for investigating the hydrogen bond characteristics of liquid water over a wide range of temperatures and pressures. Geometric definitions of a hydrogen bond often use a rectangular region on the plane of hydrogen bond distances and angles. In this work, we find that an elliptical region is more appropriate for the identification of hydrogen bonds, based on statistically favorable molecular configurations. The two-dimensional potential of mean force (PMF) landscape along the hydrogen bond distance (O–H) and angle (O–H–O) is calculated for identifying the statistically favored molecular configurations, which is then used for defining hydrogen bond formation as well as the strength of a hydrogen bond. We further propose a new approach to characterize the hydrogen bonds as strong when the PMF is lower than −2 kT. Using this definition, a consistent explanation for the different average numbers of hydrogen bonds in water is obtained in agreement with the literature. Simulations are also performed with the rigid and nonpolarizable TIP4P/2005 water model. Both water models are qualitatively consistent in predicting the distribution of double-, single-, and non-donor configurations, in line with experimental data, while the iAMOEBA water model yields more quantitatively precise results, including a 10–15% double-donor fraction at 90 °C and 1 atm. The method is also demonstrated to be applicable to the recent, and more general, three-dimensional PMF-based definition of hydrogen bonds.

The existence of two structural forms in liquid water has been a point of discussion for a long time. A phase transition between these two forms of liquid water has been proposed based on evidence from molecular simulations, and experiments have also been very recently able to track the proposed transition of the low-density liquid (LDL) form to the high-density liquid form. We propose to use the average angle an oxygen atom makes with its neighbors to describe the structural environment of a water molecule. The distribution of this order parameter is observed to have two peaks, with one peak at ∼ 109.5°, corresponding to the internal angle of a regular tetrahedron, indicating tetrahedral arrangement. The other peak corresponds to an environment with a tighter arrangement of neighboring molecules. The distribution of O-O-O angles is decomposed into two skewed distributions to estimate the fractions of the two liquid forms in water. A good similarity is observed between the temperature and pressure trends of fractions of locally favoured tetrahedral structure (LFTS) form estimated using the new order parameter and the reports in the literature, over a range of temperatures and pressures. We also compare the structural environments indicated by different order parameters and find that the order parameter proposed in this work captures the structure of first solvation shell of LFTS accurately.

The antifreeze activity of a type-III antifreeze protein (AFP) expressed in ocean pout (Zoarces americanus) is compared with that of a specific mutant (T18N) using all-atom molecular dynamics simulations. The antifreeze activity of the mutant is only 10% of the wild-type AFP. The results from this simulation study revealed the following insights into the mechanism of antifreeze action by type-III AFPs. The AFP gets adsorbed to the advancing ice front due to its hydrophobic nature. A part of the hydrophobicity is caused by the presence of clathrate structure of water molecules near the ice-binding surface (IBS). The mutation in the AFP disrupts this structure and thereby reduces the ability of the mutant to adsorb to the ice–water interface leading to the loss of antifreeze activity. The mutation, however, has no effect on the ability of the adsorbed protein to bind to the growing ice phase. Simulations also revealed that all surfaces of the protein can bind to the ice phase, although the IBS is the preferred surface.

Modern thermodynamic models incorporate the concept of association (hydrogen bonding) and they can describe very satisfactorily many properties of water containing mixtures. They have not been successful in representing water's anomalous properties and this work provides a possible explanation. We have analyzed and interpreted recent experimental data, molecular simulation results, and two‐state theory approaches and compared against the predictions from thermodynamic models. We show that the dominance of the tetrahedral structure implemented in modern thermodynamic models may be the reason for their failure for describing water systems. While this study does not prove the two‐state theories for water, it indicates that a high level of tetrahedral structure of water is not in agreement with water's anomalous properties when used in thermodynamic models.

We compared the temperature trend of the fraction of hydrogen-bonded configurations estimated in our simulations using the iAMOEBA water model with the values reported by Gartner et al, using the MB-POL water model. The MB-POL water model is a many-body forcefield for simulation of water which captures the structure and properties of water very well, albeit being computationally expensive [1]. As can be seen from fig. S1, the temperature trends of different hydrogen-bonded configurations (when all hydrogen bonds are considered) reported by us are in agreement with the results reported by Gartner et al [2].