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Thermodynamic and structural anomalies of water nanodroplets.

ABSTRACT: Liquid water nanodroplets are important in earth's climate, and are valuable for studying supercooled water because they resist crystallisation well below the bulk freezing temperature. Bulk liquid water has well-known thermodynamic anomalies, such as a density maximum, and when supercooled is hypothesised to exhibit a liquid-liquid phase transition (LLPT) at elevated pressure. However, it is not known how these bulk anomalies might manifest themselves in nanodroplets. Here we show, using simulations of the TIP4P/2005 water model, that bulk anomalies occur in nanodroplets as small as 360 molecules. We also show that the Laplace pressure inside small droplets reaches 220?MPa at 180?K, conditions close to the LLPT of TIP4P/2005. While the density and pressure inside nanodroplets coincide with bulk values at moderate supercooling, we show that deviations emerge at lower temperature, as well as significant radial density gradients, which arise from and signal the approach to the LLPT.

SUBMITTER: Malek SMA

PROVIDER: S-EPMC6008328 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Thermodynamic and structural anomalies of water nanodroplets.

Malek Shahrazad M A SMA Poole Peter H PH Saika-Voivod Ivan I

Nature communications 20180619 1

Liquid water nanodroplets are important in earth's climate, and are valuable for studying supercooled water because they resist crystallisation well below the bulk freezing temperature. Bulk liquid water has well-known thermodynamic anomalies, such as a density maximum, and when supercooled is hypothesised to exhibit a liquid-liquid phase transition (LLPT) at elevated pressure. However, it is not known how these bulk anomalies might manifest themselves in nanodroplets. Here we show, using simula ...[more]

PMID: 29921912

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Project description:We perform path-integral molecular dynamics (PIMD) simulations of H2O and D2O using the q-TIP4P/F model. Simulations are performed at P = 1 bar and over a wide range of temperatures that include the equilibrium (T≥ 273 K) and supercooled (210 ≤T < 273 K) liquid states of water. The densities of both H2O and D2O calculated from PIMD simulations are in excellent agreement with experiments in the equilibrium and supercooled regimes. We also evaluate important thermodynamic response functions, specifically, the thermal expansion coefficient αP(T), isothermal compressibility κT(T), isobaric heat capacity CP(T), and static dielectric constant ε(T). While these properties are in excellent [αP(T) and κT(T)] or semi-quantitative agreement [CP(T) and ε(T)] with experiments in the equilibrium regime, they are increasingly underestimated upon further cooling. It follows that the inclusion of nuclear quantum effects in PIMD simulations of (q-TIP4P/F) water is not sufficient to reproduce the anomalous large fluctuations in density, entropy, and electric dipole moment characteristic of supercooled water. It has been hypothesized that water may exhibit a liquid-liquid critical point (LLCP) in the supercooled regime at P > 1 bar and that such a LLCP generates a maximum in CP(T) and κT(T) at 1 bar. Consistent with this hypothesis and in particular, with experiments, we find a maximum in the κT(T) of q-TIP4P/F light and heavy water at T≈ 230-235 K. No maximum in CP(T) could be detected down to T≥ 210 K. We also calculate the diffusion coefficient D(T) of H2O and D2O using the ring-polymer molecular dynamics (RPMD) technique and find that computer simulations are in remarkable good agreement with experiments at all temperatures studied. The results from RPMD/PIMD simulations are also compared with the corresponding results obtained from classical MD simulations of q-TIP4P/F water where atoms are represented by single interacting sites. Surprisingly, we find minor differences in most of the properties studied, with CP(T), D(T), and structural properties being the only (expected) exceptions.

Project description:Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

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Thermodynamic and structural anomalies of water nanodroplets.

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Thermodynamic and structural anomalies of water nanodroplets.

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