Structure and mobility of water confined in AlPO4-54 nanotubes

We performed molecular dynamics simulations of water confined within AlPO₄-54 nanotubes. AlPO₄-54 is an artificial material made of AlO₄ and of PO₄ in tetrahedra arranged in a periodic structure forming pores of approximately 1.3 nm in diameter. This makes AlPO₄-54 an excellent candidate for practical applications, such as for water filtration and desalination. In this work, the structural and dynamical properties of the confined water are analyzed for various temperatures and water loadings. We find that the water structure is controlled by the heterogeneity of the nanopore surface with the water molecules located preferentially next to the surface of oxygens of AlPO₄-54; consequently, at very low densities, water forms helicoidal structures in string-like arrangements.

Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method

Explicit and implicit solvent models have a proven record of delivering hydration free energies of small, druglike solutes in reasonable agreement with experiment. Hydration of macromolecules, such as proteins, is to a large extent uncharted territory, with few results shedding light on quantitative consistency between different solvent models, let alone their ability to reproduce real water. In this work, based on extensive explicit solvent simulations employing TIP3P and SPC/E water models we analyze hydration free energy changes between fixed conformations of 5 diverse proteins, including large multidomain structures. For the two solvent models we find better agreement in electrostatic rather than nonpolar contributions (RMSE of 2.3 and 2.7 kcal/mol, respectively), even though absolute values of the latter are typically an order of magnitude smaller. We also highlight the importance of finite size corrections to relative protein hydration free energies, which turn out to be rather large, on the order of several kcal/mol, and are necessary for proper interpretation of results obtained under periodic boundary conditions. We further compare gathered data with predictions of the implicit solvent approach based on the Poisson equation and the surface or volume based nonpolar term. We find definitely lesser consistency than between the two explicit models (RMSE between implicit and TIP3 results of 11.3 and 8.4 kcal/mol for electrostatic and nonpolar contributions, respectively). In the process we determine the value of the protein dielectric constant and the geometric model for the dielectric boundary that provide for the best agreement. Finally, we evaluate the usefulness of surface and volume based models of nonpolar contributions to hydration free energy of large biomolecules.

Structures and thermodynamics of water encapsulated by graphene

Understanding phase behaviors of nanoconfined water has driven notable research interests recently. In this work, we examine water encapsulated under a graphene cover that offers an ideal testbed to explore its molecular structures and thermodynamics. We find layered water structures for up to ~1000 trapped water molecules, which is stabilized by the spatial confinement and pressure induced by interfacial adhesion. For monolayer encapsulations, we identify representative two-dimensional crystalline lattices as well as defects therein. Free energy analysis shows that the structural orders with low entropy are compensated by high formation energies due to the pressurized confinement. There exists an order-to-disorder transition for this condensed phase at ~480-490 K, with a sharp reduction in the number of hydrogen bonds and increase in the entropy. Fast diffusion of the encapsulated water demonstrates anomalous temperature dependence, indicating the solid-to-fluid nature of this structural transition. These findings offer fundamental understandings of the encapsulated water that can be used as a pressurized cell with trapped molecular species, and provide guidance for practical applications with its presence, for example, in the design of nanodevices and nanoconfined reactive cells.

Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations

The BACE-1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM-PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono-protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns. We also investigated the influence of the protein force field, the water model, the periodic boundary conditions artifacts (box size), as well as the ionic strength. Amber03 with TIP3P, a minimal distance of 1.0 nm between the protein and the box edges and a ionic strength of I = 0.2 M provides the optimal correlation with experiments. Overall, when using these parameters, a Pearson correlation coefficient of R = 0.84 (R²  = 0.71) is obtained for the 46 ligands, spanning eight orders of magnitude of K_d (from 0.017 nm to 2000 μM, i.e., from -14.7 to -3.7 kcal/mol), with a ligand size from 22 to 136 atoms (from 138 to 937 g/mol). After a two-parameter fit of the binding affinities for 12 of the ligands, an error of RMSD = 1.7 kcal/mol was obtained for the remaining ligands. © 2017 Wiley Periodicals, Inc.

Size and Origins of Long-Range Orientational Water Correlations in Dilute Aqueous Salt Solutions

Long-range ordering of water around solutes has been repeatedly invoked as the key to its biological function. Recently, it has been shown that in an 8 mM aqueous NaCl solution the orientational correlation between water molecules extends beyond 8 nm. This was interpreted as arising from ion-induced long-range effects on the water collective hydrogen-bond interactions. Each ion was suggested to affect >10 000 water molecules, leading to a picture involving nanoscopic "ordered domains". Using molecular dynamics simulations, we show that the very small long-range tail in the correlation function is caused primarily by pairs of water molecules belonging to different ions' hydration shells and can be made to practically disappear by rearranging the ionic positions. This means that the ion-induced water orientational ordering in millimolar salt solutions cannot be separated from ion-ion interaction effects, for which the Debye-Hückel screening length shrinks to less than 1 nm at physiological ionic strengths.

Molecular Modeling of Thermodynamic and Transport Properties for CO2 and Aqueous Brines

Molecular simulation techniques using classical force-fields occupy the space between ab initio quantum mechanical methods and phenomenological correlations. In particular, Monte Carlo and molecular dynamics algorithms can be used to provide quantitative predictions of thermodynamic and transport properties of fluids relevant for geologic carbon sequestration at conditions for which experimental data are uncertain or not available. These methods can cover time and length scales far exceeding those of quantum chemical methods, while maintaining transferability and predictive power lacking from phenomenological correlations. The accuracy of predictions depends sensitively on the quality of the molecular models used. Many existing fixed-point-charge models for water and aqueous mixtures fail to represent accurately these fluid properties, especially when descriptions covering broad ranges of thermodynamic conditions are needed. Recent work on development of accurate models for water, CO₂, and dissolved salts, as well as their mixtures, is summarized in this Account. Polarizable models that can respond to the different dielectric environments in aqueous versus nonaqueous phases are necessary for predictions of properties over extended ranges of temperatures and pressures. Phase compositions and densities, activity coefficients of the dissolved salts, interfacial tensions, viscosities and diffusivities can be obtained in near-quantitative agreement to available experimental data, using relatively modest computational resources. In some cases, for example, for the composition of the CO₂-rich phase in coexistence with an aqueous phase, recent results from molecular simulations have helped discriminate among conflicting experimental data sets. The sensitivity of properties on the quality of the intermolecular interaction model varies significantly. Properties such as the phase compositions or electrolyte activity coefficients are much more sensitive than phase densities, viscosities, or component diffusivities. Strong confinement effects on physical properties in nanoscale media can also be directly obtained from molecular simulations. Future work on molecular modeling for CO₂ and aqueous brines is likely to be focused on more systematic generation of interaction models by utilizing quantum chemical as well as direct experimental measurements. New ion models need to be developed for use with the current generation of polarizable water models, including ion-ion interactions that will allow for accurate description of dense, mixed brines. Methods will need to be devised that go beyond the use of effective potentials for incorporation of quantum effects known to be important for water, and reactive force fields developed that can handle bond creation and breaking in systems with carbonate and silicate minerals. Another area of potential future work is the integration of molecular simulation methods in multiscale models for the chemical reactions leading to mineral dissolution and flow within the porous media in underground formations.

Perspective: Quantum mechanical methods in biochemistry and biophysics

In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

Trimethylamine N-oxide stabilizes proteins via a distinct mechanism compared with betaine and glycine

We report experimental and computational studies investigating the effects of three osmolytes, trimethylamine N-oxide (TMAO), betaine, and glycine, on the hydrophobic collapse of an elastin-like polypeptide (ELP). All three osmolytes stabilize collapsed conformations of the ELP and reduce the lower critical solution temperature (LSCT) linearly with osmolyte concentration. As expected from conventional preferential solvation arguments, betaine and glycine both increase the surface tension at the air-water interface. TMAO, however, reduces the surface tension. Atomically detailed molecular dynamics (MD) simulations suggest that TMAO also slightly accumulates at the polymer-water interface, whereas glycine and betaine are strongly depleted. To investigate alternative mechanisms for osmolyte effects, we performed FTIR experiments that characterized the impact of each cosolvent on the bulk water structure. These experiments showed that TMAO red-shifts the OH stretch of the IR spectrum via a mechanism that was very sensitive to the protonation state of the NO moiety. Glycine also caused a red shift in the OH stretch region, whereas betaine minimally impacted this region. Thus, the effects of osmolytes on the OH spectrum appear uncorrelated with their effects upon hydrophobic collapse. Similarly, MD simulations suggested that TMAO disrupts the water structure to the least extent, whereas glycine exerts the greatest influence on the water structure. These results suggest that TMAO stabilizes collapsed conformations via a mechanism that is distinct from glycine and betaine. In particular, we propose that TMAO stabilizes proteins by acting as a surfactant for the heterogeneous surfaces of folded proteins.

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.

Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol

In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion by the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.

A new intermolecular potential for simulations of methanol: The OPLS/2016 model

In this work, a new rigid-nonpolarizable model of methanol is proposed. The model has three sites, located at the same positions as those used in the OPLS model previously proposed by Jorgensen [J. Phys. Chem. 90, 1276 (1986)]. However, partial charges and the values of the Lennard-Jones parameters were modified by fitting to an adequately selected set of target properties including solid-fluid experimental data. The new model was denoted as OPLS/2016. The overall performance of this model was evaluated and compared to that obtained with other popular models of methanol using a similar test to that recently proposed for water models. In the test, a certain numerical score is given to each model. It was found that the OPLS/2016 obtained the highest score (7.4 of a maximum of 10) followed by L1 (6.6), L2 (6.4), OPLS (5.8), and H1 (3.5) models. The improvement of OPLS/2016 with respect to L1 and L2 is mainly due to an improvement in the description of fluid-solid equilibria (the melting point is only 14 K higher than the experimental value). In addition, it was found that no methanol model was able to reproduce the static dielectric constant and the isobaric heat capacity, whereas the better global performance was found for models that reproduce the vaporization enthalpy once the so-called polarization term is included. Similar conclusions were suggested previously in the analysis of water models and are confirmed here for methanol.

A comprehensive scenario of the thermodynamic anomalies of water using the TIP4P/2005 model

The striking behavior of water has deserved it to be referred to as an "anomalous" liquid. The water anomalies are greatly amplified in metastable (supercooled and/or stretched) regions. This makes difficult a complete experimental description since, beyond certain limits, the metastable phase necessarily transforms into the stable one. Theoretical interpretation of the water anomalies could then be based on simulation results of well validated water models. But the analysis of the simulations has not yet reached a consensus. In particular, one of the most popular theoretical scenarios-involving the existence of a liquid-liquid critical point (LLCP)-is disputed by several authors. In this work, we propose to use a number of exact thermodynamic relations which may shed light on this issue. Interestingly, these relations may be tested in a region of the phase diagram which is outside the LLCP thus avoiding the problems associated to the coexistence region. The central property connected to other water anomalies is the locus of temperatures at which the density along isobars attain a maximum (TMD line) or a minimum (TmD). We have performed computer simulations to evaluate the TMD and TmD for a successful water model, namely, TIP4P/2005. We have also evaluated the vapor-liquid (VL) spinodal in the region of large negative pressures. The shape of these curves and their connection to the extrema of some response functions, in particular the isothermal compressibility and heat capacity at constant pressure, provides very useful information which may help to elucidate the validity of the theoretical proposals. In this way, we are able to present for the first time a comprehensive scenario of the thermodynamic water anomalies for TIP4P/2005 and their relation to the vapor-liquid spinodal. The overall picture shows a remarkable similarity with the corresponding one for the ST2 water model, for which the existence of a LLCP has been demonstrated in recent years. It also provides a hint as to where the long-sought for extrema in response functions might become accessible to experiments.

The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core

The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6.

Decoupling of viscosity and relaxation processes in supercooled water: a molecular dynamics study with the TIP4P/2005f model

We show that the TIP4P/2005f water model describes accurately the experimental viscosity and self-diffusion over a large temperature range. We then show the decoupling of viscosity and structural relaxation time in supercooled water.

Communication: Interaction of BrO radical with the surface of water

Solvation of a BrO radical in a slab of water is investigated using adaptive buffered force quantum mechanics/molecular mechanics (QM/MM) dynamics simulations. The simulation results show that the BrO radical exhibits preference towards the water surface with respect to the interior region of the water slab, despite BrO's high affinity to water. Another important finding is the weakening of (BrO)Br⋯O(water) interaction at the water surface due to competitive interactions between (BrO)Br⋯O(water) and (water)H⋯O(water). As such, the BrO-water slab interaction is dominated by (BrO)O⋯H(water) interaction, contrary to that in the gas phase, suggesting that the reactive site for the BrO radical at the air/water surface is more likely the Br site. The conclusion from this study can offer deeper insight into the reactivity of the BrO radical at the air/water interface, with regard to atmospheric implications.

Effects of Intermolecular Charge Transfer in Liquid Water on Raman Spectra

The low-frequency vibrational spectrum of liquid water is composed of contributions from the intermolecular librational and translation modes. The existence of these two modes introduces difficulty into the simulation of experimentally obtained Raman spectra. We constructed a polarizability function for a water model that includes intramolecular charge flow (CF) effects, intermolecular charge transfer (CT) effects, and intermolecular dipole-induced-dipole (DID) effects. We computed the one-dimensional (1D) Raman and terahertz (THz) spectra with all of these effects included (CFCT-DID) and compared with experimental spectra. We find that the CFCT-DID function provides a better description of the experimental results, because the CT effects reduce the polarizability only for translational motion to which parallelly polarized (VV) and perpendicularly polarized (VH) Raman spectra are sensitive. In our calculations of two-dimensional (2D) Raman and THz-Raman spectra, we observe the enhancement of echo signals in both cases. The details of the CFCT-DID function, along with its source code, are provided in the Supporting Information.

Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions

The central role played by water in fundamental processes relevant to different disciplines, including chemistry, physics, biology, materials science, geology, and climate research, cannot be overemphasized. It is thus not surprising that, since the pioneering work by Stillinger and Rahman, many theoretical and computational studies have attempted to develop a microscopic description of the unique properties of water under different thermodynamic conditions. Consequently, numerous molecular models based on either molecular mechanics or ab initio approaches have been proposed over the years. However, despite continued progress, the correct prediction of the properties of water from small gas-phase clusters to the liquid phase and ice through a single molecular model remains challenging. To large extent, this is due to the difficulties encountered in the accurate modeling of the underlying hydrogen-bond network in which both number and strength of the hydrogen bonds vary continuously as a result of a subtle interplay between energetic, entropic, and nuclear quantum effects. In the past decade, the development of efficient algorithms for correlated electronic structure calculations of small molecular complexes, accompanied by tremendous progress in the analytical representation of multidimensional potential energy surfaces, opened the doors to the design of highly accurate potential energy functions built upon rigorous representations of the many-body expansion (MBE) of the interaction energies. This Account provides a critical overview of the performance of the MB-pol many-body potential energy function through a systematic analysis of energetic, structural, thermodynamic, and dynamical properties as well as of vibrational spectra of water from the gas to the condensed phase. It is shown that MB-pol achieves unprecedented accuracy across all phases of water through a quantitative description of each individual term of the MBE, with a physically correct representation of both short- and long-range many-body contributions. Comparisons with experimental data probing different regions of the water potential energy surface from clusters to bulk demonstrate that MB-pol represents a major step toward the long-sought-after "universal model" capable of accurately describing the molecular properties of water under different conditions and in different environments. Along this path, future challenges include the extension of the many-body scheme adopted by MB-pol to the description of generic solutes as well as the integration of MB-pol in an efficient theoretical and computational framework to model acid-base reactions in aqueous environments. In this context, given the nontraditional form of the MB-pol energy and force expressions, synergistic efforts by theoretical/computational chemists/physicists and computer scientists will be critical for the development of high-performance software for many-body molecular dynamics simulations.

Premelting-Induced Smoothening of the Ice-Vapor Interface

We perform computer simulations of the quasiliquid layer of ice formed at the ice-vapor interface close to the ice Ih-liquid-vapor triple point of water. Our study shows that the two distinct surfaces bounding the film behave at small wavelengths as atomically rough and independent ice-water and water-vapor interfaces. For long wavelengths, however, the two surfaces couple, large scale parallel fluctuations are inhibited, and the ice-vapor interface becomes smooth. Our results could help explain the complex morphology of ice crystallites.

Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

The solubility of NaCl in water is evaluated by using three force field models: Joung-Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.

Accuracy limit of rigid 3-point water models

Classical 3-point rigid water models are most widely used due to their computational efficiency. Recently, we introduced a new approach to constructing classical rigid water models [S. Izadi et al., J. Phys. Chem. Lett. 5, 3863 (2014)], which permits a virtually exhaustive search for globally optimal model parameters in the sub-space that is most relevant to the electrostatic properties of the water molecule in liquid phase. Here we apply the approach to develop a 3-point Optimal Point Charge (OPC3) water model. OPC3 is significantly more accurate than the commonly used water models of same class (TIP3P and SPCE) in reproducing a comprehensive set of liquid bulk properties, over a wide range of temperatures. Beyond bulk properties, we show that OPC3 predicts the intrinsic charge hydration asymmetry (CHA) of water - a characteristic dependence of hydration free energy on the sign of the solute charge - in very close agreement with experiment. Two other recent 3-point rigid water models, TIP3PFB and H2ODC, each developed by its own, completely different optimization method, approach the global accuracy optimum represented by OPC3 in both the parameter space and accuracy of bulk properties. Thus, we argue that an accuracy limit of practical 3-point rigid non-polarizable models has effectively been reached; remaining accuracy issues are discussed.

Enthalpic and Entropic Contributions to Hydrophobicity

Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called "unhappy water" molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions

Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

Tetrahedrality and hydrogen bonds in water

We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

Continuous melting through a hexatic phase in confined bilayer water

Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The liquid between constituents in a cell is confined to such dimensions, and there is already evidence that such water can behave very differently from its bulk counterpart. A striking finding has been reported from computer simulations for two-dimensionally confined water: The liquid displays continuous or discontinuous melting depending on its density. In order to understand this behavior, we have analyzed the melting exhibited by a bilayer of nanoconfined water by means of molecular dynamics simulations. At high density we observe the continuous melting to be related to the phase change of the oxygens only, with the hydrogens remaining liquidlike throughout. Moreover, we find an intermediate hexatic phase for the oxygens between the liquid and a triangular solid ice phase, following the Kosterlitz-Thouless-Halperin-Nelson-Young theory for two-dimensional melting. The liquid itself tends to maintain the local structure of the triangular ice, with its two layers being strongly correlated yet with very slow exchange of matter. The decoupling in the behavior of the oxygens and hydrogens gives rise to a regime in which the complexity of water seems to disappear, resulting in what resembles a simple monoatomic liquid. This intrinsic tendency of our simulated water may be useful for understanding novel behaviors in other confined and interfacial water systems.

Water Determines the Structure and Dynamics of Proteins

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.