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.

Probing the triplet correlation function in liquid water by experiments and molecular simulations

Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.

Water: A Tale of Two Liquids

Water is the most abundant liquid on earth and also the substance with the largest number of anomalies in its properties. It is a prerequisite for life and as such a most important subject of current research in chemical physics and physical chemistry. In spite of its simplicity as a liquid, it has an enormously rich phase diagram where different types of ices, amorphous phases, and anomalies disclose a path that points to unique thermodynamics of its supercooled liquid state that still hides many unraveled secrets. In this review we describe the behavior of water in the regime from ambient conditions to the deeply supercooled region. The review describes simulations and experiments on this anomalous liquid. Several scenarios have been proposed to explain the anomalous properties that become strongly enhanced in the supercooled region. Among those, the second critical-point scenario has been investigated extensively, and at present most experimental evidence point to this scenario. Starting from very low temperatures, a coexistence line between a high-density amorphous phase and a low-density amorphous phase would continue in a coexistence line between a high-density and a low-density liquid phase terminating in a liquid–liquid critical point, LLCP. On approaching this LLCP from the one-phase region, a crossover in thermodynamics and dynamics can be found. This is discussed based on a picture of a temperature-dependent balance between a high-density liquid and a low-density liquid favored by, respectively, entropy and enthalpy, leading to a consistent picture of the thermodynamics of bulk water. Ice nucleation is also discussed, since this is what severely impedes experimental investigation of the vicinity of the proposed LLCP. Experimental investigation of stretched water, i.e., water at negative pressure, gives access to a different regime of the complex water diagram. Different ways to inhibit crystallization through confinement and aqueous solutions are discussed through results from experiments and simulations using the most sophisticated and advanced techniques. These findings represent tiles of a global picture that still needs to be completed. Some of the possible experimental lines of research that are essential to complete this picture are explored.

Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models

Trp-cage unfolds at different temperatures in different water models revealing the sensitivity of conformational order metrics to the choice of water models.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Triplet correlation functions in liquid water

Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M. P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O-O-O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O-O-O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed.

Triplet correlations dominate the transition from simple to tetrahedral liquids

The total, triplet, and pair contributions to the entropy with increasing tetrahedrality are mapped out for the Stillinger-Weber liquids to demonstrate the qualitative and quantitative differences between triplet-dominated, tetrahedral liquids and pair-dominated, simple liquids with regard to supercooling and crystallization. The heat capacity anomaly of tetrahedral liquids originates in local ordering due to both pair and triplet correlations. The results suggest that structural correlations can be directly related to thermodynamic anomalies, phase changes, and self-assembly in other atomic and colloidal fluids.

Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model

Secondary structural preferences of the beta-hairpin of the 2GB1 protein in the folded and unfolded ensembles are shown to be sensitive to the choice of water model.

Water and water-like liquids: relationships between structure, entropy and mobility

Liquids with very diverse underlying interactions share the thermodynamic and transport anomalies of water, including metalloids, ionic melts and mesoscopic fluids. The generic feature that characterises such water-like liquids is a density-driven shift in the nature of local order in the condensed phases. The key semiquantitative relationships between structural order, thermodynamics and transport that are necessary in order to map out the consequences of this common qualitative feature for liquid-state properties and phase transformations of such systems are reviewed here. The application of these ideas to understand and model tetrahedral liquids, especially water, is discussed and possible extensions to other complex fluids are considered.

Fluctuation-driven anisotropic assembly in nanoscale systems

We demonstrate that the self-assembly of spherical nanoparticles (NPs), grafted isotropically with polymeric ligands, into anisotropic structures is a manifestation of the fluctuations inherent in small number statistics. Computer simulations show that the organization of ligand atoms around an individual NP is not spatially isotropic for small numbers of grafts and ligand monomers. This inherent, spatially asymmetric ligand distribution causes the effective, two-body inter-NP potential to have a strong orientational dependence, which reproduces the anisotropic assembly observed ubiquitously for these systems. In contrast, ignoring this angular dependence does not permit us to capture NP self-assembly. This idea of fluctuation-driven behavior should be broadly relevant, and, for example, it should be important for the assembly of ligand-decorated quantum dots into arrays.

Structural correlations and cooperative dynamics in supercooled liquids

The relationships between diffusivity and the excess, pair and residual multiparticle contributions to the entropy are examined for Lennard-Jones liquids and binary glassformers, in the context of approximate inverse power law mappings of simple liquids. In the dense liquid where diffusivities are controlled by collisions and cage relaxations, Rosenfeld-type excess entropy scaling of diffusivities is found to hold for both crystallizing as well as vitrifying liquids. The crucial differences between the two categories of liquids emerge only when local cooperative effects in the dynamics result in significant caging effects in the time-dependent behaviour of the single-particle mean square displacement. In the case of glassformers, onset of such local cooperativity coincides with onset of deviations from Rosenfeld-type excess entropy scaling of diffusivities and increasing spatiotemporal heterogeneity. In contrast, for two- and three-dimensional liquids with a propensity to crystallise, the onset of local cooperative dynamics is sufficient to trigger crystallization provided that the liquid is sufficiently supercooled that the free energy barrier to nucleation of the solid phase is negligible. The state points corresponding to onset of transient caging effects can be associated with typical values, within reasonable bounds, of the excess, pair, and residual multiparticle entropy as a consequence of the isomorph-invariant character of the excess entropy, diffusivity and related static and dynamic correlation functions.

Water and other tetrahedral liquids: order, anomalies and solvation

In order to understand the common features of tetrahedral liquids with water-like anomalies, the relationship between local order and anomalies has been studied using molecular dynamics simulations for three categories of such liquids: (a) atomistic rigid-body models for water (TIP4P, TIP4P/2005, mTIP3P, SPC/E), (b) ionic melts, BeF(2) (TRIM model) and SiO(2) (BKS potential) and (c) Stillinger-Weber liquids parametrized to model water (mW) and silicon. Rigid-body, atomistic models for water and the Stillinger-Weber liquids show a strong correlation between tetrahedral and pair correlation order and the temperature for the onset of the density anomaly is close to the melting temperature. In contrast, the ionic melts show weaker and more variable degrees of correlation between tetrahedral and pair correlation metrics, and the onset temperature for the density anomaly is more than twice the melting temperature. In the case of water, the relationship between water-like anomalies and solvation is studied by examining the hydration of spherical solutes (Na(+), Cl(-), Ar) in water models with different temperature regimes of anomalies (SPC/E, TIP4P and mTIP3P). For both ionic and nonpolar solutes, the local structure and energy of water molecules is essentially the same as in bulk water beyond the second-neighbour shell. The local order and binding energy of water molecules are not perturbed by the presence of a hydrophobic solute. In the case of ionic solutes, the perturbation is largely localized within the first hydration shell. The binding energies for the ions are strongly dependent on the water models and clearly indicate that the geometry of the partial charge distributions, and the associated multipole moments, play an important role. However the anomalous behaviour of the water network has been found to be unimportant for polar solvation.

Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models

The relationship between local tetrahedral order, tagged particle potential energy, and coordination number is studied for mTIP3P and TIP4P models of water in the bulk as well as in the neighborhood of a small peptide. The tendency of water molecules with different binding or tagged particle potential energies to occupy environments with different degrees of disorder can be effectively illustrated by constructing tetrahedral order distributions and corresponding entropy metrics conditional on restricted ranges of local binding energy. At the state point corresponding to the onset of the density anomaly, the correlation between tetrahedral entropy versus tagged potential energy is strong and virtually identical for mTIP3P and TIP4P. In TIP4P, this correlation is retained up to temperatures as high as 300 K, while it is lost by 250 K in mTIP3P. In the 250-300 K regime that is important for biomolecular simulations, mTIP3P behaves essentially as a simple liquid while TIP4P shows the density and related anomalies characteristic of water. We also study the number of water molecules, the tetrahedral order, and the tagged molecule potential energies for water molecules as a function of the distance from the peptide for the 16-residue β-hairpin fragment of 2GB1 in mTIP3P and TIP4P solvents. The hydration shell coordination profiles (n(r)) of the number of water molecules are almost identical in the two solvents, but the radial variation in the local energies and local order show significant differences. The residue-wise variation in the tagged potential energy of water molecules within the first hydration shell is qualitatively similar in the two models. A comparison of the tetrahedral order distributions of water molecules lying at different distances from the biomolecular solute shows that the perturbation in the local tetrahedral order distributions of the bulk solvent due to the presence of the solute is marginal. Thus, in the 250-300 K regime, the mTIP3P and TIP4P water models show qualitatively different behavior in terms of the relationship between tetrahedral order and local energy, but as solvents in the neighborhood of a biomolecular solute, the differences between the two models are only quantitative and not qualitative.

Thermodynamic, diffusional, and structural anomalies in rigid-body water models

Structural, density, entropy, and diffusivity anomalies of the TIP4P/2005 model of water are mapped out over a wide range of densities and temperatures. The locus of temperatures of maximum density (TMD) for this model is very close to the experimental TMD locus for temperatures between 250 and 275 K. Four different water models (mTIP3P, TIP4P, TIP5P, and SPC/E) are compared with the TIP4P/2005 model in terms of their anomalous behavior. For all the water models, the density regimes for anomalous behavior are bounded by a low-density limit at around 0.85-0.90 g cm(-3) and a high-density limit at about 1.10-1.15 g cm(-3). The onset temperatures of the density anomaly in the various models show a much greater variation, ranging from 202 K for mTIP3P to 289 K for TIP5P. The order maps for the various water models are qualitatively very similar with the structurally anomalous regions almost superimposable in the q(tet)-τ plane. Comparison of the phase diagrams of water models with the region of liquid-state anomalies shows that the crystalline phases are much more sensitive to the choice of water models than the liquid state anomalies; for example, SPC/E and TIP4P/2005 show qualitatively similar liquid state anomalies but very different phase diagrams. The anomalies in the liquid in all the models occur at much lower pressures than those at which the melting line changes from negative to positive slope. The results in this study demonstrate several aspects of structure-entropy-diffusivity relationships of water models that can be compared with experiment and used to develop better atomistic and coarse-grained models for water.

Entropy, diffusivity and the energy landscape of a waterlike fluid

Molecular dynamics simulations and instantaneous normal mode (INM) analysis of a fluid with core-softened pair interactions and waterlike liquid-state anomalies are performed to obtain an understanding of the relationship between thermodynamics, transport properties, and the potential energy landscape. Rosenfeld scaling of diffusivities with the thermodynamic excess and pair correlation entropy is demonstrated for this model. The INM spectra are shown to carry information about the dynamical consequences of the interplay between length scales characteristic of anomalous fluids, such as bimodality of the real and imaginary branches of the frequency distribution. The INM spectral information is used to partition the liquid entropy into two contributions associated with the real and imaginary frequency modes; only the entropy contribution from the imaginary branch captures the nonmonotonic behavior of the excess entropy and diffusivity in the anomalous regime of the fluid.

Relationship between structure, entropy, and diffusivity in water and water-like liquids

Anomalous behavior of the excess entropy (S(e)) and the associated scaling relationship with diffusivity are compared in liquids with very different underlying interactions but similar water-like anomalies: water (SPC/E and TIP3P models), tetrahedral ionic melts (SiO(2) and BeF(2)), and a fluid with core-softened, two-scale ramp (2SRP) interactions. We demonstrate the presence of an excess entropy anomaly in the two water models. Using length and energy scales appropriate for onset of anomalous behavior, we show the density range of the excess entropy anomaly to be much narrower in water than in ionic melts or the 2SRP fluid. While the reduced diffusivities (D*) conform to the excess-entropy-scaling relation, D* = A exp(alphaS(e)) for all the systems (Rosenfeld, Y. Phys. Rev. A 1977, 15, 2545), the exponential scaling parameter, alpha, shows a small isochore dependence in the case of water. Replacing S(e) by pair correlation-based approximants accentuates the isochore dependence of the diffusivity scaling. Isochores with similar diffusivity-scaling parameters are shown to have the temperature dependence of the corresponding entropic contribution. The relationship between diffusivity, excess entropy, and pair correlation approximants to the excess entropy are very similar in all the tetrahedral liquids.

Excess entropy and structural transitions in a two-dimensional square-shoulder fluid

Metropolis Monte Carlo simulations on the square-shoulder fluid of Malescio and Pellicane are used to trace the temperature dependent excess entropy, the heat capacity, and configurational energy along several isochores, including those for which mechanically stable zero-temperature structures have been predicted. Thermodynamic signatures of structural phase transitions are identified along several isochores, in addition to the low-density triangular solid and stripe phase transitions identified earlier. The finite temperature phases illustrate the competition between cluster formation and stripe formation as competing mechanisms for generating minimum free energy configurations as a function of density, consistent with earlier results at zero temperature. We also critically examine the usefulness of a phase-ordering rule based on the residual multiparticle entropy (RMPE) in predicting the formation of this diverse set of ordered structures from a disordered fluid phase. For the majority of the isochores studied, the RMPE prediction and the thermodynamic evidence for a phase transition were consistent. However, this criterion fails along isochores that are in regions of coexistence. Thus, the zero-RMPE rule is only likely to be approximately predictive in systems with small phase coexistence regimes, e.g., in the case of liquid crystal forming systems.

Local order, energy, and mobility of water molecules in the hydration shell of small peptides

The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.

Transport properties of tetrahedral, network-forming ionic melts

Molecular dynamics simulations of liquid silica and beryllium fluoride are performed using the van Beest-Kramer-van Santen and transferable rigid ion model potentials, respectively, in order to compare transport properties. The ionic conductivity (sigma), shear viscosity (eta) and ionic self-diffusivities (D(+/-)) are computed over a fairly wide range of temperatures and densities and deviations from Arrhenius behavior along different isochores is studied. The Stokes-Einstein relation is shown to hold over the entire range of state points, though the effective hydrodynamic radius shows small variations due to thermal fluctuations, compression, and local tetrahedral order. Several alternative tests of the Nernst-Einstein relation are implemented which show that significant network-formation in the anomalous regime leads to a breakdown of this relationship. The relaxation times, tau(sigma) and tau(M), associated with the decay of the charge-flux and pressure ACFs respectively, are computed. In the anomalous regime, as the tetrahedral network formation progresses, tau(M) increases rapidly while tau(sigma) shows very little variation, indicating a decoupling of charge and momentum transport processes.

Fluconazole-induced Recurrent Ventricular Fibrillation Leading to Multiple Cardiac Arrests

This case report describes the successful management of a patient with diabetic ketoacidosis, who developed torsades de pointes leading to nine cardiac arrests secondary to intravenous fluconazole administration on a background of hypokalaemia and hypocalcaemia.

Relationship between structure, entropy, and mobility in network-forming ionic melts

Diffusivity, ionic conductivity, and viscosity of network-forming ionic melts are examined using molecular dynamics simulations of BeF2 and SiO2 melts. These tetrahedral, network-forming ionic melts are shown to possess a conductivity anomaly, in addition to waterlike viscosity and diffusivity anomalies, corresponding to a striking breakdown of the Nernst-Einstein relation. The contrasting scaling behavior of the different mobility measures with different structural contributions to the excess entropy is demonstrated.