Paulo A. Netz

Static and dynamic properties of stretched water

We present the results of molecular dynamics simulations of the extended simple point charge model of water to investigate the thermodynamic and dynamic properties of stretched and supercooled water. We locate the liquid–gas spinodal, and confirm that the spinodal pressure increases monotonically with T, supporting thermodynamic scenarios for the phase behavior of supercooled water involving a “non-reentrant” spinodal. The dynamics at negative pressure show a minimum in the diffusion constant D when the density is decreased at constant temperature, complementary to the known maximum of D at higher pressures. We locate the loci of minima of D relative to the spinodal, showing that the locus is inside the thermodynamically metastable regions of the phase diagram. These dynamical results reflect the initial enhancement and subsequent breakdown of the tetrahedral structure and of the hydrogen bond network as the density decreases.

Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode.

Despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform self-dockings and cross dockings between two DNA ligands (a minor groove binder and an intercalator) and four distinct receptors: 1) crystallographic DNA without intercalation gap; 2) crystallographic DNA with intercalation gap; 3) canonical B-DNA; and 4) modified B-DNA with intercalation gap. Besides being efficient in self-dockings, AutoDock is capable of correctly identifying two of the main DNA binding modes with the condition that the target possesses an artificial intercalation gap. Therefore, we suggest a default protocol to identify DNA binding modes which uses a modified canonical DNA (with gap) as receptor. This protocol was applied to dock two different Troger bases to DNA and the predicted binding modes agree with those suggested, yet not established, by experimental data. We also applied the protocol to dock aflatoxin B(1) exo-8,9-epoxide, and the results are in complete agreement with experimental data from the literature. We propose that this approach can be used to investigate other ligands whose binding mode to DNA remains unknown, yielding a suitable starting point for further theoretical studies such as molecular dynamics simulations.

Thermodynamic and dynamic anomalies for a three-dimensional isotropic core-softened potential.

Using molecular-dynamics simulations and integral equations (Rogers-Young, Percus-Yevick, and hypernetted chain closures) we investigate the thermodynamics of particles interacting with continuous core-softened intermolecular potential. Dynamic properties are also analyzed by the simulations. We show that, for a chosen shape of the potential, the density, at constant pressure, has a maximum for a certain temperature. The line of temperatures of maximum density (TMD) was determined in the pressure-temperature phase diagram. Similarly the diffusion constant at a constant temperature, D, has a maximum at a density rho(max) and a minimum at a density rho(min) < rho(max). In the pressure-temperature phase diagram the line of extrema in diffusivity is outside of the TMD line. Although this interparticle potential lacks directionality, this is the same behavior observed in simple point charge/extended water.

Waterlike hierarchy of anomalies in a continuous spherical shouldered potential

We investigate by molecular dynamics simulations a continuous isotropic core-softened potential with attractive well in three dimensions, introduced by Franzese [J. Mol. Liq. 136, 267 (2007)], that displays liquid-liquid coexistence with a critical point and waterlike density anomaly. Besides the thermodynamic anomalies, here we find diffusion and structural anomalies. The anomalies, not observed in the discrete version of this model, occur with the same hierarchy that characterizes water. We discuss the differences in the anomalous behavior of the continuous and the discrete model in the framework of the excess entropy, calculated within the pair correlation approximation.

Structural anomalies for a three dimensional isotropic core-softened potential

Using molecular dynamics simulations we investigate the structure of a system of particles interacting through a continuous core-softened interparticle potential. We found for the translational order parameter t a local maximum at a density rho(t-max) and a local minimum at rho(t-min)>rho(t-max). Between rho(t-max) and rho(t-min), the t parameter anomalously decreases upon increasing pressure. For the orientational order parameter Q(6) a maximum was observed at a density rho(t-max)<rho(Qmax)<rho(t-min). For densities between rho(Qmax) and rho(t-min), both the translational (t) and orientational (Q(6)) order parameters have anomalous behavior. We know that this system also exhibits density and diffusion anomalies. We found that the region in the pressure-temperature phase diagram of the structural anomaly englobes the region of the diffusion anomaly that is larger than the region limited by the temperature of maximum density. This cascade of anomalies (structural, dynamic, and thermodynamic) for our model has the same hierarchy as that observed for the simple point charge/extended water.

Relation between structural and dynamical anomalies in supercooled water

We step toward the elucidation of the relation between the structural and dynamic anomalies in supercooled water. We present the results of molecular dynamics simulations of the extended simple point charge (SPC/E) model of water for the translational and rotational diffusion and for the number of neighbors and hydrogen bonds. We find that the product of diffusion coefficient and relaxation time is nearly constant. The coupling between the two mobilities is explained in the framework of the structural anomalies.

An ubiquitous mechanism for water-like anomalies

Using collision-driven molecular dynamics a system of spherical particles interacting through an effective two-length-scales potential is studied. The potential can be tuned by means of a single parameter, λ, from a ramp (λ=0.5) to a square-shoulder potential (λ=1.0) representing a family of two-length-scales potentials in which the shortest interaction distance has higher potential energy than the largest interaction distance. For all the potentials, ranging between the ramp and the square-shoulder, density and structural anomalies were found, while the diffusion anomaly is found in all but in the square-shoulder potential. The presence of anomalies in square-shoulder potential, not observed in previous simulations, confirms the assumption that the two-length-scales potential is an ubiquitous ingredient for a system to exhibit water-like anomalies.

COMPUTER SIMULATION STUDIES OF ANOMALOUS DIFFUSION IN GELS: STRUCTURAL PROPERTIES AND PROBE-SIZE DEPENDENCE

We have carried out simulations of particle diffusion through polyacrylamide gel networks. The model structures were built on a diamond lattice, in a simulation box with periodic boundary conditions. The method of structure generation consists of a random distribution of knots on the lattice and interconnection between randomly chosen pairs of knots. The structures generated by this procedure approximate the topology of real polymer gels. Parameters that control the distance between knots and the degree of stretching of the chain permit us to simulate a polyacrylamide system in which the concentration of species as well as the degree of crosslinking can be compared to realistic gels as prepared by the available experimental procedures. These structures were geometrically characterized by the analysis of the pore size distribution and excluded volume. The structures thus generated are used as model networks for Monte Carlo studies of the diffusion of hard spheres in the restricted geometry. Modeling the de...

Computer simulation studies of diffusion in gels: Model structures

We have investigated particle diffusion through different obstacle geometries by computer simulations. The model structures used in this work — randomly placed point obstacles and cage-like structures — were chosen with the aim of represent a broad range of geometrical structures similar to gels and in order to be compared with our previous simulations of particle diffusion through polyacrylamide gels. The diffusion behavior was studied as a function of tracer size and obstacle concentration. The isomorphism between the diffusion of finite-sized tracers and the diffusion of point tracers in the presence of expanded obstacles was applied. Only hard-sphere interactions of the tracer with the immobile obstacles were considered and the theoretical description was made in terms of theory of the obstruction effect. In the case of randomly placed point obstacles an analytical expression for the dependence of the diffusion coefficient on tracer radius and obstacle concentration, applying the model of spherical ce...

Statistical physics and liquid water at negative pressures

Angell and his collaborators have underscored the importance of studying water under all extremes of pressure—squeezing to high pressures and stretching to negative pressures. Here we review recent results of molecular dynamics simulations of two models of liquid water, the extended simple point charge (SPC/E) and the Mahoney-Jorgensen transferable intermolecular potential with five points (TIP5P), which is closer to real water than previously proposed classical pairwise additive potentials. In particular, we describe simulations of the TIP5P model for a wide range of deeply supercooled states, including both positive and negative pressures, which reveal (i) the existence of a non-monotonic “nose-shaped” temperature of maximum density (TMD) line and a non-reentrant spinodal, (ii) the presence of a low-temperature phase transition. The TMD that changes slope from negative to positive as P decreases and, notably, the point of crossover between the two behaviors is located at ambient pressure (temperature ≈4°C, and density ≈1g/cm3). We also describe simulations of the dynamics of the SPC/E model, which reveal (iii) the dynamics at negative pressure shows a minimum in the diffusion constant D when the density is decreased at constant temperature, complementary to the known maximum of D at higher pressures, and (iv) the loci of minima of D relative to the spinodal shows that they are inside the thermodynamically metastable regions of the phase diagram. These dynamical results reflect the initial enhancement and subsequent breakdown of the tetrahedral structure and of the hydrogen bond network as the density decreases.