Niharendu Choudhury

Molecular dynamics simulation of aqueous urea solution: is urea a structure breaker?

An aqueous solution of urea is a very important mixture of biological relevance because of the definitive role of urea as protein denaturant at high concentrations. There has been an extended debate over the years on ureas influence on the structure of water. On the basis of a variety of analysis methods employed, urea has been described as a structure-breaker, a structure-maker, or as neutral toward water structure. Using molecular dynamics simulation and a nearest neighbor approach of analyzing water structure, we present here a detailed analysis of the effect of urea on water structure. By carefully choosing the nearest neighbors, allowing urea also to be a neighbor of a reference water molecule, we have conclusively shown that urea does not break the local tetrahedral structure of water even at high concentrations. A slight change in the distribution of tetrahedral order parameters as a function of urea concentration has been shown to be a result of change in the proportions of n-hydrogen-bonded water molecules. The present result thus suggests that urea is able to substitute for water in the hydrogen-bonded network nicely without breaking the tetrahedral, hydrogen-bonded structure of water.

Integral equation theory of Lennard-Jones fluids: A modified verlet bridge function approach

An integral equation theory for the Lennard-Jones fluid is investigated using a proposed new closure based on a modification of the Verlet-modified bridge function, which has been known to be very successful for hard body fluids. The structural and thermodynamic properties of the Lennard-Jones fluid calculated from this integral equation theory over a wide range of temperature and density show very good agreement with those obtained from simulation or from equation of state derived from simulation data. The gas–liquid phase diagram predicted by the present integral equation theory is shown to agree quite well with the corresponding simulation results.

Local density profiles are coupled to solute size and attractive potential for nanoscopic hydrophobic solutes

We employ constant pressure molecular dynamics simulations to investigate the effects of solute size and solute–water dispersion interactions on the solvation behavior of nanoscopic hydrophobic model solutes in water at normal temperature and pressure. The hydration behavior around a single planar atomic model solute as well as a pair of such solutes have been considered. The hydration water structure of a model nanoscopic solute with standard Lennard-Jones interaction is shown to be significantly different from that of their purely repulsive analogues. The density of water in the first solvation shell of a Lennard-Jones solute is much higher than that of bulk water and it remains almost unchanged with the increase of the solute dimensions from one to a few nanometers. On the other hand, for a purely repulsive analogue of the above model, solute hydration behavior shows a marked solute size dependence. The contact density of water in this case decreases with the increasing dimension of the solute. We also demonstrate the effect of solute–solvent attraction on the cavity formation in the inter solute region between two solutes with an inter solute separation of 6.8 Å, corresponding to the first solvent separated minimum in the free energy profile as obtained in our earlier work.We employ constant pressure molecular dynamics simulations to investigate the effects of solute size and solute–water dispersion interactions on the solvation behavior of nanoscopic hydrophobic model solutes in water at normal temperature and pressure. The hydration behavior around a single planar atomic model solute as well as a pair of such solutes have been considered. The hydration water structure of a model nanoscopic solute with standard Lennard-Jones interaction is shown to be significantly different from that of their purely repulsive analogues. The density of water in the first solvation shell of a Lennard-Jones solute is much higher than that of bulk water and it remains almost unchanged with the increase of the solute dimensions from one to a few nanometers. On the other hand, for a purely repulsive analogue of the above model, solute hydration behavior shows a marked solute size dependence. The contact density of water in this case decreases with the increasing dimension of the solute. We also...

Ab initio studies of phonon softening and high-pressure phase transitions of α-quartz SiO2

Density functional perturbation theory calculations of alpha-quartz using extended norm conserving pseudopotentials have been used to study the elastic properties and phonon dispersion relations along various high symmetry directions as a function of bulk, uniaxial and non-hydrostatic pressure. The computed equation of state, elastic constants and phonon frequencies are found to be in good agreement with available experimental data. A zone boundary (1/3, 1/3, 0) K-point phonon mode becomes soft for pressures above P=32 GPa. Around the same pressure, studies of the Born stability criteria reveal that the structure is mechanically unstable. The phonon and elastic softening are related to the high pressure phase transitions and amorphization of quartz and these studies suggest that the mean transition pressure is lowered under non-hydrostatic conditions. Application of uniaxial pressure, results in a post-quartz crystalline monoclinic C2 structural transition in the vicinity of the K-point instability. This structure, intermediate between quartz and stishovite has two-thirds of the silicon atoms in octahedral coordination while the remaining silicon atoms remain tetrahedrally coordinated. This novel monoclinic C2 polymorph of silica, which is found to be metastable under ambient conditions, is possibly one of the several competing dense forms of silica containing octahedrally coordinated silicon. The possible role of high pressure ferroelastic phases in causing pressure induced amorphization in silica are discussed.

On the Manifestation of Hydrophobicity at the Nanoscale

The manifestation of hydrophobicity at the nanoscale has been shown to depend on the topology of the solute. Using various nanoscopic hydrophobic plates, molecular dynamics simulation has been employed to explore the hydration and dewetting at the nanoscale. The topology of the solute regulates the behavior of nanoconfined water, resulting in any of the wet, dry, and intermittent wet-dry intersolute states. The present result reconciles apparently contrasting literature reports on how water behaves at extended hydrophobic surfaces and sheds light on the mechanism of dewetting.

A molecular dynamics simulation study of buckyballs in water: Atomistic versus coarse-grained models of C60

A simple coarse-grained water-C(60) model potential is proposed to study the solvation behavior of C(60) in water. Extensive molecular dynamics simulations are performed to compare the hydration behavior of the coarse-grained C(60) with that of its atomistic counterpart. In the coarse-grained description, we model the C(60) as a spherical solute and its interaction with water is represented by a simple two-body central potential as obtained from a coarse graining of the interactions of a water molecule with all the atoms of the C(60). On the other hand, the atomistic model takes into account a discrete nature of all the atoms of C(60) explicitly. Molecular dynamics simulations are carried out in an isothermal-isobaric ensemble at normal temperature and pressure. Various spatial and orientational correlations of the water around the two model C(60)s are compared. The coarse-grained model is shown to reproduce the hydration behavior of the C(60) quite well. The simplicity and the computational economy of the coarse-grained model will allow for simulations of self-assembly processes of a much larger system over a longer period of time.

Lattice dynamics and Born instability in yttrium aluminum garnet, Y3A15O12

We report lattice dynamics calculations of various microscopic and macroscopic vibrational and thermodynamic properties of yttrium aluminum garnet (YAG), Y3Al5O12, as a function of pressure up to 100 GPa and temperature up to 1500 K. YAG is an important solid-state laser material with several technological applications. Garnet has a complex structure with several interconnected dodecahedra, octahedra and tetrahedra. Unlike other aluminosilicate garnets, there are no distinct features to distinguish between intramolecular and intermolecular vibrations of the crystal. At ambient pressure, low energy phonons involving mainly the vibrations of yttrium atoms play a primary role in the manifestations of elastic and thermodynamic behavior. The aluminum atoms in tetrahedral and octahedral coordination are found to be dynamically distinct. Garnets stability can be discerned from the response of its phonon frequencies to increasing pressure. The dynamics of both octahedral and tetrahedral aluminum atoms undergo radical changes under compression which have an important bearing on their high pressure and temperature properties. At 100 GPa, YAG develops a large phonon bandgap (90-110 meV) and its microscopic and macroscopic physical properties are found to be profoundly different from that at the ambient pressure phase. There are significant changes in the high pressure thermal expansion and specific heat. The mode Grüneisen parameters show significant changes in the low energy range with pressure. Our studies show that the YAG structure becomes mechanically unstable around P = 108 GPa due to the violation of the Born stability criteria. Although this does not rule out thermodynamic crossover to a lower free energy phase at lower pressure, this places an upper bound of P = 110 GPa for the mechanical stability of YAG.

Dynamics of water at the nanoscale hydrophobic confinement

We investigate the effect of solute surface topology created by considering various intermolecular separations of the hydrophobic, paraffinlike plates on the dynamics of water confined between two such plates. The solute plates are made up of 5 n-C(18)H(38) molecules arranged in parallel in such a way that all the carbon atoms of the paraffin molecule are lying on the same plane. Results are obtained from extensive molecular dynamics simulations of aqueous solutions of paraffinlike plates in the isothermal-isobaric ensemble. A strong dependence of the translational as well as vibrational dynamics of the confined water molecules on surface topology (intermolecular distance within the paraffinlike plate) has been observed. Analysis of mean squared displacement reveals anomalous nonlinear behavior of the water molecules in the nanoconfined environment.

Correlation of Structural Order, Anomalous Density, and Hydrogen Bonding Network of Liquid Water

We use extensive molecular dynamics simulations employing different state-of-the-art force fields to find a common framework for comparing structural orders and density anomalies as obtained from different water models. It is found that the average number of hydrogen bonds correlates well with various order parameters as well as the temperature of maximum densities across the different models, unifying apparently disparate results from different models and emphasizing the importance of hydrogen bonding in determining anomalous properties and the structure of water. A deeper insight into the hydrogen bond network of water reveals that the solvation shell of a water molecule can be defined by considering only those neighbors that are hydrogen-bonded to it. On the basis of this view, the origin of the appearance of a non-tetrahedral peak at a higher temperature in the distribution of tetrahedral order parameters has been explained. It is found that a neighbor that is hydrogen-bonded to the central molecule is tetrahedrally coordinated even at higher temperatures. The non-tetrahedral peak at a higher temperature arises due to the strained orientation of the neighbors that are non-hydrogen-bonded to the central molecule. With the new definition of the solvation shell, liquid water can be viewed as an instantaneously changing random hydrogen-bonded network consisting of differently coordinated hydrogen-bonded molecules with their distinct solvation shells. The variation of the composition of these hydrogen-bonded molecules against temperature accounts for the density anomaly without introducing the concept of large-scale structural polyamorphism in water.

Integral equation theory of penetrable sphere fluids: A modified Verlet bridge function approach

Structure of penetrable sphere fluids, which are generally used to model micelles in a solvent or star polymer solutions, has been studied by integral equation theory with a very simple closure relation based on a modification of the Verlet-modified bridge function, which has been known to be very successful for hard body fluids. Conventional integral equation theories, which use Percus–Yevick and hypernetted chain closures, are unable to correctly model the behavior of the pair distribution functions of the penetrable sphere fluids, particularly in the core overlap region. The results for the pair-distribution or radial distribution functions obtained from the present theory are found to be in excellent agreement with the corresponding computer simulation results. The bridge functions at various temperatures and densities have also been compared with the corresponding results extracted from the computer simulation.