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Sundaram Balasubramanian

Publications and source records attributed to Sundaram Balasubramanian.

10 recordsLinked to original sources
PubMed2007

Evolution of intermolecular structure and dynamics in supercritical carbon dioxide with pressure: an ab initio molecular dynamics study.

The effect of pressure on supercritical carbon dioxide (scCO2) has been characterized by using Car-Parrinello molecular dynamics simulations. Structural and dynamical properties along an isotherm of 318.15 K and at pressures ranging from 190 to 5000 bar have been obtained. Intermolecular pair correlation functions and three-dimensional atomic probability density map calculations indicate that the local environment of a central CO2 molecule becomes more structured with increasing pressure. The closest neighbors are predominantly oriented in a distorted T-shaped geometry while neighbors separated by larger distances are likely oriented in a slipped parallel arrangement. The structure of scCO2 at high densities has been compared with that of crystalline CO2. The probability distributions of intramolecular distances narrow down with increasing pressure. A marginal but non-negligible effect of pressure on the instantaneous intramolecular OCO angle is observed, lending credence to the idea that intermolecular interactions between CO2 molecules in an inhomogeneous near neighbor environment could contribute to the observed instantaneous molecular dipole moment. The extent of deviation from a perfect linear geometry of the carbon dioxide molecule decreases with increasing pressure. Time constants derived from reorientational time correlation functions of the molecular backbone compare well with experimental data. Within the range of thermodynamic conditions explored here, no significant changes are observed in the frequencies of intramolecular vibrational modes. However, a blue shift is observed in the low-frequency cage rattling mode with increasing pressure.

Journal Article↗
PubMed2006

Electron donor-acceptor interactions in ethanol-CO2 mixtures: an ab initio molecular dynamics study of supercritical carbon dioxide.

The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello molecular dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercritical carbon dioxide-ethanol mixtures. The probability density distribution of CO2 molecules around ethanol in the supercritical state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 molecules themselves leads to significant deviations from linearity in the geometry of the CO2 molecule. The vibrational spectra of carbon dioxide obtained from the atomic velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the nu2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concentration in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixture when compared to its gas-phase value, in agreement with experiments.

Journal Article↗
PubMed2005

Hydration layer of a cationic micelle, C(10)TAB: structure, rigidity, slow reorientation, hydrogen bond lifetime, and solvation dynamics.

We report a theoretical study of the structure and dynamics of the water layer (the hydration layer) present at the surface of the cationic micelle decyltrimethylammonium bromide (DeTAB) by using atomistic molecular dynamics simulations. The simulated micelle consisted of 47 surfactant molecules (and an equal number of bromide ions), in good agreement with the pioneering light scattering experiments by Debye which found an aggregation number of 50. In this micelle, three partially positively charged methyl groups of each surfactant headgroup face the surrounding water. The nature of the cationic micellar surface is found to play an important role in determining the arrangement of water which is quite different from that in the bulk or on the surface of an anionic micelle, like cesium perfluorooctanoate. Water molecules present in the hydration layer are found to be preferentially distributed in the region between the three partially charged methyl headgroups. It is found that both the translational and rotational motions of water exhibit appreciably slower dynamics in the layer than those in the bulk. The solvation time correlation function (TCF) of bromide ions exhibits a long time component which is found to originate primarily from the interaction of the probe with the micellar headgroups. Thus, the decay of the solvation TCF is controlled largely by the residence time of the probe in the surface. The residence time distribution of the water molecules also exhibits a slow time component. We also calculate the collective number density fluctuation in the layer and find a prominent slow component compared to the similar quantity in the bulk. This slow component demonstrates that water structure in the hydration layer is more rigid than that in the bulk. These results demonstrate that the slow dynamics of hydration layer water is generic to macromolecular surfaces of either polarity.

Journal Article↗
PubMed2005

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe.

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.

Binding Sites↗
PubMed2005

n-Heptane under pressure: structure and dynamics from molecular simulations.

Atomistic molecular dynamics simulations have been performed in the isothermal-isobaric ensemble to explore the phase behavior of n-heptane. Motivated by recent high-pressure spectroscopic experiments on n-heptane, the present work aims at understanding the liquid-solid and the alluded to solid-solid transitions upon increasing pressure. Starting from the stabilized solid phase at 300 K and 10 kbar, we have investigated the range of these two transitions by a gradual decrease and increase of pressure, respectively. Although the solid-liquid transition has clear signatures such as the formation of gauche defects along the molecular backbone, the present model does not show any sign of a first-order solid-solid transition at high pressures. However, interesting changes in the environment around methyl groups and in their dynamics are observed. These have been substantiated by calculations of the vibrational density of states obtained from a normal-mode analysis and from the simulation trajectory.

Journal Article↗
PubMed2004

Ab initio molecular-dynamics study of supercritical carbon dioxide.

Car-Parrinello molecular-dynamics simulations of supercritical carbon dioxide (scCO(2)) have been performed at the temperature of 318.15 K and at the density of 0.703 g/cc in order to understand its microscopic structure and dynamics. Atomic pair correlation functions and structure factors have been obtained and good agreement has been found with experiments. In the supercritical state the CO(2) molecule is marginally nonlinear, and thus possesses a dipole moment. Analyses of angle distributions between near neighbor molecules reveal the existence of configurations with pairs of molecules in the distorted T-shaped geometry. The reorientational dynamics of carbon dioxide molecules, investigated through first- and second-order time correlation functions, exhibit time constants of 620 and 268 fs, respectively, in good agreement with nuclear magnetic resonance experiments. The intramolecular vibrations of CO(2) have been examined through an analysis of the velocity autocorrelation function of the atoms. These reveal a red shift in the frequency spectrum relative to that of an isolated molecule, consistent with experiments on scCO(2). The results have also been compared to classical molecular-dynamics calculations employing an empirical potential.

Journal Article↗
PubMed2004

Anomalous dielectric relaxation of water molecules at the surface of an aqueous micelle.

Dielectric relaxation of aqueous solutions of micelles, proteins, and many complex systems shows an anomalous dispersion at frequencies intermediate between those corresponding to the rotational motion of bulk water and that of the organized assembly or macromolecule. The precise origin of this anomalous dispersion is not well-understood. In this work we employ large scale atomistic molecular dynamics simulations to investigate the dielectric relaxation (DR) of water molecules in an aqueous micellar solution of cesium pentadecafluorooctanoate. The simulations clearly show the presence of a slow component in the moment-moment time correlation function [PhiMW(t)] of water molecules, with a time constant of about 40 ps, in contrast to only 9 ps for bulk water. Interestingly, the orientational time correlation function [Cmu(t)] of individual water molecules at the surface exhibits a component with a time constant of about 19 ps. We show that these two time constants can be related by the well-known micro-macrorelations of statistical mechanics. In addition, the reorientation of surface water molecules exhibits a very slow component that decays with a time constant of about 500 ps. An analysis of hydrogen bond lifetime and of the rotational relaxation in the coordinate frame fixed on the micellar body seems to suggest that the 500 ps component owes its origin to the existence of an extended hydrogen bond network of water molecules at the surface. However, this ultraslow component is not found in the total moment-moment time correlation function of water molecules in the solution. The slow DR of hydration water is found to be well correlated with the slow solvation dynamics of cesium ions at the water-micelle interface.

Colloids↗
PubMed2003

Dynamics of bound and free water in an aqueous micellar solution: analysis of the lifetime and vibrational frequencies of hydrogen bonds at a complex interface.

In order to understand the nature and dynamics of interfacial water molecules on the surface of complex systems, large scale, fully atomistic molecular dynamics simulations of an aqueous micelle of cesium perfluorooctanoate (CsPFO) surfactant molecules have been carried out. The lifetime and the intermolecular vibrational frequencies of the hydrogen bonds that the water molecules form with the hydrophilic, polar head groups (PHG) of the surfactants are calculated. Our earlier classification [S. Balasubramanian et al., Curr. Sci. 84, 428 (2003); e-print cond-mat/0212097] of the interfacial water molecules, based on structural and energetic considerations, into bound and free types is further validated by their dynamics. Lifetime correlation functions of the water-surfactant hydrogen bonds show the long-lived nature of the bound water species. Surprisingly, the water molecules that are singly hydrogen bonded to the surfactants have a longer lifetime than those that form two such hydrogen bonds. The free water molecules that do not form any such hydrogen bonds behave similarly to bulk water in their reorientational dynamics. A few water molecules that form two such hydrogen bonds are orientationally locked in for durations of the order of a few hundreds of picoseconds; that is, much longer than their average lifetime. The intermolecular vibrational frequencies of these interfacial water molecules have been studied from the power spectra of their velocity autocorrelation function. We find a significant blue shift in the librational band of the interfacial water molecules, apart from a similar shift in the near neighbor bending modes, relative to water molecules in bulk. These blue shifts suggest an increase in rigidity in the structure around interfacial water molecules. This is in good agreement with recent incoherent, inelastic neutron scattering data on macromolecular solutions [S. Ruffle et al., J. Am. Chem. Soc. 124, 565 (2002)]. The results of the present simulations appear to be rather general and should be relevant to the understanding of the dynamics of water near any hydrophilic surface.

Journal Article↗
PubMed2002

Hydrogen-bond dynamics near a micellar surface: origin of the universal slow relaxation at complex aqueous interfaces.

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

Hydrocarbons, Fluorinated↗