• Snehasis Daschakraborty

      Articles written in Journal of Chemical Sciences

    • Does polar interaction influence medium viscosity? A computer simulation investigation using model liquids

      Snehasis Daschakraborty Ranjit Biswas

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      Molecular dynamics simulations of model liquids interacting via Lennard-Jones (L-J) and Stockmayer (SM) interactions have been carried out to explore the effects of the longer-ranged dipole-dipole interaction on solvent viscosity and diffusion. Switching on of the dipolar interaction at a fixed density and temperature has been found to increase the viscosity over that of the LJ liquid, the extent of increase being a few percent to as large as ∼60% depending on the magnitude of the solvent dipole moment used in the SM potential. The simulated translational and rotational diffusion coefficients show strong dipole moment and temperature dependences, eventhough effects of these parameters on solvent-solvent radial distribution function are moderate. Interestingly, a partial solute-solvent decoupling is observed when the simulated translational and rotational diffusion coefficients are connected to the simulated viscosity coefficients via the Stokes-Einstein (SE) and Stokes-Einstein-Debye (SED) relations. In the limit of large dipole moment, simulated self-part of the van Hove correlation function at intermediate times reveals a departure from the Gaussian distribution with particle displacement. This suggests that dynamic heterogeneity is one of the reasons for the departure of centre-of-mass diffusion from the SE relation in these model systems.

    • Nonpolar solvation dynamics for a nonpolar solute in room temperature ionic liquid: a nonequilibrium molecular dynamics simulation study


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      Nonpolar solvation dynamics of a nonpolar diatomic solute in a roomtemperature ionic liquid (RTIL) has been followed via nonequilibrium molecular dynamics (MD) simulation. Frank-Condon type excitation of the solute, previously in equilibrium inRTIL solvent, has been modelled by abruptly changing the Lennard-Jones(LJ) diameter of the solute atoms and thereby disrupting the equilibrium situation. The rearrangement of the RTIL solvent molecules,which has been seen to be mostly contributed by the solute’s first solvation shell, around the excited solute results overall spectral narrowing and biphasic decay of the solvation energy; a dominant and very rapid process having sub-100 fs relaxation time, followed by a slower one relaxing at a timescale of ∼5 ps. A mode-coupling theory based calculation is also used to obtain the nonpolar solvation relaxation function fora model nonpolar solute dissolved in model RTIL solvent. The theoretical relaxation decay is not in very good agreement with the simulated nonequilibrium solvation response function; the theory predicts the short timerelaxation component slower and the longtime component faster than those of the simulated nonequilibrium relaxation. We have also checked the validity of the linear response theory (LRT) for nonpolar solvation in RTIL by looking at the equilibrium solvation energy correlation in the RTIL solvent in presence of the ground state (GS) and the excited state (ES) solute. Apparent breakdown of the LRT in the present case elucidates the probable disagreement between the theoretical and simulated nonequilibrium nonpolar solvation responsefunctions

    • Permeation pathway of two hydrophobic carbon nanoparticles across a lipid bilayer


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      The emerging area of carbon-based nanoparticles (NPs) and their increased usage in the biomedicalfield necessitate checking their biocompatibility and permeation pathway across the cell membrane. In thisstudy, we explore the permeation pathway of two NPs - a well-studied fullerene (C60) and a pristine carbon dot(CD) across a model Palmitoyloleoylphosphatidylcholine (POPC) lipid membrane. Both constrained andunconstrained all-atom molecular dynamics (MD) simulations are carried out to understand their permeationmechanism. C60 permeates the bilayer via passive permeation and stays inside the hydrophobic core, while theCDdoes not show any sign of permeation across the membrane throughout the simulation time window. The freeenergy profiles for the permeation are calculated using the umbrella sampling method. The huge barrier for thepermeation of theCDis confirmed from thePMFprofiles, while the free energy minima for the permeation of C60 are located in the bilayer interior. This mode of permeation of C60 can hint at its toxic nature to cell membraneswidely investigated in the past. The structural properties of the bilayer are also analyzed, and on a global scale, itshows no significant mechanical damage to the membrane. Thus, our study details the molecular level interactionof pristine carbon-based NPs with a lipid bilayer.

      In this work, we explored the permeation pathway of two hydrophobic carbon nanoparticles (NPs) - fullerene (C60) and carbon dot (CD) across a lipid bilayer. We assessed the free energy profile for the permeation, partition coefficient, permeability coefficient, and effects of the nanoparticles on the membrane structure.

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