• ARNAB MUKHERJEE

      Articles written in Journal of Chemical Sciences

    • Relaxation in binary mixtures: Non-ideality, heterogeneity and re-entrance

      Arnab Mukherjee Goundla Srinivas Sarika Bhattacharyya Biman Bagchi

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      Binary mixtures show many kinds of fascinating dynamical behaviour which has eluded microscopic description till very recently. In this work we show that much of the anomalous behaviour can be explained by building suitable models and carrying out theoretical and simulation studies. Specifically, three well-known problems have been addressed here. (a) Non-ideality in composition dependence of viscosity, (b) re-entrant behaviour of orientational relaxation, and (c) heterogeneity in supercooled binary mixtures. The physical origin of the dynamical behaviour of binary mixtures can be understood in terms of composition fluctuation, a study of which has also been presented in this paper.

    • Probing folding free energy landscape of small proteins through minimalistic models: Folding of HP-36 and β-amyloid

      Arnab Mukherjee Biman Bagchi

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      Folding dynamics and energy landscape picture of protein conformations of HP-36 andβ-amyloid (Aβ) are investigated by extensive Brownian dynamics simulations, where the inter amino acid interactions are given by a minimalistic model (MM) we recently introduced [J. Chem. Phys.118 4733 (2003)]. In this model, a protein is constructed by taking two atoms for each amino acid. One atom represents the backbone Cαs atom, while the other mimics the whole side chain residue. Sizes and interactions of the side residues are all different and specific to a particular amino acid. The effect of water-mediated folding is mapped into the MM by suitable choice of interaction parameters of the side residues obtained from the amino acid hydropathy scale. A new non-local helix potential is incorporated to generate helices at the appropriate positions in a protein. Simulations have been done by equilibrating the protein at high temperature followed by a sudden quench. The subsequent folding is monitored to observe the dynamics of topological contacts (Ntopo), relative contact order parameter (RCO), and the root mean square deviation (RMSD) from the real-protein native structure. The folded structures of different model proteins (HP-36 and Aβ) resemble their respective real native state rather well. The dynamics of folding showsmultistage decay, with an initial hydrophobic collapse followed by a long plateau. Analysis ofNtopo and RCO correlates the late stage folding with rearrangement of the side chain residues, particularly those far apart in the sequence. The long plateau also signifies large entropic free energy barrier near the native state, as predicted from theories of protein folding.

    • Carboxylic acid terminated, solution exfoliated graphite by organic acylation and its application in drug delivery

      KOUSHIK BHOWMIK AMRITA CHAKRAVARTY U MANJU GOUTAM DE ARNAB MUKHERJEE

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      Graphite nanosheets are considered as a promising material for a range of applications from flexible electronics to functional nanodevices such as biosensors, intelligent coatings and drug delivery. Chemical functionalizationof graphite nanosheets with organic/inorganic materials offers an alternative approach to control the electronic properties of graphene, which is a zero band gap semiconductor in pristine form. In this paper, we report the aromatic electrophilic substitution of solution exfoliated graphite nanosheets (SEGn). The highly conjugated π-electronic system of graphite nanosheets enable it to have an amphiphilic characteristic in aromatic substitution reactions. The substitution was achieved through Friedel–Crafts (FC) acylation reaction under mild conditions using succinic anhydride as acylating agent and anhydrous aluminum chloride as Lewisacid. Such reaction renders towards the carboxylic acid terminated graphite nanosheets (SEGn–FC) that usually requires harsh reaction conditions. The product thus obtained was characterized using various spectroscopicand microscopic techniques. Highly stable water-dispersed sodium salt of carboxylic acid terminated graphite nanosheets (SEGn–FC-Na) was also prepared. A comparative sheet-resistance measurements of SEGn, SEGn–FC and SEGn–FC-Na were also done. Finally, the anticancer drug doxorubicin (DOX) was loaded on water dispersible SEGn–FC-Na with a loading capacity of 0.266 mg mg−1 of SEGn–FC-Na and the release of DOX from this water-soluble DOX-loaded SEGn–FC-Na at two different temperatures was found to be strongly pHdependent.

    • Connecting diffusion and entropy of bulk water at the single particle level

      DEBASIS SAHA ARNAB MUKHERJEE

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      The relation between the dynamic (e.g., diffusion) and thermodynamic (e.g., entropy) properties of water and water-like liquids has been an active area of research for a long time. Although several studies have investigated the diffusivity and entropy for different systems, these studies have probed either the configurational entropy or the excess entropy of the overall system. In this study, we focus on the entropy of water at a single molecule level at different temperatures. We have used a method developed in our group to calculate thetranslational and rotational entropy of individual water molecules at various temperatures. We find that the single water translational and rotational entropy exhibit a transition at around 240 K. The translational entropyof individual water molecules shows a consistent variation with change in temperature whereas the variation in the case of rotational entropy is much smaller at different temperatures. We have also calculated diffusioncoefficients of water molecules at these temperatures. We find that diffusion also shows the well-known fragile to strong crossover transition at around the same temperature where transition in entropy values has been seen. We have calculated both kinetic and thermodynamic fragilities and crossover points using diffusion and single water translational entropy values. Finally, we correlate the diffusion and translational entropy of individual water molecules using an analog of the Adam-Gibbs relation.

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