<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bose, Samik</style></author><author><style face="normal" font="default" size="100%">Chakrabarty, Suman</style></author><author><style face="normal" font="default" size="100%">Ghosh, Debashree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Effect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry B</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">MAY</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">19</style></number><publisher><style face="normal" font="default" size="100%">AMER CHEMICAL SOC</style></publisher><pub-location><style face="normal" font="default" size="100%">1155 16TH ST, NW, WASHINGTON, DC 20036 USA</style></pub-location><volume><style face="normal" font="default" size="100%">120</style></volume><pages><style face="normal" font="default" size="100%">4410-4420</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for similar to 0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">19</style></issue><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">3.187</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bhattacharjee, Gaurav</style></author><author><style face="normal" font="default" size="100%">Choudhary, Nilesh</style></author><author><style face="normal" font="default" size="100%">Kumar, Asheesh</style></author><author><style face="normal" font="default" size="100%">Chakrabarty, Suman</style></author><author><style face="normal" font="default" size="100%">Kumar, Rajnish</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Effect of the amino acid L-histidine on methane hydrate growth kinetics</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Natural Gas Science and Engineering</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Crystal growth</style></keyword><keyword><style  face="normal" font="default" size="100%">Gas hydrate</style></keyword><keyword><style  face="normal" font="default" size="100%">kinetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular dynamic simulation</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">SEP</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">35</style></volume><pages><style face="normal" font="default" size="100%">1453-1462</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;In the present study, the effect of a polar amino acid, L-histidine on methane hydrate growth kinetics has been investigated. Methane hydrate formation experiments were carried out in a stirred tank reactor setup at pressure and temperature conditions of 274.15 K and 5.0 MPa respectively. Two different concentrations (0.1 and 1 wt %) of L-histidine were studied. Hydrate growth through molecular dynamic (MD) simulation was also studied; pressure and temperature conditions for the simulations were set at 10.0 MPa and 270.0 K, while the concentration of L-histidine was kept fixed at 0.94 wt %. Hydrate formation runs using MD simulation were carried out with optimal concentration of methane in water. The presence of L-histidine in the system was found to significantly enhance methane hydrate growth kinetics as compared to pure water for both experimental and MD simulation runs. Final gas consumption with 1 wt % L-histidine was found to be comparable to that with 1 wt % SDS, the most commonly used additive for hydrate promotion studies. L-histidine is a benign additive which offers considerable enhancement in methane hydrate formation kinetics and can be utilized for various hydrate based technologies such as methane storage and transport. (C) 2016 Elsevier B.V. All rights reserved.&lt;/p&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">2.96</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hande, Vrushali R.</style></author><author><style face="normal" font="default" size="100%">Chakrabarty, Suman</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Exploration of the presence of bulk-like water in AOT reverse micelles and water-in-oil nanodroplets: the role of charged interfaces, confinement size and properties of water</style></title><secondary-title><style face="normal" font="default" size="100%">Physical Chemistry Chemical Physics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">AUG</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">31</style></number><publisher><style face="normal" font="default" size="100%">ROYAL SOC CHEMISTRY</style></publisher><pub-location><style face="normal" font="default" size="100%">THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND</style></pub-location><volume><style face="normal" font="default" size="100%">18</style></volume><pages><style face="normal" font="default" size="100%">21767-21779</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The properties of water in a confined environment can be drastically different than the bulk water. In a confined system, e.g. the interior of a reverse micelle, there exist at least two distinct regions namely ``interfacial water'' characterized by markedly slower dynamics, and ``core water'', which may resemble bulk water for a larger size of the water pool. Using atomistic molecular dynamics simulations, we systematically investigate the presence of bulk-like water in AOT reverse micelles (RMs) with varying size given by w(0) = [H2O]/[AOT] = 10, 15 and 20. In order to understand the effect of the negatively charged interface of the RM, we have performed control studies for the model systems of water-in-oil (isooctane) nanodroplets with the same size of the water pool as the RM systems. In order to quantify the deviations from bulk-like behavior, we have used three kinds of structural order parameters, namely (i) number density to probe the local translational ordering, (ii) tetrahedral order and hydrogen bond distribution to probe the local orientational ordering, and (iii) dipolar orientation relative to the radial vector to capture the global orientational ordering of the water dipoles. We demonstrate that the size of the ``core water'' region that resembles bulk water decreases in the above order, i.e. orientational order parameters of water molecules are perturbed by the charged interface to a larger length scale as compared to the translational order. We have compared the translational and rotational dynamics of the water molecules for the interfacial and core regions to find that the slower dynamics persists even for the core water for the size range that we have studied although to a much lesser extent as compared to the interfacial water. Moreover, we demonstrate that the hydrophobic interface in the water-in-oil nanodroplets has a much weaker effect on the structure and dynamics of the confined water molecules as compared to the anionic RMs. Thus, the major contribution towards the structural ordering and slow dynamics of water in a charged RM system would originate from the strong electrostatic and hydrogen bonded interactions with the interface, and not due to the spatial confinement effect.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">31</style></issue><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">4.449</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bose, Samik</style></author><author><style face="normal" font="default" size="100%">Chakrabarty, Suman</style></author><author><style face="normal" font="default" size="100%">Ghosh, Debashree</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Electrostatic origin of the red solvatochromic shift of DFHBDI in RNA spinach</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry B</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">MAY</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">121</style></volume><pages><style face="normal" font="default" size="100%">4790-4798</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Interactions with the environment tune the spectral properties of biological chromophores, e.g., fluorescent proteins. Understanding the relative contribution of the various types of noncovalent interactions in the spectral shifts can provide rational design principles toward developing new fluorescent probes. In this work, we investigate the origin of the red shift in the absorption spectra of the difluoro hydroxybenzylidene dimethyl imidazolinone (DFHBDI) chromophore in RNA spinach as compared to the aqueous solution. We systematically decompose the effects of various components of interactions, namely, stacking, hydrogen bonding, and long-range electrostatics, in order to elucidate the relative role of these interactions in the observed spectral behavior. We find that the absorption peak of DFHBDI is red-shifted by similar to 0.35 eV in RNA relative to the aqueous solution. Earlier proposals from Huang and co-workers have implicated the stacking interactions between DFHBDI and nucleic acid bases to be the driving force behind the observed red shift. In contrast, our findings reveal that the long-range electrostatic interactions between DFHBDI and negatively charged RNA. make the most significant contribution. Moreover, we notice that the opposing electrostatic fields due to the RNA backbone and the polarized water molecules around the RNA give rise to the resultant red shift. Our results emphasize the effect of strong heterogeneity in the various environmental factors that might be competing with each other.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">18</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">Foreign</style></custom3><custom4><style face="normal" font="default" size="100%">3.146</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Choudhary, Nilesh</style></author><author><style face="normal" font="default" size="100%">Hande, Vrushali R.</style></author><author><style face="normal" font="default" size="100%">Roy, Sudip</style></author><author><style face="normal" font="default" size="100%">Chakrabarty, Suman</style></author><author><style face="normal" font="default" size="100%">Kumar, Rajnish</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Effect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Physical Chemistry B</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JUN</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">122</style></volume><pages><style face="normal" font="default" size="100%">6536-6542</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;In experimental studies, it has been observed that the presence of sodium dodecyl sulfate (SDS) significantly increases the kinetics of hydrate formation and the final water-to-hydrate conversion ratio. In this study, we intend to understand the molecular mechanism behind the effect of SDS on the formation of methane hydrate through molecular dynamics simulation. Hydrate formation conditions similar to that of laboratory experiments were chosen to study hydrate growth kinetics in 1 wt % SDS solution. We also investigate the effect of interactions with isolated SDS molecules on methane hydrate growth. It was observed that the hydrophobic tail part of the SDS molecule favorably interacts with the growing hydrate surface and may occupy the partial hydrate cages while the head groups remain exposed to water.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">25</style></issue><custom3><style face="normal" font="default" size="100%">&lt;p&gt;Foreign&lt;/p&gt;</style></custom3><custom4><style face="normal" font="default" size="100%">&lt;p&gt;3.177&lt;/p&gt;</style></custom4></record></records></xml>