01848nas a2200169 4500008004100000022001400041245012200055210006900177260007100246300001400317490000800331520115300339100001601492700002301508700002101531856012601552 2016 eng d a1520-610600aEffect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant0 aEffect of solvation on electron detachment and excitation energi a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAY a4410-44200 v1203 a

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.

1 aBose, Samik1 aChakrabarty, Suman1 aGhosh, Debashree uhttps://library.ncl.res.in/content/effect-solvation-electron-detachment-and-excitation-energies-green-fluorescent-protein02099nas a2200253 4500008004100000022001400041245007600055210006900131260000800200300001400208490000700222520131000229653001501539653001901554653001601573653001301589653003301602100002601635700002201661700001901683700002301702700001901725856010101744 2016 eng d a1875-510000aEffect of the amino acid L-histidine on methane hydrate growth kinetics0 aEffect of the amino acid Lhistidine on methane hydrate growth ki cSEP a1453-14620 v353 a

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.

10aAmino acid10aCrystal growth10aGas hydrate10akinetics10aMolecular dynamic simulation1 aBhattacharjee, Gaurav1 aChoudhary, Nilesh1 aKumar, Asheesh1 aChakrabarty, Suman1 aKumar, Rajnish uhttps://library.ncl.res.in/content/effect-amino-acid-l-histidine-methane-hydrate-growth-kinetics03029nas a2200157 4500008004100000022001400041245017900055210006900234260011000303300001600413490000700429520225600436100002402692700002302716856013202739 2016 eng d a1463-907600aExploration 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 water0 aExploration of the presence of bulklike water in AOT reverse mic aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcAUG a21767-217790 v183 a

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.

1 aHande, Vrushali, R.1 aChakrabarty, Suman uhttps://library.ncl.res.in/content/exploration-presence-bulk-water-aot-reverse-micelles-and-water-oil-nanodroplets-role-charged02118nas a2200169 4500008004100000022001400041245008200055210006900137260000800206300001400214490000800228520154800236100001601784700002301800700002101823856010401844 2017 eng d a1520-610600aElectrostatic origin of the red solvatochromic shift of DFHBDI in RNA spinach0 aElectrostatic origin of the red solvatochromic shift of DFHBDI i cMAY a4790-47980 v1213 a

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.

1 aBose, Samik1 aChakrabarty, Suman1 aGhosh, Debashree uhttps://library.ncl.res.in/content/electrostatic-origin-red-solvatochromic-shift-dfhbdi-rna-spinach01514nas a2200193 4500008004100000022001400041245010500055210006900160260000800229300001400237490000800251520082700259100002201086700002401108700001501132700002301147700001901170856013101189 2018 eng d a1520-610600aEffect of sodium dodecyl sulfate surfactant on methane hydrate formation: a molecular dynamics study0 aEffect of sodium dodecyl sulfate surfactant on methane hydrate f cJUN a6536-65420 v1223 a

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.

1 aChoudhary, Nilesh1 aHande, Vrushali, R.1 aRoy, Sudip1 aChakrabarty, Suman1 aKumar, Rajnish uhttps://library.ncl.res.in/content/effect-sodium-dodecyl-sulfate-surfactant-methane-hydrate-formation-molecular-dynamics-study