02339nas a2200169 4500008004100000022001400041245009200055210006900147260012500216300002300341490000800364520159300372100002201965700002301987700003402010856012502044 2013 eng d a0021-960600aInterplay between crystallization and glass transition in binary Lennard-Jones mixtures0 aInterplay between crystallization and glass transition in binary aCIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USAbAMER INST PHYSICScSEP aArticle No. 1045010 v1393 a

In this work we explore the interplay between crystallization and glass transition in different binary mixtures by changing their inter-species interaction length and also the composition. We find that only those systems which form bcc crystal in the equimolar mixture and whose global structure for larger x(A) (x(A) = 0.6, where x(A) is the mole fraction of the bigger particles) is a mixed fcc + bcc phase, do not crystallize at this higher composition. However, the systems whose equimolar structure is a variant of fcc (NaCl type crystal) and whose global structure at larger xA is a mixed NaCl + fcc phase, crystallize easily to this mixed structure. We find that the stability against crystallization of this ``bcc zone'' is due to the frustration between the locally preferred structure (LPS) and the mixed bcc + fcc crystal. Our study suggests that when the global structure is a mixed crystal where a single species contributes to both the crystal forms and where the two crystal forms have large difference in some order parameter related to that species then this induces frustration between the LPS and the global structure. This frustration makes the systems good glass former. When x(A) is further increased (0.70 <= x(A) < 0.90) the systems show a tendency towards mixed fcc crystal formation. However, the ``bcc zone'' even for this higher composition is found to be sitting at the bottom of a V shaped phase diagram formed by two different variants of the fcc crystal structure, leading to its stability against crystallization. (C) 2013 AIP Publishing LLC.

1 aBanerjee, Atreyee1 aChakrabarty, Suman1 aBhattacharyya, Sarika, Maitra uhttp://library.ncl.res.in/content/interplay-between-crystallization-and-glass-transition-binary-lennard-jones-mixtures-002993nas a2200193 4500008004100000022001400041245014800055210006900203260007100272300001600343490000800359520219900367100002702566700001602593700002302609700001802632700001902650856013002669 2013 eng d a1520-610600aQuantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant Ab initio QM/MM free-energy surfaces0 aQuantifying the mechanism of phosphate monoester hydrolysis in a a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcOCT a12807-128190 v1173 a

Understanding the nature of the free-energy surfaces for phosphate hydrolysis is a prerequisite for understanding the corresponding key chemical reactions in biology. Here, the challenge has been to move to careful ab initio QM/MM (QM(ai)/MM) free-energy calculations, where obtaining converging results is very demanding and computationally expensive. This work describes such calculations, focusing on the free-energy surface for the hydrolysis of phosphate monoesters, paying special attention to the comparison between the one water (1W) and two water (2W) paths for the proton-transfer (PT) step. This issue has been explored before by energy minimization with implicit solvent models and by nonsystematic QM/MM energy minimization, as well as by nonsystematic free-energy mapping. However, no study has provided the needed reliable 2D (3D) surfaces that are necessary for reaching concrete conclusions. Here we report a systematic evaluation of the 2D (3D) free-energy maps for several relevant systems, comparing the results of QM(ai)/MM and QM(ai)/implicit solvent surfaces, and provide an advanced description of the relevant energetics. It is found that the 1W path for the hydrolysis of the methyl diphosphate (MDP) trianion is 6-9 kcal/mol higher than that the 2W path. This difference becomes slightly larger in the presence of the Mg2+ ion because this ion reduces the plc of the conjugated acid form of the phosphate oxygen that accepts the proton. Interestingly, the BLYP approach (which has been used extensively in some studies) gives a much smaller difference between the 1W and 2W activation barriers. At any rate, it is worth pointing out that the 2W transition state for the PT is not much higher that the common plateau that serves as the starting point of both the 1W and 2W PT paths. Thus, the calculated catalytic effects of proteins based on the 2W PT mechanistic model are not expected to be different from the catalytic effects predicted using the 1W PT mechanistic model, which was calibrated on the observed barrier in solution and in which the TS charge distribution was similar to the that of the plateau (as was done in all of our previous EVB studies).

1 aPlotnikoy, Nikolay, V.1 aPrasad, Ram1 aChakrabarty, Suman1 aChu, Zhen, T.1 aWarshel, Arieh uhttp://library.ncl.res.in/content/quantifying-mechanism-phosphate-monoester-hydrolysis-aqueous-solution-evaluating-relevant-002456nas a2200229 4500008004100000022001400041245010100055210006900156260008000225300001600305490000800321520158800329653003001917653002001947653002301967653002901990100001502019700002302034700002202057700001902079856012802098 2014 eng d a0027-842400aModeling gating charge and voltage changes in response to charge separation in membrane proteins0 aModeling gating charge and voltage changes in response to charge a2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USAbNATL ACAD SCIENCEScAUG a11353-113580 v1113 a

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on mechanisms of charge transport and displacement processes. A recent example is provided by studies of cytochrome c oxidase. However, the interpretation of the observed voltage changes in terms of the number of charge equivalents and transfer distances is far from being trivial or unique. Using continuum approaches to describe the voltage generation may involve significant uncertainties and reliable microscopic simulations are not yet available. Here, we attempt to solve this problem by using a coarse-grained model of membrane proteins, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The model evaluates the gating charges and the electrode potentials (c.f. measured voltage) upon charge transfer within the protein. The accuracy of the model is evaluated by a comparison of measured voltage changes associated with electron and proton transfer in bacterial photosynthetic reaction centers to those calculated using our coarse-grained model. The calculations reproduce the experimental observations and thus indicate that the method is of general use. Interestingly, it is found that charge-separation processes with different spatial directions (but the same distance perpendicular to the membrane) can give similar observed voltage changes, which indicates that caution should be exercised when using simplified interpretation of the relationship between charge displacement and voltage changes.

10abacterial reaction center10aelectrogenicity10amembrane potential10aproton/electron transfer1 aKim, Ilsoo1 aChakrabarty, Suman1 aBrzezinski, Peter1 aWarshel, Arieh uhttp://library.ncl.res.in/content/modeling-gating-charge-and-voltage-changes-response-charge-separation-membrane-proteins-002661nas a2200193 4500008004100000022001400041245013800055210006900193260007100262300001400333490000700347520187800354100001602232700003002248700002302278700002302301700002202324856012102346 2015 eng d a0743-746300aBioactive polymersomes self-assembled from amphiphilic.PPO-glycopolypeptides: synthesis, characterization, and dual-dye encapsulation0 aBioactive polymersomes selfassembled from amphiphilicPPOglycopol a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcAPR a3402-34120 v313 a

Glycopolypeptide-based polymersomes have promising applications as vehicles for targeted drug delivery because they are capable of encapsulating different pharmaceuticals of diverse polarity as well as interacting with specific cell surfaces due to their hollow structural morphology and bioactive surfaces. We have synthesized glycopolypeptide-b-poly(propylene oxide) by ROP of glyco-N-carboxyanhydride (NCA) using the hydrophobic amine-terminated poly(propylene oxide) (PPO) as the initiator. This block copolymer is composed of an FDA-approved PPO hydrophobic block in conjugation with hydrophilic glycopolypeptides which are expected to be biocompatible. We demonstrate the formation of glycopolypeptide-based polymersomes from the self-assembly of glycopolypeptide-b-poly(propylene oxide) in which the presence of an ordered helical glycopolypeptide segment is required for their self-assembly into spherical nanoscale (similar to 50 nm) polymersomes. The polymersomes were characterized in detail using a variety of techniques such as TEM, AFM, cryo-SEM, and light-scattering measurements. As a model for drugs, both hydrophobic (RBOE) and hydrophilic (calcein) dyes have been incorporated within the polymersomes from solution. To substantiate the simultaneous entrapment of the two dyes, spectrally resolved fluorescence microscopy was performed on the glycopeptide polymersomes cast on a glass substrate. We show that it is possible to visualize individual nanoscale polymersomes and effectively probe the dyes colocalization and energy-transfer behaviors therein as well as investigate the variation in dual-dye encapsulation over a large number of single polymersomes. Finally, we show that the galactose moieties present on the surface can specifically recognize lectin RCA(120), which reveals that the polymersomes surface is indeed biologically active.

1 aDas, Soumen1 aSharma, Dharmendar, Kumar1 aChakrabarty, Suman1 aChowdhury, Arindam1 aGupta, Sayam, Sen uhttp://library.ncl.res.in/content/bioactive-polymersomes-self-assembled-amphiphilicppo-glycopolypeptides-synthesis-003078nas a2200157 4500008004100000022001400041245012000055210006900175260007100244300001600315490000800331520240600339100002402745700002302769856012802792 2015 eng d a1520-610600aStructural order of water molecules around hydrophobic solutes: length-scale dependence and solute-solvent coupling0 aStructural order of water molecules around hydrophobic solutes l a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcAUG a11346-113570 v1193 a

It has been suggested that the structure and thermodynamics of the water molecules in the hydration layer of simple hydrophobic solutes undergo an order disorder transition around a nanometer length-scale of the solute size. Using extensive atomistic molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulation studies, we have probed this order disorder transition around model hydrophobic solutes of varying size and shape (spherical, planar, and linear), as well as flexible hydrophobic homopolymer chains (n-alkanes), where the conformational fluctuations are likely to create both spatial and temporal heterogeneity on the solvent accessible surface. We have explored the structural response of the water molecules in the hydration shell due to the local variations of the length-scale (or curvature) upon hydrophobic collapse and/or local conformational changes of these polymers. We have shown that the tetrahedral order of the water molecules in the hydration shell is practically independent of the polymer size in the extended state of the polymer due to the availability of a subnanometer cross-sectional length-scale, allowing the water molecules to form hydrogen bonds around the polymer chain. Beyond a certain length of the polymer chains, the collapsed states (associated with larger solute length-scale) start to induce disorder in the surface water molecules. We demonstrate that the local structure (both local number density and tetrahedral order) of the hydration layer is dynamically coupled to the local topology of the polymer. Thus, we envisage that in a flexible (bio)polymer, the hydration shell properties will be sensitive to the local conformational state of the molecule (both spatially and temporally), and the overall observed water structure and dynamics will be dependent on the topological/chemical heterogeneity, and the time-scale of fluctuations in the local curvature (length-scale) of the solvent accessible surface. Moreover, we have demonstrated the direct coupling between the local density fluctuations of water and the local hydrophobic collapse of the polymer. For the extended state of the polymer, the local solvent density fluctuation is practically independent of the solute coordinate (length-scale), and the hydrophobic collapse of the polymer is prompted by a ``local dewetting'' process induced by these fluctuations.

1 aHande, Vrushali, R.1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/structural-order-water-molecules-around-hydrophobic-solutes-length-scale-dependence-and-102651nas a2200181 4500008004100000022001400041245010500055210006900160260008700229300002700316490000800343520189300351100002502244700002202269700002302291700003402314856012102348 2016 eng d a0021-960600aComposition dependence of the glass forming ability in binary mixtures: the role of demixing entropy0 aComposition dependence of the glass forming ability in binary mi a1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USAbAMER INST PHYSICScJUL aArticle Number: 0345030 v1453 a

We present a comparative study of the glass forming ability of binary systems with varying composition, where the systems have similar global crystalline structure (CsCl+fcc). Biased Monte Carlo simulations using umbrella sampling technique show that the free energy cost to create a CsCl nucleus increases as the composition of the smaller particles is decreased. We find that systems with comparatively lower free energy cost to form CsCl nucleus exhibit more pronounced pre-crystalline demixing near the liquid/crystal interface. The structural frustration between the CsCl and fcc crystal demands this demixing. We show that closer to the equimolar mixture, the entropic penalty for demixing is lower and a glass forming system may crystallize when seeded with a nucleus. This entropic penalty as a function of composition shows a non-monotonic behaviour with a maximum at a composition similar to the well known Kob-Anderson (KA) model. Although the KA model shows the maximum entropic penalty and thus maximum frustration against CsCl formation, it also shows a strong tendency towards crystallization into fcc lattice of the larger ``A'' particles which can be explained from the study of the energetics. Thus for systems closer to the equimolar mixture although it is the requirement of demixing which provides their stability against crystallization, for KA model it is not demixing but slow dynamics and the presence of the ``B'' particles make it a good glass former. The locally favoured structure around ``B'' particles is quite similar to the CsCl structure and the incompatibility of CsCl and fcc hinders the fcc structure growth in the KA model. Although the glass forming binary systems studied here are quite similar, differing only in composition, we find that their glass forming ability cannot be attributed to a single phenomenon. Published by AIP Publishing.

1 aNandi, Ujjwal, Kumar1 aBanerjee, Atreyee1 aChakrabarty, Suman1 aBhattacharyya, Sarika, Maitra uhttp://library.ncl.res.in/content/composition-dependence-glass-forming-ability-binary-mixtures-role-demixing-entropy02607nas a2200205 4500008004100000022001400041245012400055210006900179260007100248300001400319490000800333520180600341100001602147700001802163700002402181700002502205700002302230700001802253856013002271 2016 eng d a1520-610600aCorrelating Nitrile IR frequencies to local electrostatics quantifies noncovalent interactions of peptides and proteins0 aCorrelating Nitrile IR frequencies to local electrostatics quant a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAY a4034-40460 v1203 a

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular dynamics simulations, we have reported for the first time a linear correlation between nitrile frequencies and electric fields in a wide range of hydrogen-bonding environments that may bridge the existing gap between VSE and H-bonding interactions. We have demonstrated the robustness of this field-frequency correlation for both aromatic nitriles and sulfur-based nitriles in a wide range of molecules of varying size and compactness, including small molecules in complex solvation environments, an amino acid, disordered peptides, and structured proteins. This correlation, when coupled to VSE, can be used to quantify noncovalent interactions, specific or nonspecific, in a consistent manner.

1 aDeb, Pranab1 aHaldar, Tapas1 aKashid, Somnath, M.1 aBanerjee, Subhrashis1 aChakrabarty, Suman1 aBagchi, Sayan uhttp://library.ncl.res.in/content/correlating-nitrile-ir-frequencies-local-electrostatics-quantifies-noncovalent-interactions01847nas a2200169 4500008004100000022001400041245012200055210006900177260007100246300001400317490000800331520115300339100001601492700002301508700002101531856012501552 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 uhttp://library.ncl.res.in/content/effect-solvation-electron-detachment-and-excitation-energies-green-fluorescent-protein02098nas a2200253 4500008004100000022001400041245007600055210006900131260000800200300001400208490000700222520131000229653001501539653001901554653001601573653001301589653003301602100002601635700002201661700001901683700002301702700001901725856010001744 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 uhttp://library.ncl.res.in/content/effect-amino-acid-l-histidine-methane-hydrate-growth-kinetics03028nas a2200157 4500008004100000022001400041245017900055210006900234260011000303300001600413490000700429520225600436100002402692700002302716856013102739 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 uhttp://library.ncl.res.in/content/exploration-presence-bulk-water-aot-reverse-micelles-and-water-oil-nanodroplets-role-charged02620nas a2200157 4500008004100000022001400041245012800055210006900183260007100252300001400323490000800337520194500345100002702290700002302317856012202340 2016 eng d a1520-610600aReplica exchange molecular dynamics study of dimerization in prion protein: multiple modes of interaction and stabilization0 aReplica exchange molecular dynamics study of dimerization in pri a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcAUG a7332-73450 v1203 a

The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% beta-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present beta-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of beta-sheet extension) and the G131-V161 H-bond formation.

1 aChamachi, Neharika, G.1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/replica-exchange-molecular-dynamics-study-dimerization-prion-protein-multiple-modes02117nas a2200169 4500008004100000022001400041245008200055210006900137260000800206300001400214490000800228520154800236100001601784700002301800700002101823856010301844 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 uhttp://library.ncl.res.in/content/electrostatic-origin-red-solvatochromic-shift-dfhbdi-rna-spinach02078nas a2200145 4500008004100000245006800041210006800109260000800177300001600185490000800201520158800209100001801797700002301815856009401838 2017 eng d00aHidden electrostatic basis of dynamic allostery in a PDZ domain0 aHidden electrostatic basis of dynamic allostery in a PDZ domain cJUL aE5825-E58340 v1143 aAllosteric effect implies ligand binding at one site leading to structural and/or dynamical changes at a distant site. PDZ domains are classic examples of dynamic allostery without conformational changes, where distal side-chain dynamics is modulated on ligand binding and the origin has been attributed to entropic effects. In this work, we unearth the energetic basis of the observed dynamic allostery in a PDZ3 domain protein using molecular dynamics simulations. We demonstrate that electrostatic interaction provides a highly sensitive yardstick to probe the allosteric modulation in contrast to the traditionally used structure-based parameters. There is a significant population shift in the hydrogen-bonded network and salt bridges involving side chains on ligand binding. The ligand creates a local energetic perturbation that propagates in the form of dominolike changes in interresidue interaction pattern. There are significant changes in the nature of specific interactions (nonpolar/polar) between interresidue contacts and accompanied side-chain reorientations that drive the major redistribution of energy. Interestingly, this internal redistribution and rewiring of side-chain interactions led to large cancellations resulting in small change in the overall enthalpy of the protein, thus making it difficult to detect experimentally. In contrast to the prevailing focus on the entropic or dynamic effects, we show that the internal redistribution and population shift in specific electrostatic interactions drive the allosteric modulation in the PDZ3 domain protein.1 aKumawat, Amit1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/hidden-electrostatic-basis-dynamic-allostery-pdz-domain01693nas a2200181 4500008004100000245013400041210006900175260000800244300001400252490000800266520099700274100002201271700002701293700002601320700002301346700001901369856012301388 2017 eng d00aMolecular dynamics simulation and experimental study on the growth of methane hydrate in presence of methanol and sodium chloride0 aMolecular dynamics simulation and experimental study on the grow cMAY a5026-50330 v1053 aThe plugging of processing and transportation lines by gas hydrate formation is a challenging problem for safe exploitation of oil and gas. The existence of water soluble third component (like methanol and sodium chloride) in the aqueous phase influence the gas hydrate formation thermodynamically also possibly affects the kinetics of hydrate growth. Inorganic salt and organic molecule (alcohols) at high concentration in the aqueous phase have been used as thermodynamic inhibitors to effectively prevent the hydrate formation. This study utilizes molecular dynamics as well as an experimental method to investigate the mechanism of the hydrate formation and the effect of additives. The MD simulation showed that at moderate temperature and pressure, a low concentration (1 wt %) of methanol and NaCl enhances methane hydrate growth kinetics. Significant numbers of methanol molecules were observed inside the gas hydrate cages whereas Na⁺/Cl⁻ ions leach out during hydrate formation.1 aChoudhary, Nilesh1 aKushwaha, Omkar, Singh1 aBhattacharjee, Gaurav1 aChakrabarty, Suman1 aKumar, Rajnish uhttp://library.ncl.res.in/content/molecular-dynamics-simulation-and-experimental-study-growth-methane-hydrate-presence01960nas a2200157 4500008004100000245011600041210006900157260000800226300002600234490000600260520135200266100001801618700002301636700002001659856012301679 2017 eng d00aNucleotide dependent switching in Rho GTPase: conformational heterogeneity and competing molecular interactions0 aNucleotide dependent switching in Rho GTPase conformational hete cAPR aArticle Number: 458290 v73 aRas superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/ GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of "sub-states" such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound "OFF" state have very similar conformations, whereas the GTP bound "ON" state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the gamma- phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors.1 aKumawat, Amit1 aChakrabarty, Suman1 aKulkarni, Kiran uhttp://library.ncl.res.in/content/nucleotide-dependent-switching-rho-gtpase-conformational-heterogeneity-and-competing02686nas a2200361 4500008004100000022001400041245021300055210006900268260000800337300001400345490000700359520141200366653002201778653002601800653003401826653001101860653001301871653001501884653001401899653002301913653002401936653002501960653003301985653002502018653001802043653002502061653001302086100002302099700002002122700002302142700002802165856013102193 2017 eng d a0887-624X00aPartially bio-based poly(amide imide)s by polycondensation of aromatic diacylhydrazides based on lignin-derived phenolic acids and aromatic dianhydrides: synthesis, characterization, and computational studies0 aPartially biobased polyamide imides by polycondensation of aroma cNOV a3636-36450 v553 a

Two new bio-based diacylhydrazide monomers, namely, 4,4-(propane-1,3-diylbis(oxy))bis(3-methoxybenzohydrazide) and 4,4-(propane-1,3-diylbis(oxy))bis(3,5-dimethoxybenzohydrazide) were synthesized starting from lignin-derived phenolic acids, namely, vanillic acid and syringic acid. A series of poly(amide imide)s was synthesized by polycondensation of these diacylhydrazide monomers with commercially available aromatic dianhydrides. Poly(amide imide)s showed inherent viscosity in the range 0.44-0.56 dLg(-1) and exhibited good solubility in organic solvents. Poly(amide imide)s could be cast into transparent, flexible, and tough films from their N,N-dimethylacetamide solutions. Poly(amide imide)s showed 10% weight loss in the temperature range 340-364 degrees C indicating their good thermal stability. Glass transition temperature (T-g) of poly(amide imides)s were measured by DSC and DMA which were in the range 201-223 degrees C and 214-248 degrees C, respectively. The T-g values of poly(amide imide)s were dependent on the number methoxy substituents on aromatic rings of diacylhydrazide monomers. Molecular dynamics simulation studies revealed that chain rigidity is the dominant factor for observed trends in T-g. (c) 2017 Wiley Periodicals, Inc.

10aBiobased Polymers10aComputational studies10aGlass-transaction temperature10alignin10aMonomers10aPlant oils10aPolyimide10aReneable resources10aRenewable resources10aStep-growth polymers10astructure-property relations10aSustanaible Polymers10aThermal night10aThermosetting resins10aVanillin1 aKuhire, Sachin, S.1 aSharma, Pragati1 aChakrabarty, Suman1 aWadgaonkar, Prakash, P. uhttp://library.ncl.res.in/content/partially-bio-based-polyamide-imides-polycondensation-aromatic-diacylhydrazides-based-lignin02361nas a2200157 4500008004100000022001400041245014200055210006900197260000900266300001200275490000700287520173000294100002702024700002302051856012902074 2017 eng d a0006-296000aTemperature-induced misfolding in prion protein: evidence of multiple partially disordered states stabilized by non-native hydrogen bonds0 aTemperatureinduced misfolding in prion protein evidence of multi cFEB  a833-8440 v563 a

The structural basis of pathways of misfolding of a cellular prion (PrPc) into the toxic scrapie form (PrPsc) and identification of possible intermediates (e.g., PrP*) still eludes us. In this work, we have used a cumulative us of replica exchange molecular dynamics simulation data to construct the conformational free energy landscapes and capture the structural and thermodynamic characteristics associated with various stages of the thermal denaturation process in human prion protein. The temperature-dependent free energy surfaces consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds, thus rendering the protein prone to misfolding. We have been able to identify metastable conformational states with high beta-content (similar to 30-40%) and low alpha-content (similar to 10-20%) that might be precursors of PrPsc oligomer formation. These conformations also involve participation of the unstructured N-terminal domain, and its role in misfolding has been investigated. All the misfolded or partially unfolded states are quite compact in nature despite having large deviations from the native structure. Although the number of native contacts decreases dramatically at higher temperatures, the radius of gyration and number of intraprotein hydrogen bonds and contacts remain relatively unchanged, leading to stabilization of the misfolded conformations by non-native interactions. Our results are in good agreement with the established view that the C-terminal regions of the second and third helices (H2 and H3, respectively) of mammal prions might be the Achilles heels of their stability, while separation of B1-H1-B2 and H2-H3 domains seems to play a key role, as well.

1 aChamachi, Neharika, G.1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/temperature-induced-misfolding-prion-protein-evidence-multiple-partially-disordered-states01960nas a2200181 4500008004100000245013300041210006900174260000800243300001400251490000600265520127600271100002401547700002101571700002301592700001901615700001801634856012601652 2017 eng d00aTwo-dimensional infrared spectroscopy reveals cosolvent-composition-dependent crossover in intermolecular hydrogen bond dynamics0 aTwodimensional infrared spectroscopy reveals cosolventcompositio cAPR a1604-16090 v83 aCosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast twodimensional infrared spectroscopy experiments. Our results demonstrate the cosolventconcentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute solvent interactions is the key to the anomalous behavior.1 aKashid, Somnath, M.1 aJin, Geun, Young1 aChakrabarty, Suman1 aKim, Yung, Sam1 aBagchi, Sayan uhttp://library.ncl.res.in/content/two-dimensional-infrared-spectroscopy-reveals-cosolvent-composition-dependent-crossover01513nas a2200193 4500008004100000022001400041245010500055210006900160260000800229300001400237490000800251520082700259100002201086700002401108700001501132700002301147700001901170856013001189 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 uhttp://library.ncl.res.in/content/effect-sodium-dodecyl-sulfate-surfactant-methane-hydrate-formation-molecular-dynamics-study01998nas a2200169 4500008004100000245010200041210006900143260000800212300001400220490000700234520138400241100002001625700002301645700001501668700001901683856012601702 2018 eng d00aMolecular view of CO2 capture by polyethylenimine: role of structural and dynamical heterogeneity0 aMolecular view of CO2 capture by polyethylenimine role of struct cMAY a5138-51480 v343 aThe molecular thermodynamics and kinetics of CO2 sorption in Polyethylenimine (PEI) melt have been investigated systematically using GCMC and MD simulations. We elucidate presence of significant structural and dynamic heterogeneity associated with the overall absorption process. CO2 adsorption in a PEI membrane shows a distinct two-stage process of a rapid CO2 adsorption at the interfaces (hundreds of picoseconds) followed by a significantly slower diffusion limited release toward the interior bulk regions of PEI melt (hundreds of nanoseconds to microseconds). The spatial heterogeneity of local structural features of the PEI chains lead to significantly heterogeneous absorption characterized by clustering and trapping of CO2 molecules that then lead to subdiffusive motion of CO2. In the complex interplay of interaction and entropy, the latter emerges out to be the major determining factor with significantly higher solubility of CO2 near the interfaces despite having lower density of binding amine groups. Regions having higher free-volume (entropically favorable) viz. interfaces, pores and loops demonstrate higher CO2 capture ability. Various local structural features of PEI conformations, for example, inter- and intrachain loops, pores of different radii, and di- or tricoordinated pores are explored for their effects on the varying CO2 adsorption abilities.1 aSharma, Pragati1 aChakrabarty, Suman1 aRoy, Sudip1 aKumar, Rajnish uhttp://library.ncl.res.in/content/molecular-view-co2-capture-polyethylenimine-role-structural-and-dynamical-heterogeneity01915nas a2200193 4500008004100000245010800041210006900149260000800218300001400226490000700240520121800247100001701465700002401482700002001506700002301526700002801549700002501577856011901602 2018 eng d00aSoluble polybenzimidazoles with intrinsic porosity: synthesis, structure, properties and processability0 aSoluble polybenzimidazoles with intrinsic porosity synthesis str cMAY a1046-10570 v563 aWe have explored two novel comonomers, namely, 4,16-dicarboxyl[2.2]paracyclophane and 5,5,6,6-tetraamino-3,3,3,3-tetramethyl-1,1-spirobi[indane], for the synthesis of co-polybenzimidazoles (co-PBIs) with intrinsic porosity. Both these monomers possess twisted structures that can lead to awkward macromolecular shapes that cannot pack efficiently. The consequences of introducing these two monomers on the structure and properties of PBIs are reported. The random copolymers synthesized are amorphous and possess glass transition temperatures (T(g)s) greater than 400 degrees C. T-g decreases with increasing comonomer content indicating an increase in fractional free volume. The copolymers have low surface area. TEM and BET measurements show evidence of mesopore formation. The copolymers show significant carbon dioxide adsorption. Single chain molecular dynamics simulation of 24-mer repeat units shows intramolecular void spaces arising as a result of distorted polymer chain with reduced conformational mobility. These studies define a new synthetic strategy for bottoms-up synthesis of PBIs with intrinsic porosity. (c) 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018, 56, 1046-10571 aKumar, Vikas1 aChatterjee, Shyambo1 aSharma, Pragati1 aChakrabarty, Suman1 aAvadhani, Chilukuri, V.1 aSivaram, Swaminathan uhttp://library.ncl.res.in/content/soluble-polybenzimidazoles-intrinsic-porosity-synthesis-structure-properties-and02444nas a2200217 4500008004100000245009700041210006900138260000800207300001400215490000700229520166200236100003301898700000501931700001801936700003801954700002301992700002602015700003402041700003002075856012102105 2019 eng d00aCharge transfer liquid: a stable donor-acceptor interaction in the solvent-free liquid state0 aCharge transfer liquid a stable donoracceptor interaction in the cAUG a9371-93740 v553 a

Charge-transfer complexes have been an inspiration to develop many functional soft materials. However, most of those studies have focused on solution based assemblies wherein the explicit control of solvents and their polarity are crucial. In this context, we explore an efficient and stable charge transfer liquid using a solvent-free liquid dialkoxynaphthalene donor and a naphthalenediimide acceptor. It has been observed that irrespective of the donor-acceptor ratio, the charge-transfer liquid exhibited an unprecedented stability and retained characteristic features even at increased temperatures. The underlying intermolecular interactions leading to efficient CT have been examined by NMR techniques together with theoretical modelling studies. The concept of charge transfer liquid will be highly beneficial for the development of processable optoelectronically active materials.
 

1 aWakchaure, Vivek, Chandrakan1 a1 aGoudappagouda1 aRanjeesh, Kayaramkodath, Chandran1 aChakrabarty, Suman1 aRavindranathan, Sapna1 aRajamohanan, Pattuparambil, R1 aBabu, Sukumaran, Santhosh uhttp://library.ncl.res.in/content/charge-transfer-liquid-stable-donor-acceptor-interaction-solvent-free-liquid-state01802nas a2200229 4500008004100000022001400041245012700055210006900182260000900251300000900260490000800269520100900277653001801286653001701304653002501321653001701346100002201363700002301385700001501408700001901423856013001442 2019 eng d a0301-010400aComparison of different water models for melting point calculation of methane hydrate using molecular dynamics simulations0 aComparison of different water models for melting point calculati cJAN  a6-140 v5163 a

Molecular dynamics simulation is a powerful tool to understand the gas hydrate nucleation, growth, and dissociation at molecular level. Prerequisite of super-cooling during gas hydrate formation and a certain degree of super-healing during melting shows significant hysteresis in the transition between solid and liquid state due to large nucleation barrier. Different water models quantitatively differ in their prediction of thermodynamic and kinetic properties of bulk water, including phase behaviour. The present work carries out a systematic investigation of the effect of the chosen water model on the phase behaviour, in particular, the decomposition of methane hydrate. Void-induced melting has been used to predict the melting point of methane hydrate using TIP4P/Ice, TIP4P/2005, TIP4P, and SPC/E water models. This method avoids the need for a predetermined interface for melting point calculations and thus may have its importance in identifying dissociation kinetics of bulk hydrate.

10adecomposition10aGas hydrates10aVoid-induced melting10aWater models1 aChoudhary, Nilesh1 aChakrabarty, Suman1 aRoy, Sudip1 aKumar, Rajnish uhttp://library.ncl.res.in/content/comparison-different-water-models-melting-point-calculation-methane-hydrate-using-molecular00498nas a2200145 4500008004100000022001400041245006800055210006800123260000900191300000900200490000800209100001800217700002300235856009400258 2019 eng d a0006-349500aThermodynamic view of dynamic allostery in a PDZ domain protein0 aThermodynamic view of dynamic allostery in a PDZ domain protein cFEB  a163A0 v1161 aKumawat, Amit1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/thermodynamic-view-dynamic-allostery-pdz-domain-protein02138nas a2200193 4500008004100000022001400041245009700055210006900152260000900221300001600230490000700246520145600253100002201709700002701731700002601758700002301784700001901807856011801826 2020 eng d a0888-588500aMacro and molecular level insights on gas hydrate growth in the presence of hofmeister salts0 aMacro and molecular level insights on gas hydrate growth in the  cNOV  a20591-206000 v593 a

The effect of few monovalent salts (NaCl, NH4Cl, and GdmCl) as additives, according to the Hofrneister series on the growth of methane gas hydrates, has been studied using experiments as well as molecular dynamics (MD) simulation. Further, the Hofmeister effects on hydrate crystallization have been correlated with the methanol as an additive, which is a known thermodynamic hydrate inhibitor for hydrate growth. One of the previous studies (discussed later in this article) available in the literature concludes that methane hydrate formation from ice might show enhanced kinetics in the presence of salts; this behavior is contrary to the general usage of such salts as hydrate inhibitors. This conclusion may not necessarily be true for experiments done with liquid water, and therefore, this work explores the behavior of these salts in a lab-scale setup. In addition, current work reports detailed MD simulation studies to gain insight into the mechanism of hydrate formation in the presence of Hofmeister series salts at two different concentrations of 1 and 10 wt % in water and compare the results with hydrate formation in the methanol-water system. Our study suggests that the presence of these additives at low concentrations (1 wt %) does enhance the hydrate growth kinetics. However, at higher concentrations (10 wt %), inhibition by these additives persisted, and prolonged nucleation, as well as retarded growth, was observed.

1 aChoudhary, Nilesh1 aKushwaha, Omkar, Singh1 aBhattacharjee, Gaurav1 aChakrabarty, Suman1 aKumar, Rajnish uhttp://library.ncl.res.in/content/macro-and-molecular-level-insights-gas-hydrate-growth-presence-hofmeister-salts02320nas a2200181 4500008004100000022001400041245014200055210006900197260000900266300001100275490000800286520163300294100002001927700002201947700002301969700001901992856012702011 2020 eng d a0167-732200aMorphology and dynamics of self-assembled structures in mixed surfactant systems (SDS plus CAPB) in the context of methane hydrate growth0 aMorphology and dynamics of selfassembled structures in mixed sur cDEC  a1142960 v3193 a

Presence of small dosages of surfactants in the aqueous phase has been reported to enhance the rate of gas hydrate (clathrate) formation. In this work, using extensive atomistic molecular dynamics (MD) simulations, we have investigated how SDS (surfactant) aggregates in the presence/absence of CAPB (co-surfactant) at ambient conditions (temperature 298 K and pressure 1 bar) and at hydrate forming conditions (temperature 275 K and pressure 50 bar) resulting in altered growth kinetics of methane hydrate. We observe that SDS forms aggregates of different sizes and shapes depending on the thermodynamic condition starting from random distributions of the surfactants. In the presence of the CAPB co-surfactant, tightly packed mixed aggregates are formed. Using various structural order parameters, we demonstrate that shape of the aggregates deviates from spherical as well as cylindrical symmetry. During the aggregation process in presence of methane, the methane molecules get absorbed into the aggregates, enhance the aggregation kinetics and provide structural flexibility to the aggregates. This result is partly in agreement with previous experimental observations that SDS (with or without a co-surfactant) may form micelle-like structures under hydrate forming conditions and that methane gets absorbed by these aggregates leading to enhanced solubility of methane in the aqueous phase. Further, we have investigated the dynamics of shape fluctuations of the aggregates and observed that several distinct relaxation timescales exist in these heterogenous systems. (C) 2020 Elsevier B.V. All rights reserved.

1 aHande, Vrushali1 aChoudhary, Nilesh1 aChakrabarty, Suman1 aKumar, Rajnish uhttp://library.ncl.res.in/content/morphology-and-dynamics-self-assembled-structures-mixed-surfactant-systems-sds-plus-capb01749nas a2200157 4500008004100000022001400041245012100055210006900176260000900245300001400254490000700268520114400275100001801419700002301437856013101460 2020 eng d a1948-718500aProtonation-induced dynamic allostery in PDZ domain: evidence of perturbation-independent universal response network0 aProtonationinduced dynamic allostery in PDZ domain evidence of p cNOV  a9026-90310 v113 a

Dynamic allostery is a relatively new paradigm where certain external perturbations may lead to modulation of conformational dynamics at a distant part of a protein without significant changes in the overall structure. While most well-characterized examples of dynamic allostery involve binding with other entities like small molecules, peptides, or nucleic acids, in this work we demonstrate that chemical modifications like protonation may lead to significant dynamical allosteric response in a PDZ domain protein. Tuning the protonation states of two histidine residues (H317 and H372), we identify the allosteric pathways responsible for the dynamic response. Interestingly, the same set of residues that constitute the allosteric response network upon ligand binding seem to be responsible for protonation-induced dynamic allostery. Thus, we propose the existence of an inherent universal response network in signaling proteins, where the same set of residues can respond to varying types of external perturbations in terms of rearrangement of hydrogen-bonded network and redistribution of electrostatic interaction energies.

1 aKumawat, Amit1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/protonation-induced-dynamic-allostery-pdz-domain-evidence-perturbation-independent-universal03086nas a2200157 4500008004100000022001400041245010400055210006900159260000800228300001400236490000800250520251200258100002402770700002302794856011102817 2022 eng d a1520-610600aHow far is ``Bulk Water'' from interfaces? depends on the nature of the surface and what we measure0 aHow far is Bulk Water from interfaces depends on the nature of t cFEB a1125-11350 v1263 a

Using systematic molecular dynamics (MD) simulations, we revisit the question: At what distance from an interface do the properties of ``bulk water'' get recovered? We have considered three different kinds of interfaces: nonpolar (hydrophobic; isooctane-water interface), charged (negative; AOT bilayer), and polar (zwitterionic; POPC bilayer). In order to interrogate the extent of perturbation of the interfacial water molecules as a function of the distance from the interface, we utilize a diverse range of structural and dynamical parameters. To capture the structural perturbations, we look into local density (translational order), local tetrahedral order parameter, and dipolar orientation of the water molecules. We also explore the anisotropic diffusion of the water molecules in the direction perpendicular to the interface as well as the planar diffusion parallel to the interface in a distance dependent manner. In addition, the orientational time correlation functions have been computed to understand the extent of slowdown in the rotational dynamics. As expected, the electrostatic field emanating from the charged AOT interface seems to have the highest long-range effect on the orientational order and dynamics of the water molecules, whereas specific interactions like hydrogen bonding and electrostatic interaction lead to significant trapping and kinetic slowdown for both AOT and POPC (zwitterionic) very close to the interface. Our analysis highlights that not only the length-scale of perturbation depends on the nature of the interfaces and specific interactions but also the type of water property that we measure/calculate. Different water properties seem to have widely different length-scale of perturbation. Orientational order parameters seem to be perturbed to a much longer length-scale as compared to translational order parameters. The global orientational order of water can be perturbed even up to similar to 4-5 nm near the negatively charged AOT surface in the absence of any extra electrolyte. This observation has significant implication toward the interpretation of experimental measurements as well since different spectroscopic techniques would probe different parameters or water properties with possible mutual disagreement and inconsistency between different types of measurements. Thus, our study provides a broader and unifying perspective toward the aspect of ``context dependent'' structural and dynamical perturbation of ``interfacial water''.

1 aHande, Vrushali, R.1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/how-far-bulk-water-interfaces-depends-nature-surface-and-what-we-measure02770nas a2200157 4500008004100000022001400041245012700055210006900182260000800251300001400259490000600273520216100279100002002440700002302460856012902483 2022 eng d a2470-134300aSize-dependent order-disorder crossover in hydrophobic hydration: comparison between spherical solutes and linear alcohols0 aSizedependent orderdisorder crossover in hydrophobic hydration c cJAN a2671-26780 v73 a

Theory and computer simulation studies have predicted that water molecules around hydrophobic molecules should undergo an order-disorder transition with increasing solute size around a 1 nm length scale. Some theories predict the formation of a clathrate-like ordered structure around smaller hydrophobic solutes (<1 nm) and the formation of disordered vapor-liquid interfaces around larger solutes (>1 nm) and surfaces. Experimental validation of these predictions has often been elusive and contradictory. High-resolution Raman spectroscopy has detected that water around small hydrophobic solutes shows a signature similar to that of bulk water at lower temperature (increased ordering and a stronger hydrogen-bonded network). Similarly, water around larger solutes shows an increasing population of dangling OH bonds very similar to higher temperature bulk water. Thus, the solute size dependence of the structure and dynamics of water around hydrophobic molecules seems to have an analogy with the temperature dependence in bulk water. In this work, using atomistic classical molecular dynamics (MD) simulations, we have systematically investigated this aspect and characterized this interesting analogy. Structural order parameters including the tetrahedral order parameter (Q), hydrogen bond distribution, and vibrational power spectrum highlight this similarity. However, in contrast to the experimental observations, we do not observe any length-dependent crossover for linear hydrophobic alcohols (n-alkanols) using classical MD simulations. This is in agreement with earlier findings that linear alkane chains do not demonstrate the length-dependent order-disorder transition due to the presence of a sub-nanometer length scale along the cross section of the chain. Moreover, the collapsed state of linear hydrocarbon chains is not significantly populated for smaller chains (number of carbons below 20). In the context of our computational results, we raise several pertinent questions related to the sensitivity of various structural and dynamical parameters toward capturing these complex phenomena of hydrophobic hydration.

1 aHande, Vrushali1 aChakrabarty, Suman uhttp://library.ncl.res.in/content/size-dependent-order-disorder-crossover-hydrophobic-hydration-comparison-between-spherical