• Issue front cover thumbnail

      Volume 129, Issue 7

      July 2017,   pages  790a-1091

    • Table of Contents

      More Details Abstract Fulltext PDF
    • Preface

      BIMAN BAGCHI DAVID CLARY N SATHYAMURTHY

      More Details Abstract Fulltext PDF
    • Validity of the Rosenfeld relationship: A comparative study of the network forming NTW model and other simple liquids

      ATREYEE BANERJEE MANOJ KUMAR NANDI SARIKA MAITRA BHATTACHARYYA

      More Details Abstract Fulltext PDF

      In this paper we explore the validity of the Rosenfeld and the Dzugutov relation for the Lennard- Jones (LJ) system, its repulsive counterpart, the WCA system and a network forming liquid, the NTW model. We find that for all the systems both the relations are valid at high temperature regime with an universalexponent close to 0.8. Similar to that observed for the simple liquids, the LJ and the WCA systems show a breakdown of the scaling laws at the low temperature regime. However for the NTW model, which is a simple liquid, these scaling laws are valid even at lower temperature regime similar to that found for ionic melts. Thus we find that the NTW model has mixed characteristics of simple liquids and ionic melts. Our study further reveals a quantitative relationship between the Rosenfeld and the Arrhenius relations. For strong liquids, the validity of the Rosenfeld relation in the low temperature regime is connected to it following the Arrhenius behaviour in that regime. Finally we explore the role of pair entropy and residual multiparticle entropy in the dynamics as a function of fragility of the systems.

    • A free energy study of the liquid-liquid phase transition of the Jagla two-scale potential

      FRANCESCO RICCI PABLO G DEBENEDETTI

      More Details Abstract Fulltext PDF

      A fundamental understanding of pure-component liquid-liquid phase separation in network-forming fluids remains an open challenge. While considerable progress has been recently made in demonstrating the existence of such a phase transition in some models via rigorous free energy calculations, it remains unclear what aspects of a model are sufficient, necessary, and/or prohibited in order for it to exhibit a liquid-liquid phase transition (LLPT). Among the simplest models capable of producing water-like anomalies is the sphericallysymmetrytwo-scale Jagla potential, for which an LLPT has been identified via equation of state calculations. In this work, we perform rigorous free energy calculations to demonstrate the existence of an LLPT in the Jagla model. We also utilize finite-size scaling analysis to calculate the surface tension associated with the LLPT.In addition to the thermodynamics of the model, we investigate the relaxation times for density and bondorientational order in both liquid phases and show that, contrary to assertions in the literature, the characteristic relaxation time of bond-orientational order is not orders of magnitude slower than that of density. To the contrary, we actually identify conditions for which density is the slowly relaxing order parameter. In addition to the original parameterization of the Jagla model, we provide in the “Appendix” preliminary free energy surface calculations for select parameterizations of the generalized family of Jagla potentials spanning from the original (anomalous,water-like) Jagla model to the Lennard-Jones model. These calculations indicate that, as the parameterization moves towards the Lennard-Jones limit, the LLPT disappears within the range of parametersexplored. Throughout the paper, we compare our results for the Jagla model with those found in the literature for the ST2 model of water in order to emphasize key similarities and differences between two models that exhibit pure-component liquid-liquid phase separation.

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

      DEBASIS SAHA ARNAB MUKHERJEE

      More Details Abstract Fulltext PDF

      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.

    • Breakdown of universal Lindemann criterion in the melting of Lennard-Jones polydisperse solids

      SARMISTHA SARKAR CHANDRAMOHAN JANA BIMAN BAGCHI

      More Details Abstract Fulltext PDF

      It is commonly believed that melting occurs when mean square displacement (MSD) of a particle of crystalline solid exceeds a threshold value. This is known as the Lindemann criterion, first introduced in the year of 1910 by Lindemann. However, Chakravarty et al., demonstrated that this common wisdom is inadequatebecause the MSD at melting can be temperature dependent when pressure is also allowed to vary along the coexistence line of the phase diagram [Chakravarty C, Debenedetti P G and Stillinger F H 2007 J. Chem. Phys. 126 204508]. We show here by extensive molecular dynamics simulation of both two and three dimensional polydisperse Lennard-Jones solids that particles on the small and large limits of size distribution exhibit substantially different Lindemann ratio at melting. Despite all the dispersion in MSD, melting is found tobe first order in both the dimensions at 5–10% dispersity in size. Sharpness of the transition is incommensurate with the different rate of growth of MSD. The increased MSD values of smaller particles play a role in the segregation of them prior to melting.

    • Size and Structure of Cytochrome-c bound to Gold nano-clusters: Effect of Ethanol

      CATHERINE GHOSH M D ASIF AMIN BIMAN JANA KANKAN BHATTACHARYYA

      More Details Abstract Fulltext PDF

      Size and structure of cytochrome c (Cyt C) bound to gold nano-clusters (AuNC) were studied using fluorescence correlation spectroscopy (FCS) and circular dichroism (CD) spectroscopy. The CD spectra of Cyt C indicate that the ellipticity is almost completely lost on binding to AuNC which indicates unfolding.Addition of ethanol causes partial restoration of ellipticity and hence, structure of Cyt C. FCS data indicate that size (hydrodynamic radius, rH) of free Cyt C is 17Å which increases to 24Å on binding to AuNC. This too suggests unfolding of Cyt C upon binding to AuNCs. Both the size and conformational relaxation time of Cyt C bound to AuNC vary non-monotonically with increase in ethanol content.

    • Modeling of 1-D Nanowires and analyzing their Hydrogen and Noble Gas Binding Ability

      SUDIP PAN RANAJIT SAHA ASHUTOSH GUPTA PRATIM K CHATTARAJ

      More Details Abstract Fulltext PDF

      The theoretical calculation at the M05-2X/6-311+G(d,p) level reveals that the B–B bond length in [N ₄ ₋B ₂ ₋N ₄] ²⁻ system (1.506 Å) is slightly smaller than that of typical B=B bond in B ₂H ₂ (1.518 Å). These systems interact with each M ⁺ (M = Li, Na, K) ion very strongly with a binding energy of 213.5 (Li), 195.2 (Na) and 180.3 (K) kcal/mol. Additionally, the relief of the Coulomb repulsion due to the presence of counterion, M ⁺, the B–B bond contracts to 1.484–1.488Å in [N ₄ ₋B ₂ ₋N ₄]M ₂. We have further extended our study to [N ₄ ₋B ₂ ₋N ₄ ₋B ₂ ₋N ₄] ⁴⁻ and [N ₄ ₋B ₂ ₋N ₄-B ₂ ₋N ₄ ₋B ₂ ₋N ₄] ⁶⁻ systems. The B–B bond length is found to be 1.496Å in the former case, whereas the same is found to be 1.493Å and 1.508 Å, respectively, for the two B–B bonds present in the latter one. The M ⁺ counter-ions stabilize such negatively charged systems and thus, create a possibility to design a long 1-D nanowire. Their utilities as probable hydrogen and noble gas (Ng) binding templates are explored taking [N ₄ ₋B ₂2 ₋N ₄ ₋B ₂ ₋N ₄]Li ₄ system as a reference. It is found that each Li center binds with three H ₂ molecules with an average binding energy of 2.1 kcal/mol, whereas each Ng (Ar–Rn) atom interacts with Li center having a binding energy of 1.8–2.1 kcal/mol. The H ₂ molecules interact with Li centers mainly through equal contribution from orbital and electrostatic interaction, whereas the orbital interaction is found to be major term (ca. 51–58%) in Ng-Li interaction followed by dispersion (ca. 24–27%) and electrostatic interaction (ca. 17–24%).

    • Molecular Dynamics Investigation of Efficient SO₂ Absorption by Anion-Functionalized Ionic Liquids

      ANIRBAN MONDAL SUNDARAM BALASUBRAMANIAN

      More Details Abstract Fulltext PDF

      Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations unveil that the high uptake of SO₂ in these ionic liquids originates from the basicity of the anions and the consequent enhanced anion-SO₂ interactions. MD simulations of SO₂–IL mixtures reveal the crucial role of both cations and anions in SO₂ dissolution. Multiple-site interactions of SO₂ with the anions have been identified. The calculated solvation free energy substantiates these observations. The order of computed Henry’s law constant values with change in the anion is in fair agreement with experimentally determined SO₂ solubility order.

    • Nanoclusters of Cyanuric Acid

      M ELANGO V SUBRAMANIAN N SATHYAMURTHY

      More Details Abstract Fulltext PDF

      In this article, the self-assembly of cyanuric acid (CA) molecules into nano-structures is examined. Equilibrium geometry of CA is planar and it belongs to the D3h point group. It is shown that CA clusters form three dimensional bowls and balls. Cyclic pentamer (5-bowl) is the basic motif responsible for these non-planar geometries. It is also shown that the cyclic hexamer based clusters can be non-planar if they contain a 5-bowl. A unified criterion for the formation of bowls and balls from basic molecular building blocks emerges from this study. The role of symmetry in supramolecular self-assembly is also clearly evident from the present study.

    • A model with charges and polarizability for CS₂ in an ionic liquid

      RUTH M LYNDEN-BELL ANTHONY J STONE

      More Details Abstract Fulltext PDF

      The environment of a solute molecule in an ionic liquid is likely to have large fluctuating electrostatic fields, and so the electrostatic properties of such a solute including its charge distribution and its polarizability may make a difference to both its static and dynamic properties. We have developed a new model forthe static electrostatic distribution in the CS₂ molecule with 7 charged sites and anisotropic polarizability on the carbon site and isotropic polarizability on the sulfurs. We have investigated static and dynamic properties of the neat liquid and solutions of CS₂ in an ionic liquid, [dmim][NTf₂].

    • Excess vibrational modes of a crystal in an external non-affine field

      SASWATI GANGULY SURAJIT SENGUPTA

      More Details Abstract Fulltext PDF

      Thermal displacement fluctuations in a crystal may be classified as either “affine” or “non-affine”. While the former couples to external stress with familiar consequences, the response of a crystal when nonaffine displacements are enhanced using the thermodynamically conjugate field, is relatively less studied. We examine this using a simple model of a crystal in two dimensions for which analytical calculations are possible. Enhancing non-affine fluctuations destabilises the crystal. The population of small frequency phonon modesincreases, with the phonon density of states shifting, as a whole, towards zero frequency. Even though the crystal is free of disorder, we observe growing length and time scales. Our results, which may have implications for the glass transition and structural phase transitions in solids, are compared to molecular dynamics simulations. Possibility of experimental verification of these results is also discussed.

    • In silico studies of the early stages of aggregation of Aβ₄₂ peptides

      PRABIR KHATUA SANJOY BANDYOPADHYAY

      More Details Abstract Fulltext PDF

      Accumulation of amyloid beta (Aβ) peptide in the brain is responsible for debilitating neurodegenerative disease, namely, Alzheimer’s disease. We have carried out atomistic molecular dynamics simulation to study the early stages of the aggregation process of five full-length Aβ₄₂ peptide monomers with varying secondary structural contents in aqueous solution. Attempts have been made to study the conformational modifications of the Aβ peptide monomers and their dynamical features during the oligomer formation. Inparticular, specific molecular interactions that drive the association process leading to the formation of the stable oligomer have been identified. The calculations revealed that the helix–helix linkage plays an important role forbringing the unstructured regions of the monomers closer for self-assembly. Importantly, it is demonstrated that the contribution originating from the nonpolar interactions between the peptides and the corresponding nonpolarsolvation more than compensates the weakening effect of unfavorable inter-peptide electrostatic interactions, thereby stabilizing the nucleated oligomer.

    • Stabilisation of the [6]-prismane structure by silicon substitution

      ASIF EQUBAL SHWETHA SRINIVASAN NARAYANASAMI SATHYAMURTHY

      More Details Abstract Fulltext PDF

      Using the second-order Møller–Plesset perturbation (MP2) theoretic method and the cc-pVDZ basis set, it is shown that with an increase in the number of carbon atoms substituted by silicon, the [6]-prismane structure becomes increasingly more stable, relative to the two isolated benzene (like) structures. A similar trend is observed for germanium substituted prismanes as well. Extending this investigation, the stability of benzene-capped fullerene (C₆₀ fused with benzene) is also investigated.

    • Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

      IDA M FRIISBERG LORENZO COSTIGLIOLA JEPPE C DYRE

      More Details Abstract Fulltext PDF

      This paper investigates the relation between the density-scaling exponent γ and the virial potential energy correlation coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ system in two,three, and four dimensions. The state points studied include many low-density states at which the virial potential energy correlations are not strong. For these state points we find the roughly linear relation γ∼=3n R/d in d dimensions. This result is discussed in light of the approximate “extended inverse power law” description of generalized LJ potentials (Bailey N P et al. 2008 J. Chem. Phys. 129 184508). In the plot of γ versus R there is in all cases a transition around R ≈ 0.9, above which γ starts to decrease as R approaches unity. This is consistent with the fact that γ → 2n/d for R → 1, a limit that is approached at high densities and/or high temperatures at which the repulsive r−2n term dominates the physics.

    • Diffusing diffusivity: a new derivation and comparison with simulations

      ROHIT JAIN K L SEBASTIAN

      More Details Abstract Fulltext PDF

      Many experiments are now available where it has been shown that the probability distribution function (pdf) for the position of a Brownian particle diffusing in a heterogeneous medium is not Gaussian. However, in spite of this non-Gaussianity, the mean square displacement (MSD) still remains Fickian, i.e.,

      ⟨x²⟩ ∝ T . One possible explanation of this non-Gaussian yet Brownian behavior is that the diffusivity of the particle itself is “diffusing”. Chubynsky and Slater (Phys. Rev. Lett. 113 098302 2014) proposed a model of “diffusing diffusivity” which they were able to solve analytically at small time scales, but simulations were performed for intermediate to large time scales.We present here a class of diffusing diffusivity models and show that the problem of calculating pdf for the position of diffusing particle is equivalent to calculating the survival probability of a particle undergoing Brownian motion in the presence of a sink.We give exact analytical results for all time scales and show that the pdf is non-Gaussian at short times which crosses over to a Gaussian at longtimes. The MSD is also shown to vary linearly with time at all times. We find that our results reproduce the numerical results of Chubynsky and Slater quite well.

    • Microstructures and their lifetimes in acetamide/electrolyte deep eutectics: anion dependence

      SUMAN DAS BISWAROOP MUKHERJEE RANJIT BISWAS

      More Details Abstract Fulltext PDF

      Extensive computer simulations with deep eutectics made of acetamide (CH₃CONH₂) and lithium salts (LiX) have been performed at 303 K and 350 K to identify the solution-phase microstructures in these media and investigate the anion dependence of the size and lifetime distributions of these microstructures. In addition, we explore how the added electrolyte interferes with the natural hydrogen bonded (H-bonded) network structure of liquid acetamide. For this purpose several radial distribution functions have been analysedand visualised. The results reveal that amide–amide H-bond interaction decreases significantly upon the addition of electrolyte, and the interactions of Li⁺ and X⁻ (X⁻ being NO⁻3 , Br⁻ and ClO⁻4 ) with CH₃CONH₂ lead to heterogeneous solution structures. Furthermore, we have obtained the cluster size and lifetime distributions in order to estimate the size of local microstructures and their stability. Both these distributions are analysed by separating the contributions arising from (a)CH₃CONH₂−CH₃CONH₂, (b)Li⁺−CH₃CONH₂ and (c) Li⁺−X⁻ interactions. The size distribution of Li⁺−X⁻ clusters is found to be different from those for the other two. Also, the lifetime distributions show a pronounced anion dependence and suggest cluster stability time up to a fewnanoseconds.

    • A comparative study of the performance of some density functionals for vibronic spectra

      CH SRIDHAR REDDY M DURGA PRASAD

      More Details Abstract Fulltext PDF

      Computed vibronic spectra of four molecules, tetracene, octatetraene, anthracene and pyrene are compared to the experimental spectra with a view to determine the functional that can give the best description. Using a statistical analysis, it is found that M06-2X is best suited for reproducing the 0-0 transition energy while PBE0 and M06 are the best suited functionals for predicting the vibrational frequencies. All the functionals perform equally well in predicting the intensities of vibronic transitions.

    • A molecular dynamics calculation of solid phase of malonic acid: role of hydrogen-bond chains and the elastic constants

      SATHYA S R R PERUMAL YASHONATH SUBRAMANIAN

      More Details Abstract Fulltext PDF

      Recent studies suggest that hydrogen bonds, in particular, hydrogen bond chains play an important role in determining the properties of a substance.We report an investigation into the triclinic phase of crystalline malonic acid. One of two intermolecular interaction potentials proposed here is seen to predict the lattice parameters as well as the enthalpy of the triclinic phase in good agreement with experimental data. Structural and dynamic properties are reported. Also reported are the lifetime of the hydrogen bond and hydrogen bondchains of length l along [011] direction where l = 1 to 5. From the temperature dependence of the lifetime we have obtained the activation energies of the chains. We also report the elements of elastic constant tensor. Theresults show that the presence of the hydrogen bond chain along [011] direction leads to higher value for elastic tensor Cyyzz suggesting a strong correlation between hydrogen bond chains and the elastic constant along thatdirection. This is consistent with the recent report of Azuri I et al. 2015 Angew. Chem. Int. Ed. Engl. 54 13566 who reported that rather large Young’s modulus for certain amino acid crystals.

    • A computational investigation of the red and blue shifts in hydrogen bonded systems

      MITRADIP DAS SWAPAN K GHOSH

      More Details Abstract Fulltext PDF

      The presentwork reports results of computational investigations of hydrogen bonding, with regard to the most common red shift in the vibrational frequency, as well as the less common blue shift in several hydrogen bonded systems. A few new correlations of the frequency shifts with the calculated electrostatic parameters are proposed, thereby generating new insight into both types of the frequency shifts. Thus, the frequency shifts in X—H—-Y hydrogen bonded systems at differentH—Ydistances are shown to correlate well with the Mullikencharges on H and Y, with the positive and negative charges on Y correlating with the blue and red shift of the frequency of X—H vibration, respectively. The role played by charge transfers at other parts of the interacting system is also discussed.

    • Trajectories of Brownian particles with space-correlated noise

      EDOARDO MILOTTI

      More Details Abstract Fulltext PDF

      The Langevin equation used to model Brownian motion includes a stochastic process that is routinely assumed to be a Gaussian white noise. Spatial correlations of the noise are usually ruled out, and the paths traced by the random walkers are statistically independent. In this study, I consider instead noise which is white in time and has a Gaussian correlation in space, and by means of numerical simulation, I show how the spatial correlation determines the time evolution of the spatial separation of random walkers.

    • Facile charge transport in FeNx/Mo₂N/CNT nanocomposites for efficient hydrogen evolution reactions

      KASINATH OJHA SHIVALI BANERJEE ASHOK K GANGULI

      More Details Abstract Fulltext PDF

      Molybdenum based materials are gaining importance as electrocatalysts for hydrogen evolution reaction because of their lowcost and good electrocatalytic efficiency. Introducing iron nitride with molybdenum nitride as a composite results in efficient hydrogen evolution activity with current density of ∼120mA/cm2 at −400 mVvs. RHE. The nanocomposites were characterized using powder XRD, Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), ElectronDiffraction, ThermogravimetricAnalysis and FTIRSpectroscopy. The electrochemical investigations suggest that the electrocatalytic activity of the composite increases with iron nitride content. The composite exhibits good electrochemical stability upto 42 hours in acidic medium. The hydrogen evolution reaction (HER) follows Volmer-Heyrovsky mechanism where Volmer reaction is the rate determing step.

    • A coarse-grained model based on core-softened potentials for anomalous polymers

      RONALDO J C BATISTA EVY A SALCEDO TORRES ALAN BARROS DE OLIVEIRA MARCIA C B BARBOSA

      More Details Abstract Fulltext PDF

      Starting from an anomalous monomeric system, where particles interact via a two-scale cores oftened potential, we investigate how the system properties evolve inasmuch as particles are put together to form polymers whose chain size varies from 4 up to 32 monomers. We observed that the density and diffusionanomaly regions in the pressure versus temperature phase diagram of the monomeric system is smaller in the monomeric system when compared with the polymers. We also found that the polymers do not fold into themselves to form solid spheres instead they tend to maximize the chain-fluid contact.Also, Rouse and Reptation models can be employed to describe the polymers diffusive behaviour. But, in contrast to results of simulations where mere interacts via Lennard-Jones potentials, our results shown a much shorter entanglement length of at most 8 monomers.

    • Controlling the quantum rotational dynamics of a driven planar rotor by rebuilding barriers in the classical phase space

      ARCHANA SHUKLA SRIHARI KESHAVAMURTHY

      More Details Abstract Fulltext PDF

      The present work aims to control the rotational excitations of an ac-driven planar rotor, a model for rigid diatomic molecules, by rebuilding barriers in the classical phase space. The barriers are invariant tori with irrational winding ratios which are perturbatively constructed at desired locations in the phase space. Weestablish that constructing such barriers, equivalent to additional weak fields, can efficiently suppress the chaos leading to the control of various processes. The phase space barriers are shown to be effective in controlling the quantum dynamics as well. In particular, the efficiency of the phase space barriers towards controlling dynamical tunneling in the system is explored. Our studies are relevant to understanding the role of the chaotic regions in dynamical tunneling and for molecular alignment using bichromatic fields.

    • Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of α and β toxin nanopores in lipid membranes

      RAJAT DESIKAN SWARNA M PATRA KUMAR SARTHAK PRABAL K MAITI K G AYAPPA

      More Details Abstract Fulltext PDF

      Pore forming toxins (PFTs) are virulent proteins whose primary goal is to lyse target cells by unregulated pore formation. Molecular dynamics simulations can potentially provide molecular insights on the properties of the pore complex as well as the underlying pathways for pore formation. In this manuscript wecompare both coarse-grained (MARTINI force-field) and all-atom simulations, and comment on the accuracy of the MARTINI coarse-grained method for simulating these large membrane protein pore complexes. We report 20 μs long coarse-grained MARTINI simulations of prototypical pores from two different classes ofpore forming toxins (PFTs) in lipid membranes - Cytolysin A (ClyA), which is an example of an α toxin, and α-hemolysin (AHL) which is an example of a β toxin. We compare and contrast structural attributes such as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from the MARTINIsimulations with all-atom simulations. RMSD histograms sampled by the MARTINI simulations are about a factor of 2 larger, and the radius profiles show that the transmembrane domains of both ClyA and AHL pores undergo significant distortions, when compared with the all-atom simulations. In addition to the fully inserted transmembrane pores, membrane-inserted proteo-lipid ClyA arcs show large shape distortions with a tendency to close in the MARTINI simulations. While this phenomenon could be biologically plausible given the factthat α-toxins can form pores of varying sizes, the additional flexibility is probably due to weaker inter-protomer interactions which are modulated by the elastic dynamic network in the MARTINI force-field. We conclude that there is further scope for refining inter-protomer contacts and perhaps membrane-protein interactions in the MARTINI coarse-grained framework. A robust coarse-grained force-field will enable one to reliably carry out mesoscopic simulations which are required to understand protomer oligomerization, pore formation and leakage.

    • Unfolding intermediates of the mutant His-107-Tyr of human carbonic anhydrase II

      SRABANI TARAPHDER PUSPITA HALDER TANMOY KUMAR PAUL SATYAJIT KHATUA

      More Details Abstract Fulltext PDF

      The mutant His-107-Tyr of human carbonic anhydrase II (HCA II) is highly unstable and has long been linked to a misfolding disease known as carbonic anhydrase deficiency syndrome (CADS). High temperature unfolding trajectories of the mutant are obtained from classical molecular dynamics simulationsand analyzed in a multi-dimensional property space.When projected along a reaction coordinate these trajectories yield four distinguishable sets of structures that map qualitatively to folding intermediates of this mutant postulated earlier from experiments.We present in this article a detailed analysis of representative structures and proton transfer activity of these intermediates. It is also suggested that under suitable experimental conditions, these intermediates may be distinguished using circular dichroism (CD) spectroscopy.

    • Role of solvation structure in the shuttling of the hydrated excess proton

      RAJIB BISWAS GREGORY A VOTH

      More Details Abstract Fulltext PDF

      The classic Marcus electron transfer reaction model demonstrated that a barrierless electron transfer reaction can occur when both the reactant and product have almost similar solvation environment. In our recently developed proton model, we have incorporated the pre-solvation concept and showed that it indeed facilitates the proton diffusion in aqueous solution. In this work, we further quantify the degree of pre-solvation using different structural parameters, e.g., tetrahedral order parameter, average numbers of hydrogen bonds. All theabove said parameters exhibit a very strong correlation with the proton share parameter. The more Zundel-like configurations have almost identical solvation environment for both the water molecules and support the presolvationconcept. However, in the case of Eigen-like configurations, the central hydronium and “special pair” water have distinctly different solvation structures.

    • On the origin of spurious errors in many-body expansion for water cluster

      SOUMEN SAHA M RAM VIVEK G NARAHARI SASTRY

      More Details Abstract Fulltext PDF

      Many-body expansion (MBE) has been carried out to investigate two- to five-body energy terms and their contributions to the interaction energy (IE) of (H₂O)₁₅ cluster. We have observed that the erroneous contribution of many-body terms on IE originated from cheaper convergence thresholds set as default in popular quantum mechanics packages. The propagation of errors from smaller to higher-body terms, due to the combinatorial nature of MBE, is also observed.

    • The dynamic behavior of the exohedral transition metal complexes of B₄₀ : η⁶- and η⁷-B₄₀Cr(CO) ₃ and Cr(CO) ₃η⁷-B₄η₀-Cr(CO) ₃

      NAIWRIT KARMODAK ELUVATHINGAL D JEMMIS

      More Details Abstract Fulltext PDF

      The dynamic nature of the exohedral η⁶- and the η⁷-complexes of B₄₀ with Cr(CO) ₃ has been explored using density functional theory. The ab initio molecular dynamic simulations were performed at 1200 K to investigate the fluxionality of the heptagonal and hexagonal faces of exohedral B40 complexes. Our computations show that the coordination of the B40 faces with Cr(CO) ₃ fragment reduces its fluxionality to a limited extent. The activation barrier for the inter-conversion of the heptagonal and hexagonal rings in (CO)₃Cr(η⁶-B₄₀) complex is around 15.2 kcal/mol whereas in the (CO)₃ Cr(η⁷-B₄₀) complex, it is slightly higher at around 19.7 kcal/mol. The coordination with another Cr(CO)₃ fragment is found to be equally exergonic, with a barrier for interconversion of 21.5 kcal/mol. The HOMO-LUMO gap is almost similar as the mono-metallated complexes. The di-metallated complexes also show a dynamical behavior of the six and seven membered rings at 1200 K.

    • Vibrational echo spectral observables and frequency fluctuations of hydration shell water around a fluoride ion from first principles simulations

      DEEPAK OJHA AMALENDU CHANDRA

      More Details Abstract Fulltext PDF

      Aqueous solution of a fluoride ion at 300K is studied using the method of ab initio molecular dynamics simulation. Instantaneous fluctuations in vibrational frequencies of local OD stretch modes of deuterated water are calculated using a time-series analysis of the simulated trajectory. The vibrational spectraldiffusion of OD modes in the first and second solvation shells and also in bulk of the aqueous fluoride ionic solution are studied through calculations of the frequency time correlation function (FTCF), joint probability distributions, slope of three pulse photon echo (S3PE) and two dimensional infrared spectrum (2D-IR). The vibrational spectral dynamics in the first solvation shell shows decay with three components which can be correlated with the dynamics of intact ion-water hydrogen bonds, ion-water hydrogen bond lifetime and the escape dynamics of water molecules from the solvation shell. The vibrational spectral diffusion of OD modes in the second solvation shell and in the bulk show very similar decay behavior. The timescales obtained from FTCF, S3PE and the slope of nodal line (SNL) of 2D-IR are found to be in reasonable agreement with each others.

    • Density dependence of relaxation dynamics in glass formers, and the dependence of their fragility on the softness of inter-particle interactions

      ANSHUL D S PARMAR PALLABI KUNDU SRIKANTH SASTRY

      More Details Abstract Fulltext PDF

      Fragility, quantifying the rapidity of variation of relaxation times, is analysed for a series of model glass formers, which differ in the softness of their interparticle interactions. In an attempt to rationalize experimental observations in colloidal suspensions that softer interactions lead to stronger (less fragile) glassformers, we study the variation of relaxation dynamics with density, rather than temperature, as a control parameter.We employ density-temperature scaling, analyzed in recent studies, to address the question.We find that while employing inverse density in place of temperature leads to the conclusion that softer interactions lead to stronger behaviour, the use of scaled variables involving temperature and density lead to the opposite conclusion, similarly to earlier investigations where temperature variation of relaxation dynamics was analysed for the same systems. We rationalize our results by considering the Adam-Gibbs (AG) fragility, which incorporates the density dependence of the configurational entropy and an activation energy that may arise from other propertiesof a glass former.Within the framework of the Adam-Gibbs relation, by employing density temperature scaling for the analysis, we find that softer particles make more fragile glasses, as deduced from dynamical quantities, which is found to be consistent with the Adam-Gibbs fragility.

  • Journal of Chemical Sciences | News

© 2017 Indian Academy of Sciences, Bengaluru.