Department of Chemistry

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IIT Jodhpur

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Chemistry - An Asian Journal

Multi-pyrene assemblies supported on stannoxane frameworks: Synthesis, structure and photophysical studies

Conformational dynamics plays a critical role in the activation, deactivation, and open-close activities of ion channels in living cells. Such conformational dynamics is often inhomogeneous and extremely difficult to be directly characterized by ensemble-averaged spectroscopic imaging or only by single channel patch-clamp electric recording methods. We have developed a new and combined technical approach, single-molecule patch-clamp FRET microscopy, to probe ion channel conformational dynamics in living cell by simultaneous and correlated measurements of real-time single-molecule FRET spectroscopic imaging with single-channel electric current recording. Our approach is particularly capable of resolving ion channel conformational change rate process when the channel is at its electrically off states and before the ion channel is activated, the so-called "silent time" when the electric current signals are at zero or background. We have probed NMDA (N-methyl-D-aspartate) receptor ion channel in live HEK-293 cell, especially, the single ion channel open-close activity and its associated protein conformational changes simultaneously. Furthermore, we have revealed that the seemingly identical electrically off states are associated with multiple conformational states. On the basis of our experimental results, we have proposed a multistate clamshell model to interpret the NMDA receptor open-close dynamics.

Fulltext

Journal of the American Chemical Society

Single-molecule patch-clamp FRET microscopy studies of NMDA receptor ion channel dynamics in living cells: revealing the multiple conformational states associated with a channel at its electrical off state

Molecular dynamics simulations of bilayers in a surfactant/co-surfactant/water system with explicit solvent molecules show formation of topologically distinct gel phases depending upon the bilayer composition. At low temperatures, the bilayers transform from the tilted gel phase, Lβ′, to the one dimensional (1D) rippled, Pβ′phase as the surfactant concentration is increased. More interestingly, we observe a two dimensional (2D) square phase at higher surfactant concentration which, upon heating, transforms to the gel Lβ′phase. The thickness modulations in the 1D rippled and square phases are asymmetric in two surfactant leaflets and the bilayer thickness varies by a factor of ∼2 between maximum and minimum. The 1D ripple consists of a thinner interdigitated region of smaller extent alternating with a thicker non-interdigitated region. The 2D ripple phase is made up of two superimposed square lattices of maximum and minimum thicknesses with molecules of high tilt forming a square lattice translated from the lattice formed with the thickness minima. Using Voronoi diagrams we analyze the intricate interplay between the area-per-head-group, height modulations and chain tilt for the different ripple symmetries. Our simulations indicate that composition plays an important role in controlling the formation of low temperature gel phase symmetries and rippling accommodates the increased area-per-head-group of the surfactant molecules. This journal is © the Partner Organisations 2014.

Soft Matter

Laterally structured ripple and square phases with one and two dimensional thickness modulations in a model bilayer system

We analyze the efficacy of an output as a resource from a universal quantum cloning machine in information processing tasks such as teleportation and dense coding. For this, we have considered the 3 ⊗ 3 dimensional systems. The output states are found to be NPT states for a certain range of machine parameters. Using the output state as an entangled resource, we also study the optimal fidelities of teleportation and capacities of dense coding protocols with respect to the machine parameters and make some interesting observations. Our work is motivated from the fact that the cloning output can be used as a resource in quantum information processing and adds a valuable dimension to the applications of cloning machines. © 2013 Springer Science+Business Media New York.

Quantum Information Processing

A cloned qutrit and its utility in information processing tasks

Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. © 2014 Elsevier B.V. All rights reserved.

Physica A: Statistical Mechanics and its Applications

Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

A catalytic highly diastereo- and enantioselective synthesis of 2,6-cis-substituted tetrahydropyrans was realized using a one-pot sequential catalysis involving Henry and oxa-Michael reactions. The nitroaldol products obtained in a highly enantioselective copper(II)-catalyzed Henry reaction between nitromethane and 7-oxo-hept-5-enals were subsequently treated with a catalytic amount of camphorsulfonic acid (CSA) to give the desired tetrahydropyran derivatives in excellent yields, diastereoselectivities (dr >99:1), and enantioselectivities (ee = 98-99%). The reaction can also be used for the high stereoselective synthesis of a cis-2,6-disubstituted morpholine. © 2013 American Chemical Society.

Organic Letters

Highly stereoselective synthesis of 2,6- cis -substituted tetrahydropyrans using a one-pot sequential catalysis

Chemical dynamics simulations, based on both an analytic potential energy surface (PES) and direct dynamics, were used to investigate the intrinsic non-RRKM dynamics of the Cl--CH3Br ion-dipole complex, an important intermediate in the Cl-+CH3Br SN2 nucleophilic substitution reaction. This intermediate may dissociate to Cl -+CH3Br or isomerize to the ClCH3-Br - ion-dipole complex. The decomposition of microcanonical ensembles of the Cl--CH3Br intermediate were simulated, and the ensuing populations vs. Time of the excited intermediate and Cl -+CH3Br and ClCH3-Br- products were fit with multi-exponential functions. The intrinsic non-RRKM dynamics is more pronounced for the simulations with the analytic PES than by direct dynamics, with the populations for the former and latter primarily represented by tri-and bi-exponential functions, respectively. For the analytic PES and direct dynamics simulations, the intrinsic non-RRKM dynamics is more important for the isomerization pathway to form ClCH3-Br- than for dissociation to Cl-+CH3Br. Since the decomposition probability of Cl--CH3Br is non-exponential, the Cl --CH3Br unimolecular rate constant depends on pressure, with both high and low pressure limits. The high pressure limit is the RRKM rate constant and for the simulations with the analytic PES the rate constant decreased by a factor of 3.0, 5.6, and 4.3 in going from the high to low pressure limit for total energies of 40, 60, and 80 kcal/mol. For the direct dynamics simulations these respective factors are 2.4, 1.4, and 1.2. A separable phase space model with intermolecular and intramolecular complexes describes some of the simulation results, but overall models advanced for intrinsic non-RRKM dynamics give incomplete representations of the intermediate and product populations vs. Time determined from the simulations. © by Oldenbourg Wissenschaftsverlag, München.

Zeitschrift fur Physikalische Chemie

Models for intrinsic Non-RRKM dynamics. Decomposition of the SN2 Intermediate Cl--CH3Br

In classical and quasiclassical trajectory chemical dynamics simulations, the atomistic dynamics of collisions, chemical reactions, and energy transfer are studied by solving the classical equations of motion. These equations require the potential energy and its gradient for the chemical system under study, and they may be obtained directly from an electronic structure theory. This article reviews such direct dynamics simulations. The accuracy of classical chemical dynamics is considered, with simulations highlighted for the F- + CH3OOH reaction and of energy transfer in collisions of CO2 with a perfluorinated self-assembled monolayer (F-SAM) surface. Procedures for interfacing chemical dynamics and electronic structure theory computer codes are discussed. A Hessian-based predictor-corrector algorithm and high-accuracy Hessian updating algorithm, for enhancing the efficiency of direct dynamics simulations, are described. In these simulations, an ensemble of trajectories is calculated which represents the experimental and chemical system under study. Algorithms are described for selecting the appropriate initial conditions for bimolecular and unimolecular reactions, gas-surface collisions, and initializing trajectories at transition states and conical intersections. Illustrative direct dynamics simulations are presented for the Cl- + CH3I SN2 reaction, unimolecular decomposition of the epoxy resin constituent CH3-NH-CH=CH-CH3 versus temperature, collisions and reactions of N-protonated diglycine with a F-SAM surface that has a reactive head group, and the product energy partitioning for the post-transition state dynamics of C2H5F → HF + C2H4 dissociation. © 2012 John Wiley &amp; Sons, Ltd.

Wiley Interdisciplinary Reviews: Computational Molecular Science

Direct chemical dynamics simulations: Coupling of classical and quasiclassical trajectories with electronic structure theory

Simulation results are presented for Xe atoms colliding with the {0001} surface of hexagonal ice (Ih) with incident energies EI of 3.88, 4.56, 5.71, and 6.50 eV and incident angles θI of 0, 25, 45, and 65. The TIP4P model was used for ice and ab initio calculations were performed to determine an accurate Xe/ice potential. Three types of events were observed; that is penetration below the ice surface and then desorption, penetration with Xe remaining in ice for times greater than 6 ps trajectory, and direct scattering without surface penetration. Surface penetration is most probable for normal (θI = 0) collisions and direct scattering becomes important for θI = 45 and 65. Penetration into ice becomes deeper as EI is increased. For θI = 0 and 25, all of the Xe atoms penetrate the surface and there is no direct scattering. The probability that the Xe atoms remain trapped below the surface increases as EI is increased and is more than 70% for θI = 0 and EI = 6.50 eV. For θI of 0 and 25 the trapped Xe atoms have a thermal energy of ∼25 meV at 6 ps and are close to being thermalized. For θI of 0 and 25 the average translational energy of the scattered Xe-atoms EF is highest when θF is very close to normal and then gradually decreases for higher values of θF. For θI of 45 and 65, EF is less than 250 meV for θF varying from 0 to 40, but for larger θF the value of EF rapidly increases to ∼1/3 to 1/2 of the collision energy. The probability of the subsurface Xe desorbing is greatest between 0 and 3 ps, with as much as 65% of the desorption occurring within a 1 ps interval of this time frame. Desorption is greatly diminished at longer times consistent with Xe becoming more thermalized. Simulation results using the TIP3P model for ice are similar to those above for the TIP4P model, with the caveat that trapping below the ice surface is more pronounced for the TIP3P model. The simulation results are in overall quite good agreement with experiment. © 2013 American Chemical Society.

Journal of Physical Chemistry C

Chemical dynamics simulations of high energy xenon atom collisions with the {0001} surface of hexagonal ice

We propose a three-qubit partially entangled set of states as a shared resource for optimal and faithful quantum information processing. We show that our states always violate the Svetlichny inequality, which is a Bell-type inequality whose violation is a sufficient condition for the confirmation of genuine three-qubit nonlocality. Although our states can be physically realized from the generalized Greenberger-Horne-Zeilinger (GGHZ) states using a simple quantum circuit, the nonlocal properties of the set are quite different from the GGHZ states. Instead, they are similar to the maximal slice (MS) states, even though our states are not locally equivalent to the MS states. Unlike other two- and three-qubit partially entangled states, quantum teleportation using our states results in faithful transmission of information with unit probability and unit fidelity by performing only standard measurements for the sender, controller, and receiver. We further demonstrate that dense coding also leads to the deterministic transfer of a maximum number of bits from the sender to the receiver. We also introduce witness operators able to experimentally detect the family of states introduced. This work highlights the importance of both the local as well as nonlocal aspects of quantum correlations in multiqubit systems. © 2013 American Physical Society.