ALBERT

Description: This work investigates the computational design of a pH induced protein fold switch based on a self-consistent mean-field approach by identifying the ensemble averaged characteristics of sequences that encode a fold switch. The primary challenge to balance the alternative sets of interactions present in both target structures is overcome by simultaneously optimizing two foldability criteria corresponding to two target structures. The change in pH is modeled by altering the residual charge on the amino acids. The energy landscape of the fold switch protein is found to be double funneled. The fold switch sequences stabilize the interactions of the sites with similar relative surface accessibility in both target structures. Fold switch sequences have low sequence complexity and hence lower sequence entropy. The pH induced fold switch is mediated by attractive electrostatic interactions rather than hydrophobic-hydrophobic contacts. This study may provide valuable insights to the design of fold switch proteins.

Description: The rheology and transport dynamics of the randomly hyperbranched polymers with excluded volume interactions are investigated within the tenets of the Rouse-Zimm theory. The excluded volume interactions typically account for an effective co-volume between the nearest non-bonded monomers, modeled through a delta function pseudopotential, while the strength of such interactions is evaluated from the possible geometric orientations of the bonds. The mechanical moduli are primarily determined by the smaller eigenvalues corresponding to the collective modes. These modes with smaller relaxation rates increase with the decrease in the strength of excluded volume interaction parameter, while the local modes with higher relaxation rates remain unaffected. The internal structure of the randomly hyperbranched polymer is reflected in the intermediate frequency regime of the mechanical relaxation moduli, where the characteristic power-law behavior implies the fractal nature of the randomly hyperbranched polymers. The length of this power-law region increases either with the decrease in the strength of excluded volume interactions or with the increase in the number of shells of the randomly hyperbranched polymer, while the numerical values of the power-law exponents are strongly affected by the strength of excluded volume interactions. Intrinsic viscosity increases linearly for lower values of the excluded volume interaction parameters, while depicting a non-linear trend at higher strengths of excluded volume interactions. The randomly hyperbranched polymers are relatively more compact compared to the star polymer but less compact than that of dendrimers with the same number of monomers and same strength of excluded volume interactions. The values of the scaling exponents of the diffusion coefficient increase with decreasing the strength of excluded volume interactions. The scaling exponents of the diffusion coefficient of randomly hyperbranched polymers calculated with excluded volume exactly match with the earlier experimental results for hyperbranched polyglycidols in poly(vinyl alcohol) solutions.

Description: A detailed investigation on the molecular dynamics of ionic deep eutectic solvents (acetamide + lithium nitrate/sodium thiocyanate) is reported. The study was carried out employing dielectric relaxation spectroscopy covering seven decades in frequency (10 −1 -10 6 Hz) and in a wide temperature range from 373 K down to 173 K, accessing the dynamic observables both in liquid and glassy state. The dielectric response of the ionic system has been presented in the dynamic window of modulus formalism to understand the conductivity relaxation and its possible connection to the origin of localized motion. Two secondary relaxation processes appear below glass transition temperature. Our findings provide suitable interpretation on the nature of secondary Johari-Goldstein process describing the ion translation and orientation of dipoles in a combined approach using Ngai’s coupling model. A nearly constant loss feature is witnessed at shorter times/lower temperatures. We also discuss the ac conductivity scaling behavior using Summerfield approach and random free energy barrier model which establish the time-temperature superposition principle. These experimental observations have fundamental importance on theoretical elucidation of the conductivity relaxation and glass transition phenomena in molten ionic conductors.

Description: We have performed steady state UV-visible absorption and time-resolved fluorescence measurements and computer simulations to explore the cosolvent mole fraction induced changes in structural and dynamical properties of water/dioxane (Diox) and water/tetrahydrofuran (THF) binary mixtures. Diox is a quadrupolar solvent whereas THF is a dipolar one although both are cyclic molecules and represent cycloethers. The focus here is on whether these cycloethers can induce stiffening and transition of water H-bond network structure and, if they do, whether such structural modification differentiates the chemical nature (dipolar or quadrupolar) of the cosolvent molecules. Composition dependent measured fluorescence lifetimes and rotation times of a dissolved dipolar solute (Coumarin 153, C153) suggest cycloether mole-fraction (X THF/Diox ) induced structural transition for both of these aqueous binary mixtures in the 0.1 ≤ X THF/Diox ≤ 0.2 regime with no specific dependence on the chemical nature. Interestingly, absorption measurements reveal stiffening of water H-bond structure in the presence of both the cycloethers at a nearly equal mole-fraction, X THF/Diox ∼ 0.05. Measurements near the critical solution temperature or concentration indicate no role for the solution criticality on the anomalous structural changes. Evidences for cycloether aggregation at very dilute concentrations have been found. Simulated radial distribution functions reflect abrupt changes in respective peak heights at those mixture compositions around which fluorescence measurements revealed structural transition. Simulated water coordination numbers (for a dissolved C153) and number of H-bonds also exhibit minima around these cosolvent concentrations. In addition, several dynamic heterogeneity parameters have been simulated for both the mixtures to explore the effects of structural transition and chemical nature of cosolvent on heterogeneous dynamics of these systems. Simulated four-point dynamic susceptibility suggests formation of clusters inducing local heterogeneity in the solution structure.

Description: The paper reports a detailed simulation study on collective reorientational relaxation, cooperative hydrogen bond (H-bond) fluctuations, and their connections to dielectric relaxation (DR) in deep eutectic solvents made of acetamide and three uni-univalent electrolytes, lithium nitrate (LiNO 3 ), lithium bromide (LiBr), and lithium perchlorate (LiClO 4 ). Because cooperative H-bond fluctuations and ion migration complicate the straightforward interpretation of measured DR timescales in terms of molecular dipolar rotations for these conducting media which support extensive intra- and inter-species H-bonding, one needs to separate out the individual components from the overall relaxation for examining the microscopic origin of various timescales. The present study does so and finds that reorientation of ion-complexed acetamide molecules generates relaxation timescales that are in sub-nanosecond to nanosecond range. This explains in molecular terms the nanosecond timescales reported by recent giga-Hertz DR measurements. Interestingly, the simulated survival timescale for the acetamide-Li + complex has been found to be a few tens of nanosecond, suggesting such a cation-complexed species may be responsible for a similar timescale reported by mega-Hertz DR measurements of acetamide/potassium thiocyanate deep eutectics near room temperature. The issue of collective versus single particle relaxation is discussed, and jump waiting time distributions are determined. Dependence on anion-identity in each of the cases has been examined. In short, the present study demonstrates that assumption of nano-sized domain formation is not required for explaining the DR detected nanosecond and longer timescales in these media.

Description: The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic. The excited state lifetime of C153 decreases in MFE and DFE as compared to ETH, whereas in TFE, it increases as compared to MFE and DFE. Molecular dynamics simulation reveals that the carbon terminal away from the OH group of fluorinated ETHs has a preferential orientation near the perfluoro (CF 3 ) group of C153. In MFE and DFE, the CF 3 group of C153 prefers to have a CF 2 —F⋯H —(CHF) type of electrostatic interaction over CF 2 —F⋯F —(CH 2 ) kind of dispersion interaction which increases the rate of nonradiative decay, probably due to the electrostatic nature of the CF 2 —F⋯H —(CHF) hydrogen bond. On the other hand, in TFE, C—F⋯ F—C type of dispersion interaction, also known as fluorous interaction, takes place between the CF 3 groups of C153 and TFE which decreases the rate of nonradiative rate as compared to MFE and DFE, leading to the increased lifetime of C153 in TFE. Photophysical and MD simulation studies clearly depict that the structural organization of solvents and their interaction with the fluorocarbon group are crucial factors for the photophysical behavior of the fluorocarbon containing molecules.

Description: Micro-heterogeneity in aqueous solutions of 2-butoxyethanol (BE), a system with closed loop miscibility gap, has been explored via absorption and time-resolved fluorescence measurements of a dissolved dipolar solute, coumarin 153 (C153), in the water-rich region at various BE mole fractions (0 ≤ X BE ≤ 0.25) in the temperature range, 278 ≤ T/K ≤ 320. Evidences for both alcohol-induced H-bond strengthening and subsequent structural transition of H-bond network have been observed. Analyses of steady state and time-resolved spectroscopic data for these aqueous mixtures and comparisons with the results for aqueous solutions of ethanol and tertiary butanol indicate that alcohol aggregation in BE/water mixtures is driven by hydrophobic interaction with no or insignificant role for criticality-driven concentration fluctuations preceding phase separation. Excitation energy dependence of fluorescence emission of C153 confirms formation of aggregated structures at very low BE mole fractions. No asymptotic critical power law dependence for relaxation rates of the type, k ∝ (|T − T c |/T c ) γ , with γ denoting universal critical constant, has been observed for both solute’s rotational relaxation and population relaxation rates in these mixtures upon either approaching to critical concentration or critical temperature. Estimated activation energies for rotational relaxation rate of C153 and solution viscosity have been found to follow each other with no abrupt changes in either of them at any mixture composition. In addition, measured C153 rotation times at various compositions and temperatures reflect near-hydrodynamic viscosity coupling through the dependence, 〈τ r 〉 ∝ (η/T) p , with p = 0.8-1.0, suggesting solute’s orientational relaxation dynamics being, on an average, temporally homogeneous.

Description: Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH 3 CONH 2 ) and urea (NH 2 CONH 2 ) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions ( f ) for the mixture [ f CH 3 CONH 2 + (1 − f )NH 2 CONH 2 ] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α 2 ) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al. , J. Chem. Phys. 140 , 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Description: In this study, we have investigated the ion concentration dependent collective dynamics in two series of deep eutectic solvent (DES) systems by femtosecond Raman-induced Kerr effect spectroscopy, as well as some physical properties, e.g., shear viscosity ( η ), density ( ρ ), and surface tension ( γ ). The DES systems studied here are [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] and [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] with f = 0, 0.2, 0.4, 0.6, 0.8, and 1.0. γ of these DES systems shows near insensitivity to f , while ρ shows a moderate dependence on f . Interestingly, η exhibits a strong dependence on f . In the low-frequency Kerr spectra, obtained via the Fourier transform of the collected Kerr transients, a characteristic band at ∼70 cm −1 is clear in [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] DES especially at the larger f . The band is attributed to the intermolecular hydrogen bond of acetamide. Because of less depolarized Raman activities of intermolecular/interionic vibrational motions, which are mostly translational (collision-induced or interaction-induced) motions, of spherical ions, the intermolecular hydrogen-bonding band is clearly observed. In contrast, the intermolecular hydrogen-bonding band is buried in the other intermolecular/interionic vibrational motions, which includes translational and reorientational (librational) motions and their cross-terms, in [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] system. The first moment ( M 1 ) of the intermolecular/interionic vibrational band in these DES systems is much higher than that in typical neutral molecular liquids and shows a weak but contrasting dependence on the bulk parameter γ / ρ . The time constants for picosecond overdamped Kerr transients in both the DES systems, which are obtained on the basis of the analysis fitted by a triexponential function, are rather insensitive to f for both the DES systems, but all the three time constants (fast: ∼1–3 ps; intermediate: ∼7–20 ps; and slow: ∼100 ps) are different between the [0.78CH 3 CONH 2 + 0.22{ f  LiBr + (1 – f  )LiNO 3 }] and [0.75CH 3 CONH 2 + 0.25{ f  KSCN + (1 – f  )NaSCN}] systems. These results indicate that the intermolecular/interionic interactions in DES systems is strongly influenced by the ionic species present in these DES systems.

Description: A semi-molecular theory for studying composition dependent Stokes shift dynamics of a dipolar solute in binary mixtures of (non-dipolar ionic liquid + common dipolar solvent) is developed here. The theory provides microscopic expressions for solvation response functions in terms of static and dynamic structure factors of the mixture components and solute-solvent static correlations. In addition, the theory provides a framework for examining the interrelationship between the time dependent solvation response in and frequency dependent dielectric relaxation of a binary mixture containing electrolyte. Subsequently, the theory has been applied to predict ionic liquid (IL) mole fraction dependent dynamic Stokes shift magnitude and solvation energy relaxation for a dipolar solute, C153, in binary mixtures of an ionic liquid, trihexyltetradecylphosphonium chloride ([P 14,666 ][Cl]) with a common dipolar solvent, methanol (MeOH). In the absence of suitable experimental data, necessary input parameters have been obtained from approximate methods. Dynamic shifts calculated for these mixtures exhibit a linear increase with IL mole fraction for the most part of the mixture composition, stressing the importance of solute-IL dipole-ion interaction. Average solvation rates, on the other hand, show a nonlinear IL mole fraction dependence which is qualitatively similar to what has been observed for such binary mixtures with imidazolium (dipolar) ILs. These predictions should be re-examined in suitable experiments.