Structural Transformations, Composition Anomalies and a Dramatic Collapse of Linear Polymer Chains in Dilute Ethanol-Water Mixtures

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) approximate to 0.06-0.10 (that amounts to a volume fraction of 0.17-0.26, which is a significant range!). The bicontinuous phase is formed by aggregation of ethanol molecules, resulting in a weak phase transition whose nature is elucidated. We find that the microheterogeneous structure of the mixture gives rise to a pronounced nonmonotonic composition dependence of local compressibility and nonmonotonic dependence in the peak value of the radial distribution function of ethyl groups. A multidimensional free energy surface of pair association is shown to provide a molecular explanation of the known negative excess partial volume of ethanol in terms of parallel orientation and hence better packing of the ethyl groups in the mixture due to hydrophobic interactions. The energy distribution of the ethanol molecules indicates additional energy decay channels that explain the excess sound attenuation coefficient in aqueous alcohol mixtures. We studied the dependence of the solvation of a linear polymer chain on the composition of the water-ethanol solvent. We find that there is a sudden collapse of the polymer at x(eth) approximate to 0.05-a phenomenon which we attribute to the formation of the microheterogeneous structures in the binary mixture at low ethanol concentrations. Together with recent single molecule pulling experiments, these results provide new insight into the behavior of polymer chain and foreign solutes, such as enzymes, in aqueous binary mixtures.

Relaxation and jump dynamics of water at the mica interface

The orientational relaxation dynamics of water confined between mica surfaces is investigated using molecular dynamics simulations. The study illustrates the wide heterogeneity that exists in the dynamics of water adjacent to a strongly hydrophilic surface such as mica. Analysis of the survival probabilities in different layers is carried out by normalizing the corresponding relaxation times with bulk water layers of similar thickness. A 10-fold increase in the survival times is observed for water directly in contact with the mica surface and a non-monotonic variation in the survival times is observed moving away from the mica surface to the bulk-like interior. The orientational relaxation time is highest for water in the contact layer, decreasing monotonically away from the surface. In all cases the ratio of the relaxation times of the 1st and 2nd rank Legendre polynomials of the HH bond vector is found to lie between 1.5 and 1.9 indicating that the reorientational relaxation in the different water layers is governed by jump dynamics. The orientational dynamics of water in the contact layer is particularly novel and is found to undergo distinct two-dimensional hydrogen bond jump reorientational dynamics with an average waiting time of 4.97 ps. The waiting time distribution is found to possess a long tail extending beyond 15 ps. Unlike previously observed jump dynamics in bulk water and other surfaces, jump events in the mica contact layer occur between hydrogen bonds formed by the water molecule and acceptor oxygens on the mica surface. Despite slowing down of the water orientational relaxation near the surface, life-times of water in the hydration shell of the K ion are comparable to that observed in bulk salt solutions. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4717710]

Analysis of Parameter Values in the van der Waals and Platteeuw Theory for Methane Hydrates Using Monte Carlo Molecular Simulations

The van der Waals and Platteuw (vdVVP) theory has been successfully used to model the thermodynamics of gas hydrates. However, earlier studies have shown that this could be due to the presence of a large number of adjustable parameters whose values are obtained through regression with experimental data. To test this assertion, we carry out a systematic and rigorous study of the performance of various models of vdWP theory that have been proposed over the years. The hydrate phase equilibrium data used for this study is obtained from Monte Carlo molecular simulations of methane hydrates. The parameters of the vdWP theory are regressed from this equilibrium data and compared with their true values obtained directly from simulations. This comparison reveals that (i) methane-water interactions beyond the first cage and methane-methane interactions make a significant contribution to the partition function and thus cannot be neglected, (ii) the rigorous Monte Carlo integration should be used to evaluate the Langmuir constant instead of the spherical smoothed cell approximation, (iii) the parameter values describing the methane-water interactions cannot be correctly regressed from the equilibrium data using the vdVVP theory in its present form, (iv) the regressed empty hydrate property values closely match their true values irrespective of the level of rigor in the theory, and (v) the flexibility of the water lattice forming the hydrate phase needs to be incorporated in the vdWP theory. Since methane is among the simplest of hydrate forming molecules, the conclusions from this study should also hold true for more complicated hydrate guest molecules.

A Series of Trifacial Pd6 Molecular Barrels with Porphyrin Walls

Three new nanoscopic trigonal prisms, (tmen)6Pd6(H2L)3](NO3)12 (1), (Meen)6Pd6(H2L)3](NO3)12 (2), and (2,2'-bipy)6Pd6(H2L)3](NO3)12 (3), have been synthesized in excellent yields through single-step metalligand-coordination-driven self-assembly using 5,10,15,20-tetrakis(3-pyridyl)porphyrin (H2L) as a donor and cis-blocked PdII 90 degrees acceptors. These complexes were fully characterized by spectroscopic studies and single-crystal X-ray diffraction. All of these barrels quantitatively bind ZnII ions in the N4 pockets of the porphyrin walls at room temperature. Their corresponding zinc-embedded complexes, (tmen)6Pd6(ZnL)3](NO3)12 (1?a), (Meen)6Pd6(ZnL)3](NO3)12 (2?a), and (2,2'-bipy)6Pd6(ZnL)3](NO3)12 (3?a), were synthesized under ambient conditions by the post-synthetic binding of ZnII ions into the H2N4 pockets of the porphyrin walls of these complexes. These zinc-embedded complexes were characterized by electronic absorption, fluorescence emission, 1H NMR spectroscopy, as well as elemental analysis. Complexes 13 exhibited considerable microporosity in their solid state. Complex 1 was an efficient adsorbent for nitrogen gas and EtOH, MeOH, and water vapors.

Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Effect of pressure on the ionic conductivity of Li+ and Cl- ions in water

A molecular dynamics simulation study of aqueous solution of LiCl is reported as a function of pressure. Experimental measurements of conductivity of Li+ ion as a function of pressure shows an increase in conductivity with pressure. Our simulations are able to reproduce the observed trend in conductivity. A number of relevant properties have been computed in order to understand the reasons for the increase in conductivity with pressure. These include radial distribution function, void and neck distributions, hydration or coordination numbers, diffusivity, velocity autocorrelation functions, angles between ion-oxygen and dipole of water as well as OH vector, mean residence time for water in the hydration shell, etc. These show that the increase in pressure acts as a structure breaker. The decay of the self part of the intermediate scattering function at small wave number k shows a bi-exponential decay at 1 bar which changes to single exponential decay at higher pressures. The k dependence of the ratio of the self part of the full width at half maximum of the dynamic structure factor to 2Dk(2) exhibits trends which suggest that the void structure of water is playing a role. These support the view that the changes in void and neck distributions in water can account for changes in conductivity or diffusivity of Li+ with pressure. These results can be understood in terms of the levitation effect. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4756909]

Simulation of Influence of Bilayer Melting on Dynamics and Thermodynamics of Interfacial Water

We investigate the effect of bilayer melting transition on thermodynamics and dynamics of interfacial water using molecular dynamics simulation with the two-phase thermodynamic model. We show that the diffusivity of interface water depicts a dynamic crossover at the chain melting transition following an Arrhenius behavior until the transition temperature. The corresponding change in the diffusion coefficient from the bulk to the interface water is comparable with experimental observations found recently for water near 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles Phys. Chem. Chem. Phys. 13, 7732 (2011)]. The entropy and potential energy of interfacial water show distinct changes at the bilayer melting transition, indicating a strong correlation in the thermodynamic state of water and the accompanying first-order phase transition of the bilayer membrane. DOI: 10.1103/PhysRevLett.110.018303

Ionomer based blend as water vapor barrier material for organic device encapsulation

Blends of poly (ethylene-co-methacrylic acid) (PEMA) and poly (vinyl alcohol-co-ethylene) (EVOH) were studied for encapsulating Schottky structured organic devices. A calcium degradation test was used to determine water vapor transmission rates and to determine the moisture barrier performance of neat and blend films. Moisture barrier analysis for the neat and blend compositions was discussed concerning the interactions in the blend, diffusivity of water molecules through the unit cell systems, and the occupiable free volumes available in the unit cells using molecular dynamics simulations. The experimental results of water vapor permeation were correlated with diffusion behavior predicted from molecular dynamics simulations results. The effectiveness of the blend as a suitable barrier material in increasing the lifetime of an encapsulated Schottky structured organic device was determined.

EFFECT OF CORE-SHELL STRUCTURE OF HYDROGEL BEADS ON THE THRESHOLD CONCENTRATION OF WATER FOR SWELLING AND ITS PH SENSITIVITY

In this paper we investigate the effect of core-shell structure of Sodium Alginate based hydrogel beads and their size on certain activation threshold concentration of water for applications in swelling and pH sensing. This type of hydrogel experiences diffusive pressure due to transport of certain free charges across its interface with a solvent or electrolyte. This process is essentially a dynamic equilibrium of the electric force field, stress in the polymeric network with cage like structure and molecular diffusion including phase transformation due to pressure imbalance between the hydrogel and its surroundings. The effect of pH of the solvant on the swelling rate of these beads has been studied experimentally. A mathematical model of the swelling process has been developed by considering Nernst-Planck equation representing the migration of mobile ions and Er ions, Poisson equation representing the equilibrium of the electric field and mechanical field equation representing swelling of the gel. An attempt has been made to predict the experimentally observed phenomena using these numerical simulations. It is observed experimentally that certain minimum concentration called activation threshold concentration of the water molecules must be present in the hydrogel in order to activate the swelling process. For the required activation threshold concentration of water in the beads, the pH induced change in the rate of swelling is also investigated. This effect is analyzed for various different core-shell structures of the beads.

Solvent Sensitivity of Protein Unfolding: Dynamical Study of Chicken Villin Headpiece Subdomain in Water Ethanol Binary Mixture

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding of a small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective of this work is to explore the sensitivity of protein unfolding dynamics toward increasing concentration of the cosolvent and unravel essential features of intermediates formed in search of a dynamical pathway toward unfolding. In water ethanol binary mixtures, HP-36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as similar to 600 K to denature in pure aqueous solvent. However, an interesting course of pathway is observed to be followed in the process, guided by the formation of unique intermediates. The first step of unfolding is essentially the separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely, Phe-7, Phe-11, and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. The initial steps are similar to temperature-induced unfolding as well as chemical unfolding using DMSO as cosolvent. Subsequent unfolding steps follow a unique path. As water-ethanol shows composition-dependent anomalies, so do the details of unfolding dynamics. With an increase in cosolvent concentration, different partially unfolded intermediates are found to be formed. This is reflected in a remarkable nonmonotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states can be attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol. We further quantify the local dynamics of unfolding by using a Marcus-type theory.

Selective and Efficient Detection of Nitro-Aromatic Explosives in Multiple Media including Water, Micelles, Organogel, and Solid Support

Selective detection of nitro-aromatic compounds (NACs) at nanomolar concentration is achieved for the first time in multiple media including water, micelles or in organogels as well as using test strips. Mechanism of interaction of NACs with highly fluorescent p-phenylenevinylene-based molecules has been described as the electron transfer phenomenon from the electron-rich chromophoric probe to the electron deficient NACs. The selectivity in sensing is guided by the pK(a) of the probes as well as the NACs under consideration. TNP-induced selective gel-to-sol transition in THF medium is also observed through the reorganization of molecular self-assembly and the portable test trips are made successfully for rapid on-site detection purpose.

Calculation of Chemical Potentials and Occupancies in Clathrate Hydrates through Monte Carlo Molecular Simulations

The flexibility of the water lattice in clathrate hydrates and guest-guest interactions has been shown in previous studies to significantly affect the values of the thermodynamic properties, such as chemical potentials and free energies. Here we describe methods for computing occupancies, chemical potentials, and free energies that account for the flexibility of water lattice and guest-guest interactions in the hydrate phase. The methods are validated for a wide variety of guest molecules, such as methane, ethane, carbon dioxide, and tetrahydrodfuran by comparing the predicted occupancy values of guest molecules with those obtained from isothermal isobaric semigrand Monte Carlo simulations. The proposed methods extend the van der Waals and Platteuw theory for clathrate hydrates, and the Langmuir constant is calculated based on the structure of the empty hydrate lattice. These methods in combination with development of advanced molecular models for water and guest molecules should lead to a more thermodynamically consistent theory for clathrate hydrates.

An Efficient Probe for Rapid Detection of Cyanide in Water at Parts per Billion Levels and Naked-Eye Detection of Endogenous Cyanide

A new molecular probe based on an oxidized bis-indolyl skeleton has been developed for rapid and sensitive visual detection of cyanide ions in water and also for the detection of endogenously bound cyanide. The probe allows the naked-eye detection of cyanide ions in water with a visual color change from red to yellow ((max)=80nm) with the immediate addition of the probe. It shows high selectivity towards the cyanide ion without any interference from other anions. The detection of cyanide by the probe is ratiometric, thus making the detection quantitative. A Michael-type addition reaction of the probe with the cyanide ion takes place during this chemodosimetric process. In water, the detection limit was found to be at the parts per million level, which improved drastically when a neutral micellar medium was employed, and it showed a parts-per-billion-level detection, which is even 25-fold lower than the permitted limits of cyanide in water. The probe could also efficiently detect the endogenously bound cyanide in cassava (a staple food) with a clear visual color change without requiring any sample pretreatment and/or any special reaction conditions such as pH or temperature. Thus the probe could serve as a practical naked-eye probe for in-field experiments without requiring any sophisticated instruments.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1 `) in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH(2)group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.