From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Hydration dynamics of protein molecules in aqueous solution: Unity among diversity

Dielectric dispersion and NMRD experiments have revealed that a significant fraction of water molecules in the hydration shell of various proteins do not exhibit any slowing down of dynamics. This is usually attributed to the presence of the hydrophobic residues (HBR) on the surface, although HBRs alone cannot account for the large amplitude of the fast component. Solvation dynamics experiments and also computer simulation studies, on the other hand, repeatedly observed the presence of a non-negligible slow component. Here we show, by considering three well-known proteins (lysozyme, myoglobin and adelynate kinase), that the fast component arises partly from the response of those water molecules that are hydrogen bonded with the backbone oxygen (BBO) atoms. These are structurally and energetically less stable than those with the side chain oxygen (SCO) atoms. In addition, the electrostatic interaction energy distribution (EIED) of individual water molecules (hydrogen bonded to SCO) with side chain oxygen atoms shows a surprising two peak character with the lower energy peak almost coincident with the energy distribution of water hydrogen bonded to backbone oxygen atoms (BBO). This two peak contribution appears to be quite general as we find it for lysozyme, myoglobin and adenylate kinase (ADK). The sharp peak of EIED at small energy (at less than 2 k(B)T) for the BBO atoms, together with the first peak of EIED of SCO and the HBRs on the protein surface, explain why a large fraction (similar to 80%) of water in the protein hydration layer remains almost as mobile as bulk water Significant slowness arises only from the hydrogen bonds that populate the second peak of EIED at larger energy (at about 4 k(B)T). Thus, if we consider hydrogen bond interaction alone, only 15-20% of water molecules in the protein hydration layer can exhibit slow dynamics, resulting in an average relaxation time of about 5-10 ps. The latter estimate assumes a time constant of 20-100 ps for the slow component. Interestingly, relaxation of water molecules hydrogen bonded to back bone oxygen exhibit an initial component faster than the bulk, suggesting that hydrogen bonding of these water molecules remains frustrated. This explanation of the heterogeneous and non-exponential dynamics of water in the hydration layer is quantitatively consistent with all the available experimental results, and provides unification among diverse features.

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]

Phase inversion in agitated liquid-liquid dispersions: Anomalous effect of electrolyte

An imbalance between breakup and coalescence of drops in turbulent liquid-liquid dispersions leads to inversion of phases the dispersed phase becomes continuous and vice versa. An increase in the rate of coalescence of drops is expected to decrease the dispersed phase fraction at which inversion occurs. In the present work, we increased the rate of coalescence of drops by adding electrolyte to pure liquid-liquid dispersions. The experiments carried out for three representative liquid-liquid systems show that contrary to the expectation the addition of an electrolyte increases the dispersed phase fraction at which inversion occurs for both, oil-in-water and water-in-oil dispersions. The step-down experiments confirm that the addition of the electrolyte increases the rate of coalescence of drops in lean dispersions under the same conditions, thereby confirming an anomalous effect of the presence of an electrolyte on the stability of dispersions. (C) 2012 Elsevier Ltd. All rights reserved.

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

Synthesis of zero valent iron nanoparticles and application to removal of arsenic(III) and arsenic(V) from water

Recently nano scale zero valent iron particles (nZVI) have been considered as smart adsorbent for environmental and groundwater remediation. Although several synthetic methods are available for the preparation of nZVI, air stable nZVI are not available for remediation works. Further, challenges demand synthesis of nZVI without stabilizers and capping agents. A modified methodology for the synthesis of air stable nZVI has been developed without any capping agents and characterized by powder X-Ray Diffraction (XRD), Scanning Electron Microscopy Energy-dispersive X-Ray (SEM-EDS), Transmission Electron Microscopy (TEM) and X-Ray Photoelectron Spectroscopy (XPS). The results of the present study suggest that the synthetic nZVI are air-stable over a period of one year and consists of particles of 30-40 nm in diameter. Although a layer of less than 3 am thick oxide/hydroxide is observed by TEM and XPS, it appears to be due to oxidation of outer surface during analysis. Adsorption study has shown that the synthetic nZVI are more effective adsorbent than the commercial nZVI and can remove simultaneously arsenite As-III] and arsenate As-V] from water without prior reduction of As-V to As-III. The removal process is adsorptive rather than precipitative and the removal of As-III is greater than that of As-V.

1.5 V battery driven reduced graphene oxide-silver nanostructure coated carbon foam (rGO-Ag-CF) for the purification of drinking water

A porous carbon foam (CF) electrode modified with a reduced graphene oxide-Ag (rGO-Ag) nanocomposite has been fabricated to purify water. It can perform as an antibacterial device by killing pathogenic microbes with the aid of a 1.5 V battery, with very little power consumption. The device is recycled ten times with good performance for long term usage. It is shown that the device may be implemented as a fast water purifier to deactivate the pathogens in drinking water.

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.

Observed changes in Himalayan glaciers

In the Himalaya, large areas are covered by glaciers and seasonal snow. They are an important source of water for the Himalayan rivers. In this article, observed changes in glacial extent and mass balance have been discussed. Various studies suggest that most of the Himalayan glaciers are retreating though the rate of retreat varies from glacier to glacier, ranging from a few meters to almost 61 m/year, depending upon the terrain and meteorological parameters. In addition, mapping of almost 11,000 out of 40,000 sq. km of glaciated area, distributed in all major climatic zones of the Himalaya, suggests an almost 13% loss in area in the last 4-5 decades. The glacier mass balance observations and estimates made using methods like field, AAR, ELA and geodetic measurements, suggest a significant increase in mass wastage of Himalayan glaciers in the last 3-4 decades. In the last four decades loss in glacial ice has been estimated at 19 +/- 7 m. This suggests loss of 443 +/- 136 Gt of glacial mass out of a total 3600-4400 Gt of glacial stored water in the Indian Himalaya. This study has also shown that mean loss in glacier mass in the Indian Himalaya is accelerated from -9 +/- 4 to -20 +/- 4 Gt/year between the periods 1975-85 and 2000-2010. The estimate of glacial stored water in the Indian Himalaya is based on glacier inventory on a 1 : 250,000 scale and scaling methods; therefore, we assume uncertainties to be large.

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.

Treatment of gray water using anaerobic biofilms created on synthetic and natural fibers

Gray water treatment and reuse is an immediate option to counter the upcoming water shortages in various parts of world, especially urban areas. Anaerobic treatment of gray water in houses is an alternative low cost, low energy and low sludge generating option that can meet this challenge. Typical problems of fluctuating VFA, low pH and sludge washout at low loading rates with gray water feedstock was overcome in two chambered anaerobic biofilm reactors using natural fibers as the biofilm support. The long term performance of using natural fiber based biofilms at moderate and low organic loading rates (OLR) have been examined. Biofilms raised on natural fibers (coir, ridge-gourd) were similar to that of synthetic media (PVC, polyethylene) at lower OLR when operated in pulse fed mode without effluent recirculation and achieved 80-90% COD removal at HRT of 2 d showing a small variability during start-up. Confocal microscopy of the biofilms on natural fibers indicated thinner biofilms, dense cell architecture and low extra cellular polymeric substances (EPS) compared to synthetic supports and this is believed to be key factor in high performance at low OLR and low strength gray water. Natural fibers are thus shown to be an effective biofilm support that withstand fluctuating characteristic of domestic gray water. (C) 2013 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.

A modeling study of the processes of surface salinity seasonal cycle in the Bay of Bengal

In response to the Indian Monsoon freshwater forcing, the Bay of Bengal exhibits a very strong seasonal cycle in sea surface salinity (SSS), especially near the mouths of the Ganges-Brahmaputra and along the east coast of India. In this paper, we use an eddy-permitting (similar to 25 km resolution) regional ocean general circulation model simulation to quantify the processes responsible for this SSS seasonal cycle. Despite the absence of relaxation toward observations, the model reproduces the main features of the observed SSS seasonal cycle, with freshest water in the northeastern Bay, particularly during and after the monsoon. The model also displays an intense and shallow freshening signal in a narrow (similar to 100 km wide) strip that hugs the east coast of India, from September to January, in good agreement with high-resolution measurements along two ships of opportunity lines. The mixed layer salt budget confirms that the strong freshening in the northern Bay during the monsoon results from the Ganges-Brahmaputra river discharge and from precipitation over the ocean. From September onward, the East India Coastal Current transports this freshwater southward along the east coast of India, reaching the southern tip of India in November. The surface freshening results in an enhanced vertical salinity gradient that increases salinity of the surface layer by vertical processes. Our results reveal that the erosion of the freshwater tongue along the east coast of India is not driven by northward horizontal advection, but by vertical processes that eventually overcome the freshening by southward advection and restore SSS to its premonsoon values. The salinity-stratified barrier layer hence only acts as a ``barrier'' for vertical heat fluxes, but is associated with intense vertical salt fluxes in the Bay of Bengal.

Graphene Oxide-MnFe2O4 Magnetic Nanohybrids for Efficient Removal of Lead and Arsenic from Water

We show that the hybrids of single-layer graphene oxide with manganese ferrite magnetic nanoparticles have the best adsorption properties for efficient removal of Pb(II), As(III), and As(V) from contaminated water. The nanohybrids prepared by coprecipitation technique were characterized using atomic force and scanning electron microscopies, Fourier transformed infrared spectroscopy, Raman spectroscopy, X-ray diffraction, and surface area measurements. Magnetic character of the nanohybrids was ascertained by a vibrating sample magnetometer. Batch experiments were carried out to quantify the adsorption kinetics and adsorption capacities of the nanohybrids and compared with the bare nanoparticles of MnFe2O4. The adsorption data from our experiments fit the Langmuir isotherm, yielding the maximum adsorption capacity higher than the reported values so far. Temperature-dependent adsorption studies have been done to estimate the free energy and enthalpy of adsorption. Reusability, ease of magnetic separation, high removal efficiency, high surface area, and fast kinetics make these nanohybrids very attractive candidates for low-cost adsorbents for the effective coremoval of heavy metals from contaminated water.

Seleno-Nucleobases and Their Water-Soluble Ruthenium-Arene Half-Sandwich Complexes: Chemistry and Biological Activity

Half-sandwich organometallic ruthenium complexes of seleno-nucleobases, 3 and 4, were synthesized and characterized. The structures of both complexes were determined by X-ray crystallography and are the first crystal structures of ruthenium complexes with seleno-nucleobases. Interestingly, 3 self-assembles aided by adventitious water in DMF to give a tetranuclear square 3a center dot 6H(2)O. Complex 4 is active against Jurkat and Molt-4 cell lines but inactive against the K562 cell line, whereas 3 is completely inactive against all three cell lines. The free ligand 6-selenopurine (1) and 6-selenoguanine (2) are highly active against these cell lines. Compound 2, like its thio analogue, is unstable under UVA light, whereas 4 is stable under similar conditions, which suggests that the ruthenium complex could reduce problems associated with the instability of the free ligand, 2, under irradiation.