Excited state properties of formamide in water solution: An ab initio study

We present ab initio quantum calculation of the optical properties of formamide in vapor phase and in water solution. We employ time dependent density functional theory for the isolated molecule and many-body perturbation theory methods for the system in solution. An average over several molecular dynamics snapshots is performed to take into account the disorder of the liquid. We find that the excited stateproperties of the gas-phase formamide are strongly modified by the presence of the water solvent: the geometry of the molecule is distorted and the electronic and optical properties are severely modified. The important interaction among the formamide and the water molecules forces us to use fully quantum methods for the calculation of the excited stateproperties of this system. The excitonic wave function is localized both on the solute and on part of the solvent.

Microscopic and Spectroscopic Methods for Probing the Clay Water Interface

Clay minerals have a fundamental importance in many processes in soils and sediments such as the bioavailability of nutrients, water retention, the adsorption of common pollutants, and the formation of an impermeable barrier upon swelling. Many of the properties of clay minerals are due to the unique environment present at the clay mineral/water interface. Traditional techniques such as X-ray diffraction (XRD) and absorption isotherms have provided a wealth of information about this interface but have suffered from limitations. The methods and results presented herein are designed to yield new experimental information about the clay mineral/water interface.A new method of studying the swelling dynamics of clay minerals was developed using in situ atomic force microscopy (AFM). The preliminary results presented here demonstrate that this technique allows one to study individual clay mineral unit layers, explore the natural heterogeneities of samples, and monitor swelling dynamics of clay minerals in real time. Cation exchange experiments were conducted monitoring the swelling change of individual nontronite quasi-crystals as the chemical composition of the surrounding environment was manipulated several times. A proof of concept study has shown that the changes in swelling are from the exchange of interlayer cations and not from the mechanical force of replacing the solution in the fluid cell. A series of attenuated total internal reflection Fourier transform infrared spectroscopy (ATR-FTIR) experiments were performed to gain a better understanding of the organization of water within the interlayer region of two Fe-bearing clay minerals. These experiments made use of the Subtractive Kramers-Kronig (SKK) Transform and the calculation of difference spectra to obtain information about interfacial water hidden within the absorption bands of bulk water. The results indicate that the reduction of structural iron disrupts the organization of water around a strongly hydrated cation such as sodium as the cation transitions from an outer-sphere complex with the mineral surface to an inner-sphere complex. In the case of a less strongly hydrated cation such as potassium, reduction of structural iron actually increases the ordering of water molecules at the mineral surface. These effects were only noticed with the reduction of iron in the tetrahedral sheet close to the basal surface where the increased charge density is localized closer to the cations in the interlayer.

Active water in protein-protein communication within the membrane: the case of SRII-HtrII signal relay.

We detect internal water molecules in a membrane-embedded receptor-transducer complex and demonstrate water structure changes during formation of the signaling state. Time-resolved FTIR spectroscopy reveals stimulus-induced repositioning of one or more structurally active water molecules to a significantly more hydrophobic environment in the signaling state of the sensory rhodopsin II (SRII)-transducer (HtrII) complex. These waters, distinct from bound water molecules within the SRII receptor, appear to be in the middle of the transmembrane interface region near the Tyr199(SRII)-Asn74(HtrII) hydrogen bond. We conclude that water potentially plays an important role in the SRII --> HtrII signal transfer mechanism in the membrane's hydrophobic core.

Understanding measured water rotational temperatures and column densities in the very innermost coma of Comet 73P/Schwassmann–Wachmann 3 B

Direct sublimation of a comet nucleus surface is usually considered to be the main source of gas in the coma of a comet. However, evidence from a number of comets including the recent spectacular images of Comet 103P/Hartley 2 by the EPOXI mission indicates that the nucleus alone may not be responsible for all, or possibly at times even most, of the total amount of gas seen in the coma. Indeed, the sublimation of icy grains, which have been injected into the coma, appears to constitute an important source. We use the fully-kinetic Direct Simulation Monte Carlo model of Tenishev et al. (Tenishev, V.M., Combi, M.R., Davidsson, B. [2008]. Astrophys. J., 685, 659−677; Tenishev, V.M., Combi, M.R., Rubin, M. [2011]. Astrophys. J., 732) to reproduce the measurements of column density and rotational temperature of water in Comet 73P-B/Schwassmann–Wachmann 3 obtained with a very high spatial resolution of ∼30 km using IRCS/Subaru in May 2006 (Bonev, B.P., Mumma, M.J., Kawakita, H., Kobayashi, H., Villanueva, G.L. [2008]. Icarus, 196, 241−248). For gas released solely from the cometary nucleus at a heliocentric distance of 1 AU, modeled rotational temperatures start at 110 K close to the surface and decrease to only several tens of degrees by 10–20 nucleus radii. However, the measured decay of both rotational temperature and column density with distance from the nucleus is much slower than predicted by this simple model. The addition of a substantial (distributed) source of gas from icy grains in the model slows the decay in rotational temperature and provides a more gradual drop in column density profiles. Together with a contribution of rotational heating of water molecules by electrons, the combined effects allow a much better match to the IRCS/Subaru observations. From the spatial distributions of water abundance and temperature measured in 73P/SW3-B, we have identified and quantified multiple mechanisms of release. The application of this tool to other comets may permit such studies over a range of heliocentric and geocentric distances.

Diffusion transport of water in basalts

Studying diffusive transport in porous rocks is of fundamental importance in understanding a variety of geochemical processes including: element transfer, primary mineral dissolution kinetics and precipitation of secondary phases. Here we report new findings on the relationship between diffusive transport and textural characteristics of the pore systems on the example of mid-oceanic ridge basalts having different degree of alteration but very similar bulk pore volume. Diffusion processes in porous basalts were studied in situ using H2O -> D2O exchange experiments. The effective diffusion coefficients of water molecules increase systematically from 5.05*10**-11 to 1.19*10**-10 m**2/s for fresh and moderately altered basalts and from 2.40*10**-11 to 6.72*10**-11 m**2/s for completely altered basalt as temperature increases from 5 to 50 °C. The activation energy of the diffusion process increases from 12.29 ± 0.71 kJ/mol for fresh and moderately altered basalts to 14.3 ± 1.33 kJ/mol for completely altered basalt. The results indicate that neither the bulk porosity nor the degree of alteration can be used as proxies for the efficiency of element transport during MORB-water interaction. The formation of secondary phases that replace primary minerals and fill the pore space in the rock leads to the formation of tiny pores and phases with large specific surface area. These factors might have a dominant control on the transport properties of altered basaltic rocks.

Cation exchange capacity and water content of ODP sites from Nankai

Pore fluid chlorinity lower than seawater is often observed in accretionary wedges and one of the possible causes of pore water freshening is the smectite to illite reaction. This reaction occurs during diagenesis in the 80-150°C temperature range. Low chlorinity anomalies observed at the toe of accretionary wedges have thus been interpreted as evidence for lateral fluid migration from inner parts of the wedge and the seismogenic zone. However, temperature conditions in Nankai Trough are locally high enough for the smectite to illite transition to occur in situ. Cation exchange capacity is here used as a proxy for smectite content in the sediment and the amount of interlayer water released during the smectite to illite reaction represents in average 12 water molecules per cation charge. Water and chloride budget calculations show that there is enough smectite to explain the chlorinity anomalies by in situ reactions. The shape of the pore fluid chlorinity profiles can be explained if compaction is also taken into account in the model. Lateral flow is not needed. This argument, based solely on chloride concentration, does not imply that lateral flow is absent. However, previous estimations of lateral fluid fluxes, and of the duration of transient flow events along the de.collement, should be reconsidered.

Cotransport of water by the Na+/glucose cotransporter

Water is transported across epithelial membranes in the absence of any hydrostatic or osmotic gradients. A prime example is the small intestine, where 10 liters of water are absorbed each day. Although water absorption is secondary to active solute transport, the coupling mechanism between solute and water flow is not understood. We have tested the hypothesis that water transport is directly linked to solute transport by cotransport proteins such as the brush border Na+/glucose cotransporter. The Na+/glucose cotransporter was expressed in Xenopus oocytes, and the changes in cell volume were measured under sugar-transporting and nontransporting conditions. We demonstrate that 260 water molecules are directly coupled to each sugar molecule transported and estimate that in the human intestine this accounts for 5 liters of water absorption per day. Other animal and plant cotransporters such as the Na+/Cl−/γ-aminobutyric acid, Na+/iodide and H+/amino acid transporters are also able to transport water and this suggests that cotransporters play an important role in water homeostasis.

Local osmotic gradients drive the water flux associated with Na+/glucose cotransport

It recently was proposed [Loo, D. D. F., Zeuthen, T., Chandy, G. & Wright, E. M. (1996) Proc. Natl. Acad. Sci. USA 93, 13367–13370] that SGLT1, the high affinity intestinal and renal sodium/glucose cotransporter carries water molecules along with the cosubstrates with a strict stoichiometry of two Na+, one glucose, and ≈220 water molecules per transport cycle. Using electrophysiology together with sensitive volumetric measurements, we investigated the nature of the driving force behind the cotransporter-mediated water flux. The osmotic water permeability of oocytes expressing human SGLT1 (Lp ± SE) averaged 3.8 ± 0.3 × 10−4 cm⋅s−1 (n = 15) and addition of 100 μM phlorizin (a specific SGLT1 inhibitor) reduced the permeability to 2.2 ± 0.2 × 10−4 cm⋅s−1 (n = 15), confirming the presence of a significant water permeability closely associated with the cotransporter. Addition of 5 mM α-methyl-glucose (αMG) induced an average inward current of 800 ± 10 nA at −50 mV and a water influx reaching 120 ± 20 pL cm−2 ⋅s−1 within 5–8 min. After rapidly inhibiting the Na+/glucose cotransport with phlorizin, the water flux remained significantly elevated, clearly indicating the presence of a local osmotic gradient (Δπ) estimated at 16 ± 2 mOsm. In short-term experiments, a rapid depolarization from −100 to 0 mV in the presence of αMG decreased the cotransport current by 94% but failed to produce a comparable reduction in the swelling rate. A mathematical model depicting the intracellular accumulation of transported osmolytes can accurately account for these observations. It is concluded that, in SGLT1-expressing oocytes, αMG-dependent water influx is induced by a local osmotic gradient by using both endogenous and SGLT1-dependent water permeability.

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Packing at the protein-water interface.

We have determined the packing efficiency at the protein-water interface by calculating the volumes of atoms on the protein surface and nearby water molecules in 22 crystal structures. We find that an atom on the protein surface occupies, on average, a volume approximately 7% larger than an atom of equivalent chemical type in the protein core. In these calculations, larger volumes result from voids between atoms and thus imply a looser or less efficient packing. We further find that the volumes of individual atoms are not related to their chemical type but rather to their structural location. More exposed atoms have larger volumes. Moreover, the packing around atoms in locally concave, grooved regions of protein surfaces is looser than that around atoms in locally convex, ridge regions. This as a direct manifestation of surface curvature-dependent hydration. The net volume increase for atoms on the protein surface is compensated by volume decreases in water molecules near the surface. These waters occupy volumes smaller than those in the bulk solvent by up to 20%; the precise amount of this decrease is directly related to the extent of contact with the protein.

Significance of bound water to local chain conformations in protein crystals.

We examine how the polypeptide chain in protein crystal structures exploits the multivalent hydrogen-bonding potential of bound water molecules. This shows that multiple interactions with a single water molecule tend to occur locally along the chain. A distinctive internal-coordinate representation of the local water-binding segments reveals several consensus conformations. The fractional water occupancy of each was found by comparison of the total number of conformations in the database regardless of the presence or absence of bound water. The water molecule appears particularly frequently in type II beta-turn geometries and an N-terminal helix feature. This work constitutes a first step into assessing not only the generality but also the significance of specific water binding in globular proteins.

Detection of one slowly exchanging substrate water molecule in the S3 state of photosystem II.

The exchangeability of the substrate water molecules at the catalytic site of water oxidation in photosystem II has been probed by isotope-exchange measurements using mass spectrometric detection of flash-induced oxygen evolution. A stirred sample chamber was constructed to reduce the lag time between injection of H2(18)O and the detecting flash by a factor of more than 1000 compared to the original experiments by R. Radmer and O. Ollinger [(1986) FEBS Lett. 195, 285-289]. Our data show that there is a slow (t1/2 approximately 500 ms, 10 degrees C) and a fast (t1/2 <25 ms, 10 degrees C) exchanging substrate water molecule in the S3 state of photosystem II. The slow exchange is coupled with an activation energy of about 75 kJ/mol and is discussed in terms of a terminal manganese oxo ligand, while the faster exchanging substrate molecule may represent a water molecule not directly bound to the manganese center.

Dodecyltrimethylammonium chloride adsorption at the silica/water interface studied by Sum Frequency Generation

La génération des fréquences somme (SFG), une technique spectroscopique spécifique aux interfaces, a été utilisée pour caractériser les changements de la structure macromoléculaire du surfactant cationique chlorure de dodécyltriméthylammonium (DTAC) à l’interface silice/eau dans une plage de pH variant entre 3 et 11. Les conditions expérimentales ont été choisies pour imiter les conditions les plus communes trouvées pendant les opérations de récupération assistée du pétrole. Particulièrement, la silice a été étudiée, car elle est un des composantes des surfaces minérales des réservoirs de grès, et l’adsorption du surfactant a été étudiée avec une force ionique pertinente pour les fluides de la fracturation hydraulique. Les spectres SFG ont présenté des pics détectables avec une amplitude croissante dans la région des étirements des groupes méthylène et méthyle lorsque le pH est diminué jusqu’à 3 ou augmenté jusqu’à 11, ce qui suggère des changements de la structure des agrégats de surfactant à l’interface silice/eau à une concentration de DTAC au-delà de la concentration micellaire critique. De plus, des changements dans l’intensité SFG ont été observés pour le spectre de l’eau quand la concentration de DTAC augmente de 0,2 à 50 mM dans les conditions acide, neutre et alcaline. À pH 3, près du point de charge zéro de la surface de silice, l’excès de charge positive en raison de l’adsorption du surfactant cationique crée un champ électrostatique qui oriente les molécules d’eau à l’interface. À pH 7 et 11, ce qui sont des valeurs au-dessus du point de charge zéro de la surface de silice, le champ électrostatique négatif à l’interface silice/eau diminue par un ordre de grandeur avec l’adsorption du surfactant comme résultat de la compensation de la charge négative à la surface par la charge positive du DTAC. Les résultats SFG ont été corrélés avec des mesures de l’angle de contact et de la tension interfaciale à pH 3, 7 et 11.

Dodecyltrimethylammonium chloride adsorption at the silica/water interface studied by Sum Frequency Generation

La génération des fréquences somme (SFG), une technique spectroscopique spécifique aux interfaces, a été utilisée pour caractériser les changements de la structure macromoléculaire du surfactant cationique chlorure de dodécyltriméthylammonium (DTAC) à l’interface silice/eau dans une plage de pH variant entre 3 et 11. Les conditions expérimentales ont été choisies pour imiter les conditions les plus communes trouvées pendant les opérations de récupération assistée du pétrole. Particulièrement, la silice a été étudiée, car elle est un des composantes des surfaces minérales des réservoirs de grès, et l’adsorption du surfactant a été étudiée avec une force ionique pertinente pour les fluides de la fracturation hydraulique. Les spectres SFG ont présenté des pics détectables avec une amplitude croissante dans la région des étirements des groupes méthylène et méthyle lorsque le pH est diminué jusqu’à 3 ou augmenté jusqu’à 11, ce qui suggère des changements de la structure des agrégats de surfactant à l’interface silice/eau à une concentration de DTAC au-delà de la concentration micellaire critique. De plus, des changements dans l’intensité SFG ont été observés pour le spectre de l’eau quand la concentration de DTAC augmente de 0,2 à 50 mM dans les conditions acide, neutre et alcaline. À pH 3, près du point de charge zéro de la surface de silice, l’excès de charge positive en raison de l’adsorption du surfactant cationique crée un champ électrostatique qui oriente les molécules d’eau à l’interface. À pH 7 et 11, ce qui sont des valeurs au-dessus du point de charge zéro de la surface de silice, le champ électrostatique négatif à l’interface silice/eau diminue par un ordre de grandeur avec l’adsorption du surfactant comme résultat de la compensation de la charge négative à la surface par la charge positive du DTAC. Les résultats SFG ont été corrélés avec des mesures de l’angle de contact et de la tension interfaciale à pH 3, 7 et 11.

Geochemistry of hydrate gas and water at DSDP Hole 84-570

Molecular and isotopic measurements of gas and water obtained from a gas hydrate at Site 570, DSDP Leg 84, are reported. The hydrate appeared to be Structure I and was composed of a solid framework of water molecules enclosing methane and small amounts of ethane and carbon dioxide. Carbon isotopic values for the hydrate-bound methane, ethane, and carbon dioxide were -41 to about -44, -27, and -2.9 per mil, respectively. The d13C-C1 values are consistent with void gas values that were determined to have a biogenic source. A significant thermogenic source was discounted because of high C1/C2 ratios and because the d13C-CO2 values in these sections were also anomalously heavy (or more positive) isotopically, suggesting that the methane was formed biogenically by reduction of heavy CO2 . The isotopically heavy hydrate d13C-C2 is also similar to void gas isotopic compositions and is either a result of low-temperature diagenesis producing heavy C2 in these immature sediment sections or upward migration of deeper thermogenic gas. The salinity of the hydrate water was 2.6 per mil with dDH2O and d18OH2O values of +1 and +2.2 per mil, respectively.