Trapped Water Molecules Research Articles

Interfacial Water at Hydrophobic and Hydrophilic Surfaces: Slip, Viscosity, and Diffusion

The dynamics and structure of water at hydrophobic and hydrophilic diamond surfaces is examined via non-equilibrium Molecular Dynamics simulations. For hydrophobic surfaces under shearing conditions, the general hydrodynamic boundary condition involves a finite surface slip. The value of the slip length depends sensitively on the surface water interaction strength and the surface roughness; heuristic scaling relations between slip length, contact angle, and depletion layer thickness are proposed. Inert gas in the aqueous phase exhibits pronounced surface activity but only mildly increases the slip length. On polar hydrophilic surfaces, in contrast, slip is absent, but the water viscosity is found to be increased within a thin surface layer. The viscosity and the thickness of this surface layer depend on the density of polar surface groups. The dynamics of single water molecules in the surface layer exhibits a similar distinction: on hydrophobic surfaces the dynamics is purely diffusive, while close to a hydrophilic surface transient binding or trapping of water molecules over times of the order of hundreds of picoseconds occurs. We also discuss in detail the effect of the Lennard-Jones cutoff length on the interfacial properties.

The Thermodynamic Influence of Trapped Water Molecules on a Protein–Ligand Interaction

Water molecules doing time: Atomic-resolution crystal structures of the PPIase domain of cyclophilin G, alone and in complex with cyclosporin A, and together with MD simulations and calorimetry, reveal how trapped water molecules influence the thermodynamic profile of a protein-ligand interaction.

In vivo measurement of axon diameter distribution in the corpus callosum of rat brain

Here, we present the first in vivo non-invasive measurement of the axon diameter distribution in the rat corpus callosum. Previously, this measurement was only possible using invasive histological methods. The axon diameter, along with other physical properties, such as the intra-axonal resistance, membrane resistance and capacitance etc. helps determine many important functional properties of nerves, such as their conduction velocity. In this work, we provide a novel magnetic resonance imaging method called AxCaliber, which can resolve the distinct signatures of trapped water molecules diffusing within axons as well as water molecules diffusing freely within the extra-axonal space. Using a series of diffusion weighted magnetic resonance imaging brain scans, we can reliably infer both the distribution of axon diameters and the volume fraction of these axons within each white matter voxel. We were able to verify the known microstructural variation along the corpus callosum of the rat from the anterior (genu) to posterior (splenium) regions. AxCaliber yields a narrow distribution centered approximately 1 microm in the genu and splenium and much broader distributions centered approximately 3 microm in the body of the corpus callosum. The axon diameter distribution found by AxCaliber is generally broader than those usually obtained by histology. One factor contributing to this difference is the significant tissue shrinkage that results from histological preparation. To that end, AxCaliber might provide a better estimate of the in vivo morphology of white matter. Being a magnetic resonance imaging based methodology, AxCaliber has the potential to be used in human scanners for morphological studies of white matter in normal and abnormal development, and white matter related diseases.

Trapped Water Molecule in the Charge Separation of a Bacterial Reaction Center

Low-frequency oscillations in the absorption spectrum at 1020 nm, connected to the primary charge separation process in Rhodobacter sphaeroides, have been shown by Yakovlev et al. to be caused by rotational motion of an interstitial water molecule called "water-A". The same water molecule was shown by Potter et al. to increase the rate of charge separation by a factor of 8. We have carried out geometry optimization of water-A and its nearest atoms in the protein pocket, using density functional theory (DFT). There are strong hydrogen bonds to the axial imidazol group of the B part of the special pair (P=PAPB) and to the keto carbonyl group of ring V of the accessory chlorophyll (BA). Rotation of water-A is thus impossible in the electronic ground state. We have tried to support our speculations on other possible mechanisms by calculations. The P(+)BA(-) charge transfer state is stabilized by proton transfer from water-A and simultaneous proton transfer from the axial group of PB to water-A. After double proton transfer the hydrogen bond to the keto group disappears whereby a possibility opens up for almost free water rotation. The results therefore would explain the 32 cm(-1) oscillation of Yakovlev et al. The proposed mechanism assumes, however, that the general assumption that the activation energy disappears in the primary charge separation of bacterial photosynthesis, holds also for this special case.

Effect of Solvent on the Phase Diagram of a Simple Anisotropic Model of Globular Proteins

Anisotropic protein interactions play a role in globular protein phase transitions, including the shape of fluid-fluid coexistence curves and the formation of hemoglobin polymer fibers in sickle cell disease. Also, the solvent has been shown to play an important role in the phase behavior of some aqueous protein solutions, through the release or trapping of water molecules upon crystallization. Both anisotropy and solvent effects have been treated separately in earlier theoretical studies. Here we propose and analyze a simple, composite model that treats both anisotropy and solvent effects. We find that this model qualitatively explains some phase behavior that has been observed in protein solutions, including normal and retrograde solubility curves and lower critical points.

Viscoelastic properties of adsorbed and cross-linked polypeptide and protein layers at a solid–liquid interface

The real-time changes in viscoelasticity of adsorbed poly(L-lysine) (PLL) and adsorbed histone (lysine rich fraction) due to cross-linking by glutaraldehyde and corresponding release of associated water were investigated using a quartz crystal microbalance with dissipation monitoring (QCM-D) and attenuated total reflection Fourier transform infrared spectroscopy (ATR/FTIR). The kinetics of PLL and histone adsorption were measured through changes in mass adsorbed onto a gold-coated quartz surface from changes in frequency and dissipation and using the Voigt viscoelastic model. Prior to cross-linking, the shear viscosity and shear modulus of the adsorbed PLL layer were ∼ 3.0 × 10 −3 Pa s and ∼ 2.5 × 10 5 Pa , respectively, while after cross-linking, they increased to ∼ 17.5 × 10 −3 Pa s and ∼ 2.5 × 10 6 Pa , respectively. For the adsorbed histone layer, shear viscosity and shear modulus increased modestly from ∼ 1.3 × 10 −3 to ∼ 2.0 × 10 −3 Pa s and from ∼ 1.2 × 10 4 to ∼ 1.6 × 10 4 Pa , respectively. The adsorbed mass estimated from the Sauerbrey equation (perfectly elastic) and the Voigt viscoelastic model differ appreciably prior to cross-linking whereas after cross-linking they converged. This is because trapped water molecules were released during cross-linking. This was confirmed experimentally via ATR/FTIR measurements. The variation in viscoelastic properties increased substantially after cross-linking presumably due to fluctuation of the randomly cross-linked network structure. An increase in fluctuation of the viscoelastic properties and the loss of imbibed water could be used as a signature of the formation of a cross-linked network and the amount of cross-linking, respectively.

Dynamic Mechanism of Collagen-like Peptide Encapsulated into Carbon Nanotubes

Carbon nanotubes (CNTs)-based devices and their applications have received more and more attention, and several biomolecules have been found to be encapsulated into the inner space of the CNTs spontaneously. In this work, the molecular dynamics simulations demonstrate that a collagen-like peptide with a hydrophobic center and hydrophilic surfaces could be inserted into CNTs spontaneously but slowly. Then the dynamic mechanism of the encapsulation process was investigated by a series of steered molecular dynamics simulations. The van der Waals interaction between the peptide and the carbon nanotubes was proved to be a positive factor for this insertion process, whereas the major resistance of this process is attributed to the repelling of the trapped water molecules and the breaking of the hydrogen-bond networks of water molecules around the peptide. Because of the synthetical effect of these interactions, there is an optimal tube size corresponding to effective encapsulation of the protein into the CNTs for a given kind of protein molecule.

Hydrogen Exchange and Hydration Dynamics in Gelatin Gels

Gelatin, derived from the collagen triple helix, is the most widely used functional biopolymer and a prototype for studies of physical gels. Gelatin gels have also served as models for soft biological tissue in efforts to elucidate the molecular basis of the magnetic relaxation phenomena that govern magnetic resonance image contrast. Yet, the microstructure, hydration, and magnetic relaxation behavior of gelatin gels are not well understood. To address these issues, we report here the water 2H and 17O magnetic relaxation dispersion (MRD) profiles from gelatin gels over wide ranges of resonance frequency and pH. For the global analysis of this extensive data set, we use a generalized relaxation theory that remains valid for arbitrarily slow molecular dynamics. The strong pH dependence in the 2H profiles can be rationalized quantitatively as the result of exchange with bulk water of labile hydrogens in gelatin side chains. The global analysis of the MRD data yields hydrogen-exchange rate constants, acid dissociation constants, and orientational order parameters in agreement with independent structural, thermodynamic, and kinetic data. The MRD analysis reveals a highly mobile hydration layer at the surface of the gelatin triple helix and a small number of trapped water molecules with residence times on the order of 10(-8) s, presumably associated with structural defects and branch points in the gel. The MRD data also indicate that approximately 20% of the gelatin residues belong to flexible polypeptide chains, rather than to rigid triple-helical segments. By identifying the molecular species and motions responsible for the 2H and 17O dispersion profiles, this study takes a significant step toward a quantitative understanding of water relaxation in aqueous gels and biological tissue.

One new nickel coordination polymer with an unsymmetric 5-(4-pyridyl)-1,3,4-oxadiazole-2-thione: Synthesis, structure and characterization

A new neutral 2D coordination polymer, {[Ni(pot)2(H2O)2]·6H2O}n (1) (Hpot=5-(4-pyridyl)-1,3,4-oxadiazole-2-thione), has been prepared by reacting NiII salt with the Hpot ligand under a mixed solvents medium; 1 possesses large rectangular channels to trap water molecules. It has been characterized by IR and gas sorption property as well as TG analysis.

Trapped water molecules are essential to structural dynamics and function of a ribozyme

Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular dynamics simulation and single molecule fluorescence spectroscopy approaches, we find that a ribozyme from a subviral plant pathogen exhibits a coupled hydrogen bonding network that communicates dynamic structural rearrangements throughout the catalytic core in response to site-specific chemical modification. Trapped long-residency water molecules are critical for this network and only occasionally exchange with bulk solvent as they pass through a breathing interdomain base stack. These highly structured water molecules line up in a string that may potentially also be involved in specific base catalysis. Our observations suggest important, still underappreciated roles for specifically bound water molecules in the structural dynamics and function of noncoding RNAs.

Mesomorphic Complexes of DNA with the Mixtures of a Cationic Surfactant and a Neutral Lipid

Polyanionic DNA binds to cationic lipids to form electrostatic complexes exhibiting rich self-assembled structures. These types of complexes have been considered as a nonviral carrier in gene therapy and as a template for nanostructure construction. For the latter application where biocompatibility is not the key issue, replacement of cationic lipid by cationic surfactant is advantageous due to the wide availability of surfactant. Here we report the self-assembly behavior of the complexes of DNA with a cationic surfactant, dodecyltrimethylammonium bromide (DTAB), mixed with a neutral lipid, dioleoylphosphatidylethanolamine (DOPE), in fully hydrated state as a function of DTAB-to-DNA base pair molar ratio (x), DOPE-to-DTAB molar ratio (m) and temperature. The binary complexes of DNA with DTAB microphase separated to form hydrophilic and hydrophobic domains without long-range order. Incorporating DOPE into the complexes effectively strengthened the hydrophobic interaction and hence promoted the formations of long-range ordered mesophases, including a condensed multilamellar phase (L(alpha)(c)) at small to intermediate m (m </= approximately 4) and an inverted hexagonal phase (H(II)(c)) at large m (m > approximately 6). The lyotropic mesophase transition with respect to the change of m was properly predicted by a formula for calculating the packing parameter of amphiphile mixture. In addition to the lyotropic transition, an unusual thermotropic order-order transition (OOT) between L(alpha)(c) and H(II)(c) phases was revealed for the isoelectric complex with m = 3. This OOT was thermally reversible and was postulated to be driven by the reduction of the effective headgroup area due to the release of trapped water molecules.

Crystal Structures of the GluR5 and GluR6 Ligand Binding Cores: Molecular Mechanisms Underlying Kainate Receptor Selectivity

Little is known about the molecular mechanisms underlying differences in the ligand binding properties of AMPA, kainate, and NMDA subtype glutamate receptors. Crystal structures of the GluR5 and GluR6 kainate receptor ligand binding cores in complexes with glutamate, 2S,4R-4-methylglutamate, kainate, and quisqualate have now been solved. The structures reveal that the ligand binding cavities are 40% (GluR5) and 16% (GluR6) larger than for GluR2. The binding of AMPA- and GluR5-selective agonists to GluR6 is prevented by steric occlusion, which also interferes with the high-affinity binding of 2S,4R-4-methylglutamate to AMPA receptors. Strikingly, the extent of domain closure produced by the GluR6 partial agonist kainate is only 3 degrees less than for glutamate and 11 degrees greater than for the GluR2 kainate complex. This, together with extensive interdomain contacts between domains 1 and 2 of GluR5 and GluR6, absent from AMPA receptors, likely contributes to the high stability of GluR5 and GluR6 kainate complexes.

Structural Rationalization of a Large Difference in RNA Affinity Despite a Small Difference in Chemistry between Two 2‘-O-Modified Nucleic Acid Analogues

Chemical modification of nucleic acids at the 2'-position of ribose has generated antisense oligonucleotides (AONs) with a range of desirable properties. Electron-withdrawing substituents such as 2'-O-[2-(methoxy)ethyl] (MOE) confer enhanced RNA affinity relative to that of DNA by conformationally preorganizing an AON for pairing with the RNA target and by improving backbone hydration. 2'-Substitution of the ribose has also been shown to increase nuclease resistance and cellular uptake via changes in lipophilicity. Interestingly, incorporation of either 2'-O-[2-(methylamino)-2-oxoethyl]- (NMA) or 2'-O-(N-methylcarbamate)-modified (NMC) residues into AONs has divergent effects on RNA affinity. Incorporation of 2'-O-NMA-T considerably improves RNA affinity while incorporation of 2'-O-NMC-T drastically reduces RNA affinity. Crystal structures at high resolution of A-form DNA duplexes containing either 2'-O-NMA-T or 2'-O-NMC-T shed light on the structural origins of the surprisingly large difference in stability given the relatively minor difference in chemistry between NMA and NMC. NMA substituents adopt an extended conformation and use either their carbonyl oxygen or amino nitrogen to trap water molecules between phosphate group and sugar. The conformational properties of NMA and the observed hydration patterns are reminiscent of those found in the structures of 2'-O-MOE-modified RNA. Conversely, the carbonyl oxygen of NMC and O2 of T are in close contact, providing evidence that an unfavorable electrostatic interaction and the absence of a stable water structure are the main reasons for the loss in thermodynamic stability as a result of incorporation of 2'-O-NMC-modified residues.

A rationale for the large breathing of the porous aluminum terephthalate (MIL-53) upon hydration.

Aluminum 1,4-benzenedicarboxylate Al(OH)[O(2)C-C(6)H(4)-CO(2)]. [HO(2)C-C(6)H(4)-CO(2)H](0.70) or MIL-53 as (Al) has been hydrothermally synthesized by heating a mixture of aluminum nitrate, 1,4-benzenedicarboxylic acid, and water, for three days at 220 degrees C. Its 3 D framework is built up of infinite trans chains of corner-sharing AlO(4)(OH)(2) octahedra. The chains are interconnected by the 1,4-benzenedicarboxylate groups, creating 1 D rhombic-shaped tunnels. Disordered 1,4-benzenedicarboxylic acid molecules are trapped inside these tunnels. Their evacuation upon heating, between 275 and 420 degrees C, leads to a nanoporous open-framework (MIL-53 ht (Al) or Al(OH)[O(2)C-C(6)H(4)-CO(2)]) with empty pores of diameter 8.5 A. This solid exhibits a Langmuir surface area of 1590(1) m(2)g(-1) together with a remarkable thermal stability, since it starts to decompose only at 500 degrees C. At room temperature, the solid reversibly absorbs water in its tunnels, causing a very large breathing effect and shrinkage of the pores. Analysis of the hydration process by solid-state NMR ((1)H, (13)C, (27)Al) has clearly indicated that the trapped water molecules interact with the carboxylate groups through hydrogen bonds, but do not affect the hydroxyl species bridging the aluminum atoms. The hydrogen bonds between water and the oxygen atoms of the framework are responsible for the contraction of the rhombic channels. The structures of the three forms have been determined by means of powder X-ray diffraction analysis. Crystal data for MIL-53 as (Al) are as follows: orthorhombic system, Pnma (no. 62), a = 17.129(2), b = 6.628(1), c = 12.182(1) A; for MIL-53 ht (Al), orthorhombic system, Imma (no. 74), a = 6.608(1), b = 16.675(3), c = 12.813(2) A; for MIL-53 lt (Al), monoclinic system, Cc (no. 9), a = 19.513(2), b = 7.612(1), c = 6.576(1) A, beta = 104.24(1) degrees.

A Microporous Zinc Phosphonocarboxylate with a Zeolite ABW Framework via the Trialkyl Phosphonocarboxylate Route: In situ Synthesis and Characterization of Na[Zn(O3PC2H4CO2)]·H2O

AbstractA new zinc phosphonocarboxylate Na[Zn(O3PC2H4CO2)]·H2O (1) has been hydrothermally synthesized by base‐catalyzed hydrolysis of trimethyl 3‐phosphonopropionate. An X‐ray crystallographic study revealed that 1 consists of parallel stacked inorganic hexagonal sheets which are connected by organic −C−C−C−O− pillars forming a three‐dimensional framework with the same topology as ABW‐type zeolites. The accessible channel of 1 consisting of 22 atoms is larger than those of ABW‐type zeolites and the metal phosphonates Zn(O3PC2H4NH2) and Zn(O3PC2H4CO2H)·1.5H2O. TGA shows the trapped water molecules in 1 can be thermally removed without damage to the framework. Furthermore, dehydrated 1 is stable up to 340 °C. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)

Minimization of cavity size ensures protein stability and folding: structures of Phe46-replaced bovine pancreatic RNase A.

The Phe46 residue, located in the hydrophobic core of RNase A, was replaced with other hydrophobic residues, leucine, valine, or alanine, and their X-ray crystallographic structures were determined up to 1.50-1.80 A resolution in an attempt to examine the relationship between structural changes and conformational stability or folding kinetics. The backbone structure of F46L, F46V, and F46A was indistinguishable from that of the wild-type enzyme, retaining the correct active site structure. However, one water molecule was included in the hydrophobic core of F46A, forming two hydrogen bonds with the backbone peptide chain. The side chain of Met29 in F46V and F46A adopted two different conformations in an equal occupancy. A trapped water molecule and two conformations of Met29 represent changes that minimize the cavity volume. Nevertheless, the replacement of Phe46 with the above residues resulted in a marked decrease in both thermal stability and folding reaction. Thus, Phe46 ensures the thermal stability and the rapid and correct folding of RNase A by the role it plays in forming a highly packed, hydrophobic core.

Influence of H2O molecules on sub-nanometre scale gaps between Auleads

Electric-field induced surface modification of Au is used to create stablesub-nanometre-scale gaps between Au leads. Electron tunnelling current ismeasured as a function of the molecular environment. We explore the influence ofwater molecules on tunnelling conductance. At small voltage, water molecules donot influence the conductance. At large voltage, a strong static electric fieldbetween the leads induces trapping of H2O molecules from the water vapour. Atroom temperature, trapped water molecules increase the tunnelling barrierheight, in agreement with the workfunction of water. We estimate that theresistance of a single trapped water molecule at 5 V is of order 100 GΩ.

CHARACTERISATION OF CONDUCTING POLYMERS USING ION BEAM ANALYSIS

Complex bis terthiophene porphyrin conducting polymers were used to investigate the uptake of zinc into the freebase porphyrin unit after polymerisation by acquiring depth profiles using Rutherford Backscatting Spectrometry (RBS) analysis. Issues such as the influence of the support material and extent of polymer oxidation on the dispersion of the counter ions through the polymer films are of importance. Gaining knowledge of the dispersion of counter ions provides new insights into the redox mechanisms for conductive polymers. The results were compared to those obtained from a sample where zinc was coordinated to the porphyrin prior to the polymerisation process. Unexpectedly high concentration of both nitrogen and oxygen were found which could be due to evidence of the trapped cations from the electrolyte ( (Bu) 4 N +), and trapped water molecules, within the polymer films. The chlorine concentrations help to understand the dispersion of the perchlorate counter ion throughout the polymer films, and the combination of both RBS and Proton Induced X-ray Emission (PIXE) show that trace element impurities can be detected using ion beam analysis which other analytical techniques are unable to do.

Modeling of hydrophilic wafer bonding by molecular dynamics simulations

The role of moisture in hydrophilic wafer bonding was modeled using molecular dynamics computer simulations of interface formation between amorphous silica surfaces. Three different surface treatments were used in order to determine the effect of moisture on the formation of siloxane (Si–O–Si) bridges across the interface at two temperatures. The three surface conditions that were studied were: (a) wet interfaces containing 1 monolayer of water adsorbed at the interface (based on the room temperature bulk density of water), (b) hydroxylated interfaces with concentrations of 3–5 silanols/nm2 on each surface and no excess water molecules initially in the system, and (c) pristine interfaces that had only Si and O and no water or H present. The surfaces were slowly brought together and siloxane bond formation was monitored. In the pristine interfaces, siloxane bridges formed across the interface by the coalescence of various defect species in each surface. A bimodal distribution of siloxane bond angles formed during the first 2.5 Å of approach after the first siloxane bond was formed. These bond angles were much lower than and higher than the bulk average, indicating the formation of less stable bonds. The hydroxylated (with no excess water) and wet surfaces showed a more uniform distribution of siloxane bond angles, with no highly reactive small bond angles forming. The presence of water molecules enhanced H-bond formation across the interface, but trapped water molecules inhibited formation of the strong siloxane bridges across the interface. In real systems, high temperatures are required to remove this trapped moisture.

Magnetic local structures and dynamic behavior of water molecules in a moisture-sensitive spin-crossover system [Fe(II)(R-triazole) 3](X)· nD 2O studied by solid-state high-resolution deuterium NMR

The trapped state of crystal water molecules in a moisture-sensitive spin-crossover system of [Fe(II)(R-triazole) 3](ClO 4) 2· nD 2O was investigated by solid-state high-resolution deuterium NMR spectrum. Plus and minus sign and magnitude of hyperfine coupling constant of deuterium of crystal water molecules were determined. The hyperfine coupling constant +87 kHz of D 2O of [Fe(II)(4-NH 2-1,2,4-triazole) 3](ClO 4) 2· nD 2O indicates that the crystal water molecules are not directly bound to Fe(II) ion but sit around Fe(II) ion or triazole ligand. We demonstrated that a high-speed magic angle spinning deuterium NMR spectrum is useful for studying local magnetic structures of the high-spin phase of Fe(II) system. It was also found that most of the D 2O molecules in [Fe(II)(1-H-1,2,4-triazole) 3](ClO 4) 2· nD 2O rotate isotropically near room temperature, whereas D 2O molecules in a similar complex [Fe(II)(4-NH 2-1,2,4-triazole) 3](ClO 4) 2· nD 2O are hindered much more strongly. The complex with mobile crystal water undergoes an abrupt spin-crossover transition, while the complex with strongly trapped water molecules shows relatively gradual transition.