Translational Diffusion Of Water Research Articles

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters.

This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-dodecyl-β-maltoside (C(12)G(2)), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure, and hydration of the C(12)G(2) anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M.; et al. J. Comput. Chem. 2002, 23, 1236-1243). We find that our CHARMM and GLYCAM parameter sets yield similar results in the case of properties related to the micelle structure but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C(12)G(2) micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 and 25.4 Å for the α- and β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7-11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in α- or β-anomers.

Entropy and dynamics of water in hydration layers of a bilayer

We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme [two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (TΔS) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules.

Effect of Surface Roughness on the Static and Dynamic Properties of Water Adsorbed on Graphene

We studied the effects that deviations from a perfectly flat structure have in the adsorption of water on a single graphene sheet at room temperature. To do so we performed molecular dynamics simulations of water on top of a single sheet of carbon atoms whose positions were changed periodically or randomly and the results compared with those obtained for an ideal flat surface. Different textures were considered, and in all cases, the corresponding geometries of the single graphene layers were kept frozen through the simulations. Our results indicate that the effect of the roughness in the water molecules depends basically on the average amplitude of the distortions in the Z direction and not of their particular type (random or periodic). Binding energies and water structure are scarcely affected by corrugation, with an average number of 3.5-3 hydrogen bonds per molecule through the distance perpendicular to the surface. Analysis of water translational diffusion and spectroscopical densities of states indicates changes when water is close to the vacuum interface and far from the graphene surface.

Diffusion Tensor Imaging Detects Early Cerebral Cortex Abnormalities in Neuronal Architecture Induced by Bilateral Neonatal Enucleation: An Experimental Model in the Ferret

Diffusion tensor imaging (DTI) is a technique that non-invasively provides quantitative measures of water translational diffusion, including fractional anisotropy (FA), that are sensitive to the shape and orientation of cellular elements, such as axons, dendrites and cell somas. For several neurodevelopmental disorders, histopathological investigations have identified abnormalities in the architecture of pyramidal neurons at early stages of cerebral cortex development. To assess the potential capability of DTI to detect neuromorphological abnormalities within the developing cerebral cortex, we compare changes in cortical FA with changes in neuronal architecture and connectivity induced by bilateral enucleation at postnatal day 7 (BEP7) in ferrets. We show here that the visual callosal pattern in BEP7 ferrets is more irregular and occupies a significantly greater cortical area compared to controls at adulthood. To determine whether development of the cerebral cortex is altered in BEP7 ferrets in a manner detectable by DTI, cortical FA was compared in control and BEP7 animals on postnatal day 31. Visual cortex, but not rostrally adjacent non-visual cortex, exhibits higher FA than control animals, consistent with BEP7 animals possessing axonal and dendritic arbors of reduced complexity than age-matched controls. Subsequent to DTI, Golgi-staining and analysis methods were used to identify regions, restricted to visual areas, in which the orientation distribution of neuronal processes is significantly more concentrated than in control ferrets. Together, these findings suggest that DTI can be of utility for detecting abnormalities associated with neurodevelopmental disorders at early stages of cerebral cortical development, and that the neonatally enucleated ferret is a useful animal model system for systematically assessing the potential of this new diagnostic strategy.

ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water.

Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, T(g) = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called "no man's land" (the range 150-235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at approximately 225 K. The reorientation of the probe molecules decouples from the viscosity below approximately 225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes-Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974-12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360:324-328] and the fragile-to-strong dynamic cross-over at approximately 228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-to-strong liquid transition in water. Nature 398:492-494].

Water molecule contributions to proton spin–lattice relaxation in rotationally immobilized proteins

Spin–lattice relaxation rates of protein and water protons in dry and hydrated immobilized bovine serum albumin were measured in the range of 1H Larmor frequency from 10 kHz to 30 MHz at temperatures from 154 to 302 K. The water proton spin–lattice relaxation reports on that of protein protons, which causes the characteristic power law dependence on the magnetic field strength. Isotope substitution of deuterium for hydrogen in water and studies at different temperatures expose three classes of water molecule dynamics that contribute to the spin–lattice relaxation dispersion profile. At 185 K, a water 1H relaxation contribution derives from reorientation of protein-bound molecules that are dynamically uncoupled from the protein backbone and is characterized by a Lorentzian function. Bound-water-molecule motions that can be dynamically uncoupled or coupled to the protein fluctuations make dominant contributions at higher temperatures as well. Surface water translational diffusion that is magnetically two-dimensional makes relaxation contributions at frequencies above 10 MHz. It is shown using isotope substitution that the exponent of the power law of the water signal in hydrated immobilized protein systems is the same as that for protons in lyophilized proteins over four orders of magnitude in the Larmor frequency, which implies that changes in the protein structure associated with hydration do not affect the 1H spin relaxation.

Translational diffusion of water and its dependence on temperature in charged and uncharged clays: A neutron scattering study

The water diffusion in four different, highly compacted clays [montmorillonite in the Na- and Ca-forms, illite in the Na- and Ca-forms, kaolinite, and pyrophyllite (bulk dry density rho(b)=1.85+/-0.05 gcm(3))] was studied at the atomic level by means of quasielastic neutron scattering. The experiments were performed on two time-of-flight spectrometers and at three different energy resolutions [FOCUS at SINQ, PSI (3.65 and 5.75 A), and TOFTOF at FRM II (10 A)] for reliable data analysis and at temperatures between 27 and 95 degrees C. Two different jump diffusion models were used to describe the translational motion. Both models describe the data equally well and give the following ranking of diffusion coefficients: Na-montmorillonite<or=Ca-montmorillonite<Ca-illite<Na-illite<water<or=pyrophyllite<or=kaolinite. Uncharged clays had slightly larger diffusion coefficients than that of bulk water due to their hydrophobic surfaces. The time between jumps, tau(t), follows the sequence: Ca-montmorillonite>or=Na-montmorillonite>Ca-illite>Na-illite>or=kaolinite>pyrophyllite>or=water, in both jump diffusion models. For clays with a permanent layer charge (montmorillonite and illite) a reduction in the water content by a factor of 2 resulted in a decrease in the self-diffusion coefficients and an increase in the time between jumps as compared to the full saturation. The uncharged clay kaolinite exhibited no change in the water mobility between the two hydration states. The rotational relaxation time of water was affected by the charged clay surfaces, especially in the case of montmorillonite; the uncharged clays presented a waterlike behavior. The activation energies for translational diffusion were calculated from the Arrhenius law, which adequately describes the systems in the studied temperature range. Na- and Ca-montmorillonite (approximately 11-12 kJmol), Na-illite (approximately 13 kJmol), kaolinite and pyrophyllite (approximately 14 kJmol), and Ca-illite (approximately 15 kJmol) all had lower activation energies than bulk water (approximately 17 kJmol in this study). This may originate from the reduced number and strength of the H-bonds between water and the clay surfaces, or ions, as compared to those in bulk water. Our comparative study suggests that the compensating cations in swelling clays have only a minor effect on the water diffusion rates at these high densities, whereas these cations influence the water motion in non-swelling clays.

Water Diffusion in Nanoporous Glass: An NMR Study at Different Hydration Levels

By pulsed field gradient nuclear magnetic resonance measurements, we investigated the translational diffusion of water confined in the 200 A diameter pores of a sol-gel silica glass. The experiments, performed as a function of the hydration level, showed an enhancement of the self-diffusion coefficient when the water content corresponds to one or fewer monolayers. An explanation for this occurrence has been given in terms of a two-phase process involving a fast molecular exchange between the liquid and the vapor phase. Moreover, in partially filled pores, the surface water diffusion coefficient was measured, and was 4 times lower than the diffusion of liquid confined water in saturated spaces.

Translational diffusion of water in compacted clay systems

The translational diffusion of water in compacted clays at a high hydration level has been investigated by quasielastic neutron scattering at a time-of-flight spectrometer FOCUS (SINQ). Four compacted clays with systematic structural differences have been studied: Na-montmorillonite, Na-illite, kaolinite and pyrophyllite. The QENS experiments were performed using two different incident wavelengths in order to access a larger Q range and verify the data analysis. The translational diffusion coefficient for water in Na-montmorillonite and Na-illite are lower than those for bulk water, whereas the preliminary results for kaolinite and pyrophyllite show larger diffusion coefficient.

Solute−Solvent Contact by Intermolecular Cross-Relaxation. 2. The Water−Micelle Interface and the Micellar Interior

The intermolecular dipole-dipole cross-relaxation is measured between 19F nuclei of sodium perfluorooctanoate in micelles and 1H nuclei of the water solvent. The cross-relaxation rates for fluorines in the different moieties along the surfactant vary strongly by the resonance frequency in the investigated range of 188-470 MHz. This frequency dependence indicates that the cross-relaxation between water and amphiphilic aggregates is not controlled solely by the fast local water dynamics but significantly contributed to by the long-range translational diffusion of water. The cross-relaxation rates, analyzed in the framework of a model (Nordstierna, L.; Yushmanov, P. V.; Furó, I. J. Chem. Phys. 2006, 125, 074704), provide information about the dynamic retardation of water molecules by the micellar headgroup region and the location of the various moieties along the hydrophobic tail with respect to the water-micelle interface. Both intermolecular cross-relaxation and aggregation-induced 19F chemical shift changes indicate no direct water contact to fluorines except for those closest to the head group.

Quasi-elastic neutron scattering study of dimethyl-sulfoxide–water mixtures: Probing molecular mobility in a nonideal solution

The translational and rotational motions of water and dimethyl sulfoxide, [DMSO, (CH(3))(2)SO] have been investigated using quasi-elastic neutron scattering. Water-DMSO mixtures at five DMSO mole fractions, chi(DMSO), ranging from 0 to 0.75, were measured. Hydrogen-deuterium substitution was used to extract independently the water proton dynamics (d-DMSO-H(2)O), the DMSO methyl proton dynamics (h-DMSO-D(2)O) and to obtain background corrections (d-DMSO-D(2)O). The translational diffusion of water slows down significantly compared to bulk water at all chi(DMSO)>0. The rotational time constant for water exhibits a maximum at chi(DMSO)=0.33 that corresponds to the observed maximum of the viscosity of the mixture. Data for DMSO can be analyzed in terms of a relatively slow tumbling of the molecule about its center-of-mass in conjunction with random translational diffusion. The rotational time constant for this motion exhibits some dependence on chi(DMSO), while the translational diffusion constant shows no clear variation for chi(DMSO)>0. The results presented reinforce the idea that due to the stronger associative nature of DMSO, DMSO-water aggregates are formed over the whole composition range, disturbing the tetrahedral natural arrangement of the water molecules. As a consequence adding DMSO to water causes a drastic slowing down of the dynamics of the water molecule, and vice versa.

Contribution of the actomyosin motor to the temperature-dependent translational diffusion of water by cytoplasmic streaming in Elodea canadensis cells

The extent to which the actomyosin motor responsible for cytoplasmic streaming contributes to the translational diffusion of water in Elodea canadensis cells was studied by a nuclear magnetic resonance (NMR) spin-echo technique. The relative contribution of the actomyosin motor was determined from the corresponding apparent diffusion coefficient by the Einstein-Smolukhovsky relation. It is equal to the difference between the diffusional displacements of the cytoplasmic and the bulk water (deltaX). The NMR data show that the temperature dependence of deltaX is humpshaped, which is characteristic of enzyme reactions. At the same time, the apparent diffusion coefficient of cytoplasmic water increases with an increase in temperature. The most significant contribution of the actomyosin motor to deltaX is observed at temperatures below 20 degrees C. Within the temperature range of 20 to 33 degrees C, deltaX changes only slightly, and a further increase in temperature reduces deltaX to zero.

Anisotropic Water Diffusion in Macroscopically Oriented Lipid Bilayers Studied by Pulsed Magnetic Field Gradient NMR

The anisotropy, D ///D ⊥, of water diffusion in fully hydrated bilayers of dimyristoylphosphatidylcholine at 29°C has been measured by pulsed magnetic field gradient (pfg) NMR. By using NMR imaging hardware to produce magnetic field gradients in an arbitrary direction with respect to a stack of macroscopically aligned lipid bilayers, translational diffusion of water was measured as a function of the angle between the direction of the magnetic field gradient and the normal of the lipid membrane. The observed diffusion coefficient is found to depend strongly on this angle. The anisotropy cannot be accurately determined due to the very small value of D ⊥, but a lower limit of about 70 can be estimated from the observed diffusion coefficients. The results are discussed in terms of the relatively low permeability of water across the lipid bilayer, instrumental limitations, and/or possible defects in the lamellae.

Water rotational relaxation and diffusion in hydrated lysozyme.

This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of lysozyme is 3-7 times slower than that in the bulk depending on how the hydration shell is defined in the calculation. We have also verified that the dynamics of water translational diffusion in the vicinity of lysozyme have retardations similar to rotational relaxation. This is a common assumption in nuclear magnetic relaxation dispersion (NMRD) studies to derive residence times. In contrast to bulk water dynamics, surface water is in a dispersive diffusion regime or subdiffusion. Very good agreement of dipolar second-rank relaxation time with NMRD estimates is obtained by using appropriate dimensions of the hydration shell. Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P.

In vivo 1H magnetic resonance imaging and spectroscopy of the rat spinal cord using an inductively‐coupled chronically implanted RF coil

An inductively coupled, chronically implanted short-solenoid coil was used to obtain in vivo localized 1H NMR spectra and diffusion-weighted images from a rat spinal cord. A 5 x 8 mm two-turn elliptically shaped solenoid coil was implanted in rats at the site of a T-12 vertebral-level laminectomy. Excitation was achieved solely by a 3 x 3 cm external surface coil, and signal detection was achieved by inductively coupling the external coil to the implanted coil. The image signal-to-noise ratio (SNR) obtained with the inductively-coupled implanted coil was compared with that obtained using a linear or a quadrature external surface coil. The implanted coil provided a gain by over a factor of 3 in SNR. The implanted coil was used to measure localized 1H spectra in vivo at the T13/L1 spinal-cord level within a 1.85 x 1.85 x 4.82 mm (16.5 microL) volume. With 256 averages, a approximately 3-s repetition delay and respiratory gating, a high-quality spectrum was acquired in 13 min. In addition, water translational diffusion was measured in three orthogonal directions using a stimulated-echo imaging sequence, with a short echo time (TE), to produce a quantitative map of diffusion in a rat spinal cord in vivo.

The Dynamics of Protein Hydration Water: A Quantitative Comparison of Molecular Dynamics Simulations and Neutron-scattering Experiments

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein–water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.

Comparative Cell Shape and Diffusional Water Permeability of Red Blood Cells from Indian Elephant (Elephas maximus) and Man (Homo sapiens)

Red blood cells (RBC) from an Indian elephant (Elephas maximus) were studied by light microscopy (LM), scanning electron microscopy (SEM) and a new nuclear magnetic resonance (NMR) ‘imaging’ method based on the translational diffusion of water, NMR q-space analysis. Also, the transmembrane diffusional permeability, P d of water in RBC was measured by using a Mn2+-doping NMR technique, taking human RBC as a reference. The main diameter of the elephant RBC was measured as 9.3 ± 0.7 μm by LM, 9.3 ± 0.7 μm by ‘shrinkage-corrected’ SEM, and 9.3 ± 0.4 μm by q-space anlaysis. The value is ∼1.4 μm larger than that for the human RBC. The values of P d were, in the case of elephant RBC, 3.2 × 10−3 cm/s at 25 °C, 3.9 × 10−3 cm/s at 30 °C, 5.2 × 10−3 cm/s at 37 °C and 6.5 × 10−3 cm/s at 42 °C; all values were significantly lower than the corresponding values of P d for human RBC, namely 4.3 × 10−3 cm/s at 25 °C, 5.2 × 10−3 cm/s at 30 °C, 6.1 × 10−3 cm/s at 37 °C, 7.8 × 10−3 cm/s at 42°C. The maximal inhibition of P d (56%) was reached in 30 min at 37 °C with 2 mm p-chloromercuribenzene sulphonate (PCMBS) for both species of RBC. The basal permeability to water at 37 °C was estimated to be 2.3 × 10−3 cm/s for elephant and 2.6 × 10−3 cm/s for human RBC. The values of the activation energy for water permeability (E a,d ) was significantly higher for elephant RBC (31.9 kJ/mol) than for human RBC (25.9 kJ/mol). This indicated that features other than the number of transporters per cell are likely to be important in defining the differences in water permeability in the RBC from the two species.

Line Shape Analysis of NMR Powder Spectra of2H2O in Lipid Bilayer Systems

A NMR line shape/spin relaxation model is developed for 2H2O studies of structure and dynamics of the lipid−water interfaces of phosphatidylcholine bilayers. A line shape function describing the orientational dependence of 2H2O is derived. In addition, also expressions of the observed quadrupole splitting and the spin−lattice relaxation rate are derived within the same dynamic model. The model comprises two chemically interchanging fractions of water namely, “free”, and “bound”. There are four molecular parameters characterizing the “bound” water of the lipid water interface, namely, (1) the fraction water molecules bound to lipid molecules, (2) the local water order parameter , (3) the order parameter which describes the averaged “bound” water, and an effective correlation time (4) τc, characterizing water translational diffusion at the interface. This model allows for analyzing quadrupole splittings, spin−lattice relaxation rates, and water powder line shapes. Thus, dynamics as well as structural information about the water molecules residing in the water lipid interface may be extracted. In the reinterpretation of 2H2O powder spectra obtained for lamellar phases of dipalmitoylphosphatidylcholine (DPPC), the results clearly indicate that (Lα) > (Lβ‘) when comparing the liquid crystalline phase with 10−11 water molecules per lipid molecule and the gel phase with 3.5−4.2 water molecules per lipid molecule. Whereas the order of the perturbed water is similar in both phases, (Lα) ≈ (Lβ‘). The lateral diffusion is characterized by a correlation time τc > 60 ns but cannot be determined without measuring the spin−lattice relaxation measurements.

Structure and Dynamics in Concentrated, Amorphous Carbohydrate−Water Systems by Molecular Dynamics Simulation

We report results from molecular simulations of binary aqueous solutions of the carbohydrate stereoisomers, β-d-glucose, β-d-mannose, and d-fructose over a concentration range from zero to 80 wt % carbohydrate at 300 and 270 K. It is found that increasing carbohydrate concentration has a number of striking effects on the microscopic structure and dynamics of these solutions, including (1) a percolation threshold for connected water clusters at ca. 60 wt % carbohydrate, (2) a maximum in the hydrogen bond network strength and degree of ordering, as a function of carbohydrate concentration, at ca. 29 wt %, and (3) activated or “hopping” dynamics in the translational diffusion of water due to the influence of (1) and (2). There are appreciable differences in the magnitudes of these effects as a function of sugar type for the three stereoisomers studied. The relevance of these results is discussed in the context of the efficacy of sugars in biopreservation and lyophilization applications.

Molecular Dynamics Study of Water in Hydrogels

Abstract Molecular dynamics simulations are performed for aqueous solutions of polymers: Poly (vinyl alcohol) (PVA), Poly (vinyl methylether) (PVME), and Poly (N-isopropyl acrylamide) (PNiPAM). The distributions and dynamics of hydrogen-bonds, the translational diffusion of water, and the orientational relaxation of water are analyzed to investigate the properties of water which is highly influenced by the surrounding polymer chains. The water molecules around the polymer chains are highly hindered by the chains.