MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.

Permeability of lysozyme tetragonal crystals to water

Diffusion of water within cross-linked tetragonal crystals of hen egg-white lysozyme has been measured and simulated on a computer using the X-ray structure of water-filled channels within the crystal lattice. Relative to the self-diffusion coefficient of bulk water molecules, the experimental diffusion coefficient of water within the crystal was found to be 13 times reduced in the (001) crystallographic plane and 5 times reduced in the [001] direction. Comparison of the experimental and computer simulated diffusion coefficients shows that steric limitations for water diffusion are mostly responsible for this reduction of the water diffusion in the crystal, with the self-diffusion coefficient of intracrystalline water reduced by no more than 30–40% as compared to that of bulk water.     

Molecular dynamics simulation of liquid water under the influence of an external electric field

Molecular dynamics simulations of liquid water were performed at 258K and a density of 1.0?g/cm³ under various applied external electric field, ranging 0～10¹⁰?V/m. The influence of external field on structural and dynamical properties of water was investigated. The simple point charge (SPC) model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bonds structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected since the self-diffusion coefficient was very large. The self-diffusion coefficient decreases remarkably with increasing strength of electric field and the self-diffusion coefficient is anisotropic.     

Molecular dynamics simulations of nonionic surfactant adsorbed on subbituminous coal model surface based on XPS analysis

A molecular dynamics (MD) simulation was conducted to study the adsorption behaviour of a nonionic surfactant adsorbed on low-rank coal. Owing to the complicated chemical component and structure of the coal surface, a modified graphite surface with hydroxyl, carboxyl, and carbonyl groups was utilised for a representation of the subbituminous coal surface model. The compositions of the hydroxyl, carbonyl, and carboxyl groups on the coal surface were found to be at a proportion of 25:3:5 according to the X-ray photoelectron spectroscopy (XPS) results. The interaction of nonylphenol ethoxylate with 8 ethylene oxide groups (NPEO-8) using this coal model in an aqueous phase was then simulated. It was revealed that the nonionic surfactant molecules were adsorbed at the interface between water and coal. This agminated structure of the surfactant molecules on the surface of the coal demonstrated an attachment of the surfactant ethoxylate groups to these solid surfaces and an extension of the remaining hydrophobic portions into the solution. Therefore, a coal surface with greater hydrophobicity was created. The dynamic properties of the water molecules characterised through self-diffusion coefficients indicate greater water mobility resulting from the existence of NPEO-8.     

The self-diffusion of water in Artemia cysts

The self-diffusion coefficient of water molecules has been measured by nuclear magnetic resonance in cysts of Artemia over a wide range of hydration. Compared to the value for bulk water, the diffusion coefficient is reduced by a factor of 7 at the highest hydration and by approximately 100 at the lowest hydration. The results are used to evaluate various models that have been proposed to account for the reduction of water self-diffusion coefficients in complex systems.     

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 3(1), 4(1), and 7(1), and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.     

Nonexponential Diffusion Extinction of Spin Echo from Water Protons in Wheat Root

The method of NMR spin echo with the magnetic field pulse gradient was used for studying self-diffusion of water molecules in the radial root direction. It was shown on the basis of physiologopharmacological methods of modification of the object that the coefficients of water self-diffusion resulting from computer decomposition of nonexponential diffusion extinction of the relative echo amplitude in the root to components are related to the subcellular and supercellular organization (structure) of the root and reflect changes in water permeability of the two transport channels of plasmodesmas.     

Influence of dolichyl phosphate on permeability and stability of bilayer lipid membranes

The ionic permeability coefficients, ionic transference numbers, activation energy of ion transport and breakdown voltage of bilayer lipid membranes made from dioleoylphosphatidylcholine or its mixtures with dolichyl 12-phosphate have been studied. The electrical measurements showed that dolichyl phosphate in phospholipid bilayers decreases membrane permeability, changes membrane ionic selectivity and increases membrane stability. These results are discussed in light of the aggregation behavior and the intramolecular clustering of a dolichyl phosphate molecule in phospholipid membranes. From our data we suggest that the hydrophilic part of dolichyl phosphate molecules regulates their behavior in membranes.     

Molecular modeling study of sulfonated SIBS triblock copolymers

An important class of thermoplastic elastomers involves polystyrene and polyisobutylene blocks (SIBS). Sulfonated SIBS Triblock Copolymers (S-SIBS) are of particular interest because of potential applications for fuel cell and textile applications, where breathable, protective clothing is required. We have used multiscale modeling to gain an understanding of the static and dynamic properties of these polymer systems at detailed atomistic levels. Quantum chemistry tools were used to elucidate the bonding of water molecules and sulfonate groups. In addition, molecular dynamics was applied to calculate the polymer density at various levels of sulfonation. The structures of polymer with hydronium ions and also water were studied and the mechanism of water self-diffusion was proposed. It was found that with increase of water content the hydronium ions move further away from sulfonate groups. The self-diffusion coefficients of water were found to reproduce well experimental trends. Two different distributions of sulfonate groups were studied: one blocky and another perfectly dispersed. In the case of the blocky architecture, the water clusters are connected at a lower sulfonation level, leading to increased water diffusion coefficients as compared to the dispersed architecture.     

Transport properties of polymer solutions. A comparative approach

A variety of transport properties have been measured for solutions of the water soluble polymer poly(ethylene oxide)(PEO) with molecular weights ranging from 200 to 14,000, and volume fractions ranging from 0-80%. The transport properties are thermal conductivity, electrical conductivity at audio frequencies (in solutions containing dilute electrolyte), and water self-diffusion. These data, together with dielectric relaxation data previously reported, are amenable to analysis by the same mixture theory. The ionic conductivity and water self-diffusion coefficient, but not the thermal conductivity, are substantially smaller than predicted by the Maxwell and Hanai mixture relations, calculated using the known transport properties of pure liquid water. A 25% (by volume) solution of PEO exhibits an average dielectric relaxation frequency of the suspending water of one half that of pure water, with clear evidence of a distribution of relaxation times present. The limits of the cumulative distribution of dielectric relaxation times that are consistent with the data are obtained using a linear programming technique. The application of simple mixture theory, under appropriate limiting conditions, yields hydration values for the more dilute polymer solutions that are somewhat larger than values obtained from thermodynamic measurements.     

Effect of cholesterol on the structure and dynamic properties of unsaturated phospholipid bilayers

Molecular dynamics (MD) computer simulations of five different hydrated unsaturated phosphatidylcholine lipid bilayers built up by 18:0/18:1(n-9)cis PC, 18:0/18:2(n-6)cis PC, 18:0/18:3(n-3)cis PC, 18:0/20:4(n-6)cis PC, and 18:0/22:6(n-3)cis PC molecules with 40 mol% cholesterol, and the same five pure phosphatidylcholine bilayers have been performed at 303 K. The simulation box of a lipid bilayer contained 96 phosphatidylcholines, 64 cholesterols, and 3840 water molecules (48 phosphatidylcholine molecules and 32 cholesterols per layer and 24 water molecules per phospholipid or cholesterol in each case). The lateral self-diffusion coefficients of the lipids in these systems and mass density profiles with respect to the bilayer normal have been analyzed. It has been found that the lateral diffusion coefficients of phosphatidylcholine molecules increase with increasing number of double bonds in one of the lipid chains, both in pure bilayers and in bilayers with cholesterol. It has been found as well that the lateral diffusion coefficient of phosphatidylcholine molecules of a lipid bilayer with 40 mol% cholesterol is smaller than that for the corresponding pure phosphatidylcholine bilayer.     

Water in channel-like cavities: structure and dynamics.

Ion channels contain narrow columns of water molecules. It is of interest to compare the structure and dynamics of such intrapore water with those of the bulk solvent. Molecular dynamics simulations of modified TIP3P water molecules confined within channel-like cavities have been performed and the orientation and dynamics of the water molecules analyzed. Channels were modeled as cylindrical cavities with lengths ranging from 15 to 60 A and radii from 3 to 12 A. At the end of the molecular dynamics simulations water molecules were observed to be ordered into approximately concentric cylindrical shells. The waters of the outermost shell were oriented such that their dipoles were on average perpendicular to the normal of the wall of the cavity. Water dynamics were analyzed in terms of self-diffusion coefficients and rotational reorientation rates. For cavities of radii 3 and 6 A, water mobility was reduced relative to that of simulated bulk water. For 9- and 12-A radii confined water molecules exhibited mobilities comparable with that of the bulk solvent. If water molecules were confined within an hourglass-shaped cavity (with a central radius of 3 A increasing to 12 A at either end) a gradient of water mobility was observed along the cavity axis. Thus, water within simple models of transbilayer channels exhibits perturbations of structure and dynamics relative to bulk water. In particular the reduction of rotational reorientation rate is expected to alter the local dielectric constant within a transbilayer pore.     

Structural and dynamical properties predicted by reactive force fields simulations for four common pure fluids at liquid and gaseous non-reactive conditions

Four common pure fluids were chosen to elucidate the reliability of reactive force fields in estimating bulk properties of selected molecular systems: CH₄, H₂O, CO₂ and H₂. The pure fluids are not expected to undergo chemical reactions at the conditions chosen for these simulations. The ‘combustion’ ReaxFF was chosen as reactive force field. In the case of water, we also considered the ‘aqueous’ ReaxFF model. The results were compared to data obtained implementing popular classic force fields. In the gas phase, it was found that simulations conducted using the ‘combustion’ ReaxFF formalism yield structural properties in reasonable good agreement with classic simulations for CO₂ and H₂, but not for CH₄ and H₂O. In the liquid phase, ‘combustion’ ReaxFF simulations reproduce reasonably well the structure obtained from classic simulations for CH₄, degrade for CO₂ and H₂, and are rather poor for H₂O. In the gas phase, the simulation results are compared to experimental second virial coefficient data. The ‘combustion’ ReaxFF simulations yield second virial coefficients that are not sufficiently negative for CH₄ and CO₂, and slightly too negative for H₂. The ‘combustion’ ReaxFF parameterisation induces too strong an effective attraction between water molecules, while the ‘aqueous’ ReaxFF yields a second virial coefficient that is in reasonable agreement with experiments. The ‘combustion’ ReaxFF parameterisation yields acceptable self-diffusion coefficients for gas-phase properties of CH₄, CO₂ and H₂. In the liquid phase, the results are good for CO₂, while the self-diffusion coefficient predicted for liquid CH₄ is slower, and that predicted for liquid H₂ is about nine times faster than those expected based on classic simulations. The ‘aqueous’ ReaxFF parameterisation yields good results for both the structure and the diffusion of both liquid and vapour water.     

Concerning Measurements of the Self-Diffusion Coefficient of Water Molecules and Time of Proton Spin-Lattice Relaxation in Plant Tissues

Measurements of the coefficient of water molecules self-diffusion (D) and the time of spin-lattice relaxation (T ₁) in prosenchyme (elongated) plant cells, whose length significantly exceeding their transverse size, show that the orientation of plant tissues in the H ₀field significantly affects the measured parameters. We conclude that this effect should be taken into account in experiments on the measurement of self-diffusion coefficients and time of proton spin-lattice relaxation in plant tissues containing prosenchyme cells.     

Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions.

We have developed a Brownian dynamics algorithm for simulating probe and self-diffusion in concentrated solutions of DNA and protein. In these simulations, proteins are represented as spheres with radii given by their hydrodynamic radii, while DNA is modeled as a wormlike chain of hydrodynamically equivalent spherical frictional elements. The molecular interaction potentials employed by the program allow for intramolecular stretching and bending motions of the DNA chains, short-range Lennard-Jones interactions, and long-range electrostatic interactions. To test the program, we have carried out simulations of bovine serum albumin (BSA) probe diffusion and DNA self-diffusion in solutions of short-chain DNA as a function of both DNA concentration and solution ionic strength. In addition, we report on simulations of BSA self-diffusion as a function of BSA concentration and ionic strength. Based on a comparison to available experimental data, we find that our simulations accurately predict these transport properties under conditions of physiological salt concentration and predict the stronger concentration dependence observed at lower salt concentrations. These results are discussed in light of the nature of the intermolecular interactions in such systems and the approximations and limitations of the simulation algorithm.     

Analysis of diffusion and relaxation behavior of water in apple parenchymal cells

It has been demonstrated by an example of apple parenchymal cells that NMR spectroscopy can be used to analyze the relaxation and diffusion of water molecules in plant cells. With small diffusion times, three relaxation components have been distinguished, which correspond to water in a vacuole, in the cytoplasm, and in intercellular liquid. The coefficient of self-diffusion corresponding to these components have been determined. With large diffusion times, it is possible to distinguish two components. For the slowly relaxing component (which corresponds to water in a vacuole), the regime of restricted diffusion was observed. For a quickly relaxing component, an anomalous increase in the coefficient of self-diffusion with the time of diffusion took place.     

PFG-NMR measurements of the self-diffusion coefficients of water in equilibrium poly(HEMA-co-THFMA) hydrogels

The self-diffusion coefficients for water in a series of copolymers of 2-hydroxyethyl methacrylate, HEMA, and tetrahydrofurfuryl methacrylate, THFMA, swollen with water to their equilibrium states have been studied at 310 K using PFG-NMR. The self-diffusion coefficients calculated from the Stejskal-Tanner equation, D(obs), for all of the hydrated polymers were found to be dependent on the NMR storage time, as a result of spin exchange between the proton reservoirs of the water and the polymers, reaching an equilibrium plateau value at long storage times. The true values of the diffusion coefficients were calculated from the values of D(obs) in the plateau regions by applying a correction for the fraction of water protons present, obtained from the equilibrium water contents of the gels. The true self-diffusion coefficient for water in polyHEMA obtained at 310 K by this method was 5.5 x 10(-10) m(2)s-1. For the copolymers containing 20% HEMA or more a single value of the self-diffusion coefficient was found, which was somewhat larger than the corresponding values obtained for the macroscopic diffusion coefficient from sorption measurements. For polyTHFMA and copolymers containing less than 20% HEMA, the PFG-NMR stimulated echo attenuation decay curves and the log-attenuation plots were characteristic of the presence of two diffusing water species. The self-diffusion coefficients of water in the equilibrium-hydrated copolymers were found to be dependent on the copolymer composition, decreasing with increasing THFMA content.     

Diffusion of water in the endosperm tissue of wheat grains as studied by pulsed field gradient nuclear magnetic resonance.

Pulsed field gradient nuclear magnetic resonance has been used to measure water self-diffusion coefficients in the endosperm tissue of wheat grains as a function of the tissue water content. A model that confines the water molecules to a randomly oriented array of capillaries with both transverse dimension less than 100 nm has been used to fit the data and give a unique diffusion coefficient at each water content. The diffusion rates vary from 1.8 x 10(-10) m2s-1 at the lowest to 1.2 x 10(-9) m2s-1 at the highest moisture content. This variation can be explained in terms of an increase in water film thickness from approximately 0.5 to approximately 2.5 nm over the moisture range investigated (200-360 mg g-1).     

Self-diffusion of polymers in cartilage as studied by pulsed field gradient NMR

Pulsed field gradient (PFG) nuclear magnetic resonance (NMR) was used to investigate the self-diffusion behaviour of polymers in cartilage. Polyethylene glycol and dextran with different molecular weights and in different concentrations were used as model compounds to mimic the diffusion behaviour of metabolites of cartilage. The polymer self-diffusion depends extremely on the observation time: The short-time self-diffusion coefficients (diffusion time Delta approximately 15 ms) are subjected to a rather non-specific obstruction effect that depends mainly on the molecular weights of the applied polymers as well as on the water content of the cartilage. The observed self-diffusion coefficients decrease with increasing molecular weights of the polymers and with a decreasing water content of the cartilage. In contrast, the long-time self-diffusion coefficients of the polymers in cartilage (diffusion time Delta approximately 600 ms) reflect the structural properties of the tissue. Measurements at different water contents, different molecular weights of the polymers and varying observation times suggest that primarily the collagenous network of cartilage but also the entanglements of the polymer chains themselves are responsible for the observed restricted diffusion. Additionally, anomalous restricted diffusion was shown to occur already in concentrated polymer solutions.