Molecular dynamics study of translational and rotational diffusion in liquid ortho-terphenyl

NVT molecular dynamics simulations were performed on liquid o-terphenyl as a function of temperature in the range 320-480 K. Computed translational diffusion coefficients displayed the non-Arrhenius behavior expected of a fragile glass-forming liquid and were in good, semiquantitative agreement with experimental results. Rotational correlation functions calculated for various vectors within the molecule exhibited a very short time (0-1 ps) initial decay, followed by a reversal, which corresponds to free reorientation within the "solvent" cage prior to collision with a wall. Rotational correlation times of three orthogonal vectors fixed on the central benzene were close to equal at all temperatures, indicating nearly isotropic overall molecular reorientation. The average correlation times exhibited a non-Arrhenius temperature dependence and were in very good agreement with experimental values derived from 2D and 1H NMR relaxation times. Correlation times of vectors located on the lateral phenyl rings were used to calculate the "spinning" internal rotation diffusion coefficients, which were approximately twice as great as the overall rotational diffusion constants, indicating rapid internal rotation of the phenyl side groups over wide ranges of angle in the liquid.     

Entanglement in polystyrene detected by translational diffusion of photo-labeled molecules

The contribution of polymer diffusion studies to clarifying the entanglement problem in polymer chain liquids is reviewed. In particular, we present a phenomenological equation for a critical molecular weight M_C as a function of the diffusant and matrix molecular weights, respectively, and compare it with recent theories.     

Molecular dynamics study of anisotropic translational and rotational diffusion in liquid benzene

Equilibrium NPT and NVT molecular dynamics simulations were performed on liquid benzene over an extended range of temperature (from 260 to 360 K) using the COMPASS force field. Densities and enthalpies of vaporization (from cohesive energy densities) were within 1% of experiment at all temperatures. tumbling and spinning rotational diffusion coefficients, D(perpendicular) and D(parallel), computed as a function of temperature, agreed qualitatively with the results of earlier reported experimental and computational investigations. Generally, it was found that D(parallel)/D(perpendicular) approximately 1.4-2.5 and the activation energy for tumbling was significantly greater than for spinning about the C6 axis [Ea(D(perpendicular)) = 8.1 kJ mol(-1) and Ea(D(parallel)) = 4.5 kJ mol(-1)]. Calculated translational diffusion coefficients were found to be in quantitative agreement with experimental values at all temperatures [deviations were less than the scatter between different reported measurements]. In addition, translational diffusion coefficients were computed in the molecule-fixed frame to yield values for Dxy (diffusion in the plane of the molecule) and Dz (diffusion perpendicular to the plane). It was found that the ratio Dxy/Dz approximately 2.0, and that the two coefficients have roughly equal activation energies. This represents the first atomistic molecular dynamics study of translational diffusion in the molecular frame.     

Size and shape of fast-tumbling bicelles as determined by translational diffusion

In this study, the size and shape of an isotropic bicelle have been determined by measuring the translational diffusion as a function of the volume fraction of the lipids. A linear relation between the diffusion coefficients is obtained for both DMPC and DHPC in the bicelles. The slope of this linear function, which is strongly shape-dependent, is found to be different for the two molecules. This difference is direct evidence that the two molecules are not fully mixed in the bicelle. The shape- combined with the size-dependence of the diffusion coefficient allows us to calculate both the size and shape of the bicelle.     

A study of the relation between translational and rotational diffusion through measurement of molecular recollision

Translational and rotational diffusion rates of perdeuterated tempone (PDT) in ethanol are determined using electron paramagnetic resonance spectroscopy. The translational motion is measured on two scales: the macroscopic, as represented by the Heisenberg spin-exchange rate, and the microscopic, which entails recollisions between the same spin-exchange particle pair. The spin-exchange and recollision rates are used together to calculate the overall translational diffusion coefficient without recourse to assumptions concerning the value of the Stokes radius or collision distance. When observed as a function of solvent isothermal compressibility, the recollision time in ethanol is displaced from the common alkane curve at low temperatures but joins that curve at higher temperatures. Rotational correlation times in ethanol are obtained and show a decreasing rotation-translation coupling with increasing temperature, revealing a pattern that is qualitatively identical with respect to both collision and recollision. In comparison, an examination of PDT diffusion in toluene reveals an increasing rotation-translation coupling with increasing temperature. The contrasting behavior of the coupling in the two solvents is attributable to the degree of anisotropy in PDT rotation.     

Investigation of water diffusion into quartz using ion beam analysis techniques

Diffusion of water into quartz was studied by measuring H and ¹⁸O concentration profiles in surface layers of quartz samples treated hydrothermally in the range of 125° C to 200° C. Sample surfaces were orientated normal to the c-axis. The measurements were performed using the nuclear reactions ¹H(¹⁵N,αγ)¹²C and ¹⁸O(p,α)¹⁵N. The diffusion profiles have widths of up to 500 nm. Diffusion rate constants derived from the profiles are in the range of 10^–15 cm²/s to 10^–18 cm²/s and show a distinct temperature dependence, yielding a rough estimate of about 60 kJ/mole for the activation energy. Received: 24 June 1996 / Revised: 20 January 1997 / Accepted: 22 January 1997     

Structural insights into the mechanism of translational inhibition by the fungicide sordarin

The translational machinery has been found to be the target for a number of antibiotics. One such antibiotic sordarin selectively inhibits fungal translation by impairing the function of elongation factor 2 (eEF2) while being ineffective to higher eukaryotes. Surprisingly, sordarin is not even equally effective in impairing translation for all fungal species. The binding cavity of sordarin on eEF2 has been localized by X-ray crystallographic study and its unique specificity towards sordarin has been attributed to the species specific substitutions within a stretch of amino acids (sordarin specificity region, SSR) at the entrance of the cavity. In this study, we have analyzed the sordarin-binding cavity of eEF2 from different species both in isolated and ribosome-bound forms in order to decipher the mechanism of sordarin binding selectivity. Our results reveal that the molecular architecture as well as the microenvironment of the sordarin-binding cavity changes significantly from one species to another depending on the species specific substitutions within the cavity. Moreover, eEF2 binding to ribosome aggravates the effects of these substitutions. Thus, this study, while shedding light on the molecular mechanism underpinning the selective inhibitory effects of sordarin, will also be a helpful guide for future studies aiming at developing novel antifungal drugs with broader spectrum of activity.     

Molecular dynamics simulation study on the transient response of solvation structure during the translational diffusion of solute

The transient response function of the density profile of the solvent around a solute during the translational diffusion of the solute is formulated based on the generalized Langevin formalism. The resultant theory is applied to both neat Lennard-Jones fluids and cations in liquid water, and the response functions are obtained from the analysis of the molecular dynamics simulations. In the case of the self-diffusion of Lennard-Jones fluids, the responses of the solvation structures are in harmony with conventional pictures based on the mode-coupling theory, that is, the binary collision in the low-density fluids, the backflow effect from medium to high density fluids, and the backscatter effect in the liquids near the triple point. In the case of cations in water, the qualitative behavior is strongly dependent on the size of cations. The pictures similar to simple dense liquids are obtained for the large ion and the neutral molecule, while the solvent waters within the first solvation shell of small ions show an oscillatory response in the short-time region. In particular, the oscillation is remarkably underdumped for lithium ion. The origin of the oscillation is discussed in relation to the theoretical treatment of the translational diffusion of ions in water.     

Enhanced translational diffusion of rubrene in sucrose benzoate

The translational diffusion of rubrene in the fragile molecular glass former, sucrose benzoate (SB) (fragility index m approximately 94), has been studied from T(g)+6 K to T(g)+71 K(T(g)=337 K) by using the technique of holographic fluorescence recovery after photobleaching. In the temperature range of the measurements, the translational relaxation functions were observed to decay exponentially, indicating that Fick's law of diffusion governs the translational motion of rubrene in sucrose benzoate. The value of the translational diffusion coefficient D(T) obtained from the 1e time of the translational relaxation function varied from 5.3 x 10(-15) cm2 s(-1) at 343 K to 5.0x10(-9) cm2 s(-1) at 408 K. The temperature dependence of D(T) for diffusion of rubrene in SB is compared with that of the viscosity and the dielectric relaxation time tau(D) of SB. The temperature dependence of D(T) is weaker than that of Teta for T<1.2T(g) but tracks the reciprocal of the dielectric relaxation time 1tau(D) for 1.05T(g)相似文献   

An NMR study of translational diffusion and structural anisotropy in magnetically alignable nonionic surfactant mesophases

The diffusion of both water and surfactant components in aqueous solutions of the nonionic surfactant "C12E6"--which includes hexagonal, cubic, lamellar, and micellar mesophases--has been studied by pulsed-field-gradient NMR. Diffusion coefficients were measured in unaligned samples in all of these phases. They were also obtained in the hexagonal and lamellar phases in oriented monodomain samples that were aligned by slow cooling from the micellar phase in an 11.7 T magnet. Measured water and soap diffusion coefficients in the NMR-isotropic cubic and (high-water-content) micellar phases as well as diffusion anisotropy measurements in the magnetically aligned hexagonal phase were quantitatively consistent with the constituent structures of these phases being identical surfactant cylinders, with only the fraction of surface-associated water varying with the water-soap molar ratio. The values of the water and soap diffusion coefficients in the oriented lamellar phase suggest an increase in defects and obstructions to soap diffusion as a function of increasing water content, while those in the low-water-content micellar phase rule out the presence of inverse micelles.     

Separating the contribution of translational and rotational diffusion to protein association

The association of two proteins is preceded by a mutual diffusional search in solution. The role of translational and rotational diffusion in this process has been studied theoretically for many years. However, systematic experimental verification of theoretical results is still lacking. We report here measurements of association rates of the proteins beta-lactamase (TEM) and beta-lactamase inhibitor protein (BLIP) in solutions of glycerol and poly(ethylene glycol) of increasing viscosity. We also measured translational and rotational diffusion in the same solutions, using fluorescence correlation spectroscopy and fluorescence anisotropy, respectively. It is found that in glycerol both translational and rotational diffusion rates are inversely dependent on viscosity, as predicted by the classical Stokes-Einstein relations, while the association rate depends nonlinearly on viscosity. In contrast, the association rate depends only weakly on the viscosity of the polymer solutions, which results in a similar weak dependence of k(on) on viscosity. The data are modeled using the theory of diffusion-limited association. Deviations from the theory are explained by a short-range solute-induced repulsion between the proteins in glycerol solution and an attractive depletion interaction generated by the polymers. These results open the way to the creation of a unified framework for all nonspecific effects involved in the protein association process, as well as to better theoretical understanding of these effects. Further, they reflect on the complex factors controlling protein association within the crowded environment of cells and suggest that a high concentration of macromolecules does not significantly impede protein association.     

Enhanced translational diffusion of rubrene and tetracene in polysulfone

Translational diffusion of tetracene and rubrene in bisphenol A polysulfone (T_g = 460 K) was measured using a holographic fluorescence recovery after photobleaching (FRAP) technique. In the temperature range from 493 to 462 K, probe translation was diffusive and the translational diffusion coefficients varied from 10⁻⁸ to 10⁻¹³ cm²/s. Surprisingly, the observed translational diffusion coefficients showed a weaker temperature dependence than the rotational correlation times of the same probes. Rotational correlation times have the same temperature dependence as the viscoelastic relaxation times characteristic of the rubberlike modulus, while translational relaxation times decouple from the viscoelastic relaxation times. On average, probe molecules are translating larger and larger distances per probe rotation time as the temperature is lowered to T_g. These results can be explained qualitatively in terms of spatially heterogeneous segmental dynamics in the polysulfone matrix. © 1996 John Wiley & Sons, Inc.     

An EPR study of the triplet state of pentacene by electron spin-echo techniques and laser flash excitation

By combining the electron spin-echo technique with pulsed-laser excitation we have been able to perform an EPR study of the very short-lived (≈ 30 μs) triplet state of pentacene in naphthalene. We have obtained the orientation of the pentacene molecule in the naphthalene host crystal, the zero-field splitting parameters, and the kinetic properties of the triplet spin levels.     

A kinetic study of diffusion in the electrothermal atomizer with a graphite filter by laser excited atomic fluorescence

Laser excited atomic fluorescence-electrothermal atomizer (LEAFS-ETA) was used to study atomization and diffusion mechanisms in a novel diffusive graphite tube atomizer. The atomizer design included a hollow graphite cylinder mounted between two graphite rods which served as electrodes. One of the rods had a small graphite insert with a sampling hollow and could move backwards and forwards. After the sample was introduced into the hollow, the electrodes tightly sealed the graphite cylinder ensuring that the insert was directly in the center of the furnace. The furnace assembly was then heated and the vaporized sample diffused through the hot graphite wall. The atomic fraction of the sample vapor was excited by a laser beam which was directed along the graphite tube surface so that no gap remained between the beam and the tube surface. Fluorescence vs. time profiles for three elements — Cu, Ag and Ni — were obtained within the temperature range of 1400–2600 K. The rate constants of specific processes were measured from the decay portions of the fluorescence signals under the assumption of first-order kinetics. The Arrhenius plots were constructed and the activation energies, E_a were evaluated from their slopes. The plots obtained for Cu and Ag consisted of two linear parts, the corresponding values of E_a were: 195 kJ/mol and 77 kJ/mol for Cu (1550 K < T < 2600 K) and 238 kJ/mol and 97 kJ/mol for Ag (1430 K < T < 2280 K). The Arrhenius plot for Ni was linear within the temperature range of 1770–2530 K resulting in an E_a equal to 161 kJ/mol. The diffusion coefficients were evaluated on the basis of a steady-state diffusion model out of a hollow cylinder. The values for the diffusion coefficients were: 3.7·10⁻⁴−2.0·10⁻³ cm²/s (1750–2600 K) for Cu, 6.5·10⁻³−1.4·10⁻³ cm²/s (1750–2280 K) for Ag and 5.6·10⁻⁵−1.5·10⁻³ cm²/s (1770–2530 K) for Ni.     

Roles of translational and reorientational modes in translational diffusion of high-pressure water: comparison with soft-core fluids

The dynamics of two soft-core fluids that show the increase in diffusivity with isothermal compression is studied with the mode-coupling theory (MCT). The anomalous density dependence of the diffusivity of these fluids is reproduced by the theory, and it is ascribed to the decrease in the first peak of the structure factor. The mechanism is quite different from that of high-pressure water revealed by MCT on molecular liquids described by the interaction-site model [T. Yamaguchi, S.-H. Chong, and F. Hirata, J. Chem. Phys., 119, 1021 (2003)]. The structures used in that study, calculated by the reference interaction-site model integral equation theory, showed the increase in the height of the first peak of the structure factor between oxygen atoms, whereas the structure obtained by molecular dynamics (MD) simulations shows the decrease in the peak height. In this work, calculations with MCT are performed on the simple fluids whose structure factor is the same as that between oxygen atoms of water from MD simulation, in order to clarify the role of translational structure on the increase in diffusivity with compression. The conclusion is that both the translational and reorientational modes contribute to the increase in diffusivity, and the effect of the latter is indispensable for the anomaly alone at least above freezing temperature.     

Morphology of three lyotropic liquid crystalline biological NMR media studied by translational diffusion anisotropy.

The morphologies of three dilute liquid crystalline phases, which are widely used for biological NMR spectroscopy, are investigated by the study of tracer self-diffusion. The aqueous liquid crystalline media investigated include the common phospholipid bicelle medium, a phase consisting of a mixture of pentaethyleneglycol mono dodecyl ether and hexanol, and a medium containing cetylpyridinium bromide and hexanol. Threonine and water were used as tracer molecules for probing the aqueous environment, and tetramethylsilane (TMS) was for probing the lipophilic environment. Pulsed field gradient NMR was used to measure tracer self-diffusion rates in three orthogonal directions. Although results for the water-soluble tracers in bicelle media do not contradict the widely accepted disk-shaped bicelle model, the high TMS diffusion rate observed in the bilayer plane requires extensive transient edge-to-edge contacts of such disks. This morphology is essentially that of a heavily perforated lamellar bilayer phase and explains why this medium remains liquid crystalline well below the Onsager limit for disk-shaped nematogens. Below 25 degrees C, a bicelle mixture consisting of dimyristoyl phosphatidyl choline and dihexanoyl phosphatidyl choline remains isotropic, but tracer diffusion obstruction indicates that the particles are significantly oblate. The diffusion anisotropy in the penta(ethyleneglycol) mono dodecyl ether liquid crystals confirms the previously proposed alpha-lamellar phase. However, weak inhibition of aqueous-phase self-diffusion in the z direction points to the presence of bridge- or caplike obstructions, and the bilayers appear slightly permeable to water. If the previously proposed concentric cylinder superstructure of bilayers applies, the diffusion data indicate that the most outer cylinder must have a diameter greater than 50 microm. The tracer self-diffusion data for the cetylpyridinium bromide/hexanol medium is only compatible with a planar alpha-lamellar phase, with its local director orthogonal to the magnetic field, and a very large domain size over which the director remains parallel.     

Copper diffusion in cable-insulating materials by chemiluminescence and DSC techniques

Journal of Thermal Analysis and Calorimetry - Chemiluminescence (CL) and differential scanning calorimetry (DSC) were applied for proving the copper ion migration processes occurring within the...     

A study of solvent diffusion in thin polyimide films using laser interferometry

Using laser interferometry, we have determined in situ the thickness increase with time of thin supported polyimide films (4–8 μm in initial thickness) immersed in n-methyl-2-pyrrolidone (NMP) as a function of NMP temperature (22–120°C). Similar experiments were also performed in dimethyl sulfoxide (DMSO) at 22°C with polyimide films of 4.1 μm in thickness. For NMP, the equilibrium fractional thickness increase (about 20%) is independent of initial polyimide thickness and temperature. The time scale for reaching equilibrium sharply decreases with temperature from 2–3 days at 22°C to 30–60 min at 120°C. Compared with NMP, the rate of DMSO sorption is considerably faster, reaching equilibrium swelling of about 28% in about 5 h at 22°C. To describe the transport process, we applied a phenomenological model proposed by Astarita and Sarti¹ but reformulated in polymer fixed frame to enable straightforward comparison with the thickness data. Our analysis indicated that the transport of NMP is best described as anomalous, that is, intermediate between diffusion controlled and case II transport. The effective diffusion coefficient D_eff and the front velocity U₀ at 22°C were found to be 3–6 × 10^?12 cm²/s and 8 × 10^?9 cm/s, respectively. Our front velocity is in good accord with the value of 6 × 10^?9 cm/s obtained for a similar polyimide based on gravimetric measurements.² Both D_eff and U₀ show an activation energy of ～56 kJ/mol. For DMSO, however, the transport is clearly case II. The front velocity at 22°C was found to be about 6 × 10^?8 cm/s, which is about four times that obtained by Rutherford back-scattering spectrometry.³