Spectral signatures of the diffusional anomaly in water

Power spectra for various tagged particle quantities in bulk extended simple point charge model water [H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987)] are shown to have a regime with 1f(alpha) dependence on frequency f with alpha lying between 1 and 1.5 if the dynamical changes in the particular observable are sensitive to the multiple time-scale behavior of the hydrogen-bond network. The variations in mobility associated with the diffusional anomaly are mirrored in the scaling exponent alpha associated with this multiple time-scale behavior, suggesting that monitoring of 1f(alpha) behavior is a simple and direct method for linking phenomena on three distinctive length and time scales: the local molecular environment, hydrogen-bond network reorganizations, and the diffusivity. Our results indicate that experimental studies of supercooled water to probe the density dependence of 1f(alpha) spectral features, or equivalent stretched exponential behavior in time-correlation functions, will be of interest.     

Coherent and diffusional motion of a chemisorbed atom

Experiments indicate that there are two extreme types of motion of an atom on a solid surface. One is characterized by an average velocity and has a mean square displacement proportion to the square of the time (we call this coherent). The other (called purely diffusional) is characterized by a diffusion coefficient and has a mean square displacement proportional to time. We present a simple stochastic model to explain the microscopic origin of these two extreme types of motion. In the case in which both types of motion coexist, the motion becomes diffusional for times longer than an intrinsic time depending on the intensity of the thermal fluctuations of the atom—lattice coupling.     

Modeling diffusional transport in the interphase cell nucleus

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: Randomly distributed, noninterconnected obstacles, a random walk chain model, and a self-avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the three dimensional geometry of the fiber network on the particle diffusion is investigated in detail while varying the occupation volume, chain length, persistence length, and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self-avoiding random walk model, and, to a lesser extent, the persistence length affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.     

Non-orthogonal basis functions in the solution of diffusional problems

The diffusion equation in presence of strong potential gradients can be conveniently solved by means of a suitable set of non-orthogonal basis functions that mimic the asymptotic behaviour of the eigensolutions of the time evolution operator. This method is discussed in the context of the calculation of spectroscopic observables by means of the Lanczos algorithm, that is by representing the spectral density as a continued fraction. The modified Lanczos algorithm, which takes into account the non-orthogonality of the basis functions, is analysed in detail. In order to test the performance of the new procedure, the planar rotor subject to a cosine potential is considered, and the set of non-orthogonal functions having the correct asymptotic behaviour is derived in both cases of single and double minimum. The results of the numerical calculations clearly show the advantages of the proposed method when dealing with systems characterized by hindered motions.     

Suppression of red cell diffusional water permeability by lipophilic solutes

The inhibitory effect of a series of neutral lipophilic solutes (methanol, ethanol, n-propanol, iso-propanol, n-butanol, iso-amylalcohol, n-hexanol, diethylether, nitrobenzene, and pyridine) on the diffusional water permeability (Pd, tot) of bovine erythrocyte membrane at 25 degrees C was studied in comparison to that of p-chloromercuri benzoate (pCMB). Permeability data were obtained by measuring the transmembrane diffusional water exchange time tau(exch) using an 1H-T2 NMR technique. Maximal inhibition by approximately 50% of Pd, tot was produced by 2 mM pCMB which completely blocked the membrane water channels in 20 min, hence suggesting the channel-to-lipid diffusional water permeability ratio of about 1:1. Furthermore, the maximal inhibitory effect of pCMB in combination with the lipophilic solutes was lower than that of pCMB alone. As pCMB does not interfere with the lipid bilayer, and provided that it blocks the water channels in solute presence as well, this confirms that the solutes induce an increase in the lipid-mediated background water permeability contribution (Pd, lipid) by the formation of aqueous leaks in the membrane hydrophobic barrier. However, faster but less efficient in permeability inhibition than pCMB (either alone or combined with solutes) were the lipophilic solutes alone. Taken together, the results indicate that the lipophilic solutes suppress the membrane total permeability Pd, tot by two opposing effects: a reduction of its channel-mediated part (Pd, channel) to the extent exceeding that of a simultaneous Pd, lipid increase. The inhibitory potency of the solutes tested appears to be correlated with their solubility in the membrane medium.     

Electrochemical deposition of indium: nucleation mode and diffusional limitation

the electrochemical deposition of indium metal from InCl₃ solutions was investigated. Cyclovoltammetric experiments showed that the initial hydrogen evolution reaction, observed together with the metal deposition on Pt surface, is blocked when the surface is covered by In. At large cathodic potentials, the current is diffusion-limited. The scan rate dependence of cyclovoltammograms allowed the determination of the diffusion coefficient of In³⁺ ions, 8.18 × 10^–6 cm²/s, using the Delahay equation. The activation energy of diffusion, determined from the temperature dependence of cyclovoltammograms, is about 0.3 eV (23 kJ/mol). Chrono-amperometric experiments are consistent with the cyclovoltammetry; the In³⁺ diffusion coefficient determined using the Cottrell law is in good agreement with the value determined by the Randles-?ev?ik equation. Moreover the use of the nucleation models developed by Scharifker and Hills showed a progressive nucleation mode. Electron microscopy observations and X-ray diffraction patterns confirmed the formation of crystalline indium deposits.     

Ionic character

The concept of ionic character in and bond systems is considered in the light of recent definitions of orbital electronegativity [6, 14].

---

Zusammenfassung Das Konzept des ionischen Charakters in und Bindungen wird im Lichte neuerer Definitionen von Orbitalelektronegativitäten diskutiert.

---

Résumé Le caractère ionique des liaisons et est discuté en tenant compte des définitions récentes de l'électronégativité des orbitales.

---

---

We wish to acknowledge financial support from the National Research Council of Canada. One of us (N.C.B.) thanks the council for the award of a studentship.     

Collective effects in diffusional motion of water molecules: computer simulation

Structural Chemistry - Molecular dynamics simulation of the system containing 3,456 water molecules in the cubic periodic box was performed. Virtual temperatures were 261 and 297&;nbsp;K....     

A diffusional alternative to the Marcus free energy gap law

The results of the precise kinetic fitting of the highly exergonic electron transfer from excited perylene to tetracyanoethylene in acetonitrile were used to estimate the Stern-Volmer constant of perylene quenching by double channel electron transfer (to the ground and excited states of the radical ion pair). It appears that the Stern-Volmer constant is exactly the same as the diffusional height of the Rehm-Weller plateau, substituting the exergonic wing of the Marcus free energy gap law. Even the single channel transfer is shown to be fast enough that the quenching should be under true diffusional control at the highest available exergonicity.     

Extension of the diffusional kinetics models involving changes in activation energy

On the basis of previous modifications of the Zhuravlev and Ginstling-Brounshtein models, a generalization of kinetic diffusional models is proposed. With the assumption that the rate of the activation energy change during the reaction is inversely proportional to the reaction time, it has been shown that all diffusional kinetic equations in heterogeneous systems take the formF()=KT ⁿ , whereF() is a function of the degree of conversion andK andn are constants related to the rate constant.

---

Zusammenfassung Auf Grund vorangegangener Modifikationen der Modelle von Zhuravlev und Ginstling-Brounshtein wird eine Verallgemeinerung der kinetischen Diffusionsmodelle vorgeschlagen. Mit der Annahme, daß die Geschwindigkeit der Änderung der Aktivierungsenergie während der Reaktion umgekehrt proportional der Reaktionszeit ist, wird gezeigt, daß alle kinetischen Diffusionsgleichungen für heterogene Systeme die FormF()=KT ⁿ haben, woF() eine Funktion des Konversionsgrades undK undn mit der Geschwindigkeitskonstante in Beziehung stehende Konstanten sind.

---

- . , , , F()=KT ⁿ , F() — , K n — .

     

Chaperone-assisted protein folding in the cell cytoplasm

Folding of polypeptides in the cell typically requires the assistance of a set of proteins termed molecular chaperones. Chaperones are an essential group of proteins necessary for cell viability under both normal and stress conditions. There are several chaperone systems which carry out a multitude of functions all aimed towards insuring the proper folding of target proteins. Chaperones can assist in the efficient folding of newly-translated proteins as these proteins are being synthesized on the ribosome and can maintain pre-existing proteins in a stable conformation. Chaperones can also promote the disaggregation of preformed protein aggregates. Many of the identified chaperones are also heat shock proteins. The general mechanism by which chaperones carry out their function usually involves multiple rounds of regulated binding and release of an unstable conformer of target polypeptides. The four main chaperone systems in the Escherichia coli cytoplasm are as follows. (1) Ribosome-associated trigger factor that assists in the folding of newly-synthesized nascent chains. (2) The Hsp 70 system consisting of DnaK (Hsp 70), its cofactor DnaJ (Hsp 40), and the nucleotide exchange factor GrpE. This system recognizes polypeptide chains in an extended conformation. (3) The Hsp 60 system, consisting of GroEL (Hsp 60) and its cofactor GroES (Hsp 10), which assists in the folding of compact folding intermediates that expose hydrophobic surfaces. (4) The Clp ATPases which are typically members of the Hsp 100 family of heat shock proteins. These ATPases can unfold proteins and disaggregate preformed protein aggregates to target them for degradation. Several advances have recently been made in characterizing the structure and function of all of these chaperone systems. These advances have provided us with a better understanding of the protein folding process in the cell.     

Effects of water model and simulation box size on protein diffusional motions

We performed molecular dynamics simulations of ubiquitin with the distinct water models, TIP3P, SPC, SPC/E, and SPC/Fw, in different system sizes with different box shapes. The translational diffusion constants of pure water linearly depend on the effective box length, which is known as finite size effect, whereas the first and second rotational times of pure water are nearly constant. We then observed that both the overall translation and rotational motions of the protein are linearly correlated to the viscosity of pure water. As expected from the finite size effect in pure water, the translational diffusion of the protein is significantly affected by the system size, and rotational diffusion is nearly size-independent. After correction for the finite size effect, the SPC/E and SPC/Fw models reproduce both the translational and rotational motion of the protein relatively well. Thus, water models that reproduce the experimentally derived diffusional properties of pure water accurately are expected to also be suitable for simulating protein diffusion quantitatively.     

Analysis of transient membrane protein interactions by single-molecule diffusional mobility shift assay

Various repertoires of membrane protein interactions determine cellular responses to diverse environments around cells dynamically in space and time. Current assays, however, have limitations in unraveling these interactions in the physiological states in a living cell due to the lack of capability to probe the transient nature of these interactions on the crowded membrane. Here, we present a simple and robust assay that enables the investigation of transient protein interactions in living cells by using the single-molecule diffusional mobility shift assay (smDIMSA). Utilizing smDIMSA, we uncovered the interaction profile of EGFR with various membrane proteins and demonstrated the promiscuity of these interactions depending on the cancer cell line. The transient interaction profile obtained by smDIMSA will provide critical information to comprehend the crosstalk among various receptors on the plasma membrane.Subject terms: Fluorescence imaging, Super-resolution microscopy, Single-molecule biophysics     

Model of nanocrystal formation in solution by burst nucleation and diffusional growth

The phenomenon of burst nucleation in solution, in which a period of apparent chemical inactivity is followed by a sudden and explosive growth of nucleated particles from a solute species, has been given a widely accepted qualitative explanation by LaMer and co-workers. Here, we present a model with the assumptions of instantaneous re-thermalization below the critical nucleus size and irreversible diffusive growth above the critical size, which for the first time formulates LaMer's explanation of burst nucleation in a manner allowing quantitative calculations. The behavior of the model at large times, t, is derived with the result that the average cluster size, as measured by the number of atoms, grows approximately t, while the width of the cluster distribution grows approximately (sq root)1.We develop an effective numerical scheme to integrate the equations of the model and compare the asymptotic expressions to results from numerical simulation. Finally, we discuss the physical effects which cause real nucleation processes in solution to deviate from the behavior of the model.     

Enhanced videomicroscopy of phase transitions and diffusional phenomena in oil-water-nonionic surfactant systems

Videomicroscopy was used to observe dynamic behavior accompanying phase transformation in waternonionic surfactant mixtures and the contact of these mixtures with pure hydrocarbons. Various unusual phenomena involving growth and dissolution of the lamellar liquid crystalline phase were seen, including the formation of myelinic figures and bâtonnets by the novel procedure of heating an isotropic liquid. In some phenomena the defect structure of the liquid crystalline phase played a controlling role. For instance, initial nucleation of fluid phases was seen to occur along defects, the first such observation for liquid crystals. Various types of behavior were seen in the contacting experiments, depending on whether the temperature was well below, near, or well above the phase inversion temperature. The chief phenomena, spontaneous emulsification and intermediate phase formation, were similar in many respects to those seen previously in anionic surfactant systems and were explainable in terms of diffusion path theory. In several experiments flow produced by natural convection and/or Marangoni effects increased the rate of equilibration and was the source of rather dramatic behavior.     

Charge dynamics of a methane adsorption storage system: Intraparticle diffusional effects

The charge of natural gas adsorption storage systems is studied numerically, With emphasis given to the impact on its dynamics of intraparticle diffusional resistances to mass transport. Besides adsorption kinetics and thermal effects, the simulation model takes into account both mass transport inside the adsorbent and hydrodynamics of flow through the packed bed. Numerical results are presented for change with methane of a 50 liter cylindrical reservoir, filled with hypothetical adsorbents with diffusional time constants in the range 10^?3 s¹ D/R _p ² ≤ ∞. and with the adsorption equilibrium curve of a commercially available activated carbon with a good adsorptive storage capacity. An attempt is made to assemble the charge histories for different values ofD/R _p ² , in a single cure by using a modilied time scale.     

Charge dynamics of a methane adsorption storage system: Intraparticle diffusional effects

The charge of natural gas adsorption storage systems is studied numerically, With emphasis given to the impact on its dynamics of intraparticle diffusional resistances to mass transport. Besides adsorption kinetics and thermal effects, the simulation model takes into account both mass transport inside the adsorbent and hydrodynamics of flow through the packed bed. Numerical results are presented for change with methane of a 50 liter cylindrical reservoir, filled with hypothetical adsorbents with diffusional time constants in the range 10^–3 s¹ D/R _p ² . and with the adsorption equilibrium curve of a commercially available activated carbon with a good adsorptive storage capacity. An attempt is made to assemble the charge histories for different values ofD/R _p ² , in a single cure by using a modilied time scale.     

Voltammetric studies of diffusional and migrational transport of ferrocene derivative of tripeptide glutathione

The transport of mono- and divalent anions of S-ferrocenylmethyl-L-glutathione (FcCH2SG) was investigated voltammetrically at a microelectrode in solutions of low ionic strength. The electrooxidation reactions of the ferrocenyl group attached to biologically active glutathione neutralized with a strong base in two consecutive steps can be represented as FcCH(2)SG(-) --> Fc(+)CH(2)SG(-) + e and FcCH(2)SG(2-) --> Fc(+)CH(2)SG(2-) + e for the mono- and divalent anions of FcCH(2)SG, respectively. The limiting currents due to these electrode processes were investigated under the conditions of varying content of supporting ions. The results obtained for the electrooxidation of the monovalent anion of FcCH(2)SG deviate significantly from the theoretical predictions derived for the charge cancellation electrode processes (i.e., processes producing uncharged species upon electron transfer). The differences observed are attributed to the specific migrational behavior of the generated dipole-like product which formally bears no net charge but in fact contains two oppositely charged moieties within a molecule. To interpret the data obtained for the divalent anion of FcCH(2)SG, a recent model of the theory of migrational voltammetry has been adapted and extended. The agreement between the experimental data and the theory is obtained only for the ratio of diffusion coefficients of the electrode process product (Fc(+)CH(2)SG(2-)) and the substrate (FcCH(2)SG(2-)) smaller than 1. This leads to a conclusion that upon oxidation this molecule undergoes a conformation change and winds up because of the formation of a coordination bond. The conclusion is supported by molecular-mechanics calculations. The presented methodology allows one to study quantitatively the changes in the concentration distribution of biologically active molecules driven by migration and diffusion and to diagnose their possible structural changes upon reduction/oxidation. Both factors are essential for the proper understanding of the functionality of biologically active systems.