Protonation equilibria of glycine, 1,10-phenanthroline and 2,2-bipyridyl in ethylene glycol–water mixtures

Abstract

The solute–solvent interactions of glycine, 1,10-phenanthroline and 2,2-bipyridyl have been studied in 0–60% v/v ethylene glycol–water media by a pH metric method. The protonation constants were estimated with the computer program MINIQUAD75. Selection of the best fit chemical model of the protonation equilibria is based on the standard deviation in protonation constants and residual analysis using a sum of squares of residuals in all mass-balance equations. The observed linear variation of protonation constants with the inverse of dielectric constant of the solvent mixture can be attributed to the dominance of the electrostatic forces. The distribution of species, protonation equilibria and effects of influential parameters on the protonation constants are also presented.     

Dielectric behavior of DNA in water–organic co-solvent mixtures

The radiowave dielectric dispersions of DNA in different water–organic co-solvent mixtures have been measured in the frequency range from 100 kHz to 100 MHz, where the polarization mechanism is generally attributed to the confinement of counterions within some specific lengths, either along tangential or perpendicular to the polyion chain. The dielectric dispersions have been analyzed on the basis of two partially different dielectric models, a continuum counterion fluctuation model proposed by Mandel and a discrete charged site model, proposed by Minakata. The influence of the quality of the solvent on the dielectric parameters has been investigated in water–methanol and water–glycerol mixtures at different composition, by varying the permittivity ?_m and the viscosity η of the solvent phase. The analysis of the dielectric spectra in solvents where electrostatic and hydrodynamic interactions vary with the solvent composition suggests that both the two models are able, in principle, to account for the observed high-frequency dielectric behavior. However, while some certain assumptions are necessary about the polyion structure within the Mandel model, no structural prerequisite is needed within the Minakata model, where the polarization mechanism invoked considers a radial counterion exchange with the outer medium, which is largely independent of the local polyion conformation.     

A molecular dynamics simulation study of the effect of water–graphene interaction on the properties of confined water

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsive r^?12 potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r^?12 potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential.     

Modeling of formation and breaking of lubricant bridge in the head–disk interface by molecular dynamic simulation

The technology of heat-assisted magnetic recording (HAMR) has improved the storage density of hard disc drives. The PFPE molecules of lubricant layer adhered on the disc can transfer from the lubricant layer and form the lubricant bridge which can deteriorate the stability of read/write process. In this paper, the formation and breaking of lubricant bridge at the head–disc interface (HDI) affects HAMR stability and deserves to be investigated. Using molecular dynamic simulation, a full-atom model was built to evaluate the behaviour of the lubricant bridge. Moreover, the effects of lubricant temperature, heating-up time, disc rotation speed and bearing pressure on the HDI were studied. It has been found that the amount of transferring atoms sharply increased when the lubricant temperature was above 700 K. The loss rate of lubricant layer decreased gradually during the heating process and it took about 2.2 ns for the remaining lubricant to reach stability. Furthermore, transferring PFPE molecules can form the lubricant bridge. A shorter heating-up time makes the lubricant bridge thicker and more robust. And the duration of lubricant bridge is notably affected by heating-up time, rotation speed and bearing pressure. A shorter heating-up time leads to a longer duration of lubricant bridge, whereas a higher rotation speed and bearing pressure reduces the duration of lubricant bridge.     

Influence of polymer structure on adsorption behavior at solid–liquid interface by Monte Carlo simulation

Monte Carlo simulations for the adsorption of polymers including random copolymer, homopolymer, diblock copolymer and two kinds of triblock copolymers, respectively, in nonselective solvent at solid–liquid interface have been performed on a simple lattice model. The effect of polymer structure on adsorption properties was examined. In simulations, all polymeric molecules are modeled as self-avoiding linear chains composed of two segments A and B while A is attractive to the surface and B is non-attractive. It was found that for all polymers, the size distribution of various configurations is determined by the linked sequence of segments and the interaction energy between segment and surface. The results of simulation show that the adsorbed amount always increases with increasing bulk concentration but the adsorption layer thickness is mostly dependent on the adsorption energy at a fixed fraction of segments A. On the other hand, diblock copolymer has always the highest surface coverage and adsorbed amount, while random copolymers and homopolymers give generally the smallest surface coverage and adsorbed amount. It is shown that the sequence of polymer chains, i.e. molecular structure, is the most important factor in affecting adsorption properties at the same composition and interaction between segment and surface. The results also show that the adsorption behavior of random copolymers is remarkably different from that of block copolymers, but acting like homopolymer.     

Solvation structures of sodium halides in dimethyl sulfoxide (DMSO)–methanol (MeOH) mixtures

A constrained molecular dynamics technique has been used to study the structures and dynamics of the solvation shells of three sodium halides, namely sodium chloride (Na⁺–Cl^?), sodium bromide (Na⁺–Br^?) and sodium iodide (Na⁺–I^?) in DMSO–MeOH mixtures. In the case of Na⁺–Cl^? and Na⁺–Br^?, Na⁺ is preferentially solvated by DMSO and Cl^? and Br^? are preferentially solvated by methanol in the contact ion pair (CIP) state. In the solvent-assisted ion pair (SAIP) configuration, Na⁺ ions of Na⁺–Cl^? and Na⁺–Br^? are preferentially solvated by methanol and Cl^? and Br^? also show preferential solvation by methanol over DMSO. In the case of Na⁺–I^?, the only preferential solvation is in the SAIP state for I^? ion by methanol. These observations are supported by the calculated excess coordination numbers and spatial density maps. The heights of the transition states barriers for CIPs and SAIPs/solvent-shared ion pairs (SSHIPs) are significantly affected when the mole fraction of methanol (x_MeOH) changes from 0.0 to 0.25 because of a significant increase in the methanol density around halides. From the analysis of angular distribution functions of DMSO and methanol around the cations and anions, it is seen that DMSO and methanol molecules are present in parallel dipolar orientations (with respect to cation–solvent vector) in the first coordination shell of these three ion pairs at the CIP and SAIP states. Methanol molecules are nearly in an antiparallel (with respect to ion–solvent vector) orientation around the three halide ions.     

Quantum chemical molecular dynamics simulation of carbon nanotube–graphene fusion

Abstract

Here we report a quantum mechanical molecular dynamics (QM/MD) study of a fusion process of an open-ended carbon nanotube on a graphene hole, which results in the formation of a so-called pillared graphene structure – a three-dimensional nanomaterial consisting entirely of sp²-carbons. The self-consistent-charge density-functional tight-binding potential was adopted in this study. Two different sizes of graphene holes with 12 or 24 central carbon atoms removed from a graphene flake, and a (6,6) carbon nanotube with a compatible diameter were adopted. Formations of 6–7–6/5–8–5 defect structures were found on the fusion border between tube and graphene hole. The 6–7–6 structure was found to bear less curvature-induced strain energy and therefore to be more stable and much easier to form than the 5–8–5 structure.     

Stability analysis for binary sII hydrogen–promoter hydrates by molecular dynamics simulation

Molecular dynamics simulation was applied for the binary sII hydrogen–promoter hydrates to search the potential promoters to stabilise the hydrogen hydrates. The simulations were performed at 10.1 MPa. The simulation temperature was maintained at 260 K for 100 ps, and then it was increased at the rate of 0.1 TK/s. The cell volumes of the hydrates slowly increased with increasing temperature, and then the cell volumes rapidly increased. The temperature at which the cell volumes rapidly increased is identified as the simulated collapse temperature. The promoter which gives high simulated collapse temperature is judged to stabilise the hydrates. The simulated collapse temperature of the hydrate filled with cyclobutane is the highest among the promoters studied in this work.     

Simple assay for adsorption of proteins to the air–water interface

A rapid assay is described, based upon the Marangoni effect, which detects the formation of a denatured-protein film at the air–water interface (AWI) of aqueous samples. This assay requires no more than a 20 µL aliquot of sample, at a protein concentration of no more than1 mg/ml, and it can be performed with any buffer that is used to prepare grids for electron cryo-microscopy (cryo-EM). In addition, this assay provides an easy way to estimate the rate at which a given protein forms such a film at the AWI. Use of this assay is suggested as a way to pre-screen the effect of various additives and chemical modifications that one might use to optimize the preparation of grids, although the final proof of optimization still requires further screening of grids in the electron microscope. In those cases when the assay establishes that a given protein does form a sacrificial, denatured-protein monolayer, it is suggested that subsequent optimization strategies might focus on discovering how to improve the adsorption of native proteins onto that monolayer, rather than to prevent its formation. A second alternative might be to bind such proteins to the surface of rationally designed affinity grids, in order to prevent their diffusion to, and unwanted interaction with, the AWI.     

Prediction of predator–prey populations modelled by perturbed ODEs

In this paper we explore a stochastic model in continuous time for predator-prey interactions, which accounts for the periodical behaviour observed in many animal populations. More precisely, we consider a solution to the classical Lotka-Volterra system of equations, but we view the actual population sizes as random perturbations of the solutions to this ODE system. Namely, we assume that the perturbations follow correlated Ornstein-Uhlenbeck processes; this approach generalizes the one of Froda and Colavita [Aust N Z J Stat 2:235-254, 2005] who considered only i.i.d. errors. This type of perturbed deterministic model allows to perform parameter estimation and to predict population sizes at future times. On the other hand, the present model refines the previous one since it takes into account the variability due to external factors and the time dependence in the random component. Moreover, this more flexible model improves the predictions of population sizes at future times. In order to illustrate this last point, we analyse two data sets.     

Separation of xylose oligomers using centrifugal partition chromatography with a butanol–methanol–water system

Xylose oligomers are the intermediate products of xylan depolymerization into xylose monomers. An understanding of xylan depolymerization kinetics is important to improve the conversion of xylan into monomeric xylose and to minimize the formation of inhibitory products, thereby reducing ethanol production costs. The study of xylan depolymerization requires copious amount of xylose oligomers, which are expensive if acquired commercially. Our approach consisted of producing in-house oligomer material. To this end, birchwood xylan was used as the starting material and hydrolyzed in hot water at 200 °C for 60 min with a 4 % solids loading. The mixture of xylose oligomers was subsequently fractionated by a centrifugal partition chromatography (CPC) with a solvent system of butanol:methanol:water in a 5:1:4 volumetric ratio. Operating in an ascending mode, the butanol-rich upper phase (the mobile phase) eluted xylose oligomers from the water-rich stationary phase at a 4.89 mL/min flow rate for a total fractionation time of 300 min. The elution of xylose oligomers occurred between 110 and 280 min. The yields and purities of xylobiose (DP 2), xylotriose (DP 3), xylotetraose (DP 4), and xylopentaose (DP 5) were 21, 10, 14, and 15 mg/g xylan and 95, 90, 89, and 68 %, respectively. The purities of xylose oligomers from this solvent system were higher than those reported previously using tetrahydrofuran:dimethyl sulfoxide:water in a 6:1:3 volumetric ratio. Moreover, the butanol-based solvent system improved overall procedures by facilitating the evaporation of the solvents from the CPC fractions, rendering the purification process more efficient.     

Monte Carlo simulation of the adsorption of C2–C7 linear alkanes in aluminophosphate AlPO4-11

The adsorption behaviors of linear alkanes ranging in length from C₂ to C₇ in AlPO₄-11 have been simulated by using configurational-bias Monte Carlo technique at 313 K. The calculated heats of adsorption at zero coverage for linear alkanes, estimated by Henry coefficients, are consistent well with previously reported experimental and simulation results. The simulated isotherms for n-hexane in AlPO₄-11 at 298 K agree with the experimental data. The isotherms of C₂–C₇ linear alkane were predicted, in which butane presents a substep. The adsorbed alkane molecules are only localized in 10-membered ring channels, and adsorbed phase structures for each alkane were investigated. Total potentials for individual alkane molecule decrease with increasing number of carbon atoms. A linear change in total potential is observed for each linear alkane with increasing loading per unit cell, except that an increasing trend is found in the total potential curve of butane as the loading per unit cell is higher than two molecules.     

Influence of hydrogen bonding on the structural transition of poly(methacrylic acid) chain in water–ethanol solution by molecular dynamics simulations

The conformational structure of dilute atactic-poly(methacrylic acid) (PMA) solution in binary water–ethanol mixture was investigated by molecular dynamics simulations, over 0–0.9 ethanol (co-solvent) fraction. The radius of gyration 〈R_g〉, torsion angle distribution, intra-chain hydrogen bonds (H-bonds), and H-bonds for PMA–water, PMA–ethanol and water–ethanol, atom–atom and atom–group pair radial distribution functions were analysed. An increase in the ethanol fraction leads to chain expansion. The non-monotonic variation of 〈R_g〉, commensurate with the experimentally observed behaviour of intrinsic viscosity [η], takes place by H-bonding effects between PMA, water and ethanol, as driven by the differences in the chemical structure of water and ethanol. The PMA repeat units are closer to the CH₂ groups as compared with CH₃ groups of ethanol, in the nearest coordination shell. Water as compared with ethanol is able to coordinate closer to the PMA repeat unit centre of mass. Intra-chain H-bonding depreciates with an increase in the ethanol content in solution. The changes, across the ethanol fraction range, in chain dimensions and of predicted intrinsic viscosity by the simulations, compare well with experimental results in the literature.     

Effect of glycerol–water binary mixtures on the structure and dynamics of protein solutions

We have performed 20?ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30, and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The solvent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the incoherent intermediate scattering function, shows a nonmonotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water-containing solvents, but different from the pure glycerol case. The increase in the number of protein–glycerol hydrogen bonds in glycerol–water binary mixtures explains the slowing down of protein dynamics as the glycerol content increases. We also explored the dynamic behavior of the hydration layer. We show that the short length scale dynamics of this layer are insensitive to glycerol concentration. However, the long length scale behavior shows a significant dependence on glycerol content. We also provide insights into the behavior of bound and mobile water molecules.     

Vapor–liquid equilibria and thermophysical behavior of the SPC-HW model for heavy water

The vapor–liquid coexistence curve of the simple point charge heavy-water model (SPC-HW), [J. Chem. Phys., 114, 8064–8067 (2001)] is determined by Gibbs Ensemble Monte-Carlo (GEMC) simulation. The estimated critical conditions of the model based on the Wegner-type expansion for the order parameters and the rectilinear diameter are ρ_c = 0.300 g/cc, T _c = 661 K and P _c = 156 bars. The dielectric constant determined by isothermal–isochoric molecular dynamics is underpredicted along the coexistence curve by 29–44% in comparison with the experimental values. The analysis of the orthobaric temperature dependence of the system microstructure, in terms of the three site–site radial distribution functions, indicates that the first coordination numbers for the oxygen–oxygen and the oxygen–deuterium interactions are ～4.3 ± 0.1 and ～1.9 ± 0.1 at T = 300 K, and decrease by 15 and 55%, respectively, at criticality. The dipole–dipole correlation functions show that the orientational order in heavy water is quickly lost beyond the first oxygen–oxygen coordination shell. The model's second virial coefficient is determined by Monte-Carlo integration and used to aid the interpretation of the predicted phase equilibrium results.     

Preferential solvation and association constants of 2-exo and 2-endo norbornyl chlorides in water–acetone mixtures

Molecular dynamics simulations of 2-exo and 2-endo norbornyl chlorides are performed in water–acetone mixtures to investigate the role of preferential solvation on the dissociation process of norbornyl chlorides. Increase in the association constants between carbon (C2) and chloride (Cl) of norbornyl chlorides with an increase in mole fraction of acetone supports the experimental data for the corresponding decrease in the rates of solvolysis for both exo and endo norbornyl chlorides. When the mole fraction of water is increased in water–acetone mixtures, acetone molecules are replaced by water molecules around C2 as well as Cl of norbornyl chloride. Preferential solvation by water is analysed using running coordination numbers and excess coordination numbers around C2 and Cl.     

Application of kinetic Monte Carlo method to the vapour–liquid equilibria of associating fluids and their mixtures

Canonical kinetic Monte Carlo (C-kMC) simulations have been carried out to assess their feasibility and potential for calculating the vapour–liquid equilibria of various pure components with increasingly strong electrostatic interactions (carbon dioxide, methanol, ammonia and water) over a wide range of temperatures and for methanol/water mixtures at 298 K. The simulation results show that C-kMC is successful as a method for studying phase equilibria and thermodynamic properties. For all the examples investigated, the performance of the C-kMC method is at least as good as that of the conventional Monte Carlo (MC) methods and is efficient at low temperature where these fail. It also provides a route that is superior to the Widom method for the calculation of chemical potential. We recommend this method for this purpose and as an alternative to conventional MC for simulations of strongly associating fluids and at low temperatures.