Shear Viscosity of Model Mixtures by Nonequilibrium Molecular Dynamics. IV. Effect of Molecular Shape

Abstract

We present new results for thermodynamic properties and viscosities of pure dumbbell fluids, spherical/dumbbell mixtures, and dumbbell/dumbbell mixtures. It is evident that the interaction between dumbbell molecules is less attractive than that between spherical molecules which leads to lower viscosities. The shear viscosities and the LJ energies of both spherical Ar/dumbbell Kr (case B) and dumbbell Ar/dumbbell Kr (case C) are described quite well by the liquid mixture expression. The ideality in case C is much better than in case B which is consistent with the idea that dumbbell/dumbbell mixtures are likely to be more ideal than spherical/dumbbell mixtures. But the mixture pressures of the spherical/dumbbell mixture (case B) are described accurately by the ideal liquid mixture expression while those of the dumbbell/dumbbell mixture (case C) are not, which is not consistent with the better ideality of case C in the shear viscosity and the LJ energy than case B.     

Effect of temperature on adsorption of mixtures in porous materials

The effect of temperature on the adsorption of a simple mixture (Ar/Kr) in disordered porous materials is investigated by means of molecular simulation. In the larger mesopores of porous silica glasses, capillary condensation occurs upon decreasing the temperature. At temperatures above the capillary condensation temperature, Kr is preferentially adsorbed at the pore surface and Ar adsorption occurs in regions of low Kr density. For temperatures below the capillary condensation temperature, Ar density surprisingly increases as temperature increases, the behaviour that is consistent with an over-solubility effect. In contrast, in the disordered sub-nanoporous carbon, filling of the pores occurs in a reversible and continuous way upon decreasing the temperature, owing to the small size and amorphous shape of the pores. These results show that the crossover between capillary condensation and continuous reversible filling observed for pure fluids in pores also exists for mixtures. We also show that the Kr selectivity exhibits a minimum in the disordered porous silica that is located at the capillary condensation temperature. In contrast, in the disordered porous carbon where no capillary condensation occurs, the selectivity decreases monotonically with increasing the temperature. These results shed light on low-temperature adsorption of mixtures confined in porous materials and provide a guide to design efficient phase separation processes.     

On the nature of bonding in HCOOH...Ar and HCOOH...Kr complexes

The chemical interaction in HCOOH...Ng (Ng=Ar, Kr) complex was analyzed by topological analysis of the electron density based on Atoms-In-Molecules theory. For all computationally stable equilibrium structures of 1:1 HCOOH...Ng complexes, an intermolecular bond path with a bond critical point was found and perturbation of formic acid (FA) atomic basins and electron density was observed. The intermolecular interaction between the two complex subunits can be classified, according to its nature, as a closed-shell van der Waals type of interaction. However, one of the computed structures (complex II), pictures a noble gas atom attached linearly to the acidic O–H tail of FA. In this particular case, the electron density at the intermolecular bond critical point was found to resemble a hydrogen-bonded system and thus, may be termed a hydrogen-bond-like interaction. This change in the nature of the interaction is also shown by large perturbations of the FA properties found for this complex structure. The structural and vibrational perturbations are larger than for the other three structures and they increase for the Kr complexes compared to the Ar complex.Figure Electron density analysis of HCOOH...Ng (Ng=Ar,Kr) complex.     

Phase Equilibria of Quadrupolar Fluids by Simulation in the Gibbs Ensemble

Abstract

Vapour-liquid phase diagrams for pure fluids and mixtures of molecules with Lennard-Jones plus quadrupole-quadrupole interaction potentials were determined by Monte Carlo simulation in the Gibbs ensemble [1]. This is the first reported application of the method to molecular fluids. We have demonstrated that the Gibbs method works reliably for strongly interacting molecular fluids at liquid densities. Pure fluid calculations were performed for reduced quadrupole strengths, Q* = Q/(εσ⁵)^1/2 equal to 1 and √2, typical of molecules like C₂H₂ and C₂H₄. It was found that the critical temperature of the quadrupolar fluid increased rapidly with increasing quadrupolar strength, in good agreement with previous computer simulation and theoretical results. A single mixture with components characterized by identical Lennard-Jones parameters and Q*₁ = + 1, Q*₂ = - 1 was studied at three temperatures. A negative azeotrope was observed at the lowest temperature studied, as seen experimentally in the CO₂/C₂H₂ mixture. The perturbation theory calculations are in good agreement with the simulation results for all properties except coexisting liquid densities. The results illustrate some of the strengths and limitations of perturbation theories based on the Padé approximant for the free energy of polar fluids.     

The antitumor molecular mechanism of Alisma orientalis with c-myc DNA: multi-spectroscopic analysis and molecular simulation

Abstract

We prepared extracts of Alisma orientalis from Sichuan and Fujian Province, China. Based on the ratio of alisol B 23-acetate (23B) to alisol A 24-acetate (24A) in two Alisma orientalis extracts, we prepared two mixtures of 24A and 23B (24A:23B?=?1:3 or 1:10). The antitumor molecular mechanism of the monomers 24A and 23B, the two mixtures and the effective components of Alisma orientalis from different habitats were studied. The MTT assay suggested that the difference in the antitumor activity of Alisma orientalis from different habitats was correlated to the ratio of 24A to 23B. The multi-spectroscopic analysis suggested that the effective components, the monomers and mixtures interacted with c-myc DNA in a partial intercalation manner. The binding strength of the alisol acetates to c-myc DNA was consistent with the anticancer activity, indicating that c-myc DNA was the anticancer target. The molecular simulation indicated that the mixtures were all directly bound to different base pairs of c-myc DNA for a superimposed effect, which led to the binding strength of the mixtures to c-myc DNA was stronger than that of the monomers. The molecules in the 1:3 mixture were all bound to different base pairs of c-myc DNA. However, for the 1:10 mixture, seven molecules of 23B bound to the side chain of 24A, resulting in the mixture with a long chain structure which increased the steric hindrance of 24A. As a result, affinity between 24A and c-myc DNA in the 1:10 mixture was weaker than that in the 1:3 mixture.

The antitumor molecular mechanism of the alisol monomers 24A and 23B, the mixtures with different proportions and the effective components of Alisma orientalis from different habitats were studied. The order of the antitumor activity was as follows: Sichuan?>?Fujian, 24A-23B (1:3) > 24A-23B (1:10) > 23B?>?24A. The antitumor activity of Alisma orientalis from different habitats was consistent with the mixtures which were designed according to the contents of the active ingredients of the medicinal materials, indicating that the antitumor activity of Alisma orientalis from Sichuan is better than that from Fujian which is related to the contents of 24A and 23B and the proportion of 1:3 is better than 1:10. The binding strength of the mixtures to c-myc DNA was consistent with the anticancer activity. The mixtures were all directly bound to different base pairs of c-myc DNA for a superimposed effect, which led to the strength of the interaction of the mixtures to c-myc DNA was stronger than that of the monomers. For the 24A-23B (1:3) mixture, the four small molecules bound to c-myc DNA directly and interacted with different base pairs of c-myc DNA. While for the 24A-23B (1:10) mixture, 24A and three 23B molecules interacted with c-myc DNA, the remaining seven 23B molecules bound to the side chain of 24A, which increased the steric hindrance. The binding of the mixture to c-myc DNA was decreased.

Communicated by Ramaswamy H. Sarma     

Conformations and dynamics of surfactants in micelles and liquid crystals by nuclear magnetic relaxation

The order parameters as well as the rates of overall and internal motions of aggregated surfactants can be obtained from deuteron and carbon-13 nuclear relaxation experiments. The main contribution to the relaxation is generally the quadrupolar coupling (²H) or the short range dipolar interaction with protons (¹³C). In some cases it is convenient to derive the same information from the¹³C relaxation induced by long range dipolar interactions with a paramagnetic probe exchanging rapidly among the polar heads of surfactant molecules. This paper outlines the methods of interpretation of relaxation data by means of a rotational jump model of internal motions, taking into account most of the accessible conformers. The conformational and dynamical parameters are obtained from the magnetic field dependence of the longitudinal relaxation rates (micelles) or from the simultaneous fit of these rates and of the dipolar or quadrupolar splittings (liquid crystals). Some examples of application of these methods are given from recent works on single and double detailed surfactants.     

Structural transitions in mixed ternary noble gas clusters

The properties of noble gas systems can be greatly extended by heterogeneous mixtures of elements. The geometrical structures and energies of mixed Ar–Kr–Xe clusters were investigated using ternary Lennard-Jones (TLJ) potential. For the Ar₁₉Kr _n Xe₁₉, Ar₁₉Kr₁₉Xe _n , and Ar _n Kr₁₉Xe₁₉ (n?=?0–17) clusters investigated, the results show that only two minimum energy configurations exist, i.e., polytetrahedron and six-fold pancake. The inner core of all these clusters is composed mainly of Ar atoms, and Kr and Xe atoms are distributed on the surface with well mixed pattern for polytetrahedral and segregate pattern for six-fold pancake configurations. The relative stability property of Ar–Kr–Xe clusters with a certain composition is discussed. Moreover, the role of heterogeneity on the strain was investigated, and reduced strain energies in Ar–Kr–Xe clusters were studied to find possible ways of reducing strain. The results showed that the strain energies were affected mainly by Ar–Ar, Ar–Kr, and Xe–Xe bonds.

Characterization of polyacrylamide-stabilized Pf1 phage liquid crystals for protein NMR spectroscopy

A new polymer-stabilized nematic liquid crystal has been characterized for the measurement of biomolecular residual dipolar couplings. Filamentous Pf1 phage were embedded in a polyacrylamide matrix that fixes the orientation of the particles. The alignment was characterized by the quadrupolar splitting of the ²H NMR water signal and by the measurement of ¹H-¹⁵N residual dipolar couplings (RDC) in the archeal translation elongation factor 1. Protein dissolved in the polymer-stabilized medium orients quantitatively as in media without polyacrylamide. We show that the quadrupolar splitting and RDCs are zero in media in which the Pf1 phage particles are aligned at the magic angle. This allows measurement of J and dipolar couplings in a single sample.     

Cover crop mixtures including legume produce ecosystem services of nitrate capture and green manuring: assessment combining experimentation and modelling

Background and aims

During the fallow period, non-legume cover crop species can capture mineral nitrogen (N) and thus decrease nitrate leaching, whereas legume cover crop species can provide a green manuring service that increases N availability for the subsequent crop. The aim of our study was to investigate the ability of bispecific mixtures to simultaneously produce these two services of N management in relation to their interspecific interactions.

Methods

Three field experiments were conducted at contrasting sites from summer to autumn to evaluate 25 mixtures and 10 sole crops. We measured biomass, N acquisition, C:N ratio and soil mineral N. Ecosystem services were assessed using both experimental data and simulation model predictions.

Results

Overall, prediction of N mineralized from cover crop residues was significantly higher for mixtures than for non-legume sole crops. Predictions of nitrate leached after mixtures did not differ significantly from those after non-legume sole crops and remained significantly lower than those under bare soil, especially for mixtures with turnip rape which benefitted greatly from being in mixtures.

Conclusions

Some of the mixtures provided a choice of compromises between the two ecosystem services, which helps define solutions for adapting mixture choice according to the site’s soil and climate characteristics and to fallow period management.

     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

Solid state 13C NMR of unlabeled phosphatidylcholine bilayers: spectral assignments and measurement of carbon-phosphorus dipolar couplings and 13C chemical shift anisotropies.

The direct measurement of 13C chemical shift anisotropies (CSA) and 31P-13C dipolar splitting in random dispersions of unlabeled L alpha-phase phosphatidylcholine (PC) has traditionally been difficult because of extreme spectral boradening due to anisotropy. In this study, mixtures of dimyristoyl phosphatidylcholine (DMPC) with three different detergents known to promote the magnetic orientation of DMPC were employed to eliminate the powder-pattern nature of signals without totally averaging out spectral anisotropy. The detergents utilized were CHAPSO, Triton X-100, and dihexanoylphosphatidylcholine (DHPC). Using such mixtures, many of the individual 13C resonances from DMPC were resolved and a number of 13C-31P dipolar couplings were evident. In addition, differing line widths were observed for the components of some dipolar doublets, suggestive of dipolar/chemical shift anisotropy (CSA) relaxation interference effects. Oriented sample resonance assignments were made by varying the CHAPSO or DHPC to DMPC ratio to systematically scale overall bilayer order towards the isotropic limit. In this manner, peaks could be identified based upon extrapolation to their isotropic positions, for which assignments have previously been made (Lee, C.W.B., and R.G. Griffin. 1989. Biophys. J. 55:355-358; Forbes, J., J. Bowers, X. Shan, L. Moran, E. Oldfield, and M.A. Moscarello. 1988. J. Chem. Soc., Faraday, Trans. 1 84:3821-3849). It was observed that the plots of CSA or dipolar coupling versus overall bilayer order obtained from DHPC and CHAPSO titrations were linear. Estimates of the intrinsic dipolar couplings and chemical shift anisotropies for pure DMPC bilayers were made by extrapolating shifts and couplings from the detergent titrations to zero detergent. Both detergent titrations led to similar "intrinsic" CSAs and dipolar couplings. Results extracted from an oriented Triton-DMPC mixture also led to similar estimates for the detergent-free DMPC shifts and couplings. The results from these experiments were found to compare favorably with limited measurements made from pure L alpha PC. This detergent-based method for assigning spectra and for determining dipolar couplings and CSA in detergent-free systems should be extendable to other lipid systems. The resulting data set from this study may prove useful in future modeling of the structure and dynamics of DMPC bilayers. In addition, the fact that experiments utilizing each of the three detergents led to similar estimates for the spectral parameters of pure DMPC, and the fact that spectral parameter versus bilayer order plots were linear, indicate that the averaged conformation and dynamics of DMPC in the presence of the three detergents are very similar to those of pure L alpha DMPC.     

Physical properties of insect cuticular hydrocarbons: Model mixtures and lipid interactions

Cuticular lipids include a diverse array of hydrophobic molecules that play an important role in the water economy of terrestrial arthropods. Their waterproofing abilities are believed to depend largely on their physical properties, but little is known about interactions between different surface lipids to determine the phase behavior of the total lipid mixture. I examined the biophysical properties of binary hydrocarbon mixtures, as a model for interactions between different epicuticular lipids of insects. The midpoint of the solid/liquid phase transition (T_m) for mixtures of n-alkanes differing in chain length equaled the weighted average of the T_ms of the component lipids. This was also true for n-alkane-methylalkane mixtures. However, alkane-alkene mixtures melted at temperatures up to 17°C above the temperature predicted from the weighted average of component lipid T_m values. Hydrocarbon mixtures did not exhibit biphasic melting transitions indicative of independent phase behavior of the component lipids. Instead, melting occurred continuously, over a broader temperature range than pure hydrocarbons.     

Isobaric and Isothermal Molecular Dynamics Simulations of Diatomic Systems

Abstract

Isobaric molecular dynamics simulations were carried out for diatomic systems using different algorithms available in the literature. Two-centered Lennard-Jones potentials with and without quadrupolar interactions were used. Thermodynamic properties obtained from the isobaric algorithms compared very well with those of an equivalent simulation in the microcanonical ensemble; however, some differences were observed when similar comparisons were carried out for dynamic properties. More specifically, the constant pressure constraint affects the translational dynamics of the system because of the non-negligible differences between the momenta and the instantaneous velocities of the molecules.

Furthermore, the following studies were carried out using isobaric MD simulations: 1. Low temperature spontaneous FCC-orthorhombic (and vice versa) transition of a diatomic system with quadrupolar interactions as a function of the molecular bond length. 2. Effect of quadrupolar interaction on isobaric melting of a model diatomic system. 3. Effect of pressure on melting properties of a model diatomic system with quadrupolar interactions.     

Effects of temperature and composition on the viscosity of respiratory gases

The steady-state sensitivity of resistance pneumotachographs is proportional to viscosity. Dynamic characteristics of pneumotachographs, pressure transducers, and mass spectrometers are also viscosity dependent. We derive linear equations to approximate the viscosities of O2, N2, CO2, H2O, He, N2O, and Ar for temperatures between 20 and 40 degrees C by using published viscosity data and a nonlinear extrapolation equation. We verify the accuracy of the extrapolation equation by comparison with published data. Our linear equations for pure gas viscosities yield standard errors less than 0.35 microP. We also compare a nonlinear equation for calculating the viscosities of mixtures of gases with published measured viscosities of dry air, humid air, and He-O2 and N2-CO2 mixtures. The maximum difference between published and calculated values is 1.3% for 10% CO2 in N2. All other differences are less than 0.38%. For saturated humid air at 35 degrees C, a linear concentration-weighted combination of viscosities differs from our nonlinear equation by 4.9, 2.1, and 1.7% at barometric pressures of 32, 83, and 100 kPa, respectively. By use of our method, the viscosity of normal respiratory gases can be calculated to within 1% of measured values.     

Spaser Based on Dark Quadrupolar Mode of a Single Metallic Nanodisk

A spaser based on dark quadrupolar mode of a single metallic nanodisk coated with a layer of gain media is studied theoretically. The absorption efficiency of the metallic structure, the gain efficiency of the gain media, and the scattering efficiency of the whole nanosystem are calculated separately. It is found that the ratio of the absorption and the scattering intensities (RAS) of the dark quadrupolar mode depends strongly on the gain coefficient, which increases from 0.8 to 4.39 with gain coefficient reaches the threshold, by contrast the bright dipolar mode keeps its RAS unchanged at 0.16. This is attributed to that the gain media mainly amplifies quadrupolar eigenmode composition of the dark quadrupolar mode, thus the scattering loss caused by dipolar eigenmode composition is under effective control, which changes the RAS and leads to super low-threshold spaser. Our works may benefit the achievement of spaser system with low scattering loss.

     

Nonsputtering impulse magnetron discharge

Experiments with quasi-steady high-current discharges in crossed E × B fields in various gases (Ar, N₂, H₂, and SF₆) and gas mixtures (Ar/SF₆ and Ar/O₂) at pressures from 10⁻³ to 5 Torr in discharge systems with different configurations of electric and magnetic fields revealed a specific type of stable low-voltage discharge that does not transform into an arc. This type of discharge came to be known as a high-current diffuse discharge and, later, a nonsputtering impulse magnetron discharge. This paper presents results from experimental studies of the plasma parameters (the electron temperature, the plasma density, and the temperature of ions and atoms of the plasma-forming gas) of a high-current low-pressure diffuse discharge in crossed E × B fields.     

Synthesis of blockwise alkylated (1→4) linked trisaccharides as surfactants: influence of configuration of anomeric position on their surface activities

New carbohydrate-based surfactants consisting of hydrophilic cellobiosyl and hydrophobic glucosyl residues, methyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranosyl-(1→4)-2,3,6-tri-O-methyl-α-d-glucopyranoside 1 (GβGαMα, G: glucopyranosyl residue, α and β: α-(1→4)- and β-(1→4) glycosidic bonds, M: methyl group), 2 (G_βG_βM_α), 3 (G_βG_αM_β), 4 (G_βG_βM_β), 5 (G_βG_αE_α, E: ethyl group), 6 (G_βG_βE_α), 7 (G_βG_αE_β), 8 (G_βG_βE_β) and eight α-and β-glycoside mixtures (a mixture of 1 and 2: 1/2 = 62/38 (9), 32/68 (10); a mixture of 3 and 4: 3/4 = 69/31 (11), 32/68 (12); a mixture of 5 and 6: 5/6 = 62/38 (13), 33/67 (14); a mixture of 7 and 8: 7/8 = 59/41 (15), 29/71 (16)) were synthesized via combined methods consisting of acid-catalyzed alcoholysis of cellulose ethers and glycosylation of phenyl thio-cellobioside derivatives. Their surface activities in aqueous solution depended on their chemical structures: α- or β-(1→4) linkage between hydrophilic cellobiosyl and hydrophobic glucosyl blocks, methyl or ethyl groups of hydrophobic glucosyl block, and α- or β-linked ether group at the C-1 of hydrophobic glucosyl block. The mixing effect of α- and β-glycosides on surface activities was also investigated. As a result, ethyl β-d-glucopyranosyl-(1→4)-α-d-glucopyranosyl-(1→4)-2,3,6-tri-O-ethyl-β-d-glucopyranoside 7 (G_βG_αE_β) had the highest surface activity, and its critical micellar concentration (CMC) and γ_CMC (surface tension at CMC) values of compound 7 were 0.5 mM (ca. 0.03 wt %) and 34.5 mN/m, respectively. The surface tensions of α- and β-glycoside mixtures except for compounds 9 and 10 were almost equal to those of pure compounds. The syntheses of the mixtures of α- and β-glycosides without purification process are easier than those of pure compounds. Thus, the mixtures should be more practical compounds for industrial use as a surfactant.     

Modelling Bioaccumulation and Toxicity of Metal Mixtures

Bioaccumulation of metals in mixtures may demonstrate competitive, anticompetitive, or non-competitive inhibition, as well as various combinations of these and/or enhancement of metal uptake. These can be distinguished by plotting (metal in water)/(metal in tissue) against metal in water and comparison to equivalent plots for single-metal exposure. For the special case of pure competitive inhibition where only one site of uptake is involved, inhibition of metal accumulation in any metal mixture can be predicted from bioaccumulation of the metals when present singly. This is consistent with the commonly used Biotic Ligand Model (BLM) but does not explain bioaccumulation of metals in Hyalella azteca. Options for modelling toxicity of metal mixtures include concentration or response addition based on metal concentrations in either water or tissues. If the site of toxic action is on the surface of the organism, if this is the same as the site of metal interaction for bioaccumulation, if there is only one such type of site, and if metal bioaccumulation interactions are purely competitive (as in the BLM), then metal toxicity should be concentration additive and predictable from metal concentrations in either water or tissues. This is the simplest toxicity interaction to model but represents only one of many possibilities. The BLM should, therefore, be used with caution when attempting to model metal interactions, and other possibilities must also be considered.