Molecular dynamics simulations of dendritic polyelectrolytes with flexible spacers in salt free solution

We present the results of molecular dynamics simulations of dendritic polyelectrolytes in dilute salt-free solutions. The dendritic polyelectrolytes are modeled as an ensemble of regular-branched bead-spring chains of neutral and charged Lennard-Jones particles with explicit counterions. A wide range of molecular variables of the dendritic polyelectrolytes such as generation number, spacer length, and charge density were considered in the simulations. The effect of dendrimer size on relaxation time, the conformation of spacers, and the size dependence of the dendrimer on molecular variables are discussed and compared with a Flory type theory. The osmotic coefficients of the dilute dendritic polyelectrolyte solutions, as well as the profiles of monomers and counterions, are calculated directly from the simulations. Our simulation results show that the inner spacers of the dendrimers are extensively stretched, and the size dependence on the molecular weight deviates from the scaling prediction that assumes a Gaussian elasticity of the spacer.     

Electrosorption of sodium cellulose sulfates with different substitution patterns

Various types of sodium cellulose sulfate (SCS), dissolved in a 1M LiCl solution, were investigated by alternating current (AC)polarography. The SCS samples differed in the degree of substitution (DS), thedistribution of substituents within the anhydroglucose unit (AGU), and alongthechain, due to the method of synthesis. The goal was to study theelectrosorptionbehavior, characterized by the shape of the desorption wave in the polarogram,as a function of the chemical structure of the SCS samples. The shape of thedesorption wave reflects domains of different substitution. A superimpositionofparameters like DS and pattern of substitution on the electrosorption behaviorwas observed. The AC polarography method described can be used as a tool todistinguish between an even or uneven distribution of substituents along thecellulose chain.     

Properties of blends of methyl cellulose and carboxymethyl cellulose with different degrees of ionization in solutions and solids

The rheological properties of dilute and moderately concentrated aqueous solutions of methyl cellulose with carboxymethyl cellulose having different degrees of ionization, were examined. The solvent vapor sorption method was applied to examine the compatibility of the polymers in the solid state and elucidate how the amount of nonionized carboxy groups in carboxymethyl cellulose affects its compatibility with methyl cellulose.     

Thermochemical characteristics of cellulose acetates with different degrees of acetylation

The standard enthalpies of combustion and formation of cellulose acetates with different degrees of acetylation are determined. It is established that there is a proportional dependence of these thermochemical characteristics vs. the degree of acetylation, weight fraction of bonded acetic acid, and molar mass of the repeating unit of cellulose acetates.     

Molecular dynamics simulations of spontaneous bile salt aggregation

Bile salts are surfactants in bile that facilitate digestion, adsorption and excretion of various compounds. They have planar hydrophobic and hydrophilic faces and therefore exhibit some unusual properties; including the shape and size of the micelles that they form. Molecular dynamics simulations of the spontaneous aggregation of six bile salts (cholate (CHD), glycocholate (GCH), taurocholate (TCH), glycochenodeoxycholate (GCD), glycodeoxycholate (GDX) and glycolithocholate (GLC)) were performed in an aqueous phase to gain insight into their micellar structure. The aggregates that formed spontaneously from a random distribution of molecules ranged in size from 8 to 17 molecules. The structures are highly dynamic in nature and are on average oblate, but can vary from oblate, to spherical or prolate. Intermolecular hydrogen bonding within the micelles was found to be an important factor in determining the micelle size, structure and dynamics. The molecular arrangement within the micelles maximises the hydration of the hydrophilic chains and some favourable orientations for adjacent molecules were acquired. The dynamics of the micelles were investigated using the hydrogen-bond lifetime autocorrelation function correlation time, which exhibited a relationship with the degree of hydroxylation. Comparison of the proposed model to the three literature models showed some features of the disk shaped models of Cary and Small [M.C. Cary, D.M. Small, Arch. Intern. Med. 130 (1972) 506–527] and Kawamura et al. [H. Kawamura, Y. Murata, T. Yamaguchi, H. Igimi, M. Tanaka, G. Sugihara, J.P. Kratohvil, J. Phys. Chem. 93 (1989) 3321–3326], whereas the third, inverted helix model of Giglio et al. [E. Giglio, S. Loreti, N.V. Pavel, J. Phys. Chem. 92 (1988) 2858–2862] can be discounted. The proposed model is better than the existing models, which assumed a rigid and structured molecular arrangement.     

Molecular parameters of sodium cellulose xanthate in dilute solution

Molecular parameters of sodium cellulose xanthate in NaOH solution have been determined by means of light scattering and viscometry. The effect of the degree of substitution on the molecular configuration of sodium cellulose xanthate has been studied for three series of samples of varying degree of substitution. The expansion factor has been determined from the expression due to Orofino and Flory. The effective bond length b and the ratio of the unperturbed dimension to the dimension assuming free rotation of the chain units (R?_o²/R?_f²)^1/2, have also been determined. It is concluded that sodium cellulose xanthate in dilute solution is a loosely coiled molecule, comparable to other cellulose derivatives in chain stiffness.     

Compatibility of carboxymethyl cellulose ionized to various degrees with poly-N-vinylformamide in composite films

Composite films were obtained from aqueous solutions of blends of carboxymethyl cellulose ionized to various degrees and poly-N-vinylformamide. The composition ranges in which the polymers are compatible were determined by solvent vapor sorption and by dynamic mechanical analysis. The heat resistance of the films and the interaction of the polymers in the solid state were examined by DSC, TGA, and Fourier IR spectroscopy.     

Molecular dynamics simulations of dendrimer-encapsulated alpha-Keggin ions in trichloromethane solution

We report on molecular dynamics simulations of dendrimer-encapsulated alpha-Keggin ions in trichloromethane solution. The simulations were done within the NVE ensemble at temperatures around T = 300 K. The eight examined systems are model compounds for dendrizymes, a hybrid material where a polyoxometalate ion (the core) is surrounded by amphiphilic cationic dendrimers (the shell) such that the complete system may exhibit enzyme-like regioselectivity and substrate selectivity, e.g., in olefin oxidation. The influence of dendrimer type, dendrimer generation, and number of dendritic cations bound by electrostatic interaction to the polyoxometalate core on the structure and dynamics of the shell has been studied. It is shown that the resulting distribution of trichloromethane molecules within the shell may serve as an indicator for the shell's permeability for small molecules. The dendritic shell causes a size exclusion effect that influences the access of small molecules to the central polyoxometalate ion, i.e., to that part where the enzyme-like reaction of a dendrizyme is supposed to take place.     

Molecular dynamics simulations of the solution-air interface of aqueous sodium nitrate

Molecular dynamics simulations have been used to investigate the behavior of aqueous sodium nitrate in interfacial environments. Polarizable potentials for the water molecules and the nitrate ion in solution were employed. Calculated surface tension data at several concentrations are in good agreement with measured surface tension data. The surface potential of NaNO3 solutions at two concentrations also compare favorably with experimental measurements. Density profiles suggest that NO3- resides primarily below the surface of the solutions over a wide range of concentrations. When the nitrate anions approach the surface of the solution, they are significantly undercoordinated compared to in the bulk, and this may be important for reactions where solvent cage effects play a role such as photochemical processes. Surface water orientation is perturbed by the presence of nitrate ions, and this has implications for experimental studies that probe interfacial water orientation. Nitrate ions near the surface also have a preferred orientation that places the oxygen atoms in the plane of the interface.     

Steady and dynamic rheological behaviors of sodium carboxymethyl cellulose entangled semi-dilute solution with opposite charged surfactant dodecyl-trimethylammonium bromide

The steady and dynamic rheological behaviors of sodium carboxymethyl cellulose (NaCMC) entangled semi-dilute solution filled with different concentrations of dodecyl-trimethylammonium bromide (C₁₂TAB) were investigated. The results reveal that the zero shear rate viscosity (η₀) and dynamic modules (G′and G″) increase with C₁₂TAB concentration (C_s), and there exist three scaling regions divided by two critical C₁₂TAB concentrations (C₁, C₂ and , respectively, from steady and dynamic tests). The increase of viscosity and modules with C_s is ascribed to formation of network due to C₁₂TAB micelles bridging NaCMC chains. The two critical C₁₂TAB concentrations implies that the structure evolution of NaCMC–C₁₂TAB complex is exposed to three states with increasing C_s, i.e., no network formation, network extent progressive formation and perfect network formation, respectively. Moreover, are a little lower than C₁, C₂, indicating that the dynamic test is more sensitive to detect the structure change of the complex as compared with steady test. Furthermore, it is found that as NaCMC concentration increases, , and increase.     

Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers

Four 20 ns molecular dynamic simulations of rhodopsin embedded in different one-component lipid bilayers have been carried out to ascertain the importance of membrane lipids on the protein structure. Specifically, dimyristoyl phosphatidylcholine (DMPC), dipalmitoyl phosphatidylcholine (DPPC), palmitoyl oleoyl phosphatidylcholine (POPC), and palmitoyl linoleyl phosphatidylcholine (PLPC) lipid bilayers have been considered for the present work. The results reported here provide information on the hydrophobic matching between the protein and the bilayer and about the differential effects of the protein on the thickness of the different membranes. Furthermore, a careful analysis of the individual protein-lipid interactions permits the identification of residues that exhibit permanent interactions with atoms of the lipid environment that may putatively act as hooks of the protein to the membrane. The analysis of the trajectories also provides information about the effect of the bilayer on the protein structure, including secondary structural elements, salt bridges, and rigid-body motions.     

Effect of the reaction conditions on the degree of substitution of carboxymethyl cellulose

Cellulosic fabric composed of 84 % cotton and 16 % viscose rayon fiber was carboxymethylated. The influence of the reaction parameters (concentration of the reagents, time of reaction) on the degree of substitution was studied in the process, applying sodium hydroxide and monochloroacetic acid in one bath. Two kinds of regression equations were used to calculate approximately the degree of substitution. These polynomials can be used for the selection of reaction parameters to obtain a sample of a given degree of substitution.     

Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature

Summary We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG)d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG-and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).     

Physical properties of sodium carboxymethyl cellulose molecules adsorbed on a polyacrylonitrile ultrafiltration membrane

Ultrafiltration experiments showed that the graphical relationship between flux and pressure was a straight line through the origin, provided that the wall shear rate of the bulk fluid was higher than a certain critical value or the pressure was below a critical value. A higher critical shear rate corresponded to a higher critical pressure. For these conditions the total hydrodynamic resistance was only slightly greater than the resistance of a clean membrane for pure water. This additional resistance is attributed to a (mono-) molecular layer of macromolecules which is adsorbed on the membrane in the absence of both a concentration polarization layer and a conventional gel layer.At steady state ultrafiltration conditions, an increase of the flux was obtained after replacing the bulk solution by distilled water at constant experimental conditions, which is attributed to the removal of the concentration polarization layer whereas a mono-molecular layer of macromolecules remained adsorbed on the membrane. For these conditions the flux vs. pressure relationship showed a qualitatively similar behaviour as for ultrafiltration conditions.At a constant shear rate the flux vs. pressure relationship was a straight line through the origin for pressures below the critical pressure, the value of which increased with the shear rate. This linear relationship was reversible, showing no hysteresis. However, if the pressure was higher than its critical value, the flux vs. pressure relationship was no longer a straight line as a consequence of the occurrence of an additional hydrodynamic resistance which did not disappear entirely upon lowering the pressure below its critical value. For the explanation of these phenomena it is assumed that freely moveable parts of the adsorbed macromolecules can block the entrance region of the pores in the membrane if the pressure is beyond its critical value.On the other hand, for pressures below the critical pressure or shear rates beyond the critical shear rate, the pores of the membrane are deblocked. This blocking and deblocking of pores by parts of adsorbed macromolecules apparently takes place in a partly reversible way.     

UV spectroscopy of methanofullerene derivatives with different degrees of substitution

Compounds from the series of methanofullerenes with different degrees of functionalization were studied by UV spectroscopy. As the number of substituents increased, a hypsochromic shift of the characteristic absorption bands took place and the optical density of the solutions of the compounds at characteristic maxima decreased. A similar dependence was also noted for the ratio of the optical densities of the 258 and 329 nm bands typical for fullerene (A ₂₅₈/A ₃₂₉). An exponential dependence of the molar absorption coefficients of metanofullerenes on the degree of functionalization of the fullerene nucleus was found.     

Molecular dynamics simulations of porphyrin-dendrimer systems: toward modeling electron transfer in solution

We have performed computational simulations of porphyrin-dendrimer systems--a cationic porphyrin electrostatically associated to a negatively charged dendrimer--using the method of classical molecular dynamics (MD) with an atomistic force field. Previous experimental studies have shown a strong quenching effect of the porphyrin fluorescence that was assigned to electron transfer (ET) from the dendrimer's tertiary amines (Paulo, P. M. R.; Costa, S. M. B. J. Phys. Chem. B 2005, 109, 13928). In the present contribution, we evaluate computationally the role of the porphyrin-dendrimer conformation in the development of a statistical distribution of ET rates through its dependence on the donor-acceptor distance. We started from simulations without explicit solvent to obtain trajectories of the donor-acceptor distance and the respective time-averaged distributions for two dendrimer sizes and different initial configurations of the porphyrin-dendrimer pair. By introducing explicit solvent (water) in our simulations, we were able to estimate the reorganization energy of the medium for the systems with the dendrimer of smaller size. The values obtained are in the range 0.6-1.5 eV and show a linear dependence with the inverse of the donor-acceptor distance, which can be explained by a two-phase dielectric continuum model taking into account the medium heterogeneity provided by the dendrimer organic core. Dielectric relaxation accompanying ET was evaluated from the simulations with explicit solvent showing fast decay times of some tens of femtoseconds and slow decay times in the range of hundreds of femtoseconds to a few picoseconds. The variations of the slow relaxation times reflect the heterogeneity of the dendrimer donor sites which add to the complexity of ET kinetics as inferred from the experimental fluorescence decays.     

Molecular dynamics simulations of polyelectrolyte-polyampholyte complexes. Effect of solvent quality and salt concentration

Complexation between polyelectrolyte and polyampholyte chains in poor solvent conditions for the polyelectrolyte backbone has been studied by molecular dynamics simulations. In a poor solvent a polyelectrolyte forms a necklace-like structure consisting of polymeric globules (beads) connected by strings of monomers. The simulation results can be explained by assuming the existence of two different mechanisms leading to the necklace formation. In the case of weak electrostatic interactions, the necklace formation is driven by optimization of short-range monomer-monomer attraction and electrostatic repulsion between charged monomers on the polymer backbone. In the case of strong electrostatic interactions, the necklace structure appears as a result of counterion condensation. While the short-range attractions between monomers are still important, the correlation-induced attraction between condensed counterions and charged monomers and electrostatic repulsion between uncompensated charges provide significant contribution to optimization of the necklace structure. Upon forming a complex with both random and diblock polyampholytes, a polyelectrolyte chain changes its necklace conformation by forming one huge bead. The collapse of the polyelectrolyte chain occurs due to the neutralization of the polyelectrolyte charge by polyampholytes. In the case of the random polyampholyte, the more positively charged sections of the chain mix with negatively charged polyelectrolyte forming the globular bead while more negatively charged chain sections form loops surrounding the collapsed core of the aggregate. In the case of diblock polyampholyte, the positively charged block, a part of the negatively charged block, and a polyelectrolyte chain form a core of the aggregate with a substantial section of the negatively charged block sticking out from the collapsed core of the aggregate. In both cases the core of the aggregate has a layered structure that is characterized by the variations in the excess of concentration of monomers belonging to polyampholyte and polyelectrolyte chains throughout the core radius. These structures appear as a result of optimization of the net electrostatic energy of the complex and short-range attractive interactions between monomers of the polyelectrolyte chain.     

Molecular dynamics: conductivity of a fused salt

The electrical conductivity of a model of liquid KCl was determined by molecular dynamics computations. In a constant temperature ensemble, the linear regime for Ohm's law was shown to extend up to at least 1.5 × 10⁷ V/cm. The results compared favorably with that calculated by monitoring the power dissipation and with the zero-field value obtained via the current autocorrelation function.     

Fluorescence quenching method for the determination of sodium carboxymethyl cellulose with acridine yellow or acridine orange

In near neutral to weak basic media, sodium carboxymethyl cellulose (NaCMC) will dissociate to become a macro polymeric anion, which can react with acridine yellow (AY) or acridine orange (AO) to form an ion-association complex resulting in fluorescence quenching of the acridine dyes. The maximum fluorescence quenching wavelength is 505 nm (lambda(ex)=440 nm) for AY system and 530 nm (lambda(ex)=493 nm) for AO system, respectively. The fluorescence quenching values (DeltaF) are directly proportional to the concentrations of NaCMC and the linear ranges are 20.0-4000 microg/L for AY system and 20.0-7000 microg/L for AO system, separately. This method has high sensitivity and the detection limits for NaCMC are 58.0 microg/L (AY system) and 157.2 microg/L (AO system). The effects of coexistent substance have been investigated, and the results show that this method has a relatively good selectivity. A fluorescence quenching method for the determination of NaCMC based on the ion-association reactions of CMC polymeric anion with a basic acridine dye was developed. The method is sensitive, simple and fast.     

不同浓度下NaCl水溶液的分子动力学模拟

采用分子动力学模拟的方法在298K时对1.33mol/L,2.71mol/L,4.14mol/L和5.12mol/L的NaCl水溶液的微观结构进行了研究。模拟发现浓度对离了近程水化结构的影响不大,浓溶液中Na^+,Cl^-之间有两种缔合方式,接触缔合离子对和溶剂分隔的缔合离子对。这表明在建立可适用于高浓度条件下的电解质溶液热力学模型时应考虑离子缔合的贡献。