Structural effects of DNA on thermodynamic stability of DNA-dendronized polymer nanoclusters and nanoclusteration process

We studied the means by which DNA-dendronized polymer nanoclusters and the nanoclusteration process are affected by structural properties of the nanocluster components, including the length of dendronized polymer, wrapping radius of DNA, and surface charge densities on the DNA and dendronized polymer, by calculating the total free energy of the system and free energy of the nanoclusteration process. The most thermodynamically stable nanocluster conformation was then predicted based on the values of the free energies. It was found that the nanoclusters with longer dendronized polymers, shorter DNA wrapping radius, and larger surface charge density on both the DNA and dendronized polymers are more stable.     

Molecular structure of single DNA complexes with positively charged dendronized polymers

Positively charged dendronized polymers with protonated amine groups at the periphery and different dendron generations are cylindrically shaped nanoobjects whose radii and linear charge densities can be varied systematically. These polyelectrolytes have been complexed with DNA and subsequently adsorbed on precoated mica substrates. The analysis of scanning force microscopy data indicates that DNA wraps around the dendronized polymers. The calculated pitch is 2.30 +/- 0.27 and 2.16 +/- 0.27 nm for DNA wrapped around dendronized polymers of generation two and four, respectively. The complex with the second generation has been shown to be negatively charged, which is consistent with the theory of spontaneous overcharging of macro-ion complexes, when the electrostatic contribution to the free energy dominates over the elastic energy. The complexes may be of interest for the development of nonviral gene delivery systems.     

Effect of ionic strength, pH and polymer concentration on the separation of DNA fragments in the presence of electroosmotic flow

DNA separations in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solutions have been demonstrated. During the separations, PEO entered capillaries filled with Tris-borate (TB) free buffers by EOF and acted as sieving matrices. We have found that ionic strength and pH of polymer and free solutions affect the bulk EOF and resolution differently from that in capillary zone electrophoresis. The EOF coefficient increases with increasing ionic strength of the free TB buffers as a result of decreases in the adsorption of PEO molecules. In contrast, the bulk EOF decreases with increasing the ionic strength of polymer solutions using capillaries filled with high concentrations of free TB buffers. Although resolution values are high due to larger differential migration times between any two DNA fragments in a small bulk EOF using 10 mM TB buffers, use of a capillary filled with at least 100 mM TB free buffers is suggested for high-speed separations. On the side of PEO solutions, 1.5% PEO solutions prepared in 100 to 200 mM TB buffers are more proper in terms of resolution and speed. The separation of DNA markers V and VI was accomplished less than 29 min in 1.5% PEO solutions prepared in 100 mM TB buffers, pH 7.0 at 500 V/cm using a capillary filled with 10 mM free TB buffers, pH 7.0.     

Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs

Different microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long-range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.     

Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations

Through the use of the one-step perturbation approach, 130 free energies of base stacking and 1024 free energies of base pairing in DNA have been calculated from only five simulations of a nonphysical reference state. From analysis of a diverse set of 23 natural and unnatural bases, it appears that stacking free energies and stacking conformations play an important role in pairing of DNA nucleotides. On the one hand, favourable pairing free energies were found for bases that do not have the possibility to form canonical hydrogen bonds, while on the other hand, good hydrogen-bonding possibilities do not guarantee a favourable pairing free energy if the stacking of the bases dictates an unfavourable conformation. In this application, the one-step perturbation approach yields a wealth of both energetic and structural information at minimal computational cost.     

Liquid-crystalline polymers from cationic dendronized polymer-anionic lipid complexes

The use of cationic dendronized polymers as a polyelectrolytic system for templating thermotropic liquid-crystalline phases (LC) via complexation and self-assembly with counter-charged ionic lipids is described. The topology of the LC phases resulting from the self-assembly process, their lattice parameter, and the interpenetration of lipid chains is discussed via birefringency analysis and small-angle X-ray scattering. Depending on the generation of the dendronized polymer and the length of the alkyl chains, amorphous, lamellar, and columnar tetragonal phases are observed. A structural model is proposed which accounts for the systematic variations of alkyl chain length as well as polymer generation. Owing to the reversible nature of the ionic complexation, this process proves high relevance for nanoporous channels, biomimetic, transport, and nanotemplating applications.     

On the use of the activation energy concept to investigate analyte and network deformations in entangled polymer solution capillary electrophoresis of synthetic polyelectrolytes

The activation energy associated with the electrophoretic migration of an analyte under given electrolyte conditions can be accessed through the determination of the analyte electrophoretic mobility at various temperatures. In the case of the electrophoretic separation of polyelectrolytes in the presence of an entangled polymer network, activation energy can be regarded as the energy needed by the analyte to overcome the obstacles created by the separating network. Any deformation undergone by the analyte or the network is expected to induce a decrease in the activation energy. In this work, the electrophoretic mobilities of poly(styrenesulfonates) (PSSs) of various molecular weights (Mr 16 x 10(3) to 990 x 10(3)) were determined in entangled polyethylene oxide (PEO) solutions as a function of temperature (in the 17-60 degrees C range) and the PSS activation energies were calculated. The influences of the PSS molecular weight, blob sizes zetab of the separating network (related to the PEO concentration), ionic strength of the electrolyte and electric field strength (75-600 V/cm) were investigated. The results were interpreted in terms of analyte and network deformations and were confronted with those previously obtained for DNA migration in polymer solutions and chemical gels. For a radius of gyration Rgzetab, suggesting PSS and network deformations in the latter case. Increasing ionic strength resulted in an increase in the PSS activation energy, because of the decrease of their radii of gyration, which makes them less deformable. Finally, the activation energies of all the PSSs are a decreasing function of field strength and at high field strength tend to reach a constant value close to that for a small molecule.     

HCl-NaCl-C3H8O3-H2O体系溶液热力学性质

在恒定丙三醇质量分数x=0．1的条件下，测定了无液接电池（A）和电池（B）的电动势根据电池（A）电动势确定了丙三醇和水混合溶剂中的Ag－AgCl电极的标准电极电势，讨论了HCl的迁移性质；由电池（B）测得的电动势计算了HCl在该体系中的活度系数γA，计算的结果表明，对于所讨论的体系，在溶液中总离子强度保持恒定，HCl的活度系数服从Harned规则．在溶液组成恒定时，IgγA是温度倒数1／T的线性函数，讨论了混合物中HCl的相对偏摩尔焓及介质效应．     

From atomistic simulation to the dynamics, structure and helical network formation of dendronized polymers: the Janus chain model

It is the purpose of this paper to establish a bottom-up multiscale approach for dendronized polymers. Based on our understanding of the phenomenology of an atomistic model for this class of polymers, we introduce a "Janus chain" (JC) model which adds a vectorial degree of freedom (Janus vector)--related to the sectorial amphiphilicity--to each segment of the linear backbone of a (classical) uncharged, semiflexible, and multibead chain representation of a polymer. The JC features induced polymeric curvature and ultimately triggers complexation. JC parameters related to the topology and chemical details are obtained from the atomistic level. Available experimental observations including the formation of superstructures and double helical conformations are well reproduced by the JC model. JC is efficiently solved via Brownian dynamics simulation and can be seen as a member of a universality class which is one (two) level(s) above the magnetic (semiflexible) chain model. It therefore should allow to model not only dendronized polymers but also structures belonging to the same class-exhibiting induced (or spontaneous) curvature--such as single stranded DNA and actin filaments.     

Synthesis of an anionically chargeable, high-molar-mass, second-generation dendronized polymer and the observation of branching by scanning force microscopy

An efficient synthesis of a methacrylate-based, second-generation (G2) dendronized macromonomer and its free radical polymerization to the corresponding high-molar-mass G2 dendronized polymer are described. The molar mass is determined by gel permeation chromatography (GPC), light-scattering, and analytical ultracentrifugation and compared with values estimated from a scanning force microscopy (SFM) contour lengths analysis of individualized polymer strands on mica. The polymer carries terminal tert-butyl-protected carboxyl groups, the degree of deprotection of which with trifluoroacetic acid is quantified by NMR spectroscopy using the highest molar mass sample. SFM imaging of both protected (noncharged) and unprotected (charged) dendronized polymers on solid substrates reveals mostly linear chains but also some with main-chain branches. The nature of these branches is investigated and the degree roughly estimated to which they are formed. Finally, a synthetic model experiment is described which sheds some light on the aspect of whether chain transfer, a process that could lead to covalent branching, is of importance in the synthesis of the present dendronized polymers.     

Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA

Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].     

含[BMIM]Cl-ZnCl2和非质子溶剂的凝胶聚合物电解质的合成

以烯类单体MA、MMA、HEMA为基质,通过原位聚合,合成了同时含离子液体[BMIM]Cl-ZnCl2和非质子溶剂的一系列新型凝胶聚合物电解质,用FTIR、AC、TG等方法对其结构和性能进行了表征。研究表明,聚合物电解质具有复合物结构;[BMIM]Cl-ZnCl2和非质子溶剂PC﹑DMC的加入使聚合物电解质的室温离子电导率大大增加,达2.83×10⁻³ S/cm,且与温度的关系符合VTF方程;聚合物电解质的热分解温度大于275 ℃,显示出良好的热稳定性。     

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

A CNDO/2 molecular orbital study of the electronic and conformational modes of ibotenic acid

CNDO/2 molecular orbital calculations on the non-ionic molecule, zwitterion and mono-anion of ibotenic acid are reported. Internal energy surfaces have been calculated from which minimum energy conformations are predicted. The relative internal energies, dipole moments and net atomic populations at the minimum-energy conformations are given. The importance of using a free energy rather than internal energy approach in the construction of energy surfaces is also discussed.     

Electrokinetic effects of adsorbed neutral polymers

On the basis of a previously developed hydrodynamic model for adsorbed polymers the charge flow along a charged interface with adsorbed (uncharged) polymer is calculated. An effective electrokinetic layer thickness is defined and its dependence on the characteristics of the adsorbed polymer and the ionic strength is studied. It is found that tails are very important for the hydrodynamic effects considered because they effectively screen the solvent flow from inner parts of the absorbed layer. The electrokinetic layer thickness increases with decreasing ionic strength, and tends to a limit equal to the hydrodynamic thickness at very low ionic strength.     

A modified Poisson-Boltzmann model including charge regulation for the adsorption of ionizable polyelectrolytes to charged interfaces, applied to lysozyme adsorption on silica

The equilibrium adsorption of polyelectrolytes with multiple types of ionizable groups is described using a modified Poisson-Boltzmann equation including charge regulation of both the polymer and the interface. A one-dimensional mean-field model is used in which the electrostatic potential is assumed constant in the lateral direction parallel to the surface. The electrostatic potential and ionization degrees of the different ionizable groups are calculated as function of the distance from the surface after which the electric and chemical contributions to the free energy are obtained. The various interactions between small ions, surface and polyelectrolyte are self-consistently considered in the model, such as the increase in charge of polyelectrolyte and surface upon adsorption as well as the displacement of small ions and the decrease of permittivity. These interactions may lead to complex dependencies of the adsorbed amount of polyelectrolyte on pH, ionic strength, and properties of the polymer (volume, permittivity, number, and type of ionizable groups) and of the surface (number of ionizable groups, pK, Stern capacity). For the adsorption of lysozyme on silica, the model qualitatively describes the gradual increase of adsorbed amount with pH up to a maximum value at pHc, which is below the iso-electric point, as well as the sharp decrease of adsorbed amount beyond pHc. With increasing ionic strength the adsorbed amount decreases (for pH > pHc), and pHc shifts to lower values.     

Influence de la conformation des polyions sur la fixation de colorants—III. Etude de la fixation de l'auramine o sur des polyacides synthetiques par equilibres de dialyse

The binding of auramine O (AuO), a cationic dye which does not dimerize, to poly(methacrylic acid) (PMA) and poly(acrylic acid) (PAA) has been measured by dialysis experiments. The effects of ionization, ionic strength and polymer to dye ratio (P/D) have been systematically investigated. At low ionization and P/D = 100, the bound fraction (q) of AuO is distinctly higher with PMA than with PAA at all ionic strength; this difference can be attributed to non-electrostatic interactions. Increase of ionic strength leads to displacement of the bound dye; on the other hand, high P/D ratio favours binding. We were able to describe the binding isotherms by an ion-exchange process at constant ionization and ionic strength. Water-methanol mixtures, known to destroy the coiled conformations of PMA, lead to a decrease in q; the same is observed in unionized acidic PMA solutions where ionic interactions are suppressed. These results indicate a strong binding due to the insertion of the dye into the polyion compact core and also a weak electrostatic one; they agree with the observations of spectrofluorescence; it must be emphasized that the bound fraction of dye is not, in itself, a significant parameter of conformational states.     

Self-organizable vesicular columns assembled from polymers dendronized with semifluorinated Janus dendrimers act as reverse thermal actuators

The synthesis and structural analysis of polymers dendronized with self-assembling Janus dendrimers containing one fluorinated and one hydrogenated dendrons are reported. Janus dendrimers were attached to the polymer backbone both from the hydrogenated and from the fluorinated parts of the Janus dendrimer. Structural analysis of these dendronized polymers and of their precursors by a combination of differential scanning calorimetry, X-ray diffraction experiments on powder and oriented fibers, and electron density maps have demonstrated that in both cases the dendronized polymer consists of a vesicular columnar structure containing fluorinated alkyl groups on its periphery. This vesicular columnar structure is generated by a mechanism that involves the intramolecular assembly of the Janus dendrimers into tapered dendrons followed by the intramolecular self-assembly of the resulting dendronized polymer in a vesicular column. By contrast with conventional polymers dendronized with self-assembling tapered dendrons this new class of dendronized polymers acts as thermal actuators that decrease the length of the supramolecular column when the temperature is increased and therefore, are called reverse thermal actuators. A mechanism for this reversed process was proposed.     

The molecular mechanics of valinomycin. II: Comparative studies of alkali ion binding

We have carried out a series of molecular mechanics calculations on the alkali ion complexes of valinomycin. For the ions Na⁺, K⁺, Rb⁺, and Cs⁺ we have found three-fold rotationally symmetric conformations as the lowest energy structures, while for Li⁺ a markedly asymmetric configuration is preferred. The relative free energies of the complexes show that Li⁺ is by far the poorest binding partner in solution, followed by Na⁺, which is in turn far poorer than any of the three larger ions. The binding selectivity derives from the slower variation of the complexation free energy with ionic size than the ionic solvation free energy, so that the ionophore is unable to compete with the solvent for the smaller ions. Our calculated strain energies suggest that valinomycin's failure to form complexes with the smaller ions in solution is due partially to the rigidity of the ionophore structure, which prevents the central cavity from contracting to accommodate them. Certain geometric criteria indicate that K⁺ provides the best fit to the binding site, although there is some inconsistency between the energetic and geometric criteria of binding ability.     

Calculation of the solvation free energy of neutral and ionic molecules in diverse solvents

The solvation free energy density (SFED) model was modified to extend its applicability and predictability. The parametrization process was performed with a large, diverse set of solvation free energies that included highly polar and ionic molecules. The mean absolute error for 1200 solvation free energies of the 379 neutral molecules in 9 organic solvents and water was 0.40 kcal/mol, and for 90 hydration free energies of ions was 1.7 kcal/mol. Overall, the calculated solvation free energies of a wide range of solute functional groups in diverse solvents were consistent with experimental data.