The structure and morphology of some mesophase polymers with flexible and stiff macromolecules

Comparative analysis of the temperature behavior and phase composition of linear flexible-chain polyfluoroalkoxyphosphazene and linear stiff-chain copolyester was carried out using X-ray diffraction at elevated temperatures and DSC measurements. The main idea of the study was to examine the nature of noncrystalline phases of such mesomorphic materials and to identify their structure and specific features of the morphology. The data obtained show that both flexible-and stiff-chain polymers despite the fact, whether their macromolecules contain or not contain mesogenic groups, are able to form columnar mesophases, whereas the formation of typically LC nematic and smectic states is the inherent structural feature only of stiff-chain polymeric systems, which exhibit peculiar aperiodic layer structures.     

Effect of flexible polymers on the dielectric dispersion of rod-like macromolecules

The rotational diffusion of rod-like polar macromolecules (poly-γ-benzyl-l-glutamate or poly-n-hexylisocyanate) within entangled non polar polymer coils (polystyrene) is studied by dielectric absorption in solution. The dielectric increment as well as the rotatory diffusion constant is studied as a function of molecular weight of both components and increasing concentration of the non-polar polymer as well as the temperature. The classical theory of rotational diffusion is not obeyed if the viscosity of the polystyrene solution is taken as the medium viscosity. An increase in molecular aggregation on polystyrene addition is suspected.     

Effect of nonhomogeneous shear rates on the flow-induced crystallization of flexible macromolecules

Several observations are made regarding the role of nonhomogeneous shearing rates in the process of flow-induced fibrillar crystallization from solution. The flow geometry chosen in the present analysis is that occurring in the annular region between two concentric cylinders. Computational evaluation and discussion of the effect of stress-induced diffusion is presented in terms of the elastic dumbbell model. Significant variations in concentrations in the annular region are predicted at full development. Estimates of the dynamics of development of these profiles indicate that the length to capillary radii for full development depends upon the molecular weight of the polymer and the relative dimensions of the concentric cylinders. These results indicate the important role of stress-induced diffusion in the process of thickening of fibrillar crystals.     

A fast algorithm for the interactive docking maneuver with flexible macromolecules and probes

A new algorithm for the interactive docking maneuver is presented. Full attention is given to the flexibility of both substrate and macromolecule, i.e., all the fragments are allowed to move. It is assumed that any numerical quantity which depends only on the isolated macromolecule at energy minimum is disposable when approximate expressions are derived. The central idea is the concept of relevant docking coordinates which reflect the essential features of the macromolecular deformations during the docking maneuver and which substantially diminish the number of considered degrees of freedom (DF). The conformational energy is divided into two parts. The first part, represented by condensed potential functions, needs no approximations. For the second part, termed E_rest, a quadratic approximation in the subspace spanned by the relevant docking coordinates is used. All the pairwise interactions between the atoms of the macromolecule are eliminated. A simple computational example using the ECEPP force field is given. Atomic coordinate computations are simplified by the introduction of virtual rotation axes for the backbone. In connection with drug design the concept of pressure pattern is defined and related to quantities appearing in the energy gradient. Extensions to substrate induced allosteric transitions are discussed.     

Dilute solution rheology of flexible macromolecules (bead–rod model)

The rheological behavior of dilute solutions of flexible macromolecules is studied by means of a freely jointed multiple bead–rod model. The solution of the equations describing the mechanics of the system is obtained by means of a numerical procedure, which applies to arbitrary flow conditions. The case of the transient stress in uniaxial elongational flow is developed in some detail. A comparison with bead–spring models shows both quantitative and qualitative differences which are briefly discussed.     

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0

We report the development and validation of a novel suite of programs, FITTED 1.0, for the docking of flexible ligands into flexible proteins. This docking tool is unique in that it can deal with both the flexibility of macromolecules (side chains and main chains) and the presence of bridging water molecules while treating protein/ligand complexes as realistically dynamic systems. This software relies on a genetic algorithm to account for the flexibility of the two molecules as well as the location of bridging water molecules. In addition, FITTED 1.0 features a novel application of a switching function to retain or displace key water molecules from the protein-ligand complexes. Two independent modules, ProCESS and SMART, were developed to set up the proteins and the ligands prior to the docking stage. Validation of the accuracy of the software was achieved via the application of FITTED 1.0 to the docking of inhibitors of HIV-1 protease, thymidine kinase, trypsin, factor Xa, and MMP to their respective proteins.     

Determination of charge and molecular weight of rigid-rod polyelectrolytes

Rod-like polyelectrolytes are an interesting model system because their persistence length is independent of the ionic strength and pH of the surrounding medium and they permit the investigation of polyelectrolytes in the absence of conformational degrees of freedom. In this work, rigid-rod poly(aramide) polyelectrolytes were synthesized by the Higashi method. Electrophoresis NMR spectroscopy in conjunction with diffusion NMR spectroscopy has been applied to determine the effective charge of the polymer. The charge was determined from the balance between the force in the electric field and the hydrodynamic friction in the steady-state electrophoretic motion. Because only organic counterions were present, and were identified in the proton NMR spectra, the counterions were investigated as well, and the fraction of condensed counterions was determined directly. From the effective charge per molecule and the knowledge of the fraction of condensed counterions, the total charge per molecule was determined. Finally, from the total charge, the number of repeat units and thus the molecular weight were inferred.     

Synthesis of novel rigid-rod and tripodal azulene chromophores

Two novel azulene chromophores 1 and 2 were synthesized to study dynamics of ultrafast electron injection at the interface of TiO₂ semiconductor nanoparticles. Fluorescence quenching was observed upon binding.     

Structure and electrical conductivity of ion-implanted rigid-rod and ladder polymers

Isotropic and oriented thin films of rigid-rod, rigid-rod pseudo-ladder, and ladder polymers were ion-bombarded with ⁸⁴Kr⁺ to a dose of 4 × 10¹⁶ ions/cm². The bombardment was conducted at two conditions: one at 190 keV energy with 0.12 μA/cm² current density and the other at 200 keV energy with 2.0 μA/cm² current density. With the low current density, the polymers developed a uniform ion-bombarded layer of about 0.35 μm at the surface. This layer showed an electrical conductivity on the order of 10^?3s/cm at ambient conditions, an enhancement of 6 to 9 orders of magnitude from the pristine polymers. The enhanced conductivity was found to decrease to 10^?6s/cm after the implanted krypton was removed by heating under reduced pressure. It suggests that the enhanced conductivity was due to a synergistic effect of structural change of the polymers and chemical doping by the im-planted ions. With the high current density, most polymer films, except that of rigid-rod pseudo-ladder poly(p-(2,5-dihydroxy) phenylene benzobisthiazole) (DPBT), developed an additional fibrous network structure over the uniform ion-bombarded layer. The comparable conductivity, 53 to 157 s/cm, measured for the various ion-bombarded films in-dicated that neither the molecular structure, rigid-rod or ladder, nor the molecular packing order, isotropic or oriented, constituted significant effect on the conductivity of ion-bombarded polymers. Since krypton could not be detected in the polymers ion-bombarded with high current density, the enhanced conductivity was attributed to the structural change of the polymers. The DPBT films ion-bombarded with high current density showed holes of micron size, probably due to the decomposition of hydroxy pendents from the rigid-rod backbone. © 1993 John Wiley & Sons, Inc.     

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

We propose a rigorous method for removing rigid-body motions from a given molecular dynamics trajectory of a flexible macromolecule. The method becomes exact in the limit of an infinitesimally small sampling step for the input trajectory. In a recent paper [G. Kneller, J. Chem. Phys. 128, 194101 (2008)], one of us showed that virtual internal atomic displacements for small time increments can be derived from Gauss' principle of least constraint, which leads to a rotational superposition problem for the atomic coordinates in two consecutive time frames of the input trajectory. Here, we demonstrate that the accumulation of these displacements in a molecular-fixed frame, which evolves in time according to the virtual rigid-body motions, leads to the desired trajectory for internal motions. The atomic coordinates in the input and output trajectory are related by a roto-translation, which guarantees that the internal energy of the molecule is left invariant. We present a convenient implementation of our method, in which the accumulation of the internal displacements is performed implicitly. Two numerical examples illustrate the difference to the classical approach for removing macromolecular rigid-body motions, which consists of aligning its configurations in the input trajectory with a fixed reference structure.     

Ionic conductivity of conjugated water-soluble rigid-rod polymers

Poly[(1,7-dihydrobenzo[1,2-d:4,5-d′] diimidazole-2,6-diyl)-2-(2-sulfo)-p-phenylene], a conjugated rigid-rod polymer, was derivatized with pendants of propane-sulfonated ionomers. The derivatized rigid-rod polymer was soluble in aprotic solvents as well as in water for isotropic solutions that were processed into isotropic films. Direct-current electrical conductivity σ of the films was measured using the four-probe technique. Room-temperature σ as high as 2.9 × 10^?4S/cm was achieved on pristine isotropic films without using dopants. When the rigid-rod polymer concentration exceeded 25 wt %, the isotropic solution could be transformed into a liquid-crystalline solution that allowed deformations to be applied to produce anisotropic films. Significant increase in σ was obtained in a sheared film along both the parallel direction (∥) and the transverse direction (⊥) with a σ_∥/σ_⊥ = 5. Additionally, enhanced σ was realized in films heat-treated at about 100°C, in the derivatized polymer with higher molecular weight from dialysis, and in substituting the sulfonated ion Na⁺ by H⁺ in the pendants of the polymers. Constant-voltage measurements were applied to the polymers to monitor the σ stability for ascertaining the nature of the conductivity. No electronic contribution in σ was detected. Instead, a monotonically decreasing σ was consistently observed indicative of ionic conductivity. © 1993 John Wiley & Sons, Inc.     

Molecular factors affecting solubility in rigid-rod polyamides

The solubility of a series of para-linked, substituted phenyl, biphenyl, terphenyl, and quaterphenyl polyamides is reported. Most of these polymers are soluble in amide solvents without lithium chloride, and several are soluble in ethers and/or ketones. The results indicate that solubility in this class of polymers is affected by the position, polarizability and size of the substituents, enantiomeric purity, and the number of non-coplanar biphenyl rings per repeat unit.     

Synthesis and investigation of new water soluble sulfonated rigid-rod polynaphthoyleneimide

A new water-soluble rigid-rod sulfonated polynaphthoyleneimide (PNIS) was synthesized. The structure of PNIS has been confirmed by elemental analysis, NMR (¹H, ¹³C), full X-ray investigation of model compound. Viscosity measurements, sedimentation and light-scattering experiments of PNIS solutions confirm the suggested aggregation of this polymer and an increase of its molecular weight without being substantially changed in different types of aqueous solution. These aggregates could consist of very tightly packed rigid rods.     

Multidimensional benzobisoxazole rigid-rod polymers. I. Preparation and characterization

Two- and three-dimensional rigid-rod polymers containing benzobisoxazole structures were prepared through the polycondensation in polyphosphoric acid of 4-[5-amino-6-hydroxybenzoxazol-2-yl]benzoic acid (ABA) with trimesic acid and 1,3,5,7-tetrakis(4-carboxylatophenyl)adamantane, respectively. Thermal properties of the polymers were determined by differential scanning calorimetry, thermogravimetric/mass spectral analysis, and isothermal aging studies. The multidimensional polymers exhibited lower solution viscosities and lower thermooxidative stabilities than the one-dimensional polymer generated by the homopolymerization of ABA under identical reaction conditions. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 3451–3456, 1997     

Computation of the nonhomogeneous equilibrium states of a rigid-rod solution

The nonhomogeneous equilibrium phase behavior of a solution of rigid rods is analyzed for a periodic one-dimensional system. Stable and unstable equilibrium solutions for the distribution function are computed as extrema of the free energy of the system expressed by the nonhomogeneous generalization of Onsager's [Ann. N.Y. Acad. Sci. 51, 627 (1949)] theory, which models interaction between rods on the scale of a single rod length. Biaxial equilibrium solutions are computed in a periodic system by discretizing the Euler-Lagrange nonlinear integral equation by the finite-element method and using Newton's method to solve the resulting set of nonlinear equations. Stable states for isotropic-nematic coexistence are computed in a periodic system rather than the semi-infinite system used in previous calculations. The density and order parameter profiles evolve monotically from the isotropic phase to the nematic phase. Unstable, nonhomogeneous, equilibrium states are also computed for concentrations of rods that exceed the value for spinodal decomposition. These nonhomogeneous states are characterized by combinations of bend, twist, and splay distortions in physical space and correspond to unstable attractors in the dynamic process of isotropic-nematic spinodal decomposition. For large systems, the nonhomogeneous states develop wide, bulklike nematic regions separated by thin regions with sharp gradients in orientation. The free energy formulation was also used to compute the accurate neutral stability curve; this curve shows the limits of applicability of the low-wave-number approximations frequently used in the study of spinodal decomposition.     

Synthetic multifunctional pores: lessons from rigid-rod beta-barrels

In this account, studies on synthetic multifunctional pores formed by rigid-rod beta-barrels are summarized comprehensively. The first section outlines the evolution of synthetic multifunctional pores from the introduction of rigid-rod molecules in bioorganic chemistry and the discovery of synthetic beta-barrels in comparison with pertinent developments in related areas of research. Design strategies to position active sites at the inner surface of rigid-rod beta-barrel pores are described in the second section. The third section focuses on the characteristics of transmembrane barrel-stave pores, emphasizing the dynamic nature of supramolecular oligomers with the aid of notional phase and energy diagrams. Section four introduces multifunctionality with the use of synthetic pores as hosts of a rich collection of guests, reaching from inorganic cations to organic macromolecules like peptides, oligonucleotides, polysaccharides and polyacetylenes. In section five, practical applicability of molecular recognition by synthetic multifunctional pores is documented with non-invasive fluorometric enzyme sensing. The application of host-guest chemistry within synthetic pores to couple molecular recognition and translocation with molecular transformation is the topic of section six. The last section mentions some perspectives and challenges with synthetic multifunctional pores.