Solutions Of Rodlike Molecules Research Articles

Entropic forces drive self-organization and membrane fusion by SNARE proteins

SNARE proteins are the core of the cell's fusion machinery and mediate virtually all known intracellular membrane fusion reactions on which exocytosis and trafficking depend. Fusion is catalyzed when vesicle-associated v-SNAREs form trans-SNARE complexes ("SNAREpins") with target membrane-associated t-SNAREs, a zippering-like process releasing ∼65 kT per SNAREpin. Fusion requires several SNAREpins, but how they cooperate is unknown and reports of the number required vary widely. To capture the collective behavior on the long timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE properties such as the zippering energy landscape and the surface charge distribution. In simulations the ∼65-kT zippering energy was almost entirely dissipated, with fully assembled SNARE motifs but uncomplexed linker domains. The SNAREpins self-organized into a circular cluster at the fusion site, driven by entropic forces that originate in steric-electrostatic interactions among SNAREpins and membranes. Cooperative entropic forces expanded the cluster and pulled the membranes together at the center point with high force. We find that there is no critical number of SNAREs required for fusion, but instead the fusion rate increases rapidly with the number of SNAREpins due to increasing entropic forces. We hypothesize that this principle finds physiological use to boost fusion rates to meet the demanding timescales of neurotransmission, exploiting the large number of v-SNAREs available in synaptic vesicles. Once in an unfettered cluster, we estimate ≥15 SNAREpins are required for fusion within the ∼1-ms timescale of neurotransmitter release.

Experimental realization of crossover in shape and director field of nematic tactoids

Spindle-shaped nematic droplets (tactoids) form in solutions of rod-like molecules at the onset of the liquid crystalline phase. Their unique shape and internal structure result from the interplay of the elastic deformation of the nematic and anisotropic surface forces. The balance of these forces dictates that tactoids must display a continuous variation in aspect ratio and director-field configuration. Yet, such continuous transition has eluded observation for decades: tactoids have displayed either a bipolar configuration with particles aligned parallel to the droplet interface or a homogeneous configuration with particles aligned parallel to the long axis of the tactoid. Here, we report the first observation of the continuous transition in shape and director-field configuration of tactoids in true solutions of carbon nanotubes in chlorosulfonic acid. This observation is possible because the exceptional length of carbon nanotubes shifts the transition to a size range that can be visualized by optical microscopy. Polarization micrographs yield the interfacial and elastic properties of the system. Absorbance anisotropy measurements provide the highest nematic order parameter (S=0.79) measured to date for a nematic phase of carbon nanotubes at coexistence with its isotropic phase.

Monodisperse Oligodiacetylenes

The authors report the synthesis of a novel series of oligodiacetylenes of defined lengths (1-n). These highly soluble molecules were systematically studied for the relationship between conjugation length and optical properties. The authors conclude that the oligodiacetylenes are rigid rod-like molecules in solution reaching up to 4 nm in length.

13C-NMR Studies on Fluctuation of Rod-Like Molecules in Solution: Molecular Dynamics in a Polar Solvent of CDCl3

To investigate the molecular dynamics of rod-like molecules in solution, 13C-NMR measurements of a liquid crystalline material (4-(1-methylheptyloxycarbonyl)phenyl 4′-octyloxybiphenyl-4-carboxylate: MHPOBC) with a CDCl3 solvent are carried out. When MHPOBC leaves the solution and deposits as crystals, peak broadening, which may result from a slowing down of molecular motion, occurs simultaneously. In addition, the correlation time τc of the corresponding molecular motion is estimated to be approximately 10−8 s by the spin-lattice relaxation time T1 measurements.

Liquid-Crystalline Order in Polymer Systems: Basic Models

The liquid crystalline (LC) order appears in a variety of polymer systems, such as solutions of rod-like molecules (DNA, TMV), solutions of semiflexible molecules (long fragments of DNA), block-copolymer melts, main-chain and side-chain liquid crystalline polymer melts etc. Many LC phases have been observed in these systems; the most common being: the nematic, cholesteric, smectic or lamellar, hexagonal, and double gyroid (in block copolymers) phases. We will discuss in detail some of them and give their quantitative description in terms of order parameters. We will also present various theoretical models used to study LC ordering in the systems. The models discussed in this paper are as follows: Onsager model and its extension within the Density Functional Theories (DFT), Khohlov-Semenov model for semiflexible polymers, Kratky-Porod model, combination of the Kratky-Porod model and Maier-Saupe model, self-consistent field theoretical model and finally the Landau-Ginzburg models and their connection with the Edwards model for polymer systems. We will also briefly discuss the elasticity of polymer systems in the case of nematic ordering. We present in a pedagogical manner the general ideas which are behind various models and give references to the papers which contain the technical details.

Depolarized Dynamic Light Scattering Mesurement of Rotational Motion of Rod-like Molecules in Solution under Sinusoidal Strain.

Depolarized Dynamic Light Scattering Mesurement of Rotational Motion of Rod-like Molecules in Solution under Sinusoidal Strain.

Theory of nematic phases in solutions of rodlike molecules with hydrogen bonds

Nematic phases in dilute transitions of rodlike molecules with carboxylic acid functional groups are studied using an Onsager-like theory with the additional term in the free energy describing hydrogen bonding. It is shown that the hydrogen bonds with a proper geometry enhance nematic ordering. The behavior of the system turns out to be completely different in the cases when molecules can form only dimers and when then can form hydrogen-bonded ‘‘polymers.’’ In the latter case the molecules tend to form a completely ordered phase at low temperatures. The numbers of hydrogen bonds in the ordered phase and isotropic liquid are different. Therefore IR spectroscopy can be used for study of these systems.

DNA: A Model Compound for Solution Studies of Macromolecules

Well-defined, monodisperse, homologous series of oligonucleotides and DNA restriction fragments may now be produced and used as models of rigid and semirigid rodlike molecules in solution. Information from optical experiments on these model systems aids in the formulation and testing of theories of macromolecular dynamics in both dilute and concentrated solution.

Rotational and translational diffusion of short rodlike molecules in solution: Oligonucleotides

Rotational and translational diffusion coefficients in aqueous solution of a series of three B duplex oligonucleotides 8, 12, and 20 base pairs in length are measured by depolarized and polarized dynamic light scattering, respectively. Theoretical relations for the diffusion coefficients of short rods by Tirado and Garcia de la Torre are used in combination with the experimental data to obtain the dimensions of the molecules. The theoretical relations are self-consistent through the series and give a hydrodynamic diameter for DNA of 20±1.5 Å. The results, furthermore, show that the combination of depolarized and polarized dynamic light scattering provides a powerful method for obtaining hydrodynamic dimensions of short rodlike particles and may therefore be used in applications which follow molecular sizes and size changes.

Orientability of Rigid Rodlike Molecules in Solution and Controlled Preparation of Model Systems

ABSTRACTA survey is presented of our works on orientability of poly(p-phenylene-benzbisthiazole) (PBT) as a model for rigid rods. It starts with the solid state with specific reference to diffraction by the individual molecule. It is followed by behaviour in semidilute solutions, demonstrating increase of orientability with increasing rod alignment, with vastly higher absolute values (as expressed by rotational diffusion coefficient) than anticipated from existing theory. The origin of the discrepancy, as identified by simulations, lies in the inappropriateness of the application of mean constraints, a recognition which should have wider implications. The relaxation from the highly oriented state, also in solution, has been followed and the elementary rotational jump of rods identified, with a new method relying on in situ (synchrotron) X-ray diffraction. As a separate line, we are announcing a new model system, ellipsoidal latices of predesigned axial ratios, with wide ranging potential for the study of rigid rod behaviour in polymer and colloid science.

Effect of flow on solutions of rodlike molecules

AbstractA flow field imposed on a solution of rodlike particles tends to align the rods owing to friction between the fluid and the rods. The potential energy of rods in a steady‐state, homogeneous, and irrotational flow is superposed on the equilibrium Gibbs free energy of the quiescent solution to obtain the total free energy. The exact lattice treatment of Flory and Ronca is used in formulating the problem. Effects of flow on the orientational distribution function of rods and phase separation are analyzed with particular reference to elongational and pure shear flows. Calculations carried out for various compositions and flow characteristics reveal the presence of a region where the order parameter is sensitive to changes in prevailing flow conditions. Experimental determination of orientation by measuring flow birefringence is discussed.

On the rotational diffusion of rod-like macromolecules in lyotropic-mesomorphic phases

The rotational diffusion of rod-like macromolecules, idealized as monodisperse rods, in concentrated solution is considered. The Doi-Edwards model is modified to explain the experimentally observed increase of the rotational relaxation time with increasing concentration in the lyotropic-nematic phase of rigid rod-like molecules in solution. Our approach consists in (i) reconsidering the original Doi-Edwards model to eliminate unphysical behaviour of the rotational relaxation time at the limit of perfect order, and (ii) including concentration effects on the translational diffusivity of rods in the Doi-Edwards model. Predictions of the corrected model are compared with steady flow viscosity data for poly(n-alkylisocyanates). In the lyotropic-nematic phase a very good qualitative agreement between the theory and experiment is observed. Additionally, the model applied to a highly concentrated isotropic phase explains in a natural way the viscosity behaviour as the concentration is increased towards the criti...

The effect of restricted rotational diffusion on the dynamics of rodlike molecules in concentrated solution

AbstractThe model of Doi for the rotational dynamics of rodlike molecules in solution is compared with that of Warchol and Vaughan and Wang and Pecora. The similarities in the results for dielectric relaxation are discussed and the application of the models to the behaviour of isotropic solutions, anisotropic (lyotropic‐nematic) solutions, and mixtures of small molecules with polymers is briefly discussed.

Model calculations of the phase behaviour of rod-like particles in solution: Polydisperse systems having asymmetric distributions of rod-lengths

Model calculations have been made of the phase behaviour, and compositions of the phases in the biphasic range, for polydisperse rod-like particles in solution. The special cases of a most-probable distribution (m.p.d.), an empirically modified most-probable distribution and asymmetric Gaussian distributions are considered. It is shown that the presence of species of very low molecular length in the m.p.d. result in v o ϱ∗∗ , the volume fraction of polymer for which the system becomes wholly-anisotropic, being close to unity and thus the biphasic range for the case of this distribution is far larger than that normally found experimentally. The empirically-modified m.p.d. gives a narrower biphasic range than that for the m.p.d. Calculations for the asymmetric Gaussian distribution make it clear that v o ϱ∗∗ is determined by the low molecular length species in the distribution whilst v o ϱ∗ , the volume fraction of polymer at which the system goes from isotropic to biphasic, is determined by the high molecular length species of the distribution. It is suggested that these distributions and those considered earlier are unable to adequately explain the observed dielectric and viscosity behaviour of rod-like molecules in solution. It is necessary to introduce a small high molecular weight tail to a chosen distribution in order to obtain agreement betwee between the calculate and the observed behaviour.

Capillary and slit flow behavior of concentrated solutions of a rod-like polymer

This paper is concerned with the flow behavior of isotropic solutions of the rod-like polymer, poly(p-phenyleneterephthalamide) (PPT), in 100 percent sulfuric acid. Studies include entry flow visualization in a slit die and solution fracture, and die swell in capillaries and a slit die. It was observed that solutions of PPT exhibit nearly negligible die swell, a slip-stick type of fracture that disappears at high shear rates, and radial entry flow patterns similar to Newtonian fluids. Fracture was associated with the plateau in the shear stress vs shear rate curve. Because values of the wall shear stress (τw.) obtained from capillary measurements were in good agreement with those obtained from a cone-and-plate rheometer and values of the loss modulus (G″) obtained from small-strain dynamic oscillatory measurements, it is believed that the rheological properties lead to the flow instability. These results are in agreement with the predictions of a recent theory by Doi and Edwards for concentrated solutions of rod-like molecules. Data are also presented for a flexible chain polyamide, nylon 6,6, in 100 percent H2SO4 for the purpose of comparing the flow characteristics of rigid and flexible chain polymers.

Dependence of the primary normal-stress difference coefficient on molecular weight for concentrated solutions of rodlike molecules

The primary normal-stress difference has been measured for concentrated solutions of rodlike and flexible chain polyamides. The solutions studied here consist of poly-p-phenyleneterephthalamide (PPT) which is believed to be rodlike in 100% H2SO4 and the flexible chain polyamide, polyhexamethylene adipamide (nylon 6.6), which is also dissolved in 100% sulfuric acid. For the PPT solutions the primary normal-stress difference coefficient in the limit of zero shear rate (ψ 1(0)) is observed to be proportional toM 12.9 whereM w is the weight average molecular weight. For concentrated solutions of nylon 6.6,ψ 1(0) is found to be proportional toM 7.6 which is in reasonable agreement with values reported for other flexible chain polymers. These data point out that there are some interesting differences in the primary normal stress differences for rodlike and flexible chain polymers and at the same time provide support of the recent theoretical predictions ofDoi andEdwards for concentrated solutions of entangled rodlike molecules.

Non-Newtonian Viscoelastic Properties of Rodlike Molecules in Solution: Comment on a Paper by Kirkwood and Plock

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Viscosity of Rodlike Molecules in Solution

A theory is presented for the viscosity of rodlike molecules in solution. It does not use the diagonalization approximation of the Oseen tensor and improves the Riseman and Kirkwood theory. It is found that the diagonalization approximation amounts to reducing the effects of the hydrodynamical interactions between the segments of the molecules. A new technique is introduced to reduce the problem to an integral equation, of which the solution follows Ullman, who corrected Riseman and Kirkwood and Kirkwood and Auer.