Plasmid DNA Complexes in Powder Form Studied by Spectroscopic and Diffraction Methods.

Currently, new functional materials are being created with a strong emphasis on their ecological aspect. Materials and devices based on DNA biopolymers, being environmentally friendly, are therefore very interesting from the point of view of applications. In this paper, we present the results of research on complexes in the powder form based on plasmid DNA (pDNA) and three surfactants with aliphatic chains containing 16 carbon atoms (cetyltrimethylammonium chloride, benzyldimethylhexadecylammonium chloride and hexadecylpyridinium chloride). The X-ray diffraction results indicate a local hexagonal packing of DNA helices in plasmid DNA complexes, resembling the packing for corresponding complexes based on linear DNA. Based on the Fourier-transform infrared spectroscopy results, the DNA conformation in all three complexes was determined as predominantly of A-type. The two relaxation processes revealed by dielectric spectroscopy for all the studied complexes are connected with two different contributions to total conductivity (crystallite part and grain boundaries). The crystallite part (grain interior) was interpreted as an oscillation of the polar surfactant head groups and is dependent on the conformation of the surfactant chain. The influence of the DNA type on the properties of the complexes is discussed, taking into account our previous results for complexes based on linear DNA. We showed that the type of DNA has an impact on the properties of the complexes, which has not been demonstrated so far. It was also found that the layer of pDNA-surfactant complexes can be used as a layer with variable specific electric conductivity by selecting the frequency, which is interesting from an application point of view.

Evidence for NMR Relaxation Enhancement in a Protic Ionic Liquid by the Movement of Protons Independent of the Translational Diffusion of Cations.

The molecular dynamics, thermal stability, and ionic conductivity were studied in the protic ionic liquid 1-methylimidazolium bis(trifluoromethylsulfonyl)imide ([MIm][TFSI]). The relaxation of the 1H spin-lattice of cations in the measured frequency range (10 kHz to 20 MHz) and temperature (298 to 343 K) is sensitive mainly to slow processes occurring in the molecular dynamics of protic ionic liquid and dominated by the contribution of intermolecular translational diffusion. Molecular rotations give only a constant contribution and become significant in the higher frequency range. An interesting feature is the observed enhancement of the 1H spin-lattice relaxation below 0.03 MHz attributed to the exchange of protons (order of 10-5 s) between imidazolium cations. The measurements of the self-diffusion coefficient of hydrogen atoms of cation from 298 to 343 K additionally confirm the observed phenomenon. The coefficient for exchangeable protons -NH is higher than for the cation. The nuclear magnetic resonance (NMR) experiments provide unambiguous evidence for proton transport decoupled from molecular diffusion of ions and support the conclusion that the charge transport mechanism in the studied PIL includes contributions from both the vehicular and Grotthus mechanisms. The protic ionic liquid is thermally stable to about 573 K as shown by thermogravimetric analysis and its electrical conductivity is 5 × 10-2 S/cm at 423 K.

The viscous consequence of different trends in clustering of 1,2-diol and 1,n-diol molecules.

This paper presents the molecular basis for the quite different behavior of the viscosity of 1,2- and 1,n-diols in dependence of the length of the alkyl part of the molecules of these compounds. The experimental data on the dipolar orientational effects revealed a decidedly different role of that part of the molecules in creating a microstructure of both the hydrogen-bonded liquids. In the case of 1,n-diols, an increase in the alkyl radical length, i.e. an increasing of the distance between the OH groups within the molecule, highly stimulates molecular self-assembly in form of gradually longer and wider ribbon-like clusters. This effect yields a quite important increase in the viscosity of 1,n-diols as n increases. In the case of 1,2-diols, due to gradual separation of the hydrophilic and hydrophobic parts of the molecules, the situation is quite different. Two OH groups situated on one of the ends of the hydrocarbon radical form the clusters of a micelle-like shape, however, the dipole moment is not compensated. Along with an increase in the hydrocarbon part in 1,2-diol molecules, one only observes an increase in the intermolecular consolidation within the micelle-like entities. This manifests as a gradual decrease in the polarity of these clusters. So, actually, there are no relevant reasons for essential differences of viscosities in the series of 1,2-diols.

From supramolecular to conventional polymers: polyethylene glycol.

Increasing the polymerization degree of polyethylene glycol (PEG), HO-(CH2CH2O-)nH, entails lowering the number of hydroxyl groups per unit volume; therefore, supramolecular polymers are gradually replaced by longer and longer conventional polymers. This paper concerns an estimation of the polymerization degree (n) where PEG changes its nature from a supramolecular polymer to a conventional polymer. It was found that that virtual transformation takes place when n reaches the value of about 9. The conclusion follows from the different thermal behaviors of the dipolar orientational effects in liquid PEG detected for n below and above 9. The result reflects a diametrically different impact of the temperature on the linkages between the monomers in supramolecular and conventional polymers.

Does water belong to the homologous series of hydroxyl compounds H(CH2)nOH?

The main objective of this paper is to find a source of anomalously high value of the equilibrium permittivity of water. The source is identified to be the unusually high deformation polarizability. The conclusion follows from the analysis of the behavior of the orientational entropy increment induced by an external electric field applied to the liquids belonging to the homologous series of hydroxyl compounds H(CH2)nOH at the end of which water is located. The finding reflects the "indecision" of water about its dielectric relationship with the alcohol family: the value of the permittivity of water absolutely does not fit into alcohols (is too high), while the dipolar orientation effects (which normally determine the permittivity level) fit into alcohols quite well. It results from the presented experimental data that among all the diversity of intermolecular hydrogen-bonded structures existing in liquid water, predominant are the polar entities, i.e. the structures which more or less resemble the chains. Otherwise, the dipolar orientational effects would behave in a quite different way than what is observed in the experiment. The result is convergent with the conclusion of Wernet et al., based on the high-performance X-ray studies of water (Science, 2004).

Dipolar Self-Assembling in Mixtures of Propylene Carbonate and Dimethyl Sulfoxide as Revealed by the Orientational Entropy.

This article presents the results of static dielectric studies performed on mixtures of two strongly polar liquids important from a technological point of view: propylene carbonate (PC) and dimethyl sulfoxide (DMSO). The dielectric data were analyzed in terms of the molar orientational entropy increment induced by the probing electric field. It was found that the two polar liquids in the neat state reveal quite different molecular organization in terms of dipole-dipole self-assembling: PC exhibits a dipolar coupling of the head-to-tail type, whereas in DMSO one observes extreme restriction of dipolar association in any form. In PC + DMSO mixtures, the disintegration of the dipolar ensembles of PC molecules takes place and the progress of that process is strictly proportional to the concentration of DMSO. The static permittivity of mixtures of such differently self-organized liquids exhibits a positive deviation from the additive rule and the deviation develops symmetrically within the concentration scale.

Hierarchical Structure of Supramolecular Polymers Formed by N,N'-Di(2-ethylhexyl)urea in Solutions.

Supramolecular chain polymers formed by N,N'-di(2-ethylhexyl)urea (EHU) dissolved at low concentrations (up to 0.1 mole fraction) in heptane were investigated with the use of the dielectric spectroscopy. The experimental data show an exceptional ability of the chains for the antiparallel self-aggregation due to dipole-dipole interactions, leading to an anomalous dependence of the static permittivity of EHU + heptane solutions on temperature and concentration of the urea. The primary molecular assembly into polymeric chains is therefore followed by a secondary bundling of the chains which facilitates a longitudinal translation of the chains. That peculiarity and an asymmetry of the alkyl substituent in the EHU molecule making the system a mixture of diastereoisomers of unfavorable packing of the side group, are the most probable molecular mechanisms which prevent the crystallization of EHU-the only known liquid urea derivative.

Compliance of the Stokes-Einstein model and breakdown of the Stokes-Einstein-Debye model for a urea-based supramolecular polymer of high viscosity.

Impedance spectroscopy was used for the study of the static and dynamic behavior of the electrical conductivity of a hydrogen-bonded supramolecular polymer of high viscosity. The experimental data are discussed in the frame of the Stokes-Einstein and Stokes-Einstein-Debye models. It was found that the translational movement of the ions is due to normal Brownian diffusion, which was revealed by a fulfillment of Ohm's law by the electric current and a strictly exponential decay of the current after removing the electric stimulus. The dependence of the dc conductivity on the viscosity of the medium fulfills the Stokes-Einstein model quite well. An extension of the model, by including in it the conductivity relaxation time, is proposed in this paper. A breakdown of the Stokes-Einstein-Debye model is revealed by the relations of the dipolar relaxation time to the viscosity and to the dc ionic conductivity. The importance of the C=O···H-N hydrogen bonds in that breakdown is discussed.

Phase transition from liquid to disordered solid phase of cyclooctanone studied with dielectric methods.

The dielectric studies performed for cyclooctanone in its static dielectric regime have shown that at the phase transition from liquid to disordered (plastic) solid phase of the compound, the following singular phenomena occur: (a) the static permittivity (ε(s)) exhibits a small increase at the transition, instead of that usually observed for polar liquids, a strong decrease of the permittivity at the transition to the crystalline solid phase; (b) temperature dependence of the permittivity, ε(s)(T), is practically the same in both phases, reflecting the same dipolar orientational entropy increment induced by the probing electric field; (c) a distinct jump occurs in the slope of the frequency dependence (in log-log scale) of the dielectric losses due to an ionic current, from the "ohmic" value -1 in the liquid phase to about -0.9 just after the transition to the plastic phase; (d) a similar jump is observed in the shape of the electric modulus spectra of cyclooctanone. The results clearly show the liquid-like freedom in the molecular dynamics in the plastic phase as well as similar intermolecular interactions in both phases of cyclooctanone. The differences in the dielectric losses frequency behavior may reflect the change in the ions dynamics: from the normal translational Brownian diffusion in the liquid phase to the subdiffusional dynamics in the plastic phase.

On similarity of hydrogen-bonded networks in liquid formamide and water as revealed in the static dielectric studies.

The paper presents the experimental verification of the result obtained with the molecular dynamics simulation which revealed the differences in the topology of the hydrogen-bonded networks in liquid formamide and water, namely, the differences in their intermolecular cyclization process (I. Bakó, et al. J. Chem. Phys. 2010, 132, 014506). It is shown in our paper that the difference in the (simulated) size distribution of the hydrogen-bonded molecular rings in water (a relatively sharp maximum at about 6 molecules) and formamide (a broad maximum at about 11 molecules) strongly manifests itself in the experimental values of the Kirkwood correlation factor of the compounds. A much larger number of molecules included in the cyclic species (of more or less compensated dipole moment) leads to significant decrease of the Kirkwood correlation factor of formamide in comparison to that of water. Besides, as a consequence of an enhancement in formation of the cyclic multimers of formamide, one observes an essential reduction of the orientational entropy increment of that liquid, in comparison to the entropy effect related to liquid amides where the chain multimers are formed.

On intermolecular dipolar coupling in two strongly polar liquids: dimethyl sulfoxide and acetonitrile.

The paper presents the results of studies of the electric and dielectric properties of dimethyl sulfoxide (DMSO) and acetonitrile (ACN), two strongly polar liquids composed of the molecules of the same dipole moment value (µ ≈ 4 D) but of a quite different static dielectric permittivity (ε(S)(DMSO) >> ε(S)(ACN)). It was shown that the activation energies for both the dc ionic conductivity (σ(DC)) and the viscosity (η) are two times higher for DMSO than for ACN; however, for both of the liquids, the temperature dependence of the product σ(DC)η is quite close to the prediction of the Stokes-Einstein relation. The dielectric results are interpreted in terms of the intermolecular dipole-dipole coupling. An exceptional behavior of DMSO most certainly results from its "monomolecularity", i.e., from the lack of the dipolar coupling in that strongly polar liquid. The effect is a consequence of a very specific structure of the DMSO molecule where its rotational dynamics makes the intermolecular dipole-dipole coupling very unfavorable, in contrast to the ACN molecules.

Fractional Stokes-Einstein-Debye relation and orientational entropy effects in strongly hydrogen-bonded liquid amides.

The impedance spectroscopy studies performed for two strongly hydrogen-bonded liquid amides: N-methylpropionamide (NMP, CH(3)·NH·CO·C(2)H(5)) and N-ethylacetamide (NEA, C(2)H(5)·NH·CO·CH(3)) have shown that the two centers of the peptide linkage, -NH·CO-, active in the C=OH-N hydrogen bonds formation, exhibit quite different sensibilities to the steric screening effects. In contrast to the oxygen atom, a relatively small change (CH(3)- to C(2)H(5)-) in the screening of the hydrogen atom leads to an essential decrease of the degree of the amide self-association. As a consequence, both the static dielectric permittivity and the orientational entropy increment of NEA are essentially lower than those of NMP. However, it was found that the dynamic processes studied are only weakly influenced (in the case of dc conductivity, σ(DC)) or totally not influenced (the dielectric relaxation time, τ(D)) by the different degrees of NMP and NEA self-association. The experiment shows that for both the amides, the logσ(DC) vs. logτ(D) dependence is nonlinear and can be described with the fractional Stokes-Einstein-Debye relation, σ(DC)τ ≅ const, with the exponent s varying from about -0.8 to about -0.6 in the temperature range from 5 °C to 110 °C.

Molecular dynamics and entropy effects in hydrogen-bonded supramolecular polymer N,N'-di(2-methyl-2-pentylheptyl)urea dissolved in nonpolar medium.

On the basis of the static dielectric permittivity temperature behavior of the supramolecular polymer formed by N,N'-di(2-methyl-2-pentylheptyl)urea (MPHU) in carbon tetrachloride diluted solution (10% in mole fraction) and that of neat acetonitrile, it was found that two liquids of the same macroscopic polarity (expressed by the same value of the dielectric permittivity approximately 35) exhibit an essential difference in the field-induced orientational entropy change. A much higher entropy effect is observed for the liquid composed of not too numerous but highly polar molecular entities (MPHU + CCl(4)) than for the liquid composed of numerous but less polar entities (neat acetonitrile). The analysis of the dielectric relaxation spectra of MPHU + CCl(4) solutions was performed with the Davidson-Cole (DC) model. It was found that the DC exponent beta changes its value in a quite important range of 0.4-0.8, depending on MPHU concentration and temperature. This reflects an important deviation of the relaxation mechanism occurring in the supramolecular system investigated from that corresponding to the normal Brownian rotational diffusion (beta = 1).

Conductivity dynamics and static dielectric permittivity of highly conducting molecular liquids studied with impedance spectroscopy. Formamides.

Impedance spectroscopy was used for studies of the frequency dependence of the electric conductivity of two highly conducting liquid amides: N-methylformamide (NMF), strongly self-associated via the hydrogen bonds C=O...N-H, and N,N-dimethylformamide (DMF), which is not able to self-organize by hydrogen bonding. The studies were performed in the frequency range f = 50 kHz-100 MHz and in the temperature range T = 278.15-363.15 K. It was found that, at a given temperature, NMF exhibits static conductivity (sigma(0)) of 2 orders of magnitude higher, and conductivity relaxation time (tau(sigma)) of 2 orders of magnitude shorter, than those of DMF. On the basis on sigma(0) and tau(sigma) values, the static dielectric permittivity (epsilon) was calculated for both liquids studied and the values obtained perfectly agree with those measured with the classical dielectric methods. An empirical equation for epsilon(T) dependence for NMF and DMF is proposed.