Electrostatic Interactions in the Formation of DNA Complexes with Cis- and Trans-Isomers of Azobenzene-Containing Surfactants in Solutions with Di- and Trivalent Metal Ions.

The effect of the presence of divalent and trivalent metal ions in solutions upon DNA packaging induced by the photosensitive azobenzene-containing surfactant is considered. It has been shown that the addition of divalent and trivalent metal ions does not affect the DNA-surfactant interaction for both the cis- and the trans-isomers of the surfactant. At the same time, the ionic strength of the solution, which is provided by a certain concentration of the salt, has a huge impact. It affects the association of surfactant molecules with each other and their binding to DNA. It has been shown by computer simulation that cobalt hexamine is attracted to the N7 atom of guanine in the major groove of DNA and does not penetrate into grooves near the AT base pairs.

Influence of the Chemical Structure on the Mechanical Relaxation of Dendrimers.

The rheological properties of macromolecules represent one of the fundamental features of polymer systems which expand the possibilities of using and developing new materials based on them. In this work, we studied the shear-stress relaxation of the second generation PAMAM and PPI dendrimer melts by atomistic molecular dynamics simulation. The time dependences of relaxation modulus G(t) and the frequency dependences of the storage G'(ω) and loss G″(ω) moduli were obtained. The results were compared with the similar dependences for the polycarbosilane (PCS) dendrimer of the same generation. The chemical structure of the dendrimer segments has been found to strongly influence their mechanical relaxation. In particular, it has been shown that hydrogen bonding in PAMAM dendrimers leads to an entanglement of macromolecules and the region is observed where G'(ω) > G″(ω). This slows down the mechanical relaxation and rotational diffusion of macromolecules. We believe that our comprehensive research contributes to the systematization of knowledge about the rheological properties of dendrimers.

Alizarin as a potential protector of proteins against damage caused by hydroperoxyl radical.

Alizarin is a natural anthraquinone molecule with moderate antioxidative capacity. Some earlier investigations indicated that it can inhibit osteosarcoma and breast carcinoma cell proliferation by inhibiting of phosphorylation process of ERK protein (extracellular signal-regulated kinases). Several mechanisms of deactivation of one of the most reactive oxygen species, hydroperoxyl radical, by alizarin are estimated: hydrogen atom abstraction (HAA), radical adduct formation (RAF), and single electron transfer (SET). The plausibility of those mechanisms is estimated using density functional theory. The obtained results indicated HAA as the only thermodynamically plausible mechanism. For that purpose, two possible mechanistic pathways for hydrogen atom abstraction are studied in detail: hydrogen atom transfer (HAT) and proton-coupled electron transfer (PCET). Water and benzene are used as models of solvents with opposite polarity. To examine the difference between HAT and PCET is used kinetical approach based on the Transition state theory (TST) and determined rate constants (k). Important data used for a distinction between HAT and PCET mechanisms are obtained by applying the Quantum Theory of Atoms in Molecules (QTAIM), and by the analysis of single occupied molecular orbitals (SOMOs) in transition states for two examined mechanisms. The molecular docking analysis and molecular dynamic are used to predict the most probable positions of binding of alizarin to the sequence of ApoB-100 protein, a protein component of plasma low-density lipoproteins (LDL). It is found that alizarin links the nitrated polypeptide forming the π-π interactions with the amino acids Phenylalanine and Nitrotyrosine. The ability of alizarin to scavenge hydroperoxyl radical when it is in a sandwich structure between the polypeptide and radical species, as the operative reaction mechanism, is not significantly changed concerning its antioxidant capacity in the absence of polypeptide. Therefore, alizarin can protect the polypeptide from harmful hydroperoxyl radical attack, positioning itself between the polypeptide chain and the reactive oxygen species.

Cis-Isomers of Photosensitive Cationic Azobenzene Surfactants in DNA Solutions at Different NaCl Concentrations: Experiment and Modeling.

The DNA interaction with cis-isomers of photosensitive azobenzene-containing surfactants was studied by both experimental methods and computer simulation. It was shown that before the organization of micelles, such surfactants in the cis-conformation form associates of only a single type with a disordered orientation of molecules. In contrast, for trans-isomers, there exist two types of associates with head-to-head or head-to-tail orientations of molecules in dependence on salt concentration in a solution. The comparison of cis- and trans-isomer binding to DNA and the influence of salt concentration on the formation of their complexes with DNA were studied. It was shown that cis-isomers interact with phosphate groups of DNA and that their molecules were also located along the minor groove of DNA.

Some Features of Surfactant Organization in DNA Solutions at Various NaCl Concentrations.

The photosensitive azobenzene-containing surfactant C4-Azo-OC6TMAB is a promising agent for reversible DNA packaging in a solution. The simulation of the trans-isomer surfactant organization into associates in a solution with and without salt as well as its binding to DNA at different NaCl concentrations was carried out by molecular dynamics. Experimental data obtained by spectral and hydrodynamic methods were used to verify the results of simulation. It was shown that head-to-tail aggregates with close to antiparallel orientation of surfactant molecules were formed at certain NaCl and surfactant concentrations (below critical micelle concentration). Such aggregates have two positively charged ends, and therefore, they can be attracted to negatively charged DNA phosphates far located along the chain, as well as those that belong to different molecules. This contributes to the formation of intermolecular DNA-DNA contacts, and this way, the experimentally observed precipitation of DNA can be explained.

NMR Spectroscopic Studies of Cation Dynamics in Symmetrically-Substituted Imidazolium-Based Ionic Liquid Crystals.

Ionic liquid crystals (ILCs) present a new class of non-molecular soft materials with a unique combination of high ionic conductivity and anisotropy of physicochemical properties. Symmetrically-substituted long-chain imidazolium-based mesogenic ionic liquids exhibiting a smectic liquid crystalline phase were investigated by solid state NMR spectroscopy and computational methods. The aim of the study was to reveal the correlation between cation size and structure, local dynamics, and orientational order in the layered mesophase. The obtained experimental data are consistent with the model of a rod-shaped cation with the two chains aligned in opposite directions outward from the imidazolium core. The alignment of the core plane to the phase director and the restricted conformations of the chain segments were determined and compared to those in single-chain counterparts. The orientational order parameter S~0.5-0.6 of double-chain ionic liquid crystals is higher than that of corresponding single-chain analogues. This is compatible with the enhanced contribution of van der Waals forces to the stabilization of smectic layers. Increased orientational order for the material with Br- counterions, which exhibit a smaller ionic radius and higher ability to form hydrogen bonds as compared to that of BF4-, also indicated a non-negligible influence of electrostatic and hydrogen bonding interactions. The enhanced rod-shape character and higher orientational order of symmetrically-substituted ILCs can offer additional opportunities in the design of self-assembling non-molecular materials.

Understanding ionic mesophase stabilization by hydration: a solid-state NMR study.

The correlation between the water contribution to hydrogen bonding within ionic sublayer, mesophase order parameter, and ion translational self-diffusion in the layered ionic liquid crystalline phase is investigated. Changes in hydrogen bonding, conformational and translational dynamics, and orientational order upon hydration were followed by solid-state NMR combined with density functional theory (DFT) analysis. We observed that the smectic mesophase of monohydrated imidazolium-based ionic liquids, which was stabilized in a wider temperature range compared to that of anhydrous materials, counterintuitively exhibited a lower orientational order of organic cations. Thus the role of anisotropic alignment of cations and contribution of dispersion forces in the mesophase stability decreased upon hydration. The local dynamics of cations is controlled by the alignment of the bulky methyl-imidazolium ring, experiencing strong electrostatic and H-bond interactions in the ionic sublayer. Anisotropy of translational diffusion increased in the hydrated samples, thus supporting the layer-stabilizing effect of water. The effect of decreasing molecular order is outweighed by the contribution of water hydrogen bonding to the overall interaction energy within the ionic sublayer.

Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg-DNA Interaction.

The interaction of the regulatory biologically active peptide Glu-Asp-Arg (EDR) with DNA is considered by spectral, NMR, viscosimetry, and molecular dynamics methods. It was shown that EDR can partly penetrate into the major groove of DNA and affect the base atoms, mainly the N7 and O6 of guanine. It was observed that Mg2+ ions can promote DNA-EDR interaction due to their effective screening of the negatively charged phosphate groups of DNA. This action of Mg2+ remains in salted solution as well.

Representation of DNA environment: Spiral staircase distribution function.

In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg2+ or Na+ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na+ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.

Experimental strategies for 13C-15N dipolar NMR spectroscopy in liquid crystals at the natural isotopic abundance.

Direct dipolar spin couplings are informative and sensitive probes for a wide range of dynamic processes and structural properties at atomic, molecular and supramolecular levels in liquid crystals and other anisotropic materials. Usually, heteronuclear 13C-1H dipolar couplings in liquid crystals with natural 13C abundance are measured. Recording 13C-15N NMR dipolar spectra in unlabeled materials is challenging because of the unfavorable combination of two rare isotopes. Here we design and compare various experimental strategies to measure short- and long-range heteronuclear 13C-15N dipolar couplings in liquid crystalline samples with high molecular orientational order. New techniques were developed to record 13C and 15N spectra of naturally occurring 13C-15N spin pairs with increased signal intensity and spectral resolution while suppressing the signals of the uncoupled isotopes. Highly resolved 13C-15N dipolar spectra were recorded within an experimental time of a few hours. Coupling constants in a broad range of 10-1000 Hz between spins separated by up to five chemical bonds and distances of up to 5 Å were measured. Because of their relatively low demands on radio-frequency power levels, the experiments were easy to implement using conventional high-resolution solution-state NMR hardware. Experimental data were compared to the results of density functional theory and molecular dynamics computational analyses. The presented experimental methods to characterize the dipolar couplings in unlabeled materials provide novel routes to investigate molecular structure and dynamics in mesophases.

Theoretically possible spatial accuracy of geomagnetic maps used by migrating animals.

Many migrating animals, belonging to different taxa, annually move across the globe and cover hundreds and thousands of kilometres. Many of them are able to show site fidelity, i.e. to return to relatively small migratory targets, from distant areas located beyond the possible range of direct sensory perception. One widely debated possibility of how they do it is the use of a magnetic map, based on the dependence of parameters of the geomagnetic field (total field intensity and inclination) on geographical coordinates. We analysed temporal fluctuations of the geomagnetic field intensity as recorded by three geomagnetic observatories located in Europe within the route of many avian migrants, to study the highest theoretically possible spatial resolution of the putative map. If migratory birds measure total field intensity perfectly and take the time of day into account, in northern Europe 81% of them may return to a strip of land of 43 km in width along one of coordinates, whereas in more southern areas such a strip may be narrower than 10 km. However, if measurements are performed with an error of 0.1%, the strip width is increased by approximately 40 km, so that in spring migrating birds are able to return to within 90 km of their intended goal. In this case, migrating birds would probably need another navigation system, e.g. an olfactory map, intermediate between the large-scale geomagnetic map and the local landscape cues, to locate their goal to within several kilometres.

Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method.

Fully-atomistic molecular dynamics simulations were carried out on two similar cyanobiphenyl nematogens, HO-6OCB and 7OCB, in order to study effects of hydrogen bonds on local structure of liquid crystals. Comparable length of these two molecules provides more evident results on the effects of hydrogen bonding. The analysis of radial and cylindrical distribution functions clearly shows the differences in local structure of two mesogens. The simulations showed that anti-parallel alignment is preferable for the HO-6OCB. Hydrogen bonds between OH-groups are observed for 51% of HO-6OCB molecules, while hydrogen bonding between CN- and OH-groups occurs only for 16% of molecules. The lifetimes of H-bonds differ due to different mobility of molecular fragments (50 ps for N⋅⋅⋅H-O and 41 ps for O⋅⋅⋅H-O). Although the standard Optimized Potentials for Liquid Simulations - All-Atom force field cannot reproduce some experimental parameters quantitatively (order parameters are overestimated, diffusion coefficients are not reproduced well), the comparison of relative simulated results for the pair of mesogens is nevertheless consistent with the same relative experimental parameters. Thus, the comparative study of simulated and experimental results for the pair of similar liquid crystals still can be assumed plausible.

Coarse-grain model of the benzene ring with para-substituents in the molecule.

A new two-site coarse-grain model of the benzene ring with substituents in the para-position is proposed for use with multiscale simulations. The model uses a modified Lennard-Jones potential and introduces an additional shifting parameter to the description of the atom-atom interactions. Furthermore, the model separates sets of parameters of Van-der-Waals interactions into inter- and intramolecular. The shifting parameter is specified separately for each pair of atom types for both inter- and intramolecular interactions. The model itself consists of two superatoms. It allows for high speed calculations, "remembers" the benzene ring orientation in multiscale simulations, and can be used together with well-known sets of "united atoms" potentials. This model was tested on p-xylene, 1-ethyl-4-methylbenzene, and 1-methyl-4-propylbenzene. Structural properties for all three substances in the full-atomic model, the "united atoms" model, and the suggested coarse-grained model are discussed. The results demonstrate that the local structure derived from the coarse-grained model is very similar to that derived from the "united atoms" model.