Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path‐search algorithm

Branch migration of the Holliday junction takes place at the center of the RuvA tetramer. To elucidate how branch migration occurs, umbrella sampling simulations were performed for complexes of the RuvA tetramer and Holliday junction DNA. Although conventional umbrella sampling simulations set sampling points a priori, the umbrella sampling simulation in this study set the sampling points one by one in order to search for a realistic path of the branch migration during the simulations. Starting from the X‐ray structure of the complex, in which the hydrogen bonds between two base‐pairs were unformed, the hydrogen bonds between the next base‐pairs of the shrinking stems were observed to start to disconnect. At the intermediate stage, three or four of the eight unpaired bases interacted closely with the acidic pins from RuvA. During the final stage, these bases moved away from the pins and formed the hydrogen bonds of the new base‐pairs of the growing stems. The free‐energy profile along this reaction path showed that the intermediate stage was a meta‐stable state between two free‐energy barriers of about 10 to 15 kcal/mol. These results imply that the pins play an important role in stabilizing the interactions between the pins and the unpaired base‐pairs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Initial lamellar thickness dependency of recrystallization behavior of poly(4‐methyl‐1‐pentene)

The isothermal crystallization and subsequent melting process in semicrystalline poly(4‐methyl‐1‐pentene) were investigated via temperature‐dependent small‐ and wide‐angle X‐ray scattering and Flash DSC techniques. In a phase diagram of inversed crystalline lamellar thickness and temperature, the crystallization and melting lines can be described by two linear dependencies of different slopes and different limiting temperatures at infinite lamellar thickness. Upon subsequent heating, recrystallization lines with different slopes were observed for samples with different lamellar thickness, indicating changes in surface free energy difference between stabilized crystallites and mesomorphic phase. The surface free energy of native crystallites with extended‐chain conformation decreased with increasing lamellar thickness due to a more ordered surface region and less chain ends which changes cooperatively with mesomorphic phase. The surface free energy of stabilized crystallites remained unchanged for all lamellar thickness. Therefore, the recrystallization lines with different slopes are consequences of changes in surface free energy of mesomorphic phase. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 219–224     

Superconducting first‐order pairing: Finite‐temperature simulations

A recently developed first‐order mechanism for superconducting pairing has been extended from T = 0 K to finite temperatures. On the basis of quantum statistical considerations, we have suggested a direct pairing interaction that does not necessarily involve second‐order elements, such as the electron–phonon coupling or specific magnetic interactions submitted by spin fluctuations. The driving force for the (energy‐driven) first‐order pairing is an attenuation of the destabilizing influence of the Pauli antisymmetry principle (PAP). Only the moves of unpaired fermions are controlled by the PAP, while the moves of superconducting Cooper pairs are not. The quantum statistics of Cooper pairs is of a mixed type, as it combines fermionic on‐site and bosonic intersite properties. The strong correlation between the strength of PAP constraints and system topology in combination with the electron number has been discussed for some larger clusters. Detailed finite‐temperature simulations on first‐order pairing have been performed for four‐center–four‐electron clusters with different topologies. A canonical ensemble statistics has been employed to derive the electronic energy, the electronic configuration entropy, and the free energy of paired and unpaired states in thermal equilibrium. The simulations show that pairing can be caused by either the electronic energy or the electronic configuration entropy. The coexistence of two different sets of quantum particles in paired states (i.e., the Cooper pairs and the unpaired electrons) can lead to an enhanced configuration entropy. In this context, we discuss the possibility of an entropy‐driven high‐temperature superconductor emerging from a low‐temperature unpaired state. The charge and spin degrees of freedom of the four‐center–four‐electron systems have been studied with the help of the charge and spin fluctuations. The spin fluctuations are helpful in judging the validity of pairing theories based on magnetic interactions. The charge fluctuations are a measure for the carrier delocalization in unpaired and paired states. The well‐known proximity between Jahn–Teller activity and superconductivity is analyzed in the zero‐temperature limit. It is demonstrated that both processes compete in their ability to reduce PAP constraints. All theoretical results have been derived within the framework of the simple Hubbard Hamiltonian. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DFT plus PCM calculation for pairing specificity of Watson–Crick‐type bases in aqueous solutions

This study is aimed at explaining the preference for AT and CG pairings and the possible insertion of other tautomeric DNA base pairs such as G_enolT, that respect energetic and steric requirements including at least two hydrogen bonds and 11 ± 0.5Å distance between the 9‐CH₃ of purine and 5‐CH₃ of pyrimidine. The calculated free energy of formation ΔΔG at the DFT B3LYP/6‐31G*‐PCM/BEM level pointed out the CG and AT pairs as the most favored, followed closely by G_enolT, in good agreement with Michaelis–Menten first order kinetics (CG ≈ AT > G_enolT). Unusual DNA base pairs complexes such as AG (BEM) and CT (PCM) resulted to be stable, but it is very difficult to assume that they are likely to be included in the double strand DNA. The calculated enthalpy and dipole moments of isolated DNA bases agree well with experiment. The free energy of hydration, ΔG_hyd, was found to depend on the electrostatic term, while cavitation‐dispersion components are almost constant. The stability of DNA complexes in water resulted from PCM calculations is markedly influenced by the free energy of hydration. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Biocomplementary interaction behavior in DNA‐like and RNA‐like polymers

A series of nucleobased polymers and copolymers were synthesized through atom transfer radical polymerization (ATRP). Biocomplementary DNA‐ and RNA‐like supramolecular complexes are formed in dilute DMSO solution through nucleobase recognition. ¹H NMR titration studies of these complexes in CDCl₃ indicated that thymine‐adenine (T‐A) and uracil‐adenine (U‐A) complexes form rapidly on the NMR time scale with high association constants (up to 534 and 671 M^–1, respectively) and result in significant T_g increase. WAXD and differential scanning calorimetry analyzes in the bulk state indicate the presence of highly physical cross‐linked structures and provide further details into the nature of the self‐assembly of these systems. Furthermore, this study is of discussion on the difference in the hydrogen bond strength between T‐A and U‐A base pairs within polymer systems, indicating that the strength of hydrogen bonds in RNA U‐A pairs is stronger than that in DNA T‐A base pairs. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6388–6395, 2009     

Role of molten fraction on the structural evolution in stretching and cooling of crosslinked low‐density polyethylene: Real‐time mechano‐optical measurements

We investigated the uniaxial deformation behavior of crosslinked low‐density polyethylene in partially and substantially molten states using a real‐time true stress–strain birefringence system. The stress–birefringence behavior exhibits a multiregime behavior during stretching and holding process. The details of this regime behavior are primarily governed by the degree of unmelted crystallinity as it has a dominant role in the long‐range structural connectivity. When the long‐range physical connectivity is present, a three‐regime nonlinear stress–optical behavior was observed. When the long‐range connectivity is substantially eliminated at higher temperatures, the regime I behavior disappears. Structural studies including cooling process reveal that the lower the proportion of molten material during stretching, the higher the concentration of fibrillar structure and the shorter are the lengths of the kebabs that exhibit twisted lamellae after solidification. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1825–1841, 2005     

Nonuniversal transport behavior in heterogeneous high‐density polyethylene/graphite nanosheet composites

The direct‐current resistivity of high‐density polyethylene/graphite nanosheet composites above the percolation threshold has been measured and fitted to a power law, which gives a conductivity critical exponent (0.10 ± 0.01) and a percolation threshold (2.97 ± 0.03). These fitted parameters are in disagreement with universal theoretical predictions, and plausible explanations of the observed discrepancies are given. The sample‐to‐sample fluctuations in the relative resistivity seem to obey a power law. This fluctuation behavior, if interpreted in terms of correlation‐length fluctuations, yields a correlation‐length critical exponent, 0.52 ± 0.06, that is consistent with the mean‐field value of 1/2. Interpretations of these experimental results imply that nonuniversal transport behavior in disordered composites is caused by composites being in a nonuniversal scaling regime. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1846–1852, 2006     

Thermoresponsive brush copolymers with poly(propylene oxide‐ran‐ethylene oxide) side chains via metal‐free anionic polymerization “grafting from” technique

Thermoresponsive brush copolymers with poly(propylene oxide‐ran‐ethylene oxide) side chains were synthesized via a “grafting from” technique. Poly(p‐hydroxystyrene) was used as the backbone, and the brush copolymers were prepared by random copolymerization of mixtures of oxyalkylene monomers, using metal‐free anionic ring‐opening polymerization, with the phosphazene base (t‐BuP₄) being the polymerization promoter. By controlling the monomer feed ratios in the graft copolymerization, two samples with the same side‐chain length and different compositions were prepared, both of which possessed high molecular weights and low molecular weight distributions. The results from light scattering and fluorescence spectroscopy indicated that the brush copolymers in their dilute aqueous solutions were near completely solvated at low temperature and underwent slight intramolecular chain contraction/association and much more profound intermolecular aggregation at different stages of the step‐by‐step heating process. Above 50 °C, very turbid solutions, followed by macrophase separation, were observed for both of the samples, which implied that it was difficult for the brush copolymers to form stable nanoscopic aggregates at high temperature. All these observations were attributed, at least partly, to the distribution of the oxyalkylene monomers along the side chains and the overall brush‐like molecular architecture. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2320–2328, 2010     

Solvent‐free free‐radical frontal polymerization: A new approach to quickly synthesize poly(N‐vinylpyrrolidone)

The first synthesis of poly(N‐vinylpyrrolidone) without solvent by free‐radical frontal polymerization at ambient pressure is reported. The appropriate amounts of two reactants N‐vinyl‐2‐pyrrolidone (NVP) and initiator 2,2′‐azobis‐isobutyronitrile (AIBN) without solvent were mixed together at ambient temperature. Frontal polymerization was initiated by heating the wall of the tube with a soldering iron, and the resultant hot fronts were allowed to self‐propagate throughout the reaction vessel. Once initiated, no further energy was required for polymerization to occur. To suppress the fingers of molten monomer, a small amount of nanosilica was added. The dependence of the front velocity and front temperature on the AIBN concentration was thoroughly investigated. The as‐prepared polymers were characterized by gel permeation chromatography (GPC) and thermogravimetric analysis (TGA). Results show that without postpolymerization solvent removal, waste production can be reduced. Solvent‐free FP could be exploited as a means for preparation of PVP with the potential advantage of higher throughput than solvent‐based methods. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2177–2185, 2008     

Study of the quiescent and shear‐induced crystallization kinetics of intercalated PTT/MMT nanocomposites

An intercalated nanocomposite made of montmorillonite nanoclay, MMT, and poly(trimethylene terephthalate), PTT, was produced by twin screw extrusion and characterized by wide angle X‐ray diffraction, WAXD, and transmission electron microscopy, TEM. The quiescent isothermal and non‐isothermal and the flow‐induced crystallization of the nanocomposite were studied by differential scanning calorimetry, DSC, polarized light optical microscopy, PLOM, and rheometry. The quiescent results showed that the nanoclay acted as an efficient nucleating agent for the PTT, which result in an anticipation of the transition temperature between regimes II and III of crystallization. The fold interfacial free energy, σ_e, of the PTT in the nanocomposite during regime III was lower than in the pure state; that is, the pure PTT developed spherulites, whereas in the nanocomposite it produced a paracrystalline morphology. Under shear rate, the total times for crystallization in the nanocomposite were higher than in the pure PTT. In flow‐induced crystallization, a fibrillar nucleus must be formed as a result of chain orientation. In the nanocomposite, chain orientation only occurred after the percolated structure was broken. Therefore, the formation of a fibrillar nucleus in the nanocomposite took more time, which increased the total crystallization time. Inc. J Polym Sci Part B: Polym Phys 48: 113–127, 2010     

Polymer electrolyte membranes based on p‐toluenesulfonic acid doped poly(1‐vinyl‐1,2,4‐triazole): Synthesis,thermal and proton conductivity properties

Throughout this work, the synthesis, thermal as well as proton conducting properties of acid doped heterocyclic polymer were studied under anhydrous conditions. In this context, poly(1‐vinyl‐1,2,4‐triazole), PVTri was produced by free radical polymerization of 1‐vinyl‐1,2,4‐triazole with a high yield. The structure of the homopolymer was proved by FTIR and solid state ¹³C CP‐MAS NMR spectroscopy. The polymer was doped with p‐toluenesulfonic acid at various molar ratios, x = 0.5, 1, 1.5, 2, with respect to polymer repeating unit. The proton transfer from p‐toluenesulfonic acid to the triazole rings was proved with FTIR spectroscopy. Thermogravimetry analysis showed that the samples are thermally stable up to ～250 °C. Differential scanning calorimetry results illustrated that the materials are homogeneous and the dopant strongly affects the glass transition temperature of the host polymer. Cyclic voltammetry results showed that the electrochemical stability domain extends over 3 V. The proton conductivity of these materials increased with dopant concentration and the temperature. Charge transport relaxation times were derived via complex electrical modulus formalism (M*). The temperature dependence of conductivity relaxation times showed that the proton conductivity occurs via structure diffusion. In the anhydrous state, the proton conductivity of PVTri1PTSA and PVTri2PTSA was measured as 8 × 10^?4 S/cm at 150 °C and 0.012 S/cm at 110 °C, respectively. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1016–1021, 2010     

High‐Density DNA Functionalization by a Combination of Cu‐Catalyzed and Cu‐Free Click Chemistry

We report the regioselective Cu‐free click modification of styrene functionalized DNA with nitrile oxides. A series of modified oligodeoxynucleotides (nine base pairs) was prepared with increasing styrene density. 1,3‐Dipolar cycloaddition with nitrile oxides allows the high density functionalization of the styrene modified DNA directly on the DNA solid support and in solution. This click reaction proceeds smoothly even directly in the DNA synthesizer and gives exclusively 3,5‐disubstituted isoxazolines. Additionally, PCR products (300 and 900 base pairs) were synthesized with a styrene triphosphate and KOD XL polymerase. The click reaction on the highly modified PCR fragments allows functionalization of hundreds of styrene units on these large DNA fragments simultaneously. Even sequential Cu‐free and Cu‐catalyzed click reaction of PCR amplicons containing styrene and alkyne carrying nucleobases was achieved. This new approach towards high‐density functionalization of DNA is simple, modular, and efficient.     

First solvent‐free synthesis of poly(N‐methylolacrylamide) via frontal free‐radical polymerization

We report the first synthesis of poly (N‐methylolacrylamide) (PNMA) via free‐radical frontal polymerization (FP) with solid monomers at ambient pressure. The appropriate amounts of reactants (N‐methylolacrylamide) (NMA) and initiator (ammonium persulfate) were mixed together at ambient temperature without solvent. FP was initiated by heating the wall of the tube with a soldering iron, and the resultant hot fronts were allowed to self‐propagate throughout the reaction vessel. Once initiated, no further energy was required for polymerization to occur. To suppress the fingers of molten monomer, a small amount of nanosilica was added. We also produced PNMA with dimethyl sulfoxide (DMSO) or N‐methyl‐2‐pyrrolidone, as solvent by FP, to study the macrokinetics in FP of PNMA without fillers. The front velocity and front temperature dependence on the ammonium persulfate and N‐methyl‐2‐pyrrolidone concentration were investigated. The polymer was analyzed by thermogravimetric analysis. Results show that without postpolymerization solvent removal, waste production can be reduced. Solvent‐free FP could be exploited as a means for preparation of PNMA with the potential advantage of higher throughput than solvent‐based methods. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4322–4330, 2007     

Gas sorption environments in poly(2,6‐dimethyl‐1,4‐phenylene oxide) by xenon‐129 nuclear magnetic resonance: Effects of processing

One‐ and two‐dimensional xenon‐129 nuclear magnetic resonance (¹²⁹Xe NMR) experiments were performed on a series of poly(2,6‐dimethyl‐1,4‐phenylene oxide) (PXE) samples to characterize the sorption environments and the relative mobility of xenon in the samples. Samples of PXE in sealed NMR tubes pressurized with xenon were studied as a function of temperature, pressure, and processing. In a dense cast film of PXE, the shift relative to the free gas resonance is smaller than that observed for typical glassy polymers, indicating a higher free volume environment. Solubility rises rapidly as temperature decreases. The lower shift and rapid increase in solubility with decreasing temperature are consistent with a relatively high free volume environment for gas sorption. If PXE is antiplasticized, the shift is slightly larger, the increase in signal intensity with decreasing temperature is smaller, and the line widths are greater. This sample is a better packed glass with less free volume and slower diffusion. Samples of PXE produced by rapid precipitation have broad lines and even lower shifts corresponding to a wide distribution of higher free volume environments. The appearance of two lines at low temperatures is consistent with the presence of a bimodal distribution of environments similar to what has been observed with positron annihilation lifetime spectroscopy. The resonance closest to the free gas resonance is associated with very large free volume elements relative to those of traditional glassy polymers. In two‐dimensional experiments, there is a rapid exchange of xenon by diffusion between the two environments, indicating the close spatial proximity of the environments. Two‐dimensional experiments and one‐dimensional progressive saturation experiments reflect a rapid exchange of xenon between the sorbed state and the free gas resonance for the precipitated samples. At low temperatures, the high field peak exchanges more rapidly with the free gas. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1965–1974, 2002     

Polymer chain of freely‐jointed segments in nematic molecular mean‐field

The distribution function of orientations of a segment, which interacts with the orienting field and is within the chain with given the end‐to‐end distance‐vector, is calculated. The number of segments per chain is finite. The Lagrange method of conditional minimization of the chain free energy (the Helmholtz function) functional is used. Constraints for the segment orientations stem from fixed the chain end‐to‐end distance‐vector. Hence, Lagrange multipliers, energy, free energy, and entropy, for the chain with given the end‐to‐end distance‐vector, are calculated. Then, the distribution function of values of that vector is obtained. Furthermore, an average free energy per chain inside the polymer network with given a topological structure, the system self‐deformation, and modulus of elasticity are calculated and discussed in Gaussian limit, that is, for the number of segments per chain tending to infinity. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 138–144, 2010     

The influence of molten fraction on the uniaxial deformation behavior of polypropylene: Real time mechano‐optical and atomic force microscopy observations

In this study, we have coupled the real time mechano‐optical measurements with the off‐line structural characterization techniques including AFM, WAXS, and DSC to establish the quantitative relationships between the “true mechano‐optical behavior and developed morphology” as influenced by the fraction of molten phase present in the polypropylene films. Stretching PP in the solid state invariably leads to formation of fibrillar texture. The evolution of surface morphology in partially molten state was found to depend on the fraction of the molten phase present at the start of the deformation. If the samples are strained past the yielding in partially molten state, the birefringence begins a rapid rise. Concurrent with this, the equatorial zones of the spherulites begin to crack while meridional regions remaining intact. This leads to temporary reduction of crystallinity because of destruction of some of the crystals. If held in this strained state, the crystallite thickening was observed while the birefringence increases while the lost crystallinity is recovered. If the films are strained past the strain hardening point, the microfibrillar structure was found to dominate the surface morphology. When the films are stretched in the melting temperature range, they exhibit substantial nodular surface topology. These nodules that were absent in the solid state deformed samples are hard lamellae buried inside amorphous “soft matter”. The tangential lamellae increasingly become dominant as the processing temperature approaches substantially molten state leading to the observation of a* oriented crystallites in the X‐ray analysis. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 925–941, 2006     

DNA‐backbone radio resistivity induced by spin blockade effect

Coherent control of OH‐free radicals interacting with the spin‐triplet state of a DNA molecule is investigated. A model Hamiltonian for molecular spin singlet‐triplet resonance is developed. We illustrate that the spin‐triplet state in DNA molecules can be efficiently populated, as the spin‐injection rate can be tuned to be orders of magnitudes greater than the decay rate due to small spin‐orbit coupling in organic molecules. Owing to the nano‐second life‐time of OH free radicals, a non‐equilibrium free energy barrier induced by the injected spin triplet state that lasts approximately longer than one‐micro second in room temperature can efficiently block the initial Hydrogen abstraction and DNA damage. For a direct demonstration of the spin‐blockade effect, a molecular simulation based on an ab‐initio Car‐Parrinello molecular dynamics is deployed. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Pressure–volume–temperature data and surface tension of blends of poly(ethylene oxide) and poly(methyl acrylate) in the melt

The pressure–volume–temperature behavior of miscible blends of poly(ethylene oxide) (PEO) and poly(methyl acrylate) (PMA) was studied over extended ranges of temperature and pressure. From pressure–volume–temperature data, the reduction parameters for the Flory‐Orwoll‐Vrij equation‐of‐state were determined. It was found that reduction parameters as well as density, thermal expansion coefficient, and isothermal compressibility vary with composition in a nonlinear manner. The surface tension of the blends in the molten state was measured over the whole composition range using the sessile drop method. The surface tension was found to display negative deviation from additivity pointing toward a remarkable surface excess of PMA. Moreover, surface tension displays a minimum in the range of low PEO content at weight fraction of ～0.19. In addition, the temperature coefficient of surface tension shows negative deviation from linearity. It stays constant when PMA is in excess. Results are discussed in terms of equation‐of‐state thermodynamics. The minimum of surface tension can be well explained by weak self‐association of PEO in the bulk. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1893–1900, 2010     

Self‐emulsification and surface modification effect of fluorinated amphiphilic acrylate graft copolymers

We report on self‐emulsification and surface modification effect of novel fluorinated amphiphilic graft copolymers prepared with perfluoroalkyl acrylate and 2‐dimethylaminoethyl methacrylate using simple macromonomer technique and radical copolymerization. The interfacial properties of amphiphilic graft copolymers were characterized with light scattering, contact angle measurement, and X‐ray photoelectron spectroscopy. The preparation of fluorinated amphiphilic graft copolymer was verified using nuclear magnetic resonance and Fourier transform infrared spectroscopy. It was observed that the fluorinated amphiphilic graft copolymer has both strong hydrophobic and hydrophilic properties and shows self‐emulsification ability without addition of external surfactants. The graft copolymer shows very low surface energy even though the copolymer has low content of hydrophobic segment and better performance than random copolymer for low‐energy surface modification. The addition of small amount of the graft copolymer (0.1 wt %) into the base poly(methyl methacrylate) was sufficient to lower the surface energy less than that of poly(tetrafluoroethylene). © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Creep behavior of ultra‐thin polymer films

A novel microbubble inflation method has been used to determine the creep compliance of poly(vinyl acetate) and polystyrene ultra‐thin films (13–300 nm thick) at temperatures from below to above the glass temperature. We present results that suggest that time‐temperature and time‐thickness superposition hold in the glassy relaxation regime. Although time‐temperature superposition is found for the entire response curve for each thickness, we also find that time‐thickness superposition fails as the long‐time compliance is approached. This effect occurs because of a strong stiffening as the film thickness decreases. We also show first evidence of stiffening in the glassy regime of free standing films of polystyrene. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1952–1965, 2008