Dynamics of Adsorbed Star‐Branched Polymer Chains: A Computer Simulation Study

The simple cubic‐lattice model of polymer chains was used to study the dynamic properties of adsorbed, branched polymers. The model star‐branched chains consisted of f = 3 arms of equal lengths. The chain was modeled with excluded volume, that is, in good solvent conditions. The only interaction assumed was a contact potential between polymer segments and an impenetrable surface. This potential was varied to cover both weak and strong adsorption regimes. The classical Metropolis sampling algorithm was used for models of star‐branched polymers in order to calculate the dynamic properties of adsorbed chains. It was shown that long‐time dynamics (diffusion constant) and short‐time dynamics (the longest relaxation time) were different for weak and strong adsorption. The diffusion of weakly adsorbed chains was found to be qualitatively the same as for free nonadsorbed chains, whereas strongly adsorbed chains behaved like two‐dimensional polymers. The time‐dependent properties of structural elements such as tails, loops, and trains were also determined.

The mean lifetimes of tails, loops, and trains versus the bead number for the chain with N = 799 beads for the case of the weak adsorption ε_a = −0.3.     

Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

The interest in polynucleotide translocation through nanopores has moved from purely biological to the need of realizing nanobiotechnological applications related to personalized genome sequencing. Polynucleotide translocation is a process in which biomolecules, like DNA or RNA, are electrophoretically driven through a narrow pore and their passage can be monitored by the change in the ionic current through the pore. Such a translocation process, which will be described here offers a very promising technology aiming at ultra‐fast low‐cost sequencing of DNA, though its realization is still confronted with challenges and drawbacks. In this review, we present the main aspects involved in the polynucleotide translocation through solid‐state nanopores by discussing the most relevant experimental, theoretical, and computational approaches and the way these can supplement each other. The discussion will expose the goals that have been reached so far, the open questions, and contains an outlook to the future of nanopore sequencing. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 985–1011, 2011     

Effect of the Side‐Chain‐Distribution Density on the Single‐Conjugated‐Polymer‐Chain Conformation

The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side‐chain‐distribution density on the conformation at the isolated single‐polymer‐chain level was investigated with regiorandom (rra‐) poly(3‐hexylthiophene) (P3HT) and poly(3‐hexyl‐2,5‐thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single‐molecule spectroscopy investigation. With single‐molecule fluorescence excitation polarization spectroscopy, we found that rra‐P3HTV single molecules form highly ordered conformations. In contrast, rra‐P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side‐chain‐distribution density, that is, the spaced‐out side‐chain substitution pattern, in rra‐P3HTV favors more ordered conformations compared to rra‐P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer‐chain conformation, even at the single‐molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.     

Influence of the Helical Backbone in the Behavior of a Simple Model for Dimeric Coiled‐Coil Proteins

Using computer simulations as a tool for thought experiments, we investigate the influence of the helical backbone geometry in the association process and the final structures of a simple model which mimics parallel, two‐stranded coiled‐coil proteins. We define three types of helices: two of them have straight helical axes and 3.5 or 3.6 residues per helical turn; the third type presents a coiled helical axis, according to the canonical scheme defined by Crick. By using a Monte Carlo simulation algorithm, we observe that the three models exhibit different transition temperatures for the formation of the dimeric structure from two independent peptides, and a different behavior concerning the appearance of out‐of‐register structures. The energy minimized dimer structures present strong deviations from the correct association for straight helices with 3.6 residues/turn, especially for long peptides, deviations which are absent for the other two types when only the burial of hydrophobic residues is considered. A careful analysis of the energies for the out‐of‐register configurations and the contact maps reveals also differences between dimers resulting from the model with Crick parameterization and with 3.5 residues/turn. The results presented in this paper may be relevant for the design of simple models which use rigid α‐helices built from predicted elements of secondary structure.

Top views of the helical models used in this work.     

Effect of Poly(3‐octylthiophene) Doping on the Attachment and Proliferation of Osteoblasts

The effect of doping P3OT with ferric chloride on the attachment and proliferation of MC3T3‐E1 osteoblasts is reported. Cell density and area correlated strongly with doping concentration: cells were larger and exhibited better spreading as doping increased. Cells cultured on undoped P3OT showed a decrease in proliferation between 24 and 48 h followed by a recovery after 72 h. However, this trend diminished with increasing doping concentration, and disappeared completely at the highest dopant level investigated. Analysis of cell‐cell spatial distributions suggested that contact inhibition of proliferation occurred similarly on both undoped and doped P3OT. From these results, FeCl₃‐doping had no significant deleterious effect on attachment or proliferation of osteoblasts in vitro.

     

Photochemical Properties and Activity of Water‐Soluble Polymer/C60 Nanohybrids for Photodynamic Therapy

Water‐soluble star‐like poly(vinyl alcohol)/C₆₀ and poly{[poly(ethylene glycol) acrylate]‐co‐(vinyl acetate)}/C₆₀ nanohybrids are prepared by grafting macroradicals onto C₆₀ and are assessed as photosensitizers for photodynamic therapy. The photophysical and biological properties of both nanohybrids highlight key characteristics influencing their overall efficiency. The macromolecular structure (linear/graft) and nature (presence/absence of hydroxyl groups) of the polymeric arms respectively impact the photodynamic activity and the stealthiness of the nanohybrids. The advantages of both nanohybrids are encountered in a third one, poly[(N‐vinylpyrrolidone)‐co‐(vinyl acetate)]/C₆₀, which has linear grafts without hydroxyl groups, and shows a better photodynamic activity.

     

Cellulose Acetate-g-Polycaprolactone Copolymerization Using Diisocyanate Intermediates and the Effect of Polymer Chain Length on Surface,Thermal, and Antibacterial Properties

The need for biodegradable and biocompatible polymers is growing quickly, particularly in the biomedical and environmental industries. Cellulose acetate, a natural polysaccharide, can be taken from plants and modified with polycaprolactone to improve its characteristics for a number of uses, including biomedical applications and food packaging. Cellulose acetate-g-polycaprolactone was prepared by a three-step reaction: First, polymerization of ε-caprolactone via ring-opening polymerization (ROP) reaction using 2-hydroxyethyl methacrylate (HEMA) and functionalization of polycaprolactone(PCL) by introducing NCO on the hydroxyl end of the HEMA-PCL using hexamethyl lenediisocyanate(HDI) were carried out. Then, the NCO–HEMA-PCL was grafted onto cellulose acetate (using the “grafting to” method). The polycaprolactone grafted cellulose acetate was confirmed by FTIR, the thermal characteristics of the copolymers were investigated by DSC and TGA, and the hydrophobicity was analyzed via water CA measurement. Introducing NCO-PCL to cellulose acetate increased the thermal stability. The contact angle of the unreacted PCL was higher than that of cellulose acetate-g-PCL, and it increased when the chain length increased. The CA-g-PCL50, CA-g-PCL100, and CA-g-PCL200 showed very high inhibition zones for all three bacteria tested (E. coli, S. aureus, and P. aeruginosa).     

Coarse‐grained models and collective phenomena in membranes: Computer simulation of membrane fusion

We discuss the role coarse‐grained models play in investigating collective phenomena in bilayer membranes and place them in the context of alternative approaches. By reducing the degrees of freedom and applying simple effective potentials, coarse‐grained models can address the large time scales and length scales of collective phenomena in membranes. Although the mapping from a coarse‐grained model onto chemically realistic models is a challenge, such models provide a direct view on the phenomena that occur on the length scales of a few tens of nanometers. Their relevance is exemplified by the study of fusion of model membranes. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1441–1450, 2003     

Contact bactericides and fungicides on the basis of amino‐functionalized poly(norbornene)s

This study is aimed at investigating the microbiocidal potential of amino‐functionalized poly(norbornenes) in the solid state. A series of norbornene‐type monomers that carry secondary or tertiary amine functions as well as hexyl and dodecyl groups were prepared. Ring‐opening metathesis polymerization was used to prepare homopolymers of the amine bearing monomers and random copolymers of amine‐ and alkyl‐substituted monomers of high average molar mass. The resulting polymers were characterized by nuclear magnetic resonance, thermogravimetry, differential scanning calorimetry, infrared spectroscopy, and contact angle measurements, and their contact biocidal potential was evaluated according to the Japanese Industry standard Z2801. Tested microorganisms comprised Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Candida albicans, and Aspergillus niger. Microbiocidal activity of selected polymer films against E. coli, S. aureus, and A. niger was found, whereas against C. albicans and P. aeruginosa microbiostatic behavior was observed. Moreover, the most potent copolymer revealed no cytotoxicity rendering a biocidal polymer with potential applications in mammalian‐, and in particular, human‐related fields. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

The Chain Stretching Effect on the Morphology and Rheological Properties of Phase‐Separating Polymer Blends Subjected to Simple Shear Flow

Summary: The spinodal decomposition of a binary mixture subjected to simple shear flow is investigated in the framework of the modified time‐dependent Ginzburg‐Landau (TDGL) equation with an external velocity term. The domain growth and related rheological properties of a binary mixture under shear flow are simulated in three dimensions by means of the cell dynamics scheme (CDS). The simulation results show that the domain growth is anistropic and depends on the terminal relaxation time of the polymer chain. It is found that lamellae‐like domains with the normal parallel to the velocity gradient direction are observed when the terminal relaxation time is long enough. This result has also been confirmed by carefully checking the scattering functions in different incident light directions and the evolution of the domain size in different directions. In addition, when the chain stretching effect is strong, the transients of the excess shear viscosity are much higher than the case without the chain stretching effect. The terminal relaxation time of the chain also has an important effect on the first and second normal stress differences.

The time evolution of the morphology for the case with strong chain stretching effect.     

Cross‐Coupling of Aryl‐Bromide and Porphyrin‐Bromide on an Au(111) Surface

Cross‐coupling is of great importance in organic synthesis. Here it is demonstrated that cross‐coupling of aryl‐bromide and porphyrin‐bromide takes place on a Au(111) surface in vacuo. The products are oligomers consisting of porphyrin moieties linked by p‐phenylene at porphyrin’s meso‐positions. The ratio of the cross‐coupled versus homocoupled bonds can be regulated by the reactant concentrations. Kinetic Monte Carlo simulations were applied to determine the activation barrier. It is expected that this reaction can be employed in other aryl‐bromide precursors for designing alternating co‐polymers incorporating porphyrin and other functional moieties.     

Simulation of Polymer Aggregates as a Method to Investigate the Solvent Effect on Blend Complexation and the Relative Strength of H‐Bonding Groups in Blends

Simulations of polymer‐solvent and polymer‐polymer aggregates, in which the study of hydrogen bonding plays an important role, have been carried out with two blend systems. The aim was to examine the influence of the solvent on blend complexation and to compare the strength of different hydrogen bonds in a blend system. We quantified the strength of one hydrogen bond in the blend environments. For this we used the EVOCAP software, developed by our institute. It allows the building of large molecular aggregates with realistic and homogeneous densities, with an implemented positioning algorithm of the molecules under consideration and their excluded volume, and a charge equilibration method for the partial charge calculation. In the simulated aggregates the specific interaction energy of the hydrogen atom forming the hydrogen bond was a useful indicator for our studies. Through a direct correlation of this specific‐interaction energy with the strength of the hydrogen bond, we supported the experimental result that, in toluene, complex formation between poly(methyl methacrylate) (PMMA) and PSOH, a hydroxyl‐modified polystyrene, is possible, but not in tetrahydrofuran. Varying the proton‐donor polymer, also a hydroxyl‐modified polystyrene, in blends of poly(vinyl methyl ether) (PVME) with groups of different donor strength, we reconstructed the experimental row of increasing hydrogen‐bond strengths.     

Conformational Analysis,RIS Models and Single‐Chain Properties of Structurally Modified Polycarbonates, 1. Effect of Cyclohexyl and Phenyl Ring Substitutions

Conformational properties of segments and chains of structurally different polycarbonates are investigated in detail. Conformational analysis and rotational isomeric state (RIS) models for some of the polycarbonates and single‐chain properties of all the polycarbonates are reported here for the first time. Substitution of the methyl group on the bisphenol phenyl rings results in increased energy barriers to rotations as well as changes in positions of local minima, compared to the case without substitutions. Conformational structure about the isopropylidene linkage C_α atom is not altered by ortho methyl substitutions on the rings. Substitution by a cyclohexyl ring rigidly attached to the C_α atom restricts conformational mobility within the bisphenol unit. Rotational flexibility of the phenyl–oxygen bond is hindered by additional substitutions on the cyclohexyl ring. The carbonate group prefers the trans–trans conformation in all the polycarbonates. The energy difference between the cis–trans and trans–trans states of the carbonate group is lowered by the ortho methyl substituent on the phenyl rings. There is a reduction in 〈R²〉, 〈S²〉, and C_n accompanying the substitutions. The introduction of other substituents on a cyclohexyl polycarbonate results in an increase in all chain dimensions including the persistence length. Also, the cyclohexyl or trimethylcyclohexyl substituents do not significantly alter the overall average shape of the chains. Substitutions both on the phenyl rings and at the isopropylidene linkage lead to a compaction of the polymer chain, but the effect is more pronounced when due to substituents on phenyl rings.     

Antimicrobial anilinium polymers: The properties of poly(N,N‐dimethylaminophenylene methacrylamide) in solution and as coatings

Antimicrobial polymers have been widely reported to exert strong biocidal effects against bacteria. In contrast with antimicrobial polymers with aliphatic ammonium groups, polymers with anilinium groups have been rarely studied and applied as biocidal materials. In this study, a representative polymer with aniline side functional groups, poly(N,N‐dimethylaminophenylene methacrylamide) (PDMAPMA), was explored as a novel antimicrobial polymer. PDMAPMA was synthesized and its physicochemical properties evaluated. The methyl iodide‐quaternized polymer was tested against the Gram‐positive Staphylococcus aureus, with a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 16–32 and 64–128 μg mL^?1, respectively. Against the Gram‐negative Escherichia coli, the MIC and MBC were both 64–128 μg mL^?1. To broaden the range of applications, PDMAPMA was coated on substrates via crosslinking to endow the surface with contact‐kill functionality. The effect of charge density of the coatings on the antimicrobial behavior was then investigated, and stronger biocidal performance was observed for films with higher charge density. This study of the biocidal behavior of PDMAPMA both in solution and as coatings is expected to broaden the application of polymers containing aniline side groups and provide more information on the antimicrobial behavior of such materials. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1908–1921     

Synthesis of cationic diacetylene‐co‐carbazole‐co‐fluorene polymers and their sensitive fluorescent quenching properties with DNA

Two neutral precursor conjugated copolymers based 2,7‐diethynylfluorene and 3,6‐diethynylcarbazole units in the main chain ( PFC and PF2C ) were prepared by Hay coupling polymerization. Their cationic copolymers ( CPFC and CPF2C ) were prepared by the methylation of their diethylpropylamino groups with CH₃I. For comparison, neutral conjugated homopolymers of 2,7‐diethynylfluorene ( PF ), 3,6‐diethynylcarbazole units ( PC ) and their cationic polymers ( CPF and CPC ) were also prepared with the same method. A comparative study on the optical properties of cationic polymers CPFC and CPF2C in DMF and DMF/H₂O showed that they underwent water‐induced aggregation. The spectral behaviors of CPFC and CPF2C with calf thymus DNA showed that a distinct fluorescent quenching took place with minute addition of CT DNA (3.3 × 10^?13 M). The results showed that the polymers would be promising biosensor materials for sensitive detection of DNA. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4168–4177, 2010     

Smart Poly(N‐isopropylacrylamide) Containing Iridium(III) Complexes as Water‐Soluble Phosphorescent Probe for Sensing and Bioimaging of Homocysteine and Cysteine

Homocysteine (Hcy) and cysteine (Cys) are two important kinds of amino acids in human bodies. Herein, we synthesized an iridium(III) complex‐functionalized poly(N‐isopropylacrylamide) and its hydrogel, which could be used as the excellent phosphorescent bioprobe for sensing Hcy and Cys. Their detection can be realized in aqueous system through the variations in absorption and photoluminescence spectra. Furthermore, living cell imaging experiments demonstrate that the phosphorescent bioprobe is membrane permeable and can monitor the changes of Hcy and Cys within living cells. In addition, the probe is also thermoresponsive, and its photoluminescence intensified with increasing temperature. These results suggests that this bioprobe has promising application in biomedical fields.     

Monte Carlo Simulation of the Topology and Conformational Behavior of Hyperbranched Molecules: Pd–Diimine‐Catalyzed Polyethylene

A kinetic Monte Carlo model was developed to simulate the polymerization of ethylene with palladium–α‐diimine catalyst wherein hyperbranched molecules are formed through a chain‐walking mechanism. The total degree of branching and the distribution of short branches obtained with the model agree well with reported ¹³C NMR experimental results. Different chain topologies were generated by varying the probability of chain walking, P_w , which controls the competition between chain‐walking and monomer insertion. Molecular Monte Carlo simulations were subsequently conducted to study the conformations of isolated molecules (created by the kinetic Monte Carlo scheme) to relate molecular shape and topology. Our results provide evidence that the topology varies from predominantly linear with many short branches at low P_w to a densely branched, globular structure at high P_w . In contrast to experimental observations, our results for the molecular weight (N) dependence of the radius of gyration (R_g ∝ N^v) indicate that the branching topology has an effect on this relation, i. e., high‐P_w molecules have a smaller scaling exponent v. The simulated N‐dependence of the second virial coefficient exhibits a similar behavior. We also discuss the unusual conformational behavior of highly branched polymers obtained when P_w → 1.