Preparation of UV-cured cellulose nanocrystal-filled epoxidized natural rubber and its application in a triboelectric nanogenerator.

Cellulose nanocrystal (CNC) is an abundant biopolymer possessing high strength and biodegradability. In the present work, the extraction of CNCs from Napier grass stems was carried out. The CNCs were subsequently modified by maleic anhydride, called M-CNC, before being incorporated into the epoxidized natural rubber (ENR). The compounds were later cured by ultraviolet (UV) irradiation under various conditions. The obtained optimum condition was then used to fabricate the biocomposites filled with various CNC and M-CNC loadings for triboelectric nanogenerator (TENG) performance measurements. Output voltage and current increased continuously with increasing filler loading. Regardless of the filler type, an increase in filler loading enhanced TENG output. ENR/M-CNC exhibited a superior TENG output to ENR/CNC due to the greater electron transfer capability of the biocomposites, as proven by the reduction in the ionization potential (IP) value obtained from the quantum calculation. In this study, ENR/M-CNC5 exhibited the maximum output voltage (80.3 V), current (7.4 µA), and power density (1.32 W/m2) at a load resistance of 9 MΩ.

Clickable styryl dyes for fluorescence labeling of pyrrolidinyl PNA probes for the detection of base mutations in DNA.

Fluorescent hybridization probes are important tools for rapid, specific and sensitive analysis of genetic mutations. In this work, we synthesized novel alkyne-modified styryl dyes for conjugation with pyrrolidinyl peptide nucleic acid (acpcPNA) by click chemistry for the development of hybridization responsive fluorescent PNA probes. The free styryl dyes generally exhibited weak fluorescence in aqueous media, and the fluorescence was significantly enhanced (up to 125-fold) upon binding with DNA duplexes. Selected styryl dyes that showed good responses with DNA were conjugated with PNA via sequential reductive alkylation-click chemistry. Although these probes showed little fluorescence change when hybridized to complementary DNA, significant fluorescence enhancements were observed in the presence of structural defects including mismatched, abasic and base-inserted DNA targets. The largest increase in fluorescence quantum yield (up to 14.5-fold) was achieved with DNA carrying base insertion. Although a number of probes were designed to give fluorescence response to complementary DNA targets, probes that are responsive to mutations such as single nucleotide polymorphism (SNP), base insertion/deletion and abasic site are less common. Therefore, styryl-dye-labeled acpcPNA is a unique probe that is responsive to structural defects in the duplexes that may be further applied for diagnostic purposes.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA.

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system.

Conformationally Gated Charge Transfer in DNA Three-Way Junctions.

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.

New series of triply bridged dinuclear Cu(II) compounds: synthesis, crystal structure, magnetic properties, and theoretical study.

Five new triply bridged dinuclear Cu(II) compounds have been synthesized, and their magnetic properties have been measured and characterized. The magnetic coupling constants (J) of these compounds plus a previously structurally characterized compound of the same type have been derived by appropriate fitting of the experimentally measured molar susceptibility variation with the temperature. Two of the compounds are ferromagnetically coupled, and three are antiferromagnetically coupled with J values in the [+150, -40] cm(-1) range. The validity of the structural aggregate Addison's parameter as a qualitative magneto-structural correlation is confirmed. The origin of the magnetic interactions and the magnitude of the magnetic coupling have been analyzed by means of density functional theory-based calculations using a variety of state of the art exchange-correlation potentials. It is shown that the long-range separated LC-ωPBE provides the overall best agreement with experiment for this family as well as for a set of previously reported hetero triply bridged dinuclear Cu(II) compounds, especially for ferromagnetic systems.

Effects of various halogen anions and cations of alkali metals on energetics of excess charge recombination in stilbene donor-acceptor capped DNA hairpins.

DNA hairpin conjugates with a stilbenedicarboxamide (Sa) hole donor and a stilbenediether (Sd) hole acceptor are considered as model systems for studying charge recombination (CR) of excess charges in DNA. Using the method of thermodynamic integration, we estimated the relative free energies of this process in hairpins with three adenine:thymine pairs between Sa and Sd surrounded by 1 M aqueous solutions of ionic compounds M(+)Cl(-) (M = Li, Na, K) and Na(+)X(-) (X = F, Cl, Br, I). The values of this quantity were calculated with respect to the free energy for the same hairpin in the 1 M NaCl aqueous solution. Based on the results obtained, we conclude that halogen anions have no significant influence on the rate of the CR reaction. By contrast, cations of other alkali metals can considerably change the potential barrier of the process, thus affecting the reaction rate. Different results obtained for cations and anions were attributed to the fundamental distinction in the electrostatic interactions of M(+) and X(-) species with negatively charged phosphate groups of the hairpin. In addition, our results show that the relative free energy of CR is larger for cations that are able to be closer to Sd and Sa structural units. The latter correlation suggests that the replacement of Na(+) by cations of other alkali metals enables one to change the CR rate modifying it in either direction.

Toward the design of ferromagnetic molecular complexes: magnetostructural correlations in ferromagnetic triply bridged dinuclear Cu(II) compounds containing carboxylato and hydroxo bridges.

In the present work we present a comprehensive study of the magneto-structural correlations of a series of ferromagnetic triply heterobridged Cu(II) dinuclear compounds containing [Cu(2)(mu-O(2)CR)(mu-OH)(mu-X)(L)(2)](2+) ions (where X = OH(2), Cl(-), OMe(-) and L = bpy, phen, dpyam) which have the particularity of being all ferromagnetic. The present theoretical study, based on hybrid density functional theory (DFT) calculations, leads to strong conclusions about the role of the pentacoordination geometry of the Cu(II) ions (square base pyramidal (SP) or trigonal bipyramidal (TBP) coordination) and the nature of the third bridging ligand in determining the final value of the magnetic coupling constants in this series of compounds. These investigations point toward the existence of a maximum value for the ferromagnetic interaction and may offer some useful information to synthetic chemists aiming at obtaining new compounds with enhanced ferromagnetism.

Insight into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA x DNA duplex.

Molecular dynamics (MD) simulations and experimental measurements of the stability of a novel pyrrolidinyl PNA binding to DNA (PNA x DNA) in both parallel and antiparallel configurations were carried out. For comparison, simulations were also performed for the DNA x DNA duplex. The conformations of the three simulated systems were found to retain well-defined base pairing and base stacking as their starting B-like structure. A large gas-phase energy repulsion of the two negatively charged sugar-phosphate backbones of the DNA strands was found to reduce the stability of the DNA x DNA duplex significantly compared with that of the PNA x DNA complexes, especially in the antiparallel binding configuration. In addition, the antiparallel PNA x DNA was observed to be less solvated than that of the other two systems. The simulated binding free energies and the experimental melting temperatures for the three investigated systems are in good agreement, indicating that the antiparallel PNA x DNA is the most stable duplex.

Pi stack structure and hole transfer couplings in DNA hairpins and DNA. A combined QM/MD study.

Many key characteristics of hole transfer (HT) in DNA have been derived from spectroscopic studies of DNA hairpins. Because the capping groups in the hairpins can remarkably influence the structure and flexibility of the pi stack, and therefore, the charge transfer rate, the question arises of whether the HT parameters obtained for hairpins may be transferred to DNA oligomers. On the basis of large-time scale QM/MD simulations, we compare structural and electronic parameters of AT stacks in hairpins and DNA oligomers. We find that even in short hairpins, Sa-AA-Sd and Sa-AAA-Sd, the effects of the capping chromophores on the structure of the pi stack and the HT couplings properly averaged over MD trajectories are relatively small, and therefore, the hairpins are good models to study hole transfer through DNA. By contrast, the calculations of the electronic couplings based on the average structures of the systems lead to essential errors in the HT rate and the misleading statement that the charge transfer properties of DNA domains within hairpins are quite different from those of normal sequences.

Molecular-dynamics simulations of pyronine 6G and rhodamine 6G dimers in aqueous solution.

We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.