Impedimetric Detection of DNA Damage with the Sensor Based on Silver Nanoparticles and Neutral Red

Novel electrochemical DNA‐sensor based on glassy carbon electrode (GCE) modified with Ag nanoparticles, Neutral red covalently attached to its surface and native DNA adsorbed on modifier coating was developed for the estimation of DNA damage on example of model system based on Fenton reagent. As was shown, the oxidation process resulted in synchronous increase of electron transfer resistance and capacitance measured by electrochemical impedance spectroscopy (EIS). The contribution of each sensor component on the signal was specified and sensitivity estimated against similar surface coatings. The shift of EIS parameters was found to be higher than that of similar biosensors reported. The DNA sensor was tested on the estimation of antioxidant capacity of green tea infusions again the results of coulometric titration with electrogenerated bromine.     

Formation of a vanillic Mannich base — theoretical study

One-pot anti-Mannich reaction of vanillin, aniline and cyclohexanone was successfully catalyzed by ionic liquid triethanolammonium chloroacetate, at room temperature. Yield of the obtained Mannich base was very good and excellent diastereoselectivity was achieved. Mechanism of the reaction was investigated using the density functional theory. The reaction started with a nucleophilic attack of aniline nitrogen at the carbonyl group of vanillin. The intermediate α-amino alcohol formed in this way was further subjected to protonation by the triethanolammonium ion yielding the imminium ion. Theoretically, the obtained imminium ion and the enol form of cyclohexanone can build the protonated Mannich base via the anti and syn pathways. The chloroacetic anion spontaneously abstracts the proton yielding the final product of the reaction anti 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H). The syn pathway requires lower activation energy but the anti pathway yields a thermodynamically more stable product, which implies that the examined Mannich reaction is thermodynamically controlled.     

Parameterization of electrostatic interactions for molecular dynamics simulations of heterocyclic polymers

The paper focuses on the problem of electrostatic interactions in molecular dynamics simulations of thermal properties of heterocyclic polymers. The study focuses on three thermoplastic polyimides synthesized on the basis of 1,3‐bis‐(3′,4‐dicarboxyphenoxy)benzene (dianhydride R) and three diamines: 4,4′‐bis‐(4″‐aminophenoxy) diphenylsulfone (diamine BAPS), 4,4′‐bis‐(4″‐aminophenoxy) biphenyl (diamine BAPB), and 4,4′‐bis‐(4''‐aminophenoxy) diphenyloxide (diamine BAPO). In the molecular dynamics simulations these polyimides were described by the Gromos53a5 force field. To parameterize the electrostatic interactions four methods of calculating the partial atomic charges were chosen: B3LYP/6–31G*(Mulliken), AM1(Mulliken), HF/6–31G*(Mulliken), and HF/6–31G*(ChelpG). As our parameterization is targeted to reproduce thermal properties of the thermoplastic polyimides, the choice of proper partial charges was finalized on a basis of the closest match between computational and experimental data for the thermal expansion coefficients of the polyimides below glass transition temperatures. Our finding clearly show that the best agreement with experimental data is achieved with the Mulliken partial atomic charges calculated by the Hartree‐Fock method with 6–31G* basis set. Furthermore, in addition to the thermal expansion coefficients this set of partial atomic charges predicts an experimentally observed relationship between glass transition temperatures of the three polyimides under study: . A mechanism behind the change in thermal properties upon the change in the chemical structure in considered polyimides may be related to an additional spatial ordering of sulfone groups due to dipole‐dipole interactions. Overall, the modified force‐field is proved to be suitable for accurate prediction of thermal properties of thermoplastic polyimides and can serve as a basis for building up atomistic theoretical models for describing other heterocyclic polymers in bulk. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 912–923     

Substituting CF2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2′‐β or 2′‐α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF₂ group for the O4′ atom (O4′‐CF₂ modification) leads to a preference of the BI relative to AI DNA‐like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4′‐CF₂ derivative. Consequently, the O4′‐CF₂ modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.     

Coating Platinum Nanoparticles with Methyl Radicals: Effects on Properties and Catalytic Implications

It was recently reported that the reaction of methyl radicals with Pt⁰ nanoparticles (NPs), prepared by the reduction of Pt(SO₄)₂ with NaBH₄, is fast and yields as the major product stable (Pt⁰‐NPs)?(CH₃)_n and as side products, in low yields, C₂H₆, C₂H₄, and some oligomers. We decided to study the effect of this coating on the properties of the Pt⁰‐NPs. The results show that the coating can cover up to 75 % of the surface Pt⁰ atoms. The rate constant of the reaction, k( ^. CH₃+Pt⁰‐NPs), decreases with the increase in the surface coverage, leading to competing reaction paths in the solution, which gradually become dominant, affecting the composition of the products. The methyl coating also affects the zeta potential, the UV spectra, and the electrocatalytic reduction of water in the presence of the NPs. Thus, the results suggest that binding alkyl radicals to Pt⁰ surfaces might poison the NPs catalytic activity. When the Pt⁰‐NPs are prepared by the reduction of a different precursor salt, PtCl₆^2?, nearly no C₂H₄ and oligomers are formed and the methyl coating covers a larger percentage of the surface Pt⁰ atoms. The difference is attributed to the morphology of the Pt⁰‐NPs: those prepared from Pt(SO₄)₂ are twinned nanocrystals, whereas those prepared from PtCl₆^2? consist mostly of single crystals. Thus, the results indicate that the side products, or most of them at least, are formed on the twinned Pt⁰ nanocrystal edges created between (111) facets. In addition, the results show that Pt⁰‐NPs react very differently compared with other noble metals, for example, Au⁰ and Ag⁰; this difference is attributed in part to the difference in the bond strength, (M⁰‐NP)?CH₃, and should be considered in heterogeneous catalytic processes involving alkyl radicals as intermediates.     

The Trifluoromethyl Anion

First evidence for the existence of free trifluoromethyl anion CF₃^? has been obtained. The 3D‐caged potassium cation in [K(crypt‐222)]⁺ is inaccessible to CF₃^?, thus rendering it uncoordinated (“naked”). Ionic [K(crypt‐222)]⁺ CF₃^? has been characterized by single‐crystal X‐ray diffraction, solution NMR spectroscopy, DFT calculations, and reactivity toward electrophiles.     

Structure and electronic properties of hollow‐caged C60 fullerene‐derived (MN4)nC6(10 − n) (M = Zn,Mg, Fe,n = 1−6) complexes

Unique hollow‐caged (MN₄)_nC_{6(10 ? n)} (M = Zn, Mg, Fe, n = 1?6) complexes designed by introduction of n porphyrinoid fragments in C₆₀ fullerene structure were proposed and the atomic and electronic structures were calculated using LC‐DFT MPWB95 and M06 potentials and 6‐311G(d)/6‐31G(d) basis sets. The complexes were optimized using various symmetric configurations from the highest O_h to the lowest C₁ point groups in different spin states from S = 0 (singlet) to S = 7 (quindectet) for M = Fe to define energetically preferable atomic and electronic structures. Several metastable complexes were determined and the key role of the metal ions in stabilization of the atomic structure of the complexes was revealed. For Fe₆N₂₄C₂₄, the minimum energy was reported for C_2h, D_2h, and D_4h symmetry of pentet state S = 2, so the complex can be regarded as unique molecular magnet. It was found that the metal partial density of states determine the nature of HOMO and LUMO levels making the clusters promising catalysts. © 2014 Wiley Periodicals, Inc.     

Thermal Effects and Structural Changes of Photosynthetic Reaction Centers Characterized by Wide Frequency Band Hydrophone: Effects of Carotenoids and Terbutryn

Photothermal characteristics and light‐induced structural (volume) changes of carotenoid‐containing and noncontaining photosynthetic reaction centers (RCs) were investigated by wide frequency band hydrophone. We found that the presence of carotenoid either does not play considerable role in the light‐induced conformational movements, or these rearrangements are too slow for inducing a photoacoustic (PA) signal. The kinetic component with a few tens of microseconds, exhibited by the carotenoid‐less RCs, appears to be similar to that of triplet state lifetimes, identified by other methods. The binding of terbutryn to the acceptor side is shown to affect the dynamics of the RC. Our results do not confirm large displacements or volume changes induced by the charge movements and by the charge relaxation processes in the RCs in few hundreds of microseconds time scale that accompanies the electron transfer between the primary and secondary electron acceptor quinones.