Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA

Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.     

Accurate relativistic adapted gaussian basis sets for francium through ununoctium without variational prolapse and to be used with both uniform sphere and gaussian nucleus models

Accurate relativistic adapted Gaussian basis sets (RAGBSs) for ₈₇Fr up to ₁₁₈Uuo atoms without variational prolapse were developed here with the use of a polynomial version of the Generator Coordinate Dirac‐Fock method. Two finite nuclear models have been used, the Gaussian and uniform sphere models. The largest RAGBS error, with respect to numerical Dirac‐Fock results, is 15.4 miliHartree for Ununoctium with a basis set size of 33s30p19d14f functions. © 2013 Wiley Periodicals, Inc.     

A Multivariate Curve Resolution Approach to the Study of the Degradation Kinetics of Valsartan under Photolytic and Acid Conditions

The analysis of UV‐spectrophotometric data with second‐order chemometrics techniques, including multivariate curve resolution with alternating least‐squares (MCR‐ALS) and hybrid hard‐ and soft MCR (HS‐MCR), was examined as an alternative tool for studying the kinetics of drug degradation under stress conditions, employing valsartan (VAL) as a model drug. Despite small structural and spectroscopic differences between VAL and its degradation products, MCR‐ALS and HS‐MCR were able to detect the generation of two photoneutral degradation products (DP‐1 and DP‐2) and a single acid hydrolysis product (DP‐3), providing good approximations to their pure spectra and concentration profiles, from which estimations of the kinetic profiles and rate constants were obtained. Kinetic models based on first‐order reactions explained the degradation processes. MCR‐ALS and HS‐MCR analyses yielded similar rate constants; however, the latter was capable of more properly fitting the experimental data to a kinetic model in the case of drug photolysis. The results were confirmed by comparison with data obtained by HPLC analysis of the degraded samples.     

Interactions between rotenone and humic acids by means of FT-IR and fluorescence spectroscopies

The aim of this work was to ascertain, on a comparative basis, the compositional, structural and functional differences occurring between three humic acids (HAs), HA S1 (isolated from a Mediterranean brown soil), HA S2 (isolated from a Bavarian brown soil), and HA SR (a Suwannee River standard aquatic HA, purchased from IHSS), and to investigate the influence of their intrinsic properties on the types of binding mechanisms toward the pesticide rotenone. Original HAs and their corresponding HA–rotenone products, obtained by two different interaction protocols, were analyzed for elemental and functional group composition, and spectroscopic techniques, such as Fourier-transform infrared (FT IR) with Fourier self-deconvolution (FSD) and fluorescence both in the single-scan and in three-dimensional modes. The HA S1 sample appeared to be characterized by a greater aromaticity degree and lower polarity with respect to the HA S2, featured by a mixed aromatic/aliphatic character, whereas mainly aliphatic and acidic resulted the HA SR. The data obtained suggested that the low water-soluble, non-polar pesticide rotenone resulted preferentially adsorbed onto HAs by hydrophobic interaction, that was the prevailing mechanism in the order HA S1 > HA S2 >>> HA SR, whereas hydrogen bonds resulted predominant in the opposite order.     

Dynamics of transitions in population interactions

A two-species model with transitions between population interactions is studied. Rich dynamics is observed as the number and quality of equilibria change when model parameters and functional responses vary. Existence and stability of equilibria and nonexistence of periodic solutions are established, existence of some bifurcation phenomena are analytically and numerically studied, explicit threshold values are computed to determine the kind of interaction (mutualism, competition, host-parasite) between the species, and several numerical examples are provided to illustrate the main results in this work.     

Analysis of confinement potential fluctuation and band-gap renormalization effects on excitonic transition in GaAs/AlGaAs multiquantum wells grown on (1 0 0) and (3 1 1)A GaAs surfaces

The competition between confinement potential fluctuations and band-gap renormalization (BGR) in GaAs/Al_xGa_1−xAs$\mathrm{GaAs}/{\mathrm{Al}}_x{\mathrm{Ga}}_{1-x}\mathrm{As}$ quantum wells grown on [1 0 0] and [3 1 1]A GaAs substrates is evaluated. The results clearly demonstrate the coexistence of the band-tail states filling related to potential fluctuations and the band-gap renormalization caused by an increase in the density of photogenerated carriers during the photoluminescence (PL) experiments. Both phenomena have strong influence on temperature dependence of the PL-peak energy (E_PL(T))$(E_{\mathit{PL}}(T))$. As the photon density increases, the E_PL can shift to either higher or lower energies, depending on the sample temperature. The temperature at which the displacement changes from a blueshift to a redshift is governed by the magnitude of the potential fluctuations and by the variation of BGR with excitation density. A simple band-tail model with a Gaussian-like distribution of the density of state was used to describe the competition between the band-tail filling and the BGR effects on E_PL(T).     

Thermal and spectroscopic study of the lanthanide 2-aminoterephthalate compounds in the solid state

Lanthanides 2-aminoterephthalate compounds were synthetized and characterized on the basis of TG–DTA data in order to study their thermal behavior, as well as to establish hydration grade and stoichiometry, while TG/FTIR system identified the gaseous products evolved during the thermal decomposition of these compounds in each step of the TG curve, in which water and carbon dioxide were the main products with a small amount of carbon monoxide and ammonia. Through the FT-IR spectroscopic data of the compounds in the solid state, information concerning the coordination mode of the carboxylate groups to the metal was provided, and by analysis of fluorescence, with excitation at 405 nm, the respective electronic transitions supported by the data reported in the literature were identified. In addition, the excitation was made for the ligand salt and acid with the aim of understanding the contribution of the ligand in the emission of the compounds. In summary, the ligand influenced on the fluorescence of lanthanide ions, being more intense for the compounds of La, Ce, Pr, and Nd, making this material interesting for optical and photonic applications.     

Significant Substituent Effect on the Anomerization of Pyranosides: Mechanism of Anomerization and Synthesis of a 1,2‐cis Glucosamine Oligomer from the 1,2‐trans Anomer

Aminoglycosides containing a 2,3‐trans carbamate group easily undergo anomerization from the 1,2‐trans glycoside to the 1,2‐cis isomer under mild acidic conditions. The N‐substituent of the carbamate has a significant effect on the anomerization reaction; in particular, an N‐acetyl group facilitated rapid and complete α‐anomerization. The differences in reactivity due to the various N‐substituents were supported by the results of DFT calculations; the orientation of the acetyl carbonyl group close to the anomeric position was found to contribute significantly to the directing of the anomerization reaction. By exploiting this reaction, oligoaminoglycosides with multiple 1,2‐cis glycosidic bonds were generated from 1,2‐trans glycosides in a one‐step process.     

Modular CeCl3·7H2O-catalyzed multi-component synthesis of 1,2,3,4-tetrasubstituted pyrroles under microwave irradiation and their further trichloroisocyanuric acid-mediated conversion into 5-sulfenylpyrrole derivatives

A modular, multicomponent synthesis of 1,2,3,4-tetrasubstituted pyrroles promoted by the inexpensive CeCl₃·7H₂O, is reported. The reaction was carried out under microwave irradiation, affording good yields of products in short time. Scope and limitations were explored and a plausible reaction mechanism is discussed. The resulting heterocycles were smoothly and efficiently converted into their corresponding 5-arylsulfenyl derivatives by reaction with diaryl disulfides and trichloroisocyanuric acid in EtOAc.