Genomic clustering of the Trypanosoma cruzi nonlong terminal L1Tc retrotransposon with defined interspersed repeated DNA elements

We have analyzed the genomic distribution and organization of the long interspersed nucleotide element (LINE) L1Tc, a nonlong terminal repeat (LTR) retrotransposon of Trypanosoma cruzi. The results indicate that the L1Tc element is dispersed along the parasite genome and that in some regions it is organized in tandem repeats. The data allowed us to define the existence of short direct-repeated sequences flanking the genomic L1Tc elements. Relevant is the finding that the LINE L1Tc is located in genomic regions rich in short interspersed nucleotide elements (SINE)-like sequences. In particular, the L1Tc element is found associated to E13-related sequences, redefined in this work and renamed RS13Tc, and to a newly described RS1Tc sequence. The RS1Tc sequence is present, per haploid genome, in about 3,200 copies. Northern blot analysis showed that the RS1Tc is being transcribed into RNAs of different sizes. The analysis of the chromosomal distribution of these elements in various strains of T. cruzi suggested that this type of clustering might be a common feature of the genome of these parasites.     

Radiolysis in H2O/D2O mixtures. Hydrogen production under LOCA simulation

The hydrogen isotope radiolytic yields, G(H₂), G(HD) and G(D₂) were determined in H₂O/D₂O mixtures under chemical conditions close to a LOCA in a PHWR like Atucha I Nuclear Station, that is 2·10^–3 MH₃BO₃ and p(H+D)=8.5±0.2. The total hydrogen radiolytic yield G(H₂+HD+D₂) as a function of the deuterium atom fraction goes through a flat maximum at about 0.58. This result in dicates that the 4% flammability limit for hydrogen in the reactor's containment with be reached sooner than what is expected assuming a linear combination of pure H₂ and D₂ radiolytic yields. Hydrogen radiolytic production in 10^–3 M KBr in H₂O/D₂O mixtures gives the same results as in the boric solutions suggesting a bimolecular B(OH) ₄ ^– +OH reaction. Identical isotope concentration factors were calculated for both solutions.     

A theoretical study on the low-lying excited states of 2,2':5',2'-terthiophene and 2,2':5',2':5',2'-quaterthiophene.

The nature and properties of the low-lying singlet and triplet valence excited states of 2,2':5',2'-terthiophene (terthiophene) and 2,2':5',2':5',2'-quaterthiophene (tetrathiophene) are discussed on the basis of high-level ab initio computations. The spectroscopic features determined experimentally for short alpha-oligothiophenes are rationalised on theoretical grounds. Special attention is devoted to the nonradiative decay process through intersystem crossing (ISC) from the singlet to the triplet manifold, which is known to be relatively less efficient in tetrathiophene. Along the geometry relaxation of the S1 state of terthiophene, the S1 and T2 states become degenerate, which leads to a favourable situation for the occurrence of ISC. The parallel process is expected to be less favoured in tetrathiophene because of the less efficient spin-orbit coupling and the increase of the S1-T2 energy gap.     

Sulfate Ions in Titania Polymorphs

Sol-gel titania was sulfated by using sulfuric acid as hydrolysis catalyst, or by impregnating with ammonium sulfate fresh samples prepared with nitric acid or ammonium hydroxide as hydrolysis catalyst. Samples were characterized with X-ray powder diffraction, infrared spectroscopy, thermogravimetry and atomic absorption spectroscopy. Sulfate ions were found anchored to brookite and anatase phases, because they have short O—O atomic bond lengths slightly larger than the largest O—O bond length of sulfate ion. Since the shortest O—O atomic bond in anatase is smaller than the one in brookite, the sulfate ions are then less deformed when they are anchored to anatase, and consequently more stable. Therefore when the sample temperature is raised, the brookite with sulfate ions was transformed mainly to anatase and not into rutile, which is the most probably transformation when these ions are not involved. Sulfate ions also hindered anatase and brookite crystallite growing and stabilized the crystalline structure of anatase. When the sulfate ions are lost the crystalline anatase phase is transformed into rutile, leaving a large number of vacancies that favored atom diffusion and consequently the growing of rutile crystallites. The crystalline evolution of the samples as a function of the annealing temperature is almost independent of the sulfating method.     

Synthesis of S,N-chelating heterocyclic thionates of palladium(II). Crystal structure of cis-[Pd(pym2S)(PPh3)2] (pym2S = pyrimidine-2-thionate)

The synthesis of mononuclear palladium(II) complexes containing chelating heterocyclic thionates is described. The new compounds of general formula cis-[Pd(RS-N)(L) _x ](ClO₄) [x = 2, L = PPh₃, RS-N = pyridine-2-thionate (py2S) (1), pyrimidine-2-thionate (pym2S) (2), imidazolidine-2-thionate (imzdS) (3), 1-methylimidazoline-2 thionate (mimzS) (4), 1,3-thiazoline-2-thionate (tzdS) (5); x = 1, L = dppe, RS-N = pyridine-2-thionate (py2S) (6), pyrimidine-2-thionate (pym2S) (7), imidazolidine-2-thionate (imzdS) (8), 1-methylimidazole-2 thionate (mimzS) (9) and 1,3-thiazoline-2-thionate (tzdS) (10)] were prepared by directly reacting the hydroxo-complexes [{Pd(PPh₃)₂(-OH) }₂](ClO₄)₂ and [ {Pd(dppe)(-OH) }₂](ClO₄)₂ with the corresponding heterocyclic thiones (RS-N)H. The complexes have been characterized by partial elemental analyses, conductance measurements and spectroscopic methods (I.r., FAB, ¹H- and ³¹P-n.m.r.). No evidence for monomer-dimer equilibrium was found in solution. The crystal structure of (2) has been determined by X-ray diffraction analysis.     

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine homodimers were determined by the MP2 and CCSD(T) calculations utilizing a wide range of split-valence, correlation-consistent, and bond-functions basis sets. Complete basis set MP2 (CBS MP2) stacking energies extrapolated using aug-cc-pVXZ (X = D, T, and for pyrimidine dimer Q) basis sets equal to -5.3, -12.3, and -11.2 kcal/mol for the first three dimers, respectively. Higher-order correlation corrections estimated as the difference between MP2 and CCSD(T) stacking energies amount to 2.0, 0.7, and 0.9 kcal/mol and lead to final estimates of the genuine stacking energies for the three dimers of -3.4, -11.6, and -10.4 kcal/mol. The CBS MP2 stacking-energy estimate for guanine dimer (-14.8 kcal/mol) was based on the 6-31G(0.25) and aug-cc-pVDZ calculations. This simplified extrapolation can be routinely used with a meaningful accuracy around 1 kcal/mol for large aromatic stacking clusters. The final estimate of the guanine stacking energy after the CCSD(T) correction amounts to -12.9 kcal/mol. The MP2/6-31G(0.25) method previously used as the standard level to calculate aromatic stacking in hundreds of geometries of nucleobase dimers systematically underestimates the base stacking by ca. 1.0-2.5 kcal/mol per stacked dimer, covering 75-90% of the intermolecular correlation stabilization. We suggest that this correction is to be considered in calibration of force fields and other cheaper computational methods. The quality of the MP2/6-31G(0.25) predictions is nevertheless considerably better than suggested on the basis of monomer polarizability calculations. Fast and very accurate estimates of the MP2 aromatic stacking energies can be achieved using the RI-MP2 method. The CBS MP2 calculations and the CCSD(T) correction, when taken together, bring only marginal changes to the relative stability of H-bonded and stacked base pairs, with a slight shift of ca. 1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases.     

Short synthesis of the CDEF ring system of lactonamycin

[reaction: see text]. A synthesis of the CDEF fragment of lactonamycin is achieved in eight steps (six pots) from the known and readily available anhydride 4 via a Diels-Alder reaction between tricycle 13 and 2,3-dimethylbenzoquinone.     

Thermal study of vermiculites and mica-vermiculite interstratifications

Simultaneous DTA-TG has been carried out on a set of natural vermiculite samples. Based on their dehydration behaviour the samples can be divided in two groups: (a) those with DTA endothermic peak temperatures at 140°–150°C and 240°–270°C (pure vermiculties) and (b) those with peak temperatures at 95°–115°C (vermiculite with mica or mica-vermiculite interstratifications). The low temperature at which the endothermic effect in group (b) appears is discussed on the basis of dilution due to the inert layers of mica, differences in chemical composition, and lowering of interlamellar water bond energy.     

Surface tension and density of mixtures of 1,3-dioxolane+alkanols at 298.15 K: analysis under the extended Langmuir model

Surface tensions (sigma) for [1,3-dioxolane+methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, and 1-pentanol] and excess molar volumes (v(E)) for [1,3-dioxolane+methanol, ethanol, 1-propanol, 2-propanol, and 2-butanol] at the temperature 298.15 K and normal atmospheric pressure have been determined as a function of mole fractions. The magnitude of these experimental quantities is discussed in terms of the nature and type of intermolecular interactions in binary mixtures. In order to analyze the surface tension behavior, the extended Langmuir (EL) model was used and the results obtained for the systems containing 1,3-dioxolane were compared with those of other formerly published series: [1,4-dioxane+alkanes] and [1,4-dioxane+alcohols].     

Investigations of a novel process to the framework of benzo[c]cinnoline

A novel synthetic process leading to the framework of benzo[c]cinnoline has been discovered and investigated. The process is composed of two separate reactions, the first of which is a partial reduction of the nitro groups of the 2,2'-dinitrobiphenyl, a process that we believe proceeds via a SET mechanism to yield the hydroxyamino and nitroso groups. In the following step the cyclization takes place under formation of the -N=N- bond. We believe that this process take place via a radical mechanism through the nitroso radical anion. The novel process affords either benzo[c]cinnoline or benzo[c]cinnoline N-oxide, both in high yields, 93% and 91%, respectively. To obtain benzo[c]cinnoline, the reaction is conducted with an alcohol as solvent and an alkoxide as the base, while for benzo[c]cinnoline N-oxide, water is used as solvent with sodium hydroxide as the base. To establish the latter procedure, statistical experimental design and multivariate modeling were utilized to reveal the response surface for the reaction and to determine the optimal conditions for the reaction. A proposal for the complex reaction mechanism is given. During the corroboration of the mechanism, a new deoxygenation reaction for converting benzo[c]cinnoline N-oxide into benzo[c]cinnoline was discovered. The reaction is conducted by treating the N-oxide with sodium ethoxide at elevated temperature to achieve near-quantitative conversion into benzo[c]cinnoline in a yield of 96%.