Ab initio study of naphtho-homologated DNA bases

Naphtho-homologated DNA bases have been recently used to build a new type of size-expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naphtho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like forms of naphtho-thymine (yyT) and naphtho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naphtho-guanine (yyG) and naphtho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphtho-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naphtho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.     

Metric Properties of Projections in Semi-Hilbertian Spaces

Several results on norms of projections on a Hilbert space are extended for the operator seminorm defined by a positive semidefinite operator . The authors were supported in part by UBACYT I030, ANPCYT PICT 03-09521, PIP 2188/00.     

Modular phosphite-oxazoline/oxazine ligand library for asymmetric pd-catalyzed allylic substitution reactions: scope and limitations-origin of enantioselectivity

A library of phosphite-oxazoline/oxazine ligands L1-L15 a-h has been synthesized and screened in the Pd-catalyzed allylic substitution reactions of several substrate types. These series of ligands can be prepared efficiently from easily accessible hydroxyl amino acid derivatives. Their modular nature enables the substituents/configurations in the oxazoline/oxazine moiety, alkyl backbone chain and in the biaryl phosphite moiety to be easily and systematically varied. By carefully selecting the ligand components, therefore, high regio- and enantioselectivities (ee values up to 99 %) and good activities have been achieved in a broad range of mono- and disubstituted linear hindered and unhindered liner and cyclic substrates. The NMR studies on the Pd-pi-allyl intermediates provide a deeper understanding about the effect of the ligand parameters on the origin of enantioselectivity. It also indicates that the nucleophilic attack takes place predominantly at the allylic terminal carbon atom located trans to the phosphite moiety.     

Discovery and antibacterial activity of lucensimycin C from Streptomyces lucensis

Protein synthesis is one of the key and validated antibacterial targets and its inhibition has led to the development of highly successful clinical drugs. Ribosomal protein S4 (RPSD) is a part of ribosomal machinery and a new potential target for antibacterial agents. Screening of microbial extracts using antisense sensitized rpsD strain in Staphylococcus aureus followed by chemical analysis led to the isolation of a new compound lucensimycin C, which is a key biosynthetic intermediate of the other lucensimycins. Isolation, structure elucidation, antibiotic activity, and biogenesis have been described.     

Photodegradation of soil organic matter and its effect on gram-negative bacterial growth

To learn more about the role of the reactive oxygen species (ROS) in the production of bioavailable products of the dissolved organic matter, we investigate here the effect of the photolysis (lambda(exc) > 320 nm) of a soil extract (SE) on the growth of bacteria isolated from the same soil as used for obtaining the extract. Comparative experiments with Aldrich humic acid (AHA) as substrate were performed. The photodegradation of the SE was evaluated with different techniques-UV-visible absorption spectroscopy, fluorescence excitation emission matrices (EEM) and Fourier transform infrared spectroscopy (FTIR). Known ROS scavengers were employed to study the effect of photochemically produced ROS on the photodegradation of the substrates. To evaluate the effect of irradiation on the bioavailability of the SE and AHA, photolyzed and nonphotolyzed substrates were added to different culture media and the growth of Pseudomonas sp. isolated from the soil and a strain of Escherichia coli were studied. The different results obtained were assigned to the dissimilar metabolisms of both bacteria.     

1,2,4,5-benzenetetracarboxylate- and 2,2'-bipyrimidine-containing cobalt(II) coordination polymers: preparation, crystal structure, and magnetic properties

Three new mixed-ligand cobalt(II) complexes of formula [Co2(H2O)6(bta)(bpym)]n.4nH2O (1), [Co2(H2O)2(bta)(bpym)]n (2), and [Co2(H2O)4(bta)(bpym)]n.2nH2O ( 3) (bpym = 2,2'-bipyrimidine and H 4bta = 1,2,4,5-benzenetretracaboxylic acid) have been synthesized and characterized by single crystal X-ray diffraction. 1 is a chain compound of mer-triaquacobalt(II) units which are linked through regular alternating bis-bidentate bpym and bis-monodentate bta groups. 2 and 3 are three-dimensional compounds where aquacobalt(II) ( 2) and cis-diaquacobalt(II) ( 3) entities are linked by bis-bidentate bpym ( 2 and 3) and tetrakis- ( 2 and 3) and octakis-monodentate ( 2) bta ligands. The cobalt atoms in 1- 3 exhibit somewhat distorted octahedral surroundings. Two bpym-nitrogen atoms ( 1- 3) and either two bta-oxygens ( 2) or one bta-oxygen and a water molecule ( 1 and 3) build the equatorial plane, whereas the axial positions are filled either by two water molecules ( 1) or by a bta-oxygen atom and a water molecule ( 2 and 3). The values of the cobalt-cobalt separation across the bridging bpym vary in the range 5.684(2)-5.7752(7) A, whereas those through the bta bridge cover the ranges 5.288(2)-5.7503(5) A (across the anti-syn carboxylate) and 7.715(3)-11.387(1) A (across the phenyl ring). The magnetic properties of 1- 3 have been investigated in the temperature range 1.9-290 K. They are all typical of an overall antiferromagnetic coupling with the maxima of the magnetic susceptibility at 14.5 ( 1) and 11.5 K ( 2 and 3). Although exchange pathways through bis-bidentate bpym and carboxylate-bta in different coordination modes are involved in 1- 3, their magnetic behavior is practically governed by that across the bpym bridge, the magnitude of the exchange coupling being J = -5.59(2) ( 1), -4.41(2) ( 2), and -4.49(2) ( 3) with the Hamiltonian H = - JS 1 S 2.     

Coordination and haptotropic migration of Cr(CO)3 in polycyclic aromatic hydrocarbons: the effect of the size and the curvature of the substrate

In this work, we study the reaction mechanism of the tricarbonylchromium complex haptotropic rearrangement between two six-membered rings arranged like in naphthalene of four polycyclic aromatic hydrocarbons (PAHs). It has been found that the reaction mechanism of this haptotropic migration can either occur in a single step or stepwise depending on the interaction between the orbitals of the Cr(CO)3 and the PAH fragments. Our results show that the size of the cyclic system favors the metal migration whereas the curvature of the organic substrate tends to slow down the rearrangement. We discuss the key factors that help to explain this behavior through orbital and energy decomposition analysis.     

Hydrogen-bonding interactions in 2-thiophen-3-ylmalonic acid

Formation of intra- and intermolecular hydrogen bonds in 2-thiophen-3-ylmalonic acid, the precursor of a polythiophene derivative bearing two carboxylic acid groups in the side chain, have been examined by Fourier transform infrared (FTIR) spectroscopy and ab initio quantum mechanical calculations. Interactions found in the FTIR spectra recorded for the melted and solid states are in good agreement with results provided by MP2/6-31+G(d,p) calculations on monomers and dimers, respectively. Specifically, inter- and intramolecular hydrogen bonds were detected in the solid and melted states, respectively. Calculations on dimers stabilized by intermolecular hydrogen bonds exclusively and by both intra- and intermolecular interactions indicated that the former structures are significantly more stable than the latter ones, which is fully consistent with experimental observations. On the other hand, intramolecular interactions in isolated monomers are favored in the melted state, which is dominated by a thermally driven entropic process.     

New families of balanced symmetric functions and a generalization of Cusick,Li and Stǎnicǎ’s conjecture

In this paper we provide new families of balanced symmetric functions over any finite field. We also generalize a conjecture of Cusick, Li, and Stǎnicǎ about the non-balancedness of elementary symmetric Boolean functions to any finite field and prove part of our conjecture.