Estudo de sistema molecular confinado

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo de estirilpironas de Cryptocarya mandioccana por espectrometria de massas e análise configuracional por ressonância magnética nuclear e dicroísmo circular

Pós-graduação em Química - IQ

Identification of quinolactin alkaloids from fungi associated to Brazilian red algae Dichotomaria marginata by LC-PDA-MS and LC-MSn

Fungi isolated from marine organisms have been shown to produce several interesting secondary metabolites with important biological activities. Such chemical diversity may be associated to environmental stress conditions and may represent an important source of NCE for bioprospection. Quinolactins belong to a rare fungi-alkaloid class with a unique N-methyl-quinolone moiety fused to a lactam ring and present several bioactivities1. Fungi strain Dm1 was isolated from red alga Dichotomaria marginata, collected from Brazil SE coast, and was grown in sterile rice solid media at 26oC 2, which was then extracted with MeOH. The MeCN fr. from the MeOH extract was chromatographed over Sephadex LH-20 and fr. 4 afforded quinolactin (QL) alkaloids B1, B2 and A, whereas fr. 5 afforded quinolactin D1 after purification by HPLC-DAD. Structural determination of pure compounds was based on HRMS, UV, and NMR spectral analyses, in addition to comparison with literature data and Antimarin® databank. UV data indicated the presence of similar chromophores with λmax at ca. 247 and 320nm. HRMS and tandem MS analyses using both negative and positive ion modes for the isolated compounds indicated their molecular formula and structural features, as for QL B1: C15H16O2N2 [M+H 257], which showed one fragment at m/z 214 [-CHNO]; QL B2: C15H16O3N2 [M+H 273], with product ions at m/z 230 [-CHNO.] and m/z 186 [-C4H9NO.]; for QL A: C16H18N2O2 [M+H 271], which presented one ion at m/z 214, due to loss of fragment (-C4H9) from the molecular ion; and for QL D1: C16H18N2O3 [M+H 287], with product ions at m/z 186 [-CHNO] and m/z 230 [-C4H9]. Such data suggested fragmentation proposals, e.g. for Quinolactin B1 (Fig. 1), which confirmed the structures of the isolated quinolactins, and may represent an important contribution for the sustainable exploration of marine biodiversity.

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda)

The binding selectivity of the M(phen)(edda) (M = Cu, Co, Ni, Zn; phen = 1,10-phenanthroline, edda = ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(11) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N4O2 octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling. (C) 2008 Elsevier B.V. All rights reserved.

Ab initio study and NMR analysis of the complexion of citric acid with ion lithium

Quantum mechanics calculations at the ab initio HF/3-21G* level were carried out with Nuclear Magnetic Resonance (NMR) measurements to characterize citric acid and lithium interactions. The results indicate the formation of a tridentate organometallic compound with one lithium and one citric acid molecule and a tridentate and bidentate compound of two lithium atoms and one citric acid molecule. The results are in agreement with the experimental and theoretical data. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Amorphous carbon nitrogenated films prepared by plasma immersion ion implantation and deposition

In this work, an investigation was conducted on amorphous hydrogenated-nitrogenated carbon films prepared by plasma immersion ion implantation and deposition. Glow discharge was excited by radiofrequency power (13.56 MHz, 40 W) whereas the substrate-holder was biased with 25 kV negative pulses. The films were deposited from benzene, nitrogen and argon mixtures. The proportion of nitrogen in the chamber feed (R-N) was varied against that of argon, while keeping the total pressure constant (1.3 Pa). From infrared reflectance-absorbance spectroscopy it was observed that the molecular structure of the benzene is not preserved in the film. Nitrogen was incorporated from the plasma while oxygen arose as a contaminant. X-ray photoelectron spectroscopy revealed that N/C and O/C atomic ratios change slightly with R-N. Water wettability decreased as the proportion of N in the gas phase increased while surface toughness underwent just small changes. Nanoindentation measurements showed that film deposition by means of ion bombardment was beneficial to the mechanical properties of the film-substrate interface. The intensity of the modifications correlates well with the degree of ion bombardment. (c) 2006 Elsevier B.V. All rights reserved.

Plasma-polymerized hexamethyldisilazane treated by nitrogen plasma immersion ion implantation technique

This paper describes the effect of nitrogen Plasma Immersion Ion Implantation (PIII) on chemical structure, refraction index and surface hardness of plasma-polymerized hexamethyldisilazane (PPHMDSN) thin films. Firstly, polymeric films were deposited at 13.56 MHz radiofrequency (RF) Plasma Enhanced Chemical Vapour Deposition (PECVD) and then, were treated by nitrogen PIII from 15 to 60 min. Fourier Transformed Infrared (FTIR) spectroscopy was employed to analyse the molecular structure of the samples, and it revealed that vibrations modes at 3350 cm(-1), 2960 cm(-1), 1650 cm(-1), 1250 cm(-1) and 1050 cm(-1) were altered by nitrogen PIII. Visible-ultraviolet (vis-UV) spectroscopy was used to evaluate film refractive index and the results showed a slight increase from 1.6 to 1.8 following the implantation time. Nanoindentation revealed a surface hardness rise from 0.5 to 2.3 GPa as PIII treatment time increased. These results indicate nitrogen PIII is very promising in improving optical and mechanical properties of PPHMDSN films.

Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the quick cryo-soaking technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)(8) barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu(32), Asp(34), Asp(91), and solvent molecules. In the proposed acid base catalytic mechanism, His(12) and His(47) play key roles and are supported by a network of hydrogen bonds between Asp(34), Asp(52), Trp(230), Asp(233), and Asn(252).

Protein-Ion Binding Process on Finite Macromolecular Concentration. A Poisson-Boltzmann and Monte Carlo Study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C-terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C-terminus introduced a negative charge at an all-positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide's primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel-like activity on anionic bilayers with a well-defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans-negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Spectroscopic investigation of a new hybrid glass formed by the interaction between croconate ion and calcium polyphosphate

In this work, a new organic-inorganic hybrid material has been synthesized by the incorporation of croconate ion into a calcium polyphosphate coacervate. The hybrid so obtained was characterized by means of electronic and vibrational spectroscopies. The material is a homogeneous mixture described by a structural model, which includes helical chains of polyphosphate ions, where the calcium ion occupies the internal vacancies of the structure. The croconate ion appears to be occupying the regions outside the polymeric structure, surrounded by several water molecules. The electronic spectrum of the incorporated material shows a broad band peaking at the same wavelength region (363 nm) observed for the aqueous solution of croconate ion, and manifesting the Jahn-Teller effect as evidenced by the doublet structure of the band. The infrared spectrum is widely dominated by the absorption bands of the polyphosphate ion and the appearance of the carbonyl stretching band at ca. 1550 cm(-1) indicates the presence of croconate ion incorporated in the structure. The Raman spectrum of the material shows several vibrational bands related to the oxocarbon moiety; most of them are shifted in comparison with the free ion. These shifts can be understood in terms of strong hydrogen bonding interactions between water molecules and the oxocarbon moiety. The low temperature methodology proposed here can be well used in the preparation of new phosphate glasses containing organic moieties opening the route to an entirely new class of hybrid glasses. (c) 2004 Elsevier B.V All rights reserved.

Numerical simulation of magnetic-field-enhanced plasma immersion ion implantation in cylindrical geometry

Recent studies have demonstrated that the sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field. In this paper, a two-dimensional computer simulation of a magnetic-field-enhanced PHI system is described. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded vacuum chamber filled with uniform molecular nitrogen plasma. A static magnetic field is created by a small coil installed inside the target holder. The vacuum chamber is filled with background nitrogen gas to form a plasma in which collisions of electrons and neutrals are simulated by the Monte Carlo algorithm. It is found that a high-density plasma is formed around the target due to the intense background gas ionization by the magnetized electrons drifting in the crossed E x B fields. The effect of the magnetic field intensity, the target bias, and the gas pressure on the sheath dynamics and implantation current of the PHI system is investigated.

Mixed pseudohalide complexes of copper(II). Crystal and molecular structure of [Cu(N-3)(NCS)(tmen)](n) and of [Cu(N-3)(NCO)(tmen)]2 (tmen = N,N,N ',N '-tetramethylethylenediamine)

The compounds [Cu(N-3)(NSC)(tmen)](n) (1), [Cu(N-3)(NCO)(tmen)](n) (2) and [Cu(N-3)(NCO)(tmen)](2) (3) (tmen = N,N,N',N'-tetramethylethylenediamine) were synthesized and studied by i.r. spectroscopy. Single crystals of compounds (1) and (3) were obtained and characterized by X-ray diffraction. The structure of compound (1) consists of neutral chains of copper(II) ions bridged by a single azido ligand showing the asymmetric end-to-end coordination fashion. Each copper ion is also surrounded by the other three nitrogen atoms: two from one N,N,N',N'-tetramethylethylenediamine and one from a terminal bonded thiocyanate group. Compound (2) decomposes slowly in acetone and the product formed [Cu(N-3)(NCO)(tmen)](2) (3) crystallizes in the monoclinic system (P2(1)). The structure of (3) consists of dimeric units in which the Cu atoms are penta-coordinated and connected by p(1,3) bridging azido and cyanate ligands. In both cases the five coordinated atoms give rise to a slightly distorted square-based pyramid coordination geometry at each copper ion. The thermal behavior of [Cu(N-3)(NSC)(tmen)](n) (1) and [Cu(N-3)(NCO)(tmen)](n) (2) were investigated and the final decomposition products were identified by X-ray powder diagrams.

Design of Gaussian basis sets to the theoretical interpretation of IR-spectrum of hexaaquachromium (III) ion, tetraoxochromium (IV) ion, and tetraoxochromium (VI) ion

The Generator Coordinate Hartree-Fock (GCHF) method is employed to design 16s, 16s10p, 24s17p13d, 25s17p13d, and 26s17p Gaussian basis sets for the H ((2)S), O ((3)P), O(2-) ((1)S), Cr(3+) ((4)F), Cr(4+) ((3)F), and Cr(6+) ((1)S) atomic species. These basis sets are then contracted to (4s) for H ((2)S), (6s4p) for O ((3)P), and O(2-) ((1)S), (986p3d) for Cr(3+) ((4)F), (10s8p3d) for Cr(4+) ((3)F), and (13s7p) for Cr(6+) (1S) by a standard procedure. For evaluation of the quality of those basis sets in molecular calculations, we have accomplished studies of total and orbital (HOMO and HOMO-1) energies at the HF-Roothaan level for the molecular species of our interest. The results obtained with the contracted basis sets are compared to the values obtained with our extended basis sets and to the standard 6-311G basis set from literature. Finally, the contracted basis sets are enriched with polarization function and then utilized in the theoretical interpretation of IR-spectrum of hexaaquachromium (III) ion, [Cr(H(2)O)(6)](3+), tetraoxochromium (IV) ion, [CrO(4)](4-), and tetraoxochromium (VI) ion, [CrO(4)](2-). The respective theoretical harmonic frequencies and IR-intensities were computed at the density functional theory (DFT) level. In the DFT calculations we employed the Becke's 1988 functional using the LYP correlation functional. The comparison between the results obtained and the corresponding experimental values indicates a very good description of the IR-spectra of the molecular ions studied, and that the GCHF method is still a legitimate alternative for selection of Gaussian basis sets. (C) 2003 Elsevier B.V. All rights reserved.

Glass structure and ion dynamics of lead-cadmium fluorgermanate glasses

Glass structure and fluorine motion dynamics are investigated in lead-cadmium fluorgermanate glasses by means of differential scanning calorimetry, Raman scattering, x-ray absorption (EXAFS), electrical conductivity (EC), and F-19 nuclear magnetic resonance (NMR) techniques. Glasses with composition 60PbGeO(3)-xPbF(2)-yCdF(2) (in mol %), with x+y=40 and x=10, 20, 30, 40, are studied. Addition of metal fluorides to the base PbGeO3 glass leads to a decrease of the glass transition temperature (T-g) and to an enhancement of the ionic conductivity properties. Raman and EXAFS data analysis suggest that metagermanate chains form the basic structural feature of these glasses. The NMR study leads to the conclusion that the F-F distances are similar to those found in pure crystalline phases. Experimental results suggest the existence of a heterogeneous glass structure at the molecular scale, which can be described by fluorine rich regions permeating the metagermanate chains. The temperature dependence of the NMR line shapes and relaxation times exhibits the qualitative and quantitative features associated with the high fluorine mobility in these systems. (C) 2004 American Institute of Physics.