Ferric and ferrous iron in nitroso-myoglobin: computer simulations of stable and metastable states and their infrared spectra

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O-2, which only bind to ferrous (Fe-II) iron, NO binds to both ferrous and ferric (Fe-II) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ob initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta'-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe-II-NO, which ex- hibits only two minima (the eta(2) coordination mode for Fe-II is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe-III than for Fe-II. We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.

Comments on some recent measurements of anomalously steep N2O and O3tracer spectra in the stratospheric surf zone

Recent aircraft measurements, primarily in the extratropics, of the horizontal variance of nitrous oxide (N2O) and ozone (O3) in the middle stratosphere indicate that horizontal spectra of the tracer variance scale nearly as k−2, where k is the spatial wavenumber along the aircraft flight track [Strahan and Mahlman, 1994; Bacmeister et al., 1996]. This spectral scaling has been regarded as inconsistent with the accepted picture of stratospheric tracer motion; large-scale quasi-two-dimensional tracer advection typically yields a k−1 scaling (i.e., the classical Batchelor spectrum). In this paper it is argued that the nearly k−2 scaling seen in the measurements is a natural outcome of quasi-two-dimensional filamentation of the polar vortex edge. The accepted picture of stratospheric tracer motion can thus be retained: no additional physical processes are needed to account for deviations from the Batchelor spectrum. Our argument is based on the finite lifetime of tracer filaments and on the “singularity spectrum” associated with a one-dimensional field composed of randomly spaced jumps in concentration.

QCD sum rule calculation for the charmonium-like structures in the J/psi phi and J/psi omega invariant mass spectra

Using the QCD sum rules we test if the charmonium-like structure Y(4274), observed in the J/psi phi invariant mass spectrum, can be described with a D(s)(D) over bar (s0)(2317)+ h.c. molecular current with J(PC) = 0(-+). We consider the contributions of condensates up to dimension ten and we work at leading order in alpha(s). We keep terms which are linear in the strange quark mass m(s). The mass obtained for such state is mD(s)D(s0) = (4.78 +/- 0.54) GeV. We also consider a molecular 0(-+) D (D) over bar (0)(2400)+ h.c. current and we obtain m(DD0) = (4.55 +/- 0.49) GeV. Our study shows that the newly observed Y(4274) in the J/psi phi invariant mass spectrum can be, considering the uncertainties, described using a molecular charmonium current. (C) 2011 Elsevier B.V. All rights reserved.

Dilepton mass spectra in p plus p collisions at root s=200 GeV

PHENIX has measured the electron-positron pair mass spectrum from 0 to 8 GeV/c(2) in p + p collisions at root s = 200 GeV. The contributions from light meson decays to e(+)e(-) pairs have been determined based on measurements of hadron production cross sections by PHENIX. Within the systematic uncertainty of similar to 20% they account for all e(+)e(-) pairs in the mass region below similar to 1 GeV/c(2). The e(+)e(-) pair yield remaining after subtracting these contributions is dominated by semileptonic decays of charmed hadrons correlated through flavor conservation. Using the spectral shape predicted by PYTHIA, we estimate the charm production cross section to be 544 +/- 39(stat) +/- 142(syst) +/- 200(model) pb. which is consistent with QCD calculations and measurements of single leptons by PHENIX. (C) 2008 Elsevier BV. All rights reserved.

Electron paramagnetic resonance and the thermoluminescence emission mechanism of the 280 degrees C peak in natural andalusite crystal

Samples of natural andalusite (Al(2)SiO(5)) crystal have been investigated in terms of thermoluminescence (TL) and electron paramagnetic resonance (EPR) measurements. The TL glow curves of samples previously annealed at 600 degrees C for 30 min and subsequently gamma-irradiated gave rise to four glow peaks at 150, 210, 280 and 350 degrees C. The EPR spectra of natural samples heat-treated at 600 degrees C for 30 min show signals at g = 5.94 and 2.014 that do not change after gamma irradiation and thermal treatments. However, it was observed that the appearance of a paramagnetic center at g=1.882 for the samples annealed at 600 degrees C for 30 min followed gamma irradiation. This line was attributed to Ti(3+) centers. The EPR signals observed at g=5.94 and 2.014 are due to Fe(3+). Correlations between EPR and TL results of these crystals show that the EPR line at g=1.882 and the TL peak at 280 degrees C can be attributed to the same defect center. (C) 2011 Elsevier B.V. All rights reserved.

UV optical absorption spectra analysis of beryl crystals from Brazil

The spectral decomposition analysis was applied to the optical absorption spectra of green and colorless beryl crystals from the Brazilian Eastern Pegmatitic province in the natural state, Submitted to heat treatment and irradiated with UV light The attributions of the lines were made taking into account highly accurate quantum mechanical calculations The deconvolution of the green beryl spectra revealed four lines, two of them around 12,000 cm(-1) (1 5eV) and two of them around 34,000 cm(-1) (4.2 eV) attributed to Fe(2+) and Fe(3+), respectively The deconvolution of the colorless beryl spectra without any treatment, after heating and for the same heat treatment followed by UV light irradiation revealed five lines The analysis of ratio relations showed that the lines at 36,400 cm(-1) (4.5 eV) and 41,400 cm(-1) (5 1 eV) belongs to a single defect attributed to a silicon dangling bond defect (=Si). Discussions and comparison with reported defects in quartz have supported the allocation of the lines at 61,000 cm(-1) (7.6 eV) and 43,800 cm(-1) (5 4 eV) to diamagnetic oxygen vacancy defect ( Si-Si ) and unrelaxed ( Si Si ) defect, respectively Finally, the line at 39.100 cm(-1) (4.8 eV), quite polarized along the c-axis, was attributed to a (Fe(2+) OH(-)) defect in the structural channels (C) 2009 Elsevier B V All rights reserved

Correlation between electron paramagnetic resonance and thermoluminescence in natural sodalite

Samples of natural sodalite, Na(8)Al(6)Si(6)O(24)Cl(2), submitted to gamma irradiation and to thermal treatments, have been investigated using the thermoluminescence (TL) and electron paramagnetic resonance (EPR) techniques. Both, natural and heat-treated samples at 500A degrees C in air for 30 min, present an EPR signal around g = 2.01132 attributed to oxygen hole centers. The EPR spectra of irradiated samples show an intense line at g = 2.0008 superimposed by a hyperfine multiplet of 11 lines due to an O(-) ion in an intermediate position with respect to two adjacent Al nuclei. In the TL measurements, the samples were annealed at 500A degrees C for 30 min and then irradiated with gamma doses varying from 0.001 to 20 kGy. All the samples have shown TL peaks at 110, 230, 270, 365, and 445A degrees C. A correlation between the EPR g = 2.01132 line and the 365A degrees C TL peak was observed. A TL model is proposed in which a Na(+) ion acts as a charge compensator when an Al(3+) ion replaces a Si(4+) lattice ion. The gamma ray destruction of the Al-Na complex provides an electron trapped at the Na and a hole trapped at a non-bridging oxygen ion adjacent to the Al(3+) ion.

Thermoluminescence and optical absorption studies of natural grossular minerals

The optical absorption spectra of two samples of grossular have been measured at room temperature. An intense charge transfer band (UVCT) of iron extends to the visible and near infrared region. Some peaks associated to Fe3+ ions in tetrahedral and octahedral positions have been identified and their energy levels were computed. Mn2+ and Fe2+ ions are responsible with some bands and probably these ions occupy dodecahedral positions. No change in the intensity of optical absorption spectra were found after gamma dose, but only the 505 nm band decreases with irradiation. The OH spectra, consisting of OH overtones at 2750nm and asymmetric OH bands in the near infrared region were observed in the two samples. The heat treatment produces Fe2+ -> Fe3+ and Mn2+ -> Mn3+ by oxidation. This last was observed in sample II only. The thermally stimulated luminescence of both grossular samples has been investigated. Due to differences in iron and manganese concentration, not only a large difference has been observed in their optical absorption behavior, but also a striking difference in their thermoluminescent behavior. Actually, it is not clear whether other impurities such as Ti, Na and K that are present in quite different concentration in grossular I and II are also contributing to the thermoluminescenct properties of both samples. (C) 2008 Elsevier Ltd. All rights reserved.

Resolution and Absolute Configuration Assignment of a Natural Racemic Chromane from Peperomia obtusifolia (Piperaceae)

The resolution of the natural racemic chromane 3,4-dihydro-5-hydroxy-2,7-dimethyl-8-(3 ``-methyl-2 ``-butenyl)-2-(4`-methyl-1`,3`-pentadienyl)-2H-1-benzopyran-6-carboxylic acid (1) isolated from the leaves of Peperomia obtusifolia has been accomplished using stereoselective HPLC. The absolute coil figuration of the resolved enantiomers was determined by the analysis of optical rotations and CD spectra. The finding of a racemic mixture instead of an enantiomerically pure metabolite raises questions about the final steps in the biosynthesis of this class of natural products, suggesting that the intramolecular chromane ring formation step may not be enzymatically controlled at all in P. obtusifolia. Chirality 21:799-801, 2009. (C) 2008 Wiley-Liss, Inc.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

Julocrotine, N-(2,6-dioxo-l-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data. (C) 2007 Wiley Periodicals, Inc.

Compósitos de borracha natural com polianilina

Compósitos de borracha natural (Hevea brasiliensis)-BN/polianilina - PANI, com diferentes composições foram obtidos através da polimerização por emulsão do monômero anilina na presença da BN e do ácido dodecilbenzeno sulfônico (DBSA). Filmes finos e homogêneos foram obtidos por prensagem a quente. Os compósitos foram caracterizados por condutividade elétrica, FTIR, UV-vis-NIR, DSC e difração de raios X. Compósito com condutividade elétrica cerca de 14 ordens de grandeza maior que a BN foi obtido. Este alto valor de condutividade é atribuído à formação da PANI no estado dopado no compósito, que foi verificado através das técnicas de UV-vis-NIR e FTIR. Os resultados obtidos com a técnica de DSC e difratometria de raios X indicaram que os polímeros são imiscíveis e que a presença da borracha não altera significantemente a fase cristalina da PANI-DBSA no compósito.

Synthesis, characterization, and application of modified silica in the removal and preconcentration of lead ions from natural river water

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

The interaction between heparin and Lys49 phospholipase A(2) reveals the natural binding of heparin on the enzyme

We have studied at a molecular level the interaction of heparins on bothropstoxin-1 (BthTx-1), a phospholipase A(2) toxin. The protein was monitored using gel filtration chromatography, dynamic light scattering (DLS), circular dichroism (CD), attenuated total reflectance Fourier transform infrared (ATR-FTIR) and intrinsic tryptophan fluorescence emission (ITFE) spectroscopy. The elution profile of the protein presents a displacement of the protein peak to larger complexes when interacting with higher concentration of heparin. The DLS results shows two R-h at a molar ratio of 1, one to the distribution of the protein and the second for the action of heparin on BthTx-I structures, and a large distribution with the increase of protein. The interaction is accompanied by significant changes in the CD spectra, showing two common features: a decrease in signal at 208 nm (3 and 6 kDa heparins) and an isodichroic point near 226 nm (3 kDa heparin). FTIR spectra indicate that only a few amino acid residues are involved in this interaction. Alterations in the ITFE by binding heparins suggest that the initial binding occurs on the ventral face of BthTx-1. Together, these results add an experimental and structural basis on the action mechanism of the heparins over the phospholipases A(2) and provide a molecular model to elucidate the interaction of the enzyme-heparin complex at a molecular level. (c) 2005 Elsevier B.V. All rights reserved.

Resolution and Absolute Configuration Assignment of a Natural Racemic Chromane from Peperomia obtusifolia (Piperaceae)

The resolution of the natural racemic chromane 3,4-dihydro-5-hydroxy-2,7-dimethyl-8-(3 ''-methyl-2 ''-butenyl)-2-(4'-methyl-1',3'-pentadienyl)-2H-1-benzopyran-6-carboxylic acid (1) isolated from the leaves of Peperomia obtusifolia has been accomplished using stereoselective HPLC. The absolute coil figuration of the resolved enantiomers was determined by the analysis of optical rotations and CD spectra. The finding of a racemic mixture instead of an enantiomerically pure metabolite raises questions about the final steps in the biosynthesis of this class of natural products, suggesting that the intramolecular chromane ring formation step may not be enzymatically controlled at all in P. obtusifolia. Chirality 21:799-801, 2009. (C) 2008 Wiley-Liss, Inc.

Vibrational spectra of pilocarpine hydrochloride crystals

Pilocarpine is a natural substance with potential application in the treatment of several diseases. In this work Fourier Transform (FT)-Raman spectrum and the Fourier Transform infra red (FT-IR) spectrum of pilocarpine hydrochloride C11H17N2O2+.Cl- were investigated at 300 K. Vibrational wavenumber and wave vector have been predicted using density functional theory (B3LYP) calculations with the 6-31 G(d,p) basis set. A comparison with experiment allowed us to assign most of the normal modes of the crystal.