A theoretical study on the XeF(2) molecule

A relativistic four-component study was performed for the XeF(2) molecule by using the Dirac-Coulomb (DC) Hamiltonian and the relativistic adapted Gaussian basis sets (RAGBSs). The comparison of bond lengths obtained showed that relativistic effects on this property are small (increase of only 0.01 angstrom) while the contribution of electron correlation, obtained at CCSD(T) or CCSD-T levels, is more important (increase of 0.05 angstrom). Electron correlation is also dominant over relativistic effects for dissociation energies. Moreover, the correlation-relativity interaction is shown to be negligible for these properties. The electron affinity, the first ionization potential and the double ionization potential are obtained by means of the Fock-space coupled cluster (FSCC) method, resulting in DC-CCSD-T values of 0.3 eV, 12.5 eV and 32.3 eV, respectively. Vibrational frequencies and some anharmonicity constants were also calculated under the four-component formalism by means of standard perturbation equations. All these molecular properties are, in general, ill satisfactory agreement with available experimental results. Finally, a partition in terms of charge-charge flux-dipole flux (CCFDF) contributions derived by means of the quantum theory of atoms in molecules (QTAIM) in non-relativistic QCISD(FC)/3-21G* calculations was carried out for XeF(2) and KrF(2). This analysis showed that the most remarkable difference between both molecules lies on the charge flux contribution to the asymmetric stretching mode, which is negligible in KrF(2) but important in XeF(2). (c) 2008 Elsevier B.V. All rights reserved.

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis (Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

A Model Coupling Vibrational and Rotational Motion for the DNA Molecule

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

Hydrogen bond and the resonance effect on the formamide-water complexes

The interaction of formamide and the two transition states of its amide group rotation with one, two, or three water molecules was studied in vacuum. Great differences between the electronic structure of formamide in its most stable form and the electronic structure of the transition states were noticed. Intermolecular interactions were intense, especially in the cases where the solvent interacted with the amide and the carbonyl groups simultaneously. In the transition states, the interaction between the lone pair of nitrogen and the water molecule becomes important. With the aid of the natural bond orbitals, natural resonance theory, and electron localization function (ELF) analyses an increase in the resonance of planar formamide with the addition of successive water molecules was observed. Such observation suggests that the hydrogen bonds in the formamidewater complexes may have some covalent character. These results are also supported by the quantitative ELF analyses. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

HYDROGEN SULFIDE AS A CRYOGENIC MEDIATOR OF HYPDXIA-INDUCED ANAPYREXIA

Hypoxia causes a regulated decrease in body temperature (Tb), a response that has been aptly called anapyrexia, but the mechanisms involved are not completely understood. The roles played by nitric oxide (NO) and other neurotransmitters have been documented during hypoxia-induced anapyrexia, but no information exists with respect to hydrogen sulfide (H(2)S), a gaseous molecule endogenously produced by cystathionine beta-synthase (CBS). We tested the hypothesis that HA production is enhanced during hypoxia and that the gas acts in the anteroventral preoptic region (AVPO; the most important thermosensitive and thermointegrative region of the CNS) modulating hypoxia-induced anapyrexia. Thus, we assessed CBS and nitric oxide synthase (NOS) activities [by means of H2S and nitrite/nitrate (NO(x)) production, respectively] as well as cyclic adenosine 3',5'-monophosphate (cAMP) and cyclic guanosine 3',5'-monophosphate (cGMP) levels in the anteroventral third ventricle region (AV3V; where the AVPO is located) during normoxia and hypoxia. Furthermore, we evaluated the effects of pharmacological modifiers of the H2S pathway given i.c.v. or intra-AVPO. I.c.v. or intra-AVPO microinjection of CBS inhibitor caused no change in Tb under normoxia but significantly attenuated hypoxia-induced anapyrexia. During hypoxia there were concurrent increases in H2S production, which could be prevented by CBS inhibitor, indicating the endogenous source of the gas. cAMP concentration, but not cGMP and NOR, correlated with CBS activity. CBS inhibition increased NOS activity, whereas H2S donor decreased NO. production. In conclusion, hypoxia activates H2S endogenous production through the CBS-H(2)S pathway in the AVPO, having a cryogenic effect. Moreover, the present data are consistent with the notion that the two gaseous molecules, H(2)S and NO, play a key role in mediating the drop in Tb caused by hypoxia and that a fine-balanced interplay between NOS-NO and CBS-H(2)S pathways takes place in the AVPO of rats exposed to hypoxia. (C) 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Low content cerium oxide nanoparticles on carbon for hydrogen peroxide electrosynthesis

A comparative study using different proportions of CeO2/C (4%, 9% and 13% CeO2) was performed to produce H2O2, a reagent used in the oxidation of organic pollutants and in electro-Fenton reactions for the production of the hydroxyl radical (OH center dot), a strong oxidant agent used in the electrochemical treatment of aqueous wastewater. The CeO2/C materials were prepared by a modified polymeric precursor method (PPM). X-ray diffraction analysis of the CeO2/C prepared by the PPM identified two phases. CeO2 and CeO2. The average size of the crystallites in these materials was close to 7 nm. The kinetics of the oxygen reduction reaction (ORR) were evaluated by the rotating ring-disk electrode technique. The results showed that the 4% CeO2/C prepared by the PPM was the best composite for the production of H2O2 in a 1 mol L-1 NaOH electrolyte solution. For this material, the number of electrons transferred and the H2O2 percentage efficiency were 3.1 and 44%, respectively. The ring-current of the 4% CeO2/C was higher than that of Vulcan carbon, the reference material for H2O2 production, which produced 41% H2O2 and transferred 3.1 electrons per molecule of oxygen. The overpotential for this reaction on the ceria-based catalyst was substantially lower (approximately 200 mV), demonstrating the higher catalytic performance of this material. Gas diffusion electrodes (GDE) containing the catalyst were used to evaluate the real amount of H2O2 produced during exhaustive electrolysis. The 4% CeO2/C GDE produced 871 mg L-1 of H2O2, whereas the Vulcan carbon GDE produced a maximum amount of only 407 mg L-1. Thus, the 4% CeO2/C electrocatalyst prepared by the PPM is a promising material for H2O2 electrogeneration in alkaline media. (C) 2011 Elsevier B.V. All rights reserved.

Effect of endogenous hydrogen sulfide inhibition on structural and functional renal disturbances induced by gentamicin

Animal models of gentamicin nephrotoxicity present acute tubular necrosis associated with inflammation, which can contribute to intensify the renal damage. Hydrogen sulfide (H2S) is a signaling molecule involved in inflammation. We evaluated the effect of DL-propargylglycine (PAG), an inhibitor of endogenous H2S formation, on the renal damage induced by gentamicin. Male Wistar rats (N = 8) were injected with 40 mg/kg gentamicin (im) twice a day for 9 days, some of them also received PAG (N = 8, 10 mg·kg-1·day-1, ip). Control rats (N = 6) were treated with saline or PAG only (N = 4). Twenty-four-hour urine samples were collected one day after the end of these treatments, blood samples were collected, the animals were sacrificed, and the kidneys were removed for quantification of H2S formation and histological and immunohistochemical studies. Gentamicin-treated rats presented higher sodium and potassium fractional excretion, increased plasma creatinine [4.06 (3.00; 5.87) mg%] and urea levels, a greater number of macrophages/monocytes, and a higher score for tubular interstitial lesions [3.50 (3.00; 4.00)] in the renal cortex. These changes were associated with increased H2S formation in the kidneys from gentamicin-treated rats (230.60 ± 38.62 µg·mg protein-1·h-1) compared to control (21.12 ± 1.63) and PAG (11.44 ± 3.08). Treatment with PAG reduced this increase (171.60 ± 18.34), the disturbances in plasma creatinine levels [2.20 (1.92; 4.60) mg%], macrophage infiltration, and score for tubular interstitial lesions [2.00 (2.00; 3.00)]. However, PAG did not interfere with the increase in fractional sodium excretion provoked by gentamicin. The protective effect of PAG on gentamicin nephrotoxicity was related, at least in part, to decreased H2S formation.

Local Structure of Hydrogen-Bonded Liquids

Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding. This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified. Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.

Massenspektrometrische Wasserdampfmessung in der oberen Troposphäre und unteren Stratosphäre

Diese Arbeit beschreibt die Entwicklung des flugzeuggetragenen Atmosphärischen Ionisations-Massenspektrometers AIMS-H2O zur Messung von Wasserdampf in der oberen Troposphäre und unteren Stratosphäre (UTLS) und erste Flugzeugmessungen mit dem Instrument. Wasserdampf beeinflusst das Klima in der UTLS aufgrund seiner Strahlungseigenschaften und agiert als wichtiger Parameter bei der Bildung von Zirruswolken und Kondensstreifen. Deshalb sind genaue Wasserdampfmessungen für das Verständnis vieler atmosphärischer Prozesse unerlässlich. Instrumentenvergleiche wie sie im SPARC Report No. 2 und dem Bericht der AUQAVIT Kampagne zusammengefasst sind, haben gezeigt, dass große Abweichungen zwischen einzelnen Methoden und Instrumenten bestehen. Diese Unsicherheiten limitieren das Verständnis des Einflusses von Wasserdampf auf die Dynamik und die Strahlungseigenschaften in der UTLS. Die in dieser Arbeit vorgestellte Entwicklung einer neuen Messmethode für Wasserdampf mit dem Massenspektrometer AIMS-H2O ist deshalb auf die genaue Messung niedriger Wasserdampfkonzentrationen in der UTLS fokussiert. Mit AIMS H2O wird Umgebungsluft in einer neu entwickelten Gasentladungsquelle ionisiert. Durch eine Reihe von Ionen-Molekül-Reaktionen entstehen H3O+(H2O) und H3O+(H2O)2 Ionen. Diese Ionen werden genutzt, um die Wasserdampfkonzentration in der Atmosphäre zu bestimmen. Um die erforderliche hohe Genauigkeit zu erzielen, wird AIMS H2O im Flug kalibriert. In dem zu diesem Zweck aufgebauten Kalibrationsmodul wird die katalytische Reaktion von Wasserstoff und Sauerstoff auf einer Platinoberfläche genutzt, um definierte Wasserdampfkonzentrationen für die Kalibration im Flug zu erzeugen. Bei ersten Messungen auf der Falcon während der Kampagne CONCERT 2011 konnte dabei eine Genauigkeit von 8 bis 15% für die Messung der Wasserdampfkonzentration in einem Messbereich von 0,5 bis 250 ppmv erreicht werden. Die Messfrequenz betrug 4 Hz, was einer räumlichen Auflösung von etwa 50 m entspricht. Der Vergleich der Messung des Massenspektrometers mit dem Laserhygrometer Waran zeigt eine sehr gute Übereinstimmung im Rahmen der Unsicherheiten. Anhand zweier Fallstudien werden die Messungen von AIMS H2O während CONCERT 2011 detailliert analysiert. In der ersten Studie werden zwei Flüge in eine stratosphärische Intrusion über Nordeuropa untersucht. In dieser Situation wurde stratosphärische Luft bis hinunter auf 6 km Höhe transportiert und war dadurch mit der Falcon erreichbar. Es konnte gezeigt werden, dass AIMS-H2O sehr gut für die genaue Messung niedriger Wasserdampfkonzentrationen, in diesem Fall bis etwa 3,5 ppmv, geeignet ist. Der Vergleich der Messung mit Analysen des ECMWF Integrated Forecast Systems zeigt eine gute Übereinstimmung der gemessenen Wasserdampfstrukturen mit der dynamischen Tropopause. Unterschiede tauchen dagegen beim Vergleich der Wasserdampfkonzentrationen in der unteren Stratosphäre auf. Hier prognostiziert das Modell deutlich höhere Feuchten. Die zweite Fallstudie beschäftigt sich mit der Verteilung der relativen Feuchte in jungen Kondensstreifen im Vergleich zu ihrer direkten Umgebung. Dabei wurde für drei Messsequenzen im Abgasstrahl von Flugzeugen beobachtet, dass die relative Feuchte innerhalb des Kondensstreifens im Vergleich zur Umgebung sowohl bei unter- als auch übersättigten Umgebungsbedingungen in Richtung Sättigung verschoben ist. Die hohe Anzahl an Eispartikeln und die damit verbundene große Eisoberfläche in jungen Kondensstreifen führt also zu einer schnellen Relaxation von Gasphase und Eis in Richtung Gleichgewicht. In der Zukunft soll AIMS-H2O auch auf HALO für die genaue Messung von Wasserdampf bei ML-CIRRUS und weiteren Kampagnen eingesetzt werden.

Reflection of solar wind hydrogen from the lunar surface

The solar wind continuously flows out from the Sun and directly interacts with the surfaces of dust and airless planetary bodies throughout the solar system. A significant fraction of solar wind ions reflect from an object's surface as energetic neutral atoms (ENAs). ENA emission from the Moon was first observed during commissioning of the Interstellar Boundary Explorer (IBEX) mission on 3 December 2008. We present the analysis of 10 additional IBEX observations of the Moon while it was illuminated by the solar wind. For the viewing geometry and energy range (> 250 eV) of the IBEX-Hi ENA imager, we find that the spectral shape of the ENA emission from the Moon is well-represented by a linearly decreasing flux with increasing energy. The fraction of the incident solar wind ions reflected as ENAs, which is the ENA albedo and defined quantitatively as the ENA reflection coefficient RN, depends on the incident solar wind speed, ranging from ~0.2 for slow solar wind to ~0.08 for fast solar wind. The average energy per incident solar wind ion that is reflected to space is 30 eV for slow solar wind and 45 eV for fast solar wind. Once ionized, these ENAs can become pickup ions in the solar wind with a unique spectral signature that reaches 3vSW. These results apply beyond the solar system; the reflection process heats plasmas that have significant bulk flow relative to interstellar dust and cools plasmas having no net bulk flow relative to the dust.

A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1

The 3.0-Å structure of a 190-residue fragment of intercellular adhesion molecule-1 (ICAM-1, CD54) reveals two tandem Ig-superfamily (IgSF) domains. Each of two independent molecules dimerizes identically with a symmetry-related molecule over a hydrophobic interface on the BED sheet of domain 1, in agreement with dimerization of ICAM-1 on the cell surface. The residues that bind to the integrin LFA-1 are well oriented for bivalent binding in the dimer, with the critical Glu-34 residues pointing away from each other on the periphery. Residues that bind to rhinovirus are in the flexible BC and FG loops at the tip of domain 1, and these and the upper half of domain 1 are well exposed in the dimer for docking to virus. By contrast, a residue important for binding to Plasmodium falciparum-infected erythrocytes is in the dimer interface. The presence of A′ strands in both domains 1 and 2, conserved hydrogen bonds at domain junctions, and elaborate hydrogen bond networks around the key integrin binding residues in domain 1 make these domains suited to resist tensile forces during adhesive interactions. A subdivision of the intermediate (I) set of IgSF domains is proposed in which domain 1 of ICAM-1 and previously described I set domains belong to the I1 set and domain 2 of ICAM-1, ICAM-2, and vascular cell adhesion molecule-1 belong to the I2 set.

On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions

The electronic nature of low-barrier hydrogen bonds (LBHBs) in enzymatic reactions is discussed based on combined low temperature neutron and x-ray diffraction experiments and on high level ab initio calculations by using the model substrate benzoylacetone. This molecule has a LBHB, as the intramolecular hydrogen bond is described by a double-well potential with a small barrier for hydrogen transfer. From an “atoms in molecules” analysis of the electron density, it is found that the hydrogen atom is stabilized by covalent bonds to both oxygens. Large atomic partial charges on the hydrogen-bonded atoms are found experimentally and theoretically. Therefore, the hydrogen bond gains stabilization from both covalency and from the normal electrostatic interactions found for long, weak hydrogen bonds. Based on comparisons with other systems having short-strong hydrogen bonds or LBHBs, it is proposed that all short-strong and LBHB systems possess similar electronic features of the hydrogen-bonded region, namely polar covalent bonds between the hydrogen atom and both heteroatoms in question.

Chemical synthesis of the precursor molecule of the Aequorea green fluorescent protein, subsequent folding, and development of fluorescence

The present paper describes the total chemical synthesis of the precursor molecule of the Aequorea green fluorescent protein (GFP). The molecule is made up of 238 amino acid residues in a single polypeptide chain and is nonfluorescent. To carry out the synthesis, a procedure, first described in 1981 for the synthesis of complex peptides, was used. The procedure is based on performing segment condensation reactions in solution while providing maximum protection to the segment. The effectiveness of the procedure has been demonstrated by the synthesis of various biologically active peptides and small proteins, such as human angiogenin, a 123-residue protein analogue of ribonuclease A, human midkine, a 121-residue protein, and pleiotrophin, a 136-residue protein analogue of midkine. The GFP precursor molecule was synthesized from 26 fully protected segments in solution, and the final 238-residue peptide was treated with anhydrous hydrogen fluoride to obtain the precursor molecule of GFP containing two Cys(acetamidomethyl) residues. After removal of the acetamidomethyl groups, the product was dissolved in 0.1 M Tris⋅HCl buffer (pH 8.0) in the presence of DTT. After several hours at room temperature, the solution began to emit a green fluorescence (λmax = 509 nm) under near-UV light. Both fluorescence excitation and fluorescence emission spectra were measured and were found to have the same shape and maxima as those reported for native GFP. The present results demonstrate the utility of the segment condensation procedure in synthesizing large protein molecules such as GFP. The result also provides evidence that the formation of the chromophore in GFP is not dependent on any external cofactor.

The Involvement of Hydrogen Peroxide in the Differentiation of Secondary Walls in Cotton Fibers1

H2O2 is a widespread molecule in many biological systems. It is created enzymatically in living cells during various oxidation reactions and by leakage of electrons from the electron transport chains. Depending on the concentration H2O2 can induce cell protective responses, programmed cell death, or necrosis. Here we provide evidence that H2O2 may function as a developmental signal in the differentiation of secondary walls in cotton (Gossypium hirsutum) fibers. Three lines of evidence support this conclusion: (a) the period of H2O2 generation coincided with the onset of secondary wall deposition, (b) inhibition of H2O2 production or scavenging the available H2O2 from the system prevented the wall differentiation process, and (c) exogenous addition of H2O2 prematurely promoted secondary wall formation in young fibers. Furthermore, we provide support for the concept that H2O2 generation could be mediated by the expression of the small GTPase Rac, the accumulation of which was shown previously to be strongly induced during the onset of secondary wall differentiation. In support of Rac's role in the activation of NADPH oxidase and the generation of reactive oxygen species, we transformed soybean (Glycine max) and Arabidopsis cells with mutated Rac genes. Transformation with a dominantly activated cotton Rac13 gene resulted in constitutively higher levels of H2O2, whereas transformation with the antisense and especially with dominant-negative Rac constructs decreased the levels of H2O2.

Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.

DNA fragments with stretches of cytosine residues can fold into four-stranded structures in which two parallel duplexes, held together by hemiprotonated cytosine.cytosine+ (C.C+) base pairs, intercalate into each other with opposite polarity. The structural details of this intercalated DNA quadruplex have been assessed by solution NMR and single crystal x-ray diffraction studies of cytosine-rich sequences, including those present in metazoan telomeres. A conserved feature of these structures is the absence of stabilizing stacking interactions between the aromatic ring systems of adjacent C.C+ base pairs from intercalated duplexes. Effective stacking involves only the exocyclic keto groups and amino groups of the cytidine bases. The apparent absence of stability provided by stacking interactions between the bases in this intercalated DNA has prompted us to examine the available structures in detail, in particular with regard to unusual features that could compensate for the lack of base stacking. In addition to base-on-deoxyribose stacking and intra-cytidine C-H...O hydrogen bonds, this analysis reveals the presence of a hitherto unobserved, systematic intermolecular C-H...O hydrogen bonding network between the deoxyribose sugar moieties of antiparallel backbones in the four-stranded molecule.