Reactive electron scattering from biomolecules and technologically relevant molecules

The role of a set of gases relevant within the context of biomolecules and technologically relevant molecules under the interaction of low-energy electrons was studied in an effort to contribute to the understanding of the underlying processes yielding negative ion formation. The results are relevant within the context of damage to living material exposed to energetic radiation, to the role of dopants in the ion-molecule chemistry processes, to Electron Beam Induced Deposition (EBID) and Ion Beam Induced Deposition (IBID) techniques. The research described in this thesis addresses dissociative electron attachment (DEA) and electron transfer studies involving experimental setups from the University of Innsbruck, Austria and Universidade Nova de Lisboa, Portugal, respectively. This thesis presents DEA studies, obtained by a double focusing mass spectrometer, of dimethyl disulphide (C2H6S2), two isomers, enflurane and isoflurane (C3F5Cl5) and two chlorinated ethanes, pentachloroethane (C2HCl5) and hexachloroethane (C2Cl6), along with quantum chemical calculations providing information on the molecular orbitals as well as thermochemical thresholds of anion formation for enflurane, isoflurane, pentachloroethane and hexachloroethane. The experiments represent the most accurate DEA studies to these molecules, with significant differences from previous work reported in the literature. As far as electron transfer studies are concerned, negative ion formation in collisions of neutral potassium atoms with N1 and N3 methylated pyrimidine molecules were obtained by time-of-flight mass spectrometry (TOF). The results obtained allowed to propose concerted mechanisms for site and bond selective excision of bonds.

Twin peak distribution of electron emission profile and impact ionization of ambient molecules during laser ablation of silver target

Laser-induced plasma generated from a silver target under partial vacuum conditions using the fundamental output of nanosecond duration from a pulsed Nd:yttrium aluminum garnet laser is studied using a Langmuir probe. The time of flight measurements show a clear twin peak distribution in the temporal profile of electron emission. The first peak has almost the same duration as the laser pulse while the second lasts for several microseconds. The prompt electrons are energetic enough ('60 eV) to ionize the ambient gas molecules or atoms. The use of prompt electron pulses as sources for electron impact excitation is demonstrated by taking nitrogen, carbon dioxide, and argon as ambient gases.

Transition metal atoms encapsulated in adamantane molecules

We performed a first principles total energy investigation on the structural, electronic, and magnetic properties of 3d-transition metal-encapsulated adamantane molecules (TM@C(10)H(16). with TM = Cr, Mn, Fe, Co, and Ni). We find that the C-C interactions are strong enough to maintain the molecular rigidity upon TM incorporation, although outward relaxations and formation energies are large. We built a microscopic model that explains the electronic structure of those molecules. (C) 2011 Elsevier B.V. All rights reserved.

Radiative association of C and P, and Si and P atoms

The rate coefficients for the formation of carbon monophosphide (CP) and silicon monophosphide (SiP) by radiative association are estimated for temperatures ranging from 300 to 14 100 K. In this temperature range, the radiative association rate coefficients are found to vary from 1.14 x 10(-18) to 1.62 x 10(-18) cm(3) s(-1) and from 3.73 x 10(-20) to 7.03 x 10(-20) cm(3) s(-1) for CP and SiP, respectively. In both cases, rate coefficients increase slowly with the increase in temperature.

Radiative association of Ti and O atoms

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Radiative association of Ti and O atoms

Rate coefficients for the radiative association of titanium and oxygen atoms to form the titanium monoxide (TiO) molecule are estimated. The radiative association of Ti(F-3) and O(P-3) atoms is dominated by an approach along the C-3 Delta potential energy curve, accompanied by spontaneous emission into the X-3 Delta ground state of TiO. For temperatures ranging from 300-14 000 K, the total rate coefficients are found to vary from 4.76 x 10(-17) to 9.96 x 10(-17) cm(3) s(-1), respectively.

Identification of adsorbed molecules via STM tip manipulation: CO, H₂O, and O₂ on TiO₂ anatase (101)

While Scanning Tunneling Microscopy (STM) has evolved as an ideal tool to study surface chemistry at the atomic scale, the identification of adsorbed species is often not straightforward. This paper describes a way to reliably identify H2O, CO and O2 on the TiO2 anatase (101) surface with STM. These molecules are of a key importance in the surface chemistry of this and many other (photo-) catalytic materials. They exhibit a wide variety of contrasts in STM images, depending on the tip condition. With clean, metallic tips the molecules appear very similar, i.e., as bright, dimer-like features located in the proximity of surface Ti5c atoms. However, each species exhibits a specific response to the electric field applied by the STM tip. It is shown that this tip–adsorbate interaction can be used to reliably ascertain the identity of such species. The tip–adsorbate interactions, together with comparison of experimental and calculated STM images, are used to analyse and revisit the assignments of molecular adsorbed species reported in recent studies.

Transport and Distribution of Hydroxyl Radicals and Oxygen Atoms from H2O Photodissociation in the Inner Coma of Comet 67P/Churyumov-Gerasimenko

With a combination of the Direct Simulation Monte Carlo (DSMC) calculation and test particle computation, the ballistic transport process of the hydroxyl radicals and oxygen atoms produced by photodissociation of water molecules in the coma of comet 67P/Churyumov-Gerasimenko is modelled. We discuss the key elements and essential features of such simulations which results can be compared with the remote-sensing and in situ measurements of cometary gas coma from the Rosetta mission at different orbital phases of this comet.

The invariant system of coordinates of antibody molecules: prediction of the "standard" C alpha framework of VL and VH domains.

A new approach of comparing protein structures that does not involve the procedure of superposition is suggested. An invariant system of coordinates for immunoglobulin molecules that is based on the geometrical symmetry inherent to the variable domain light-chain (VL)-heavy-chain (VH) complex is described. The coordinates of the Calpha atoms in 22 immunoglobulin structures are calculated in the invariant system of coordinates. We found that 76 identical positions in this Calpha framework are symmetrical about the twofold axis. Comparison of the identical positions in these molecules allows us to select 96 positions in the light chains and 87 positions in the heavy chains whose Calpha atom coordinates are approximately the same. To check whether the average coordinates of Calpha atoms in these positions complies with the stereochemical requirements, we calculated Calpha-Calpha distances. Seventy-three positions of the light chains and 72 positions of the heavy chains satisfy the Calpha-Calpha distance criterion. The Calpha atoms in these positions are used for constructing the "standard" Calpha framework of VL and VH complexes. The average coordinates of Calpha atoms are presented.

Disarray Of Glomerular And Tubular Cell Adhesion Molecules In The Course Of Experimental Bothrops Moojeni Envenomation.

In this study, we show that administration of Bothrops moojeni venom in rats induces a general disturbance in the distribution and content of the tight junctional protein ZO-1, the cell-matrix receptor beta 1 integrin, the cytoskeletal proteins, vinculin and F-actin, and of the extracellular matrix component laminin in renal corpuscles and cortical nephron tubules. These findings suggest that cell-cell and cell-matrix adhesion proteins may be molecular targets in the B. moojeni-induced kidney injury.

Lsa21, a novel leptospiral protein binding adhesive matrix molecules and present during human infection

Background: It has been well documented over past decades that interaction of pathogens with the extracellular matrix (ECM) plays a primary role in host cell attachment and invasion. Adherence to host tissues is mediated by surface-exposed proteins expressed by the microorganisms during infection. The mechanisms by which pathogenic leptospires invade and colonize the host remain poorly understood since few virulence factors contributing to the pathogenesis of the disease have been identified. Whole-genome sequencing analysis of L. interrogans allowed identification of a repertoire of putative leptospiral surface proteins. Results: Here, we report the identification and characterization of a new leptospiral protein that exhibits extracellular matrix-binding properties, called as Lsa21 (leptospiral surface adhesin, 21 kDa). Compatible with its role in adhesion, the protein was shown to be surface-exposed by indirect immunofluorescence. Attachment of Lsa21 to laminin, collagen IV, and plasma fibronectin was specific and dose dependent. Laminin oxidation by sodium metaperiodate reduced the protein-laminin interaction in a concentration-dependent manner, indicating that laminin sugar moieties are crucial for this interaction. The gene coding for Lsa21 is present in pathogenic strains belonging to the L. interrogans species but was not found in the saprophytic L. biflexa serovar Patoc strain Patoc 1. Loss of gene expression occurs upon culture attenuation of pathogenic strains. Environmental factors such as osmolarity and temperature affect Lsa21 expression at the transcriptional level. Moreover, anti-Lsa21 serum labeled liver and kidney tissues of human fatal cases of leptospirosis. Conclusion: Our data suggest a role of Lsa21 in the pathogenesis of leptospirosis.

Characterization of Novel OmpA-Like Protein of Leptospira interrogans That Binds Extracellular Matrix Molecules and Plasminogen

Leptospira interrogans is the etiological agent of leptospirosis, a zoonotic disease of human and veterinary concern. The identification of novel proteins that mediate host-pathogen interactions is important for understanding the bacterial pathogenesis as well as to identify protective antigens that would help fight the disease. We describe in this work the cloning, expression, purification and characterization of three predicted leptospiral membrane proteins, LIC10258, LIC12880 (Lp30) and LIC12238. We have employed Escherichia coli BL21 (SI) strain as a host expression system. Recently, we have identified LIC12238 as a plasminogen (PLG)-binding receptor. We show now that Lp30 and rLIC10258 are also PLG-receptors of Leptospira, both exhibiting dose-dependent and saturating binding (K(D), 68.8 +/- 25.2 nM and 167.39 +/- 60.1 nM, for rLIC10258 and rLIC12880, respectively). In addition, LIC10258, which is a novel OmpA-like protein, binds laminin and plasma fibronectin ECM molecules and hence, it was named Lsa66 (Leptospiral surface adhesin of 66 kDa). Binding of Lsa66 to ECM components was determined to be specific, dose-dependent and saturable, with a KD of 55.4 +/- 15.9 nM to laminin and of 290.8 +/- 11.8 nM to plasma fibronectin. Binding of the recombinant proteins to PLG or ECM components was assessed by using antibodies against each of the recombinant proteins obtained in mice and confirmed by monoclonal anti-polyhistidine antibodies. Lsa66 caused partial inhibition on leptospiral adherence to immobilized ECM and PLG. Moreover, this adhesin and rLIC12238 are recognized by antibodies in serum samples of confirmed leptospirosis cases. Thus, Lsa66 is a novel OmpA-like protein with dual activity that may promote the attachment of Leptospira to host tissues and may contribute to the leptospiral invasion. To our knowledge, this is the first leptospiral protein with ECM and PLG binding properties reported to date.

T cells, adhesion molecules and modulation of apoptosis in visceral leishmaniasis glomerulonephritis

Background: Immune complex deposition is the accepted mechanism of pathogenesis of VL glomerulopathy however other immune elements may participate. Further in the present study, no difference was seen between immunoglobulin and C3b deposit intensity in glomeruli between infected and non-infected dogs thus T cells, adhesion molecules and parameters of proliferation and apoptosis were analysed in dogs with naturally acquired VL from an endemic area. The dog is the most important domestic reservoir of the protozoa Leishmania (L.) chagasi that causes visceral leishmaniasis (VL). The similarity of VL manifestation in humans and dogs renders the study of canine VL nephropathy of interest with regard to human pathology. Methods: From 55 dogs with VL and 8 control non-infected dogs from an endemic area, kidney samples were analyzed by immunohistochemistry for immunoglobulin and C3b deposits, staining for CD4+ and CD8+ T cells, ICAM-1, P-selectin and quantified using morphometry. Besides proliferation marker Ki-67, apoptosis markers M30 and TUNEL staining, and related cytokines TNF-alpha, IL-1 alpha were searched and quantified. Results: We observed similar IgG, IgM and IgA and C3b deposit intensity in dogs with VL and non-infected control dogs. However we detected the Leishmania antigen in cells in glomeruli in 54, CD4+ T cells in the glomeruli of 44, and CD8+ T cells in 17 of a total of 55 dogs with VL. Leishmania antigen was absent and T cells were absent/scarse in eight non-infected control dogs. CD 4+ T cells predominate in proliferative patterns of glomerulonephritis, however the presence of CD4+ and CD8+ T cells were not different in intensity in different patterns of glomerulonephritis. The expression of ICAM-1 and P-selectin was significantly greater in the glomeruli of infected dogs than in control dogs. In all patterns of glomerulonephritis the expression of ICAM-1 ranged from minimum to moderately severe and P-selectin from absent to severe. In the control animals the expression of these molecules ranged from absent to medium intensity. It was not observed any correlation between severity of the disease and these markers. There was a correlation between the number of Leishmania antigen positive cells and CD4+ T cells, and between the number of CD4+ T cells and CD8+ T cells. In dogs presenting different histopathological patterns of glomerulonephritis, parameters of proliferation and apoptosis were studied. Ki-67, a proliferative marker, was not detected locally, but fewer apoptotic cells and lower TNF-alpha expression were seen in infected animals than in non-infected controls. Conclusion: Immunopathogenic mechanisms of VL glomerulonephritis are complex and data in the present study suggest no clear participation of immunoglobulin and C3b deposits in these dogs but the possible migration of CD4+ T cells into the glomeruli, participation of adhesion molecules, and diminished apoptosis of cells contributing to determine the proliferative pattern of glomerulonephritis in VL.

Radio-frequency spectroscopy of (6)Li p-wave molecules: Towards photoemission spectroscopy of a p-wave superfluid

We study rf spectroscopy of a lithium gas with the goal to explore the possibilities for photoemission spectroscopy of a strongly interacting p-wave Fermi gas. Radio-frequency spectra of quasibound p-wave molecules and of free atoms in the vicinity of the p-wave Feshbach resonance located at 159.15G are presented. The spectra are free of detrimental final-state effects. The observed relative magnetic-field shifts of the molecular and atomic resonances confirm earlier measurements realized with direct rf association. Furthermore, evidence of molecule production by adiabatically ramping the magnetic field is observed. Finally, we propose the use of a one-dimensional optical lattice to study anisotropic superfluid gaps as most direct proof of p-wave superfluidity.

Crystallization and preliminary X-ray diffraction analysis of recombinant chlorocatechol 1,2-dioxygenase from Pseudomonas putida

Chlorocatechol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida (Pp 1,2-CCD) is considered to be an important biotechnological tool owing to its ability to process a broad spectrum of organic pollutants. In the current work, the crystallization, crystallographic characterization and phasing of the recombinant Pp 1,2-CCD enzyme are described. Reddish-brown crystals were obtained in the presence of polyethylene glycol and magnesium acetate by utilizing the vapour-diffusion technique in sitting drops. Crystal dehydration was the key step in obtaining data sets, which were collected on the D03B-MX2 beamline at the CNPEM/MCT - LNLS using a MAR CCD detector. Pp 1,2-CCD crystals belonged to space group P6(1)22 and the crystallographic structure of Pp 1,2-CCD has been solved by the MR-SAD technique using Fe atoms as scattering centres and the coordinates of 3-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus (PDB entry 2boy) as the search model. The initial model, which contains three molecules in the asymmetric unit, has been refined to 3.4 A resolution.