Ligand-Induced structural changes in TEM‑1 probed by molecular dynamics and relative binding free energy calculations

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM- 1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70−Oγ and Lys73−Nζ, Lys73−Nζ and Ser130−Oγ, and Ser70−Oγ−Ser130−Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

Detection of quasi-periodic processes in complex systems: how do we quantitatively describe their properties?

It has been shown that in reality at least two general scenarios of data structuring are possible: (a) a self-similar (SS) scenario when the measured data form an SS structure and (b) a quasi-periodic (QP) scenario when the repeated (strongly correlated) data form random sequences that are almost periodic with respect to each other. In the second case it becomes possible to describe their behavior and express a part of their randomness quantitatively in terms of the deterministic amplitude–frequency response belonging to the generalized Prony spectrum. This possibility allows us to re-examine the conventional concept of measurements and opens a new way for the description of a wide set of different data. In particular, it concerns different complex systems when the ‘best-fit’ model pretending to be the description of the data measured is absent but the barest necessity of description of these data in terms of the reduced number of quantitative parameters exists. The possibilities of the proposed approach and detection algorithm of the QP processes were demonstrated on actual data: spectroscopic data recorded for pure water and acoustic data for a test hole. The suggested methodology allows revising the accepted classification of different incommensurable and self-affine spatial structures and finding accurate interpretation of the generalized Prony spectroscopy that includes the Fourier spectroscopy as a partial case.

Periplasmic nitrate reductases: structural and spectroscopic studies

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica, especialidade Bioquímica-Física, pela Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa

Molybdenum-containing proteins from Sulphate Reducing Bacteria: studying proteins with novel cofactors and revealing new features of old enzymes

Dissertação apresentada para a obtenção do Grau de Doutor em Bioquímica, especialidade de Bioquímica-Física pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Microstructure, mechanical properties and chemical degradation of brazed AISI 316 stainless steel/alumina systems

The main aims of the present study are simultaneously to relate the brazing parameters with: (i) the correspondent interfacial microstructure, (ii) the resultant mechanical properties and (iii) the electrochemical degradation behaviour of AISI 316 stainless steel/alumina brazed joints. Filler metals on such as Ag–26.5Cu–3Ti and Ag–34.5Cu–1.5Ti were used to produce the joints. Three different brazing temperatures (850, 900 and 950 °C), keeping a constant holding time of 20 min, were tested. The objective was to understand the influence of the brazing temperature on the final microstructure and properties of the joints. The mechanical properties of the metal/ceramic (M/C) joints were assessed from bond strength tests carried out using a shear solicitation loading scheme. The fracture surfaces were studied both morphologically and structurally using scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and X-ray diffraction analysis (XRD). The degradation behaviour of the M/C joints was assessed by means of electrochemical techniques. It was found that using a Ag–26.5Cu–3Ti brazing alloy and a brazing temperature of 850 °C, produces the best results in terms of bond strength, 234 ± 18 MPa. The mechanical properties obtained could be explained on the basis of the different compounds identified on the fracture surfaces by XRD. On the other hand, the use of the Ag–34.5Cu–1.5Ti brazing alloy and a brazing temperature of 850 °C produces the best results in terms of corrosion rates (lower corrosion current density), 0.76 ± 0.21 μA cm−2. Nevertheless, the joints produced at 850 °C using a Ag–26.5Cu–3Ti brazing alloy present the best compromise between mechanical properties and degradation behaviour, 234 ± 18 MPa and 1.26 ± 0.58 μA cm−2, respectively. The role of Ti diffusion is fundamental in terms of the final value achieved for the M/C bond strength. On the contrary, the Ag and Cu distribution along the brazed interface seem to play the most relevant role in the metal/ceramic joints electrochemical performance.

A fluorescente bicyclic Calix[4] Arene-Oxacyclophane with planar chirality: Resolution, chiroptical, properties, and absolute configuration.

A new inherently chiral calix[4]arene ICC 1 has been disclosed. The dissymmetry of 1 is generated from a chirality plane in the quinol moiety of a 1,3-bridged bicyclic calix[4]arene. ICC 1 has been resolved by enantioselective HPLC, and the chiroptical properties of both isolated antipodes (pS)-1 and (pR)-1 confirm their enantiomeric nature. The absolute configuration of the (pS)-1/(pR)-1 enantiomeric pair was established through time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (CD) spectra. (C) 2014 Elsevier Ltd. All rights reserved.

Chiroptical and emissive properties of a calix[4]arene-containing chiral poly (P-phenylene ethynylene) with enantioselective recognition ability

Supramolecular chirality was achieved in solutions and thin films of a calixarene-containing chiral aryleneethynylene copolymer. The observed chiroptical activity, which is primarily allied with the formation of aggregates of high molecular weight polymer chains, is the result of a combination of intrachain and interchain effects. The former arises by the adoption of an induced helix-sense by the polymer main-chain while the latter comes from the exciton coupling of aromatic backbone transitions. The co-existence of bulky bis-calixKlarene units and chiral side-chains on the polymer skeleton prevents efficient pi-stacking of neighbouring chains, keeping the chiral assembly highly emissive. In contrast, for a model polymer lacking calixarene moieties, the chiroptical activity is dominated by strong interchain exciton couplings as a result of more favourable packing of polymer chains, leading to a marked decrease of photoluminescence in the aggregate state. The enantiomeric recognition abilities of both polymers towards (R)- and (S)-alpha-methylbenzylamine were examined. It was found that a significant enantiodiscrimination is exhibited by the calixarene-based polymer in the aggregate state.

Homo-and heteropolymetallic 3-(2-pyridyl)pyrazolate manganese and rhenium complexes

fac-[MBr(CO)(3)(pypzH)] (M = Mn, Re; pypzH = (3-(2-pyridyl) pyrazole) complexes are prepared from fac[ MBr(CO)(3)(NCMe)(2)] and pypzH. The result of their deprotonation depends on the metallic substrate: the rhenium complex affords cleanly the bimetallic compound [fac-{Re(CO)(3)(mu(2)-pypz)}] 2 (mu(2)-pypz = mu(2)-3-(2pyridyl-. 1N) pyrazolate-2. 1N), which was crystallographically characterized, whereas a similar manganese complex was not detected. When two equivalents of pyridylpyrazolate are used, polymetallic species [fac-M(CO) 3(mu(2)-pypz)(mu(3)-pypz) M'] (mu(3)-pypz = mu(3)-3-(2-pyridyl-kappa N-1) pyrazolate-1 kappa 2N, N: 2. 1N:; M = Mn, M' = Li, Na, K; M = Re, M' = Na) are obtained. The crystal structures of the manganese carbonylate complexes were determined. The lithium complex is a monomer containing one manganese and one lithium atom, whereas the sodium and potassium complexes are dimers and reveal an unprecedented coordination mode for the bridging 3-(2-pyridyl) pyrazolate ligand, where the nitrogen of the pyridyl fragment and the nitrogen-1 of pyrazolate are chelated to manganese atoms, and each nitrogen-2 of pyrazolate is coordinated to two alkaline atoms. The polymetallic carbonylate complexes are unstable in solution and evolve spontaneously to [fac-{Re(CO) 3(mu(2)-pypz)}](2) or to the trimetallic paramagnetic species [MnII(mu(2)-pypz) 2{fac-{MnI(CO) 3(mu(2)-pypz)}(2)}]. The related complex cis-[MnCl2(pypzH)(2)] was also synthesized and structurally characterized. The electrochemical behavior of the new homo-and heteropolymetallic 3-(2-pyridyl) pyrazolate complexes has been studied and details of their redox properties are reported.

NiII, CuII and ZnII complexes with a sterically hindered scorpionate ligand (TpmsPh) and catalytic application in the diasteroselective nitroaldol (Henry) reaction

The Ni-II and Zn-II complexes [MCl(Tpms(Ph))] (Tpms(Ph) = SO3C(pz(Ph))(3), pz = pyrazolyl; M = Ni 2 or Zn 3) and the Cu-II complex [CuCl(Tpms(Ph))(H2O)] (4) have been prepared by treatment of the lithium salt of the sterically demanding and coordination flexible tris(3-phenyl-1-pyrazolyl)methanesulfonate (Tpms(Ph))(-) (1) with the respective metal chlorides. The (Tpms(Ph))(-) ligand shows the N-3 or N2O coordination modes in 2 and 3 or in 4, respectively. Upon reaction of 2 and 3 with Ag(CF3SO3) in acetonitrile the complexes [M(Tpms(Ph))-(MeCN)](CF3SO3) (M = Ni 5 or Zn 6, respectively) were formed. The compounds were obtained in good yields and characterized by analytic and spectral (IR, H-1 and C-13{H-1} NMR, ESI-MS) data, density functional theory (DFT) methods and {for 4 and [(Bu4N)-Bu-n](Tpms(Ph)) (7), the tatter obtained upon Li+ replacement by [(Bu4N)-Bu-n](+) in Li(Tpms(Ph))} by single crystal X-ray diffraction analysis. The Zn-II and Cu-II complexes (3 and 4, respectively) act as efficient catalyst precursors for the diastereoselective nitroaldol reaction of benzaldehydes and nitroethane to the corresponding beta-nitroalkanols (up to 99% yield, at room temperature) with diastereoselectivity towards the formation of the anti isomer, whereas the Ni-II complex 2 only shows a modest catalytic activity.

Micro – and nanofibers and liquid crystals for ligth-scattering shutters: Simulation of electrp-optical properties

This work demonstrates the feasibility of using polymeric micro- and nanofiber-composed films and liquid crystals as electrically switchable scattering light shutters. We present a concept of electro-optic device based on an innovative combination of two mature technologies: optics of nematic liquid crystals and electrospinning of nanofibers. These devices have electric and optical characteristics far superior to other comparable methods. The simulation presented shows results that are highly consistent with those of experiments and that explain the working mechanism of the devices.

Synthesis of Sub-5 NM Co-Doped SnO2 nanoparticles and their structural microstructural, optical and photocatalytic properties

A swift chemical route to synthesize Co-doped SnO2 nanopowders is described. Pure and highly stable Sn1-xCoxO2-delta (0 <= x <= 0.15) crystalline nanoparticles were synthesized, with mean grain sizes <5 nm and the dopant element homogeneously distributed in the SnO2 matrix. The UV-visible diffuse reflectance spectra of the Sn1-xCoxO2-delta samples reveal red shifts, the optical bandgap energies decreasing with increasing Co concentration. The samples' Urbach energies were calculated and correlated with their bandgap energies. The photocatalytic activity of the Sn1-xCoxO2-delta samples was investigated for the 4-hydroxylbenzoic acid (4-HBA) degradation process. A complete photodegradation of a 10 ppm 4-HBA solution was achieved using 0.02% (w/w) of Sn0.95Co0.05O2-delta nanoparticles in 60 min of irradiation. (C) 2014 Elsevier B.V. All rights reserved.

Probabilistic models for mechanical properties of prestressing strands

This study focus on the probabilistic modelling of mechanical properties of prestressing strands based on data collected from tensile tests carried out in Laboratório Nacional de Engenharia Civil (LNEC), Portugal, for certification purposes, and covers a period of about 9 years of production. The strands studied were produced by six manufacturers from four countries, namely Portugal, Spain, Italy and Thailand. Variability of the most important mechanical properties is examined and the results are compared with the recommendations of the Probabilistic Model Code, as well as the Eurocodes and earlier studies. The obtained results show a very low variability which, of course, benefits structural safety. Based on those results, probabilistic models for the most important mechanical properties of prestressing strands are proposed.

Mechanical properties of stent-graft materials

An aneurysm is a localized blood-filled dilatation of an artery whose consequences can be deadly. One of its current treatments is endovascular aneurysm repair, a minimally invasive procedure in which an endoprosthesis, called a stent-graft, is placed transluminally to prevent wall rupture. Early stent-grafts were custom designed for the patient through the assembling of off-the-shelf components by the operating surgeon. However, nowadays, stent-grafts have become a commercial product. The existing endoprostheses differ in several aspects, such as shape design and materials, but they have in common a metallic scaffold with a polymeric covering membrane. This article aims to gather relevant information for those who wish to understand the principles of stent-grafts and even to develop new devices. Hence, a stent-graft classification based on different characteristics is presented and the desired features for an ideal device are pointed out. Additionally, the materials currently in use to fabricate this type of endoprosthesis are reviewed and new materials are suggested.

Calix[4]arene-carbazole-containing polymers: synthesis and properties

New highly fluorescent calix[4]arene-containing phenylene-alt-ethynylene-3,6- and 2,7-carbazolylene polymers (CALIX-PPE-CBZs) have been synthesized for the first time and their photophysical properties evaluated. Both polymers were obtained in good isolated yields (70-84%), having M-w ranging from 7660-26,700 g mol(-1). It was found that the diethynyl substitution (3,6- or 2,7-) pattern on the carbazole monomers markedly influences the degree of polymerization. The amorphous yellow polymers are freely soluble in several nonprotic organic solvents and have excellent film forming abilities. TG/DSC analysis evidences similar thermal behaviors for both polymers despite their quite different molecular weight distributions and main-chain connectivities (T-g, in the range 83-95 degrees C and decomposition onsets around 270 degrees C). The different conjugation lengths attained by the two polymers dictates much of their photophysical properties. Thus, whereas the fully conjugated CALIX-PPE-2,7-CBZ has its emission maximum at 430 nm (E-g = 2.84 eV; Phi(F) = 0.62, CHCl3), the 3,6-linked counterpart (CALIX-PPE-3,6-CBZ) fluoresces at 403 nm with a significant lower quantum yield (E-g = 3.06 eV; Phi(F) = 0.31, CHCl3). The optical properties of both polymers are predominantly governed by the intrachain electronic properties of the conjugated backbones owing to the presence of calix[4]arenes along the polymer chain which disfavor significant interchain interactions, either in fluid- or solid-state.

Molybdenum – and tungsten(II) monometallic 3-(2-pyridyl)pyrazole and bimetallic 3-(2-pyridyl)pyrazolate complexes

Molybdenum and tungsten complexes containing the pypzH (3-(2-pyridyl)pyrazole) ligand as a chelating bidentate are prepared: [Mo(CO)(4)(pypzH)], cis-[MoBr(eta(3)-allyl)(CO)(2)(pypzH)], cis-[MoCl(eta(3)-methallyl)(CO)(2)(pypzH)], [MI2(CO)(3)(pypzH)] (M = Mo, W) from [Mo(CO)(4)(NBD)] or the adequate bis(acetonitrile) complexes. The deprotonation of the molybdenum allyl or methallyl complexes affords the bimetallic complexes [cis-{Mo(eta(3)-allyl)(CO)(2)(mu(2)-pypz)}](2) or [cis-{Mo(eta(3)-methallyl)(CO)(2)(mu(2)-pypz)}](2) (mu(2)-pypz = mu(2)-3-(2-pyridyl-kappa N-1) pyrazolate-2 kappa N-1). The allyl complex was subjected to an electrochemical study, which shows a marked connection between both metallic centres through the bridging pyridylpyrazolates.