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112. Pursuing the stabilisation of crystalline nanostructured magnetic manganites through a green low temperature hydrothermal synthesisArianna Minelli, Paolo Dolcet, Stefano Diodati, Sandra Gardonio, Claudia Innocenti, Denis Badocco, Stefano Gialanella, Paolo Pastore, Luciano Pandolfo, Andrea Caneschi, Angela Trapanati, Silvia Gross, 2017, izvirni znanstveni članek Opis: A quick, easy and green water-based synthesis protocol involving coprecipitation of oxalates combined with hydrothermal treatment resulted in the crystallisation of nanostructured manganites at a relatively low temperature (180 °C). The subcritical hydrothermal approach was shown to play a key role in stabilising phases which are generally achieved at much higher temperatures and under harsher conditions, thus disclosing an exciting alternative for their synthesis. Through this mild wet chemistry approach, the compounds CuMnO2, ZnMn2O4 and ZnMnO3 were synthesised as nanocrystalline powders. Noticeably, the optimised route proved to be effective in stabilising the exotic polymorph cubic spinel ZnMnO3 in pure form. This is particularly notable, as very few records concerning this compound are available in the literature. The compounds were fully characterised from compositional, structural, morphological and magnetic points of view.
Ključne besede: nanostructured manganites, low temperature wet chemistry synthesis
Objavljeno v RUNG: 28.03.2017; Ogledov: 4366; Prenosov: 0
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113. Vpliv metformina in sorodnih ksenobiotikov na viabilnost celic raka dojkeSara Klemenčič, 2017, diplomsko delo Opis: Farmacevtska industrija se danes med drugim sooča tudi z negativnimi vplivi svojih proizvodov na okolje. Tak primer je metformin, ki spada med najpogosteje predpisana zdravila v procesih zdravljenja diabetesa tipa II in je hkrati v fazi kliničnih raziskav kot zdravilo za zdravljenje rakavih obolenj. Deluje tako, da zavira celično dihanje, niža proizvodnjo ATP in aktivira z AMP-aktivirano protein kinazo (AMPK), ki je glavni metabolični senzor v evkariontskih celicah. V diplomskem delu smo želeli ugotoviti, ali metformin in sorodni ksenobiotiki, povezani z delovanjem AMPK (spojina C in bromokrotonska kislina), vplivajo na rast visoko invazivnih celic adenokarcinoma dojke MDA-MB-231. To smo storili s pomočjo spektrofluorimetričnega testa viabilnosti z barvilom Presto Blue, ki temelji na sposobnosti zdravih celic, da reducirajo barvilo po vstopu v celico. Pokazali smo, da obstaja linearna zveza med številom celic MDA-MB-231 v populaciji in fluorescenčnim signalom barvila, kar potrjuje ustreznost izbrane metode. Celice smo gojili 48 h pri optimalnih pogojih in v prisotnosti različnih koncentracij vsake od treh učinkovin. Pokazali smo, da viabilnost celic pojema z naraščanjem koncentracije učinkovine. Rezultati kažejo, da inhibicija kataboličnih in oksidativnih procesov v celici (mitohondrijsko dihanje, oksidacija maščobnih kislin in aktivacija AMPK) negativno vpliva na rast in preživetje celic MDA-MB-231. Z našimi rezultati smo prispevali k boljšemu razumevanju mehanizma delovanja metformina in sorodnih zdravilnih učinkovin usmerjenih proti kataboličnemu metabolizmu.
Ključne besede: viabilnost, metformin, bromokrotonska kislina, spojina C, dorzomorfin, AMPK, rak dojke, MDA-MB-231
Objavljeno v RUNG: 31.01.2017; Ogledov: 14182; Prenosov: 242
 Celotno besedilo (1,08 MB) |
114. Formation of Hybrid Electronic States in FePc Chains Mediated by the Au(110) SurfaceMaria Grazia Betti, Pierluigi Gargiani, Carlo Mariani, Stefano Turchini, Nicola Zema, Sara Fortuna, Arrigo Calzolari, Stefano Fabris, 2012, izvirni znanstveni članek Opis: Iron–phthalocyanine (FePc) molecules deposited on the Au(110) surface self-organize in ordered chains driven by the reconstructed Au channels. The interaction process induces a rehybridization of the electronic states localized on the central metal atom, breaking the 4-fold symmetry of the molecular orbitals of the FePc molecules. The molecular adsorption is controlled by a symmetry-determined mixing between the electronic states of the Fe metal center and of the Au substrate, as deduced by photoemission and absorption spectroscopy exploiting light polarization. DFT calculations rationalize this mixing of the Fe and Au states on the basis of symmetry arguments. The calculated electronic structure reproduces the main experimental spectral features, which are associated to a distorted molecular structure displaying a trigonal bipyramidal geometry of the ligands around the metal center.
Ključne besede: phthalocyanine, Au(110), gold, surface, DFT, density functional theory, calculation, simulation
Objavljeno v RUNG: 13.10.2016; Ogledov: 4946; Prenosov: 0
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115. Structural phases of ordered FePc-nanochains self-assembled on Au(110)Betti Maria Grazia, Pierluigi Gargiani, Carlo Mariani, Roberto Biagi, Jun Fujii, Giorgio Rossi, Andrea Resta, Stefano Fabris, Sara Fortuna, Xavier Torrelles, Manvendra Kumar, Maddalena Pedio, 2012, izvirni znanstveni članek Opis: Iron-phthalocyanine molecules deposited on the Au(110) reconstructed channels assemble into one-dimensional molecular chains, whose spatial distribution evolves into different structural phases at increasing molecular density. The plasticity of the Au channels first induces an ordered phase with a 5×5 symmetry, followed by a second long-range ordered structure composed by denser chains with a 5×7 periodicity with respect to the bare Au surface, as observed in the low-energy electron-diffraction (LEED) and grazing incidence X-ray diffraction (GIXRD) patterns. The geometry of the FePc molecular assemblies in the Au nanorails is determined by scanning tunneling microscopy (STM). For the 5×7 phases, the GIXRD analysis identifies a “4-3” rows profile along the [001] direction in the Au surface and an on-top FePc adsorption site, further confirmed by density functional theory (DFT) calculations. The latter also reveals the electronic mixing of the interface states. The chain assembly is driven by the molecule–molecule interaction and the chains interact with the Au nanorails via the central metal atom, while the chain–chain distance in the different structural phases is primarily driven by the plasticity of the Au surface.
Ključne besede: STM, LEED, DFT, density functional theory, phthalocyanine, Au(110), gold, surface
Objavljeno v RUNG: 13.10.2016; Ogledov: 4824; Prenosov: 0
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116. Spin and orbital configuration of metal phthalocyanine chains assembled on the Au(110) surfaceGargiani Pierluigi, Giorgio Rossi, Roberto Biagi, Valdis Corradini, Maddalena Pedio, Sara Fortuna, Arrigo Calzolari, Stefano Fabris, Julio Criginski Cezar, N. B. Brookes, Maria Grazia Betti, 2013, izvirni znanstveni članek Opis: The spin and orbital configuration of magnetic metal phthalocyanines (MPcs) deposited on metallic substrates are strongly influenced by the rehybridization of the molecular states with the underlying metal. FePc, CoPc, and CuPc isolated molecules are archetypal systems to investigate the interrelationship between magnetic moments and orbital symmetry after deposition on a metallic substrate. MPcs form long-range ordered chains self-assembled along the reconstructed channels of the Au(110) surface. X-ray magnetic circular dichroism from the L2,3 absorption edges of Fe, Co, and Cu shows that the orbital and spin configuration are strongly modified upon adsorption on the Au(110) surface if the orbitals responsible of the magnetic moment are involved in the interaction process. The magnetic moment for a single layer of molecular chains is completely quenched for the CoPc molecules, fully preserved for the CuPc and reduced for the FePc ones. The modified magnetic configuration is confined to the very interface layer, i.e., to the MPc molecules bound to the metal substrate up to the compact packing of the single layer. The different response can be rationalized in terms of the symmetry/orientation of the metal-ion d states interacting with the substrate states, as indicated by density functional theory calculations in agreement with experimental findings.
Ključne besede: phthalocyanine, Au(110), gold, self-assembly, pattern, configuration, density functional theory, DFT, CuPc, FePc
Objavljeno v RUNG: 12.10.2016; Ogledov: 4813; Prenosov: 0
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117. Distance-based configurational entropy of proteins from molecular dynamics simulationsFederico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, izvirni znanstveni članek Opis: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes.
In particular:
reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;
the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;
backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);
the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface.
This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Ključne besede: entropy, protein, molecular dynamics, simulations, MD
Objavljeno v RUNG: 12.10.2016; Ogledov: 4326; Prenosov: 221
Celotno besedilo (2,40 MB) |
118. In silico generation of peptides by replica exchange Monte Carlo: Docking-based optimization of maltose-binding-protein ligandsAnna Russo, Pasqualina Liana Scognamiglio, Rolando Pablo Hong Enriquez, Carlo Santambrogio, Rita Grandori, Daniela Marasco, Antonio Giordano, Giacinto Scoles, Sara Fortuna, 2015, izvirni znanstveni članek Opis: Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
Ključne besede: peptides, docking, optimisation, computation, maltose binding protein, probe, ligand
Objavljeno v RUNG: 12.10.2016; Ogledov: 4054; Prenosov: 140
Celotno besedilo (4,27 MB) |
119. Chelating effect in short polymers for the design of bidentate binders of increased affinity and selectivitySara Fortuna, Federico Fogolari, Giacinto Scoles, 2015, izvirni znanstveni članek Opis: The design of new strong and selective binders is a key step towards the development of new sensing devices and effective drugs. Both affinity and selectivity can be increased through chelation and here we theoretically explore the possibility of coupling two binders through a flexible linker. We prove the enhanced ability of double binders of keeping their target with a simple model where a polymer composed by hard spheres interacts with a spherical macromolecule, such as a protein, through two sticky spots. By Monte Carlo simulations and thermodynamic integration we show the chelating effect to hold for coupling polymers whose radius of gyration is comparable to size of the chelated particle. We show the binding free energy of flexible double binders to be higher than that of two single binders and to be maximized when the binding sites are at distances comparable to the mean free polymer end-to-end distance. The affinity of two coupled binders is therefore predicted to increase non linearly and in turn, by targeting two non-equivalent binding sites, this will lead to higher selectivity.
Ključne besede: chelation, polymer, multivalency, bidentate, free energy, thermodynamic integration, Monte Carlo
Objavljeno v RUNG: 11.10.2016; Ogledov: 4094; Prenosov: 152
Celotno besedilo (1,68 MB) |
120. Accurate estimation of the entropy of rotation-translation probability distributionsFederico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, izvirni znanstveni članek Opis: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno v RUNG: 11.10.2016; Ogledov: 4445; Prenosov: 0
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