Iron | EPFL Graph Search

Iron is a chemical element with the symbol Fe () and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, just ahead of oxygen (32.1% and 30.1%, respectively), forming much of Earth's outer and inner core. It is the fourth most common element in the Earth's crust, being mainly deposited by meteorites in its metallic state, with its ores also being found there. Extracting usable metal from iron ores requires kilns or furnaces capable of reaching or higher, about higher than that required to smelt copper. Humans started to master that process in Eurasia during the 2nd millennium BCE and the use of iron tools and weapons began to displace copper alloys—in some regions, only around 1200 BCE. That event is considered the transition from the Bronze Age to the Iron Age. In the modern world, iron alloys, such as steel, stainless steel, cast iron and special steels, are by far the most

Optimization methods and objective functions for analysis of metabolic network models

Zhaleh Hosseini

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichiometric balances while taking into account gene-protein-reaction associations. Several methods have already been developed for the analysis of these models. These methods are mainly used to optimize a single or combination of objective functions subject to different constraints. In this thesis, we have summarized the optimization methods and objective functions by classifying them based on biological and mathematical features. Particularly, we suggest reformulations to convert some of the complex optimization classes to simpler ones. One of the reformulations is the conversion of mixed-integer linear fractional programming (MILFP) to mixed-integer linear programming (MILP). We show that this conversion is useful in studying coupling relationships in thermodynamically constrained metabolic network models. Coupling determines how different components of the network such as metabolites or reactions are interrelated. Particularly, flux Coupling Analysis (FCA) is a method for evaluating the dependencies between metabolic reactions. In FCA, two reactions are considered as coupled if the activity of one, constrains the activity of the other. So far, FCA has been used for analyzing metabolic reactions in flux-balanced models. In this work, we developed a new formulation, Thermodynamic Flux Coupling Analysis (TFCA), which calculates flux couplings of metabolic models that are subjected to thermodynamic constraints. With TFCA, we show that adding thermodynamic constraints can significantly change the coupling relationship of reactions of the network. Moreover, we show that calculating coupling relations helps in reducing the number of combinations of bidirectional reactions (BDRs), which in turn will facilitate the analysis of the metabolic network. In addition to proposing several mathematical reformulations to gain global optimality, we also addressed the issue of finding the proper cellular objective function in different conditions of cellular metabolism. This is not always straight-forward, since the metabolic activities of some organisms are not well-characterized, e.g., metabolism of dormancy phase in some bacteria and parasites. In this thesis, we studied the metabolic behaviour of dormant malaria parasite using genome-scale model of Plasmodium falciparum. We examined known and novel objective functions and scored them based on the modelâs consistency with experimental gene expression data. Our results suggested that minimizing energy dissipation can best describe the metabolic activities of the malaria parasites in the dormancy phase. In the last chapter, we focus on studying another poorly characterized metabolic system that is the process of iron reduction in Clostridium acetobutylicum. Research has shown that this organism can reduce Fe(III), but the mechanism behind this reduction is yet to be identified. In this thesis, we analyzed the metabolism of C. acetobutylicum using its reconstructed genome-scale metabolic network model and experimental transcriptomics data in the presence or absence of Fe(III). By performing several computational studies, we suggested that NAD(P) is involved in the reduction of iron and is the potential physiological electron donor to Fe(III).

EPFL2020

Iron Complexes for Hydrogen Activation and Catalytic Hydrogenation

Simona Mazza

Inspired by Nature several groups have developed structural and functional iron complexes mimicking the active site of the iron-hydrogenases, which show high reactivity in the H2 cleavage. Usually pendant bases have been incorporated onto families of Fe complexes in order to achieve active systems. In the view of these recent developments, in chapter two, we investigated the possibility of synthesizing novel iron (II) complexes bearing an amine internal base and providing an open site for substrate binding as catalysts for H2 activation. Pentacoordinated Fe(II) low spin complexes [(PhPNP)Fe(CO)(bdt)] (1), [(PhPNP)Fe-(CO)(Nbt)] (4), [(CyPNP)Fe(CO)(Nbt)] (5), [(dppe)Fe(CO)(Nbt)] (6) and the paramagnetic complex [(CyPNP)FeCl2] (10) have been synthesized and fully characterised. Unfortunately, when these complexes were tested as catalysts for hydrogenation reaction of a wide range of unsaturated substrates, no appreciable reactivity was observed. Same behaviour was observed in the case of complexes [(CyPNP)Fe(CO)(Cp)] (11) and [(CyPNP)Fe(CH3CN)(Cp)] (12) where the Cp ligand was installed in order to modulate the electronic and steric properties on the iron center. In chapter three, a new class of well-defined iron pincer complexes is reported. Several Fe(II) complexes supported by a 2,6-bis(phosphinito)pyridine ligand (PONOP) have been synthesized and fully characterised. In particular, the Fe-hydride complexes [(iPrPONOP)-Fe(CO)(H)Br] (14) and (iPrPONOP)Fe(CO)(H)(CH3CN) (15) could activate H2 at room temperature. Moreover, complexes 14 and 15 served as catalysts for the selective hydrogenation of aldehydes at room temperature. In presence of sodium formate as hydrogen donor, 14 and 15 showed an excellent reactivity in hydrogen transfer reaction of aldehydes. The mechanism of hydrogen activation and hydrogenation is discussed based on the observed reactivity of iron complexes. The feature of being chemoselective towards aldehydes and a broad functional-group tolerance make these iron-hydride systems remarkable in the class of the earth-abundant-metal hydrogenation catalysts. Chapter four is dedicated to the tuning of the Fe-PONOP systems reported in chapter three in order to synthesize similar iron(II) complexes exhibiting enhanced reactivity for H2 activation and hydrogenation of unsaturated substrates. As first attempt, complexes [(CyPONOP)Fe(CO)Br2] (22) and the analogous chloride [(CyPONOP)Fe(CO)Cl2] (23) bearing the stronger donor CyPONOP ligand were synthesized and tested as catalysts for hydrogenation reaction, but none of the substrates employed was reduced. As second attempt, the CO ligand was substituted with the better donor ligand tert-butyl isocyanide in presence of iPrPONOP as pincer ligand. Several Fe-PONOP complexes were synthesized and fully characterized. In particular the Fe-hydride complex [(iPrPONOP)Fe(tBuNC)(H)Br] (25) exhibited reactivity towards hydrogenation of aldehydes under the same reaction conditions reported for 14. No reaction was observed in presence of acetophenone, cyclohexene and 1-decene demonstrating that, although spectroscopically different, 25 did not exhibit enhanced reactivity relative to 14.

EPFL2015

Diel quenching of Southern Ocean phytoplankton fluorescence is related to iron limitation

Nina Schuback

Evaluation of photosynthetic competency in time and space is critical for better estimates and models of oceanic primary productivity. This is especially true for areas where the lack of iron (Fe) limits phytoplankton productivity, such as the Southern Ocean. Assessment of photosynthetic competency on large scales remains challenging, but phytoplankton chlorophyll a fluorescence (ChlF) is a signal that holds promise in this respect as it is affected by, and consequently provides information about, the photosynthetic efficiency of the organism. A second process affecting the ChlF signal is heat dissipation of absorbed light energy, referred to as non-photochemical quenching (NPQ). NPQ is triggered when excess energy is absorbed, i.e. when more light is absorbed than can be used directly for photosynthetic carbon fixation. The effect of NPQ on the ChlF signal complicates its interpretation in terms of photosynthetic efficiency, and therefore most approaches relating ChlF parameters to photosynthetic efficiency seek to minimize the influence of NPQ by working under conditions of sub-saturating irradiance. Here, we propose that NPQ itself holds potential as an easily acquired optical signal indicative of phytoplankton physiological state with respect to Fe limitation. We present data from a research voyage to the Subantarctic Zone south of Australia. Incubation experiments confirmed that resident phytoplankton were Fe-limited, as the maximum quantum yield of primary photochemistry, F-v/F-m, measured with a fast repetition rate fluorometer (FRRf), increased significantly with Fe addition. The NPQ "capacity" of the phytoplankton also showed sensitivity to Fe addition, decreasing with increased Fe availability, confirming previous work. The fortuitous presence of a remnant warm-core eddy in the vicinity of the study area allowed comparison of fluorescence behaviour between two distinct water masses, with the colder water showing significantly lower F-v/F-m than the warmer eddy waters, suggesting a difference in Fe limitation status between the two water masses. Again, NPQ capacity measured with the FRRf mirrored the behaviour observed in F-v/F-m, decreasing as F-v/F-m increased in the warmer water mass. We also analysed the diel quenching of underway fluorescence measured with a standard fluorometer, such as is frequently used to monitor ambient chlorophyll a concentrations, and found a significant difference in behaviour between the two water masses. This difference was quantified by defining an NPQ parameter akin to the Stern-Volmer parameterization of NPQ, exploiting the fluorescence quenching induced by diel fluctuations in incident irradiance. We propose that monitoring of this novel NPQ parameter may enable assessment of phytoplankton physiological status (related to Fe availability) based on measurements made with standard fluorometers, as ubiquitously used on moorings, ships, floats and gliders.

2020