Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated Basis sets of at least triple-zeta quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD (T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBEO, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results

A quantum-mechanical study of the reaction mechanism of sulfite oxidase.

The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2

What is the giant wall gecko having for dinner ? Conservation genetics for guiding reserve management in Cabo Verde

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systemsinfo:eu-repo/semantics/publishedVersio

Revisiting the origin of the bending in group 2 metallocenes AeCp2 (Ae = Be–Ba)

Metallocenes are well-established compounds in organometallic chemistry, and can exhibit either a coplanar structure or a bent structure according to the nature of the metal center (E) and the cyclopentadienyl ligands (Cp). Herein, we re-examine the chemical bonding to underline the origins of the geometry and stability observed experimentally. To this end, we have analysed a series of group 2 metallocenes [Ae(C5R5)2] (Ae = Be–Ba and R = H, Me, F, Cl, Br, and I) with a combination of computational methods, namely energy decomposition analysis (EDA), polarizability model (PM), and dispersion interaction densities (DIDs). Although the metal–ligand bonding nature is mainly an electrostatic interaction (65–78%), the covalent character is not negligible (33–22%). Notably, the heavier the metal center, the stronger the d-orbital interaction with a 50% contribution to the total covalent interaction. The dispersion interaction between the Cp ligands counts only for 1% of the interaction. Despite that orbital contributions become stronger for heavier metals, they never represent the energy main term. Instead, given the electrostatic nature of the metallocene bonds, we propose a model based on polarizability, which faithfully predicts the bending angle. Although dispersion interactions have a fair contribution to strengthen the bending angle, the polarizability plays a major role

Life cycle assessment tool of electricity generation in Portugal

ABSTRACT: This article presents and describes the LCA4Power tool, developed in this work to assess the potential environmental impacts, as, for example, the contribution to global warming, of electricity generation in continental Portugal, not considering the Madeira and Azores archipelagos. Based on a life cycle perspective, the tool considers the life cycles of various available technologies for producing electricity, on a cradle-to-gate perspective, excluding distribution and final use. It was implemented in MS Excel™ using emission factors obtained from the literature and other sources, instead of raw life cycle inventory data. The current version of the tool includes wind and hydroelectric power as renewable energy sources, and thermal and combined heat and power generation from fossil fuels as non-renewable energy sources. The combination of the aforementioned electricity generation technologies is responsible for more than 90% of the electricity generated in continental Portugal. Results were validated comparing the tool’s predictions with data from other LCA studies of electricity production, showing a good agreement, in particular for the greenhouse gas emissions. As added value, this tool provides a user-friendly way of simulating the potential environmental impacts of different endogenous energy mixes in Portugal, thus support decision making and communication. Future developments of the tool will include other technologies for electricity generation and its application to support decision making through the analysis of future scenarios for electricity generation in Portugal.info:eu-repo/semantics/publishedVersio

Insights into the habitat associations, phylogeny, and diet of Pipistrellus maderensis in Porto Santo, northeastern Macaronesia

Around 60 % of all bat species occur in islands, and nearly one in four is an insular endemic. Bats are often the only native terrestrial mammals in oceanic islands, and despite increasing anthropogenic pressures, little is known about the distribution, natural history, and population status of most insular bat populations. The sub-tropical archipelago of Madeira is composed of the volcanic islands of Madeira, Porto Santo, and Desertas and is home to the Macaronesian endemic Pipistrellus maderensis, to the endemic subspecies Nyctalus leisleri verrucosus, and to Plecotus austriacus. Pipistrellus maderensis is known to both Madeira and Porto Santo, whereas the other two species have only been recorded in the former. However, no bats have been recorded in Porto Santo for over 15 years, raising fears that bats are probably extinct in the island. In July 2021, we conducted an island-wide acoustic survey using AudioMoth passive acoustic recorders, leading to the detection of Pipistrellus maderensis in 28 out of the 46 sampling sites (60 %). The species' activity was strongly associated with artificial water sources, and genetic samples from six captured individuals revealed that the populations of Pipistrellus maderensis in Porto Santo and Madeira have a close phylogenetic affinity. Furthermore, using DNA metabarcoding, we found that the species feeds on a wide variety of insects, including several economically important pest species and disease vectors. These findings emphasise the need to target more conservation and research efforts towards extant island bat populations and the potential ecosystem services they provide

Effect of Type of Biomass used in the Hydrothermal Liquefaction of Microalgae on the Bio Crude Yields and Quality

Hydrothermal liquefaction (HTL) is an energy-efficient technology that converts biomass with high moisture content, such as lignocellulosic material and aquatic biomass, into bio-oil which can be used as a precursor in the production of renewable biofuels. The current state of technology is mostly at a laboratory scale with relatively low Technology Readiness Levels (TRL). Most HTL research takes place in batch reaction systems, but there is growing interest in scaling up the technology through the use of continuous units. The process is influenced by several factors and operational parameters, which affect the performance of the process in terms of production and bio-oil quality. HTL is highly dependent on the type of biomass used. The main advantages in relation to other thermochemical processes is the possibility of using wet biomass, avoiding the high cost of the drying process. In this work several types of biomasses were studied, different types of micro algae (i. e. Spirulina, Chlorella Vulgaris, algae grown in industrial effluents), and grass. Growing microalgae has a significant cost in the production process of liquid biofuels. So, it was also tested algae cultivated in industrial effluents which has advantages from an economic and environmental point of view. Also, the grass wastes, have high moisture content and so its adequate to be process in HTL. In all the tests, four different products were obtained: gases, aqueous and organic (biocrude) products and solids. All these fractions were characterized to suggest their most favourable application. The gases were mainly composed of Hydrogen, Oxygen, Carbon Monoxide, Carbon Dioxide and Hydrocarbons until C4. Bio oil composition was the parameter most affected by biomass type. So, when microalgae were used, it was observed higher content of nitrogenous compounds, like pyrroles, indoles, pyrazines and other nitrogen-containing compounds, probably formed from the protein fraction of the algae. In all the bio-oils it was also detected the presence of oxygenated compounds, such as ketones, esters, phenols, fatty acids, alcohols, that maybe were produced from the lipids and carbohydrates. Hydrocarbons, including alkanes, alkenes, alkynes and aromatics compounds were also present. The composition of the biomass used has a higher effect on the bio-oil composition, so it is important an extensive characterization of the feedstock in order to select the best raw material to be used in HTL process depending on the intended application. This paper analyses the effect of biomass composition in the HTL to assess its viability to be used to produce biofuels or valuable chemicals