Resonating holes vs molecular spin-orbit coupled states in group-5 lacunar spinels

The valence electronic structure of magnetic centers is one of the factors that determines the characteristics of a magnet. This may refer to orbital degeneracy, as for jeff = 1/2 Kitaev magnets, or near-degeneracy, e.g., involving the third and fourth shells in cuprate superconductors. Here we explore the inner structure of magnetic moments in group-5 lacunar spinels, fascinating materials featuring multisite magnetic units in the form of tetrahedral tetramers. Our quantum chemical analysis reveals a very colorful landscape, much richer than the single-electron, single-configuration description applied so far to all group-5 GaM4X8 chalcogenides, and clarifies the basic multiorbital correlations on M4 tetrahedral clusters: while for V strong correlations yield a wave-function that can be well described in terms of four V4+V3+V3+V3+ resonant valence structures, for Nb and Ta a picture of dressed molecular-orbital jeff = 3/2 entities is more appropriate. These internal degrees of freedom likely shape vibronic couplings, phase transitions, and the magneto-electric properties in each of these systems

The diabatic picture of electron transfer, reaction barriers and molecular dynamics

Diabatic states have a long history in chemistry, beginning with early valence bond pictures of molecular bonding and extending through the construction of model potential energy surfaces to the modern proliferation of methods for computing these elusive states. In this review, we summarize the basic principles that define the diabatic basis and demonstrate how they can be applied in the specific context of constrained density functional theory. Using illustrative examples from electron transfer and chemical reactions, we show how the diabatic picture can be used to extract qualitative insight and quantitative predictions about energy landscapes. The review closes with a brief summary of the challenges and prospects for the further application of diabatic states in chemistry.National Science Foundation (U.S.) (NSF-CAREER Award (CHE-0547877)David & Lucile Packard FoundationAlfred P. Sloan Foundatio

A molecular modelling journey from packing to conformational polymorphism

The efficient and reproducible crystallisation of a polymorph showing the desired properties and functionalities is crucial in a variety of fields, such as the pharmaceutical sector. Characterising thermodynamics and mechanisms of polymorphic transitions at the molecular level is thus a key step towards developing a rational design of crystallisation processes and products. Despite its relevance, a systematic computational analysis of polymorphism and polymorphic transitions still represents a major challenge. In this thesis, metadynamics is employed in combination with state-of-the-art techniques, such as committor analysis and Markov State Models, to provide insight into polymorphism in molecular systems. The first part of the work focuses on packing polymorphism. The investigation of the transition between phases I and III in bulk carbon dioxide aims at testing a set of computational tools able to characterise in detail thermodynamics and mechanism of polymorphic transitions. This set-up is then applied and further developed for the study of CO2 confined in cylindrical nanopores, unveiling a complex landscape of ordered structures, unaccessible in unconfined conditions. Next, the serendipitous and irreproducible discovery of a new polymorph of succinic acid, γ, provides a challenging context to tackle the study of conformational polymorphism. Form γ presents folded conformers in its unit cell, while the other known polymorphs show planar molecules. From molecular dynamics and metadynamics, γ appears labile and metastable, a characteristic that might hinder its crystallisation. The study of the conformational behaviour of succinic acid in water reveals fast interconversions within a network of nine conformers, both folded and planar, among which the folded conformation observed in γ is the most thermodynamically stable. The high flexibility of this molecule is relevant in determining the nucleation mechanism. Simulations of supersaturated solutions and of crystal seeds dissolution suggest that nucleation cannot be classical, but it is rather likely to be a multi-step process

Development of novel biocatalysts and biosystems for green chemistry

The chemical synthesis currently employed in the manufacture of cosmetics presents limitations such as unwanted side reactions and the need of strong chemical conditions. In order to overcome these drawbacks, novel enzymes have been developed to catalyse the targeted bioconversions contributing to the solution of the environmental concerns of the industrial activities moving them towards sustainable biotechnologies. This work was mainly aimed at developing improved biocatalysts based on feruloyl esterases (FAEs) and glucuronoyl esterases (GEs) for the production of compounds with antioxidant activity. Novel fungal FAEs and GEs, identified through a bioinformatics approach from the analysis of 300 fungal genomes by the “Westerdijk Fungal Biodiversity Institute”, were expressed in Pichia pastoris and characterized. FAE from Aspergillus wentii was selected as the most promising enzyme to be subjected to site-directed mutagenesis to further fine-tune the enzyme towards its application in bioconversions. A homology model of this enzyme was developed and five site-directed variants were designed, expressed in P. pastoris and characterized assessing substrate specificity, solvent and thermo tolerance. This analysis led to the development of a rational designed variant with tenfold improved hydrolytic activity and a variant with enhanced thermo and solvent tolerance. As a second approach to develop improved biocatalysts based on FAEs, directed evolution was applied to the already characterized FAEs from Fusarium oxysporum (FoFaeC) and from Myceliophthora thermophila (MtFae1a). Two complete methodologies for the construction and the automated screening of evolved variants collections were developed and applied to the generation of 30,000 mutants libraries and their screening. Randomly mutated variants of FoFaeC and MtFae1a were generated through error prone-polymerase chain reaction and expressed in Yarrowia lipolytica and Saccharomyces cerevisiae, respectively. Thanks to the development of ad hoc chromogenic substrates for high-throughput assays on solid and in liquid media, screening for higher extracellular FAE activity than the wild type enzymes led to the selection of improved enzyme variants. The best evolved variants of both MtFae1a and FoFaeC were characterized for their thermotolerance, solvent tolerance and specificity towards methylated cinnamic substrates and subjected to small molecular docking studies to assess substrate interactions. In addition, MtFae1a evolved variants were tested in transesterification reactions in detergentless microemulsions for the production of target compounds selected for their potential antioxidant activity. Thus, although the screening strategy was based on the selection of evolved variants with improved hydrolytic activity, it was possible to obtain MtFae1a variants with both hydrolytic and synthetic enhanced activities to be potentially exploited in cosmetic industry. Finally, with the aim of identifying novel FAEs with non-conserved sequences, different fungal strains isolated from lignocellulosic biomasses during biodegradation under natural conditions and belonging to the microbial collection of Department of Agriculture (University of Naples “Federico II”) were screened for the production of different enzymes having potentially synergistic actions on lignocellulose conversion. This led to the selection of a novel fungal species showing FAE activity production induced by different carbon sources. Genome and transcriptome sequencing and analysis confirmed the presence of genes related to plant cell wall degrading enzymes