Computational Investigations of Catalyzed Organic Reactions: Carbocatalysis, Biocatalysis, Metal and Organo Catalysis

This thesis comprises most of the computational results obtained during the three year Chemistry Ph.D course, during which the research activity mainly focused on investigating catalyzed reaction mechanisms. Catalysis is a vast phenomenon and this dissertation does not presume to cover its extent, nor to be a mere list of computational investigations. The purpose is to stress out that computational organic chemistry is a tool to be exploited to explain how and why some reactions prefer to cover one path rather than another by interpreting computation outcomes. Among the immense world of catalysts, the activity of carbon nanoparticles, enzymes, metal complex and proline in catalyzed organic reactions were investigated. Commercially available software for molecular computations were used to carry out the investigations. The thesis is divided in few parts; the former (Part I) provides some insights into the computational methods used during the PhD activity where Quantum-Mechanics (QM), Molecular-Mechanics (MM) and hybrid QM/MM methods are briefly described. Parts II-V gather the results obtained during the PhD activity. In Part II, two examples of carbo-catalyzed reactions are reported, while Part III and IV collect the computational evidences achieved by analysing the reaction mechanism of enzymatic and metal- (or organo-) catalyzed reactions respectively. The last Part (V) includes two, among the many, side works that were carried out during the PhD course. A résumé of the computational results is reported in Part VI

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease

The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, M-pro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C-60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, M-pro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C-70 as an innovative scaffold for the inhibition of SARS-CoV-2 M-pro. At odds with masitinib, both C-60 and C-70 interact more strongly with SARS-CoV-2 M-pro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to M-pro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding

Engineering the Fullerene-protein Interface by Computational Design: The Sum is More than its Parts

Of all the amino acids, the surface of \u3c0-electron conjugated carbon nanoparticles has the largest affinity for tryptophan, followed by tyrosine, phenylalanine, and histidine. In order to increase the binding of a protein to a fullerene, it should suffice to mutate a residue of the site that binds to the fullerene to tryptophan, Trp. Computational chemistry shows that this intuitive approach is fraught with danger. Mutation of a binding residue to Trp may even destabilize the binding because of the complicated balance between van der Waals, polar and non-polar solvation interactions

Deciphering the Reactive Pathways of Competitive Reactions inside Carbon Nanotubes

: Nanoscale control of chemical reactivity, manipulation of reaction pathways, and ultimately driving the outcome of chemical reactions are quickly becoming reality. A variety of tools are concurring to establish such capability. The confinement of guest molecules inside nanoreactors, such as the hollow nanostructures of carbon nanotubes (CNTs), is a straightforward and highly fascinating approach. It mechanically hinders some molecular movements but also decreases the free energy of translation of the system with respect to that of a macroscopic solution. Here, we examined, at the quantum mechanics/molecular mechanics (QM/MM) level, the effect of confinement inside CNTs on nucleophilic substitution (SN2) and elimination (syn-E2 and anti-E2) using as a model system the reaction between ethyl chloride and chloride. Our results show that the three reaction mechanisms are kinetically and thermodynamically affected by the CNT host. The size of the nanoreactor, i.e., the CNT diameter, represents the key factor to control the energy profiles of the reactions. A careful analysis of the interactions between the CNTs and the reactive system allowed us to identify the driving force of the catalytic process. The electrostatic term controls the reaction kinetics in the SN2 and syn/anti-E2 reactions. The van der Waals interactions play an important role in the stabilization of the product of the elimination process

Enhanced Uptake and Phototoxicity of C60@albumin Hybrids by Folate Bioconjugation

Fullerenes are considered excellent photosensitizers, being highly suitable for photodynamic therapy (PDT). A lack of water solubility and low biocompatibility are, in many instances, still hampering the full exploitation of their potential in nanomedicine. Here, we used human serum albumin (HSA) to disperse fullerenes by binding up to five fullerene cages inside the hydrophobic cavities. Albumin was bioconjugated with folic acid to specifically address the folate receptors that are usually overexpressed in several solid tumors. Concurrently, tetramethylrhodamine isothiocyanate, TRITC, a tag for imaging, was conjugated to C-60@HSA in order to build an effective phototheranostic platform. The in vitro experiments demonstrated that: (i) HSA disperses C-60 molecules in a physiological environment, (ii) HSA, upon C-60 binding, maintains its biological identity and biocompatibility, (iii) the C-60@HSA complex shows a significant visible-light-induced production of reactive oxygen species, and (iv) folate bioconjugation improves both the internalization and the PDT-induced phototoxicity of the C-60@HSA complex in HeLa cells

Amino acid-driven adsorption of emerging contaminants in water by modified graphene oxide nanosheets

Graphene oxide nanosheets have shown promising adsorption properties toward emerging organic contaminants in drinking water. Here, we report a family of graphene oxide nanosheets covalently modified with amino acids and the study on their adsorption properties toward a mixture of selected contaminants, including pharmaceuticals, additives, and dyes. Graphene oxides modified with l-glutamic acid and l-methionine (GO-Glu and GO-Met) were synthesized and purified with a scalable and fast synthetic and purification procedure, and their structure was studied by combined X-ray photoelectron spectroscopy and elemental analysis. An amino acid loading of about 5% and a slight reduction (from 27% down to 14-20% oxygen) were found and associated with the adsorption selectivity. They were compared to unmodified GO, reduced GO (rGO), GO-lysine, and to the reference sample GO-NaOH. Each type of modified GO possesses a higher adsorption capacity toward bisphenol A (BPA), benzophenone-4 (BP4), and carbamazepine (CBZ) than standard GO and rGO, and the adsorption occurred within the first hour of contact time. The maximum adsorption capacity (estimated from the adsorption isotherms) was strictly related to the amino acid loading. Accordingly, molecular dynamics simulations highlighted higher interaction energies for the modified GOs than unmodified GO, as a result of higher van der Waals and hydrophobic interactions between the contaminants and the amino acid side chains on the nanosheet surface

Chemical Tailoring of β-Cyclodextrin-Graphene Oxide for Enhanced Per- and Polyfluoroalkyl Substances (PFAS) Adsorption from Drinking Water

We report on the synthesis of β-cyclodextrin (βCD) modified graphene oxide (GO) nanosheets, having different sized alkyl linkers (GO-Cn-βCD) and their exploitation as sorbent of per- and polyfluoroalkyl substances (PFAS) from drinking water. βCD were functionalized with a pending amino group, and the resulting precursors grafted to GO nanosheets by epoxide ring opening reaction. Loading of βCD units in the range 12 %–36 % was estimated by combined XPS and elemental analysis. Adsorption tests on perfluorobutanoic acid (PFBA), a particularly persistent PFAS selected as case study, revealed a strong influence of the alkyl linker length on the adsorption efficiency, with the hexyl linker derivative GO-C6-βCD outperforming both pristine GO and granular activated carbon (GAC), the standard sorbent benchmark. Molecular dynamic simulations ascribed this evidence to the favorable orientation of the βCD unit on the surface of GO which enables a strong contaminant molecules retention

Facile high-yield synthesis and purification of lysine-modified graphene oxide for enhanced drinking water purification

Lysine-covalently modified graphene oxide (GO-Lys) was prepared by an innovative procedure. Lysine brushes promote enhanced adsorption of bisphenol A, benzophenone-4 and carbamazepine contaminants from tap water, with a removal capacity beyond the state of the art

Core-shell graphene oxide-polymer hollow fibers as water filters with enhanced performance and selectivity

Commercial hollow fiber filters for micro- and ultrafiltration are based on size exclusion and do not allow the removal of small molecules such as antibiotics. Here, we demonstrate that a graphene oxide (GO) layer can be firmly immobilized either inside or outside polyethersulfone-polyvinylpyrrolidone hollow fiber (Versatile PES (R), hereafter PES) modules and that the resulting core-shell fibers inherits the microfiltration ability of the pristine PES fibers and the adsorption selectivity of GO. GO nanosheets were deposited on the fiber surface by filtration of a GO suspension through a PES cartridge (cut-off 0.1-0.2 mu m), then fixed by thermal annealing at 80 degrees C, rendering the GO coating stably fixed and unsoluble. The filtration cut-off, retention selectivity and efficiency of the resulting inner and outer modified hollow fibers (HF-GO) were tested by performing filtration on water and bovine plasma spiked with bovine serum albumin (BSA, 66 kDa, approximate to 15 nm size), monodisperse polystyrene nanoparticles (52 nm and 303 nm sizes), with two quinolonic antibiotics (ciprofloxacin and ofloxacin) and rhodamine B (RhB). These tests showed that the microfiltration capability of PES was retained by HF-GO, and in addition the GO coating can capture the molecular contaminants while letting through BSA and smaller polystyrene nanoparticles. Combined XRD, molecular modelling and adsorption experiments show that the separation mechanism does not rely only on physical size exclusion, but involves intercalation of solute molecules between the GO layers

Core–shell graphene oxide–polymer hollow fibers as water filters with enhanced performance and selectivity

Commercial hollow fiber filters for micro- and ultrafiltration are based on size exclusion and do not allow the removal of small molecules such as antibiotics. Here, we demonstrate that a graphene oxide (GO) layer can be firmly immobilized either inside or outside polyethersulfone–polyvinylpyrrolidone hollow fiber (Versatile PES®, hereafter PES) modules and that the resulting core–shell fibers inherits the microfiltration ability of the pristine PES fibers and the adsorption selectivity of GO. GO nanosheets were deposited on the fiber surface by filtration of a GO suspension through a PES cartridge (cut-off 0.1–0.2 μm), then fixed by thermal annealing at 80 °C, rendering the GO coating stably fixed and unsoluble. The filtration cut-off, retention selectivity and efficiency of the resulting inner and outer modified hollow fibers (HF-GO) were tested by performing filtration on water and bovine plasma spiked with bovine serum albumin (BSA, 66 kDa, ≈15 nm size), monodisperse polystyrene nanoparticles (52 nm and 303 nm sizes), with two quinolonic antibiotics (ciprofloxacin and ofloxacin) and rhodamine B (RhB). These tests showed that the microfiltration capability of PES was retained by HF-GO, and in addition the GO coating can capture the molecular contaminants while letting through BSA and smaller polystyrene nanoparticles. Combined XRD, molecular modelling and adsorption experiments show that the separation mechanism does not rely only on physical size exclusion, but involves intercalation of solute molecules between the GO layers