Alexandre F. Gomes

The Biginelli Reaction with an Imidazolium–Tagged Recyclable Iron Catalyst: Kinetics, Mechanism, and Antitumoral Activity

The present work describes the synthesis, characterization, and application of a new ion-tagged iron catalyst. The catalyst was employed in the Biginelli reaction with impressive performance. High yields have been achieved when the reaction was carried out in imidazolium-based ionic liquids (BMI⋅PF6, BMI⋅NTf2, and BMI⋅BF4), thus showing that the ionic-liquid effects play a role in the reaction. Moreover, the ion-tagged catalyst could be recovered and reused up to eight times without any noticeable loss in activity. Mechanistic studies performed by using high-resolution electrospray-ionization quadrupole-time-of-flight mass (HR-EI-QTOF) spectrometry and kinetic experiments indicate only one reaction pathway and rule out the other two possibilities under the development conditions. The theoretical calculations are in accordance with the proposed mechanism of action of the iron catalyst. Finally, the 37 dihydropyrimidinone derivatives, products of the Biginelli reaction, had their cytotoxicity evaluated in assays against MCF-7 cancer cell linages with encouraging results of some derivatives, which were virtually non-toxic against healthy cell linages (fibroblasts).

Mechanistic Studies on Lewis Acid Catalyzed Biginelli Reactions in Ionic Liquids: Evidence for the Reactive Intermediates and the Role of the Reagents

This paper describes the use of common Lewis acids supported in imidazolium-based ionic liquids as the catalysts to promote the Biginelli reaction. The ionic liquid effect and the reaction mechanism are discussed on the basis of nuclear magnetic resonance (NMR), electrospray ionization mass spectrometry (ESI-MS), and theoretical calculations. Indeed, the results showed that the ionic medium plays a fundamental role in the synthesis of biologically active dihydropyrimidinones due to the stabilization of the charged intermediates proposed in the mechanism. When conducted in an ionic liquid as solvent, the reaction mechanism is more complex than in other Lewis acid catalyzed Biginelli reactions.

On the use of 2,1,3-benzothiadiazole derivatives as selective live cell fluorescence imaging probes

Newly designed 2,1,3-benzothiadiazole-containing fluorescent probes with four excited state intramolecular proton transfer (ESIPT) sites were successfully tested in live cell-imaging assays using a confluent monolayer of human stem-cells (tissue). All tested dyes were compared with the commercially available DAPI and gave far better results.

Chemical cross-linking with a diazirine photoactivatable cross-linker investigated by MALDI- and ESI-MS/MS

Crystallography and nuclear magnetic resonance are well-established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross-linking of proteins coupled with mass spectrometry allows low-resolution characterization of proteins and protein complexes based on measuring distance constraints from cross-links. In this work, we have investigated cross-linking by means of a heterobifunctional cross-linker containing a traditional N-hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross-links compared with homobifunctional, NHS-based cross-linkers. Cross-linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra- and intermolecular cross-links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross-links, which facilitates identification.

Ionically Tagged Iron Complex‐Catalyzed Epoxidation of Olefins in Imidazolium‐Based Ionic Liquids

A new ionophilic ligand and a new ionically tagged imidazolium-based iron(III) complex were synthesized and applied in the air oxidation (also hydrogen peroxide) of alkenes in imidazolium-based ionic liquids. At least ten recycling reactions were performed. The epoxidized olefin was obtained in very good yields of 84-91 %. Some important mechanistic insights are also provided based on electrospray ionization quadrupole-time of flight mass spectrometry for the oxidation reaction. These results indicate that oxidations can take place by two different pathways, depending on the reaction condition: a radical or a concerted mechanism. These results contribute towards a better understanding of iron-catalyzed oxidation mechanisms.

Iron Complex with Ionic Tag‐Catalyzed Olefin Reduction under Oxidative Conditions—A Different Reaction for Iron

An iron(III) complex with ionic tags was applied to the reduction of alkenes in imidazolium-based ionic liquids (ILs) under oxidative conditions. The catalyst is very efficient to promote reactions of biomass derivatives. At least ten recycling reactions were performed without any loss of catalytic activity. Some important mechanistic insights for this new reaction are also provided based mostly on electrospray ionization quadrupole-time of flight mass spectrometry (ESI-QTOF-MS).

Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking

Traveling-wave ion mobility (TWIM) coupled to mass spectrometry (MS) has emerged as a powerful tool for structural and conformational analysis of proteins and peptides, allowing the analysis of isomeric peptides (or proteins) with the same sequence but modified at different residues. This work demonstrates the use of the novel TWIM-MS technique to separate isomeric peptide ions derived from chemical cross-linking experiments, which enables the acquisition of distinct product ion spectra for each isomer, clearly indicating modification on different sites. Experiments were performed with four synthetic peptides, for which variable degrees of mobility separation were achieved. In cases of partially overlapping mobility arrival time distributions (ATDs), extracting the ATDs of fragment ions belonging to each individual isomer allowed their separation into two distinct ATDs. Accumulation over regions from the specific ATDs generates the product ion spectrum of each isomer, or a spectrum highly enriched in their fragments. The population of both modified peptide isomers was correlated with the intrinsic reactivities of different Lys residues from reactions conducted at different pH conditions.

Synthesis, spectroscopic characterization, DFT studies, and initial antibacterial assays in vitro of a new palladium(II) complex with tryptophan

A new palladium(II) complex with the amino acid L-tryptophan (Pd-TRP) was synthesized in aqueous solution and characterized by chemical and spectroscopic methods. Elemental, ESI-QTOF mass spectrometric, and thermal analyses of the solid compound permitted proposing the [Pd(C11H11N2O2)2] · 2H2O composition. Infrared, Raman, and UV-Vis spectroscopic data indicate the coordination of the ligand to Pd(II) through monodentate oxygen of carboxylate and through nitrogen of the amino group. The 1H and 13C NMR spectroscopic data confirm coordination through the carboxylate, while 15N NMR data confirm coordination of nitrogen of NH2. Density functional theory studies confirmed nitrogen and oxygen coordination to palladium(II) as a minimum of the potential energy surface with calculations of the hessians showing no imaginary frequencies. Biological studies were performed to provide information concerning the antibacterial activities of the compound. The Pd-TRP complex was shown to be active against Gram-positive and Gram-negative pathogenic bacterial strains.

Catalytic Aminolysis (Amide Formation) from Esters and Carboxylic Acids: Mechanism, Enhanced Ionic Liquid Effect, and its Origin

This paper describes the use of imidazolium‐based ionic liquids {1‐n‐butyl‐3‐methylimidazolium tetrafluoroborate [BMI‐BF4], 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate [BMI‐PF6], and 1‐n‐butyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide [BMI‐NTf2]} as efficient supports for Lewis and Brønsted acids ,which are promoters of the aminolysis of some esters, fatty acids, and fatty acid esters (among others) to form amide derivatives. Some esters and carboxylic acids were tested to demonstrate the generality of the methodology, and the corresponding amides were obtained in high yields. Recycling reactions (at least eight reuses) without a notable loss in activity could be performed by using CdO and SnCl2 as catalysts in BMI‐NTf2 as the ionic medium. Brønsted acids, such as H2SO4 and HCl, were also tested with impressive results; however, it was not possible to perform recycling reactions because of catalyst leaching. The same was true when using BF3⋅OEt2 as the catalyst. Mechanistic insights and the ionic‐liquid effect were investigated by using 13C{1H} NMR spectroscopy, which showed that there is a strong interaction of the imidazolium cation with the CO and CC bonds of methyl oleate, most likely through CH⋅⋅⋅π interactions, π‐stacking interactions, and ion‐pair formation in the presence of a metal catalyst. Electrospray ionization–quadrupole time‐of‐flight experiments allowed a better understanding of the reaction mechanism. The results could explain the enhanced ionic‐liquid effect on the stabilization of the formed intermediates, which facilitated the amide bond formation.

Conformational dynamics of α-synuclein: insights from mass spectrometry

The aggregation and deposition of α-synuclein in Lewy bodies is associated with the progression of Parkinsons disease. Here, Mass Spectrometry (MS) is used in combination with Ion Mobility (IM), chemical crosslinking and Electron Capture Dissociation (ECD) to probe transient structural elements of α-synuclein and its oligomers. Each of these reveals different aspects of the conformational heterogeneity of this 14 kDa protein. IM-MS analysis indicates that this protein is highly disordered, presenting in positive ionisation mode with a charge state range of 5 ≤z≤ 21 for the monomer, along with a collision cross section range of ∼1600 Å(2). Chemical crosslinking applied in conjunction with IM-MS captures solution phase conformational families enabling comparison with those exhibited in the gas phase. Crosslinking IM-MS identifies 3 distinct conformational families, Compact (∼1200 Å(2)), Extended (∼1500 Å(2)) and Unfolded (∼2350 Å(2)) which correlate with those observed in solution. ECD-Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry (ECD-FT-ICR MS) highlights the effect of pH on α-synuclein structure, identifying the conformational flexibility of the N and C termini as well as providing evidence for structure in the core and at times the C terminus. A hypothesis is proposed for the variability displayed in the structural rearrangement of α-synuclein following changes in solution pH. Following a 120 h aggregation time course, we observe an increase in the ratio of dimer to monomer, but no gross conformational changes in either, beyond the significant variations that are observed day-to-day from this conformationally dynamic protein.