It is widely accepted that the sharing of electrons constitutes a bond. Conversely, molecular interactions that do not involve electron transfer, such as van der Waals forces and electrostatics are defined as "non-bonding" or "non-covalent" interactions. More recently computational and experimental observations have shown situations where the division between "bonding" and "non-bonding" interactions is blurred. One such class of interactions are known as σ-hole interactions. Chapter 1 provides a literature review of investigations into the nature of σ-hole interactions, highlighting the individual contributing factors. Chapter 2 provides a detailed analysis into the nature of chalcogen-bonding interactions. Synthetic molecular balances are employed for experimental measurements of conformational free energies in different solvents, facilitating a detailed examination of the energetics and associated solvent and substituent effects on chalcogen-bonding interactions. The chalcogen-bonding interactions examined were found to have surprisingly little solvent dependence. The independence of the conformational free energies on solvent polarity, polarisability and H-bond characteristics showed that electrostatic, solvophobic or dispersion forces were not dominant factors in accounting for the experimentally observed trends. A molecular orbital analysis provided a quantitative relationship between the experimental free energies and the molecular orbital energies, which was consistent with chalcogen-bonding interactions being dominated by an n→σ* orbital delocalisation. Chapters 3 and 4 both use the molecular orbital modelling approach established in Chapter 2 to investigate the potential partial covalency in H-bonding and carbonyl···carbonyl interactions. H-bonding is generally considered to be an electrostatically dominated interaction. However, computational results have suggested a partial covalent character in H-bonding. The molecular orbital analysis revealed an n→σ* electron delocalisation in all H-bonding systems evaluated. However, no quantitative correlation could be found with experimental free energies. Similarly, the nature of carbonyl···carbonyl interactions has been subject to debate, with electrostatic or an n→π* electron delocalisation having been proposed as the dominant factors. The molecular orbital analysis employed here showed that n→π* delocalisation was exceptionally geometry dependent. Studies of literature systems reveal that n→π* delocalisation contributes to overall stability of a range of systems, with a quantitative link between molecular orbital energy and conformational free energies.

A thorough knowledge of non-covalent amino acid interactions within a protein structure is essential for a complete understanding of its conformation, stability and function. Among all the amino acids that usually make up a protein, tryptophan is distinguished both by its rarity and size of its side chain formed by an indole group. It is able to provide various types of indispensable interactions within the protein and between different polypeptide chains, but also between the protein and a biological membrane. In addition, it is the most commonly used natural fluorophore. Databases of solved protein structures are commonly used to study amino acid interactions and allow more or less complex analyzes of the issue. Thus many non-covalent interactions that may occur between tryptophan and other amino acids have been found. However, most of these analyzes focus on specific interactions and do not follow up the tryptophan's environment as a whole, where all amino acids interact. Some newly developed methods have been used in this Thesis, specifically the occurrence profiles of the individual amino acids around the indole group of tryptophan and the results were compared with an available literature. The amino acid that has the greatest preference for tryptophan turned out to be tryptophan again, and...

Les interactions non-covalentes (NCI pour Non-Covalent Interactions) stabilisant les complexes non-covalents biologiques (NCX pour Non-Covalent compleXes) régissent la majorité des processus cellulaires indispensables au développement et au bon fonctionnement de tout organisme vivant. Toutes les fonctions de l'ADN, tels que son conditionnement, sa réplication et la régulation de son expression, sont permises par la formation et la dissociation de NCI avec des protéines. La compréhension des bases de ces processus cellulaires de l'ADN au niveau moléculaire est un sujet d'actualité et d'une importance fondamentale. Des informations essentielles peuvent être obtenues par spectrométrie de masse (MS pour Mass Spectrometry) qui joue un rôle de plus en plus important dans ce domaine. Malgré la technologie avancée déjà mise en ¿uvre, le développement de nouveaux concepts d'ionisation et d'activation implémentent perpétuellement la MS. Les travaux de thèse exposés à travers ce manuscrit présente l'étude de la stabilité des NCI maintenant les NCX biologiques par la comparaison des voies de fragmentations observées en mode positif et en mode négatif mais aussi par l'application de certains concepts récents de la MS comme : (i) l'utilisation d'agents de " superchargement " et, (ii) le développement et l'utilisation d'une source V-EASI (pour Venturi Easy Ambiant Sonic-spray Ionization) permettant l'aspiration libre de la solution et la désorption/ionisation des analytes par la seule vélocité du gaz de nébulisation. / Non-covalent interactions (NCI) stabilizing biological non-covalent complexes (NCX) lead most of cellular processes compulsory for the development and the functioning of all living organisms. All DNA functions, such as its conditioning, its replication and the regulation of its expression, are allowed by the formation and the dissociation of NCI with proteins. The comprehension of cellular processes basis of DNA at the molecular level is both topical and fundamental. Crucial information can be obtained by mass spectrometry (MS) which plays an increasing role in this field. Despite the already advanced technology applied, the development new ionization and activation concepts implement perpetually the MS. The Ph.D. work described through this manuscript presents the study of NCI maintaining the biological NCX by the comparison of fragmentation pathways observed in positive ion mode and in negative ion mode but also by the application of some recent MS concepts like: (i) the use of supercharging reagents and, (ii) the development and the use of a Venturi Easy Ambiant Sonic-spray Ionization (V-EASI) source allowing the free aspiration of the solution and the desorption/ionization of the analytes only by the velocity of the spraying gas.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / This work presents the synthesis of five new planned [2]rotaxanes whith thread derivates succinamide [R1R2NC(O)CH2CH2C(O)NR1R2, where R1 = R2 = Pr, i-Pr, Bu, i-Bu e R1 = CH2Cy e R2 = CH2Ph]. The compounds were obtained by a five-component clipping reaction. Several studies have been conducted with these compounds such as: deslipping reactions, structural analysis, molecular dynamics by using solution 1H NMR spectroscopy and intra and intermolecular interactions using Hirshfeld surface. From these results, it was observed that the deslipping reaction was highly effective when microwave irradiation was employed and the reaction has shown to be an efficient model for the synthesis of macrocycles. Moreover, it was possible to calculate the rotational energy barrier of the macrocycle around the thread of [2]rotaxanes. In addition, when the Hirshfeld surface was used, it was possible to demonstrate all of the non-covalent interactions between the submolecular components as well as the intermolecular interactions of [2]rotaxane. / Este trabalho apresenta a síntese planejada de cinco novos [2]rotaxanos com filamentos lineares derivados da succinamida [R1R2NC(O)CH2CH2C(O)NR1R2, onde R1 = R2 = Pr, i-Pr, Bu, i-Bu e R1 = CH2Cy e R2 = CH2Ph]. A síntese dos compostos foi realizada através de uma reação cinco componentes utilizando o método clipping. Diversos estudos foram realizados com esses compostos, como: dissociação dos subcomponentes moleculares (deslipping), estruturais, de dinâmica molecular utilizando RMN de 1H em solução e das interações inter/intramolecular utilizando superfície de Hirshfeld. Através dos resultados foi possível verificar que a reação de deslipping foi altamente eficiente quando utilizado irradiação de micro-ondas, sendo um ótimo modelo para a síntese de macrociclos. Além disso, foi possível calcular a energia da barreira rotacional do macrociclo ao redor do filamento linear para os [2]rotaxanos em questão. Com a utilização da superfície de Hirshfeld foi possível demonstrar todas as interações intra e intermoleculares para os [2]rotaxanos.

Cette thèse est développée en 3 chapitres. Le premier chapitre décrit un travail d’ethnopharmacologie dans deux communautés de métis de l’Amazonie péruvienne. Les résultats montrent un inventaire de 46 plantes regroupées en fonction de leurs utilisations et préparations traditionnelles. Les activités in vitro contre trois parasites (Plasmodium falciparum, Leishmania donovani, Trypanosoma brucei gambiense) et leur cytotoxicité sont rapportées. Parmi toutes ces plantes Grias neuberthii (Lecythidaceae) et Costus curvibracteatus (Costaceae) ont montré une forte activité antiparasitaire, associé à une forte cytotoxicité pour C. curvibracteatus.Le deuxième chapitre décrit l’exploration, par spectrométrie de masse (SM) dans un milieu biomimétique reproduisant la vacuole digestive de Plasmodium (VDP), des liaisons intermoléculaires formé entre l’hème et des ligands. Les résultats pour des ligands de la famille des méthoxyflavones suggèrent qu’il n’existe pas de relation positive entre la stabilité de la liaison à l’hème et l’activité biologique contre deux souches de P. falciparum (3D7 et W2). Une corrélation est suggérée entre la présence d’une substitution méthoxylé en R5 de la flavone, la liaison à l’hème et l’hydrophobicité (cLogP). Cette relation peut s’expliquer en partie par l’influence des liaisons hydrogène avec le du groupe carbonyle. Des analyses d’arrimage moléculaire ont été aussi développées dans le but de comprendre les forces électrostatiques impliquées dans cette liaison. Le même type d’étude a été appliquée à des sondes fluorescentes originales dérivées de l’artémisinine (ART). La stabilité évaluée par CID montre des similitudes de comportement vis-à-vis de l’hème entre une des sonde et l’ART. La stabilité de trois sondes en différentes conditions mimant la biologie de Plasmodium a été évaluée.Le troisième chapitre détaille le développement d’une méthode de biodéréplication d’extraits bruts, en utilisant la méthodologie de liaison à l’hème par SM. La plante Piper coruscans (Piperaceae) a été utilisée pour l’application. La visualisation des adduits formés par SM a été faite de manière rapide par l’intermédiaire de réseaux moléculaires L’isolement des produits ciblés a été faite avec la chromatographie de partage liquide et chromatographie liquide préparative en un ou deux étapes. Treize molécules ont été isolées dont dix produits déjà connus dans la littérature : six flavanones, trois chalcones, un alkylamide; une indanone isolée pour la première fois comme produit naturel, et deux produits naturels nouveaux : une kavalactone et un dérivé de l’acide cinnamique. Parmi toutes ces molécules, une chalcone valide l’activité biologique de la plante et montre une liaison intermédiaire avec l’hème. / This work is developed in 3 chapters. The first chapter describes an ethopharmacological work in two Mestizos communities from Peruvian Amazonia. Results include an inventory of 46 plants grouped according to their uses and traditional preparations. In vitro activities on three parasites (Plasmodium falciparum, Leishmania donovani, Trypanosoma brucei gambiense) and their cytotoxicity are reported. Among all these plants Grias neuberthii (Lecythidaceae) and Costus curvibracteatus (Costaceae) showed a strong antiparasitic activity, associated with a strong cytotoxicity for C. curvibracteatus.The second chapter describes the exploration by mass spectrometry (MS) in a biomimetic environment mimicking the digestive vacuole of Plasmodium (DVP), the intermolecular bond between heme and ligands. Results for methoxyflavones suggested that there is no positive relation between the stability of the heme adduct and the biological activity on two P. falciparum strains (3D7 and W2). A correlation was suggested between the presence of a methoxy substitution in R5 of the flavone, heme binding and hydrophobicity (cLogP). This relation could be partially explained by the influence of the carbonyl group on hydrogen bounding. Docking analyses were performed to understand the electrostatic forces involved in the binding. The same kind of study was applied on original fluorescent probes based on artemisinin skeleton (ART). Stability of the heme adduct with the probes, evaluated by CID, showed similarities with ART. Stability of three probes in different conditions mimicking Plasmodium biology were evaluated.The third chapter presents the development of a crude extract biodereplication method, using heme-binding methodology by MS. The plant Piper coruscans (Piperaceae) was selected for this application. MSMS adducts visualization was performed by molecular networking. Targeted products were isolated by centrifugal partition chromatography or preparative liquid chromatography, in one or two steps. Thirteen molecules were isolated, including ten already known products: six flavanones, three chalcones, one alkylamide, one indanone isolated for the first time like a natural product and two new coumpounds: one kavalactone and one cinnamic acid derivative. Among all these molecules, a chalcone validated the biological activity of the plant and showed an intermolecular bound with heme.

Intermolecular Interactions in Proteins - Abstract Mgr. Jiří Kysilka Non-covalent interactions are responsible for the protein folding and the molecular recognition during the protein interaction with other molecules, including various ligands, other proteins and solvent molecules. In order to understand these processes, exhibited by protein molecules, a proper description of non-covalent interactions is needful. Most methods that are computationally available for the systems of biological interest have difficulties handling with the dispersion term. In this thesis, a density functional theory / coupled clusters (DFT/CC) correction scheme is utilized for a set of small molecules, interacting with a graphitic surface. The results serve as a benchmark for the interaction of the functional groups of proteins with hydrophobic environment. In the following part of this thesis, the role of non-covalent interactions in proteins was studied for the processes of protein-protein interaction and protein hydration. Interaction interfaces has been localized in a set of 69 protein dimers and their composition has been characterized. Interfaces has been shown to prefer branched-chain hydrophobic amino acids (Ile, Leu, Val), aromatic amino acids (Phe, Tyr) and exclude the charged amino acids except of Arg. It was...

Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...

Phosphonium ions readily compare to ammonium ions in regards to their aggregate characteristics, thermal stability, and antibacterial activity. Ionic aggregation in phosphonium-based polymers provides thermoreversible crosslinks, ideal for reversible self-assembly, self-healing, and smart response. In polymers, these ionic functionalities aggregate, providing improved moduli, and altering the size and structure of ionic aggregates regulates polymer melt processability. This dissertation highlights phosphonium-based chemistry for the synthesis of novel step-growth ionomers and structure-property relationships in ionic polymers. The synthesis of phosphonium endcapping reagents for melt polyester reactions afforded a thermally stable ionic functionality that controlled molecular weight. Weak association was present with phosphonium ions at low ion concentrations below 7.7 mole %. The use of novel ionic bisacetoacetate monomers in the formation of networks from Michael addition reactions led to the synthesis of ionic networks with increased and broadened glass transitions and improved tensile stresses at break and strains at break compared to those in the non-ionic networks. The first electrospun fibers from Michael addition crosslinking reactions are reported, and equilibrium ionic liquid uptake experimental results indicated that ionic functional networks absorb close to three times the amount of ionic liquid as non-ionic, poly(ethylene glycol)-based films. Chain-extending polyurethanes with a phosphonium diol and subsequently varying the hard segment content led to changes in ionic aggregation, crystallinity, and thermal transitions in the polymers. Additionally, novel phosphonium-based methacrylate monomers incorporated into diblock copolymers with styrene exhibited microphase separation. Overall, the inclusion of phosphonium ions pendant to or in the main chain of various types of polymers led to changes in morphology, improved tensile properties, enhanced moduli, broadened transitions, changes in crystalline melting points, changes in solubility, and appearance of ionic aggregation. / Ph. D.

Coiled coils are a well-known protein structure prevalent in eukaryotic function, synthetic applications, and de novo protein design. Coiled-coil folding is often described using heptad repeat positions labeled abcdefg where a and d positions occupy the interface between the coils, e and g positions flank the interface, and the b, c, and f positions face the solvent-exposed surface. The a, d, e, and g positions have been extensively studied in the coiled-coil literature. There is a lack of investigation on the impact of the b, c, and f positions on coiled-coil folding. Chapter 1 is an introduction to the heptad repeat of coiled coils and the impact on folding of each heptad repeat position. In Chapter 2 we introduce a non-covalent interaction among the b, c, and f positions of a coiled-coil trimer that significantly enhances thermodynamic stability. We identify characteristics of the f-position residue (hydrogen bond donating ability and hydrophobicity) that lead to the greatest amount of stability. Chapter 3 introduces crystal structures and molecular dynamic simulations of the interaction to identify the mechanism of stabilization. Further thermodynamic studies find a key salt-bridge interaction between the b and c positions that are influenced by the f-position residue. Chapter 4 explores the impact of salt on the non-covalent interaction and determines that the interaction is sensitive to salt screening and is ionic in nature. It also explores more characteristics of the f-position amino acid, in particular the hydrogen bond donating component. In Chapter 5 we insert the solvent-exposed interaction into helix bundles of differing length and oligomeric state. We find that stability is not only dependent upon amino acid identity but also the length and stoichiometry of a coiled coil.

L’avènement de la microscopie biphotonique et des techniques dites de « super-résolution » ont permis d’améliorer les performances de la microscopie de fluorescence et de l’appliquer à l’imagerie intravitale et à l’analyse des tissus biologiques. Ces techniques requièrent néanmoins l’emploi de sondes aux propriétés optiques et biologiques optimisées.Plusieurs séries de colorants cationiques basés sur le motif vinyl-triphénylamine (TP) ont été développés pour le marquage d’ADN. Ces fluorophores rouges ou jaunes dont l’émission de fluorescence est commutée par l’interaction avec l’ADN sont des ligands de petit sillon de l’hélice B et possèdent des sections efficaces d’absorption à deux photons élevées.Les TP marquent l’ADN du noyau des cellules fixées ou en apoptose avec une intensité et un contraste élevés. Elles sont non-cytotoxiques, photostables et sont perméables à la membrane cellulaire. L’optimisation des propriétés a permis d’obtenir la TP-2Bzim, qui possède une brillance biphotonique parmi les plus élevées rapportées dans la littérature pour des molécules de faible poids moléculaire (383 GM) et permet une détection en microscopie biphotonique à basse concentration et à faible puissance d’excitation. En cellules vivantes, les TP sont localisées dans les mitochondries mais, sous excitation mono- ou bi-photonique constante, elles déclenchent l’apoptose de la cellule et se relocalisent dans le noyau. Le phénomène peut être imagé par fluorescence, et les TP pourraient donc être employées comme photosensibilisateurs théranostiques.Enfin, une stratégie de synthèse pour fonctionnaliser la TP-2Bzim a été développée. Elle a ainsi pu être couplée à des oligonucléotides et à un PNA pour la détection d’hybridation par fluorescence et à l’acide folique et à la spermidine pour le ciblage de cellules cancéreuses. / Significant advances were made in the field of in vivo fluorescence imaging thanks to the recent development of biphotonic microscopy and super-resolution techniques, rendering intravital imaging and biological tissues analysis possible. Those techniques however require the use of new probes with optimized optical and biological properties.Several series of cationic dyes for DNA staining were developed based on the vinyl-triphenylamine (TP) scaffold. Those new switchable yellow or red fluorophores bind in the minor-groove of DNA and display high two-photon absorption cross-sections. Two anionic derivatives were also designed for staining HSA.In fixed or apoptotic cells, the cationic dyes stain nuclear DNA with a high brightness and contrast. They are non-cytotoxic, photostable and cell permeant. The molecule with the most optimized properties, TP-2Bzim, has one of the highest two-photon brightness to date (383 GM in DNA), allowing sensible detection in biphotonic microscopy at low concentration and excitation power. In live cells, the dyes are localized in the mitochondria, but it appears that upon constant mono- or bi-photonic excitation they trigger cell apoptosis within a few minutes and are released in the nucleus. Since the phenomenon can be imaged by fluorescence microscopy, the TP dyes could thus be used as photosensitizers for theranostics.A synthetic pathway was also developed to functionalize the TP-2Bzim. It was then coupled by “click-chemistry” to short oligonucleotides or PNA sequences for fluorescence in situ hybridization, and to folic acid and spermidine for cancer cells targeting.