The thesis entitled “Unravelling the Nature of Halogen and Chalcogen Intermolecular Interactions by Charge Density Analysis" consists of five chapters. A basic introductory section describes the topics relevant to the work and the methods and techniques utilized. The main focus of the present work is to characterize the interaction patterns devoid of strong classical hydrogen bonds. The case studies include halogen bonds and hydrogen bonds involving bromine (as a halogen bond donor and hydrogen bond acceptor), intermolecular chalcogen bond formation involving sulphur, type I Br Br contacts, type II F F and F S interactions and S-H S hydrogen bonds. Chapter 1 discusses experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one which has been carried out to quantify the topological features of a short C Br···O halogen bond with nearly linear geometry (2.922Å, C Br···O=172.7) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the “- hole” on bromine while the interaction energy is comparable to that of a moderate O-H O hydrogen bond. In addition, the energetic contribution of C-H···Br interaction is demonstrated to be on par with that of the C-Br···O halogen bond in stabilizing the crystal structure. Chapter 2 discusses an organic solid, 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole that has been designed to serve as an illustrative example to quantitatively evaluate the relative merits of halogen and chalcogen bonding in terms of charge density features. The compound displays two polymorphic modifications, one crystall zing in a non-centrosymmetric space group (Z =1) and the other in a centrosymmetric space group with two molecules in the asymmetric unit (=2). Topological analysis based on QTAIM clearly brings out the dominance of chalcogen bond over the halogen bond along with an indication that halogen bonds are more directional compared to chalcogen bonds. The cohesive energies calculated with the absence of both strong and weak hydrogen bonds as well as stacking interaction are indicative of the stabilities associated with the polymorphic forms. Chapter 3 discusses the role of a type I C-Br Br-C contact and what drives the contact i.e. how a dispersive interaction is stabilized by the remaining contacts in the structure. In the process we observe the role the Br2Cl motif which is quite unique in its nature. Also the role of the bromine atoms in stabilizing the stacking interactions has been shown by the electrostatic potentials which are oriented perpendicular to the plane of the benzene ring. Chapter 4 discusses the enigmatic type II C-F F-C and C-FS-C interactions in pentafluorophenyl 2,2- bithiazole. Both the interactions are shown to be realistic “-hole” interactions based on high resolution X-ray charge density analysis. As fluorine is the most electronegative element, its participation in halogen bonding wherein the electrostatic potential around the atom gets redistributed to form regions of electron depletion and accumulation had time and again been speculated but never observed. In this chapter the experimental charge dnsity analysis clearly identifies the “-hole” on fluorine and distinguishes the C-F S-C interaction as a halogen bond rather than the chalcogen bond. Chapter 5 discusses the experimental charge density analysis of the hitherto unexplored S-H S hydrogen bond in crystal structures. The work highlights how relatively small is the number of crystal structures which are constructed by the S-H S hydrogen bond compared to the X-H S hydrogen bond via Cambridge Structural Database (CSD) analysis. The potential S-H S hydrogen bond is studied in three isomeric mercaptobenzoic acids with experimental charge density collected on 2-mercaptobenzoic acid and theoretical estimates made on 3- and 4-mercaptobenzoic acid. The strength and directionality of the S-H S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of intramolecular S O halogen bond.

Ce travail a pour objet de synthétiser de nouveaux matériaux hybrides organiques-inorganiques, de types silsesquioxanes pontants. La structure locale et les propriétés de luminescence sont caractérisées en vue d’applications potentielles dans le domaine de la photonique durable comme les concentrateurs solaires.Dans ce contexte, trois familles distinctes de matériaux sont synthétisées, basées sur six précurseurs pouvant s’auto-assembler à travers des liaisons hydrogènes et dont les parties sililées peuvent être poly-condensées lors de la réaction sol-gel. Ces précurseurs diffèrent par leur sous structure organique i.e. 1) structure linéaire où la partie organique est basée sur le groupement malonamide (P2-m et P4-m); 2) structure linéaire dans laquelle un aromatique sépare deux groupements amide et/ou thioamide (P(UU), P(UT) and P(TT)) et 3) une structure à trois embranchements dont la partie organique est basée sur des groupements amides (t-UPTES (5000)).Les deux hybrides organiques inorganiques (M2-m et M4-m) résultant de l’hydrolyse condensation des précurseurs P2-m et P4-m sont synthétisés en présence de lanthanides. On étudie l’impact de la présence d’un ou deux groupes malonamides sur la structure locale et les propriétés de photoluminescence.Les hybrides organiques-inorganiques (H(UU), H(UT) and H(TT)) sont obtenus par hydrolyse condensation des précurseurs des précurseurs (P(UU), P(UT) and P(TT)). Des composés organiques modèles des trois sous structurels organiques sont également synthétisés. L’impact de la substitution du groupement urée par le groupement thio-urée sur la structure locale des modèles et des hybrides est étudié par spectroscopie vibrationnelle. Les mécanismes de compressions et les propriétés optiques des matériaux sont ensuite analysés à la lumière des différents types de liaisons hydrogènes (urée-urée, urée-thio-urée et thio-urée--thio-urée) mises en évidence dans ces composés.es hybrides basés sur les précurseurs t-UPTES(5000) sont synthétisés selon différentes stratégies. En changeant la concentration de HCl et d’eau ou en effectuant la synthèse dans un environnement contrôlé, on montre une amélioration des propriétés optiques de ce système, en particulier, le rendement quantique absolu et le coefficient d’absorption. De plus, les mécanismes de recombinaison responsables de l’émission sont étudiés à travers la comparaison entre les propriétés de luminescence des modèles organiques et inorganiques.Finalement, de par leur affinité pour les ions lanthanides les précurseurs P2-m and P4-m ont été dopés par des ions Eu3+. La structure locale des hybrides correspondants montre une coordination entre l’hybride et l’hôte. Grâce à un rendement quantique de luminescence très élevé pour ces matériaux, des concentrateurs solaires luminescents peuvent être développés présentant un maximum de rendement quantique absolu de 0.60+/-0.06 et un rendement de conversion optique de 12.3% dans la région spectrale (300-380 nm). / The present work aims to synthesize new organic-inorganic hybrid materials, bridge silsesquioxanes type, and characterize the local structure and photoluminescence properties overlooking potential applications in the area of sustainable photonics, namely, in solid-state lighting as luminescent solar concentrators.In this context, three distinct families of materials based on six precursors which differ in their structural organization are synthesized, i.e. precursors with structure: 1) linear where the organic component is based on malonamide group (P2-m and P4-m); 2) linear which is added an aromatic ring whose organic part is based on amide and/or thioamide (P(UU), P(UT) and P(TT)) and 3) tri-branched which the organic component is based on amide group (t-UPTES (5000)).Two organic-inorganic hybrids (M2-m and M4-m) which results from hydrolysis and condensation of the precursors P2-m and P4-m are synthetized. The role of the presence of one or two malonamide groups is studied in terms of local structure and photoluminescence properties.Three organic-inorganic hybrids (H(UU), H(UT) and H(TT)) based on (P(UU), P(UT) and P(TT)) aresynthesized and structurally characterized aiming to study the role of the hydrogen bond in the self-assembling of these materials. The presence of different types of hydrogen bonds (bifurcated, linear and cyclic) induces different conformations which affect the physical properties (mechanical and optical) of the materials.Hybrids based on t-UPTES(5000) precursor are synthesized based on different synthesis strategies. Changing the concentration of HCl and water content as well as the synthesis in a controlled environment allow the improvement of the optical properties of this system, in particular, the absolute quantum yield and the absorption coefficient. In addition, it is studied the recombination mechanisms responsible for the emission through the comparison between the corresponding photoluminescence properties of the organic and inorganic models.Finally, due to the structural simplicity of the precursors and affinity with lanthanide ions, P2-m and P4-m precursors are doped with Eu3+. The local structure of the corresponding hybrids shows local coordination between the ion and host. Efficient materials concerning the quantum yield values lead to the development of luminescent solar concentrators with a maximum absolute quantum yield of 0.600.06 and optical conversion efficiency in the absorption spectral region (300-380 nm) of 12.3%.

No presente trabalho utilizamos as espectroscopias eletrônica e vibracional, com o apoio de simulação computacional de líquidos para estudar o comportamento solvatocrômico e ionocrômico de diaminoantraquinonas. Adicionalmente estudamos a potencialidade da 1,2-diaminoantraquinona (1,2-DAAQ) no reconhecimento de ânions em superfícies de prata. Utilizando espectroscopia de absorção obtivemos espectros da 1,2-DAAQ e alguns isômeros em diversos solventes. Estes resultados foram analisados por métodos empíricos de solvatocromismo, principalmente, pela escala solvatocrômica de Kamlet-Taft. Esta análise nos propiciou um conhecimento preciso sobre o comportamento da 1,2-DAAQ em meio solvente e serviu de suporte para o estudo do ionocromismo, e da interação com as superfícies. Através da simulação computacional geramos estruturas de soluções da 1,2-DAAQ em três solventes e analisamos a estrutura destas soluções via análise das Funções de Distribuição Radial de pares, o que nos possibilitou uma visão no nível microscópico do efeito das interações com o solvente. As estruturas geradas serviram de base para o cálculo do espectro de absorção para comparação com os valores experimentais. Baseado nesta comparação foi possível especular que a estrutura da 1,2-DAAQ é afetada pelo solvente no estado excitado. Utilizando espectroscopia no infravermelho e eletrônica foi possível caracterizar o tipo de interação entre a 1,2-DAAQ e o ânion fluoreto, como sendo por ligação de hidrogênio de força moderada. A atribuição vibracional da 1,2-DAAQ foi realizada com base nos espectros Raman, auxiliada por cálculos de freqüência. A atribuição foi utilizada para a determinação da orientação da 1,2-DAAQ nas superfícies de prata e principalmente para estudar a natureza desta interação. A análise destes resultados nos permitiu traçar um panorama bastante claro sobre esta interação além de auxiliar no entendimento do uso da 1,2-DAAQ como sonda aniônica de superfícies. Finalmente, através da espectroscopia Raman ressonante foi possível confirmar e detalhar a atribuição da transição eletrônica observada na região do visível, característica das diaminoantraquinonas. / In the present work, the ionochromic and solvatochromic behavior of several diaminoantraquinones were investigated by means of optical and vibrational spectroscopies, alongside computational simulation. The UV-Vis spectra of 1,2- diaminoantraquinone (1,2-DAAQ) were analyzed using empirical solvatochromic scales, like the Kamlet-Taft. Such analysis enabled an accurate description of its solvatochromic behavior that was instrumental to understand its interaction with anions and metallic surfaces. Computational simulation provided the structures of 1,2-DAAQ solutions in three different solvents, and the analyses of the radial distribution functions revealed a microscopic view of its interactions with the solvents. The obtained structures were the departing points for the calculation of the electronic spectrum, then compared with the experimental one. The results suggest that the structure of 1,2-DAAQ is substantially affected by the solvent in the excited state. Infrared spectroscopy clearly indicates that the interaction of the 1,2-DAAQ and fluoride involves a hydrogen bonding of moderate strength. Raman spectroscopy and quantum chemical calculations provided the means for the vibrational assignment that was instrumental to understand the orientation of the molecule in its interaction with silver surface.

The studies on cocrystals and salts presented in the the chapters clearly bring out the influence of intermolecular interactions as the main evaluators of the cocrystal-salt regime. The observations made in Chapter 2 indicate that in case if the cocrystal formation is through hydrogen bonds the location of the proton decides the nature of the complex in the energy landscape. The observation that the coformer controls the topology of intermolecular space as demonstrated in Chapter 3 provides insights into the importance of directionality rather than strength of intermolecular interactions. Indeed halogen bonding in cocrystals gain importance in this context.

The nature of interactions within a molecule, i.e. chemical bonding, is well understood today. However, our understanding about intermolecular interactions, which has great relevance in nature, is still evolving. Historically there are two types of intermolecular interactions, van der Waals interaction and hydrogen bonding. However, there has been an upsurge of interest in the halogen bonding and lithium bonding during the last decade. The main emphasis of our research is to understand these interactions in detail, in particular non-conventional hydrogen bond acceptors. In this work, weakly bound complexes are studied using Pulsed Nozzle Fourier Transform Microwave Spectrometer, which has been fabricated in our laboratory and various theoretical methods. FTMW spectroscopy in the supersonic beam provides accurate structural information about the near-equilibrium geometry of small dimers and trimers in isolation. The home-built Pulsed Nozzle Microwave spectrometer, having a spectral range of 2-26.5 GHz has been used to record the microwave spectrum of these complexes. The spectrometer consists of a Fabry-Perot cavity, electronic circuit and pumps. Fabry-Perot cavity is the interaction zone of the molecules and radiation. The electronic circuit is used for the polarization and detection of the signal. Mechanical and diffusion pumps are used to maintain the vacuum inside the cavity. The gas molecules of interest are then mixed with a carrier gas and pulsed supersonically inside the cavity through a nozzle of 0.8 mm diameter. The emission from the complexes formed during the expansion is detected by super-heterodyne detection technique and then Fourier transformed. The first chapter of the thesis gives a brief introduction to intermolecular interactions, hydrogen bonding, halogen bonding, lithium bonding and molecular 2 of clusters. The chapter also includes a brief introduction to rotational spectroscopy. The second chapter of the thesis discusses the experimental and theoretical methods. It includes a detailed discussion of the mechanical and electrical parts of the spectrometer and the software used, which is developed in Labview 7.1. The various theoretical methods (ab initio and DFT) and the basis sets are discussed along with Atoms In Molecules Theory and the criteria used to characterize hydrogen bond. In the third chapter, to understand the ability of saturated hydrocarbons to act as hydrogen bond donor and acceptor, interaction of CH4 with H2S is studied using rotational spectroscopy as well as theoretical methods such as ab initio and Atoms In Molecules theory. Three progressions were obtained for the CH4•••H2S complex using microwave spectroscopy. The progressions were independently fitted to a linear top Hamiltonian. Absence of J10 transition in Progression II confirms the presence of higher internal angular momentum state, m=1. This also confirms the internal rotation of the monomers in the complex. Progressions II and III have negative centrifugal distortion constants. Hence both the states are from some excited internal rotation/torsional motion with strong vibrational-rotational coupling. The moment of inertia obtained from the experimental rotational constant confirms the structure in which sulphur of H2S is close to CH4. This also supports the structure in which CH4 is the hydrogen bond donor, if such an interaction is present. AIM analysis and the potential energy barrier for internal rotation show orientational preference and hence hydrogen bonding. The ab initio results show that CH4•••HSH interaction is more favorable than CH3H•••SH2. Ab initio and AIM studies also gave a structure where there is direct interaction between C and S. This is interesting since the electronegativities of C and S are comparable. Experimentally obtained negative distortion constants for the other two states, confirm excited state rotational-vibrational coupling. The experimental data give a floppy structure having internal rotation. In the fourth chapter the complex chosen for investigation is benzene-ethylene. Experiments in condensed phase and theoretical works show evidence of - stacking in benzene dimer, but there is no gas phase spectroscopic evidence available for the same. The lack of permanent dipole moment in the -stacked geometry of benzene dimer is the hindrance in the experimental observation of the same using microwave spectroscopy. Substitution of one of the benzene with ethylene in the -stacked structure will result in a complex having permanent dipole moment. C6H6 C2H4 complex can have, in addition to -stacking, C-H/interaction. There could be a competition between C6H6 and C2H4, either of which can act as H-bond donor. Experiments show the evidence of C-H/interaction, where C2H4 is the hydrogen bond donor. To ascertain hydrogen bond interaction AIM analysis has been carried out. The results show C-H/interaction, where one of the C2H4 hydrogen interacts with the benzene. Even though the aim was to get the -stacked geometry, it could not be obtained. However theory and AIM supports the formation of -stacked complex. In the fifth chapter using theoretical methods the ability of radicals as acceptor of hydrogen, lithium and chlorine bonds are examined with CF3 radical as the model system. As hydrogen bonds are highly sensitive to the environment, the effect of substitution of hydrogen by fluorine is also analyzed. It is found that, even though CH3 and CF3 radicals are topologically different, they interact in a similar fashion. AIM analysis of CF3HY satisfies all the eight criteria proposed by Koch and Popelier for hydrogen bonding. Here the hydrogen bond formed is charge transfer assisted. The interaction energies of the complexes are inversely proportional to the dipole moment of hydrogen bond donors and are proportional to the charge transfer occurring in the complex. Interaction energies from ab initio calculations confirm complexation of CF3 radical with LiY(Y=F, Cl, Br) and ClF. AIM analysis of CF3LiY and CF3ClF complexes show a bond critical point between Li/Cl and the C of CF3 and the condition of mutual penetration is also met. In CF3LiY complexes the interaction energies and charge transferred are directly proportional to the dipole moment of the Li bond donor. In the sixth chapter in order to extend the concept of non-conventional hydrogen bond acceptors to transition metals, complexes of Fe (Fe(CO)5) with HX (X=F,Cl,Br) have been studied theoretically. DFT calculations show that the structure in which the hydrogen of HX interacting with Fe through the sixth co-ordination site is a stable geometry. AIM analysis shows the presence of a bond critical point between the iron and the hydrogen of HX and hence bond formation. Q obtained from NBO analysis shows that there is charge transfer from the organometallic system to the hydrogen bond donor. However the interaction energies of the complexes are proportional to the dipole moment of hydrogen bond donors and are inversely proportional to the charge transfer for these complexes. H-bonding leads to the stabilization of square pyramidal geometry. ‘Hydrogen bond radius’ of iron has also been defined. Studies on the interaction of Fe(CO)5 with ClF and ClH showed that Fe can also act as a chlorine bond acceptor. Seventh chapter provides the overall conclusion and also discusses future direction.

Le but de cette thèse est une revisite du potentiel SIBFA. Ceci inclut un travail et une réflexion sur la méthodologie de cette approche avec une implémentation proposant une utilisation plus large. De plus, une nouvelle calibration de champ de forces raffiné est permise aujourd’hui. En effet, la décomposition d’énergie intermoléculaire SAPT donne accès à toutes les composantes avec rigueur. La reproduction des résultats ab-initio par un potentiel analytique laisse entrevoir des applications prometteuses. Au-delà du coup de calcul considérablement réduit par rapport aux méthodes de chimie quantique, son intégration dans un code de dynamique moléculaire ouvre les portes à de nombreuses études encore plus prometteuses hors de portée de la chimie quantique. Enfin l’optimisation de ce code, avec une parallélisation bien étudiée, en feront un outil majeur de la biochimie. Dans une première partie, nous introduirons les notions et principes essentiels à la dynamique moléculaire. Un premier chapitre exposera la mécanique classique utilisé dans les programmes les plus distribués et utilisés. Un second chapitre introduira les méthodes permettant un meilleur traitement des interactions non-covalentes essentielles dans les études de complexes ligand-récepteur. Une seconde partie abordera de manière plus concrète la stratégie d’implémentation de SIBFA dans Tinker. Celle-ci s’organisera autour de trois chapitres, traitant chaque composante énergétique intermoléculaire. L’objectif de cette thèse est de proposer un socle solide autour du traitement des interactions non covalentes dans le cadre des champs de forces polarisables de dernières générations et de présenter le modèle d’eau hybride AMOEBA/SIBFA. / The purpose of this thesis is to revisit the potential of SIBFA (Sum of Interactions Between Fragments Ab initio computed) [...]

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...

<p>One in eight woman develop breast cancer in the United States of America and is the most common type of cancer in the world. Breast cancer has the highest rate of death compared to any other form of cancer. Triple Negative Breast Cancer (TNBC) is the most lethal type of breast cancer, which is the most fatal of all breast cancer types. TNBC is onerous to treat since it lacks all the three most commonly targeted hormones and receptors. Current patients afflicted with TNBC are treated with platinum core chemotherapeutics, namely Cisplatin. Despite the anticancer effects shown by Cisplatin, TNBC attenuates its effect and develops a resistance eventually, which results in reoccurrence of TNBC after few years. Hence there is a demand for effective and alternative ways to treat TNBC. To inhibit the TNBC cell proliferation, blocking the key glycolytic enzyme Lactase Dehydrogenase B (LDHB) is studied and validated. Galloflavin (GF), a proven LDHB inhibitor is utilized in this series of studies and analysis. In addition, Electrochemotherapy, which involves the application of electrical pulses (EP) were utilized to enhance the uptake of GF. The combination of Electrochemotherapy (ECT) with LDHB is a novel way to treat TNBC to produce an alternative to traditional chemotherapy. EP+GF will be subjected onto TNBC cells at various concentrations and pulse parameters. The purpose of this study is to test the effect of alternative chemotherapeutic drug delivery methods for TNBC patients for decrease in mortality rate and improve quality of life. Results indicate TNBC cell viability is the least for EP+GF treatments and the maximum Reactive Oxygen Species (ROS) levels and a maximum decrease in Glucose and Lactate uptake for EP+GF treatments relative to control. Immunoblotting studies indicate the inhibition of LDHB is the most on EP+GF treatments, indicating that this could be a novel modality to treat TNBC.<br></p>

L’objectif de ces travaux est d’analyser les propriétés rhéologiques de l’acétate de cellulose, un polymère biosourcé. Afin de faciliter la mise en œuvre de l’acétate de cellulose, il est usuel d’y incorporer des plastifiants. Dans le but de développer la transformation de ce polymère par des procédés industriels conventionnels, il est nécessaire d’obtenir davantage d’informations rhéologiques pour différentes conditions d’écoulement. Le comportement rhéologique particulier d’un acétate de cellulose plastifié de degré de substitution 2,45 a été étudié à l’aide de différentes mesures rhéologiques. Des mesures viscoélastiques dans le régime linéaire ont été menées et des comportements inattendus ont été mis en évidence. Par rapport à des polymères thermoplastiques conventionnels, la structure et les dynamiques des relaxations des chaînes macromoléculaires d’acétate de cellulose semblent être plus complexes que celles des polymères synthétiques communs. Ces observations ont été confirmées par des mesures dans le régime non linéaire. Les résultats suggèrent que le comportement viscoélastique des chaînes d’acétate de cellulose n’est pas contrôlé par des enchevêtrements mais plutôt par une autre longueur de corrélation définie par l’existence de points d’interactions fortes entre les chaînes nommés stickers. Ces interactions engendrent un comportement d’échelle inhabituel suivant le taux de plastifiant et la température. / This present work deals with the rheological properties of cellulose acetate which is a biobased polymer manufactured from cellulose. In order to facilitate its forming process, cellulose acetate is usually blended with plasticizers. As the conventional industrial processes need rheological information for different flow conditions, viscoelastic behaviour of a plasticized cellulose acetate with a degree of substitution of 2,45 was investigated by various rheology experiments. Measurements in the linear regime were carried out for various plasticizer contents and some unexpected behaviours have been highlighted. Compared to conventional thermoplastic polymers, the structure and dynamics of the macromolecular chains of cellulose acetate seem to be more complex than that of common synthetic polymers. This was confirmed by measurements in the nonlinear domain. The results suggests that the viscoelastic behaviour of cellulose acetate chains is not controlled by entanglements but rather by another correlation length related to strong interactions between chains, named stickers. These interactions confer to the polymer dynamics an unusual scaling behaviour depending on plasticizer content and temperature.

No description available.