Our understanding of the folding of membrane proteins lags behind that of soluble proteins due to the challenges posed by the exposure of hydrophobic regions during in vitro chemical denaturation and refolding experiments. While different folding models are accepted for soluble proteins, only the two-stage model and the long-range interactions model have been proposed so far for helical membrane proteins. To address our knowledge gap on how different membrane proteins traverse their folding landscapes, Chapter 2 investigates the structural features of SDS-denatured states and the kinetics for reversible unfolding of sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis. pSRII is difficult to denature, and only SDS can dislodge the retinal chromophore without rapid aggregation. Even in 30% SDS (0.998 $\mathit{\Chi}_{SDS}$), pSRII retains the equivalent of six out of seven transmembrane helices, while the retinal binding pocket is disrupted, with transmembrane residues becoming more solvent-exposed. Folding of pSRII from an SDS-denatured state harbouring a covalently-bound retinal chromophore shows deviations from an apparent two-state behaviour. SDS denaturation to form the sensory opsin apo-protein is reversible. This chapter establishes pSRII as a new model protein which is suitable for membrane protein folding studies and has a unique folding mechanism that differs from those of bacteriorhodopsin and bovine rhodopsin. In Chapter 3, SDS-denatured pSRII, acid-denatured pSRII and sensory opsin obtained by hydroxylamine-mediated bleaching of pSRII were characterised by solution state NMR. 1D $^1$H and $^{19}$F NMR were first used to characterise global changes in backbone amide protons and tryptophan side-chains. Residue-specific changes in backbone amide chemical shifts and peak intensities in 2D [$^1$H,$^{15}$N]-correlation spectra were analysed. While only small changes in the chemical environment of backbone amides were detected, changes in backbone amide dynamics were identified as an important feature of SDS- and acid-denatured pSRII and sensory opsin. $^{15}$N relaxation experiments were performed to study the backbone amide dynamics of SDS-denatured pSRII, reflecting motions on different timescales, including fast fluctuations of NH bond vectors on the ps-ns timescale and the lack of exchange contributions on the µs timescale. These studies shed insight on differences in the unfolding pathways under different denaturing conditions and the crucial role of the retinal chromophore in governing the structural integrity and dynamics of the pSRII helical bundle. Hydrogen bonds play fundamental roles in stabilising protein secondary and tertiary structure, and regulating protein function. Successful detection of hydrogen bonds in denatured states and during protein folding would contribute towards our understanding on the unfolding and folding pathways of the protein. Previous studies have demonstrated residue-specific detection of stable and transient hydrogen bonds in small globular proteins by measuring $^1{\it J}_{NH}$ scalar coupling constants using NMR. In Chapter 4, different methods for measuring $^1{\it J}_{NH}$ scalar coupling were explored using RalA, a small GTPase with a mixed alpha/beta fold, as proof-of-concept. Detection of hydrogen bonds was then attempted with OmpX, a beta-barrel membrane protein, both in its folded state in DPC micelles and in the urea-denatured state. While $^1{\it J}_{NH}$ measurement holds promise for studying hydrogen bond formation, further optimisation of NMR experiments and utilisation of perdeuterated samples are required to improve the precision of such measurements in large detergent-membrane protein complexes. Naturally occurring split inteins can mediate spontaneous trans-splicing both in vivo and in vitro. Previous studies have demonstrated successful assembly of proteorhodopsin from two separate fragments consisting of helices A-B and helices C-G via a splicing site in the BC loop. To complement the in vitro unfolding/folding studies, pSRII assembly in vivo was attempted by introducing a splicing site in the loop region of the beta-hairpin constituting the BC loop of pSRII. The expression conditions for the N- and C-terminal pSRII-intein segments were optimised, and the two segments co-expressed. However, the native chromophore was not observed. Further optimisation is required for successful in vivo trans-splicing of pSRII and application of this approach towards understanding the roles of helices and loops in the folding of pSRII.

Work reported in this thesis mainly comprises of the assignments and analysis of the rotational spectra and structures of three weakly bound complexes: C2H4•••H2S, C6H5CCH•••H2O and C6H5CCH•••H2S. All the data have been collected using a home built Pulsed Nozzle Fourier Transform Microwave Spectrometer. Apart from this, the thesis also deals with a criterion of classifying a weakly bound complex to a ‘hydrogen-bonded’ one. First chapter of the thesis gives a brief intermolecular interactions and molecular clusters of π system. It also briefly touches on the structural determination by rotational spectroscopy and the basic information one can gain from the rotational spectrum. Second chapter of the thesis gives a brief introduction to the experimental and theoretical methodology. It also gives a description of the software used in the FTMW spectrometer which was rebuilt using Labview 7.1. Third chapter of the thesis deals with the rotational spectra and structure of eight isotopologoues of C2H4•••H2S complex. The lines are split into four components for the parent isotopologue due to the presence of large amplitude motion. The smaller splitting is 0.14 MHz and the higher splitting is 1.67 MHz in (B+C)/2 for the parent isotopologue. Spectral splitting pattern of the isotopologues confirmed that smaller splitting is due to the rotation of ethylene about its C-C bond axis along with the contraction of S-H bond whereas the larger motion arises due to the interchange of equivalent hydrogens of H2S in the complex. A detailed spectral analysis and ab initio calculation for this system have been described in chapter III. The fourth chapter of the thesis describes the rotational spectroscopic studies of five isotopologues of C6H5CCH•••H2O complex. Rotational spectra unequivocally confirm the structure of the complex to be a one where H2O is donating one of its hydrogen to the acetylenic π cloud forming a O-H••• π bond whereas the ring ortho C-H bond forms C-H•••O bond with the water oxygen. For theparent isotopomer the lines are split into two components due to the rotation of H2O about its C2 symmetric axis. The fifth chapter of thesis describes the rotational spectroscopic and ab initio studies of five isotopologues of C6H5CCH•••H2S complex. Rotational spectra indicate the structure to be the one where H2S is sitting on the top of the phenyl ring and shifted towards the acetylenic group. The sixth chapter of the thesis describes a criterion for calling a complex to be hydrogen bonded based on the dynamic structure rather than the static structure of the complex. The question asked is if the anisotropy of the interaction is strong enough to hold the ‘hydrogen bond’ when one takes dynamics into account. The proposed criterion is that the zero point energy of the motion which takes the hydrogen away from the acceptor should be much less than the barrier height of the respective motion supporting at least one bound level below the barrier. Ab initio calculations have been done on four model systems Ar2•••H2O, Ar2•••H2S, C2H4••• H2O and C2H4••• H2S to emphasize this criterion.

Les concepts de la chimie supramoléculaire peuvent être exploités avantageusement pour contrôler la structure et les propriétés des matériaux moléculaires. Dans une approche productive, les composantes moléculaires du matériau peuvent être choisies pour pouvoir s'engager dans des interactions fortes et prévisibles avec leurs voisins. Cette stratégie, appelée la tectonique moléculaire, est caractérisée par la préparation de molécules particulières appelées tectons (du grec tectos, qui signifie constructeur) qui, par design rationnel, s’associent de manière prévisible via de multiples interactions non-covalentes afin de générer l’architecture désirée. Ce processus est réversible et guidé par la présence de fonctions chimiques complémentaires, appelées groupements de reconnaissance, qui sont orientées de manière à conférer un aspect directionnel aux interactions intermoléculaires. Ceci permet de positionner les molécules voisines de façon prédéterminée. Les contraintes imposées par les interactions s’opposent souvent à la tendance naturelle des molécules à former une structure compacte et permettent donc à d'autres molécules invitées d’occuper un volume appréciable dans le matériau, sans toutefois contribuer directement à l'architecture principale. Appliquée à la cristallisation, cette approche peut générer des cristaux poreux, analogues aux zéolites. Les ponts hydrogène offrent une interaction non-covalente de choix dans cette stratégie car ils sont forts et directionnels. L’exploration d’une multitude de fonctions chimiques connues pour pouvoir participer à la formation de ponts hydrogène a permis de créer une grande diversité de nouveaux matériaux lors de l’évolution du domaine du génie cristallin. Une molécule classique, qui illustre bien la stratégie tectonique et qui a eu un fort impact dans le domaine de la chimie supramoléculaire, est l’acide 1,3,5-benzènetricarboxylique, communément appelé acide trimésique. L’acide trimésique donne une orientation trigonale à trois groupements carboxyles, favorisant ainsi la formation d'un réseau hexagonal retenu par ponts hydrogène. Nous avons visé une modification dans laquelle les groupements -COOH de l'acide trimésique sont remplacés par deux autres groupements de reconnaissance, jusqu’ici peu exploités en chimie supramoléculaire, l’oxime et l’hydrazone. Nous rapportons la synthèse et la cristallisation de différentes trioximes et trihydrazones analogues à l'acide trimésique. Les cristaux obtenus ont été analysés par diffraction des rayons-X et leurs structures ont été déterminées. L’auto-assemblage de différentes trioximes et trihydrazones en 2D par adsorption sur graphite a également été étudié en utilisant la microscopie à balayage à effet tunnel. Nos résultats nous permettent de comparer l'organisation en 2D et en 3D de différents analogues de l'acide trimésique. / The concepts of supramolecular chemistry can be exploited advantageously to control the structure and properties of molecular materials. In a productive approach, the molecular components of a material can be specifically selected to engage in strong and predictable interactions with their neighbours. This strategy, called molecular tectonics, is based on designing particular molecules called tectons (from the Greek word tectos, meaning builder) that self-associate in predictable ways via multiple non-covalent interactions, thereby generating a desired architecture. This process is reversible and guided by the presence of complementary chemical functions, named supramolecular synthons, specifically oriented to direct intermolecular interactions. This predisposes neighbouring molecules to be positioned in a predetermined fashion. The constraints arising from these interactions often tend to counter the natural tendency of molecules to form compact structures, thereby leaving significant volume within the material for guest molecules that do not directly contribute to the main architecture. When applied to crystallisation, this approach can generate potentially porous crystals similar to zeolites. Hydrogen bonds are an ideal non-covalent interaction for the strategy of molecular tectonics because of their strength and directionality. The field of crystal engineering has evolved greatly through exploration of various chemical functions known to assemble through hydrogen bonds. Such exploration has revealed a variety of new materials. A classic molecule that well represents the tectonic strategy and has had a larger impact in the field of supramolecular chemistry is benzene-1,3,5-tricarboxylic acid, commonly referred to as trimesic acid. Trimesic acid imparts a trigonal orientation to three carboxyl groups (COOH), favouring the formation of a hexagonal network supported by hydrogen bonds characteristic of these groups. We aimed to replace the COOH groups of trimesic acid by less-commonly used synthons in supramolecular chemistry derived from oximes and hydrazones. Herein, we report the synthesis and crystallisation of a series of trigonal trioximes and trihydrazones analogous to trimesic acid. Crystals were analysed by X-ray diffraction and their structures were determined. Self-assembly of the trioximes and trihydrazones in 2D by adsorption on graphite was also studied by scanning tunnelling microscopy. Together, our results enabled us to compare the 2D and 3D organisation of different analogues of trimesic acid.

Notre étude a pour objet la conception, la synthèse ainsi que l’étude structurale d’architectures supramoléculaires obtenues par auto-assemblage, en se basant sur les concepts de la tectonique moléculaire. Cette branche de la chimie supramoléculaire s’occupe de la conception et la synthèse de molécules organiques appelées tectons, du grec tectos qui signifie constructeur. Le tecton est souvent constitué de sites de reconnaissance branchés sur un squelette bien choisi. Les sites de reconnaissance orientés par la géométrie du squelette peuvent participer dans des interactions intermoléculaires qui sont suffisamment fortes et directionnelles pour guider la topologie du cristal résultant. La stratégie envisagée utilise des processus d'auto-assemblage engageant des interactions réversibles entre les tectons. L’auto-assemblage dirigé par de fortes interactions intermoléculaires directionnelles est largement utilisé pour fabriquer des matériaux dont les composants doivent être positionnés en trois dimensions (3D) d'une manière prévisible. Cette stratégie peut également être utilisée pour contrôler l’association moléculaire en deux dimensions (2D), ce qui permet la construction de monocouches organisées et prédéterminées sur différents types des surfaces, tels que le graphite.Notre travail a mis l’accent sur le comportement de la fonction amide comme fonction de reconnaissance qui est un analogue du groupement carboxyle déjà utilisé dans plusieurs études précédentes. Nous avons étudié le comportement d’une série de composés contenant un noyau plat conçu pour faciliter l'adsorption sur le graphite et modifiés par l'ajout de groupes amide pour favoriser la formation de liaisons hydrogène entre les molécules ainsi adsorbées. La capacité de ces composés à former de monocouches organisées à l’échelle moléculaire en 2D a été examinée par microscopie à effet tunnel, etleur organisation en 3D a également été étudiée par cristallographie aux rayons X. Dans notre étude, nous avons systématiquement modifié la géométrie moléculaire et d'autres paramètres afin d'examiner leurs effets sur l'organisation moléculaire. Nos résultats suggèrent que les analyses structurales combinées en 2D et 3D constituent un important atout dans l'effort pour comprendre les interactions entre les molécules adsorbées et l’effet de l’interaction avec la surface du substrat. / Our study involves the design, synthesis and structural analysis of supramolecular architectures obtained by self-assembly, based on the concepts of molecular tectonics. This branch of supramolecular chemistry explores the properties of molecules called tectons,from the Greek word tectos, meaning builder. Tectons typically incorporate sites of recognition connected to well-chosen skeletons with defined geometries. The sites of recognition, oriented by the geometry of the skeleton, can participate in intermolecular interactions that are sufficiently strong and directional to control the topology of the resulting assembly. This strategy is thereby based on self-assembly processes involving reversible interactions between tectons. Self-assembly directed by strong directional intermolecular interactions is widely used to produce materials whose components must be positioned in three dimensions (3D) in a predictable way. This strategy can also be used to control molecular association in two dimensions (2D), thereby allowing the construction of predictably organized and predetermined nanopatterns on various surfaces, such as graphite.Our work has focused on the behavior of the amide groups as primary sites of intermolecular interaction. These groups are analogues of carboxyl groups, which have been widely used in previous studies of directed molecular assembly. We have studied the 3D and 2D association of compounds with flat cores designed to favor the formation of sheets and to facilitate adsorption on graphite, modified by the addition of amide groups to promote the formation of intermolecular hydrogen bonds. The ability of these compounds to form predictably ordered 2D nanopatterns has been examined by scanning tunneling microscopy, and their organization in 3D has also been investigated by X-ray crystallography. In our study, we have systematically altered molecular geometry and other parameters to examine their effect on molecular organization. Our results suggest that combined structural analyses in 2D and 3D are an important asset in the effort to understand why molecules aggregate in particular ways and how these preferences can be altered by underlying surfaces.

La chimie supramoléculaire est un domaine qui suscite depuis quelques années un intérêt grandissant. Le domaine s’appuie sur les interactions intermoléculaires de façon à contrôler l’organisation moléculaire et ainsi moduler les propriétés des matériaux. La sélection et le positionnement adéquat de groupes fonctionnels, utilisés en combinaison avec un squelette moléculaire particulier, permet d’anticiper la façon dont une molécule interagira avec les molécules avoisinantes. Cette stratégie de construction, nommé tectonique moléculaire, fait appel à la conception de molécules appelées tectons (du mot grec signifiant bâtisseur) pouvant s’orienter de façon prévisible par le biais d’interactions faibles et ainsi générer des architectures supramoléculaires inédites. Les tectons utilisent les forces intermoléculaires mises à leur disposition pour s’orienter de façon prédéterminée et ainsi contrecarrer la tendance à s’empiler de la manière la plus compacte possible. Pour ce faire, les tectons sont munies de diverses groupes fonctionnels, aussi appelés groupes de reconnaissance, qui agiront comme guide lors de l’assemblage moléculaire. Le choix du squelette moléculaire du tecton revêt une importance capitale puisqu’il doit permettre une orientation optimale des groupes de reconnaissance. La stratégie de la tectonique moléculaire, utilisée conjointement avec la cristallisation, ouvre la porte à un domaine de la chimie supramoléculaire appelé le génie cristallin. Le génie cristallin permet l’obtention de réseaux cristallins poreux soutenus par des interactions faibles, pouvant accueillir des molécules invitées. Bien que toutes les interactions faibles peuvent être mises à contribution, le pont hydrogène est l’interaction prédominante en ce qui a trait aux réseaux cristallins supramoléculaires. La force, la directionnalité ainsi que la versatilité font du pont hydrogène l’interaction qui, à ce jour, a eu le plus grand impact dans le domaine du génie cristallin. Un des groupements de reconnaissance particulièrement intéressants en génie cristallin, faisant appel aux ponts hydrogène et offrant plusieurs motifs d’interaction, est l’unité 2,4-diamino-1,3,5-triazinyle. L’utilisation de ce groupement de reconnaissance conjointement avec un cœur moléculaire en forme de croix d’Onsager, qui défavorise l’empilement compact, permet l’obtention de valeurs de porosités élevées, comme c’est le cas pour le 2,2’,7,7’-tétrakis(2,4-diamino-1,3,5-triazin-6-yl)-9,9’-spirobi[9H-fluorène]. Nous présentons ici une extension du travail effectué sur les cœurs spirobifluorényles en décrivant la synthèse et l’analyse structurale de molécules avec une unité dispirofluorène-indénofluorényle comme cœur moléculaire. Ce cœur moléculaire exhibe les mêmes caractéristiques structurales que le spirobifluorène, soit une topologie rigide en forme de croix d’Onsager défavorisant l’empilement compact. Nous avons combiné les cœurs dispirofluorène-indénofluorényles avec différents groupements de reconnaissance de façon à étudier l’influence de l’élongation du cœur moléculaire sur le réseau cristallin, en particulier sur le volume accessible aux molécules invitées. / Supramolecular chemistry is a field of rapidly increasing interest in recent years. The field uses weak intermolecular interactions to control molecular organisation and therefore modulate the properties of materials. Adequate selection and positioning of functional groups, combined with a carefully selected molecular core to which the groups are attached, allows for the creation of molecules with a high degree of predictability in the way they will interact with their neighbours. This approach to the design and construction of materials, called molecular tectonics, is based on subunits called tectons (derived from the Greek word for builder), which use weak interactions to organise themselves in a predictable manner and generate novel supramolecular architectures. In favorable cases, the interactions can counter the general tendency shown by molecules to pack together in a compact manner. Instead, specific functional groups direct molecular recognition and help guide the process of auto-assembly. At the same time, the molecular core of the tecton is also of capital importance as it must allow an optimal orientation of the recognition groups. The molecular tectonics approach, used jointly with crystallisation, opens the door to new opportunities in crystal engineering. For example, crystal engineering now allows the logical creation of porous crystalline networks that can accept guest molecules. Although any type of weak interaction can hold such networks together, the hydrogen bond is favored for constructing porous supramolecular networks. The strength, directionality and versatility of the hydrogen bond accounts for its special importance in the domain of crystal engineering. A recognition group of particular interest in crystal engineering is the 2,4-diamino-1,3,5-triazinyl unit. This unit forms hydrogen bonds according to various standard motifs. The use of this recognition group, joined to molecular cores specifically designed to inhibit close packing, such as Onsager crosses, allows for the construction of supramolecular networks with high porosity, as shown by the behaviour of 2,2’,7,7’-tetrakis(2,4-diamino-1,3,5-triazin-6-yl)-9,9’-spirobi[9H-fluorene]. We present here an extension of previous studies of spirobifluorenyl cores by describing the synthesis and structural analysis of molecules with related dispirofluorene-indenofluorenyl cores. This new core offers the same characteristics as the spirobifluorenyl core, namely rigid topology and an Onsager cross molecular shape which are known to inhibit close packing. We have combined this core with a variety of recognition groups to verify the influence of the molecular core on the crystalline networks generated, particularly on the volume accessible to guest molecules.

The research work reported in this thesis is focused on the chiral analysis, quantification of enantiomeric composition, assignment of absolute configuration of molecules with chosen functional groups. The weak intra-molecular hydrogen bonding interactions are detected by exploiting several multinuclear and multi-dimensional techniques. Pulse sequences have been designed to manipulate the spin dynamics to derive specific information from the complex NMR spectra encountered in diverse situations. Broadly, the thesis can be classified in to three sections. The section I containing two chapters reports the introduction of new chiral auxiliaries and protocols developed for enantiomeric discrimination, measurement of enantiomeric contents, assignment of absolute configuration for molecules possessing specific functional groups using chiral solvating and derivatizing agents. The section II, reports NMR experimental evidence for the observation of the rare type of intramolecular hydrogen bonds involving organic fluorine in biologically important organic molecules, that are corroborated by extensive DFT based theoretical calculations. The section II also discusses the H/D exchange mechanism as a tool for quantification of HB strengths in organic building blocks. The section III reports the two different novel NMR methodologies designed for deriving information on the scalar interaction strengths in an orchestrated manner. The designed sequences are able to completely eradicate the axial peaks, prevents the evolution of unwanted couplings and also yields ultrahigh resolution in the direct dimension, permitting the accurate measurement of scalar couplings for a particular spin. The brief summary about each chapter is given below. Chapter 1 provides a general introduction to one and two dimensional NMR spectroscopy. The pedagogical approach has been followed to discuss the conceptual understanding of spin physics and the NMR spectral parameters. The basic introduction to chirality, existing approaches in the literature for discrimination of enantiomers and the assignment of absolute configuration of molecules with chosen functional groups and their limitations are briefly discussed. The brief introduction to hydrogen bond, experimental methods to obtain the qualitative information about the strengths of hydrogen bonds, and the theoretical approaches employed in the thesis to corroborate the NMR experimental findings have been provided. The mechanism of H/D exchange, the utilization of exchange rates to derive strengths of intra-molecular hydrogen bond in small molecules have also been discussed. This chapter builds the bridge for the rest of the chapters. Each of these topics are discussed at length in the corresponding chapters. Part I: NMR Chiral Analysis: Novel Protocols Chapter 2 discusses a simple mix and shake method for testing the enantiopurity of primary, secondary and tertiary chiral amines and their derivatives, amino alcohols. The protocol involves the in-situ formation of chiral ammonium borate salt from a mixture of C2 symmetric chiral BINOL, trialkoxyborane and chiral amines. The proposed concept has been convincingly demonstrated for the visualization of enantiomers of a large number of chiral and pro-chiral amines and amino alcohols. The protocol also permits the precise measurement of enantiomeric composition. The significant advantage of the protocol is that it can be performed directly in the NMR tube, without any physical purification. The structure of the borate complex responsible for the enantiodifferentiation of amines has also been established by employing multinuclear NMR techniques and DFT calculations. From DOSY and 11B NMR experiments it has been ascertained that there are only two possible complexes or entities which are responsible for differentiating enantiomers. From the combined utility of DFT calculations and the 11B NMR chemical shifts, the structure of the borate complex has been determined to be an amine-coordinated complex with the N atom of the amine. Chapter 3 discusses a simple chiral derivatizing protocol involving the coupling of 2-formylphenylboronic acid and an optically pure [1,1-binaphthalene]-2,2-diamine for the rapid and accurate determination of the enantiopurity of hydroxy acids and their derivatives, possessing one or two optically active centres. It is established that this protocol is not only rapid method for discrimination of enantiomers but also highly effective for assigning the absolute configuration of various chiral hydroxy acids and their derivatives. The developed protocol involves the coupling of 2-formylphenylboronic acid with (R)-[1,1-binaphthalene]-2,2-diamine, and 2-formylphenylboronic acid with (S)-[1,1-binaphthalene]-2,2-diamine as chiral derivatizing agents. The absence of aliphatic peaks from the derivatizing agent, large chemical shift separation between the discriminated peaks of diastereomers, and the systematic change in the direction of displacement of peaks for an enantiomer in a particular diastereomeric complex, permitted the unambiguous assignment of absolute configuration. Part II : Rare Type of Intramolecular Hydrogen Bonding In chapter 4 The rare occurrence of intramolecular hydrogen bonds of the type N–H˖˖˖F–C, in the derivatives of imides and hydrazides in a low polarity solvent, is convincingly established by employing multi-dimensional and multinuclear solution state NMR experiments. The observation of 1hJFH, 2hJFN, and 2hJFF of significant strengths, where the spin polarization is transmitted through space among the interacting NMR active nuclei, provided strong and conclusive evidence for the existence of intra-molecular hydrogen bonds. Solvent induced perturbations and the variable temperature NMR experiments unambiguously supported the presence of intramolecular hydrogen bond. The two dimensional HOESY and 15N–1H HSQC experiments reveals the existence of multiple conformers in some of the investigated molecules. The 1H DOSY experimental results discarded any possibility of self or cross-dimerization of the molecules. The results of DFT based calculations, viz., Quantum Theory of Atoms In Molecules (QTAIM) and Non Covalent Interaction (NCI), are in close agreement with the NMR experimental findings. In chapter 5 the rates of hydrogen/deuterium (H/D) exchange determined by 1H NMR spectra have been utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted Benz amides and anilines. The theoretical fitting of the time dependent variation in the integral areas of 1H NMR resonances to the first order decay function permitted the determination of H/D exchange rate constants (k) and their precise half-lives (t1/2) with high degree of reproducibility. The comparative study also permitted the determination of relative strengths of hydrogen bonds and the contribution from electronic effects on the H/D exchange rates. Part III: Novel NMR Methodologies for the Precise Measurement of 1H-1H Couplings Chapter 6 describes two novel NMR methodologies developed for the precise measurement of 1H-1H couplings. Poor chemical shift dispersion and the pairwise interaction among the entire coupled network of protons results in the severely complex and overcrowded one dimensional 1H NMR spectra, hampering both the resonance assignments and the accurate determination of nJHH. The available two-dimensional selective refocusing (SERF) based experiments suffer from the evolution of magnetization from uncoupled protons as intense uninformative axial peaks. This creates ambiguity in the identification of peaks belonging to the coupled partners of a selectively excited proton, hindering the extraction of their interaction strengths. This challenge has been circumvented by designing two novel experimental technique, cited as “Clean-G-SERF” and “PS-Clean-G-SERF”. The Clean-G-SERF technique completely eradicates the axial peaks and suppresses the evolution of unwanted couplings while retaining only the couplings to the selectively excited proton. The method permits the accurate determination of spin-spin couplings even from a complex proton NMR spectrum in an orchestrated manner. The PS-Clean-G-SERF technique has been designed for the complete elimination of axial peaks and undesired couplings, with a blend of ultra-high resolution achieved by real time broad band mononuclear decoupling has been discussed in this chapter. The spin dynamics involved in both these pulse sequences have been discussed. The diverse applications of both these novel experiments have been demonstrated.

La précipitation et la dissolution du carbonate de calcium (CaCO3) sont des processus clés dans les systèmes naturels en raison de leur association intime avec le cycle du carbone terrestre. La précipitation se produit généralement sur des substrats étrangers en abaissant les barrières énergétiques qui contrôlent la nucléation. Ce processus appelé nucléation hétérogène résulte d'une interaction entre la sursaturation du fluide et les différentes énergies d’interface entre substrat-noyau-fluide. Malgré l’importance des énergies d’interface sur le devenir de la nucléation hétérogène, la littérature actuelle reste rare dans leurs valeurs absolues, limitant la précision de la modélisation du transport réactif. La formation des biominéraux constitue un réservoir majeur des carbonates dans la lithosphère. Des études récentes ont révélé des nucléations par multi-étapes impliquant la formation du carbonate de calcium amorphe (ACC), un intermédiaire métastable durant les premiers stades de la formation des biominéraux. De tels précurseurs amorphes permettent de réaliser les formes complexes des biominéraux, tandis que leur stabilité et leur cinétique de cristallisation sont contrôlées par de multiples facteurs. L'élucidation des mécanismes sous-jacents est bénéfique pour le développement de matériaux biomimétiques.Le premier objectif est de développer une compréhension prédictive des valeurs d'énergie d’interface régissant la nucléation hétérogène du CaCO3 en fonction des propriétés physico-chimiques spécifiques des substrats, comme l'hydrophobicité. Cette dernière est étudiée en utilisant de la phlogopite avec et sans substitution par le fluor produisant des substrats hydrophobes et hydrophiles. La technique de diffusion des rayons X aux petits angles en incidence rasante a été employée in situ pour obtenir des valeurs d’énergie effective d’interface. Il est intéressant de noter que les valeurs extraites pour les deux substrats sont similaires, et thermodynamiquement les deux fournissent un bon modèle pour la nucléation, alors que leurs mécanismes sont différents. La caractérisation ex situ par microscopie à force atomique a montré que le substrat hydrophile favorise la formation et la stabilisation d’ACC, tandis que le substrat hydrophobe favorise la formation de calcite. Ces résultats soulignent la flexibilité structurelle intrinsèque du CaCO3 et son avantage dans les processus de nucléation hétérogènes.Le deuxième objectif est de fournir une description atomistique de l'hydrophobicité du substrat. L'adsorption d'eau sur la phlogopite a été réalisée in situ par spectroscopie de photoélectrons à pression ambiante pour étudier l'effet de la substitution par le fluor et de différents types de contre-ions (K+, Na+ vs. Cs+). Ces résultats ont été interprétés par des simulations de dynamique moléculaire et la théorie de bond-valence. La combinaison de ces techniques montre que l'hydrophobicité du substrat provient d'une compétition entre deux facteurs: l'hydratation des contre-ions par rapport à celle du substrat.Le but final est d'étudier les mécanismes moléculaires par lesquels Mg2+, une impureté chez les précurseurs amorphes biogéniques, augmente la persistance cinétique d’ACC. La technique de diffusion inélastique incohérente des neutrons a été combinée avec la spectroscopie de corrélation de photons X pour élucider la dynamique à l'échelle nanométrique de l'eau et des ions dans les ACC. Les résultats montrent que la présence de Mg2+ augmente la diffusion atomique dans le solide tout en amplifiant la rigidité du réseau des liaisons hydrogène. Ces résultats contre-intuitifs sont abordés en considérant différents facteurs cinétiques inclus dans l’équation décrivant le taux de nucléation au sein de la théorie classique de la nucléation. Dans l'ensemble, ces résultats indiquent l'importance de l'eau comme stabilisant cinétique de la structure amorphe et de l'existence de barrières stériques qui abaissent le taux de cristallisation. / Precipitation and dissolution of calcium carbonate (CaCO3) are key processes in both natural and engineered systems due to their intimate association with the Earth’s carbon cycle. Precipitation usually occurs on foreign substrates since they lower the energetic barriers controlling nucleation events. This so-called heterogeneous nucleation results from the interplay between the fluid supersaturation and the interfacial free energies present at the substrate-nucleus-fluid interfaces. Despite the relevance of interfacial energies for the fate of heterogeneous nucleation, the current literature remains scarce in their absolute values, which limits the accuracy of reactive transport modelling. Of particular relevance to the carbon cycle, the formation of biominerals accounts for a major reservoir of the carbonate minerals in the lithosphere. Recent studies have revealed the existence of multistep nucleation pathways that involve formation of amorphous calcium carbonate (ACC), a metastable intermediate during the early stages of biomineral formation. Such amorphous precursors allow molding of the intricate shapes of biominerals, while their stability and crystallization kinetics are effectively controlled by multiple factors. Elucidating the underlying mechanisms is beneficial for the development of biomimetic materials.The first goal of this dissertation is to develop a predictive understanding of interfacial energy values governing CaCO3 heterogeneous nucleation as a function of specific physico-chemical properties of the substrates, such as hydrophobicity. This last was investigated using phlogopite, a common mica, with and without fluorine substitution yielding hydrophobic and hydrophilic substrates. In situ time-resolved Grazing-Incidence Small Angle X-ray Scattering experiments were performed to obtain effective interfacial energy values. Interestingly, the extracted values for both substrates were similar, and thermodynamically these substrates provide a good template for nucleation, but the pathways differ. By ex situ Atomic Force Microscopy characterization, the hydrophilic substrate was shown to promote the formation and stabilization of ACC, whereas the hydrophobic one favored the formation of calcite. These results point to the intrinsic structural flexibility of CaCO3 and its advantage in heterogeneous nucleation processes.The second goal is to provide an atomistic description of the substrate hydrophobicity/hydrophilicity. Water adsorption on phlogopite was studied in situ using Near-Ambient Pressure X-ray Photoelectron Spectroscopy to investigate the effect of fluorine substitution and the influence of different types of counterions (K+, Na+ vs. Cs+). The results of the spectroscopy experiments were further interpreted using molecular dynamics simulations and bond-valence theory. The combination of these techniques shows that the substrate hydrophobicity stems from a competition between two factors: hydration of counterions vs. that of substrate.The final goal is to study the molecular mechanisms by which Mg2+, a common impurity in biogenic amorphous precursors, increases the kinetic persistence of ACC. Inelastic Incoherent Neutron Scattering and X-ray Photon Correlation Spectroscopy were combined to elucidate the nanoscale dynamics of water and ions within ACC. The presence of Mg2+ was shown to enhance the atomic diffusion within the solid while simultaneously increasing the stiffness of the hydrogen bond network. These counter-intuitive results are addressed by considering the different factors included in the pre-exponential term of the nucleation rate equation within the framework of the classical nucleation theory. Overall, the results point to the importance of water as a kinetic stabilizer, and to the existence of steric barriers that lower the crystallization rate.

Dans cette thèse, nous étudions la stabilité et les propriétés des glaces d’eau de haute pression (entre 5 et 300 GPa) et de haute température (entre 300 et 2000 K) comportant ou non des inclusions de NaCl dans leur structure cristalline. Pour attendre ces conditions propres aux intérieurs des exoplanètes océans, nous utilisons une approche théorique basée sur des dynamiques moléculaires ab initio. Nous montrons que l’analyse de la dynamique des liaisons entre hydrogènes et oxygènes permet de distinguer toutes les phases de la glace présentant une structure cubique volume-centrée. En particulier, nous présentons la première description ab initio de la phase plastique, et nous mettons en évidence la présence de multiples transitions dans la phase superionique. Ensuite, nous montrons que jusqu’à 5.9 % en masse de NaCl peuvent être inclus dans la structure de la glace à 1600 K. L’inclusion des ions Na+ et Cl- stimule le désordre orientationel des molécules d’eau par rapport à la glace d’eau pure. À partir de 2.5 % en masse de NaCl, la conduction superionique s’étend à l’ensemble de la gamme de pression étudiée, et la symétrisation des liaisons hydrogènes se produit à plus haute pression. Enfin, nous décrivons les structures de cœur des dislocations vis ayant des vecteurs de Burgers <110> et <111> dans la glace X à 80 GPa, ce qui constitue une étape préliminaire importante à la construction de lois rhéologiques pour les glaces cubiques de haute pression. / In this thesis we study the stability and the properties of pure and NaCl-bearing dense water ices at high pressure (between 5 and 300 GPa) and high temperature (between 300 and 2000 K). To reach these conditions that correspond to the interiors of ocean exoplanets, we employ a theoretical approach based on ab initio molecular dynamics simulations. We show that a detailed analysis of the hydrogen bond dynamics allows to distinguish all the different ice phases presenting a body-centered cubic sub-lattice of oxygen atoms. In particular, we present the first ab initio description of the plastic phase of water ice. We also reveal the multiple transitions that occur in the superionic domain. Next, we show that ice VII' can incorporate up to 5.9 wt% NaCl in its structure at 1600 K. The inclusion of Na+ and Cl- ions enhances the orientation disorder of the water molecules in comparison to the pure ice. From 2.5 wt% NaCl, superionic conduction expands over the entire pressure range studied, and the hydrogen symmetrisation is shifted towards higher pressures. Last, we describe the <110> and <111> screw dislocation core structures of ice X at 80 GPa. This constitutes a first step towards the construction rheological laws for high-pressure cubic ices.

No description available.

This thesis titled, “Nature of Local Interactions at cisPro-Aro Peptide Sequences in Proteins: Evidences for van der Waals type Interactions. Design and Synthesis of Novel Covalent Surrogates for the Peptide Hydrogen Bond”, describes two important studies. The first is to gain a thorough understanding of the nature of interactions that govern cisPro stability at Pro-Aro sequences, which described in the first four chapters. The final chapter describes the synthesis of novel 4-carbon covalent surrogates for the peptide H-bonding interaction. Chapter 1: Local Interactions Governing cisPro Stability: Refining the Model Peptides Chapter 1 Section A: Understanding the role of inter-side chain CH•••Aro interaction in cis-trans isomerization at Pro-Aro and Aro-Pro Sequences. This chapter is divided into two sections. In the first section an exhaustive overview of earlier investigations into the nature of local interactions at Xaa-cisPro-Aro and Aro-cisPro-Xaa peptide sequences, by various groups, are discussed. Most studies have found evidence for the close assemblage between side chains of residues flanking cisPro motifs, when at least one of them is an aromatic group. An electronic C-H•••π nature has been proposed for these assemblies and they are proposed to influence the cisPro stability. We highlight those features in these studies that indicate that these interactions are not always electronically tunable, are insensitive to presence of strong chaotropes in the solvent and occur at protein sequences lacking Pro or cisPro; all of which contradict the electronic C-H•••π model for these inter-side chain assemblages and their perceived influence on cisPro stability. Chapter 1 Section B: Investigation of the Nature of H Xaa•••Aro interaction at Xaa-Pro-Pro-Phe-sequences In Section B, we design and synthesize Pro-Aro containing short peptide models to investigate the nature of local C-H•••Aro interactions in them. We synthesize a series of homologous Pro-Pro-Aro containing peptides (modeled based on earlier studies) and investigate the relative populations of its four Xaa-Pro rotamers using extensive 1D and 2D NMR techniques including TOCSY, HSQC and ROESY. We find several drawbacks that make this a relatively deficient model. Firstly, their relative populations of the rotamers (the most important data for current investigation) cannot be determined with high fidelity as they are dependent on the solvent polarity, solute concentration and chemical shift degeneracy of crucial NMR signals for the rotamers. Importantly, the populations of a few rotamers are influenced by strong 13-membered ring backbone H-bonds. Notably, some of the cisPro rotamers do not even contain the inter-side chain assembly, whose nature is under investigation. Design of novel models – unconstrained by H-bonds We design the Acyl-Pro-Pro-Aro-OMe peptides that lack the possibility of forming the 13-membered ring H-bonded structures. Thorough 1D and 2D NMR analyses of these models reveal that strong Type VI β-turn type 10-membered ring H-bonds are formed in the rotamers of these models – hence precluding their applications for current study. Interestingly, the relative rotamer populations are strongly influenced by solvent polarity and are entirely different from those of the corresponding C-terminal amide models. We further discover that the Pro-Pro-Aro motif is not essential to express the inter-side chain interactions – Ala-Pro-Aro are sufficient. Formation of the 10-membered H-bonding interactions, however, are not precluded. Chapter 2: Design and Synthesis of Acyl-Pro-Phe-OMe: Novel models to investigate the role of HαXaa•••Aro interactions on Xaa-cisPro-Aro stability. Chapter 2 Section A: Design, Synthesis and Conformational Analysis of Ibu-Pro-Phe-OMe Chapter 2 is divided into two sections. In Section A, we replace the amino acid at the N-terminal of the putative Pro residue with simple isosteric isobutyryl group, the resulting minimalist dipeptide model shows the exclusive influence of desired inter-side chain interactions in the cisPro rotamer. Solvent polarity and temperature coefficient studies reveal that absence of any intramolecular H-bonding or Oπ* interactions in it. 1D and 2D NMR analyses clearly indicate the close proximity between the side chains of Ibu and Phe exclusively in the cisPro rotamer. The Kc/t value decreases upon mutation of Phe to Ala. All these features favor the Ibu-Pro-Phe-OMe as an ideal minimalistic model for investigating the nature of Ibu•••Ph assemblages in the cisPro rotamer. Chapter 2 Section B: Investigation of CH•••Aro /Alp•••Alp interactions in Ibu-cisPro-Xaa-OMe In Section B, the 1D and 2D NMR analyses of the complete set of the aliphatic and aromatic analogues Ibu-Pro-Xaa-OMe were investigated. DMSO-d6 was found to be the best solvent for mimicking both the folded and the unfolded local environments of these short peptide sequences. The HαIbu•••Aro assemblage is observed in Aro analogues, but cannot be electronically tuned. The aliphatic analogues also surprisingly contain the HαIbu•••Alp interactions! The Kc/t values (cisPro %) increase in the aliphatic analogues too, where the aliphatic side chain is long. Increase in cisPro stability is not due to ring current effects or intramolecular H-bonds or Oπ* interactions. It seems to be due to van der Waals type interactions between the involved side chains, either of which need not be aromatic in nature. Chapter 3: Nature of Inter-Side Chain Interactions at Acyl-cisPro-Aro Sequences: Evidence for van der Waals Interactions Chapter 3 Section A: Investigation of nature of inter-side chain interactions in R-CO-cisPro-Phe-OMe Chapter 3 has two sections. Section A describes the systematic design and synthesis of Acyl-Pro-Phe-OMe homologues where first the steric bulk and hence the surface area of the aliphatic side chain of the acyl group is varied. Interaction of the phenyl ring of Phe seems to occur with the Cα-Cβ σ-bond of the acyl group. Branching at either Cα or Cβ seems to destabilize the cisPro rotamer. Aliphatic•••Aromatic interactions overwhelm the cisPro rotamer population to be greater than that of transPro. In the analogues where the acidity of the acyl Cα-H bond is increased, the Kc/t does not increase correspondingly. The Δδ(trans-cis) ppm shifts of HαAcyl protons are dependent exclusively on its acidity rather than on the Kc/t values. In carbamyl-Pro, which entirely lack the HαAcyl proton, the Kc/t values are significantly high and improve as the aliphatic surface on the alkoxy group increases. Introduction of benzyloxy carbamyl group at Pro renders almost the same Kc/t values as that of ethyloxy carbamate. All these data contradict the C-H•••π interaction model and strongly support a van der Waals type interaction between the Acyl (preceding cisPro) group’s Xα-Yβ σ-bond and the Aro or Alp side chains (succeeding cisPro). Chapter 3 Section B: Evidence for the Van der Waals nature of Inter Side Chain (Acyl•••S.C.Aro/Alp) interactions- Determination of Interactions energies In Section B, a thorough investigation of both aliphatic•••aliphatic and aliphatic•••aromatic interactions on the background of homologous Acyl-Pro-Aro/Alp-OMe peptide models is undertaken. These models uniquely allow the delineation of contribution of the van der Waals interactions and the ring current effects to the cis/trans isomerization in these peptides. We see that the energy of the van der Waals component of these aliphatic•••aliphatic and aliphatic…aromatic interactions increase linearly with increase in Kc/t, in both DMSO-d6 and D2O. On other hand, energy from the ring current effects largely remains invariant. The Acyl•••Aro/Alp interactions are not hydrophobic and are facilitated by conformational effects. Chapter 4: Crystallographic evidence for van der Waals interaction-mediated stabilization of cisPro conformers Chapter 4 Section A: Systematic crystallization and crystal structure analyses of homologous Xaa-cisPro-Alp and Xaa-cisPro-Aro rotamers: Evidence for van der Waals interactions Chapter 4 has two sections, both of which present crystallographic evidence for the van der Waals nature of the Xaa•••Aro interactions at Xaa-cisPro-Aro sequences. Section A describes the unique crystal structures of five of the Acyl-Pro-Alp-OMe analogues that have been synthesized in the current study. All of them remarkably crystallize with two features: 1) the Acyl-Pro peptide bond adopts the cisPro rotamer in all; and 2) the aliphatic side chains of the acyl group and the Alp side chain are involved in van der Waals type interactions. The cisPro rotamers of even the bulkiest motifs, namely Ibu-Pro-Val-OMe, Piv-Pro-Ile-OMe and Piv-Pro-Leu-OMe crystallize, stabilized by van der Waals packing between aliphatic groups of the acyl and the Leu/Ile/Val side chains. Where the side chains are not long enough to make sub-van der Waals contacts with each other, their acyl C′-Cα σ-bond rotations are restricted due to Oσ* interactions involving the charge on the acyl carbonyl O. Where this occurs, the short space between the acyl and Alp side chains are filled in by aliphatic groups from neighbouring molecules at sub van der Waals distances. The Pro, Alp and χ1(Alp) dihedral angles are restricted to narrow range of values, irrespective of the length of Alp side chain, indicating that this backbone conformation is a conformational minimum when i+3i backbone H-bond is removed, with Pro at the i+1st position. This is further substantiated in Piv-Pro-Gly-OMe, which crystallizes in trans-Pro form, but still adopts similar backbone dihedral angles in spite of lacking any Alp side chain for interactions with the acyl group. Three of the Acyl-Pro-Aro-OMe models also crystallize in cisPro rotamer forms – both exhibit van der Waals type contacts between the Acyl group and backbone of Phe, rather than the aromatic ring of Phe. The phenyl ring of Phe may or may not form intramolecular Ph•••Pro inter-side chain contacts – which is not a pre-requisite for cisPro stabilization. No C-H••• interactions are observed anywhere in these peptides – van der Waals type contacts alone predominate in all cases. There are no abnormal distortions in bond angles or lengths even in the most sterically hindered cases, signifying that the conformations of these cisPro rotamers involving aliphatic•••aliphatic type contacts are natural minima. Chapter 4 Section B: Mining the PDB for Statistical Evidence of van der Waals interactions Section B of chapter 4 describes the data mining and statistical analyses of Xaa-cisPro-Phe, Xaa-cisPro-Val and Xaa-cisProLeu sequences in the PDB. The PEARL program was used to mine the PDB data. The overall frequency of 5.3% for appearance of cisPro among all Xaa-Pro peptide bonds, improves when Xaa is Phe or Tyr. However, several anomalies highlight the need for refining the analyses set to only those sequences where the side chains of Xaa and Aro/Alp face each other. In this refined set, clearly, inter side chain Xaa•••Alp/Aro contacts take precedence over even Aro•••Pro interactions at Aro-cisPro sequences (where Xaa is Aro). The Phe and the Leu side chains induce similar conformational effects on the preceding Xaa-Pro backbone. So does Val. Strong aliphatic•••aliphatic inter side chain contacts at van der Waals distances are observed to flank cisPro in several proteins. Substitution at the Cα of Xaa governs the proximity of the approaching side chain of Alp / Aro residue. The Cα-H of Xaa steers away from the Aro side chain at Xaa-Pro-Phe sequences, as the Aro group gets closer to it – implying the absence of ordered C-H••• contacts between them. There is consistent parallel alignment between Cα-Cβ -bond of Xaa and the C -C bond of the approaching side chain of Alp or Aro group – clearly highlighting the presence of van der Waals type interactions between them. All these evidences clearly point towards the van der Waals nature of local interactions at cisPro-Aro/Alp peptide sequences. Chapter 5: A novel 4-carbon covalent surrogate model for peptide H-Bond Chapter 5 describes the design and synthesis of novel 4-carbon covalent surrogates for the peptide H-bond (HBS). These surrogates would allow the unique constraining of two peptide strands in their extended conformations. The covalent HBS contain four orthogonal functional groups for independent extension at all of the four ends – similar to an endogenous inter-strand peptide H-bond. The synthesis of the surrogate is achieved by directly using natural chiral amino acid derivatives, beginning from amino alcohols obtained from reduction of desired amino acids. Suitably N-protected alcohols undergo oxidation to aldehyde followed by Grignard addition of allyl magnesium bromide, TBDMS protection of the homoallylic alcohol and reductive ozonolysis of the olefin to get a primary alcohol which is subject to Fukuyama-Mitsunobu reaction with desire protected peptide. The residue preferences that produce strongest inter-strand H-bonds were explored. The designed 4-carbon covalent HBS was incorporated using this methodology in a Gramicidin-S analogue, its first structural mimic containing only a single turn motif. This HBS model will have wide applications for constraining peptides in a number of secondary structures.