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Interaction preferences in protein - DNA complexes Dávid Jakubec Abstract Interactions of proteins with DNA lie at the basis of many fundamental bio- logical processes. Despite ongoing efforts, the rules governing the recognition of specific nucleic acid sequences have still not been universally elucidated. In this work, I attempt to explore the recognition process by splitting the intricate network of contacts at the protein - DNA interface into contribu- tions of individual amino acid - nucleotide pairs. These pairs are extracted from existing high-resolution structures of protein - DNA complexes and in- vestigated by bioinformatics and computational-chemistry based methods. Criteria of specificity based on the coupling of observed geometrical prefer- ences and the respective interaction energies are introduced. The application of these criteria is used to expand the library of amino acid - nucleotide pairs potentially significant for direct sequence recognition. Electrostatic poten- tial maps are calculated for individual nucleotides as well as for selected complexes to investigate the physical basis of the observed specificity. 1

<p>A significant development in mass spectrometry instrumentation and software in the past decade has led to its application in solving complex biological problems. One of the emerging areas is Chemical Proteomics that involves design and use of chemical reagents to probe protein functions in ‘a live cell’ environment. Another aspect of Chemical Proteomics is the identification of target proteins of a drug or small molecule. This is assisted by photoreactive groups, which on exposure to UV light, covalently link the target proteins that can be purified by affinity-based enrichment followed by mass-spectrometric identification. This phenomenon of Photoaffinity labeling (PAL) has been widely used in a broad range of applications. Herein, we have designed chemical tools to study Zika endocytosis and phosphoproteomics.</p> <p>Zika virus has attracted the interest of researchers globally, following its outbreak in 2016. While a significant development has been made in understanding the structure and pathogenesis, the actual mechanism of Zika entry into host cells is largely unknown. We designed a chemical probe to tag the live virus, leading to the identification of the virus receptors and other host factors involved in viral entry. We further validated neural cell adhesion molecule (NCAM1) as a host protein involved in early phase entry of Zika virus into Vero cells.</p> <p>The second aspect is the development of the DIGE (Difference Gel Electrophoresis) technology for phosphoproteomics. Phosphoproteins are known to be involved in various signaling pathways and implicated in multiple diseased states. We designed chemical reagents composed of titanium (IV) ion, diazirine and a fluorophore, to covalently label the phosphoproteins. Cyanine3 and cyanine5 fluorophores were employed to reveal the difference in phosphorylation between samples for the comparative proteomics. Thus far, we have successfully demonstrated the labeling of standard phosphoproteins in both simple and complex protein mixtures, and the future efforts are towards applying the technology to identify phosphoproteins in a cell lysate.</p>

Diese Arbeit befasst sich mit dem Einfluss der molekularen Struktur von 2,5-Diphenyl-1,3,4-Oxadiazol-Derivaten auf die Präparierung dünner Schichten mittels Vakuumdeposition. Dünne Schichten von diesen Substanzen wurden auf Si/SiO2 aufgedampft und ihre Struktur systematisch mittels XSR, AFM und IR untersucht. Das Ergebnis zeigt, dass die Schichtstrukturen offenbar von Substratetemperatur (Ts) abhängig sind. Im untersuchten Ts-Bereich bilden etherverbrückte Oxadiazole immer geordnete Schichten und die Schichtperiodicität hängt linear von der Längen der aliphatischen Ketten, während sich bei den amidverbrückten Oxadiazolen nur bei hohen Ts geordnete Schichten bilden können. Diese Unterschiede sind auf die intermolekularen Wasserstoffbrücken zurückzuführen. Der Tilt-Winkel der Moleküle ist durch die Wechselwirkung zwischen dem aromatischen Teil bestimmt. Die Wechselwirkungen zwischen den Kopfgruppen können durch Tempern abgeschwächt werden und führen zur Strukturumwandlung von Schichten, die auf etherverbrückten Oxadiazolen basieren. Alle Schichten von etherverbrückten Oxadiazolen haben Doppelschicht-Struktur, aber amidverbrückte Oxadiazole bilden nur Doppelschicht-Strukturen, wenn die Moleküle eine Kopfgruppe besitzen. / The correlations between the chemical structures of the 2,5-diphenyl-1,3,4-oxadiazole compounds and their corresponding vapour deposited film structures on Si/SiO2 were systematically investigated with AFM, XSR and IR for the first time. The result shows that the film structure depends strongly on the substrate temperature (Ts). For the compounds with ether bridge group, the film periodicity depends linearly on the length of the aliphatic chain. The films based on those oxadiazols have ordered structure in the investigated substrate temperature region, while die amide bridged compounds form ordered film only at high Ts due to the formation of intermolecular H-bond. The tilt angle of most molecules is determined by the pi-pi complexes between the molecules. The intermolecular interaction between head groups leads to the structural transformation during the thermal treatment after deposition. All the ether bridged oxadiazoles form films with bilayer structure, while amide bridged oxadiazole form film bilayer structure only when the molecule has a head group.

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.

Thin-film organic field effect transistors (OFETs) have attracted growing interest in recent years due to their promising electrical, optical and mechanical properties. Especially, oligothiophenes and their derivates are candidates with good prospects for application as the organic semiconducting material in such devices. They possess an extended, polarisable aromatic π-electron system that promotes a high structural arrangement of the molecules. The charge transport in the organic film is realised in the direction perpendicular to the plane of the thiophene rings via a hopping transport mechanism. Thus, a good π-π-overlap and a consequent stacking of the thiophene molecules in the film perpendicular to the gate substrate is essential to achieve excellent electric properties such as high charge carrier mobilities and low resistive losses. The highly polarisable thiophene-based molecules are also very attractive materials that are potentially applicable as the field-sensitive organic semiconducting component of a ferroelectric OFET device. In such a device, the dielectric gate element of a conventional OFET setup is substituted by a ferroelectric substrate. The electric field that is induced by the polarisation of the ferroelectric material serves as gate field and controlls the charge injection and charge density inside the device. In this thesis, thiophene-based molecules are investigated in detail with respect to their application as field-sensitive organic semiconducting component in a ferroelectric OFET device employing quantum-chemical ab initio and DFT-based methods. We demonstrate that the phosphonic acids can bind the organic molecules to the dielectric or ferroelectric material and well-anchored, robust self-assembled monolayers are formed. Furthermore, special focus is put on the influence of the intermolecular interactions among the organic molecules on the technologically relevant structural and electronic properties. It is found that the CN···HC hydrogen bond link the molecules into extended ribbons, but the π-π-stacking-stacking interaction is the main driving force in the self-assembly of the molecules. We also establish in detail the influence of the electric field on the phosphonic acid anchoring molecule and some quarterthiophene derivates. For the latter, the strongest field-sensitivity is obtained for an external electric field aligned parallel to the extension of the thiophene framework. Hence, they are suitable to act as the field-sensitive organic components in devices that take advantage of a band-gap engineering. Moreover, the present results emphasise the importance of the adsorption morphology of the molecules in the film in a π-stacked fashion with their longitudinal axis oriented parallel to the (orthonormal) electric field induced by the ferroelectric substrate.

Il est désormais possible, en utilisant le modèle de densité électronique résolue en spin (CRM2), de combiner les diffractions des rayons X et des neutrons (polarisés) pour déterminer les distributions électroniques de charge et de spin de matériaux magnétiques cristallins. Cette méthode permet la mise en évidence des chemins d’interactions rendant compte de l’ordre magnétique. Le modèle résolu en spin a été appliqué aux complexes de coordination avec un métal de transition portant la majorité du moment magnétique, il a été ensuite utilisé pour étudier les radicaux purs organiques contenant des électrons non appariés délocalisés sur un groupement chimique et les matériaux inorganiques. Dans le radical Nit(SMe)Ph, la modélisation des densités de charge et de spin a permis, en accord avec les résultats antérieurs, de montrer que le spin est délocalisé sur le groupe O-N-C-N-O (fonction nitronyle nitroxyde). Elle a également permis de montrer l’implication des liaisons hydrogène dans les interactions magnétiques ferromagnétique observé en dessous de 0.6K. Cette étude a mis en évidence une répartition dissymétrique de la population de spin sur les deux groupes N—O dont seuls les calculs CASSCF permettent de reproduire l’amplitude. Cette dissymétrie proviendrait d’une combinaison d’effets moléculaires et cristallins. Dans le radical p-O2NC6F4CNSSN de la famille des dithiadiazolyles, la modélisation par affinement joint montre que la majorité du spin est porté par le groupement –CNSSN en accord avec les travaux antérieurs. Grace aux propriétés topologiques de la densité de charge, des interactions halogène, chalcogène et π ont été mis en évidence. Certaines de ces interactions favorisent des couplages magnétiques, notamment les contacts S…N2 entre molécules voisines pouvant contribuer à l’ordre ferromagnétique observé à très basse température (1.3K). Quant au matériau inorganique, YTiO3, les densités de charge en phases paramagnétique et ferromagnétique ont été déterminées ainsi que la densité de spin dans la phase ferromagnétique. Les résultats de cette étude montrent que les orbitales d les plus peuplées en électrons de l’atome de Ti sont dxz et dyz.. L’ordre orbital présent dans ce matériau est observé à 100 et à 20 K suggérant que l’ordre orbitalaire est lié à la distorsion des octaèdres. La fonction d’onde de l’électron non apparié est une combinaison linéaire de ces orbitales t2g / X-ray and neutron diffraction methods can be combined to determine simultaneously electron charge and spin densities in crystals based on spin resolved electron density model developed at CRM2. This method enables to carry out the study of interaction paths leading to the observed ferromagnetic order. First applications of this model were to coordination complexes, where the unpaired electron is mainly located on the transition metal, then generalized to explore organic radicals and to inorganic materials. In radical Nit(SMe)Ph, the modeling of the experimental charge and spin densities showed localization of spin density on O-N-C-N-O group (nitronyl -nitroxyde function), in agreement with previous works. It is also evidenced the involvement of the hydrogen bonds in the magnetic interactions leading to the ferromagnetic transition at very low temperature (0.6K). This study revealed dissymmetrical spin population of the two N-O groups that only CASSCF-type calculations can reproduce in amplitude (not DFT). This dissymmetry originates from both molecular and crystal effects. In radical p-O2NC6F4CNSSN belonging to the family of dithiadiazolyl, the joint refinement showed that the majority of the spin is distributed on -CNSSN group in agreement with the previous works. From topological properties of the charge density, halogen, chalcogen and π interactions have been highlighted. The most important magnetic interactions are observed through the network formed by contacts S ... N2 between neighboring molecules leading to the ferromagnetic order below 1.23K. Concerning the inorganic material, YTiO3, the charge densities in both paramagnetic and ferromagnetic phases and spin density were modelled. The results show that the most populated d orbitals of Ti atom are dxz and dyz. The orbital ordering evidenced in this material is observed at 100 and 20 K due to the orthorhombic distorsion. The wave function of the unpaired electron is a linear combination of these particularly populated t2g orbitals

The thesis entitled “Organic fluorine in crystal engineering: Consequences on molecular and supramolecular organization” consists of six chapters. The main theme of the thesis is to address the role of substituted fluorine atoms in altering the geometrical and electronic features in organic molecules and its subsequent consequences on crystal packing. The thesis is divided into three parts. Part I deals with compounds that are liquids under ambient conditions, crystal structures of which have been determined by the technique of in situ cryocrystallography. Part II demonstrates the utilization of in situ cryocrystallography to study kinetically trapped metastable crystalline phases that provide information about crystallization pathways. In part III, crystal structures of a series of conformationally flexible molecules are studied to evaluate the consequences of fluorine substitution on the overall molecular conformation. The genesis and stabilization of a particular molecular conformation has been rationalized in terms of variability in intermolecular interactions in the crystalline state. Part I. In situ cryocrystallography: Probing the solid state structures of ambient condition liquids. Chapter 1 discusses the crystal structures of benzoyl chloride and its fluorinated analogs. These compounds have been analysed for the propensity of adoption of Cl···O halogen bonded dimers and catemers. The influence of conformational and electronic effects of sequential fluorination on the periphery of the phenyl ring has been quantified in terms of the most positive electrostatic potential, VS,max (corresponding to σ-hole) on the Cl-atom. It is shown that fluorine also exhibits “amphoteric” nature like other heavier halogens, particularly in presence of electron withdrawing groups. Although almost all the derivatives pack through C–H···O, C–H···F, C–H···Cl, Cl···F, C–H···π and π···π interactions, the compound 2,3,5,6-tetrafluorobenzoyl chloride exhibited a not so commonly observed Cl···O halogen bonded catemer. On the other hand, the proposed Cl···O mediated dimer is not observed in any of the structures due to geometrical constraints in the crystal lattice. Chapter 2 presents the preferences of fluorine to form hydrogen bond (C–H···F) and halogen bonds (X···F; X= Cl, Br, I). Crystal structures of all three isomers of chloro-, bromo-and iodo-fluorobenzene have been probed in order to gain insights into packing interactions preferred by fluorine and other heavier halogens. It has been observed that homo halogen…halogen (Cl···Cl, Br···Br and I···I) contacts prevail in most of the structures with fluorine being associated with the hydrogen atom forming C–H···F hydrogen bond. The competition between homo and hetero halogen bonds (I···I vs I···F) is evident from the packing polymorphism exhibited by 4-iodo fluorobenzene observed under different cooling protocols. The crystal structures of pentafluoro halo (Cl, Br, I) benzenes were also determined in order to explore the propensity of formation of homo halogen bonds over hetero halogen bonds. Different dimeric and catemeric motifs based on X···F and F···F interactions were observed in these structures. Chapter 3 focuses on the effect of different cooling protocols in generating newer polymorphs of a given liquid. The third polymorph (C2/c, Z'=6) of phenylacetylene was obtained by sudden quenching of the liquid filled in capillary from a hot water bath (363 K) to the nitrogen bath (< 77 K). Also, different polymorphs were obtained for both 2¬fluoro phenylacetylene (Pna21, Z'=1) and 3-fluoro phenylacetylene (P21/c, Z'=3) when crystallized by sudden quenching in contrast to the generally followed method of slow cooling which results in isostructural forms (P21, Z'=1). The rationale for these kinetically stable “arrested” crystalline configurations is provided in part II of the thesis. Part II. Tracing crystallization pathways via kinetically captured metastable forms. Chapter 4 explains the utilization of the new approach of sudden quenching of liquids (detailed in chapter 3) to obtain kinetically stable (metastable) crystalline phases that appear to be closer to the unstructured liquids. Six different examples namely, phenylacetylene, 2-fluorophenylacetylene, 3-fluorophenylacetylene, 4-fluorobenzoyl chloride, 3-chloro fluorobenzene and ethyl chloroformate are discussed in this context. In each case, different polymorphs were obtained when the liquid was cooled slowly (100 K/h) and when quenched sharply in liquid nitrogen. The relationship between these metastable forms and the stable forms (obtained by slow cooling) combined with the mechanistic details of growth of stable forms from metastable forms provides clues about the crystallization pathways. Part III. Conformational analysis in the solid state: Counterbalance of intermolecular interactions with molecular and crystallographic symmetries. Chapter 5 describes the crystal structures of a series of conformationally flexible molecules namely, acetylene and diacetylene spaced aryl biscarbonates and biscarbamates. While most of the molecules adopt commonly anticipated anti (transoid) conformation, some adopt unusual cisoid and gauche conformations. It is shown that the unusually twisted conformation of one of the compounds [but-2-yne-bis(2,3,4,5,6¬pentafluorocarbonate)] is stabilized mainly by the extraordinarily short C–H···F intermolecular hydrogen bond. The strength of this rather short C–H···F hydrogen bond has been authenticated by combined single crystal neutron diffraction and X-ray charge density analysis. It has also been shown that the equi-volume relationship of H-and F-atoms (H/F isosterism) can be explored to access various possible conformers of a diacetylene spaced aryl biscarbonate. While biscarbonates show variety of molecular conformations due to absence of robust intermolecular interactions, all the biscarbamates adopt anti conformation where the molecules are linked with antiparallel chains formed with N–H···O=C hydrogen bonds. Chapter 6 presents a unique example where the commonly encountered crystallographic terms namely, high Z' structure, polymorphism, phase transformation, disorder, isosterism and isostructuralism are witnessed in a single molecular species (parent compound benzoylcarvacryl thiourea and its fluorine substituted analogs). The origin of all these phenomenon has been attributed to the propensity of formation of a planar molecular dimeric chain mediated via N–H···O [R2 (12)] and N–H···S [R2 (8)] dimers.

Introduction The chemistry of transitional metal complexes bearing σ-bonded H−X (X = H, Si, C) species/fragments, the so called σ-complexes, are key intermediates in catalytic processes such as hydrogenation, hydrosilylation, alkane functionalization etc. Particularly, the σ-H2 complexes form the best-known group of σ-complexes in which H2 is bound to the metal center in η2-fashion. Several well characterized examples of η2-silane and η2-borane complexes have also been reported. Moreover, in recent years, the carbon analogues of these complexes in which alkanes are coordinated through η2-C-H bonds to the metal center have been attracting the attention of organometallic chemists. An approach towards direct functionalization of σ-bonds in simple alkanes is the heterolytic activation of the C−H bond using highly electrophilic complexes. After all, for fine catalyst design and the selective functionalization of H−H, silanes or simple alkanes, it is necessary to understand the bonding nature of these σ-complexes in depth. Objectives The objectives of this work are as follows a) An attempt to stabilize and gain insights into the bonding nature and reactivity behavior of various sigma ligands on ruthenium center [Ru(η2-HX)(Tpms)(PPh3)2][OTf], (X = H, SiR (R = Me3 or Me2Ph) and CH3). b) Synthesis, characterization and reactivity studies of electrophilic ruthenium(II) complexes bearing (C6F5)2PCH2CH2P(C6F5)2 (dfppe) ligand towards heterolysis of H2. c) An approach towards preparation of insoluble molecular clusters from [Ru(P(OH)3)(dppe)2][OTf]2 complex and Zn, Cd and Cu acetates to realize σ-bond activation under heterogeneous conditions. Significant results In our attempts to gain insights into the bonding nature and reactivity behavior of σ-H2, silane and methane complexes, we followed two strategies to generate these complexes in solution. First, we synthesized and well characterized two new Ru(II)-complexes [RuH(Tpms)(PPh3)2] and [Ru(OTf)(Tpms)(PPh3)2], (OTf = trifluoromethane sulfonate) where Ru-H and Ru-OTf are the key reactive centers, followed by their subsequent reactions with electrophilic reagents such as HOTf, Me3SiOTf and CH3OTf and with H2, PhMe2SiH and CH4 at low temperature, respectively. These reactions finally resulted in the characterization of σ-H2 and σ-silane complexes, however, no σ-methane complex was observed even at low temperature (Scheme 1). Scheme 1 In order to realize highly eletrophilic metal complexes, a chelating fluorinated phosphine ligand 1,2-bis-(pentafluorophenylphosphino)ethane, (C6F5)2PCH2CH2P(C6F5)2 (dfppe) was employed and the synthesis and structural characterization of a series of new, Ru(II) hydride complexes [RuH(P(OMe)3)(bpy)(dfppe)][OTf], cis-[RuH2(dfppe)(PPh3)2] and [RuH(CO)Cl(PPh3)(dfppe)] were accomplished. Protonation reaction of the hydride complexes [RuH(P(OMe)3)(bpy)(dfppe)][OTf] (Scheme 2) and [RuH(CO)Cl(PPh3)(dfppe)] (Scheme 3) with HOTf at low temperature gave free H2 and five-coordinate species [Ru(P(OMe)3)(bpy)(dfppe)][OTf]2 and [Ru(CO)Cl(PPh3)(dfppe)][OTf], respectively. Surprisingly, in all these reactions, dihydrogen complexes are formed which were unobservable in which the H2 ligand was found to be highly labile. Reaction of is-[Ru(bpy)(dfppe)(OH2)(P(OMe)3)][OTf]2 with H2 however, resulted in the heterolytic activation of the H–H bond and concomitant protonation of H2O to give the corresponding hydride complex cis-[Ru(H)(bpy)(dfppe)(P(OMe)3)][OTf] and H3O+ (Scheme 2) . Scheme 2 Scheme 3 In an attempt to prepare insoluble molecular clusters in order to realize σ-bond activation under heterogeneous conditions, we studied the reactivity of highly electrophilic [Ru(P(OH)3)(dppe)2]2+ (dppe = (C6H5)2PCH2CH2P(C6H5)2) complex with various metal acetates. Usage of Zn(OAc)2.2H2O afforded a novel [Ru2(dppe)4P2(OH)2O4Zn2(OAc)(DMP)(OTf)][OTf]2 (Ru-Zn ) soluble bimetallic complex (Scheme 4) which was characterized in detail by NMR and single crystal X-ray crystallography. To achieve the expected insoluble molecular cluster further studies are required to tune the electronics and the sterics around the phosphorous acid moiety. Scheme 4

The importance of weak interactions between molecules to life and all parts of science and engineering is unquestionable and there have been an enormous interest in such interactions. Among all the weak interactions, hydrogen bonding is the most popular and it has enjoyed the most attention of the scientific community. Halogen bonding is gaining more popularity in the recent time, as its importance to biological molecules and crystal engineering has been recognized. In this work, a Pulsed Nozzle Fourier Transform Microwave spectrometer has been used to study the rotational spectra of molecules and hydrogen bonded complexes. Structural information is obtained from the rotational spectra. Ab initio electronic structure, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theoretical methods have been used to characterize the weak intermolecular interactions, including hydrogen bonding, halogen bonding and lithium bonding. In Chapter I, introduction to weak interaction is discussed. A brief introduction of different experimental and theoretical methods is presented. Chapter II discusses in detail about the different methods used to investigate weak interaction, both experimentally and theoretically, in this work. In our lab, we use Pulsed Nozzle Fourier Transform Microwave spectrometer to determine the complexes spectra and structures. We generate MW radiation with the help of electronic devices and use Balle-Flygare cavity where molecular interaction takes place. We inject the sample inside the cavity in form of supersonic molecular beam through a pulsed nozzle, parallel to MW radiation. The detailed instrumental discussion about MW spectrometer has been done in this Chapter. We extensively use theoretical methods to probe weak bonding and characterize them. Ab initio and DFT calculations are used to optimize the structure of the complexes and predict their rotational spectra. Atoms in Molecules theory and Natural Bond Orbital theory are then used with the ab initio wave functions to understand the weak interactions in depth. Discussion about these methods and software used for the analysis will also be discussed. In Chapter III, rotational spectrum of Hexafluoroisopropanol (HFIP) monomer is presented. HFIP is an interesting molecule as it offers many possibilities as hydrogen bond donor and acceptor. It has the OH group which can both accept/donate a hydrogen bond and in addition it has a very acidic CH group. It is the only solvent that can dissolve polyethylene terephthalate, a normally difficult-to-dissolve polymer, and clearly it has unique interactions with this difficult to solve polymer. We have recorded and fitted rotational spectra of five different isotopologues of HFIP which helped us in determining its accurate structure. Though, it can exist in synclinical and antiperiplanar conformers, only the later has been detected in our molecular beam spectrometer. This happens to be the global minimum structure of HFIP. Combination of experimental observations and ab initio calculations provided many evidences which confirmed the presence of antiperiplanar conformer, experimentally. Since, the rotational constants for both conformers were very close, it was always challenging to pick up one conformer as experimentally observed structure. A prototype molecule, hexafluoroisobutene (HFIB) shows doubling of rotational transitions due to tunnelling/counter rotation of the two CF3 groups through a small barrier. Interestingly, such motion has no barrier in HFIP and hence no splitting in transitions was observed. Potential energy surface calculated for counter-rotation of the two CF3 groups is consistent with this observation. This barrier is different from eclipsed-staggered exchange barrier, observed by 60 counter rotation of both terminal CF3 groups, for which the barrier height is very large and tunnelling cannot occur. The origin/lack of the small barrier in HFIB/HFIP has been explored using Natural Bond Orbital (NBO) method which helped in understanding intramolecular bonding in these molecules. Along with HFIB, other prototype molecules were also considered for the analysis e.g. hexafluoroacetone, hexafluoroacetone imine, hexafluoroisobutane, hexafluoroisopropylamine. In the last section of this Chapter, we have discussed the generalized behaviour of molecules which have CF3-C-CF3 groups. In Chapter IV, rotational spectrum of HFIP•••H2O complex is presented. Aqueous solution of HFIP stabilizes α-helical structure of protein, a unique property of this solvent. The main objective of this Chapter is understanding the interaction between HFIP and H2O. Microwave spectrum of HFIP•••H2O was predicted and recorded. Three isotopologues were investigated. Though, this complex could in principle have several structural conformers, detailed ab initio calculations predicted two conformers and only one was observed. Though, the rotational constants for both structures were somewhat similar, lack of a dipole transitions, larger intensity of b-dipole transitions over c-dipole transitions and isotopic substitution analysis positively confirm the structure in which HFIP acts as the hydrogen bond donor. The linear O-H•••O hydrogen bond in HFIP-H2O complex is significantly stronger than that in water dimer with the H•••O distance of 1.8 Å. The other structure for this complex, not found in experiment is cyclic with both C-H•••O and O-H•••O hydrogen bonds, both of which are bent with H•••O distances in the range 2.2-2.3 Å. Both AIM and NBO calculations have been used to characterize the hydrogen bond in this complex. In Chapter V, a comprehensive study on hydrogen bonding, chlorine bonding and lithium bonding have been done. A typical hydrogen bonded complex can be represented as A•••H-D, where A is the acceptor unit and H-D is the hydrogen bond donor unit. Many examples are known in literature, both experimentally and theoretically, in which the A-H-D bond angles are not linear. Deviation from linearity also results in the increase in A•••H bond lengths, as noted above for the two structures of HFIP•••H2O complex. Though this has been known for long, the distance between A and D being less than the sum of their van der Waals ‘radii’ is still used as a criterion for hydrogen bonding by many. Our group has recently shown the inappropriateness of van der Waals ‘radii’ and defined hydrogen bond ‘radii’ for various donors, DH and A. A strong correlation of DH hydrogen bond ‘radii’ with the dipole moment was noted. In this Chapter, we explored in detail the angular dependence of hydrogen bond ‘radii’. Electron density topology around DH (D = F, Cl and OH) has been analyzed in detail and shown to be elliptical. For these molecules, the two constants for H atom treated as an ellipse have been determined. It is hoped that these two constants will be used widely in analyzing and interpreting H•••A distances, as a function of D-H•••A angles, rather than one ‘radius’ for H and acceptor atoms. In Chapter VI, Detailed analysis and comparisons among hydrogen bond, chlorine bond and lithium bond, have been done. Hydrogen can be placed in group 1 as well as group 17 of the periodic table. Naturally, lithium bonding and halogen bonding have been proposed and investigated. There have been numerous investigations on the nature of hydrogen bonding and the physical forces contributing to it. In this Chapter, a total of one hundred complexes having H/Cl/Li bonding have been investigated using ab initio, AIM and NBO theoretical methods. Various criteria proposed in the literature have been examined. A new criterion has been proposed for the characterization of closed shell (ionic/electrostatic) and open shell (covalent) interactions. It has been well known that the D-H bond weakens on the D-H•••A hydrogen bond formation and H•••A bond acquires a fractional covalency. This Chapter shows that for D-Li•••A complexes, the ionicity in D-Li is reduced as the Li•••A bond is formed This comprehensive investigation of H/Cl/Li bonding has led us to propose a conservation of bond order, considering both ionic and covalent contributions to both D-X and X•••A bonds, where DX is the X-bond donor and A is the acceptor with X = H/Cl/Li. Hydrogen bond is well understood and its definition has been recently revised [Arunan et al. Pure Appl. Chem., Vol. 83, pp. 1619–1636, 2011]. It states “The X–H•••Y hydrogen bond angle tends toward 180° and should preferably be above 110°”. Using AIM theory and other methods, this fact is examined and presented in Appendix A. In second part of appendix A, a discussion about calling H3¯ complex as trihydrogen bond and its comparison with FHF¯ complex, is presented. In Appendix B, there is tentative prediction and discussion about the HFIP dimer. Condense phase studies show that HFIP have strong aggregation power to form dimer, trimer etc. During, HFIP monomer study, we have unassigned lines which are suspected to be from HFIP dimer. These are tabulated in the Appendix B as well.