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.

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.

The results of a systematic 35Cl, 81Br, and 127I SSNMR spectroscopic study of a series of halogen-substituted anilinium halide salts are presented. Solid-state NMR of these nuclides, bromine-/81 and iodine-127 in particular, is not well established. Twenty-one compounds thought to exhibit halogen bonding were prepared based on modified literature procedures, and two crystal structures were solved. Experiments show that collection of SSNMR spectra of the anions is feasible, though ultrahigh magnetic fields (21.1 T) and variable offset data acquisition were found to be essential. Electric field gradient and chemical shift tensors are measured experimentally for all 21 compounds, significantly expanding the body of data for the quadrupolar halogen nuclei. Quadrupolar coupling constants for chlorine-35 ranged from 2.12 to 6.04 MHz, for bromine-81 from 12.3 to 45.3 MHz, and for iodine-127 from 57.50 to 152.50 MHz. Gauge-including projector-augmented wave density functional theory (GIPAW-DFT) calculations were used to provide insight as to how the NMR parameters vary with local environment and long-range crystal packing. Overall, calculations reproduced the experimental trends in quadrupolar coupling constants and chemical shift tensor span (Ω) but failed to provide quantitative agreement within experimental error. Experimental and computational data were analyzed in order to provide insight into how halogen bonding influences NMR parameters. Several trends were elucidated from this study, including an inverse correlation between Ω and the length of the shortest halogen-halide contact (d). In selected bromine compounds, for example, Ω (81Br) was measured to increase from 120 to 240 ppm as d decreased from 3.838 to 3.443 Å. In summary, this study has demonstrated the feasibility and utility of quadrupolar halogen SSNMR, and that these techniques may prove useful in characterizing halogen bonding interactions in solids.

Solid-state nuclear magnetic resonance (SSNMR) has proven to be a useful tool in the characterization of non-covalent interactions such as hydrogen bonding and cation-π interactions. In recent years, the scientific community has manifested a renewed interest towards an important class of non-covalent interaction, halogen bonding (XB), as it has applications in various fields such as crystal engineering and biological processes. This dissertation demonstrates that NMR parameters measured in the solid state are sensitive to changes in electronic structure, which are caused by halogen bonds. A series of halogen bonded compounds exhibiting interactions between different diiodoperfluorobenzenes (p- C6F4I2, o- C6F4I2, sym- C6F3I3, p- C6H4I2) and various halogen bond acceptors have been synthesized as part of this work. These new halogen bonded compounds were characterized with a combined theoretical and experimental SSNMR, X-ray diffraction (XRD) methods. The complete multinuclear magnetic resonance spectroscopy of the nuclei involved directly in the halogen bond (13C, 14/15N, 31P, 77Se, 35/37Cl and 79/81Br) were recorded at multiple magnetic fields (4.7, 9.4, 11.75 and 21.1 T). The specialized SSNMR experiments provided high-resolution spectra of quadrupolar nuclei, which were WURST-QCPMG or solid-echo type experiments combined with the variable offset cumulative spectral (VOCS) method, as for spin 1/2 nuclei cross polarization magic angle spinning (CPMAS) experiments were usually appropriate. This dissertation will discuss successful applications of SSNMR spectroscopy to characterize halogen bonds, it will demonstrate the significant changes in NMR observables in the presence of XB interaction and thus establish that NMR parameters are very sensitive to halogen bonding interaction. Furthermore, this work explains why the NMR parameters are correlated with the halogen bonding interaction. The different trends observed between the NMR observables and the halogen bonding were further understood with a ZORA-DFT natural localized molecular orbital (NLMO) study.

Electrostatic interactions such as halogen bonding and pnictogen bonding interactions have gained a lot of interest in the field of crystal engineering and pharmaceutical science. In the first part of this thesis, we expand our knowledge on anion coordinated halogen bonded cocrystals by looking at a series of cocrystals made from 3-iodoethynyl pyridine and 3-iodoethynylbenzoic acid. We utilize the power of mechanochemistry to create the new cocrystals made with phosphonium salts and use multinuclear solid-state nuclear magnetic resonance spectroscopy and X-ray diffraction and characterize them. We found that mechanochemistry is a fast and powerful tool to explore and synthesize new halogen bonded cocrystals and ³¹P solid-state NMR is a rapid way to identify the formation of a cocrystal. In the second part, we look at the versatility of the pnictogen atom, specifically antimony, as a pnictogen bond donor and a halogen bond acceptor. We evaluate these electrostatic interactions with nuclear quadrupolar resonance and found that nuclear quadrupole resonance is a strong spectroscopy tool to probe these types of electrostatic interactions.

Les travaux décrits dans ce manuscrit utilisent les principes de la tectonique moléculaire pour générer des polymères de coordination hautement fluorés et /ou chiraux pour une application potentielle en séparation chirale. La synthèse de 13 porphyrines de type A2B2 substituées en position méso par deux pyridines et par deux chaines fluorées et/ou alkyles a été mise au point. Des réseaux de coordination ont été obtenus en présence de Zn(II) et de Cd(II) et caractérisés par diffraction des RX sur monocristal (DRX). Une analyse systématique des interactions supramoléculaires et notamment de interactions F---F présentes à l’état solide a été conduite. Des réseaux à base de liaisons halogènes ont également été obtenus en présence de di- et tri-iodoarènes et caractérisés par DRX.Le premier chapitre est une introduction générale sur la tectonique moléculaire, le deuxième chapitre décrit les voies des synthèses utilisées pour générer les ligands chiraux et fluorés et leur caractérisation à l’état solide. Le troisième chapitre présente la structure des réseaux mono, bi, et tridimensionnels formés en présence de Zn(II) ou de Cd(II), l’analyse structurale met en évidence un nombre croissant d’interaction F---F en fonction du nombre de fluors présents à la périphérie du macrocycle porphyrinique. Le dernier chapitre se concentre sur l’utilisation des liaisons halogènes de type N---I impliquant des porphyrines ou des tectons de type bipyridine et une série d’ iodofluoroarenes. / This manuscript focuses on the use of molecular tectonics to generate chiral and / or fluorinated coordination polymers based on porphyrin building blocks for potential application in chiral separation. Synthesis of novel A2B2 fluorinated porphyrin tectons is described and their combinations with metal ions and haloarenes molecules are characterized by X-Ray diffraction.The first chapter gives a general introduction on molecular tectonics; the second chapter focuses on the synthetic routes used for the synthesis of highly fluorinated and/or chiral porphyrins and their solid state characterization by X-Ray diffraction analysis, highlighting the importance of the number of fluorine atoms present at the periphery of the tecton on the crystal packing. The third chapter presents the mono-, bi- and three dimensional networks formed by a combination of the porphyrins with Zn(II) or Cd(II). In the solid state, short F---F contacts were observed depending on the number of fluorine atoms present on the porphyrin backbone. The last chapter focuses on the use of halogen bonds, by merging the neutral porphyrin or bipyridine tectons with a series of iodofluoroarenes. The crystalline materials described in this work can be used as potential candidates for the separation of chiral and fluorinated molecules.

Thyroid hormones, which are secreted by the thyroid gland, are one of the most important halogenated compounds in the body. Thyroid hormones control almost every processes in the body including growth, body temperature, protein synthesis, carbohydrate and fat metabolism, heart rate, and cardiovascular, renal and brain function. Thyroid gland secretes L-thyroxine or 3,3',5,5'-tetraiodothyronine (T4) as a prohormone. While the biologically active hormone 3,3',5-triiodothyronine (T3) is produced by selective phenolic ring deiodination of T4, selective tyrosyl ring deiodination of T4 produces a biologically less active metabolite 3,3',5'-triiodothyronine (rT3). Tyrosyl and phenolic ring deiodination of T3 and rT3, respectively, also produces a biologically inactive metabolite 3,3'-diiodothyronine (3,3'-T2). Regioselective deiodinations of thyroid hormones are catalysed by three isoforms of a selenoenzyme iodothyronine deiodinase (DIO1, DIO2, DIO3). DIO1 can remove iodine from both the tyrosyl and phenolic rings of thyroid hormones, whereas DIO2 and DIO3 are selective towards phenolic and tyrosyl ring, respectively. Although the Figure 1. (A) Deiodination of thyroid hormones by iodothyronine deiodinases (DIOs) (A) and naphthyl-based selenium and/or sulphur compounds (B). mystery behind the origin of regioselectivity of deiodination by DIOs remains unsolved, formation of halogen bonding between selenium in the active site of DIOs and iodine of thyroid hormones has been widely accepted as the mechanism of deiodination. Halogen bonding, a noncovalent interaction between halogen and an electron donor such as nitrogen, oxygen, sulphur, selenium etc., elongates the C-I bond and impart a carbanionic character on the carbon atom that gets protonated after the removal of iodide. Apart from the deiodination, thyroid hormones also undergo decarboxylation, oxidative deamination, sulphate-conjugation to form iodothyronamines, iodothyroaetic acids and sulphated thyroid hormones, respectively. Figure 2. (A) Proposed mechanism of deiodination of thyroid hormones by deiodinase mimics. (B) Halogenation of uracil- and cytosine-containing nucleosides by hypohalous acid (HOX). Recently, naphthyl-based selenium/sulphur-containing compounds, such as compound 1 (Figure 1B), have been reported to mediate the selective tyrosyl ring deiodination of T4 and T3 to form rT3 and 3,3'-T2, respectively. Interestingly, replacement of the selenol moiety in compound 1 with a thiol decreases the activity, whereas replacement of the thiol moiety with another selenol dramatically increases the deiodination activity. Based on the detailed experimental and theoretical investigations, a mechanism involving the Se···I halogen bonding was proposed (Figure 2A). In addition to the halogen bonding between selenium and iodine atom, chalcogen bonding between two nearby chalcogen atoms was also shown to be important for the deiodination activity. Another important class of halogenated compounds in the body are the halogenated nucleosides. Myeloperoxidase and eosinophil peroxidase are heme-containing enzymes, which can convert halide ions (X¯) into a toxic reactive halogen species hypohalous acid (HOX) in presence of hydrogen peroxide (H2O2). Uracil- and cytosine-containing nucleosides are known to undergo halogenation at the 5-position of the nucleobase to form the halogenated nucleosides (Figure 2B). Interestingly, halogenated nucleosides such as 5-halo-2'-deoxyuridine are known to be incorporated in the DNA of dividing cells essentially substituting for thymidine. Incorporation of halogenated nucleosides into the DNA leads to mutagenesis, carcinogenesis and loss of genome integrity. Thymidylate synthase (TSase), the key enzyme involved in the biosynthesis of 2'-deoxythmidine-5'-monophosphate (dTMP) from 2'-deoxyuridine-5'-monophosphate (dUMP), can catalyse the dehalogenation of halogenated nucleotides in presence of external thiols. This thesis consists of five chapters. The first chapter provides a general introduction to halogen bonding, thyroid hormones and halogenated nucleosides. This chapter also briefly describes the halogen bond-mediated biochemical and biomimetic deiodinations of thyroid hormones by iodothyronine deiodinases and naphthyl-based organoselenium compounds. Dehalogenation of halogenated nucleotides by thymidylate synthase and thiol-based small molecules has also been discussed in this chapter. The second chapter of this thesis contains the regioselective deiodination of iodothyronamines (TAMs) by deiodinases mimics. TAMs are the endogenous metabolites produced by the decarboxylation of β-alanine side chain of thyroid hormones (THs). 3,3',5-triiodothyronamine (T3AM) and 3,5-diiodothyronamine (3,5-T2AM) undergoes selective tyrosyl ring deiodination by deiodinase mimics to form 3,3'-diiodothyronamine (3,3'-T2AM) and 3-iodothyronamine (3-T1AM), respectively. Interestingly, when the initial rates of deiodinations of T3 and T3AM were compared, deiodination of T3 was found to be several fold faster than that of T3AM under identical reaction conditions. To understand the ability of the iodine atoms to form Figure 3. (A) HPLC chromatogram of deiodination of T3. (B) Proposed mode of interaction of dimeric T3 and monomeric T3AM with organoselenium compounds. halogen bonding, a model selenolate (MeSe¯) was optimized with the T3 and T3AM. Although both T3 and T3AM forms the expected Se···I halogen bonding with MeSe¯, the strength of halogen bonding was found to be less for T3AM than T3. Furthermore, detailed kinetic and spectroscopic studies indicate that T3 and T3AM exist as dimeric and monomeric species in solution. The dimerization of T3 in solution was shown to have remarkable impact on the activation energy and pre-exponential factor of the deiodination reactions. Single crystal X-Ray crystallography and theoretical calculations indicated that in addition to Se···I halogen bonding, I···I halogen bonding may play an important role in the deodination of thyroid hormones by deiodinase mimics. Furthermore, the presence of heteroatoms such as nitrogen, oxygen and sulphur in the close proximity of one of the selenium atoms of deiodinase mimics was shown to have significant effect on the rate of deiodination reactions. The third chapter of the thesis focusses on the conformational polymorphism and conformation-dependent halogen bonding of L-thyroxine. Synthetic version of L-thyroxine (T4) is a life-saver for millions of people who are suffering from hypothyroidism, a thyroidal disorder recognised by low levels of T4 and elevated levels of TSH in blood plasma. Synthetic version of L-thyroxine is available in the Figure 4. Ball and stick model of the single crystal X-Ray structure of the conformational polymorphs of L-thyroxine. Form I and Form II was exclusively crystallized from methanol and acetonitrile, respectively. Water molecules are omitted for clarity. market with various brand names. However, adverse effects have been observed in the patients when they switch their brand of thyroxine. Based on these observations, the American Thyroid Association (ATA), the Endocrine Society (TES), and the American Association of Clinical Endocrinologists (AACE) declared that the different brands of T4 are not bioequivalent, thus leading to differences in the bioavailability of the drug. We have shown that the commercially available thyroxine exists in at least two stable forms (Form I and Form II) with different three-dimensional structures (Figure 4). These two forms exhibit different intermolecular interactions in crystal packing, spectral behaviours, thermal stabilities, optical activity and very interestingly, different solubility in acidic and basic pH. At pH 4, solubility of Form I is about 42% and 45% greater than that of Form II and bulk T4, respectively, whereas at pH 9, the solubility of Form II is about 38% and 42% higher than that of Form I and bulk T4, respectively. As T4 is a narrow therapeutic index drug, these differences in solubility may have remarkable impact on the bioavailability of the drug. In addition to this, we have shown that the ability of the iodine atoms in the C-I bonds to form halogen bond with donor atoms can be altered by changing the relative orientation of tyrosyl and phenolic rings in T4. In the fourth chapter, the three-dimensional structures and conformations of thyroid hormones (THs) and iodothyronamines (TAMs) are discussed. TAMs, the endogenous decarboxylated metabolites of THs, exhibit different binding affinities to the transport proteins and iodothyronine deiodinases (DIOs) compared to the THs. Figure 5. Change in the structure and conformations of thyroid hormones and iodothyronamines with the decarboxylation of amino acid side chain and deiodination of phenolic and tyrosyl ring. Furthermore, the substrate specificities of DIOs have been found to be dependent on the position of iodine atoms on the phenolic and tyrosyl ring of TAMs and THs. Single crystal X-ray structures of TAMs indicate that decarboxylation of amino acid side chain of THs induces significant changes in the structure and conformation. Furthermore, the positional isomers of THs and TAMs exhibit remarkably different conformations, which may have significant effect on the binding of these metabolites to the active site of DIOs. In addition to the structure and conformations, different categories of the intermolecular halogen···halogen (X···X) interactions in the crystal packing of THs and TAMs have also been discussed. Natural bond orbital (NBO) analysis have been done on the halogen-bonded geometries to understand the electronic nature of these interactions. In the fifth chapter, the dehalogenation of halogenated nucleosides and nucleobases by naphthyl-based sulphur/selenium compounds is discussed. Purine and pyrimidine nucleosides are halogenated at various positions of the aromatic ring by different peroxidases such as myeloperoxidase and eosinophil peroxidase present in the white blood cells. Incorporation of the halogenated nucleosides into the DNA of replicating cells leads to DNA-strand breaks, mutagenesis, carcinogenesis and loss of Figure 6. (A) Dehalogenation of halogenated nucleosides. Effect of base-pairing wih adenine and guanine on the deiodination of IU (B) and debromination of BrU (C) by compound 2. genome integrity. We have shown that the naphthalene-based organoselenium compounds such as compound 2 can mediate the dehalogenation of 5-iodo-2'-deoxyuridine (5-IdUd) and 5-bromo-2'-deoxyuridine (5-BrdUd) to produce 2'-deoxyuridine (dUd) (Figure 6A). The deiodination of 5-IdUd was found to be faster than the debromination of 5-BrdUd by compound 2. The mechanism of dehalogenation of halogenated nucleosides by compound 2 was found to be dependent on the nature of halogen. While the deiodination of 5-IdUd by compound 2 follow halogen bond-mediated pathway like thyroid hormones, debromination of 5-BrdUd follow a Michael addition-elimination pathway. Similar results were obtained when 5-iodo-2'-deoxycytidine (5-IdCd) or 5-bromo-2'-deoxycytidine (5-BrdCd) was used as substrate for dehalogenation reaction. Base-pairing of 5-iodouracil (IU) and 5-bromouracil (5-BrU) with adenine and guanine has a significant effect on the rate of dehalogenations of IU and BrU by compound 2 (Figure 6B and 6C).

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.

Weak intermolecular interactions have very strong impact on the structures and properties of life giving molecules like H2O, DNA, RNA etc. These interactions are responsible for many biological phenomena. The directional preference of some of these interactions is used for designing different synthetic approaches in the supramolecular chemistry. The work reported in this Thesis comprises of investigations of weak intermolecular interactions in gas phase using home-built Pulsed Nozzle Fourier Transform Microwave (PN-FTMW) spectrometer as an experimental tool and ab-initio and Atoms in Molecules (AIM) theory as theoretical tools. The spectrometer which is coupled with a pulsed nozzle is used to record pure rotational spectra of the molecular clusters in a jet cooled molecular beam. In the molecular beam molecules/complexes are free from interactions with other molecules/complexes and thus, spectroscopy in the molecular beams provides information about the 'isolated' molecule/complex under investigation. The rotational spectra of the molecules/complexes in the molecular beam provide their geometry in the ground vibrational states. These experimental geometries can be used to test the performance and accuracy of theoretical models like ab-initio theory, when applied to the weakly bound complexes. Further the AIM theory can be used to gain insights into the nature and strength of the intermolecular interactions present in the system under investigation. Chapter I of this Thesis gives a brief introduction of intermolecular interactions. Other than hydrogen bonding, which is considered as the most important intermolecular interaction, many other intermolecular interactions involving different atoms have been observed in past few decades. The chapter summarizes all these interactions. The chapter also gives a brief introduction to the experimental and theoretical methods used to probe these interactions. In Chapter II, the experimental and theoretical methods used in this work are summarized. Details of our home-built PN-FTMW spectrometer are given in this chapter. The chapter also discusses briefly the theoretical methods like ab-initio, AIM and Natural bond orbital (NBO) analysis. We have made few changes in the mode of control of one of our delay generators which have also been described. Chapter III and Chapter V of this Thesis are dedicated to the propargyl alcohol complexes. Propargyl alcohol (PA) is a molecule of astrophysical interest. It is also important in combustion chemistry since propargyl radical is considered as the precursor in soot formation. Moreover, PA is a multifunctional molecule, having a hydroxyl (-OH) and an acetylenic (-C≡C-H) group. Both of the groups can individually act as hydrogen bond acceptor as well as donor and thus PA provides an exciting possibility of studying many different types of weak interactions. Due to internal motion of -OH group, PA monomer can exist in gauche as well as trans form. However, rotational spectra of PA-monomer show the presence of only gauche conformer. In Chapter III, rotational spectra of Ar•••PA complex are discussed. The pure rotational spectra of the parent Ar•••PA complex and its two deuterated isotopologues, Ar•••PA-D (OD species) and Ar•••PA-D (CD species), could be observed and fitted within experimental uncertainty. The structural fitting confirmed a structure in which PA is present as gauche conformer and argon interacts with both the O-H group and the acetylenic group leading to Ar•••H-O and Ar•••π interactions respectively. Presence of these interactions was further confirmed by AIM theoretical analysis. In all the three isotopologues c-type rotational transitions showed significant splitting. Splitting patterns in the three isotopologues suggest that it originates mainly due to the large amplitude motion of the hydroxyl group and the motion is weakly coupled with the carbon chain bending motion. No evidence for the complex with trans conformer of PA was found. Although, we could not observe Ar•••trans-PA complex experimentally, we decided to perform ab-initio and AIM theoretical calculations on this complex as well. AIM calculations suggested the presence of Ar•••H-O and a unique Ar•••C interaction in this complex which was later found to be present in the Ar•••methanol complex as well. This prompted us to explore different possible interactions in methanol, other than the well known O-H•••O hydrogen bonding interactions, and eventually led us to an interesting interaction which we termed as carbon bond. Chapter IV discusses carbon bonding interaction in different complexes. Electrostatic potential (ESP) calculations show that tetrahedral face of methane is electron-rich and thus can act as hydrogen/halogen bond acceptor. This has already been observed in many complexes, e.g. CH4•••H2O/HF/HCl/ClF etc., both experimentally and theoretically. However, substitution of one of the hydrogens of methane with -OH leads to complete reversal of the properties of the CH3 tetrahedral face and this face in methanol is electron-deficient. We found that CH3 face in methanol interacts with electron rich sites of HnY molecules and leads to the formation of complexes stabilized by Y•••C-X interactions. This interaction was also found to be present in the complexes of many different CH3X (X=OH/F/Cl/Br/NO2/NF2 etc.) molecules. AIM, NBO and C-X frequency shift analyses suggest that this interaction could be termed as "carbon bond". The carbon bonding interactions could be important in understanding hydrophobic interactions and thus could play an important role in biological phenomena like protein folding. The carbon bonding interaction could also play a significant role in the stabilization of the transition state in SN2 reactions. In Chapter V of this Thesis rotational spectra of propargyl alcohol dimer are discussed. Rotational spectra of the parent dimer and its three deuterated (O-D) isotopologues (two mono-substituted and one bi-substituted) could be recorded and fitted within experimental uncertainty. The fitted rotational constants are close to one of the ab-initio predicted structure. In the dimer also propargyl alcohol exists in the gauche form. Atoms in molecules analysis suggests that the experimentally observed dimer is bound by O-H•••O, O-H•••π and C-H•••π interactions. Chapter VI of the thesis explores the 'electrophore concept'. To observe the rotational spectra of any species and determine its rotational constant by microwave spectroscopy, the species should have a permanent dipole moment. Can we obtain rotational constants of a species having no dipole moment via microwave spectroscopy? Electrophore concept can be used for this purpose. An electrophore is an atom or molecule which could combine with another molecule having no dipole moment thereby forming a complex with a dipole moment, e.g. Argon atom is an electrophore in Ar•••C6H6 complex. The microwave spectra of Ar•••13CC5H6 and Ar•••C6H5D complexes were recorded and fitted. The A rotational constant of these complexes was found to be equal to the C rotational constant of 13CC5H6 and C6H5D molecules respectively and thus we could determine the C rotational constant of microwave 'inactive' 13CC5H6. This concept could be used to obtain the rotational spectra of parallel displaced benzene-dimer if it exists. We recently showed that the square pyramidal Fe(CO)5 can act as hydrogen bond acceptor. Appendix I summarizes the extension of this work and discusses interactions of trigonal bipyramidal Fe(CO)5 with HF, HCl, HBr and ClF. Our initial attempts on generating a chirped pulse to be used in a new broadband spectrometer are summarized in Appendix II. Preliminary investigations on the propargyl•••water complex are summarized in Appendix III.

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.