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Whilst biodiesel has many advantages as a renewable-energy fuel and as a substitute source of petroleum diesel, it suffers from poor performance at both low temperatures and high pressures. Not only does biodiesel crystallise at low temperatures below ~0 °C, but it also crystallises under the high pressures experienced in common-rail and injector systems within diesel engines. Crystalline solids induced by temperature and pressure can clog filters and injectors in the diesel engine, thereby causing engine failure. This thesis focuses on developing an enhanced understanding of the behaviour of biodiesel using a range of spectroscopy and diffraction techniques. The crystallisation behaviour of biodiesel at high pressure (0.1 GPa to 4 GPa) or low temperature (0 °C to -40 °C) was studied in this work. Structural phase transitions of the components of biodiesel induced by both temperature and pressure were observed. On account of the complex nature of biodiesel, it proved difficult to characterise these changes in biodiesel itself. Instead, one of the main components, methyl stearate, was therefore investigated. The crystallisation behaviour of methyl stearate is temperature-sensitive. A new polymorph of form II was successfully characterised by single crystal diffraction - by growing crystals from a saturated carbon disulfide solution at room temperature while data collection was conducted at 120 K. Form III was obtained by crystallisation from melt followed by slow cooling. Structural characterisation using single crystal diffraction showed disordered packing behaviour of the molecules in this form. The crystal structure of form IV was obtained using a combination of synchrotron X-ray powder diffraction and high resolution neutron powder diffraction. It was crystallised from the melt by quench cooling at low temperature. The thermal expansion behaviour of this form was also investigated in this work. Furthermore, a phase transition from form IV to form V was observed in neutron diffraction experiments for a fully deuterated sample, but no evidence for this transition was observed in X-ray diffraction studies. Due to the complexity of methyl stearate and the limitations of the experimental data, the crystal structure of form V was not solved. In addition to the temperature studies, the crystallisation behaviour of methyl stearate under variable pressure conditions was investigated in this work. A diamond-anvil cell was employed to generate high-pressure environments. Synchrotron high-pressure X-ray powder diffraction and Raman spectroscopy showed that pressures of as little as 0.1 GPa can induce form IV of methyl stearate to convert to form II. Four phase transitions in the pressure range of 0.1 GPa to 6.3 GPa were also observed. The phase behaviour of methyl stearate induced by pressure is reversible and form II was recovered when the pressure was released. The structure of these high-pressure phases of methyl stearate have still to be determined. High-pressure neutron powder diffraction experiments have also been conducted with form IV of methyl stearate using a Paris-Edinburgh Press. Fluorinert (FC-87) was employed as pressure-transmitting medium to generate hydrostatic condition. No evidence of a phase transition was observed in the pressure range up to 3.31 GPa.

Yes / Properties of a matter are intrinsically dependent upon the internal arrangement of molecules in the solid state. Therefore, knowledge of 3-dimensional structure of the matter is prerequisite for structure-property correlations and design of functional materials. Over the past century, X-ray crystallography has evolved as a method of choice for accurate determination of molecular structure at atomic resolution. The structural information obtained from crystallographic analysis paved the way for rapid development in electronic devices, mineralogy, geosciences, materials science, pharmaceuticals, etc. Knowledge of the structural information of active pharmaceutical ingredients (APIs) is prerequisite for rational drug design and synthesis of new chemical entities for development as new medicines. Over the past two decades, X-ray crystallography has played a key role in the design of pharmaceutical cocrystals-crystalline solids containing an API and one or more of pharmaceutically acceptable coformers. These materials have proved promising for fine-tuning several important properties of APIs. This short review highlights the history of crystallography, early breakthroughs, and the role of crystallography in understanding physicochemical properties of pharmaceutical cocrystals. / S. Aitipamula gratefully acknowledges the financial support from the Institute of Chemical and Engineering Sciences of A*STAR (Agency for Science, Technology and Research), Singapore. V. R. Vangala thanks Royal Society of Chemistry for Researcher Mobility Grant (2015/17).

Diffusion plays an important role in a number of processes like heterogeneous catalysis, corrosion, separation and purification of chemicals of industrial importance, steel hardening, fuel cells, and solid electrolytes for batteries. It also plays a vital role in several biological processes like transport across biomembranes, nerve impulse, flow of blood and permeation of ingested drug. The elementary process of diffusion in solids is quite different from those in liquids. Similarly, the mode of diffusion in porous solid where different regimes such Knudsen regime exists bears little similarity to those in a dense close-packed crystalline solid. Chapter 1 provides a brief introduction to basics of diffusion in different phases of condensed matter. Among the various phases discussed are liquids, close-packed crystalline solids (e.g., body-centered cubic solids), amorphous solids (e.g. glasses) and microporous crystalline solids (e.g., zeolites). Diffusion in these widely differing phases often bears no resemblance to each other; the rate of diffusion in these phases varies over many orders of magnitude and the elementary step and mechanism in the diffusion process are very different. Brief introduction to theories for diffusion in these phases is provided. Various experimental techniques to measure diffusivities are discussed. Different microscopic models to explain the Quasi Elastic Neutron Scattering (QENS) spectra of these phases yield an insight into the elementary step of the diffusion process. Notwithstanding the fact that completely different models are invoked to explain diffusion in different phases, there are certain underlying generic behaviour across these widely differing phases as the recent work on size dependence of diffusion in these phases demonstrate. Diffusion of a molecule or species (in the context of diffusion within condensed phases) without loss of generality may be said to occur in a medium. A universal behaviour observed is that self diffusivity exhibits a maximum as a function of the size of the diffusant when the diffusant is confined to a medium, as a result of what is known as the Levitation Effect. Such a maximum in self diffusivity has been seen in widely differing medium: microporous solids, dense liquids, ions in polar solvents, etc. The aim of the thesis is to investigate and further explore such universal behaviour and demonstrate for the first time the existence of common trends across different condensed phases in spite of difference in the detail at the microscopic level. In Chapter 2, we report a molecular dynamics study of diffusion of diatomic species AB within zeolite Y. The bond length of A-B as well as the interaction of A and B with the host zeolite atoms are varied. The results demonstrate that for the symmetric case (when A=B or AA), there exists a preferred bond length (determined by the bottleneck or window diameter) when the diffusivity is maximum. This is in agreement with previous results on monatomic species which also exhibit a similar diffusivity maximum. More importantly, no such maximum is seen when the interaction asymmetric is introduced in AB. Slight asymmetry in the interaction gives rise to a weak maximum while large asymmetry in interaction obliterates the diffusivity maximum. These results suggest that the importance of interaction between the diffusant and the medium in Levitation Effect or size-dependent diffusivity maximum. Further, it also demonstrates for the first time the close association between an inversion centre (in a statistical sense and not in the crystallographic sense) and the Levitation Effect. In Chapter 3, a study of size dependence of solutes in a Lennard-Jones liquid is reported. Einstein and others derived the reciprocal dependence of the self-diffusivity D on the solute radius ru for large solutes based on kinetic theory. We examine here (a) the range of ru over which Stokes-Einstein (SE) dependence is valid and (b) the precise dependence for small solutes outside of the SE regime. We show through molecular dynamics simulations that there are two distinct regimes for smaller solutes: (i) the interaction or Levitation Effect (LE) regime for solutes of intermediate sizes and (ii) the D 1/ru2 for still smaller solutes. We show that as the solute-solvent size ratio decreases, the breakdown in the Stokes-Einstein relationship leading to the LE regime has its origin in dispersion interaction between the solute and the solvent. These results explain reports of enhanced solute diffusion in solvents existing in the literature seen for small solutes for which no explanation exists. Several properties have been computed to understand the nature of solute motion in different regimes. We investigate in Chapter 4, the dependence of self diffusivity on the size of the diffusant in a disordered medium with the objective of understanding the experimentally observed correlation between self diffusivity and activation energy seen in a wide variety of glasses. Typically, it is found in many ionic glasses that a higher conductivity is associated with lower activation energy and vice versa. Our understanding of transport in glasses as provided by existing theories does not offer an explanation of this correlation. We have carried out molecular dynamics simulation as a function of the size of the impurity atom or diffusant (both neutral and charged) in a model host amorphous matrix. We find that there is a maximum in self diffusivity as a function of the size of the impurity atom suggesting that there is an appropriate size for which the diffusivity is maximum. The activation energy is found to be the lowest for this size of the impurity. A similar maximum has previously been found in other condensed phases such as confined fluids and dense liquids and has its origin in the Levitation Effect. The implications of this result for understanding ionic conductivity in glasses are discussed. Our result suggests that there is a relation between microscopic structure of the amorphous solid, diffusivity or conductivity and activation energy. The nature of this relationship is discussed in terms of the Levitation parameter showing that diffusivity is maximum when the size of the neck or doorway radius is comparable with the size of the diffusant. Our computational results here are in excellent agreement with independent experimental results which show that structural features of the glass are important in determining the ionic conductivity. In Chapter 5, we report results of molecular dynamics investigations into neutral impurity diffusing within an amorphous solid as a function of the size of the diffusant and density of the host amorphous matrix. We find that self diffusivity exhibits an anomalous maximum as a function of the size of the impurity species. An analysis of properties of the impurity atom with maximum diffusivity shows that it is associated with lower mean square force, reduced backscattering of velocity autocorrelation function, near-exponential decay of the intermediate scattering function (as compared to stretched-exponential decay for other sizes of the impurity species) and lower activation energy. These results demonstrate the existence of well known size-dependent diffusivity maximum in disordered solids. Further, we show that the diffusivity maximum is observed at lower impurity diameters with increase in density. This is explained in terms of the levitation parameter and the void structure of the amorphous solid. We demonstrate that these results imply contrasting dependence of self diffusivity (D) on the density of the amorphous matrix, . D increases with  for small sizes of the impurity but shows an increase followed by a decrease for intermediate sizes of the impurity atom. For large sizes of the impurity atom, D decreases with increase in . These contrasting dependence arises naturally from the existence of Levitation Effect. In Chapter 6, we discuss size dependence of impurity diffusion in an ordered system. We report molecular dynamics simulation studies to understand the role of impurity size and impurity-host interaction on impurity diffusivity in a body centered cubic solid. The simulation studies have been performed for a set of impurity-host interaction parameter ih (i=impurity, h=host atom) for a range of impurity sizes in rigid and flexible bcc solids. A double maximum is seen corresponding to two different sizes of the impurity species. Anomalous maximum is seen for a larger size of the impurity species in the case of the rigid host as compared to flexible host. The second anomalous diffusivity disappears with decrease in ih in flexible bcc solid. For one of the ih where double diffusivity maxima are observed, various properties are analysed to understand the anomalous diffusion behaviour. The impurity with anomalous diffusion has lower activation energy as compared to other impurities. Among the two anomalous impurities, the impurity with higher diffusivity has lower activation energy. The anomalous regime impurities as associated with velocity autocorrelation function with little or no backscattering, minimum average mean square force due to host atoms, lower activation energy. The self intermediate scattering function shows faster decay and a single relaxation time for anomalous regime impurity and two relaxation times for other impurity sizes. The wavenumber dependence of diffusivity of impurities shows oscillatory behaviour except for the anomalous regime impurities which show monotonic dependence on wavenumber. Chapter 7 discusses the influence of temperature induced solid-liquid phase transition on the size-dependent diffusivity. We report results for two distinct cases: (a) when the phase change is associated with corresponding changes in density and (b) when the phase change occurs at constant density. The latter is carried out so as to obtain the influence of disorder on the size-dependent diffusion or Levitation Effect. Studies with variable density are useful to understand the effect of disorder as well as change in density on size-dependent diffusivity. Two diffusivity maxima in the solid face-centred cubic phase is seen when the impurity-medium interaction is sufficiently large. One of these diffusivity maximum disappears with decrease in h. The impurities near the diffusivity maximum show velocity autocorrelation function with little backscattering, minimum in the average mean square force, lower activation energy, faster decay of self intermediate scattering function with a single relaxation time and a monotonic decay in wavevector dependence of diffusivity. Chapter 8 reports molecular dynamics simulations of a model guest tetrahedral molecule AX4 with differing bond lengths lAX have been carried out in a sphere with different surface roughness. The rotational-diffusion coefficient Dr shows a maximum for a particular value of lAX. This corresponds to the distance at which the interaction of the guest with the atoms of the host is most favourable. Although, the intensity of the maximum decreases with increase in the roughness of the confining surface, it is seen that the maximum exists even for a reasonably high degree of roughness. The observed maximum arises from the minimum in the torque on the tetrahedral molecule from its interaction with the confining medium due to mutual cancellation of forces. Activation energy for rotation is seen to be also a minimum for the bond length for which Dr is a maximum. These results suggest that there is a maximum in the rotational-diffusion coefficient when the rotating molecule is confined to a sphere of comparable size similar to the maximum in translational diffusion coefficient seen in porous solids and known as the Levitation Effect. On increase in the roughness of the sphere surface, the value of lAX at which the maximum in Dr is seen decreases. This is similar to the shift seen in the size of the diffusant corresponding to maximum diffusivity in the case of translational diffusivity. In Chapter 9 possible extensions to the work reported in the previous chapters and the directions to take are discussed. Symmetry plays an important role in size dependent diffusivity maximum in microporous crystalline solids; it would be interesting to investigate if similar role of symmetry exists in case of liquids and other disordered solids. Previous work from this laboratory on ions in water has shown the importance of electrostatic interactions. In the light of this, it would be interesting to see the influence of long-range interactions in breakdown of Stokes-Einstein relationship in liquids. Effect of density of the medium on impurity diffusion can be studied over a wide range of densities in case of supercritical fluids such as ions in water (where electrostatic interactions are present) and these can provide greater insight into dependence of diffusion on density. The origin of two diffusivity maxima in case of body-centered and face-centred cubic solids needs a detailed investigation to understand its origin. Quantification of disorder and its effect on size dependence of diffusion would be of interest. A detailed comparison with experimental data of matrix isolated molecules to understand and verify the dependence of rotational diffusivity on the size of the molecule as well as the cavity radius would be instructive.

The thesis entitled "Phase Behaviour in Crystalline Solids: Exploring the Structure Guiding Factors via Polymorphism, Phase Transitions and Charge Density Studies" consists of five chapters divided into two parts. A basic introductory section describes the topics relevant to the work and the methods and techniques utilized. Part A contains two chapters that discuss the structural aspects related to polymorphism, solvatomorphism, conformational preferences and phase transitions exhibited by active pharmaceutical ingredients (APIs). It also discusses the structure-property correlations in API crystal forms and the possible utility of second harmonic generation (SHG) for their bulk characterization. Part B has three chapters that discuss experimental and theoretical charge density analyses of intra-and intermolecular interactions that play structure guiding roles in some of the APIs discussed in Part A. The main focus of the present work is to characterize the interaction patterns devoid of strong classical hydrogen bonds. The case studies include multifurcated C - H …O hydrogen bonds, the “carbon bonding” and chalcogen interactions involving Se and S atoms. In addition to charge density studies, in situcryocrystallography and molecular complexation experiments have been employed to examine structural consequences of chalcogen bonding. Further, Appendices 1 and 2 describe phase transition studies on the inorganic mineral kröhnkite and its high temperature phase transitions leading to novel inorganic structural types. Part A: Polymorphism and phase behaviour in Active Pharmaceutical Ingredients (APIs) Chapter 1 discusses case studies of polymorphism, supramolecular preference sand phase transitions exhibited by active pharmaceutical ingredients (APIs). Section 1.1 deals with the polymorphism of an anti-oxidant drug candidate ebselen and its hydroxyl derivative. The potential of organoselenium compounds to form a Se…O chalcogen bonded supramolecular recognition unit (synthon) has been established in these polymorphs and its generality is substantiated with the help of a Cambridge Structural Database (CSD) analysis. Section 1.2 demonstrates the utility of the ‘chalcogen bonded supramolecularsynthon’ in generating molecular complexes of APIs. A series of salts and co-crystals of the amyotrophic lateral sclerosis drug Riluzole have been synthesized in order to evaluate the structure directing role of S…O chalcogen bonded synthon in their crystal structures. Section 1.3adescribes the generation of polymorphs and solvatomorphs of the antidepressant drug candidate fenobamand associated phase transitions. The tautomeric preference in this molecule has been rationalized from the crystal structure analysis and abinitioenergy calculations. Further, section 1.3b utilizes chemical derivatization as a means to experimentally simulate thetautomeric preference and molecular conformations in several derivatives of fenobam and thiofenobam. Section 1.4 describes the issue of solvatomorphism and the generation of the fifth solvatomorph of gallic acid, its structural complexity and temperature induced phase transitions. The ability of solvent water molecules to drive structural diversity, by forming ‘hydration synthons’,is demonstrated in this case. Chapter 2 presents a novel methodology for the detection of polymorphic impurities in APIs based on second harmonic generation (SHG).The SHG based method has been employed to polymorphic mixtures of fenobam, hydrochlorothiazide, pyrazinamide, tolbutamide, curcumin, febuxostat and nimesulide.The conventional methods such as powder X-ray diffraction (profile fitting analysis), FT-IR, Raman spectroscopy and thermal analysesto detect the presence of polymorphic impuritiesin bulk API samples are employed on the mixtures of these API samples and the impurity detection limits are compared with the proposed SHG methodology. The APIs used in these case studies were screened for their SHG efficiency using quantum chemical calculations of hyperpolarizability and HOMO-LUMO charge redistribution behaviour. Further, a correlation with the crystal symmetry, relative packing arrangement of molecules and the observed SHG efficiency have been discussed in of some of these cases. Part B: Exploring the nature and structural consequences of nonbonding interactions in molecular crystals Chapter 3 discusses the electron density features of quasi-trifurcated CH…Cl/CH…O interaction motifs leading to ‘carbon bonding’ and a trifurcated CH…O hydrogen bond motif. Section 3.1 describes the experimental and theoretical charge density analyses of quasi-trifurcated CH…Cl and CH…O motifsand investigates the existence of “carbon bonding” in solid state. The experimental charge density evidence for “carbon bonding” have been analyzed in cases of fenobam and dimethylamine: 4-hydroxybenzoic acid complex. The existence of this unconventional interaction, which roughly mimics the transition state geometry of SN2 (bimolecular nucleophilic substitution) reaction, is further established by a CSD analysis. Section 3.2 describes the experimental and theoretical charge density analyses of ferulic acid and compares the topological features associated with a trifurcated CH…O hydrogen bond motif, with corresponding strong classical OH…O hydrogen bonds. The study demonstrates the “Gulliver effect” of weak interactions in charge density terms. Charge density based interaction energy calculations via EPMM and EML methods have been utilized in this context to evaluate the relative strength of such interactions. Chapter 4 discusses the charge density features of intermolecular chalcogen bonding interactions involving selenium and sulphur atoms.Section 4.1 describes the experimental and theoretical charge density analyses of ebselen and its hydroxyl derivative. The charge density characterization of the conserved chalcogen bond synthon (discussed in chapter 1, section 1.1) has been carried out and electronic nature and geometric dependence of Se…O interactions have been explored. The mechanism of drug action of ebselen has been correlated with the experimentally observed charge density distribution around the intramolecular SeC and SeN bonds. Section 4.2 explores the homochalcogen interactions such as S…SandSe…Se in phenol analogues. In situ cryocrystallographic studies on thiophenol, selenophenol and their solid solutions are described. Veggard’s law-like behaviour observed in these solid solutions have been rationalized and the S…S and Se…Sehomochalcogen interactions have been evaluated in these liquid systems which are devoid of any other packing forces such as strong hydrogen bonds. Chapter 5 discusses the conformation locking potential of intramolecular S…O chalcogen bonding in sulfadrugs. Section 5.1 discusses conformation locking in the antibioticdrugsulfamethizole. A two pronged approach has been adopted in the study; a) generation of cocrystals and salts of sulfamethizole for the ‘experimental simulation’ of the molecular conformation, b) evaluation of charge density distribution around the intramolecular S…O interaction region in sulfamethizole. Section 5.2 describes the effect of ‘simple hybridized orbital geometry’ in the formation of intramolecular S…O chalcogen bonding. The experimental charge density analysis of the carbonic anhydrase inhibitor drug acetazolamide has been carried out and the two different intramolecular S…O geometries have been compared in terms of the charge density topology. The analysis highlights the advantage of “orbital geometry” consideration over the conventional distance-angle criteria in assessing nonbonded interactions.

Thin-film materials from μm thickness down to single-atomic-layered 2D materials play a central role in many novel electronic and optical applications. Coherent, nonlinear optical (NLO) μ-spectroscopy offers insight into the local thickness, stacking order, symmetry, or electronic and vibrational properties. Thin films and 2D materials are usually supported on multi-layered substrates leading to (multi-) reflections, interference, or phase jumps at interfaces during μ-spectroscopy, which all can make the interpretation of experiments particularly challenging. The disentanglement of the influence parameters can be achieved via rigorous theoretical analysis. In this work, we compare two self-developed modeling approaches, a semi-analytical and a fully vectorial model, to experiments carried out in thin-film geometry for two archetypal NLO processes, second-harmonic and third-harmonic generation. In particular, we demonstrate that thin-film interference and phase matching do heavily influence the signal strength. Furthermore, we work out key differences between three and four photon processes, such as the role of the Gouy-phase shift and the focal position. Last, we can show that a relatively simple semi-analytical model, despite its limitations, is able to accurately describe experiments at a significantly lower computational cost as compared to a full vectorial modeling. This study lays the groundwork for performing quantitative NLO μ-spectroscopy on thin films and 2D materials, as it identifies and quantifies the impact of the corresponding sample and setup parameters on the NLO signal, in order to distinguish them from genuine material properties.

In the last few years a renewed interest has reappeared in materials that were highly investigated in the 50s-70s, like manganese perovskites, spinel chalcogenides and vanadium oxides. The first two classes of materials are nowadays intensively studied due to the colossal magnetoresistance effect, which is the magnetoresistance associated with a ferromagnetic-paramagnetic transition. Vanadium oxides are known to form many compounds and most of them undergo metal-to-insulator phase transitions, with a high increase in the electrical conductivity (MIT). Many technological applications derive from the variation of the physical properties around the phase transition temperature. Although many efforts have been done in order to understand their electronic structures and to elucidate the MIT mechanisms, the vanadium oxides are still matter of debate in science.The present study has been performed in order to understand the electronic structure of these very intriguing materials. The role of different dopants that induce strong changes in the electronic and magnetic properties has been investigated making use of two spectroscopic techniques, namely X-ray photoelectron and X-ray emission spectroscopy.

The details of the interplay between the electronic structure and the magnetic properties of matter represent a state of the art challenge. In the present work spectroscopic investigations on the electronic structure of some interesting materials are presented. The achieved information has been used in order to answer specific questions related to the magnetic behavior of the investigated materials. For the transition metal dicyanamide compounds it is shown that the electronic states arising from carbon and nitrogen remain roughly unchanged for all compositions. A model for the magnetic superexchange interaction was proposed. In this model the geometry of the crystallographic structure accounts for a particular interaction pattern while the occupancy of the 3d transition metal band is the factor which triggers the changeover from antiferromagnetic to ferromagnetic interaction. In the case of six-membered ferric-wheel molecules the comparison between experimental and theoretical data issued estimations for the magnitude of magnetic exchange interactions. The information on the electronic structure of the LaNi5-xMex (Me=Cu, Al) allowed a better understanding of their magnetic behavior. The changes induced in the electronic structure of the parent compound by partial substitutions of nickel by copper or aluminum are discussed.

Spontaneous Raman spectroscopy (SR) is a versatile method for analysis and visualization of ferroelectric crystal structures, including domain walls. Nevertheless, the necessary acquisition time makes SR impractical for in situ analysis and large scale imaging. In this work, we introduce broadband coherent anti-Stokes Raman spectroscopy (B-CARS) as a high-speed alternative to conventional Raman techniques and demonstrate its benefits for ferroelectric domain wall analysis. Using the example of poled lithium niobate, we compare the spectral output of both techniques in terms of domain wall signatures and imaging capabilities. We extract the Raman-like resonant part of the coherent anti-Stokes signal via a Kramers–Kronigbased phase retrieval algorithm and compare the raw and phase-retrieved signals to SR characteristics. Finally, we propose a mechanism for the observed domain wall signal strength that resembles a Cerenkov-like behavior, in close analogy to domain wall signatures obtained by secondharmonic generation imaging.We, thus, lay here the foundations for future investigations on other poled ferroelectric crystals using B-CARS.