Neste trabalho, a reação O(3P) + HBr → OH + Br, que se insere no contexto da química atmosférica, mais especificamente nos ciclos de destruição catalítica do ozônio, foi estudada empregando superfícies de energia potencial ab initio de alta qualidade. Construímos superfícies para os estados eletrônicos 3A\" e 3A\', baseadas na expansão de muitos corpos, com potenciais de dois corpos ajustados por funções \"switched-MLJ\" e potenciais de três corpos interpolados utilizando o método RKHS. Os pontos ab initio utilizados foram obtidos no nível de teoria MRCISD+Q/CBS+SO. A superfície final para o estado eletrônico 3A\" foi corrigida por um fator multiplicativo de modo que reproduzisse cálculos benchmark para a altura de barreira, em que foram considerados efeitos relativísticos (escalares e spin-órbita), correlação caroço-valência e correlação de ordem alta (excitações triplas e quádruplas). As principais características da SEP 3A\" são dois mínimos de van der Walls no canal de entrada e saída e um estado de transição com uma barreira energética de 5,01 kcal mol-1. A SEP 3A\' tem um estado de transição linear em 6,45 kcal mol-1. O valor obtido para a entalpia de reação, a 0 K, foi de -15,7 kcal mol-1, muito próximo do valor experimental de -15,14 kcal mol-1. Calculamos constantes de velocidade, no intervalo de 200 a 1000 K, utilizando a teoria do estado de transição variacional com contribuições de tunelamento multidimensional (ICVT/µOMT) e com uma aproximação de espalhamento reativo quântico (QM/JS). Estes valores estão em ótima concordância com os dados experimentais da literatura, em todo intervalo de temperatura em que estão disponíveis: de 221 a 554 K para reação O + HBr e de 295 a 419 K para reação O + DBr. As constantes de velocidade, a 298 K e em cm3 molécula-1 s-1, obtidas para a reação O + HBr são: 3,62·10-14 (ICVT/µOMT) e 3,35·10-14 (QM/JS), enquanto que o valor experimental é 3,78·10-14. A qualidade destes resultados reforça nossa confiança nos procedimentos e aproximações utilizadas, abrindo caminho para a caracterização, em alto nível, de uma grande variedade de reações em fase gasosa. / In this work, the O(3P) + HBr → OH + Br reaction, which is relevant to atmospheric chemistry, specially for the catalytic ozone depletion, was studied using high-level ab initio potential energy surfaces. We constructed surfaces for the 3A\" and 3A\' electronic states, based on the many-body expansion, with the two-body potentials adjusted by the switched-MLJ function and the three-body potentials interpolated using the RKHS method. The ab initio points were calculated at the MRCISD+Q/CBS+SO level of theory. The main features of the 3A\" are the presence of two van der Waals minima, at the entrance and exit channels, and a transition state with a barrier height of 5.01 kcal mol-1. The 3A\' PES has a linear transition state at 6.45 kcal mol-1. We obtained the enthalpy of reaction, at 0 K, of -15.7 kcal mol-1, in close agreement with the experimental value of -15.14 kcal mol-1. Rate constants, in the temperature range from 200 to 1000 K, were calculated using the variational transition state theory with contributions of multidimensional tunneling (ICVT/µOMT) and also a quantum reactive scattering approach (QM/JS). Their values are in fair agreement with the experimental data in the literature in the whole temperature range available: from 221 to 554 K for the O + HBr reaction, and from 295 to 419 K for the O + DBr reaction. At 298 K, the calculated rate constants, in cm3 molecule-1 s-1, for the O + HBr reaction are 3.62·10-14 (ICVT/µOMT) and 3.35·10-14 (QM/JS); and the experimental value is 3.78·10-14. The quality of these results reinforces our confidence in the procedures and approximations used, leading to the possibility of high-level characterization of a variety of gas phase reactions.

Este trabalho teve como foco principal a caracterização espectroscópica dos haletos de berílio, BeCl, BeBr e BeI. O conhecimento acerca dessas espécies foi ampliado significativamente através do cálculo de parâmetros de difícil caracterização experimental. Como os poucos trabalhos experimentais realizados para esses haletos apresentam resultados inconclusivos para a transição C 2Σ+ - X 2Σ+, através do cálculo acurado de probabilidades de transição foi possível oferecer uma nova interpretação para os dados existentes, apresentando inclusive resultados para as outras transições eletrônicas até o presente desconhecidas. Cálculos utilizando o método de Interação de Configurações Multirreferencial (MRCI) com um conjunto de funções de base consistentes na correlação de qualidade quintupla-zeta foram utilizados para se obter as curvas de energia potencial associadas ao primeiro e segundo canais de dissociação para os estados dubleto e quarteto dessas espécies. Parâmetros espectroscópicos como as constantes vibracionais we, wexe, a constante rotacional Be e a distância de equilíbrio foram determinados para os estados de mais baixa energia. Além disso, foram calculadas a energia de excitação (Te) e a energia de dissociação (De) com e sem a inclusão de efeitos spin-órbita. Os resultados obtidos expandiram significativamente nosso conhecimento sobre os estados eletrônicos dessa espécies. Para os estados já investigados experimentalmente, houve boa coerência entre os parâmetros calculados e experimentais. As diferenças de energia entre os dois canais no limite de dissociação para as moléculas BeCl, BeBr e BeI obtidas neste trabalho foram, respectivamente: 21835, 21889 e 21998 cm-1, em concordância com o respectivo resultado experimental das três espécies (21980 cm-1). A determinação teórica da energia de dissociação D0 foi bastante satisfatória. Obtivemos 92,24; 72,77 e 51,75 kcal·mol-1, respectivamente, para as moléculas BeCl, BeBr e BeI incluindo os efeitos spin-órbita, comparados a 91,78, 71 e 57 kcal·mol-1. Para uma análise mais completa das curvas de energia potencial, elas também foram obtidas considerando-se os efeitos relativísticos. A constante de acoplamento spin-órbita calculada na região de equilíbrio de cada uma das moléculas BeCl, BeBr e BeI foi, respectivamente: 41, 207 e 324 cm-1, em boa concordância com os resultados experimentais: 52,8, 198 e 361,1 cm-1, respectivamente. A separação spin-órbita no limite de dissociação calculada foi de 823, 3446 e 6975 cm-1 (BeCl, BeBr e BeI), também coerentes com resultados experimentais: 882, 3685,24 e 7603,15 cm-1, respectivamente. Foi ainda realizada uma análise detalhada sobre os canais de dissociação das moléculas HBeP e BePH. A construção de um diagrama de energias relativas permitiu obter um conjunto de dados importantes a respeito de todos os possíveis canais de dissociação. Em particular é mostrado a estabilidade relativa e a energia no limite de dissociação. Para a energia no limite de dissociação obtivemos resultados consistentes com os valores experimentais. Nossos cálculos para os três primeiros canais de dissociação HBeP = H + Be resultaram nos seguintes valores: H (2Sg) + Be (X 4Σ+), 0 cm-1; H (2Sg) + Be (a 2π), 426 cm-1 (exp. 502 cm-1); H (2Sg) + Be (b 2Σ-), 1896 cm-1 (exp. 1976 cm-1). Por fim, pela primeira vez na literatura, o calor de formação e de atomização foram calculados para estas espécies. Para os isômeros HBeP e BePH, a energia de atomização a 298,15 K calculada foi de 119,02 kcal·mol-1 e 107,40 kcal·mol-1, respectivamente; para o calor de formação a 298,15 K, obtivemos 86,14 e 97,76 kcal·mol-1 para as espécies HBeP e BePH, respectivamente. / This work has mainly focused on the spectroscopic characterization of the beryllium halides, BeCl, BeBr and BeI. Knowledge about these species was substantially increased through the calculation of parameters that are difficult to access in an experimental characterization. As the few experimental works carried out for these halides presented inconclusive results for the C 2Σ+ - X2Σ+ transition, we carried out accurate calculations of transition probabilities, thus offering a new interpretation about the existing data, including also results for other electronic transitions as yet unknown. Calculations using the method Multireference Configuration Interaction (MRCI) along with correlation-consistent basis set functions of quintuple-zeta quality were used to obtain the potential energy curves associated with the first and second dissociation channels for the doublet and quartet states of these species. Spectroscopic parameters such as vibrational constants We, WeXe, the rotational constant Be and the equilibrium distance were determined for the low-lying states. Furthermore, we also calculated the excitation energy (Te) and the dissociation energy (De) with and without the inclusion of spin-orbit effects. The obtained results significantly expanded our knowledge about the electronic states of this species. For states already investigated experimentally, there was good consistency between the calculated and the experimental parameters. The energy differences between the two channels in the dissociation limit for BeCI, BeBr and Bel molecules obtained in this work were: 21835, 21889 and 21998 cm-1, in agreement with the corresponding experimental results of the three species (21 980 cm-1). The theoretical determination of the dissociation energy D0 was very satisfactory. We obtained 92.24, 72.77, and 51.75 kcal·mol-1, respectively, for the BeCl, BeBr and BeI molecules including spin-orbit effects, compared to 91.78, 71 and 57 kcal . mol-1. For a more complete analysis of the potential energy curves, they also were obtained considering relativistic effects. The calculated spin-orbit coupling constants in the equilibrium region of BeCl, BeBr and BeI molecules were respectively 41, 207 and 324 cm-1, in good agreement with the experimental results: 52.8, 198, and 361.1 cm-1, respectively. The calculated spin-orbit splitting in the dissociation limit was 823, 3446 and 6975 cm-1 (BeCl, BeBr and BeI) also consistent with the experimental results: 882, 3685.24 and 7603.15 cm-1, respectively. Additionally, a detailed analysis of the dissociation channels of HBeP and BePH molecules was performed. The construction of a relative energies diagram allowed us to derive a set of important data for all the possible dissociation channels. In particular, it is shown the relative stability and the energy in the dissociation limit. For the energy in the dissociation limit, we obtained results consistent with the experimental values. Our calculations for the first three dissociation channels HBeP = H + Be resulted in the following values: H (2Sg) + Be (X 4Σ+), 0 cm-1; H (2Sg) + Be (a 2π), 426 cm-1 (exp. 502 cm-1); H (2Sg) + Be (b 2Σ-), 1896 cm-1 (exp. 1976 cm-1). Finally, for the first time in the literature, the heat of formation and the atomization energy were calculated for these species. For the HBeP and BePH isomers, the atomization energy calculated at 298.15 K was 119.02 and 107.40 kcal . mol-1, respectively; for the heat of formation at 298.15 K, we obtained 86.14 and 97.76 kcal· mol-1 for HBeP and BePH species, respectively.

Ce travail de thèse se situe à l'interface entre la chimie théorique, le calcul scientifique et les mathématiques appliquées. On s'intéresse aux différents algorithmes utilisés pour résoudre les équations spécifiques qui apparaissent dans le cadre de la dynamique moléculaire utilisant des champs de forces polarisables dans un cadre massivement parallèle. Cette famille de modèles nécessite en effet de résoudre des équations plus complexes que les modèles classiques usuels et rend nécessaire l'utilisation de supercalculateurs pour obtenir des résultats significatifs. On s'intéressera plus précisément à différents cas de conditions aux limites pour rendre compte des effets de solvatation comme les conditions aux limites périodiques traitées avec la méthode du Particle Mesh Ewald et un modèle de solvatation continu discrétisé par décomposition de domaine : le ddCOSMO. Le plan de cette thèse est le suivant : sont d'abord passées en revue les différentes stratégies parallèles en dynamique moléculaire en général, sont ensuite présentées les façons de les adapter au cas des champs de forces polarisables. Après quoi sont présentées différentes stratégies pour s'affranchir de certaines limites liées à l'usage de méthodes itératives en dynamique moléculaire polarisable en utilisant des approximations analytiques pour l'énergie de polarisation. Ensuite, l'adaptation de ces méthodes à différents cas pratiques de conditions aux limites est présentée : d'abord en ce qui concerne les conditions aux limites périodiques traitées avec la méthode du Particle Mesh Ewald et ensuite en ce qui concerne un modèle de solvatation continue discrétisé selon une stratégie de décomposition de domaine. / This works is at the interface between theoretical chemistry, scientific computing and applied mathematics. We study different algorithms used to solve the specific equations that arise in polarizable molecular dynamics in a massively parallel context. This family of models requires indeed to solve more complex equations than in the classical case making the use of supercomputers mandatory in order to get significant results. We will more specifically study different types of boundary conditions that represent different ways to model solvation effects : first the Particle Mesh Ewald method to treat periodic boundary conditions and then a continuum solvation model discretized within a domain decomposition strategy : the ddCOSMO. The outline of this thesis is as follows : first, the different parallel strategies in the general context of molecular dynamics are reviewed. Then several methods to adapt these strategies to the specific case of polarizable force fields are presented. After that, strategies that allow to circumvent certain limits due to the use of iterative methods in the context of polarizable molecular dynamics are presented and studied. Then, the adapation of these methods to different cases of boundary conditions is presented : first in the case of the Particle Mesh Ewald method to treat periodic boundary conditions and then in the case of a particular continuum solvation model discretized with a domain decomposition strategy : the ddCOSMO. Finally, various numerical results and applications are presented.

This thesis describes the development of several spectroscopic methods based on impulsive vibrational spectroscopy as well as of the technique itself. The first chapter describes the ultrafast time domain Raman spectrometer including the development of two noncollinear optical parametric amplifiers for sub-10 fs pulse generation with 343 or 515 nm pumping. In the first spectroscopic study we demonstrate, for the first time, that impulsive vibrational spectroscopy can be used for recording transient Raman spectra of molecules in excited electronic states. We obtain spectra of beta-carotene with comparable, or better, quality than established frequency domain based nonlinear Raman techniques. The following two chapters address the questions on the fate of vibrational coherences when generated on a reactive potential energy surface. We photoexcite bacteriorhodopsin and observe anharmonic coupling mediated vibrational coherence transfer to initially silent vibrational modes. Additionally, we are able to correlate the vibrational coherence activation with the efficiency of the isomerisation reaction in bR. Upon generation of vibrational coherence in the second excited electronic state of beta-carotene, by excitation from the ground electronic state, we are able to follow the wavepacket motion out of the Franck-Condon region. We observe vibrationally coherent internal conversion, through a conical intersection, into the first excited electronic state and are hence able to demonstrate that electronic surface crossings can occur in a vibrationally coherent fashion. Additionally, we find strong evidence for vibronic coupling mediated back and forth crossing between the two electronic states. As a combination of this work we develop a IVS based technique that allows for the direct recording of background and baseline free Raman spectra in the time domain. Several proof of principle experiments highlight the capabilities of this technique for time resolved Raman spectroscopy. In the final chapter we present work on weak-field coherent control. Here, we address the question of whether a photochemical reaction can be controlled by the phase term of an electric excitation field, in the one photon excitation limit. We study the systems rhodamine 101, bacteriorhodopsin, rhodopsin and isorhodopsin and, contrary to previous reports, find no evidence for one photon control.

III-Nitride semiconductors are very promising in both electronics and optical devices. The ability of the III-Nitride semiconductors as light emitters to span the electromagnetic spectrum from deep ultraviolet light, through the entire visible region, and into the infrared part of the spectrum, is a very important feature, making this material very important in the field of light emitting devices. In fact, the blue emission from Indium Gallium Nitride (InGaN), which was awarded the 2014 Nobel Prize in Physics, is the basis of the common and important white light emitting diode (LED). Quantum dots (QDs) have properties that make them very interesting for light emitting devices for a range of different applications, such as the possibility of increasing device efficiency. The spectrally well-defined emission from QDs also allows accurate color reproduction and high-performance communication devices. The small size of QDs, combined with selective area growth allows for an improved display resolution. By control of the polarization direction of QDs, they can be used in more efficient displays as well as in traditional communication devices. The possibility of sending out entangled photon pairs is another QD property of importance for quantum key distribution used for secure communication. QDs can hold different exciton complexes, such as the neutral single exciton, consisting of one electron and one hole, and the biexciton, consisting of two excitons. The integrated PL intensity of the biexciton exhibits a quadratic dependence with respect to the excitation power, as compared to the linear power dependence of the neutral single exciton. The lifetime of the neutral exciton is 880 ps, whereas the biexciton, consisting of twice the number of charge carriers and lacks a dark state, has a considerably shorter lifetime of only 500 ps. The ratio of the lifetimes is an indication that the size of the QD is in the order of the exciton Bohr radius of the InGaN crystal making up these QDs in the InGaN QW. A large part of the studies of this thesis has been focused on InGaN QDs on top of hexagonal Gallium Nitride (GaN) pyramids, selectively grown by Metal Organic Chemical Vapor Deposition (MOCVD). On top of the GaN pyramids, an InGaN layer and a GaN capping layer were grown. From structural and optical investigations, InGaN QDs have been characterized as growing on (0001) facets on truncated GaN pyramids. These QDs exhibit both narrow photoluminescence linewidths and are linearly polarized in directions following the symmetry of the pyramids. In this work, the neutral single exciton, and the more rare negatively charged exciton, have been investigated. At low excitation power, the integrated intensity of the PL peak of the neutral exciton increases linearly with the excitation power. The negatively charged exciton, on the other hand, exhibits a quadratic power dependence, just like that of the biexciton. Upon increasing the temperature, the power dependence of the negatively charged exciton changes to linear, just like the neutral exciton. This change in power dependence is explained in terms of electrons in potential traps close to the QD escaping by thermal excitation, leading to a surplus of electrons in the vicinity of the QD. Consequently, only a single exciton needs to be created by photoexcitation in order to form a negatively charged exciton, while the extra electron is supplied to the QD by thermal excitation. Upon a close inspection of the PL of the neutral exciton, a splitting of the peak of just below 0.4 meV is revealed. There is an observed competition in the integrated intensity between these two peaks, similar to that between an exciton and a biexciton. The high energy peak of this split exciton emission is explained in terms of a remotely charged exciton. This exciton state consists of a neutral single exciton in the QD with an extra electron or hole in close vicinity of the QD, which screens the built-in field in the QD. The InGaN QDs are very small; estimated to be on the order of the exciton Bohr radius of the InGaN crystal, or even smaller. The lifetimes of the neutral exciton and the negatively charged exciton are approximately 320 ps and 130 ps, respectively. The ratio of the lifetimes supports the claim of the QD size being on the order of the exciton Bohr radius or smaller, as is further supported by power dependence results. Under the assumption of a spherical QD, theoretical calculations predict an emission energy shift of 0.7 meV, for a peak at 3.09 eV, due to the built-in field for a QD with a diameter of 1.3 nm, in agreement with the experimental observations. Studying the InGaN QD PL from neutral and charged excitons at elevated temperatures (4 K to 166 K) has revealed that the QDs are surrounded by potential fluctuations that trap charge carriers with an energy of around 20 meV, to be compared with the exciton trapping energy in the QDs of approximately 50 meV. The confinement of electrons close to the QD is predicted to be smaller than for holes, which accounts for the negative charge of the charged exciton, and for the higher probability of capturing free electrons. We have estimated the lifetimes of free electrons and holes in the GaN barrier to be 45 ps and 60 ps, in consistence with excitons forming quickly in the barrier upon photoexcitation and that free electrons and holes get trapped quickly in local potential traps close to the QDs. This analysis also indicates that there is a probability of 35 % to have an electron in the QD between the photoexcitation pulses, in agreement with a lower than quadratic power dependence of the negatively charged exciton. InN is an attractive material due to its infrared emission, for applications such as light emitters for communication purposes, but it is more difficult to grow with high quality and low doping concentration as compared to GaN. QDs with a higher In-composition or even pure InN is an interesting prospect as being a route towards increased quantum confinement and room temperature device operation. For all optical devices, p-type doping is needed. Even nominally undoped InN samples tend to be heavily n-type doped, causing problems to make pn-junctions as needed for LEDs. In our work, we present Mg-doped p-type InN films, which when further increasing the Mg-concentration revert to n-type conductivity. We have focused on the effect of the Mg-doping on the light emission properties of these films. The low Mg doped InN film is inhomogeneous and is observed to contain areas with n-type conductivity, so called n-type pockets in the otherwise p-type InN film. A higher concentration of Mg results in a higher crystalline quality and the disappearance of the n-type pockets. The high crystalline quality has enabled us to determine the binding energy of the Mg dopants to 64 meV. Upon further increase of the Mg concentration, the film reverts to ntype conductivity. The highly Mg doped sample also exhibits a red-shifted emission with features that are interpreted as originating from Zinc-Blende inclusions in the Wurtzite InN crystal, acting as quantum wells. The Mg doping is an important factor in controlling the conductivity of InN, as well as its light emission properties, and ultimately construct InN-based devices. In summary, in this thesis, both pyramidal InGaN QDs and InGaN QDs in a QW have been investigated. Novel discoveries of exciton complexes in these QD systems have been reported. Knowledge has also been gained about the challenging material InN, including a study of the effect of the Mg-doping concentration on the semiconductor crystalline quality and its light emission properties. The outcome of this thesis enriches the knowledge of the III-Nitride semiconductor community, with the long-term objective to improve the device performance of III-Nitride based light emitting devices.

The prediction of ground state properties of atomistic systems is of vital importance in technological advances as well as in the physical sciences. Fundamentally, these predictions are based on a quantum-mechanical description of many-electron systems. One of the hitherto most prominent theories for the treatment of such systems is density functional theory (DFT). The main reason for its success is due to its balance of acceptable accuracy with computational efficiency. By now, DFT is applied routinely to compute the properties of atomic, molecular, and solid state systems. The general approach to solve the DFT equations is to use a density-functional approximation (DFA). In Kohn-Sham (KS) DFT, DFAs are applied to the unknown exchangecorrelation (xc) energy. In orbital-free DFT on the other hand, where the total energy is minimized directly with respect to the electron density, a DFA applied to the noninteracting kinetic energy is also required. Unfortunately, central DFAs in DFT fail to qualitatively capture many important aspects of electronic systems. Two prime examples are the description of localized electrons, and the description of systems where electronic edges are present. In this thesis, I use a model system approach to construct a DFA for the electron localization function (ELF). The very same approach is also taken to study the non-interacting kinetic energy density (KED) in the slowly varying limit of inhomogeneous electron densities, where the effect of electronic edges are effectively included. Apart from the work on model systems, extensions of an exchange energy functional with an improved KS orbital description are presented: a scheme for improving its description of energetics of solids, and a comparison of its description of an essential exact exchange feature known as the derivative discontinuity with numerical data for exact exchange. An emerging alternative route towards the prediction of the properties of atomistic systems is machine learning (ML). I present a number of ML methods for the prediction of solid formation energies, with an accuracy that is on par with KS DFT calculations, and with orders-of-magnitude lower computational cost. / Att kunna förutsäga egenskaper hos atomistiska system utgör en viktigdel av vår teknologiska utveckling, samt spelar en betydande roll i defysikaliska vetenskaperna. Sådana förutsägelser bygger på en kvantmekaniskbeskrivning av mångelektronsystem. En av de mest framståendeteorierna för att behandla den här typen av system är täthetsfunktionalteorin(DFT). Den främsta orsaken till dess framgång är attden lyckas kombinera skaplig noggrannhet med en bra beräkningseffektivitet.DFT används numera rutinmässigt för att beräkna storheterhos atomer, molekyler, och fasta kroppar. Generellt sett löses ekvationerna inom DFT genom att man inför entäthetsfunktionalapproximation (DFA). I Kohn-Sham (KS) DFT, användsDFAer för att approximera utbytes-korrelationsenergin. Inom orbitalfriDFT, där målet är att direkt minimera den totala energin med avseendepå elektrontätheten, så approximerar man också den icke-interageranderörelseenergin hos elektronerna. Dessvärre så fallerar många centralaDFAer att kvalitativt beskriva många viktiga aspekter hos elektronsystem.Två viktiga exempel är beskrivningen av lokaliserade elektroner,samt beskrivningen av system där det förekommer elektronytor. I denna avhandling använder jag modellsystem för att konstruera enDFAför elektronlokaliseringsfunktionen (ELF). Samma tillvägagångssättappliceras sedan för att studera den kinetiska energitätheten i gränsen avlångsamt varierande elektrontätheter, där effekten av elektronytor effektivtinkluderas. Förutom arbetet som berör modellsystem, så presenterasen utökad variant av en utbytes-energifunktional med en förbättrad KSorbitalbeskrivning: ett schema för att förbättra dess energiegenskaperför solida material, samt en jämförelse av dess beskrivning av en viktigegenskap hos den exakta utbytesenergin, vilket utgörs av diskontinuiteteri dess derivata. Ett mera nyligen uppkommet samt alternativt sätt att kunna förutsägaegenskaper hos atomistiska system utgörs av maskinlärning (ML).Jag presenterar ett antal ML-modeller för att kunna förutsäga formeringsenergierhos fasta material med en noggrannhet som är i linje medresultat som uppnås av beräkningar med hjälp av KS DFT, och med enberäkningseffektivitet som är flera storleksordningar snabbare.

Three distinct aspects, disorder, polymorphism and co-crystal formation have been addressed in molecular crystals in terms of intra- and intermolecular interactions involving halogens, weak hydrogen bonds and van der Waals interactions. A basic introductory chapter highlights the importance of these three aspects followed by a foreword to the contents. Chapter 1 employs in situ cryo-crystallization techniques to study the crystal and molecular structures of compounds which are liquids at room temperature. Section 1.1 deals with the crystal structure analyses of low melting chloro- and bromo-substituted anilines which reveal both the importance of hydrogen bonds and weak interactions involving different halogens. The halogen⋅⋅⋅halogen interactions are compared with fluorine and iodine substituted compounds to bring out the relevance of both size and polarizability characteristics. Section 1.2 describes the crystal structures of benzyl derivative compounds utilizing the concept of in situ cryo-crystallization. This analysis brings out the correlation between acidity of benzyl derivative compounds with its preference of either a (sp2)C-H⋅⋅⋅π or (sp3)C-H⋅⋅⋅π interactions in the crystal packing. Chapter 2 consists of two sections dealing with the preference of halogen⋅⋅⋅halogen interactions in supramolecular chemistry. Section 2.1 discusses a statistically large number of crystal structures in halogen substituted benzanilide compounds. It reveals the importance of hetero halogen F⋅⋅⋅X (Cl, Br), homo halogen X⋅⋅⋅X (F, Cl, Br, I), C-X⋅⋅⋅π and C-H⋅⋅⋅F interactions in terms of their directionality and preferences to complement a primary N-H⋅⋅⋅O hydrogen bond in directing the three-dimensional supramolecular assembly. Section 2.2 deals with solvent induced polymorphism which highlights the role of weak interactions in two case studies. The preference and directionality of C-H⋅⋅⋅F and Cl⋅⋅⋅Cl interactions lead to dimorphic modifications in case of 3-chloro-N-(2-fluorophenyl)benzamide whereas in case of 2-iodo-N-(4-bromophenyl)benzamide the interactions are through C-H⋅⋅⋅π and I⋅⋅⋅I contacts. Further, the analysis is supported using morphological evidence, DSC (Differential scanning calorimetry) and Powder X-ray diffraction data. Chapter 3 has three sections, concentrating on disorder and its consequence in crystal structures. Section 3.1 discusses the apparent shortening of the C(sp3)–C(sp3) bond analysed via a variable temperature X-ray diffraction study in racemic 1,1′-binaphthalene-2,2′-diyl diethyl bis(carbonate). Variable temperature single crystal X-ray diffraction studies show that the shortening is entirely due to positional disorder and not due to thermal effects. A supercell formation at T≤150 K depicts the formation of a Z'= 2 structure. Section 3.2 deals with crystal structure analysis of Ethyl-4-(2-fluorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate which clarifies the discrepancy in the higher value of the residual electron density in the literature in terms of positional disorder of fluorine at ortho sites. The existence of fluorine atom at the para position on the phenyl ring of another isomeric molecule leads to disorder induced conformational polymorphism through the involvement of the ethyl group. The static disorder of ethyl group which is associated with only one molecule (Z′=2) could be resolved at 120 K. This supports the results of the previous section (3.1). Section 3.3 reports crystal structure analysis of disordered fluorine in benzanilide compounds. The preference of interactions involving fluorine in either ortho sites or meta sites could be one of the reasons for the positional disorder of both possible sites. With one of the structure showing high Z′ value due to differences in the occupancy of disordered fluorine atom. CSD (Cambridge Structural Database) analysis indicates that the percentage of disorder in halogenated crystal structures having halogen atom at either ortho site or meta site decreases from fluorine to iodine. Further, the analysis points out that the disorder in fluorine containing compounds is mostly localized at the fluorine position whereas for other halogenated disordered structures, the disorder appears at other parts of the molecule. Chapter 4 discusses co-crystal formation and analysis of intermolecular interactions. It consists of two sections. Section 4.1 discusses co-crystal formation of nicotinamide with benzoic acid and seven other derivatives by changing the functional group at different positions of benzoic acid. Hydroxyl (-OH) group at 4/3-postion of benzoic acid prefers phenol⋅⋅⋅pyridine synthon when at 2-position it prefers acid⋅⋅⋅pyridine synthon. The preference of amide anticatemer over dimer synthon is supported by additional C-H⋅⋅⋅O hydrogen bonds. In case of 3,5-dinitro-2-hydroxy benzoic acid, the disorder in hydroxyl (-OH) group at ortho site leads to salt formation. Section 4.2 describes co-crystal study of adenine and thymine (AT) as free nucleobases. This result reveals the formation of AT (2:1) complex with both Hoogsteen and “quasi-Watson-Crick” hydrogen bonds. The hydrogen bonded bases using the Hoogsteen and the “quasi-Watson-Crick” interactions generate a hexagonal supramolecular motif. Four water molecules are located inside the hexagonal void of this complex. A high temperature study on the same crystal shows that at 313K, one of the water molecules escapes from the lattice resulting in the small change in unit cell parameters. However, the space group remains the same and the hexagonal void remains unaltered. With further increase in temperature, the crystal deteriorates irreversibly which clearly brings out the importance of water molecule in the molecular recognition of adenine-thymine complex. Chapter 5 discusses crystal structure analysis of trans-atovaquone (antimalarial drug), its new polymorph form including one stereoisomer (cis) and five other derivatives with different functional groups. Based on the conformational features of these compounds and the characteristics of the nature of hydrogen bonding and other weak intra and intermolecular interactions, docking studies with cytochrome bc1 complex provide valuable insight into the atomistic details of protein-inhibitor interactions. The docking results reveal that atovaquone and its derivatives, owing to their nature of hydrogen bond and the propensity towards the formation of weaker hydrogen bonds involving the chlorine atom as well appear as good candidates for drug evaluation.

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