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We study in this thesis work the spectroscopic and thermodynamic quantities of some substances such as ammonium halides (NH4Cl, NH4I), ferroelectric crystals of tris-sarcosine calcium chloride (TSCC), tris-sarcosine calcium bromide (TSCB), organic compounds of carbon tetrachloride (CCl4) and s-triazine (C3N3H3) close to the phase transitions. Various physical and chemical properties of those materials have been measured near the critical points and have been reported in the literature. In this study, the spectroscopic parameters of the frequency shifts, intensity and bandwidths are calculated as functions of temperature or pressure near the phase transitions in ammonium halides using the experimental data from the literature. The spectroscopic parameters are related to the crystal volume and the specific heat in these compounds. The thermodynamic quantities of the specific heat, thermal expansion and the isothermal compressibility are also calculated in the solid and liquid phases of carbon tetrachloride using the experimental data. In another part of this thesis work, we analyze the temperature dependence of the spontaneous polarization and the dielectric susceptibility at fixed pressures for TSCC and TSCB by using the experimental data from the literature. The temperature dependence of the damping constant for the s-triazine is also calculated here close to the I-II transition. We use the theoretical models on the basis of the observations in the literature to calculate the critical behaviour of these physical quantities and we compare the results with the observed data. Various experimental studies in the literature give us the opportunity to find the proper way of fitting the calculated and observed results. This study gives us the chance of a better understanding of the critical behavior of the studied materials by verifying the values of some critical exponents and the types of transitions as expected by different theoretical models.

Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Brédas, Jean-Luc; Committee Member: Kippelen, Bernard; Committee Member: Marder, Seth; Committee Member: Sherrill, David; Committee Member: Whetten, Robert. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (Ph. D.)--Brandeis University, 2010. / "UMI:3390481." MICROFILM COPY ALSO AVAILABLE IN THE UNIVERSITY ARCHIVES. Includes bibliographical references.

Les cristaux moléculaires présentent des applications importantes dans l'électronique/l'optoélectronique, les systèmes 'host-guest', ou encore pour des systèmes mécaniques photo-actifs.Les propriétés mentionnées ci-dessus sont sensiblement affectées par le polymorphisme, qui influence le comportement de chaque composé présent dans une forme cristalline définie. Ce phénomène est rendu difficile à étudier de par la présence d'interactions de dispersion et/ou liaisons hydrogène.Avec l'objectif de décrire précisément ces interactions, et pour prédire des propriétés électroniques, une approche de mécanique quantique (QM) a été adoptée, utilisant la Théorie de la Fonctionnelle de la Densité (DFT).Les avancements les plus importants dans l'étude des cristaux examinées, sont: i) une prédiction correcte de la stabilité relative entre olymorphes, similaire aux résultats prévus par des méthodes plus coûteuses, peut être obtenue par l'utilisation d'une ombinaison entre la DFT et des corrections semi-empiriques moins coûteuses; ii) Le benchmark réalisé ici peut être utile dans le cadre de la création de nouveaux corrections pour la dispersion en DFT; iii) la rédiction de la structure de quatre formes cristallines d'un composé 'host-guest' précédemment synthétisé a été réalisée, notamment grâce aux calculs des déplacements chimiques (RMN) ayant permis de compléter et corriger l'interprétation RMN des résultats expérimentaux; iv) un protocole calculatoire pour l'étude des procédés photophysiques et photochimiques d'un cristal moléculaire thermochromique a été mis en place, basé sur la caractérisation des clusters de molécules extraits du cristal 'bulk' par la mécanique quantique. / Molecular crystals find relevant applications in electronics/optoelectronics, host-guest systems, or photo-activated mechanical systems. The properties mentioned above are severely affected by polymorphism, which influences the behaviour of each compound in a definite crystalline form. This is complicated by the dispersion and/or hydrogen bond interactions, which govern the molecular displacement within the solid. In order to describe accurately these interactions, and to predict advanced electronic properties, a quantum (QM) computational approach has been adopted, at the Density Functional Theory (DFT) level. The more notable advancements in the characterization of the studied crystals are: i) the demonstration that a wise combination of DFT and costless semiempirical corrections for dispersion leads to predict accurately the relative stability between polymorphs, almost at the same level of higher and costly methods; ii) The benchmarking carried out against these last can be exploited to design new dispersion-correction schemes for DFT iii) the structural prediction of four crystal forms of a solid host-guest compound previously synthetized, for that we addressed and clarified some lacks on the experimental NMR interpretation, through calculated NMR chemical shifts; iv) the optimization of a computational protocol for the study of the photophysical-photochemical processes of a thermochromic molecular crystal – based on the QM characterization of clusters of molecules extracted from the bulk crystal.

In the past decade the interest in molecular electronic devices has escalated. The synthesis of molecular crystals has improved, providing single crystals or thin films with mobility comparable with or even higher than amorphous silicon. Their mechanical flexibility admits new types of applications and usage of electronic devices. Some of these organic crystals also display magnetic effects. Furthermore, the fullerene and carbon nanotube allotropes of carbon are prominent candidates for various types of applications. The carbon nanotubes, in particular, are suitable for molecular wire applications with their robust, hollow and almost one-dimensional structure and diverse band structure. In this thesis, we have theoretically investigated carbon based materials, such as carbon nanotubes, pentacene and spiro-biphenalenyl neutral radical molecular crystals. The work mainly deals with the electron structure and the transport properties thereof. The first studies concerns effects and defects in devices of finite carbon nanotubes. The transport properties, that is, conductance, are calculated with the Landauer approach. The device setup contains two metallic leads attached to the carbon nanotubes. Structural defects as vacancies and bending are considered for single-walled carbon nanotubes. For the multi-walled carbon nanotubes the focus is on inter-shell interaction and telescopic junctions. The current voltage characteristics of these systems show clear marks of quantum dot behaviour. The influence of defects as vacancies and geometrical deformations are significant for infinite systems, but in these devices they play a minor role. The rest of the studies concern molecular crystals, treated with density-functional theory (DFT). Inspired by the enhance of the electrical conductivity obtained experimentally by doping similar materials with alkali metals, calculations were performed on bundles of single-walled carbon nanotubes and pentacene crystals doped with potassium. The most prominent effect of the potassium intercalation is the shift of Fermi level in the nanotube bands. A sign of charge transfer of the valence electrons of the potassium atoms. Semi-conducting bundles become metallic and metallic bundles gain density of states at the Fermi level. In the semi-conducting pristine pentacene crystals structural transitions occur upon doping. The herringbone arrangement of the pristine pentacene molecules relaxes to a more π-stacked structure causing more dispersive bands. The charge transfer shifts the Fermi level into the lowest unoccupied molecular orbital band and turns the crystal metallic. Finally, we have studied molecular crystals of spiro-biphenalenyl neutral radicals. According to experimental studies, some of these materials show simultaneous electrical, optical and magnetical bistability. The electronic properties of these crystals are investigated by means of DFT with a focus on the possible intermolecular interactions of radical spins.

The main objective of this thesis is to provide a deeper understanding of the charge transport phenomena occuring in molecular crystals. The focus is on the stability and the dynamics of the polaron as the charge carrier. To achieve this goal, a series of numerical calculations are performed using the semi-emprical "Holstien-Peierls" model. The model considers both intra- (Holstein) and inter- (Peierls) molecular interactions, in particular the electron-phonon interactions. First, the stability of the polaron in an ordered two dimensional molecular lattice with an excess charge is studied using Resilient backPropagation, RPROP, algorithm. The stability is defined by the "polaron formation energy". This formation energy is obtained for a wide range of parameter sets including both intra- and inter-molecular electron-phonon coupling strengths and their vibrational frequencies, transfer intergral and electric field. We found that the polaron formation energies lying in the range of 50-100 meV are more interesting for our studies. The second step to cover is the dynamical behaviour of the polaron. Using the stable polaron solutions acheived in the first step, an electric field is applied as an external force, pushing the charge to move. We observed that the polaron remains stable and moves with a constant velocity for only a limited range of parameter sets. Finally, the impact of disorder and temperature on the charge dynamics is considered. Adding disorder to the system will result in a more restricted parameter set space for which the polaron is dynamically stable and mobile. Temperature is included in the Newtonian equations of motion via a random force. We observed that the polaron remains localized and moves with a diffusive behaviour up to a certain temperature. If the temperature increases to values above this critical temperature, the localized polaron becomes delocalized. All this research work is coded in MATLAB software , allowing us to run the calculations, test and validate our results.

No / We investigated five different methods for evaluating the electrostatic interaction between atoms in force field calculations on organic solids. Atomic charges and multipoles were obtained by fitting them to the molecular electrostatic potential, calculated in vacuum with an ab initio quantum mechanical method. Multipole moments were derived using three schemes, differing in the order in which the monopoles, dipoles and quadrupoles were fitted. For comparison, Gasteiger charges were also calculated. Using these electrostatic models, the lattice parameters and the molecular geometry of 48 organic crystals were optimised with the DREIDING force field. During the optimisation, the atomic multipoles were rotated with their local environment to account for molecular flexibility. For comparative reasons, rigid-body optimisations were performed on a subset of structures. The results were analysed in terms of structural parameters of the lattice and the molecules, and, for the ten polymorphic systems present in the test set, in terms of relative stability. On average, the multipole methods were not superior to the point charge methods for the full optimisation. For rigid molecules, however, the multipole models gave a substantial improvement in lattice parameters. No evidence was found that parameters for van der Waals energies need to be refitted for a specific electrostatic model. Energy differences between polymorphs were less than 5 kcal mol¿1 in eight out of ten cases, independent of the electrostatic model used. The results show that our use of distributed multipoles to describe the intra-molecular as well as inter-molecular electrostatic interactions does lead to an improvement in accuracy for rigid molecules, but not for flexible molecules. The investigation shows that accurate descriptions of the intra-molecular as well as the inter-molecular energies are crucial for the successful optimisation of crystal structures of organic solids.

Crystallographically solids with well defined crystal structures are normally assumed to be highly ordered. However, it is not uncommon to find considerable degree of disorder amongst many of these crystalline substances. Disorder among crystalline substances often arise from the rotational motion which leads to the well known class of plastic crystalline substances. Typically, globular molecules such as methane, carbon tetrachloride or adamantane exhibit plastic crystalline phase with significant amount of orientational disorder. In many other substances, disorder arises from torsional motion as in the case of biphenyl, p- or o-terphenyls, stilbene or azobenzenes. In case of molecules with flexible segment, such as alkanes or surfactants, motion of the terminal methyl group or terminal ethyl group is responsible for the observed disorder. Chapter 1 discusses various aspects of disorder in crystals. A new pressure induced solid phase of biphenyl is reported at room temperature. Isothermal-isobaric ensemble variable shape simulation cell Monte Carlo calculations are reported on biphenyl at 300K as a function of pressure between 0-4 GPa. The potential proposed by Williams for inter-molecular and Benkert-Heine-Simmons(BHS) for intramolecular interactions have been employed. Different properties indicating changes in the crystal structure, molecular structure, distributions of inter- and intra-molecular energy are reported as a function of pressure. With increase in pressure beyond 0.8 GPa, the dihedral angle distribution undergoes a change from a bimodal to an unimodal distribution. The changes in IR and Raman spectra across the transition computed from ab initio calculations are in agreement with the experimental measurements. It is shown that at pressures larger than 0.8 GPa, competition between inter-molecular interactions with intra-molecular terms v/z., conjugation energy and the ortho-ortho repulsion favors a planar biphenyl due to better packing and consequently a predominant inter-molecular term. The exact value of the transition pressure will depend on the accuracy of the inter- and intra-molecular potentials employed here. p-terphenyl has been modeled at 300K and atmospheric pressure with different potential models. Modified Fihppini parameters for mtermolecular interactions and BHS potential for inter-ring torsion predict the structure of p-terphenyl reasonably well. Pressure variation calculations are carried out with this combination of inter- and intra-molecular potential. The structure as a function of pressure upto 5 GPa has been compared with experimental structure provided by Puschnig et al. The transformation of functional form of the potential energy curve (associated with the inter-ring flipping) from W-shaped to [/-shaped form as a function of pressure has been observed. This is in excellent agreement with previous studies of polyphenyls including biphenyl and p-hexaphenyl. The complete planarization of molecules occurs when the pressure range is 1.0 GPa-1.5 GPa. Molecular simulation of solid stilbene in the isothermal-isobaric ensemble with variable shape simulation are reported. Structure has been characterized by means of lattice parameters and radial distribution functions. Simulations show existence of pedal-like motion at higher temperatures in agreement with the recent X-ray diffraction measurements by Ogawa and co-workers and several others previously. Difference in energy between the major and minor conformers, barrier to conformational change at both the crystallographic sites have been calculated. Temperature dependence of the equilibrium constant between the two conformers as well as the rate of conversion between the con-formers at the two sites have been calculated. These are in agreement with the recent analysis by Harada and Ogawa of non-equilibrium states obtained by rapid cooling of stilbene. Volume and total intermolecular energy suggest existence of two transitions in agreement with previous Raman phonon spectroscopic and calorimetric studies. They seem to be associated with change from order to disorder at the two sites. Ab initio calculations coupled with simulations suggest that the disorder accounts for only a small part of the observed shortening in ethylene bond ength. A Monte Carlo simulation with variable shape simulation cell has been carried out on stilbene. The study attempts to investigate the disorder at various pressures upto 4 GPa. It is seen that the population of minor conformers at sites 1 and 2 decrease with increase in pressure. Population of minor conformers at site 2 decreases to zero by 1.5 GPa. In contrast, the population of minor conformers at site 1 remains finite for the runs reported here. It is seen that the population of minor conformers at site 1 is higher than at site 2 at room temperature which is to be expected on the basis of the activation energies. Associated changes in the unit cell as well as molecular conformation are discussed. Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been earned out with variable shape simulation cell. Low temperature crystalline phase and the room temperature plastic crystalline phases have been studied employing the Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low temperature ordered tetragonal phase of adamantane. The high pressure ordered phase appears to be characterized by a slightly larger shift of the first peak towards lower value of r in C-C, C-H and H-H rdfs as compared to the low temperature tetragonal phase. Co-existence curve between the crystalline and plastic crystalline phase has been obtained approximately upto a pressure of 4 GPa. We investigate the equation of state, variation of lattice parameters and the distortion of molecular geometry of low temperature phase of adamantane upto 26 GPa pressure. A rigid and a flexible model of adamantane have been studied using variable shape simulation within the isothermal-isobaric ensemble. Including six low frequency modes obtained from density functional theory carried out on a single-molecule has incorporated the flexibility. These calculations used Becke 3-parameter method and Lee-Yang-Parr electron correlation functional with 6-31G(d) basis set. The simulated equation of state and variation of c/a ratio as a function of pressure are compared with the experimental results. The results are in good agreement with high pressure experiments. Nature of distortion in molecular geometry obtained from the calculation are also in good agreement with the experiment.

University of Macau / Institute of Chinese Medical Sciences