Water is known to take on highly organized structures to influence the reactivity of chemical and biological systems; despite this, water is often only implicitly or approximately included in theoretical studies of biochemical systems, if not omitted entirely. Many of the current models for biological processes predate an understanding of the complex behaviour of water, yet these models have not been updated. This thesis presents an exploration of how a better of water might affect the models used to describe neurotransmission. Two classes of systems are investigated, representing the two main categories of neurotransmission: that which occurs along the length of a neuron, and that which occurs between one neuron and another cell. Lipid bilayers are studied using molecular dynamics, and neurotransmitters are studied using Car-Parrinello molecular dynamics. The results indicate that water structures may play a more specific role in neurotransmission than was previously thought.

Abstract This thesis focuses on the molecular-level chemistry of the solvation of aluminum salts. Fundamental aspects such as, structural characteristics of the aluminum molecules, hydrolysis, acidity, solvation structure, effect of counter ions, and chemical stability are discussed herein. Static computations augmented with the conductor-like screening model (COSMO) were used to investigate hundreds of planar and cyclic configurations of dimeric, trimeric, tetrameric, and pentameric aluminum complexes. Car–Parrinello molecular dynamics (CPMD) calculations were used to expand investigations to aqueous environments. This thesis consists of four articles and one additional article. The first paper focuses on the structural analysis of the hydrolysis products of AlCl3 · 6H2O. Dimeric, trimeric, and tetrameric aluminum (chloro)hydroxides were investigated in both gas and liquid phase. The liquid environment was modeled by using COSMO. The second and the additional paper concentrate on the chemistry of aluminum sulfate complexes. The second article focuses on identifying hydrolysis products of AlCl3 · 6H2O in the presence of sulfate (H2SO4). The additional paper focuses on the structural characteristics of the hydrolysis products of Al2 (SO4)3 · 18H2O. Structural information was deduced from the ESI MS results with the aid of computational methods. Detected cationic structures closely resembled the aluminum chlorohydrate analogues introduced in the first paper. The third and fourth articles are devoted to the hydrolysis, stability, and dynamics of dimeric and pentameric aluminum (chloro)hydroxides in aquatic environments. During the CPMD simulations, several spontaneous associative hydration reactions were detected in the primary hydration shell of the complexes. Dimeric aluminum chlorohydrates were detected to be stable in liquid conditions, whereas the pentameric aluminum complexes experienced significant topological changes during the simulations. Constrained simulations were used to reveal the role of chloride ions in the hydrolysis processes of dimeric complexes. The effect of the empirical van der Waals corrections to the dynamics of the simulations was also tested for the pentameric system. The results of this thesis showed unequivocally that computational chemistry provides effective tools for structural analysis of inorganic complexes such as, aluminum chlorohydrates and sulfates in both gas and liquid phase. In addition, calculations provided answers to the anomalies detected in the experiments. Hence, theoretical methods are highly recommended to be used alongside with conventional experimental methods in the interpretation of the aluminum species in aqueous solutions and to widen the overall chemical perspective of the hydrolysis of aluminum salts.

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<p>The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium.</p><p>This thesis describes computer simulations of Al³⁺(<i>aq</i>), Fe²⁺(<i>aq</i>), Fe³⁺(<i>aq</i>) and Cu²⁺(<i>aq</i>). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. </p><p>All the ion-water coordination figures in this thesis are octahedral, except in the Cu²⁺(<i>aq</i>) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu²⁺(<i>aq</i>), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. </p><p>Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.</p>

The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium. This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.

The subject of the present licentiate thesis is density functional theorybased electronic structure calculations of organic thermoelectric materials and novel organic molecules. We used the Car-Parrinello molecular dynamics method in order to investigate the electronic structure of “green energy” and “greenchemistry” compounds. First, we have investigated the electronic structure of the poly(3,4-ethylene-dioxythiophene) (PEDOT) and its derivatives - the best studied and successfully implemented by industry organic thermoelectric material. Its transparency, low toxicity and high stability in the oxidized state are combined withan ability to produce electrical current when applying a temperature gradient. This makes PEDOT a perfect “organic metal” and a first candidate for organic thermoelectrogenerators - devices that can produce “green energy” from a temperature difference. The average structures found in these quantum dynamical simulations agree well with earlier static electronic structure studies. The energy gap of two, four and six unit oligomers of PEDOT was calculated and was found to lie in the range of previous theoretical studies. We have also calculatedthe point-charge distributions along the polymer backbone in order to investigate the polaron formed by doping agents of PEDOT. Our analysis allowed us to predict possible localization of the charge in the center of the polymer chain. However, further calculations of the twelve unit PEDOT and its selenium and tellurium derivatives will provide more information. First-principles calculations for the tellurium derivative of PEDOT are here presented for the first time. The second part of our investigation concerns theoretical calculations of novel piperidine-containing acetylene glycols. These molecules were newly synthesized by our experimental collaborators and are expected to provideplant growth stimulation properties, the same as its diacetylene analogs. We performed quantum mechanical calculations of four compounds, presented ananalysis of the highest occupied and lowest unoccupied molecular orbitals and collected detailed information on point-charges for further parametrization of novel molecules for future computational studies. According to these results, the low production yield found in the experiments cannot be attributed to chemical instability in these novel compounds. / <p>QC 20150629</p> / ScalTEG SSF

Conductive polymers are also known as "organic metals" due to their semiconducting properties. They are found in a wide range of applications in the field of organic electronics. However, the growing number of experimental works is not widely supported with theoretical calculations. Hence, the field of conductive polymers is experiencing lack of understanding of mechanisms occurring in the polymers. In this PhD thesis, the aim is to increase understanding of conductive polymers by performing theoretical calculations.        The polymers poly(3,4-ethylenedioxythiophene) (PEDOT) together with its selenium (PEDOS) and tellurium (PEDOTe) derivatives, poly(p-phenylene) (PPP) and naphthobischalcogenadiazoles (NXz) were studied. Several computational methods were applied for analysis of mentioned structures, including density functional theory (DFT), tight-binding modelling (TB), and Car-Parrinello molecular dynamics (CPMD) calculations. The combination of CPMD and DFT calculations was applied to investigate the PEDOT, PEDOS and PEDOTe. The polymers were studied using four different functionals in order to investigate the full picture of structural changes, electronic and optical properties. Temperature effects were studied using molecular dynamics simulations. Wide statistics for structural and molecular orbitals analysis were collected.         The TB method was employed for PPP. The formation and motion of the excitations, polarons and bipolarons, along the polymer backbone was investigated in presence of electric and magnetic fields. The influence of non-magnetic and magnetic impurities was determined.        The extended π-conjugated structures of NXz were computed using B3LYP and ωB97XD functionals in combination with the 6-31+G(d) basis set. Here, the structural changes caused by polaron formation were analyzed. The combined analysis of densities of states and absorption spectra was used for understanding of the charge transition. / <p>QC 20170928</p>