Density Functional Theory is used in order to shed light on the reaction mechanisms and the origins of stereoselectivity in enantioselective organocatalytic reactions. The reactions investigated are the dipeptide-catalyzed aldol reaction, the cinchona thiourea-catalyzed nitroaldol reaction and the prolinol derivative-catalyzed hydrophosphination reaction. We can justify the stereoselectivity in the reactions from the energies arising from different interactions in the transition states. The major contributions to the energy differences are found to be hydrogen bond-type attractions and steric repulsions. This knowledge will be useful in the design of improved catalysts as well as general understanding of the basis of selection in other reactions. / QC 20101111

Polymer electrolyte fuel cells (PEFC) convert the chemically bound energy in a fuel, e.g. hydrogen, directly into electricity by an electrochemical process. Examples of future applications are energy conversion such as combined heat and power generation (CHP), zero emission vehicles (ZEV) and consumer electronics. One of the key components in the PEFC is the membrane / electrode assembly (MEA). Both the membrane and the electrodes consist of proton conducting polymers (ionomers). In the membrane, properties such as gas permeability, high proton conductivity and sufficient mechanical and chemical stability are of crucial importance. In the electrodes, the morphology and electrochemical characteristics are strongly affected by the ionomer content. The primary purpose of the present thesis was to develop experimental techniques and to use them to characterise proton conducting polymers and membranes for PEFC applications electrochemically at, or close to, fuel cell operating conditions. The work presented ranges from polymer synthesis to electrochemical characterisation of the MEA performance. The use of a sulfonated dendritic polymer as the acidic component in proton conducting membranes was demonstrated. Proton conducting membranes were prepared by chemical cross-linking or in conjunction with a basic functionalised polymer, PSU-pyridine, to produce acid-base blend membranes. In order to study gas permeability a new in-situ method based on cylindrical microelectrodes was developed. An advantage of this method is that the measurements can be carried out at close to real fuel cell operating conditions, at elevated temperature and a wide range of relative humidities. The durability testing of membranes for use in a polymer electrolyte fuel cell (PEFC) has been studied in situ by a combination of galvanostatic steady-state and electrochemical impedance measurements (EIS). Long-term experiments have been compared to fast ex situ testing in 3 % H2O2 solution. For the direct assessment of membrane degradation, micro-Raman spectroscopy and determination of ion exchange capacity (IEC) have been used. PVDF-based membranes, radiation grafted with styrene and sulfonated, were used as model membranes. The influence of ionomer content on the structure and electrochemical characteristics of Nafion-based PEFC cathodes was also demonstrated. The electrodes were thoroughly investigated using various materials and electrochemical characterisation techniques. Electrodes having medium Nafion contents (35<x<45 wt %) showed the best performance. The mass-transport limitation was essentially due to O2 diffusion in the agglomerates. The performance of cathodes with low Nafion content (<30 wt %) is limited by poor kinetics owing to incomplete wetting of platinum (Pt) by Nafion, by proton migration throughout the cathode as well as by O2 diffusion in the agglomerates. At large Nafion content (>45 wt %), the cathode becomes limited by diffusion of O2 both in the agglomerates and throughout the cathode. Furthermore, models for the membrane coupled with kinetics for the hydrogen electrode, including water concentration dependence, were developed. The models were experimentally validated using a new reference electrode approach. The membrane, as well as the hydrogen anode and cathode characteristics, was studied experimentally using steady-state measurements, current interrupt and EIS. Data obtained with the experiments were in good agreement with the modelled results. / QC 20101014

<p>Polymer electrolyte fuel cells (PEFC) convert the chemically bound energy in a fuel, e.g. hydrogen, directly into electricity by an electrochemical process. Examples of future applications are energy conversion such as combined heat and power generation (CHP), zero emission vehicles (ZEV) and consumer electronics. One of the key components in the PEFC is the membrane / electrode assembly (MEA). Both the membrane and the electrodes consist of proton conducting polymers (ionomers). In the membrane, properties such as gas permeability, high proton conductivity and sufficient mechanical and chemical stability are of crucial importance. In the electrodes, the morphology and electrochemical characteristics are strongly affected by the ionomer content. The primary purpose of the present thesis was to develop experimental techniques and to use them to characterise proton conducting polymers and membranes for PEFC applications electrochemically at, or close to, fuel cell operating conditions. The work presented ranges from polymer synthesis to electrochemical characterisation of the MEA performance.</p><p>The use of a sulfonated dendritic polymer as the acidic component in proton conducting membranes was demonstrated. Proton conducting membranes were prepared by chemical cross-linking or in conjunction with a basic functionalised polymer, PSU-pyridine, to produce acid-base blend membranes. In order to study gas permeability a new in-situ method based on cylindrical microelectrodes was developed. An advantage of this method is that the measurements can be carried out at close to real fuel cell operating conditions, at elevated temperature and a wide range of relative humidities. The durability testing of membranes for use in a polymer electrolyte fuel cell (PEFC) has been studied in situ by a combination of galvanostatic steady-state and electrochemical impedance measurements (EIS). Long-term experiments have been compared to fast ex situ testing in 3 % H2O2 solution. For the direct assessment of membrane degradation, micro-Raman spectroscopy and determination of ion exchange capacity (IEC) have been used. PVDF-based membranes, radiation grafted with styrene and sulfonated, were used as model membranes. The influence of ionomer content on the structure and electrochemical characteristics of Nafion-based PEFC cathodes was also demonstrated. The electrodes were thoroughly investigated using various materials and electrochemical characterisation techniques. Electrodes having medium Nafion contents (35<x<45 wt %) showed the best performance. The mass-transport limitation was essentially due to O2 diffusion in the agglomerates. The performance of cathodes with low Nafion content (<30 wt %) is limited by poor kinetics owing to incomplete wetting of platinum (Pt) by Nafion, by proton migration throughout the cathode as well as by O2 diffusion in the agglomerates. At large Nafion content (>45 wt %), the cathode becomes limited by diffusion of O2 both in the agglomerates and throughout the cathode. Furthermore, models for the membrane coupled with kinetics for the hydrogen electrode, including water concentration dependence, were developed. The models were experimentally validated using a new reference electrode approach. The membrane, as well as the hydrogen anode and cathode characteristics, was studied experimentally using steady-state measurements, current interrupt and EIS. Data obtained with the experiments were in good agreement with the modelled results. Keywords: polymer electrolyte fuel cell, proton conducting membrane, porous electrode, gas permeability, degradation, water transport</p>

Multivariate regression of several different quantum chemical descriptors was used to build a model for the reactivity of nucleophilic aromatic substitution reactions, i.e. SNAr reactions, through predictingthe molecular reaction site’s Gibb’s free activation energy (ΔG‡). The datasets used for training provided data of ΔG‡ for several differing halide leaving groups including chloride, bromide, and fluoride. A set of descriptors were tested for the different leaving groups revealing that dissimilar leaving groups are more dependent on certain descriptors than others, meaning each model has to be tailored for the specific leaving groups. Excellent correlations (R2 = 0.93) were achieved between the predicted ΔG‡ and the experimental ΔG‡.The ability of the model to predict regioselectivity in aromatic compounds with multiple leaving groups was tested and successfully predicted the correct regioselectivity through the calculation of ΔΔG‡ in each case tested. However, the model’s validity outside of the training dataset was put into doubt through low R2 values when the model was tested with several external datasets. An unknown factor arose which is speculated to be because of how differing nucleophiles and solvents affect the ΔG‡. One of these tests yielded excellent correlations (R2 = 0.9525) which could be because of similarities between solvents and nucleophiles between the training dataset but a similar factor between predicted ΔG‡ and the experimental ΔG‡ could still be observed.

<p>Individual proteins, and small collections of proteins, have been extensively studied for at least two hundred years. Today, more than 350 genomes have been completely sequenced and the proteomes of these genomes have been at least partially mapped. The inventory of protein coding genes is the first step toward understanding the cellular machinery. Recent studies have generated a comprehensive data set for the physical interactions between the proteins of <i>Saccharomyces cerevisiae</i>, in addition to some less extensive proteome interaction maps of higher eukaryotes. Hence, it is now becoming feasible to investigate important questions regarding the evolution of protein-protein networks. For instance, what is the evolutionary relationship between proteins that interact, directly or indirectly? Do interacting proteins co-evolve? Are they often derived from each other? In order to perform such proteome-wide investigations, a top-down view is necessary. This is provided by network (or graph) theory.</p><p>The proteins of the cell may be viewed as a community of individual molecules which together form a society of proteins (nodes), a network, where the proteins have various kinds of relationships (edges) to each other. There are several different types of protein networks, for instance the two networks studied here, namely metabolic networks and protein-protein interaction networks. The metabolic network is a representation of metabolism, which is defined as the sum of the reactions that take place inside the cell. These reactions often occur through the catalytic activity of enzymes, representing the nodes, connected to each other through substrate/product edges. The indirect interactions of metabolic enzymes are clearly different in nature from the direct physical interactions, which are fundamental to most biological processes, which constitute the edges in protein-protein interaction networks.</p><p>This thesis describes three investigations into the evolution of metabolic and protein-protein interaction networks. We present a comparative study of the importance of retrograde evolution, the scenario that pathways assemble backward compared to the direction of the pathway, and patchwork evolution, where enzymes evolve from a broad to narrow substrate specificity. Shifting focus toward network topology, a suggested mechanism for the evolution of biological networks, preferential attachment, is investigated in the context of metabolism. Early in the investigation of biological networks it seemed clear that the networks often display a particular, 'scale-free', topology. This topology is characterized by many nodes with few interaction partners and a few nodes (hubs) with a large number of interaction partners. While the second paper describes the evidence for preferential attachment in metabolic networks, the final paper describes the characteristics of the hubs in the physical interaction network of <i>S. cerevisiae</i>.</p>

Individual proteins, and small collections of proteins, have been extensively studied for at least two hundred years. Today, more than 350 genomes have been completely sequenced and the proteomes of these genomes have been at least partially mapped. The inventory of protein coding genes is the first step toward understanding the cellular machinery. Recent studies have generated a comprehensive data set for the physical interactions between the proteins of Saccharomyces cerevisiae, in addition to some less extensive proteome interaction maps of higher eukaryotes. Hence, it is now becoming feasible to investigate important questions regarding the evolution of protein-protein networks. For instance, what is the evolutionary relationship between proteins that interact, directly or indirectly? Do interacting proteins co-evolve? Are they often derived from each other? In order to perform such proteome-wide investigations, a top-down view is necessary. This is provided by network (or graph) theory. The proteins of the cell may be viewed as a community of individual molecules which together form a society of proteins (nodes), a network, where the proteins have various kinds of relationships (edges) to each other. There are several different types of protein networks, for instance the two networks studied here, namely metabolic networks and protein-protein interaction networks. The metabolic network is a representation of metabolism, which is defined as the sum of the reactions that take place inside the cell. These reactions often occur through the catalytic activity of enzymes, representing the nodes, connected to each other through substrate/product edges. The indirect interactions of metabolic enzymes are clearly different in nature from the direct physical interactions, which are fundamental to most biological processes, which constitute the edges in protein-protein interaction networks. This thesis describes three investigations into the evolution of metabolic and protein-protein interaction networks. We present a comparative study of the importance of retrograde evolution, the scenario that pathways assemble backward compared to the direction of the pathway, and patchwork evolution, where enzymes evolve from a broad to narrow substrate specificity. Shifting focus toward network topology, a suggested mechanism for the evolution of biological networks, preferential attachment, is investigated in the context of metabolism. Early in the investigation of biological networks it seemed clear that the networks often display a particular, 'scale-free', topology. This topology is characterized by many nodes with few interaction partners and a few nodes (hubs) with a large number of interaction partners. While the second paper describes the evidence for preferential attachment in metabolic networks, the final paper describes the characteristics of the hubs in the physical interaction network of S. cerevisiae.

In the present thesis, the reaction mechanisms of several di-zinc hydrolases have been explored using quantum chemical modeling of the enzyme active sites. The studied enzymes are phosphotriesterase (PTE), aminopeptidase from Aeromonas proteolytica (AAP), glyoxalase II (GlxII), and alkaline phosphatase (AP). All of them contain a binuclear divalent zinc core in the active site. The density functional theory (DFT) method B3LYP functional was employed in the investigations. The potential energy surfaces (PESs) for various reaction pathways have been mapped and the involved transition states and intermediates have been characterized. The hydrolyses of different types of substrates were examined, including phosphate esters (PTE and AP) and the substrates containing carbonyl group (AAP and GlxII). The roles of zinc ions and individual active-site residues were analyzed and general features of di-zinc enzymes have been characterized. The bridging hydroxide stabilized by two zinc ions has been confirmed to be capable of the nucleophile in the hydrolysis reactions. PTE, AAP, and GlxII all employ the bridging hydroxide as the direct nucleophile. Furthermore, it is shown that either one of or both zinc ions provide the main catalytic power by stabilizing the negative charge developing during the reaction and thereby lowering the barriers. In the cases of GlxII and AP, one of zinc ions also contributes to the catalysis by stabilizing the leaving group. These features perfectly satisfy the two requisites for the hydrolysis, i.e. sufficient nucleophilicity and stabilization of charge. A competing mechanism, in which the bridging hydroxide acts as a base, was shown to have significantly higher barrier in the case of PTE. For phosphate hydrolysis reactions, it is important to characterize the nature of the transition states involved in the reactions. Associative mechanisms were observed for both PTE and AP. The former uses a step-wise associative pathway via a penta-coordinated intermediate, while the latter proceeds through a concerted associative path via penta-coordinated transition states. Finally, with PTE as a test case, systematic evaluation of the computational performance of the quantum chemical modeling approach has been performed. This assessment, coupled with other results of this thesis, provide an effective demonstration of the usefulness and powerfulness of quantum chemical active-site modeling in the exploration of enzyme reaction mechanisms and in the characterization of the transition states involved. / QC 20100715 / Quantum Chemical Modeling of Binuclear Zinc Enzymes

The aim of this thesis was to investigate carbon based molecular materials at first principles levels. Special attention has been paid to simulations of X-ray spectroscopies, including near edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron, and X-ray emission spectroscopy, which can provide detailed information about core, occupied and unoccupied molecular orbitals of the systems under investigation. Theoretical calculations have helped to assign fine spectral structures in high resolution NEXAFS spectra of five azabenzenes (pyridine, pyrazine, pyrimidine, pyridazine and s-triazine), and to identify different local chemical environments among them. With the help of NEXAFS, the characters of important chemical bonds that might be responsible for the unique magnetic properties of the tetracyanoethylene compound has been revealed. Calculations have demonstrated that X-ray spectroscopies are powerful tools for isomer identification and structure determination of fullerenes and endohedral metallofullerenes. A joint experimental and theoretical study on metallofullerene Gd@C82 has firmly determined its equilibrium structure, in which the gadolinium atom lies above the hexagon on the C2 axis. It is found that the gadolinium atom could oscillate around its equilibrium position and that its oscillation amplitude increases with increasing temperature. In this thesis, several new computational schemes for large-scale systems have been proposed. Parallel implementation of a central insertion scheme (CIS) has been realized, which allows to effectively calculate electronic structures of very large systems, up to 150,000 electrons, at hybrid density functional theory levels. In comparison with traditional computational methods, CIS provides results with the same high accuracy but requires only a fraction of computational time. One of its applications is to calculate electronic structures of nanodiamond clusters varying from 0.76 nm (29 carbons) to 7.3 nm (20,959 carbons) in diameter, which enabled to resolve the long-standing debate about the validity of the quantum confinement model for nanodiamonds. Electronic structures and X-ray spectroscopies of a series of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths have been calculated, which have made it possible to interpret the existing experimental results. / QC 20100727

This thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree-Fock calculations. Density matrix purification, which is a method used to construct the density matrix for a given Fock matrix, is also discussed. The methods described are not only applicable in the Hartree-Fock case, but also in Kohn-Sham Density Functional Theory calculations, where the Coulomb and exchange matrices are parts of the Kohn-Sham matrix. Screening techniques for reducing the computational complexity of both Coulomb and exchange computations are discussed, including the fast multipole method, used for efficient computation of the Coulomb matrix. The thesis also discusses how sparsity in the matrices occurring in Hartree-Fock and Kohn-Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them. / QC 20100817

This thesis presents a theoretical study on optical properties of molecular materials. Special emphasis has been put on the influence of solvent environment, nuclear vibrations, and aggregation effects on molecular properties like linear and nonlinear polarizabilities, one- and two-photon absorption probabilities. All calculations have been performed by means of time independent and dependent quantum chemical methods at the Hartree-Fock and density functional theory levels. Solvation models that include both long range and short range interactions have been employed for calculations of optical properties of molecules in solutions. Pure vibrational and zero-point vibrationally averaged contributions have been taken into account for linear and nonlinear polarizabilities. The linear coupling model is applied to simulate vibronic profiles of optical absorption spectra. The computational strategies described in this thesis are very useful for the design of efficient molecular photonic materials. More specifically, the nonmonotonic behavior of the solvatochromic shifts and the first hyperpolarizability of para-nitroaniline (pNA) with respect to the polarity of the solvents have been theoretically confirmed for the first time. The significant contributions of the hydrogen bonding on the electronic structures of pNA are revealed. Vibrational contributions to the linear and nonlinear polarizabilities of methanol, ethanol and propanol have been calculated both at the static limit and in dynamic optical processes. The importance of vibrational contributions to certain nonlinear optical processes have been demonstrated. A series of end-capped triply branched dendritic chromophores have been studied with the result that their second order nonlinear optical properties are found strongly dependent on the mutual orientations of the three chromophores, numbers of caps and the conjugation length of the chromophores. Several possible mechanisms for the origin of the Q-band splitting of aluminum phthalocyanine chloride have been examined. Calculated vibronic one-photon absorption profiles of two molecular systems are found to be in very good agreement with the corresponding experiments, allowing to provide proper assignments for different spectral features. Furthermore, effects of vibronic coupling in the nonradiative decay processes have been considered which helps to understand the aggregation enhanced luminescence of silole molecules. The study of molecular aggregation effects on two-photon absorption cross sections of octupolar molecules has highlighted the need to use a hybrid method that combines density functional response theory and molecular dynamics simulations for the design of molecular materials. / QC 20100820