QC 20110520

α-helical membrane proteins constitute 20-30% of all proteins in a cell and are involved in many essential cellular functions. The structure is only known for a few hundred of them, which makes structural models important. The most common structural model of a membrane protein is the topology which is a two-dimensional representation of the structure. This thesis is focused on three different aspects of membrane protein structure: improving structural predictions of membrane proteins, improving the level of detail of structural models and the concept of dual topology. It is possible to improve topology models of membrane proteins by including experimental information in computer predictions. This was first performed in Escherichia coli and, by using homology, it was possible to extend the results to 225 prokaryotic organisms. The improved models covered ~80% of the membrane proteins in E. coli and ~30% of other prokaryotic organisms. However, the traditional topology concept is sometimes too simple for complex membrane protein structures, which create a need for more detailed structural models. We created two new machine learning methods, one that predicts more structural features of membrane proteins and one that predicts the distance to the membrane centre for the amino acids. These methods improve the level of detail of the structural models. The final topic of this thesis is dual topology and membrane protein evolution. We have studied a class of membrane proteins that are suggested to insert either way into the membrane, i.e. have a dual topology. These protein families might explain the frequent occurrence of internal symmetry in membrane protein structures.

The current thesis deals with one important branch of the physics of ultrafast processes, namely modeling of femtosecond nuclear dynamics. We suggest a new type of time resolved spectroscopy, the phase sensitive infrared-x-ray pump probe spectroscopy, which combines rich opportunities of IR laser techniques in quantum control of molecular systems with the site selectivity of x-rays. We have developed and applied a dynamical theory of x-ray pump-probe spectroscopy to study different molecular systems. Special attention is paid to design of the wave packets of desirable shape and spectral composition. Such a quantum control of the nuclear wave packet enables the study of molecular properties in regions that are unavailable by standard x-ray spectroscopies. The IR - x-ray pump probe spectroscopy is nicely suited to perform mapping of wave packet trajectories, to study revival phenomena, femtosecond chemical dynamics, and proton transfer, to mention a few examples. Our simulations show that the phase of the infrared pulse strongly influences the trajectory of the nuclear wave packet, and hence, the x-ray spectrum. Such a dependence is caused by the transfer of the phase of the IR field to the wave packet through the interference of the one (x-ray) and two-photon (IR + x-ray) excitation channels. The time resolved x-ray spectra are sensitive to the shape, duration and delay time between the pulses. The phase of the IR pulse influences the molecular dynamics also when the Rabi period becomes comparable with the period of vibrations, breaking down the rotating wave approximation. We predict a phase memory effect which is a promising technique in studies of chemical dynamics on different time scales. It is shown that the final state interaction with the pump affects the probe spectrum when the pump and probe pulses overlap. In a further step, we explore the electronic recoil effect in x-ray photoelectron spectroscopy, which has recently attracted attention of experimentalists due to its sensitivity to intramolecular interaction. We show that an IR field enhances the manifestation of the recoil effect through the formation of extensive vibrational wave packets. The theory of x-ray Raman scattering from molecules with strong spin-orbit coupling accompanied by electron-hole interaction is developed and applied to simulations of resonant x-ray Raman scattering of the HCl molecule. Special attention is paid to the theoretical methodologies to reduce the computational cost of our wave packet codes. / QC 20100825

Diss. (sammanfattning) Linköping : Univ., 2004. / Härtill 6 uppsatser.

Diss. (sammanfattning) Stockholm : Stockholms universitet, 2009.

No description available.

The present thesis is concerned with the theoretical studies on artificial water splitting process. As the quick development of research on utilizing of solar energy, which is a green, clean, and renewable energy source, many research groups focus their attention on artificial photo-synthesis systems inspired by the photosystem I and II. The overall reaction in these artificial systems is water splitting to oxygen and hydrogen. Artificial water splitting can generally be divided into two half reactions, catalytic water oxidation and catalytic proton reduction. There is an increasing interest and demand to understand the detailed mechanism of these two key parts. Since DFT (density functional theory) in particular, has proven to be a powerful and popular tool in exploring reaction mechanisms, B3LYP and M06 functionals were employed to provide a theoretical explanation of these two important reactions in this thesis. For water oxidation reaction, many efficient Water Oxidation Catalysts (WOCs) based on Ru, Ir, etc., have been reported over the last several years. The discovery of mononuclear ruthenium WOCs carrying anionic ligands is one of the major breakthroughs recently. WOCs bearing anionic ligands are able to efficiently drive catalytic water oxidation with relatively higher Turnover Numbers (TON) and Turnover Frequencies (TOF). Therefore the influence of anionic ligands gained our attention. We decided to carry out a detailed investigation on this effect, and try to propose a full mechanism of this catalytic water oxidation as well. We found that 1) The anionic ligands exert a promoting influence on the ligand exchange between picoline and water, which facilitates the formation of aqua-Ru complex, 2) The anionic ligands facilitate the complex access to higher oxidation states, which is necessary for the OO bond formation, and 3) The work of OO bond formation is in progress. For the proton reduction reaction, the transport or movement of protons is vital and interesting in many biological and chemical processes, including the hydrogen uptake/production, the reduction of CO2 to formate, and the reduction of O2 to water. It is often related to energy storage and utilization. However, the details of these processes are still ambiguous. In most natural hydrogenase enzymes or synthetic catalysts based on iron or nickel, the incorporation of a pendant amine is a frequently occurring feature. This internal amine base seems to facilitate this proton transfer by acting as a proton relay. Our calculated results showed that the internal base allows for a splitting of one high enthalpy-high entropy barrier into two: one with a high enthalpy-low entropy barrier and the other with a low enthalpy-high entropy barrier, resulting in a low free energy of activation for proton transfer. Our results can serve as a guideline in the development of new catalysts, not only for proton reduction catalysts, but also for any process that involves proton transfer from a metal hydride to an external base, such as C-H activation and functionalization catalysts. A thorough understanding on the mechanism of water splitting can help generate a strategy to enhance the catalytic performance on both water oxidation and proton reduction. We can tune or modify the synthetic complex by accelerating the slow step (rate-determining step) in the overall catalytic cycle, and can construct artificial water splitting systems with improved performance. / <p>QC 20120920</p>

This thesis deals with two disjoint subdiciplines of quantum chemistry.  One isthe most used electronic structure method today, density functional theory(DFT), and the other one of the least used electronic structure methods,valence bond theory (VB).  The work on DFT is based on previous developments inthe department in density functional response theory and involves studies ofhyperfine coupling constants which are measured in electron paramagneticresonance experiments.  The method employed is a combination of arestricted-unrestriced approaches which allows for adequate description of spinpolarization without spin contamination, and spin-orbit corrections to accountfor heavy atom effects useing degenerate perturbation theory.  The work anvalence bond theory is a new theoretical approach to higher-order derivatives.The orbital derivatives are complicated by the fact that the wave functions areconstructed from determinants of non-orthogonal orbitals. An approach based onnon-orthogonal second-quantization in biorthogonal basis sets leads tostraightforward derivations without explicit references to overlap matrices.These formulas are relevant for future applications in time-dependent valencebond theory. / QC 20101006

A very important trend for studying biomolecules is computational chemistry. In particular, nowadays it is possible to use theoretical methods to figure out the catalytic mechanism of enzyme reactions. Quantum chemistry has become a powerful tool to achieve a description of biological processes in enzymes active sites and to model reaction mechanisms. The present thesis uses Density Functional Theory (DFT) to investigate catalytic mechanism of methyltransferase enzymes. Two enzymes were studied – Glycine N-MethylTransferase (GNMT) and Guanidinoacetate Methyltransferase (GAMT). Different models of the enzyme active sites, consisting of 20 to 100 atoms, are employed. The computed energetics are compared and are used to judge the feasibility of the reaction mechanisms under investigation. For the GNMT enzyme, the methyl transfer reaction was found to follow an SN2 reaction mechanism. The calculations demonstrate that the mechanism is thermodynamically reasonable. Based on the calculations it was concluded that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to carboxylate group raise the barrier. In the GAMT enzyme the methyl transfer reaction was found to follow a concerted asynchronous mechanism which includes transfer of a methyl group accompanied by a proton transfer taking place simultaneously in the same kinetic step. The calculated barrier agrees well with the experimental rate constant. i / QC 20101124

<p>The present thesis is devoted to theoretical studies of light pulse propagation through different linear and nonlinear media. One dimensional holographic photonic crystals and one dimensional impurity band based photonic crystals are investigated as linear media. The effects of angular dependence of the band structures and pulse delay with respect to the light polarization are analyzed. A strict theory of nonlinear propagation of a few strong interacting light beams is presented and applied in the field of nonlinear optics. The key idea of this approach is a self-consistent solution of the nonlinear wave equation and the density matrix equations of the material beyond the so-called rotating wave approximation. The results of numerical studies led to a successful interpretation of recent experimental data [<i>Nature</i>, 415:767, 2002]. A theoretical study of the NO molecule by means of two-color infrared -- X-ray pump probe spectroscopy is presented. It was found that the phase of the infrared field strongly influences the trajectory of the nuclear wave packet, and hence, the X-ray spectrum. The dependence of the X-ray spectra on the delay time, the duration and the shape of the pulses are studied.</p>