The cyclic nitrone 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), and the lesser known linear phenyl-N-tert-butylnitrone (PBN) and its phosphorylated analogues have been used as spin traps for the investigation of free radicals in biological systems. Theoretical work on these molecules suggests that there are important differences in their properties between biological systems and isolated molecules in the gas phase, most likely resulting from intra and intermolecular hydrogen bonding. Most dielectric solvation models such as the polarized continuum model and COSMO are incapable of direct determination of solvent-spin trap chemical interactions. To examine this, hybrid models incorporating COSMO for long range effects and discrete solvent molecules for short range effects, at the DFT/B3LYP/6-31G* level of theory, have been used to study the stabilization and alteration of the spin trap molecules properties in protic and aprotic polar solvents. The hybrid models have been successfully implemented to support the prominent role played by hydrogen bonding interactions in the stabilization of spin traps.

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Two computer simulation studies were performed; one to help understand the structure-function relationships of prolyl peptides (Part I) and the other to help predict more efficient pharmaceutical drug delivery by molecular modification of small peptides (Part II). In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between <i>cis</i> and <i>trans</i> conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of <i>cis</i> to <i>trans</i> conformers was obtained. Our simulation generated much lower <i>%cis</i> for both peptides as compared with experimental values and possible problems in our computational schemes are presented. However, our results were encouraging in that they predicted preference of <i>trans</i> conformers for both peptides and higher <i>%cis</i> for Ace-Tyr-Pro-NMe, compared to Ace-Asn-Pro-NMe, which agrees with experimental results. Part II applied semi empirical (AMS0L) and microscopic simulation (POLARIS) methods to obtain the solvation free energies of a series of phenylalanyl peptides with various degrees of methylation on their backbone nitrogens. It was clearly predicted that as a peptide length increased, so solvation free energy decreased, indicating less favorable permeability through the cell membrane system, in agreement with data in the literature. AMSOL also showed that solvation free energy change upon methylation was variable depending on the position of the substituted backbone nitrogen, which disagrees with the literature. However, non-systematic solvation free energy change of small amines upon methylation was successfully predicted by AMSOL, in good accord with experimental data. / Master of Science

Solvation-thermodynamics models based on computational quantum mechanics, such as the conductor-like screening model (COSMO), provide a good alternative to traditional group-contribution methods for predicting thermodynamic phase behavior. Two COSMO-based thermodynamic models are COSMO-RS (real solvents) and COSMO-SAC (segment activity coefficient). The main molecule-specific input for these models is the sigma profile, or the probability distribution of a molecular surface segment having a specific charge density. Generating the sigma profiles represents the most time-consuming and computationally expensive aspect of using COSMO-based methods. A growing number of scientists and engineers are interested in the COSMO-based thermodynamic models, but are intimidated by the complexity of generating the sigma profiles. This thesis presents the first free, open-literature database of 1,513 self-consistent sigma profiles, together with two validation examples. The offer of these profiles will enable interested scientists and engineers to use the quantum-mechanics-based, COSMO methods without having to do quantum mechanics. This thesis summarizes the application experiences reported up to October 2004 to guide the use of the COSMO-based methods. Finally, this thesis also provides a FORTRAN program and a procedure to generate additional sigma profiles consistent with those presented here, as well as a FORTRAN program to generate binary phase-equilibrium predictions using the COSMO-SAC model. / Master of Science

京都大学 / 新制・課程博士 / 博士(工学) / 甲第25287号 / 工博第5246号 / 京都大学大学院工学研究科材料工学専攻 / (主査)教授 杉村 博之, 教授 邑瀬 邦明, 准教授 小林 圭 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

<p>The copper-binding ability of the prion protein may be closely connected to its function. Identifying the exact function of the prion protein can clarify the underlying mechanism in prion diseases. In this work, the copper-binding octapeptide region in the human prion protein has been studied. The structural characteristics of the binding site are examined by quantum chemical structural optimization. The calculations aim at identifying a substitute for copper(II) to be used in NMR-spectroscopic studies of the copper-binding region. The dynamical and structural features of the peptide region are investigated in molecular dynamics simulations. Aspects of importance in the development of model systems in molecular dynamics simulation are addressed.</p>

<p>The electronic and geometrical structure of free neutral clusters and liquids have been studied using synchrotron-radiation based photoelectron and Auger electron spectroscopy in combination with lineshape modeling. A novel experimental setup has been developed for studies of liquids, based on the liquid microjet technique. Theoretical lineshapes have been computed using both classical (molecular dynamics) and quantum mechanical (mainly density functional theory) methods.</p><p>Clusters are finite ensembles of atoms or molecules, ranging in size from a few to several thousand atoms. Apart from being fundamentally interesting, clusters are also promising as building blocks for nano-technology. In this thesis results are presented for rare-gas and molecular clusters, ranging from weakly van-deer-Waals bonded to hydrogen bonded. It is shown that the combination of core-level photoelectron spectroscopy (XPS) and lineshape modeling can be used to estimate the sizes of clusters. A model for treating the effect of inter-molecular nuclear relaxation upon ionization is proposed. The structure of single-component molecular clusters are investigated by molecular dynamics simulations, validated against XPS data. Finally, the radial structure of a two-component molecular cluster is investigated by XPS.</p><p>Liquids have been studied for centuries, but still many questions remain regarding the microscopic properties. With the recent development of the liquid microjet technique, new insight into the atomic structure can be obtained. In this thesis we study aqueous solutions using photoelectron and Auger electron spectroscopy (AES). We investigate the structure of surface active molecules by XPS, study the Auger decay after core-level ionization in aqueous potassium chloride (KCl), and follow the changes in molecular structure of glycine as a function of pH.</p>

Title: Solvent effects on ion pairing and photoionization in water Author: Mgr. et Ing. Eva Pluhařová Department: Physical and Macromoleculer Chemistry Advisor: Prof. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: Various methods of theoretical chemistry, namely classical molecular dynamics simulations with empirical force fields, ab initio molecular dynamics, enhanced sampling methods, and ab initio calculations were used to provide new insight into ion pairing and photoionization in aqueous solutions. Systems mod- eling aqueous solutions of decreasing size were investigated by computational methods of increasing level of sophistication. In a classical molecular dynamics study of concentrated lithium salt solutions, the electronic continuum correction to account for polarization provided qualita- tive improvement over the conventional non-polarizable force fields and enabled molecular interpretation of neutron scattering measurements. The same model- ing approach was also successful in predicting the affinity of halide ions to the solution/oil interface. By combining ab initio molecular dynamics and potential of mean force cal- culations, we designed a reliable computational protocol for calculating the free energy profile for an ion pair...

Molecular modelling has become a well-established tool for studying biological mole- cules, moreover with the prospect of being useful for drug development. The thesis summarises research on the methodological advances in the treatment of molecular flexibility and intermolecular interactions. Altogether, seven original publications are accompanied by a text which aims to provide a general introduction to the topic as well as to emphasise some consequences of the computer-aided drug design. The molecular flexibility is tackled by a study of a drug-DNA interaction and also by an investigation of small drug molecules in the context of implicit solvent models. The approaches which neglect the conformational freedom are probed and compared with experiment in order to suggest later, how to cope with such a freedom if in- evitable. The noncovalent interactions involving halogen atoms and their importance for drug development are briefly introduced. Finally, a model for a faithful description of halogen bonds in the framework of molecular mechanics is developed and its per- formance and limits are tested by a comparison with benchmark ab initio calculations and experimental data. 1