NR 20140805

Results of ab initio and density functional theory calculations on the structure and vibrational frequencies of hypophosphite anion indicate earlier experimental assignments of the fundamental vibrational modes are correct while the recent reassignments of several modes proposed by Bickley et al. are inconsistent with the calculated 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.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24176号 / 理博第4867号 / 新制||理||1696(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)准教授 倉重 佑輝, 教授 谷村 吉隆, 教授 吉村 一良 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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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...

Os estudos de modelagem molecular das interações entre ligantes baseado em oxindóis (isaepy, isapn, [Cu(isapn)]², isaenim e o SU9516) e as proteínas kinases dependentes de ciclina (CDK1 e CDK2) são apresentados neste trabalho. Uma inibição na atividade da CDK1 e CDK2, que catalisam a fosforilação de grupos específicos em proteínas, tem implicações na indução da apoptose celular. O objetivo é tentar determinar qual destes ligantes potencializa a inibição da síntese de ATP (adenosina trifosfato) em ADP (adenosina difosfato) no sítio ativo da CDK1 e CDK2 para, desta forma, induzir a apoptose de células cancerígenas. Os estudos realizados neste trabalho indicam que dentre os ligantes analisados, o isaepy e o isapn obtiveram melhores resultados de estabilidade e ligações de hidrogênio entre aminoácidos dentro do sítio. Analisamos a influência do íon Cu no aumento da eficácia do isapn na atividade inibitória (complexo [Cu(isapn)]²) e comparamos os resultados obtidos dos estudos do isapn e [Cu(isapn)]², quando inseridos no sítio de ligação do ATP da CDK1, com medidas de eletroforese em gel. Verificamos que os nossos resultados foram corroborados com as medidas de eletroforese. Também discutimos os resultados de cálculos de acoplamento hiperfino para o Cu no [Cu(isapn)]² em diferentes ambientes químicos e fizemos a comparação destes resultados com medidas de EPR. Desta forma, conseguimos verificar o ambiente químico do íon Cu e um aumento da estabilidade do isapn dentro do sítio estudado com a inserção do íon Cu. Este trabalho visa contribuir para a síntese de novos ligantes que aumentem a eficácia da inibição da síntese de ATP em ADP nas CDKs e também para a minimização dos custos através da diminuição da realização de experimentos que se baseiam em métodos de tentativa e erro. / Molecular modeling studies of the interaction of oxindol based ligands (isaepy, isapn [Cu(isapn)]²,isaenim and SU9516) with Cyclin Dependent Kinases proteins (CDK1 and CDK2) are presented here. CDK1 and CDK2 catalyze the phosphorylation of specific groups in proteins and inhibition of its activities implies in induction of cancer cells apoptosis. The goal is to determine which ligands increase the inhibition of ATP (adenosine triphosphate) into ADP (adenosine diphosphate) synthesis which occurs inside the CDK1 and CDK2 active site. We analyze the influence of the Cu ion on increasing the inhibitory activity in isapn ([Cu(isapn)]² metal complex). Comparisons between the results obtained from studies of the isapn and [Cu(isapn)]² inserted into the ATP binding site of CDK1 with measurements of gel electrophoresis were performed. The hyperfine coupling at Cu ion in [Cu(isapn)]² in different chemical environments are here obtained and the results are compared with EPR measurements. This work aims to contribute to the development of new ligands which increase the inhibition of the synthesis of ATP into ADP in the CDKs moreover we aim to assist in the reduction of the costs of measurements that are based on trial and error aproaches.

Os estudos de modelagem molecular das interações entre ligantes baseado em oxindóis (isaepy, isapn, [Cu(isapn)]², isaenim e o SU9516) e as proteínas kinases dependentes de ciclina (CDK1 e CDK2) são apresentados neste trabalho. Uma inibição na atividade da CDK1 e CDK2, que catalisam a fosforilação de grupos específicos em proteínas, tem implicações na indução da apoptose celular. O objetivo é tentar determinar qual destes ligantes potencializa a inibição da síntese de ATP (adenosina trifosfato) em ADP (adenosina difosfato) no sítio ativo da CDK1 e CDK2 para, desta forma, induzir a apoptose de células cancerígenas. Os estudos realizados neste trabalho indicam que dentre os ligantes analisados, o isaepy e o isapn obtiveram melhores resultados de estabilidade e ligações de hidrogênio entre aminoácidos dentro do sítio. Analisamos a influência do íon Cu no aumento da eficácia do isapn na atividade inibitória (complexo [Cu(isapn)]²) e comparamos os resultados obtidos dos estudos do isapn e [Cu(isapn)]², quando inseridos no sítio de ligação do ATP da CDK1, com medidas de eletroforese em gel. Verificamos que os nossos resultados foram corroborados com as medidas de eletroforese. Também discutimos os resultados de cálculos de acoplamento hiperfino para o Cu no [Cu(isapn)]² em diferentes ambientes químicos e fizemos a comparação destes resultados com medidas de EPR. Desta forma, conseguimos verificar o ambiente químico do íon Cu e um aumento da estabilidade do isapn dentro do sítio estudado com a inserção do íon Cu. Este trabalho visa contribuir para a síntese de novos ligantes que aumentem a eficácia da inibição da síntese de ATP em ADP nas CDKs e também para a minimização dos custos através da diminuição da realização de experimentos que se baseiam em métodos de tentativa e erro. / Molecular modeling studies of the interaction of oxindol based ligands (isaepy, isapn [Cu(isapn)]²,isaenim and SU9516) with Cyclin Dependent Kinases proteins (CDK1 and CDK2) are presented here. CDK1 and CDK2 catalyze the phosphorylation of specific groups in proteins and inhibition of its activities implies in induction of cancer cells apoptosis. The goal is to determine which ligands increase the inhibition of ATP (adenosine triphosphate) into ADP (adenosine diphosphate) synthesis which occurs inside the CDK1 and CDK2 active site. We analyze the influence of the Cu ion on increasing the inhibitory activity in isapn ([Cu(isapn)]² metal complex). Comparisons between the results obtained from studies of the isapn and [Cu(isapn)]² inserted into the ATP binding site of CDK1 with measurements of gel electrophoresis were performed. The hyperfine coupling at Cu ion in [Cu(isapn)]² in different chemical environments are here obtained and the results are compared with EPR measurements. This work aims to contribute to the development of new ligands which increase the inhibition of the synthesis of ATP into ADP in the CDKs moreover we aim to assist in the reduction of the costs of measurements that are based on trial and error aproaches.

La spintronique est un nouveau domaine de recherche qui exploite l'influence de la caractéristique quantique de l’électron (le spin) sur la conduction électrique. Pour réaliser des composants de spintronique innovants, l’obtention des semi-conducteurs ferromagnétiques à température ambiante devenait un challenge international. Dans ce contexte, après les premières prédictions théoriques de la haute température de Curie de Zn1-xCoxO et les rapports contradictoires sur l'état magnétique de ce système, nous nous sommes attaché à étudier le semi-conducteur magnétique dilué Zn1-xCoxO. Une étude ab initio des propriétés structurales, électroniques et magnétiques du Zn1-xCoxO a été effectuée en utilisant la méthode de pseudopotentiels dans le cadre de la théorie de la fonctionnelle de la densité (DFT) avec les deux approximations GGA et GGA+U. En parallèle, des films minces de Zn1-xCoxO ont été synthétisés par co-pulvérisation cathodique magnétron en condition réactive avec différentes conditions d’élaboration. Les propriétés structurales, morphologiques, électriques et magnétiques ont été analysées par différentes techniques de caractérisation et confrontées à celles obtenues par l’étude ab inito. / Spintronic is a new field of research exploiting the effect of the quantum property of the electron (spin) on the electrical conduction. In order to realize innovative spintronic components, ferromagnetic semiconductors obtained at room temperature became an international challenge. In this context and following initial reports of high Curie temperature and contradictory reports on the magnetic states of this system, we investigated the diluted magnetic semiconductor Zn1-xCoxO. An ab initio study of structural, electronic and magnetic properties of Zn1-xCoxO was performed using the pseudopotentials method within the framework of density functional theory (DFT) with both GGA and GGA+U approximations. In parallel, thin films of Zn1-xCoxO were synthesised by reactive magnetron co-sputtering with different deposition conditions. The structural, morphological, electrical and magnetic properties were analyzed by various characterization techniques and compared with those obtained by ab inito study.