I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

The Design and Synthesis of Transition Metal Complexes Supported by Non-innocent Ligand Scaffolds for Small Molecule Activation

This dissertation focuses on the incorporation of non-innocent or multifunctional moieties into different ligand scaffolds to support one or multiple metal centers in close proximity. Chapter 2 focuses on the initial efforts to synthesize hetero- or homometallic tri- or dinuclear metal carbonyl complexes supported by para-terphenyl diphosphine ligands. A series of [M₂M’(CO)₄]-type clusters (M = Ni, Pd; M’ = Fe, Co) could be accessed and used to relate the metal composition to the properties of the complexes. During these studies it was also found that non-innocent behavior was observed in dinuclear Fe complexes that result from changes in oxidation state of the cluster. These studies led to efforts to rationally incorporate central arene moieties capable managing both protons and electrons during small molecule activation.

Chapter 3 discusses the synthesis of metal complexes supported by a novel para-terphenyl diphosphine ligand containing a non-innocent 1,4-hydroquinone moiety as the central arene. A Pd⁰-hydroquinone complex was found to mediate the activation of a variety of small molecules to form the corresponding Pd⁰-quinone complexes in a formal two proton ⁄ two electron transformation. Mechanistic investigations of dioxygen activation revealed a metal-first activation process followed by subsequent proton and electron transfer from the ligand. These studies revealed the capacity of the central arene substituent to serve as a reservoir for a formal equivalent of dihydrogen, although the stability of the M-quinone compounds prevented access to the PdII-quinone oxidation state, thus hindering of small molecule transformations requiring more than two electrons per equivalent of metal complex.

Chapter 4 discusses the synthesis of metal complexes supported by a ligand containing a 3,5-substituted pyridine moiety as the linker separating the phenylene phosphine donors. Nickel and palladium complexes supported by this ligand were found to tolerate a wide variety of pyridine nitrogen-coordinated electrophiles which were found to alter central pyridine electronics, and therefore metal-pyridine π-system interactions, substantially. Furthermore, nickel complexes supported by this ligand were found to activate H-B and H-Si bonds and formally hydroborate and hydrosilylate the central pyridine ring. These systems highlight the potential use of pyridine π-system-coordinated metal complexes to reversibly store reducing equivalents within the ligand framework in a manner akin to the previously discussed 1,4-hydroquinone diphosphine ligand scaffold.

Chapter 5 departs from the phosphine-based chemistry and instead focuses on the incorporation of hydrogen bonding networks into the secondary coordination sphere of [Fe₄(μ₄-O)]-type clusters supported by various pyrazolate ligands. The aim of this project is to stabilize reactive oxygenic species, such as oxos, to study their spectroscopy and reactivity in the context of complicated multimetallic clusters. Herein is reported this synthesis and electrochemical and Mössbauer characterization of a series of chloride clusters have been synthesized using parent pyrazolate and a 3-aminophenyl substituted pyrazolate ligand. Efforts to rationally access hydroxo and oxo clusters from these chloride precursors represents ongoing work that will continue in the group.

Appendix A discusses attempts to access [Fe₃Ni]-type clusters as models of the enzymatic active site of [NiFe] carbon monoxide dehydrogenase. Efforts to construct tetranuclear clusters with an interstitial sulfide proved unsuccessful, although a (μ₃-S) ligand could be installed through non-oxidative routes into triiron clusters. While [Fe₃Ni(μ₄-O)]-type clusters could be assembled, accessing an open heterobimetallic edge site proved challenging, thus prohibiting efforts to study chemical transformations, such as hydroxide attack onto carbon monoxide or carbon dioxide coordination, relevant to the native enzyme. Appendix B discusses the attempts to synthesize models of the full H-cluster of [FeFe]-hydrogenase using a bioinorganic approach. A synthetic peptide containing three cysteine donors was successfully synthesized and found to chelate a preformed synthetic [Fe₄S₄] cluster. However, efforts to incorporate the diiron subsite model complex proved challenging as the planned thioester exchange reaction was found to non-selectively acetylate the peptide backbone, thus preventing the construction of the full six-iron cluster.

Los artefactos retocados del nivel C4d1j de Isturitz: estudio arqueopetrológico desde la Tipología Analítica

Homenaje a Georges Laplace, realizado en Vitoria-Gasteiz el 13, 14 y 15 de noviembre de 2012. Edición a cargo de Aitor Calvo, Aitor Sánchez, Maite García-Rojas y Mónica Alonso-Eguíluz.

Isotope shift studies in the rare earths and lead

Isotope shifts of K_α1 x-ray transitions were measured for the Neodymium isotopes Nd 142, 143, 144, 145, 146, 148 and 150, the Samarium isotopes Sm 147, 148, 149, 150, 152 and 154, the Gadolinium isotopes Gd 154, 155, 156, 157, 158 and 160, the Dysprosium isotopes Dy 162 and 164, the Erbium isotopes Er 166, 168 and 170, the Hafnium isotopes Hf 178 and 180 and the Lead isotopes Pb 204, 206, 207 and 208. A curved crystal Cauchois spectrometer was used. The analysis of the measurement furnished the variation of the mean square charge radius of the nucleus, δ˂r²˃, for 23 isotope pairs. The experimental results were compared with theoretical values from nuclear models. Combining the x-ray shifts and the optical shifts in Nd and Sm yielded the optical mass shifts. An anomaly was observed in the odd-even shifts when the optical and the x-ray shifts were plotted against each other.

轴向为烷氧基配位的萘酞菁硅配合物的光谱及光稳定性

研究了4种轴向为烷氧基配位的萘酞菁硅配合物（NcSi（OR）2，R为CH3、C2H3、C3H7和C4H9）在DMSO、DMF、CH2Cl2中的Q带吸收光谱和光降解动力学及其稳定性。研究结果表明，这4种萘酞菁配合物在相同溶剂中随着轴向配位烷氧基碳链的增长其最大吸收波长逐渐增加，并且在DMSO、CH2Cl2溶剂中随着轴向配位烷氧基碳链的增长光稳定性逐渐增强；对于同一配合物，溶剂对其光稳定性影响顺序为：DMSO〉CH2Cl2〉DMF。

Efeitos do uso de antiinflamatório e do exercício aeróbico sobre a regeneração tecidual e perfil biomecânico do tendão calcâneo de ratos após ruptura completa

Ruptura do tendão calcâneo é uma das lesões tendíneas mais frequentes. Embora a maioria dos trabalhos sugira que o exercício seja benéfico na cicatrização tendínea, não há consenso sobre o efeito do antiinflamatório neste contexto. Trabalhos experimentais tentam reproduzir lesão aguda deste tendão, em diferentes espécies animais. Neste estudo, descrevemos uma técnica de tenotomia completa do tendão calcâneo direito em ratos e, em seguida, avaliamos os efeitos do uso do antiinflamatório e do exercício aeróbico, isoladamente e em combinação, sobre a proliferação celular e o perfil biomecânico do tendão calcâneo, durante o processo de cicatrização após tenotomia. Estudo experimental com 156 ratos machos adultos, da raça Wistar, com idade média de 3 meses e peso médio de 300g. Após anestesia com tiopental e com auxílio da microscopia de luz, foi realizada incisão longitudinal posterior de cinco milímetros, em direção proximal, a partir da tuberosidade posterior do calcâneo da pata direita do rato. Foi feito corte transversal do tendão calcâneo, a sete milímetros da tuberosidade do calcâneo, com preservação do tendão plantar. Utilizamos as técnicas de Hematoxilina e Eosina, Picrosirius-red e Resorcina-fucsina de Weigert para avaliação da cicatrização tendínea e das fibras dos sistemas colágeno e elástico. Após a tenotomia, metade dos animais receberam tenoxicam intramuscular por 7 dias e no 8o dia iniciou-se protocolo de exercício em esteira na metade de cada grupo. Os ratos foram divididos aleatoriamente em 4 grupos de tratamento: A sem antiinflamatório E sem exercício (controle); B com antiinflamatório E com exercício; C sem antiinflamatório E com exercício; D com antiinflamatório E sem exercício. Os animais foram eutanasiados com 1, 2, 4 e 8 semanas após a tenotomia, para avaliação histológica pelo PCNA, e biomecânica através do teste de resistência à tração e da medida do ciclo locomotor. Foram realizados análise de variância, teste de Kruskal-Wallis e o método de Bonferroni, no programa R Project, versão 2.11.1. O tempo cirúrgico médio foi de 1 minuto e 24 segundos, sem complicações observadas até a 8a semana pós-operatória. Observamos proliferação celular e fibrilogênese com duas semanas, e diminuição da celularidade e das fibras elásticas na 8a semana, além de mudanças na organização estrutural do sistema colágeno. Encontramos pico da imunomarcação com PCNA na 2a semana em todos os grupos, exceto no grupo A, cujo pico aconteceu com 1 semana da tenotomia. Evidenciamos resistência à tração significativamente maior (p=0,02) nos ratos submetidos ao exercício, 8 semanas após ruptura. Nos grupos com antiinflamatório, observamos um ciclo locomotor mais estável durante todo o tempo avaliado. Consideramos a técnica cirúrgica experimental de tenotomia completa do tendão calcâneo, realizada com auxílio da microscopia de luz e preservação do tendão plantar, simples, rápida, com sinais de cicatrização tendínea normal e de fácil reprodução em ratos. O exercício aeróbico, iniciado precocemente após tenotomia completa do tendão calcâneo, é significativamente benéfico na sua recuperação biomecânica e o uso combinado com antiinflamatório confere maior estabilidade na marcha, o que pode proteger contra rerruptura tendínea em ratos

Alveolar nitric oxide and its role in pediatric asthma control assessment

Resumen Background: Nitric oxide can be measured at multiple flow rates to determine proximal (maximum airway nitric oxide flux; Jaw(NO)) and distal inflammation (alveolar nitric oxide concentration; CA(NO)). The main aim was to study the association among symptoms, lung function, proximal (maximum airway nitric oxide flux) and distal (alveolar nitric oxide concentration) airway inflammation in asthmatic children treated and not treated with inhaled glucocorticoids. Methods: A cross-sectional study with prospective data collection was carried out in a consecutive sample of girls and boys aged between 6 and 16 years with a medical diagnosis of asthma. Maximum airway nitric oxide flux and alveolar nitric oxide concentration were calculated according to the two-compartment model. In asthmatic patients, the asthma control questionnaire (CAN) was completed and forced spirometry was performed. In controls, differences between the sexes in alveolar nitric oxide concentration and maximum airway nitric oxide flux and their correlation with height were studied. The correlation among the fraction of exhaled NO at 50 ml/s (FENO50), CA(NO), Jaw(NO), forced expiratory volume in 1 second (FEV1) and the CAN questionnaire was measured and the degree of agreement regarding asthma control assessment was studied using Cohen's kappa. Results: We studied 162 children; 49 healthy (group 1), 23 asthmatic participants without treatment (group 2) and 80 asthmatic patients treated with inhaled corticosteroids (group 3). CA(NO) (ppb) was 2.2 (0.1-4.5), 3 (0.2-9.2) and 2.45 (0.1-24), respectively. Jaw(NO) (pl/s) was 516 (98.3-1470), 2356.67 (120-6110) and 1426 (156-11805), respectively. There was a strong association (r = 0.97) between FENO50 and Jaw(NO) and the degree of agreement was very good in group 2 and was good in group 3. There was no agreement or only slight agreement between the measures used to monitor asthma control (FEV1, CAN questionnaire, CA(NO) and Jaw(NO)). Conclusions: The results for CA(NO) and Jaw(NO) in controls were similar to those found in other reports. There was no agreement or only slight agreement among the three measure instruments analyzed to assess asthma control. In our sample, no additional information was provided by CA(NO) and Jaw(NO).

新型掺铒离子氧氟碲酸盐玻璃的光谱性质

探求新的具有优良的热学和光学性能的基质玻璃系统，是获得具有宽带宽和增益平坦的掺Er^3＋光纤放大器（EDFA）的一种有效途径。制备了一种新型氧氟碲酸盐玻璃TeO2-BaF2-LaF3，并对其热学性能和光学性质进行了测试。应用乍得-奥菲尔特（Judd-Ofelt）理论计算了Er^3＋离子的J-O理论参量和荧光寿命r。探讨了氟化物的引入对碲酸盐玻璃结构的改变的影响，并分析了其对玻璃的热学性质和光学性质的影响。实验发现，获得的氧氟碲酸盐玻璃具有优良的热学稳定性（△T=156.6C），宽的荧光半峰全宽（72nm）