A series of complexes of the type [Rh(diphos)(C(_7)H(_8))](BF(_4)) (1) have been synthesised and two of these species [diphos = Bu(^1)(_2)P(CH(_2))(_2)PBu(^1)(_2), Cy(_2)P(l,2-trans-cyclopentane)PCy(_2)] have been characterised by X-ray crystallography. The influence of the chelating diphosphine on the structural characteristics and NMR parameters of these compounds has been investigated. Complexes of the type (1) are active catalysts for the hydroformylation of l-hexene(120ºC, 450psi 2:1 H(_2):C0). However, they are inactive for the related hydroesterification process and this is attributed to the stability of [Rh(diphos)(CO)(_2)]^ under the reaction conditions. Detailed studies of the reactions of type (1) complexes with H(_2) have been undertaken. The products from these reactions are dependent on both the diphosphine and the solvent employed. In THF and CD(_2)Cl(_2), dimeric hydrides were observed, whilst in CDCl(_3) hydrido-chloro-complexes of the type [Rh(_z)(diphos)(_2)(|µCl)H(_2)](^2+) were formed. In the former solvents, three types of hydrides have been identified by NMR studies, namely [Rh(_2)(diphos)(_2)H(_6)], [Rh(_2)(diphos)(_2)H(_4)] and [Rh(_2)(diphos)(_2)H(_4)](^2+). The oxidative-addition reactions of alkyl-, acyl- and formyl-halide with Rh(I) complexes have been investigated. The reaction with ClCO(_2)Me with [Rh(dppe)Cl](_2) and [Rh(dppe)](_2)(BF(_4))(_2) led to the formation of diphosphine-rhodium(III)-halide species (H(_3)NOH)[Rh(dppe)Cl(_4)] and [Rh(_2)(dppe)(_2)(µ-Cl)(_3)Cl(_2)](BF(_4)) respectively. Alternative routes to these complexes have been investigated starting from RhCl(_3).3H(_2)O/diphosphines and a series of the novel halide bridged dimers have been characterised, including by X-ray crystallography and their reaction chemistry explored. In the synthesis of the cationic rhodium complexes from neutral chloro-complexes with AgBF(_4), the novel silver complexes [Ag(_2)(µ-Bu(^t)(_2)P(CH(_2))(_3)PBu(^t)(_2))(_2)](BF(_4))(_2), [{Ag(H(_2)O)}(_2)(µ-Bu(^t)(_2)P(CH(_2))(_2)PBu(^t)(_2))](BF(_4))(_2), and [Ag(C(_6)D(_6))(_3)BF(_4)] have been isolated as by-products and characterised by X-ray crystallography.

Nucleic acids are responsible for the storage of genetic information and directly participate in gene replication, transcription and expression, and thereby the control of nucleic acids leads to the regulation of genetic information flow and gene expression. Meanwhile, many non-coding RNAs are in-volved in signal transduction directly. Moreover, nucleic acid-based therapeutic strategies have been lead to drug candidates and are effective tools in drug discovery and disease study at the molecular level as well as the genetic level. Consequently, the 3D crystal structure study and related functional research on natural and unnatural nucleic acids have become very popular area, expanding their potential appli-cation in medicinal and biological chemistry. Since oxygen, sulfur, selenium and tellurium are in the same elemental family (VIA) in the peri-odic table, we anticipate that oxygen atoms in nucleic acids can most likely be replaced with the other chalcogen atoms without causing significant perturbations. Owing to the special K edge and unique properties of selenium, our lab has completed the chemical and enzymatic synthesis of unnatural nucle- ic acids with selenium substitutions at various positions. The selenium functionality in nucleic acid is es-sential for nucleic acids’ structural determination at the atomic level. Additionally this novel elemental feature (atomic size and electronic nature) provides nucleic acids with unique properties. In addition, the selenium derivatization can facilitate crystal growth. Other chalcogen elements are applicable as well to modify nucleic acid, generating some special biofunctions, like the application of phosphorthioate oligonucleotide in gene therapy. This dissertation will outline the chalcogen elements (especially selenium) modifications of nucleic acids, including syntheses strategies, structure studies and potential therapeutic applications. Our research work here tries to show that (1) Selenium functionality is able to facilitate the crystal structure determination, by both helping solve phase problem and accel-erating crystal growth; (2) Selenium functionality can generate special capability to nucleic acids, like improved base pair fidelity, novel atomic interactions and feasibility to be biological chemistry probe; (3) Selenium derivatized oligonucleotides are extraordinary good candidates for gene therapy discovery, considering its stability under nuclease environment. In general, these atom-specific replacements gen-erate a new paradigm of nucleic acids. INDEX WORDS: Nucleic acid, Selenium, X-ray crystal structure, Biofunction, Therapeutics

Reaction of the thiosemicarbazone ligands, [4-(p-bromophenyl)thiosemicarbazone of salicylaldehyde (H2L1), 4-(p-X-phenyl)thiosemicarbazone of o-vanillin {X = F (H2L2), X = Cl (H2L3) and X = OMe (H2L4)}, 4-(p-bromophenyl)thiosemicarbazone of 5-bromosalicylaldehyde (H2L5), and 4-(p-chlorophenyl)thiosemicarbazone of o-hydroxynaphthaldehyde (H2L6)] with [MoO2(acac)2] afforded a series of new oxidomolybdenum(VI) complexes [Mo(VI)O2L1–6(solv)] (1–6) {where solv (solvent) = DMSO (1, 3, 5 & 6) and H2O (2 & 4)}. The molecular structures of 2 and 3 were determined by X-ray crystallography, demonstrating the dibasic tridentate behavior of ligands. The cyclic voltammogram pattern is similar for 1–6, which includes two irreversible reduction processes within the potential window −0.71 to −0.66 V and −0.92 to −0.85 V corresponding to the metal centered reduction from Mo(VI)/Mo(V) and Mo(V)/Mo(IV) respectively. Catalytic potential of 1–6 was tested for the oxidation of styrene and cyclohexene. The effect of various parameters such as the amount of catalyst, oxidant, NaHCO3, and solvent was checked to optimize the conditions for the best performance of the catalyst. 100% product selectivity for the formation of cyclohexene oxide from cyclohexene and ∼98–99% product selectivity for the oxidation of styrene to styrene oxide was observed.

Five novel compounds were synthesized and characterized. Crystal structures were determined using Rigaku Mercury 375/MCCD(XtaLAB mini) diffractometer with graphite monochromated MoKα radiation. The crystal structures of [Rh2(NPhCOCH3)4•xNCC6H4R where x = 1 or 2 and R=H, 2-CH3,3-CH3 and 4-CH3 were solved to an R1 value of less than 5 (R1= Σ||Fo| - |Fc|| / Σ |Fo|). In each of the nitrile complexes, the rhodium is five or six coordinate and possesses pseudo D4h symmetry. The complexes were also characterized by NMR and IR spectroscopy. [Rh2(CO2CCH3)(PhCOCF3)3] was also synthesized. In this complex, each rhodium atom is six coordinate, thus each rhodium is in an octahedral environment. Details of each synthesized complex are discussed.

Orientador: Luis Eduardo Soares Netto / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-14T00:45:19Z (GMT). No. of bitstreams: 1 Discola_karenFulan_D.pdf: 5792872 bytes, checksum: ee9797756e3c67c12d00e2c76271feee (MD5) Previous issue date: 2009 / Resumo: Glutarredoxinas (Grxs) são pequenas oxidorredutases que possuem pelo menos um resíduo de cisteína conservado em seus sítios ativos e têm atividade dissulfeto redutase dependente de tiol. Embora Grxs estejam envolvidas em diversos processos celulares, como enovelamento protéico e proteção contra espécies reativas de oxigênio, poucos substratos biológicos dessas enzimas são conhecidos. Na levedura Saccharomyces cerevisiae, oito Grxs foram identificadas (ScGrx1-8); destas ScGrx1-2 são ditiólicas e possuem o motivo Cys-Pro-Tyr-Cys em seus sítios ativos. Ambas Grxs ditiólicas são citosólicas, embora ScGrx2 também seja encontrada na mitocôndria. Neste trabalho, mostramos que ScGrx2 possui atividade específica como oxidorredutase quinze vezes maior do que ScGrx1, embora estas enzimas compartilhem 64% de identidade e 85% de similaridade de seqüência. A análise cinética bi-substrato mostrou que ScGrx2 possui tanto um menor KM para glutationa quanto um maior turnover que ScGrx1. Com o intuito de compreender melhor estas diferenças bioquímicas, determinamos os valores de pKa da cisteína N-terminal (Cys27) dos sítios ativos destas duas proteínas e demonstramos que estes parâmetros não justificam a diferença de atividade observada. Tentando identificar características estruturais relacionadas a essa diferença de atividade, determinamos as estruturas cristalográficas de ScGrx2 na forma oxidada e do mutante ScGrx2-C30S ligado à glutationa a 2.05 e 1.91 Å de resolução, respectivamente, e comparamos estas estruturas com as estruturas de ScGrx1 descritas por Håkansson & Winther, 2007. As análises estruturais nos permitiram formular a hipótese de que substituições dos resíduos Ser23 e Gln52 de ScGrx1 por Ala23 e Glu52 em ScGrx2 poderiam modificar a capacidade da cisteína C-terminal do sítio ativo de atacar o dissulfeto misto formado entre a cisteína Nterminal e glutationa. Nossa hipótese foi testada através de ensaios enzimáticos com proteínas mutantes. Acreditamos que as diferenças funcionais e estruturais observadas entre ScGrx1 e ScGrx2 possam refletir em variações na especificidade por substratos e indicam que estas enzimas possuem funções biológicas não redundantes em S. cerevisiae. / Abstract: Glutaredoxins (Grxs) are small thiol-dependent oxidoreductases with disulfide reductase activity endowed by at least one cysteine at their active sites. Although Grxs are implicated in many cellular processes, including protein folding and protection against reactive oxygen species, few of their targets are known. In the yeast Saccharomyces cerevisiae, eight Grxs isoforms were identified (ScGrx1-8). Two of them (ScGrx1-2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Both dithiol glutaredoxins are cytosolic, however ScGrx2 is also located at the mitochondria. In spite of the fact that ScGrx1 and ScGrx2 share 85% of amino acid sequence similarity, we have shown that ScGrx2 is fifteen times more active as oxidoreductase than ScGrx1. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that ScGrx2 possesses both a lower KM for glutathione and a higher turnover than ScGrx1. To better comprehend these biochemical differences, the pKa of the N-terminal active site cysteines (Cys27) of these two proteins were determined. Since the pKa values of ScGrx1 and ScGrx2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. In an attempt to better understand the mechanisms and differences between yeast dithiol Grxs activities, we elucidated the crystallographic structures of ScGrx2 in the oxidized state and of the ScGrx2-C30S mutant with a glutathionyl mixed disulfide at resolutions of 2.05 and 1.91 Å, respectively. Comparisons among these structures and those of ScGrx1 (Håkansson & Winther, 2007) provided insights into the remarkable functional divergence between these enzymes. We hypothesize that the substitutions of Ser23 and Gln52 in ScGrx1 by Ala23 and Glu52 in ScGrx2 can modify the capability of the active site C-terminal cysteine to attack the mixed disulfide between the N-terminal active site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between ScGrx1 and ScGrx2 may reflect variations in substrate specificity and non-redundant biological functions. / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18344号 / 農博第2069号 / 新制||農||1024(附属図書館) / 学位論文||H26||N4851(農学部図書室) / 31202 / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

A new cyanoscorpionate - tris(4-cyano-3,5-diphenylpyrazolyl)borate (TpPh2,4CN) has been synthesized and characterized. The thallium complex of this ligand TlTpPh2,4CN has also been prepared and characterized by FT-IR, 1H NMR, and single-crystal X-ray-diffraction. The complex TlTpPh2,4CN crystalized in the monoclinic space group C2/c with unit cell a = 14.6697(10) Å, b = 13.9493(10) Å, c = 19.3347(12) Å, and b= 91.761(2)°. Structural comparison of TlTpPh2,4CN with analogous complexes demonstrated the effects of both steric and electron-withdrawing substituents on coordination geometry and the electronic properties of the metal ion. There were short contacts between the cyano groups and neighboring thallium ions that also indicated the ligand’s potential to form coordination polymers.

The research presented in this thesis focused on pseudorotaxanes and supramolecular polymers based on a new recognition motif, the dibenzo-24-crown-8/paraquat recognition motif. Main kinds of pseudorotaxanes and rotaxanes and various protocols used for the study of them were discussed first. By preparation and characterization of a series of pesudorotaxanes based on DB24C8 and paraquat derivatives, it was found that these complexes were stabilized by N+...O interactions, C-H...O hydrogen bonding, and face-to-face p-stacking interactions. Because methyl protons of paraquat are involved in hydrogen bonding to the host, the substitution of any methyl hydrogen on paraquat causes apparent association constant of the pseudorotaxane to decrease. The concentration dependence of apparent association constants, Ka,exp, of fast exchange host-guest systems was studied for the first time by using complexes based on viologens and crown ethers as examples. While the bis(hexafluorophosphate) salts of paraquat derivatives are predominantly ion paired in acetone (and other low dielectric constant solvents presumably) the complex based on dibenzo-24-crown-8 and paraquat is not ion paired in solution, resulting in concentration dependence of Ka,exp. However, four complexes of two different bis(m-phenylene)-32-crown-10 (BMP32C10) derivatives and bis(p-phenylene)-34-crown-10 (BPP3C10) with viologens are ion paired in solution, as shown by the fact that Ka,exp is not concentration dependent for these systems involving hosts with freer access to bound guests. X-ray crystal structures support these soluton-based assessments in that there is clearly ion pairing of the cationic guest and its PF6- counterions in the solid states of the latter four examples, but not in the former. The complexes based on the new dibenzo-24-crown-8/paraquat recognition motif are thus different from the complexes based on two old recognition motifs: the BPP34C10/BMP32C10-paraquat and DB24C8-ammonium motives. In order to compare these recognition motives further, the selectivity between two hosts, DB24C8 and BPP34C10, and two guests, dimethyl paraquat and dibenzyl ammnonium salt, was discussed. By individual and competitive complexation studies, it was demonstrated that DB24C8 is a better host than BPP34C10 for paraquat, and that paraquat is a better guest than dibenzyl ammonium salt for DB24C8. Finally the DB24C8-paraquat recognition motif was successfully applied in the preparation the first star-shaped supramolecular polymer based on a tetraparaquat guest and a DB24C8 functionalized polystyrene oligomer. A model system based on this guest and DB24C8 was also studied for comparison. It was found that the complexation in these two systems is cooperative, as are most biological complexations of multitopic species. Due to the ready availability of DB24C8 and paraquat derivatives, the new recognition motif should prove to be very valuable for self-assembly of other more sophisticated supramolecular systems. / Master of Science

The novel compound, [Rh2(N-{2,4,6-CH3}C6H2)COCH3)4] was synthesized. Crystal structures of [Rh2(N-{2,4,6-CH3}C6H2)COCH3)4]·2NCC6H5 and Ba1.5[Fe(C10H13N2O7)][Co(CN)6]·9H2O were determined employing a Rigaku Mercury375R/M CCD (XtaLAB mini) diffractometer with graphite monochromated Mo-Kα radiation. For [Rh2(N-{2,4,6-CH3}C6H2)COCH3)4]·2NCC6H5, the space group was P-421c(#114) with unit cell dimensions: a =11.0169(14)Å, c =21.499(3)Å, V = 2609.4(6)Å3. Each rhodium had approximately octahedral coordination and was bound to another rhodium atom, two nitrogens (trans to each other), two oxygens (trans to each other), and one benzonitrile nitrogen (trans to rhodium). For Ba1.5[Fe(C10H13N2O7)][Co(CN)6]·9H2O the space group was: P-1(#2) with unit cell dimensions: a=13.634Å, b=13.768Å, c=17.254Å and α=84.795°, β=87.863°, γ=78.908°, V=3164.5Å3. The iron atom (nearly octahedral) was coordinated to one chelating ligand (derived from ethylenediaminetetraacetic acid) and the nitrogen of a cyanide ligand. The carbon of the cyanide ligand was bound to cobalt (octahedral). Thus, the cyanide ligand serves as a bridge between the two metals.

Thiostrepton (TS: TS; C72H85N19O18S5) is a thiazoline antibiotic that is effective against Gram-positive bacteria and the malarial parasite, Plasmodium falciparum. Tight binding of TS to the bacterial L11-23S ribosomal RNA (rRNA) complex of the large 50S ribosomal unit inhibits protein biosynthesis. The TS producing organism, Streptomyces azureus, biosynthesizes thiostrepton-resistance methyltransferase (TSR), an enzyme that uses S-adenosyl-L-methionine (AdoMet) as a methyl donor, to modify the TS target site. Methylation of A1067 (Escherichia coli ribosome numbering) by TSR circumvents TS binding. The S. azureus tsr gene was overexpressed in E. coli and the protein purified for biochemical characterization. Although the recombinant protein was produced in a soluble form, its tendency to aggregate made handling a challenge during the initial stages of establishing a purification protocol. Different purification conditions were screened to generate an isolation protocol that yields milligram quantities of protein with little aggregation and sufficient purity for crystallographic studies. Enzymological characterization of TSR was carried out using an assay to monitor AdoMet-dependent ([methyl-3H]-AdoMet) methylation of the rRNA substrate by liquid scintillation counting. During the optimization of assay, it was found that, although this method is frequently employed, it is very time and labour intensive. A scintillation proximity assay was investigated to evaluate whether it could be a method for collecting kinetic data, and was found that further optimization is required. Comparative sequence analysis of TSR has shown it to be a member of the novel Class IV SpoUT family of AdoMet-dependent MTases. Members of this class possess a non-canonical AdoMet binding site containing a deep trefoil knot. Selected SpoUT family proteins were used as templates to develop a TSR homology model for monomeric and dimeric forms. Validation of the homology models was performed with structural validation servers and the model was then used as the basis of ongoing mutagenesis experiments. The X-ray crystal structure of TSR bound with AdoMet (2.45 Å) was elucidated by our collaborators, Drs. Mark Dunstan and Graeme Conn (University of Manchester). This structure confirms TSR MTase’s membership in the SpoUT MTase family with a deep trefoil knot in the catalytic domain. The AdoMet bound in the crystal structure is in an extended conformation not previously observed in SpoUT MTases. RNA docking simulations revealed some features that may be relevant to binding and recognition of TSR to the L11 binding domain of the RNA substrate. Two structure-activity studies were conducted to investigate the TS-rRNA interaction and TS solubility. Computational analyses of TS conformations, molecular orbitals and dynamics provided insight into the possible modes of TS binding to rRNA. Single-site modification of TS was attempted, targeting the dehydroalanine and dehydrobutyrine residues of the antibiotic. These moieties were modified using the polar thiol, 2-mercaptoethanesulfonic acid (2-MESNA). Similar modifications had been previously used to improve solubility and bioavailability of antibiotics. The resulting analogue was structurally characterized (NMR and mass spectrometry) and showed antimicrobial activity against Bacillus subtilis and Staphylococcus aureus.