The bonding in a series of ligand-bridged metal dimer complexes has been characterized by He(I) and He(II) photoelectron spectroscopy and approximate molecular orbital calculations. Bridging ligands such as carbonyl, nitrosyl, methylene and pyrazolyl in the complexes [CpFe(NO)]₂, [Cp*Fe(NO)]₂, [CpRu(NO)]₂, [Cp*Co(CO)]₂, [CpFe(CO)₂]₂, [Cp*Fe(CO)₂]₂, [CpFe(CO)]₂-μCO-μCH₂, [Cp*Fe(CO)]₂-μCO-μCH₂, [CpFe(NO)]₂- μCh₂, [CpRu(NO)]₂-μCH₂, [CpCo(CO)]₂-μCH₂, [CpRh(CO)]₂-μCH₂, [Ir(pyrazolyl)(CO)₂]₂, [Ir(3-methylpyrazolyl)(CO)₂]₂ and [Ir(3,5-dimethylpyrazolyl)(CO)₂]₂ are investigated and their effects upon metal-metal interactions are surveyed. Due to the presence of two d⁷ or d⁸ late metal atoms per molecule, these complexes display many overlapping ionization bands in a narrow valence ionization region. Attention has been given to modelling the photoelectron single ionization with asymmetric and symmetric Gaussians. The overlapping ionizations are successfully represented in terms of the model bandshapes. Thermodynamic relationships between bond dissociation and photoelectron ionization energies are also investigated. With relationships of this type, trends in bond energies may be correlated with ionization energies. Ligand inductive and bonding effects as well as small changes in molecular geometry cause shifts in the metal-based ionizations, which aid chemical understanding and interpretation of the molecular orbital picture. By comparing a series of related metal dimers, the assignment of related ionizations in the photoelectron spectra becomes apparent. Changes in ligand π accepting ability and changes in metal and formal oxidation states are also probed. Addition information is provided by vibrational fine structure in Cp₂Os, [CpFe(NO)]₂, and [Cp*Co(CO)]₂ and spin-orbit splitting in Cp₂Os. The metal-ligand backbonding combinations are found to be the most stable interactions and are responsible for the stability of the metal dimers. Metal-metal interactions are found to be relatively unimportant. Ligands with stronger π accepting abilities allow for more stabilized supported metal dimer complexes.

The kinetics for the bridge-to-chelate isomerization of the dppe ligand in H4Ru4(CO)10(dppe) have been investigated by UV-vis and NMR spectroscopies over the temperature range of 308-328 K. The isomerization of the ligand-bridged cluster 1,2-H4Ru4(CO)10(dppe) was found to be reversible by 31P NMR spectroscopy, affording a Keq = 15.7 at 323 K in favor of the chelating dppe isomer. The forward (k1) and reverse (k-1) first-order rate constants for the reaction have been measured in different solvents and in the presence of ligand trapping agents (CO and PPh3). On the basis of the activation parameters and reaction rates that are unaffected by added CO and PPh3, a sequence involving the nondissociative migration of a phosphine moiety and two CO groups between basal ruthenium centers is proposed and discussed. The substitution of the MeCN ligands in the activated cluster 1,2-Os3(CO)10(MeCN)2 by the diphosphine ligands dppbz proceeds rapidly at room temperature to furnish a mixture of bridging and chelating Os3(CO)10(dppbz) isomers and the ortho-metalated product HOs3(CO)9[μ-(PPh2)C=C{PPh(C6H4)}C4H4]. Thermolysis of the bridging isomer 1,2-Os3(CO)10(dppbz) under mild conditions gives the chelating isomer 1,1-Os3(CO)10(dppbz), molecular structure of both the isomers have been determined by X-ray crystallography. The kinetics for the ligand isomerization has been investigated by UV-vis and 1H NMR spectroscopy in toluene solution over the temperature range of 318-343 K. On the basis of kinetic data conducted in the presence of added CO and the Eyring activation parameters, a non-dissociative phosphine migration across one of the Os-Os bonds is proposed. Ortho metalation of one of the phenyl groups associated with the dppbz ligand is triggered by near-UV photolysis of the chelating cluster 1,1-Os3(CO)10(dppbz). The triosmium cluster 1,2-Os3(CO)10(MeCN)2 reacts with the diphosphine ligand 3,4­bis(diphenylphosphino)-5-methoxy-2(5)H-furanone (bmf) at 25 ºC to give the bmf-bridged cluster 1,2-Os3(CO)10(bmf). Heating 1,2-Os3(CO)10(bmf) leads to an equilibrium with the chelating isomer 1,1-Os3(CO)10(bmf). The molecular structure of each isomer has been crystallographically determined, and the kinetics for the isomerization has been investigated by UV-vis and 1H NMR spectroscopy. The reversible nature of the diphosphine isomerization has been confirmed by NMR measurements, and the forward (k1) and reverse (k-1) first-order rate constants for the bridge-to-chelate isomerization have been determined. Thermolysis of the SEQ CHAPTER h r 11,1-Os3(CO)10(bmf) cluster (>110 ºC) leads to regiospecific activation of C-H and P-C bonds, producing the hydrido clusters HOs3(CO)9[µ-PPh2C=C{PPh(C6H4)} CH(OMe)OC(O)] and the benzyne clusters HOs3(CO)8(μ3-C6H4)[µ-PPhC=C(PPh2)CH(OMe)OC(O)]. The hydride and benzyne clusters, which exist as a pair of diastereomers, have been fully characterized in solution by IR and NMR spectroscopy, and the molecular structure of one benzyne cluster (major diastereomer) has been determined by X-ray crystallography.

In chapter 1, I discuss how ligand architecture in tripodal nitrogen-rich ligands can drastically affect the structure of zinc complexes featuring these ligands. The synthesis and characterization of zinc tris(1-methylimidazol-2-ylthio)methyl ([Titm^Me]) and tris(1-Pribenzimidazol-2-ylthio)methyl ([Titm^iPr,benzo]) complexes is presented. The ligand in [Titm^Me]Zn complexes binds the metal to form carbatrane structures that exhibit unusually long and flexible Zn–C bonds. The bonding between the zinc and the carbon in these complexes can therefore be more accurately described as a zwitterionic interaction between a carbanion and a zinc cation. Density functional theory calculations demonstrate that the energy profile for the Zn–C bond is shallow, such that large variations of the Zn–C distance result in very little change in the energy of the complex. The benzannulated ligand [Titm^iPr,benzo] allows access to a rare monomeric zinc hydride species [κ³-Titm^iPr,benzo]ZnH that can react with either CO₂ to produce a zinc formate, or B(C₆F₅)₃ to form the ion pair [κ⁴-Titm^iPr,benzo]ZnHB(C₆F₅)₃. The coordination chemistry of the [Titm^iPr,benzo] ligand also extends to the other metals of group 12. In chapter 2, I report the use of the [Titm^Me] and [Titm^iPr,benzo] zinc complexes presented in chapter 1 as biomimetic models for zinc enzymes. First, [Titm^Me] zinc complexes present structural similarities with the active site of carbonic anhydrase, and can be used to study the binding of carbonic anhydrase inhibitors to the enzyme active site. Then, [κ⁴-Titm^iPr,benzo]ZnX (X = MeB(C₆F₅)₃, BPh₄) complexes and their interactions with ligands of relevance towards antibiotic resistance is reported. The non coordinating nature of the anions in [κ⁴-Titm^iPr,benzo]ZnX (X = MeB(C₆F₅)₃, BPh₄) lead to the formation of a Lewis acidic zinc cationic center, which can be coordinated by an additional ligand of biological interest. The binding of simple β-lactams to the [κ⁴-Titm^iPr,benzo]ZnX complexes can be probed using X-ray diffraction and Nuclear Magnetic Resonance (NMR) spectroscopy, thereby providing a way to model the binding of antibiotics to the active site of the metallo-β-lactamases enzymes responsible for broad antibiotic resistance. The binding of β-lactams can be compared to larger ring size lactams and linear amides. [κ⁴-Titm^iPr,benzo]ZnX (X = MeB(C₆F₅)₃, BPh₄) also allows for the study of the binding of potential metallo-β-lactamases inhibitors, such as, for example, glycinamide, picolinamide, and piperazine-2,3-dione. Binding studies between [κ⁴-Titm^iPr,benzo]ZnX and substrates bearing structural similarities to antibiotics reveal secondary interactions involving peripheral functional groups the cationic zinc center in [κ⁴-Titm^iPr,benzo]ZnX. These studies provide guidelines to modify existing antibiotics, in order to decrease their sensitivity to metallo-β-lactamases. In chapter 3, I explore the reactivity of previously characterized tris(2-pyridylthio)methyl [Tptm] zinc complexes. First, an improved synthesis of [κ⁴-Tptm]ZnF using Me₃SnF as the fluorinating agent is reported. The fluorine atom in [κ⁴-Tptm]ZnF acts as a Lewis base, as illustrated by its reaction with B(C₆F₅)₃ to form [κ⁴-Tptm]ZnFB(C₆F₅)₃, in which the fluorine is transferred to the borane group. The fluoride ligand in [κ⁴-Tptm]ZnF also acts as a hydrogen bond and halogen bond acceptor and is capable of forming adducts with H₂O, indole, and iodopentafluorobenzene. [κ⁴-Tptm]ZnF undergoes metathesis with Ph₃CCl to form Ph₃CF, thereby providing a rare example of C–F bond formation promoted by a zinc complex. Then, [κ³-Tptm]ZnH is used as a catalyst for the hydrosilylation of aldehydes and ketones using phenylsilane to produce tris alkoxysilane products. The catalyst is very active with aldehydes, and shows slower reactivity towards dialkyl ketones. The reaction proceeds via insertion of the carbonyl group in the Zn–H bond to form a zinc alkoxide, which then undergoes metathesis with the silane to generate the desired product and regenerate the zinc hydride species. The complicated NMR spectroscopic features of the products resulting from the hydrosilylation of prochiral ketones are explained by the presence of different diastereomers. Finally, we report that [κ³-Tptm]ZnH is a catalyst for the hydrosilylation of silylformates to methoxy silanes with (EtO)₃SiH, (MeO)₃SiH and κ⁴-N(CH₂CH₂O)₃SiOMe. We show that CO₂ can be reduced to methoxy silane species in a one pot reaction using (MeO)₃SiH and catalytic amounts of [κ³-Tptm]ZnH. In chapter 4, I report the synthesis and characterization of a silicon based analogue of [Titm^iPr,benzo], namely the tris(1-Pribenzimidazol-2-yldimethylsilyl)methyl [Tism^iPr,benzo] ligand. The ligand possesses unique structural features, due to the proximity between the dimethylsilyl groups and the methyl carbanion. The formation of [κ⁴-Tism^iPr,benzo]Li proceeds via the doubly base stabilized silene intermediate [κ³-C(SiMe₂benzimid^iPr)₂]SiMe₂. [κ⁴-Tism^iPr,benzo]Li can be used as a precursor for copper and nickel [Tism^iPr,benzo] and [C₃-Tism^iPr,benzo] complexes, where [C3-Tism^iPr,benzo] represents the isomerized tris carbene version of [Tism^iPr,benzo]. [κ³-C(SiMe₂benzimid^iPr)₂]SiMe₂ reacts with ZnMe₂ to produce [κ³-C(SiMe₃)(SiMe₂benzimid^iPr)₂]ZnMe, which can be transformed to the phenoxide compound. This compound acts as a catalyst for the hydrosilylation of CO₂ to silyl formates and methoxy silanes. [κ³-C(SiMe₂benzimid^iPr)₂]SiMe₂ itself reacts with CO₂ to produce an unusual β-lactone.

No description available.

Thesis (Ph.D.)--York University, 2008. Graduate Programme in Chemistry. / Typescript. Includes bibliographical references (leaves 183-207). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:NR39001

Thesis (M.S. in Bio. E.)--School of Biomedical Engineering, Georgia Institute of Technology, 2004. Directed by Cheng Zhu. / Includes bibliographical references (leaves 79-84).

published_or_final_version / Pharmacology and Pharmacy / Doctoral / Doctor of Philosophy

Selected nucleic acid binding species (aptamers) have been shown to undergo conformational changes in the presence of ligands, and have been adapted to function as biosensors. We were interested in whether the secondary structures of aptamers could be rationally engineered to undergo ligand dependent conformational changes. To this end, we used rational and computational design methods to generate a number of aptamer biosensors. First, we built upon previous work that showed that antisense oligonucleotides bearing reporter moieties could be used to denature aptamers. Upon addition of ligands, the conformational equilibrium is shifted towards release of the antisense oligonucleotide and a concomitant increase in fluorescence. We attempted to adapt this format to the potential detection of ricin, but were unsuccessful. In order to better evaluate rational designs, we attempted to use computational modeling methods. Again, aptamer biosensors have previously been engineered based on ligand-induced reorganization of secondary structure (as opposed to oligonucleotide displacement), a so-called 'slip-structure' model. We developed an algorithm to evaluate different lisp structures, predicted both aptamers and aptazymes that should have undergone ligand-dependent changes in conformation, and experimentally evaluated the computationally predicted sequences. A number of robust biosensors that could respond to the cytokine VegF and the small molecule flavin were discovered. The computational model was further adapted to an aptamer biosensor that underwent a larger conformational change upon ligand-binding, an antiswitch. In this model, binding of the ligand stabilizes one hairpin structure at the expense of a competing structure (as opposed to merely changing the register of the hairpin as in the previously described slip structure model). Again, we were able to computationally identify a number of antiswitches that upon synthesis were responsive to the ligand theophylline. Finally we again attempted to use rational design methods to optimize not just the degree of signal but also the kinetic performance of aptamer biosensors. To this end, we developed biosensors that signaled within seconds the presence of the coagulation protein thrombin. / text

No description available.

The optimisation of ligand-macromolecule interactions is fundamental to the design of therapeutic agents. The GRID method is a procedure for determining energetically favourable ligand binding sites on molecules of known structure using an empirical energy potential. In this thesis, it has been extended, tested, and then applied to the design of anti-influenza agents. In the GRID method, the energy of a hydrogen-bond is determined by a function which is dependent on the length of the hydrogen-bond, its orientation at the hydrogen-bond donor and acceptor atoms, and the chemical nature of these atoms. This function has been formulated in order to reproduce experimental observations of hydrogen-bond geometries. The reorientation of hydrogen atoms and lone-pair orbitals on the formation of hydrogen-bonds is calculated analytically. The experimentally observed water structures of crystals of four biological molecules have been used as model systems for testing the GRID method. It has been shown that the location of well-ordered waters can be predicted accurately. The ability of the GRID method to assist in the assignment of water sites during crystallographic refinement has been demonstrated. It has also been shown that waters in the active site of an enzyme may be both stabilized and displaced by a bound substrate. Ligands have been designed to block the highly conserved host cell receptor site of the influenza virus haemagglutinin in order to prevent the attachment of the virus to the host cells. The protein was mapped energetically by program GRID and specific ligand binding sites were identified. Ligands, which exploited these binding sites, were then designed using computer graphics and energy minimization techniques. Some of the designed ligands were peptides and these were synthesised and assayed. Preliminary results indicate that they may possess anti-influenza activity.