Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

Carbon-carbon bond forming reactions from bis(carbene)-platinum(II) complexes and olefin polymerization and oligomerization using group 4 post-metallocene complexes

A long-standing challenge in transition metal catalysis is selective C–C bond coupling of simple feedstocks, such as carbon monoxide, ethylene or propylene, to yield value-added products. This work describes efforts toward selective C–C bond formation using early- and late-transition metals, which may have important implications for the production of fuels and plastics, as well as many other commodity chemicals.

The industrial Fischer-Tropsch (F-T) process converts synthesis gas (syngas, a mixture of CO + H₂) into a complex mixture of hydrocarbons and oxygenates. Well-defined homogeneous catalysts for F-T may provide greater product selectivity for fuel-range liquid hydrocarbons compared to traditional heterogeneous catalysts. The first part of this work involved the preparation of late-transition metal complexes for use in syngas conversion. We investigated C–C bond forming reactions via carbene coupling using bis(carbene)platinum(II) compounds, which are models for putative metal–carbene intermediates in F-T chemistry. It was found that C–C bond formation could be induced by either (1) chemical reduction of or (2) exogenous phosphine coordination to the platinum(II) starting complexes. These two mild methods afforded different products, constitutional isomers, suggesting that at least two different mechanisms are possible for C–C bond formation from carbene intermediates. These results are encouraging for the development of a multicomponent homogeneous catalysis system for the generation of higher hydrocarbons.

A second avenue of research focused on the design and synthesis of post-metallocene catalysts for olefin polymerization. The polymerization chemistry of a new class of group 4 complexes supported by asymmetric anilide(pyridine)phenolate (NNO) pincer ligands was explored. Unlike typical early transition metal polymerization catalysts, NNO-ligated catalysts produce nearly regiorandom polypropylene, with as many as 30-40 mol % of insertions being 2,1-inserted (versus 1,2-inserted), compared to <1 mol % in most metallocene systems. A survey of model Ti polymerization catalysts suggests that catalyst modification pathways that could affect regioselectivity, such as C–H activation of the anilide ring, cleavage of the amine R-group, or monomer insertion into metal–ligand bonds are unlikely. A parallel investigation of a Ti–amido(pyridine)phenolate polymerization catalyst, which features a five- rather than a six-membered Ti–N chelate ring, but maintained a dianionic NNO motif, revealed that simply maintaining this motif was not enough to produce regioirregular polypropylene; in fact, these experiments seem to indicate that only an intact anilide(pyridine)phenolate ligated-complex will lead to regioirregular polypropylene. As yet, the underlying causes for the unique regioselectivity of anilide(pyridine)phenolate polymerization catalysts remains unknown. Further exploration of NNO-ligated polymerization catalysts could lead to the controlled synthesis of new types of polymer architectures.

Finally, we investigated the reactivity of a known Ti–phenoxy(imine) (Ti-FI) catalyst that has been shown to be very active for ethylene homotrimerization in an effort to upgrade simple feedstocks to liquid hydrocarbon fuels through co-oligomerization of heavy and light olefins. We demonstrated that the Ti-FI catalyst can homo-oligomerize 1-hexene to C₁₂ and C₁₈ alkenes through olefin dimerization and trimerization, respectively. Future work will include kinetic studies to determine monomer selectivity by investigating the relative rates of insertion of light olefins (e.g., ethylene) vs. higher α-olefins, as well as a more detailed mechanistic study of olefin trimerization. Our ultimate goal is to exploit this catalyst in a multi-catalyst system for conversion of simple alkenes into hydrocarbon fuels.

Selectivity, activity, and stability of ruthenium-carbene based olefin metathesis initiators

The olefin metathesis reaction has found many applications in polymer synthesis and more recently in organic synthesis. The use of single component late metal olefin metathesis catalysts has expanded the scope of the reaction to many new applications and has allowed for detailed study of the catalytic species.

The metathesis of terminal olefins of different steric bulk, different geometry as well as electronically different para-substituted styrenes was studied with the ruthenium based metathesis initiators, trans-(PCy₃)₂Cl₂Ru=CHR, of different carbene substituents. Increasing olefin bulk was found to slow the rate of reaction and trans internal olefins were found to be slower to react than cis internal olefins. The kinetic product of a11 reactions was found to be the alkylidene, rather than the methylidene, suggesting the intermediacy of a 2,4-metallacycle. The observed effects were used to explain the mechanism of ring opening cross metathesis and acyclic diene metathesis polymerization. No linear electronic effects were observed.

In studying the different carbene ligands, a series of ester-carbene complexes was synthesized. These complexes were found to be highly active for the metathesis of olefinic substrates, including acrylates and trisubstituted olefins. In addition, the estercarbene moiety is thermodynamically high in energy. As a result, these complexes react to ring-open cyclohexene by metathesis to alleviate the thermodynamic strain of the ester-carbene ligand. However, ester-carbene complexes were found to be thermolytically unstable in solution.

Thermolytic decomposition pathways were studied for several ruthenium-carbene based olefin metathesis catalysts. Substituted carbenes were found to decompose through bimolecular pathways while the unsubstituted carbene (the methylidene) was found to decompose unimolecularly. The stability of several derivatives of the bis-phosphine ruthenium based catalysts was studied for its implications to ring-closing metathesis. The reasons for the activity and stability of the different ruthenium-based catalysts is discussed.

The difference in catalyst activity and initiation is discussed for the bis-phosphine based and mixed N-heterocyclic carbene/phosphine based ruthenium olefin metathesis catalysts. The mixed ligand catalysts initiate far slower than the bis-phosphine catalysts but are far more metathesis active. A scheme is proposed to explain the difference in reactivity between the two types of catalysts.

Geochemistry and resonance ionization of platinum-group elements

Experimental studies were conducted with the goals of 1) determining the origin of Pt- group element (PGE) alloys and associated mineral assemblages in refractory inclusions from meteorites and 2) developing a new ultrasensitive method for the in situ chemical and isotopic analysis of PGE. A general review of the geochemistry and cosmochemistry of the PGE is given, and specific research contributions are presented within the context of this broad framework.

An important step toward understanding the cosmochemistry of the PGE is the determination of the origin of POE-rich metallic phases (most commonly εRu-Fe) that are found in Ca, AJ-rich refractory inclusions (CAI) in C3V meteorites. These metals occur along with γNi-Fe metals, Ni-Fe sulfides and Fe oxides in multiphase opaque assemblages. Laboratory experiments were used to show that the mineral assemblages and textures observed in opaque assemblages could be produced by sulfidation and oxidation of once homogeneous Ni-Fe-PGE metals. Phase equilibria, partitioning and diffusion kinetics were studied in the Ni-Fe-Ru system in order to quantify the conditions of opaque assemblage formation. Phase boundaries and tie lines in the Ni-Fe-Ru system were determined at 1273, 1073 and 873K using an experimental technique that allowed the investigation of a large portion of the Ni-Fe-Ru system with a single experiment at each temperature by establishing a concentration gradient within which local equilibrium between coexisting phases was maintained. A wide miscibility gap was found to be present at each temperature, separating a hexagonal close-packed εRu-Fe phase from a face-centered cubic γNi-Fe phase. Phase equilibria determined here for the Ni-Fe-Ru system, and phase equilibria from the literature for the Ni-Fe-S and Ni-Fe-O systems, were compared with analyses of minerals from opaque assemblages to estimate the temperature and chemical conditions of opaque assemblage formation. It was determined that opaque assemblages equilibrated at a temperature of ~770K, a sulfur fugacity 10 times higher than an equilibrium solar gas, and an oxygen fugacity 10⁶ times higher than an equilibrium solar gas.

Diffusion rates between -γNi-Fe and εRu-Fe metal play a critical role in determining the time (with respect to CAI petrogenesis) and duration of the opaque assemblage equilibration process. The diffusion coefficient for Ru in Ni (D^Ru_Ni) was determined as an analog for the Ni-Fe-Ru system by the thin-film diffusion method in the temperature range of 1073 to 1673K and is given by the expression:

D^Ru_Ni (cm² sec^-1) = 5.0(±0.7) x 10^-3 exp(-2.3(±0.1) x 10¹² erg mole^-1/RT) where R is the gas constant and T is the temperature in K. Based on the rates of dissolution and exsolution of metallic phases in the Ni-Fe-Ru system it is suggested that opaque assemblages equilibrated after the melting and crystallization of host CAI during a metamorphic event of ≥ 10³ years duration. It is inferred that opaque assemblages originated as immiscible metallic liquid droplets in the CAI silicate liquid. The bulk compositions of PGE in these precursor alloys reflects an early stage of condensation from the solar nebula and the partitioning of V between the precursor alloys and CAI silicate liquid reflects the reducing nebular conditions under which CAI were melted. The individual mineral phases now observed in opaque assemblages do not preserve an independent history prior to CAI melting and crystallization, but instead provide important information on the post-accretionary history of C3V meteorites and allow the quantification of the temperature, sulfur fugacity and oxygen fugacity of cooling planetary environments. This contrasts with previous models that called upon the formation of opaque assemblages by aggregation of phases that formed independently under highly variable conditions in the solar nebula prior to the crystallization of CAI.

Analytical studies were carried out on PGE-rich phases from meteorites and the products of synthetic experiments using traditional electron microprobe x-ray analytical techniques. The concentrations of PGE in common minerals from meteorites and terrestrial rocks are far below the ~100 ppm detection limit of the electron microprobe. This has limited the scope of analytical studies to the very few cases where PGE are unusually enriched. To study the distribution of PGE in common minerals will require an in situ analytical technique with much lower detection limits than any methods currently in use. To overcome this limitation, resonance ionization of sputtered atoms was investigated for use as an ultrasensitive in situ analytical technique for the analysis of PGE. The mass spectrometric analysis of Os and Re was investigated using a pulsed primary Ar⁺ ion beam to provide sputtered atoms for resonance ionization mass spectrometry. An ionization scheme for Os that utilizes three resonant energy levels (including an autoionizing energy level) was investigated and found to have superior sensitivity and selectivity compared to nonresonant and one and two energy level resonant ionization schemes. An elemental selectivity for Os over Re of ≥ 10³ was demonstrated. It was found that detuning the ionizing laser from the autoionizing energy level to an arbitrary region in the ionization continuum resulted in a five-fold decrease in signal intensity and a ten-fold decrease in elemental selectivity. Osmium concentrations in synthetic metals and iron meteorites were measured to demonstrate the analytical capabilities of the technique. A linear correlation between Os⁺ signal intensity and the known Os concentration was observed over a range of nearly 10⁴ in Os concentration with an accuracy of ~ ±10%, a millimum detection limit of 7 parts per billion atomic, and a useful yield of 1%. Resonance ionization of sputtered atoms samples the dominant neutral-fraction of sputtered atoms and utilizes multiphoton resonance ionization to achieve high sensitivity and to eliminate atomic and molecular interferences. Matrix effects should be small compared to secondary ion mass spectrometry because ionization occurs in the gas phase and is largely independent of the physical properties of the matrix material. Resonance ionization of sputtered atoms can be applied to in situ chemical analysis of most high ionization potential elements (including all of the PGE) in a wide range of natural and synthetic materials. The high useful yield and elemental selectivity of this method should eventually allow the in situ measurement of Os isotope ratios in some natural samples and in sample extracts enriched in PGE by fire assay fusion.

Phase equilibria and diffusion experiments have provided the basis for a reinterpretation of the origin of opaque assemblages in CAI and have yielded quantitative information on conditions in the primitive solar nebula and cooling planetary environments. Development of the method of resonance ionization of sputtered atoms for the analysis of Os has shown that this technique has wide applications in geochemistry and will for the first time allow in situ studies of the distribution of PGE at the low concentration levels at which they occur in common minerals.

Estimation of catalyst activity profiles and deactivation parameters from reactor operating data with applications to naphtha reforming

Techniques are developed for estimating activity profiles in fixed bed reactors and catalyst deactivation parameters from operating reactor data. These techniques are applicable, in general, to most industrial catalytic processes. The catalytic reforming of naphthas is taken as a broad example to illustrate the estimation schemes and to signify the physical meaning of the kinetic parameters of the estimation equations. The work is described in two parts. Part I deals with the modeling of kinetic rate expressions and the derivation of the working equations for estimation. Part II concentrates on developing various estimation techniques.

Part I: The reactions used to describe naphtha reforming are dehydrogenation and dehydroisomerization of cycloparaffins; isomerization, dehydrocyclization and hydrocracking of paraffins; and the catalyst deactivation reactions, namely coking on alumina sites and sintering of platinum crystallites. The rate expressions for the above reactions are formulated, and the effects of transport limitations on the overall reaction rates are discussed in the appendices. Moreover, various types of interaction between the metallic and acidic active centers of reforming catalysts are discussed as characterizing the different types of reforming reactions.

Part II: In catalytic reactor operation, the activity distribution along the reactor determines the kinetics of the main reaction and is needed for predicting the effect of changes in the feed state and the operating conditions on the reactor output. In the case of a monofunctional catalyst and of bifunctional catalysts in limiting conditions, the cumulative activity is sufficient for predicting steady reactor output. The estimation of this cumulative activity can be carried out easily from measurements at the reactor exit. For a general bifunctional catalytic system, the detailed activity distribution is needed for describing the reactor operation, and some approximation must be made to obtain practicable estimation schemes. This is accomplished by parametrization techniques using measurements at a few points along the reactor. Such parametrization techniques are illustrated numerically with a simplified model of naphtha reforming.

To determine long term catalyst utilization and regeneration policies, it is necessary to estimate catalyst deactivation parameters from the the current operating data. For a first order deactivation model with a monofunctional catalyst or with a bifunctional catalyst in special limiting circumstances, analytical techniques are presented to transform the partial differential equations to ordinary differential equations which admit more feasible estimation schemes. Numerical examples include the catalytic oxidation of butene to butadiene and a simplified model of naphtha reforming. For a general bifunctional system or in the case of a monofunctional catalyst subject to general power law deactivation, the estimation can only be accomplished approximately. The basic feature of an appropriate estimation scheme involves approximating the activity profile by certain polynomials and then estimating the deactivation parameters from the integrated form of the deactivation equation by regression techniques. Different bifunctional systems must be treated by different estimation algorithms, which are illustrated by several cases of naphtha reforming with different feed or catalyst composition.