Because bimolecular interactions in water are poorly understood, three tactics commonly used to improve binding affinity in ligand design were investigated: (1) increasing apolar surface area, (2) introducing a conformational constraint, and (3) targeting a cation-[pi] interaction. Thermodynamic parameters of binding ligands to the Grb2 SH2 domain were determined by isothermal titration calorimetry (ITC), and structural data was obtained by X-ray crystallography. The apolar surface area of the pTyr+1 residue in Ac-pTyr-Acnc-Asn-NH₂ was varied by incrementally increasing the size of the cyclic Acnc residue from a 3-membered to a 7-membered ring. Increasing apolar surface area resulted in an increase in Ka due to a more favorable [delta]H⁰ that was dominated a less favorable [delta]S⁰. Structural analyses showed that all ligands bound in a similar mode, so differences in binding thermodynamics were attributed to the pTyr+1 residue. The thermodynamics of binding tripeptides wherein pTyr+1 was an n-alkyl group were studied. Ka increased when Ala was mutated to Abu, but additional methylene groups had no effect on Ka due to strong entropy-enthalpy compensation. While [delta]H⁰ was weakly correlated with buried surface area, there was no change in [delta]H⁰ between one methylene and two methylene groups, presumably because an enthalpic penalty is associated with a gauche interaction between C-[beta] and C-[gamma] of the Xaa side chain that was noted in the crystal structure. An olefin was installed in an attempt to alleviate the energetic penalty incurred from the gauche interaction, but the introduction of the constraint resulted in equipotent ligands. A putative cation-[pi] interaction between Arg67 and various aromatic groups was probed by varying the [pi]-donating capability of groups attached to a tripeptide scaffold. Although crystal structures demonstrated that three of the aryl groups were close enough to Arg67 to form a cation-[pi] interaction, only a modest increase in Ka was observed relative to analogues having only an N-acetyl group. Furthermore, a simple cyclohexyl group in place of aryl groups resulted in ligands that were equipotent with indolyl- and phenyl- derived analogues, so any cation-[pi] interaction is not significant. / text

Redox cofactors and amino-acid free radicals play important roles in biology. Although many of the same cofactors and amino acids that form these radicals are found across a broad range of biological systems, identical cofactors can have different reduction potentials. The local environment plays a role in defining these redox potentials. An understanding of this local-environment effect can shed more light on how redox chemistry works in nature. Our laboratory has developed a library of model proteins that are well suited to study amino-acid radicals. a3X is a de novo designed protein that is composed of 67 residues. It forms a three-helix bundle connected by two glycine loops. The radical site is located at position 32 on the central a-helix. The a3X protein is designed to be well-folded and thermodynamically stable across a broad pH range. Paper 1 describes the structural and electrochemical characterization of a3Y, a tyrosine variant of a3X. We were able to obtain a unique Faradaic response from Y32 at both low and high pH, using differential pulse voltammetry. In addition, we successfully redesigned α3Y by introducing a histidine in close proximity to Y32, creating a tyrosine/histidine pair. Our goal in creating this pair was to study proton-coupled electron transfer (PCET) in a well-structured and solvent-sequestered protein environment.  In paper 2 we illustrated the redox reversibility of Y32 and produced the first ever Pourbaix diagram for a tyrosine radical in a protein. The formal potential of the Y32-OŸ/Y32-OH redox couple was determined to be 918 ± 2 mV vs. the normal hydrogen electrode (NHE) at pH 8.40.  While at pH 5.52, the formal potential of the Y32-OŸ/Y32-OH redox couple was recorded at 1.07 V. Papers 3 and 4 utilize a3W to study cation-π interactions. In paper 3, we showed how solvation can affect the strength of these interactions by -0.9 kcal/mol. In Paper 4, we were able to monitor the disruption of the cation-π interaction with the use of high-pressure fluorescence and were able to calculate the interaction energy for a solvent exposed cation-π. The aim of the work described in this thesis was to use model proteins to study tyrosine radicals to gain a broader perspective and better understanding of the versatility of biological electron transfer and to measure cation-π interactions and how they behave in different environments. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

The cation&ndash;&pi; interaction has been long-established to play an important role in molecular recognition, supramolecular chemistry, and molecular biology. In contrast, its potential application in small-molecule catalysis, especially as a selectivity-determining factor in asymmetric synthesis has been overlooked until very recently. This dissertation begins with an extensive literature review on the state-of-the-art research on the application of cation&ndash;&pi; interactions in non-enzymatic catalysis of organic and organometallic transformations. The research in this field has been largely inspired and guided by the related biosynthetic systems incorporating the same type of interactions.</p> / Chemistry and Chemical Biology

Thesis advisor: Shih-Yuan Liu / Described herein are two projects on the application and effects of BN/CC isosterism on indole-containing compounds. In the first chapter, the synthetic route to an unnatural boron and nitrogen-containing analogue of tryptophan (BN-tryptophan) via late-stage functionalization of BN-indole is disclosed and its spectroscopic properties are reported with respect to the natural amino acid, tryptophan. The incorporation of BN-tryptophan into proteins expressed in E. coli using selective pressure incorporation, a residue specific method of unnatural amino acid incorporation, is then reported and its reactivity and fluorescence in the proteins characterized. In the second chapter, the synthesis of a BN-indole-containing aromatic scaffold is reported and the cation-π binding ability characterized by nuclear magnetic resonance (NMR) monitored titrations is disclosed. The resulting chemical shifts were analyzed using a non-linear curve fitting procedure and the extracted association constants (Ka’s) compared with the natural indole scaffold. Computations were also performed to support the titration results. / Thesis (PhD) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

The UN predicts that by 2050 there will water shortages throughout the globe. Current sources for safe, clean drinking water are being over mined and exhausted. Seawater provides an alternative water source, but a high salt content makes it unsuitable for the majority of applications. However, reverse osmosis lowers the salt content producing water that is safe for human consumption. Reverse osmosis uses a semi-permeable membrane to prevent the transport of salt but allows for the transport of water. Currently these membranes are susceptible to fouling and contamination, which reduces their efficiency. Graphene-oxide membranes offer a new material for reserves osmosis membranes. Sheets of graphene-oxide are stacked in a layered structure. The separation between the sheets can be controlled using physical confinement, resulting in limited ion permeation of abundant cations in seawater, like Na+ and K+. This is believed to be due to the separation of 0.76 nm between the graphene sheets, forcing the ions to lose its surrounding water molecules, making it unfavourable for the ion to travel through the membrane. Molecular dynamics simulations can give an atomic level insight into the molecular processes within GO membranes. Recent simulations have shown that charged species are attracted to graphene surfaces due to polarisation of the pi-electron system. This work has managed to incorporate these ion-pi interactions into molecular dynamics simulations. Including ion-pi interactions caused some ions, like Na+ and K+, to prefer to lose water molecules and reside at a graphene surface. This work observed the same phenomena when ions were confined to graphene channel ranging from 1.3 nm - 0.7 nm. This observation could have a large impact on whether dehydration is limiting the permeation of these two ions, or if there are additional processes that limit their molecular transport.

No description available.

Cationâ Ï interaction is an important determinant in protein structure and function. Among the three proteinogenic aromatic amino acids, tryptophan (Trp) is the strongest cationâ Ï donor. We reported the asymmetric syntheses of tryptophan regioisomers in which the amino acid side chain is attached at different position of the indole moiety. These new tryptophan regioisomers can effect a different mode of cationâ Ï interaction. In nature, dramatic increases in binding affinity can be achieved through multivalent binding. Following a fragmentation-dimerization approach, we synthesized Taxol-based dimer in which the baccatin III core of Taxol is coupled with flexible PEG linker. However, microtubule assembly assay suggested that these new dimers are not capable of effecting bivalent binding to the Taxol binding sites in microtubules. Memory of chirality (MOC) is an emerging theme in asymmetric synthesis in which the dynamic chirality of the reactive intermediate "memorizes" the static chirality of the reactant. Using dynamic 1D and 2D NMR and density functional theory (DFT) methods, we studied the MOC effect of 1,4-benzodiazepin-2-ones. Reconstruction of the reaction pathway using DFT calculations supported our proposed contra steric, retention of configuration mechanism. / Ph. D.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.