Movement of a Spherical Brownian Particle Between Infinite Parallel Plates: Hindered Dispersion and Sedimentation

The dispersion of an isolated, spherical, Brownian particle immersed in a Newtonian fluid between infinite parallel plates is investigated. Expressions are developed for both a 'molecular' contribution to dispersion, which arises from random thermal fluctuations, and a 'convective' contribution, arising when a shear flow is applied between the plates. These expressions are evaluated numerically for all sizes of the particle relative to the bounding plates, and the method of matched asymptotic expansions is used to develop analytical expressions for the dispersion coefficients as a function of particle size to plate spacing ratio for small values of this parameter.

It is shown that both the molecular and convective dispersion coefficients decrease as the size of the particle relative to the bounding plates increase. When the particle is small compared to the plate spacing, the coefficients decrease roughly proportional to the particle size to plate spacing ratio. When the particle closely fills the space between the plates, the molecular dispersion coefficient approaches zero slowly as an inverse logarithmic function of the particle size to plate spacing ratio, and the convective dispersion coefficent approaches zero approximately proportional to the width of the gap between the edges of the sphere and the bounding plates.

Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c

Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.

Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.

Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c

A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.

Studies of the serotonin type 3A receptor and the chemical preparation of tRNA

This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT₃AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.

In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT₃A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT₃AR, which establishes a binding orientation for these drugs.

In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT₃A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.

In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.

Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, K_B, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT₃A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.

Investigations of the conductor-semiconductor interface

I. Schottky barriers produced by polymeric sulfur nitride, (SN)_x, on nine common III-V and II-VI compound semiconductors are compared to barriers formed by Au. The conductor (SN)_x produces significantly higher barriers to n-type semiconductors and lower barriers to p-type semiconductors than Au, the most electronegative elemental metal. The barrier height improvement, defined as ɸ(SN)_x - ɸ(Au), is smaller on covalent semiconductors than on ionic semiconductors; (SN)x barriers follow the ionic-covalent transition. Details of (SN)_x film deposition, samples preparation, and barrier height measurements are described.

II. The rate of dissolution of amorphous Si into solid Al is measured. The rate of movement of the amorphous Si/Al interface is found to be much faster than predicted by a simple model of the transport of Si through Al. This result is related to defects in the growth of epitaxial Si using the solid phase epitaxy process.

New Catalytic Methods for the Preparation of Tryptophans and Pyrroloindolines: Total Synthesis of (+)-Naseseazines A and B and (–)-Aspergilazine A

Tryptophan and unnatural tryptophan derivatives are important building blocks for the total synthesis of natural products, as well as the development of new drugs, biological probes, and chiral small molecule catalysts. This thesis describes various catalytic methods for the preparation of tryptophan derivatives as well as their functionalization and use in natural product total synthesis.

Herein, the tandem Friedel–Crafts conjugate addition/asymmetric protonation reaction between 2-substituted indoles and methyl 2-acetamidoacrylate to provide enantioenriched trytophans is reported. This method inspired further work in the area of transition metal catalyzed arylation reactions. We report the development of the coppercatalyzed arylation of tryptamine and tryptophan derivatives. The utility of these transformations is highlighted in the five-step syntheses of the natural products (+)-naseseazine A and B. Further work on the development of a mild and general Larock indolization protocol to access unnatural tryptophans is also discussed.

Preparation and attempted resolution of benzoyl-malic acid

The final object of this research was to prepare m-nitrobenzoyl malic acid and to separate it, if possible, into the four stereoisomers predicted by the Huggins' theory of the benzene ring. Inasmuch as the quantity of m-nitro- benzoyl chloride available was limited it was thought better to first prepare i-benzoyl malic acid and then attempt to resolve it. The resolution of m-nitrobenzoyl malic acid could probably be accomplished by a similar method.