Chemistry Commons^™

New Insights Into The Mechanism Of Dna Replication On Unmodified And Benzo[A]Pyrene Modified Templates Using Surface Plasmon Resonance, Richard George Federley

Wayne State University Dissertations

DNA synthesis is critical to cell survival, and the enzyme DNA polymerase has had a great deal of time to evolve efficient strategies to perform synthesis. A variety of effects are induced by the identity of the incoming dNTP, and its ability to effectively base pair with the templating base. The presence of the next correct dNTP is known to induce a conformational change of the polymerase and lead to an increase in KF-DNA binding. Conversely, the presence of an incorrect dNTP is shown to lead to a destabilization and reduction in the levels of KF-DNA complexes formed. Using surface …

Laser-Assisted Single-Molecule Refolding, Rui Zhao

Wayne State University Dissertations

Non-coding RNAs must fold into precise secondary and tertiary structures in order to perform the biological functions. Due to the flexibility of RNA, the RNA folding energy landscape can be rugged and full of local minimum (kinetic trap). To provide a means to study kinetically trapped RNAs, we have developed a new technique combining single-molecule FRET detection with laser induced temperature jump. We have calibrated the magnitude of the temperature jump with 1˚C accuracy using gold micro-size sensor. The accuracy of temperature calibration was confirmed by close agreement between single-molecule and bulk DNA duplex melting experiments.

HIV 1 DIS RNAs …

Astrochemical Dynamics: Fundamental Studies Relevant To Titan's Atmosphere, Wilson Kamundia Gichuhi

Wayne State University Dissertations

This work presents results of primary fundamental photodissociation and state-specific ion-molecule dynamical studies that are relevant to understanding the formation and growth mechanisms of unsaturated hydrocarbon molecules, haze layers and aerosols in Titan's upper atmosphere. In the diacetylene dimer, it is shown, via laboratory studies combined with electronic structure calculations that the photodissociation of the dimer readily initiates atomic hydrogen (H) loss and atomic H transfer reactions forming two prototypes of resonantly stabilized free radicals, C8H3 and C4H3, respectively. In ethylamine cation, high-level ab initio calculations identify the complex dissociation pathways for the ground state CH3CH2NH2+ radical cation at 233.3 …

Artificial And Natural Nucleic Acid Self Assembling Systems, Marcus Wood

Wayne State University Dissertations

Nucleic acids are good candidates for nanomachine construction. They participate in all the processes of life, and so can function as structural building blocks and dynamic catalysts. However, to use nucleic acids as nanomachines, a better understanding of their material properties, how to design structures using them, and their dynamics is needed. We have tried to address these issues, in a small way, with nucleic acid force field development, an attempt at nanostructural design and synthesis using DNA, and a study of the RNA/protein regulatory dynamics of the tryptophan regulatory attenuation protein.

Development Of Chemical Inducers Of Dimerization For Screening Competitive Histone Deactelyase Inhibitors, Emily Lynn Aubie

Wayne State University Dissertations

Histone Deacetylase (HDAC) proteins are transcriptional regulators that affect histone proteins, which are involved in packaging of DNA into chromosomes. HDACs have been linked to the proliferation of cancer through their role in transcriptional regulation. Due to these findings, HDAC inhibitors have been explored as anti-cancer agents. Several HDAC inhibitors are currently in various stages of clinical trials, and the inhibitor suberoyl anilide hydroxamic acid (SAHA) has been FDA approved for treatment of cutaneous T-Cell lymphoma. Currently, most of the known HDAC inhibitors are non-selective, which causes non-specific binding to the active sites of all HDAC isoforms, including those not …

Synthesis And Characterization Of Metal Chalcogenide Nanostructured Materials For Thermoelectric Applications, Shreyashi Ganguly

Wayne State University Dissertations

The synthesis and characterization of metal chalcogenide nanostructured materials with the potential to exhibit enhanced thermoelectric (TE) properties is reported. The tellurides, specifically PbTe and Bi⊂2⊂Te⊂3⊂ (Bi⊂2⊂Te⊂3⊂–Sb⊂2⊂Te⊂3⊂ alloys) were selected as these are well established TE materials in bulk form. The approaches used for nanostructuring are (1) sol-gel assembly of discrete nanoparticles of PbTe, Bi⊂2⊂Te⊂3⊂, and Bi⊂2⊂Te⊂3⊂–⊂2⊂Te⊂3⊂ alloys, and (2) formation of heterostructured nanocomposites of PbTe nanoparticles in bulk Bi⊂2⊂Te⊂3⊂ (p– or n–doped) matrices.

Aerogels and xerogels of PbTe nanoparticles were synthesized by sol–gel assembly of discrete nanoparticles, leading to interconnected networks of nanoparticles and pores. The PbTe aerogel exhibited …

Synthesis, Redox Properties, And Langmuir Monolayer Formation Of Selected 3d- And 4d- Metalloamphiphiles, Sree Ramadevi Shanmugam

Wayne State University Dissertations

Transition metals containing amphiphilic compounds integrate various geometric, electronic, magnetic, and electrochemical properties together with the film forming properties. These compounds thereby find potential towards the fabrication of responsive films. This dissertation confers the synthesis and analysis of film forming properties of various redox-active metalloamphiphiles. Two new azido and thiocyanto bridged copper-based amphiphiles were synthesized and characterized by IR, UV-visible, and EPR spectroscopies, mass spectrometry, cyclic voltammetry, and elemental analysis. The redox studies show that both these complexes exhibit redox reversibility with only the azido bridged complex showing good redox cycling of about 50 times with minimal decomposition of less …

Thiomaleic Anhydride: A Linchpin For Organic Synthesis And Structural Verification Of A Nonprotein Antifreeze Oligosaccharide, Md Yeajur Rahaman Sardar

Wayne State University Dissertations

This dissertation consists of two parts of which the first develops the utility of α,β-unsaturated monothioanhydrides as a linchpins in multicomponent coupling reactions by processes involving addition to the double bond, cyclization onto the anhydride, and finally exploitation of the rich chemistry of the thioacid liberated in the cyclization. The second part of the thesis is concerned with verification of the structure of a nonprotein antifreeze oligosaccharide by the total synthesis of various authentic oligosaccharides and the comparison of spectroscopic data.

Chapter one starts with the introduction of the general characteristics and reactivity of thioacids, and their potential for application …

Chemical Synthesis Of Peptides And Peptide Thioesters, Indrajeet Sharma

Wayne State University Dissertations

This dissertation describes investigations toward the development of a new chemistry for the block synthesis of peptides and peptidyl thioesters. A direct approach for the Fmoc-SPPS of peptidyl thioesters is also delineated in this thesis.

In the first part of chapter one, the difficulty and importance of chemical synthesis of peptides is explained, and a brief survey of available methods is given. The second part of chapter one presents the challenges inherent in the synthesis of peptidyl thioesters by Fmoc-SPPS.

The second chapter outlines the investigations conducted towards the development of a new chemistry for epimerization-free block synthesis of peptides …

Electronic Excitations In Branched Conjugated Oligomers: A Quasiparticle View And Tight-Binding Models, Hao Li

Wayne State University Dissertations

This dissertation focuses on the theoretical understanding and simulation of the excited state electronic structures of organic conjugated molecules. The exciton scattering (ES) approach has been extended for efficient calculation of optical spectra of large branched conjugated oligomers. The methodology of tight-binding (lattice) model, originally developed in condensed matter theory, has been extended to the building block structure of conjugated molecules for explicit description of the electronic excitations.

Within the ES approach, the electronic excitations in quasi-1D molecular structures are attributed to standing waves that represent quantum quasiparticles (excitons) scattered at the molecular vertices. Excitation energies can be found by …

Synthesis Of Peptide-Ligand Conjugates And Their Applications, Nitinkumar Dilipkumar Jabre

Wayne State University Dissertations

Three research areas pertaining to this dissertation, (i) synthesis strategies of peptide-ligand conjugates, (ii) their applications and (iii) chemistry of ferryls were surveyed in the introduction chapter. Next, the divergent and dual divergent strategies for the synthesis of non-heme ligand-peptide conjugates were developed. Using these strategies various peptide-ligand conjugates were synthesized via solution as well as solid phase synthesis. The scope and the functional group compatibility of these strategies were also established. The utility of the dual divergent strategy has been demonstrated by synthesizing a small library of metal-binding LHRH analogues. This work showcased the ability of the dual divergent …

Isolation And Analysis Of Peptides Binding To Helix 69 Of E. Coli 23 S Rrna From M13 Phage Display, Moninderpal Kaur

Wayne State University Dissertations

Peptides binding to helix 69 of domain IV or residues 1906-1924, of 23 S rRNA of E.coli were being selected from a heptapeptide phage library. An experimental system including biotin labeling of RNA and then affinity selection through four rounds was being followed. After sequencing phage clones of the fourth round, two peptide sequences dominated the phage pool, STYTSVS and NQVANHQ. The later sequence was a unique sequence since this sequence contained an abundance of amino acid residues that are also present in the ribosome recycling factor, RRF, and known to make contacts with H69. Phage-display methodology demonstrated the rapid …

Applications Of Electronic Structure Theory To Problems In Unimolecular Dissociation And Inorganic And Biochemical Systems, Jia Zhou

Wayne State University Dissertations

In this dissertation, ab initio classical trajectory calculations have been carried out to study the dissociation of acetone radical cation, pentane-2,4-dione radical cation, and 1,3-cyclobutanedione radical cation. For acetone radical cation and pentane-2,4-dione radical cation, MP2 with bond additivity corrections generates a better potential energy surface at low cost and is thus used for molecular dynamics calculations. The dissociation of acetone radical cation is found to favor the loss of the newly formed methyl group in agreement with the experiments. The branching ratios of methyl loss were also calculated with different amount of excess energy and of specific mode excitation. …

Transition Metal-Mediated Higher-Order Cycloaddition Reactions: Application To The Total Synthesis Of Complex Natural Products, Bilal Abou Aleiwi

Wayne State University Dissertations

ABSTRACT

TRANSITION METAL-MEDIATED HIGHER-ORDER CYCLOADDITION REACTIONS: APPLICATION TO THE TOTAL SYNTHESIS OF COMPLEX NATURAL PRODUCTS

by

BILAL ABOU ALEIWI

October 2010

Advisor: Dr. James H. Rigby

Major: Chemistry (Organic)

Degree: Doctor of Philosophy

Chromium (0)-mediated [6ð + 2ð] and [6ð + 2ð + 2ð] cycloaddition reactions between cyclic trienes and alkynes is reported. The development, investigation and the application of these reactions in the total synthesis of complex ring systems and natural products is described. Two natural products, namely, ∆ 9(12) -Capnellene and Echinopines A and B were targeted.

An investigation led to the successful development of a methodology to …

Experimental And Theoretical Analysis Of The Electronic Behavior In Five-Coordinate Iron(Iii) And Six-Coordinate Cobalt(Iii) Complexes With Electroactive Phenol-Rich Ligands, Marco Mathieu Allard

Wayne State University Dissertations

Three 5 coordinate high-spin Iron(III) complexes containing pentadentate N2O5 ligands were synthesized and characterized, namely, (1) [FeIII(L1)] and (2) [FeIII(L2)]. Structural differences in ligand design,N,N,N'-tris(3,5-di-tert-butyl-2-hydroxybenzyl)benzene-1,2-diamine for (1) and N,N,N'-tris-(3,5-di-tert-butyl-2-hydroxybenzyl)-N'-methyl-benzene-1,2-diamine for (2), result in complexes that due to their forced geometry, asymmetry, and slightly different electronic structures are able to foster phenoxyl radicals although show a sensitive dependence to both the solvent and the electrolyte system in the cyclic voltammetry. In the presence of TBAClO4 (1) exhibits a two-electron oxidation, whereas in the presence of TBAPF6 (2), , shows three distinct phenolato/phenoxyl radical couples. Both (1) and (2) were redox-cycled 30 …

Development And Applications Of Thioacids In Peptide Chemistry And Exploration Of Methods Toward The Stereochemical Elucidation And Synthesis Of Virgineone, Kasinath Sana

Wayne State University Dissertations

ABSTRACT

DEVELOPMENT AND APPLICATIONS OF THIOACIDS IN PEPTIDE CHEMISTRY AND EXPLORATION OF METHODS TOWARD THE STEREOCHEMICAL ELUCIDATION AND SYNTHESIS OF VIRGINEONE

by

KASINATH SANA

December 2010

Advisor: David Crich

Major: Chemistry

Degree: Doctor of Philosophy

This dissertation describes investigations toward the development of methods for the synthesis of peptidyl thioacids and thioesters, with particular emphasis on applications in peptide chemistry, and the exploration of methods toward the assignment of the relative and absolute configuration of virgineone and its total synthesis.

The first part of chapter one introduces the general characteristics and reactivity of thioacids, and describes their potential for application …

Synthetic Levers Enabling Control Of Phase, Size And Morphology In Transition Metal Phosphide Nanoparticles (Fe, Ni), Elayaraja Muthuswamy

Wayne State University Dissertations

ABSTRACT

SYNTHETIC LEVERS ENABLING CONTROL OF PHASE, SIZE AND MORPHOLOGY IN TRANSITION METAL PHOSPHIDE NANOPARTICLES (FE, NI)

by

ELAYARAJA MUTHUSWAMY

May 2011

Advisor:Dr. Stephanie L. Brock

Major: Chemistry

Degree: Doctor of Philosophy

This dissertation study focuses on (1) development of a synthetic strategy to control phase in nanoscale iron phosphides; (2) extension of the developed phase control strategy to the nanoscale nickel phosphide system with simultaneous control on size and morphology and (3) illustration of the enhanced reactivity of nanoscale oxide systems.

A synthetic strategy to control phase in nanoscale iron phosphides was developed to prepare phase-pure samples of …

Dechalcogenative Allylic Selenosulfide And Disulfide Rearrangements For Cysteine Modification And Glycoligation, Venkataraman Subramanian

Wayne State University Dissertations

This thesis describes investigations directed at the development of methods for the selenosulfide and disulfide rearrangements for the permanent functionalization of thiols, and in particular of cysteine and carbohydrate based thiols. Emphasis is placed on the newly invented silver mediated allylic desulfurative rearrangement for the primary modification of thiols and the synthesis of complex oligosaccharide mimics.

Chapter one introduces the concept of chemoselective ligations for the modification of macromolecules like carbohydrates and proteins. It overviews the native and non-native ligation techniques for their modification of such entities with a attention focusing on thiol based ligation techniques. The later part of …

Metal Chalcogenide Nanocrystal Assembly: From Synthesis To Applications, Qinghong Yao

Wayne State University Dissertations

This dissertation study is focused on (1) the application of an oxidation-induced sol-gel assembly method to formation of CdTe aerogels; (2) extension of existing aerogel compositions and properties by an alternative synthetic approach: cation-exchange reactions; and (3) probing the functionality of CdSe aerogels as optical sensors of Lewis base analytes.

Highly porous CdTe aerogels were successfully synthesized by sol-gel assembly of CdTe nanocrystals with thiolate or nonthiolate (phosphine oxide) ligated surfaces by treatment with tetranitromethane. Both phosphine oxide-capped and the thiolate-capped aerogels exhibit similar structure, morphology and porosimetry properties, suggesting that precursor ligation does not have a no major effect …

Synthesis And Characterization Of Metal Complexes Containing Tetrazolate, Poly(Tetrazolyl)Borate, And Aryl Pentazole Ligands As High Energy Density Materials, Dongmei Lu

Wayne State University Dissertations

Heavier alkaline earth metal tetrazolates have been prepared as cryatals contain aqua ligands and as anhydrous powders, and were characterized by spectral and analytical methods. Potassium bis(tetrazolyl)borate complexes K(BH₂(RCN₄)₂)(H₂O)_n (R = H, Me, NMe₂, and NiPr₂) and their 18-crown-6 adducts have been synthesized. In the solid state, complexes where R = H and Me have B-N bonds to the nitrogen atoms proximal to the carbon atom, whereas those with R = NMe₂ and NiPr₂ possess isomeric B-N bonds to the nitrogen atoms distal to the …

The Synthesis, Structure, And Properties Of Group 2 Poly(Pyrazolyl)Borates And Their Use For The Atomic Layer Deposition Of Group 2 Borates, Mark J. Saly

Wayne State University Dissertations

A series of heavy alkaline earth complexes containing TpR2-based ligands has been synthesized, structurally characterized, and their properties were investigated. Salt metathesis routes involving MI2 (M = Ca, Sr, Ba) with either KTpEt2 or KTpnPr2 afforded MTpEt22 or MTpnPr22 in good to moderate yields. All of these complexes are volatile and exceptionally thermally stable, and have acceptable properties for use as group 2 atomic layer deposition (ALD) precursors. In addition, a series of group 2 complexes containing BpR2-based ligand systems were synthesized. Treatment of MI2 (M = Ca, Sr, Ba) with two equivalents of TlBptBu2, KBp, and KBpiPr2 in tetrahydrofuran …

I. Microwave-Influenced Diversity-Oriented Synthesis Of Biologically Relevant Small & Natural-Product-Like Molecules Via Multicomponent Coupling Reactions Ii. Synthetic Studies Toward The Total Synthesis Of The Repeating Tetrasaccharide Unit Of Zwitterionic Polysaccharide Ps A1, Soumava Santra

Wayne State University Dissertations

Microwave-influenced diversity-oriented synthesis of biologically relevant small and natural-product-like molecules via multicomponent coupling reactions (MCCRs) have been investigated. Cheap, readily available starting materials in conjunction of microwave irradiation and employment of environmentally benign solvent (e.g. water) provided a common platform that allowed to access a wide array of structurally and skeletally diverse molecules. The investigation allowed us to establish a new paradigm of diversity-activity relationships (DARs) by tuning reacting components of the MCCRs and proved that in contrary to the conventional use of microwave as a rate accelerating tool, it can be used to influence reactivity of molecules. The method …

Synthesis Of Functionalized Gpi Anchors And Related Glycoconjugates, Benjamin M. Swarts

Wayne State University Dissertations

This dissertation is divided into two chapters describing the background, significance, and synthesis of GPI anchors and GPI-anchored molecules. GPI anchors are a class of complex glycolipids with the primary purpose of attaching cell surface proteins/glycoproteins to the cell membrane. The first chapter is focused on the synthesis of functionalized GPI anchors, and begins with an introductory look at the discovery, structure, biosynthesis, and biological functions of GPIs. Then, after surveying progress and achievements in GPI synthesis, including discussion about current strategic shortcomings in the field that prevent the chemical synthesis of various GPI derivatives, our approach to accessing uniquely …

Photodissociation Dynamics In Titan's Atmosphere, Welvidanalage Ruchira Silva

Wayne State University Dissertations

Photodissociation dynamics of molecules relevant to understanding Titan's atmosphere (diacetylene, cyanoacetylene and heptane isomers) are carried out under collisionless condition using the DC slice imaging technique. In diacetylene photodissociation, two-photon processes dominate at 243 nm and 212 nm whereas at 121.6 nm, a one-photon dissociation process dominates. Direct measurement of the lifetime of metastable triplet diacetylene confirms sub-microsecond lifetimes. Photodissociation of cyanoacetylene at 193.3 nm proceeds on the S1 potential energy surface with an exit barrier. In heptane photodissociation, the dissociation occurs on the ground state or low-lying triplet states with nonradiative electronic relaxation. Time-of-flight mass spectroscopy studies in this …

I-Kinetic And Mechanistic Investigations Of Amino Acid Substrates Reactivities With Ferryl Species, Ahmed Ibrahim Youssef Abouelatta

Wayne State University Dissertations

ABSTRACT

I-KINETIC AND MECHANISTIC INVESTIGATIONS OF AMINO ACID SUBSTRATES REACTIVITIES WITH FERRYL SPECIES

II-SYNTHESIS AND CHARACTERIZATION OF DERIVATIVES OF THE BN-TPEN LIGAND AND THEIR METAL COMPLEXES

by

AHMED IBRAHIM YOUSSEF ABOUELATTA

MAY 2011

Advisor: Dr. Jeremy Jacob Kodanko

Major: Chemistry (Organic)

Degree: Doctor of philosophy

The reactivity of tryptophan, methionine, aspartic acid, glutamic acid, histidine and hydrochloride salt of lysine amino acid substrates with the N4Py ferryl species was studied by UV-vis spectroscopy and product characterization. Based on kinetic isotope effect studies and product analysis, an ET-PT mechanism was proposed for the reaction of tryptophan substrate with N4Py ferryl and …

Determination Of Size Distributions In Heterodisperse Systems Of Homogeneous, Non-Absorbing Spheres From Angular Light Scattering Extrema, Werner Bergman

Wayne State University Dissertations

No abstract provided.