Chemistry Commons^™

Spectroelectrochemical Elucidation Of The Kinetics Of Two Closely Spaced Electron Transfers, Robert L. Keesey, Michael D. Ryan

Chemistry Faculty Research and Publications

The use of spectroelectrochemistry to facilitate the analysis of an EE mechanism was reported in this work. Using a set of spectra as a function of potential, the spectra of all three oxidation states were determined using evolving window factor analysis. From these spectra, the concentration of each species in solution was determined for each potential. Using these data, the current was calculated. Unlike the direct measurement of current, the current due to each redox process was determined, allowing one to analyze each redox process separate from the other. With the use of the Butler–Volmer equation, the redox potential and …

Structural Characterization Of Zn(Ii)-, Co(Ii)-, And Mn(Ii)-Loaded Forms Of The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Ye Tao, Jacob E. Shokes, Wade C. Mcgregor, Robert A. Scott, Richard C. Holz

Chemistry Faculty Research and Publications

The Zn, Co, and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectra of the N-acetyl-l-ornithine deacetylase (ArgE) from Escherichia coli, loaded with one or two equivalents of divalent metal ions (i.e., [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)], [Co(II)Co(II)(ArgE)], [Mn(II)_(ArgE)], and [Mn(II)Mn(II)(ArgE)]), were recorded. The Fourier transformed data (FT) for [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)] and [Co(II)Co(II)(ArgE)] are dominated by a peak at 2.05 Å, that can be fit assuming five or six light atom (N,O) scatterers. Inclusion of multiple-scattering contributions from the outer-shell atoms of a histidine-imidazole ring resulted in reasonable Debye–Waller factors for these contributions and a slight reduction …

Sprectral Data For "Generation Of Molecular Complexity From Cyclooctatetraene Using Dienyliron And Olefin Metathesis", Mohamed F. El-Mansy, Anobick Sar, Subhabrata Chaudhury, Nathaniel J. Wallock, William A. Donaldson

Natural Products Synthesis via Organoiron Methodology

Spectral data used in the course of researching "Generation of molecular complexity from cyclooctatetraene using dienyliron and olefin metathesis methodology".

Transformation of the simple hydrocarbon cyclooctatetraene into a variety of polycyclic skeletons was achieved by sequential coordination to iron, reaction with electrophiles followed by allylated nucleophiles, decomplexation and olefin metathesis.

On The Electronic Spectroscopy Of Closed Shell Cations Derived From Resonance Stabilized Radicals: Insights From Theory And Franck-Condon Analysis, T. P. Troy, S. H. Kable, T. W. Schmidt, Scott A. Reid

Chemistry Faculty Research and Publications

Context. Recent attention has been directed on closed-shell aromatic cations as potential carriers of the diffuse interstellar bands. The spectra of mass-selected, matrix-isolated benzylium, and tropylium cations were recently reported. The visible spectrum of benzylium exhibits a large Franck-Condon (FC) envelope, inconsistent with diffuse interstellar band carriers.

Aims. We perform a computational analysis of the experimentally studied benzylium spectrum before extending the methods to a range of larger, closed-shell aromatic cations to determine the potential for this class of systems as diffuse interstellar band carriers.

Methods. Density functional theory (DFT), time-dependent ((TD)DFT), and multi-configurational self-consistent field second-order perturbation theory (MRPT2) …

Generation Of Molecular Complexity From Cyclooctatetraene Using Dienyliron And Olefin Metathesis Methodology, Mohamed F. El-Mansy, Anobick Sar, Subhabrata Chaudhury, Nathaniel J. Wallock, William A. Donaldson

Chemistry Faculty Research and Publications

Transformation of the simple hydrocarbon cyclooctatetraene into a variety of polycyclic skeletons was achieved by sequential coordination to iron, reaction with electrophiles followed by allylated nucleophiles, decomplexation and olefin metathesis.

A Density Functional Theory And Laser Flash Photolysis Investigation Of Carbofuran Photodegradation In Aqueous Medium, A. Atifi, M. Talipov, H. Mountacer, Michael D. Ryan, M. Sarakha

Chemistry Faculty Research and Publications

Density functional theory (DFT) approach was used to study the photodegradation of Carbofuran in aqueous medium. This computational method enables us to assign the electronic transitions and interpret the dissociative behavior upon irradiation based on a thermodynamical analysis of the bond dissociation energies (BDE) of Carbofuran. According to these calculations, phenoxy C---O bond appears weaker than the C---N bonds. Hence, it was predicted that the photodegradation of Carbofuran should occur with an initial homolytic dissociation of the C---O bond of the carbamate moiety. Laser Flash Photolysis (LFP) results clearly indicate the formation of the phenoxyl radical, which support the outcome …

The Impact Of Ligand Design On The Coordination Chemistry And Reactivity Of Metal Pincer Complexes, Sarath Wanniarachchi

Dissertations (1934 -)

Pincer ligands are uninegative tridentate metal-coordinating agents of the form [XZY]- where Z is the central, anchoring Lewis donor while X and Y are flanking Lewis donors. Ever since initial reports of transition metal pincer complexes were published in the late 1970's, there has been burgeoning interest in such complexes because of their desirable robust nature, generally simple syntheses, and the spectacular chemical transformations that they can mediate. In this research project, two new sets of pincer ligands with a diarylamido anchor and either two pyrazolyl nitrogenous flanking donors (NNN pincer) or one pyrazolyl and one diphenylphosphine donor (NNP pincer) …

Synthesis And Characterization Of Iron(Ii) Complexes Modeling The Active Site Structure Of Nonheme Iron Dioxygenases, Jacob Baus

Master's Theses (2009 -)

The aerobic degradation of polycyclic aromatic compounds, which are widespread contaminants in soils and groundwaters, is carried-out in large part by various Fe-containing dioxygenases that perform the cis-dihydroxylation and oxidative cleavage of aromatic rings. Recently, a new Fe dioxygenase family emerged that catalyzes a remarkable set of transformations; the distinguishing feature of these enzymes is that their monoiron(II) centers are coordinated by three histidines residues (i.e., imidazole ligands) in a facial geometry - a departure from the "canonical" 2-histidine-1-carboxylate facial triad that is dominant among nonheme monoiron enzymes. Members of the "3His family" are capable of oxidatively cleaving C-C bonds …

Computational Study Of Vibrational Qubits In Anharmonic Linear Ion Traps, Lei Wang

Dissertations (1934 -)

A string of cold ions confined in a linear trap represents a man-made quantum object with a broad range of applications in atomic and molecular spectroscopy, such as high-precision measurement of atomic properties. An efficient isolation from the environment guarantees excellent coherent properties of such systems and makes them suitable for practical realization of the quantum information processing. The pioneering theoretical [Cirac and Zoller] and experimental [Wineland and Monroe] work in 1990s resulted in the explosive expansion of this field during the last decade. In this dissertation an alternative new method for controlling the quantized motional/vibrational states of ions in …

Design, Synthesis And Study Of Polycyclic Aromatic Hydrocarbons And Their Cation Radicals, Tushar Navale

Dissertations (1934 -)

The unifying theme of most of optoelectronic devices revolves around the charge carrier mobility of the organic materials used in the conductive layers, which is a measure of how easily the electron/hole moves in a particular pi conjugated organic material. When pi conjugated materials are incorporated in these devices, molecules are generally layered in random orientation. Consequently, the efficiency of charge transport in the conducting layers of these devices is governed not only by the intramolecular electron/hole transport through the backbone of the molecule but also by the intermolecular electron/hole transport between the molecules and hence packing of these molecules …

Synthesis And Study Of Electro-Active Organic Molecules For Optoelectronic Applications, Shriya Wadumethrige

Dissertations (1934 -)

Electro-active organic materials have received considerable attention in the emerging area of molecular electronics and nanotechnology not only because of the attractive optical and electronic properties but also the advantages of organic materials such as low cost, easy processing, and great opportunities for structural modification. These materials are now being considered as active components in electronic and optoelectronic devices such as light emitting diodes for display applications, thin film transistors for low-cost and ultra-dense logic and memory circuits, photodiodes for optical information processing, and photovoltaic cells for solar energy harvesting. Therefore the electro-active organic materials have become a focus of …

Design And Synthesis Of Polycyclic Aromatic Hydrocarbons For Emission And Through-Space Charge Delocalization Studies, Vijay Vyas

Dissertations (1934 -)

Over the past decades, a variety of pi-conjugated organic materials have been explored as potential charge transport materials in conducting layers of photovoltaic devices. The performance of these devices critically depend on the efficiency with which the charge carriers (electrons and/or holes) move within the pi-conjugated materials present in their hole and electron conducting layers before their collection at the electrode. Hence, a large amount of research effort is devoted not only to the preparation of new pi-conjugated organic molecules for charge transport applications but also in understanding the nature of charge transport along the molecule (intra-chain) as well as …

Assignments Of Backbone 1h, 13c And 15n Resonances In H-Ras (1–166) Complexed With Gppnhp At Physiological Ph, Casey O'Connor, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

The small GTPase Ras is an important signaling molecule acting as a molecular switch in eukaryotic cells. Recent findings of global conformational exchange and a putative allosteric binding site in the G domain of Ras opened an avenue to understanding novel aspects of Ras function. To facilitate detailed NMR studies of Ras in physiological solution conditions, we performed backbone resonance assignments of Ras bound to slowly hydrolysable GTP mimic, guanosine 5′-[ß, γ-imido]triphosphate at pH 7.2. Out of 163 non-proline residues of the G domain, signals from backbone amide proton, nitrogen and carbon spins of 127 residues were confidently assigned with …

Synthesis And Structural Characterization Of Iron(Ii) Complexes With Tris(Imidazolyl)Phosphane Ligands: A Platform For Modeling The 3-Histidine Facial Triad Of Nonheme Iron Dioxygenases, Michael M. Bittner, Jacob Baus, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

Several monoiron(II) complexes containing tris(imidazolyl)phosphane (TIP) ligands have been prepared and structurally characterized by using X-ray crystallography and NMR spectroscopy. Two TIP ligands were employed: tris(2-phenylimidazol-4-yl)phosphane (4-TIP^Ph) and tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphane (2-TIP^Ph2). These tridentate ligands resemble the 3-histidine (3His) facial triad found recently in the active sites of certain nonheme iron dioxygenases. Three of the reported complexes are designed to serve as convenient precursors to species that model the enzyme–substrate intermediates of 3His dioxygenases; thus, each contains an [Fe(κ³-TIP)]²⁺ unit in which the remaining coordination sites are occupied by easily displaced ligands, such as solvent …

Visible And Infrared Spectroelectrochemistry Of Cobalt Porphinones And Porphinediones, Florentina Tutunea, Michael D. Ryan

Chemistry Faculty Research and Publications

The visible and infrared spectroelectrochemistry of the redox chemistry of Co^II–porphinone complexes were examined and compared with similar studies of the respective iron complexes. Cobalt(II) porphinone complexes undergo a one-electron reduction and two one-electron oxidations within the potential region that was studied in this work. The one electron spectroelectrochemical reduction of Co^II(P) (P = octaethylporphyrin (OEP), octaethylporphinone (OEPone), and octaethylporphinedione (OEPdione)) were studied using visible spectroscopy, and their cobalt(I) complexes were characterized. The same reduction was examined by FTIR spectroscopy for P = OEPone and OEPdione. The infrared spectra showed downshifts of the ν_CO band …

Reactivity Of Tri(2-Furyl)Phosphine (Pfu3) With [Mn2(Co)10–N(Ncme)N] (N = 0–2): X-Ray Structure Of Mer-[Mn(Co)3(Η1-C4H3O)(Pfu3)2], Santana Karmaker, Shishir Ghosh, Shariff E. Kabir, Daniel T. Haworth, Sergey V. Lindeman

Chemistry Faculty Research and Publications

In the search for new examples of systems that self-assemble into cyclic metal–organic architectures, the six isomers of X,Y′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L_XY, and their silver(I) trifluoromethanesulfonate complexes were prepared. Five of the six silver complexes gave crystals suitable for single crystal X-ray diffraction, with only the microcrystalline derivative of 2,3′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L₂₃, proving to be unsuitable for this analysis. Of the structurally characterized silver(I) complexes, that with L₂₂ showed an unusual trans-spanning chelating coordination mode to silver. At the same time the ligand was also bound to a second silver center …

Scope And Mechanistic Study Of The Coupling Reaction Of Α,Β-Unsaturated Carbonyl Compounds With Alkenes: Uncovering Electronic Effects On Alkene Insertion Vs Oxidative Coupling Pathways, Ki Hyeok Kwon, Do W. Lee, Chae S. Yi

Chemistry Faculty Research and Publications

The cationic ruthenium-hydride complex [(C₆H₆)(PCy₃)(CO)RuH]⁺BF₄^– (1) was found to be a highly effective catalyst for the intermolecular conjugate addition of simple alkenes to α,β-unsaturated carbonyl compounds to give (Z)-selective tetrasubstituted olefin products. The analogous coupling reaction of cinnamides with electron-deficient olefins led to the oxidative coupling of two olefinic C–H bonds in forming (E)-selective diene products. The intramolecular version of the coupling reaction efficiently produced indene and bicyclic fulvene derivatives. The empirical rate law for the coupling reaction of ethyl cinnamate with propene was …

Improved Potential Energy Surface Of Ozone Constructed Using The Fitting By Permutationally Invariant Polynomial Function, M. Ayouz, Dmitri Babikov

Chemistry Faculty Research and Publications

New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are added to …

Recent Applications Of The Simple Hydrocarbon Cyclooctatetrene As A Starting Material For Complex Molecule Synthesis, Kevin W. Glaeske, William A. Donaldson

Chemistry Faculty Research and Publications

Cyclooctatetraene [COT], a simple non-aromatic cyclic polyene, is capable of undergoing a variety of oxidation and cycloaddition reactions to afford polycyclic structures. In addition, complexation of COT or the cycloaddition products with transition metals facilitates bond formation. Recent developments in the reactivity of COT and application to the synthesis of naturally occurring and non-naturally occurring compounds is reviewed.

Spectroscopy And Dynamics Of The Predissociated, Quasi-Linear S2 State Of Chlorocarbene, Chong Tao, Craig A. Richmond, Calvin Mukarakate, S. H. Kable, Eric C. Brown, Richard Dawes, Phalgun Lolur, Scott A. Reid

Chemistry Faculty Research and Publications

In this work, we report on the spectroscopy and dynamics of the quasi-linear S₂ state of chlorocarbene, CHCl, and its deuterated isotopologue using optical-optical double resonance (OODR) spectroscopy through selected rovibronic levels of the S₁ state. This study, which represents the first observation of the S₂ state in CHCl, builds upon our recent examination of the corresponding state in CHF, where pronounced mode specificity was observed in the dynamics, with predissociation rates larger for levels containing bending excitation. In the present work, a total of 14 S₂ state vibrational levels with angular momentum ℓ = 1 …

Potential Energy And Dipole Moment Surfaces Of Hco- For The Search Of H- In The Interstellar Medium, M. Ayouz, I. Mikhailov, Dmitri Babikov, M. Raoult, S. Galtier, O. Dulieu, V. Kokoouline

Chemistry Faculty Research and Publications

Potential energy and permanent dipole moment surfaces of the electronic ground state of formyl negative ion HCO− are determined for a large number of geometries using the coupled-cluster theory with single and double and perturbative treatment of triple excitations ab initio method with a large basis set. The obtained data are used to construct interpolated surfaces, which are extended analytically to the region of large separations between CO and H− with the multipole expansion approach. We have calculated the energy of the lowest rovibrational levels of HCO− that should guide the spectroscopic characterization of HCO− in laboratory experiments. The study …

Polysaccharide Ecocomposite Materials: Materials: Synthesis, Characterization And Application For Removal Of Pollutants And Bacteria, Simon Duri, Bilal El-Zahab, Chieu D. Tran

Chemistry Faculty Research and Publications

A novel, simple and totally recyclable method has been developed for the synthesis of nontoxic, biocompatible and biodegradable composite materials from cellulose and chitosan. In this method, [BMIm+Cl-], an ionic liquid (IL), was used as a solvent to dissolve and synthesize the [CEL+CS] composite materials. Since the IL can be removed from the materials by washing them with water, and recovered from the washed solution, the method is totally recyclable. XRD, FTIR, NIR and SEM were used to characterize the materials and to confirm that CEL and CS were successfully regenerated by the method without any chemical transformation. More importantly, …

A Chemical Proteomic Probe For Detecting Dehydrogenases: Catechol Rhodanine, Xia Ge, Daniel S. Sem

Chemistry Faculty Research and Publications

The inherent complexity of the proteome often demands that it be studied as manageable subsets, termed subproteomes. A subproteome can be defined in a number of ways, although a pragmatic approach is to define it based on common features in an active site that lead to binding of a common small molecule ligand (ex. a cofactor or a cross-reactive drug lead). The subproteome, so defined, can be purified using that common ligand tethered to a resin, with affinity chromatography. Affinity purification of a subproteome is described in the next chapter. That subproteome can then be analyzed using a common ligand …

Nmr Line Shapes And Multi-State Binding Equilibria, Evgenii L. Kovrigin

Chemistry Faculty Research and Publications

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule …

Charge Delocalization In Self-Assembled Mixed-Valence Aromatic Cation Radicals, Tushar Navale, Khushabu Thakur, Vijay Vyas, Shriya Wadumethrige, Ruchi Shukla, Sergey V. Lindeman, Rajendra Rathore

Chemistry Faculty Research and Publications

The spontaneous assembly of aromatic cation radicals (D^+•) with their neutral counterpart (D) affords dimer cation radicals (D₂^+•). The intermolecular dimeric cation radicals are readily characterized by the appearance of an intervalence charge-resonance transition in the NIR region of their electronic spectra and by ESR spectroscopy. The X-ray crystal structure analysis and DFT calculations of a representative dimer cation radical (i.e., the octamethylbiphenylene dimer cation radical) have established that a hole (or single positive charge) is completely delocalized over both aromatic moieties. The energetics and the geometrical considerations for the formation …

Preparation, Properties, And Reactivity Of Carbonylrhodium(I) Complexes Of Di(2-Pyrazolylaryl)Amido-Pincer Ligands, Sarath Wanniarachchi, Brendan J. Liddle, Sergey V. Lindeman, James R. Gardinier

Chemistry Faculty Research and Publications

A series of six carbonylrhodium(I) complexes of three new and three previously reported di(2-3R-pyrazolyl)-p-Z/X-aryl)amido pincer ligands, (^RZX)Rh(CO), (R is the substituent at the 3-pyrazolyl position proximal to the metal; Z and X are the aryl substituents para- to the arylamido nitrogen) were prepared. The metal complexes were studied to assess how their properties and reactivities can be tuned by varying the groups along the ligand periphery and how they compared to other known carbonylrhodium(I) pincer derivatives. This study was facilitated by the discovery of a new CuI-catalyzed coupling reaction between 2-(pyrazolyl)-4-X-anilines (X = Me or …

Reactivity Of Acyclic (Pentadienyl)Iron(1+) Cations: Synthetic Studies Directed Toward The Frondosins, Do W. Lee, Rajesh K. Pandey, Sergey V. Lindeman, William A. Donaldson

Chemistry Faculty Research and Publications

A short, 4-step route to the scaffold of frondosin A and B is reported. The [1-methoxycarbonyl-5-(2′,5′-dimethoxyphenyl)pentadienyl]Fe(CO)₃⁺ cation was prepared in two steps from (methyl 6-oxo-2,4-hexadienoate)Fe(CO)₃. Reaction of this cation with isopropenyl Grignard or cyclohexenyllithium reagents affords (2-alkenyl-5-aryl-1-methoxycarbonyl-3-pentene-1,5-diyl)Fe(CO)₃ along with other addition products. Oxidative decomplexation of these (pentenediyl)iron complexes, utilizing CuCl₂, affords 6-aryl-3-methoxycarbonyl-1,4-cycloheptadienes via the presumed intermediacy of a cis-divinylcyclopropane.

Removal Of 2,4-Dichlorophenoxyacetic Acid By Calcined Zn–Al–Zr Layered Double Hydroxide, Allen Chaparadza, Jeanne Hossenlopp

Chemistry Faculty Research and Publications

The adsorption equilibrium, kinetics, and thermodynamics of removal of 2,4-dichlorophenoxy-acetic acid (2,4-D) from aqueous solutions by a calcined Zn–Al layered double hydroxide incorporated with Zr⁴⁺ were studied with respect to time, temperature, pH, and initial 2,4-D concentration. Zr⁴⁺ incorporation into the LDH was used to enhance 2,4-D uptake by creating higher positive charges and surface/layer modification of the adsorbent. The LDH was capable of removing up to 98% of 2,4-D from 5 to 400 ppm aqueous at adsorbent dosages of 500 and 5000 mg L⁻¹. The adsorption was described by a Langmuir-type isotherm. The percentage 2,4-D …

Analysis Of Binding Site Hot Spots On The Surface Of Ras Gtpase, Greg Buhrman, Casey O'Connor, Brandon Zerbe, Bradley M. Kearney, Raeanne Napoleon, Elizaveta A. Kovrigina, Sandor Vajda, Dima Kozakov, Evgenii L. Kovrigin, Carla Mattos

Chemistry Faculty Research and Publications

We have recently discovered an allosteric switch in Ras, bringing an additional level of complexity to this GTPase whose mutants are involved in nearly 30% of cancers. Upon activation of the allosteric switch, there is a shift in helix 3/loop 7 associated with a disorder to order transition in the active site. Here, we use a combination of multiple solvent crystal structures and computational solvent mapping (FTMap) to determine binding site hot spots in the “off” and “on” allosteric states of the GTP-bound form of H-Ras. Thirteen sites are revealed, expanding possible target sites for ligand binding well beyond the …

Nmr And Computational Studies Of Nad(P)(H) Cofactor Binding, Junghwa Kim

Master's Theses (2009 -)

Tuberculosis (TB) is one of the most dangerous diseases in a sense of spread method. According W.H.O., one third of world population has this disease and annual one of these infected people spreads 10 -15 people unintentionally. To protect human from this bacterial, the unique feature of mycrobacterial [sic] TB was studied previously. The unique cell wall, peptidoglycan, has high content of DAP (diaminopimelic acid). The disruption of synthesis DAP results in cell death due to instability of cell wall. One way to inhibiting synthesis of DAP is to modify cofactor which acts with dehydrogenase. To do that the study …