Chemistry Commons^™

Structure, Dynamics, And Redox Reactivity Of An All-Purpose Flavodoxin, Sharique Khan, Ahmadullah Ansari, Monica Brachi, Debarati Das, Wassim El Housseini, Shelley Minteer, Anne Frances Miller

Chemistry Faculty Research & Creative Works

The Flavodoxin Of Rhodopseudomonas Palustris CGA009 (Rp9Fld) Supplies Highly Reducing Equivalents To Crucial Enzymes Such As Hydrogenase, Especially When The Organism Is Iron-Restricted. By Acquiring Those Electrons From Photodriven Electron Flow Via The Bifurcating Electron Transfer Flavoprotein, Rp9Fld Provides Solar Power To Vital Metabolic Processes. To Understand Rp9Fld's Ability To Work With Diverse Partners, We Solved Its Crystal Structure. We Observed The Canonical Flavodoxin (Fld) Fold And Features Common To Other Long-Chain Flds But Not All The Surface Loops Thought To Recognize Partner Proteins. Moreover, Some Of The Loops Display Alternative Structures And Dynamics. To Advance Studies Of Protein–protein Associations …

Investigation Of Electron Transfer In The Ksha-Kshb-R286a Protein Complex From Mycobacterium Tuberculosis, Elyse Tavares

Honors Program Theses and Projects

With drug-resistant bacteria such as Mycobacterium tuberculosis being a serious public health problem, infected individuals have minimal treatment options. By investigating the electron transfer within 3-ketosteroid-9��-hydroxylase (KshAB), a protein involved in the energy production pathway of this bacteria, it will allow for potential inhibitors of this enzyme to be designed as antibiotics against tuberculosis. The purpose of this project is to stop the interaction between the KshA and KshB complexes to prevent the bacteria from gaining energy by breaking down steroids like cholesterol. To achieve this goal, an arginine at the 286th position of the KshB protein was mutated to …

Using Cyclic-Step Chronopotentiometry To Explore Electron Mobility In Dye-Sensitized Solar Cells, Jasmine Hopson, Ian Mcneil

Honors Projects

In this project, we are making dye-sensitized solar cells using titanium dioxide and the dye from raspberries. We are exploring how electrons diffuse through these systems. To do this, we perform cyclic chronopotentiometry where we cycle between periods of applying a voltage to achieve a certain current and periods where the current is stopped. We focus on the time-dependent decay of the voltage when the current is stopped and fit these decays with a bi-exponential model. We compare the results of devices with and without lithium perchlorate in the electrolyte solution since lithium lowers the energies of the acceptor states …

Exploring Electron-Sink Behaviors Of Molecular Assemblies, Yume Mai

Boise State University Theses and Dissertations

Metal carbonyl clusters, such as the [Ni₃₂C₆(CO)₃₆]^6- anion, have been documented to display electron-sink phenomena. However, such large clusters suffer from inefficient yields due to their demanding and unreliable synthesis routes. To approach this obstacle, we investigated the electrochemical properties of Fe₂(μ-PPh₂)₂(CO)₆, an organometallic complex known to experience a reversible two-electron transfer process. In this work, we report a modular synthetic strategy for expanding the electron-sink capacity of molecular assemblies by installing Fe₂(μ-PPh₂)₂(CO)₆ redox mediators to arylisocyanide ligands. …

Synthesis Of Novel Porphyrin Derived Molecules For The Study Of Self Assembly And Photophysical Properties, Alex Nguyen

Williams Honors College, Honors Research Projects

The photochemical capabilities of self-assembling porphyrins holds the potential to eliminate the use of fossil fuels. Porphyrins have the ability to absorb solar energy to excite its electrons within the highly conjugated π system of the porphyrin ring. The excited electron can then be donated thus creating a charge separated state between the porphyrin donor and the electron acceptor. With self-assembly of porphyrin monomers into a supramolecular structure, this charge separated state can be emphasized and prolonged so the energy potential generated can be harvested. Here, the synthesis of porphyrin derivatives substituted with biologically found molecules is described. The lysine …

Ru(Ii)-Diimine Complexes And Cytochrome P450 Working Hand-In-Hand, Celine Eidenschenk, Lionel Cheruzel

Faculty Publications, Chemistry

With a growing interest in utilizing visible light to drive biocatalytic processes, several light-harvesting units and approaches have been employed to harness the synthetic potential of heme monooxygenases and carry out selective oxyfunctionalization of a wide range of substrates. While the fields of cytochrome P450 and Ru(II) photochemistry have separately been prolific, it is not until the turn of the 21st century that they converged. Non-covalent and subsequently covalently attached Ru(II) complexes were used to promote rapid intramolecular electron transfer in bacterial P450 enzymes. Photocatalytic activity with Ru(II)-modified P450 enzymes was achieved under reductive conditions with a judicious choice of …

Building On Nature: Spectroscopic Studies Of Photosynthesis-Inspired Pigments, Fused Light Harvesting Proteins, And Bacterial Reaction Center Mutants, Kaitlyn Faries

Arts & Sciences Electronic Theses and Dissertations

Photosynthesis is the dominant form of solar energy conversion on the planet, making it critical to understand the fundamentals of the process in order to effectively mimic and improve upon it for human energy needs. The initial stages of photosynthesis include light harvesting and chemical conversion of that harvested energy via electron transport, with both of these stages relying on pigments (or chromophores) such as chlorophyll and specific protein architectures for the processes. In this work, the fundamental underpinnings of photosynthetic light harvesting and electron transport are explored via spectroscopy of various photosynthetic systems with altered natural pigments and proteins. …

Distinct Properties Underlie Flavin-Based Electron Bifurcation In A Novel Electron Transfer Flavoprotein Fixab From Rhodopseudomonas Palustris, H. Diessel Duan, Carolyn E. Lubner, Monika Tokmina-Lukaszewska, George H. Gauss, Brian Bothner, Paul W. King, John W. Peters, Anne-Frances Miller

Chemistry Faculty Publications

A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV–visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to …

Fhbc, A Hexa‐Peri‐Hexabenzocoronene–Fluorene Hybrid: A Platform For Highly Soluble, Easily Functionalizable Hbcs With An Expanded Graphitic Core, Tushar S. Navale, Maxim V. Ivanov, Mohammad M. Hossain, Rajendra Rathore

Chemistry Faculty Research and Publications

Materials based upon hexa‐peri‐hexabenzocoronenes (HBCs) show significant promise in a variety of photovoltaic applications. There remains the need, however, for a soluble, versatile, HBC‐based platform, which can be tailored by incorporation of electroactive groups or groups that can prompt self‐assembly. The synthesis of a HBC–fluorene hybrid is presented that contains an expanded graphitic core that is highly soluble, resists aggregation, and can be readily functionalized at its vertices. This new HBC platform can be tailored to incorporate six electroactive groups at its vertices, as exemplified by a facile synthesis of a representative hexaaryl derivative of FHBC. Synthesis of …

Unraveling The Coulombic Forces In Electronically Decoupled Bichromophoric Systems During Two Successive Electron Transfers, Maxim V. Ivanov, Shriya Wadumethrige, Denan Wang, Rajendra Rathore

Chemistry Faculty Research and Publications

Coulombic forces are vital in modulating the electron transfer dynamics in both synthetic and biological polychromophoric assemblies, yet quantitative studies of the impact of such forces are rare, as it is difficult to disentangle electrostatic forces from simple electronic coupling. To address this problem, the impact of Coulombic interactions in the successive removal of two electrons from a model set of spirobifluorenes, where the interchromophoric electronic coupling is nonexistent, is quantitatively assessed. By systematically varying the separation of the bifluorene moieties using model compounds, ion pairing, and solvation, these interactions, with energies up to about 0.4 V, are absent at …

Oxidation Of Substituted Catechols At The Air-Water Interface: Production Of Carboxylic Acids, Quinones, And Polyphenols, Elizabeth A. Pillar, Marcelo I. Guzman

Chemistry Faculty Publications

Anthropogenic activities contribute benzene, toluene, and anisole to the environment, which in the atmosphere are converted into the respective phenols, cresols, and methoxyphenols by fast gas-phase reaction with hydroxyl radicals (HO(•)). Further processing of the latter species by HO(•) decreases their vapor pressure as a second hydroxyl group is incorporated to accelerate their oxidative aging at interfaces and in aqueous particles. This work shows how catechol, pyrogallol, 3-methylcatechol, 4-methylcatechol, and 3-methoxycatechol (all proxies for oxygenated aromatics derived from benzene, toluene, and anisole) react at the air-water interface with increasing O3(g) during τc ≈ 1 μs contact time and contrasts their …

Mechanism Of Rapid Electron Transfer Reactions Involving Cytochrome Bc1, Cytochrome C And Cytochrome Oxidase, Jeremy Erik Durchman

Graduate Theses and Dissertations

Electron transfer between mitochondrial proteins complexes represents the primary means by which living things acquire the requisite energy for survival. The coupling of electron transfer to proton translocation creates an electrochemical gradient that drives the synthesis of highly energetic compounds such as ATP. The purpose of these studies is to measure rates of electron transfer and elucidate the important governing factors in the redox events involving cytochrome bc1, cytochrome c and cytochrome oxidase. Using rapid initiation of redox events triggered by laser flash excitation of ruthenium compounds, and strategically monitoring unique spectral properties of these proteins in the visible region …

Electron Transfer During Metal-Assisted And Stain Etching Of Silicon, Kurt W. Kolasinski

Chemistry Faculty Publications

The etching of silicon in fluoride solutions is limited by the kinetics of charge transfer not thermodynamics. This characteristic is what gives fluoride etching its great versatility in making different types of nanostructures as the result of self-limiting chemistry. This review approaches the kinetics of electron transfer from silicon and metal coated silicon to a solution phase species from a fundamental point of view in order to establish a better understanding of the mechanisms of nanostructure formation during metal assisted and stain etching of silicon. Band bending calculations demonstrate that diffusion of holes away from low work function metals such …

Electrochemical Catalysis: A Dft Study, Li Li, Zi-Dong Wei

Journal of Electrochemistry

In this review, we focus on achievements in electro-catalysis based on the density function theory study. The relationships among the electrode potential, electronic structure of catalysts and electro-catalytic activity are summarized in three parts: the adsorption and desorption of species, electron transfer, and stability of catalysts. The electrode potential and the electronic structure (d-band center or Fermi (HOMO) energy) of catalysts significantly influence the formation, adsorption and desorption of surface species on electrode. The electro-catalytic activity can be improved by modulating the electrode potential and electronic structure of catalysts.

Electron Transfer In Pnicogen Bond, Liangyu Guan

Masters Theses

Abstract is available for download as a separate file.

Co2 Reduction Under Periodic Illumination Of Zns, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

The photoreduction of CO₂ to formate (HCOO^–) in sphalerite (ZnS) aqueous suspensions is systematically studied in the presence of Na₂S hole scavenger. A series of cut-on filters at λ_cut-on ≥ 280, 295, 305, 320, and 400 nm are used to measure the reaction rate of formate production. The dependence of the measured reaction rates on λ_cut-on indicates that a wavelength of λ = 345 nm is associated with the actual bandgap of the semiconductor nanocrystallites suspended in water. The results from apparent quantum yield measurements during periodic illumination experiments suggest that (1) valence-band …

Size-Dependent Interactions Of Metal Nanoparticles With Fluorophores And Semiconductors, Liyana A. Wajira Ariyadasa

Dissertations

In recent years, nanoscale metallic particles have gained considerable interest due to their potential applications in advanced technology. Despite such interest, synthetic procedures that produce gram-scale, well-defined metallic nanoparticles with controlled size and shape, especially with diameters less than 5 nm remains a challenge. Our work has focused on developing synthetic procedures that produce well-defined platinum and palladium metal nanoparticles in the 1-5 nm size range. Thioether ligands were used as stabilizers and resulted in metal nanoparticles with controlled size. The nanoparticles were characterized using transmission electron microscopy (TEM), x-ray diffraction (XRD), selected area electron diffraction (SAED), x-ray photoelectron spectroscopy …

The Mechanism Of Galvanic/Metal-Assisted Etching Of Silicon, Kurt W. Kolasinski

Chemistry Faculty Publications

No abstract provided.

Charge-Pairing Interactions Control The Conformational Setpoint And Motions Of The Fmn Domain In Neuronal Nitric Oxide Synthase, Mohammad Mahfuzul Haque, Mekki Bayachou, Mohammed A. Fadlalla, Deborah Durra, Dennis J. Stuehr

Chemistry Faculty Publications

The NOS (nitric oxide synthase; EC 1.14.13.39) enzymes contain a C-terminal flavoprotein domain [NOSred (reductase domain of NOS)] that binds FAD and FMN, and an N-terminal oxygenase domain that binds haem. Evidence suggests that the FMN-binding domain undergoes large conformational motions to shuttle electrons between the NADPH/FAD-binding domain [FNR (ferredoxin NADP-reductase)] and the oxygenase domain. Previously we have shown that three residues on the FMN domain (Glu(762), Glu(816) and Glu(819)) that make charge-pairing interactions with the FNR help to slow electron flux through nNOSred (neuronal NOSred). In the present study, we show that charge neutralization or reversal at each of …

Effect Of Side Chains On Organic Donor (D) And Acceptor (A) Complexes And Photophysical Properties Of D-A Dyads, Amarnath Bheemaraju

Open Access Dissertations

This dissertation aims to understand the effect of incompatible side chains on the complexes of pi-conjugated electron-rich donors and electron-deficient acceptors in solution. The role of incompatible side chains were studied in simple mixtures of organic donor and acceptor molecules that form donor-acceptor complexes. The incompatible branched and linear alkane side chains on the acceptor and donor respectively prevented complex formation between naphthalene diimide acceptor and naphthalene ether donor. However, the incompatible hydrocarbon-fluorocarbon and polar-non polar side chain pairs did not affect complex formation between the donor and acceptor. In quaterthiophene-naphthalene diimide dyads, the incompatibility of the side chain on …

Reduced Electronic Spaces For Modeling Donor/Acceptor Interactions, Robert J. Cave, Stephen T. Edwards '06, John A, Kouzelos '07, Marshall D. Newton

All HMC Faculty Publications and Research

Diabatic states for donor (D) and acceptor (A) interactions in electron transfer (ET) processes are formulated and evaluated, along with coupling elements (H_DA) and effective D/A separation distances (r_DA), for reduced electronic spaces of variable size, using the generalized Mulliken Hush model (GMH), applicable to an arbitrary state space and nuclear configuration, and encompassing Robin−Day class III and as well as class II situations. Once the electronic state space is selected (a set of n ≥ 2 adiabatic states approximated by an orbital space based on an effective 1-electron (1-e) Hamiltonian), the charge-localized GMH …

Intermolecular Electron Transfer Reactivity And Dynamics Of Cytochrome C – Nanoparticle Adducts, Adrienne M. Carver

Open Access Dissertations

Interprotein electron transfer (ET) is crucial for natural energy conversion and a fundamental reaction in the pursuit of understanding the broader problem of proteinprotein interactions and reactivity. Simplifying the complicated nature of these natural systems has driven development of biomimetic approaches. Functionalized gold nanoparticles offer simplified, tunable surfaces that can serve as a proxy to study the reactivity and dynamics of proteins. Amino-acid functionalized gold nanoparticles (Au-TX) served as a complementary partner to cytochrome c (Cyt c) and catalyzed its ET reactivity without altering the native structure. Redox mediator and EPR experiments confirmed that the redox potential and coordination environment …

Molecular Designs Toward Improving Organic Photovoltaics, Arpornrat Nantalaksakul

Doctoral Dissertations 1896 - February 2014

Organic photovoltaics (OPVs) that have been studied to date have poor power conversion efficiencies. This dissertation focuses on various molecular designs that could lead to both a fundamental understanding of photoinduced charge separation at a molecular level and also provide a solution to improve bulk properties of organic materials to overcome the poor efficiencies of OPV devices.

The effect of molecular architectures on the efficiency of electron transfer, a primary step in OPVs functioning, is evaluated in this work. We have shown that even though dendrimer provides an interesting architecture for efficient electron transfer due to the presence of multiple …

Coupling Coherence Distinguishes Structure Sensitivity In Protein Electron Transfer, Tatiana Prytkova, Igor V. Kurnikov, David Beratan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantum mechanical analysis of electron tunneling in nine thermally fluctuating cytochrome b562 derivatives reveals two distinct protein-mediated coupling limits. A structure-insensitive regime arises for redox partners coupled through dynamically averaged multiple-coupling pathways (in seven of the nine derivatives) where heme-edge coupling leads to the multiple-pathway regime. A structure-dependent limit governs redox partners coupled through a dominant pathway (in two of the nine derivatives) where axial-ligand coupling generates the single-pathway limit and slower rates. This two-regime paradigm provides a unified description of electron transfer rates in 26 ruthenium-modified heme and blue-copper proteins, as well as in numerous photosynthetic proteins.

Ferritin: Mechanistic Studies And Electron Transfer Properties, Bo Zhang

Theses and Dissertations

Ferritins are ubiquitous iron storage proteins in living systems. Although much is known about the iron deposition process in ferritin and a mechanism has been developed, several important issues still remain unknown. One lingering question is the less than stoichiometric quantities of hydrogen peroxide detected in previous studies on animal ferritins. Extensive experimental data on identifying the species in competition for peroxide equivalents point to a surprising conclusion that H2O2 generated in the ferroxidase reaction is consumed by amine buffers that are commonly employed in in vitro ferritin studies, while non-nitrogen containing buffers, such as acetate, phosphate, and carbonate, do …

Multistate Effects In Calculations Of The Electronic Coupling Element For Electron Transfer Using The Generalized Mulliken−Hush Method, Michael Rust '01, Jason Lappe '00, Robert J. Cave

All HMC Faculty Publications and Research

A simple diagnostic is developed for the purpose of determining when a third state must be considered to calculate the electronic coupling element for a given pair of diabatic states within the context of the generalized Mulliken−Hush approach (Chem. Phys. Lett. 1996, 275, 15−19). The diagnostic is formulated on the basis of Löwdin partitioning theory. In addition, an effective 2-state GMH expression is derived for the coupling as it is modified by the presence of the third state. Results are presented for (i) a model system involving charge transfer from ethylene to methaniminium cation, (ii) a …

Article Are Hydrogen Bonds Unique Among Weak Interactions In Their Ability To Mediate Electronic Coupling?, Emily Cukier '03, Sarah Daniels '02, Eric Vinson '01, Robert J. Cave

All HMC Faculty Publications and Research

Superexchange effects on the electronic coupling element for electron transfer are investigated using water dimers and atomic donors and acceptors. We compare the electronic coupling elements obtained with H-bonded dimers to those obtained for other water dimer geometries at given donor−acceptor and oxygen−oxygen distances. The H-bonded orientation does not yield significantly different coupling elements from non-H-bonded orientations at a given oxygen−oxygen distance. In addition, the distance dependence of the coupling mediated by H-bonds is not significantly different from that for other dimer geometries. It is found that protonation of the intervening waters has a significant effect on coupling elements for …

A Theoretical Study Of The Electronic Coupling Element For Electron Transfer In Water, Newt E. Miller '99, Matthew C. Wander '97, Robert J. Cave

All HMC Faculty Publications and Research

The electronic coupling element for electron transfer between a donor and acceptor in water is examined using simulations combining molecular dynamics and semiempirical quantum mechanics. In the first phase of the simulations a model donor and acceptor are solvated in water, using realistic potentials. Following equilbration, molecular dynamics simulations are performed with the donor, acceptor, and water at approximately 300 K, under periodic boundary conditions. In the second phase of the simulation, the electronic coupling element between the donor and acceptor is calculated for a number of time slices, in the presence of the intervening water molecules (those having a …

Distance Dependence Of Electron Transfer Along Artificial Beta-Strands At 298 And 77 K, S. R. L. Fernando, Gennady V. Kozlov, Michael Y. Ogawa

Chemistry Faculty Publications

Photoinduced electron-transfer rate constants were measured for a series of binuclear metallopeptides consisting of a [Ru(bpy)(2)(cmbpy)](2+) electron donor tethered to a Co-III(NH3)(5) electron acceptor by an oligovaline peptide chain (bpy = 2,2'-bipyridine, cmbpy = 4-carboxy-4'-methyl-2,2'-bipyridine). These compounds were shown by H-1 NMR to adopt the conformational properties found within the individual strands of a beta-pleated sheet in both aqueous and methanol solutions. Emission lifetime measurements and HPLC product analysis show that the binuclear donor/acceptor compounds undergo photoinduced electron transfer (ET). The values of k(et) decrease with increasing donor/acceptor distance according to the expression k(et) = k' exp[-beta(r(-)r(0))]. A distance attenuation …

Electron Transfer Across A Peptide-Peptide Interface Within A Designed Metalloprotein, Gennady V. Kozlov, Michael Y. Ogawa

Chemistry Faculty Publications

Mechanistic studies of biological electron-transfer (ET) reactions have involved the use of surface-derivatized proteins, protein−protein complexes, and polypeptide-bridged donor−acceptor compounds. These latter studies seek to use well-defined model systems to better define the role of the intervening protein matrix in mediating biological electron transfers. However, whereas many in vivo ET reactions occur across a noncovalent protein−protein interface, the primary role of the peptide spacers found in current model systems is to provide a covalent link between the donor and acceptor sites. As such, these systems are poorly suited to probe the mechanisms of ET reactions occurring across a peptide−peptide interface.