Kinetics and Mechanisms of Electron Transfer Reactions of Metal Complexes Ormond Jerry Parker Iowa State University
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Structure-Function Relationship of Metalloproteins
RESEARCH ACTIVITIES Structure-Function Relationship of Metalloproteins Department of Life and Coordination-Complex Molecular Science Division of Biomolecular Functions FUJII, Hiroshi Associate Professor KURAHASHI, Takuya Assistant Professor CONG, Zhiqi IMS Fellow OHTSUKI, Akimichi Post-Doctoral Fellow WANG, Chunlan Graduate Student TANIZAWA, Misako Secretary Metalloproteins are a class of biologically important A d4 high-spin manganese(III) ion forms a Robin-Day Class II macromolecules, which have various functions such as oxygen mixed-valence system, in which electron transfer is occurring transport, electron transfer, oxidation, and oxygenation. These between the localized phenoxyl radical and the phenolate. This diverse functions of metalloproteins have been thought to is in clear contrast to a d8 low-spin nickel(II) ion with the depend on the ligands from amino acid, coordination struc- same salen ligand, which induces a delocalized radical (Robin- tures, and protein structures in immediate vicinity of metal Day Class III) over the two phenolate rings, as previously ions. In this project, we are studying the relationship between reported by others. The present findings point to a fascinating the electronic structures of the metal active sites and reactivity possibility that electron transfer could be drastically modu- of metalloproteins. lated by exchanging the metal ion that bridges the two redox centers. 1. One-Electron Oxidation of One-electron Oxidation Electronically-Diverse Manganese(III) and N N N N Nickel(II) Salen Complexes: Transition from M M R O O R R O O R Localized to Delocalized Mixed-Valence tBu tBu 3+ 2+ tBu tBu Ligand Radicals1) M = Mn , Ni t R = Bu, OCH3, Ph Electron Transfer Ligand radicals from salen complexes are unique mixed- Figure 1. -
Mineral Formation and Sorption Mechanisms in Marine Ferromanganese-Rich Sediments
Mineral Formation and Sorption Mechanisms In Marine Ferromanganese-rich Sediments Amy Leanne Atkins Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Earth and Environment October 2014 The candidate confirms that the work submitted is her own, except where work, which has formed part of jointly authored publications has been included. The contributions of the candidate and the other authors to this work have been indicated overleaf. The candidate confirms that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from this thesis may be published without proper acknowledgement. ii Declaration Chapter 4 is a reproduction of a peer-reviewed publication in the journal Geochimica et Cosmochimica Acta as: Atkins A. L., Shaw S., Peacock C. L. (2014) Nucleation and growth of todorokite: Implications for trace-metal cycling in marine sediments. Geochim. Cosmochim. Acta. 144, 109-125. TEM images presented in chapter 4 were collected by Michael Ward at the Leeds Electron Microscopy and Spectroscopy centre with the guidance of the candidate. All other experimental work has been conducted by the candidate. The interpretation of the experimental data, and preparation of the manuscript has been undertaken by the candidate with the help and guidance of her supervisors: Caroline L. Peacock and Sam Shaw. Chapter 5 is a reproduction of a manuscript currently in the final stages of preparation for submission to the journal Geochimica et Cosmochimica Acta as: Atkins A. -
Concepts and Tools for Mechanism and Selectivity Analysis in Synthetic Organic Electrochemistry
Concepts and tools for mechanism and selectivity analysis in synthetic organic electrochemistry Cyrille Costentina,1,2 and Jean-Michel Savéanta,1 aUniversité Paris Diderot, Sorbonne Paris Cité, Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université–CNRS 7591, 75205 Paris Cedex 13, France Contributed by Jean-Michel Savéant, April 2, 2019 (sent for review March 19, 2019; reviewed by Robert Francke and R. Daniel Little) As an accompaniment to the current renaissance of synthetic organic sufficient to record a current-potential response but small electrochemistry, the heterogeneous and space-dependent nature of enough to leave the substrates and cosubstrates (of the order of electrochemical reactions is analyzed in detail. The reactions that follow one part per million) almost untouched. Competition of the the initial electron transfer step and yield the products are intimately electrochemical/chemical events with diffusional transport under coupled with reactant transport. Depiction of the ensuing reactions precisely mastered conditions allows analysis of the kinetics profiles is the key to the mechanism and selectivity parameters. within extended time windows (from minutes to submicroseconds). Analysis is eased by the steady state resulting from coupling of However, for irreversible processes, these approaches are blind on diffusion with convection forced by solution stirring or circulation. reaction bifurcations occurring beyond the kinetically determining Homogeneous molecular catalysis of organic electrochemical reactions step, which are precisely those governing the selectivity of the re- of the redox or chemical type may be treated in the same manner. The same benchmarking procedures recently developed for the activation action. This is not the case of preparative-scale electrolysis accom- of small molecules in the context of modern energy challenges lead to panied by identification and quantitation of products. -
Arxiv:1706.09241V1 [Cond-Mat.Mtrl-Sci] 28 Jun 2017 Based Electrolyte Supercapacitors Remain Somewhat Sim- Confinement Might Have a Drastic Influence on the Sol- Ilar
Confinement Effects on an Electron Transfer Reaction in Nanoporous Carbon Electrodes Zhujie Li1;2;3, Guillaume Jeanmairet2;3, Trinidad M´endez-Morales1;2;3, Mario Burbano1;3, Matthieu Haefele1, Mathieu Salanne1;2;3 1Maison de la Simulation, CEA, CNRS, Univ. Paris-Sud, UVSQ, Universit´eParis-Saclay, F-91191 Gif-sur-Yvette, France 2Sorbonne Universit´es,UPMC Univ Paris 06, CNRS, Laboratoire PHENIX, F-75005 Paris, France and 3R´eseau sur le Stockage Electrochimique´ de l'Energie´ (RS2E), FR CNRS 3459, France∗ Nanoconfinement generally leads to drastic effect on the physical and chemical properties of ionic liquids. Here we investigate how the electrochemical reactivity in such media may be impacted inside nanoporous carbon electrodes. To this end, we study a simple electron transfer reaction using molecular dynamics simulations. The electrodes are held at constant electric potential by allowing the atomic charges on the carbon atoms to fluctuate. We show that the Fe3+=Fe2+ couple dissolved in an ionic liquid exhibits a deviation with respect to Marcus theory. This behavior is rationalized by the stabilization of a solvation state of the Fe3+ cation in the disordered nanoporous electrode that is not observed in the bulk. The simulation results are fitted with a recently proposed two solvation state model, which allows us to estimate the effect of such a deviation on the kinetics of electron transfer inside nanoporous electrodes. Nanoconfinement effects strongly impact on many liq- a supercapacitor16. Among the various questions raised uid properties, such as transport, diffusion coefficients, by this study, the most important ones are: How is the phase transitions, and solvation structures1{4. -
Crystallographic Determination of Wild Type, Mutant and Substrate
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. Crystallographic Determination of Wild Type, Mutant and SubstrateSubstrate---- Analogue Inhibited Structures of Bacterial Members of a Family of Superoxide Dismutases bybyby Simon Hardie Oakley Submitted as part of the requirements for the degree of Doctor of Philosophy Institute of Fundamental Sciences, Chemistry Massey University, New Zealand 2009 i "Part of the inhumanity of the computer is that, once it is competently programmed and working smoothly, it is completely honest." Isaac Asimov (1920-92), author, inventor of the word “robotics”. ii 0.1 Abstract Crystallographic Determination of Wild Type, Mutant and Substrate-Analogue Inhibited Structures of Bacterial Members of a Family of Superoxide Dismutases The iron and manganese superoxide dismutases are a family of metallo-enzymes with highly conserved protein folds, active sites and dimer interfaces. They catalyse the elimination of the cytotoxic free radical superoxide to molecular oxygen and hydrogen peroxide by alternate reduction then oxidation of the active- site with the concomitant transfer of protons from the solvent. There are many key aspects of enzymatic function that lack a structural explanation. The focus of this study is on three crystal structures. The iron-substituted manganese superoxide dismutase from Escherichia coli complexed with azide, a substrate-mimicking inhibitor, was solved to 2.2 Å. This “wrong” metal form shows a binding pattern seen previously in the manganese superoxide dismutase from Thermus thermophilus. -
Surface Geochemistry of the Clay Minerals
Proc. Natl. Acad. Sci. USA Vol. 96, pp. 3358–3364, March 1999 Colloquium Paper This paper was presented at the National Academy of Sciences colloquium ‘‘Geology, Mineralogy, and Human Welfare,’’ held November 8–9, 1998 at the Arnold and Mabel Beckman Center in Irvine, CA. Surface geochemistry of the clay minerals GARRISON SPOSITO*†,NEAL T. SKIPPER‡,REBECCA SUTTON*, SUNG-HO PARK*, ALAN K. SOPER§, AND JEFFERY A. GREATHOUSE¶ *Earth Sciences Division, Mail Stop 90y1116, Ernest Orlando Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720; ‡Department of Physics and Astronomy, University College, Gower Street, London WC1E 6BT, United Kingdom; §ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom; and ¶Department of Chemistry, University of the Incarnate Word, 4301 Broadway, San Antonio, TX 78209 ABSTRACT Clay minerals are layer type aluminosilicates (6) and in the construction of environmental liners (7). Major that figure in terrestrial biogeochemical cycles, in the buff- impact on industrial organic synthesis comes in the many ering capacity of the oceans, and in the containment of toxic designed catalysts developed from clay minerals with adsorbed waste materials. They are also used as lubricants in petroleum polymeric cations (8). extraction and as industrial catalysts for the synthesis of many Certain clay minerals are isostructural with mica (1, 2) but organic compounds. These applications derive fundamentally are not as well crystallized because of random isomorphic from the colloidal size and permanent structural charge of cation substitutions in their structure (9, 10). These cation clay mineral particles, which endow them with significant substitutions lead to a negative net surface charge that induces surface reactivity. -
Oxidation-Reduction Reactions
Oxidation-Reduction Reactions What is an Oxidation-Reduction, or Redox, reaction? Oxidation-reduction reactions, or redox reactions, are technically defined as any chemical reaction in which the oxidation number of the participating atom, ion, or molecule of a chemical compound changes. Some common redox reactions include fire, rusting of metals, browning of fruit, and photosynthesis. In simpler terms, redox reactions involve the transfer of electrons from one substance to another. In a redox reaction, electrons can never be “lost”; if one substance loses electrons, another substance must gain an equal number of electrons. Therefore, oxidation and reduction always happen at the same time; they are a matched set. What is Oxidation? Oxidation is the loss of electrons by an atom, ion, or molecule. The atom, ion, or molecule that is oxidized will become more positively charged. Oxidation may also involve the addition of oxygen or the loss of hydrogen. What is Reduction? Reduction is the gain of electrons by an atom, ion, or molecule. The atom, ion, or molecule that is reduced will become more negatively charged. Reduction may also involve the loss of oxygen or the gain of hydrogen. Tips for determining if an atom, ion, or compound has been Oxidized or Reduced: • Remembering one of the two following mnemonics can be of assistance in determining the difference between oxidation and reduction: 1) OIL RIG- Oxidation Is Loss (of electrons), Reduction Is Gain (of electrons) or 2) LEO GER- Loss of Electrons- Oxidation, Gain of Electrons- Reduction • Atoms of metals tend to lose electrons to form positive ions (oxidation) • Atoms of non-metals tend to gain electrons to form negative ions (reduction). -
Design and Fine-Tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics
1 Design and Fine-tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics Parisa Hosseinzadeh and Yi Lu Abstract: 1. Introduction A significant portion of biological processes are involved with providing vital energy sources such as ATP, and controlling the flow of energy through living systems. These bioenergetics processes, the most important of which are photosynthesis and respiration, require electron transfer (ET) between different redox partners. Metalloproteins are one of the most widely used ET centers in biology. They can be classified into three major classes: cupredoxins, which include type 1 copper (T1Cu) proteins and CuA centers [1- 10], cytochromes [10-17], and iron-sulfur (FeS) proteins [10,18-24]. Each class of ET proteins transfer electrons between different redox partners which possess different reduction potentials (E°) (Figure 1). Therefore, the ET centers need to adjust their E° in a way that matches those of their redox partners. No single class of protein can cover the entire range of physiological E°, which is between ~ -1V, at which protons are reduced to H2, and 1V, at which water is oxidized to O2. Cupredoxins usually function at the high end of the E°, while FeS proteins are mostly involved in ET reactions possessing relatively low E° [10]. The E°’s of FeS proteins overlap significantly with those of cytochromes that often have intermediate E° among the three classes of ET proteins. Figure 1. Reduction potential range of metal centers in electron transfer metalloprotein. Adapted from ref. [10] 2 In this review, we first describe the importance of tuning E° of ET centers, including the metalloproteins described above. -
Light Induced Electron Transfer of Metal Complexes
Electron and Proton Transfer in Chemistry and Biology, edited by A. Müller et al. Studies in Physical and Theoretical Chemistry, Vol. 78 €> 1992 Elsevier Science Publishers B.V. All rights reserved. Light Induced Electron Transfer of Metal Complexes A. Vogler and H. Kunkely Institut für Anorganische Chemie Universität Regensburg Universitätsstraße 31 D-8400 Regensburg (Germany) * Summary Light induced electron transfer of metal complexes has been studied extensively during the last decade. This interest was stimulated by attempts to develop an artificial photosyn• thesis for the conversion and chemical storage of solar energy. Even if this goal has not yet been achieved photochemical redox processes of coordination compounds are now much better understood. In this review the various possibilities of photoinduced electron transfer are discussed and illustrated by selected examples. A distinction is made between intra- and intermolecular electron transfer which may occur as a direct optical transition or by an excited state electron transfer mechanism. Introduction The study of photochemical electron transfer processes involving coordination compounds (refs. 1-17) has become an important research subject during the last 10 years. These investigations were initiated, at least partially, by the desire to create an artificial photosynthetic system for the conversion and chemical storage of solar energy (refs. 18-20). It is well known that natural photosynthesis requires a light induced electron transfer as the basic process employing chlorophyll as the key compound. In order to imitate nature we have to improve our knowledge of photoredox processes. Coordination compounds, particularly those of transition metals, are excellent candi• dates for such studies. Metal complexes are generally redox active. -
Arsenic Adsorption Onto Minerals: Connecting Experimental Observations with Density Functional Theory Calculations
Minerals 2014, 4, 208-240; doi:10.3390/min4020208 OPEN ACCESS minerals ISSN 2075-163X www.mdpi.com/journal/minerals Article Arsenic Adsorption onto Minerals: Connecting Experimental Observations with Density Functional Theory Calculations Heath D. Watts 1,*, Lorena Tribe 2 and James D. Kubicki 1,3,* 1 Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA 2 Division of Science, The Pennsylvania State University, Berks, Reading, PA 19610, USA; E-Mail: [email protected] 3 Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA * Authors to whom correspondence should be addressed; E-Mails: [email protected] (H.D.W.); [email protected] (J.D.K.); Tel.: +1-814-865-3951 (J.D.K.); Fax: +1-814-867-2378 (J.D.K). Received: 24 December 2013; in revised form: 25 February 2014 / Accepted: 6 March 2014 / Published: 27 March 2014 Abstract: A review of the literature about calculating the adsorption properties of arsenic onto mineral models using density functional theory (DFT) is presented. Furthermore, this work presents DFT results that show the effect of model charge, hydration, oxidation state, and DFT method on the structures and adsorption energies for AsIII and AsV onto Fe3+-(oxyhydr)oxide cluster models. Calculated interatomic distances from periodic planewave and cluster-model DFT are compared with experimental data for AsIII and AsV adsorbed to Fe3+-(oxyhydr)oxide models. In addition, reaction rates for the adsorption of AsV on α-FeOOH (goethite) (010) and Fe3+ (oxyhydr)oxide cluster models were calculated using planewave and cluster-model DFT methods. Keywords: arsenic; density functional theory (DFT); kinetics; thermodynamics; adsorption; computational chemistry; planewave DFT; reaction rates; As—Fe bond distances Minerals 2014, 4 209 1. -
Nature of the First Electron Transfer in Electrochemical Ammonia Activation in a Nonaqueous Medium
Nature of the First Electron Transfer in Electrochemical Ammonia Activation in a Nonaqueous Medium The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Schiffer, Zachary et al. "Nature of the First Electron Transfer in Electrochemical Ammonia Activation in a Nonaqueous Medium." Journal of Physical Chemistry C 123, 15 (April 2019): 9713-9720 © 2019 American Chemical Society As Published http://dx.doi.org/10.1021/ACS.JPCC.9B00669 Publisher American Chemical Society (ACS) Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/124016 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Nature of the First Electron Transfer in Electrochemical Ammonia Activation in a Non-Aqueous Medium Zachary J Schiffer1, Nikifar Lazouski1, Nathan Corbin1, Karthish Manthiram1,* 1Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA *Corresponding Author: 617-715-5740, [email protected] 1 Abstract Decreasing costs of renewable sources of electricity will increase the viability of electrochemical processes in chemical manufacturing. To this end, improved understanding of electrochemical N-H bond activation is essential to develop electrochemical routes for nitrogen-containing chemicals. In this work, we investigate electrochemical ammonia activation in acetonitrile, a prototypical non-aqueous solvent for electro-organic syntheses. Non-aqueous environments are desirable for electro- organic syntheses due to large electrochemical stability windows and high solubility for organic products. We find that ammonia oxidation in acetonitrile proceeds through an outer-sphere mechanism involving an initial electron transfer as the rate-determining step, likely producing an ammonia radical cation. -
The Role of Cytochrome C in the Electron Transport Chain
The Role of Cytochrome c in the Electron Transport Chain Rebecca Rosamond, Ashleigh Keeler, Josh Diaz Texas A&M University, College Station, TX 77843 Introduction Cytochrome c Applications in Research Iron is an important element for sustaining life. Iron appears in many different Heme iron metal center forms in the body, one of which is in a heme type protein, a cytochrome. These Electrochemistry12 cytochromes bind heme as a cofactor and function as electron transfer agents, • Octahedral geometry • Coordinated by 6 ligands • Cytochrome c encapsulated most commonly in the electron transport chain. The electron transport chain (ETC) within a methyl-modified silica is a series of complexes and molecules that transfer electrons from donors to o 4 nitrogen atoms of the porphyrin ring film to enhance electrochemical acceptors via redox reactions coupled with the transport of protons across the reduction rates inner mitochondrial membrane to create a concentration gradient.1 This gradient is . Tetradentate chelating ligand • Advancements in this field help then used to supply the energy for ATP synthase to generate ATP, the principle to create more efficient molecule for providing energy to cells. The complexes and molecules the ETC o 1 sulfur atom of biotechnologies Cyt c redox reaction to sense H O consists of are Complex I, Ubiquinone, Complex II, Complex III, cytochrome c, and methionine residue 2 2 Complex IV (cytochrome c oxidase). Of these complexes and molecules Complex o 1 nitrogen atom of III, cytochrome c, and Complex IV contain heme type proteins. Cytochrome c is histidine imidazole ring unique as it is not part of a larger complex, and freely diffuses through the inner Biosensors11 2 membrane to react with Complex III and cytochrome c oxidase.