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Synthesis and Kinetics Study of Diiron-Hydrogenase Active Site Mimics

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Synthesis and Kinetics Study of Diiron-Hydrogenase Active Site Mimics SYNTHESIS AND KINETICS STUDY OF DIIRON-HYDROGENASE ACTIVE SITE MIMICS A THESIS SUBMITTED TO THE GRADUATE SCHOOL IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE MASTERS OF SCIENCE BY KATHERINE MACRI Committee Approval: Committee Advisor Date Committee Member Date Committee Member Date Departmental Approval: Departmental Chairperson Date Graduate Office Check: Dean of Graduate School Date SYNTHESIS AND KINETICS STUDY OF DIIRON-HYDROGENASE ACTIVE SITE MIMICS A THESIS SUBMITTED TO THE GRADUATE SCHOOL IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE MASTERS OF SCIENCE BY KATHERINE MACRI ADVISOR: JESSE W. TYE BALL STATE UNIVERSITY MUNCIE, INDIANA JULY 2012 Acknowledgements I would like to thank my advisor Dr. Jesse Tye for all of his help and support over the past two years. I appreciate his patience and understanding, as well the encouragement and guidance I needed to help me reach my goals. Special thanks to my committee, Dr. Daesung Chong and Dr. Robert Sammelson for their support, guidance and helpful suggestions. I would also like to thank Amanda Atkins for helping me get started, and the Ball State chemistry department for making my time here a fun and enjoyable experience. To my friends and family, thank you for all your love and support. I would not be where I am today without your help and encouragement. Special thanks to Dr. Ann Cutler and Dr. Jason Ribblett for constantly pushing me to reach my full potential. Thanks for never giving up on me. ABSTRACT Thesis: Synthesis and Kinetics Study of Diiron-Hydrogenase Active Site Mimics Student: Katherine Macri Degree: Master of Science College: Sciences and Humanities Date: July 2012 Pages: 92 The hydrogenase enzyme is an effective replacement for the expensive platinum catalysts used in hydrogen fuel cells today. However, many enzymes themselves are found in extreme environments and are inactive under standard conditions, but current active site models have a much larger over-potential for H+ reduction than the actual enzyme. Most research today involves the improvement of these synthetic models in an attempt to lower reduction potential, increase reaction kinetics, or improve catalytic activity. Research focuses on the synthesis of active site models with a carbon chain bridgehead linker of varying length. Synthesis of these molecules is achieved by the reaction of a dithiol with triiron dodecacarbonyl under an inert atmosphere to avoid the formation of by-products. Dithiols with four or more carbon atoms must first be converted to cyclic disulfides before the reaction with the iron dodecacarbonyl. This prevents the formation of an unwanted side product. Both butyl- and pentyldithiolatohexacarbonyldiiron model complexes have been characterized by IR, NMR, and X-ray spectroscopy. Active site models can also feature two unlinked sulfur atoms. These models have two conformational isomers that depend on the spatial location of the R-group bonded to each sulfur atom. This research also focuses on the synthesis of unlinked active site models with a variety of R-groups, and a temperature controlled NMR study of the isomeration reaction to determine the reaction rate. TABLE OF CONTENTS Page Number List of Figures i. List of Schemes and Tables iii. Chapter 1 Review of Literature I. Discovery of Hydrogenase Enzymes 2 II. Use as a Fuel Cell Catalyst 3 III. Classes of Hydrogenase Enzymes 6 i. [NiFe]-Hydrogenases 7 ii. [FeFe]-Hydrogenases 9 iii. [Fe]-Hydrogenases 11 IV. Synthetic Models 13 i. Synthetic [NiFe]-Hydrogenase Models 13 ii. Synthetic [FeFe]-Hydrogenase Models 16 iii. Synthetic [Fe]-Hydrogenase Models 24 Chapter 2 Synthesis of [FeFe]-Hydrogenase Active Site Mimics with Bridged Sulfur Atoms I. Introduction 28 II. General Experimental 29 III. Synthesis of Cyclic Disulfides 30 IV. Synthesis of Methanedithiol Precursors 33 V. Synthesis of Diiron-dithiolato Complexes 36 VI. Results and Conclusions 39 VII. Data 44 Chapter 3 Preliminary Kinetics Study of [FeFe]-Hydrogenase Active Site Mimics I. Introduction 48 II. General Experimental 49 III. Synthesis of Unlinked Models 50 IV. Solvent Study 53 V. Results and Conclusions 54 VI. Data 59 References 62 Appendix 67 i LIST OF FIGURES Page Number Chapter 1 Review of Literature Figure 1.1 Graphic Representation of a Hydrogen Fuel Cell 6 1.2 Active Site of [NiFe]-Hydrogenase 8 1.3 Inactive for of the [NiFe]-Hydrogenase. 9 1.4 [FeFe]-Hydrogenase Active Site 10 1.5 Proposed Active Site of [Fe]-Hydrogenase 12 1.6 Structure of [Ni(bme-daco)Fe(CO)4] 14 1.7 Structure of {P2Ni(μ-S)2Fe}-motifs. 14 1.8 Trinuclear {Nix(μ-S)zFey}-complexes 15 1.9 Structure of μ-(1,3-propanedithiolato)hexacarbonyldiiron 16 1.10 [FeFe]-Hydrogenase Active Site Models 17 1.11 Select Redox States of [FeFe]-Hydrogenase Enzyme 19 1.12 Stable Diferrous Specious with Bridging CO Ligand 20 1.13 Mixed-valent Fe(I) – Fe(II) Synthetic Complexes 20 1.14 Synthetic Hydride Models 22 1.15 Ruthenium-based Active Site Model 22 1.16 [Fe]-Active Site Models with Pyridinol Ligand 25 Chapter 2 Synthesis of [FeFe]-Hydrogenase Active Site Mimics with Bridged Sulfur Atoms 2.1 Structure of Products (1 – 6) 40 2.2 Structure of Products (7 – 9) 41 2.3 Proposed Structure of [Fe4S4] Dimer 43 ii Chapter 3 Preliminary Kinetics Study of [FeFe]-Hydrogenase Active Site Mimics 3.1 Conformation of Isomers A and B 49 3.2 Structure of Products (10 – 14) 55 3.3 1H NMR of Isomerization Reaction 56 iii LIST OF SCHEMES AND TABLES Page Number Chapter 1 Introduction and Background Literature Chapter 2 Synthesis of [FeFe]-Hydrogenase Active Site Mimics with Bridged Sulfur Atoms Schemes 2.1 Reversible thiol-disulfide interchange reaction. 31 2.2 Oxidation of thiols to disulfides with molecular bromine 32 on a hydrated silica gel support. 2.3 Possible pathway for the formation of diiron-dithiolate 42 complexes. Chapter 3 Preliminary Kinetics Study of [FeFe]-Hydrogenase Active Site Mimics Table 3.1 Relative Concentrations and Equilibrium Constants for 58 [Fe(CO)3SR]2 Isomers Chapter 1 Review of Literature I. Discovery of Hydrogenase Enzymes II. Use as a Fuel Cell Catalyst III. Types of Hydrogenase Enzymes i. [NiFe]-Hydrogenases ii. [FeFe]-Hydrogenases iii. [Fe]-Hydrogenases IV. Synthetic Models i. [NiFe]-Hydrogenase Models ii. [FeFe]-Hydrogenase Models iii. [Fe]-Hydrogenase Models 2 I. DISCOVERY OF HYDROGENASE ENZYMES Many microorganisms use the hydrogenase enzyme to catalyze the oxidation- reduction equilibrium of dihydrogen, as shown in the following reaction, 2H+ + 2e- ↔ H2. Since its discovery in 1931, the hydrogenase enzyme has been divided into three different classes based on the metal ions present at its active site. All are believed to be unrelated and are classified as [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]- hydrogenases. Most hydrogenases found in nature belong to the [NiFe]-H2ase or [FeFe]- H2ase class. [Fe]-hydrogenases are different because they contain a mononuclear iron active site and no iron-sulfur bonds characteristic of the other hydrogenases. The production of dihydrogen has many biotechnological applications, including an alternative to carbon based fossil fuels as an energy source. The hydrogenase enzyme was discovered after Stephenson and Stickland demonstrated that colon bacteria evolved H2 during growth and could use H2, but not 1 N2, to reduce other substrates. A hydrogenase was thought to be the enzyme responsible. Over the years, the hydrogenase enzyme was isolated from prokaryotes 3 found in both Bacteria and Archaea domains.2 The majority of organisms able to metabolize H2 are prokaryotes, but some eukaryotes have been discovered to produce 2 H2 using an [FeFe]-hydrogenase. These species have hydrogenases instead of mitochondria.2 In 2007, Vignais and Billoud reported that over 450 hydrogenases have been sequenced. Many of these enzymes are found in the same organism, and often individual species will contain hydrogenases with different metal centers.2 Until 1984, it was believed that all hydrogenases contained nickel as a cofactor in the active site. The absence of a strong electron paramagnetic resonance (EPR) signal from nickel in the anaerobe Megasphaera elsdenii led researchers to conclude the metal was not found at the active site.1 A variety of other [FeFe]-hydrogenases were soon isolated, the majority of them found in anaerobic bacteria. Extensive EPR spectroscopy of the enzyme lead to the discovery of multiple [4Fe-4S] clusters thought to be involved in the H2 catalysis. A variety of different clusters were synthesized and compared to the known data. The findings suggest a binuclear active site structure, but this was not proven until 1999.2 In recent years, the discovery of the mononuclear [Fe]-hydrogenase has led to a third class of hydrogenase enzymes. II. USE AS A FUEL CELL CATALYST The hydrogenase enzymes found in nature have many parallels to the dihydrogen fuel cell. A fuel cell generates electricity through an electrochemical reaction. Hydrogen is the most commonly used fuel, but hydrocarbons or alcohols will 4 also work as reducing agents.3 All fuel cells contain an anode, cathode, and electrolyte. In the hydrogen fuel cell, H2 enters the cell at the anode where it is oxidized into protons and electrons by a catalyst. The positively charged ions travel through the electrolyte to the cathode. Simultaneously, the electrons are channeled through a wire producing an electric current. Both protons and electrons are reunited at the cathode with oxygen and react with the help of another catalyst to form water. The only by-product is heat which
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