Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 Palladium(II) and platinum(II) synthetic peptidases: residue- and sequence-selective hydrolysis and the photochemistry of sulfoxides, S,C-sulfonium ylides, and sulfilimines: unimolecular bond cleavage Stacey Anne Stoffregen Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Inorganic Chemistry Commons, and the Organic Chemistry Commons Recommended Citation Stoffregen, Stacey Anne, "Palladium(II) and platinum(II) synthetic peptidases: residue- and sequence-selective hydrolysis and the photochemistry of sulfoxides, S,C-sulfonium ylides, and sulfilimines: unimolecular bond cleavage" (2007). Retrospective Theses and Dissertations. 15926. https://lib.dr.iastate.edu/rtd/15926 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Palladium(II) and platinum(II) synthetic peptidases: residue- and sequence-selective hydrolysis and the photochemistry of sulfoxides, S,C-sulfonium ylides, and sulfilimines: unimolecular bond cleavage by Stacey Anne Stoffregen A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Chemistry (Biomolecular Science) Program of Study Committee: William Jenks, Major Professor Robert Angelici Mark Gordon Emily Smith Theresa Windus Iowa State University Ames, Iowa 2007 UMI Number: 3274868 UMI Microform 3274868 Copyright 2007 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, MI 48106-1346 ii TABLE OF CONTENTS ABSTRACT iv CHAPTER 1. The development of synthetic peptidases: a general review 1.1 Dissertation organization 1 1.2 Properties of the amide group 2 1.3 Hydrolysis of amide bonds 3 1.4 Proteolytic reagents 5 1.5 Metal-ion binding to amides 6 1.6 Palladium(II) and platinum(II) reagents for peptide and protein hydrolysis 7 1.7 References 11 CHAPTER 2. Thioether complexes of palladium(II) and platinum(II) as artificial peptidases: residue-selective peptide cleavage by a palladium complex 2.1 Abstract 17 2.2 Introduction 18 2.3 Experimental procedures 20 2.4 Results and discussion 26 2.5 Conclusions 36 2.6 Acknowledgments 37 2.7 Supporting information description 37 2.8 References 38 CHAPTER 3. The photochemistry and photophysics of sulfur and selenium ylides: a general review 3.1 General introduction to sulfur- and selenium-containing compounds 44 3.2 Nomenclature and properties of sulfur- and selenium-containing compounds 44 3.3 Thermal reactions of sulfoxides, selenoxides, sulfinic esters, and sulfonic esters 47 3.4 Unimolecular photochemistry of sulfoxides and selenoxides 51 3.5 Properties, preparation, and reactivity of carbenes 61 3.6 References 67 CHAPTER 4. Photochemical reactivity of S,C-sulfonium ylides: potential carbene precursors 4.1 Abstract 77 4.2 Introduction 78 4.3 Experimental details 79 4.4 Results and discussion 83 4.5 Conclusions 92 4.6 Acknowledgement 93 4.7 Supporting information description 93 4.8 References 93 iii CHAPTER 5. Correlation of thiophene-S-oxide and selenophene-Se-oxide excited states with deoxygenation products 5.1 Abstract 98 5.2 Introduction 99 5.3 Computational details 102 5.4 Results and discussion 104 5.5 Conclusions 120 5.6 Acknowledgement 121 5.7 Supporting information description 121 5.8 References 121 CHAPTER 6. Sulfur and selenium ylide bond enthalpies 6.1 Abstract 125 6.2 Introduction 126 6.3 Computational methods 127 6.4 Results and discussion 127 6.5 Summary 147 6.6 Acknowledgement 148 6.7 Supporting information description 148 6.8 References 148 CHAPTER 7. Elimination reactions of N-sulfilimines and S,C-sulfonium ylides 7.1 Abstract 154 7.2 Introduction 155 7.3 Computational details 158 7.4 Results and discussion 158 7.5 Summary and conclusions 164 7.6 Acknowledgement 165 7.7 Supporting information description 165 7.8 References 165 CHAPTER 8. General conclusions 169 APPENDIX A. Supporting information for Chapter 2 173 APPENDIX B. Supporting information for Chapter 4 178 APPENDIX C. Supporting information for Chapter 5 213 APPENDIX D. Supporting information for Chapter 6 229 APPENDIX E. Supporting information for Chapter 7 300 iv ABSTRACT In this dissertation the photochemistry of sulfoxides, sulfilimines, and S,C-sulfonium ylides was explored both computationally and experimentally. Dibenzothiophene-S-oxide has been previously shown to undergo deoxygenation to form dibenzothiophene and a reactive intermediate believed to be O(3P). In this study, the photochemistry of S,C- sulfonium ylides of thiophenes was explored and shown to result in unimolecular bond scission of the S-C ylidic bond to give the corresponding sulfide and a reactive intermediate, analogous to the chemistry of dibenzothiophene-S-oxide. Chemical trapping studies provide indirect evidence that the reactive intermediate produced upon photolysis is a carbene. The mechanism of unimolecular bond cleavage for sulfoxides was further explored computationally by generating the potential energy surfaces (PES) of thiophene-S-oxide and selenophene-Se-oxide as a function of S-O and Se-O bond length using the CASSCF [18,14] method. Energy corrections were obtained with a second-order perturbation theory (MRMP2). The results for thiophene-S-oxide and selenophene-Se-oxide indicate that the second triplet excited state of each provide nearly barrierless route toward S-O and Se-O bond dissociation. The potential energy diagrams offer a new explanation for the experimentally observed unimolecular bond cleavage of DBTO and DBSeO, in which intersystem crossing from an excited singlet state to a dissociative T2 state provides a pathway to deoxygenation products. This mechanism is consistent with the increased quantum yields of deoxygenation that were experimentally observed for heavy-atom substituted sulfoxides. The bond dissociation enthalpies (BDEs) of several sulfoxides, sulfilimines, S,C- sulfonium ylides, and selenoxides were also estimated by applying MP2/6- 311++G(3df,2p)//MP2/6-31G(d,p), G3, and other computational methods. Selenoxides v have the weakest ylide bond strengths, followed by N-H sulfilimines and CH2-S,C- sulfonium ylides. Sulfilimine and S,C-sulfonium ylides are stabilized by electron withdrawing substituents on N or C, respectively. Incorporation of the S or Se atom into a ring system that stands to gain aromaticity upon deoxygenation results in weaker BDEs. Finally, the elimination reactions of sulfoxides, sulfilimines, and S,C-sulfonium ylides were studied computationally. We report the reaction enthalpies and activation barriers of the forward and reverse reactions for related sulfilimines, S,C-sulfonium ylides, and a sulfoxide. Our results indicate that a major factor affecting the relative ease of reactivity is the strength of the S-Cα bond. Resonance stabilization of the ylide nitrogen of sulfilimines and the ylide carbon of sulfonium ylides with electron-withdrawing groups effectively delocalizes the charge rendering the ylide less nucleophilic and thereby less reactive toward eliminations. Additionally, our results show that among the compounds tested, the S-Cα bond of compounds with electron-withdrawing substituents is the strongest, further limiting the reactivity of these ylides. The estimated reaction enthalpies of S,C- sulfonium ylides from this study suggest that these compounds would be viable reactants for mild preparation of a variety of alkenes. 1 CHAPTER 1 The development of synthetic peptidases: a general review 1.1 Dissertation organization. This dissertation containing eight chapters and five appendices investigates aspects of bioinorganic chemistry and organic photochemistry. Chapter 1 is a general review of the hydrolysis of peptides and proteins. Chapter 2 is a paper that was published in 2005 in Inorganic Chemistry, which discusses the development of Pd(II) and Pt(II) thioether complexes that selectively hydrolyze peptide bonds. The author of this dissertation performed the bulk of the experiments, wrote the paper, and mentored undergraduate Amanda Griffin who synthesized and characterized the binuclear complex. Chapter 3 is a general review of the chemistry of sulfoxides, selenoxides, S,C- sulfonium ylides, and sulfilimines. Chapter 4 is a paper being prepared for publication in the Journal of Organic Chemistry that discusses the photochemistry of thiophene-based S,C-sulfonium ylides. The author of this dissertation performed all of the experiments and wrote the paper. Chapter 5 is a paper being prepared for publication in the Journal of the American Chemical Society. The chapter describes a computational study designed to provide a correlation of thiophene-S-oxide excited states with the products of photochemical deoxygenation. The author of this dissertation performed the bulk of the calculations, wrote the paper, and mentored undergraduate Pearl Dickerson who performed the initial HF/6-31G(d) calculations on selenophene-Se-oxide. Chapter 6 is a paper that has been submitted for publication in the Journal