Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2008 Ultrafast fluorescence spectroscopy used as a probe to explore excited state photophysics of biologically and environmentally relevant systems Prasun Mukherjee Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Physical Chemistry Commons Recommended Citation Mukherjee, Prasun, "Ultrafast fluorescence spectroscopy used as a probe to explore excited state photophysics of biologically and environmentally relevant systems" (2008). Retrospective Theses and Dissertations. 15645. https://lib.dr.iastate.edu/rtd/15645 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]. Ultrafast fluorescence spectroscopy used as a probe to explore excited state photophysics of biologically and environmentally relevant systems by Prasun Mukherjee A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Physical Chemistry Program of Study Committee: Jacob W. Petrich, Major Professor Mark S. Gordon Mark S. Hargrove Xueyu Song Hans Stauffer Iowa State University Ames, Iowa 2008 Copyright © Prasun Mukherjee, 2008. All rights reserved. UMI Number: 3307072 UMI Microform 3307072 Copyright 2008 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 Dedicated to my parents iii TABLE OF CONTENTS ACKNOWLEDGEMENT vi CHAPTER I. GENERAL INTRODUCTION 1 Excited State Photophysics of Hypericin: Understanding the Nature of Non-naturally Occurring Complexes with Proteins 1 Photomovements in Ciliates: Structure Elucidation of Novel Hypericin Like Pigment 5 Solvation Dynamics 6 Room Temperature Ionic Liquids (RTILs) 9 Dielectric Relaxation in Protein Environment 16 Micelle 20 Thesis Organization 22 References 23 CHAPTER II. EXPERIMENTAL AND CALCULATION METHODS 38 Generation of Laser Pulses 38 Group Velocity Dispersion 43 Ti-Sapphire Oscillator 46 Time Correlated Single Photon Counting (TCSPC) 50 Tripler 55 Fluorescence Upconversion Spectroscopy 59 Calculation of Reorganization Energy 65 Experimental Procedure and Data Analysis for Solvation Dynamics Experiments 68 Calculation of the “Zero-time” Emission Spectrum 73 References 76 CHAPTER III. INTERACTION OF GLUTATHIONE S-TRANSFERASE WITH HYPERICIN: A PHOTOPHYSICAL STUDY 79 Abstract 79 Introduction 80 Materials and Methods 83 Results and Discussion 85 Conclusions 93 Acknowledgements 94 References 94 CHAPTER IV. MARISTENTORIN, A NOVEL PIGMENT FROM THE POSITIVELY PHOTOTACTIC MARINE CILIATE Maristentor dinoferus, IS STRUCTURALLY RELATED TO HYPERICIN AND STENTORIN 99 Abstract 99 Introduction 100 Materials and Methods 103 Results 105 Discussion 109 Conclusions 116 Acknowledgements 116 iv References 117 CHAPTER V. ASSESSING THE ROLES OF THE CONSTITUENTS OF IONIC LIQUIDS IN DYNAMIC SOLVATION: COMPARISON OF AN IONIC LIQUID IN MICELLAR AND BULK FORM 120 Abstract 120 Introduction 121 Materials and Methods 123 Results 128 Discussion 129 Conclusions 137 Acknowledgements 138 References 138 CHAPTER VI. DYNAMIC SOLVATION IN PHOSPHONIUM IONIC LIQUIDS: COMPARISON OF BULK AND MICELLAR SYSTEMS AND CONSIDERATIONS FOR THE CONSTRUCTION OF THE SOLVATION CORRELATION FUNCTION, C(t) 142 Abstract 142 Introduction 143 Materials and Methods 145 Results 149 Discussion 152 Conclusions 165 Acknowledgements 165 References 165 CHAPTER VII. CHARACTERIZATION OF THE INTERACTIONS OF FLUORESCENT PROBES WITH PROTEINS: COUMARIN 153 AND 1,8- ANS IN COMPLEX WITH HOLO- AND APOMYOGLOBIN 171 Abstract 171 Introduction 172 Materials and Methods 173 Results and Discussion 175 Conclusions 181 Acknowledgements 182 References 182 CHAPTER VIII. SOLVATION DYNAMICS IN PROTEIN ENVIRONMENTS: COMPARISON OF FLUORESCENCE UPCONVERSION MEASUREMENTS OF COUMARIN 153 IN MONOMERIC HEMEPROTEINS WITH MOLECULAR DYNAMICS SIMULATIONS 187 Abstract 187 Introduction 188 Materials and Methods 193 Results 197 Discussion 197 Conclusions 202 v Acknowledgements 204 References 204 CHAPTER IX. GENERAL CONCLUSIONS 209 VITA 214 vi ACKNOWLEDGEMENT I would like to express my heartfelt gratitude and appreciation to my research advisor, Dr. Jacob W. Petrich. It is obvious that without his invaluable guidance, constant support and help, the research works described here would never have been possible. It is my ultimate pleasure to work with him. I would also express my humble gratitude to all my committee members, Dr. Mark S. Gordon, Dr. Mark S. Hargrove, Dr. Xueyu Song and Dr. Hans Stauffer for all their help. I am highly grateful to all of our group members. I express my special thanks to Dr. Mintu Halder for training me in the laboratory. I thank Pramit Chowdhury and Lindsay Sanders Headley for their generous help in showing me the intrinsic details of numerous calculation and analysis methods. It has turned out to be a great experience working with Ramkrishna Adhikary and Sayantan Bose and I enjoyed sharing the workspace with them. I admit that I have been benefited a lot through the discussions with them on various basic concepts. I am thankful to Ramkrishna Adhikary for carefully reading the first two chapters of this thesis and giving helpful comments. I would also like to thank Dr. Ranjan Das, Dr. Govindarajan Krishnamoorthy, Charles Barnes, Alyse Hurd, Alex Reynolds, Frank Maistrovich, Tessa Calhoun and Erin Campbell. I have been privileged to work with all these wonderful people in the laboratory. The research described in this thesis involves lot of collaborations. I thank Dr. Daniel W. Armstrong and his group members for providing us with the ionic liquids and helping us with chromatographic separations. For protein work, I thank Dr. Mark S. Hargrove and his group members for collaborating with us and letting us use his laboratory for our protein preparation work. Dr. Xueyu Song deserves special thanks as he always helped us with the vii theoretical aspects. I am gratefully indebted to him for providing the program of “zero-time” spectrum calculation. I am thankful to Dr. William M. Atkins and Weiya D. Lu for providing us with the GST proteins. For pigment work, I thank Dr. Christopher S. Lobban, Bruce Fulton and Kamel Harrata for providing immense help. I also thank the members from NADC and Dr. Pavol Miskovsky and Dr. Zhiqun Lin for collaborating with us. I would like to thank Dr. Basudeb Saha for helping and teaching me various experiments in Physical and Analytical Chemistry laboratory. I would also like to thank Dr. Bob Doyle for his generous support while performing the microscopy experiments. I am also very grateful to all the members of the Chemistry department for making my stay here a wonderful one. I thank all of my friends, especially Supratim Giri, Ramkrishna Adhikary, Sayantan Bose, for their company. I am grateful to many of my teachers for building me up. I am thankful to Dr. Sambhu N. Datta (with whom I have done my Masters research) for his guidance and to Dr. Anindya Datta for helping me in choosing this laboratory for my graduate studies. Two of my college professors, Dr. Gobinda De and Dr. Anirban Misra, need special mention. I am gratefully thankful to them for guiding me during my college days. I must admit that without their constant help I would probably not ending up here. Last but not the least I would like to express my sincere thanks to my parents for their love, support, patience and understanding. This work would never have been possible without their constant encouragement. I dedicate the thesis to my parents. My interest in Chemistry grew initially while discussing many Chemistry problems with my father. I also thank all my family members and relatives for their love and support. 1 CHAPTER I. GENERAL INTRODUCTION With the help of ultrafast laser techniques there has been tremendous progress in understanding various important molecular phenomenon occurring on the nanosecond (109 s), picosecond (1012 s), and even femtosecond (1015 s) time regimes. The importance of such short time scale measurements can be appreciated by considering that many biological and chemical phenomena, for example, hydrogen atom (or proton) transfer and electron transfer, occur on these time scales. This thesis mainly deals with four main topics, namely (a) understanding the differential interaction of hypericin with two different isoforms of Glutathione S-transferase (GST) proteins, (b) characterization and structure elucidation of a novel hypericin like pigment from a marine ciliate Maristentor dinoferus, (c) solvation dynamics in room temperature ionic liquids (RTILs) especially focusing on a comparison of bulk solvent versus its micellar form in water and (d) solvation dynamics in protein environments. In this chapter I will briefly overview various systems, which are studied here, with the help of the instrumentation available in our laboratory. Special emphasis was given to the current available literature and the motivation of the work discussed here. Excited State Photophysics of Hypericin: Understanding the Nature