Photo-Induced Electron Transfer Studies in Donor-Bridge-Acceptor Molecules

by

Subhasis Chakrabarti

BS, Presidency College, Calcutta University, India, 2000

MS, Indian Institute of Technology, Mumbai, India, 2002

Submitted to the Graduate Faculty of

Arts and Science in partial fulfillment

of the requirements for the degree of

Doctor of Philosophy

University of Pittsburgh

2008

UNIVERSITY OF PITTSBURGH

FACULTY OF ARTS AND SCIENCES

This dissertation was presented

by

Subhasis Chakrabarti

It was defended on

September 8, 2008

and approved by

Dr. David Pratt, Professor, Chemistry

Dr. Sunil Saxena, Professor, Chemistry

Dr. Hyung J. Kim, Professor, Chemistry

Dissertation Advisor: Dr. David H. Waldeck, Professor, Chemistry

ii

Copyright by Subhasis Chakrabarti

2008

iii

PHOTO-INDUCED ELECTRON TRANSFER STUDIES IN DONOR-BRIDGE-ACCEPTOR MOLECULES

Subhasis Chakrabarti, PhD

University of Pittsburgh, 2008

Abstract

Electron transfer reactions through Donor-Bridge-Acceptor (DBA) molecules are

important as they constitute a fundamental chemical process and are of intrinsic importance in

biology, chemistry, and the emerging field of nanotechnology. Electron transfer reactions

proceed generally in a few limiting regimes; nonadiabatic electron transfer, adiabatic electron

transfer and solvent controlled electron transfer. This study is going to address two different

regimes (nonadiabatic and solvent controlled) of electron transfer studies. In the nonadiabatic

limit, we are going to explore how the electron tunneling kinetics of different donor-bridge-

acceptor molecules depends on tunneling barrier. Different parameters like free energy,

reorganization energy, and electronic coupling which govern the electron transfer were

quantitatively evaluated and compared with theoretical models. In the solvent controlled limit we

have shown that a change of electron transfer mechanism happens and the kinetics dominantly

depends on solvent polarization response.

This study comprises of two different kinds of Donor-Bridge-acceptor molecules, one

having a pendant group present in the cleft between the donor and acceptor hanging from the

bridge and the other having no group present in the cleft. The electron transfer kinetics critically

depend on the pendant unit present in the cavity between the donor and the acceptor moieties.

The electronic character of the pendant unit can tune the electronic coupling between the donor

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and the acceptor. If the cavity is empty then solvent molecule(s) can occupy the cavity and can

influence the electron transfer rate between donor and acceptor. It has been shown that water

molecules can change the electron transfer pathways in proteins. This study has experimentally

shown that few water molecules can change the electron transfer rate significantly by forming a

hydrogen bonded structure between them. This experimental finding supports the theoretical

predictions that water molecules can be important in protein electron transfer.

Understanding the issues outlined in this work are important for understanding and

controlling electron motion in supramolecular structures and the encounter complex of reactants.

For example, the efficiency of electron tunneling through water molecules is essential to a

mechanistic understanding of important biological processes, such as bioenergetics. Also, the

influence of friction and its role in changing the reaction mechanism should enhance our

understanding for how nuclear motions affect long range electron transfer.

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TABLE OF CONTENTS

ACKNOWLEDGEMENT .................................................................................................. XVII

1.0 INTRODUCTION.1

1.1 Prologue.1

1.2 Electron Transfer Theory...2

1.3 Reorganization Energy and Reaction Free Energy7

1.4 Electronic Coupling.11

1.5 Dynamic Solvent Effect...13

1.6 Summary..15

1.7 References18

2.0 PENDANT UNIT EFFECT ON ELECTRON TUNNELING IN U-SHAPED

MOLECULES..21

2.1 Introduction..21

2.2 Modeling the Rate Constant...25

2.3 Experimental....28

2.4 Results and Analysis30

2.5 Theoretical Calculations..40

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2.6 Discussion44

2.7 Conclusion...46

2.8 Acknowledgement...47

2.9 Appendix..48

2.10 References..52

3.0 COMPETING ELECTRON TRANSFER PATHWAYS IN HYDROCARBON

FRAMEWORKS: SHORT-CIRCUITING THROUGH-BOND COUPLING BY NON-

BONDED CONTACTS IN RIGID U-SHAPED NORBORNYLOGOUS SYSTEMS

CONTAINING A CAVITY-BOUND AROMATIC PENDANT GROUP.56

3.1 Introduction..57

3.2 Experimental............................63

3.3 Results..............65

3.4 Discussion82

3.5 Conclusion...87

3.6 Acknowledgements..88

3.7 Appendix..89

3.8 References................92

4.0 SOLVENT DYNAMICAL EFFECTS ON ELECTRON TRANSFER IN U-SHAPED

DONOR-BRIDGE-ACCEPTOR MOLECULES..96

4.1 Introduction..96

4.2 Background......................99

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4.3 Experimental..104

4.4 Results and Analysis..107

4.5 Discussion and Conclusion120

4.6 Acknowledgement.123

4.7 Appendix124

4.8 References..128

5.0 EXPERIMENTAL DEMONSTRATION OF WATER MEDIATED ELECTRON-

TRANSFER THROUGH BIS-AMINO ACID DONOR-BRIDGE-ACCEPTOR

OLIGOMERS....130

5.1 Acknowledgement.137

5.2 Appendix................................138

5.3 References......162

6.0 CONCLUSION..165

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LIST OF TABLES

Table 2.1 Solvent parameters used in the molecular solvation model..........34

Table 2.2 Solute parameters used in the molecular solvation model ...34

Table 2.3 Best fit of rG (295 K) values for U-shaped molecules ......36

Table 2.4 Best fit of V and 0 (295 K) values for U-shaped molecules ..38

Table 2.5 Twist angles (degrees) and closest distances () between the pendant group and

acceptor and donor groups and the closest distance between the donor and acceptor

....42

Table 2.6 Fluorescence decay of DBA molecules in toluene...48

Table 2.7 Fluorescence decay of DBA molecules in mesitylene..49

Table 2.8 Fluorescence decay of DBA molecules in p-Xylene50

Table 2.8 Fluorescence decay of DBA molecules in acetonitrile.51

Table 3.1 Charge transfer (CT) emission maxima ( max ) of 2DBA in different solvents at 295 K

and Solvent Parameters, n, S (295K) and f for each solvent . ..68

Table 3.2 r G and 0 ; determined from the charge transfer emission spectra, using E00 = 3.40

73

eV ..........................................................................................................72

Table 3.3 ( )rG LE CS values for 1DBA and 2DBA in different solvents

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Table 3.4 Best fit of electronic coupling and reorganization energy (from the kinetic fit and from

CT emission spectra) for 1DBA and 2DBA..76

Table 3.5 Fluorescence decay of DBA molecules in toluene...89

Table 3.6 Fluorescence decay of DBA molecules in p-Xylene90

Table 3.7 Fluorescence decay of DBA molecules in acetonitrile.91

Table 4.1 Properties of solvent NMP at 303K106

Table 4.2 Fitting parameters for compound 1, 2 and 3 in NMP at 295K112

Table 4.3 Fluorescence decay of 1DBA molecules in NMP...124

Table 4.4 Fluorescence decay of 2DBA molecules in NMP...125

Table 4.4 Fluorescence decay of 3DBA molecules in NMP...126

Table 5.1 Electron transfer parameters (V, G, Total) and rotamer populations for D-SSS-A

and D-RRS-A..135

Table 5.2 NMR analysis of conformer ratio...151

Table 5.3 D-SSS-A and D-RRS-A in water and DMSO excited at 330 nm...160

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LIST OF FIGURES

Figure 1.1 Diagram illustrating the two pictures (adiabatic and nonadiabatic) for the electron

transfer.3

Figure 1.2 Energetics of relevant electron transfer reactions are shown for the reactant state (top

panel) and the transition state (bottom panel). Both electronic (r) and nuclear (q) coordinates(r, q)

are involved in the reaction......5

Figure 1.3 The multiple interactions between the solute and solvent molecules according to

Matyushov model...10

Figure 1.4 U-shaped Donor-Bridge-Acceptor molecules studied in chapter 2,3 and 4...15

Figure 1.5 Model peptide systems studied in chapter 5 and 6..16

Figure 2.1 Diagram illustrating the adiabatic (the solid curves) - strong coupling - and

nonadiabatic (the diabatic dashed curves) weak coupling..25

Figure 2.2 Absorption spectra (left) and emission spectra (right) of 1 (black), 2 (green), 3 (blue)

and 4 (red) in acetonitrile (A) and mesitylene (B) 30

Figure 2.3 The experimental rG values are plotted for 1 (diamond), 2 (triangle), 3 (circle) and 4

(square) in mesitylene. The lines show the rG values predicted from the molecular model with

the solvent parameters given in Table 2.1.35

xi

Figure 2.4 Experimental rate constant data are plotted versus 1/T, for 1 (diamond), 2 (triangle),

3 (circle) and 4 (square) in mesitylene (black) and acetonitrile (gray). The lines represent the

b