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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
iv
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.
v
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
vi
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
vii
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
viii
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
ix
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
x
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
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