Terranova ZL 032014 D

EXPLORING THE STRUCTURE AND DYNAMICS OF IONIC LIQUIDS USING
MOLECULAR DYNAMICS
A Dissertation
Submitted to the Graduate School

of the University of Notre Dame
in Partial Fulfillment of the Requirements
for the Degree of
Doctor of Philosophy
by
Zachary L. Terranova
Steven A. Corcelli, Director
Graduate Program in Chemistry and Biochemistry

Notre Dame, Indiana
March 2014
EXPLORING THE STRUCTURE AND DYNAMICS OF IONIC LIQUIDS USING

MOLECULAR DYNAMICS
Abstract
by
Experimental studies of solvation dynamics in imidazolium-based ionic liquids
(ILs) have revealed complex kinetics over a broad range of time scales from femtoseconds to tens of nanoseconds. Microsecond-length molecular dynamics (MD)
simulations of coumarin 153 (C153) in a series of imidazolium-based ILs were performed to reveal the molecular-level mechanism for solvation dynamics over the full
range of time scales accessed in the experiments. An analysis of the structure of the
IL in the vicinity of the probe molecule revealed preferential solvation by the cations.
Despite this observation, decomposition of the solvation response into components
from the anions and cations and also from translational and rotational motions show
that translations of the anions are the dominant contributor to solvation dynamics.
The kinetics for the translation of the anions into and out of the first solvation shell
of the dye were found to mimic the kinetic profile of the solvation dynamics response.
This mechanism for solvation dynamics contrasts dramatically with conventional polar liquids in which solvent rotations are generally responsible for the response.
The structure and dynamics of water as measured experimentally in ILs have
revealed local ion rearrangements that occur an order of magnitude faster than complete randomization of the liquid structure. Simulations of an isolated water molecule
embedded in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6 ], were
performed to shed insight into the nature of these coupled water-ion dynamics. The
theoretical calculations of the spectral diffusion dynamics and the infrared absorption
spectra of the OD stretch of isolated HOD in [bmim][PF6 ] agree well with experiment.
The infrared (IR) absorption lineshape of the OD stretch is narrow and blue-shifted
in the IL compared to the OD stretch of HOD in H2 O. Decomposition of the OD
frequency time correlation function revealed the translation of the anions dominate
the spectral diffusion dynamics.
DEDICATION
To my complement, treasure, and companion, Kelly.

And Harrison Ford.
ii
CONTENTS
FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
TABLES
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xi
ACKNOWLEDGEMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
xii
CHAPTER 1: INTRODUCTION . . . . . . . . . . . . . .
1.1 Ionic Liquids . . . . . . . . . . . . . . . . . . . .
1.1.1 Polarity of ILs . . . . . . . . . . . . . . . .
1.2 Solvation Dynamics . . . . . . . . . . . . . . . . .
1.2.1 Solvation Dynamics in ILs . . . . . . . . .
1.3 Vibrational Spectroscopy . . . . . . . . . . . . . .
1.3.1 Spectroscopic Studies in ILs . . . . . . . .
1.3.1.1 Spectroscopic Characterization of
1.3.1.2 Vibrational Reporters in ILs . . .
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CHAPTER 2: THE MECHANISM OF SOLVATION DYNAMICS IN [emim][BF4 ]

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Theoretical Methodology . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.1 Solvation Response Calculations . . . . . . . . . . . . . . . . .
2.2.2 Decomposition of the Solvation Response by Solvent Component
2.2.3 Decomposition of the Solvation Response by Translations and
Rovibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2.4 Molecular Dynamics Simulations . . . . . . . . . . . . . . . .
2.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . .
2.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
CHAPTER 3: SIMULATIONS OF THE SOLVATION RESPONSE
RIES OF IONIC LIQUIDS . . . . . . . . . . . . . . . . . . . .
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2 Methodology . . . . . . . . . . . . . . . . . . . . . . . . .
3.2.1 Decomposition of the Solvation Response . . . . . .
3.2.2 Molecular Dynamics Simulations . . . . . . . . . .
3.3 Solvation Dynamics Results . . . . . . . . . . . . . . . . .
3.4 Charge Scaling . . . . . . . . . . . . . . . . . . . . . . . .
iii
IN A SE. . . . . .
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16
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57
3.4.1 Self-Diffusion Coefficients . . . . . . . . . . . . . . . . . . . .

3.4.2 Charge Scaling Effects on Solvation Dynamics . . . . . . . . .
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
57
60
62
CHAPTER 4: REGARDING THE VALIDITY OF LINEAR RESPONSE THEORY IN SOLVATION DYNAMICS SIMULATIONS OF IONIC LIQUIDS
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Computational Methods . . . . . . . . . . . . . . . . . . . . . . . . .
63
63
65
66
CHAPTER 5: A MOLECULAR DYNAMICS INVESTIGATION OF THE VIBRATIONAL SPECTROSCOPY OF ISOLATED WATER IN AN IONIC
LIQUID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.2 Theoretical Methodology . . . . . . . . . . . . . . . . . . . . . . . . .
5.2.1 Spectroscopic Maps . . . . . . . . . . . . . . . . . . . . . . . .
5.2.2 Infrared Absorption Spectrum . . . . . . . . . . . . . . . . . .
5.2.3 Spectral Diffusion and Decomposition of the FFCF . . . . . .
5.2.4 Molecular Dynamics Simulations . . . . . . . . . . . . . . . .
5.3.1 IR Absorption . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.3.2 Spectral Diffusion . . . . . . . . . . . . . . . . . . . . . . . . .
5.4 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . .
75
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81
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85
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92
97
3.5
CHAPTER 6: MONITORING INTRAMOLECULAR PROTON TRANSFER

WITH TWO-DIMENSIONAL INFRARED SPECTROSCOPY . . . . . . 98
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
6.2 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
6.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . 107
CHAPTER 7: SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
7.1 Alternative Systems of Interest . . . . . . . . . . . . . . . . . . . . . 114
APPENDIX A: SOLVATION RESPONSE FUNCTION FITS . . . . . . . . . 124
APPENDIX B: MALONALDEHYDE TWO-DIMENSIONAL INFRARED SPECTRA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
BIBLIOGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
iv
FIGURES
1.1
1.2
1.3
2.1
2.2
2.3
2.4
2.5
The structures of imidazolium cations and inorganic anions studied

here. These geometries were calculated with density functional theory
(DFT) with a B3LYP functional and the aug-cc-pVDZ basis set. The
cations are 1-butyl-3-methyl imidazolium, [bmim], 1-ethyl-3-methyl
imidazolium, [emim], while the anions are tetrafluoroborate, [BF4 ], dicyanamide, [DCA], trifluoromethanesulfonate, [TfO], hexafluorophosphate, [PF6 ]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The structure coumarin 153 (C153) with the differences in charge density, q, predicted upon excitation as calculated and validated by
Cinacchi et al.[1] . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The experimental solvation relaxation time as a function of the solvent

viscosity[2] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
Calculated (black) and experimental[2, 3] (green) solvation response

functions in the range from 50 fs to 1 ns. . . . . . . . . . . . . . . . .
23
Fits of the calculated (black) and experimental (green) solvation responses of C153 in the IL [emim][BF4] to a stretched exponential function, A exp((t/ ) ), in the time range between 10 ps and 1 ns. The
data are shown as filled circles, while the fits are lines. The quality of
the fits in terms of the correlation coefficient, r2 , are excellent: r2 =
0.9987 for the theoretical data and r2 = 0.9983 for the experimental
data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24
The calculated total simulated solvation response (black) is decomposed using the methodology described in Section 2.2.2 into contributions from the anions (red), the cations (blue), and the internal
motions of the C153 solute (purple). . . . . . . . . . . . . . . . . . .
25
The radial distribution function, g(r), for C153-[emim] and C153-[BF4 ]

pairs, where r is defined as the distance between the center-of-mass
positions of the relevant pair of molecules. . . . . . . . . . . . . . . .
28
The solvation responses of [emim] (blue) and [BF4 ] (red) decomposed

into contributions from translational (solid) and rovibrational (dashed)
motions. For reference, the total solvation response minus the contribution from the internal motions of the C153 solute is also shown
(black). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
30
2.6
2.7
The residence-time correlation function (RTCF) for the anions and

cations in the first solvation shell of the C153 solute. The first solvation
shell was defined as any molecule whose center-of-mass lies within 5.6
A of the center-of-mass of the C153 probe. . . . . . . . . . . . . . . .
31
A schematic depiction of the mechanism of solvation dynamics in

C153/[emim][BF4 ]. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
33
3.1
Optimized structures of imidazolium cations and inorganic anions studied in this chapter. The cations are 1-butyl-3-methyl imidazolium,
[bmim], 1-ethyl-3-methyl imidazolium, [emim], while the anions are
tetrafluoroborate, [BF4 ], dicyanamide, [DCA], trifluoromethanesulfonate,
[TfO], hexafluorophosphate, [PF6 ]. . . . . . . . . . . . . . . . . . . . 36
3.2
The calculated (dashed) and experimental (solid) solvation response

functions for [emim][BF4 ] (black), [bmim][BF4 ] (red), [bmim][DCA](green),
[emim][TfO](blue), and [bmim][PF6 ] (brown) over the range 50 fs to 1
ns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.3
Time constants for experiment and calculated response functions derived from a fit to a single exponential, A exp((t/ )), in the range
from 50 ps to 400 ps. . . . . . . . . . . . . . . . . . . . . . . . . . . .
44
The calculated total solvation response (black) is decomposed into

contributions from the [BF4 ] anions (red), the [bmim] cations (blue),
and the internal motions of the C153 solute (purple). . . . . . . . . .
46

contributions from the [DCA] anions (red), the [bmim] cations (blue),
47

contributions from the [PF6 ] anions (red), the [bmim] cations (blue),
48

contributions from the [TfO] anions (red), the [emim] cations (blue),
49
The radial distribution function, g(r), for C153-[cation] and C153[anion] pairs, where r is defined as the distance between the center-ofmass positions of the relevant pair of molecules. . . . . . . . . . . . .
50
3.4
3.5
3.6
3.7
3.8
3.9
The solvation responses of [bmim] (blue) and [BF4 ] (red) decomposed

motions. For reference, the total solvation response is also shown (black). 52
3.10 The solvation responses of [bmim] (blue) and [DCA] (red) decomposed
vi
3.11 The solvation responses of [bmim] (blue) and [PF6 ] (red) decomposed
3.12 The solvation responses of [emim] (blue) and [TfO] (red) decomposed
3.13 The residence-time correlation function (RTCF) for the anions and
cations in the first solvation shell of the C153 solute. The first solvation
shell was defined as any molecule whose center-of-mass lies within the
first solvation shell, defined as the first minimum of the cation-C153
g(r). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
3.14 Calculated self-diffusion coefficients for [emim] (blue) and [BF4 ] (red)
for varied unit charges. Experimental measurements (dashed) selfdiffusion coefficients for this IL in the range of 298-303 K are reported
to vary from 4.4 5.4 1011 m2 /s for [emim] and 3.6 4.2 1011
m2 /s for [BF4 ].[4] . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
58
3.15 The calculated (solid) solvation response functions for [emim][BF4 ]

where the charge scaling parameter was varied from 1.0 (orange),
0.825 applied to the entire [emim] cation(red) 0.80 applied to the entire [emim] cation (black), or 0.80 applied to the imidazolium ring
(turquoise), along with experimental measurements (black filled circles) over the range 50 fs to 1 ns. . . . . . . . . . . . . . . . . . . . .
61
4.1
4.2
4.3
4.4
5.1
The normalized solvation response without the contribution of the dye

for the nonequilibrium S(t) (black) and equilibrium C1 (t) (red), and
C0 (t) (green) from 50 fs to 1 ns. The inset is the identical response
including intramolecular interactions of the dye molecule responsible
for the large oscillations below 10 ps. . . . . . . . . . . . . . . . . . .
68
A comparison of two decomposition strategies as applied to C0 (t) showing auto- and cross-correlation decomposition (top), to the alternative
method defined in Eq. 4.4 that calculates the contribution of the relevant component relative to the total response. . . . . . . . . . . . . .
70
The normalized solvation response decomposed into anion (top) and

cation (bottom) contributions for nonequilibrium S(t) (black) and
equilibrium C1 (t) (red), and C0 (t) (green) from 50 fs to 1 ns. . . . . .
71
The normalized solvation responses of S(t) (black), C1 (t) (red), and

C0 (t) (green) decomposed into contributions due to translational (solid)
and rovibrational (dashed) motions. . . . . . . . . . . . . . . . . . . .
72
The orientational time-correlation function for an OD bond in H2 O

(black) and in the [bmim][PF6 ] IL (turquoise). . . . . . . . . . . . . .
86
vii
5.2
Vibrational line shapes for the OD stretch of dilute HOD in H2 O and

in the [bmim][PF6 ] IL. The spectra were arbitrarily scaled to have the
same maximum intensity. . . . . . . . . . . . . . . . . . . . . . . . . .
87
5.3
Distribution functions, F (E), for the projection of the electric field

projected along the OD of HOD in H2 O (black) and in the [bmim][PF6 ]
IL (turquoise). The distribution of electric fields in the IL resulting
from cations (blue) and anions (red) are also shown. The distribution
functions have all been scaled to have the same value at their maximum. 90
5.4
Normalized CE (t) for HOD in H2 O and HOD in the [bmim][PF6 ] IL.

Also shown is a comparison between C (t) (red) and CE (t) for HOD
in the IL. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
91
Decomposition of normalized CE (t) for the OD stretch of HOD isolated

in the [bmim][PF6 ] IL in terms of the contributions from the cations
(blue) and anions (red). . . . . . . . . . . . . . . . . . . . . . . . . .
95
Decomposition of normalized CE (t) for the OD stretch of HOD isolated

in the [bmim][PF6 ] IL in terms of the contributions from the translational (solid) and rovibrational (dashed) components from cations
(blue) and anions (red). . . . . . . . . . . . . . . . . . . . . . . . . .
96
6.1
Proton transfer reaction coordinate in malonaldehyde. . . . . . . . . .
99
6.2
(top) Potential energy curves for the intramolecular proton transfer in

malonaldehyde generated with DFT and SCCDFTB. The DFT barrier height is 3.2 kcal/mol while SCCDFTB predicts a barrier of 2.6
kcal/mol. (middle) Free energy profile from a QM/MM simulation of
malonaldehyde in water with a barrier height of 4.1 kcal/mol. (bottom)
Anharmonic CD vibrational frequencies as a function of the proton
transfer reaction coordinate for malonaldehyde in the gas-phase. The
frequencies were fit to Eq. 6.2, where A0 = 1534.0, A1 = 91.5, A2 =
11.8, A3 = 2106.5, A4 = 42.7, and A5 = 7.0. . . . . . . . . . . . . . . 102
6.3
(a) CD stretch IR absorption spectrum of labeled malonaldehyde in

aqueous solution. (b-d) Chemical exchange 2D IR spectra for waiting
times of 0, 15, and 50 ps. . . . . . . . . . . . . . . . . . . . . . . . . . 105
6.4
(top) Reaction coordinate time correlation function along with a fit

to a single exponential with a time constant of 28.8 ps. (bottom)
Evolution of the normalized volumes of the diagonal and off-diagonal
peaks in the 2D IR spectra as a function of the waiting time. Both
curves were fit to a single exponential yielding time constants of 29.7
and 28.3 ps for the diagonal and off-diagonal peaks, respectively. . . . 109
7.1
The simulated solvation response (black) is decomposed using the

methodology described in Chapter 2 into contributions from the rovibrational (dashed pink) and the translational motions of the fictitious
dipole molecule (solid blue). . . . . . . . . . . . . . . . . . . . . . . . 112
5.5
5.6
viii
7.2
The calculated solvation relaxation time as a function of the inverse

cube root of the molecular volume. . . . . . . . . . . . . . . . . . . . 113
7.3
The optimized structures of cations and anions. The cations are 1butyl-3-methyl imidazolium, [bmim], 1-ethyl-3-methyl imidazolium,
[emim], triethyl sulfonium, [S222 ], and tri(methoxymethyl)-methyl phosphonium, and [Tmet]. The anions are tetrafluoroborate, [BF4 ], trifluoromethane sulfonate, [TfO], 1-pyrazolide, [Pyrazo], 1,2,3,-triazolium, [Triazo], and bistrifluoromethylsulfonylimide, [Tf2 N] . . . . . . . . . . . . 116
7.4

contributions from the [TfO] anions (red), the [bmim] cations (blue),
and the internal motions of the C153 solute (purple). . . . . . . . . . 117
7.5

contributions from the [Pyrazo] anions (red), the [emim] cations (blue),
7.6

contributions from the [Tf2 N] anions (red), the [emim] cations (blue),
7.7

contributions from the [Triazo] anions (red), the [emim] cations (blue),
7.8

contributions from the [BF4 ] anions (red), the [S2 22] cations (blue),
7.9

contributions from the [BF4 ] anions (red), the [Tmet] cations (blue),
7.10 The calculated total solvation response (black) is decomposed into

contributions from the [Pyrazo] anions (red), the [Tmet] cations (blue),
A.1 Fits of the calculated (black) and experimental (red) solvation responses of C153 in the IL [emim][BF4] to a single exponential function
in the time range between 50 ps and 400 ns. The data are shown as
filled circles, while the fits are lines. . . . . . . . . . . . . . . . . . . . 125
ix
B.1 Chemical exchange 2D IR spectra for waiting times of 0 ps. . . . . . . 132
B.2 Chemical exchange 2D IR spectra for waiting times of 10 ps. . . . . . 133
B.11 Chemical exchange 2D IR spectra for waiting times of 100 ps. . . . . 142
TABLES
2.1
PARAMETERS FOR A STRETCHED EXPONENTIAL FIT . . . .
26
3.1
SELF-DIFFUSION COEFFICIENTS FROM MD SIMULATIONS . .
41
5.1
IR ABSORPTION DATA . . . . . . . . . . . . . . . . . . . . . . . .
88
A.1 IDEAL MULTIPLICATIVE CONSTANTS . . . . . . . . . . . . . . . 130
xi
ACKNOWLEDGEMENT
I owe many of my achievements and successes to the hard work, encouragement

and support of others. I am truly appreciative for all of the guidance, support,
and wisdom my advisor, Professor Steven A. Corcelli, has conveyed to me during my
graduate studies. His invaluable insight combined with his affable demeanor enriched
my graduate experience. I consider myself to be extremely fortunate to have been
surrounded by so many talented people throughout my time here. The Corcelli group
members, past and present, have been especially helpful in the conversations and
entertainment we have shared: Cory Ayres, Lindsay Baxter, Ryan Forrest, Danyal
Floisand, Mary C. Sherman, Clyde Daly, Jonathan Walker, Dr. Hannah Fox, Dr.
Ryan Haws, Dr. Laura Kinnaman, Dr. Carrie Miller, Dr. Kristina Furse (Davis). I
am gracious for the artistic and computational knowledge shared with me by Dr.
Kristina Furse (Davis) and Dr. Charles F. Vardemann II.
I have been touched by so many in my years here at Notre Dame. Mary C.
Sherman, Kelsey M. Stocker, Ryan P. Forrest, Steve Asiala, James Marr, and Joseph
Michalka provided me with the friendship and fortitude to withstand the isolating
and occasionally crushing nature of graduate school all while tolerating my antics
while in lab. When I reflect on the encouragement I received from those who inspired
me to go to graduate school, Torgny B. Hallin, Michael Seibert, Professor Scott Reid,
Professor Alanah Fitch, Professor Augustine Agyeman, and Mike Grady, I am forever
grateful. My siblings Lindsey, Ryan, Jacob, Kevin, Hannah, Julianna, and Luke and
my mothers, Kelly Hodge and Barb Maggio, have always generously provided love
and support. Dr. Kent and Dr. Diana, Tom, and Denise Nelson have additionally
xii
extended their love and help whenever necessary. Professionally I am appreciative of

the guidance and personal conversations shared with Associate Dean John Lubker,
Mimi Beck, and my administrative assistant Donna Frahn.
I am thankful for the helpful questions, comments, and challenges presented by
my committee members Professor J. Daniel Gezelter, Professor S. Alex Kandel, and
Professor Jeffrey Peng. In particular, I am very thankful for the advice I received
from my personal coffee connoisseur Professor J. Daniel Gezelter thereby enabling
my addiction. I would be remiss if I did not acknowledge Lets Spoon Frozen Yogurt
for supplying 20% of my meals any given week. It was a pleasure teaching with Professor A. Graham Lappin, who contributed greatly to my teaching philosophy and
personal edification. I am sincerely thankful for the assistance provided by Professor Ed Maginn and his group members, specifically Dr. Craig M. Tenney, Dr. Hao
Wu, Dr. Marcos Perez-Blanco, and Dr. Yong Zhang. The computational wizards
at the Center for Research Computing, specifically Dr. Paul Brenner, Dr. Timothy
Stitt, Dr. Dodi Heryadi, Rich Sudlow, and Jim Bulger, have been instrumental to
my success here at Notre Dame. Without their technical expertise and training, I
would not have averaged 500,000 CPU hours every month. Many thanks for the time
and input given by the additional multidisciplinary members CoMSEL supergroup.
I also want to thank Cheryl Copley, Deb Bennett, Mary Prorok, and Eric Kuehner,
and the additional staff in the Department of Chemistry and Biochemistry for their
help. Additionally, I am thankful for the office and janitorial staff of the Department of Chemical and Biochemical Engineering for their kindness, cleanliness, and
coffee. I am gracious to our experimental collaborators Professor Mark Maroncelli
and Professor Michael Fayer for generously sharing data.
Finally, and most importantly, I would like to acknowledge the patience, support,
comfort, and compassion my wife, Kelly, and my sons, Jack and Owen, give to me each
day. The laughter and love that is shared in our house motivates me to continually
xiii
achieve my best. I could not have risen to the level I am now without them.
xiv
CHAPTER 1
INTRODUCTION
Ionic liquids (ILs) are gaining considerable attention because of their attractive
properties as environmentally friendly alternatives to volatile organic solvents[5, 6]
and their applications involving the production, storage, and efficient utilization
of energy[7] while also demonstrating tremendous promise in a variety of liquid
separation and extraction strategies.[8] ILs exhibit unique physical properties relative to conventional liquids in terms of vapor pressure, viscosity, electrical and
thermal conductivity, solubility of polar and nonpolar molecules, and low melting
point.[9] Moreover, these properties can be tuned to specific applications by chemically modifying the molecules that comprise the liquid, and/or by forming multicomponent mixtures of anions and cations, making ILs highly adaptable for a
variety of tasks. The use of ILs has made significant advances in electrochemical
applications[7, 10, 11], the processing of lignocellulose[1215], and thermally stable
high performance lubricants[16, 17], the practical aspects of complete control of these
reactions lies in fostering an understanding of the complex dynamics of these liquids.
In general, dynamics play an important role in determining mass and heat transport properties of reactions, which are crucial to many energy related applications.
Many proposed and actual applications of ILs involve charge-transfer reactions (e.g.
dye-sensitized solar cells, batteries, and many catalytic reactions), so understanding the detailed microscopic mechanisms and time scales of solvation dynamics in
ILs is of pressing relevance. While the solvation response has been measured in a
range of ILs, the exact molecular mechanism responsible for their complex kinetic
1
profiles has not been determined until now. This dissertation sets out to develop
a fundamental understanding of the complex intermolecular interactions in ILs that
are responsible for microscopic structures and dynamics that ultimately manifest in
macroscopic physical properties by using molecular dynamics (MD) simulations to
calculate theoretical quantities directly comparable to experimental measurements of
solvation dynamics and infrared (IR) spectroscopy.
This dissertation is organized such that a brief overview of ILs and background
material concerning solvation dynamics and IR spectroscopy are presented in the
first chapter. The second chapter focuses on calculating solvation dynamics in a
common IL, [emim][BF4 ], thus allowing a direct comparison with our experimental
collaborators. Chapter 3 then expands the solvation dynamics study over a series
of imidazolium-based ILs in addition to analyzing the effects of charge scaling on IL
properties. In Chapter 4 the validity of linear response theory as applied to solvation dynamics simulations in ILs over the entire response time is explored. The fifth
chapter describes the spectroscopic signatures of an isolated water molecule in an IL,
which acts as a probe of structure and dynamics within ILs, in addition to shedding
insight into water-ion interactions. Deviating from ILs, Chapter 6 presents calculations of multidimensional infrared spectroscopy of a non-perturbative vibrational
reporter to monitor the kinetics of proton transfer processes in aqueous solution. Finally, Chapter 7 contains concluding remarks and a summary of this work, as well as
proposed alternative systems of interest.
1.1 Ionic Liquids

ILs represent an important class of solvents with melting points below 100 C
composed entirely of ions and present a unique environment to test our theoretical
understanding of condensed phase dynamics. Unlike common inorganic salts such
as NaCl, these ions remain in the liquid state at ambient conditions due to weak
2
electrostatic interactions and frustrated packing that inhibits crystal formation. ILs
possess the advantages offered by aqueous solutions (i.e. nonflammable, high solubility of a range of compounds, efficient conductivity, etc.) and avoid certain limitations
by having a large potential window, excellent thermal stability, and the control of a
range of physicochemical properties.
Traditional molten salts were used in electrodeposition processes[18, 19] but with
operable temperatures of 1000 C, practical solution-phase applications are impossible. First generation ILs were synthesized with the goal of developing lower
temperature molten salts based on eutectic mixtures of chloroaluminates. These ILs
were able to operate at a lower temperature, however their extremely hygroscopic
nature resulted in an overproduction of HCl which limited their applicability. The
second generation ILs use ammonium, phosphonium, and most commonly imidazolium cations paired with discrete anions which offer more air and water stable
operable conditions[20] and ushered in a new era of intense IL research.
The cations examined in this dissertation, 1-butyl-3-methyl imidazolium, [bmim],
1-ethyl-3-methyl imidazolium, [emim], offer certain complexities that separate them
from inorganic cations K+ and Na+ (Figure 1.1). Their larger size and thus increased
charge delocalization decreases the lattice energy allowing these compounds to remain
liquid below 100 C. While studies examining the dependence of certain properties
on the alkyl-chain length have found changes in the viscosity[21, 22], solubility of
gases[23], and structural heterogeneity,[24, 25] the choice of the anion offers greater
control over the physicochemical properties. The favored IL 1-ethyl-3-methyl imidazolium tetrafluoroborate [emim][BF4 ] was first introduced in 1992[26] followed by
the addition of another highly fluorinated anion, hexafluorophosphate [emim][PF6 ]
in 1994[27]. Unfortunately the melting point 58-60 C made [emim][PF6 ] cumbersome until the introduction of [bmim][PF6 ] and [bmim][BF4 ] the following year.[28]

These cation anion pairs dominated the IL literature for a decade, however concerns
Cations
Anions
[bmim]
[BF4]
[PF6]
[emim]
[DCA]
[TfO]
Figure 1.1. The structures of imidazolium cations and inorganic anions

studied here. These geometries were calculated with density functional
theory (DFT) with a B3LYP functional and the aug-cc-pVDZ basis set.
The cations are 1-butyl-3-methyl imidazolium, [bmim], 1-ethyl-3-methyl
imidazolium, [emim], while the anions are tetrafluoroborate, [BF4 ],
dicyanamide, [DCA], trifluoromethanesulfonate, [TfO],
hexafluorophosphate, [PF6 ].
over their aptitude to form HF gas[29] prompted the appearance of alternative anions. Trifluoromethanesulfonate, [TfO], anions emerged as interesting ILs given their
relatively lower viscosities and stability.[30] The only non-fluorinated anion surveyed
in this dissertation, dicyanamide [DCA], relies on the highly electronegative carbonnitrogen triple bond to delocalize the charge resulting in some unique properties.
Presenting some of the lowest viscosities and highest conductivities for all ILs[31],
DCA based ILs are often considered in solar cell applications.[32, 33]
1.1.1 Polarity of ILs

The polarity of a solvent is informative regarding its solvating capability. A
common empirical measure of the polarity relies on the sensitivity of solvatochromic
probes reporting on various interactions in the solvent commonly reported on the
(30)
Reichardts solvent polarity parameter ET
(30)
scale. Representative ET
values range
from 63.1 kcal/mol for water and 30.7 kcal/mol for tetramethylsilane, the least polar
compound. Despite large variations in the different structural motifs that comprise
(30)
the classes of ILs, the ET
values fall within a very narrow window around 47-49

(30)
kcal/mol.[3436] This suggests ILs are more polar than acetonitrile (ET
(30)
kcal/mol) and less polar than methanol (ET

(30)
medium chain alcohols (butanol = ET
of 45.6
of 55.6 kcal/mol), more similar to
of 49.1 kcal/mol).[34]
Another descriptor of the solvent polarity is the dielectric constant, , which

characterizes the loss of intermolecular Coulombic interaction energy in the condensed
phase relative to vacuum. A large found in water or formaldehyde, = 80 and 84
respectively, is a reflection the ability of the solvent to efficiently shield the solute
charges, thus enabling effective solvation of polar or charged species. With that
definition is is reasonable to speculate that a system composed entirely of charged
species would have a larger than water. However, experimental measurements
on a range of ILs indicate for these systems are in the range of 815, similar
5
to pentanol (=15.1) and octanol(=8.8).[37] The modest is an indication of the

diverse environment of structured charge density and modulated screening efficiency
presented by these systems. Most notable, however, is the appreciable range that the
polarity can be altered solely by differing the components of the liquid.
1.2 Solvation Dynamics

Solvation dynamics refers to molecular reorganizations in response to a perturbation in the geometric or electronic structure of a solute and are particularly important
for charge-transfer reactions whose kinetic rates are determined almost exclusively
by solvent reorganization. Solvent reorganization also influences the kinetic rates
and mechanisms of other classes of chemical reactions that involve polar transition
states.[38] Solvation dynamics are measured in time-dependent fluorescence Stokes
shift (TDSS) experiments. TDSS experiments employ fluorescent probe molecules to
measure the response of the environment to a sudden perturbation of the charge distribution of the probe molecule.[3941] In brief, the experiment begins with an initial
laser pulse, v(0) that electronically excites the probe molecule. This excitation occurs
effectively instantaneously, such that the molecular geometry of the probe molecule is
unchanged, but its charge distribution is significantly altered. After the initial excitation, the solvent environment begins to reorganize to accommodate the new charge
distribution. The reorganization stabilizes the excited electronic state of the probe
relative to its ground electronic state, and subsequent fluorescence, v(t), is redshifted
with respect to the initial fluorescence, v(0). The time scales of the environment
reorganization are typically characterized by a solvation response function,
S(t) =
v(t) v()
v(0) v()
(1.1)
where v() is the emission frequency after the environment has completely responded
to the excited state charge distribution of the dye.

A suitable fluorescent probe molecule that can capture the dynamics of the solvation environment over the necessary timescales while being minimally perturbative to
the system is tantamount to the success of solvation dynamics measurements. Often
fluorescent molecules that are sensitive to environmental polarities have been used
to shed insight into a variety of physicochemical properties. Typically these probes
possess an electron donating group, often an amino group, and an electron withdrawing group that is positioned at a maximal distance from the amino group to achieve
a transfer of electron density that produces the large excited state dipole moment.
There are two classes of probe molecules depending on their ability to hydrogen bond
with the solvent.
Hydrogen bonding probes can complicate interpretations of the solvation timescales
because these interactions can destabilize the Franck-Condon excited state and can
potentially cause a blue shift in the absorption spectrum. Common hydrogen bonding probes such as 6-propionyl-2-(N,N,-dimethylamino) naphthalene (PRODAN) and
4-aminophthalimide (4-AP) have been used to examine the solvation properties of
ILs, however the kinetics of their excited state are complex and debated. Differing
theoretical studies disagree on the existence of a twisted intramolecular or planar
intramolecular charge transfer state, thus impeding a straightforward interpretation
of the spectra.[4246] Additionally, measurements utilizing 4-AP are extremely sensitive to the degree of hydrogen bonding present in the solvation environment, and
in the present context introduce an additional complexity when describing solvation
dynamics.[4750]. Because of these complications, rigid 7-aminocoumarins are typically used as solvatochromic laser dyes. Coumarin 153 (C153), the probe of choice for
this study, is a dye within the class of 7-aminocoumarins that possess a highly dipolar
excited state whose fluorescence is strongly sensitive to the solvent environment providing exceptional quantum yield. Theoretical investigations determined the HOMO
Figure 1.2. The structure coumarin 153 (C153) with the differences in
charge density, q, predicted upon excitation as calculated and validated
by Cinacchi et al.[1]
LUMO excitation corresponds to a transition with a substantial change

in the partial charges (Figure 1.2), and thus the dipole moment. Since intersystem
crossing is strongly forbidden in C153 its transition to ground electronic state is by
fluorescence exclusively, with a lifetime of 35 ns.[51]
Probe dependency remains an unresolved issue. An extensive examination by
Maroncelli et al. revealed significant differences in solvation relaxation time scales
independent of the quality and experimental conditions.[52] The assumption that
solvation dynamics is an inherent property of the media is invalid given the differences
in relaxation times for different probe molecules within the same IL.[53] Examining
the solvation dynamics of ILs is entirely dependent on the quality and location of
the probe molecule. Given the heterogeneous nature of these systems[5464] it is
conceivable a degree of preferential solvation persists, a topic explored further in
Chapters 2 and 3.
1.2.1 Solvation Dynamics in ILs

The majority of the solvation dynamics measurements on ILs employ the timecorrelated single photon counting (TCSPC) technique to measure the TDSS following
optical excitation of the probe molecule.[3436, 52, 6572] TCSPC has a time resolution of approximately 20 ps, therefore any solvation dynamics occurring faster than
20 ps are left largely unresolved. Since the TDSS often persists to 10 ns in ILs,
TCSPC is an ideal technique to capture these relatively long time scales. In practice,
though, TCSPC will miss about half of the total solvation response.[71] Several investigators have utilized fluorescence upconversion spectroscopy with sub-100 fs time
resolution[73, 74] to measure faster portions of the TDSS in ILs.[7579] By combining
the two measurement techniques, the full solvation response from 10 fs to 10 ns
is elucidated.[75, 76, 78, 79] Recently, Maroncelli, Ernsting, and coworkers have measured the TDSS of coumarin 153 (C153) in a series of ILs from 50 fs to 20 ns.[2, 3]
Immediately apparent in their results is a complex, highly nonexponential kinetic
profile with a noticeable plateau in the region between 1 and 10 ps, where the TDSS
slows appreciably. Trends with respect to varying the identity of the cations and
anions are not immediately apparent, although the slowest time scales do correlate
with viscosity (Figure 1.3).[2, 65, 69, 80]
There have been numerous experimental measurements [2, 3, 3436, 52, 6572, 75
80] in addition to a number of theoretical and simulation studies[8193] of solvation
dynamics in ILs. Kim and coworkers have examined important aspects IL dynamics,
including solvation dynamics, with both united and all-atom fully-flexible models.[84
86, 91] For the united atom studies, solvation responses were computed to time scales
as long as 1 ns, whereas shorter time scales of 10 ps were considered for the all-atom
simulations. In these studies, the solute was modeled either as a diatomic or with
a benzene-like structure. Kobrak and coworkers performed simulations of solvation
dynamics that closely mimic experiment in so much as the all-atom, fully-flexible
liquids contain a realistically modeled C153 solute.[87, 88] The solvation response
was computed to 10 ps, and a number of decomposition strategies were employed to
understand the factors responsible for the onset of solvation dynamics in ILs. In par-
Figure 1.3. The experimental solvation relaxation time as a function of the

solvent viscosity[2]
10
ticular, Kobrak emphasizes the importance of the translations of the ions to the early
solvation response.[88] This is in stark contrast to conventional polar liquids, whose
short-time solvation dynamics are dominated by rotations.[41] Kobrak encountered
some difficulties in applying certain decomposition strategies to his calculated solvation response functions because of the non-pairwise additive nature of the Ewald
summation technique.[9496] Roy and Maroncelli performed extensive equilibrium
and nonequilibrium simulations of a variety of model solutes, as well as a fully atomistic C153 probe, in a coarse grained IL model.[82] For the C153 solute the computed
solvation response was in generally good agreement with experiment with the amplitude of the short time response being slightly overestimated. Roy and Maroncelli
also noted the importance of translational motions of the IL molecules to the inertial solvation response, as well as reasonable agreement between the equilibrium
and nonequilibrium solvation response functions implying the validity of the linear
response approximation. Most recently, Schmollngruber, Schrder, and Steinhauser
investigated with the solvation dynamics of C153 in three imidazolium-based ILs.[81]
Their simulations utilized an electronically polarizable force field, and their results
for the solvation response functions agree well with experiment, although the long
time decay was slightly too slow. Once again, translational motions of the molecules
were implicated as being particularly important to the solvation response. By decomposing the total response in terms of auto- and cross-correlation functions for the
anions and cations, Schmollngruber, Schrder, and Steinhauser found that the anion
and cation auto-correlation functions were similar, and the cross-correlation functions
were highly anti-correlated.
1.3 Vibrational Spectroscopy

Complementing measurements of solvation dynamics, ultrafast vibrational spectroscopy is an effective tool for probing the structure and dynamics in condensed
11
phase systems. Vibrational frequencies are susceptible to subtle changes in the surrounding electric field, shifting in frequency relative to the magnitude and direction
of the oncoming electric field relative to the transition dipole of the vibration. This
information is experimentally captured in the line shape of the IR absorption spectrum and can reflect the distribution of electric fields surrounding the probe. This
simplified perspective can result in motional narrowing, where the line shape appears
to be more narrow than the actual distribution of frequencies, yet is informative regarding the dynamics of the surrounding solvent. For example, if the dynamics of
the surrounding solvent are slower than the vibrational frequency of interest the line
shape will be a Gaussian distribution identical to the distribution of the frequencies.
However if self averaging occurs resulting in motional narrowing, the line shape is
Lorentzian, the direct result of a Fourier transformation of an exponential decay.
The linear vibrational spectrum can be in principle be obtained by performing a
Fourier transformation of the quantum mechanical dipole moment time correlation
function (TCF)
Z
I() =
dt expit h(t)
(0)i
(1.2)
where
is the fully quantum mechanical dipole operator. While this approach is
exact, it is computationally intractable to determine the quantum mechanical TCF. A
common approximation is to treat the translational degrees of freedom classically and
replace the quantum mechanical dipole operator with the classical dipole moment.
This oversimplification can result in large errors when calculating relevant frequencies
of interest, when ~ > kT , or when the Born-Oppenheimer potential deviates from a
harmonic approximation. Alternatively, the IR absorption spectra can be computed
from knowledge of the frequency and transition dipole moment trajectories using the
semiclassical fluctuating frequency approximation (FFA),[97]
12
I() =
E
D
Rt
dteit
~ (t)
~ (0)ei 0 d ( ) et/2T1 ,
(1.3)
where h i represents a classical ensemble average, (t) = (t) hi is the fluctuation of the frequency from its average value, hi, and
~ (t) is the transition dipole
moment vector. The FFA expression, 1.3, approximately captures the effects of
inhomogeneous broadening, motional narrowing, rotational broadening, and nonCondon transition dipole moments on the vibrational line shape. The quality of the
resulting spectrum then solely depends on the method of acquiring the frequency
trajectory and transition dipole moment. As further discussed in Chapter 4, the vibrational frequencies for the IR spectra of water in ILs were obtained by connecting
solvent configurations to vibrational frequencies via an empirical relationship. Alternatively, mixed quantum mechanics/molecular mechanics simulations employing
the self-consistent-charge density functional tight binding (SCC-DFTB) were used to
generate the frequencies in Chapter 6 for a tangential project that focused on proton
transfer in aqueous solution.
1.3.1 Spectroscopic Studies in ILs

1.3.1.1 Spectroscopic Characterization of ILs
Typical imidazolium-based ILs have weak absorption in the 250400 nm region
and slight fluorescence around 300600 nm. Most interesting however, is the shift of
the emission maximum to longer wavelengths when increasing the excitation wavelength [98] inconsistent with Kashas rule resulting from the large degree of spatial heterogeneity similarly observed in highly viscous media such as glasses and
polymers.[99] The absorption and fluorescent properties of ILs are extremely dependent on the purity of the mixtures, as spurious spectroscopic signatures can result
from contaminants.[100] In the context of solvation dynamics, C153 has an absorp-
13
tion and emission fluorescence maximum that is orders of magnitude more intense
than the absorption and fluorescence behavior of imidazolium ILs, so convolution of
the spectrum is not observed.
1.3.1.2 Vibrational Reporters in ILs

X-ray spectroscopy, NMR, and vibrational spectroscopy have been used to characterize the structure in bulk ILs.[25, 101104] Ultrafast two-dimensional infrared
(2D IR) spectroscopy measurements of ILs have the potential to elucidate important dynamical motifs that differ from conventional solvents. 2D IR spectroscopy
has already proven itself as a powerful technique for investigating the structure and
dynamics of liquids by monitoring the response of a vibration to the evolution of its
local environment, a process called spectral diffusion. The frequencies of vibrational
reporters are exquisitely sensitive to changes in their local environment, particularly
to changes in electrostatics, hydrogen bonding, and chemical processes. For example,
the OH and OD stretch frequencies of HOD are known to depend hydrogen bonding:
an increase in hydrogen-bond strength red-shifts the OH and OD stretch vibrational
frequencies. The inhomogeneous IR absorption line shape of liquid water reflects the
range of different hydrogen bonding environments present. [105107] The spectral
diffusion time scales revealed by 2D IR have been shown to directly relate to hydrogen
bond rearrangement processes in liquid water.[108111]
Previous work examining isolated water in ILs determined a water molecule is
bridged by two anions in an IL, existing in a A HOH A complex. As a result
of this proximity, the anions are most responsible for influencing the OH stretch
frequency.[112114] Investigations varying the lengths of the cation alkyl chains in
imidazolium-based ILs suggest the chains do not have an influence on the OH stretching frequency.[112, 115] Recently, the dynamics of HOD isolated in an IL was investigated with vibrational spectroscopy.[116] The linear IR absorption spectrum
14
of the OD stretch frequency of dilute HOD in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6 ], revealed a blue-shifted and a significantly narrowed
vibrational line shape compared to the spectrum of HOD in water. The blue-shift
suggests weaker OD interactions with the ionic environment and is characteristic
of a relatively isolated OD stretch, for example the free OD stretches at a liquid
D2 O/vacuum interface.[117119] The 2D IR measurements monitored spectral diffusion of the OD stretch of HOD in the IL. An important quantity accessible by
both simulation and experiment is the frequency fluctuation time correlation function (FFCF), C(t) = h(t)(0)i, where (t) is the deviation of the frequency
from its equilibrium value, (t) = (t) hi. As a water molecule samples different
molecular environments, the FFCF decays to zero. This can be approximately related
to the spectral diffusion measurements quantified experimentally using the center line
slope (CLS) method.[120, 121] Measurements of the amplitudes and timescales of the
FFCF thus give information about the dynamics of the environment surrounding the
HOD molecule. Two times scales were found: 6.9 2.1 ps and 72 20 ps. The
faster of the two relaxation timescales was attributed to changes in the local structure
of the anions bridged by the water and the subsequent motions of the cations. The
slower relaxation time was assigned to orientational relaxation, though a discrepancy
of approximately one order of magnitude exists between the 72 ps timescale and
the 2.3 ns response in optical heterodyne detected optical Kerr effect experiments in
[bmim][PF6 ].[122]
15
CHAPTER 2
THE MECHANISM OF SOLVATION DYNAMICS IN [emim][BF4 ]
2.1 Introduction
Recall from Chapter 1, that solvation dynamics are measured in time-dependent
fluorescence Stokes shift (TDSS) experiments which employ fluorescent probe molecules
to measure the response of the environment to an instantaneous perturbation of the
charge distribution of the probe molecule.[3941] The experiment begins with an initial laser pulse, v(0) that electronically excites the probe molecule. This excitation
occurs effectively instantaneously, such that the molecular geometry of the probe
molecule is unchanged, but its charge distribution is significantly altered. After the
initial excitation, the solvent environment begins to reorganize to accommodate the
new charge distribution. The reorganization stabilizes the excited electronic state of
the probe relative to its ground electronic state, and subsequent fluorescence, v(t), is
red shifted with respect to the initial fluorescence, v(0). The time scales of the environment reorganization are typically characterized by a solvation response function,
S(t) =
v(t) v()
v(0) v()
(2.1)
to the excited state charge distribution of the dye, achieving an equilibrium solvation
structure around the newly formed charges.
Experimental studies of solvation dynamics in imidazolium-based ionic liquids
(ILs) have revealed complex kinetics over a broad range of time scales from fem16
toseconds to tens of nanoseconds. This chapter presents calculations of the solvation

response over the full range of time scales (from 10 fs to 10 ns) accessed in measurements of C153 in 1-ethyl-3-methyl imidazolium ([emim]) and tetrafluoroborate
([BF4 ]). These calculations utilized microsecond-length molecular dynamics (MD)
simulations with the C153 and IL molecules modeled in full atomistic detail necessary to capture the highly nonexponential kinetic profile, including the plateau in
the region between 1 and 10 ps. The calculated response is compared directly with
experiment, and analysis of the simulations with decomposition strategies developed
previously to understand solvation dynamics in complex biological systems[123126]
provide insights into the mechanism of solvation dynamics in this imidazolium-based
IL.
2.2 Theoretical Methodology

2.2.1 Solvation Response Calculations
The solvation response of C153 in [emim][BF4 ] was computed using methodology
that has been utilized and validated extensively in previous MD studies of solvation
dynamics.[127129] The central quantity in this approach is E(t) = Ee (t) Eg (t),
which represents the difference in the interaction energy of the probe molecule with
its environment for its excited (Ee ) and ground (Eg ) electronic states. The electronic states are modeled classically as two different distributions of atomic-centered
charges, which have been derived and validated previously from density functional
theory calculations.[1] This allows for the calculation of the equilibrium time correlation function for the fluctuations in the solvation energy differences within a MD
simulation,
C(t) =
hE(t)E(0)i
,
h(E)2 i
17
(2.2)
where E(t) = E(t) hEi and h i is an ensemble average in the ground electronic state of the probe. Within linear response theory, which will be specifically
examined in Chapter 4, in addition to previous studies have generally found to be applicable to solvation dynamics in ILs at early times in the response,[89] C(t) is equal
to S(t), thus allowing direct comparisons with experiment.[129, 130] During calculations of E(t), the longranged electrostatic interactions between C153 and the IL
molecules were computed with the damped shifted force (DSF) method.[131] The DSF
method is used as an alternative to the traditional Ewald summation technique,[94
96] and facilitates decomposition of the solvation response (see 2.2.2) because it is
based explicitly on a pairwise sum.
2.2.2 Decomposition of the Solvation Response by Solvent Component

The total solvation response can be decomposed into contributions from the different constituents present in the liquid. Such decompositions are made possible
P
because of the additive nature of the solute interaction energy, E(t) = E (t),
where E (t) is the solute interaction energy with solvent component , in this case
the anions, cations, and intramolecular electrostatic interactions within the probe
itself. Unfortunately, there is not a unique decomposition of Eq. (2.1) simply based
on expressing E (t) as a sum. However, one decomposition strategy is formally
compatible with linear response theory,[90, 124, 132]
hE (t)E(0)i
,
C (t) =
h(E)2 i
(2.3)
where superscript signifies the solvent component of interest. Previous investigations have confirmed empirically that, when linear response theory holds, C(t)
corresponds to the contributions to S(t) from the solvent components (note that S(t)
does uniquely decompose due to the additive property E(t)).[132, 133] Kobrak and
18
Znamenskiy[90] were the first to employ Eq.(2.3) in the context of solvation dynamics
in ILs. They decomposed the solvation response of the solute betaine-30 in 1-butyl3-methyl imidazolium ([bmim]) and hexafluorophosphate ([PF6 ]) over the range from
1 to 5 ps and found that the anion dominates the response on this timescale.
2.2.3 Decomposition of the Solvation Response by Translations and Rovibrations

The solvation response functions for the anions and cations of the IL can be further
decomposed into contributions from their respective translational and rovibrational
motions. The translational contribution, Etrans

, to E for the cations and anions
are computed by regarding each relevant IL molecule as a single point charge located
at its center of charge. The rovibrational contribution, Erovib

, to E is then just
obtained as the difference, Erovib

= E Etrans
. With these definitions, the
correlation functions for the cations and anions decompose into translational and
rovibrational contributions,
C (t) = Ctrans
(t) + Crovib
(t)
(2.4)
(t)
(t) and Crovib
(t) are computed with Eq.(2.3) using Etrans
where the functions Ctrans
and Erovib
(t) in place of E (t).
2.2.4 Molecular Dynamics Simulations

The MD simulations were performed using the Large-scale Atomic/Molecular
Massively Parallel Simulator (LAMMPS)[134] program with periodic boundary conditions and a cubic simulation box containing 256 [emim] cations, 256 [BF4 ] anions,
and one C153 molecule. All of the molecules were modeled as fully flexible, except
for covalent bonds containing hydrogen which were fixed at equilibrium lengths using
the SHAKE algorithm.[135] For the C153 and [emim] molecules force-field parame-
19
ters for the bonds, bends, dihedrals, and atomic-centered Lennard-Jones sites were
adopted from the generalized Amber force field (GAFF).[136] Parameters for [BF4 ]
are not available in the GAFF, so these parameters were obtained from Liu et al.[137]
Atomic-centered partial charges for the IL molecules and the ground state of C153
were calculated via the Merz-Singh-Kollman[138] analysis of the electron density of
the optimized geometry of the molecules obtained with density functional theory
(DFT) with a B3LYP functional and the aug-cc-pVDZ basis set. The change in
the partial charges for C153 upon electronic excitation were calculated and validated
previously by Cinacchi et al.[1] thus the excited state partial charges for C153 are
obtained by simply adding these changes to the computed ground state charges. In
the MD simulations the long-ranged electrostatic interactions were computed with
the particle-mesh Ewald summation method with a 15
A real-space cutoff.[94, 139]
This same cutoff distance was utilized when computing interactions between LennardJones sites.
Since imidazolium-based ILs are known to exhibit slow (nanosecond) relaxation
dynamics, we employed a rigorous equilibration protocol before performing the production run simulations from which the solvation response function was calculated.
Following an initial period of minimization, the temperature was slowly raised from
0 K to 300 K over a period of 200 ps. This was followed by a 4 ns simulation in the
NPT ensemble (300 K and 1 atm) using a Nose-Hoover thermostat and barostat.[140]
The size of the simulation box was isotropically scaled to reflect the average density
and was then simulated in the NVT ensemble for 1 ns at 300 K, the temperature
was raised to 600 K over 1 ns to destroy any pseudo-stable ionic cages that may
have formed. Next, the temperature was reduced back to 300 K in 1 ns, followed by
the NVT simulation for 1 ns at constant temperature of 300 K. The final velocities
were scaled to 300 K and a pre-production NVE simulation was performed for 11
ns. Production-runs (comprising a total of 5.015 s) were performed in the NVE
20
ensemble with a 2 fs integration time step and a collection resolution of 10 fs.

A 100 ns control simulation of pure [emim][BF4 ] was performed to validate the
IL force-field. The average density of the liquid was found to be 1.19 g/cc, which
compares reasonably well to experiment (1.28 g/cc).[141] It is important to note
that the partial charges for [emim] and [BF4 ] were empirically scaled by a factor of
0.80, guided by DFT calculations,[142] to achieve better agreement with experiments
where dynamic properties are of interest. Charge scaling has become a fairly common practice in IL MD simulations and a valid means of increasing diffusion.[143]
The scaling factor is further addressed in Chapter 3, though, in brief, it can be regarded as an additional force-field parameter whose physical role is to account, in an
approximate and empirical fashion, for the effects of electronic polarizability. This
adjustment decreases the calculated density from 1.27 g/cc in a simulation with full
charges[137] to 1.19 g/cc with scaled charges. However, the computed self-diffusion
constants, 8.1 1011 m2 /s for [emim] and 5.5 1011 m2 /s for [BF4 ], compare more
favorably with experiment (5.0 1011 m2 /s and 4.2 1011 m2 /s) than diffusion
constants reported for simulations with full charges (1.1 1011 m2 /s and 0.9 1011
m2 /s).[137]
2.3 Results and Discussion

The calculated solvation response for C153 in [emim][BF4 ] is shown in Figure 2.1
along with the experimental measurement[2, 3] for direct comparison. The simulated
solvation response is in good overall agreement with experiment and it reproduces
the complex non-exponential decay, including the plateau in the 1 10 ps regime
reminiscent of dynamics in supercooled liquids. The pronounced oscillations in the
calculated response at times less than 10 ps are due to internal motions of the C153
probe molecule and will be discussed in more detail below. While the calculated response is qualitatively similar to experiment over all timescales, it decays too quickly
21
in the regime beyond 10 ps. To quantify the differences in the long-time decay between experiment and theory, both solvation response curves were fit with a stretched
exponential function, A exp((t/ ) ), in the range from 10 ps to 1 ns (Table 2.1 and
Figure 2.2). A stretched exponential is ideal over this range as it captures the superposition of an indefinite number of single exponential decays all weighted by a
distribution of relaxation times.[144]
The time constant, , is shorter in the theoretical result (81.4 ps) than in the
experiment (115.7 ps). It has been empirically established that the long-time decay of
the solvation response in imidazolium-based ILs is viscosity dependent.[7, 65, 69, 80]
Thus, the slightly too large self-diffusion constants for the molecules in the neat
[emim][BF4 ] simulation Section 2.2.4 are a likely culprit for the slightly too fast longtime decay of the solvation response. While it is beyond the scope of the present study,
it might be possible to utilize the experimental solvation response data to further
refine the dynamical properties of the IL force-field via the empirical charge scaling
factor discussed in Section 2.2.4 and Chapter 3. While modest discrepancies in the
long-time decay exist, the calculated solvation response captures the complex kinetic
behavior of the experimental measurement, thus validating the simulations directly
with experiment, and we will now proceed to further analyze the simulations to
uncover the molecular mechanisms responsible for solvation dynamics in [emim][BF4 ].
Figure 2.3 shows the decomposition of the total calculated solvation response of
C153 in [emim][BF4 ] into contributions from the anions, cations, and internal motions
of the C153 solute. It is immediately apparent that the anions dominate the solvation
response. Not only is the anion contribution substantially larger than that of the
cations or C153 for all time scales, it also mimics closely the characteristic shape of
the total response curve. The internal motions of the C153 solute do not contribute
to the decay of the solvation response (i.e. the C153 component of the response
22
Figure 2.1. Calculated (black) and experimental[2, 3] (green) solvation

response functions in the range from 50 fs to 1 ns.
23
Figure 2.2. Fits of the calculated (black) and experimental (green) solvation
responses of C153 in the IL [emim][BF4] to a stretched exponential
function, A exp((t/ ) ), in the time range between 10 ps and 1 ns. The
data are shown as filled circles, while the fits are lines. The quality of the
fits in terms of the correlation coefficient, r2 , are excellent: r2 = 0.9987 for
the theoretical data and r2 = 0.9983 for the experimental data.
24
Figure 2.3. The calculated total simulated solvation response (black) is

decomposed using the methodology described in Section 2.2.2 into
contributions from the anions (red), the cations (blue), and the internal
motions of the C153 solute (purple).
25
TABLE 2.1
PARAMETERS FOR A STRETCHED EXPONENTIAL FIT
Experiment
Theory
0.38
0.32
(ps)
115.7
81.4
0.55
0.74
Parameters for a stretched exponential, A exp((t/ ) ), fit to the calculated and experimental solvation response functions in the range from 10 ps to 1 ns.
is generally flat). However, these motions do engender pronounced oscillations in

the total response function. Such oscillations in the solvation response have been
observed in high temporal resolution measurements in solution[145] and for a dye
molecule (Hoechst 33258) bound to DNA.[146] For H33258 bound to DNA an analysis
of the oscillations computed with theoretical methodology similar to that employed
in the present work yielded reasonably good agreement with experiment.[125] The
decomposition in Figure 2.3, which is formally consistent with the linear response
approximation, results in a less ambiguous interpretation than the analysis in terms
of auto- and cross-correlation functions presented most recently by Schmollngruber,
Schrder, and Steinhauser,[81] where it is not clear that the anions are the dominant
contributor to the solvation response over all timescales.
The results shown in Figure 2.3 suggest that the [BF4 ] anions play a particularly
important role in determining the solvation response. To begin to understand the role
of the anions in the solvation response, we first focused on the structure of the IL in
the vicinity of the C153 probe. Shown in Figure 2.4 are radial distribution functions,
26
g(r), for the center-of-mass of the cations and anions relative to the center-of-mass
of the C153 solute. The most striking feature is the dramatic enhancement of [emim]
cations in the vicinity of the C153 molecule, represented by the pronounced peak near
4
A and the corresponding depletion of [BF4 ] anions close to C153. The preferential
solvation of C153 by [emim] is perhaps not surprising, since the molecules can align
their flat surfaces and take advantage of favorable stacking interactions. While
the radial distribution function shown in Figure 2.4 does not give a full characterization of the three-dimensional solvent structure around the non-spherical C153 solute,
it does indicate that the [emim] cations are, on average, more proximal to the C153
solute than the [BF4 ] anions. This observation is consistent with previous studies of
the three-dimensional solvent structure around aromatic compounds in imidazolium
ILs.[147, 148] The observation of preferential solvation creates a conundrum for understanding solvation dynamics in [emim][BF4 ]. Conventionally, solvation dynamics
is dominated by molecules close to the fluorescent dye molecule. In this case, however, the anions, which have been implicated as the dominant player in the response
dynamics (Figure 2.3), are generally further away from the C153 dye molecule than
the cations. Before we resolve this issue, it is worth noting that the observation of
preferential solvation has broader implications. In most experiments that employ an
exogenous spectroscopic probe molecule, the general assumption is that the presence
of the solute does not greatly alter the native structure and dynamics of interest.
In this case, the C153 molecule is apparently inducing structure in the IL. This implies that there is some ambiguity as to whether the experiment is really measuring
dynamics that are native to the neat IL. Preferential solvation effects could also be
relevant to the interpretations of other experiments on IL structure and dynamics.
To determine which specific motions of the [emim] and [BF4 ] molecules are most
relevant to solvation dynamics, we further decomposed the anion and cation solvation responses into contributions from translations and rovibrations (Figure 2.5).
27
Figure 2.4. The radial distribution function, g(r), for C153-[emim] and
C153-[BF4 ] pairs, where r is defined as the distance between the
center-of-mass positions of the relevant pair of molecules.
28
Focusing first on the [BF4 ] anions the results are unambiguous: translational motions of the anions dominate the total response, whereas [BF4 ] rovibrational motions
are negligible. Note that the shape of the anion translational decomposition nearly
perfectly mimics the total solvation response. Since the [BF4 ] molecule is symmetric
and possesses no permanent dipole moment it is not surprising that its rovibrational
motions do not affect the solvation dynamics. However, since solvation dynamics in
conventional polar liquids is governed mostly by rotational motions of the solvent,
the central importance of the translational motions of [BF4 ] to the solvation response
of C153 in [emim][BF4 ] is unusual and warrants further investigation. The cations
also exhibit unusual and interesting behavior in Figure 2.5. The translations of the
cations are also a significant contributor to the total solvation response (but still significantly less than the anion translations), however these contributions are largely
offset by the cation rotations, which are uniformly negative in sign on all time scales.
Negative values of the cation rotational contribution to the total solvation response
indicate that these motions are actually counterproductive, on average, to stabilizing
the excited state charge distribution of the C153 solute.
The final unresolved issue for obtaining a complete view of the mechanism of
solvation dynamics in the [emim][BF4 ] IL is to determine which specific translational
motions of the [BF4 ] anion are relevant. For this we computed the residence-time
correlation function (RTCF) for the anions and cations in the first solvation shell of
the C153 solute, hn(0)n(t)i, where n(t) = 1 if the molecule of interest is in the first
solvation shell and n(t) = 0 if it is not (Figure 2.6). For the purposes of the RTCF
calculation the first solvation shell was defined as any molecule whose center-of-mass
lies within 5.6
A of the center-of-mass of the C153 probe. 5.6
A was chosen because
it is the first minimum of the C153-[emim] radial distribution function. The RTCF
describes the time scales for molecules, either anions or cations, to enter or leave the
first solvation shell of the solute. The RTCF for the anion is generally similar to
29
Figure 2.5. The solvation responses of [emim] (blue) and [BF4 ] (red)
decomposed into contributions from translational (solid) and rovibrational
(dashed) motions. For reference, the total solvation response minus the
contribution from the internal motions of the C153 solute is also shown
(black).
30
Figure 2.6. The residence-time correlation function (RTCF) for the anions
and cations in the first solvation shell of the C153 solute. The first
solvation shell was defined as any molecule whose center-of-mass lies within
5.6
A of the center-of-mass of the C153 probe.
31
the solvation response. It appears to exhibit the same unusual kinetic profile as the
solvation response, which is suggestive that these anionic translational motions are
relevant for the response. In contrast, the RTCF for the cations is significantly slower
than the anions and its shape is qualitatively different from the solvation response.
The time scales for the decay of the anion RTCF are similar, although clearly slower,
than the solvation response. However, the difference in the times scales is likely due to
the somewhat arbitrary definition of the solvation shell. Changing the cutoff distance
for the solvation shell alters the time scales for the RTCF decay of both anions and
cations, but the qualitative profiles are unchanged (data not shown). The results in
Figures (2.42.6) support a solvation dynamics mechanism in [emim][BF4 ] where the
translational motion of the anions into and out of the first solvation shell of the C153
probe molecule potentially play an important role.
2.4 Summary
Extensive MD simulations have revealed the detailed molecular motions responsible for solvation dynamics of C153 in the imidazolium-based IL [emim][BF4 ] (Figure
2.7). Solvation dynamics in liquids generally involves collective motions of the solvent
environment in the vicinity of the fluorescence probe molecule. In this case, however,
we have identified a particular molecular motion that appears to be especially relevant to solvation dynamics in [emim][BF4 ], namely the translational motion of the
[BF4 ] anion into and out of the first solvation shell of C153. This proposed mechanism is consistent with a number of previous simulation studies that have implicated
translational motions and/or motions of the anions as being especially relevant to
solvation dynamics in imidazolium-based ILs.[82, 86, 8890] The MD simulations
have also revealed that the IL forms a specialized structure around the C153 solute,
in which the first solvation shell is enriched in [emim] while the second solvation
shell is enriched in [BF4 ]. An important question remains for future studies: how
32
Figure 2.7. A schematic depiction of the mechanism of solvation dynamics

in C153/[emim][BF4 ].
33
general is this anion-translation mechanism? It seems likely that other imidazoliumbased ILs, whose cations can preferentially solvate dyes with fused ring structures,
will exhibit this mechanism. However, as one deviates from the structural motifs
of the C153/[emim][BF4 ] system, new solvation dynamics mechanisms could emerge.
This presents both challenges and opportunities for the theoretical and experimental
communities interested in designing ILs with properties selectively tuned for specific
applications.
34
CHAPTER 3
SIMULATIONS OF THE SOLVATION RESPONSE IN A SERIES OF IONIC
LIQUIDS
3.1 Introduction
In the previous chapter microsecond-length molecular dynamics (MD) simulations of coumarin 153 (C153) in 1-ethyl-3-methyl imidazolium tetrafluoroborate,
[emim][BF4 ], were performed to reveal the molecular-level mechanism for solvation
dynamics. In that particular system it was the translational motion of the [BF4 ] anion
into and out of the first solvation shell of C153 that dominated the solvation response.
Given the sensitivity of certain properties to variations in the cation and anion constituents in the IL[9, 2125], it is necessary to understand if this anion-translation
mechanism can be generalized to other imidazolium-based ILs. This chapter presents
calculations of the solvation response of C153 in a series of imidazolium-based ILs
comprised of cations and anions seen in Figure 3.1. Two cations, 1-butyl-3-methyl imidazolium, [bmim], and 1-ethyl-3-methyl imidazolium, [emim], were paired with four
different anions, tetrafluoroborate, [BF4 ], dicyanamide, [DCA], trifluoromethanesulfonate, [TfO], hexafluorophosphate, [PF6 ], to create five unique systems, [emim][BF4 ],
[bmim][BF4 ], [bmim][DCA], [bmim][PF6 ], and [emim][TfO] allowing a direct comparison to experiment. Studying this series where size, shape, and charge distribution of
the cations and anions varies is helpful to determine if any trends or generalizations
regarding the solvation mechanism are present.
Additionally, this chapter investigates the effects of charge scaling. Transport
properties such as the mean-square displacement (MSD), diffusion coefficients, and
35
Cations
Anions
[bmim]
[BF4]
[PF6]
[emim]
[DCA]
[TfO]
Figure 3.1. Optimized structures of imidazolium cations and inorganic

anions studied in this chapter. The cations are 1-butyl-3-methyl
imidazolium, [bmim], 1-ethyl-3-methyl imidazolium, [emim], while the
anions are tetrafluoroborate, [BF4 ], dicyanamide, [DCA],
trifluoromethanesulfonate, [TfO], hexafluorophosphate, [PF6 ].
36
viscosity are all affected by modifications to the charges. The accuracy of a molecular
dynamics simulation is dependent on the proper selection of the force field parameters. Force fields are an approximation to the intra- and inter-molecular interactions
that attempt to capture the properties of molecules accurately and efficiently over a
range of conditions. A force field contains three kids of parameters that determine
bonded interactions, electrostatics, and short range interactions. Bonded parameters are generally calculated from quantum mechanics, whereas electrostatics and
short-range interactions are more difficult to parametrize. Accurately representing
this interplay between long-range and short-range interactions is key to achieving a
correct description of the system, and it truly matters how the force field deals with
charge transfer and polarization. Some force fields are more general, such as OPLS,
GAFF, or CHARMM, meant to be transferable over a range of molecules and temperatures while others are created and parameterized to match specific experimental
properties.
Classical, or non-polarizable, force fields use static partial charges for each atomic
site to model the electrostatic interactions. In IL systems, non-polarizable force
fields typically underestimate dynamic and transport properties due to a neglect
of the electronic polarization and charge transfer effects present in the condensed
phase. Ideally using a fully polarizable force field would adequately capture the
movement of electron densities, and various studies have examined the inclusion of
polarizability.[81, 143, 149151] Polarizable models consistently show faster translational and rotational relaxations, higher self-diffusion and conductivity, and lower
shear viscosity when compared to non polarized models. This is a consequence of
a weakening of the long-range interactions caused by enhanced screening. However,
due to the sluggish dynamics and the the long timescales required for accurate descriptions of solvation dynamics calculations, simulating hundreds of molecules in a
fully polarizable model for microseconds is computationally prohibitive.
37
Utilizing fixed charges in a non-polarizable force field requires careful insight into
how one deals with charge transfer and polarization. While not modeling the atomic
sites as being explicitly responsive to their local environment, fixed-charge force fields
accomplish an effective representation by scaling the charges of the molecules and
using existing generalized force fields, or undergo a complete reparameterization of the
short-range interactions and keep the unit charges 1. Adopting the latter method,
Koddermann et al.[152] showed that through reparameterization and matching the
experimentally derived observables (density, self-diffusion coefficients, and rotational
correlation dynamics) they were able to reproduce viscosity, the heats of vaporization
and dynamic properties maintaining full unit charges on all molecules. While this
force field is transferable to imidazolium cations with various alkyl chain lengths, it
requires dynamical properties as inputs to fit these short range parameters, which
presents a difficulty as these experiments for a range of cation and anion pairs are
sparse.
Reducing the net charges, entertainingly referred as Poor mans polarization,[143]
is grounded in electronic structure calculations. A number of studies performing ab
initio calculations of non-isolated IL ions revealed the net charges are reduced due to
charge transfer and polarization.[153158] In principle, charge transfer occurs when
the charge density is shifted from one ion to another ion via orbital overlap. Quantifying this effect was carried out when a systematic study involving XPS, NMR, and
corroborating evidence from DFT calculations determined significant charge transfer
and polarization are present in these ILs.[103] Taken together, a reduced point charge
is representative of this screened partial charge. In Section 3.4 the effects of varying
the overall scaled charges on the dynamics in ILs are discussed.
38
3.2 Methodology
3.2.1 Decomposition of the Solvation Response
Recall the total solvation response can be decomposed into contributions from the
different constituents present in the liquid. Such decompositions are made possible
because of the additive nature of the solute interaction energy, E(t) = E (t),
where E (t) is the solute interaction energy with solvent component , in this case
the anions, cations, and intramolecular electrostatic interactions within the probe
itself. Unfortunately, there is not a unique decomposition of C(t) simply based on
expressing E (t) as a sum. However, one decomposition strategy is formally compatible with linear response theory,[90, 124, 132]
C (t) =
hE (t)E(0)i
,
h(E)2 i
(3.1)
where superscript signifies the solvent component of interest. Note that could
also correspond to other components such as rotations and translations of cations
and anions, thus allowing further insight.

Similar to [emim][BF4 ] in Chapter 2, cubic simulation boxes were created containing 256 cations, 256 anions, and one C153 molecule for each of the following systems:
[bmim][BF4 ], [bmim][DCA], [bmim][PF6 ], and [emim][TfO]. The solvation dynamics
calculations presented in Section 3.3 employed a charge scaling parameter, , of 0.80
and 0.84, respectively, based on DFT calculations and simulations of [emim][BF4 ]
and [bmim][BF4 ] which found the ideal scaling parameter for these systems.[142]
Lacking an exhaustive investigation into the appropriate scaling parameter for these
systems, was assumed to be cation dependent where the [emim] cation-based systems, [emim][BF4 ] and [emim][TfO], = 0.80, while for [bmim] cation-based systems,
39
[bmim][BF4 ],[bmim][PF6 ], and [bmim][DCA], = 0.84. The validity of this assumption is examined below in Section 3.4.1. For the analysis of charge scaling, identical
systems were created however the net charge was scaled appropriately. All of the
molecules were modeled as fully flexible, except for covalent bonds containing hydrogen which were fixed at equilibrium lengths using the SHAKE algorithm.[135] The
force field parameters for the bonds, bends, dihedrals, and atomic-centered LennardJones sites for [BF4 ] and [PF6 ] were obtained from Liu et al.[137], while the parameters for [DCA] were taken from Lopes et al.[159] For C153, [emim], [bmim], and [TfO],
parameters were adopted from the generalized Amber force field (GAFF).[136] All
atomic-centered partial charges for the IL molecules and the ground state of C153
were derived using the Merz-Singh-Kollman[138] scheme to interpret the electron
density of the optimized geometry of the molecules obtained with density functional
theory (DFT) with a B3LYP functional and the aug-cc-pVDZ basis set. The change
in the partial charges for C153 upon electronic excitation were calculated identical
to Chapter 2. In the MD simulations the long-ranged electrostatic interactions were
computed with the particle-mesh Ewald summation method with a 15
A real-space
cutoff.[94, 139] This same cutoff distance was utilized when computing interactions
between Lennard-Jones sites. The equivalent equilibration protocol was employed
whereby each system undergoes a total of 22 ns of minimization, NPT, NVT, and
NVE ensemble simulations explicitly laid out in Chapter 2. All production-runs were
performed in the NVE ensemble with a 2 fs integration time step and a collection
resolution of 10 fs for trajectories 2.0 s long.
Simulations of the pure ILs were performed for 100 ns to validate our force field
and charge scaling parameter. Determining a reliable a self-diffusion coefficient requires considerable amounts of simulation time, though to ensure sufficient convergence, multiple checkpoints from the trajectory were used as starting points in the
calculation. Using the Einstein relation, limt MSD = 6Dt, in the linear range of
40
TABLE 3.1
SELF-DIFFUSION COEFFICIENTS FROM MD SIMULATIONS
System
D+ [sim]
[bmim][BF4 ]
0.84
1.7
[bmim][DCA]
0.84
[bmim][PF6 ]
[emim][TfO]
[emim][BF4 ]
[sim]
[lit]
[lit]
D+
Ref
1.2
1.4
1.3
[161]
1.7
2.0
0.4
0.5
[160]a
0.84
0.6
0.3
0.8
0.6
[162]
0.80
3.0
1.3
1.1
1.6
[81]a
0.84
1.9
0.9
0.80
8.1
5.5
5.0
4.2
[163]
1.0
0.3
0.2
0.80ring
6.8
4.9
Polarizable MD simulation results. The ion self-diffusion coefficients D+/ (in units
of 1011 m2 /s) from MD simulations along with literature values for the IL systems.
The net unit charge of the cations and anions is given by .
0.1 1000 ps, self-diffusion coefficients were calculated (Table 3.1). In all cases the
simulated ILs compare favorably with experiment, albeit predicting faster dynamics.
In the absence of experimental data for [bmim][DCA] and [emim][TfO], transport
properties calculated using parameters from polarizable force fields [81, 160] indicate our MD simulations are in reasonable agreement. See Section 3.4, in particular
Subsection 3.4.1, for a discussion regarding the implications of charge scaling on the
dynamic properties.
41
3.3 Solvation Dynamics Results

Shown in Figure 3.2 are the calculated solvation responses for C153 in [emim][BF4 ],
[bmim][BF4 ], [bmim][DCA], [emim][TfO], and [bmim][PF6 ], along with the experimental measurements[2, 3] for direct comparison. The experimental results were
scaled by a multiplicative constant to bring the results into maximum coincidence
for comparative purposes (Appendix A). The simulated solvation response is able to
capture the complex non-exponential decay, including the plateau in the 1 10 ps
regime, and agrees well with experiment. For all the ILs systems studied here, the
decay response is qualitatively similar to experiment over the entire range, however
it consistently predicts a more rapid decay than experimental measurements, with
the exception of [bmim][DCA]. The calculated response function for [bmim][DCA]
predicts faster short-time and slower long-time dynamics than experimental observations, most likely due to inaccurate approximations in the force field parameters for
this anion.
To facilitate comparison to experiment, the solvation response functions were fit
with a single exponential, A exp((t/ )), in the range from 50 ps to 400 ps seen
in Appendix A. The theoretical time constants are lower than those measured by
experiment (Figure 3.3), however it appears to be a systematic underestimation due
to overscaling the charges that led to slightly larger self-diffusion constants reported
in Table 3.1. This phenomena is examined in greater detail in Section 3.4 where varied
charge scaling parameters are used to refine the the dynamical properties of the IL
force field to improve the ability of the simulation to reproduce the experimental
solvation response data. Although the simulations report response functions that are
faster than experimental measurements, the calculated solvation response captures
the non-exponential kinetic behavior, thereby validating the simulations directly with
experiment. Figures 3.4-3.7 shows the decomposition of the total calculated solvation
response of C153 in [bmim][BF4 ], [bmim][DCA], [bmim][PF6 ], and [emim][TfO] into
42
Figure 3.2. The calculated (dashed) and experimental (solid) solvation

response functions for [emim][BF4 ] (black), [bmim][BF4 ] (red),
[bmim][DCA](green), [emim][TfO](blue), and [bmim][PF6 ] (brown) over the
range 50 fs to 1 ns.
43
Figure 3.3. Time constants for experiment and calculated response

functions derived from a fit to a single exponential, A exp((t/ )), in the
range from 50 ps to 400 ps.
44
contributions from the anions (red), cations (blue), and internal motions of the C153
solute (purple). In all cases the anions dominate the solvation response. Not only is
the anion contribution substantially larger than that of the cations or C153 for all
time scales, the anions are responsible for the the characteristic shape of the total
response curve. The internal motions of the C153 solute do not contribute to the
decay of the solvation response (i.e. the C153 component of the response is generally
flat).
The decomposition results indicate the anions play a particularly important role
in determining the solvation response. Further insight regarding the role of the anions
in the solvation response, is gained by analyzing the structure of the IL in the vicinity of the C153 probe. Shown in Figure 3.8 are radial distribution functions, g(r),
for the center-of-mass of the cations and anions relative to the center-of-mass of the
C153 solute, including the results from [emim][BF4 ] reported in Chapter 2. Immediately apparent is the proximity at which the relatively larger imidazolium cations
are to the C153 molecule compared to the smaller, mostly spherical anions. The
non-spherical anion, [DCA], shows a small enhancement near 4
A before mimicking
similar charge ordering seen in the other ILs. While the radial distribution function
shown in Figure 3.8 does not give a full characterization of the three-dimensional solvent structure around the non-spherical C153 solute, it does indicate that the cations
are, on average, closer to the C153 solute than the anions. This observation is consistent with previous studies of the three-dimensional solvent structure around aromatic
compounds in imidazolium-based ILs,[147, 148] though confirms that despite the diversity of the molecular environments in these ILs, preferential solvation of C153 by
the imidazolium-based cations is persistent. Given the favorable stacking interactions between C153 and the imidazolium ring and the heterogeneous nature of
these systems,[5464] it is conceivable a degree of preferential solvation is present.
Preferential solvation as first understood in mixtures of polar and non-polar solvents
45
Figure 3.4. The calculated total solvation response (black) is decomposed

into contributions from the [BF4 ] anions (red), the [bmim] cations (blue),
and the internal motions of the C153 solute (purple).
46

into contributions from the [DCA] anions (red), the [bmim] cations (blue),
47

into contributions from the [PF6 ] anions (red), the [bmim] cations (blue),
48

into contributions from the [TfO] anions (red), the [emim] cations (blue),
49
Cations
Anions
Figure 3.8. The radial distribution function, g(r), for C153-[cation] and
C153-[anion] pairs, where r is defined as the distance between the
center-of-mass positions of the relevant pair of molecules.
50
was first described in terms of dielectric enrichment[164, 165] where the solute is
surrounded by solvent molecules to form an associated complex in thermodynamic
equilibrium. Studies examining the effects of preferential solvation of C153 in tolueneacetonitrile and toluene-methanol mixtures[166] and more recently in IL-surfactant
solutions[167] have highlighted the implications of these non-ideal systems. In most
experiments that employ a spectroscopic probe molecule, the general assumption is
that the presence of the solute does not alter the native structure and dynamics of
interest. Figure 3.8 reveals the C153 molecule is apparently inducing structure in
the ILs. This suggests that there is some ambiguity as to whether the experiment is
really measuring dynamics that are native to the neat IL.
Further decomposition of the component solvation responses in Figures 3.9-3.12
identifies specific motions, translations and rovibrations, of the cation and anion
molecules necessary for effective charge accommodation. The results are unambiguous: translational motions of the anions (solid red) dominate the total response for
all imidazolium-based ILs studeied here, whereas anion rovibrational motions (red
dashed) are negligible, or slightly negative in the case of [bmim][DCA]. The translations of the cations (solid blue) are also a significant contributor to the total solvation response, however these contributions are offset by the cation rotations, which
are negligible or negative in sign on all time scales. Negative values of the [DCA]
and cation rotational contribution to the total solvation response indicate that these
motions are actually counterproductive to stabilizing the excited state charge distribution of the C153 solute.
Solvation dynamics in conventional polar liquids is governed mostly by librational and rotational motions of the solvent molecules proximal to the fluorescent
dye molecule. The results of the solvation response decomposition presented in Figures 3.4-3.12 indicate the translational motions of the anions are essential to the
solvation response of C153 in imidazolium-based ILs. To determine which specific
51
Figure 3.9. The solvation responses of [bmim] (blue) and [BF4 ] (red)
(dashed) motions. For reference, the total solvation response is also shown
(black).
52
Figure 3.10. The solvation responses of [bmim] (blue) and [DCA] (red)
(black).
53
Figure 3.11. The solvation responses of [bmim] (blue) and [PF6 ] (red)
(black).
54
Figure 3.12. The solvation responses of [emim] (blue) and [TfO] (red)
(black).
55
Figure 3.13. The residence-time correlation function (RTCF) for the anions
and cations in the first solvation shell of the C153 solute. The first solvation
shell was defined as any molecule whose center-of-mass lies within the first
solvation shell, defined as the first minimum of the cation-C153 g(r).
56
translational motions of the anions are relevant we computed the residence-time correlation function (RTCF) for the anions and cations in the first solvation shell of
the C153 solute, hn(0)n(t)i, where n(t) = 1 if the molecule of interest is in the first
solvation shell and n(t) = 0 if it is not (Figure 3.13). For the purposes of the RTCF
calculation the first solvation shell was defined as any molecule whose center-of-mass
lies within the first solvation shell, defined as the first minimum of the cation-C153
g(r) (top panel in Figure 3.8). The RTCF reports on the time scales for molecules,
either anions or cations, that enter or leave the first solvation shell of the solute. The
RTCF for the anions share the characteristic shape of the solvation response, which
is suggestive that these anionic translational motions are relevant for the response.
In contrast, the RTCF for the cations is significantly slower than the anions and
its shape is qualitatively different from the solvation response. The time scales for
the decay of the anion RTCF are similar, although clearly slower, than the solvation
response. However, the difference in the times scales is likely due to the somewhat
arbitrary definition of the solvation shell. The results in Figures (3.83.13) support
a solvation dynamics mechanism in ILs where the translational motion of the anions
into and out of the first solvation shell of the C153 probe molecule potentially play
an important role.
3.4 Charge Scaling

3.4.1 Self-Diffusion Coefficients
Force fields inherently contain a variety of approximations to model intra- and
inter-molecular interactions and rely on extensive parameterization and analytic expressions to describe the potential energy. Traditional non-polarizable force fields
utilize force constants, reference angles, Lennard-Jones parameters and static unit
charges to describe the molecular interactions. The charge scaling parameter, , can
57
Figure 3.14. Calculated self-diffusion coefficients for [emim] (blue) and

[BF4 ] (red) for varied unit charges. Experimental measurements (dashed)
self-diffusion coefficients for this IL in the range of 298-303 K are reported
to vary from 4.4 5.4 1011 m2 /s for [emim] and 3.6 4.2 1011 m2 /s
for [BF4 ].[4]
58
be thought of as an additional mutable parameter set on improving the accuracy of

the force field. MD Simulations employing ions with a static net charge of 1 drastically underestimate the dynamics of the system, thus requiring the simulations to
either be performed at elevated temperatures,[168] or reducing the overall charge on
the ions by introducing a scaling parameter. As discussed above, 100 ns simulations
of each IL were performed to determine the self-diffusion coefficients (Table 3.1) for
a given charge scaling parameter, .
Modifying for identical systems results in dramatic changes to the self-diffusion
constant. For example, six systems of pure [emim][BF4 ] were simulated for 100 ns
with ranging from 0.80-0.85 to calculate the self-diffusion coefficient (Figure 3.14).
Included in Figure 3.14 are experimental measurements (dashed) of the self-diffusion
coefficients for [emim][BF4 ] in the range of 298-303 K are reported to vary from
4.4 5.4 1011 m2 /s for [emim] and 3.6 4.2 1011 m2 /s for [BF4 ].[4] Particularly
interesting is the linear dependence of the diffusion on , predicting unit charges
scaled by 82.5% as being most appropriate for both the cation and anion to reproduce
the transport properties observed experimentally.
To examine whether is an inherent characteristic of the cation, the scaling parameter appropriate for [emim][BF4 ], 0.80, and for [bmim][BF4 ], 0.84, were applied
to [emim][TfO] to calculate the self-diffusion coefficient. Polarizable MD simulations,
which in the absence of any experimental evidence represent the most accurate determination for the self-diffusion coefficients, reports D+ = 1.1 1011 m2 /s and
D = 1.6 1011 m2 /s, indicating = 0.84 (D+ = 1.9 1011 m2 /s and D =
0.9 1011 m2 /s) as being more representative of the dynamics of the system than
when = 0.80. When = 0.80, excessive reduction of the charges results in D+ that
is almost triple the reported literature value 3.0 1011 m2 /s and 1.1 1011 m2 /s,
respectively.[81]
For [emim][BF4 ] the atomic partial charges were scaled by a factor of 0.80, which
59
increased the self-diffusion coefficients from 0.31011 m2 /s for [emim] and 0.21011
m2 /s for [BF4 ] with full unit charges to 8.1 1011 m2 /s for [emim] and 5.5 1011
m2 /s for [BF4 ]. It is conceivable that the alkyl chain of the cation will play a minor
role in the polar regions of increased charge density, and applying a uniform charge
scaling factor to the entire molecule is too drastic. In fact, if the atomic partial
charges on the imidazolium ring are scaled while the charge density on the alkyl chain
is unchanged the computed self-diffusion coefficients, 6.8 1011 m2 /s for [emim] and
4.9 1011 m2 /s for [BF4 ], compare more favorably with experiment (5.0 1011
m2 /s and 4.2 1011 m2 /s).[163]
3.4.2 Charge Scaling Effects on Solvation Dynamics

Response functions characterizing the solvation dynamics are a excellent measure
of the validity of a force field. The decay profile contains a wealth of information
regarding the temporal evolution of collective dynamics over a broad range (fs to ns).
The consequences of altering the electrostatic interactions of the molecules results in
pronounced changes in the timescales of solvation. Figure 3.15 highlights the striking
differences in the solvation response brought about by modifying the Coulombic interactions. As expected, from the dramatic reduction in the self-diffusion, simulations
using full unit charges ( = 1) for the IL molecules results in a solvation response
that overestimates the decay timescale. The response function in a simulation where
the partial charges for the IL molecules were scaled by 0.80 (as reported in Chapter
2) is in good qualitative agreement with experiment (filled black circles), though it
decays too quickly in the regime beyond 10 ps. Reducing the partial charges only on
the imidazolium ring (turquoise) improves the translational dynamics (see Section
3.4.1), though also decays too quickly beyond 10 ps. Examining the dependence of
the self-diffusion coefficient on suggested partial charges reduced by 0.825 (Figure
3.14) are necessary to reflect the dynamics observed experimentally. However the
60
Figure 3.15. The calculated (solid) solvation response functions for

[emim][BF4 ] where the charge scaling parameter was varied from 1.0
(orange), 0.825 applied to the entire [emim] cation(red) 0.80 applied to the
entire [emim] cation (black), or 0.80 applied to the imidazolium ring
(turquoise), along with experimental measurements (black filled circles)
over the range 50 fs to 1 ns.
61
solvation response utilizing the scaled charges of 0.825 only modestly improves the
long time dynamics, relative to experiment.
The unsophisticated approach of tuning the partial charges of the molecules as
a means to improve agreement with experimental measurements of the solvation
response is not ideal. To be thoroughly correct, a full reparameterization of the force
field is necessary to adequately describe the complicated combination of molecular
interactions observed in solvation dynamics.
3.5 Summary
The calculated solvation response of C153 in a series of imidazolium-based ILs,
[emim][BF4 ], [bmim][BF4 ], [bmim][DCA], [emim][TfO], and [bmim][PF6 ] identify a
general solvation mechanism. The particular molecular motion that appears to be
especially relevant to solvation dynamics in imidazolium-based ILs are the the translational motions of the anions into and out of the first solvation shell of C153, regardless
of the composition of the IL. It is conceivable postulate that as one deviates from the
structural motifs whereby the cations cannot preferentially solvate dyes with favorable
aromatic interactions, new solvation dynamics mechanisms will emerge. Investigating the impacts of charge scaling revealed the linear dependence of the self-diffusion
coefficient on the effective scaling parameter. Charge-scaled models are able to reproduce the complexities of the solvation response function, and are ideally suited to
reproduce collective properties where the use of polarizable models is impractical.
62
CHAPTER 4
REGARDING THE VALIDITY OF LINEAR RESPONSE THEORY IN
SOLVATION DYNAMICS SIMULATIONS OF IONIC LIQUIDS
4.1 Introduction
Observing the evolution of solvent reorganization in the vicinity of an excited
probe molecule provides unique insight into molecular interactions responsible for
accommodating a charge perturbation. In particular, discerning these molecular
mechanisms is important to understanding the role of solvents in charge-transfer
reactions whose kinetic rates are influenced by solvent reorganization.[38] Central
to the study of solvation dynamics is linear response, which makes the assumption
that the dynamics of a system responding to a nonequilibrium state are equivalent
to the response to thermal fluctuations identical in amplitude and frequency in an
equilibrium system.
Time dependent fluorescence Stokes-shift (TDSS) measurements investigating
these solvation dynamics rely on an ultrafast laser pulse with energy hv(0), that
electronically excites a fluorescent probe molecule such as Coumarin-153 (C153),
4-aminophthalamide (4-AP), or PRODAN. This excitation is essentially occurring
instantaneously following the Franck-Condon principle, where the molecular geometry of the probe molecule is unchanged, but the charge distribution is significantly
altered such that a large change in the dipole is achieved. The subsequent fluorescent
emission of the probe, v(t), is continuously shifted to longer wavelengths over time,
as the solvent molecules reorganize to establish new equilibrium positions relative
63
to the new charge distribution. TDSS experiments monitor this temporal evolution
with a time dependent solvent response function,
S(t) =
v(t) v()
v(0) v()
(4.1)
to the excited state charge distribution of the probe.[3941] Linear response theory
equates the nonequilibrium response function S(t) to the equilibrium time correlation
function (TCF), C0(1) (t), of the fluctuations in the solvent effect on the electronic
energy gap,[129, 169]
S(t)
= C0(1) (t) =
hE(0)E(t)i0(1)
h(E)2 i0(1)
(4.2)
where E(t) = E(t) hEi0(1) and h...i0(1) is an ensemble average with the
probe molecule modeled in the ground or excited electronic state, respectively. Here
E(t) = Ee (t) Eg (t) the difference in the interaction energy of the probe molecule
with its environment for the excited (Ee ) and ground (Eg ) electronic states. An
important criteria for the validity of linear response theory is that the time-dependent
distribution of E(t) be adequately described by a Gaussian distribution.[130, 170]
Deviations from linear response occur when the electronic transition of the probe
molecule undergoes significant change in magnitude, size, or when the excitation
alters the solvation structure in such a way that it is no longer similar to ground
state fluctuations, e.g. altering the hydrogen bonding capabilities.[41, 128]
In Chapters 2 and 3, we postulated the solvation mechanism in imidazoliumbased ILs is dominated by translational movements of anions into and out of the
first solvation shell surrounding the probe molecule.[171] Our calculations compare
favorably with experiment, though they rely on the validity of linear response in order
to appropriately characterize the system. A study using all-atom molecular dynamics
64
simulations which included polarization effects calculated C0 (t) and C1 (t) for three
ILs over the entire duration of the response, however no direct comparison to S(t)
was achieved due to the significant computational costs.[81] Simulations explicitly
comparing the nonequilibrium response S(t) and C(t) in ILs were performed by Shim
et al. using a diatomic and benzene-like probes and united-atom representations of
the IL molecules, where they found sufficient similarity between S(t) and C(t).[89]
While their findings have been used as justification for applying linear response theory
in solvation dynamics simulations of ILs, due to computational limitations at that
time, the simulations only calculated the solvation response out to 2 ps. Given
experimental evidence that the solvation response is known to persist for nanoseconds
in ILs[2, 3], examining the applicability of linear response theory over the entire
relaxation timescale is warranted.
4.2 Computational Methods

The simulation box was constructed and equilibrated using an identical protocol
as in our previous study of [emim][BF4 ], as discussed in Chapter 2. In brief, a total
of 256 [emim] cations, 256 [BF4 ] anions, and one C153 molecule comprised the three
systems. All of the molecules were modeled as fully flexible, except for covalent bonds
containing hydrogen which were fixed using the SHAKE algorithm.[135] For C153 and
the [emim] molecules force-field parameters were obtained from the generalized Amber force field (GAFF).[136] Parameters for [BF4 ] were adopted from Liu et al.[137]
Partial charges for the IL molecules and the ground state of C153 were calculated via
the Merz-Singh-Kollman[138] analysis of the electron density of the optimized geometry of the molecules obtained with density functional theory (DFT) with a B3LYP
functional and the aug-cc-pVDZ basis set. The partial charges for [emim] and [BF4 ]
were empirically scaled by a factor of 0.80, guided by DFT calculations,[142] to
achieve better agreement with experiments where dynamic properties are of interest.
65
In the MD simulations the long-ranged electrostatic interactions were computed with

the particle-mesh Ewald summation method with a 15
This same cutoff distance was utilized when computing interactions between LennardJones sites. The the longranged electrostatic interactions between C153 and the IL
molecules calculated for E(t), were computed with the damped shifted force (DSF)
method.[131] The DSF method is a useful alternative to the traditional Ewald summation techniques,[9496] and provides a straightforward description based explicitly
on a pairwise sum.
Simulations of C0 (t) were calculated using identical methods described earlier
(Chapter 2). Similar conditions were employed for the calculation of C1 (t), however
the cations and anions were equilibrated in the presence of an excited C153 molecule.
Note, the excited state partial charges for C153 were calculated and validated previously by Cinacchi et al.,[1] thus the excited state partial charges for C153 are obtained
by simply adding these changes to the computed ground state charges. Independent trajectories generated from the ground state equilibrium simulation were used
as starting configurations for the nonequilibrium calculations, whereby the partial
charges of C153 were abruptly switched to reflect the excited state charge distribution. Production-runs (comprising a total of 5.015 s for C0 (t), 2.0 s for C1 (t),
and 5.0 s for S(t)) were performed using the large-scale atomic/molecular massively
parallel simulator (LAMMPS).[134]

As seen in Figure 4.1, the ground and excited state equilibrium TCFs C0 (t) and
C1 (t), results are nearly identical and fully compatible with the nonequilibrium S(t)
response function. The inset contains the total solvation response including the
oscillations due to internal motions of the C153 probe molecule. These oscillations in
the solvation response have been observed in high temporal resolution measurements
66
in solution[145] and for a dye molecule (Hoechst 33258) bound to DNA.[146] To

facilitate comparison, these oscillations can be subtracted from the total response,
which is shown in the main panel of Figure 4.1. The calculated response functions
all include an ultrafast inertial relaxation followed by a complex non-exponential
decay, which is known to be viscosity dependent.[7, 65, 69, 80] The equilibrium C0 (t)
(green) better reproduces the short-time inertial component of S(t) (black) than C1 (t)
(red), a consequence of the similar solvent configurations explored in C0 (t) and S(t)
simulations at early time.
Certain systems exist where S(t) is equal to C(t), though this is due entirely
to coincidental timescales of certain motions, and not because the linear response
approximation is valid.[172, 173] Decomposition of the total solvation response into
contributions arising from the different constituents present in the liquid is necessary
to rule out any accidental timescale correlations. Taking advantage of the additive
P
nature of the solute interaction energy, E(t) = E (t), where E (t) is the
solute interaction energy with solvent component , i.e. the anions, cations, and
intramolecular electrostatic interactions within the probe itself. The decomposition
of S(t) is uncomplicated such that
S (t) =
E (t) hE ()i1
hE (0)i0 hE ()i1
(4.3)
where the overbar represents an average over nonequilibrium trajectories and the
superscript signifies the solvent component of interest. Calculating the component
contributions to C (t) in a way that is formally compatible with linear response
theory is given as,[124, 126, 132, 169]
hE (t)E(0)i
C (t) =
.
h(E)2 i
(4.4)
This formalism importantly retains the same amount of information without invoking
67
Figure 4.1. The normalized solvation response without the contribution of

the dye for the nonequilibrium S(t) (black) and equilibrium C1 (t) (red),
and C0 (t) (green) from 50 fs to 1 ns. The inset is the identical response
including intramolecular interactions of the dye molecule responsible for
the large oscillations below 10 ps.
68
any cross-correlations that are often incapable of providing a clear molecular mechanism for solvation dynamics. Unfortunately, a commonly reported decomposition
scheme utilizes binomial multiplication providing auto- and cross-correlation terms
that are inadequate at identifying distinct components responsible for solvation.
The two alternative decomposition schemes applied to C0 (t) are shown in Figure
4.2. The top panel contains the auto- and cross-correlation functions contrasted with
the proper decomposition for a complex perturbation in the bottom panel. The autocorrelation of the anion-anion component in top panel shows the dominance of the
anion-anion contribution (red) followed by the cation-cation (blue) auto-correlation
term. The dashed lines represent the cross-correlation terms (anion-cation, aniondye, and cation-dye), which are mostly negligible, with exception to the anion-cation
cross-correlation contribution. While this does contain interesting information about
the interactions between components, this unnecessarily complicates the interpretation of the solvation mechanism by indicating there is a degree of anti-correlation
between the constituents, without exposing the exact intricacies necessary to understand solvation. It is possible to remove the ambiguity by employing Eq. 4.4 to
determine the contribution from each component relative to the total response, as
seen in the bottom panel of Figure 4.2. It is then straightforward to understand
the importance of the anions in solvating C153 without any obscure cross-correlation
terms. Using the latter decomposition scheme, Figure 4.3 presents the component
solvation response for anion (top) and cation (bottom) contributions for nonequilibrium S(t) (black) and equilibrium C1 (t) (red), and C0 (t) (green). The decompositions
for C0(1) (t) that are consistent with S (t), fitting with linear response theory.
The solvation response functions for the anions and cations can be further decomposed into contributions resulting from their respective translational and rovi
brational motions. The translational contribution, Etrans
, to E for the cations
and anions are computed by regarding each relevant IL molecule as a single point
69
Figure 4.2. A comparison of two decomposition strategies as applied to

C0 (t) showing auto- and cross-correlation decomposition (top), to the
alternative method defined in Eq. 4.4 that calculates the contribution of
the relevant component relative to the total response.
70
Figure 4.3. The normalized solvation response decomposed into anion (top)
and cation (bottom) contributions for nonequilibrium S(t) (black) and
equilibrium C1 (t) (red), and C0 (t) (green) from 50 fs to 1 ns.
71
Figure 4.4. The normalized solvation responses of S(t) (black), C1 (t) (red),
and C0 (t) (green) decomposed into contributions due to translational
(solid) and rovibrational (dashed) motions.
72
charge located at its respective center of charge. The rovibrational contribution,
Erovib
, to E is then obtained as the difference, Erovib
= E Etrans
. With
these definitions, the correlation functions for the cations and anions decompose into
translational and rovibrational contributions,
C (t) = Ctrans
(t) + Crovib
(t)
(4.5)
where the functions Ctrans

(t) and Crovib
(t) are computed with Eq. 4.4 using Etrans
(t)
and Erovib
(t) in place of E (t).
The translational and rovibrational contributions originating from the anions

(top) and the cations (bottom) are displayed in Figure 4.4, where the translational
component (solid) and rovibrational component (dashed) lines are presented for S(t)
(black), C1 (t) (red), and C0 (t) (green). In agreement with our previous study, translations of the anion are the dominant contributor to the solvation response with a
negligible rovibrational contribution.[171] Because the anion possesses a lack of symmetry and therefore no permanent dipole, the contributions arising from rovibrational
motions are expected to be trivial. The translational motion of cations also contribute
to the total solvation response, albeit to a lesser degree than the translational movements of the anions, however these contributions are largely negated by rotational
motion of the cations. In this sense the anti-correlation effect can be understood as
the rotations of cation molecules as being counterproductive in stabilizing the excited
state charge distribution of the C153 solute.
Using the appropriate decomposition strategy that unambiguously identifies the
respective motion of the constituents in the IL responsible for accommodating the
charge perturbation, we are able to confidently identify the solvation mechanism in
[emim][BF4 ]. Given the level of agreement between the component decomposition and
translational/rovibrational analysis of S(t), C1 (t), and C0 (t), we do not anticipate
any breakdown in linear response theory and thus validates the use of linear response
73
theory in simulating solvation dynamics of ILs.
74
CHAPTER 5
A MOLECULAR DYNAMICS INVESTIGATION OF THE VIBRATIONAL
SPECTROSCOPY OF ISOLATED WATER IN AN IONIC LIQUID
5.1 Introduction
Our understanding of water-ion interactions is derived primarily from studies of
dilute aqueous salt solutions in which the ions are fully hydrated and water-water
interactions are perturbed but still prevalent. Studying water at dilute concentrations
in an ionic liquid (IL) reverses this scenario; the water is isolated in a sea of ions and
the water-water interactions are negated. The water/IL system provides a unique
opportunity to investigate the dynamics of water in a highly electrolytic environment.
Moreover, the isolated water molecule can serve as a reporter of the structure and
dynamics of the IL.
Despite their promise as environmentally friendly solvents and in clean and renewable energy applications,[7, 1017] widespread industrial adoption of many ILs
is plagued by their large viscosities.[174] While impurities such as water are known
to alter the physical properties and chemical reaction rates in hygroscopic ILs,[20,
175, 176] the addition of this cosolvent is gaining in popularity as a means to reduce
viscosity.[177] Thus, understanding the behavior of water in ILs and how water alters
the properties of ILs has important practical implications.
Many ILs are hygroscopic and complete removal of water is nearly impossible.[178
180] A variety of experimental[5458] and computational[5964] studies have aimed to
understand the influence of water on the properties of ILs. These studies suggest that
75
some ILs have nanoscale structuring with polar and nonpolar regions.[60, 61, 181
186] As the water concentration in these ILs increase, the polar domains collapse with
the formation of larger water clusters stabilized by a hydrogen-bond network.[60, 187]
Previous work examining isolated water in ILs determined a water molecule is bridged
by two anions in an IL, existing in an A HOH A complex. As a result of
this proximity, the anions were assumed to be most responsible for influencing the
OH stretch frequency.[112114] Investigations varying the lengths of the cation alkyl
chains in imidazolium-based ILs suggest the chains do not have an influence on the
OH stretching frequency.[112, 115]
X-ray spectroscopy, NMR, and vibrational spectroscopy have been used to understand structure in bulk ILs. [25, 101, 102, 104] Ultrafast two-dimensional infrared
(2D IR) spectroscopy measurements of ILs have the potential to elucidate important dynamical motifs that differ from conventional solvents. 2D IR spectroscopy
has already proven itself as a powerful technique for investigating the structure and
dynamics of liquids by monitoring the response of a vibration to the evolution of its
local environment, a process called spectral diffusion. The frequencies of vibrational
reporters are exquisitely sensitive to changes in their local environment, particularly
to changes in electrostatics, hydrogen bonding, and chemical processes. For example, the OH and OD stretch frequencies of HOD are known to depend on hydrogen
bonding: an increase in hydrogen-bond strength red-shifts the OH and OD stretch
vibrational frequencies. The inhomogeneous IR absorption line shape of liquid water
reflects the range of different hydrogen bonding environments present. [105107] The
spectral diffusion time scales revealed by 2D IR have been shown to directly relate
to hydrogen bond rearrangement processes in liquid water.[108111]
Recently, the dynamics of HOD isolated in an IL was investigated with vibrational
spectroscopy.[116] The linear IR absorption spectrum of the OD stretch frequency
of dilute HOD in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6 ],
76
revealed a blue-shifted and a significantly narrowed vibrational line shape compared

to the spectrum of HOD in water. The blue-shift suggests weaker OD interactions
with the ionic environment and is characteristic of a relatively isolated OD stretch,
for example the free OD stretches at a liquid D2 O/vacuum interface.[117119] The 2D
IR measurements monitored spectral diffusion of the OD stretch of HOD in the IL.
An important quantity accessible by both simulation and experiment is the frequency
fluctuation time correlation function (FFCF), C(t) = h(t)(0)i, where (t) is
the deviation of the frequency from its equilibrium value, (t) = (t) hi. As a
water molecule samples different molecular environments, the FFCF decays to zero.
This can be approximately related to the spectral diffusion measurements quantified
experimentally using the center line slope (CLS) method.[120, 121] Measurements of
the amplitudes and timescales of the FFCF thus give information about the dynamics
of the environment surrounding the HOD molecule. Two times scales were found: 6.9
2.1 ps and 72 20 ps. The faster of the two relaxation timescales was attributed to
changes in the local structure of the anions bridged by the water and the subsequent
motions of the cations. The slower relaxation time was assigned to orientational
relaxation, though a discrepancy of approximately one order of magnitude exists
between the 72 ps timescale and the 2.3 ns response in optical heterodyne detected
optical Kerr effect experiments in [bmim][PF6 ].[122]
The objective of this chapter is to utilize molecular simulation to understand
the factors responsible for the spectral diffusion timescales for HOD isolated in the
[bmim][PF6 ] IL. In Section 5.2 the theoretical methodology necessary to compute
the linear IR absorption spectrum of HOD in [bmim][PF6 ], as well as the FFCF, is
discussed. In addition, approaches to decompose the FFCF into contributions from
specific motions of the anions and cations are presented. In Section 5.3 results for the
IR absorption spectrum, the FFCF, and its decompositions are shown and discussed.
Finally, some concluding remarks can be found in Section 5.4.
77
5.2 Theoretical Methodology

5.2.1 Spectroscopic Maps
In order to calculate the IR absorption spectrum and the spectral diffusion dynamics of the OD stretch of isolated HOD in [bmim][PF6 ] within an MD simulation,
one must have a model for relating the OD vibrational frequency and its transition
dipole moment to the instantaneous solvent environment of the HOD molecule. We
will adopt an approach that has shown considerable success in describing the vibrational spectroscopy of HOD in water[188191] and in electrolyte solutions,[192]
whereby the relevant spectroscopic quantities (i.e. the OD vibrational frequency and
transition dipole moment) are empirically related to the electric field of the environment projected along the OD bond of interest. The motions of the environment cause
the projected electric field, and thus the OD vibrational frequency, to fluctuate. From
the vibrational frequency and transition dipole moment dynamics the IR spectrum
and FFCF can be calculated.
The projection of the electric field along the OD bond axis, EOD , due to a collection of N solvent point-charges, {qi }, is given in atomic units by
EOD = rOD
N
X
qi riD
i=1
2
riD
(5.1)
where rOD is the unit vector along the OD bond, riD is the distance between charge i
and the D atom, and riD is a unit vector between site i and the D atom. For calculations of EOD the long-range electrostatic interactions were corrected with the damped
shifted force (DSF) method.[131] One motivation for utilizing the DSF method rather
than traditional Ewald summation techniques[9496] is that DSF treats the interactions as a pairwise sum, thus lending itself to straightforward decomposition in terms
of the contributions of the anions and cations in the IL.
The empirical relationship that relates the OD vibrational stretch frequency,
78
OD , to EOD was developed by Lin, Auer, and Skinner in HOD for aqueous NaBr
solutions[192]
OD = 2762.6 cm

cm1
cm1
2
3640.8
Eef f 56641
Eef
f.
au
au2
(5.2)
Here an effective electric field, Eef f , was introduced to account for the blue-shifts in
the OD stretch frequency observed experimentally with increasing salt concentrations,
Eef f = EH2 O + aEcat + bEan ,
(5.3)
where a and b are empirical parameters, 0.81379 and 0.92017, respectively. EH2 O ,
Ecat , and Ean are contributions to EOD from water, cations, and anions, respectively. This spectroscopic map was designed to be applicable for all aqueous salt
concentrations, and when no ions are present the map is conveniently appropriate for
HOD in H2 O. The unequal weighting of the contributions for the cations and anions
reproduces the smaller OD frequency shifts observed in electrolyte solutions.
Because non-Condon effects are known to be important in the vibrational spectroscopy of water,[191] calculations of the IR absorption spectrum of HOD also requires a spectroscopic map for the magnitude of transition dipole moment, 0 , for the
OD stretch relative to its value in the gas phase, 0g ,
0
= 0.71116 + 75.591 Eef f
0g
(5.4)
It is important to emphasize that the spectroscopic maps given by Eqs. (5.3) and
(5.4) were developed in the context of aqueous alkali halide salt solutions, and not
specifically for water in ILs. Comparisons of the results for the IR absorption spectrum and the FFCF for isolated HOD in [bmim][PF6 ] directly with experiment will
79
both provide validation and reveal the extent to which the spectroscopic maps are
transferable.
5.2.2 Infrared Absorption Spectrum

The IR absorption spectra were computed from knowledge of the frequency and
transition dipole moment trajectories using the semiclassical fluctuating frequency
approximation (FFA),[97]
Z
I() =
D
E
Rt
dteit
~ (t)
~ (0)ei 0 d ( ) et/2T1 ,
(5.5)
where h i represents a classical ensemble average, (t) = (t) hi is the fluctuation of the frequency from its average value, hi, and
~ (t) is the transition dipole
moment vector,
~ (t) = 0 x10 rOD ,
(5.6)
assumed to be in the direction of the OD bond, rOD . In Eq. (5.6), x10 = h1 |

x| 0i
is the matrix element of the position operator computed assuming Morse oscillator
ground, |0i, and first excited-state, |1i, vibrational wavefunctions. For convenience,
x10 can also be related, empirically, to the OD stretch frequency,
x10
= 0.0880 A 1.105 105
A
cm1

OD .
(5.7)
The FFA expression, Eq. (5.5), approximately captures the effects of inhomogeneous broadening, motional narrowing, rotational broadening, and non-Condon transition dipole moments on the vibrational line shape. The effects of lifetime broaden
ing are captured empirically via the exp(t 2T1 ) factor, where T1 is the vibrational
population lifetime, 1.8 ps for the OD stretch of HOD in water.[193] T1 has not
been determined for HOD in [bmim][PF6 ]. For the calculation of the IR absorption
80
spectrum of HOD in [bmim][PF6 ] the value 1.8 ps was assumed to be qualitatively

representative of the population lifetime.
5.2.3 Spectral Diffusion and Decomposition of the FFCF

Spectral diffusion of the OD stretch vibrational frequency of HOD is a sensitive
reporter of the dynamics of its local solvation environment. These dynamics are often
quantified in terms of the normalized FFCF,
C (t) =
h(t)(0)i
.
C (0)
(5.8)
C (t) is accessible experimentally and can be computed from frequency trajectories

obtained during MD simulations using, for example, the spectroscopic maps described
in Subsection 5.2.1. The FFCF has been measured for HOD in water[191] and in
the [bmim][PF6 ] IL.[116] For HOD in water, the long-time (1.5 ps) decay of the
FFCF have been attributed to hydrogen bond rearrangements. FFCFs computed
using the spectroscopic maps developed by Skinner and coworkers generally have the
same long-time decay rate as the hydrogen-bond time correlation function for a given
empirical water model.[111] The quantitative agreement of the long-time FFCF decay
with experiment, however, varies by water model. Water models without electronic
polarizability generally have FFCFs and hydrogen-bond time correlation functions
that decay too quickly.[188]
For a multicomponent solution, like the [bmim][PF6 ] IL, it would be physically
insightful to decompose the FFCF into contributions from the respective components
(i.e. from the anions and the cations). A straightforward decomposition is somewhat
hindered by the quadratic form of the empirical frequency map, Eq. (5.2), where the
total frequency shift, , is not a simple sum of contributions from anions, an ,
and cations, cat : 6= an + cat . However, the effective electric field, Eef f ,
81
from which the frequencies are computed is naturally a sum of contributions from the
anions and cations, Eq. (5.3). Note that, for isolated water in an IL, the contribution
to the effective electric field from other water molecules can be ignored. Fortuitously,
the normalized time correlation function of the electric field fluctuations,
CE (t) =
hE(t)E(0)i
,
CE (0)
(5.9)
where E(t) = Eef f hEef f i is the fluctuation of the effective electric field from its
average value, is an excellent surrogate for C (t) . For a linear relationship between
the electric field and the vibrational frequency, the two normalized correlation functions are identical. For a quadratic relationship between the field and the frequency,
the functions can differ. However, for HOD in [bmim][PF6 ] the normalized correlation functions are almost quantitatively identical (vide infra). Thus, we will proceed
to decompose CE (t) and assume that the qualitative insights are relevant for C (t) .
Since E(t) can be expressed as a linear sum, Eq. (5.3), CE (t) can be decomposed
into contributions from anions and cations using the same approach that has proven
successful in unraveling the factors that influence solvation response functions in
ILs,[90, 171] proteins,[132] and DNA,[123126, 194]
CE (t) =
X C (t) X hE (t)E(0)i
E
=
,
CE (0)
CE (0)
(5.10)
where represents the solvent component of interest. This method of decomposing, CE (t), and C (t) by proxy, is rigorously consistent with the linear response
approximation, and has not previously been applied in the context of understanding
vibrational spectral diffusion in multicomponent liquids.
Each of the solvent component correlation functions, CE (t), in Eq. (5.10) can also
be further separated into contributions that arise from their respective translational
and rotational motions. The translational contribution to E , E ,trans , is calculated
82
by regarding each relevant IL molecule as a single point charge located at its center
of charge. The rovibrational contribution to E is then just the difference E ,rovib =
E E ,trans . These definitions allow the solvent component correlation functions
for the cations and anions to be decomposed into their respective translational and
rovibrational contributions,
CE (t) = CE,trans (t) + CE,rovib (t) ,
(5.11)
where the functions CE,trans (t) and CE,rovib (t) are computed with Eq. (5.10), but
with E ,trans (t) and E ,rovib (t) in place of E (t).

For our control calculations on dilute HOD in water, a cubic simulation box of 512
H2 O molecules was constructed with periodic boundary conditions. The vibrational
spectroscopy of neat water is complicated by intra- and inter-molecular coupling, of
the OH stretches. Considering dilute HOD in H2 O is preferable because the OD
stretch is spectrally isolated from all other vibrational modes and limits intra- and
inter-molecular vibrational coupling. For our calculations of the vibrational spectroscopy of dilute HOD in H2 O, we can regard each bond as the OD vibration of
interest. Here we are taking advantage of the fact that a single HOD molecule
in H2 O is indistinguishable from a neat H2 O simulation.[188] The atomic-centered
partial charges and other force-field parameters for the H2 O molecule are from the
SPC/E model.[195]
The cubic simulation box of ILs was constructed with 256 [bmim] cations, 256
[PF6 ] anions, and one D2 O molecule with periodic boundary conditions. A D2 O
molecule was used because its dynamics are not particularly different from HOD, and
both OD bonds could be considered the vibration of interest, thus providing a twofold
83
increase of our statistics. The MD simulations were performed using the Largescale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program.[134] All
molecules were modeled as fully flexible, except for covalent bonds containing hydrogen or deuterium which were fixed at equilibrium lengths using the SHAKE
algorithm.[135, 196] For the [bmim] molecules force-field parameters for the bonds,
bends, dihedrals, and atomic-centered Lennard-Jones sites were adopted from the
generalized Amber force field (GAFF).[136] Minor dihedral angle modifications were
made to better match density functional theory calculations carried out with a B3LYP
functional and the aug-cc-pVDZ basis set. Parameters for [PF6 ] are not available in
the GAFF and were obtained from Liu et al.[137] Atomic-centered partial charges
for the IL molecules were calculated via the Merz-Singh-Kollman[138] analysis of the
electron density of the optimized geometry of the molecules obtained with DFT with
a B3LYP functional and the aug-cc-pVDZ basis set. In an attempt to more accurately
model the dynamics of the system, the partial charges were empirically scaled by a
factor of 0.84, as suggested by DFT calculations for a similar IL, [bmim][BF4 ].[142]
Treating the charge scaling factor as a tunable force field parameter to approximately
describe the effects of electronic polarizability is commonly used as a means to more
accurately capture diffusion in ILs.[143] The long-ranged electrostatic interactions
in the simulations were computed with the particle-mesh Ewald summation method
with a 15
Out of concern for the long relaxation dynamics, we rely on a rigorous equilibration procedure identical to our previous work simulating ILs. In brief, the molecules
are allowed to relax during a minimization procedure after which the temperature
is slowly raised from 0 K to 300 K and maintained at 300 K for 4 ns in the NPT
ensemble controlled by a Nose-Hoover thermostat and barostat.[140] The size of the
simulation box was isotropically scaled to reflect the average density and was then
simulated in the NVT ensemble for 1 ns at 300 K, the temperature was slowly raised
84
to 600 K over 1 ns to destroy any pseudo-stable ionic cages that may have formed.
Next, the temperature was reduced back to 300 K in 1 ns, followed by an NVT simulation for 1 ns at constant temperature of 300 K. The final velocities were scaled to
300 K and a pre-production NVE simulation was performed for 11 ns. A total of 50
ns of continuous dynamics for the D2 O:IL system and 5 ns for the neat H2 O systems
were collected in the NVE ensemble with a 2 fs integration time step and a collection
resolution of 4 fs.
As a preliminary validation of the simulations and force-fields, we calculated the
orientational time correlation function for an OD bond in neat H2 O and in the
[bmim][PF6 ] IL, given as hP2 (
rOD (0) rOD (t))i, where P2 (x) is the second-order Legendre polynomial (Figure 5.1). The oscillations below 1 ps are indicative of water
librational motion and will be discussed in more detail in Subsection 5.3.1. The reorientational dynamics are clearly much faster in H2 O than in the IL. Experimental
measurements of the OD anisotropy decay in [bmim][PF6 ] were collected out to 40
ps, and a biexponential fit revealed two time constants: 2.4 and 24.7 ps.[116] The calculated rotational correlation function was fit to a tri-exponential function for t 1
ps (Figure 5.1). The three time constants were 3.5 ps, 19.4 ps, and 85.6 ps. The
first two time constants agree fairly well with experiment and serve as a validation
of the simulations. The longer time decay (85.6 ps) would not be resolvable in the
experiment because of the population lifetime of the OD vibrational reporter.

5.3.1 IR Absorption
The calculated IR absorption spectra for the OD stretch of dilute HOD in H2 O

and in [bmim][PF6 ] are shown in Figure 5.2. It is immediately apparent that the
line width is narrowed dramatically in the IL by 128 cm1 and is blue-shifted by
85
Rotational Correlation
IL
H2O
0.1
0.01
0.1
t (ps)
10
100
Figure 5.1. The orientational time-correlation function for an OD bond in

H2 O (black) and in the [bmim][PF6 ] IL (turquoise).
86
Figure 5.2. Vibrational line shapes for the OD stretch of dilute HOD in
H2 O and in the [bmim][PF6 ] IL. The spectra were arbitrarily scaled to have
the same maximum intensity.
87
TABLE 5.1
IR ABSORPTION DATA
HOD in H2 O
HOD in [bmim][PF6 ]
max (cm1 )
FWHM (cm1 )
Theory
2548
148
Expa
2510
170
Theory
2712
20
Expa
2678
21
Ref. [116]. Summary of the theoretical and experimental IR absorption line shapes for
the OD stretch of HOD in H2 O and in [bmim][PF6 ]. max is the frequency of maximum
absorption and FWHM is the full-width at half the maximum absorption.
164 cm1 (Table 5.1). Experimentally, the spectrum shifts by 168 cm1 and narrows
by 149 cm1 . The agreement between theory and experiment for the differences
in the line shapes between the aqueous and IL environments are excellent, which
validates both the simulations and the spectroscopic maps. Consistent with previous
studies[112, 113, 115] the peak of the OD stretch spectrum of HOD in water is to the
blue of experiment and the spectrum is slightly too narrow. In the IL the peak in the
spectrum is again to the blue of experiment, but its width is almost exactly correct.
As discussed previously, there is some ambiguity about the vibrational lifetime of
HOD in the IL, and the spectrum in Figure 5.2 assumes T1 = 1.8 ps, the same value
as HOD in H2 O. However, the lifetime is likely longer because the HOD molecule is
not hydrogen bonding and the 2D IR spectrum were collected out to 40 ps implying a
T1 longer than 1.8 ps. Therefore, the 20 cm1 width of the spectrum can be regarded
as an upper-bound. Taking T1 = provides a lower bound of 16 cm1 . The
significant narrowing of the spectrum in the IL solvent relative to aqueous solution
88
is a reflection of the absence of hydrogen bonding sites on the IL molecules and a

reduction in the diversity of solvent environments to inhomogeneously broaden the
line shape.
Examining the distribution of electric fields present in water and in the IL is physically insightful for understanding the contributions to the IR absorption spectrum
of HOD in these two liquids. Figure 5.3 shows distribution functions, F (E), for the
projection of the electric field along the OD bond of HOD in H2 O and in [bmim][PF6 ].
In the IL the electric field of interest is Eef f , as defined in Eq. (5.3). The electric
field distribution for HOD in water exhibits a characteristic shoulder on the low-field
side of F (E). These small values of the field correspond to frequencies on the blue
side of the IR absorption spectrum, which have been attributed in previous studies
to HOD molecules whose OD bond is not engaged as a hydrogen-bond donor. The
electric field distribution for HOD in the IL is significantly narrowed and is centered
almost exactly at the same location of the shoulder in the water distribution. The
difference in widths between the two distributions is consistent with the calculated
and experimentally observed narrowing in the IR absorption spectrum, and suggests
that the origin of the change in width is mostly inhomogeneous in nature. Figure 5.3
also shows distribution functions for the effective electric fields from the cations and
anions. Note that the distribution for the total effective field should not be a sum of
the contributions from the cations and anions. Interestingly, the distribution of fields
from the anions mimics the total, whereas the distribution function for the cations is
narrow and centered almost at zero. These results confirm that the anions interacts
more strongly with the HOD molecule and are the dominant contributor to the IR
absorption spectrum.
89
F(E)
IL
Cation
Anion
H2O
-0.02
0.02
0.04
E (au)
0.06
0.08
Figure 5.3. Distribution functions, F (E), for the projection of the electric
field projected along the OD of HOD in H2 O (black) and in the
[bmim][PF6 ] IL (turquoise). The distribution of electric fields in the IL
resulting from cations (blue) and anions (red) are also shown. The
distribution functions have all been scaled to have the same value at their
maximum.
90
Figure 5.4. Normalized CE (t) for HOD in H2 O and HOD in the

[bmim][PF6 ] IL. Also shown is a comparison between C (t) (red) and CE (t)
for HOD in the IL.
91
5.3.2 Spectral Diffusion

Figure 5.4 shows the normalized electric field correlation function, CE (t), for
the OD stretch of dilute HOD in H2 O and isolated HOD in [bmim][PF6 ]. Also
shown in Figure 5.3 is the FFCF, C (t), which is nearly identical to CE (t) at all
times, particularly for t > 1 ps. While the FFCF is directly related to spectral
diffusion measurements, CE (t) serves as an exemplary surrogate and the two functions
will be regarded as interchangeable for the remainder of the paper. As discussed
in Subsection 5.2.2, CE (t) is amenable to decomposition strategies that can offer
additional physical insight regarding the physical motions responsible for spectral
diffusion.
Immediately apparent in Figure 5.3 is a dramatic difference in the long-time decay
of the FFCF for HOD in the aqueous environment, where the decay is complete in under 5 ps, versus in the IL solvent, where the function persists beyond 100 ps. For HOD
in water, CE (t) was fit to a tri-exponential function, which revealed three timescales:
37 fs, 297 fs, and 0.86 ps. In previous studies the faster timescales were attributed
to hydrogen bond fluctuations, while the slowest time was related to hydrogen-bond
rearrangement processes.[197, 198] Given that the viscosity of the [bmim][PF6 ] IL
is 450 times larger than the viscosity of water,[199] it is not surprising that more
large-scale rearrangement of solvent structures takes considerably longer in the IL
than in aqueous solution, though the specific motions cannot be assigned until we
consider physical decompositions of CE (t) below.
A similar tri-exponential fit of CE (t) for HOD in the IL revealed time constants
of 54 fs, 1.6 ps, and 38 ps. Experimentally, two timescales were identified for spectral
diffusion: 6.9 2.1 ps and 72 20 ps.[116] Spectral diffusion occurring on a 50
fs timescale, as predicted in our calculations, would be difficult to resolve experimentally, so we cannot make a direct comparison. The other two calculated time
constants are too fast compared to experiment by about a factor of 4 for the 1.6 ps
92
time and a factor of two for the longest, 38 ps timescale. For HOD in water it has
been established that spectral diffusion occurs too quickly in non-polarizable water
models, by about a factor of approximately 1.52.[200] It is therefore likely that quantitatively reproducing the spectral diffusion timescales for HOD isolated in ILs would
also require electronically polarizable force fields. Nonetheless, the qualitative agreement between experiment and theory is reasonable enough to proceed to decompose
CE (t) for HOD in the IL to achieve additional physical insight. Already, the simple
absence of nanosecond timescales in both simulation and experiment demonstrate
that the OD vibrational reporter is insensitive to longer-time rearrangements that
have been observed in both theoretical and experimental investigations of solvation
dynamics in [bmim][PF6 ].[2, 79, 88, 90, 201, 202]
Before progressing to decompositions of CE (t) for HOD in the IL, it is important
to discuss the sub-picosecond damped oscillation that is evident in the electric field
correlation function for both HOD in water and HOD in the IL. Such oscillations
have been experimentally verified for spectral diffusion of HOD in liquid water and
assigned to a oscillatory stretching motion of the hydrogen bond between the OD
vibrational reporter and a neighboring water molecule.[203] The peak in the oscillation occurs at 120 fs for HOD in water, but at 280 fs for HOD in [bmim][PF6 ].
Also, the oscillation is considerably more pronounced in the IL. The decompositions
discussed below will reveal that the oscillation is related to translational motion of
the water relative to the anions. Thus, the physical interpretation is similar in the IL,
only now it is an oscillatory stretch within a [PF6 ] HOD [PF6 ] complex. Experimentally, significant oscillations were observed for the spectral diffusion of D2 O
in the [bmim][PF6 ] IL having a period of 0.3 ps. However, these oscillations were
assigned as quantum mechanical coherence oscillations due to anharmonic coupling
between the symmetric and asymmetric stretches of D2 O (i.e. the same oscillations
were observed in the center-line-slope of the diagonal and cross peaks of the symmet-
93
ric and asymmetric stretches of D2 O in the 2D IR spectra). Here, the OH and OD

vibrational frequencies of HOD are too far out of resonance to support oscillations
due to coherent energy transfer. Moreover, such an effect would also not be captured
using the theoretical approach utilized in this paper.
Figure 5.5 shows results for decomposing CE (t) for the OD stretch of HOD in
the IL in terms of contributions from the [PF6 ] anions and the [bmim] cations. It
is immediately apparent that the anions are the dominant contributor to spectral
diffusion over all timescales; the cations never contribute more than 10% to CE (t).
The long time decay of both the anion and cation correlation functions are similar to
the 38 ps decay of the total correlation function (36 ps for the anions and 43 ps for
the cations). This suggest that the long-time decay is a collective process involving
reorganization of both the anions and cations. The pronounced 280 fs oscillation in
CE (t) is clearly visible only in the anion component, however both the anion and
cation correlation functions have smaller amplitude vibrations superimposed upon
the decay at short times. Additional physical insight can be obtained by further
decomposing the anion and cation contributions to the spectral diffusion process into
contributions from translational and rovibrational motions of these molecules relative
to the OD bond of interest (Figure 5.6). From this analysis it is clear that the longtime spectral diffusion dynamics are dominated by translational motions of the anion
relative to the OD bond. Translational and rotational motions are nearly equal
contributors to the cation portion of the correlation function. The pronounced 280
fs oscillation in CE (t) is only present in the anion translational correlation function.
Thus, we can now assign this feature to a vibrational motion between the HOD
molecule and a neighboring [PF6 ] anion. A much smaller amplitude and higher
frequency oscillation is also present in the total correlation function, which can now
clearly be assigned to rovibrational motions of the anions.
94
1
IL
Cation
Anion
0.8
C(t)
0.6
0.4
0.2
0
0.01
0.1
1
t (ps)
10
100
Figure 5.5. Decomposition of normalized CE (t) for the OD stretch of HOD

isolated in the [bmim][PF6 ] IL in terms of the contributions from the
cations (blue) and anions (red).
95
1
IL
Cation-Trans
Cation-Rovib
Anion-Trans
Anion-Rovib
0.8
C(t)
0.6
0.4
0.2
0
-0.2
0.01
0.1
1
t (ps)
10
100
Figure 5.6. Decomposition of normalized CE (t) for the OD stretch of HOD

isolated in the [bmim][PF6 ] IL in terms of the contributions from the
translational (solid) and rovibrational (dashed) components from cations
(blue) and anions (red).
96
5.4 Concluding Remarks

A combined MD simulation and spectroscopic map approach has been utilized to
investigate the vibrational spectroscopy and spectral diffusion dynamics of the OD
stretch of HOD isolated in the [bmim][PF6 ] IL. Excellent agreement between experiment and theory was achieved for the dramatic shift and change in width of the
IR absorption spectrum for the OD stretch of HOD in the IL relative to in aqueous
solution. This result served to validate the spectroscopic maps that were originally
developed for aqueous electrolyte solutions. The spectral diffusion dynamics were
calculated and the agreement with experiment was more modest. The theoretical
timescales were too fast compared to experiment, which is perhaps expected for the
non-polarizable force fields used in the MD simulations. Decompositions of the total
spectral diffusion dynamics in terms of contributions from anions and cations revealed
that the anions dominate the response at all times. Further decompositions revealed
that translational motions of the anions relative to the OD bond of interest was, by
far, the most important component of the spectral diffusion dynamics. The decompositions also allowed us to assign a pronounced oscillation in the calculated FTCF
to a OD [PF6 ] vibrational motion. Overall, the results of this paper demonstrate
the utility of the MD/spectroscopic map approach for determining unambiguously
the signature of specific physical motions in complex heterogeneous solvents in linear
and 2D IR experiments.
97
CHAPTER 6
MONITORING INTRAMOLECULAR PROTON TRANSFER WITH
TWO-DIMENSIONAL INFRARED SPECTROSCOPY
6.1 Introduction
Proton transfer (PT) plays a critical role in many chemical, photochemical, catalytic, and biomolecular processes.[204, 205] It remains an important challenge to
elucidate the factors that affect the kinetic rates and mechanisms of PT in realistic
contexts. Novel spectroscopic approaches for monitoring PT processes in real time
are therefore essential. Because of its sub-picosecond time resolution and superb
sensitivity of infrared reporters to their local environments, chemical exchange twodimensional infrared (2D IR) spectroscopy[206, 207] has the ability to offer tremendous insight regarding the dynamics of thermally activated PT. Chemical exchange
2D IR spectroscopy requires a suitable IR active mode whose vibrational frequency is
sensitive, i.e. strongly coupled, to the PT reaction coordinate. A potential strategy
is to monitor directly the bonds in which the transferring proton participates. While
such an approach is necessarily completely non-perturbative, a likely drawback is the
complexity of the resulting spectra because of tunneling and nonadiabatic effects.[208]
An alternative approach is to introduce a spectroscopic reporter whose vibrational
frequency is sensitive to the PT process, but whose presence is minimally perturbative
to the motion (e.g. mechanism and kinetics) of the transferring proton of interest.
Selective deuteration of carbon atoms in the vicinity of the PT event can potentially
offer a means to monitor the reaction with minimal perturbation. Site-specific C-D
98
Figure 6.1. Proton transfer reaction coordinate in malonaldehyde.
bonds generally absorb between 2100-2300 cm1 , a region of the IR spectrum that
is mostly absent of other vibrational transitions in biomolecular contexts, and are
known to be excellent reporters of their chemical environment.[209, 210] Moreover,
since carbon is rarely the donor or acceptor in most PT processes of interest, C-D
vibrations will be adiabatically decoupled from the PT reaction.
The use of CD to monitor the kinetics of PT processes using chemical exchange
2D IR spectroscopy was demonstrated and analyzed computationally for the model
compound malonaldehyde (3-hydroxy-2-propenal, Figure 6.1). Malonaldehyde contains an intramolecular hydrogen bond across which a proton can transfer between
symmetric donor and acceptor oxygen atoms (OA H OB ), a process that has been
studied extensively by both theory[211214] and experiment.[215218] In this study,
one of the carbonyl/enol carbon atoms, a direct neighbor to the proton transfer event,
is deuterated. This particular CD vibrational reporter is likely to be exquisitely
sensitive to the PT event because of (1) its spatial proximity, (2) the known sensitivity of CD vibrational frequencies to the movement of charge via the vibrational
Stark effect,[219] and, most importantly, (3) the coupling of the CD bond to the
dramatic change in the electronic structure of the malonaldehyde molecule upon
99
intramolecular PT. The chemical environment of the carbon-atom to which the deuterium probe is attached changes markedly from HOA CD=C to OA =CDC when
the proton transfers. In essence, this change in the electronic structure of the malonaldehyde molecule results in a substantial alteration of the force constant of the CD
bond. In the gas phase, density functional theory (DFT) at the B3LYP/6-311+G(d,
p) level of theory/basis set predicts a 179 cm1 shift in the harmonic vibrational
frequency of CD vibrational probe. This large shift contrasts significantly with the
< 10 cm1 shifts observed due to the vibrational Stark effect in previous experimental studies,[209, 210, 219] which provides a qualitative indication of the importance
of the electronic structure change to the CD vibrational frequency as well as an
important experimental design principle. Classically, labeling the carbonyl/enol carbon atoms in malonaldehyde with a deuterium should have a negligible effect on the
kinetic rate of intramolecular PT because the free energy profile for the PT process
will be unchanged and there is more than a 1000 cm1 mismatch between the O-H
and CD vibrational frequencies. Quantum mechanically, however, there could be an
indirect effect due to altering the zero-point-energy of the proton on the labeled side
of the molecule relative to the unlabeled side of the molecule. Also, nonadiabatic
coupling of nuclear motions to the electronic structure of the molecule could be relevant. These potentially interesting quantum mechanical effects will be ignored for
the purposes of the present proof-of-concept study.
6.2 Methodology
2D IR spectroscopy has been utilized to investigate complexation reactions in
solution,[206, 207, 220] including hydrogen-bond formation and dissociation processes. In particular, Nydegger, Rock, and Cheatum have used 2D IR spectroscopy to
investigate CD labeled formic acid dimmer in hexane solution.[220] Unfortunately,
the interpretation of the spectra was complicated by the presence of an accidental
100
Fermi resonance so the kinetics of the intermolecular double PT process could not
be elucidated. The technique requires that the reactant (A) and product (B) species
have well-defined spectral signatures. At zero waiting time, peaks appear along the
diagonal that correspond to A and B. As the waiting time is increased, off-diagonal
peaks appear that correspond to the formation of A from B and B from A. Kinetic
rate constants for both the forward and back reactions, as well as the equilibrium
constant between A and B can then be extracted from the growth of the off-diagonal
peaks and the decay of the diagonal peaks (the effects of vibrational population relaxation must also be taken into account). In this study, the 2D IR spectra of CD
labeled malonaldehyde in aqueous solution will be calculated to demonstrate how
the technique is applicable to the study of thermally-induced PT reactions. Because
the intramolecular PT reaction is symmetric in malonaldehyde, the resulting 2D IR
spectra will be symmetric and the diagonal peaks should decay at the same rate as
the off-diagonal peaks grow (neglecting vibrational population relaxation).
In order to calculate the 2D IR spectrum of CD labeled malonaldehyde it is first
necessary to map the instantaneous CD vibrational frequency to the PT reaction
coordinate,
R(OA H) cos(OB OA H)
R(OA OB )
(6.1)
where R(OA H) is the distance from the transferring proton to the donor oxygen
atom, R(OA OB ) is the distance between the donor and acceptor oxygen atoms, and
(OB OA H) is the angle between the OA H and OA OB bonds (see Figure 6.1). The
transition state for the intramolecular PT is located at a value of = 0.5. Using DFT
with the B3LYP functional and a 6-311+G(d, p) basis set, optimized geometries of
malonaldehyde in the gas-phase were obtained for 40 values of constrained between
0.1 and 0.9. All gas-phase electronic structure calculations were performed in Gaussian 09.[221] The energies of the optimized geometries are plotted in the top panel
101
Figure 6.2. (top) Potential energy curves for the intramolecular proton
transfer in malonaldehyde generated with DFT and SCCDFTB. The DFT
barrier height is 3.2 kcal/mol while SCCDFTB predicts a barrier of 2.6
kcal/mol. (middle) Free energy profile from a QM/MM simulation of
malonaldehyde in water with a barrier height of 4.1 kcal/mol. (bottom)
Anharmonic CD vibrational frequencies as a function of the proton
transfer reaction coordinate for malonaldehyde in the gas-phase. The
frequencies were fit to Eq. 6.2, where A0 = 1534.0, A1 = 91.5, A2 = 11.8,
A3 = 2106.5, A4 = 42.7, and A5 = 7.0.
102
of Figure 6.2. DFT predicts a barrier to PT of 3.2 kcal/mol, which agrees well with
higher level quantum chemistry calculations (e.g., MP2/cc-pVTZ and CCSD(T)/ccpVDZ predict barriers of 2.8 and 3.9 kcal/mol, respectively).[222, 223] For each of
the geometries (i.e. values of ), the anharmonic CD vibrational frequency of interest was calculated using previous methodology.[224227] Briefly, the CD bond is
stretched from 0.88 to 1.44
A in 0.08
A increments, holding the rest of the molecule
fixed. At each increment, the molecular energy is calculated with B3LYP/6-311+G(d,
p) yielding the Born-Oppenheimer potential energy curve for the CD stretch, which
is fit to a Morse oscillator. The Morse parameters are sufficient to determine the 01
vibrational frequency, since the energy levels are known analytically for a Morse oscillator. The CD vibrational frequencies are shown as a function of in the bottom
panel of Figure 6.2. Note the extraordinary sensitivity of the CD stretch to the PT
reaction coordinate. The mapping of the CD stretch frequency to is completed by
utilizing an appropriately flexible fitting function,
() = A0 exp [A1 exp [A2 ]] + A3 + A4 + (A5 )2
(6.2)
Next, the malonaldehyde molecule was simulated in aqueous solution using a

mixed quantum mechanics/molecular mechanics (QM/MM) approach in which the
malonaldehyde molecule was modeled using self-consistent-charge density functional
tight binding (SCCDFTB)[228, 229] methodology and the water was modeled with
SPC/E.[195] DFTB is a computationally efficient semi-empirical quantum chemistry
method that is parameterized against local density approximation (LDA) DFT calculations for atoms and pairs of atoms within a tight binding framework. The SCC
correction improves the accuracy of DFTB by incorporating electronic polarization
effects.[230] In the top panel of Figure 6.2, the SCCDFTB method was used to calculate the potential energy curve for the intramolecular PT in malonaldehyde. To
facilitate a direct comparison with the DFT result, the molecular geometries opti103
mized with DFT were utilized for the SCCDFTB energy calculations. The DFT
and SCCDFTB potential energy curves are qualitatively similar. The two primary
differences are in the barrier region (SCCDFTB predicts a 1.5 kcal/mol lower barrier
than DFT) and in the repulsive parts of the potential.
The SCCDFTB-based QM/MM molecular dynamics (MD) simulations of malonaldehyde solvated by 2932 water molecules were performed in AMBER 10.[231]
The simulations employed periodic boundary conditions with a cubic simulation box,
and the long-ranged electrostatic interactions were treated with the particle mesh
Ewald (PME) method.[139] The SHAKE[196] algorithm was used to constrain the
geometry of the rigid SPC/E water molecules. Our equilibration protocol involved
(1) 500 steps of steepest descent minimization, (2) 500 steps of conjugate gradient
minimization, (3) a gradual defrost from 0 K to 300 K over 200 ps of simulation in
the NVT ensemble with a Langevin thermostat and a 1 fs time step, (4) 200 ps of
simulation in the NPT ensemble, (5) rescaling the simulation box size to the average
of the last 50 ps of the NPT simulation (45
A), (6) 100 ps of NVT simulation,
(7) rescaling the velocities to 300 K, and (8) 100 ps of NVE simulation. A 105 ns
trajectory in the NVE ensemble was then collected for analysis.
For each snapshot in the production run trajectory, the instantaneous value of
the PT reaction coordinate, Eq. (6.1), was calculated. A histogram of (t) was
constructed, P (), from which the free energy, F , of the intramolecular PT reaction
in malonaldehyde could be calculated using the relationship F = kB T ln(P ) (middle
panel of Figure 6.2). The free energy barrier height for the PT reaction in aqueous
solution in solution was 4.3 kcal/mol, which is in excellent agreement with a previous
SCCDFTB simulation of malonaldehyde in water (4.2 kcal/mol).[232] From the
time dependence of , a trajectory of the CD stretch vibrational frequency, (t),
was constructed via the relationship in Eq. (6.2).
As described in Chapter 1, knowledge of (t) is sufficient to calculate linear IR
104
Figure 6.3. (a) CD stretch IR absorption spectrum of labeled

malonaldehyde in aqueous solution. (b-d) Chemical exchange 2D IR
spectra for waiting times of 0, 15, and 50 ps.
105
absorption using Eq. 1.3 within a semiclassical framework with well-characterized

approximations. For the calculations of the 2D IR spectra of the CD stretch of
labeled malonaldehyde in aqueous solution, it is assumed that the instantaneous C
D stretch frequency is solely determined by the value of . In reality, fluctuations
of the solvent will also affect the CD stretch frequency. However, from previous
studies of solvatochromic shifts of CD stretch frequencies,[210] the magnitude of the
solvent effects are approximately an order of magnitude smaller than the effects of
intramolecular PT.
In 2D IR spectroscopy, three separate femtosecond IR pulses interact with the
sample, and the subsequent response is measured. The three pulses have specific wave
vectors labeled k1 , k2 , and k3 corresponding to the their sequence. The rephasing
signal is observed in the kRP = -k1 + k2 + k3 direction, while the non-rephasing signal
is described as kN R = k1 k2 + k3 direction. Within the Condon approximation and
assuming that only two vibrational states are relevant, the three-pulse echo response
functions are given by[191]
RRP (t3 , t2 , t1 ) = exp(i h10 i t3 + i h10 i t1 )RP (t3 , t2 , t1 )

(6.3)
RN R (t3 , t2 , t1 ) = exp(i h10 i t3 i h10 i t1 )N R (t3 , t2 , t1 )
where
Z t1

Z t1 +t2 +t3
RP (t3 , t2 , t1 ) = exp i
d 10 ( ) i
d 10 ( )
0
t1 +t2
Z t1

Z t1 +t2 +t3
N P (t3 , t2 , t1 ) = exp i
d 10 ( ) i
d 10 ( )
0
(6.4)
t1 +t2
where RRP and RN P are the rephasing and non-rephasing responses, respectively.
The waiting time, Tw , is synonymous with t2 in the equations above. The 2D IR
signal S(3 , t2 , 1 ) is given by the sum of the rephasing and non-rephasing signals,
106
S(3 , t2 , 1 ) Re [SRP (3 , t2 , 1 ) + SN P (3 , t2 , 1 )]
(6.5)
where
Z
SRP (3 , t2 , 1 ) =
dt3 exp(i3 t3 i1 t1 )RRP (t3 , t2 , t1 )
dt1
Z0
Z0
dt3 exp(i3 t3 + i1 t1 )RN P (t3 , t2 , t1 )
dt1
SN P (3 , t2 , 1 ) =
0
(6.6)
where SRP and SN P are the rephasing and non-rephasing signals, respectively.

Shown in the Figure 6.4(a) is the IR absorption spectrum for the CD stretch
of labeled malonaldehyde. As expected, the spectrum exhibits a pair of sharp absorbances, which are separated by 153 cm1 . The peak near 2150 cm1 corresponds
to when the transferable proton is proximal to the CD label, and the peak near
2300 cm1 is when the proton is distal relative to the label. A total of 18 chemical
exchange 2D IR spectra with waiting times spanning 0-500 ps were also calculated.
In Figure 6.4 (b-d) the 2D IR spectra for three representative waiting times, 0, 15,
and 50 ps, are reported (additional spectra for Tw over the range 0 to 500 ps can be
found in Appendix B). Analogously to the 1D IR absorption spectrum, the 2D IR
spectra all exhibit peaks on the diagonal separated by approximately 153 cm1 (note
that at infinite waiting time that a diagonal slice through the 2D IR spectrum should
yield the 1D spectrum). As the waiting time increases, the intensity of the diagonal
peaks decrease and the off-diagonal peaks grow into the spectra. The off-diagonal
peaks correspond to circumstances where the transferable proton was initially on the
side of the malonaldehyde containing the CD reporter and it transfers to the other
side of the molecule within the waiting time, or vice versa. By monitoring the decay
of the diagonal peaks and the growth of the cross peaks as function of the waiting
107
time, the kinetics of the PT process should be elucidated.

To quantify that the kinetics observed in the 2D IR spectra corresponded to the
time scale of intramolecular PT in malonaldehyde, the time correlation function of
the fluctuations of the PT reaction coordinate was computed (top panel of Figure
6.4). The time correlation function was fit reasonably by a single exponential with a
time constant of 28.8 ps, which is in reasonable agreement with previous theoretical
investigations in the gas-phase.[213] Next, the normalized volumes of the diagonal and
off-diagonal peaks were calculated as a function of the waiting time (bottom panel
of Figure 6.4). The decay and growth in volume of the diagonal and off-diagonal
peaks were also reasonably well-described by single exponentials with time constants
of 29.7 and 28.3 ps, respectively. The congruity of the PT lifetime and the kinetics
for the decay and growth of the diagonal and off-diagonal peaks on the computed 2D
IR spectra demonstrates the potential utility of the peripheral CD labeling strategy
and the use of chemical exchange 2D IR spectroscopy to monitor intramolecular PT.
The use of chemical exchange 2D IR spectroscopy of a peripheral (and minimally
perturbative) CD vibrational reporter to monitor PT processes in real-time has been
demonstrated computationally. While CD vibrations have notoriously low absorptivity that may make 2D IR measurements difficult (but not impossible),[220, 233]
the strategy of monitoring site-specific vibrational labels, rather than the transferring
proton itself, has general applicability in a broad range of contexts. Other kinds of
vibrational reporters (e.g. nitrile, azido, etc.) with substantially better absorptivity are also viable because they would be sensitive to the redistribution of charge
that occurs in proton and electron transfer processes via the vibrational Stark effect.
Finally, this work demonstrates how theory and computation can be used to guide
the development of new experiments by directly computing the relevant experimental
observables.
108
Figure 6.4. (top) Reaction coordinate time correlation function along with
a fit to a single exponential with a time constant of 28.8 ps. (bottom)
Evolution of the normalized volumes of the diagonal and off-diagonal peaks
in the 2D IR spectra as a function of the waiting time. Both curves were fit
to a single exponential yielding time constants of 29.7 and 28.3 ps for the
diagonal and off-diagonal peaks, respectively.
109
CHAPTER 7
SUMMARY
The challenges and opportunities presented when characterizing the structure

and dynamics of condensed phased reactions are considerable. Utilizing theory and
computational techniques are necessary complements to the interpretation of experimental observables. Comprehending the magnitude of precise solvent movements are
important for understanding electron and proton transfer reactions in the condensed
phase, as it is these dynamics that often determines the kinetics of solution-phase reactions. In particular, the decay of a solvation response function, S(t) yields a wealth
of information about reorganizational rates relevant to these charge-transfer reactions
in addition to developing our intuition regarding solute-solvent and solvent-solvent
interactions. An understanding of solvation dynamics has dramatically influenced
our understanding of the rates of chemical reactions in conventional dipolar media,
as solvation dynamics are known to govern the reaction rates of electron or proton
transfer.[39, 41] At the very minimum ILs are binary systems with heterogenous
regions of diverse dynamics with the ability to participate and influence chemical reactions. With the excellent thermal and chemical stability, superior solvating ability,
and controllable physicochemical properties, ILs represent a fascinating class of solvents poised to take on important challenges in energy research. Given the immense
undertaking to synthesize a fraction of the estimated 1018 possible combinations, accurate theoretical simulations are necessary to elucidate the complex, many-bodied
interactions responsible for certain macroscopic properties. This dissertation addresses the need for a fundamental understanding of the complex intermolecular
110
interactions in ILs that are responsible for microscopic structures and dynamics that
ultimately manifest in macroscopic physical properties.
In Chapters 2 and 3, we identified the persistence of preferential solvation, where
the cations are, on average, closer to the the aromatic solute than the anions. While
presenting some ambiguity in the interpretation of simulations and experiments that
depend on a spectroscopic probe to be a passive observer of the local environment,
scientists and engineers can utilize this knowledge to selectively tune solubility of
compounds by choosing the right combination of cation and anion constituents.
The mechanism of solvation in ILs is distinctly different from conventional dipolar
solvents, where collective dipole-dipole interactions in the vicinity of the fluorescence
probe molecule are the most dominant interaction. In ILs, the media is no longer
a single component liquid, rather a heterogeneous mixture, and because of their
different shapes, sizes, and charge distributions the ions respond differently to the
charge perturbation. However, extensive MD simulations in a series of imidazoliumbased ILs, [emim][BF4 ], [bmim][BF4 ], [bmim][DCA], [emim][TfO], and [bmim][PF6 ]
revealed a general solvation dynamics mechanism despite these differences in ions.
Consistently, the translational motion of the anions into and out of the first solvation
shell of C153 are most responsible for the solvation response. While initially this
mechanism appears distinct from polar solvents, if considering particular cation-anion
pairs form a molecule with a fictitious dipole moment, it is the rotation of these
fictitious molecules that dominate the response (Figure 7.1). The concept of the
fictitious dipole molecule is a proof-of-concept, with the current definition identifying
any anions with 7.75
A of the center-of-mass of the cations. The distance 7.75
A was
identified as the first minimum in the radial distribution function of the center-ofmass of the cations relative to the center-of-mass of the anions.
Analogous to experimental observations that the solvation relaxation is correlated
with viscosity (Chapter 1), a comparable resemblance is found when relating the
111
Figure 7.1. The simulated solvation response (black) is decomposed using

the methodology described in Chapter 2 into contributions from the
rovibrational (dashed pink) and the translational motions of the fictitious
dipole molecule (solid blue).
112
Figure 7.2. The calculated solvation relaxation time as a function of the

inverse cube root of the molecular volume.
113
theoretical solvation time to the inverse of the cube root of the molecular volume
(Figure 7.2). Predicting relevant solvation time scales is beyond the scope of this
study, though a survey of additional ILs would be beneficial.
One of the most daunting scientific challenges facing our society today is the
production of environmentally clean and renewable energy. Chemists and engineers
are no longer dependent on varying the reaction conditions as a means for control over
rates and products; now selectivity over the reaction media represents a paradigm
shift in our approach to chemical reactions in the condensed phase. This research
which characterized the structure and dynamics in ILs in unprecedented detail, will
benefit other scientists and engineers who are seeking to control the properties of ILs
for advanced applications in energy research.
7.1 Alternative Systems of Interest

This dissertation considers only binary compositions of common ILs, though
ternary mixtures and beyond are achievable and would present a more complicated
solvation mechanism. Previous studies have found that consistent with imidazoliumbased ILs, the solvation dynamics are extremely slow however ILs using ammonium
and phosphonium cations do not display an ultrafast component, suggesting an alternative solvation mechanism is in effect.[6769, 234] Beyond relatively planar cations
and spherical anions, preliminary investigations including planar anions and approximately spherical cations challenge the validity of the mechanism suggested in Chapters 2 and 3.
Four different cations 1-butyl-3-methyl imidazolium, [bmim], 1-ethyl-3-methyl imidazolium, [emim], triethyl sulfonium, [S222 ], and tri(methoxymethyl)-methyl phosphonium, [Tmet] were paired with five anions tetrafluoroborate, [BF4 ], trifluoromethane sulfonate, [TfO], 1-pyrazolide, [Pyrazo], 1,2,3,-triazolium, [Triazo], and bistrifluoromethylsulfonylimide, [Tf2 N] to create seven unique systems (Figure 7.3). The
114
cation [Tmet] is preferred over the non-ether containing counterpart tributyl-methyl

phosphonium, [P3331 ], because recent studies have identified the introduction of etherbonds significantly improves transport properties.[235237] Shown in Figures 7.47.10 are the solvation response and decomposition for [bmim][TfO], [emim][Pyrazo],
[emim][Tf2 N], [emim][Triazo], [S222 ][[BF4 ], [Tmet][BF4 ], and [Tmet][Pyrazo]. Consistent with the imidazolium-based ILs and spherical anions presented in Chapter 3, the
anion contribution is substantially larger than that of the cations or C153 for all time
scales of the solvation response. Decompositions of the individual ion components
into translational and rovibrational contributions have not been performed, so it is
unclear if the mechanism of solvation where the translational motion of the anions
into and out of the first solvation shell of C153 is present. This represents an exciting
avenue for future study.
115
Cations
Anions
[bmim]
[BF4]
[Tmet]
[emim]
[Triazo]
[Tf2N]
[Pyrazo]
[S222]
[TfO]
Figure 7.3. The optimized structures of cations and anions. The cations are
1-butyl-3-methyl imidazolium, [bmim], 1-ethyl-3-methyl imidazolium,
[emim], triethyl sulfonium, [S222 ], and tri(methoxymethyl)-methyl
phosphonium, and [Tmet]. The anions are tetrafluoroborate, [BF4 ],
trifluoro-methane sulfonate, [TfO], 1-pyrazolide, [Pyrazo], 1,2,3,-triazolium,
[Triazo], and bistrifluoromethylsulfonylimide, [Tf2 N]
116

into contributions from the [TfO] anions (red), the [bmim] cations (blue),
117

into contributions from the [Pyrazo] anions (red), the [emim] cations
(blue), and the internal motions of the C153 solute (purple).
118

into contributions from the [Tf2 N] anions (red), the [emim] cations (blue),
119

into contributions from the [Triazo] anions (red), the [emim] cations (blue),
120

into contributions from the [BF4 ] anions (red), the [S2 22] cations (blue),
121

into contributions from the [BF4 ] anions (red), the [Tmet] cations (blue),
122

into contributions from the [Pyrazo] anions (red), the [Tmet] cations
(blue), and the internal motions of the C153 solute (purple).
123
APPENDIX A
SOLVATION RESPONSE FUNCTION FITS
As mentioned in Chapter 3, the experimental results observed in Figure 3.2 were

scaled by a multiplicative constant to bring the results into maximum coincidence for
comparative purposes. A systematic analysis identified the ideal multiplicative constant, k, by minimizing the root-mean-square deviation (RMSD) of the experimental
measurements to the normalized simulated response (Table A.1).
Also shown in this appendix are the solvation response functions fit to a single
exponential A exp((t/ )) in the range from 50 to 400 ps as referred to in Chapter
3.
124
Figure A.1. Fits of the calculated (black) and experimental (red) solvation
responses of C153 in the IL [emim][BF4] to a single exponential function in
the time range between 50 ps and 400 ns. The data are shown as filled
circles, while the fits are lines.
125
126
127
128
129
TABLE A.1
IDEAL MULTIPLICATIVE CONSTANTS
RMSD (102 )
[emim][BF4 ]
1.17
3.9
[bmim][BF4 ]
0.78
3.2
[bmim][DCA]
0.945
2.7
[emim][TfO]
0.79
6.1
[bmim][PF6 ]
0.71
8.0
Ideal multiplicative constants, k, for experimental solvation response data that minimized the root-mean-square deviation (RMSD) for each IL system.
130
APPENDIX B
MALONALDEHYDE TWO-DIMENSIONAL INFRARED SPECTRA
Shown in this appendix are chemical exchange two-dimensional infrared (2D IR)
spectra for the CD stretch of labeled malonaldehyde in aqueous solution for waiting
times, Tw in the range 0 to 500 ps referred to in Chapter 6.
131
Figure B.1. Chemical exchange 2D IR spectra for waiting times of 0 ps.
132
133
134
135
136
137
138
139
140
141
142
143
144
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EXPLORING THE STRUCTURE AND DYNAMICS OF IONIC LIQUIDS USING

Submitted to the Graduate School

Steven A. Corcelli, Director

Graduate Program in Chemistry and Biochemistry

EXPLORING THE STRUCTURE AND DYNAMICS OF IONIC LIQUIDS USING

To my complement, treasure, and companion, Kelly.

CHAPTER 2: THE MECHANISM OF SOLVATION DYNAMICS IN [emim][BF4 ]

3.4.1 Self-Diffusion Coefficients . . . . . . . . . . . . . . . . . . . .

CHAPTER 6: MONITORING INTRAMOLECULAR PROTON TRANSFER

The structures of imidazolium cations and inorganic anions studied

The experimental solvation relaxation time as a function of the solvent

Calculated (black) and experimental[2, 3] (green) solvation response

The radial distribution function, g(r), for C153-[emim] and C153-[BF4 ]

The solvation responses of [emim] (blue) and [BF4 ] (red) decomposed

The residence-time correlation function (RTCF) for the anions and

A of the center-of-mass of the C153 probe. . . . . . . . . . . . . . . .

A schematic depiction of the mechanism of solvation dynamics in

The calculated (dashed) and experimental (solid) solvation response

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The solvation responses of [bmim] (blue) and [BF4 ] (red) decomposed

3.15 The calculated (solid) solvation response functions for [emim][BF4 ]

The normalized solvation response without the contribution of the dye

The normalized solvation response decomposed into anion (top) and

The normalized solvation responses of S(t) (black), C1 (t) (red), and

The orientational time-correlation function for an OD bond in H2 O

Vibrational line shapes for the OD stretch of dilute HOD in H2 O and

Distribution functions, F (E), for the projection of the electric field

Normalized CE (t) for HOD in H2 O and HOD in the [bmim][PF6 ] IL.

Decomposition of normalized CE (t) for the OD stretch of HOD isolated

Decomposition of normalized CE (t) for the OD stretch of HOD isolated

Proton transfer reaction coordinate in malonaldehyde. . . . . . . . . .

(top) Potential energy curves for the intramolecular proton transfer in

(a) CD stretch IR absorption spectrum of labeled malonaldehyde in

(top) Reaction coordinate time correlation function along with a fit

The simulated solvation response (black) is decomposed using the

The calculated solvation relaxation time as a function of the inverse

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

The calculated total solvation response (black) is decomposed into

7.10 The calculated total solvation response (black) is decomposed into

PARAMETERS FOR A STRETCHED EXPONENTIAL FIT . . . .

SELF-DIFFUSION COEFFICIENTS FROM MD SIMULATIONS . .

A.1 IDEAL MULTIPLICATIVE CONSTANTS . . . . . . . . . . . . . . . 130

I owe many of my achievements and successes to the hard work, encouragement

extended their love and help whenever necessary. Professionally I am appreciative of

1.1 Ionic Liquids

Figure 1.1. The structures of imidazolium cations and inorganic anions

1.1.1 Polarity of ILs

Reichardts solvent polarity parameter ET

the classes of ILs, the ET

values fall within a very narrow window around 47-49

kcal/mol) and less polar than methanol (ET

medium chain alcohols (butanol = ET

of 55.6 kcal/mol), more similar to

Another descriptor of the solvent polarity is the dielectric constant, , which

to pentanol (=15.1) and octanol(=8.8).[37] The modest is an indication of the

1.2 Solvation Dynamics