ELECTRONIC PHOTODISSOCIATION SPECTROSCOPY
OF METAL-POLYPYRIDINE COMPLEX IONSbySHUANG XU
B.S., Nanjing University, China, 2010

A thesis submitted to the
Faculty of the Graduate School of the
University of Colorado in partial fulfillmentof the requirement for the degree ofDoctor of Philosophy

Department of Physics

2016This thesis entitled:
ELECTRONIC PHOTODISSOCIATION SPECTROSCOPY
OF METAL-POLYPYRIDINE COMPLEX IONSbySHUANG XU
has been approved for the Department of Physics

Professor J. Mathias Weber

Professor W. Carl Lineberger

Date

The final copy of this thesis has been examined by the signatories, and wefind that both the content and the form meet acceptable presentation standardsof scholarly work in the above mentioned discipline.

iii
Xu, Shuang (Ph. D., Chemical Physics, Department of Physics)
Electronic Photodissociation Spectroscopy of Metal-Polypyridine Complex Ions
Thesis directed by Professor J. Mathias Weber

The properties of many important molecules are only known from condensed phasestudies, where the interaction with solvent or other chemical environments masks the intrinsic
properties of the solute molecule. Consequently, these intrinsic properties cannot be easily
obtained from condensed phase experiments. Spectroscopy of gas-phase molecular ions in vacuo
is an attractive alternative to spectroscopic studies in the condensed phase. Ions in vacuo are
isolated systems and free from perturbation inflicted by a chemical microenvironment, such as asolvent or crystal lattice. Consequently, it becomes possible to examine the intrinsic propertiesof the ions in vacuo. Furthermore, gas-phase ions can be trapped, cooled and mass-analyzed,
which provides researchers with the opportunity for controlling and selecting ion species andconditions. This thesis comprises my work on photodissociation spectroscopy of several series ofmetal-polypyridine ions in vacuo. These species have been extensively studied in inorganic
chemistry because they serve as potential candidates for broad industrial applications and also
as prototypical systems to study fundamental scientific questions such as the mechanisms ofmetal-ligand interaction and chemical reaction. This thesis describes the first investigation ofsuch systems in the gas phase using laser spectroscopy in the visible and UV spectral ranges.
In this work, the gas-phase ions are produced by electrospray ionization. The ions aretrapped and buffer-gas cooled in a cryogenic quadrupole ion trap and then undergo massselection in a time-of-flight mass spectrometer. The selected ion species are irradiated by a laser
pulse with widely tunable photon energy. If photoabsorption leads to dissociation, fragments will
be separated and analyzed by a reflectron. The yield of fragment ions is monitored as a functionof photon energy and recorded as a photodissociation spectrum. While absorption spectra iniv

solutions of the species studied here are usually broad and featureless, the photodissociation
spectra acquired in the gas phase show new resolved features, often even at room temperature.
Four series of ions were studied and the results are presented in this thesis. The first two
are [Cu(bpy)-L]+ and [Ru(bpy)(tpy)-L]2+, where bpy = 2,2’-bipyridine and tpy = 2,2′:6′,2′′terpyridine, and L represents a variable ligand. The choices for L in the two types of complexes
are different, but they both form a series from weakly (e.g. N2) to strongly interacting ligands(e.g. Cl, CH3CN). It is found that the ligand can dramatically shift the molecular orbitals andchange the electronic structure of the ion. Another critical element in the ion is the metal. To
explore how the metal affects the properties of the ion, the photodissociation spectra of a seriesof [MII(bpy)3]2+ ions were measured. Here, M represents a transition metal, and in this study,
several first-row transition metals and the d6-column metals are included (Mn, Fe, Co, Ni, Cu, Zn,
Ru, Os). The experimental data suggest that the [MII(bpy)3]2+ ions can have significantly different
excitation energies, excited-state lifetimes and symmetries. Finally, the complex ion can begenerated in microsolvated states by condensing solvent molecules onto the bare ion in the
cryogenic ion trap. By experimenting on mass-selected ions solvated by a well-defined numberof solvent molecules, it is possible to observe the solvation effect in a stepwise fashion, i.e. one
solvent molecule at a time. The target ion used in this study is [Ru(bpy)(tpy)-OH2]2+ and it is foundthat solvation by only four water molecules already contributes more than 75% of the fullsolvatochromic shift exhibited in its bulk solution. By comparing the geometry and the spectrumof each solvation stage, the evolution of the solvatochromic shift can be linked to the formationof solvation shells.
Apart from the experimental work, computations based on density functional theory
were carried out to provide more ground-state information of the systems. Excited-statecalculations were performed using time-dependent density functional theory and are comparedwith the experimental results. This comparison is used to assign the measured spectra, and togauge the reliability of the calculations.

v

To my family.

vi
Acknowledgements
I would like to express my deepest gratitude to the Weber research group. It is a vibrant,
friendly and talented group with which I feel so fortunate to spend the past five years of mydegree pursuit. In particular, the group leader and my advisor, Professor J. Mathias Weber, is aknowledgeable scientist, patient mentor and considerate friend, who has taught me how to be adiligent researcher, guided me through perplexing technical predicaments, tolerated mybrainlessness and indulged my recklessness. I feel blessed to have been able to join his group andembarked on an adventure in ion spectroscopy when I arrived in Boulder bearing only Josephson
junctions in my mind. This transition would have been forbidden had I not been lucky to gain thetrust and guidance of Professor Weber and the predecessors of my project, Dr. Sydney Kaufman
and Casey Christopher. I am also in debt to other group members, Dr. Benjamin Knurr, Michael
Thompson, Curtis Beimborn, who work on different projects but have offered tremendous help
at times, and James Smith, who often inspires me to rethink many things I have done. I would
like to thank the three short-term group members, Luke Long, Martin Meissner and Dr. Jacob
Ramsey for having been memorable companions. I will never forget the moments of cheers andlaughs in and out of the lab with these wonderful mates.
I must thank the technicians, engineers and other scientists who have worked or talked
with me because they are an indispensable source of craft and wisdom. The JILA machine shop,
electronic shop and computing group have lent critical help in the construction and maintenanceof my hardware and software. Nothing would have been possible without the assistance fromthese omnipotent technical masters. Thanks also go to the JILA supply office personnel who haveprocessed our frequent purchase requests and kept our experiment running timely. The weekly

viimeetings with the “supergroup” participated by Professor Veronica Bierbaum, Professor Carl
Lineberger, Professor Barney Ellison and their coworkers have been incentive and resourceful. I
have received valuable remarks and learned fascinating science in this small community. I am
also grateful to the National Science Foundation for supporting my research under Grant
CHE-1361814.
Next, I need to acknowledge a special group of people who hardly understand what I am
doing but have been forever unconditionally encouraging – my family. As most Chinese families
tend to stay close together for cultural and economic causes, I am extremely lucky to have my
open-minded parents and grandparents caring and supporting me when I decided to take a long
journey to the west. I hope I will be able to repay their solicitude and sacrifice by more than justmaking them proud. There is no word that is strong enough to express my gratitude to my wife,
Dr.-to-be Guoyu Wang, for her constant tender and merry company, and persistentunderstanding and supporting. We have gone through years of geographical separation and now
she is lured aboard my somewhat adventurous journey in America. Although much excitement
has come along in the migration, both of us long for a settle-down in the next chapter of our life,
which is just around the corner as I graduate. I will have to ensure that she will never regret her
choice.
Last but not least, I want to extend thanks to all my previous teachers and friends, whohave been a big part in making me who I am. Maybe I should also mention the random people I
have encountered in the concert hall, on the trail, at the party, on the soccer field and even on
the Internet, who have enriched my life with the different colors and endless joy.

viiiContents
1

2

Introduction........................................................................................................ 1
1.1

Interest in organometallic compounds....................................................................1

1.2

Why in vacuo? .......................................................................................................2

1.3

In this thesis ..........................................................................................................4

Methods ............................................................................................................. 6
2.1

Overview ...............................................................................................................6

2.2

Ion preparation.................................................................................................... 10

2.2.1

Electrospray ionization source ................................................................................. 10

2.2.2

Ion guides and pre-trap ion optics ........................................................................... 15

2.2.3

Cryogenic ion trap .................................................................................................... 20

2.2.4

Modifying ions in the trap and the pre-trap ............................................................ 25

2.3

Mass selection and mass analysis ......................................................................... 26

2.3.1

Reflectron time-of-flight mass spectrometer .......................................................... 26

2.3.2

Ion detection ............................................................................................................ 31

2.3.3

Mass gate ................................................................................................................. 32

2.3.4

Analyzing photofragments ....................................................................................... 33

2.4

Photodissociation spectroscopy ........................................................................... 36

2.4.1

Concepts ................................................................................................................... 36

2.4.2

Conditions and caveats ............................................................................................ 38

2.4.3

Messenger tagging ................................................................................................... 41

2.4.4

Multiphoton processes ............................................................................................ 43

2.5

Laser sources ....................................................................................................... 43

ix
2.5.1

Overview .................................................................................................................. 43

2.5.2

Nd:YAG pump ........................................................................................................... 45

2.5.3

OPO and SHG/SFM stage ......................................................................................... 47

2.5.4

Dye laser ................................................................................................................... 49

2.6
2.6.1

Timing sequence ...................................................................................................... 51

2.6.2

Data acquisition........................................................................................................ 55

2.6.3

Data processing ........................................................................................................ 57

2.6.4

Baseline and scaling correction ................................................................................ 59

2.7

3

References........................................................................................................... 60

The role of the ligands....................................................................................... 63
3.1

Introduction ........................................................................................................ 63

3.2

Copper bipyridine complexes ............................................................................... 65

3.2.1

Background .............................................................................................................. 65

3.2.2

Methods ................................................................................................................... 67

3.2.3

Results and discussions ............................................................................................ 69

3.3

Ruthenium polypyridine complexes...................................................................... 88

3.3.1

Background .............................................................................................................. 88

3.3.2

Methods ................................................................................................................... 90

3.3.3

Results and discussions ............................................................................................ 92

3.4

4

Operation Control ................................................................................................ 51

References......................................................................................................... 117

The role of the metal ...................................................................................... 124
4.1

Introduction and background – tris(2,2’-bipyridine)-metal complexes ................. 124

4.2

Methods ............................................................................................................ 127

x
4.3

5

Results and discussions ...................................................................................... 129

4.3.1

Computational........................................................................................................ 129

4.3.2

M = Cu .................................................................................................................... 131

4.3.3

M = Mn, Co, Ni, Zn.................................................................................................. 133

4.3.4

M = Fe, Ru, Os ........................................................................................................ 139

4.4

Summary ........................................................................................................... 151

4.5

Appendix ........................................................................................................... 154

4.6

References......................................................................................................... 166

The role of the solvent .................................................................................... 172
5.1

Introduction ...................................................................................................... 172

5.2[(tpy)(bpy)RuII-OH2]2+ solvated by 0 - 4 H2O molecules ......................................... 174

5.2.1

Background ............................................................................................................ 174

5.2.2

Methods ................................................................................................................. 175

5.2.3

Bare complex and calculations............................................................................... 178

5.2.4

The hydrated clusters............................................................................................. 186

5.2.5

Solvatochromic behavior ....................................................................................... 190

5.3

Summary ........................................................................................................... 196

5.4

References......................................................................................................... 197

6

Summary and conclusions ............................................................................... 199

7

Bibliography ................................................................................................... 201

xi

Lists of Tables
Table 2.1

Specifications of each differential pumping chamber in operation. .................... 16

Table 2.2

Lengths and typical RF amplitudes of all four octupole ion guides. ..................... 18

Table 2.3

OPO and SFM/SHG output ranges in nm. ............................................................. 48

Table 2.4

Specifications of the dyes in current study........................................................... 51

Table 2.5

Detailed timing sequence with example values. .................................................. 52

Table 3.1

Calculated ground-state properties of the complexes under study (PBE0/def2TZVP). Binding energies are for the ligand L in [Cu-L]+, except for Cu+ where thebinding energy is given for Cu and bpy+. Partial charges were determined using
natural population analysis.46 ............................................................................... 72

Table 3.2

Experimental and computed excitation energies. The experimental energies list
the first discernible peaks in each electronic band. Computed energies are
determined at the EOM-EE-CCSD/cc-pVTZ level unless indicated otherwise.
Computed adiabatic excitation energies are in parentheses. All energies are givenin cm-1.................................................................................................................... 76

Table 3.3

Experimental values were determined by fitting Lorentzian profiles with 100 cm-1
full width at half-maximum (which corresponds to the width of the 0-0 band) tothe clearly discernible peak features in Figure 3.6. The error in these peak
positions is ± 10 cm-1. Calculated values are for totally symmetric ground statevibrational modes of [Cu-N2]+ obtained with PBE0/def2-TZVP (harmonic
approximation). Additional totally symmetric modes are listed in Table 3.4. ..... 79

Table 3.4

Comparison of the calculated vibrational modes in [Cu-N2]+ and Cu+. Numbers are
given in cm-1. ......................................................................................................... 81

Table 3.5

Chemicals used in the synthesis of Ru2+. .............................................................. 91

Table 3.6

Ligand binding energies EL calculated for [Ru-L]2+ using the B3-LYP functional... 94

Table 3.7

The positions of spectroscopic features observed in the spectra of [Ru-L]2+ for L =H2O and CO2 at 180 K trap temperature, compared to their positions as predictedby TDDFT (B3-LYP functional, shifted by -1210 cm-1). No comparison is made forfeature V in each case (see text). .......................................................................... 96

xii
Table 3.8

Charge distribution calculated for [Ru-L]2+ with natural binding orbitals using the
B3-LYP functional. ............................................................................................... 102

Table 3.9

Calculated selected transition energies (B3-LYP, shifted by -1210 cm-1) sorted by
the dominant orbitals involved in the transition. ............................................... 103

Table 3.10

Lowest energy calculated electronic transition energies and oscillator strengths
for L = H2O (B3LYP functional, not shifted). Only contributions of 10% and greater
are shown............................................................................................................ 107

Table 3.11

Lowest energy calculated electronic transition energies and oscillator strengths
for L = CO2 (B3LYP functional, not shifted). Only contributions of 10% and greater
are shown............................................................................................................ 109

Table 3.12

Lowest energy calculated electronic transition energies and oscillator strengths
for L = CH3CN (B3LYP functional, not shifted). Only contributions of 10% andgreater are shown. .............................................................................................. 111

Table 3.13

Lowest energy calculated electronic transition energies and oscillator strengths
for L = N2 (B3LYP functional, not shifted). Only contributions of 10% and greater
are shown............................................................................................................ 113

Table 3.14

Lowest energy calculated electronic transition energies and oscillator strengths
for Ru2+ (B3LYP functional, not shifted). Only contributions of 10% and greater are
shown. ................................................................................................................. 115

Table 4.1

Metal salts used for production of [MII(bpy)3]2+ in this work. All chemicals wereused as received.................................................................................................. 127

Table 4.2

Calculated ground-state energies for the [MII(bpy)3]2+ species in this study (incm-1) with different symmetries (D3, C2, C1) and spin configurations. The lowest
energy for each species is listed in bold font...................................................... 129

Table 4.3

Calculated geometric properties and binding energies of [MII(bpy)3]2+. ............ 131

Table 4.4

Transition energies and oscillator strengths for selected calculated excited states(TDDFT with59 and without spin-orbit interaction) of [Ru(bpy)3]2+ compared toexperimentally observed features. Solvatochromic shifts are calculated only fordiscernible features in both aqueous solution and gas phase spectra. ............. 144

Table 4.5

Transition energies and oscillator strengths for selected calculated excited states(TDDFT without spin-orbit interaction, B3LYP/def2-tzvp) of [Fe(bpy)3]2+ compared
to experimentally observed features. Solvatochromic shifts are calculated only fordiscernible features in both aqueous solution and gas phase spectra. ............. 147

xiii
Table 4.6

Transition energies and oscillator strengths for selected calculated excited statesof [Os(bpy)3]2+ (TDDFT with62 and without spin-orbit interaction) compared toexperimentally observed features. Solvatochromic shifts are calculated only fordiscernible features in both aqueous solution and gas phase spectra. ............. 150

Table 4.7

Experimental and calculated band positions and other characteristics forcomplexes with D3 symmetry. ............................................................................ 152

Table 4.8

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Mn(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.10). .................... 154

Table 4.9

Calculated (B3LYP/def2-tzvp) energies (E) and oscillator strengths (f) of some of
the intense electronic transitions of [Fe(bpy)3]2+ in the region of our spectrum.
Only orbitals with contribution greater than 10% are shown (see Figure 4.11)......
..................................................................................................................... 155

Table 4.10

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Co(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.12). .................... 156

Table 4.11

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Ni(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.13). .................... 157

Table 4.12

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Cu(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.14). .................... 158

Table 4.13

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Zn(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.15). .................... 160

Table 4.14

Calculated (B3LYP/ecp-10-mdf) energies (E) and oscillator strengths (f) of some of
the intense electronic transitions of [Fe(bpy)3]2+ in the region of our spectrum.
Only orbitals with contribution greater than 10% are shown (see Figure 4.16) 161

Table 4.15

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Ru(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.17). .................... 162

Table 4.16

Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Os(bpy)3]2+ in the region of our spectrum. Only orbitals
with contribution greater than 10% are shown (see Figure 4.18). .................... 164

xiv
Table 5.1

Zero-point corrected binding energies of water molecules in [Ru-OH2]2+·(H2O)nclusters. The binding energy for n =2 is the same for both conformers. The values
for n = 3 and 4 are upper limits, based on the most strongly bound isomers found
for these cluster sizes. ........................................................................................ 181

Table 5.2

Experimental and calculated energies (in cm-1) of selected spectroscopic featuresof [Ru-OH2]2+·(H2O)n clusters at 180 K trap temperature. .................................. 192

xv

List of Figures
Figure 2.1

This flowchart shows the three major steps of our experiment (main blocks, blue).
Listed in the appended blocks (white) are the technologies utilized to implement
each step. The letter/number symbols in the parentheses refer to the parts of
instrumentation as labeled in Figure 2.2. ............................................................... 6

Figure 2.2

Schematics of the experimental apparatus. A - electrospray needle; B - desolvation
capillary; C - skimmer; D - octupole ion guide; E - quadrupole bender; F - helium
cryostat; G - ion trap and accelerator assembly; H - x-y deflectors and Einzel lens;I - mass gate; J - reflectron; K - microchannel plate; L - pyroelectric joulemeter. The
inset zooms in on the trap region. This figure is adapted from Ref.1 ..................... 7

Figure 2.3

Illustration of our ESI setup and microscopic mechanism of the process in positive
ion mode (see text). .............................................................................................. 12

Figure 2.4

Elements from ESI to the ion trap (see text). ....................................................... 16

Figure 2.5

Octupole ion guides. All rods have a diameter of 3 mm and placed on a circle of
9 mm in diameter. Adjacent rods are driven by 10 MHz AC signal of opposite
phases, forming a radial potential in the cylindrical space. ................................. 17

Figure 2.6

The scheme of the pre-trap in the second differential pumping chamber. The
skimmers are pulsed to generate loading (red) and unloading (blue) potentials toform ion packets from a continuous flow of ions (green). ................................... 19

Figure 2.7

Schematic of the ion trap assembly. The trap is mounted on the 4 K cold head of aclosed-cycle helium cryostat via a sapphire plate and OFHC copper mounts. A
radiation shield attached to the 40 K stage of the cryostat encloses the trap
assembly. The acceleration unit (G3-5) of the time-of-flight mass spectrometer iscoupled with the ejection ion optics of the trap (G3a). ....................................... 20

Figure 2.8

Operation of the ion trap on a time axis. At T1, buffer gas is pulsed into the trap
and the injecting period starts with RF on and an uphill potential inside the trap.
After ca. 95 ms of accumulation, at T2 a signal is sent to switch off the RF and thetrap ejects with a downhill potential. The red and blue lines represent the DC
potential energy the ion experience. The actual AC trapping potential (present
only during loading) is not shown......................................................................... 23

Figure 2.9

The photodissociation spectrum of crystal violet anion with different ion storage
times: 95 ms (red) and 45 ms (blue). Ion trap is held is at 10 K in both cases.
Significant hot band to the left the rising edge emerges when the storage time isshorter................................................................................................................... 25

xvi
Figure 2.10

Adaptor circuit for the Willamette high voltage switch. ...................................... 29

Figure 2.11

The two functions of the reflectron: (a) refocusing the same ion species that havepicked up different speeds from the acceleration zone; (b) separating the parent
ions and the fragments. Note that the geometry is not drawn to scale. ............. 30

Figure 2.12

Home-built voltage dividers for MCP (a) and CEM (b). ........................................ 31

Figure 2.13

Illustration of mass gate in open and closed configurations (not to scale).......... 32

Figure 2.14

Schematic illustration of the photodissociation process. The target ion is excitedby a photon to an electronic excited state. After relaxation to the electronic
ground state, it becomes vibrationally hot. If a dissociation channel is energeticallyaccessible, the ion will follow this channel and dissociate into fragments. ......... 37

Figure 2.15

Potential problems of photodissociation spectroscopy. The red line is thedissociation curve accessible to the ions in the higher vibrational states of theelectronic ground state. (a) The total energy of the ion needs to overcome thedissociation threshold to produce fragments. (b) Multiple photofragments from
ABn+ ion. (c) Jablonski diagram. S0 – electronic ground state (singlet); S1, S2 – singlet
excited states; T1 – triplet excited state; E – excitation; F – fluorescence; P –phosphorescence; IC – internal conversion; ISC – intersystem crossing. ............ 39

Figure 2.16

Messenger tagging examples. (a) DDDA2- tagged with up to 17 D2 molecules (traptemperature at 7 K). Different RF amplitudes are favored by different sizes. (b)[Ru(bpy)3]2+ tagged with up to 8 N2 molecules (trap temperature at 25 K). Inset
shows the n=4 adduct and the mass resolution m/∆m ≈ 2000. ........................... 42

Figure 2.17

Beam diagram of our current laser system (see text). ......................................... 44

Figure 2.18

Anatomy of Innolas Spitlight 600 Nd:YAG pump laser. ........................................ 46

Figure 2.19

Anatomy of the visible OPO and the SHG/SFM stage. ......................................... 49

Figure 2.20

The optical schematics of Sirah dye laser (adapted from Sirah Cobra-Stretch dyelaser datasheet27).................................................................................................. 50

Figure 2.21

The full timing sequence of an experiment with 10 Hz ion source. Pulses withinsignificant widths are presented as sticks. Channel numbers are shown on theleft and the functions are provided on the right. The diagram shows a full cycle fora single data point, which contains two periods, one with laser on (orange) andthe other with laser off (purple). Dotted lines illustrate synchronization hierarchy.
Red lines are handled by PG 1; blue by PG 2 (see text). Green lines present the RF
power supply and the green shadows indicate the uncertainty of T 2’-T2. QS is thexvii
result of E AND T4 and the actual trigger of the Q-switch. OS is the trigger for oneof the two oscilloscopes in an alternate fashion (see §2.6.2). ............................. 53
Figure 2.22

AND circuit for triggering pulses. .......................................................................... 55

Figure 3.1

Mass spectrum showing the formation of Cu+, [Cu-OH2]+ and [Cu-OHCH3]+. The
arrows point to the ions containing 63Cu only. ..................................................... 68

Figure 3.2

The photodissociation spectrum of [CuI(bpy)]+ at room temperature (upper) andthe fluorescence excitation spectrum of [ZnII(bpy)]2+ at 93 K in water and methanol(lower). In the upper panel, gray dots are raw data and black solid line is 50-point
sliding average. The data for [ZnII(bpy)]2+ were extracted from the work by Kotlicka
and Grabowski.34................................................................................................... 70

Figure 3.3

The structures for [Cu-L]+ (L = N2, D2, H2O, CH3OH and Cl) ................................... 72

Figure 3.4

Time-of-flight traces for electronic photodissociation of [Cu-L]+ complexes at
33870 cm-1 (L = N2, H2O and Cl). The ion signals on the right represent the parent
ions, while the smaller peaks are fragment ion signals. Only one fragment mass isobserved in each case. .......................................................................................... 73

Figure 3.5

Photodissociation spectra at 250 K for L = N2, D2, H2O, CH3OH and Cl monitoring
the loss of L. The spectrum of Cu+ at room temperature is included for reference.
The data points in the photodissociation spectra are the raw data; the full lines
are the same data smoothed by a 10-point sliding average. Spectra in the same
panel are rescaled for comparison and do not reflect relative intensity. ............ 74

Figure 3.6

Photodissociation spectrum of L = N2 with trap temperature at 70 K. The photon
energy axis is relative to the 0–0 band position of the ππ* electronic band, which
is found at 32580 cm-1. The full line represents experimental data, the stick
spectrum shows calculated totally symmetric (ground state) vibrations of [Cu-N2]+(see also Table 3.3). The 0–0 band is marked with a higher intensity for clarity, but
we note that we cannot make any quantitative statements on the expected band
intensities. ............................................................................................................. 77

Figure 3.7

Leading molecular orbitals for the two lowest energy transitions in [Cu-N2]+. The
upper panel shows the allowed transition to the ππ* state, the lower panel shows
the orbitals involved in the (symmetry forbidden) σπ* transition to the dark statecalculated 968 cm-1 below the bright ππ* state (see also Table 3.2). ................. 78

Figure 3.8

Photodissociation spectrum of [Cu-OH2]+ ions (monitoring the loss of water) at
50 K. ...................................................................................................................... 82

xviiiFigure 3.9

Leading molecular orbitals for the lowest energy transitions in [Cu-OH2]+ (seeTable 3.2 for calculated energies). ....................................................................... 83

Figure 3.10

Photodissociation spectrum of [Cu-Cl]+ ions (monitoring the loss of Cl) at room
temperature (top) and at 50 K (bottom). The data points in the photodissociation
spectra are the raw data, the full lines are the same data smoothed by 20-point
sliding average. ..................................................................................................... 85

Figure 3.11

Leading molecular orbitals for the two bright energy transitions in [Cu-Cl]+ (seeTable 3.2 for calculated energies). ....................................................................... 86

Figure 3.12

Structural template of the complexes under study. The ligand L represents a small
molecule (H2O, CO2, CH3CN, N2). .......................................................................... 89

Figure 3.13

Calculated minimum energy structures of [Ru-L]2+ for L = H2O and CO2 (the latterwith two different isomers). Carbon atoms are shown in brown, nitrogen in blue,
ruthenium in gold, oxygen in red, and hydrogen in white. .................................. 93

Figure 3.14

Photodissociation spectra of [Ru-L]2+ with L = H2O (top) and L = CO2 (bottom) at
180 K trap temperature. Dots are raw data; full lines are 30-point sliding averages.
The resolved features are labeled I through V (see also Table 3.7). The verticalcolumns represent transitions predicted by TDDFT calculations. The calculatedtransition energies are shifted by -1210 cm-1 for B3-LYP (open columns) and -2420
cm-1 for PBE0 (filled columns). .............................................................................. 95

Figure 3.15

Calculated minimum energy structures of [Ru-L]2+ for L = CH3CN and N2 (the latterwith two different isomers). Carbon atoms are shown in brown, nitrogen in blue,
ruthenium in gold, oxygen in red, and hydrogen in white. .................................. 98

Figure 3.16

Photodissociation spectra of [Ru-L]2+ with L = CH3CN (top) and at room
temperature (red) and at 30 K trap temperature (blue), and with L = N 2 (bottom)
at room temperature (red) and at 70 K (blue). Dots are raw data; full lines are 30point sliding averages. The vertical columns represent transitions predicted by
TDDFT calculations. The calculated transition energies are shifted by -1210 cm-1
for B3-LYP (open columns) and - 1210 cm-1 for PBE0 (filled columns). ................ 99

Figure 3.17

Light intensity dependence of fragment ion yield. The laser was set to thewavelength of peak absorption for each species. The full lines show linear fits;
their length indicates which data points were included in the fitting. The legend
indicates the ligand L. ......................................................................................... 101

Figure 3.18

Calculated molecular orbital levels for [Ru-L]2+ and bare Ru2+. ......................... 105

xix
Figure 3.19

Calculated orbitals contributing to transitions for L = H2O. Orbital numbers are
given as mentioned in Table 3.10....................................................................... 108

Figure 3.20

Calculated orbitals contributing to transitions for L = CO2. Orbital numbers are
given as mentioned in Table 3.11....................................................................... 110

Figure 3.21

Calculated orbitals contributing to transitions for L = CH3CN. Orbital numbers are
given as mentioned in Table 3.12....................................................................... 112

Figure 3.22

Calculated orbitals contributing to transitions for L = N2. Orbital numbers are given
as mentioned in Table 3.13. ............................................................................... 114

Figure 3.23

Calculated orbitals contributing to transitions for Ru2+. Orbital numbers are given
as mentioned in Table 3.14. ............................................................................... 116

Figure 4.1

General structure of [M(bpy)3]n+ ions. ................................................................ 125

Figure 4.2

Photodissociation spectra for the [Cu(bpy)3]2+. The grey points are raw data; thefull lines represent 10-point sliding averages to guide the eye. The vertical bars arecalculated A (red) and B (blue) transitions, shifted by -1610 cm-1. .................... 132

Figure 4.3

Photodissociation spectrum of [Ni(bpy)3]2+ (top) compared to that of [Cu(bpy)-N2]+(bottom).57 Note that the two spectra have slightly shifted wavenumber axes toemphasize their similarity. The points in the upper trace are raw data; the full lineis 5-point sliding average to guide the eye. ........................................................ 134

Figure 4.4

Photodissociation spectra of the [MII(bpy)3]2+ complexes studied here (M is notedin the corresponding panel). The grey points are raw data; the full lines represent
10-point sliding averages. The vertical bars are calculated A2 (red) and E (blue)transitions for each metal; they are shifted by a certain amount to match theexperimental results (see text). .......................................................................... 136

Figure 4.5

Photodissociation action spectrum of [Ru(bpy)3]2+·N2 at 25 K trap temperature(upper) compared to the UV/vis absorption spectrum of an aqueous solution ofRu(bpy)3Cl2 (25 M). The data points in the photodissociation spectrum are raw
data; the full line is 30-point slide average. The vertical bars are calculated A2 (red)and E (blue) transitions; they are shifted by 800 cm-1 to the blue to match theexperimental results. Distinct features are labeled by Roman numerals as
discussed in the text. .......................................................................................... 140

Figure 4.6

Zoom-in onto the MLCT band of the photodissociation spectrum of [Ru(bpy)3]2+·N2in Figure 4.5. The full grey line is the absorption spectrum in aqueous solution asshown in the lower panel of Figure 4.5, scaled to have the same MLCT peakintensity as the photodissociation spectrum. The calculated transitions (lower

xxpanel) are displayed as bars (full: Heully et al.59; open: this work). Both calculated
spectra is graphically offset by 800 cm-1 to allow easier comparison andassignment. Note the logarithmic scale for the oscillator strength. .................. 142
Figure 4.7

Comparison of TDDFT calculations (B3LYP/def2-tzvp) for [Ru(bpy)3]2+ (filledcolumns) and [Ru(bpy)3]2+·N2 (open columns). .................................................. 145

Figure 4.8

Photodissociation action spectrum of [Fe(bpy)3]2+·N2 at 25 K trap temperaturecompared to the UV/vis absorption spectrum of its aqueous solution adaptedfrom Ref.24 (top). The points in the photodissociation spectrum are raw data; thefull line is a 20-point sliding average. The lower panel shows A2 (red) and E (blue)transitions calculated using ecp-10-mdf and def2-tzvp basis sets for Fe. The results
are shifted by 3390 cm-1 to the red to better match the experimental results. Notethe logarithmic scale for the oscillator strength. ............................................... 146

Figure 4.9

Left: Photodissociation action spectrum of [Os(bpy)3]2+·N2 at 25 K trap
temperature with TDDFT calculation using B3LYP/def2-tzvp (unshifted). The data
points in the photodissociation spectrum are raw data; the full line is 40-point
sliding average. Right: Zoom into the MLCT band (gray points and green line) andcomparison with the absorption spectrum (gray line) in acetonitrile solution
measured by Shaw et al.61 (upper panel) and calculated spectra (lower panel, fullcolumns: Ronca et al.62; open columns: this work). The gray columns represent
singlet transitions and the black are transitions to the triplet manifold, enabled byspin-orbit coupling. Note the logarithmic scale for the oscillator strength. ...... 149

Figure 4.10

Molecular orbitals of [Mn(bpy)3]2+ involved in the transitions listed in Table 4.8...
.................................................................................................................. 154

Figure 4.11

Molecular orbitals of [Fe(bpy)3]2+ involved in the transitions listed in Table 4.9. ...
.................................................................................................................. 155

Figure 4.12

Molecular orbitals of [Co(bpy)3]2+ involved in the transitions listed in Table 4.10. .
.................................................................................................................. 156

Figure 4.13

Molecular orbitals of [Ni(bpy)3]2+ involved in the transitions listed in Table 4.11...
.................................................................................................................. 157

Figure 4.14

Molecular orbitals of [Cu(bpy)3]2+ involved in the transitions listed in Table 4.12. .
.................................................................................................................. 159

Figure 4.15

Molecular orbitals of [Zn(bpy)3]2+ involved in the transitions listed in Table 4.13. .
.................................................................................................................. 160

xxi
Figure 4.16

Molecular orbitals of [Fe(bpy)3]2+ involved in the transitions listed in Table 4.14. .
.................................................................................................................. 161

Figure 4.17

Molecular orbitals of [Ru(bpy)3]2+ involved in the transitions listed in Table 4.15. .
.................................................................................................................. 163

Figure 4.18

Molecular orbitals of [Os(bpy)3]2+ involved in the transitions listed in Table 4.16. .
.................................................................................................................. 165

Figure 5.1

Mass spectrum showing the formation of [Ru-OH2]2+·(H2O)n with instrument
parameters optimized for n = 3. Mass peaks marked with asterisk are unidentified.
............................................................................................................................. 176

Figure 5.2

Photodissociation action spectrum of [Ru-OH2]2+ at 180 K trap temperature.
Circles are raw data; the line is a 15-point sliding average. Vertical bars arecalculated transition energies (B3LYP/def2-TZVP), shifted by -1210 cm-1. ........ 178

Figure 5.3

Calculated minimum energy structures of [Ru-OH2]2+·(H2O)n showing the lowest
energy structure for n = 0 and 1 and several low-energy structures for n ≥ 2. Theirenergies relative to the lowest energy conformer at 0 K are shown in the brackets.
Carbon atoms are shown in brown, nitrogen in blue, ruthenium in gold, oxygen in
red, and hydrogen in white................................................................................. 180

Figure 5.4

The photodissociation action (observation time: green - 16 s; blue - 20 s) anddepletion spectra (red) of the bare aqua complex [Ru-OH2]2+. Slow beam action
spectrum shows up to 24000 cm-1. All three spectra can be considered to beequivalent within the signal-to-noise ratio of the experiment. ......................... 183

Figure 5.5

Data points are 𝑌𝑃 (𝜆 = 442 nm)/𝑃 as a function of 𝑒 − 𝜎𝜆 = 442 nm𝐹. Linear
fitting (red) returned 𝛼 = 1.00........................................................................... 185

Figure 5.6

Photodissociation spectra for [Ru-OH2]2+·H2O (left) and [Ru-OH2]2+·(H2O)2. Upper
panels: photodepletion spectra and calculated vertical excitation spectra(B3LYP/def2-TZVP, columns, shifted by -1210 cm-1). For [Ru-OH2]2+·(H2O)2, theopen columns represent the 2-A isomer and the filled columns represent the 2-B
isomer. Lower panels: photodissociation action spectra monitoring the yield of[Ru-OH2]2+ (open circles, grey full lines) and Ru2+ (filled circles, black full lines).
Circles are raw data points; the full lines are 15-point sliding averages. ........... 186

Figure 5.7

Photodissociation spectra for [Ru-OH2]2+·(H2O)3 (left) and [Ru-OH2]2+·(H2O)4(right). The top panels contain the photodepletion spectra and the lower panels
show the action spectra monitoring different photofragments as labeled. The dots
are raw data points; the full lines are 30-point sliding averages. ...................... 189

xxii
Figure 5.8

Band envelopes of all clusters. Experimental data (data points) were smoothed(red curves) with 200-point sliding average (100 points for n = 4). The smoothedcurves were interpreted as band envelopes. Arrows above the smoothed curves
are the band envelope peaks listed in Table 5.2. Error bars are estimated fromsmall variations in the peak position when using different gliding averages. The
solution spectrum is adapted from Ref.12 .......................................................... 191

Figure 5.9

Overview of TDDFT spectra for all isomers. Left: B3LYP/def2-TZVP; right:
B3LYP/def2-SV(P). ............................................................................................... 193

Figure 5.10

Summary of solvatochromic behavior of [Ru-OH2]2+·(H2O)n compared to bulk
aqueous solution12 (horizontal line). The center of gravity positions of the MLCT
bands are shown as filled blue squares, the envelope peaks as filled red triangles.
Results from TDDFT calculations are shown as open circles (def2-TZVP) and open
squares (def2-SV(P)). The dashed lines are meant to guide the eye. Numericalvalues are listed in Table 5.2, and error bars (where given) are determined fromGaussian error propagation of the errors listed in Table 5.2. ............................ 194

1

1
1.1

Introduction

Interest in organometallic compounds
Organometallic compounds are essential compounds in many fields of chemistry. They

are systems which raise a number of fundamental questions in coordination chemistry, such as
the nature of the chelating motif, metal-ligand interaction type and strength, effects of ligand
substitution, etc. They also bear great significance in practical terms. For example, manyorganometallic species are found to be important intermediates in synthetic processes; someothers are known for their excellent performance as catalysts.
Chemical engineers have devoted tremendous efforts to developing cost-effective
synthetic pathways and catalysts, but their methodologies have been largely empirical. In orderto modify a chemical reaction to make it follow a desired fashion, e.g. lower threshold, higher
efficiency, or product selectivity, one needs to understand how the reaction is affected orcontrolled by all parameters. For decades, research in the field of physical chemistry, or chemical
physics, has been dedicated to looking into these chemical problems using the methods ofphysics. Nevertheless, scientists have not been able to acquire insights with sufficiently
fundamental details until recently. Recent advances in experimental and computational methods
and techniques have opened many possibilities to investigate a variety of systems, which
hopefully will lead to a more thorough understanding of the mechanisms of important chemical
processes.
Driven by their potential applications and scientific significance, researchers have been
studying organometallic compounds for decades. Most experiments have been performed incondensed phase, i.e. in solutions or crystals. The most pursued questions center around2
stability, geometry and reactivity. In particular, laser spectroscopy, as a widely deployedexperimental method, has collected very useful information regarding the electronic andvibrational structure of a large number of organometallic compounds. Advanced computational
methods and capabilities allow for predicting the properties of unknown species. Among theefforts towards more fundamental understanding and more sophisticated exploitation oforganometallic compounds, the present work is concerned with the application of laser
spectroscopy to selected metal organic ions in vacuo. This approach can be expected to uncover
new details that cannot be observed in the condensed phase and serve as benchmark fortheoretical computations.

1.2

Why in vacuo?
Molecules in vacuo are isolated and free from short range interactions with solvent or

crystal lattice. Therefore, the properties of the system are unperturbed by its chemical
environment, which becomes an important advantage when one needs to learn about the
intrinsic properties of certain species. Traditional experiments in the condensed phase are often
easier from a practical point of view. For example, to measure an absorption spectrum of acompound, one only needs to dissolve it and put the solution in a commercial spectrometer after
synthesis and purification. However, there are inevitable drawbacks of working with solutions.
First, every solute is subject to solvatochromism once it is dissolved in a solvent. The magnitude
of solvatochromic shifts varies from a few to thousands of cm-1, depending on the polarity of thesolvent, the specific solute and the different absorption bands. Therefore, to obtain the intrinsic
spectrum of a certain species, such shifts need to be corrected. Solvatochromism is just one of

3
the many side effects caused by the interaction between the solute and the solvent. Anotherproblem in solution is speciation, since many chemical species may coexist in a solution. For
example, solvating the ionic compound AB in water may actually lead to a variety of ions inaddition to A+ and B-, such as AH+, AOH+, A(H2O)+, A(H2O)2+, AB2- and many more. As a result, a“traditional” UV/vis absorption measurement records the collective response of all existentspecies, but may not be able to yield a spectrum of just one particular species.
One particular aspect concerning spectroscopy is the peak width. It is desirable to observewell-resolved, sharp spectral features, so that it is possible to assign individual transitions.
However, spectra taken in solutions are often broad and featureless, which hinders detailed
assignment. One factor causing broadening is thermal excitation, resulting in hot bands, eventhough experiments on frozen solutions can be used to suppress this effect. An alternative
medium that compensates some of the drawbacks of solutions is to use diluted crystals which
can be cooled down to very low temperatures. This method has the potential to resolve some ofthe speciation and temperature issues in solutions but synthesis can be challenging. In addition,
it is impossible to grow a crystal without impurities to a size that allows spectroscopic
examination, and the phonon modes of crystals are often observed in parallel with otherabsorption features, adding unwanted components to the spectra. Furthermore, because
solvent- or lattice-assisted de-excitation often dominates over the intrinsic dynamics of thesystem under study, the width of the peak obtained in the condensed phase may not represent
the intrinsic photophysical properties of the species in question.
New experimental approaches need to be explored to circumvent the problems
mentioned above, and experiments in vacuo are a promising alternative. Many techniques can

4
be applied to ions in vacuo, which opens many possibilities of experimental control. For example,
buffer gas cooling can be used to cool ions to a temperature as low as the boiling point of thebuffer gas. Mass spectrometry is a powerful tool to analyze and select gas-phase ions by masscharge ratio, nearly eliminating speciation problems. To generate ions in the gas phase, one may
choose from a variety of techniques, such as electrospray ionization, laser ablation, electron
attachment, etc., based on the nature of the ions under study. Certain species are unstable ornon-existent in solutions or solids, such as uncommon charge states, radicals, or clusters, but it
is possible to produce them in vacuo. In summary, experiments on mass-selected, cryogenically
prepared ions in vacuo can serve as a complement to more conventional measurements,
providing researchers with opportunities to study unperturbed, well-defined ionic systems underideal conditions that are often unavailable in solutions or solids. Many new discoveries have been
made since cryogenic ion spectroscopy has been applied to systems that have already beenthoroughly studied in more “traditional” experiments.

1.3

In this thesis
The theme of my work is photodissociation spectroscopy applied to electrosprayed,buffer-gas cooled and mass-selected ions. This study focuses on the UV and visible spectral
ranges, investigating the electronic states of the ions so prepared. The experimental apparatus ishome-built and a large part was designed and constructed as part of my graduate work. The
apparatus and the relevant techniques will be described in detail in Chapter 2. The next chapterswill introduce studies on several series of metal-polypyridine complex ions. An organometallic
complex ion is composed of one or more metal atoms and several ligands. The targets in this5
study are chosen specifically to explore the role of the ligands (Chapter 3) and the role of themetal (Chapter 4) by changing one unit (ligand or metal) at a time. Another interesting topic
related to these complex ions is microsolvation, where the ion is solvated by only a few solvent
molecules. It can be conceived as an intermediate state between the gas phase and thecondensed phase. One can perform the experiments in vacuo on the solvated systems to explore
the role of solvents, and to follow solvation one molecule at a time - one example will bepresented in Chapter 5. The last chapter contains concluding remarks and outlooks.

6

2

Methods

This chapter has been reproduced in part with permission from Shuang Xu, Samer Gozem, Anna
I. Krylov, Casey R. Christopher, J. Mathias Weber, Ligand Influence on the Electronic Spectra of
Monocationic Copper–Bipyridine Complexes, Physical Chemistry Chemical Physics 2015, 17 (47),pp.31938-31946. Copyright 2015, Royal Society of Chemistry.1

2.1

Overview
The goal of the present work is to measure absorption spectra of molecular ions in thegas phase at low temperatures. The whole experiment can be decomposed into three major
steps: ion preparation, mass selection and photodissociation spectroscopy, as described in a
flowchart shown in Figure 2.1. Since the ion source used in the present work is new, it will be
described in detail in this chapter.

Ion preparation•Electrospray ionization(A-B)•Cryogenic ion trap
(F-G2)

Mass selection•Wiley-McLaren time-offlight mass spectrometry(G3-I)

Photodissociation
spectroscopy•Tunable light source(laser)•Fragment detection andanalysis(L-K)

Figure 2.1
This flowchart shows the three major steps of our experiment (main blocks, blue).
Listed in the appended blocks (white) are the technologies utilized to implement each step. The
letter/number symbols in the parentheses refer to the parts of instrumentation as labeled in
Figure 2.2.

7

Figure 2.2
Schematics of the experimental apparatus. A - electrospray needle; B - desolvation
capillary; C - skimmer; D - octupole ion guide; E - quadrupole bender; F - helium cryostat; G - iontrap and accelerator assembly; H - x-y deflectors and Einzel lens; I - mass gate; J - reflectron; K microchannel plate; L - pyroelectric joulemeter. The inset zooms in on the trap region. This figure
is adapted from Ref.1

We use electrospray ionization to prepare ions in the gas phase, then cool the ions to lowtemperatures in a cryogenic ion trap. Next, we select the ion species of interest by its mass-tocharge ratio using time-of-flight mass spectrometry. Finally, we measure the photodissociation
spectrum of the ion species by tuning the wavelength of the laser and monitoring the laser
induced change of ion signals (yield of fragments or loss of parent ions). To perform all thesefunctions, the instrumentation encompasses the following major parts, as shown in Figure 2.2:
the ion source (A-E), the cryogenic ion trap (F-G), the mass spectrometer (G-K) and the laser
system. The following paragraph provides a more detailed description of the fundamental

8
processes from the perspective of ions. Specific technical details are explained in individual
sections featuring different parts of the apparatus.
We use electrospray ionization to extract the ions of interest from solution (§2.2.1). Afterelectrospraying, ions enter the first vacuum chamber through a heated desolvation capillary. The
ions are accumulated into ion packets in an octupole ion guide and trap in the second differential
pumping chamber and then directed by octupole ion guides through the third and the fourth
differential pumping stages until they reach the cryogenic ion trap (§2.2.2).
The cryogenic ion trap is a 3-dimensional quadrupole ion trap (Paul trap) and is mounted
on the cold head of a closed-cycle helium cryostat. Inside the trap the ions are cooled by collisions
with a buffer gas pulse (§2.2.3). The lowest ion temperature that has been achieved in ourapparatus is estimated to be around 30 K. After some time (typically 95 ms) for storage andcooling, all ions in the trap are ejected into the accelerator of the time-of-flight mass
spectrometer.
Our time-of-flight mass spectrometer consists of an accelerator, a pulsed mass gate anda reflectron, and can be divided into two stages (§2.3). The first stage is between the accelerator
and a pulsed mass gate located at the first space focus, and is used for mass selection of thetarget ions, while the second stage containing the reflectron is for mass anlaysis of the fragments.
The mass gate is a device that can either deflect the ions from their normal trajectory (closedmode) or let the ions pass (open mode). It is programmed to be open only at the time when theions under investigation arrive (§2.3.3). Immediately behind the mass gate is the laser interaction
region, where the ions are irradiated by a laser pulse. The laser pulse is timed to intercept thefocused and mass-selected ions after they are transmitted through the mass gate. The9wavelength of the laser radiation is widely tunable (220-2500 nm), realized by a combination ofa beta barium borate based optical parametric oscillator pumped by an Nd:YAG laser and afrequency conversion stage (§2.5).
We are interested in the absorption spectra of mass selected ions, and we use
photodissociation spectroscopy to obtain information on these spectra (§2.4). If an ion is excitedby a photon, and fluorescence can be neglected, the absorbed photon energy will be eventuallyredistributed to the vibrational modes of the ion. When certain conditions (§2.4.2) are met, thevibrationally hot ion can undergo unimolecular decay and fragmentation, resulting inphotofragment ions with different mass-to-charge ratios. The photofragment ions are massanalyzed by the second stage of the mass spectrometer. Here, a reflectron is used to separate
the undissociated parent ions and the photofragment ions (§2.3.4). A dual microchannel plate
detector is used to detect the ions (§2.3.2).
Typical experimental procedures start with optimizing the parent ion intensity. When themass gate is kept open, the entire mass spectrum can be used to analyze the components of theion packet out of the ion trap. The mass spectra have a typical mass resolution (m/∆m) greaterthan 2000, enough to distinguish 1/4 atomic mass unit in the mass range we typically work with(mass-to-charge ratio ≤ 500). One can conveniently watch the intensity change of different ionson the mass spectrum when tuning the source and trap parameters and find the optimal
combination for the target ion. After maximizing the signal for the target ion, we need to searchand optimize the photo-induced signal. This is usually done by fixing the laser at a wavelengththat the target is most likely to absorb, then adjusting the laser pulse timing and the ion trajectory
to achieve optimal spatial and temporal overlap between the ion packet and the laser pulse, so10that the yield of photofragments or the loss of the parent ions is maximized. Photodissociation
spectra are acquired by varying the photon energy and monitoring the photo-induced changes inparent or fragment ion signal as well as the laser pulse energy. Since in this laser system eachcrystal configuration has a limited tunable range, change of crystals may be necessary to cover
the desired spectral range. A full spectrum spanning over a few hundred nanometers is usually aconcatenation of several overlapping scans with different crystal configurations (§2.5.3).
Along with our experiments we use the Turbomole2,3 program suite (v6.2) to perform
quantum chemistry computations to assist the interpretation of our experimental results. The
methods are based on density functional theory4 and we will describe the details for each study
in its designated chapter.

2.2

Ion preparation

2.2.1 Electrospray ionization source
2.2.1.1 Principle and instrumentation
Electrospray ionization (ESI) is the most suitable method for our experiment because ourtargets, organometallic ions, are usually soluble but unstable under harsh conditions that often
come along with other methods such as laser ablation. ESI was invented as a soft method to
extract fragile solute ions from solution5 and often used with mass spectrometry to analyze theproducts from the extraction. This approach was first demonstrated by Dole.6 Fenn developed
this method for biological macromolecules in the late 1980s and was awarded the 2002 Nobel
Prize in Chemistry.7 The principle of ESI is based on the fact that the total charge that a droplet
of a certain size can carry has an upper limit. If the charge on a droplet exceeds this limit, or in11other words, the size of the droplet falls below the minimum that can carry the resident charge,
the droplet will fissure into smaller droplets. The fundamental mechanism is the competition
between the surface tension that holds the droplet together and the Coulomb repulsion thattends to break the droplet apart. In 1882, Lord Rayleigh investigated the case of a spherical
droplet theoretically. 8 By balancing the two effects, he derived the critical condition known as
the Rayleigh limit
𝑞 2 = 8𝜋 2 𝜀𝛾𝐷3
which states that q, the charge a spherical droplet with diameter D can carry scales with 𝐷3/2 .
The prefactor depends on the permittivity of the environment 𝜀 and the surface tension
coefficient of the solvent 𝛾. However, it has been observed in reality that a charged droplet
fissures before reaching the Rayleigh limit because deviation from a spherical shape due tomechanical deformation lowers the maximum charge that the droplet can carry.9
A cartoon showing our basic setup together with the microscopic mechanism (positive
ion mode in this example) is presented in Figure 2.3. The spraying needle for ESI is a commercial
assembly (Analytica of Branford). Silica capillary tubing (75 m ID, 193 m OD, Polymicro
Technologies) is threaded through the spraying needle and extends 1-2 mm out of the needle tip.
Dry N2 gas (30-40 psi) is fed through the hollow space in the spray needle, serving as nebulizing
gas around the tip. The solution containing the ions under study is pumped to the spraying needle
at a rate of 25-75 µL/h by a syringe pump (New Era, model NE-1000) and flows through the silica
capillary tubing to the tip of the spraying needle. The spraying needle assembly is biased with a
DC voltage of ±3-4 kV against the counterelectrode, which is the desolvation capillary in our case.
At the exit of the silica capillary tubing, a cone-shaped jet known as the Taylor cone is formed

12
due to the strong electric field at the tip of the spraying capillary10 (see Figure 2.3). Droplets
containing a net excess of either positive or negative ions (depending on the polarity of theneedle bias) break away from the tip of the Taylor cone and fly towards the desolvation capillary
under the effect of the electric field; this process is aided by the nebulizing gas flow. Solvent starts
to evaporate and the droplets are shrinking and approaching the Rayleigh limit. Some droplets
may already fissure before reaching the desolvation capillary.

Figure 2.3
Illustration of our ESI setup and microscopic mechanism of the process in positive
ion mode (see text).

13
The desolvation capillary is made of stainless steel and is 58.4 mm long. It has an ID of
0.5 mm and serves as a duct for ions from ambient pressure to the first vacuum chamber(10-1 mbar). It is housed in a cylindrical copper mount which is heated to about 80 °C with a
cartridge heater (OmegaDyne CSH-1011001, 100 W) to facilitate desolvation inside the capillary.
A type K thermocouple and a temperature controller (Omega CN9000A) are used to monitor andregulate the temperature. Because the front end of the desolvation capillary is directly exposedto the spray, it can be coated or even clogged by deposition of the solute over time. This leads tounstable or vanishing ion signals, so it must be cleaned and flushed every few hours to restore
the ion signal. The rate of the deposition is proportional to the amount of the solute dispensed
per unit time, i.e. the syringe pumping rate times the solute concentration. Therefore, thecapillary will need to be cleaned more frequently if higher pumping rates or concentrations areused.

2.2.1.2 Performance of ESI
The performance of ESI has two measures – ion beam intensity and stability – anddepends on many parameters. This section summarizes my observations from my own practiceand discusses some important parameters to be adjusted to optimize the performance of oursetup. More general and systematic discussions on ESI can be found in literature. 5,7,9,11–14
Solvent. As the starting point of ESI, the properties of the solution play an important role.
Generally, better performance can be achieved by using solvents with higher volatility, higher
polarity and lower viscosity. In most of the experiments in this work, we used pure methanol ora methanol-water mixture (𝑣: 𝑣 = 9: 1). The choice of solvent may be governed by the properties

14of the solute or other considerations. For example, if the solute is an oxidant, or if methanol canbind to the ion forming unwanted adducts, acetonitrile may be used in lieu of methanol.
Solute concentration. The proper concentration of the solution for ESI depends on thesolute. The typical range we have been working with is 0.5-5 mM. Many organometallic
complexes are easy to electrospray. For certain species such as [Ru(bpy)3]2+ (bpy=2,2’-bipyridine)
one can use a concentration as low as 50 µM and still obtain good ion beam intensity. This
concentration can be a rough guideline for deciding the amount of similar species when theyneed to be synthesized. Higher concentrations may increase ion beam intensity, but it canaccelerate the deposition of solute on the desolvation capillary. Therefore, we prefer low
concentrations and will increase the concentration only when the signal can no longer be
improved by other parameters but is still insufficient.
Solution pumping rate. Although increasing pumping rates may improve the ion signal, it
does more harm than good. Doubling the rate may increase the ion signal by only 30%, but
exacerbates the deposition problem on the desolvation capillary and sometimes can cause
electric arcing between the ESI electrodes. Therefore, we typically pump the solution no fasterthan 40 µL/h, except if absolutely necessary.
Nebulizing gas pressure. The pressure of the nebulizing gas is critical to the stability of
ESI. The optimal pressure, however,is not significantly influenced by other parameters, and wehave been using a value between 38-40 psi for all our experiments.
Electrospray voltage. ESI performance usually is not very sensitive to the magnitude ofthe electrospray voltage. The choice depends on the polarity of the solvent and the stability of
the ions. If the target ions are fragile, lower voltages are favored in order to better preserve the15ions. Typical functioning voltage is around 3 kV, but we have used values throughout the range
2-4 kV.
Position of the spray needle. The spray needle assembly is mounted on a three-axis
translation stage with insulators to allow adjusting and optimizing its position relative to thedesolvation capillary during operation. The distance between the spray needle and the capillary
determines the electric field in between and is typically about 3-4 mm at 3 kV spray voltage. A
too short distance can result in arcing and destruction of the target ions.
Temperature of the desolvation capillary. The temperature of the desolvation capillary
is set close to the boiling point of the solvent (ca. 80 °C, depending on the actual solvent).
Lowering the temperature decreases the productivity but is necessary if the target ions are heatsensitive.

2.2.2 Ion guides and pre-trap ion optics
Since the ions are sprayed at ambient pressure, a series of differential pumping stages areneeded to reach the high vacuum required for time-of-flight mass spectroscopy (10-6 - 10-7 mbar).
Our apparatus has four differential pumping stages leading to the ion trap and three stages fromthe ion trap to the flight tube. The pressure, approximate mean free path and pumping device ofeach chamber when an experiment is running are tabulated in Table 2.1.

16
Table 2.1

Specifications of each differential pumping chamber in operation.

chamberpressure(mbar)

mean free path
(m)

I

1

10-5

II

0.1

10-4

III

10-4

0.1

IV
“the trap chamber”

10-6

10

V

10-7

100

VII
“the flight chamber”

10-8

1000

Figure 2.4

pump
65 m3/h rotary vane pump,
Leybold Trivac D65 B
65 m3/h rotary vane pump,
Leybold Trivac D65 B
685 L/s turbomolecular pump,Pfeiffer HiPace 700
1100 L/s turbomolecular pump,
Leybold Turbovac 1000 C
230 L/s turbomolecular pump,Pfeiffer TMU261
520 L/s turbomolecular pump,Pfeiffer TMU521

Elements from ESI to the ion trap (see text).

The section of the apparatus from the ESI source to the ion trap is provided in Figure 2.4.
The first two chambers are separated by a stainless steel skimmer (1.5 mm aperture) locatedabout 5 mm downstream from the exit of the desolvation capillary. To maximize the number of17ions entering the skimmer, a small tube lens (3 mm long) is inserted right after the desolvation
capillary to focus the ions. Usually a gentle gradient of electric potential is created to limit the ion
speed and prevent collision-induced dissociation as the pressures in the first and second chamber
are still relatively high.
From the second differential pumping chamber to the ion trap, the ions are guided by asequence of four octupole ion guides across the chambers. Octupole ion guides are devices thatconsist of eight metal rods placed in parallel with equal spacing in a circular pattern (seeFigure 2.5).

Figure 2.5
Octupole ion guides. All rods have a diameter of 3 mm and placed on a circle of
9 mm in diameter. Adjacent rods are driven by 10 MHz AC signal of opposite phases, forming aradial potential in the cylindrical space.

18
When each rod is driven with an AC signal (10 MHz) with opposite phase to its neighborrods, an effective potential is created along the radius, restricting the motion of ions in thecylindrical space surrounded by the rods. The performance of octupole ion guides has been
experimentally and theoretically investigated by Tosi, Jones and Gerlich.15–17
All of our octupole guides and their AC drivers were built by the machine shop and theelectronic shop at JILA. Each rod has a diameter of 3 mm, and all eight rods enclose a cylindricalvolume with a diameter of 9 mm, as shown in Figure 2.5.
The four octupole guides have different lengths (see Table 2.2) and therefore are
powered by individual impedance-matched AC drivers. The AC amplitude and DC bias of each
octupole can be tuned for the best performance. Typical values of the AC amplitude for each
octupole guide are listed in Table 2.2.

Table 2.2

Lengths and typical RF amplitudes of all four octupole ion guides.
octupole
length (mm)peak-to-peakamplitude (V)III
139 313

III
304

IV
39

480 440240 500

The ions are guided by octupoles in both the second and the third chambers. These twochambers are separated by a skimmer that is identical to the one between the first two chambers.
These two skimmers together with the octupole guide in the second chamber act as a pre-trap
for ions as shown in Figure 2.6.

19

Figure 2.6
The scheme of the pre-trap in the second differential pumping chamber. The
skimmers are pulsed to generate loading (red) and unloading (blue) potentials to form ion
packets from a continuous flow of ions (green).

The skimmers are pulsed to create trapping and ejection potentials along the axis of theoctupole guide to load and unload ions. During the loading period the ions from ESI continuously
flow into the octupole guide zone and get trapped by the axial potential, while during theunloading period all trapped ions are released as an ion packet. The purpose of the pre-trap is toprepare ion packets and to prevent ions from entering the cryogenic trap in a continuous flow.
The third and fourth chamber are separated by a gate valve and an aperture with 9 mm
ID. Inside the fourth chamber the ions go through the third octupole guide before reaching ahome-built quadrupole ion bender, which can deflect the ions by 90 degrees either towards theion trap or towards a channel electron multiplier (CEM) detector (Sjuts Optotechnik GmbH, KBL
10RS/90) mounted on the opposite side. The purpose of the bender is to separate the neutral
gas beam from the first few vacuum stages from the ions. The CEM can be used to detect ions
before the trap injection ion optics and to test and troubleshoot the ion source and transmission
through the octupole up to this point.

20
Between the bender and the ion trap, another short octupole guide, a small Einzel lensand an additional aperture are used to inject the ions into the Paul trap.

2.2.3 Cryogenic ion trap
2.2.3.1 Trap setup
Our ion trap and its power supply were purchased from Jordan TOF Products. It is a 3D
quadrupole trap, also known as Paul trap. It consists of three electrodes – a central ring electrodeand two hyperbolic end caps (G1/2), which are spaced by ceramic rings, as shown in Figure 2.7.

Figure 2.7
Schematic of the ion trap assembly. The trap is mounted on the 4 K cold head of aclosed-cycle helium cryostat via a sapphire plate and OFHC copper mounts. A radiation shieldattached to the 40 K stage of the cryostat encloses the trap assembly. The acceleration unit (G35) of the time-of-flight mass spectrometer is coupled with the ejection ion optics of the trap(G3a).

The trap is mounted on the cold head of a helium cryostat (Sumitomo F-70L, 1.5 Watt at
4.2 K), with three layers sandwiched in between. The layer closest to the trap is a 1-mm-thick

21
sapphire substrate for electric insulation from the cold head, while maintaining good thermal
contact. The other two layers are mounting and adapter plates made of OFHC copper. The trap
is enclosed in a radiation shield which is also made of OFHC copper and is electrically grounded.
It has dimensions of 66.6 mm × 95.2 mm × 90 mm (length × height × width) and is attached to
the 40 K shroud of the cryostat. There is an aperture with 16-mm diameter in both the entrance
and the exit wall of the radiation shield. Two tube lenses are used to optimize ion transportationin and out of the trap . At the trap entrance, the tube lens is 12.7 mm long and has an ID of
12.7 mm. The tube lens at the trap (G3-a) exit is 15.2 mm long and has an ID of 11.5 mm, and its
upstream end is covered with a fine wire mesh (88.6% transmission). All electric connections
inside the radiation shield use gauge 34 magnet wires, except for the ring electrode of trap, whichuses gauge 28 to avoid resistive heating since it is driven by high-amplitude radio frequency. Allwires inside the radiation shield are wound around the cold head inside the shield. They arewound around the 40 K shroud as well to limit heat flow onto the trap. All cold units are coatedwith Apiezon N grease to improve thermal contact.
There are two silicon diode temperature sensors near the trap. One (Lakeshore DT-670CU-1.4L) is embedded in the cold head; the other (Lakeshore DT-670-SD) is attached near thebottom of the trap. Both sensors are used to enable measurement of the temperatures during
operation. The temperature of the trap is controlled by a Lakeshore 336 Temperature Controller.
To slow down and cool the ions, the ions are decelerated by the DC voltages on theentrance tube lens and the entrance end cap of the trap. In addition, buffer gas is pulsed into thetrap by a general valve (Parker General Valve Series 99) via a ceramic tubing and a notch on the22first ceramic ring. The backing pressure of the buffer gas supply is 40 psi and the average pressurein the chamber is usually kept at several 10-6 mbar.
After the ions are cooled in the trap for a certain period of time, they need to betransferred from the trap to the time-of-flight mass spectrometer and accelerated. This isrealized by implementing extended electrodes on and outside of the radiation shield (G3-b/c).
They are both thin (0.64 mm) plates, each with a 12.7-mm orifice. G3-b is mounted on the heatshield while G3-c is outside the heat shield and coupled with the accelerator units of time-offlight mass spectrometer (G4/5). These electrodes are driven with the same voltage as the exiting
tube lens (G3-a) and act as an elongated lens (G3). The end caps (G1/2) are operated in concert
with G3 to create an electric field to eject the ions (see §2.2.3.2 for details).

2.2.3.2 Operation and performance
The operating principle of a quadrupole ion trap is described in detail in the literature.18,19
In brief, the central ring electrode is driven by a radio frequency (RF) signal with a DC bias,
creating an effective 3D potential well inside to trap the ions. The RF amplitude and the DC bias
determine the shape of the potential and are adjusted to optimize the ion signal of different
species in each experiment. In our setup, the ring electrode is driven with 1 MHz RF by the power
supply provided by the trap manufacturer. The DC bias is applied via this power supply as well.
The peak-to-peak amplitude of the RF signal is tunable between 0-4 kV.
The operation of the ion trap is somewhat similar to the pre-trap. It can be divided into
two steps: injection/trapping and ejection. For a 10-Hz trapping cycle, the ions are trapped for23
ca. 95% of the period (ca. 95 ms) while ejection takes only a few microseconds. Figure 2.8 shows
the timing scheme of a single trapping cycle.

Figure 2.8
Operation of the ion trap on a time axis. At T1, buffer gas is pulsed into the trap
and the injecting period starts with RF on and an uphill potential inside the trap. After ca. 95 msof accumulation, at T2 a signal is sent to switch off the RF and the trap ejects with a downhill
potential. The red and blue lines represent the DC potential energy the ion experience. The actual
AC trapping potential (present only during loading) is not shown.

In the following description, we will refer to the electrodes as denoted in Figure 2.8. At
T1, the general valve is open to release a short pulse (a few ms) of buffer gas. Meanwhile the RFof the ring electrode is on and electrodes G1/2/3 are biased to create an uphill potential for theincoming ions. The ions are decelerated by the electric field (ca. 30 V/cm) and cooled by collisions
with buffer gas molecules if the trap is at low temperature. After storing and cooling the ions forca. 95 ms, a trigger pulse is sent to the RF power supply to switch off the RF signal, terminating
the loading period. For ejection, the voltage configuration of G1/2/3 is flipped to create adownhill potential (ca. 200 V/cm) so that the ions in the trap can be ejected towards the next

24stage. This operation is delayed by 0.5-1 µs after the switching off the RF and lasts for 4-8 µs.
After the trap is depleted, the RF and the uphill potential inside the trap are resumed to set theconditions for injection in the next cycle. The actual timing scheme is slightly more complex andwill be discussed in more detail in §2.6.1.
There are three major factors influencing the ion trapping performance - the RF amplitude,
the DC bias and the buffer gas pressure. The optimal combination of these factors depends on
the ion species. In general, higher RF amplitudes and buffer gas pressures are needed for ionswith greater mass-to-charge ratio. However, such settings can lead to RF induced heating of theions and and can destroy fragile species. To vary the input amount of buffer gas one can adjust
either the duration or the amplitude of the pulse signal that drives the general valve. The only
indication of the buffer gas input is the average ambient pressure inside the chamber, which isusually held on the order of 10-6 mbar.
The ion cooling efficiency depends on the buffer gas type and pressure as well as the ion
storage time. Longer storage times allow better cooling, which is a natural conclusion and can beshown qualitatively by comparing the electronic spectra of crystal violet at 20-Hz cycles (45 ms
storage time) vs 10-Hz cycles (95 ms storage time). While the trap temperature is the same (10K), significant hot bands arise when the storage time is short, as shown in Figure 2.9. To ensurethat all ions in an ion packet spend the same amount of storage time inside the trap, the packet
needs to be formed before it enters the trap. To achieve this goal, a pre-trap is implemented
using the skimmers and the octupole guide in the second differential pump stage (see §2.2.2).

25

Figure 2.9
The photodissociation spectrum of crystal violet anion with different ion storage
times: 95 ms (red) and 45 ms (blue). Ion trap is held is at 10 K in both cases. Significant hot bandto the left the rising edge emerges when the storage time is shorter.

The choice of buffer gas is also important when cooling ions. When the trap is cold, it isnormally good practice to use a buffer gas that will not condense in the trap. For example, helium
is mostly used in our experiment at 10 K. However, there are exceptions when we need to attach
messenger tags or solvent molecules to ions in the trap. In such case, nitrogen, deuterium orwater vapor is used even if the trap temperature is below the freezing point of the gas (see §2.4.3).

2.2.4 Modifying ions in the trap and the pre-trap
While the ions are cooled in the cryogenic ion trap, they are allowed to interact withbuffer gas, providing the possibility of producing new species. Messenger tagging is usually
performed in the cryogenic ion trap (see §2.4.3). If solvent vapor is used as the buffer gas, one

26
may be able to generate solvated species in the gas phase (see Chapter 5). Such processes usuallyrequire low temperatures because of the decreasing binding energies as the number of attachedsolvents grows. However, the lowest possible ion temperature is limited due to the condensationof the buffer gas being used. To alleviate the conflicting requiremens for adduct formation andthe target temperature to which the adducts need to be cooled, we can separate these twoprocesses by using the pre-trap to form the adducts first and then transfering the adducts to thecryogenic trap to cool them. For example, in the study of ruthenium complexes (§3.3), theacentonitrile adduct was formed in the pre-trap by leaking acentonitrile vapor into the vacuum
chamber containing the pre-trap. Afterwards, we were able to cool the ions in the main trap withtemperature held at 30 K. Although this specific acentonitrile adduct was ready to form at room
temperature, other adducts may require lower temperatures. Therefore, to broaden the rangeof species to which this method is applicable, we plan to redesign the pre-trap and to integrate
it with a liquid nitrogen cooled dewar and temperature control.

2.3

Mass selection and mass analysis

2.3.1 Reflectron time-of-flight mass spectrometer
The theory of time-of-flight mass spectrometry (ToF-MS) can be easily derived using
Newtonian mechanics. Consider a case where an ion with mass-to-charge ratio 𝑚/𝑧 isaccelerated by an electric field with potential difference 𝑈. The final speed that the ion acquires
will be
𝑣=√

2𝑈
𝑚/𝑧

27
Suppose the ion flies a distance of 𝐿, the total time of flight will be

𝑡=

𝐿
𝑚/𝑧
= 𝐿√
𝑣
2𝑈

Obviously, by measuring the time of flight, one can distinguish ions with different mass-to-charge
ratios. However, because the ions are initially spread in a certain volume in space, 𝐿 and 𝑈 are
not same for all ions, which leads to an uncertainty in the time of flight and impairs the mass
resolution. To alleviate this problem, Wiley and McLaren developed a dual stage accelerator
which can spatially focus the ions and reduce the uncertainty in 𝑡.20,21
Our time-of-flight mass spectrometer follows Wiley-McLaren’s design and is modified
from a commercial angular reflectron ToF-MS (Jordan TOF Products D-850). The acceleration
region is inside the trap chamber and immediately follows the ion trap ejection electrodes (seeFigure 2.7). The accelerator electrodes (G4/5) are coupled with the last ejecting electrode (G3-c)of the ion trap, forming a dual stage accelerator in together. G4 is a metal plate of the samematerial and dimensions as G3-c except that the orifice is covered by a wire mesh (90%transmission). G5 is a combination of a plate like G4 and a 265-mm-long tube (44.5 mm ID).
After an ion packet is ejected from the trap it drifts through G3 within a few microseconds.
When the ion packet reaches the acceleration zone, G4/5 are pulsed to high voltages toaccelerate the ions. However, because the ion packet contains ions of different mass-to-charge
ratios but they are all ejected by the same electric field, different ions will arrive at theacceleration region at slightly different times.
When the acceleration field is turned on after a certain delay relative to the ejection,some ions have already passed the acceleration zone while some have not arrived yet. Only

28
those with certain mass-to-charge ratios are in the proper acceleration zone. As a result, the final
mass spectrum shows only a window of mass-to-charge ratios.
There is an alternative that allows the mass spectrum to show all components in the trap
in a single shot. If the end caps of the Paul trap are used as acceleration electrodes, all ions in
the trap will be accelerated at the same time. This scheme also improves the mass resolution
owing to the absence of the drifting section. But because the buffer gas is pulsed into the trap
and the local pressure inside the trap is estimated to be four orders of magnitude higher thanthe pressure in the surrounding chamber, the collision rate is much higher. As a result,acceleration from the trap may heat and even dissociate the target ions. Since we are mostlyinterested in spectroscopy at low temperatures and the resolution of the mass spectrometer is
not our priority, this alternative is only used for initial characterization of the mass spectrum atroom temperature.
Ions with the same mass-to-charge ratio can be at slightly different places in theacceleration zone when the voltages are pulsed. Using Wiley-McLaren’s scheme, the voltages on
the accelerator electrodes are configured to spatially and temporally focus the ions at the laserinteraction region to maximize the number of ions that can be irradiated. A removablemicrochannel plate detector is located at the laser interaction region to check the quality of thespace focus (see Figure 2.11 in Ref.22). For cations we typically use -325 V and -3800 V for G4 andG5, respectively. The power supplies for G4 and G5 are products of FUG (HCN35-6 500). The
pulsing switches are Willamette MHVSW-008V for G4 and Behlke GHTS 60 for G5. The Willamettehigh voltage switch is used with a customized circuit (shown in Figure 2.10) to improve the pulse
quality.

29

Figure 2.10

Adaptor circuit for the Willamette high voltage switch.

Once the ion packet completely enters the long tube of G5, all acceleration units arepulled to ground potential, so that the ion packet will not experience any electric field when it
exits G5. Between the trap chamber and the flight chamber is the fifth differential pumping
chamber, which houses a set of ion optics to steer and focus the ion packet. It includes a pair of
X-Y deflectors and an Einzel lens, both home-built. The deflectors are two pairs of parallel metal
plates (45.7 mm long, 30.5 mm apart) and the Einzel lens is a sequence of three cylindricalelectrodes (45.7 mm long, 30.5 mm ID).
In the flight tube, the pressure is at 10-7 - 10-8 mbar, corresponding to a mean free pathof 100-1000 meters, so the ions should not encounter any collisions during their ca. 2.5-meterflight. The ions are mass selected by mass-to-charge ratio by a pulsed mass gate (see §2.3.3) sothat only the ions of interest can interact with the laser.23

30
At the end of the flight chamber a dual-stage reflectron is installed. The main purpose of
the reflectron in our apparatus is to separate the parent ions from charged and uncharged
photofragments, but it also improves the resolution of the mass spectrometer (see §2.3.4 andFigure 2.11). Because the accelerator focuses the ions to the laser interaction region rather thanthe detector, the same ions will spread again beyond the laser interaction region and result in a
broader peak on the mass spectrum. The reflectron can be used to correct this spreading by
refocusing the ions to the final detector as shown in Figure 2.11(a). With this device we canachieve a mass resolution m/Δm up to 2000.

Figure 2.11 The two functions of the reflectron: (a) refocusing the same ion species that havepicked up different speeds from the acceleration zone; (b) separating the parent ions and thefragments. Note that the geometry is not drawn to scale.

31
2.3.2 Ion detection
At the end of the ion trajectory we use a 40-mm dual microchannel plate (MCP, Jordan
TOF Products, C-726) to detect the ions. The MCP detector is powered by a Bertan 225-05R highvoltage power supply through a home-built voltage dividing circuit shown in the left panel of
Figure 2.12.

Figure 2.12

Home-built voltage dividers for MCP (a) and CEM (b).

The dual stage MCP has an amplification factor of ca. 106. The current from the anode isregistered as a voltage by an oscilloscope using a 50 Ω terminator. The ion count can be easily
estimated from the peak voltage registered on the oscilloscope. For 1 V peak voltage, the current
is 20 mA. Dividing the current by the amplification factor and using half its value to estimate an
average, the area under a single peak with 20 ns width is approximately 10 mA  20 ns / 106 =32
2·10-16 C. The detection efficiency of an MCP is typically ca. 25 %, so this charge pulse corresponds
to about 5000 ions, assuming that each ion initially ejects one electron from the MCP surface.
The CEM detector located near the ion bender is driven by a slightly different circuit,shown in the right panel of Figure 2.12.

2.3.3 Mass gate
The mass gate is a simplified and more robust version of the design by Stoermer et al.23 It
consists of a stack of parallel metal shims with a thickness of 0.5 mm, placed at 5 mm distance toeach other. The mass gate is “open” when all shims are at ground potential and “closed” when
adjacent shims are biased at ca. ±80 V with opposite polarities (see Figure 2.13). The positive andnegative voltages compensate in the far field, so ions only experience an electric field in theimmediate vicinity of the mass gate assembly.

Figure 2.13

Illustration of mass gate in open and closed configurations (not to scale).

33
The mass gate is installed right before the laser interaction region. The mass gate is open
for about 300 ns only when the ions of interest arrive, so only these ions will pass the mass gate
and enter the laser interaction region. The transmission window can be narrowed down to asingle mass peak in the m/z region we typically work at (ca. 200-600 u/e). Other ion species are
deflected out of the ion trajectory leading to the detector when the mass gate is closed.
However, this scheme cannot separate different ions that to have the same mass-to-charge ratio
within one atomic unit (e.g. HPO4- and SO4-) or isomers of the same atomic composition (e.g.
2/3/4-nitrophenolate). The former situation is rare and often can be avoided by carefully
choosing the reagents when preparing the solution, but isomers sometimes present real
problems. We try to use pure isomers wherever possible – this equals to a chemical selection
before ESI. For example, we purchased the three isomers of nitrophenol to prepare thecorresponding nitrophenolate solutions separately. But if isomerization occurs after ESI, we will
have no control nor information of the isomers. In this case, spectroscopy becomes necessary to
determine the structure of the isomers if possible. Likewise, cluster isomers cannot be selectedby pre-ESI chemistry.

2.3.4 Analyzing photofragments
Since the parent ions and the fragments continue to fly after laser irradiation at the same
speed, one needs to distinguish between them and analyze the fragment mass. This is realized
by using the reflectron as a secondary mass analyzer.
Assume the parent ions with mass-to-charge ratio (𝑚/𝑧)𝑝 will arrive at the MCP detector
at time tp. The corresponding variables for the fragment are noted by the same symbols with

34
subscript f. Let the speed of the parent ions and the fragments before entering the reflectron bev0 and reflectron voltage be V. For simplicity, consider a single-stage reflectron in which the fieldstrength is constant E and proportional to V. The time that the parent ions spend in the reflectronis
𝑡𝑝,𝑟 =

2𝑣0𝐸(𝑚/𝑧)𝑝𝑡𝑓,𝑟 =

2𝑣0𝐸(𝑚/𝑧)𝑓

For the fragments

Since the parent ions and the fragments are flying at the same speed v0 in other sections of the
trajectory between the irradiation and the detector, the total time of flight registered on themass spectrum is then 𝑡𝑝,𝑟 or 𝑡𝑓,𝑟 plus the flight time before and after the reflectron, which is thesame for both parent and fragment ions. As a result, (𝑡𝑝,𝑟 − 𝑡𝑓,𝑟 ) is equal to (𝑡𝑝 − 𝑡𝑓 ), thedifference of the total time of flight between the parent ions and the fragments. Mathematically
it is easy to obtain(𝑚/𝑧)𝑓 = (𝑚/𝑧)𝑝 −𝐸(𝑡𝑝 − 𝑡𝑓 )2𝑣0

but here 𝐸 and 𝑣0 are not precisely known and cannot be easily measured. Consequently there
is no directly way to calculate (𝑚/𝑧)𝑓 . However, one can adjust the reflectron voltage to alter
the field strength to E’ such that the new total time of flight of the fragments 𝑡′𝑓 is equal to 𝑡𝑝 .
Now the fragment ions should appear at the original position of the parent ions on the time-offlight trace. Following the previous argument, this means that the time spent by parent ions in35
the reflectron with the original field and by the fragment ions with the modified field are thesame, given by𝑡′𝑓,𝑟 =

2𝑣0
= 𝑡𝑝,𝑟𝐸′(𝑚/𝑧)𝑓Using the equation for 𝑡𝑝,𝑟 it follows that(𝑚/𝑧)𝑓 𝐸 ′ 𝑉 ′==(𝑚/𝑧)𝑝 𝐸
𝑉
where 𝑉′ is the new reflectron voltage. Now we can calculate the mass-to-charge ratio of thefragment using a simple relationship𝑉′(𝑚/𝑧)𝑓 = 𝑉 (𝑚/𝑧)𝑝Equation 2.1

In brief, one only needs to find a pair of reflectron voltages 𝑉 and 𝑉′ that bring the parent ionsand the fragments, respectively, to the same time-of-flight, and then use the above equation to
calculate the mass-to-charge ratio of the fragments.
Although this is a very convenient way to determine the mass-to-charge ratio of the𝑉′fragments, it may not apply to all fragments, because 𝑉 has a limited range of accessible values
in practice. If the mass-to-charge ratio of the fragment is too small, the adjusted reflectron
voltage 𝑉′ needs to be very low, which impairs the efficiency of ion detection. There is a minimum
value for 𝑉′ below which ion detection becomes impractical. Note that since the fragments may
carry less charge than the parent ions, (𝑚/𝑧)𝑓 can be greater than (𝑚/𝑧)𝑝 . But the highest
voltage of the reflectron is 4500 V, which imposes an upper limit of the largest (𝑚/𝑧)𝑓 that canbe analyzed according to Equation 2.1. It is however worth noting that photodissocation
spectroscopy can still be performed without identifying the fragments.

36
The reflectron in our apparatus has two stages and they are biased proportionally – thesecond stage at voltage 𝑉 while the first at 𝑝𝑉 (0 < 𝑝 < 1). The mathematical description issimilar to the single-stage reflectron case as discussed before and the method of analyzing
fragments is still valid. The advantage of the two-stage reflectron is that it can refocus the ion
beam at an arbitrary position downbeam, i.e., on the MCP detector.
If detecting charged fragments is impossible, neutral fragments may be detected instead.
To enable this option another MCP detector is installed behind the reflectron.

2.4

Photodissociation spectroscopy

2.4.1 Concepts
Traditionally, one measures an absorption spectrum by measuring the attenuation of light
passing through the sample under study, then calculates the absorption coefficient using Beer’slaw. However, a minimum number density of absorbers (108 cm-3 for the most sensitive cavity
ringdown experiments) is needed to practically observe this attenuation. In the condensed phaseor dense gaseous targets, this minimum number density is usually readily achieved.
With mass selected ions, each ion packet we are able to generate has only 10 3 - 105 ions.
Even if every ion can absorb a photon, the intensity change for a millijoule laser pulse is on theorder of one part per trillion or lower, which is beyond the possibility of detection. Therefore, we
employ a less direct method to measure the absorption spectrum – photodissociation
spectroscopy.

37

Figure 2.14 Schematic illustration of the photodissociation process. The target ion is excitedby a photon to an electronic excited state. After relaxation to the electronic ground state, it
becomes vibrationally hot. If a dissociation channel is energetically accessible, the ion will follow
this channel and dissociate into fragments.

As illustrated in Figure 2.14, when an ion is excited by a photon, the absorbed photon
energy can be redistributed to the vibrational modes of the ion. If there is a sufficiently weakbond in the ion, it may be cleaved because the ion is vibrationally hot and ready for unimoleculardecay. Once the ion breaks into fragments, we can use the reflectron to separate and analyze thefragments. By scanning the photon energy and monitoring the yield of the fragments, aphotodissociation spectrum can be recorded. A spectrum recorded by monitoring the formationof a fragment ion is called photofragment action spectrum. Alternatively, one can monitor theloss of the parent ions. The spectrum recorded in this way is called a parent ion depletion
spectrum. Both methods have been used in this work.

38
In order to apply photodissociation spectroscopy, there are certain conditions to be met.
Moreover, since this is an indirect method to measure the absorption, the connection between
the yield of photofragments to the actual absorption across section may not be straightforward.
To report a photodissociation spectrum as an alternative representation of an absorption
spectrum, some assumptions need to be made and the raw data need to be processed
accordingly.

2.4.2 Conditions and caveats
The first premise of photodissociation spectroscopy is that the photodissociation process does
happen, which is not always the case. It requires that the excited ions have sufficient excess ofenergy to induce dissociation. This problem is illustrated in Figure 2.15(a). The dissociationthreshold is set by the bond dissociation energy to yield fragments plus any potential energy
barrier on the path to dissociation. If the energy absorbed through the excitation plus the internalenergy prior to absorption cannot overcome this threshold, dissociation will not occur. There are
two solutions if this is the case. One is to increase the laser intensity or to use multiple laser shots
so that the ions can have the chance of absorbing multiple photons to gain enough energy todissociate (see §2.4.4). The other is the messenger tagging method as introduced in §2.4.3. By
introducing an adduct that is composed of the ion in question and one or more weakly boundmolecule(s), such that an energetically accessible dissociative channel is created to enable
photodissociation spectroscopy. For a weakly bound tag, it is a reasonable assumption that the
spectrum of the original ion remains largely unperturbed. In the present experiment, thegeneration of such adducts is usually achieved in the ion trap at lower temperatures.

39

Figure 2.15 Potential problems of photodissociation spectroscopy. The red line is thedissociation curve accessible to the ions in the higher vibrational states of the electronic groundstate. (a) The total energy of the ion needs to overcome the dissociation threshold to produce
fragments. (b) Multiple photofragments from ABn+ ion. (c) Jablonski diagram. S0 – electronic
ground state (singlet); S1, S2 – singlet excited states; T1 – triplet excited state; E – excitation; F –fluorescence; P – phosphorescence; IC – internal conversion; ISC – intersystem crossing.

The next question is, if one is able to take a photodissociation spectrum, to what extent
does it represent the actual absorption spectrum of the target? There are several situations
where caution should be taken. First, if an ion has more than one dissociation channel, it may
have multiple photofragments, as illustrated in Figure 2.15(b). As in practice we are monitoring
one photofragment at a time, we need to sum over the yield of all photofragments to obtain the

40total spectrum. Since the detection efficiencies for different fragment ions may be different, thismay not be feasible. As an alternative, the parent ion depletion spectrum may be better torepresent the absorption spectrum if multiple dissociation channels exist. Chapter 5 presents an
example of this case.
An ion in the excited state can have different fates, as illustrated by a Jablonski diagramin Figure 2.15(c). Sometimes the ions can release the absorbed energy via non-dissociative
channels such as radiative decay. Moreover, even a vibrationally hot ion with sufficient energy
may live too long to decay before parent-fragment separation. In this case, neither the depletion
spectrum nor the sum of action spectra of all fragments is equal to the absorption spectrum. This
brings about the concept of quantum yield. The photodissociation quantum yield 𝑄𝑝𝑑 is the ratioof the observed number of dissociation to the number of all excited ions. It can be formulated as
𝑄𝑝𝑑 = (1 − 𝑄𝑛𝑑 )(1 − 𝑒𝜏0− ∫𝜏 𝑘(𝐸,𝑇,𝑡)𝑑𝑡)

where 𝑄𝑛𝑑 is the part of non-dissociative decay and depends on the wavelength. When 𝑄𝑛𝑑 ≠0, 𝑄𝑝𝑑 is less than unity, indicating that the photodissociation spectrum may deviate from theabsorption spectrum, unless 𝑄𝑛𝑑 is constant over the whole spectral range in question. The
second term 1 − 𝑒𝜏0− ∫𝜏 𝑘(𝐸,𝑇,𝑡)𝑑𝑡

accounts for the fact that photodissociation must take place ona finite time scale - from the time when ions are irradiated (𝜏0 ) to the time when fragments are
separated from the parent ions, i.e. when ions enter the reflectron (𝜏). The dissociation rate 𝑘 isa function of the total energy of the excited ion, 𝐸, and the ion temperature prior to irradiation,
𝑇. In many cases, particularly for ions with few vibrational degrees of freedom, or with energy
content far above the dissociation threshold, photodissociation usually occurs within a few tens

41
of picoseconds. The period 𝜏 − 𝜏0 is on the order of 10 µs, and the term 1 − 𝑒𝜏0− ∫𝜏 𝑘(𝐸,𝑇,𝑡)𝑑𝑡

canbe presumed to be unity in these cases. This may not hold, however, if 𝐸 is very close to thedissociation threshold. In this case, the photodissociation process may be slow compared to 𝜏 −𝜏0 and 𝑒𝜏0− ∫𝜏 𝑘(𝐸,𝑇,𝑡)𝑑𝑡

becomes significant and reflects an effect called kinetic shift. One can

examine whether kinetic shift effects are present by changing the ion speed to vary the timeinterval 𝜏 − 𝜏0 and then comparing spectra taken under different settings. If the spectra show
intensity differences in the low energy range, a significant kinetic shift is present.
Finally, even if an ion species meets all other conditions for photodissociation
spectroscopy and has 100% photodissociation quantum yield upon excitation, the absorption
cross section still has to be large enough to produce sufficient amounts of fragments to be
detected. One example where this condition is not met will be presented in Chapter 4.

2.4.3 Messenger tagging
As mentioned in §2.4.2, one situation where photodissociation spectroscopy is not
feasible is when the bond dissociation energies in the parent ion are too high to achievedissociation upon excitation with a single photon. For example, in the study of [Ru(bpy)3]2+, thebinding energy of a bpy ligand is almost 4 eV, much greater than the energy of visible photons.
Therefore, photodissociation is energetically inaccessible for a single-photon process in thevisible spectral region. This situation is much more common in infrared spectroscopy because thephoton energy is lower. Under such circumstances, a technique known as messenger tagging may
be used. One or more molecules can be attached to the target ion to create a weakly boundadduct. These molecules, usually referred to as messenger tags, are usually small and inert, and42they ideally do not alter the spectroscopic properties of the parent ion and can dissociate fromthe parent ion after the complex absorbs a photon. Typically used messenger tags are Ar, N2 andD2.24,25 Because of the weak interaction between the messenger tag and the target ion, theadduct can only be produced under gentle conditions and in a cold environment. In our
experiments, this is done in the cryogenic ion trap by condensing buffer gas molecules to thetarget ion. We have succeeded in tagging some ions with multiple D 2 and N2 molecules (seeFigure 2.16).

Figure 2.16 Messenger tagging examples. (a) DDDA2- tagged with up to 17 D2 molecules (traptemperature at 7 K). Different RF amplitudes are favored by different sizes. (b) [Ru(bpy) 3]2+
tagged with up to 8 N2 molecules (trap temperature at 25 K). Inset shows the n=4 adduct and themass resolution m/∆m ≈ 2000.

43
Slightly higher RF amplitude and buffer gas input aid the formation of larger adducts, but
if these two parameters are significantly increased, the fragile adducts will eventually bedestroyed in collisions with the background gas due to RF heating of the stored ions. Shown in
Figure 2.16 are the mass spectra for dodecanedioic acid dianion (DDDA2-) tagged with D2 (trap at
10 K) and [Ru(bpy)3]2+ with N2 (trap at 25 K). The influence from the RF amplitude to the tagging
result is clearly seen for the case of DDDA2-.

2.4.4 Multiphoton processes
For species with high dissociation thresholds, absorption of a single photon may notprovide sufficient energy to induce dissociation (§2.4.2). If the product of laser intensity andabsorption cross section is sufficiently large, the ions may absorb multiple photons andeventually gain enough energy to dissociate. To determine whether this is the case, one can vary
the laser intensity and measure the dissociation signal at the same wavelength as a function of
the intensity. Fitting the resulting curve with a polynomial reveals how many photons the target
has absorbed. If it is indeed a multiphoton process, the data need to be evaluated differently
than with single photon dissociation, e.g., the photon number has to be replaced by its square
for a two-photon process.

2.5

Laser sources

2.5.1 Overview
The schematics of our entire laser system is depicted in Figure 2.17. It consists of a Nd:YAG
pump laser (Innolas Spitlight 600), an optical parametric oscillator (OPO, GWU preciScan ULD)

44
with its frequency upconversion stage (GWU uvScan) and a Sirah Cobra-Stretch dye laser. The
visible OPO is pumped by the third harmonic of the pump laser (355 nm) and generates tunableradiation from 415 nm to 2500 nm. The output of the OPO can be used for second harmonic
generation (SHG) and sum frequency mixing (SFM) with the fundamental output (1064 nm) of
the pump laser to generate UV radiation from 220 to 414 nm. The dye laser is pumped by thefundamental (1064 nm) or the second harmonic (532 nm) of the pump laser. The tuning range
depends on the dye in use. The wavelength scan is realized by using a customized LabVIEW userinterface to send serial commands to the built-in program provided by the manufacturer. The
scan modes are slightly different and will be discussed individually for the OPO and the dye laserin §2.6.2.

Figure 2.17

Beam diagram of our current laser system (see text).

45
The laser beams are routed using high reflection mirrors purchased from cvi, LEO andThorlabs. The final output beam is lifted using a periscope such that it propagates through a CaF2
window into the chamber at the level of the ion trajectory. During the experiment the laser
intensity is monitored by a pyroelectric joulemeter (Coherent J8LP), while other power meters(Coherent PM30 and PM10) are used when calibrating and tuning the power of the system.

2.5.2 Nd:YAG pump
The primary laser source in our system is an Innolas Spitlight 600 pump laser. It consistsof a cavity that generates radiation pulses of 1064 nm and additional stages for second (532 nm)
and third (355 nm) harmonic generation. The optical structure of the pump laser is shown in
Figure 2.18. The resonator is formed by a high reflector and an output coupler. Inside theresonator, an Nd:YAG rod pumped by a Xe arc lamp acts as the laser medium. To generate laser
pulses, a Pockels cell in the resonator serves as an active Q-switch. The intensity of the output
pulse can be changed by adjusting the holdoff voltage and the time delay of the Q-switch. One
can also insert a λ/4 wave plate operate the resonator at a fixed Q with disabled Pockels cell for
testing purposes. The laser transition is 4F3/2 → 4I11/2 in the Nd3+ ion at 1064 nm.26

46

Figure 2.18

Anatomy of Innolas Spitlight 600 Nd:YAG pump laser.

The laser pulse from the resonator is then directed to another Nd:YAG rod, which has
been pumped by the same flash lamp at the same time as the first rod, but is seated outside theresonator. The population conversion built up in the second rod amplifies the energy of theoriginal laser pulse to about 600 mJ. The pulse duration is about 5 ns.
In order to pump the visible OPO and the dye laser, shorter wavelengths are needed. The
fundamental 1064 nm pulse passes a Type I KD*P (potassium dideuterium phosphate) crystal
which doubles the frequency and produces a 532 nm pulse. The power can be optimized byadjusting the crystal angle, and the typical value is 200 mJ/pulse. Now the 532 nm pulse and theresidual 1064 pulse propagate collinearly towards a second KD*P crystal where they undergo
sum frequency mixing to produce a 355 nm pulse. The energy of the 355 nm pulse is usually 100
to 150 mJ. Each crystal is housed in an oven and held at 70 °C to stabilize the performance of
non-linear conversion. In order to separate all the frequency components, a series of dichroic
mirrors are used. To prevent the 355 nm beam being back-reflected into the resonator, an
additional rejection mirror is placed between the KD*P crystals.

47
Since a good beam profile and a reasonable power density of the 355 nm pulse are
required to optimize the performance of the OPO and avoid damage, we routinely use aphotographic film screen to “print” and examine the beam profile, ensuring that the power
density is below 0.6 J/cm2.

2.5.3 OPO and SHG/SFM stage
The OPO is pumped by the third harmonic (355 nm) of the Nd:YAG laser. The pump beam
is introduced to the OPO resonator by a periscope. The resonator consists of a Porro prism, a λ/4
wave plate, an output coupler and a Type II beta barium borate (BBO) crystal. The use of the
Porro prism and the λ/4 wave plate is to reduce the beam divergence which would result if a
simple high reflector was used. The BBO crystal works as the frequency converter that can divide
the pump beam into two colors, namely the signal and the idler, observing energy conservation
𝜔𝑝𝑢𝑚𝑝 = 𝜔𝑠𝑖𝑔𝑛𝑎𝑙 + 𝜔𝑖𝑑𝑙𝑒𝑟
where 𝜔𝑝𝑢𝑚𝑝 , 𝜔𝑠𝑖𝑔𝑛𝑎𝑙 and 𝜔𝑝𝑢𝑚𝑝 are the frequencies of the pump, the single and the idler. By
convention, 𝜔𝑠𝑖𝑔𝑛𝑎𝑙 > 𝜔𝑖𝑑𝑙𝑒𝑟 . The output photons must also observe the conservation of
momentum:⃗𝒌𝑝𝑢𝑚𝑝 = ⃗𝒌𝑠𝑖𝑔𝑛𝑎𝑙 + ⃗𝒌𝑖𝑑𝑙𝑒𝑟
where ⃗𝒌𝑝𝑢𝑚𝑝 , ⃗𝒌𝑠𝑖𝑔𝑛𝑎𝑙 and ⃗𝒌𝑖𝑑𝑙𝑒𝑟 are the wave vectors of the pump, the single and the idler.
When the BBO crystal is rotated by a precision motor, the wavelength fulfilling the phasematching condition is changed, leading to a tunable output. There are two crystals in the setup,referred to as “blue” and “red”. One of them is chosen at a time depending on the wavelength
to be generated. The “blue” crystal is used to generate signal of 415-515 nm and idler of 1140-

48
2450 nm. The “red” crystal is used to generate signal of 505-710 nm and idler of 710-1190 nm(see Table 2.3).
The output from oscillator passes through a UV filter and a quartz compensator to filter
the residual pump beam and correct the beam direction of the output. The separation of thecollinear signal beam and idler beam is achieved by a Pellin-Broca prism located downbeam.
To generate tunable light in the UV range, an additional stage is installed following the
OPO to convert its output to higher frequencies. The GWU uvScan in our setup functions in twomodes – second harmonic generation (SHG) and sum frequency mixing (SFM). SHG takes solely
the OPO output as input while SFM takes 1064 nm beam from the pump laser in addition.
As shown in Figure 2.19, there are two non-linear optical crystals placed in sequence inthis stage. The first crystal can be either “UV1” or “UV2”, which is used in accordance with “blue”
or “red” crystal, respectively. In either case, the other crystal in the sequence is working as acompensator for the beam walk caused by the frequency converting crystal. The crystal
configurations and their according wavelength outputs are shown in Table 2.3. Frequency tuning
is realized by rotating the crystals using precision motors, same as the OPO.

Table 2.3

OPO and SFM/SHG output ranges in nm.
OPO crystal

signal

idler

SHG

SFM

blue
red

415-515505-7101140-2450
710-1190

220-257257-354299-350
350-404

49

Figure 2.19

Anatomy of the visible OPO and the SHG/SFM stage.

The wavelength calibration of the OPO is performed via a five-point polynomial fitting
suite built in the preciScan software. A diffraction grating-based UV-Vis spectrometer (Avantes,
AvaSpec-2048- USB2-DT) is used to measure the wavelength. The linewidth is about 5 cm-1 andthe pulse width is 5 ns. Pulse energies are between 10 and 25 mJ, depending on the wavelength.
Calibration of SFM/SHG is done by optimizing the output UV power and using the same built-in
polynomial fitting suite.

2.5.4 Dye laser
Dye lasers are known for narrow linewidth and high conversion efficiency, which make ita highly desirable light source for laser spectroscopy. In our experiment, we take advantage of its
intense photon fluence to target some ions that have small absorption cross sections or highbinding energies. In §2.6.2 we mentioned these as unideal situations, but with sufficient laser

50intensity, we have the opportunity to compensate the weak absorption or trigger multiphoton
process to overcome these difficulties.

Figure 2.20 The optical schematics of Sirah dye laser (adapted from Sirah Cobra-Stretch dyelaser datasheet27).

Shown in Figure 2.20, our Sirah Cobra-Stretch dye laser has two dye cells serving as thegain medium and the amplifier, respectively. The pump beam is split into the primary pump, thepre-amp and main-amp beams, which are delayed one after another. The primary pump beam
excites the dye in the first cell and creates the seed signal. When the pre-amp beam reaches thesame cell, the seed signal can be amplified. The wavelength selection is performed by a gratingbased monochromator and the linewidth is only a few picometers. The output exits the resonatorand then is amplified by the second cell, which is pumped by the main-amp beam.
So far we have used two kinds of dye - Coumarin 307 and Pyrromethene 579. Their
specifications are listed in Table 2.4. The pump beam is generated by the Nd:YAG pump laser.

51
Table 2.4

Specifications of the dyes in current study.
dyepumpmaximum
conversion
efficiency
tunable range

2.6

Coumarin 307
355 nmPyrromethene 579
532 nm30%

53%

480-540 nm

566-611 nm

Operation Control

2.6.1 Timing sequence
The combination of ion trapping, ToF-MS and laser irradiation demands a sophisticatedtiming sequence for the involving units to act in concert. We use two digital pulse generators(abbreviated “PG”) to control the timing of the experiment. The whole timing scheme isillustrated in Figure 2.21 and Table 2.5, which also contains example values.

52
Table 2.5

Detailed timing sequence with example values.

controller
PG 1(triggeredinternally at
20 Hz)RF power
supplyPG 2(triggered
externally by
T2* at 10 Hz)

channel
T1
T2
T3
T4
T5
T8
T 2’
T 2*
A
B
G
E

event
buffer gas“RF off”
flash lamp
“laser-on”“laser-off”
unload pre-trap
swtich off RFejectionacceleration
oscilloscopes
mass gate
Q-switch

sync
T0
T1
T1
T1
T1
T1
T2
T 2’
T 2*
A
A
G

delay
0
45 msc-186 µsd
0000-1 µsf
0.5 µs6 µs
025 µs
200 nswidtha
1 µs
1 µs
1 µs
100 µse100 µse
1 µs
1 µs
4 µs
8 µs
1 µs
300 ns1 µs

duty cycleb
1/0/0
1/0/0
3/1/3
3/1/1
1/0/0
-

a The 1-µs widths are used just for TTL triggering.
b The format is written as cycle off (no pulse output)/cycle on/cycles waited to start. Duty

cycle is not applicable for RF power supply and PG 2.
c 95 ms storage time is realized by 45 ms delay plus the skipped cycle of 50 ms.
d The value is set such that the Q-switch is triggered about 215 µs after the flash lamp tocatch the best population inversion.
e The width of T

4 and T5 is set to be sufficiently long to perform AND operation with

Channel E and B.
f Due to the mechanism of how the RF power supply switches off the RF signal, this delay

is uncertain. See text for detailed explanation.

53

Figure 2.21 The full timing sequence of an experiment with 10 Hz ion source. Pulses withinsignificant widths are presented as sticks. Channel numbers are shown on the left and thefunctions are provided on the right. The diagram shows a full cycle for a single data point, whichcontains two periods, one with laser on (orange) and the other with laser off (purple). Dottedlines illustrate synchronization hierarchy. Red lines are handled by PG 1; blue by PG 2 (see text).
Green lines present the RF power supply and the green shadows indicate the uncertainty of
T2’-T2. QS is the result of E AND T4 and the actual trigger of the Q-switch. OS is the trigger for oneof the two oscilloscopes in an alternate fashion (see §2.6.2).

Because the flash lamp of the pump laser must be triggered at 20 Hz, it is handled by
Channel T3 of Quantum Composers Model 9618 (“PG 1”), whose fundamental output (T 0) is set
to have 20-Hz repetition rate. The generation of ion packets is at 10 Hz (20 Hz if ion cooling is notnecessary) and is initiated by the buffer gas pulse on Channel T 1. The pre-trap is triggered by

54
Channel T8 to unload the ions. The timing scheme of the main trap has been briefly described in§2.2.3. After an accumulation time of ca. 95 ms, Channel T2 sends a transistor-transistor logic(TTL) signal to the RF power supply of the ion trap. After receiving this signal, the power supply
will wait until the RF passes zero from negative and then switches off the RF. Since T 2 may comeat any moment during an RF period, the time difference between T2 and the actual time when RF
is switched off, noted as T2’, is uncertain between 0 and 1 µs, shown by the green shadows in
Figure 2.21 on axis T2. Since the trigger for ion ejection is handled by the power supply too andsynchronized to T2’ rather than T2 (green dotted lines in Figure 2.21), the rest of the timing
sequence (acceleration, detection, laser pulse, etc.) all has to be referenced to T2’. Therefore, theTTL output (for ion ejection, noted as T2*) of the RF power supply is also used to trigger a second
pulse generator (Quantum Composers Model 9518, “PG 2”) that handles the rest of the timing
sequence.
Channel A on PG 2 is synchronized to T2* and triggers the acceleration of ToF-MS; its delay
and width vary with the mass-to-charge ratio of the target ion. For mass selection, the mass gate
is triggered by Channel G, which is synchronized to Channel A and tuned to be open only for thetarget ion species. Channel E triggers the Pockels cell of the pump laser to allow the laser pulseintercept the ion packet in time. Since we need to measure the ion signal with “laser-on” and“laser-off”, the laser pulse should be produced at 5 Hz. However, Channel E on PG 2 cannot
achieve this on its own, since PG 2 is externally triggered by T2* at 10 Hz and duty cycle settings
will not work. While PG 1 can output 5 Hz pulses using duty cycle settings, the uncertainty of T2’T2 is translated to every channel on PG 1 in respect to the ion packet (see Figure 2.21). To
circumvent the problem, we use a logic AND gate that takes Channel E and a “laser-on” signal

55from PG 1 (T4). The output will be the right timing owing to Channel E but also the right frequency
of T4 (5 Hz, orange in Figure 2.21). This method is also applied to trigger the oscilloscopes. Since
two oscilloscopes are required to monitor the laser induced and the background ion signal
respectively, the scope triggering (Channel B, 10 Hz) needs to go through the AND gate with T4(laser-on) or T5 (laser-off, purple in Figure 2.21) pulse to select the correct oscilloscope (laser-on
for Scope A, laser-off for Scope B). The implementation circuit diagram of the AND gate is shownin Figure 2.22.

Figure 2.22

AND circuit for triggering pulses.

2.6.2 Data acquisition
To acquire a photodissociation spectrum, we scan the wavelength and monitor the ion
signals and laser pulse energy. The scanning schemes are slightly different for the OPO and the
dye laser.
The GWU OPO program processes commands remotely sent from a home-written
LabVIEW program to perform continuous scans, which means the wavelength changes
continuously and samples are collected without stopping the motors. Therefore, in order to keep

56
the spectral resolution as good as possible, the scan rate needs to be sufficiently slow so that theenergy difference of adjacent data points is equal to or less than the linewidth of the laser. For
example, in the spectral range around 600 nm (16666 cm-1), with the linewidth being 5 cm-1, thestep of the data points should be less than 0.2 nm. Assuming each data point takes about 1.6 s(at 20-Hz repetition rate of the laser), the scan rate should be slower than 8 nm/min. However,in practice all species we have worked with turned out to have absorption bands that are
intrinsically much broader, therefore faster scan rates have been applied without loss of
information.
For the dye laser, the original control program by the manufacturer is modified and added
to our data acquisition and processing modules. Unlike the GWU OPO, the dye laser performs“burst” scans, which means that the wavelength is kept constant for each data point and thendriven to the next value for the next data point.
We use two Tektronix TDS 2022 (2-channel, 200 MHz, 2GS/s) oscilloscopes to measure
the laser induced ion signal and the background separately. The current from the MCP anode(§2.3.2) is collected using a 50 Ω terminator. The intensity of the laser pulses is measured by apyroelectric joulemeter (§2.5.1) and the signal is collected by the same oscilloscope thatmeasures the laser induced ion signal (Scope A). The analog input signals at the oscilloscopes are
digitized by the oscilloscopes and transmitted to the LabVIEW program via serial ports. For eachdata point, the wavelength, background signal, laser induced signal and laser intensity, areaveraged over 16 or 8 ion shots (samples). Each scan is defined by the boundary wavelengths andthe scan rate (OPO) or the step size (dye). After each scan, the raw data are immediately saved
and processed according to the choice of action or depletion spectrum by customized modules

57
built in the LabVIEW program. The processed data are saved as a list of photon energy versus ion
signal corrected for photon fluence and background (see §2.6.3).

2.6.3 Data processing
The raw data initially collected by the LabVIEW program consist of ion signals, laser
intensity and wavelength. The processing involves background correction and normalization ofion signals to photon number and is automatically performed by the LabVIEW program.and theevaluated spectrum is saved as a separate data file. The operations performed by the program
are discussed in this section.
In an action spectrum (see §2.4.2), the intensity of fragment ions, 𝑌(𝜆), actually contains
two parts: unimolecular decay of metastable ions, 𝑌𝑚𝑑 , and photodissociation, 𝑌𝑝𝑑 (𝜆). The decay
signal from metastable ions is the simply the background fragment signal without laser irradiationand is caused mainly by collisional activation during ion ejection from the trap or during
acceleration. Since 𝑌𝑚𝑑 is measured immediately after every measurement of 𝑌(𝜆), it can beused as the approximate background at the time when 𝑌(𝜆) is measured, and variations of theion source intensity are minimized this way. A simple subtraction 𝑌(𝜆) − 𝑌𝑚𝑑 returns 𝑌𝑝𝑑 (𝜆).
𝑌𝑝𝑑 (𝜆) is a function of the wavelength 𝜆 and proportional to the product of the amountof parent ions 𝑃 , the photon number 𝑁(𝜆) , the absorption cross section 𝜎(𝜆) and thephotodissociation quantum yield 𝑄𝑑
𝑌𝑝𝑑 (𝜆) = 𝑃 ∙ 𝑁(𝜆) ∙ 𝜎(𝜆) ∙ 𝑄𝑑
In this equation, the photon number 𝑁(𝜆) can be easily derived from the laser intensity 𝐼(𝜆) as
measured:58
𝑁(𝜆) =𝐼(𝜆)ℎ𝑐/𝜆where ℎ is the Planck constant and 𝑐 is the speed of light. Therefore, 𝜎(𝜆) can be represented by
𝜎(𝜆) =ℎ𝑐[𝑌(𝜆)−𝑌𝑚𝑑] 1
𝑃∙𝑄𝑑
𝜆𝐼(𝜆)

Equation 2.2

On the right side of Equation 2.2, the first term can be calculated directly from raw data, but thesecond term is difficult to measure in absolute units. Because the reflectron is usually configured
to optimize the fragment signal, the intensity of the parent ions cannot be measured
simultaneously. In principle, one can use the metastable decay background as a scale of theparent ion 𝑌𝑚𝑑 ∝ 𝑃, but since 𝑌𝑚𝑑 is often a small number, normalizing with 𝑌𝑚𝑑 worsens signalto-noise. When the ion source is working properly, the yield of parent ion is a stable quantitywith random shot fluctuations. Therefore, we assume it to be constant during a single scan (lessthan 30 minutes). The statistical fluctuations can be smoothed out by averaging over many scans.
The photodissociation quantum yield 𝑄𝑑 has been discussed in §2.4.2. Under ideal conditions,
𝑄𝑑 is close to unity. Assuming 𝑄𝑑 is independent on the wavelength, the first term inEquation 2.2, denoted as 𝜎′(𝜆), is then proportional to the absorption cross section 𝜎(𝜆) andcan be obtained from the raw data acquired in our experiment, so we can report 𝜎′(𝜆) insteadof 𝜎(𝜆) in our work.
Similarly, for a depletion spectrum, the loss of the parent ion can be linked to theabsorption cross section by
𝜎(𝜆) =ℎ𝑐[𝑃 − 𝑌𝑃 (𝜆)] 1𝜆𝐼(𝜆)𝑃 ∙ 𝑄𝑑59
where 𝑌𝑃 (𝜆) is the parent ion signal with the laser on and other symbols are defined as before.
The difference in this case is that the “background” parent ion signal 𝑃 can be measured directly.
We then obtain the relative absorption cross section in the limit of small ion depletion
𝜎′(𝜆) =ℎ𝑐[𝑃 − 𝑌𝑃 (𝜆)]𝜆𝐼(𝜆)𝑃

If the same assumption of 𝑄𝑑 can be made, 𝜎 ′ (𝜆) is a good representation of 𝜎(𝜆).
Normally, because 𝑃 is a large number and 𝑃 − 𝑌𝑃 (𝜆) is small, depletion spectra are often noisierthan action spectra. If the fraction of the loss of parent ion is significant, the extraction of 𝜎(𝜆) isless straightforward. One may use the modified Lambert-Beer law28
𝑌𝑃 (𝜆)= 1 − 𝛼 + 𝛼𝑒 −𝜎(𝜆)𝐹(𝜆)𝑃
where 𝛼 is a parameter indicating the overlap between laser and ion packet, and 𝐹(𝜆) is thephoton fluence. The overlap parameter can be determined by measuring the intensity
dependence of the parent ion depletion at the peak of the absorption profile. Chapter 5 will
provide a concrete example where this method is deployed.

2.6.4 Baseline and scaling correction
The oscilloscopes used to measure the ion signals have non-zero baseline values. To
measure the baseline, the laser beam is blocked before a scan begins and the reading of eachchannel of the oscilloscopes is recorded and saved. These values will be subtracted from the ion
and laser pulse energy measurements to eliminate this artifact.
The oscilloscopes may also have slightly different scaling factors, which can skew large
readings. This is a potential problem for depletion spectra as the parent ion signal is usually large.

60
Therefore, when laser is blocked, the parent ion signals on both oscilloscopes are recorded. The
ratio of these two values is calculated and used to rescale the data collected by the two
oscilloscopes during the scan.

2.7

References

1.

Xu, S., Gozem, S., Krylov, A. I., Christopher, C. R. & Weber, J. M. Ligand influence on theelectronic spectra of monocationic copper-bipyridine complexes. Phys. Chem. Chem. Phys.
17, 31938–31946 (2015).

2.

Weigend, F. & Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence andquadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys.
Chem. Chem. Phys. 7, 3297–3305 (2005).

3.

Weigend, F., Häser, M., Patzelt, H. & Ahlrichs, R. RI-MP2: optimized auxiliary basis sets anddemonstration of efficiency. Chem. Phys. Lett. 294, 143–152 (1998).

4.

Parr, R. G. & Yang, W. Density-Functional Theory of Atoms and Molecules. Oxford
University Press: New York (1989).

5.

Yamashita, M. & Fenn, J. B. Electrospray ion source. Another variation on the free-jettheme. J. Phys. Chem. 88, 4451–4459 (1984).

6.

Dole, M. et al. Molecular Beams of Macroions. J. Chem. Phys. 49, 2240 (1968).

7.

Fenn, J. B., Mann, M., Meng, C. K. A. I., Wong, S. F. & Whitehouse, C. M. Electrosprayionization for mass spectrometry of large biomolecules. Science 246, 64–71 (1989).

8.

Rayleigh, F. R. S. On the equilibrium of liquid conducting masses charged with electricity.
Philos. Mag. Ser. 5 14, 184–186 (1882).

9.

Hoffmann, E. & Stroobant, V. Mass Spectrometry: Principles and Applications. John Wiley& Sons, Ltd. (2006).

10.

Taylor, G. Disintegration of water drops in an electric field. Proc. R. Soc. A Math. Phys. Eng.
Sci. 280, 383–397 (1964).

11.

Blades, A. T., Ikonomou, M. G. & Kebarle, P. Mechanism of electrospray mass
spectrometry. Electrospray as an electrolysis cell. Anal. Chem. 63, 2109–2114 (1991).

61
12.

Ikonomou, M. G., Blades, A. T. & Kebarle, P. Electrospray-ion spray: a comparison of
mechanisms and performance. Anal. Chem. 63, 1989–1998 (1991).

13.

Kebarle, P. & Tang, L. From ions in solution to ions in the gas phase. Anal. Chem. 65, 972A–
986A (1993).

14.

Kebarle, P. & Verkerk, U. H. Electrospray: from ions in solution to ions in the gas phase,what we know now. Mass Spectrom. Rev. 28, 898–917 (2009).

15.

Tosi, P., Fontana, G., Longano, S. & Bassi, D. Transport of an ion beam through an octopole
guide operating in the r.f.-only mode. Int. J. Mass Spectrom. Ion Process. 93, 95–105(1989).

16.

Gerlich, D. Inhomogeneous RF fields : a versatile tool for the study of processes with slow
ions. Advances in Chemical Physics: State-Selected and State-To-State Ion-Molecule
Reaction Dynamics, Part 1. Experiment 82 (1992)

17.

Jones, R. M. & Gerlich, D. Simple radio-frequency power source for ion guides and ion
traps. Rev. Sci. Instrum. 68, 3357–3362 (1997).

18.

Dawson, P. H. Ion Storage in three-dimensional, rotationally symmetric, quadrupole fields.
I. Theoretical treatment. J. Vac. Sci. Technol. 5, 1 (1968).

19.

March, R. E. An Introduction to Quadrupole Ion Trap Mass Spectrometry. J. Mass
Spectrom. 32, 351–369 (1997).

20.

Guilhaus, M. Principles and instrumentation in time-of-flight mass spectrometry. J. Mass
Spectrom. 30, 1519–1532 (1995).

21.

Wiley, W. C. & McLaren, I. H. Time-of-Flight Mass Spectrometer with Improved Resolution.
Rev. Sci. Instrum. 26, 1150 (1955).

22.

Marcum, J. C. Electronic photodissociation spectroscopy of Electrosprayed anions (2011).
University of Colorado, Boulder.

23.

Stoermer, C. W., Gilb, S., Friedrich, J., Schooss, D. & Kappes, M. M. A high resolution dual
mass gate for ion separation in laser desorption/ionization time of flight mass
spectrometry. Rev. Sci. Instrum. 69, 1661 (1998).

24.

Garand, E., Stipdonk, M. J. Van & Johnson, M. A. Isomer-Specific IR-IR Double Resonance
Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap. J.
Phys. Chem. Lett. 3, 1099-1105 (2012).

25.

Thompson, M. C., Baraban, J. H., Matthews, D. A., Stanton, J. F. & Weber, J. M. Heavy atom

62
vibrational modes and low-energy vibrational autodetachment in nitromethane anions. J.
Chem. Phys. 142, 234304 (2015).
26.

Geusic, J. E., Marcos, H. M. & Van Uitert, L. G. Laser oscillations in nd-doped yttrium
aluminum, yttrium gallium and gadolinium garnets. Appl. Phys. Lett. 4, 182–184 (1964).

27.

Cobra-Stretch Dye Laser Datasheet. (2015)

28.

Schweizer, A. et al. Electronic photodissociation spectroscopy of Au4+.Arn, n=0-4:
Experiment and theory. J. Chem. Phys. 119, 3699–3710 (2003).

63

3
3.1

The role of the ligands

Introduction
Ligands play very important roles in organometallic complexes. The properties of ligands,

such as their electron affinity, polarizibility, aromaticity and geometry, can profoundly influence
the properties of a complex. Different ligands often lead to different complex stability andreactivity, which have been some of the main focuses of study in inorganic chemistry. One of thedirections that researchers have been pursuing is to characterize the function of a specific ligand
and its influence on the properties of the complex. This is difficult to achieve in the condensed
phase, since many other factors influence the behavior of a complex, such as the chemical
microenvironment caused by the solvent. In order to systematically investigate ligand influence,
one needs systems that have few and controllable variables. One common approach to make asystematic analysis is to alter one single ligand in a complex at a time and observe the change inthe properties of the complex.1–10 But this approach also poses challenges because such
experiments usually involve heteroleptic and undercoordinated compounds. Heteroleptic
compounds often require delicate syntheses and can undergo speciation processes in solution,even if the syntheses succeed. Undercoordinated compounds are rarely stable in the condensed
phase because the open coordination sites are vulnerable to the chemical environment. Thesedifficulties can be avoided if the compound is prepared in the gas phase. As we have introduced
in previous sections, solvents and counterions are automatically eliminated in the gas phase. In
addition, mass selection allows us to obtain pure samples and interrogate a single species at a
time.

64
Many of the properties are connected with the electronic structures of the compound. A
fundamental question in this context is how a ligand modifies the electronic structure of thewhole complex. This question can be theoretically approached by ligand field theory, which iscapable of explaining some of the important properties, such as spin configuration and color,
particularly for homoleptic compounds with high symmetry. Experimentally, the electronic
spectra can be measured by applying laser spectroscopy to compounds in the gas phase, thereby
excluding any effects related to solvent interaction.
Our focus in this chapter lies on the ligand influence in organometallic ions. We selecteda series of compounds with a single variable ligand. The fixed part in the series is ideally stable,
non-reactive and well-studied, so that the influence of the variable ligand can be unambiguously
tracked. We have looked into two series of complexes.
The first series consists of several copper(I) mono-2,2’-bipyridine (bpy) complexes. They
take the form [Cu-L]+, where boldface Cu represents the fixed part, CuI-bpy, and L represents thevariable ligand. In this case, L was chosen to be N2, D2, H2O, CH3OH and Cl, forming a series fromweakly to strongly interacting ligands. One major merit of studying this series is that Cu I isformally a closed-shell metal core so Cu does not have d-d bands and its first electronic excitation
is a ππ* transition localized on the bpy ligand (except L = Cl). Consequently, the effects of theadditional ligand are expected to be reflected in the ππ* band of the system. We measured thephotodissociation spectrum of [Cu-L]+ with different L and examined the influence of L bycomparing the spectra.
The second series we studied consists of dicationic ruthenium polypyridyl complexes,
denoted as [Ru-L]2+, where Ru = RuII(bpy)(tpy) and tpy = 2,2’;6’,2”-terpyridine. L is again the65variable ligand, in this study H2O, CO2, CN3CN and N2. The complexes based on Ru have been
extensively studied because they are often involved in catalytic applications, from wateroxidation11,12 and CO2 reduction13,14 to nitrogen fixation.15 This type of complex has a brightabsorption band in the visible range that has the character of a metal-to-ligand charge transfer
transition. Since Ru is an undercoordinate species, the attack of an extra ligand can be expected
to alter its properties, which will be important for the function of the complex in catalysis.
Therefore, it is imperative to study the electronic structure of [Ru-L]2+ in aid of understanding
fundamental aspects of its function. Note that species like [Ru-L]2+ are often intermediates andtheir isolation is often not possible in solution. Our experiment provides the first characterizationof these transient ion species without the presence of a chemical environment.

3.2

Copper bipyridine complexesThis section has been reproduced in part with permission from Shuang Xu, Samer Gozem, Anna
I. Krylov, Casey R. Christopher, J. Mathias Weber, Ligand Influence on the Electronic Spectra of
Monocationic Copper–Bipyridine Complexes, Physical Chemistry Chemical Physics 2015, 17 (47),pp.31938-31946. Copyright 2015, Royal Society of Chemistry.16

3.2.1 Background
Copper based compounds have been widely studied because they have many applications
in both chemical research and industry and they are relatively inexpensive owing to the large
abundance of copper on earth. A recent example for their potential use is their promise as
inexpensive water oxidation catalysts, as reported by Barnett et al.17 and Chen et al.,18 but their

66
photophysics and photochemistry are equally fascinating.19,20 In particular, complexes containing
monovalent CuI serve as an ideal system to study ligand effects and ligand-ligand interactions
because – at least in a qualitative formal charge picture – the metal core is in a closed-shell
configuration (d10) and their spectra should therefore be free from complications by transitions
between d-orbitals. 21–25
Diimines form a very common group of bidentate metal chelating ligands. Complexes of
CuI and some diimine ligands have found potential applications in solar energy conversion andtherefore their electronic structure and photophysical properties are under extensive study.26–29
Complexes containing 2,2’-bipyridine (bpy) and 1,10-phenanthroline have received more
attention because of the basic form of the ligands. In most experimental studies, fully
coordinated complexes with a variety of ligands are synthesized and characterized, however,there seems to be a lack of studies of undercoordinated complexes despite of theirsimplicity.30–32 This study will focus on mono-bpy complexes of CuI.
The electronic structure of bpy has been studied for decades. 33–38 It is of C2v symmetry
and its ground state is an A1 state. Therefore, the only optically allowed transitions are those to
the A1, B1 and B2 states. The first excited state S1 (11A2, nπ*) is not optically accessible due tosymmetry restrictions. The transition to the S2 state (11B1, nπ*) is very weak, while the transition
to the S3 state (11B2, ππ*) is bright.38 All these transitions are in the UV spectral region. When bpy
is chelated to a metal ion, one would expect that these transitions will be shifted and that thenature of states and their order may be modified. In the simplest case where the metal is a closedshell ion (CuI and ZnII), there will be no low-lying d-d bands or charge transfer bands. The norbitals involved in the lowest energy excited states of bpy will convert into σ-orbitals to bind67
with the metal. The lowest dark transition will therefore have σπ* nature instead of nπ*, but thefirst bright transition will still be the ππ* band (to the S2 state). In fact, this reasoning is supported
by experiments on [ZnII(bpy)]2+. The ππ* transition of [Zn(bpy)]2+ in solution was found at ca.
32600 cm-1,34 shifted by 3200 cm-1 to the red compared to the analogous bpy solution without
Zn2+, but the band profile is largely preserved.39 Therefore, we anticipate similar results for[CuI(bpy)]+ (denoted as Cu+ in the following). To understand more complicated systems wheremultiple ligands are present, one may start by asking what happens if another ligand is added to
Cu+. To carry out this study in a systematic fashion, we have examined a series of complexes in
the formula [Cu-L]+, where L is a variable and selectable ligand. By taking advantage of this very
simple system in isolation (in vacuo), we are able to investigate the role of the additional ligand
in detail.

3.2.2 Methods
The instrumentation for the experiment has been described in detail in Chapter 2. To
generate a particular [Cu-L]+ species, we prepared a solution with equal concentration ofcopper(II) salt and 2,2’-bipyridine in a 1:4 mixture of distilled water and methanol (HPLC grade,
EMD Millipore). Copper(II) nitrate hydrate (99.999%, trace metals basis, for L = N 2, D2, H2O andCH3OH) and 2,2’-bipyridine (ReagentPlus grade, ≥99%) were purchased from Sigma-Aldrich, while
copper(II) chloride dehydrate (99+%, ACS grade, for L = Cl) was purchased from Alfa Aesar. All
chemicals were used without further purification. The concentration was 5 mM, and the solution
was pumped to the ESI needle at 25 μL/hr. The spraying needle was held at +3 kV and thedesolvation capillary was heated to 70 °C in order to achieve optimal ion intensity.

68
While [Cu-OHCH3]+, [Cu-OH2]+ and [Cu-Cl]+ were formed directly in the solution andextracted to gas phase by ESI, [Cu-N2]+ and [Cu-D2]+ were formed in the trap where ambient N2
or D2 molecules dock onto Cu+. A mass spectrum with mass peaks for Cu+, [Cu-OH2]+ and [CuOHCH3]+ is shown in Figure 3.1.

Figure 3.1
Mass spectrum showing the formation of Cu+, [Cu-OH2]+ and [Cu-OHCH3]+. The
arrows point to the ions containing 63Cu only.

We calculated the ground state properties (dissociation thresholds, natural charges, andvibrational frequencies) of the molecules under study with density functional theory40 (DFT) using
the PBE0 functional41 and def2-TZVP42 basis sets for all atoms. We also calculated the excitationenergies and the respective oscillator strengths for the excited states to aid our assignment of
the spectrum. These calculations were performed using the Turbomole suite of programs. 43

69
However, our results of the excited states turned out to be unsuitable to describe theexperimental observations. Therefore, higher-level calculations using the “equation-of-motion
for excitation energies coupled-cluster approach with single and double excitations” (EOM-EECCSD)44,45 were performed by Professor Anna Krylov’s group at the University of Southern
California.16

3.2.3 Results and discussions
3.2.3.1 [CuI(bpy)]+
Before adding the ligand L, it is constructive to obtain some information about Cu+ itself
for comparison. This was feasible because we were able produce this ion by ESI, and the binding
energy of Cu and bpy+ is estimated to be 415 kJ/mol (34680 cm-1), roughly in the spectral range
where we expect the ππ* bands of metal-bpy complexes. The upper panel of Figure 3.2 shows
the photodissociation spectrum of Cu+ monitoring the yield of bpy+ acquired at room
temperature. One can immediately notice the resemblance of this spectrum to the fluorescence
excitation spectrum of [ZnII(bpy)]2+ taken by Kotlicka and Grabowski,34 shown in the lower panelof Figure 3.2.

70

Figure 3.2
The photodissociation spectrum of [CuI(bpy)]+ at room temperature (upper) andthe fluorescence excitation spectrum of [ZnII(bpy)]2+ at 93 K in water and methanol (lower). In
the upper panel, gray dots are raw data and black solid line is 50-point sliding average. The datafor [ZnII(bpy)]2+ were extracted from the work by Kotlicka and Grabowski.34

The positions of the two resolved peaks are almost identical, indicating the same amountof shift compared to the bare bpy as a corroborative trend for d10 metal ions. The first peak isfound at 32580 cm-1, slightly below the calculated binding energy. Therefore, it is likely that theinternal energy stored in the ion at room temperature is a contributing factor to overcoming thedissociation threshold. In fact, upon lowering the trap temperature to 50 K, nearly no
photofragments were detected, corroborating this speculation. This may also account for the

71
difference of the relative peak intensity between Cu+ and [ZnII(bpy)]2+ since the lower-energy
peak in the photodissociation spectrum of Cu+ may have been suppressed due to kinetic effects.

3.2.3.2 L = N2, D2, H2O, CH3OH and Cl
We first performed DFT calculations for the ground state of all species to glance at thebasic properties. Several important properties are summarized in Table 3.1, and the geometries
are provided in Figure 3.3. The results largely meet our expectations. All species are singlets in
the ground state except for [Cu-Cl]+, which is a doublet. The binding energy increases in the orderof N2 < D2 < H2O ≈ CH3OH < Cl. The charge analysis provides a qualitative picture of the charge
distribution. For L = N2, D2, H2O and CH3OH, the charge on Cu or bpy is fairly close to that in Cu+,
indicating a small polarization effect from the additional ligand, and the ligand L is more or lessneutral. In contrast, Cl has a much larger electronegativity and therefore attracts electron densityfrom the copper core. However, the formal charge on Cu is +1.174 and on Cl is -0.512, not quite
close to +2 and -1 as one might imagine based on formal charges. One conceivable explanationis that the bpy ligand lends π electron density to the copper core when Cl oxidizes it from theother side. As a result, the net valence on Cu is reduced but a higher valence on bpy is induced,
as predicted by the calculation.

72
Table 3.1
Calculated ground-state properties of the complexes under study (PBE0/def2TZVP). Binding energies are for the ligand L in [Cu-L]+, except for Cu+ where the binding energy is
given for Cu and bpy+. Partial charges were determined using natural population analysis.46
species
1Cu+
1[Cu-N ]+2
1[Cu-D ]+2
1[Cu-OH ]+2
1[Cu-OHCH ]+3
2[Cu-Cl]+

Figure 3.3

Binding energy[kJ/mol]
415
29
58
106
87
247

charge on Cu/ligand L/bpy+0.886 / – / +0.114+0.918 / -0.081 / +0.163+0.850/-0.003/+0.153+0.846 / +0.055/ +0.099+0.829/+0.066/+0.105+1.174 / -0.512 / +0.338

The structures for [Cu-L]+ (L = N2, D2, H2O, CH3OH and Cl)

We measured the photodissociation spectra of [Cu-L]+ by monitoring the loss of the Lligand. As shown in Table 3.1, according to the ground state calculations, the binding energies of
the L ligand in all cases are less than 290 kJ/mol (24000 cm-1), allowing dissociation by UV

73
photons. The loss of the L ligand was found to be the only dissociation channel of these ions when
the photon energy was fixed at 33870 cm-1 (see Figure 3.4).

Figure 3.4
Time-of-flight traces for electronic photodissociation of [Cu-L]+ complexes at-133870 cm (L = N2, H2O and Cl). The ion signals on the right represent the parent ions, while thesmaller peaks are fragment ion signals. Only one fragment mass is observed in each case.

Figure 3.5 shows the photodissociation spectra for all the species at 250 K trap
temperature in the UV region, together with Cu+ (room temperature) on the top for comparison.
The absorption profile in this spectral range represents the same ππ* transition located on thebpy moiety. All spectra have a discernible peak in the region of 32260 -33070 cm-1. The spectralenvelopes are quite distinct with different ligands, but the experimental signatures are broad in
all cases.

74

Figure 3.5
Photodissociation spectra at 250 K for L = N2, D2, H2O, CH3OH and Cl monitoring
the loss of L. The spectrum of Cu+ at room temperature is included for reference. The data points
in the photodissociation spectra are the raw data; the full lines are the same data smoothed by
a 10-point sliding average. Spectra in the same panel are rescaled for comparison and do notreflect relative intensity.

Computational description of this series of complexes turned out to be surprisingly
difficult. Time-dependent density functional theory (TD-DFT) completely failed to model theelectronic spectra. Different functionals including PBE0, B3LYP and BNL47,48 were used but yielded

75
inconsistent results. The computed excitation energies were often off by more than 6500 cm-1
compared to experimentally observed values. Coupled-cluster calculations using the CC2 model
also failed, probably because of a multi-configurational character of the ground state, as
evaluated by the D1 diagnostic proposed by Janssen and Nielsen.49 Calculations at the EOM-EECCSD level of theory yielded better results, but the vertical excitation energies were still
consistently 4840 cm-1 (0.6 eV) higher than the experiment. Excited state optimization led tosmall improvements of the excited state energies of the ππ* state. The difference between the
adiabatic and the experimental energy for the ππ* state is 3230 cm-1, 3550 cm-1, and 4440 cm-1
for L = N2, H2O and Cl, still significantly larger than typical deviations of EOM-CCSD, estimated to
be at 2400 cm-1 (0.3 eV).
The calculations did confirm the ππ* nature of the transition near 32300 cm-1. In addition,a lower-lying dark state was found to exist in all species. This kind of electronic structure isanalogous to bare bpy, where a dark nπ* state lies below the bright ππ* state. The only differenceis that in the coordination complex the dark state becomes a σπ* state as the bpy binds to themetal core. The computational results are summarized in Table 3.2.

76
Table 3.2
Experimental and computed excitation energies. The experimental energies list
the first discernible peaks in each electronic band. Computed energies are determined at the
EOM-EE-CCSD/cc-pVTZ level unless indicated otherwise. Computed adiabatic excitation energies
are in parentheses. All energies are given in cm-1.
speciesexperimental

Cu+[Cu-N2]+

32580
–a
32580

[Cu-OH2]+

–a
–b
32830

[Cu-Cl]+

–b
–a
–b
–b
21940
–b
–a
32420

calculated(adiabatic)
36537
37505
(35811)
31940
34763
37827
(37263)
9840
10485
14841
15083
26616
(20487)
28068
28471
37263
(35972) c

term

oscillator
strength

type

1A

0

σπ*

1B
2

0.047

ππ*

1A

2
1B
2

0
2.9×10-4

σπ*
MLCT to H2O

1B
2

0.045

ππ*

2B
2
2A
2
2B
2
2B
1

1.1×10-5
02.2×10-4
2×10-6

2A

1

0.056

2B
2
2A
2

2.4×10-5
02B
20.205c2

CT from Cl to bpy

ππ*

a This transition is symmetry-forbidden.
b This band is allowed, but has negligible calculated oscillator strength, and is too weak to

be observed experimentally.
c These values were computed using EOM-SF-CCSD instead of EOM-EE-CCSD.

In the following paragraphs we will discuss individual cases separately, starting with L =N2. The spectrum of [Cu-N2]+ shows a clear peak at 32580 cm-1, followed by a plateau which
extends shortly beyond 34000 cm-1. Lowering the trap temperature has a dramatic influence on
the spectrum. Figure 3.6 shows the photodissociation spectrum of this ion at 70 K trap
temperature. The plateau in the spectrum at higher temperature becomes a sequence of well-77
resolved peaks. The leading molecular orbitals involved in the two lowest electronic transitions
are plotted in Figure 3.7.

Figure 3.6
Photodissociation spectrum of L = N2 with trap temperature at 70 K. The photon
energy axis is relative to the 0–0 band position of the ππ* electronic band, which is found at
32580 cm-1. The full line represents experimental data, the stick spectrum shows calculated
totally symmetric (ground state) vibrations of [Cu-N2]+ (see also Table 3.3). The 0–0 band ismarked with a higher intensity for clarity, but we note that we cannot make any quantitative
statements on the expected band intensities.

78

Figure 3.7
Leading molecular orbitals for the two lowest energy transitions in [Cu-N2]+. The
upper panel shows the allowed transition to the ππ* state, the lower panel shows the orbitals
involved in the (symmetry forbidden) σπ* transition to the dark state calculated 968 cm-1 below
the bright ππ* state (see also Table 3.2).

Since there is only one bright transition in this region, the observed substructure of theabsorption band is likely due to vibrational progressions in the Franck–Condon envelope of theelectronic band. Considering the already difficult challenge of theoretically describing theelectronic structure, Franck–Condon simulations were beyond our computational resources.
However, if we assume that the vibrational frequencies in the ground and excited states are not
too far apart, we can manually pick out candidates for Franck-Condon active vibrations byinspecting the vibrational modes of [Cu-N2]+ in its ground state, similar to an earlier approach inthe study of bpy.50 Geometry optimization of the ππ* state in bpy (TDDFT with PBE0/def2-TZVP)
revealed that the main geometry changes of bpy from its ground state to its ππ* state are thelength of the central C-C bond and the CNC bond angle in the rings. Therefore, the totallysymmetric vibrations along these coordinates are the most probable contributors to the excitedstate vibrational features. The modes identified this way are mainly ring deformation modes and79
the energies of these modes are calculated and tabulated in Table 3.3. Bending and stretchingmodes of the CH groups, the N2 stretch and the Cu-N2 stretching mode should not be very FranckCondon active. If we set the electronic band origin at the first peak and mark the Franck-Condon
active modes on the energy axis according to their vibrational energies, we are able toqualitatively reproduce the band contour in fairly good agreement with the experimental result,as in Figure 3.6. One may also extract the vibrational energies from the experimental data.

Table 3.3
Experimental values were determined by fitting Lorentzian profiles with 100 cm -1
full width at half-maximum (which corresponds to the width of the 0-0 band) to the clearly
discernible peak features in Figure 3.6. The error in these peak positions is ± 10 cm-1. Calculated
values are for totally symmetric ground state vibrational modes of [Cu-N2]+ obtained with
PBE0/def2-TZVP (harmonic approximation). Additional totally symmetric modes are listed inTable 3.4.
experimental [cm-1]
179 a
347
639
747
1004 b1355 b1467

calculated [cm-1]
170/240381
673
783
1055/1098
1318/1326/1366
1538

assignment
skeletal bipy bending modes
central C-C stretch
CNC bending ring deformation
CCC bending ring deformation
ring deformation modes
central C-C stretching modes
CH bend and central CC stretcha This feature is wider than the others and likely combines two unresolved vibrational

peaks.
b Several of the modes listed could contribute since they have similar character.

If we further lower the trap temperature, nitrogen starts condensing in the trap, hindering
the generation of [Cu-N2]+. We were not able to generate a stable ion signal and measure thespectrum at temperatures lower than 70 K using our current setup. The residual width of the80vibrational features comes from the finite temperature, the excited-state lifetime, or a
combination of these two contributions.
Since N2 is chemically inert under most circumstances, one might tend to believe that
adding an N2 molecule as a ligand may not significantly change the electronic structure of theoriginal host. This assumption is corroborated by comparing the spectrum of [Cu-N2]+ and Cu+.
The peak positions are the same and the spectral profiles are very similar. There is a differencein the relative intensity of the band origin and the rest of the Franck-Condon envelope. However,we were monitoring the loss of N2 from [Cu-N2]+, and the threshold for this process is muchsmaller (see Table 3.1), therefore the 0-0 band is no longer suppressed by kinetic shift effects
that affect the photodissociation spectrum of Cu+. One other piece of evidence that supports theabove assumption is that the calculated frequencies of the vibrational modes in [Cu-N2]+ and Cu+
are very similar. This comparison is based on the calculations of the normal modes of both ionsin their ground state, which are listed in Table 3.4. The difference of the vibrational frequencies
is less than 5 cm-1 in most cases.

81
Table 3.4
Comparison of the calculated vibrational modes in [Cu-N2]+ and Cu+. Numbers are
given in cm-1.
Cu+
195
229
-a
372
670
778
1048
1099
1143
1208
1314
1319
1357
1472
1532
1636
1658
-a
3210
3217
3237
3257

[Cu-N2]+
170
240
311
381
673
783
1055
1098
1143
1205
1318
1326
1363
1474
1538
1637
1661
2262
3211
3218
3238
3251

assignment
pyridine-Cu-pyridine bend and central C-C stretch
bipy bend around central C-C bondCu-N2 stretch
central C-C stretch
CNC bending ring deformation
CCC bending ring deformation
CNC bending ring deformation
CC stretching ring deformation
CH bend
CH bendcentral CC stretch and CN stretching ring deformation
central CC stretch and CH bend
central CC stretch and CN stretching ring deformation
CH bend
CH bend and central CC stretch
CH bend and ring deformation
ring deformation
N-N stretch in N2 ligand
CH stretch
CH stretch
CH stretch
CH stretcha These modes involve the N+
2 ligand and are not present in Cu .

The spectrum of [Cu-D2]+ resembles that of [Cu-N2]+. Calculations found that the binding
energy of D2 and Cu+ is 58 kJ/mol, much higher than N2 and Cu+. The absorption maximum of [CuD2]+ is at roughly the same position as that of [Cu-N2]+ but the spectrum of [Cu-D2]+ has different
widths. These results imply that D2 may have a stronger impact on the relaxation dynamics of the82
excited state than N2 does. Consequently, neither N2 nor D2 would be useful as tags forundercoordinated metal complexes.
In the case of L = H2O, lowering the trap temperature also sharpens the spectrum but
does not lead to equally well-resolved features as in L = N2, despite that the trap temperature is
at 50 K, lower than for L = N2 (see Figure 3.8).

Figure 3.8
50 K.

Photodissociation spectrum of [Cu-OH2]+ ions (monitoring the loss of water) at

It is quite clear though, that the band contour of [Cu-OH2]+ is the similar to that of[Cu-N2]+. The band origin of [Cu-OH2]+ is shifted by 240 cm-1 towards higher energies compared
to [Cu-N2]+ and Cu+, but the major vibrational features can be found at the same distances fromthe band origin, indicating a very similar Franck-Condon progression. Calculations for [Cu-OH2]+
revealed a weak transition, lying 3065 cm-1 below bright ππ* transition. The main orbitals
involved in this transition are plotted in Figure 3.9. It has charge transfer character from Cu to83
the H2O ligand and is likely too weak to be observed in our experiment. However, its existence islikely to provide another de-excitation channel and shorten the lifetime of the ππ* state, which
can explain the greater spectral width of [Cu-OH2]+ even though the trap temperature in this caseis lower.

Figure 3.9
Leading molecular orbitals for the lowest energy transitions in [Cu-OH2]+ (seeTable 3.2 for calculated energies).

Since a water/methanol mixture was used for ESI, [Cu-OHCH3]+ was formed by the samemechanism as [Cu-OH2]+ but with a smaller ion intensity. Their spectra look almost identical (seeFigure 3.5). Considering that water and methanol both bind to the metal via the oxygen in the
ROH moiety (R = H or CH3), it appears that the immediate chelating moiety on the ligand dictates
its influence on the electronic structure of the complex.

84
Despite having a much stronger interacting ligand, [Cu-Cl]+ shows a very similar profile in
the UV region, with the band origin at 32424 cm-1, slightly shifted to the red compared to theothers. The substructure also looks similar to the Franck-Condon envelope in [Cu-OH2]+ and[Cu-N2]+. However, an important difference of [Cu-Cl]+ is the presence of an unpaired electron.
Therefore, its electronic structure is somehow unique among the series. Its ground state isdoublet and it exhibits a bright transition in the visible region. Figure 3.10 shows the full range
spectra of [Cu-Cl]+ with the trap at room temperature and at 50 K. Interestingly, the visible band
exhibits different shapes at the two temperatures. Considering the binding energy of Cu+ and Cl
is calculated to be 247 kJ/mol, it is likely that the lower energy edge of the visible band issuppressed at the low temperature due to kinetic shift. Both the visible and the UV bands in the
cryogenic spectra have significant residual spectral widths, which again supports the assumptionthat excited-state lifetime is the limiting factor for the width of the observed features.

85

Figure 3.10 Photodissociation spectrum of [Cu-Cl]+ ions (monitoring the loss of Cl) at room
temperature (top) and at 50 K (bottom). The data points in the photodissociation spectra are theraw data, the full lines are the same data smoothed by 20-point sliding average.

86

Figure 3.11 Leading molecular orbitals for the two bright energy transitions in [Cu-Cl]+ (seeTable 3.2 for calculated energies).

The calculations were able to predict the bright transition in the visible range andidentified it as ligand-to-ligand Cl-to-bpy charge-transfer (see Figure 3.11). The vertical energy(26616 cm-1) is again ca. 4840 cm-1 (0.6 eV) higher than the experimental value (21940 cm-1), butthere is a large difference (6130 cm-1) between the vertical and adiabatic excitation energies forthis state due to a significant excited state relaxation along the Cu-Cl stretching coordinate. Theband in the visible spectral range is very broad, and the band origin is less clear, likely because
there are several closely lying electronic states calculated to be in the same region (seeTable 3.2).

3.2.3.3 Summary
We studied the role of the variable ligand L in [Cu-L]+ complex ions by photodissociation
spectroscopy and computational analysis. Our study has covered species with L = D2, N2, H2O,

87
CH3OH and Cl in the visible and UV spectral range. All species show a similar band in the UV withthe origin near 32500 cm-1, which is assigned to the B2 π-π* transition localized on the bpy moiety.
Owing to the well-resolved spectrum of [Cu-N2]+ at a low trap temperature, we conclude that thesubstructure of this band is a Franck-Condon envelope contributed primarily by ring deformation
modes of bpy. Excited state lifetime is a dominating factor affecting the width of the observed
features and depends on the ligand. N2 has little influence on the electronic spectrum of Cu+, andis less perturbative than D2. H2O creates a weakly accessible MLCT state below the bright π-π*transition, which is likely to shorten the excited state lifetime. The striking similarity between the
spectra for L = H2O and CH3OH suggests that CH3OH has the same effect. Cl as a ligand alters theelectronic structure quite substantially by bringing in multiple lower-lying states, some of which
are in the visible region and at least one of them is strong enough to be observed in our
experiment. The lifetime decreases from N2 to H2O to Cl due to an increasing number of lower
lying electronic states that offer efficient de-excitation pathways. All complexes have a symmetry
forbidden A2 state closely below the π-π* state, inherited from bare bpy. While the nature of theligand does not significantly change the position of the bright π-π* transition, it drasticallychanges the excited-state dynamics.

88
3.3

Ruthenium polypyridine complexesThis section has been reproduced in part with permission from Shuang Xu, James E. T. Smith and
J. Mathias Weber, Ligand Influence on the Electronic Spectra of Dicationic Ruthenium-BipyridineTerpyridine Complexes, The Journal of Physical Chemistry A 2016, 120 (15), pp.2350–2356.
Copyright 2016, American Chemical Society.52
3.3.1 Background
Ruthenium polypyridine complexes form an important group of organometallic
compounds. They have found a wide range of applications, e.g. in dye-sensitized solar cells,53–55
or as photo- and electrochemical catalysts for water oxidation and CO2 reduction.11,13,14,56–64 Oneof their characteristic photophysical properties is strong absorption of visible light. For example,
tris(bipyridine)-ruthenium(II) has an extinction coefficients of about 14,000 M-1cm-1 at 452 nm.65
The transitions in this region have charge-transfer character and can drive reactions that can beused in artificial photosynthesis. In addition, ruthenium polypyridine complexes also haveapplications in biochemistry as shape- and enantio-selectively dyes binding to DNA and otherbiomolecules.66,67
Ruthenium coordination complexes have six coordination sites. For many applications ofruthenium polypyridine complexes, only some of the six coordination sites are occupied by theorganic polypyridine framework, and one or more sites are open. These open coordination sites
afford binding with other ligands, triggering interesting chemistry. For example, it is proposedthat the binding of water or CO2 to an open coordination site is the starting point of a catalytic
cycle for water oxidation or CO2 reduction.14,68 The interaction with such additional ligands
influences the photophysical and photochemical properties of the complex by changing the

89electronic structure of the complex, but it is not a trivial task to predict such ligand effects indetail. Experimentally, the biggest difficulty is that complexes formed in this way are rather
reactive. They are often unstable with regard to exchanging a particular type of ligand withsolvents or other reagents, and purification and isolation may not be even possible. As a result,controlling specific ligands and characterizing a single species is difficult under typical conditions
in solution. Therefore, utilization of mass selected ions in the gas phase provides a powerfulalternative that allows unprecedented and precise selection of the composition of the complex.
Owing to the absence of reaction partners in vacuo, many unstable species become accessible insuch experiments.

Figure 3.12 Structural template of the complexes under study. The ligand L represents a small
molecule (H2O, CO2, CH3CN, N2).

We have studied a series of ruthenium polypyridine complexes built on the[(tpy)(bpy)RuII-L]2+ structural template (denoted [Ru-L]2+), shown in Figure 3.12. Five of the six
coordination sites of the Ru atom are occupied by 2,2’:6’,2”-terpyridine (tpy) and 2,2’-bipyridine(bpy), leaving the last coordination site open for coordination to a small molecular ligand L. This
structure and its derivatives have been investigated by several other groups recently as an

90
important prototypical complex for the study of electrochemical and photoelectrochemical
catalysis.69–71 In this work, we made selections of L based on some proposed catalytic cycles inwhich [Ru-L]2+ is an important intermediate. The first species, [Ru-OH2]2+ (L = H2O), has been
invoked as the starting point of a catalytic circle using Ru2+ as a water oxidation catalyst.72 The
complex [Ru-OCO]2+ (L = CO2) may be an intermediate in CO2 reduction catalysis where CO2 isconverted to formate.56 Many of the reactions of Ru2+ and similar catalysts have been studied via
cyclic voltammetry experiments in acetonitrile solution. Acetonitrile is a very common solvent
and frequently used as a displaceable ligand, and it is conjectured that the catalytic cycle isinitialized by photon induced ligand substitution of [Ru-NCCH3]2+ (L = CH3CN).62,73 Hence, we
included [Ru-NCCH3]2+ in this study, too. Ruthenium complexes are also known for nitrogen
fixation ability. Nitrogen is usually a very inert molecule and is rarely used as a molecular ligand
in transition metal chemistry. However, it can bind to suitable undercoordinated transition metal
complexes and form a dinitrogen complex. The first isolation of a dinitrogen complex,
Ru(NH3)5-N2, in 196715 inspired the study of many transition metal containing nitrogen-fixing
agents, but despite growing interest, there have been relatively few spectroscopic studies on
dinitrogen complexes. Inspired by our work on [Cu-N2]+, we applied similar experimental
conditions and found the existence of [Ru-N2]2+ (L = N2).

3.3.2 Methods
The instrumentation for this experiment is the same as for the others reported in thisthesis (see Chapter 2). To generate the [Ru-L]2+ species, first we need to synthesize the part thatis common to all complexes in this series, Ru2+. The corresponding procedures were found in

91
literature70 and adapted to meet our needs. In brief, 0.25 mmol of 2,2’-bipyridine, 2,2’:6’,2”terpyridine and RuCl3 were dissolved in 15 mL ethanol and 5 mL water. To the solution 1.25 mmol
LiCl and 0.05 mL triethylamine were added and then refluxed for 4 hours at 90 C. The crude
solution was filtered, diluted 1:100 with ethanol, and electrosprayed without further purification.
The species with L = H2O, CO2 and N2 were formed in the trap by interaction with water vapor,
CO2 and N2 in the buffer gas. The lowest temperatures for formation of these complexes arearound 180 K (for water and CO2 adducts) and 70 K (for N2 adducts), respectively, since the ligand
gases freeze out at lower temperatures. The acetonitrile adduct was formed by admittingacetonitrile vapor into the second differential pumping stage where the Ru2+ complex ion cancapture an acetonitrile ligand. Since it was formed outside the cryogenic trap, we were able tolower trap temperatures down to 30 K. The specifications of the chemicals used in this study arelisted in Table 3.5.

Table 3.5

Chemicals used in the synthesis of Ru2+.
chemical name2,2’-bipyridine
2,2’:6’,2”-terpyridine
RuCl3
LiCl
triethylamine
ethanolacentonitrile

providerSigma Aldrich
Alfa Aesar
Alfa Aesar
Alfa Aesar
Alfa Aesar
Decon Labs
Sigma Aldrich

grade
>99%
97%
99.9%
99%
99%
100%
99.8%

The ground state geometry of each ion under study was calculated using density
functional theory40 (DFT) with def2-TZVP42 basis sets for all atoms. Two functionals, PBE041 and92
B3LYP,74,75 were employed to test the sensitivity of the results to the functional used. Singlet
excitation energies were calculated by time-dependent DFT (TDDFT) with the same basis sets andfunctionals. In order to improve the agreement with the experimental spectra, all predictedtransition energies were shifted to lower energies by constant offsets for all species under study.
These shifts were -1210 cm-1 for B3-LYP and -2420 cm-1 for PBE0. Charges were computed using
natural population analysis.46 All computations were performed using the Turbomole program
suite.43

3.3.3 Results and discussions
3.3.3.1 L = H2O and CO2
The aqua complex, [Ru-OH2]2+, and its derivatives have been studied in the context ofwater oxidation catalysis as it is proposed to be the initial complex of the catalytic cycle.68 The
ground state geometry optimized by DFT is shown in Figure 3.13.

93

Figure 3.13 Calculated minimum energy structures of [Ru-L]2+ for L = H2O and CO2 (the latterwith two different isomers). Carbon atoms are shown in brown, nitrogen in blue, ruthenium ingold, oxygen in red, and hydrogen in white.

The oxygen atom of the water ligand is bonded to the Ru core, forming an angle of 123
between the Ru-O bond and the aqua plane, consistent with sp3 hybridization on the O atom.
The CO2 complex has two stable 1 isomers, one with the CO2 ligand binding to the Ru atom
through an O atom, the other binding with the C atom to the metal in a metalloformate motif.
While this metalloformate motif is very common in metal-CO2 systems76 in the context of CO2
reduction catalysis, here it is calculated to be 444 kJ/mol higher in energy than the end-on isomer.
Therefore, we only consider the latter here. However, unlike many other cases, the Ru-O-C angle
in this complex is 156 instead of 180, which could be a result of the sp2 hybridization of theoxygen atoms in the CO2 ligand. The remaining lone pair on the O atom may have a very weak

94
interaction with the nearest CH group on the bpy. The binding energy of the L ligand is 106 kJ/mol
for L = H2O and 39 kJ/mol for L = CO2.

Table 3.6

Ligand binding energies EL calculated for [Ru-L]2+ using the B3-LYP functional.
species[Ru-OH2]2+[Ru-OCO]2+[Ru-NCCH3]2+[Ru-NN]2+

EL[kJ/mol]
106
39
164
87

The photodissociation spectra of [Ru-OH2]2 and [Ru-OCO]2+ at 180 K trap temperature areremarkably similar (see Figure 3.14). Both species exhibit broad, partially resolved electronic
bands within the 1MLCT envelope. The width of the observed features is likely due to lifetime
broadening, which has its origin in the ultrashort intersystem crossing lifetimes that are wellknown for Ru complexes.77 Transition energies predicted by TDDFT calculations recover theexperimental spectroscopic pattern of both complexes with similar quality (see Table 3.7),
although at higher energies the calculations for the aqua complex are in slightly better agreementwith experimental values than in the case of the CO2 complex.

95

Figure 3.14 Photodissociation spectra of [Ru-L]2+ with L = H2O (top) and L = CO2 (bottom) at
180 K trap temperature. Dots are raw data; full lines are 30-point sliding averages. The resolved
features are labeled I through V (see also Table 3.7). The vertical columns represent transitions
predicted by TDDFT calculations. The calculated transition energies are shifted by -1210 cm-1 for
B3-LYP (open columns) and -2420 cm-1 for PBE0 (filled columns).

96
Table 3.7
The positions of spectroscopic features observed in the spectra of [Ru-L]2+ for L =H2O and CO2 at 180 K trap temperature, compared to their positions as predicted by TDDFT (B3LYP functional, shifted by -1210 cm-1). No comparison is made for feature V in each case (seetext).
feature[Ru-OH2]2+[Ru-OCO]2+

I
17500 /
17583
17500 /
17634

Eexp / Ecalc [eV] ± 250 cm-1
II
III
IV
19200 / 21370 / 22580 /
18551
20487
21535
19440 / 22340 / 23550 /
18631
21212
22261

V
23960
25080

The lowest electronic bands (feature I) are found at 17500 cm-1 and are assigned to the
S1 state for both complexes (see Table 3.7). They are predominantly transitions from the highest
occupied molecular orbital (HOMO, Ru based) to the lowest unoccupied molecular orbital(LUMO, tpy based). Feature II, assigned to the S2 state in each case, is a shoulder at slightly higher
energy (see Table 3.7). These two features in the spectrum of [Ru-OCO]2+ are weaker incomparison with those of [Ru-OH2]2+. However, note that the calculated binding energy of theCO2 ligand is even lower than that of the H2O ligand (see Table 3.6), and no kinetic shift effects
are observed for [Ru-OH2]2+ (to be discussed in Chapter 5, also see Ref.78), so we rule out kinetic
shift effects for the [Ru-OCO]2+ complex as well.
The feature next higher in energy is attributed to the S3 state in both complexes. The twodominant features (IV and V) in both spectra are around the peak of the 1MLCT envelope, which
is at ca. 23400 cm-1 for the aqua complex and at ca. 24200 cm-1 for the CO2 complex. The higher
energy feature (V) in the aqua complex has been observed to diminish in relative intensity as
solvent molecules are added to the complex, despite the fact that there is no change in the(relatively weak) calculated oscillator strength.78 Therefore, it can be assumed that feature V is

97
composed of the weak electronic band calculated in this energy range and the Franck-Condon
envelope built on the more intense band (feature IV). The similarity in the calculated andexperimental spectra of the aqua- and CO2 complexes suggests that this is the case for both ofthese species.
Since [Ru-OH2]2+ is soluble in water, by comparing the absorption maximum of theaqueous solution and the center position of feature IV and V, its solvatochromic shift in aqueous
solution can be determined to be ca. -2420 cm-1. A more detailed study of the solvatochromic
shift and of solvation effects will be presented in Chapter 5.
It is important to note that kinetic shift effects that would skew the overall shape of thespectrum can be excluded, based on our work on the aqua complex.78 Since the calculated
binding energy of the CO2 ligand is even lower than that of the aqua ligand (see Table 3.6), we
rule out kinetic shift effects for the [Ru-OCO]2+ complex as well.

3.3.3.2 L = CH3CN and N2
The complexes with CH3CN and N2 are rather different than the other two in this series.
Some of the calculated information is summarized in Table 3.6. The acetonitrile and molecular
nitrogen ligands have Ru-N-C and Ru-N-N angles of close to 180 (see Figure 3.15). Hybridization
can explain the ligand alignment in these cases just as in L = H2O and L = CO2. Different from waterand carbon dioxide, the linear arrangement of acetonitrile and nitrogen ligands is consistent withthe sp hybrid orbitals of the binding N atoms in acetonitrile and nitrogen.

98

Figure 3.15 Calculated minimum energy structures of [Ru-L]2+ for L = CH3CN and N2 (the latterwith two different isomers). Carbon atoms are shown in brown, nitrogen in blue, ruthenium ingold, oxygen in red, and hydrogen in white.

The spectra of [Ru-NCCH3]2+ and [Ru-N2]2+ do not exhibit clearly resolved features likethose of [Ru-OH2]2+ or [Ru-OCO]2+ (see Figure 3.16), even at cryogenic trap temperatures. The
absence of resolved features at low temperatures supports the explanation that the large widthof the electronic bands is due to the ultrashort intersystem crossing rather than thermal
population, as already invoked for [Ru-OH2]2+ and [Ru-OCO]2+. The calculated spectra for L =CH3CN and N2 appear more congested around the most prominent bands than for the other twocomplexes. The lowest energy excitations are less pronounced than in the spectra of the latter,
despite having similar oscillator strengths predicted by calculations. The spectrum of[Ru-NCCH3]2+ has a peak at 23150 cm-1 with a pronounced high-energy tail. The spectra taken atroom temperature and at 30 K trap temperature are not very different from each other, although
the low temperature spectrum is overall somewhat narrower, most likely due to the suppressionof hot bands.

99

Figure 3.16 Photodissociation spectra of [Ru-L]2+ with L = CH3CN (top) and at room
temperature (red) and at 30 K trap temperature (blue), and with L = N2 (bottom) at room
temperature (red) and at 70 K (blue). Dots are raw data; full lines are 30-point sliding averages.
The vertical columns represent transitions predicted by TDDFT calculations. The calculatedtransition energies are shifted by -1210 cm-1 for B3-LYP (open columns) and - 1210 cm-1 for PBE0
(filled columns).

The solvatochromic shift for L = CH3CN in bulk acetonitrile solution13 is ca. 1050 cm-1 tothe red, much smaller than for the complex with L = H2O in aqueous solution78 (ca. 2420 cm-1 tothe red). This may seem to be counterintuitive, considering that acetonitrile has a much stronger
dipole moment than water. However, since the comparison is made between [Ru-L]2+ and the100solution with L as the solvent, the very first solvent molecule as a ligand has already induced ashift via the interaction with the metal core. In this case, the higher calculated binding energy ofCH3CN to Ru2+ is consistent with the larger dipole moment of CH3CN. The polarity of the solvent,while important, has a smaller effect on the solvatochromic shift than the interaction strength ofa solvent acting as a ligand coupled to the metal center.
The spectrum of [Ru-N2]2+ has a broad absorption profile peaking around 26130 cm-1 (at70 K trap temperature), and the only discernible structure is a broad shoulder at ca. 23400 cm-1.
The room temperature spectrum shows strong hot bands.
The envelopes of the calculated excited states are consistent with the experimentallyobserved spectra. Interestingly, the calculated energies for the S1 states are significantly higher
than for L = H2O and CO2 (18631 cm-1 for L = CH3CN, 21051 cm-1 for L = N2). The calculated
oscillator strength for the transition to the S1 state for L = N2 is an order of magnitude smaller
than for any of the other ligands under study.
Despite the relatively high binding energy of the CH3CN ligand (calculated to be
164 kJ/mol), there is no indication for kinetic shift effects, judging from the difference between
the spectra at room temperature and at 30 K trap temperature. The binding energy of the N 2
ligand is calculated at 87 kJ/mol, ruling out kinetic shift effects.

3.3.3.3 Calculated electronic properties
The binding energy of the ligand L and Ru2+ by calculation lies between 39 and 164 kJ/mol(3260 and 13710 cm-1), well below the spectral range of our spectra. In theory, photo-induced
loss of L should be a single-photon process. One can test this assumption by measuring the

101
fragment yield as a function of laser intensity.

Figure 3.17 shows the results of suchmeasurements. It clearly demonstrates the linear relationship between the fragment yield andthe laser intensity, the evidence of a single-photon process. Note that in the case of L = H2O,
saturation effects may be at play for the largest intensities used here.

Figure 3.17 Light intensity dependence of fragment ion yield. The laser was set to thewavelength of peak absorption for each species. The full lines show linear fits; their length
indicates which data points were included in the fitting. The legend indicates the ligand L.

The charge distributions for the ground state complexes calculated from natural orbitals(see Table 3.8) show only few general trends. The small molecular ligands carry only little positive
charge in each case. This is not unexpected, since the canonical inorganic chemistry picture

102
invokes σ donation to the metal and π back donation to the ligand,79 so the net charge on theligand may not change much.

Table 3.8
Charge distribution calculated for [Ru-L]2+ with natural binding orbitals using the
B3-LYP functional.
species[Ru-OH2]2+[Ru-OCO]2+[Ru-NCCH3]2+[Ru-NN]2+
Ru2+

Ru

L

+0.65
+0.66
+0.57
+0.54
+0.74

+0.16
+0.09
+0.20
+0.11
-

charge [e]bonding atom in L /in free molecule-0.86 / -0.92-0.54 / -0.49-0.34 / -0.32+0.006 / 0
-

bpy

tpy

+0.50
+0.53
+0.48
+0.52
+0.55

+0.69
+0.72
+0.75
+0.83
+0.71

The ligands can be polarized by the presence of the central Ru ion, and the polarization is
generally stronger for the O-coordinating ligands than for the N-coordinating ligands. The charge
on the Ru atom becomes less positive upon chelation, and the O-coordinating complexes have asimilar and more positive charge on the Ru atom than the N-coordinating ligands, which are again
similar to each other regarding the charge on Ru. The charge on the bpy does not show asystematic variation, but the charge on tpy becomes more positive along the series H2O < CO2 <CH3CN < N2. Compared to Ru2+, i.e., the complex without the ligand L, there are only smallchanges introduced by the O-coordinating ligands, whereas the effect of acetonitrile is somewhat
stronger, and N2 changes the charge on the tpy substantially. The changes in charge distributions
cannot be related to simple properties of the small ligands that would be immediately apparent
as their origin, such as ionization potential, electric dipole moment or polarizability. We note,however, that the charge on the binding atom of the ligand L is roughly correlated with the charge

103
distribution on Ru and tpy. The charge on the Ru ion becomes more positive as the charge on thebinding atom in the ligand L becomes more negative. In other words, the charge on the binding
atom in the ligand stabilizes (or destabilizes) the positive charge on the Ru ion.
TDDFT calculations yielded self-consistent results with B3LYP and PBE0 functionals, as
shown by the columns in Figure 3.14 and Figure 3.16. They qualitatively reproduced the spectralenvelopes however the absolute values were off by different amounts (as stated in the captions).
The character of the transitions is similar for all the complexes under study. The lowest twotransitions all are HOMOLUMO and (HOMO-1)LUMO, with the HOMO mainly of metal dorbital character, and the LUMO having π* character on tpy (see Table 3.9).

Table 3.9
Calculated selected transition energies (B3-LYP, shifted by -1210 cm-1) sorted by
the dominant orbitals involved in the transition.
Species[Ru-OH2]2+[Ru-OCO]2+[Ru-NCCH3]2+[Ru-NN]2+
Ru2+

HOMO
 LUMO
17581
17661
18710
21048
12742

Calculated transition energy using B3-LYP [cm-1]
HOMO-1HOMO-2 HOMO
HOMO-1HOMO-1
 LUMO  LUMO  LUMO+1  LUMO+1  LUMO+2
18548
20484
21532
22661
24032
18629
21210
22500
23065
23952
19597
21371
20161
22823
24274
22581
25000
23790
25565
26935
13629
15403
21371
23548
23871

The transitions at higher energies often involve a mixture of several initial and final
orbitals (see §3.3.3.5), but all can be characterized as metal to ligand charge transfer (MLCT)
transitions to a π* orbital on tpy and/or bpy. The TDDFT calculations predict for all complexes
that one transition has a significantly higher oscillator strength than the other transitions in thisenergy range. Its dominant character is (HOMO-1)  (LUMO+1). All four species also have chargetransfer states from Ru to the small molecular ligand L, but they are mostly calculated to be at

104
higher energies and have lower oscillator strengths. For example, the lowest MLCT state in theaqua complex that involves the aqua ligand is calculated at 25003 cm-1, and it does notcorrespond to an experimentally observed feature. The exception in this series is [Ru-OCO]2+,
where the lowest energy MLCT transition involving the CO2 ligand is calculated at 21212 cm-1.
Overall, the similarity in the character of the excitations suggests that the changes in the
spectra are caused by the differences in the charge distributions and orbital stabilization anddestabilization. The role of the binding atom in the ligand L is highlighted by the similarities
between spectra for complexes with the same binding atoms (H2O and CO2 versus CH3CN andN2).
Calculations on the excited states allow a comparison of the properties of theundercoordinated complex Ru2+ with the different experimentally accessible complexes. The
lowest three transitions to LUMO have much lower energies than in the fully coordinatedcomplexes. This can be traced to the MO energies, since the LUMO in Ru2+ is destabilized by theaddition of the ligand L (see Figure 3.18).

105

Figure 3.18

Calculated molecular orbital levels for [Ru-L]2+ and bare Ru2+.

3.3.3.4 Summary
We have studied the 1MLCT spectra of [Ru-L]2+ complexes with different small molecularligands L by cryogenic photodissociation spectroscopy and density functional theory. A
comparison of the spectra shows a strong influence of the ligand on the electronic structure of
the complex. The aqua complex and the complex with L = CO2 have similar spectra, with several
partially resolved electronic bands. In contrast, the complexes with L = CH3CN and N2 have much
more congested spectra, and different electronic bands cannot be resolved at all, even at trap
temperatures down to 30 K. Electronic spectra predicted by TDDFT calculations are in goodqualitative agreement with the experimental data. The charge distribution in the complex is on
the binding atom of the ligand L is roughly correlated with the charge distribution on Ru and tpy.

106
Our data for the two complexes for which solvatochromic shift data are available (L = CH3CN andH2O) show that the strength of the interaction of a solvent molecule in the role of a coordinating
ligand is more important than the polarity of the solvent.

3.3.3.5 Appendix
The excited-state analysis by theory also provided detailed information of each transition,
including its character and involved molecular orbitals. The orbitals involved in the prominenttransitions are listed in Table 3.10 through Table 3.14, and the contours are plotted in
Figure 3.19 and Figure 3.23.

107
Table 3.10
Lowest energy calculated electronic transition energies and oscillator strengths
for L = H2O (B3LYP functional, not shifted). Only contributions of 10% and greater are shown.
Transition

E [cm-1] / f [10-2]

12
3

18793 / 0.53
19761 / 0.8521696 / 1.15

4522584 / 0.31
22745 / 0.2567823551 / 0.005
23632 / 2.37
23874 / 10.991025245 / 1.61
26213 / 0.01

1127987 / 0.13

orbitals(see Figure 3.19)
114  115 (96.2%)
113  115 (95.9%)
112  115 (66.1%)
114  116 (24.5%)
114  117 (86.8%)
114  116 (53.1%)
113  116 (26.2%)
112  117 (91.3%)
112  116 (92.4%)
113  116 (56.8%)
113  117 (13.1%)
114  116 (12.7%)
112  115 (11.9%)
113  117 (69.7%)
113  122 (40.8%)
114  122 (27.0%)
113  124 (12.4%)
112  122 (64.8%)
112  126 (14.2%)

characterd  tpyd  tpyd  tpyd  bpyd  tryd  bpyd  tpyd  tpyd  bpyd  H2Od  H2O

108

Figure 3.19 Calculated orbitals contributing to transitions for L = H2O. Orbital numbers are
given as mentioned in Table 3.10.

109
Table 3.11
Lowest energy calculated electronic transition energies and oscillator strengths
for L = CO2 (B3LYP functional, not shifted). Only contributions of 10% and greater are shown.
Transition

E [cm-1] / f [10-2]12
3

18873 / 0.78
19841 / 0.53
22422 / 1.05

422503 / 0.02

523471 / 0.72

624116 / 0.03

7824277 / 11.0
24761 / 0.02

925165 / 1.17

1025245 / 1.68

1126777 / 0.07

1237100 / 0.55

orbitals(see Figure 3.20)
120  121 (92.9%)
119  121 (91.6%)
118  121 (52.9%)
120  122 (34.1%)
120  123 (78.2%)
120  122 (15.1%)
120  122 (34.9%)
119  122 (23.3%)
119  123 (16.8%)
120  123 (11.5%)
118  121 (11.0%)
118  123 (29.2%)
120  128 (27.9%)
119  128 (15.0%)
118  122 (10.7%)
119  122 (73.9%)
118  123 (37.2%)
119  128 (26.2%)
118  122 (15.7%)
119  123 (59.4%)
118  128 (20.0%)
118  122 (70.7%)
118  123 (21.1%)
120  129 (36.8%)
119  128 (33.3%)
118  128 (50.3%)
118  121 (17.6%)
119  125 (13.3%)

characterd  tpyd  tpyd  tpyd  bpyd  tpyd  bpyd  tpyd  tpyd  bpyd  tpyd  CO2

110

Figure 3.20 Calculated orbitals contributing to transitions for L = CO2. Orbital numbers are
given as mentioned in Table 3.11.

111
Table 3.12
Lowest energy calculated electronic transition energies and oscillator strengths
for L = CH3CN (B3LYP functional, not shifted). Only contributions of 10% and greater are shown.
Transition

E [cm-1] / f [10-2]

1
2
3

19922 / 0.51
20809 / 0.59
22342 / 0.10422584 / 0.28

523309 / 1.38

623874 / 0.01

724035 / 10.8824358 / 0.21

925487 / 0.22

orbitals(see Figure 3.21)
120  121 (90.8%)
119  121 (90.8%)
120  123 (76.1%)
120  122 (21.6%)
120  122 (48.0%)
118  121 (38.6%)
120  123 (12.0%)
119  122 (33.7%)
119  123 (27.0%)
118  121 (23.4%)
120  122 (12.6%)
118  123 (71.2%)
118  122 (26.9%)
119  122 (64.3%)
118  121 (12.6%)
120  122 (10.1%)
118  122 (71.3%)
118  123 (26.2%)
119  123 (57.6%)
118  121 (20.0%)

characterd  tpyd  tpyd  tpyd  bpyd  tpyd  bpyd  tpyd  tpyd  bpy

112

Figure 3.21 Calculated orbitals contributing to transitions for L = CH3CN. Orbital numbers are
given as mentioned in Table 3.12.

113
Table 3.13
Lowest energy calculated electronic transition energies and oscillator strengths
for L = N2 (B3LYP functional, not shifted). Only contributions of 10% and greater are shown.

Transition

E [cm-1] / f [10-2]

12322261 / 0.03
23793 / 0.46
25003 / 1.99

425407 / 0.21

526213 / 2.566726778 / 6.85
27342 / 0.02

828141 / 1.02

928165 / 1.97

1029923 / 0.10

orbitals(see Figure 3.22)
116  117 (99.1%)
115  117 (98.6%)
116  118 (65.7%)
116  119 (22.4%)
116  119 (74.5%)
116  118 (22.3%)
114  117 (65.2%)
115  119 (27.3%)
115  118 (81.2%)
114  118 (85.7%)
114  119 (12.5%)
114  119 (64.9%)
115  119 (12.0%)
116  119 (46.6%)
114  117 (22.1%)
114  119 (16.7%)
116  127 (59.9%)
116  124 (15.0%)
116  128 (13.1%)

characterd  tpyd  tpyd  bpyd  tpyd  tpyd  bpyd  bpyd  tpyd  tpyd  N2

114

Figure 3.22 Calculated orbitals contributing to transitions for L = N2. Orbital numbers are given
as mentioned in Table 3.13.

115
Table 3.14
Lowest energy calculated electronic transition energies and oscillator strengths
2+
for Ru (B3LYP functional, not shifted). Only contributions of 10% and greater are shown.
Transition

E [cm-1] / f [10-2]

113953 / 0.96

214841 / 0.11

316615 / 1.02

422584 / 0.22

523068 / 0.04

623471 / 0.11

723955 / 0.28

824761 / 8.56

925044 / 3.22

1025116 / 0.004

1136374 / 0.121227020 / 1.56

13
14
15

28149 / 13.27
29036 / 0.75
30165 / 0.25

orbitals(see Figure 3.23)
109  110 (71.1%)
109  113 (13.0%)
108  110 (10.7%)
108  110 (69.1%)
108  113 (14.5%)
109  110 (14.2%)
107  110 (70.3%)
107  113 (25.5%)
109  111 (80.4%)
109  112 (15.7%)
109  113 (72.4%)
109  110 (12.4%)
108  113 (72.1%)
108  110 (14.8%)
109  112 (75.2%)
109  111 (15.0%)
108  111 (81.5%)
108  112 (11.7%)
108  112 (54.6%)
107  113 (25.0%)
107  111 (84.3%)
107  112 (10.9%)
107  112 (76.7%)
106  110 (10.9%)
107  111 (10.7%)
107  113 (40.0%)
108  112 (23.0%)
107  110 (17.0%)
106  110 (81.9%)
105  110 (97.5%)
109  114 (93.3%)

characterd  tpyd  bpy/tpy
d  tpyd  tpyd  bpy/tpy

116

Figure 3.23 Calculated orbitals contributing to transitions for Ru2+. Orbital numbers are given
as mentioned in Table 3.14.

117
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Takeuchi, K. J., Thompson, M. S., Pipes, D. W. & Meyer, T. J. Redox and spectral propertiesof monooxo polypyridyl complexes of ruthenium and osmium in aqueous media. Inorg.
Chem. 23, 1845–1851 (1984).

71.

Jakubikova, E. et al. Electronic structure and spectroscopy of [Ru(tpy)2]2+,[Ru(tpy)(bpy)(H2O)]2+, and [Ru(tpy)(bpy)Cl]+. Inorg. Chem. 48, 10720–10725 (2009).

72.

Liu, F. et al. Mechanisms of Water Oxidation from the Blue Dimer to Photosystem II. Inorg.
Chem. 47, 1727–1752 (2008).

73.

Hecker, C. R., Fanwick, P. E. & McMillin, D. R. Evidence for dissociative photosubstitution
reactions of [Ru(trpy)(bpy)(NCCH3)2+. Crystal and molecular structure of[Ru(trpy)(bpy)(py)](PF6)2•(CH3)2CO. Inorg. Chem. 30, 659–666 (1991).

74.

Lee, C., Yang, W. & Parr, R. G. Development of the Colle-Salvetti correlation-energy
formula into a functional of the electron density. Phys. Rev. B 37, 785–789 (1988).

75.

Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic
behavior. Phys. Rev. A 38, 3098–3100 (1988).

76.

Benjamin J. Knurr. Structures and Charge Distributions of cluster anions studied by infrared
photodissociation spectroscopy (2015).

77.

Yoon, S., Kukura, P., Stuart, C. M. & Mathies, R. A. Direct observation of the ultrafast
intersystem crossing in tris(2,2′-bipyridine)-ruthenium(II) using femtosecond stimulated
Raman spectroscopy. Mol. Phys. 104, 1275–1282 (2006).

123

78.

Xu, S. & Weber, J. M. Absorption Spectrum of a Ru(II)-Aquo Complex in Vacuo: Resolving
individual charge-transfer transitions. J. Phys. Chem. A 119, 11509–11513 (2015).

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Pelikán, P. & Boča, R. Geometric and electronic factors of dinitrogen activation ontransition metal complexes. Coord. Chem. Rev. 55, 55–112 (1984).

124

4

The role of the metal

This chapter has been reproduced in part with permission from Shuang Xu, James E. T. Smith, J.
Mathias Weber, The electronic spectrum of cryogenic ruthenium-tris-bipyridine dications invacuo, The Journal of Chemical Physics, 2016, 145 (2), 024304, Copyright 2016, AIP Publishing1
and Shuang Xu, James E. T. Smith, J. Mathias Weber, UV Spectra of Tris(2,2'-bipyridine)-M(II)Complex Ions in Vacuo (M = Mn, Fe, Co, Ni, Cu, Zn) (under revision).

4.1

Introduction and background – tris(2,2’-bipyridine)-metal complexes
Perhaps not surprisingly, the role of the metal in organometallic compounds is offundamental importance. For transition metals, the d-shell configuration dictates thecoordination properties of the metal and its complexes, as different configurations result indifferent spins, geometries, stabilities and electronic structures. It has been a long pursued topic
in inorganic chemistry to characterize the properties of coordination complex as a function of themetal it contains, in order to establish some trend or series based on the metal’s place in the
periodic table. A commonly adopted strategy is to prepare a series of complexes with the same
ligands but an altering metal core. However, exceptions and anomalies are frequent and defy
simple and general conclusions. One of the inevitable drawbacks of such traditional experiments
is the presence of reaction media, such as the solvent or the crystal lattice. Typical complications
caused by these media include changing reaction kinetics, shifting the spectra and adding
undesired reactants, and therefore pose great difficulties to observe the intrinsic properties of
the target species. Experiments in the gas phase can avoid these complications. We chose toinvestigate a group of some of the most-studied complexes2,3 - tris(2,2’-bipyridine)-metal

125
complexes and obtained unprecedented details of their electronic structure by applying
photodissociation spectroscopy to these ions in vacuo.
Tris(2,2’-bipyridine)-metal complex ions, denoted [M(bpy)3]n+ (see Figure 4.1), areprototypical systems to study fundamental properties such as bonding, stability, steric effects
and photophysics.2,3

Figure 4.1

General structure of [M(bpy)3]n+ ions.

Among the [M(bpy)3]n+ species, complexes containing a d6 metal (M = Fe, Ru, Os) havereceived most attention because of their remarkable extinction coefficients for visible light, 4–24
but complexes involving other kinds of metals2,3 have been studied as well, particularly with firstrow transition metals.25–36 The earliest spectroscopy experiments on these complexes date backto 1937 and were reported by Yamasaki, who recorded the UV/vis absorption spectra of[MII(bpy)3]2+ (M = Fe, Co, Ni, Cu, Zn) in solutions.37 He compared the spectrum of free bipyridine
in water and that of the chelates and noticed that the spectral envelopes in the UV range were
all similar, except that the bands of [MII(bpy)3]2+ were shifted to longer wavelengths compared126
to free bipyridine, and that the shift depended on the metal. Such bathochromic shifts weretheoretically described by Schläfer as the result of the Stark effect on the ligands due to thecharged central metal ion.38 Nearly three decades later, Palmer and Piper measured theabsorption spectra of [MII(bpy)3]2+ (M = Fe, Co, Ni, Cu, Ru) in single crystals using polarized light.39
They were able to assign the bands in the visible range based on symmetry and polarization, but
no information on the UV bands was reported. Several other groups observed a metal dependent
splitting in the circular dichroism of [MII(bpy)3]n+ (n = 2, 3) ions in their UV bands.40,41 The
interaction of the bpy ligands, which in the case of D 3 symmetric complexes are equivalent,causes the π-π* bands to split into A2 and E components.12,41,42 The resulting splitting of thecircular dichroism response was used to determine the chirality of the complex. However, it was
realized that the actual assignment of the pair was inconclusive without further theoreticalinsight.35,36,43 Despite much previous effort, [MII(bpy)3]2+ complexes have been spectroscopicallystudied only in solutions or single crystals until recently, and low temperature data are scarce,
especially in the UV spectral region.
In this work, we studied the properties of several members of the [MII(bpy)3]2+ family (M= Mn, Fe, Co, Ni, Cu, Zn, Ru, Os) by photodissociation spectroscopy in vacuo. We have obtained
spectra of these species at low temperature and observe features that are obscured in solution
spectra by solvent-solute interaction and hot bands at higher temperatures. Despite cryogenic
preparation in vacuo, the spectra are still only partially resolved, but they show clear differences
for different central metal ions, and the spectra are in qualitative agreement with computational
predictions based on time-dependent density functional theory (TDDFT).

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4.2

Methods
The instrumentation for the experiment has been described in detail in Chapter 2. To

prepare [MII(bpy)3]2+ containing the first-row metals, a divalent metal salt (see Table 4.1) is codissolved with threefold excess of 2,2’-bipyridine (Sigma-Aldrich, ≥99%) in a 1:9 mixture (byvolume) of water and methanol (HPLC grade, EMD Millipore). The solution is used forelectrospray without further treatment.

Table 4.1
Metal salts used for production of [MII(bpy)3]2+ in this work. All chemicals wereused as received.
metal
salt
source and specified purity
Mn
MnCl2
Alfa Aesa, 97%
Fe
FeCl2
Alfa Aesa, 99%
Co
CoCl2
Sigma-Aldrich, 99%
Ni
NiI2
Sigma-Aldrich, 99.999%
Cu
CuCl2
Alfa Aesa, +99%
Zn
ZnCl2
Sigma-Aldrich, >98%
Ru
Ru(bpy)3Cl2
Sigma-Aldrich, 99.95%
Os
K2OsCl6
Alfa Aesar, Os 38.7%[Ru(bpy)3]2+ is generated by electrospraying a solution of Ru(bpy)3Cl2·6H2O inwater/methanol (1:9) solution . [Os(bpy)3]2+ requires synthesis. The procedures were found inliterature44 and were modified to be compatible with electrospray. In brief, K2OsCl6 and 2,2’bipyridine were mixed in glycerol (Alfa Aesar, 99%+) and refluxed at 240 °C for 1 hour. The green
mixture was cooled, diluted with water, then NH4PF6 (Alfa Aesar, 99.5%) was added. The resulting
solution was filtered to collect the dark green precipitation (mainly Os(bpy)3(PF6)2). The solid was
dissolved in acetonitrile for electrospray without further purification.

128
For [MII(bpy)3]2+ where M is a d6 metal, the binding energy of a bpy ligand is generally sohigh that photodissociation is energetically forbidden even in the UV region. Therefore, we used
N2 molecules as a messenger tag and measured photodissociation action spectra of[MII(bpy)3]2+·N2 for these species. This was done by injecting dry N2 into the 25-K ion trap as thebuffer gas. We were able to form adducts with up to 8 N 2 molecules (see §2.4.3, Figure 2.16).
For all other species, despite that the bpy biding energy is sufficiently low to allow
photodissociation in the UV. However, due to their low absorption cross sections in the visible
range,39 we were not able to produce observable photofragments due to limited laser power andparent ion intensity. Consequently, we were able to register only the UV bands for these species(M = Mn, Co, Ni, Cu, Zn).
We used density functional theory45 (DFT) with def2-TZVP basis sets46 for all atoms andthe B3-LYP functional47,48 to calculate the ground state geometry of each species for different
multiplicities. Different symmetry restrictions (D3, C2) were applied to explore the lowest energy
geometry, and these calculations were validated through calculations without symmetry
restriction. Excitation energies were calculated by time-dependent DFT (TDDFT49–51) with thesame basis sets and functionals, assuming that total spin was conserved. Charge analyses were
performed using natural population analysis.52 All computations were done using the Turbomole
program suite.53,54

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4.3

Results and discussions

4.3.1 Computational
We performed the geometry optimization for all species with and without symmetry
restrictions. The results are listed Table 4.2. Since the calculation without symmetry restriction(C1) preserves all degrees of freedom in the system, the configuration with minimum energy canbe considered as the absolute minimum. If the energy resulting from a certain symmetryrestricted calculation is very close to the minimum energy calculated without symmetry
restriction, this is evidence that the ion adopts this symmetry.

Table 4.2
Calculated ground-state energies for the [MII(bpy)3]2+ species in this study (in-1cm ) with different symmetries (D3, C2, C1) and spin configurations. The lowest energy for eachspecies is listed in bold font.
M
Mn
Co
Ni
Cu
Zn
Fe
Ru
Os

D3
low spinhigh spin-71740.134 (S=2)-71741.012-71738.611 (S=4)-78046.200-78047.370-81463.891-81463.891-85058.364-88839.177-74807.644-74807.559-43004.382-43001.255-42889.563-42886.958

C1

C2-71741.013 a-78047.372 a-81463.892 a-85059.299-88839.176-74807.647 b-43004.382 b-42889.562 b-78047.302 a-85059.259

a high-spin configurationb low-spin configuration

Following this logic, from Table 4.2, we can immediately conclude that all species follow
D3 symmetry in their ground state, except [Cu(bpy)3]2+, which takes C2 symmetry, probably due

130
to strong Jahn-Teller distortion as is often the case in other Cu II complexes.55 This suggests a
fundamentally different electronic configuration in [Cu(bpy)3]2+ than in the rest of the series.
Indeed, the electronic spectrum of [Cu(bpy)3]2+ appears to be distinct from others boththeoretically and experimentally. Therefore, [Cu(bpy)3]2+ is discussed alone in §4.3.2.
For the species with D3 symmetry, according to experiments by Burstall and Nyholm56,[MII(bpy)3]2+ takes the highest possible spin multiplicity for M = Mn, Co, Ni, Zn. This observationis corroborated by our DFT calculations as well. Lower spin states of these species are higher inenergy compared to the highest possible spin state, except for M = Ni, where the singlet andtriplet states are within 0.1 kJ/mol. The opposite is true for M = Fe, Ru, Os, i.e. the d6 metals, andall of their ground states are singlet states. The d6-metal complex ions are also distinct regarding
their complex geometries and binding energies.
Shown in Table 4.3 are geometric data together with calculated binding energies of the
bpy ligand and the charge distribution on the metal. The d6-metal complex ions have shorter
metal-nitrogen bond lengths than the other complexes studied here. The charge on the metal ismuch lower than in other species, meaning Fe, Ru and Os are significantly reduced by the bpy
ligands. More importantly, the binding energy of the bpy ligand in M = Fe, Ru, Os is remarkably
higher than that of the others. While for M = Mn, Co, Ni, Cu, Zn, the binding energy lies between
147 and 232 kJ/mol (12100 and 19360 cm-1), which is well below our spectral range in the UV andshould not result in kinetic shift effects that could distort the spectral profile, the high binding
energy in M = Fe, Ru, Os ( > 333 kJ/mol, 27830 cm-1) demands messenger tagging to perform
photodissociation spectroscopy. Consequently, we will discuss the d6 metal complexes in §4.3.4,
separate from the other species. The complex with M = Cu is different from all others, since it

131
has different symmetry. It will therefore also be discussed separately, in §4.3.2. The othercomplexes (M = Mn, Co, Ni, Zn) will be discussed in §4.3.3.

Calculated geometric properties and binding energies of [MII(bpy)3]2+.

Table 4.3

M
Mn
Co
Ni
Cu a
Zn
Fe
Ru
Os

bindingenergy(kJ/mol)
204
194
232
147
166
333
379
424

NN distance(Å)

NCCN dihedral(degrees)

M-N bond
length (Å)

chargeon M (e)

2.71
2.68
2.67
2.67/2.72
2.70
2.61
2.64
2.62

10.35
5.42
5.61
4.08/14.3
7.66
2.28
1.58
1.53

2.29
2.18
2.14
2.12/2.30
2.21
2.02
2.10
2.10

1.44
1.43
1.36
1.38
1.66
0.73
0.55
0.80

a In C symmetry, the bpy ligand on the C axis has a slightly different structure than the22other two bpy ligands. In the Cu entry, the number after the slash belongs to the bpy on the C 2
axis. For the M-N bond length, 2.12 Å is the average bond length of the two M-N bonds of theoff-axis bpy ligands.

4.3.2 M = Cu
The ground state of [Cu(bpy)3]2+ is a doublet, similar to many other CuII complexes. Strong
Jahn-Teller distortion of this species results in C2 symmetry, with two elongated Cu-N bonds on
the bpy ligand along the C2 axis (see Table 4.2). The spectrum of [Cu(bpy)3]2+ is broad and almostfeatureless. The allowed electronic transitions are of A and B symmetry. The TDDFT calculations
show that there are a significant number of transitions of similar intensity distributed throughout
the observed spectral region. Assuming that broad Franck-Condon envelopes are present formost of the transitions, such a high density of electronic states is almost certain to be responsible

132
for much of the broadness of the absorption profile. The computed spectrum is able toqualitatively reproduce the experimental spectral profile if the most intense B transition isaligned with the observed peak at 34600 cm-1. This requires a shift of -1610 cm-1 of the calculated
spectrum, which is applied in Figure 4.2. We tentatively assign the peak at 34600 cm-1 to the mostintense B transition. It has π-π* character and mainly involves the bpy ligand on the C2 axis. Notethat not all transitions in this region are of π-π* character, as some transitions involve orbitals
with significant density on Cu. Using the solution spectrum from Yamasaki,37 the solvatochromic
shift in aqueous solution is estimated to be ca. 1040 cm-1.

Figure 4.2
Photodissociation spectra for the [Cu(bpy)3]2+. The grey points are raw data; thefull lines represent 10-point sliding averages to guide the eye. The vertical bars are calculated A(red) and B (blue) transitions, shifted by -1610 cm-1.

133
4.3.3 M = Mn, Co, Ni, Zn
These species show D3 symmetry in the ground state and have similarities regarding the
calculated charges on the metal atoms and the binding energies of the bpy ligands. It is therefore
conceivable that their electronic structures should also bear significant similarities, which issubstantiated by our calculations and experimental observations.
The spectrum of [Ni(bpy)3]2+ displays the most resolved structure among all species in thisstudy. The level of spectroscopic detail in our spectrum exceeds that in the previously reported
spectra measured in frozen solutions at 77 K.35,36 The spectrum shows a prominent peak at 33150
cm-1, followed by a series of smaller peaks. The calculated spectrum is qualitatively consistent
with the experimental observations, but needs to be shifted by -2820 cm-1 to better match thecalculated pattern to the experimental spectrum. The most intense peak in the experimental
spectrum is identified as the strongest calculated A2 transition, which has π-π* character. The
substructure of the band closely resembles that of [(bpy)Cu-N2]+ except that the peaks are 480
cm-1 higher in energy. Based on this similarity, the substructure in [Ni(bpy)3]2+ can be attributed
to the Franck-Condon envelope belonging to vibrations on the bpy ligands (mainly ring
deformation modes), similar to [(bpy)Cu-N2]+ (see Figure 4.3, §3.2.3 and Ref.57).

134

Figure 4.3
Photodissociation spectrum of [Ni(bpy)3]2+ (top) compared to that of [Cu(bpy)-N2]+
57(bottom). Note that the two spectra have slightly shifted wavenumber axes to emphasize theirsimilarity. The points in the upper trace are raw data; the full line is 5-point sliding average to
guide the eye.

The main differences between the spectra of [Ni(bpy)3]2+ and [Cu(bpy)-N2]+ are the peak
positions and widths. The vibrational bands in the Franck-Condon progression of the [Ni(bpy)3]2+
spectrum are broader than those in the spectrum of [Cu(bpy)-N2]+. Since the spectrum of[Ni(bpy)3]2+ was acquired at a lower trap temperature (25 K) than for [Cu(bpy)-N2]+ (70 K), we canrule out hot bands as a cause of the residual broadening. Note that an important broadening

135
mechanism in [Cu(bpy)-L]+complexes is lifetime broadening due to internal conversion to lower
lying states.57 Therefore, the same mechanism may be at play here as well. In fact, ourcalculations show that there are many more lower lying states in [Ni(bpy)3]2+ than in [Cu(bpy)N2]+, which lends credence to this argument.
Another possible factor contributing to the spectral width is the overlap of multiple bands.
Notably, the interaction among the three bpy ligands leads to splitting of their otherwise
degenerate π-π* bands into A2 and E bands, with the E band usually at a lower energy. Although
the intensities of the lower lying bands are typically weaker, their Franck-Condon progressions
will overlap with the more intense A2 band envelope and lower the observed contrast of thevibrational structures belonging to the A2 band. Our TDDFT calculations put the splitting of theA2 and E bands in [Ni(bpy)3]2+ at ca. 400 cm-1 and predict an intensity ratio of A2:E ≈ 2.2. But if thiswas true, the E transition would be resolved as a separate peak to the red of the prominent A2
peak. However, our spectrum does not show any partially resolved feature on the low-energy
slope of the A2 peak. We can obtain an estimated upper limit on the A2-E splitting by the half
width of the A2 peak, i.e. 120 cm-1, which is very close to the splitting estimated by Bray et al.35
to be 100 cm-1. This small amount of energy difference leads to more overlapping of theenvelopes built on different origins, and thus more severe congestion of the substructures. Both
excited state lifetime and A2-E splitting may contribute to the width of the substructure of theobserved bands, but it is likely in the case of [Ni(bpy)3]2+ that the main contribution comes fromlifetime broadening, since the low-energy slope of the dominant peak shows no substructure,and it can be fitted with high fidelity by a Lorentzian line shape.

136

Figure 4.4
Photodissociation spectra of the [MII(bpy)3]2+ complexes studied here (M is notedin the corresponding panel). The grey points are raw data; the full lines represent 10-point sliding
averages. The vertical bars are calculated A2 (red) and E (blue) transitions for each metal; they
are shifted by a certain amount to match the experimental results (see text).

The spectra of the complexes with M = Mn, Co, Ni and Zn are shown in Figure 4.4, together
with our TDDFT calculations. The spectra of [Co(bpy)3]2+ and [Zn(bpy)3]2+ qualitatively resemble

137
that of [Ni(bpy)3]2+, but they have less resolved substructure. The prominent peaks in these
spectra are at similar positions, 33470 cm-1 for [Co(bpy)3]2+ and 33230 cm-1 for [Zn(bpy)3]2+, close
to that of [Ni(bpy)3]2+ (33150 cm-1). Therefore, we assign them to the same A2 π-π* band.
[Co(bpy)3]2+ and [Zn(bpy)3]2+ also shows extensive features following the A2 band, which again
can be attributed to the Franck-Condon progressions building on the A2 band. However, thesubstructures are less distinct compared to [Ni(bpy)3]2+. The calculated spectra need to be offset
by -2980 cm-1 for [Zn(bpy)3]2+ and -2420 cm-1 for [Co(bpy)3]2+ to match experimental andcalculated spectra. There are weakly discernible shoulders on the low energy side of thedominant A2 features for Co and Zn, which we tentatively interpret as experimental signatures of
the accompanying E bands. The calculated A2-E splittings and A2:E intensity ratios for [Co(bpy)3]2+
and [Zn(bpy)3]2+ are all similar to that calculated for [Ni(bpy)3]2+, but they fit better to theexperimental spectra than for [Ni(bpy)3]2+. A more notable and extensive shoulder can be foundin the even lower energy region in the spectra of M = Co and Zn but much less so for M = Ni. It isalmost 1610 cm-1 to the red of the intense A2 peak, therefore, it is unlikely to be related to the E
band. A more plausible candidate for this feature is a set of lower-lying π-π* states, which is also
predicted by the calculations, though the calculated energies are somewhat lower than theposition of this shoulder.
If we assume that the width is limited by excited state lifetime, the difference of thespectral width for different species suggests that the lifetime depends on the metal atom, or –more precisely – on the exact electronic structure of the complex. We note that simpler
electronic structures (i.e., fewer lower lying states) do not necessarily result in longer lifetimes.
An interesting case is [Zn(bpy)3]2+, which contains a d10 metal, so its electronic structure does not

138
allow low-lying d-d or MLCT transitions. However, the prominent feature that is observed in theexperimental spectrum and assigned to the second A2 state (the 5th excited state overall) is
broader than the analogous feature in the [Ni(bpy)3]2+ spectrum, which belongs to the 22nd
excited state. Obviously the sheer number of lower lying states is not as relevant as the coupling
to some of them and coupling seems to be dependent on the metal itself. Within our present
computational treatment, no simple trend can be found that would explain the different widthsof these spectra.
With the gas-phase spectrum, it is possible to calculate the absolute solvatochromic shift
in the condensed phase. The solution spectrum of [Zn(bpy)3]2+ in a frozen mixture of methanol
and water at 77 K is available from the literature,32 and comparison with our data shows asolvatochromic shift of ca. -830 cm-1 for this solvent mixture.
Finally, the [Mn(bpy)3]2+ spectrum has a broad and featureless band in the same range as
for all other spectra in this series. No detailed information can be extracted, except a generalsimilarity in the calculated pattern. The calculated spectrum in Figure 4.4 is shifted by-2420 cm-1, purely for consistency with the treatment of the related species (M = Co, Ni, Zn) in
this series. The dominant A2 and E transitions fall in the same region as everyone else and match
the position of the experimentally observed band. Because the calculated spectrum is equallysparse, we assume that the width of the features is caused by even shorter lifetimes comparedto the others. This may not be very surprising as [Mn(bpy)3]2+ is a sextet and may have access tomany intersystem crossing pathways.

139
4.3.4 M = Fe, Ru, OsThis group of [MII(bpy)3]2+ species makes up almost half of the literature on tris(bpy)metal complexes. Unlike the other species in the present work, they have much brighter MLCT
bands in the visible region, making their solutions strongly colored. This photophysical property
makes them potentially useful as photosensitizers or light harvesting dyes and is the main reason
for the attention they have received. Due to the high binding energy of the bpy ligands in these
species, we had to resort to N2 tagging and measured the photodissociation spectra of[MII(bpy)3]2+·N2. The loss of N2 from the parent ions is the only significant fragment channel, evenin the UV. We will start our discussion with M = Ru, because [Ru(bpy)3]2+ is the most studiedcomplex of the three.
The photodissociation spectrum of [Ru(bpy)3]2+·N2 throughout the visible and near UV isshown in Figure 4.5 together with the solution spectrum. Similar to [Mn(bpy)3]2+, the intense A2and E transitions with π-π* character predicted by theory in the UV region appear only as a broad
and featureless peak (feature IX) at 36100 cm-1. In contrast, in the visible range, the two featuresthat are barely resolved in aqueous solution at ca. 22100 cm-1 and 23200 cm-1 are now two veryclear, well resolved bands peaking at 23160 cm-1 (feature IV) and 24660 cm-1 (feature V). Several
shoulders appear at lower energies (features I - III, the onset at about 18700 cm-1), and around26230 cm-1 (feature VI). Some weaker and broader bands (VII, VIII) are observed around 29500
cm-1 and 32000 cm-1. These transitions in the visible and near UV have been attributed to MLCT
states.58 The two main peaks in the visible MLCT band show considerable shifts compared tosolutions. Features IV and V are shifted by -1060 cm-1 and -1460 cm-1 in aqueous solution,
respectively, and their relative intensities also change. Such differences are not unexpected

140
because the intensity of hot bands in the solution spectrum is higher, which may lead to changes
in the overall peak shapes. The overview spectrum in vacuo reported by Kirketerp and Nielsen15
at room temperature appears more similar to the solution spectra, which supports this argument.

Figure 4.5
Photodissociation action spectrum of [Ru(bpy)3]2+·N2 at 25 K trap temperature(upper) compared to the UV/vis absorption spectrum of an aqueous solution of Ru(bpy) 3Cl2 (25M). The data points in the photodissociation spectrum are raw data; the full line is 30-point slide
average. The vertical bars are calculated A2 (red) and E (blue) transitions; they are shifted by 800
cm-1 to the blue to match the experimental results. Distinct features are labeled by Roman
numerals as discussed in the text.

141
Although our TDDFT calculation using B3LYP/def2-TZVP yield a spectral pattern that isqualitatively consistent with the experimental spectrum, the calculated energies are somewhat
too low. The calculated spectrum is shifted by 800 cm-1 to the blue to match the most intense
bands in the experimental spectrum. Using the shifted calculation to aid the assignment of theobserved features, we identify the two intense bands IV and V as E transitions, and feature VI
tentatively as an A2 transition. The assignment of features VII and VIII has been controversial.
Meyer and coworkers assigned feature VII to an MLCT transition based on molecular orbitalarguments,5 but others speculated that features in this region could be metal centeredtransitions.58 Our TDDFT calculations suggest that both features are predominantly MLCT bands.
Finally, the most intense feature in the spectrum (IX) can be attributed mostly to two unresolved
intense transitions of π–π* character, one of A2 symmetry and one of E symmetry, similar to thefeatures exhibited in the spectra of other species in this region (see §4.3.3).
The lower-energy features (I-V) are not well represented by our simple approach. Heully
et al.,59 who used TDDFT calculations including spin-orbit coupling, were able to provide asimulated spectrum that better matches our result. The effect of the spin-orbit operator on the
ground and excited states in the MLCT band region is discussed in Ref.59 The three highest
occupied orbitals in the ground state of [Ru(bpy)3]2+ are metal-centered, two of e symmetry andone of a1 symmetry. Only those will be significantly affected and mixed by the (atomic) spin-orbit
operator, while the spin-orbit splittings on the ligand-centered virtual orbitals are expected to besmall. Here, only singlet excited states are considered since direct transitions to the triplet
manifold are electric dipole forbidden, and absorption cross sections may be too low for to be142
observed. Figure 4.6 shows more detail of the MLCT bands in the experimental photodissociation
spectrum.

Figure 4.6
Zoom-in onto the MLCT band of the photodissociation spectrum of [Ru(bpy)3]2+·N2in Figure 4.5. The full grey line is the absorption spectrum in aqueous solution as shown in thelower panel of Figure 4.5, scaled to have the same MLCT peak intensity as the photodissociation
spectrum. The calculated transitions (lower panel) are displayed as bars (full: Heully et al.59; open:
this work). Both calculated spectra is graphically offset by 800 cm-1 to allow easier comparison
and assignment. Note the logarithmic scale for the oscillator strength.

Assuming that the onset of the experimental spectrum represents the very first transition,
the calculated transitions by Heully et al.59 are about 800 cm-1 too low in energy. This is the same

143
amount of shift that has been applied to our calculations in Figure 4.5. Therefore, we show theshifted calculation results by Heully et al.59 as well as our own in the same graph to compare withthe experiment in Figure 4.6. The lowest energy feature in the experimental spectrum (I) is rather
weak and has an onset at ca. 18700 cm-1. It rises to a shoulder at 18900 cm-1 with a plateau that
continues until the photodissociation yield steps up again. We assign this feature to the lowest
three dipole allowed states calculated by Heully et al.59 The lowest discernible band in the
spectrum is probably dominated by the 2E’ transition (the S2 state) because of its higher oscillator
strength. The S1 state (1A2’) may be slightly lower than 18700 cm-1, based on the difference of
200 cm-1 between the S1 state and the S2 state, and because it has a much smaller oscillator
strength as calculated by Heully et al., we may not be able to observe it. Feature II, beginning at
20100 cm-1, has some substructure and extends up to 21200 cm-1. It can be assigned to a
combination of the 3A2’ and 6E’states. A shoulder at 21900 cm-1 (III) is consistent with the 8E’
state, and the two most intense features in the MLCT region can be easily assigned to the 11E’
(IV) and the 12E’ states (V). Clearly, the calculations taking the spin-orbit coupling into accountcan describe the low energy region of the electronic spectrum in a much more accurate way thanour simple TDDFT calculations do. Unfortunately, no assignment from spin-orbit correctedcalculations is available for the higher energy features. Note that in both Heully et al.’s59 and ourwork, the calculated oscillator strengths for the lower energy transitions relative to the mostintense MLCT features are too low by a factor of 10-100, compared to the experiment. The
summary of the assignments using calculations with and without spin-orbit coupling presented
in Table 4.4.

144
Table 4.4
Transition energies and oscillator strengths for selected calculated excited states
59(TDDFT with and without spin-orbit interaction) of [Ru(bpy)3]2+ compared to experimentallyobserved features. Solvatochromic shifts are calculated only for discernible features in bothaqueous solution and gas phase spectra.
computationalenergystatea[cm-1]
1A2’
18065
2E’
18242
3E’
18478
2A2’
19197
3A2’
19487
with
4E’
19714
spin-orbit coupling
59(Heully et al. )
6E’
20007
8E’
20827
5A2’
20844
9E’
21004
6A2’
21842
11E’
22015
12E’
23411
2E
22429
3E
23507
3A2
27014
without
spin-orbit coupling
4E
28516(this work)
9E
31659
14E
36066
8A2
36783

oscillator
strengths
2·10-61.3·10-3
3.8·10-4
2.2·10-7
6·10-41.7·10-5
8.4·10-4
9.6·10-4
2.9·10-4
1.3·10-5
6.8·10-5
1.3·10-2
1·10-1
1.7·10-2
2.0·10-1
6.8·10-3
2.0·10-2
1.5·10-1
4.2·10-1
7.6·10-1

energy[cm-1]

experimental (this work)
solvatochromic
featurebshift, aq. [cm-1]

18900

I

20100

II
-

c

21900

III

23160
24660
23160
24660
26230
29500
32000

IV
V
IV
V
VI
VII
VIII

-1060
-1460
-710
-1240
-1170

36100

IX

-1320

a The state designation follows that given in Ref.59 Calculated values shown in bold areassigned to the corresponding experimentally observed features.
b See Figure 4.5.
c Cannot be determined due to lack of resolved feature in the solution spectrum.

It is worth questioning whether the presence of the N2 tag affects the electronic
spectrum. Previous work by Nielsen and coworkers established that the presence of an
acetonitrile molecule does not have a significant effect on the room temperature spectrum of

145[Ru(bpy)3]2+.60 One may expect that the binding energy of the N2 tag to [Ru(bpy)3]2+ (calculated
to be ca. 5 kJ/mol) is smaller than that of acetonitrile, because the latter has a sizeable electric
dipole moment. Therefore, it is convincing that the presence of the N2 tag will not have asignificant effect on the spectrum. Since our TDDFT calculations give a reasonable qualitativedescription of the experimental spectrum, we performed exploratory TDDFT calculations forstates up to 30000 cm-1 for complexes with and without N2 tagging. The results are almost
identical, confirming that the effects of an N2 tag on the overall pattern of the electronic
spectrum are negligible (see Figure 4.7).

Figure 4.7
Comparison of TDDFT calculations (B3LYP/def2-tzvp) for [Ru(bpy)3]2+ (filledcolumns) and [Ru(bpy)3]2+·N2 (open columns).

[Fe(bpy)3]2+. This ion has an electronic structure very similar to that of [Ru(bpy)3]2+, but
the transitions are found at lower energies. The full spectrum, shown in Figure 4.8, can be also

146
divided into MCLT and π-π* regions. The calculated spectrum of [Fe(bpy)3]2+ using B3LYP/def2TZVP is able to qualitatively reproduce the experimental spectral profile. Analogous to thetreatment of the [Ru(bpy)3]2+ data, a shift of -3390 cm-1 is applied to the calculated spectrum toalign the first intense transition to the first prominent feature (II).

Figure 4.8
Photodissociation action spectrum of [Fe(bpy)3]2+·N2 at 25 K trap temperaturecompared to the UV/vis absorption spectrum of its aqueous solution adapted from Ref.24 (top).
The points in the photodissociation spectrum are raw data; the full line is a 20-point sliding
average. The lower panel shows A2 (red) and E (blue) transitions calculated using ecp-10-mdf anddef2-tzvp basis sets for Fe. The results are shifted by 3390 cm-1 to the red to better match theexperimental results. Note the logarithmic scale for the oscillator strength.

147
Assignments can be made based on the shifted, calculated spectrum as listed in Table 4.5.
The solvatochromic shift of [Fe(bpy)3]2+ in aqueous solution is calculated by comparing our
experimental data with the solution spectrum.24

Table 4.5
Transition energies and oscillator strengths for selected calculated excited states(TDDFT without spin-orbit interaction, B3LYP/def2-tzvp) of [Fe(bpy)3]2+ compared toexperimentally observed features. Solvatochromic shifts are calculated only for discerniblefeatures in both aqueous solution and gas phase spectra.
computationalenergy oscillatorstate[cm-1]
strength2E
22153
2.3·10-3
3E23437
3.6·10-2
4E
24634
7.5·10-2
5E25774
6.8·10-3
4A2
29343
2.5·10-2
6E30044
1.5·10-2
11E
34063
8.2·10-2
14E
35846
3.6·10-1
8A2
36749
6.4·10-1

energy[cm-1]
19300
19970
21570
23230

experimental
solvatochromic
featureashift, aq. [cm-1]
b
I
II
-1170
III
-1200
b
IV
-

26480

V

-580

29310

VI

-740

34360

VII

-860

a See Figure 4.8.
b Cannot be determined due to lack of resolved feature in the solution spectrum.

It should be noted that in the cases of [Fe(bpy)3]2+ and [Ru(bpy)3]2+ calculations using thedef2-TZVP basis set attribute the electronic transitions to different types of molecular orbitals,
even though the transitions appear to have the same character judging from experimental
observation. It is realized that this is simply because the basis set for Fe in def2-TZVP does not
apply an effective core potential as it does for Ru. To make the calculations comparable, we used
an ecp-10-mdf basis set (for the Fe atom only) and recovered a similar result as for [Ru(bpy) 3]2+.

148
The same shift (-3390 cm-1) needs to be applied to match the low energy region, i.e., the MLCT
region of the spectrum. The description of the MLCT bands using the ecp-10-mdf basis set is very
similar to the def2-TZVP result, but the energies of the higher transitions are significantly
underestimated (see Figure 4.8). Unfortunately, higher-level computations considering spinorbit coupling are currently beyond our computational resources, which prevents more detailed
discussions on the MLCT region.
[Os(bpy)3]2+. Our experimental spectrum of [Os(bpy)3]2+ shows less distinct features thanfor M = Fe and Ru. Because the parent ion intensity of [Os(bpy)3]2+·N2 was five times lower thanthose of [Ru(bpy)3]2+·N2 and [Fe(bpy)3]2+·N2, the signal-to-noise ratio is worse in this case. It is
however clear that the spectral profile in [Os(bpy)3]2+ is different from the spectra of the othertwo complexes, even though the main bands are found in the same energy regions and are
predicted by calculations to have the same overall character (see Figure 4.9).

149

Figure 4.9
Left: Photodissociation action spectrum of [Os(bpy)3]2+·N2 at 25 K trap
temperature with TDDFT calculation using B3LYP/def2-tzvp (unshifted). The data points in thephotodissociation spectrum are raw data; the full line is 40-point sliding average. Right: Zoom
into the MLCT band (gray points and green line) and comparison with the absorption spectrum(gray line) in acetonitrile solution measured by Shaw et al.61 (upper panel) and calculated spectra(lower panel, full columns: Ronca et al.62; open columns: this work). The gray columns represent
singlet transitions and the black are transitions to the triplet manifold, enabled by spin-orbit
coupling. Note the logarithmic scale for the oscillator strength.

We compare our experimental results with our own TDDFT calculations and withcomputational work including spin-orbit coupling by Ronca et al.62 Our calculation of singlet
transitions reproduces several strong transitions but again fails to account for spectral features
observed in the lower energy range. The calculations by Ronca et al.62 corroborate our
calculations for singlet transitions, but predict more states in the low energy region, which canbe assigned to experimental features. Tentative assignments using the same strategy as
employed for [Ru(bpy)3]2+ are given in Table 4.7.

150
Table 4.6
Transition energies and oscillator strengths for selected calculated excited states
2+of [Os(bpy)3] (TDDFT with62 and without spin-orbit interaction) compared to experimentallyobserved features. Solvatochromic shifts are calculated only for discernible features in bothaqueous solution and gas phase spectra.
computational
stateasingletexcitations

Ronca
et al. aspin-orbit
coupling

this work singlet excitations

S1: 1A2
S2,3: 1E
S4,5: 2E
S6: 2A2
S7,8: 3E
ST2,3: 1E
ST8,9: 3E
ST22,23:
8E
ST25,26:
9E
ST34,35:
12E
1A2
2E
3E
3A2
8E
12E
7A2

energy[cm-1]
18083
19373
20043
21019
22108
16091
16962

oscillator
strengths
1.0·10-201.38·10-1
2·10-32.06·10-1
1.5·10-2
2.1·10-2

20527

6.0·10-2

20785

5.8·10-2

22672

1.7·10-1

18015
20268
22094
24610
29838
36110
36709

2.7·10-3
4.2·10-2
2.1·10-1
9.3·10-3
2.3·10-1
3.8·10-1
7.3·10-1

experimental (thiswork)
energyfeatureb[cm-1]
17740
II
20700

III

22310
16140

IV
I

17740
20700
22310
24160
27890

II
III
IV
V
VI

36530

VIII

a The state designation follows that given in Ref.62 Calculated values shown in bold areassigned to the corresponding experimentally observed features.
b See Figure 4.9.

Spin-orbit coupling is stronger in atoms with higher nuclear charge, such as Os, leading toultrafast decay channel of singlet excited states into the triplet manifold. As a result, the lifetimeof excited states in Os complexes is presumably shorter,5 which also broadens the spectrum. The

151
absorption spectrum by Shaw et al.61 was measured in acetonitrile solution and in the visible
range. The solvatochromic shift can be determined only for features III-V in our spectrum, and its
magnitude is about 930 cm-1.

4.4

Summary
All [MII(bpy)3]2+ species in this study show broad absorption profiles in the UV region from

29000 to 37900 cm-1. The spectra contain multiple π-π* transitions on the bpy ligands in thisspectral range. In solution spectra,37 most [MII(bpy)3]2+ species exhibit only a broad double-peakfeature in the UV. Here, we are able to resolve some of the substructures that underlie thisfeature. The spectra for M = Co, Ni, Zn are very similar, with some variation in the overall widthof observed features and with small differences in their absolute positions. The spectra of otherspecies show only a single broad, largely unstructured band. Results from TDDFT calculations arein qualitative agreement with the experimental spectra. The most intense UV transition for eachspecies with D3 symmetry is of A2 symmetry, one branch of the π-π* transitions. For most species,
the calculated excitation energies are higher than experimental values, which is not unexpected,
since the calculations yield vertical excitation energies.
The species containing d6 metals (M = Fe, Ru, Os) show bright and broad transitions in thevisible, which are characterized as MLCT bands. The band energies follow the order Fe > Ru > Os,
consistent with our TDDFT calculations. While TDDFT calculations without spin-orbit interaction
qualitatively recover the overall spectral profiles, it is necessary to incorporate spin-orbit
interaction to interpret the smaller features observed on the low-energy onset of the spectra, atleast for M = Ru and Os. Computational work by Heully et al.59 and Ronca et al.62 provides a much

152
better description of the electronic structures of [Ru(bpy)3]2+ and [Os(bpy)3]2+ in the low energy
region.
Since we have only the spectrum in the UV region for all the [M II(bpy)3]2+ species in thiswork, we summarize the spectral behavior from both experiment and theory in Table 4.7 only
for the π-π* bands.

Table 4.7
Experimental and calculated band positions and other characteristics forcomplexes with D3 symmetry.
M
Mn
Fe
Co
Ni
Zn
Ru
Os

dominant transitions(experimental) [cm-1]
A2
E34350 a
34360
33880
33470
33150
33150
33230
32910
36100 a36530 aA2-E splitting in dominantbands [cm-1]
experimental calculated
411
480
903
320
347
428
320
532
717
599

shift ofTDDFT [cm-1]
-2420
-2420
-2420
-2820
-2980
+800
0

solvatochromic
shift of the A2
peak b [cm-1]
-910
-680
-680
-660
-1320
-

a The spectrum is broad and the A /E transitions cannot be discriminated. The number is2

the peak location in this case.
b shift for aqueous solution 37 relative to values in vacuo.

Previous studies have attempted to describe the physical and chemical properties of thecomplexes as a function of the metal and to form trends along the periodic table. In the past,absorption wavelength has been used as a parameter to describe the interaction strength
between the metal and the ligand, based on the argument that stronger interaction leads to agreater shift of the absorption wavelength of the ligand upon chelation.63,64 For instance, thebathochromic shift of the UV band of the bpy ligand has been used for attempts to describe the153[MII(bpy)3]2+ series along these lines. Modern quantum chemistry methods allow us better
describe this interaction and its results, such as geometric parameters and charge distribution.
The results of our DFT calculations have been summarized in Table 4.3. We cannot observe any
simple correlation between these physical properties and our spectroscopy data, or find a simple
trend that would reflect the empirical order of stability established by Irving and Williams65. The
experimental spectra in this work show new spectroscopic details and our results can be used tobenchmark existing computational methods and to provide solid assignments of many of the
bands observed in [M(bpy)3]2+ complex ions. The observation of Franck-Condon envelopes inmany of the complexes studied here highlights the power of cryogenic ion spectroscopy in vacuo
for the study of metal-organic complexes.

154
4.5

Appendix

Table 4.8
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Mn(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.10).

Figure 4.10

Transition
10E

E [cm-1] / f [10-2]
34200 / 15.6

5A234440 / 19.1

16E

35730 / 13.5

9A236130 / 32.1

20E

40000 / 5.6

11A240250 / 7.8

orbitals
24a1 β  44e β (27.6%)
44e α  46e α (20.8%)43e β  44e β (17.8%)
25a1 α  46e α (14.4%)43e β  44e β (43.2%)
44e α  46e α (31.7%)
24a1 β  23a2 β (13.5%)43e β  23a2 β (62.0%)44e α  23a2 α (31.7%)
24a1 β  23a2 β (59.1%)
25a1 α  23a2 α (27.1%)
44e α  24a2 α (20.2%)43e α  23a2 α (18.3%)43e β  24a2 β (16.2%)
25a1 α  24a2 α (36.8%)
24a1 β  24a2 β (32.4%)

Molecular orbitals of [Mn(bpy)3]2+ involved in the transitions listed in Table 4.8.

155
Table 4.9
Calculated (B3LYP/def2-tzvp) energies (E) and oscillator strengths (f) of some of
the intense electronic transitions of [Fe(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.11).

Figure 4.11

Transition
11E
14E

E [cm-1] / f [10-2]
34037 / 8.2
35811 / 35.6

8A236779 / 64.1

orbitals
44e  47e (78.9%)
24a1  45e (28.8%)43e  23a2 (27.3%)
44e  47e (13.5%)43e  45e (13.4%)
24a1  23a2 (40.6%)43e  45e (28.0%)
44e  47e (18.7%)

Molecular orbitals of [Fe(bpy)3]2+ involved in the transitions listed in Table 4.9.

156
Table 4.10
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Co(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.12).

Figure 4.12

Transition
12E

E [cm-1] / f [10-2]
34521 / 5.1

13E34601 / 9.8

6A2

34763 / 13.9

16E35569 / 18.3

9A235972 / 34.4

orbitals43e β  45e β (45.4%)44e β  45e β (22.9%)25a1 α  46e α (15.1%)
24a1 β  45e β (60.4%)
25a1 α  46e α (19.5%)44e α  46e α (11.4%)
44e α  46e (41.8%)43e β  45e β (28.7%)44e β  45e β (11.4%)43e β  23a2 β (38.9%)44e α  23a2 α (32.5%)44e β  23a2 β (16.4%)
24a1 β  23a2 β (48.4%)
25a1 α  23a2 α (31.9%)

Molecular orbitals of [Co(bpy)3]2+ involved in the transitions listed in Table 4.10.

157
Table 4.11
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Ni(bpy)3]2+ in the region of our spectrum. Only orbitals with contribution
greater than 10% are shown (see Figure 4.13).

Figure 4.13

Transition
8E

E [cm-1] / f [10-2]
34309 / 3.7

10E34524 / 6.9

5A2

34635 / 13.7

14E35515 / 17.1

8A2

35985 / 37.5

orbitals
44e α  46e α (63.9%)25a1 α  46e α (14.3%)
25a1 β  45e β (45.6%)
25a1 α  46e α (42.4%)44e β  45e β (40.5%)44e α  46e α (40.0%)44e β  23a2 β (56.8%)
44e α  23a2 α (29.4%)
25a1 β  23a2 β (43.5%)
25a1 α  23a2 α (35.4%)

Molecular orbitals of [Ni(bpy)3]2+ involved in the transitions listed in Table 4.11.

158
Table 4.12
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Cu(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.14).
Transition
18B

E [cm-1] / f [10-2]
34037 / 8.1

22A

35004 / 14.7

25B

35730 / 7.4

27B

36134 / 23.5

30B
31B

37102 / 10.8
37182 / 9.7

34B

37989 / 10.6

orbitals
66b α  71a α (34.1%)
66b β  71a β (29.0%)59b β  70a β (12.0%)
66b β  68b β (26.3%)
64a β  70a β (17.2%)
69a α  71a α (11.5%)
66a α  68b α (11.3%)62b β  70a β (17.7%)58b β  70a β (13.4%)61b β  70a β (10.8%)69a β  69b β (37.9%)70a α  69b α (33.1%)
60b β  70a β (46.2%)
59b β  70a β (31.6%)60b β  70a β (30.5%)68a β  69b β (67.2%)
69a α  69b α (17.1%)

159

Figure 4.14

Molecular orbitals of [Cu(bpy)3]2+ involved in the transitions listed in Table 4.12.

160
Table 4.13
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Zn(bpy)3]2+ in the region of our spectrum. Only orbitals with contribution
greater than 10% are shown (see Figure 4.15).

Figure 4.15

Transition
1E
2E
1A2

E [cm-1] / f [10-2]
34521 / 7.6
34763 / 9.3
34843 / 18.2

3E
2A235650 / 15.3
36214 / 35.3

orbitals
45e  46e (94.7%)
25a1  46e (93.3%)45e  46e (85.2%)
25a1  23a2 (11.1%)
45e  23a2 (91.3%)
25a1  23a2 (83.1%)
45e  46e (7.1%)

Molecular orbitals of [Zn(bpy)3]2+ involved in the transitions listed in Table 4.13.

161
Table 4.14
Calculated (B3LYP/ecp-10-mdf) energies (E) and oscillator strengths (f) of some of
the intense electronic transitions of [Fe(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.16)

Figure 4.16

Transition
1E

E [cm-1] / f [10-2]
17885 / 0.03

1A2
3E

18585 / 0.007
24548 / 4.0

4E
6E
13E

25792 / 7.3
31143 / 1.635053 / 19.1

14E

36181 / 27.7

8A237045 / 58.2

orbitals
23a1  47e (52.3%)
43 e  47e (39.4%)
43 e  47e (93.3%)43e  44e (70.0%)
23a1  44e (18.2%)
43e  22a2 (96.1%)
43e  23a2 (98.3%)
43e  46e (53.0%)
23a1  46e (14.8%)
43e  46e (35.9%)42e  22a2 (20.1%)
22a1  44e (17.7%)
43e  46e (33.1%)
22a1  22a2 (31.8%)42e  44e (22.6%)

Molecular orbitals of [Fe(bpy)3]2+ involved in the transitions listed in Table 4.14.

162
Table 4.15
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Ru(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.17).
Transition
1A2
1E
2E

E [cm-1] / f [10-2]
20850 / 0.12
20883 / 0.01
22429 / 1.7

3E23507 / 20

4E
6E28516 / 230799 / 0.4

9E31659 / 15

14E

36066 / 428A236783 / 76

orbitals
23a1  22a2 (99.3%)
23a1  44e (97.9%)43e  22a2 (77.5%)43e  44e (21.5%)43e  44e (76.0%)
43e  22a2 (21.6%)
43e  23a2 (98.5%)
23a1  48e (28.8%)
23a1  47e (20.7%)43e  45e (18.4%)
43e  48e (14.2%)
43e  47e (10.0%)43e  45e (46.4%)
23a1  46e (20.2%)
43e  24a1 (17.2%)
22a1  44e (44.1%)
42e  44e (23.6%)42e  44e (52.0%)
22a1  22a2 (21.4%)
43e  46e (10.2%)

163

Figure 4.17

Molecular orbitals of [Ru(bpy)3]2+ involved in the transitions listed in Table 4.15.

164
Table 4.16
Calculated energies (E) and oscillator strengths (f) of some of the intenseelectronic transitions of [Os(bpy)3]2+ in the region of our spectrum. Only orbitals with
contribution greater than 10% are shown (see Figure 4.18).
Transition
1A2
1E
2E

E [cm-1] / f [10-2]
18015 / 0.27
18708 / 0.01
20268 / 4.2

3E22094 / 21.2

4E
6E

26579 / 1.8
28654 / 4.7

8E29838 / 22.7

12E

36110 / 38.2

7A236709/ 73.2

orbitals
23a1  22a2 (99.5%)
23a1  44e (98.3%)
43e  22a2 (85.7%)
43e  44e (13.5%)43e  44e (83.9%)43e  22a2 (13.0%)43e  23a2 (97.2%)
23a1  46e (81.2%)
43e  24a1 (9.3%)
43e  45e (44.2%)
43e  24a1 (36.2%)
23a1  46e (14.1%)
22a1  44e (49.9%)42e  44e (26.4%)
42e  44e (65.3%)
22a1  22a2 (13.1%)

165

Figure 4.18

Molecular orbitals of [Os(bpy)3]2+ involved in the transitions listed in Table 4.16.

166
4.6

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172

5

The role of the solvent

This chapter has been reproduced in part with permission from Shuang Xu, James E. T. Smith, J.
Mathias Weber, Hydration of a Binding Site with Restricted Solvent Access – Solvatochromic Shiftof the Electronic Spectrum of a Ruthenium Polypyridine Complex, One Molecule at a Time, The
Journal of Physical Chemistry A 2016, 120 (39), pp.7650–7658. Copyright 2016, American
Chemical Society.1

5.1

Introduction
While experiments in vacuo allow the investigation of intrinsic properties of ions, there isoften a lack of connection between isolated systems that are computationally easier to treat andsystems in an environment (e.g. solutions), where additional chemistry occurs via interaction
between solute and solvent. For instance, when studying homogeneous catalysts, even thoughprobing important intermediates in the catalytic cycle in vacuo has, undoubtedly, potential foryielding important results, one may still find it difficult to use such information to gauge how
electronic modification changes performance in catalysis, because homogeneous catalysts workin solution after all, and the effects of solvation may eventually need to be taken into account toproperly understand the mechanism. Recent work by Garand and coworkers has shown thatsolvation of a ruthenium catalyst by a number of water molecules indeed induces oxidation of
the aqua ligand in the complex.2 In this sense, the isolated ions may be too simple to address therelevant mechanisms in catalysis. However, solvation effects can be studied in an
unprecedentedly clear fashion by using solvated cluster ions, i.e. employing photodissociation
spectroscopy of ions solvated with a well-defined number of solvent molecules.

173
One of the important solvation effects is the solvatochromic shift, which is the shift ofabsorption peak of a compound in solution compared to that of the bare compound. The shift is
usually dependent on the nature of the solvent and is typically measured as a relative shift indifferent solvents. The “absolute” shift is unattainable unless the spectrum of the unsolvatedcompound (e.g. gas phase) is available. There are some interesting questions in this regard, forexample: What is the role of individual solvent molecules and solvation shells? What is theircontribution to the total solvatochromic shift?
Theorists have designed several approaches to model the solvation process and tocompute the solvatochromic shift. One approach that reflects the collective influence of solvent
is to treat the solvent as a continuum with given dielectric permittivity (“COnductor-like
Screening MOdel”, COSMO)3 or polarizability (as in “Dielectric Polarizable Continuum Model”, DPCM).4,5 This approach (implicit models) circumvents the high computational cost that would
incur if individual solvent molecules were considered (explicit models). Sometimes, the latterapproach is necessary. Intuitively, as the number of solvent molecule incorporated in thecalculation grows, the accuracy improves but the computational cost quickly becomesprohibitive. Then the question is, how many solvent molecules should be taken into account, if
needed, to yield a result with reasonable accuracy?
To answer this question, one needs to compare the performance of calculations to theresults from experiments. However, the control of the microsolvation environment, particularly,of the number of solvent molecules present is impossible in solution. In gas-phase experiments,
it is possible to produce solvated cluster ions by condensing solvent molecules on the solute ionsin an ion trap.2,6–10 Furthermore, combination of mass spectrometry with spectroscopy allows

174
selectively studying the properties of ionic species surrounded by well-defined number of solvent
molecules. This development opens the possibility of capturing an “intermediate” state ofmolecular ions between the condensed phase and the gas phase. Experimental results of ionssolvated by a defined number of solvent molecules then become available to benchmark
theoretical computations on exactly the same systems.

5.2[(tpy)(bpy)RuII-OH2]2+ solvated by 0 - 4 H2O molecules

5.2.1 BackgroundIn §3.3 we presented our study of a series of ruthenium polypyridine complexes, one ofwhich is [(tpy)(bpy)RuII-OH2]2+ (bpy = 2,2’-bipyridine, tpy = 2,2’:6’2”-terpyridine), denoted as [RuOH2]2+. It is believed to be the starting point in the catalytic cycle of water oxidation driven by thecatalyst Ru2+. By comparing our photodissociation spectrum of [Ru-OH2]2+ in vacuo11 and its
spectrum in aqueous solution,12 we were able to measure the absolute solvatochromic shift ofthe visible MLCT band. However, as pointed out in §5.1, it remains unknown how watermolecules contribute to the overall solvatochromic shift.
The solvatochromic behavior of the 1MLCT band in aqueous solution is a very interesting
problem. One can construct a simple picture by considering the following. The MLCT transitions
involve the Ru2+ ion as well as the hydrophobic bpy and tpy ligands. Solvent access to Ru2+ isrestricted to a single coordination site, which is occupied by an aqua ligand in aqueous solution.
The polypyridine ligands have a small amount of positive charge in the ground state. 13 Upon
excitation, they gain partial negative charge, making them more hydrophobic. Hydration candestabilize a proton on the aqua ligand, as observed in infrared spectroscopic studies,2 which

175
offers the possibility of “launching” proton transfer into the solvent environment. As aconsequence, a change in the electronic structure of the complex is introduced and the 1MLCT
band can be expected to report on this change.
One way to follow how the electronic structure evolves with hydration is to measureelectronic spectra of stepwise hydrated species. Previously, Garand and coworkers2 have probed
the vibrational structure of mass selected [Ru-OH2]2+·(H2O)n clusters (n = 0 – 4) and showed thatthe interaction between the aqua ligand and the Ru center is strongly affected by the presenceof solvent molecules. In particular, the presence of H-bonded networks serves to assist in chargetransfer into the Ru-OH2 bond, anticipating proton transfer into the microhydration environment
in the first step of the water oxidation reaction. To study the electronic structure, we measured
the electronic spectra in the MLCT region of mass selected [Ru-OH2]2+·(H2O)n clusters (n = 0 – 4).
As found earlier by Garand and coworkers, the first few solvent water molecules form a network
anchored on the aqua ligand2 so we can selectively probe the solvatochromic shift induced bysolvent effects on the Ru2+ environment, one solvent molecule at a time. The experimental
results can be used to compare with computations to show whether and to what extent
theoretical predictions are accurate.

5.2.2 Methods
The instrumentation for the experiment has been described in detail in Chapter 2 and themethod of generating [Ru-OH2]2+ has been reported in §3.3. To produce [Ru-OH2]2+·(H2O)nclusters the temperature of the ion trap was set between 160-180 K and water vapor was
introduced as the buffer gas to condense water molecules onto the ions in the trap. The use of

176
water vapor as buffer gas was found to be crucial to the formation of larger clusters, but the highpartial pressure of water vapor in the trap results in condensation on the trap electrodes andcauses unstable ion signal after a certain amount of experiment time. As a result, the trap
temperature had to be raised to defrost about every 5 hours. An example of mass spectrum isshown in Figure 3.1 with instrument parameters optimizing larger clusters.

Figure 5.1
Mass spectrum showing the formation of [Ru-OH2]2+·(H2O)n with instrument
parameters optimized for n = 3. Mass peaks marked with asterisk are unidentified.

We measured the photodissociation spectra of all [Ru-OH2]2+·(H2O)n clusters. Since theclusters exhibit multiple dissociation pathways and thus different photofragments (see §5.2.4),

177
as mentioned in §2.4.2, the full absorption spectrum is better represented by the depletion
spectrum rather than fragment action spectra. However, because the absorption cross section of[Ru-OH2]2+ is very high (the maximum extinction is 15000 M-1cm-1 at 476 nm12) and the OPO
output in this wavelength region is very intense, up to 30% loss of parent ions in each ion packet
was observed with radiation near 476 nm. Since this is cannot be justified as a small factionalloss, we must adopt the modified Lambert-Beer’s law to calculate the absorption cross section
according to §2.6.3.14
For computations we used the Turbomole suite15,16 of programs to perform geometry
optimization, population analysis and excited state calculations. Ground state structures for[Ru-OH2]2+·(H2O)n (n = 0 – 4, multiple isomers) and related species were optimized employing
density functional theory17 using the B3LYP17,18 functional and def2-TZVP basis sets for all atoms.
Electronic excitation spectra were calculated using time-dependent DFT with the same functionalin two different sets of calculations. In one series, we used def2-TZVP basis sets again for all
atoms. This approach yields a qualitative description of the bare complex,13 and we therefore
judge it to be an appropriate tool for the clusters under study. All calculated excitation energies
in this series reported here are shifted by -1210 cm-1 to improve agreement with theexperimental spectrum for n = 0. However, with our resources these calculations were only
possible up to n = 3. In order to obtain calculated values for the solvatochromic shifts of all cluster
sizes, we repeated the calculations starting from the same optimized ground state structures, butwith def2-SV(P) basis sets for all atoms. The latter series was shifted by +2420 cm-1 to improve
agreement with the experimental spectrum for n = 0.

178
5.2.3 Bare complex and calculations
The photodissociation spectrum of [Ru-OH2]2+ at room temperature and at 180 K(Figure 5.2) has been discussed in detail in §3.3.3. We will briefly repeat the main observations
regarding the bare ion here in order to help understand the spectra of the solvated ion.

Figure 5.2
Photodissociation action spectrum of [Ru-OH2]2+ at 180 K trap temperature.
Circles are raw data; the line is a 15-point sliding average. Vertical bars are calculated transitionenergies (B3LYP/def2-TZVP), shifted by -1210 cm-1.

The 1MLCT band, which is a mostly featureless broad band at 21010 cm-1 (476 nm) insolution,12 reveals rich, partially resolved substructure in vacuo, even at room temperature.11 At
180 K,13 a signature corresponding to the first excited singlet state (S1) is observed at
17300 cm-1, followed by two discernible bands at 19300 cm-1 and 21400 cm-1, which we assign to
the S2 and S3 excited states. The two most intense signatures are peaks at 22600 cm-1 and
23900 cm-1. TDDFT calculations qualitatively reproduce the experimentally observed pattern.

179
Several weak bands predicted by the calculations near 22000 cm-1 are likely obscured by theenvelope of the stronger electronic bands in the region. The band envelope of the 1MLCT band
extracted from the gas phase spectrum is found at 23390 cm-1, resulting in a total solvatochromic
shift of -2380 cm-1 in aqueous solution. No resolved vibrational structure was observed in theelectronic bands. The singlet excited states are thought to decay on ultrashort timescales via
intersystem crossing to the triplet manifold19 due to the large spin-orbit interaction typical for Ru
compounds. The width of the observed bands is most likely caused by a combination of lifetime
broadening and spectral congestion from the Franck-Condon envelopes of the excited electronic
bands as well as hot bands.11
When [Ru-OH2]2+ is solvated by water, a water network is expected to form around theaqua ligand, as confirmed by our calculations of the ground state geometry for all clusters in thisstudy, which are summarized in Figure 5.3.

180

Figure 5.3
Calculated minimum energy structures of [Ru-OH2]2+·(H2O)n showing the lowest
energy structure for n = 0 and 1 and several low-energy structures for n ≥ 2. Their energies
relative to the lowest energy conformer at 0 K are shown in the brackets. Carbon atoms areshown in brown, nitrogen in blue, ruthenium in gold, oxygen in red, and hydrogen in white.

The calculated structure of the monohydrate, [Ru-OH2]2+·H2O is consistent with work by
Garand and coworkers.2 Only one low-lying stable isomer is found, and the solvent moleculebinds directly to the aqua ligand. Structures where the water ligand binds to one of thepolypyridine ligands are ca. 29 kJ/mol and more above this low-lying geometry. There are two
low lying structural motifs for the dihydrate, [Ru-OH2]2+·(H2O)2. In one motif (2-A), the aqua
ligand and the two solvent molecules form a chain, where the second solvent molecule can beviewed as the onset of the second solvation shell. This isomer is lowest in energy at both 0 K and
180 K. In the other isomer (2-B), the two solvent molecules are equivalent, both acting as H-bond181
acceptors from the aqua ligand. The 2-B isomer is 0.1 kJ/mol higher in energy (zero-point
corrected) at 0 K and 0.7 kJ/mol higher at 180 K. The threshold energies for loss of the “second”
water molecule are very similar for both isomers, and the two isomers can be viewed as
isoenergetic. Some of the structural motifs of the tri- and tetrahydrates have also been discussed
in Ref.2 The additional water molecules continue to build the H bonding network anchored at theaqua ligand. The calculated lowest energy structures have four membered rings (isomers 3-A and
4-A). These structures are calculated to be significantly lower in energy than the others we found(ca. 7.8 kJ/mol for n = 3 and 11.3 kJ/mol for n = 4). Hydration around the polypyridine ligands ispossible with greater n values but is less favorable than at the aqua ligand. According to
exploratory calculations, a probable conformer of this type is at least 29 kJ/mol higher in energy
than those with hydration around the aqua ligand. Therefore, we believe the conformers in
Figure 5.3 are the main contributors to the population in our experiment.
The binding energy of additional water molecules decreases with the size of clusters,
which is also expected (see Table 5.1

Zero-point corrected binding energies of watermolecules in [Ru-OH2]2+·(H2O)n clusters. The binding energy for n =2 is the same for bothconformers. The values for n = 3 and 4 are upper limits, based on the most strongly boundisomers found for these cluster sizes.Table 5.1). Note that the binding of the aqua ligand issignificantly higher than the solvent water molecules, reflecting the direct interaction with themetal ion.

Table 5.1
Zero-point corrected binding energies of water molecules in [Ru-OH2]2+·(H2O)nclusters. The binding energy for n =2 is the same for both conformers. The values for n = 3 and 4
are upper limits, based on the most strongly bound isomers found for these cluster sizes.

182

water molecule binding energy [kJ/mol]aqua ligand
90
solvent, n = 1
58solvent, n = 2
50solvent, n = 3
47solvent, n = 4
49
Since [Ru-OH2]2+ has its absorption maximum at 442 nm, absorption of a photon at thiswavelength (equivalent to ca. 270 kJ/mol energy input) will suffice to “evaporate” more than one
solvent molecule, if existent, which results in the presence of multiple dissociation pathways andphotofragments for n ≠ 0. Indeed, we did observe two dominant decay channels: the loss of allsolvent molecules at lower energies within the 1MLCT band and the loss of all water molecules(solvent and aqua ligand) at higher energies. In addition to the fragment action spectra, we alsomeasured the photodepletion spectra of all cluster sizes. This study illustrates the issue raised in§2.4.2 - the connection and difference between absorption, photodissociation action anddepletion spectra.
As pointed out in §2.4.2, for photodissociation spectroscopy to faithfully represent theabsorption spectrum, the primary condition is that any non-dissociative fate after
photoexcitation during the observation window of the experiment should be negligible. For thepresent case, photon emission from [Ru-OH2]2+ has been found to be very weak,12 which fulfills
the requirement. Photodissociation of the parent ion on must occur in the time scale of theexperiment (ca. 15 s), and this condition is of particular importance at low photon energies. To
verify that this condition is also met, we recorded the photodissociation spectrum of [Ru-OH2]2+
with a slower ion beam, allowing more time of flight after photoexcitation (20 s versus 16 s),and detected no difference compared to the result from the faster beam (see Figure 5.4).

183

Figure 5.4
The photodissociation action (observation time: green - 16 s; blue - 20 s) anddepletion spectra (red) of the bare aqua complex [Ru-OH2]2+. Slow beam action spectrum shows
up to 24000 cm-1. All three spectra can be considered to be equivalent within the signal-to-noise
ratio of the experiment.

For the bare aqua complex [Ru-OH2]2+, which has only one photodissociation pathway,
photodissociation action and depletion spectra are identical. However, this is not true forsolvated species. For the latter, adding the action spectra of all photodissociation pathways
should in principle yield the absorption spectrum. However, in this experiment, the fragments
may have different detection efficiencies and backgrounds so the signals in different action
spectra may not be comparable. Moreover, strong and different kinetic shift effects in the action
spectra were observed for different photofragments (see §5.2.4). We will therefore use
photodepletion data to present the absorption spectrum. Because the spectrum of bare
[Ru-OH2]2+ shows no kinetic shift effects, and the calculated binding energies of solvent watermolecules in [Ru-OH2]2+·(H2O)n clusters are substantially lower than that of the aqua ligand (see184
Table 5.1), it can be assumed that photodissociation of the clusters upon photoexcitation is fasterthan for the bare aqua complex. Consequently, the photodepletion spectra of the clusters should
also be free of kinetic shift effects and are therefore representative of the absorption spectra.
In this experiment, each laser pulse depletes up to 30% of the parent ion in a single shot,
the approximate linear relationship between the depletion ratio and the absorption cross nolonger holds. To calculate the absorption cross section, one needs to use the modified LambertBeer law introduced in §2.6.314
𝑌𝑃 (𝜆)= 1 − 𝛼 + 𝛼𝑒 −𝜎(𝜆)𝐹(𝜆)𝑃
where 𝛼 is a parameter indicating the overlap between laser and ion packet, and 𝐹(𝜆) is thephoton fluence. The overlap parameter 𝛼 can be extracted from the fluence dependence of thedepletion. We set the laser at 442 nm where the absorption of [Ru-OH2]2+ peaks and measured
the ratio of surviving parent ion and the total parent ion 𝑌𝑃 (𝜆 = 442 nm)/𝑃. Then we varied thephoton fluence 𝐹 by inserting neutral density filters and plotted 𝑌𝑃 (𝜆 = 442 nm)/𝑃 as afunction of 𝑒 −𝜎(𝜆=442 nm)𝐹 (see Figure 5.5).

185

Figure 5.5
Data points are 𝑌𝑃 (𝜆 = 442 nm)/𝑃 as a function of 𝑒 −𝜎(𝜆=442 nm)𝐹 . Linear fitting(red) returned 𝛼 = 1.00.

Using the data from Ref.12 the maximum absorption cross section can be calculated to be
5.7 × 10−17 cm2 . Here 𝜎(𝜆 = 442 nm) is taken as this number, which should have a value thatis sufficiently accurate for extracting the overlap parameter 𝛼 in this step. Fitting of the data using
the function f(x) = 1 − 𝛼 + 𝛼x yielded an almost 100% overlap between laser and ion packet(𝛼 = 1.00, standard error 0.05). As a result, the absorption cross section 𝜎(𝜆) can be linked tothe observed signal via
𝜎(𝜆) = − ln (𝑌𝑃 (𝜆)) /𝐹(λ)𝑃This equation will be used in lieu of the linear approximation for representing theabsorption spectra processed from our photodepletion data in this chapter.

186
5.2.4 The hydrated clusters
Figure 5.6 shows the depletion and action spectra for the monohydrate and the dihydrate
clusters (n = 1 and 2). The depletion spectrum appears to have less substructure in the 1MLCT
band, while the action spectra demonstrate similar substructure as in the bare aqua complex.
This is due to the inherently lower signal-to-noise ratio for depletion spectra. The lower panel
contains the action spectra of both photofragments: Ru2+and [Ru-OH2]2+, the inset being thelatter.

Figure 5.6
Photodissociation spectra for [Ru-OH2]2+·H2O (left) and [Ru-OH2]2+·(H2O)2. Upper
panels: photodepletion spectra and calculated vertical excitation spectra (B3LYP/def2-TZVP,
columns, shifted by -1210 cm-1). For [Ru-OH2]2+·(H2O)2, the open columns represent the 2-A
isomer and the filled columns represent the 2-B isomer. Lower panels: photodissociation action
spectra monitoring the yield of [Ru-OH2]2+ (open circles, grey full lines) and Ru2+ (filled circles,
black full lines). Circles are raw data points; the full lines are 15-point sliding averages.

187
It is clear that the action spectra depend on the photofragment formation efficiencies.
The fragment channel corresponding to the loss of a single water molecule (presumably thesolvent, calculated threshold energy 57.9 kJ/mol) clearly shows the low energy onset (S1 and S2
states). The fragment channel corresponding to the loss of two water molecules – albeit
detectable – is significantly suppressed at low photon energies, but this channel (calculated
threshold energy 147.6 kJ/mol) takes over and dominates the shape of the spectrum above
19400 cm-1. This can be explained by interpreting the loss of the water molecules as a sequential
process, with an energy-dependent change in survival probability of the [Ru-OH2]2+ intermediate
fragment ion (i.e., after the solvent molecule has been lost). With sufficient energy input, this ion
will also lose the aqua ligand, leading to the observed increase of the branching ratio into in the
Ru2+ fragment channel for higher photon energies.
By comparing with the bare aqua complex, we find that all discernible electronic bandsof [Ru-OH2]2+·H2O are red-shifted by ca. 320 cm-1. This can be interpreted as the solvatochromic
shift of each electronic band caused by the presence of a single solvent water molecule. The
center of gravity and the envelope of the 1MLCT band exhibit a much stronger red-shift of ca.
570 cm-1. This may be due to a shortening of the Franck-Condon progressions on the high energy
side of each band, which exacerbates the red-shift of the overall envelope. The TDDFT
calculations qualitatively reflect the observed red-shift of the individual bands, but they show no
drastic changes in oscillator strengths.
The substructure in the 1MLCT region of the dihydrate spectra is less distinct than that of
the monohydrate. The 1MLCT band center of gravity and envelope shift by -720 cm-1 and-800 cm-1, respectively. The two isomers of the dihydrate result in similar calculated TDDFT

188
spectra, and the differences between the calculated spectra are not sufficient to unambiguously
assign the experimental spectrum to one particular isomer. Similar to the monohydrate, Ru2+and [Ru-OH2]2+ were the only observable photofragments. Again, the yields of the two fragments
show different photon energy dependence, but the Ru2+ channel becomes dominant occurs at
ca. 21000 cm-1, higher in energy than in the case of the monohydrate. This is not surprisingbecause the loss the two or three water molecules demands higher energy input. The S1 and S2
states are not resolved in any of the dihydrate spectra. Monitoring the generation of[Ru-OH2]2+·H2O did not yield any significant signal in the entire spectral region, which means thatthe survival probability of the [Ru-OH2]2+·H2O intermediate fragment ion is vanishingly small on
the time scale of our experiment. While TDDFT calculations qualitatively predict the red-shift ofthe dihydrate, the magnitude of the shift is underestimated.
Parent ion intensities for clusters with n = 3 and 4 were at the edge of the sensitivity ofour photodissociation spectrometer, resulting in a low signal-to-noise ratio, but the spectra forthese species can still be observed (see Figure 5.7).

189

Figure 5.7
Photodissociation spectra for [Ru-OH2]2+·(H2O)3 (left) and [Ru-OH2]2+·(H2O)4(right). The top panels contain the photodepletion spectra and the lower panels show the action
spectra monitoring different photofragments as labeled. The dots are raw data points; the fulllines are 30-point sliding averages.

The depletion spectra show further red-shifts of the 1MLCT band center of gravity andenvelope. As seen in the smaller clusters, Ru2+ and [Ru-OH2]2+ are still the dominating
photofragments and the yield of Ru2+ is suppressed in the lower energy region. Note that theaction spectra are scaled to fit the panel, therefore, the visual intensities are not comparable.

190
5.2.5 Solvatochromic behavior
Figure 5.8 shows all the depletion spectra obtained in this study together with thesolution spectrum adapted from Ref.12 From the spectra of the solute at different stages ofhydration it is possible to determine the solvatochromic shift for each cluster and to comparewith the solution spectrum. However, because the spectra have very different shapes and they
progressively lose spectroscopic detail as solvation increases (see Figure 5.8), they cannot bedirectly compared to the solution spectrum. Therefore, a reference point that can be used for all
spectra needs to be determined in order to quantitatively evaluate the spectral shifts at different
stages of solvation. A good numerical measure for the solvatochromic shift would be the peakshift of the envelope of each spectrum. We applied two approaches to fulfill this task. In one
approach, the center of gravity of the 1MLCT band for each spectrum was determined by first
integrating the curve underneath the experimental 1MLCT band. Integration limits were the lowenergy end of the experimental data and the point where the 200-point sliding average(100-point for n = 4) went through a minimum on the high energy side of the band. The center ofgravity is at the energy where the area under the experimental data reaches half the value of thefull integral (arrows shown under the smoothed curves in Figure 5.8). Uncertainties are estimatedfrom the sensitivity of the procedure to the choice of integration interval.

191

Figure 5.8
Band envelopes of all clusters. Experimental data (data points) were smoothed(red curves) with 200-point sliding average (100 points for n = 4). The smoothed curves wereinterpreted as band envelopes. Arrows above the smoothed curves are the band envelope peaks;
arrows under the curves point at the center of gravity (both values are listed in Table 5.2). Error
bars are estimated from small variations in the peak position when using different gliding
averages. The solution spectrum is adapted from Ref.12

192
Table 5.2
Experimental and calculated energies (in cm-1) of selected spectroscopic featuresof [Ru-OH2]2+·(H2O)n clusters at 180 K trap temperature.
n

ECOG [cm-1] a

Eenv [cm-1] b

0
1
2
3
4
bulk

23470 (80)22900 (80)22180 (80)21780 (160)21610 (240)23390 (100)22820 (100)22020 (100)21940 (160)21530 (240)21010 (100)

ES8 [cm-1] cdef2-SV(P)def2-TZVP
22390
22850
22000
22530
21710
22350
21490
22120
21340

a Center of gravity of the 1MLCT band for each cluster size.
b Peak of band envelope. The bulk value was extracted from the data in Ref.12
c Calculated values for the most intense transition (S ) using the B3LYP functional with the8basis sets for all atoms as listed. Values are rounded to 10-cm-1 accuracy. For cluster sizes withmore than one isomer, an average of all values is reported. All def2-TZVP results were shifted by-1210 cm-1. All def2-SV(P) values were shifted by +2420 cm-1.

In the other approach, we employed a sufficiently broad smoothing function to determine
the peak of the envelope of the spectrum. A 200-point sliding average was used on the curves
shown in Figure 5.8, except for n = 4, where the smaller number of data points made 100-point
sliding average necessary. Error bars are estimated from small variations in the peak position
when using different sliding averages. Note that while the center of gravity is not necessarily thesame as the peak position, the results yielded from both methods lie well within the error barsof each other. Therefore, the solvatochromic shifts determined using the two procedures are
consistent with each other and we define the overall solvatochromic shift by using the difference
between the peak of the band envelope and the peak of the solution spectrum 12 (-2380 cm-1,
0.295 eV).

193
We performed TDDFT calculations using two different basis sets - def2-TZVP and def2SV(P) – for all cluster sizes and all the isomers in Figure 5.3. Both basis sets were able toqualitatively reproduce the spectral envelope for all cluster sizes up to n = 3. For n =4, only
B3LYP/def2-SV(P) yielded converged results, which are shown as stick spectra in Figure 5.9.

Figure 5.9
Overview of TDDFT spectra for all isomers. Left: B3LYP/def2-TZVP; right:
B3LYP/def2-SV(P).

194
The electronic structures for the different isomers of the clusters are very similar.
Although the calculations correctly predicted increasing red-shift as more solvent molecules arepresent, the magnitudes of the red-shift are all underestimated. The description does not
improve with increasing basis set size from def2-SV(P) to def2-TZVP (see Figure 5.10).

Figure 5.10 Summary of solvatochromic behavior of [Ru-OH2]2+·(H2O)n compared to bulk
aqueous solution12 (horizontal line). The center of gravity positions of the MLCT bands are shownas filled blue squares, the envelope peaks as filled red triangles. Results from TDDFT calculations
are shown as open circles (def2-TZVP) and open squares (def2-SV(P)). The dashed lines are meant
to guide the eye. Numerical values are listed in Table 5.2, and error bars (where given) aredetermined from Gaussian error propagation of the errors listed in Table 5.2.

The experimental and theoretical descriptions of the solvatochromic behavior of[Ru-OH2]2+ are summarized in Figure 5.10, from the bare aqua complex through the first fourwater adducts to bulk hydration. The overall envelope shifts to ca. 78% of the full bulk

195
solvatochromic shift with four solvent water molecules present, which highlights the importanceof the water network that incorporates the aqua ligand. It is clear that the solvatochromic shift
induced by each additional solvent molecule is not monotonic from n = 0 – 4. For the first twosolvent molecules, the solvatochromic shifts are ca. -650 cm-1 after each added solvent molecule,
while for n > 2, the sequential shift slows to ca. -280 cm-1 per added solvent molecule. Geometry
optimization reveals that the water network of the first solvation “shell” is filled at n = 2, whichcoincides with the turning point of the curve in Figure 5.10. This may suggest that the slower redshift with progressive solvation reflects saturation of the aqua ligand with H-bonds. Here theterm “shell” refers to the water network building around the aqua ligand only and neglects thepossible solvation sites around the polypyridine ligands.
One may predict the solvatochromic behavior beyond this point, assuming the effects ofcontinuing addition of solvent water molecules follows a linear extrapolation of the data for n =2 – 4. In this very simple picture, it can be estimated that the bulk solvatochromic shift is reachedafter addition of ca. 6 solvent water molecules. T This extrapolation is almost certainly too simple,
because it is entirely conceivable that the shift per added solvent molecule will continue todiminish as the number of solvent molecules grows. Moreover, the water network may spreadbeyond the vicinity of the aqua ligand and begin to interact with the organic ligands when thecluster size exceeds a certain point. Despite the obvious shortcomings of the extrapolation, it isinstructive to compare the solvated ion [Ru-OH2]+·(H2O)n at n  6 with the microsolvation
environment of a Ru2+ ion (without organic ligands) in bulk aqueous solution. The solid angle on
the Ru2+ ion in the complex that is accessible to hydration only amounts to ca. 15% of a full sphereand there are 7 water molecules (including the aqua ligand) in this space. This is comparable to196a solution in which an uncoordinated Ru2+ ion is surrounded by ca. 50 water molecules, whichcorresponds to roughly 1 M solution of an atomic ion. It is also in line with results by Williams
and collaborators20,21 on the behavior of large hydrated clusters in terms of water binding energy
and vibrational spectroscopy.

5.3

Summary
To study the role of solvent, we applied photodissociation spectroscopy on mass-selectedwater-solvated [Ru-OH2]2+ ions in vacuo. Upon photoexcitation, [Ru-OH2]2+·(H2O)n clusters
sequentially lose water molecules, likely by unimolecular decay of a vibrationally hot molecule inits electronic ground state. Kinetic shift effects are obvious in action spectra but negligible for thephotodepletion spectra of all ions under study. We measured the electronic spectrum of[Ru-OH2]2+ solvated by up to 4 water molecules. The 1MLCT band of the complex shifts towards
lower energies upon addition of solvent water molecules at a rate of -650 cm-1 per added solventat first and then -280 cm-1. The rate changes at n = 2 where the aqua ligand is saturated with Hbonds and the first solvation “shell” is closed. In the dihydrate (n = 2), this shift recovers 55% of
the solvatochromic shift in bulk aqueous solutions of [Ru-OH2]2+, while the tetrahydrate spectrum
shows 78% of the bulk solvatochromic shift. This observation highlights the importance of thefirst few solvent molecules for the electronic structure of this complex.
To further study this topic, larger clusters and colder ion temperatures may be interesting
to investigate. The current restriction in our setup is the optimal temperature for cluster
formation, which forces the ion trap temperature to be 180 K and prevents us from cooling theclusters down to lower temperatures. Therefore, inspired by Garand and coworkers 22, we will

197
implement an additional ion trap specifically for cluster formation and then transport the clusters
to the main trap and cool them.

5.4

References

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Xu, S., Smith, J. E. T. & Weber, J. M. Hydration of a binding site with restricted solvent
access: solvatochromic shift of the electronic spectrum of a ruthenium polypyridine
complex, one molecule at a time. J. Phys. Chem. A 120, 7650–7658 (2016).

2.

Duffy, E. M., Marsh, B. M. & Garand, E. Probing the hydrogen-bonded water network at
the active site of a water oxidation catalyst: [Ru(bpy)(tpy)(H2O)]2+·(H2O)0–4. J. Phys. Chem.
A 119, 6326–6332 (2015).

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Klamt, A. & Schüürmann, G. Cosmo - a new approach to dielectric screening in solventswith explicit expressions for the screening energy and its gradient. J. Chem. Soc. Perkin
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Skyner, R. E., McDonagh, J. L., Groom, C. R., Van, M. T. & Mitchell, J. B. O. A review ofmethods for the calculation of solution free energies and the modelling of systems insolution. Phys. Chem. Chem. Phys. 17, 6174–6191 (2015).

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Cramer, C. J. & Truhlar, D. G. Implicit solvation models: equilibria, structure, spectra, anddynamics. Chem. Rev. 99, 2161–2200 (1999).

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Spence, T. G., Burns, T. D., Guckenberger, G. B. & Posey, L. A. Wavelength-dependent
photodissociation of [Fe(bpy)3·(CH3OH)n]2+ clusters, n=2-6, triggered by excitation of themetal-to-ligand charge-transfer transition. J. Phys. Chem. A 101, 1081–1092 (1997).

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Stockett, M. H. & Brøndsted Nielsen, S. Communication: Does a single CH3CN molecule
attached to Ru(bipy)32+ affect its absorption spectrum? J. Chem. Phys. 142, 171102 (2015).

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Houmøller, J. et al. On the photoabsorption by permanganate ions in vacuo and the roleof a single water molecule. New experimental benchmarks for electronic structure theory.
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Xu, S. & Weber, J. M. Absorption spectrum of a Ru(II)-aquo complex in vacuo: resolving
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Jakubikova, E. et al. Electronic structure and spectroscopy of [Ru(tpy)2]2+,[Ru(tpy)(bpy)(H2O)]2+, and [Ru(tpy)(bpy)Cl]+. Inorg. Chem. 48, 10720–10725 (2009).

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Xu, S., Smith, J. E. T. & Weber, J. M. Ligand influence on the electronic spectra of dicationicruthenium- bipyridine-terpyridine complexes. J. Phys. Chem. A 120, 2350–2356 (2016).

14.

Schweizer, A. et al. Electronic photodissociation spectroscopy of Au4+·Arn, n=0-4:
experiment and theory. J. Chem. Phys. 119, 3699–3710 (2003).

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Weigend, F. & Ahlrichs, R. Balanced basis sets of split valence, triple zeta valence andquadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Phys.
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Weigend, F., Häser, M., Patzelt, H. & Ahlrichs, R. RI-MP2: optimized auxiliary basis sets anddemonstration of efficiency. Chem. Phys. Lett. 294, 143–152 (1998).

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19.

Yoon, S., Kukura, P., Stuart, C. M. & Mathies, R. A. Direct observation of the ultrafast
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Prell, J. S., Obrien, J. T. & Williams, E. R. Structural and electric field effects of ions inaqueous nanodrops. J. Am. Chem. Soc. 133, 4810–4818 (2011).

21.

Donald, W. A. et al. Average sequential water molecule binding enthalpies ofM(H2O)19-1242+ (M = Co, Fe, Mn, and Cu) measured with ultraviolet photodissociation at 193
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6

Summary and conclusions

This thesis summarizes my doctoral work on photodissociation spectroscopy of metalpolypyridine complex ions. I investigated the influence of ligands on electronic structure using
two series of complexes, [Cu(bpy)-L]+ and [Ru(bpy)(tpy)-L]2+, where L is a variable ligand. The
photophysical properties of the complexes are found to be critically dependent on the ligand L,
and influence of the ligand is characterized within each series. The role of the metal is studied ina series of [MII(bpy)3]2+ ions, where M stands for a transitional metal. Different metal cores leadto distinct spectral properties. The excited-state lifetime, absorption maxima and absorption
cross sections are all dictated by the nature of the metal and differ for different metals. There isno clear trend based on the position of the metal in the periodic table. Lastly, I studied solvation
effects on the MLCT band of a water oxidation catalyst, [Ru(bpy)(tpy)-OH2]2+, by measuring thephotodissociation spectrum of its solvated form with up to four solvent water molecules. It is thefirst time to experimentally observe the evolution of solvatochromic shift of an organometallic
complex with addition of one solvent molecule at a time. In this case, the first four solvent
molecules already bring about more than 75% of the bulk solvatochromic shift of this complex.
In addition to experimental investigations, I also performed quantum chemistry calculations
based on (time-dependent) density functional theory and used the computational results toassist the interpretation of the experimental data. The experiments also serve to provide
benchmarks for theory so that theoretical methods can be compared and tested.
The experiment has room for improvement. First, our method relies onphotodissociation, and the resulting photodissociation spectra are not always representative of
the underlying absorption spectra, and sometimes this method is even unfeasible. As a result, we200
may resort to messenger tagging. However, no tag is completely innocent. It demands more
effort to study the impact of tagging on electronic spectra, although it is probably small. Second,
despite mass-selection, it is impossible to distinguish isomers, which may exist and contribute tothe observed spectrum simultaneously, particularly for clusters. Infrared spectroscopy can serve
to contribute additional information on the structure of the complex under study. Therefore, aninfrared system is being implemented and will be used to identify different bonding motifs insidepossible isomers. Third, the actual temperature or the internal energy of the ions is difficult todetermine quantitatively, and we are investigating candidate molecules to be used as molecular
thermometers. Improvements along those lines will allow to extract additional information onmolecular ionic systems from their spectra and to further push the frontier of understanding thefundamental properties of these systems.

201

7

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