Sample Preparation for Femtosecond Electron Diffraction

$Page 1: Sample Preparation for Femtosecond Electron Diffraction$
Sample Preparation for Femtosecond ElectronDiffraction: Photodissociation of Triiodide

by

Cindy Lee

A thesis submitted in conformity with the requirementsfor the degree of Master of ScienceGraduate Department of Chemistry

University of Toronto

Copyright c© 2008 by Cindy Lee

Abstract

Sample Preparation for Femtosecond Electron Diffraction: Photodissociation of

Triiodide

Cindy Lee

Master of Science

Graduate Department of Chemistry

University of Toronto

2008

Femtosecond electron diffraction is a relatively new technique used to study reaction

pathways at the femtosecond (10−15 s) time scale. With this technique, it will be possible

to observe reactive intermediates and short-lived transient states and the timeframe in

which they occur. The photodissociation of triiodide is an ideal molecular reaction to

study. The dynamics are within the time resolution range of our current setup and the

iodine atoms are excellent scatters of electrons.

Before reactions can be studied by femtosecond electron diffraction studies, suitable

samples of the molecule or system of interest must be prepared. The sample preparation

for these experiments is not trivial, especially for molecular systems such as triiodide.

Three methods of preparing samples of triiodide for these experiments were per-

formed: dropcasting, spincoating, and melting with slowly cooling. The latter two showed

promise in producing samples that gave diffraction.

ii

Acknowledgements

Ever since I participated in the WISEST (Women in Scholarship Engineering Science and

Technology) summer research program in the summer of 2001, I was hooked on research.

There was so much to explore in this world! Then I was chosen as a student in the RISE

(Reactive Intermediates Student Exchange) program after my second year of undergrad

at the University of Alberta and was sent to work at the University of Toronto in the

Department of Chemistry. I have these two great programs to thank for opening the

door to research for me and my decision to do my graduate studies at the U of T.

The course of my master’s degree has not been a smooth one, so I have many people

to thank to help me get past all the curve balls life threw at me and allowed me to reach

this point in my academic career.

First, I must express endless gratitude to my two generous supervisors M. Cynthia

Goh and R. J. Dwayne Miller. They have provided me with great guidance, encour-

agement, and support throughout my degree. I will always look to them as my role

models.

Of course one spends a great deal of their time in the lab, so I thank everyone in

the Goh and Miller groups who helped me and took the time away from their work

for amusing conversations. I want to thank the senior scientists in the Goh and Miller

groups, Jane Goh, Richard Loo, Ralph Ernstorfer, and German Sciaini, for all their

help and sharing their expertise and creative ideas. I will be forever grateful to my

fellow graduate students in the Goh and Miller groups for keeping me sane while I slowly

became a “lab rat.” From the Miller group, I’d like to thank Lili Zhu and Dan Elliott

for their help and work in the sample preparation project, Christoph Hebeisen for letting

me reach my goal, and Sadia Khan for being the most helpful person in the world. From

the Goh group, I would like to congratulate those who survived the Great Purge of 2007

and especially thank Emina Veletanlic for her company in lab, Richard Kil and Jordan

Ang for putting up with my Oilers and Habs loving ways, and Rob Graham for being the

iii

best chair I have ever worked for. I would like to give special thanks to visiting students

Frederic Cunin and Jahangir Valiani for brightening our lab with their presence while

they were here and to the undergraduates who made the lab just a little bit more lively.

There is life outside the lab! I need to thank all my wonderful friends, who are now

scattered around the world in Toronto, Athabasca, Edmonton, Calgary, Vancouver, and

Hong Kong, and all my teammates whom I played with in U of T intramurals and around

the GTA. Special thanks goes to fellow chemist Tom Hsieh for eating out with me and

taking me to Jays games, Megan Bowen for being the only other sports fan in Toronto,

and my awesome roommates Ariana Haalboom and Shirley Juarez for making my home

at Graduate House a happy place to be. I am forever grateful towards my best friends

Linda Li, Jenna Li, Michelle Wong, and Christiana Yeong for always being there for me

and providing me with advice and a little bit of a social life. I also need to thank Victor

Ma and Albert Ma for their encouragement and the crazy adventures during their visits

to Toronto.

Lastly, I have to give my biggest thank you and appreciation to my family. Despite

my moving 3000 km from home, my family has been there for me every step of the way.

I would like to thank my parents Xue Mei Lee and Bob Ning Lee, my brother Roger Lee,

my cousin Olivia Hu, my grandpa Men Tong Wu, and especially my grandma Lian You

Wu for everything they have done for me and giving me more support than I could ever

ask for.

iv

Contents

1 Introduction 1

1.1 Femtochemistry &

Femtosecond Electron Diffraction . . . . . . . . . . . . . . . . . . . . . . 1

1.1.1 Electron Diffraction . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.1.2 Time-Resolved Electron Diffraction . . . . . . . . . . . . . . . . . 4

Diffractometer Setup . . . . . . . . . . . . . . . . . . . . . . . . . 4

1.1.3 Crystallization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Thin Films . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

1.2 Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2 Photodissociation of Triiodide 9

2.1 Triiodide in Femtosecond Electron Diffraction . . . . . . . . . . . . . . . 9

2.1.1 Photodissociation of Triodide . . . . . . . . . . . . . . . . . . . . 9

Solid-State Photodissociation . . . . . . . . . . . . . . . . . . . . 11

2.2 Triiodide Candidates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2.2.1 Crystal Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

2.2.2 Preparation & Physical Properties of TBAT, TEAT, TPPT . . . 14

2.3 Previous Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3 Dropcasting Triiodide 16

3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

v

3.2 Results & Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

3.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

4 Spincoating Triiodides 19

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

4.2 Characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

4.2.1 Facets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

4.3 Spincoating Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

4.3.1 Solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

4.3.2 Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

4.3.3 Number of Drops . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4.3.4 Concentration & Spin Speed . . . . . . . . . . . . . . . . . . . . . 24

4.3.5 Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

4.3.6 Cellulose Acetate . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

4.4 Floating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

4.4.1 Polyvinylalcohol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

4.5 Reproducibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

4.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

5 Melted Films 36

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

5.1.1 Melted Crystals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

5.2 Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

5.3 Results & Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

6 Summary 46

Bibliography 48

vi

List of Figures

1.1 Examples of physical, chemical, and biological changes and their timescales. 2

1.2 Setup scheme for femtosecond electron diffraction. . . . . . . . . . . . . . 5

1.3 Faceting of a thin film of TBAT in progress. . . . . . . . . . . . . . . . . 6

2.1 Electronic spectrum of triiodide in dichloromethane. . . . . . . . . . . . . 10

2.2 Chemical structures and crystal packing of TBAT, TEAT, and TPPT. . 13

2.3 Absorption spectra of (a) TBAT, (b) TEAT, and (c) TPPT in dichloromethane. 14

3.1 A dropcasted film of TPPT with cellulose acetate. . . . . . . . . . . . . . 17

4.1 Spincoated crystalline films of (a) TBAT, (b) TEAT, (c) TPPT. . . . . . 21

4.2 Absorption spectra of spincoated films of (a) TBAT, (b) TEAT, (c) TPPT. 21

4.3 Spincoated TBAT films on (a) air-dried, (b) blow-dried, and (c) wiped

glass slides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4.4 Crystals of TEAT formed at the edge of slide when too many drops are

applied during spincoating. . . . . . . . . . . . . . . . . . . . . . . . . . . 24

4.5 Channels were evident for thicker films of spincoated TBAT. . . . . . . . 25

4.6 Weak electron diffraction off a spincoated sample of TBAT. . . . . . . . . 26

4.7 Films of (a) TBAT and (b) TPPT spincoated onto carbon-coated mica. . 27

4.8 Films of (a) TBAT, (b) TEAT, (c) TPPT with cellulose acetate under the

optical microscope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

4.9 Absorption spectra of (a) TBAT, (b) TEAT, (c) TPPT with cellulose acetate. 28

vii

4.10 Film of TPPT is altered after contact with water. . . . . . . . . . . . . . 30

4.11 (a) A faceted film of spincoated TBAT with cellulose acetate and (b) the

incomplete formation of a crystalline film from an old solution. . . . . . . 31

4.12 (a) A spincoated film of TBAT with cellulose acetate and (b) the same

film after 3 days. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

4.13 (a) TBAT films immediately after spincoated and (b) TBAT films after

sitting in atmospheric conditions for a few minutes. . . . . . . . . . . . . 32

4.14 Examples of unsuccessful films. . . . . . . . . . . . . . . . . . . . . . . . 33

5.1 Schematic of the apparatus for making melted films. . . . . . . . . . . . . 37

5.2 Melted crystals of TBAT recrystallized by slow cooling. . . . . . . . . . . 38

5.3 Melted crystals of TEAT recrystallized by slow cooling. . . . . . . . . . . 39

5.4 Absorption spectrum of a melted film of TBAT. . . . . . . . . . . . . . . 41

5.5 A melted film of TBAT made from melting and cooling between glass and

(a) PVA on glass and (b) PVA with PAA on glass. . . . . . . . . . . . . 41

5.6 A melted film of TBAT made from melting and cooling between glass and

NaCl polished salt. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.7 Electron diffraction image of TBAT made from melting and cooling be-

tween glass and KCl polished salt at 80 kV. . . . . . . . . . . . . . . . . 43

5.8 Electron diffraction image of TBAT made from melting and cooling be-

tween glass and carbon-coated KCl polished salt at 55 kV. . . . . . . . . 43

5.9 Electron diffraction taken at different areas of a melted film at 50 kV. . . 44

viii

List of Abbreviations

TBAI Tetra-n-butylammonium iodide

TBAT Tetra-n-butylammonium triiodide

TEAI Tetraethylammonium iodide

TEAT Tetraethylammonium triiodide

TPPI Tetraphenylphosphonium iodide

TPPT Tetraphenylphosphonium triiodide

PAA Polyacrylic acid

PVA Polyvinyl alcohol

ix

Chapter 1

Introduction

1.1 Femtochemistry &

Femtosecond Electron Diffraction

The realm of femtochemistry sees chemical reactions on the femtosecond (10−15 s) time

scale. On this order, it is possible to observe molecular vibrations, dissociations, and to

follow a chemical reaction, where reactants go through transition states and intermediates

to the final product [1, 2]. Figure 1.1 gives examples of chemical, physical, and biological

changes that occur at the milli-, micro-, pico-, and femtosecond time scales.

In the past century, new techniques such as X-ray diffraction, electron diffraction,

NMR, etc. has allowed the determination of the 3-dimensional structure of complex

molecules. Along with the development of lasers with extremely short, femtosecond,

pulses, it has been possible to add a temporal element to these experiments. One such

technique is known as time-resolved electron diffraction (as referred to as femtosecond

electron diffraction or ultrafast electron diffraction). This new technique can allow the

elucidation of chemical reaction pathways.

Traditionally, chemical reactions are studied by isolating or trapping intermediates

and then extrapolating possible transition states and pathways. For reactions with very

1

Chapter 1. Introduction 2

Figure 1.1: Examples of physical, chemical, and biological changes and their timescales.

Reprinted from Ahmed H. Zewail’s nobel lecture c© The Nobel Foundation 1999 with

permission.


reactive intermediates, they cannot be isolated or trapped. Time-resolved electron diffrac-

tion is one possible way to monitor a reaction. Diffraction patterns change with changes

in structure.

1.1.1 Electron Diffraction

Electrons are very small negatively charged particles (mass = 9.1095 x 10−31 kg). They

exhibit particle-wave duality, and thus can be expressed as a wave with a wavelength

that can be described by de Broglie’s equation

λ =h

mv=

h√2meV

(1.1)

with the resolution

d ∼ λ

sin(θ)(1.2)

This wave property allows the diffraction of electrons. At 55 keV, the wavelength λ

is about 5 pm. The theoretical spatial resolution at this wavelength is about 0.05 A.

Being negatively charged, electrons also interact with matter. They feel the attraction

of the positively charged nuclei and repulsion of the surrounding electrons of atoms.

Together, these forces allow electrons to scatter off matter.

Crystals are highly ordered solids formed from repeating units called unit cells. Within

crystals are lattice planes. Lattice planes act similarly to diffraction gratings, where the

spacings between planes are analogous to spacing between gratings. Therefore, diffraction

patterns off crystals correspond to the spacing between lattice planes and follow Bragg’s

Law.

nλ = 2d sin(θ) (1.3)


High-resolution structures have been determined by electron diffraction. Several pro-

teins have had their 3-dimensional structures elucidated in this way with angstrom resolu-

tion. This showed that electron diffraction is appropriate for obtaining spatial resolution

in time-resolved experiments.

1.1.2 Time-Resolved Electron Diffraction

Time-resolved experiments utilize a pump-probe technique. In studying a reaction, the

pump pulse induces a reaction in the sample. The probe pulse is the electron pulse that

will produce the diffraction pattern. A time delay stage is placed to vary the time between

the optical pulse and the electron probe. In this way, it is possible to get multiple one

shot images at different times to make a molecular movie [3].

Diffractometer Setup

A diffractometer setup requires an optical pulse source as the pump pulse, an electron

source for generating the probe pulse, a sample, and a detector [4]. The optical pulse is

split into two: one becomes the pump pulse and the other generates the probe pulse.

The optical pulses must be on the order of femtoseconds to produce femtosecond

resolution. These pulses are used to excite the sample and to propagate the electron

pulse. Thus, it is necessary to have a femtosecond optical pulse to generate femtosecond

electron pulses. Figure 1.2 shows the setup scheme.

The electron pulse is generated by the photoelectric effect. The optical pulse hits a

photocathode (the electron source) and an electron pulse is propagated. The electron

pulse is the limit of time resolution. Because the electrons are negatively charged, they

exhibit repulsive forces on each other, or space charge effects, expanding the duration

of the pulse. An extraction pinhole anode is placed to set the initial free-space electron

beam diameter and final electron number. A magnetic lens then focuses the electron

beam to optimize the sharpness of the diffraction pattern.


Figure 1.2: Setup scheme for femtosecond electron diffraction. (Courtesy of M. Harb.)

The sample is placed on a translation stage. For irreversible reactions, it is necessary

to move the sample to a new area for collecting subsequent sets of data. Section 1.2

discusses the sample criteria in detail.

Finally, a phosphorus screen coupled with a CCD camera is used to detect the scat-

tered electrons and to capture the diffraction pattern.

1.1.3 Crystallization

The crystallization process consists of two stages: nucleation and growth. Nucleation is a

thermodynamically disfavored event. The molecule of interest must come out of solution,

where it is more entropically favoured to be in. After the nucleation stage is reached,

the nuclei will increase to a critical size and passes over the free energy barrier. In the

second stage, the nuclei continue to grow and become ordered crystals.

Amorphous precipitation forms when the process is not under equilibrium. There is

no nucleation stage. The precipitate is quickly formed and is highly disordered.


Thin Films

The crystallization process can occur on the surface of a substrate in the formation of

a thin film. The process also involves nucleation and growth, but can be described in

three stages: (1) nucleation, (2) growth of nuclei and formation of larger islands, and (3)

coalescence of the islands and formation of networks containing empty channels [5].

Figure 1.3 depicts a film frozen in the crystallization process (due to incomplete

faceting). The nucleation sites grow as circles, or islands, until they meet another growing

island. They then coalesce and form empty channels at the meeting points to create a

“facet” with straight edges.

Figure 1.3: Faceting of a thin film of TBAT in progress. The circles represent nucleation

sites as they grow outward.

A concern for electron diffraction of thin films is lattice mismatch. Lattice mismatch

occurs when the substrate is made of crystalline material. If the lattice constant of

the substrate is about 0.2% similar to that of the compound, the film may assume a

“pseudomorphism” where the film adopts the structure of the substrate for about the

first 10 nm. Since the films in electron diffraction are typically 100 nm or thinner, this

would be a significant problem. When there is a greater difference in lattice constants,

only the first few atomic layers are affected and would not create any problems in the

experiment.


1.2 Sample Preparation

Sample preparation for femtosecond electron diffraction is not a trivial task. The major

criteria for a sample are that it must be electron transparent, crystalline, and undergo the

desired reaction when photoexcited. However, the sample must also be able to withstand

the experimental conditions: withstand excitation, withstand vacuum, and especially

for solid samples, be free standing or on a electron transparent support, and have large

uniform areas (if studying irreversible processes).

Electron transparency is necessary for the electron beam to pass through the sample

to generate a diffraction pattern. If the sample is too thick, there will be many inelastic

collisions degrading the diffraction pattern, or the electrons could be blocked completely.

Samples that are too thin can also be problematic. There may not be enough material to

generate a strong diffraction signal. The velocity mismatch between the excitation pulse

and the electron pulse is minimal in thinner samples. As a general starting point, the

sample should be approximately 100 nm to 300 nm thick for organic samples.

Crystallinity is crucial for diffraction. The periodic lattice planes of a crystal diffract

electron into a periodic pattern. Single crystalline samples produce patterns with single

distinct peaks. Polycrystalline diffraction patterns are basically single crystalline diffrac-

tion patterns rotated 360 degrees, generating a ring pattern instead of distinct peaks.

Amorphous samples will result in diffuse scattering. Polycrystalline and single crystalline

samples are both appropriate for time-resolved electron diffraction experiments.

It is not enough for the sample to be crystalline; it must also undergo the desired

reaction when excited with the pump laser. There are few reactions that occur in the

solid state, which limits the types of reactions that can be probed with this technique.

However, there are developments to introduce liquid and gas samples, which would allow

many more reactions to be studied.

To enhance signal to noise ratio for reversible processes, the sample must remain

intact and stable after photoexcitation. The pump laser can carry a lot of energy, which


may damage the sample through heating. Because an electron transparent sample is so

thin, it is susceptible to damage from the laser and from excitation.

Experiments are carried out in a high vacuum environment (10−7 Torr) in order to

avoid scattering of electrons with particles in the air. This means samples must have low

vapour pressure and remain intact when introduced to this environment.

The films must be free standing or on an electron transparent support. This is

required for electron transmission. If a film is strong, it can be free standing and placed

on a grid to hold it. Silicon nitride windows can be used as a support for films. The

silicon nitride in these windows are amorphous and result in diffuse scattering, which will

not interfere with diffraction. They are made to be very thin, about 40 nm, which allows

the transmission of electrons.

Irreversible samples have a disadvantage in that a new area is needed for each mea-

surement. This requires not only a large film, but also uniformity across it to average

shots. The same thickness and crystallinity is required to ensure accurate measurements

of the reaction. Otherwise, changes to the diffraction pattern cannot be attributed to

the reaction, but rather, to the differences between sample areas.

Sample preparation of molecular species for femtosecond electron diffraction is a chal-

lenging task. Similar to protein crystallography, various approaches and conditions must

be attempted to obtain appropriate samples for experiments.

Chapter 2

Photodissociation of Triiodide

2.1 Triiodide in Femtosecond Electron Diffraction

Triiodide is an ideal molecular compound for femtosecond electron diffraction experi-

ments. It undergoes a photodissociation reaction, which can be initiated by an optical

pulse. It also contains a heavy atom, iodine. Heavy atoms scatter electrons better due

to their higher number of protons and electrons. Stronger scattering produce higher

intensity peaks, which facilitate the analysis of diffraction patterns.

The ultraviolet-visible (UV-Vis) absorption spectrum of triiodide in dichloromethane

has two distinctive peaks: an upper band at about 290 nm and a lower band at about

370 nm (see Figure 2.1)[6]. Excitation of either band can induce the photodissociation

of the triiiodide.

2.1.1 Photodissociation of Triodide

The photodissociation of triiodide is a well-studied reaction. The primary photodissoci-

ation reaction of triiodide is

I−3 + hv → I−2 + I

9

Chapter 2. Photodissociation of Triiodide 10

Figure 2.1: Electronic spectrum of triiodide in dichloromethane displaying 4 bands (A)

∼565 nm (B) ∼440 nm (C) 364 nm and (D) 294 nm. Reprinted from Spectrochimica Acta

Part A: Molecular Spectroscopy, Vol 30(9), W. Gabes and D. J. Stufkens, Electronic ab-

sorption spectra of symmetrical and asymmetrical trihalide ions, pages 1835-1841 c©1974

with permission from Elsevier.

There have been many studies done on the photodissociation of triiodide in gas phase,

solution, and solid state and by ab initio [7, 8, 9, 10, 11, 12, 13, 14, 15, 16]. The appearance

of I−2 was found to occur within 300 fs when I−3 , excited at 308 nm, photodissociates in

ethanol [11]. The coherent vibrational motion of the photoproduct decays around 4 ps,

attributing this short time scale to interactions with the polar solvent. Other studies of

I−3 in ethanol found that exciting at different wavelengths (266nm and 400nm) changes

the yield of I−2 [13]. At 400 nm, the yield of I−2 was unity and at 266nm, the yield was

only 0.8, suggesting alternate channels of dissociation.

There is evidence in gas phase I−3 of other two- or three- body dissociations in addition

to the primary reaction seen in ethanol:

I−3 + hv → I2 + I−

I−3 + hv → I− + I + I

Photodissociation of I−3 in gas phase was found to occur as early as 400 fs following

390 nm excitation [7]. As expected, the vibrational motion of the photoproducts lasted


longer than those in solution phase.

Solid-State Photodissociation

Poulin et al. studied I−3 in the solid state [15]. In their experiment, they used single

crystals of triiodide compounds (tetra-n-butylammonium triiodide (TBAT), tetraethy-

lammonium triodide (TEAT), and tetraphenylphosphonium triodide (TPPT) ) and ex-

cited each at 300 nm. Taking advantage of the fact the photoproduct I−2 absorbs in the

visible and near-infrared where I−3 does not, its appearance was monitored by observing

absorbances at wavelengths of 600 to 800 nm. Based on the appearance of I−2 , the pho-

todissociation of all three triiodides were found to occur on a timescale of 400 fs, which

is within our setup range. The I−2 absorption decay varied between compounds, likely

due to the varying constraints of their crystal structures (see Section 2.2.1 for crystal

parameters). Recombination following dissociation occurred in TBAT after 1.1 ps to 1.3

ps, and in TEAT, after 1.4 ps to 1.7 ps. Recombination was not observed in TPPT in

neither experiment nor molecular simulations.

Time-resolved electron diffraction experiments may be able to analyze exactly what

happens during the course of the photodissociation and also the time frame in which the

events occur.

2.2 Triiodide Candidates

Tetra-n-butylammonium triiodide (TBAT), tetraethylammonium triodide (TEAT), and

tetraphenylphosphonium triodide (TPPT) were chosen as triiodide candidates for fem-

tosecond electron diffraction experiments. The photodissociation reaction of I−3 in TBAT,

TEAT, and TPPT had already been studied confirming that photodissociation can oc-

cur in the solid state in these compounds. Simulation of the photodissociation reaction

in TBAT, TEAT, and TPPT were carried out and determined that it was possible to


observe changes in the diffraction pattern as the reaction progresses [17].

2.2.1 Crystal Structure

TBAT, TEAT, and TPPT each grow into different crystal structures. As seen in the solid

state experiments, this influences the recombination reactions in these compounds. The

triiodide ion in each crystal differs in bond length and linearity. Each compound gives a

different diffraction pattern. Figure 2.2 shows the chemical structure and the packing of

the three triiodides.

TBAT grows as a triclinic P-1 crystal [18, 19]. The parameters are: a=15.7926 A,

b=15.9936 A, c=9.5785 A, α=74.486◦, β=101.529◦, γ=96.638◦, with Z=4. There are two

nearly linear I−3 ions with asymmetrical bond lengths of 2.951 A, 2.887 A and 2.941 A,

2.910 A.

TEAT grows in two orthorhombic crystalline modifications, Cmca and Pnma [20]. In

modification I, Cmca, the crystal parameters are: a=14.208 A, b=15.220 A, c=14.061 A,

α=β=γ=90◦, with Z=8. There are two independent I−3 ions at special positions of 2/m

symmetry. The bond lengths of the two symmetrical I−3 ions are 2.928 A and 2.943 A.In

modification II, Pnma, the crystal parameters are: a=14.552 A, b=13.893 A, c=15.156

A, α=β=γ=90◦, with Z=8. There are two independent I−3 ions that are nearly linear,

but have asymmetric bond lengths of 2.912 A, 2.961 A, and 2.892 A, 2.981 A.

TPPT grows as a monoclinic P2/n crystal with the following parameters: a=10.2102

A, b=7.5555 A, c=15.3253 A, α=γ=90◦, β=93.16◦ with Z=2 (both TPP+ and I−3 ions

sit on two-fold axes) [21]. The I−3 ions are slightly bent at an angle of 175.27◦ with the

iodine atoms 2.9180 A from each other.


Figure 2.2: Chemical structures of (a) TBAT, (c) TEAT, and (e) TPPT and their crystal

packing, (b)(d)(f) respectively. Reprinted from Science, Vol 313, P. R. Poulin and K.

A. Nelson, Irreversible Organic Crystalline Chemistry Monitored in Real Time, pages

1756-1760 c© 2006 with permission from AAAS.


2.2.2 Preparation & Physical Properties of TBAT, TEAT, TPPT

TBAT, TEAT, and TPPT were prepared by reacting iodine with their iodide parent (RI)

[22].

RI + I2 → RI3

TBAI, TEAI, and TPPI were dissolved in absolute ethanol or a mixture of ethanol

and methanol. I2 was dissolved in absolute ethanol and added in excess to the iodide

solutions. The resulting crystals were filtered and washed with cold ethanol, hexane, and

again with cold ethanol. After drying, the crystals were recrystallized. Figure 2.3 shows

the absorption spectra of each triiodide dissolved in dichloromethane. All three triiodide

compounds have the two main triiodide absorption peaks at ∼300 nm and ∼370 nm.

Figure 2.3: Absorption spectra of (a) TBAT, (b) TEAT, and (c) TPPT in

dichloromethane.

The triiodides were recrystallized by two methods: dissolving the triiodide in hot

ethanol to saturation and slowly cooled to room temperature, and dissolving in ethanol

at room temperature and recrystallized by slow evaporation. Supersaturated solutions

produced very fine, small crystals. Slow evaporation resulted in large crystals. TBAT

crystals were dark brown, TEAT crystals were reddish brown and TPPT crystals were

gold coloured.


These triiodides are unique because their cations have large hydrophobic side groups

that influence their solubility. All three were found to be insoluble in highly non-polar

solvents, such as hexane. They were slightly soluble in polar solvents such as alcohols

with decreasing solubility as the alkyl chain of the alcohol increased. TEAT was the most

soluble in polar solvents followed by TBAT and TPPT. Polar protic solvents, such as

dichloromethane and acetone, showed the highest solubility. TBAT was the most soluble

in these solvents followed by TEAT and TPPT.

The literature melting point of TBAT is 68-71 ◦C [23]. The melting point of TEAT

was found to be 150◦C and that of TPPT to be > 150◦C. The relatively low melting point

of TBAT brought about the idea of creating films by melting and cooling (see Chapter

5: Melted Films).

2.3 Previous Work

Previous work in the group has been unsuccessful in producing suitable molecular samples

for electron diffraction, and in particular, for studying the photodissociation of triiodide

[17, 24]. Both top-down and bottom-up approaches were attempted. Some attempts

yielded failures, while others had the potential for success. The top-down approaches

involved microtoming, laser ablation, and AFM etching. The bottom-up approaches in-

volved iodine-doped polyisoprene, 1-methyl-3-propylimidazolium triiodide (an ionic liq-

uid), spincoating, and films from slow cooling after melting. Iodine-doped polyisoprene

and 1-methyl-3-propylimidazolium triiodide proved unsuccessful due to the loss of triio-

dide under vacuum conditions.

This thesis focuses on bottom-up approaches to produce thin films of triiodide: drop-

casting, spincoating, and films from slow cooling after melting, or “melted films”.

Chapter 3

Dropcasting Triiodide

3.1 Introduction

Dropcasting is a technique where the solution of a compound in a volatile non-polar

solvent is dropped onto a surface of water, casting a film. The film is then collected onto

a grid or wafer and dried for electron diffraction experiments. Dropcasting is commonly

used in the sample preparation for electron microscopy [25].

Cellulose acetate was used to facilitate the formation a film with the triiodide. Cellu-

lose acetate is the acetyl ester of cellulose, a polysaccharide of β(1→4) linked D-glucose

units. The polymer is weakly polar due to the acetyl groups. Cellulose acetate is soluble

in acetone, but not in water, at room temperature. Due to the partial hydrolysis of sur-

face ester groups, cellulose acetate also carries some negative charge. This may interact

with the cation of the triiodide compounds [26].

Dichloromethane and acetone in a 1:1 ratio was used as the solvent. Dichloromethane

was the hydrophobic solvent used to spread the triiodide into a film on the surface of

water. Acetone dissolves both cellulose acetate and triiodide. Cellulose acetate is not

soluble in dichloromethane requiring acetone to be added to the solvent.

16

Chapter 3. Dropcasting Triiodide 17

3.2 Results & Discussion

Solutions of cellulose acetate alone, TEAT with cellulose acetate, and TPPT with cellu-

lose acetate were tested. Dropcasting triiodide without cellulose acetate did not produce

any films, only precipitate on the surface of the water. Drops of cellulose acetate so-

lution produced clear, colourless films. This means cellulose acetate was necessary for

dropcasting triiodide films. Films about an inch in diameter were formed from 10 µL of

solutions containing a cellulose acetate component.

Though the films were large in diameter, they were not very uniform. Recall that

large uniform areas were required for samples with irreversible reactions. The center of

the film was more concentrated, and hence thicker than other areas.

TPPT has the lowest solubility among the three triiodides. Casted films were light

yellow and translucent. Unfortunately the TPPT was not soluble enough to produce

suitable thin films. When the TPPT and cellulose acetate solutions were dropcasted, the

films had large crystals in them (see Figure 3.1). The crystals were microns wide and

microns thick. This non-uniformity and thickness made the film unsuitable for electron

diffraction experiments.

Figure 3.1: A dropcasted film of TPPT with cellulose acetate: (a) This picture shows

that the film is not uniform, with a concentration in the centre of the film (b) Crystals

of TPPT embedded in the film.

Chapter 3. Dropcasting Triiodide 18

TEAT and cellulose acetate solutions produced yellow films upon casting. However,

due to the higher solubility of TEAT in water than TBAT and TPPT, the yellow colour

disappeared within seconds leaving a clear colourless cellulose acetate film.

Films of TBAT with cellulose acetate made from this method, by R. Loo, did not give

diffraction despite looking very similar, by eye and by AFM, to spincoated samples of

TBAT with cellulose acetate that did give diffraction. The difference could be due to the

crystallization process in dropcasting. The crystalllization of TBAT with cellulose acetate

happens over a longer duration in spincoating than in dropcasting. (The spincoating of

TBAT with cellulose acetate is discussed in Section 4.3.6). Slower processes promote

crystallinity. Dropcasted films tend to have poor crystallinity, which has been mentioned

in literature on sample preparation for electron microscopy [25].

3.3 Conclusions

Dropcasting TPPT with cellulose acetate has proved unsuccessful in producing uniform

thin films. TEAT with cellulose acetate films dissolved due to the higher solubility of

TEAT in water.

This method was unable to produce films that would be suitable for femtosecond

electron diffraction experiments. The dropcasting technique inherently produces samples

of poor crystallinity. Thus, this method is deemed inappropriate for sample preparation

for electron diffraction experiments.

Chapter 4

Spincoating Triiodides

4.1 Introduction

Spincoating is a common method of generating thin films. It can produce crystalline

films by recrystallization on a substrate. Spincoating involves dropping a solution onto a

spinning substrate, which removes excess solution, and a film is formed after the solvent

has evaporated.

There are many parameters that can be altered to produce a film with desirable char-

acteristics. Cleaning of substrate, concentration, spin speed, number of drops, substrate

material, and introduction of cellulose acetate were parameters that were examined for

TBAT, TEAT, and TPPT.

Facet size and thickness were used as determinants of suitability for diffraction ex-

periments. Occasionally, films were tested for the ability to diffract, but time on these

instruments were extremely limited (see Chapter 6). It was assumed that the presence

of faceting indicated the film was crystalline and not amorphous. And the thickness can

be an indicator of electron transparency.

19

Chapter 4. Spincoating Triiodides 20

4.2 Characterization

Films were characterized by facet size and thickness. Faceting could be observed by eye

for large facets or under an optical microscope for smaller facets. The films were also

observed under an optical microscope to measure facet sizes and to examine their quality.

Thickness was measured qualitatively by UV-Vis absorption and quantitatively by a

Wyko profilometer. The Wyko profilometer has a vertical resolution of 1 nm; however,

there is a slight error in the profilometry measurements due to the procedure used. Films

were scraped with tweezers and the height difference between the scraped area and intact

film were measured. There was some residual film left from the scraping, which increases

the height for the scraped area. For very thin films, profilometry measurements were not

possible due to this reason.

4.2.1 Facets

Solutions of TBAT, TEAT, and TPPT in dichloromethane were used to test faceting.

TBAT and TEAT exhibited this type of crystalline film, but with different looking facets

(see Figure 4.1). TPPT films did not have this characteristic, but it is still possible

that TPPT films are crystalline based on the snowflake-like areas of the films. By eye,

crystalline TBAT films were reddish-brown and/or slightly purple, TEAT films were

yellow, and TPPT films were light yellow. Absorption spectra of the films in Figure 4.2

show they contain triiodide based on the ∼290 nm and/or ∼370 nm peaks. There is a

noticeable broad band spanning between 400 nm and 700 nm in the TBAT spectrum.

The cause for this is unknown but could be due to the reaction of triiodide reverting back

to I2 and I− (I−3 → I2 + I−) because I2 absorbs at around 500 nm.

It should be noted that the facet sizes varied on the same films, especially at the

edges of the substrate. Areas of the each film were randomly selected for facet width

measurements and the average was used for comparison.


Figure 4.1: Spincoated crystalline films of (a) TBAT, (b) TEAT, (c) TPPT.

Figure 4.2: Absorption spectra of spincoated films of (a) TBAT, (b) TEAT, (c) TPPT.


4.3 Spincoating Parameters

4.3.1 Solvents

For the majority of the conditions tested, TBAT in dichloromethane was used. TBAT

has the highest solubility in dichloromethane of all the solvents tested. Acetone was also

tested as a solvent, but has lower solubility and lower vapour pressure.

Acetone was more inconsistent at producing films than dichloromethane. It did not

spread very well. However, on occasion, it was able to produce a faceted film. The

thickness and facet sizes were generally about the same as with dichloromethane.

4.3.2 Cleaning

All slides were sonicated in 1:1 absolute ethanol and deionized water before being subject

to the various cleaning techniques. Slides were either air-dried, blow-dried with nitrogen

gas, or wiped with tissue.

The cleaning technique had the largest impact on facet size of all the conditions tested.

Facet sizes were different for all three cleaning methods. Blow-dried slides had the largest

facets, between 0.1 mm and 2 mm. Wiped slides had the smallest, between 30 µm and

0.1 mm, which is about 10 times smaller than the blow-dried slides. Air-dried slides had

facet sizes between these two. The thickness of the films, however, were approximately

the same for all three kinds of cleaning.

The difference in facet sizes between the cleaning methods could be explained by the

number of nucleation sites. Particles left on the substrate can induce nucleation. The

tissue used in wiping slides could leave particles and fibers. This could explain why wiped

slides had the smallest facet sizes. Smaller facet sizes indicate more nucleation sites (each

facet centre grows until its growing edge meets the edge of another growing facet). Air

dried slides were found to have some particles on its surface. This was evident from the

increased number of holes in those films, which is a common defect in spincoating. It


Figure 4.3: Spincoated TBAT films on (a) air-dried, (b) blow-dried, and (c) wiped glass

slides.

also explains the medium sized facets. Blow-dried slides are likely the cleanest because

the method blows off particles from the slide and does not introduce new particles. This

results in larger facets.

4.3.3 Number of Drops

20 mg/mL solutions of TBAT and TEAT in dichloromethane were used to test the

influence of the number of drops, ie. volume, on film thickness and faceting during

spincoating.

The facet size was not affected by the number of drops and, the thickness of the film

was independent of the number of drops used during the spincoating process. There was

no direct correlation between number of drops and thickness. The likely explanation is

that excess solution is driven off the slide during spinning. No matter how much excess

was used, approximately the same amount of solution would stay on the slide to produce

a film.

Although, a problem with using too many drops was encountered. Because the solvent

dichloromethane is very volatile, the solution would begin to evaporate as more solution

was being dropped onto the slide. The TEAT samples had small crystals formed at the

edge and corners of the slide with only the centre of the slide having a faceted film.

For a film to be uniformly covering the slide, a slight excess of solution should be


Figure 4.4: Crystals of TEAT formed at the edge of slide when too many drops are

applied during spincoating.

used. Too little volume and the film does not cover the entire slide. Too much and large

crystals may form.

4.3.4 Concentration & Spin Speed

The influence of concentration and spin speed were tested using various concentrations

and spin speeds on blow-dried and wiped glass slides: 4, 7, 10, 20 mg/mL of TBAT in

dichloromethane and 1, 3, 5, 8 krpm.

The facet size remained the same as the concentration increased and at different spin

speeds for both blow-dried and wiped slides. And as expected, the thickness of the film

increased as the concentration increased and decreased as the spin speed increased.

Absorption spectra were compared to determine relative thicknesses. These showed

an obvious trend in the thickness as the concentration and spin speed varied. The thickest

films were about 200 nm produced from 20 mg/mL of TBAT solution spun at the lowest

speed 1 krpm. The thinnest films were only a few nanometers thick produced from 4

mg/mL solutions spun at the highest speed 8 krpm. With each 3 mg/mL increase in

concentration, the films were approximately 20 to 30 nm thicker. The effect of spinning

at a higher rate resulted in films that were approximately 5 to 10 nm thinner with each


increase in krpm.

The facet edges, or channels, were noticeably deeper as the film thickness increased

(see Figure 4.5). Edges are where two facets meet. This would create a problem for

election diffraction because the channels increase the surface roughness and may cause

irregular diffraction patterns.

Figure 4.5: Channels were evident for thicker films of spincoated TBAT.

During the profilometry measurements, it was found that the thickness of each facet

varied, in some cases, by a few nanometers. If the difference is large enough, this may

create a problem when a subsequent area is taken for electron diffraction, the pattern

will exhibit a different intensity at another location on the film.

4.3.5 Substrates

Different substrates could interact with the solution differently depending on crystallinity

and/or hydrophobicity of the surface. As mentioned in Section 1.1.3, lattice constants

have an influence on the first layers of a film. The hydrophobicity of the surface influences

how well a solution spreads, and thus, the formation of a film.

Glass, silicon nitride wafers and windows, and carbon-coated mica were tested. All

substrates are amorphous, which would avoid problems with lattice mismatching. Spin-

coating a film onto silicon nitride windows would directly generate samples for electron


diffraction experiments. Films formed on the other substrates must be floated off and

picked up on a support for use in diffraction experiments.

Silicon nitride wafers produced similar results to glass. Films formed on the silicon

nitride windows were assumed to have the same characteristics as those formed on silicon

nitride wafers. The thickness and facet sizes of films formed on silicon nitride were

approximately the same as those formed on glass.

Silicon nitride windows were initially difficult to handle. The windows were made

by M. Harb at the nanotech facility at Cornell University. The original design had the

windows spaced fairly closed to each other on a wafer with scribing that was not deep

enough to easily separate the individual windows. Due to the extreme thinness of the

windows (40nm) any disturbances resulted in the breakage of the windows, rendering

them useless. A new design spaced the windows farther apart and were more easily

separated from one another. Direct vacuum, from the spincoater, under the windows

caused breakages, but was managed by using double-sided tape to hold the windows to

the spincoater’s chuck instead. Figure 4.6 shows diffuse scattering of a TBAT sample

spincoated onto a silicon nitride window but weak diffraction can be seen.

Figure 4.6: Weak electron diffraction off a spincoated sample of TBAT.

Carbon was deposited by evaporation onto freshly cleaved mica. Mica is known to be

atomically smooth. The carbon would provide an amorphous layer on the mica to prevent

lattice mismatches. The carbon layer would be beneficial for the electron diffraction


by prevent surface charging and would not affect the diffraction pattern because it is

amorphous and would only diffusely scatter electrons. It also facilitates the floating

process.

Unfortunately, the deposited carbon was not a smooth layer on the mica. This resulted

in many particles on the surface of the substrate, which causes defects in spincoated films.

Spincoating solutions on these substrates resulted in many holes in the films or induced

crystallization (see Figure 4.7).

Figure 4.7: Films of (a) TBAT and (b) TPPT spincoated onto carbon-coated mica.

4.3.6 Cellulose Acetate

The goal in spincoating is to generate a film and to float it off its substrate, which

will be picked up by a support, such as a grid, mesh, or window that allows electron

transmittance. The film must be sturdy to remain intact once it is floated onto the water

surface and picked up. The triiodide films were very fragile and broke into pieces upon

sitting on the water surface. Large areas are needed for electron diffraction experiments.

For the same purpose as the dropcasting, cellulose acetate was used to fortify the triiodide

films (see Section 3.1).

In general, the facet appearance was the same as those of films without cellulose

acetate (see Figure 4.8). The absorption spectra of these films show the unique triiodide


peaks at ∼290 nm and ∼370 nm (see Figure 4.9). The spectra resembled those of

the triiodides without cellulose acetate, with the exception of TBAT (see Figure 2.3).

(Cellulose acetate does not absorb in the UV-visible region.) TBAT with cellulose acetate

spectra lacked the broad absorption between 400 nm and 600 nm seen in the TBAT films.

If the broad band was an indicator of I2 (see Section 4.2.1) then the addition of cellulose

acetate prevented the reaction I−3 → I2 + I−.

Figure 4.8: Films of (a) TBAT, (b) TEAT, (c) TPPT with cellulose acetate under the

optical microscope.

Figure 4.9: Absorption spectra of (a) TBAT, (b) TEAT, (c) TPPT with cellulose acetate.

With higher concentrations of cellulose acetate, 10 mg/mL, striations formed. These

are wave-like appearances in the film that correlate to differences in thickness. These

striations did not appear at lower (2 mg/mL) cellulose acetate concentrations. Lower

ratios of cellulose acetate to triiodide were also favoured for diffraction purposes: more

triiodide in the film would result in higher intensity diffraction peaks.


Cellulose acetate not only fortified the film, but also altered its crystallization. In

TBAT with cellulose acetate, the facets were larger and the crystallization was slower.

These facets were about 70 mm to 1 cm wide, whereas facets from TBAT solutions ranged

from 0.1 mm to 2 mm. This implies there were fewer nucleation sites. Cellulose acetate

may interact with TBAT in a way to cause this effect.

Using the purple colour of the TBAT film an indicator for faceting, it was possi-

ble to observe the time required for a slide to be covered by a crystalline film, ie. the

crystallization process. Complete crystallization of films of TBAT without cellulose ac-

etate typically took under a minute. Crystallization of TBAT with cellulose acetate took

longer than a minute. The slow crystallization can be watched as the purple areas grew

outwards and larger. Slower crystallization usually yields higher crystallinity.

Solutions of TEAT with cellulose acetate generated faceted films similar to those

without cellulose acetate. These films were floated off. However, similar to the problem

encountered with dropcasting TEAT with cellulose acetate, the yellow colour of the film

disappeared after a few seconds. TEAT is too soluble for floating onto water. For use of

TEAT in electron diffraction, TEAT samples need to be spincoated directly onto silicon

nitride windows or a similar support.

Films of TPPT with cellulose acetate looked the same as those of TPPT. These films

were floated and tested for diffraction. Though the absorption spectrum showed the two

characteristic peaks of triiodide, at 310 nm and 370 nm, the sample did not diffract.

There was about 25% electron transmittance so the sample thickness was not an issue.

Possible reasons for no diffraction could be that the film was not crystalline, cellulose

acetate may interfere with the lattice structure, or there was not enough triiodide in the

film. It could also be possible that water may alter film crystallinity. Figure 4.10 shows

noticeably change in film morphology after exposure to water.


Figure 4.10: Film of TPPT is altered after contact with water.

4.4 Floating

The films tended to be very fragile and broke apart into very small pieces when floating

was attempted. These pieces were too small to pick up on a mesh or grid to be useful for

diffraction experiments. Films with large facets that were floated tended to break apart

at the facet edges. This is probably because the film is thinner at the edge or channel

between facets. PVA was used to facilitate the floating process.

4.4.1 Polyvinylalcohol

To faciliate the floating of the spincoated films, polyvinylalcohol (PVA) was first spin-

coated onto the glass substrate. PVA is a water-soluble polymer made from the hydrolysis

of polyvinyl acetate. PVA was used as a sacrificial layer on the substrate to float the

triiodide film. Once the film makes contact with the water, the PVA layer will dissolve

and the film will float off intact.

The PVA layer is still amorphous but changes the hydrophobicity of the surface

of the substrate. The layer also affects the surface roughness. Solutions of TBAT in

dichloromethane and acetone spincoated on PVA yielded films that did not cover the

entire slide and/or films with many holes. Solutions of TBAT, TEAT, and TPPT with

cellulose acetate spincoated on PVA yielded films that covered the entire slide and did


not have holes.

4.5 Reproducibility

Reproducibility was a major problem that was encountered. There were a few interesting

factors that had an influence on the reproducibility of films. The dichloromethane used

to prepare solutions had to be fresh from the bottle to yield crystalline films. The type of

vial used to store the solutions had an impact on the lifetime of the solution. TBAT with

cellulose acetate solutions had to be made fresh. Old solutions resulted in incomplete

crystallization (nucleation sites that cease to continue growth, see Figure 4.11). However,

some solutions of TBAT in acetone had to be aged at least a day to produce faceted films.

Figure 4.11: (a) A faceted film of spincoated TBAT with cellulose acetate and (b) the

incomplete formation of a crystalline film from an old solution.

Samples made with the same conditions would give different diffraction results: some

would give diffraction while others did not. Also, samples tended to degrade over time.

Humidity was thought to be a factor because this degradation was more prominent during

the humid summers in Toronto. The lifetime of a film was extended after being placed

in a desiccator.

Figure 4.12 shows the degradation of TBAT with cellulose acetate was visible under

an optical microscope. The surface of the film becomes less defined with a wet look. This


could be due to the absorption of water from the air.

Figure 4.12: (a) A spincoated film of TBAT with cellulose acetate and (b) the same film

after 3 days.

The films changed colour with time after spincoating. Initially, the films were clear

and the colour of their respectively compounds, but within a few minutes, the films

becomes somewhat opaque (see Figure 4.13). The absorption spectra of the films were

not affected, however, suggesting that only the surface is affected.

Figure 4.13: (a) TBAT films immediately after spincoated and (b) TBAT films after

sitting in atmospheric conditions for a few minutes.

Some of the unsuccessfully formed films resulted in droplets, crystallized droplets,

and incomplete crystallization (see Figure 4.14).


Figure 4.14: Unsuccessful films: (a) crystallized droplets of TBAT, (b) crystallized

droplets of TEAT (c) droplets of TBAT, and (d) incomplete faceting of TBAT films.


4.6 Conclusions

A summary of conditions tested:

Solvents: dichloromethane, acetone

Cleaning Method: air dry, blow dry, wiping with a tissue

Number of Drops: 1, 3, 5, 10, 20

Concentration: 1, 4, 7, 10, 20 mg/mL

Spin Speed: 1, 3, 5, 8 krpm

Substrate: glass, silicon nitride (silicon nitride windows), carbon-coated mica,

PVA coated glass

Addition of cellulose acetate

Cleaning had the biggest impact on facet size, where blow-dried slides produced the

largest facets and wiped slides produced the smallest. The number of drops did not

influence thickness nor facet size, but overly excessive amounts resulted in less ideal

films. Concentration and spin speed can control the thickness, but did not have an

influence on facet size. PVA helps to float films off their substrates more easily. Cellulose

acetate reinforces the films to make them float off in larger pieces better and may improve

crystallinity of the films, by slowing down the crystallization process and reducing the

number of nucleation sites.

It was found that ideal films were those with the largest facets. This avoids problems

with surface roughness and thickness. Channels between facets were found to be notice-

ably deeper than facets, which increase overall surface roughness. Neighbouring facets

were found to differ in thickness. Also, each facet is formed from one nucleation site and

is thought to be similar to single crystals in crystallinity. Large facets reduce the number

of channels and offer a uniform film for multiple areas to be used in electron diffraction

experiments, especially for irreversible reactions such as the photodissociation of triiodie.


Films of TEAT and TPPT were not tested for diffraction, therefore could potentially

diffract. There were problems with floating TEAT due to its high solubility in water,

but it can be spincoated directly onto silicon nitride windows, a process that does not

require floating. TPPT with cellulose acetate films did not diffract for various possible

reasons. These films can be made with different parameters to perhaps produce films

that do diffract.

The largest problem with this method of sample preparation was reproducibility.

Weak diffraction was given by spincoated samples of TBAT and strong diffraction was

given by spincoated samples of TBAT with cellulose acetate. This indicates potential for

this method. Once problems with reproducibility are overcome, spincoating parameters

can be optimized.

Chapter 5

Melted Films

5.1 Introduction

Crystallization from liquid to solid was employed to make thin films. Liquids are highly

disordered and rapid cooling leads to amorphous solids. However, if cooled slowly, the

molecules can orient to pack into an ordered crystal. In a specially designed apparatus,

the compound can be cooled at a controlled rate and pressure can be applied to create

thin crystalline films.

The apparatus used for producing these films consisted of a copper cylinder with

a cylindrical hole bored through it, a cylindrical block, and a cylindrical platform (see

Figure 5.1). The sample is placed on the platform in the cylindrical hole. The block is

placed in the hole above the sample, but not touching the sample. The cylinder is heated

by wrapping a heating coil around the cylinder. The temperature was controlled by a

PID controller with a RPt resistor for active feedback. Once the sample was melted,

nitrogen gas enters the cylinder through an inlet to apply pressure to the top of the

cylindrical block, which in turn, applies pressure to the sample.

36

Chapter 5. Melted Films 37

Figure 5.1: Schematic of the apparatus for making melted films. Reprinted from D.

Elliott’s master’s thesis entitled Organic sample preparation for femtosecond electron

diffraction: tetra-n-butylammonium triiodide and 1,2-Di(2-dimethyl-5-phenylthiophen-

3-yl) perfluorocyclopentene c© 2008 with permission.


5.1.1 Melted Crystals

Crystals of TBAT and TEAT were melted and slowly cooled to observe the crystals

formed from this method. The TBAT crystals used in these experiments were made by

slow evaporation in ethanol. These were large crystals but with very rough surfaces that

could be seen by eye. TEAT crystals were made from recrystallization by cooling a super

saturated hot solution of ethanol. These crystals were not as large as the TBAT crystals

and had more deformities.

TBAT and TEAT crystals were placed on a glass slide and heated on a hot plate, to

85◦C and 150◦C respectively. The liquid was left to slowly cool to room temperature on

the cooling hot plate. Figure 5.2 and 5.3 shows pictures of the crystals, under an optical

microscope, taken before and after the melting. Both TBAT and TEAT formed crystals

after the slow cooling.

Figure 5.2: Melted crystals of TBAT recrystallized by slow cooling: (a) TBAT crystals

prior to melting; (b) and (c) the formation of crystals after slow cooling.

Sandwiching the melted compound between two substrates and applying pressure on

the substrates will spread the compound into a thin liquid layer. Upon slow cooling, this

liquid layer should crystallize into a thin film. Powder X-ray diffraction experiments con-

firmed the crystallinity of melted films matched that of TBAT powder [24]. Parameters

that could potentially influence film formation are cooling rate, substrate, and pressure.


Figure 5.3: Melted crystals of TEAT recrystallized by slow cooling: (a) TEAT crystals

prior to melting; (b) and (c) the formation of crystals after slow cooling.

5.2 Substrates

As mentioned in Section 1.1.3, lattice mismatch is a concern with thin films and should

be avoided. Samples were made by sandwiching liquid TBAT between one glass slide

and various substrates. Substrates that were used for making melted films were glass,

NaCl and KCl polished salts, carbon-coated KCl, and PVA-coated glass. Salt substrates

facilitated the floating process due to their high solubility in water. KCl was carbon-

coated, by evaporation, to counter the lattice mismatch from the salts by creating an

amorphous barrier. Carbon can also help prevent surface charging of samples, which is

beneficial in electron diffraction experiments.

Polyvinylalcohol (PVA) was spincoated onto glass to provide an alternate inexpensive

substrate that could easily float off films and also serve as an amorphous substrate. (Sec-

tion 4.4.1 discusses the properties of PVA.) A problem encountered during spincoating

experiments was that the films must be floated off the same day the PVA was spincoated

onto the slide. The PVA layer would otherwise dry to a point in which it was harder to

dissolve and floating of the film was extremely difficult. The whole procedure for making

a melted film takes at least a day and the apparatus is heated, both of which made it

almost impossible to float off the melted film from the substrate after it is made.

As an alternative, PVA with polyacrylic acid films were used instead [27]. Polyacrylic


acid (PAA) is a water-soluble polymer made from the polymerization of the monomer.

With the addition of PAA to PVA solutions, the films were able to float off the substrate

even after a few days.

TBAT crystals were placed between one glass slide and various substrates. The

crystals were heated past their melting point of 68-71◦C and then cooled. Various cooling

rates were applied, for example 35◦C over 12 hours or 24 hours. These samples were

subjected to different pressures, between 10 to 20 psi, to obtain a film of suitable thickness

for electron diffraction. The resulting films were examined under an optical microscope

to look at crystal morphology. UV-Vis absorption and a Wyko profilometer were used

for measuring the thickness.

5.3 Results & Discussion

One sample was not subjected to external pressure or controlled cooling. The liquid

TBAT was sandwiched between two glass slides, one of which was coated with PVA. The

sample was left to cool to room temperature uncontrolled. The thickness of this sample

was about 15.5 µm. The absorption spectrum in Figure 5.4 clearly shows all unique

peaks of triiodide (310, 390, and 470 nm). There was some concern that the 470 nm was

absorption from I2, which absorbs around 500 nm, but TBAT has a weak peak around

455 nm [6].

Under the optical microscope, the film appeared to have holes that were oriented (see

Figure 5.5). Other glass and PVA or PVA with PAA samples that were cooled from

85◦C to 30◦C over 24 hours (2.29◦C per hour) also exhibited this feature. At a slower

cooling rate, 85◦C to 50◦C over 24 hours (1.46◦C per hour), these holes disappeared. A

combination of fast cooling rates and insufficient pressure were attributed to the creation

of these holes.

One sample of the PVA with PAA films was taken to be tested for electron diffrac-


Figure 5.4: Absorption spectrum of a melted film of TBAT.

Figure 5.5: A melted film of TBAT made from melting and cooling between glass and

(a) PVA on glass and (b) PVA with PAA on glass.


tion. Results showed diffuse scattering and limited electron transmittance. Profilometry

measurements discovered the film to be about 1.2 µm to 2.5 µm thick, explaining the

diffraction results. All samples made with glass were too thick (0.6 µm to 5.5 µm) for

electron diffraction. All glass substrates were 1 sq in in diameter and were subject to 20

psi. Higher pressures than 20 psi are required, or smaller glass slides need to be used,

to test if PVA or PVA with PAA can be used as a substrate. (Pressure is applied via

nitrogen pushing down on a cylindrical block, which in turn applies pressure on the top

of the substrate. A smaller substrate area would result in higher pressure.)

Another feature that was noticed in the microscope images was the presence of a

domain-like structure that made up the films. Samples made on NaCl also displayed this

domain-like appearance under the optical microscope (see Figure 5.6). The area of the

domains ranged from 10 to 150 µm2 on the NaCl sample. (These were cooled from 85◦C

to 60◦C over 2 hours and had a thickness of 1.5 µm.) It is possible that each domain can

represent a single crystal, similarly to each facet in spincoated films.

Figure 5.6: A melted film of TBAT made from melting and cooling between glass and

NaCl polished salt.

Other samples of TBAT were made from NaCl and KCl substrates and cooled over

longer periods of time: 85◦C to 50◦C over 24 hours (1.46◦C per hour) and over 72 hours

(0.49◦C per hour). These parameters produce films that diffracted. Unfortunately, the

pattern was streaked, as seen in Figure 5.7. The streaking was attributed to the beam


size being close to the grain size. There was also some concern for lattice mismatch.

Figure 5.7: Electron diffraction image of TBAT made from melting and cooling between

glass and KCl polished salt at 80 kV.

KCl polished salts were carbon-coated, by evaporation, to prevent the lattice mis-

match by creating an amorphous barrier. However, diffraction off the films still exhibited

a streaked pattern and resembled diffraction rings (see Figure 5.8).

Figure 5.8: Electron diffraction image of TBAT made from melting and cooling between

glass and carbon-coated KCl polished salt at 55 kV.

A problem with sample uniformity was evident during the electron diffraction experi-

ments. Shots were taken at different sections of the same film and the diffraction patterns

were noticeably different (see Figure 5.9). The intensity varied and the peaks were in a

different position, as if the pattern were rotated. This difference may be due to the way


Figure 5.9: Electron diffraction taken at different areas of a melted film at 50 kV.

the film forms domains. Each domain could be orientated in a slightly different direction

and have a different thickness. The non-uniformity of the film presents a problem with

irreversible samples such as TBAT. However, it may be possible to carry out multiple

shots with the same area.

Another concern was that samples placed in the vacuum chamber exhibited decreasing

abilities to diffract over the course of a few days.

5.4 Conclusions

This method of melting crystals of TBAT and slow cooling between two substrates has

been successful in generating and reproducing thin film samples that give diffraction.

Several substrates and cooling rates were tested. Samples made from polished salts and

carbon-coated polished salts gave diffraction. Samples from PVA were too thick for

diffraction, but if made thinner, diffraction could be possible.

A couple of features were noticed in the films under the microscope: aligned holes

and a domain-like appearance. The aligned holes were determined to be an artifact due

to insufficient pressure and too fast a cooling rate. The liquid layer was not spread

completely before the crystallization process began. The domains are thought to be

similar to single crystals. It would be ideal for these domains to be as large as possible


for electron diffraction.

Optimization of this method is needed to obtain appropriate the thickness, crys-

tallinity, and removal of the streaking pattern for femtosecond electron diffraction exper-

iments.

Chapter 6

Summary

The major bottleneck of this project was accessibility to the diffractometer or any instru-

ment to test samples for their ability to diffract. Many samples were produced without

testing for diffraction.

The diffractometer had limited availability due to ongoing experiments and the extra

time required to pump down the chamber after a new sample is introduced to the setup.

The number of samples or space for samples was also limited by the translation stage

inside the chamber. This makes it harder to test multiple samples at the same time. There

were also unfortunate times when one or more parts of the setup were malfunctioning

and took time to repair.

It is possible to use a transmission electron microscope (TEM) with diffraction ca-

pabilities to test the samples. However, the higher current of electrons in a TEM tends

to melt or degrade organic samples. There was a transient diffraction pattern witnessed

with some samples, but this is not a practical means of testing for diffraction. The diffrac-

tion was so transient that its pattern cannot be captured with a camera. As well, the

sample that was tested in a TEM will have melted or degraded and no longer usable for

time-resolved experiments. In any case, it would be ideal to test with conditions closer

to that of the actual experiment.

46

Chapter 6. Summary 47

Three methods were performed: dropcasting, spincoating, and melted films.

Dropcasting TBAT, TEAT, and TPPT with cellulose acetate resulted in films that

were not suitable for electron diffraction. This is a poor technique for generating films

with high crystallinity.

There was some success with spincoating. TBAT films spincoated directly onto silicon

nitride windows gave weak diffraction. Perhaps some optimization could lead to samples

that give good, strong diffraction. TBAT with cellulose acetate films did give diffraction

with single peaks. However, these films were hard to reproduce.

The most success so far with triiodide films, in terms of reproducibility, was the

melted film method. It must be noted that these were the only samples tested at a

higher kV (55 to 80 kV) with a new setup that recently came online. Higher energy

increase the intensity of peaks. A beam block was also installed to allow higher currents

of electrons for diffraction. Optimization of this technique could reduce or eliminate the

streaking in the diffraction pattern. Though, it could be possible to carry out pump-

probe experiments with the streaking in the pattern, if changes can still be detected and

analyzed.

With the new setup that can potentially reach 100 kV and the development of ap-

paratuses for liquid and gas samples, it may be possible in the near future not only to

achieve better results with solid state samples, but also to experiment on compounds in

the liquid/solution and gas phase. This will open to the door to study a wider variety of

reactions.

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Sample Preparation for Femtosecond Electron Diffraction

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