development of chemical imaging methods for …
TRANSCRIPT
The Pennsylvania State University
The Graduate School
College of Engineering
DEVELOPMENT OF CHEMICAL IMAGING METHODS FOR ORGANIC
FUNCTIONAL GROUPS ON MODEL SURFACES
A Thesis in
Chemical Engineering
by
Min Yang
Submitted in Partial Fulfillment
of the Requirements
for the Degree of
Master of Science
August 2009
The thesis of Min Yang was reviewed and approved* by the following:
Seong H. Kim
Associate Professor of Chemical Engineering
Thesis Advisor
Robert Rioux
Friedrich G. Helfferich Assistant Professor of Chemical Engineering
Darrell Velegol
Professor of Chemical Engineering
Andrew Zydney
Walter L. Robb Chair and Professor of Chemical Engineering
Head of the Department of Chemical Engineering
*Signatures are on file in the Graduate School
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ABSTRACT
This research proposes a strategy to identify, quantify, and image various organic
functional groups on carbonaceous surfaces. These functional groups include hydroxyl,
carboxylic acid, carbonyl, and carbon sp2 unsaturated species. The strategy is to apply
derivatization reactions to each individual carbonaceous functional group so that different
tagging elements will attach to each specific group. X-ray photoelectron spectroscopy
(XPS) and auger electron spectroscopy (AES) techniques obtain the imaging of these
tagged elements to show the distribution of corresponding carbonaceous functional
groups.
A library of derivatizing reactions targeting each individual organic group has
been constructed; conversion and selectivity of these derivatizing reactions have been
studied as well. Model surfaces used in the reactions are self-assembled monolayers
(SAMs) and polymers containing functional groups. The procedures include: Vapor
phase reaction with trifluoroacetic anhydride (TFAA) or trichloroacetic anhydride
(TClAA) derivatizes hydroxyl groups. Liquid phase reaction with mental ions, such as
barium hydroxide, zinc hydroxide, or cadmium hydroxide, tags carboxylic acid groups.
Vapor phase reaction with trifluoroethyl hydrazine (TFH) derivatizes carbonyl groups.
Osmium tetroxide derivatizes unsaturated carbon species.
After confirming completion and selectivity of each reaction, XPS and AES
chemical imaging techniques, combined with TFAA or TClAA reaction, map the
distribution of hydroxyl groups; and using TFH reaction maps the distribution of
carbonyl groups.
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TABLE OF CONTENTS
LIST OF FIGURES .....................................................................................................vii
LIST OF TABLES....................................................................................................... x
ACKNOWLEDGEMENTS.........................................................................................xii
Chapter 1 Motivation ..................................................................................................1
1.1 Introduction to the grand challenge in tribochemistry ..................................3
1.2 State-of-art surface analysis techniques ........................................................10
1.2.1 XPS.......................................................................................................10
1.2.2 AES.......................................................................................................11
1.2.3 ToF-SIMS.............................................................................................12
1.2.4 IR spectroscopy ....................................................................................13
1.2.5 SPM ......................................................................................................14
1.3 Strategy to develop chemical imaging methods for organic groups .............15
1.3.1 Review of derivatizing reactions ..........................................................15
1.3.2 Hydroxyl group reactions .....................................................................16
1.3.3 Carboxylic acid group reactions...........................................................17
1.3.4 Carbonyl group reactions .....................................................................18
1.3.5 Alkene group reactions.........................................................................18
1.3.6 Summary ......................................................................................................19
Chapter 2 Preparation of Model Surfaces...................................................................21
2.1 Self-assembled monolayers (SAMs) ..............................................................21
2.1.1 Preparation of SAMs ............................................................................22
2.1.2 XPS analysis of SAMs .........................................................................23
2.1.3 PM-RAIRS analysis of SAMs..............................................................27
2.2 Preparation of SAM patterned samples ..........................................................30
2.2.1 Preparation for stamps..........................................................................30
2.2.2 Stamping...............................................................................................33
v
2.2.3 Testing the quality of the pattern..........................................................34
2.2.3.1 PM-RAIRS test for SAM packing .............................................35
2.2.3.2 Optical Microscopy Images .......................................................38
2.2.3.3 SEM images ...............................................................................40
2.3 Polymer thin film coated on silicon wafer......................................................41
2.3.1 Preparation of polymer thin films.........................................................41
2.3.2 Making patterns on the polymer films..................................................43
2.4 Summary.........................................................................................................45
Chapter 3 Stoichiometry and Selectivity of Reactions ...............................................46
3.1 Preparation .....................................................................................................46
3.2 Hydroxyl group (alcohol) reactions................................................................48
3.2.1 XPS peak analysis of TFAA test ..........................................................49
3.2.2 Information depth and probability........................................................52
3.2.3 TFAA test conversion and selectivity ..................................................56
3.2.4 TClAA test............................................................................................58
3.3 Carboxylic acid group reactions .....................................................................63
3.3.1 Barium hydroxide reaction ...................................................................64
3.3.2 Other metal ion reactions......................................................................68
3.3.3 Cationic dyes and ammonium ion tests ................................................70
3.3.4 Compatibility test .................................................................................73
3.4 Carbonyl group reactions................................................................................75
3.5 Alkene group reactions ...................................................................................78
3.6 Summary of SAMs reactions..........................................................................81
3.7 Quantification data for model polymers .........................................................82
Chapter 4 Chemical Imaging ......................................................................................84
4.1 AES imaging of SAMs ...................................................................................84
4.2 XPS and AES imaging of polymer films........................................................87
vi
Chapter 5 Conclusion and Future Work .....................................................................96
References…………………………………………………………………………….99
vii
LIST OF FIGURES
Figure 1-1: Representation of the tribochemistry between two contacting surfaces...2
Figure 1-2: SEM image of a MEMS device used to investigate tribological phenomena............................................................................................................3
Figure 1-3: Vapor phase lubrication on a MEMS device ............................................4
Figure 1-4: ToF-SIMS of the liquid-like polymeric species found in the contacting area. .....................................................................................................5
Figure 1-5: Friction coefficient of DLC at various RH conditions. ............................6
Figure 1-6: ToF-SIMS imaging of wear tracks on DLC films produced in dry and humid environments. ............................................................................................7
Figure 1-7: Raman analysis of wear tracks of DLC after friction test in dry and humid environments, with crystalline diamond and graphite for reference. ........8
Figure 1-8: XPS C1s peak of wear tracks of hydro-generated DLC films after friction tests in (a) dry and (b) humid environments. ...........................................9
Figure 2-1: XPS C 1s high resolution peak deconvolution analysis of SAMs............24
Figure 2-2: PM-RAIRS data for (a)CH3, (b)OH, and (c)COOH terminated SAMs....28
Figure 2-3: PDMS molecular structure........................................................................31
Figure 2-4: Procedures to make PDMS stamps...........................................................32
Figure 2-5: Optical microscope image of PDMS stamp..............................................32
Figure 2-6: Micro-contact printing procesure..............................................................34
Figure 2-7: (a) Schematic stamping with MUDA onto gold surface,(b)FESEM images of pattern obtained after stamping for 10 seconds and 10 minutes. .........35
Figure 2-8: PM-RAIRS spectra for (a)COOH and (b)OH SAMs printing..................37
Figure 2-9: Optical microscopy images of water pattern on OH SAM patterns with CH3 backfilling(a,c); COOH SAM patterns with CH3 backfilling(b,d) .......39
viii
Figure 2-10: Optical Microscopy Images of CH3 SAMs pattern with COOH backfilling. ............................................................................................................39
Figure 2-11: SEM image of pattern sample surface. ...................................................40
Figure 2-12: Thickness of PVMK, PVA and PAA as a function of concentration. ....42
Figure 2-13: Optical Microscopy images of PVMK thin film surface at both bright and dark fields ............................................................................................43
Figure 2-14: Number of passes needed to remove film layers with O2/Ar plasma .....44
Figure 2-15: Schematic O2/Ar plasma etching of Polymer film through the holes on Al foil...............................................................................................................44
Figure 2-16: Etching of patterns on polymer thin film................................................45
Figure 3-1: Schematic for vapor phase reaction. .........................................................48
Figure 3-2: C 1s, O 1s, and F 1s peaks of OH SAM before and after TFAA test .......51
Figure 3-3: Schematic of SAMs and the probability based on depth profile ..............54
Figure 3-4: Selectivity of TFAA towards OH group...................................................58
Figure 3-5: C 1s, O 1s and Cl 2p peaks of OH SAM before and after TClAA test. ...60
Figure 3-6: Selectivity of TClAA towards OH group .................................................63
Figure 3-7: Molecular structure of Toluidine Blue......................................................64
Figure 3-8: Ba(OH)2 test on COOH groups. ...............................................................67
Figure 3-9: Ba(OH)2 selectivity tests...........................................................................68
Figure 3-10: Ba(OH)2 solution and water compatibility tests on OH-TFAA reaction. ................................................................................................................74
Figure 3-11: Molecular structure of the carbonyl SAM. .............................................75
Figure 3-12: Molecular structure of TFMPH. .............................................................75
Figure 3-13: Selectivity of TFH towards carbonyl groups. .........................................77
Figure 3-14: Os 4d peak on propene SAM before and after OsO4 test.......................79
Figure 3-15: Os 4p3/2 peak on propene SAM before and after OsO4 test ...................80
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Figure 3-16: Conversion calculation based on C1s and Os 4d peak deconvolution ...80
Figure 3-17: OsO4 selectivity tests on various groups surface ....................................81
Figure 4-1: SEM image of COOH patterned, OH backfilled SAM sample after TClAA and Ba(OH)2 tests ...................................................................................85
Figure 4-2: AES spectra of two regions: (a) COOH SAM and (b) OH SAM after TClAA and Ba(OH)2 reactions.............................................................................86
Figure 4-3: (a) Cl tagged on OH-SAM and (b) F tagged on OH SAM. Both peaks decrease with the number of scans ......................................................................87
Figure 4-4: F 1s (a) and Auger (b) peaks.....................................................................89
Figure 4-5: XPS C 1s and F 1s imaging for three reactions in Table 4.2 ....................92
Figure 4-6: Auger imaging for three reactions in Table 4.2 ........................................94
Figure 5-1: SEM images and AES spectra of nano-particles on COOH SAM patterns .................................................................................................................98
x
LIST OF TABLES
Table 2-1: Organo-thiols chemical information. .........................................................23
Table 2-2: Three polymers used for reactions and their solvents. ...............................41
Table 3-1: Escape probability of photoelectron from a specific atom in SAMs. ........54
Table 3-2: Ratio of different carbon species of OH SAM...........................................55
Table 3-3: Ratio of different carbon species of OH SAM after TFAA test. ...............55
Table 3-4: XPS raw data for C, O, and F atomic percentage for both OH SAM and after TFAA reaction. ......................................................................................56
Table 3-5: XPS corrected data for C, O, and F atomic percentage for both OH SAM and after TFAA reaction. ............................................................................56
Table 3-6: Conversion of F from TFAA Tests. ...........................................................57
Table 3-7: XPS raw data for C, O, and Cl atomic percentages for both OH SAM and after TClAA reaction .....................................................................................61
Table 3-8: XPS corrected data for C, O, and Cl atomic percentage for both OH SAM and after TClAA reaction............................................................................62
Table 3-9: Conversion of Cl after TClAA tests...........................................................62
Table 3-10: XPS raw data of C, O, and Ba for both COOH SAM and after Ba(OH)2 reaction ..................................................................................................65
Table 3-11: XPS corrected data of C, O, and Ba for both COOH SAM and after Ba(OH)2 reaction ..................................................................................................66
Table 3-12: Conversion of Ba in Ba(OH)2 tests. .........................................................66
Table 3-13: XPS raw data of C, O, and Zn(or Cd) for COOH SAM and after Zn(OH)2 or Cd(OH)2 test. .....................................................................................69
Table 3-14: XPS corrected data of C, O, and Zn (or Cd) for COOH SAM and after Zn(OH)2 or Cd(OH)2 test. ............................................................................69
Table 3-15: Conversion of Zn(OH)2 tests....................................................................69
xi
Table 3-16: Toluidine Blue reaction conversions........................................................71
Table 3-17: XPS raw data for C, O, and N for COOH SAM and after TMAC test. ...71
Table 3-18: XPS corrected data for C, O, and N for COOH SAM and after TMAC test.........................................................................................................................72
Table 3-19: List of chemicals used to tag COOH group. ............................................73
Table 3-20: Carbonyl group reaction conversion ........................................................77
Table 3-21: Summary of derivatizing reactions. .........................................................82
Table 3-22: Quantification data for model polymers ..................................................83
Table 3-23: TFAA, TClAA and TFH test conversions ...............................................83
Table 4-1: Derivatization reactions for XPS imaging and AES imaging ...................89
xii
ACKNOWLEDGEMENTS
I would like to acknowledge Dr. S.H. Kim, as my advisor, for the extensive
guidance over the past one and a half years. I would like to thank Dr. A. Erdemir for his
generous help with my work. I would also like to thank Dr. Kim’s research group
members, Anna Barnette, Erik Hsiao, Matthew Marino, and Aimee Tu, as well as past
group members, Dr. David Asay, Dr. Don Kim, Dr. Sunhee Park, and Hye Rin Kwag.
Without these people’s professional and generous help, my project would not have
progressed as successfully as it did. In addition, I would like to thank Mr. Vince Bojan,
Dr. Tad Daniel, and Dr. Josh Stapleton for all their help with using the state-of-the-art
instruments. I would also like to thank Mr. Donald Lucas, Mr. David DeCapria, and Mr.
Steven Black for their technical support to our laboratories. This work was supported by
the United States Air Force Office of Scientific Research (Grant FA9550-08-1-0010).
1
Chapter 1
Motivation
The central concept behind this research is development of chemical imaging
methods to study organic functional groups on carbon-based surfaces and application of
those methods to the understanding of tribochemical reaction processes. Tribochemistry
refers to chemical reactions occurring between lubricant molecules (or environment) and
those of contacting surfaces.[1] Reaction products, produced under certain environmental
conditions, can lubricate surfaces.[2] Those reactions are very complicated and can be
explained by different reaction mechanisms, such as oxidation, thermal degradation,
catalysis, and polymerization.[1,3-6] Despite state-of-the-art techniques, the tribochemical
aspect of the tribology processes in terms of carbonaceous groups has not been fully and
thoroughly understood.
Nakayama et al proposed a model to explain the tribophysical and tribochemical
phenomena based on three different areas in a sliding friction system, as shown in Figure
1.1.[7] Nakayama suggests that inside the contacting area, the contacting surface is
pressed from the applied load and sheared from the sliding action.[8] The temperature may
also rise in the contacting region causing chemical reactions between the two contacting
surfaces. In the vicinity of the contacting area, electrical charging, called tribocharging,
can take place in semi-conductors and insulators.[9-11] Tribocharging changes the surface
potential and thus generates an electric field in the contact area. A triboplasma, produced
2
by this electric field, causes tribochemical reactions in the vicinity of the contact area. [9-
11] Outside the contact area, where no physical contact with the friction process occurs,
the reaction may be due to traditional reactions such as a catalytic or an acid-base
reaction. [2,5,6]
A plethora of tribology examples exist in which tribochemistry plays an
underlying role that is still not widely understood. Two examples in tribology that
indicate the difficulties associated with tribochemistry involvement are: (i) vapor phase
lubrication of microelectromechanical systems (MEMS) via short chain alcohols, and (ii)
environmental effects on friction/wear of carbon-based materials, such as diamond-like-
carbon (DLC), diamond and graphite.
Figure 1-1: Representation of the tribochemistry between two contacting surfaces [4]
3
1.1 Introduction to the grand challenge in tribochemistry.
Figure 1.2 shows the inside of a MEMS’ sidewall friction device used for the
purpose of investigating tribological phenomena.[12] The device consists of
polycrystalline silicon, covered with an organic monolayer.[12,13] It works by applying a
normal load while a shaft moves from side to side. The post moves perpendicular to the
contact at an applied load while the shuttle moves back and forth parallel to the contact.
Figure 1.3(a) shows the decrease in friction and improved lifetime of this MEMS device
in the presence of vapor phase lubrication of short chain alcohols, as compared to
environment without alcohols.[12,14] Asay et al used 1-pentanol vapor at a 15% saturated
pressure and a 95% saturated pressure, which are both above the partial pressure needed
for monolayer coverage, as a lubricant during the sliding process to decrease the friction
coefficient and prolong the lifetime of the device. Figure 1.3a shows that under the dry
N2 condition (green line in the figure), the friction coefficient increases dramatically after
103 cycles and the device fails within 2 minutes, due to wear and adhesion.[15] By
contrast, while under a 15% partial pressure of 1-pentanol, the friction coefficient
remains about 0.2 and no observed failure occurs after about 11 days or even longer.
Figure 1-2: SEM image of an MEMS device used to investigate tribological phenomena[12]
00
1
4
Figure 1.3(b) illustrates a liquid-like product formed in the contacting region that is not
soluble in hot 1-pentanol.[12,14] In addition, data collected with time of flight secondary
ion mass spectroscopy (ToF-SIMS) of the same 1-pentanol lubrication from a pin-on-disk
tribometer appear in Figure 1.4.[12,14] After complicated interpretation of the SIMS data,
apparently some polymeric species formed in the contacting region. More information is
necessary to determine exactly what this polymeric product is, what functional groups are
present, and how functional groups distribute throughout the contacting region.
Figure 1-3: Vapor phase lubrication on a MEMS device [12]
5
Another example involving tribochemistry is the humidity effect on the frictional
performance of diamond-like-carbon (DLC) films. DLC film is mechanically hard and
strong, and chemically inert to acid and base,[16,17] so that the film is appropriate for
manufacturing hard disks, engine parts, machine tools, and sensors.[18-21] DLC films are
grown in a plasma-enhanced chemical vapor phase deposition system using methane,
acetylene, or benzene as plasma.[22] DLC consists of hydrogen atoms, sp2 bonded and sp3
bonded carbon atoms.[23, 24] Environmental conditions during the tribology tests, such as
vacuum environment or in vapor phases, like H2O, O2, N2, H2 or their mixtures, affect the
frictional response of DLC.[18, 25]
Figure 1.5 shows the adverse effect of relative humidity (RH) on friction
coefficients of a DLC film using a ball-on-disk tribology test system.[26] Erdemir, et al
0 20 40 60 80 100 120 140 160 180 2000
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Polymeric species formed by tribochemical reactions
Figure 1-4: ToF-SIMS of the liquid-like polymeric species found in the contacting
area[12, 14]
6
designed a tribology test starting with a dry nitrogen gas environment. When the friction
coefficient reached ~0.012, these researchers filled the system with humid nitrogen, and
found that the friction coefficient increased dramatically. On restoring the dry nitrogen
system, the low coefficient returned immediately. This process was reproducible. Figure
1.5 shows that at a 24% RH, the coefficient is about 0.04; at a 27% RH, the coefficient is
slightly higher than 0.04.
The tribology test result in Figure 1.5 suggests the presence of some physical
and/or chemical changes occurring on the sliding area during the test. Figure 1.6 shows
typical ToF-SIMS images of the area covering both inside and outside wear tracks: (a)
formed in dry nitrogen, and (b) formed in humid nitrogen. After the test in dry nitrogen,
the major difference between the areas inside and outside the wear track, in Figure
1.6(a), is the decrease of oxygen and the increase of C2H and C2H2 in the track, while O
Figure 1-5: Friction coefficient of DLC at various RH conditions [33]
7
and OH are dominant outside track. After the test in dry nitrogen, the difference between
areas inside and outside the wear track in Figure 1.6(b) is not obvious; both areas are
covered mainly by O and OH.
Other than ToF-SIMS, Raman spectroscopy and x-ray photoelectron spectroscopy
(XPS) were also used to study chemical information on wear track area.[29-32] Figure 1.7
shows that Raman peaks observed after tests in both dry and humid conditions overlap
with each other. The area studied includes both inside and outside wear tracks. Although
Raman spectra suggested no difference in dry and humid conditions, perhaps surfaces (a
few nanometers in scale) may be different from the bulk, or spatial features at nano-scale
is beyond the limit of the Raman technique.[33]
In Figure 1.8, XPS C 1s peaks of the sliding area in both dry and humid conditions
show that, C-C bonding at 285.2eV contribute mainly to the carbon peak.[33] However,
a. dry nitrogen b. humid nitrogen
Figure 1-6: ToF-SIMS imaging of wear tracks on DLC films produced in dry and
humid environments [33]
8
the C-O and C=O bonds at 286.3 and 288eV are more prominent on the surface tested in
a humid environment than in a dry environment.[31, 33] C-O bond can be ether (C-O-C) or
hydroxyl (C-OH) groups, and the C=O bond can be ketone (CC(=O)C), aldehyde
(CC(=O)H), or carboxylic acid (COOH), but neither of them can be indentified.
To summarize those studies about DCL or MEMS tribochemistry tests, using
analytical techniques such as ToF-SIMS, Raman and XPS are not sufficient to show the
chemical identities of these carbonaceous groups and how they distribute on the DLC
films or MEMS’ surfaces after tribology tests.
Figure 1-7: Raman analysis of wear tracks of DLC after friction test in dry and humid
environments, with crystalline diamond and graphite for reference. [33]
9
Figure 1-8: XPS C1s peak of wear tracks of hydro-generated DLC films after friction
tests in (a) dry and (b) humid environments.[33]
(b)
10
1.2 State-of-art surface analysis techniques
The current state-of-the-art surface analysis techniques can provide insights into
the study of various carbonaceous surfaces. The following discussion considers whether
or not, XPS and Auger electron spectroscopy (AES), ToF-SIMS, infrared spectroscopy
(IR), and scanning probe microscopy (SPM) can answer these questions.
1.2.1 XPS
XPS is a widely used tool to collect elemental information as well as chemical
states or bonding environments of atoms on surfaces. The photoelectron process refers to
the process that photon irritation causes electron emission from core levels of atoms.[34]
The X-ray source, used in this research, is Al source with energy of 1486.6 eV.[35] The
detector collects emitted electrons and records intensity of electrons as a function of
kinetic energy (KE). Converting KE to binding energy (BE) uses Al source energy minus
the KE detected.[34] Most elements (Li-U) have core electrons with specific binding
energies, as listed in the XPS element handbook.[35] Analyzing feature peaks of elements
provides chemical information. The quantification of different elements, or in some cases
the same element in different chemical environments, can be conducted by deconvoluting
specific peaks, such as the example shown in Figure 1.8.[36] However, Obtaining an
accurate ratio between different species of the same element is not always easy,
especially when the species’ BEs are close to each other. Besides, the same BE can be
assigned to different bonds, for example, the BEs of C-O in both C-OH and C-O-C are
the same.
11
XPS chemical imaging capability for specific elements has been previously
proved.[38-40] Imaging organic groups, on the other hand, is not feasible. For example,
imaging the C-OH group on a surface containing C-OH, COOH, C=O and CH3 groups
can not be realized by the XPS imaging technique because the energy difference between
C species in various functional groups is not large enough to be distinguished. Therefore,
to apply chemical imaging to organic functional groups is a significant challenge; XPS
imaging capability has to be combined with other techniques.[36] In addition, typical XPS
imaging resolution is above 10 μm,[41] which is not as high as some other surface analysis
techniques, such as AES and SPM. This problem is due to the difficulty of focusing an x-
ray beam on smaller than 10μm on the surface compared to focusing an electron beam or
using a sharp tip (will be discussed in 1.2.5).[34] If XPS is combined with a synchrotron,
the X-ray beam can focus on a much smaller spot, but this technique is not available for
this study.
1.2.2 AES
Compared to XPS imaging capability, scanning AES provides a higher spatial
resolution (<1 μm) for chemical imaging purposes; thus, it is a very useful tool for high-
resolution identification of elements.[34] The principle of AES is: primary electrons (3
keV to 10 keV) irradiate the surface causing an electron (1st electron) from the core level
to be expelled. A hole, created in the core level, causes another electron (2nd electron)
from an outer level to be filled in. The excess energy from the 2nd electron filling the core
12
level then causes the third electron (3rd electron) from the outer levels to be expelled
towards the detector.[34, 42] This third electron is defined as Auger electron.
However, the analysis of AES has limitations in terms of chemical bonding
information. For example, a carbon AES peak cannot be deconvoluted into peaks
indicating different carbon bonding. Also, element sensitivity of AES is not as high as
XPS.[42] Another potential problem with the AES technique is the electron stimulated
desorption (ESD) phenomena observed for certain elements, such as F and Cl. ESD
causes the F and Cl elements to desorb from the top of the adsorbed self-assembled
monolayers (SAMs).[43-45] It was observed in this study that, ESD occurred on the surface
of SAMs so fast that the F or Cl peaks decreased to zero within 10 seconds. However, if
F and Cl elements are embedded within polymer films, their signals can still be detected,
even after longer irradiation periods. Scanning AES is usually a complement with other
techniques like XPS to obtain a more complete analysis of chemical surfaces.
1.2.3 ToF-SIMS
As a extensively used surface analysis technique, ToF-SIMS analyzes the mass of
particles such as ions and neutral species (atoms or molecules) irradiated directly from
the sample surface by energetic primary ions beam (such as Ar+).[47,48] Two types of
SIMS in terms of analyzer are: 1) Dynamic SIMS uses a primary beam (about 1mA cm-2)
of higher current density so that the damage to the surface is significant and rapid, but
still allows obtaining high detection sensitivity. 2) Static SIMS has a lower primary beam
current density (lower than 1nA cm-2), delaying damage to the surface, but detection
13
sensitivity is lower as a compromise.[48,49] ToF-SIMS is one of the most widely used
static SIMS because its detector has a higher sensitivity to lower fragment concentrations,
and it has the ability to collect all the ions generated simultaneously.[49] The molecular
ion imaging of ToF-SIMS can provide a resolution of 100nm. However, the interpretation
of the mass spectra is quite challenging due to various possible fragmentations from
unknown samples.[48,51] Besides, the bombardment of the surface by energetic primary
particles causes irreversible damage. Therefore, the identification of carbonaceous groups
on an unknown sample only by ToF-SIMS itself is very difficult; other techniques should
be combined for the study.
1.2.4 IR spectroscopy
IR spectroscopy can provide molecular information of almost any surface. An IR
instrument does not require a high vacuum system, and can be operated at ambient
conditions, or at low or high pressure conditions.[36,52,55] The basis of the principle of the
IR technique is the fact that molecules can be identified by their specific vibrational
modes (rotation or vibration), which correspond to certain frequencies.[52] The IR detector
collects transmitted light and records its intensity at different wavelengths. The versatility
of the IR technique includes Fourier Transform IR (FTIR), Attenuated Total Reflection
IR (ATR-IR), Reflection Absorption IR (RAIRS), and Polarization Modulation-
Reflection Absorption IR (PM-RAIRS). The IR technique is common in studies of
organic functional groups on surfaces, and it is one of the few methods that can provide
structural information about molecules on surfaces. While the limitation of IR is its
14
relatively poor spatial (>10μm) and depth resolutions (>1μm).[61,62] For the study of
tribochemisty on MEMS or DLC films, differentiating the surface (<10 nm thick) from
the bulk material by IR is difficult. Besides, IR is not capable to provide quantitative
information on concentrations of organic groups directly.
1.2.5 SPM
SPM techniques such as scanning tunneling microscopy (STM) and atomic force
microscopy (AFM), use sharp tips as probes. STM uses a probe tip of an electronically
conductive material and AFM uses a cantilever with a sharp tip, for very closely
approaching the surface during the scanning process.[63-65] The sharp tip makes possible
obtaining images with atomic resolution, which cannot be obtained by other microscopic
techniques. Thus, AFM and STM have a spatial resolution as high as 0.1 nm and depth
resolution of 0.1 nm or lower.[66-68]
Forces between AFM tips and surfaces include van der Waals force and
electrostatic or magnetic forces.[69,70] Although the observation of the atoms on the
surface provides great scope for studying the atomic and molecular structures of surfaces,
chemical information is not accessible without combining special techniques, such as
chemical force microscopy (CFM). CFM uses a chemically modified AFM tip which
interacts with a specific functional group. However, this technique is applicable only to
samples with previously known surface topography.[71, 72]
15
1.3 Strategy to develop chemical imaging methods for organic groups.
This study proposes a strategy to develop chemical imaging methods for organic
groups, using XPS imaging and scanning AES techniques. As discussed before,
examining the spectra in Figure 1.8 visualizes the problem with XPS. The C 1s peak
shows the possibility for several chemical states. Although the approaches to deconvolute
the C 1s peak have been extensively studied and work well, to use those approaches
properly still needs special care. Overlap is an important problem in the process of peak
fitting due to the XP spectrometer’s resolution limit, and some chemical states may be
buried under the spectrum as well.[36,119,120] Besides, two different functional groups may
be assigned to the same binding energy position. Even more difficult is dealing with an
unknown surface. Therefore, the idea of a “labeling method” to tag certain functional
groups by organic derivatizing reactions would be very convenient and useful.
1.3.1 Review of derivatizing reactions
In the literature, chemical derivatizing reactions of organic functional groups, in
combination with XPS, have been widely used to study the concentrations of those
groups on carbonaceous surfaces, such as polymers thin films,[73-77] carbon
nanotubes,[78,79] black carbons,[80,81] carbon fiber,[83,84] and glassy carbon.[85] Organic
functional groups in these studies include, but are not limited to, hydroxyl, carboxylic
acid, carbonyl, amine, and unsaturated carbon bonding. Probe elements existing in
derivatizing agents include fluorine, chlorine, barium, osmium, nitrogen, and silicon.
Choosing appropriate reactions and probe elements should follow an established
16
protocol: First and most important, the reaction should be selective for only one specific
organic group and inert to other functional groups. Second, the reaction product should
be inert to other functional groups. Third, probe elements in the derivatizing agents
should have a good sensitivity in XPS and/or AES analysis. Fourth, reactions should be
reproducible and have good yields. And last, preferably, the reactions are to occur under
mild conditions. Vapor phase reactions are commonly used in this field since they can
prevent the derivatizing agent and sample from physical contact, in order to minimize
sorption and/or surface swelling.[92] But for SAM samples, the SAM is no more than 2
nm thick, thus the liquid phase reaction can also be applied since the physical contact
should not affect the reaction result. Still, this assumption needs evidence to prove it.
1.3.2 Hydroxyl group reactions
Derivatizing reactions for hydroxyl groups have established that trifluoroacetic
anhydride (TFAA) undergoes an esterification reaction in a vapor phase with hydroxyl
groups.[86-90] Both phenolic and aliphatic hydroxyl groups are reactive in this reaction,
producing acetic ester groups with fluorine atoms as the probe. For example, TFAA has
proved to react with surface hydroxyl groups on polyvinyl alcohol (PVA) and poly(p-
hydroxystyrene) (PHS) with near 100% conversions.[84] Based on the same reaction
mechanism, expectedly, trichloroacetic anhydride (TClAA) will have the same reactivity
towards hydroxyl groups, after optimizing reaction conditions. Besides, phenolic alcohol
groups can also be differentiated from aliphatic alcohols, carboxylic acids, and carbonyls
by reacting with 2,4-dinitrofluorobenzene [C6H3F(NO2)2]. [102,118]
17
1.3.3 Carboxylic acid group reactions
Two major types of reaction can be applied to derivatize carboxylic acid groups: a
vapor phase reaction with a trifluoroethanol (TFE) /pyridine /di-tert-butylcarbodiimide
(DTBC) mixture[89,91-93] or an ionic bonding reaction with basic dyes.[94,95] The reaction
with TFE is based on the dicyclohexylcarbodiimide (DCC) peptide coupling mechanism,
in the presence of DTBC and pyridine.[83] It has been proved that carboxylic acid groups
on both polyacrylic acid (PAA) and poly(p-benzoic acid) (PBA) surfaces can react with a
TFE mixture to a 100% completion.[83,92]
Many different cationic dyes have also been used to tag acidic molecules, such as
DNA, RNA in life sciences.[54] These dyes bind only with the ionized carboxylic acid
group, not other functional groups. Toluidine blue [C15H16N3SCl], acridine orange
[C17H19N3HCl], and neutral red [C15H17N4Cl] are commercially available and their
molecules are relatively small, compared to molecules of other dyes. However, they
could still be too big for surface reactions, such as reactions with SAMs. Tetramethyl
ammonium chloride (TMAC) containing ammonium ions can also react with carboxylic
acid. All of these derivatizing agents use N as the probe element.
Epichlorohydrin (ECH) has also been studied as a derivatizing agent, but the
reaction efficiency proved to be too low since the reaction product has long soft branches
that bury the neighboring unreacted functional groups. Carboxylic acid groups also react
to metal ions in a water solution to form salt. Those metal ions include sodium hydroxide,
barium hydroxide, and cadmium hydroxide.[37,118] These salt-formation reactions are
18
preferred because they are easy to carry out and reproducible, and they provide versatile
probe elements to choose from.
1.3.4 Carbonyl group reactions
Based on the condensation reaction mechanism, carbonyl groups react with
hydrazone and fluorinated derivatives of hydrazines, such as trifluoromethyl phenyl
hydrazine(TFMPH), pentafluorophenyl hydrazine (PFPH) and trifluoroethyl hydrazine
(TFH).[81,88-92,96-101] Lyakhovich, et al studied the reaction between carbonyl groups and
hydrazine, and found that the reaction stoichiometry can be 1:1, 2:1, or any number in
between, depending on the reaction condition.[97]
The problem with TFMPH is steric hindrance due to its phenyl ring structure,
which may cause low reaction efficiency. TFMPH also attracts a significant amount of
fluorine on other surfaces, such as poly(ethylene terephthalate) (PET). This may be due
to the π−π interactions in the phenyl ring and π electron system on those surfaces.[83,92]
PFPH is in a solid state at room temperature and it requires a high temperature reaction
condition. TFH has been proved a good derivatizing agent for carbonyl groups.[81, 90, 97]
1.3.5 Alkene group reactions
To distinguish sp2 unsaturated carbon from sp3 saturated carbon, osmium tetroxide
(OsO4) and ruthenium tetroxide (RuO4) have been used to oxidize unsaturated molecules,
such as the addition reaction with alkene and alkyne bonds.[103,104] Since the AES peak of
Ru has a overlap with the AES peak of C, Os turns out to be a better choice for AES
19
analysis. Addition reactions to derivatize alkene groups also include reactions with
hypochlorous acid [HOCl] or diborane [B2H6], due to their oxidizing capability.
1.3.6 Summary
To summarize previous research, F or Cl can be used as probe to tag OH groups; F,
N, Ba, or Ca can be used as probe to tag COOH groups; F or N can be used as probe to
tag C=O groups, and Os can be used as probe to tag C=C groups. Most previous research
focused on the identification or quantification of one organic functional group on a
carbonaceous surface. If more than one type of organic group exists on the surface, each
group is derivatized and quantified separately. For example, when studying
concentrations of hydroxyl, carbonyl and carboxylic acid groups on black carbon
surfaces, Fairbrother, et al applied the TFAA test, the TFH test, and the TFE test to three
separate black carbon samples, all using the same probe “F” as the tag.[83] They
calculated hydroxyl concentration by the TFAA test, calculated carboxylic acid
concentration by the TFE test, and calculated carbonyl concentration by the TFH test,
respectively. Those concentrations are just average values for each group; the distribution
of each type of group is still unknown.
The current research proposes that instead of using only one probe for one organic
group, various probe elements should be prepared so that multiple reactions can be
accomplished on the same sample with each probe element standing for each organic
functional group. Combining this protocol with XPS imaging and scanning AES
20
techniques, the distribution of organic functional groups can be obtained on both
controlled surfaces and unknown surfaces.
Chapter 2 discusses the preparation and characterization of model surfaces
containing organic functional groups, which are used for derivatizing reactions. Chapter 3
describes the reaction mechanism, conversion, and selectivity for each functional group.
Chapter 4 focuses on the XPS/AES images that show the chemical mapping of each
organic functional group and their derivatization reactions. Chapter 5 concludes and
provides extension for future work based on this research.
21
Chapter 2
Preparation of Model Surfaces
Before any further investigation into unknown surfaces, a library of derivatizing
reactions needs to be established on structurally and chemically well-defined model
surfaces with each organic functional group. Several important factors should be taken
into consideration while choosing model surfaces: (a) Model surfaces may go through a
series of reactions, therefore, non-specific adsorption (physisorption) should be negligible
compared to chemical reaction (chemisorption), so that selectivity and conversion tests
will not be affected by factors other than reaction. (b) The preparation of model surfaces
should be simple and reproducible. (c) Analytical techniques to obtain chemical and
molecular information, and other properties of surface should be available. Based on
these considerations, two methods were chosen for preparing controlled model surfaces:
(i) SAMs prepared on gold surfaces, and (ii) polymer thin films spin-coated on silicon
wafers.
2.1 SAMs
SAMs are one of the most straightforward and widely studied models for
depositing controlled organic thin films, in particular, organo-thiols on gold surfaces.[105]
The terminated functional groups, including methyl (R-CH3), hydroxyl (R-OH), carbonyl
(RC(=O)R’), carboxylic acid (R-COOH), and alkene (R-C=C), determine the chemical
22
properties of the SAMs. The method for preparing SAMs is very simple and
reproducible; also, the quality of SAMs can be characterized by PM-RAIRS and XPS.
2.1.1 Preparation of SAMs
The organo-thiols chemicals were purchased, commercially, from Sigma-Aldrich
company. The names of chemicals, molecular structures, and functional groups of the
organo-thiols used in this study appear in Table 2.1. The gold wafers, purchased from
Sigma-Aldrich, consisted of a gold layer (1000 nm thickness) with a highly orientated
polycrystalline bonded on a silicon wafer <100> through a titanium adhesive[106]. The
organo-thiols were dissolved in 100% ethanol at concentrations ranging from 5~20mM.
Following processes prepared the gold wafers: (1) gold wafers were cut into appropriate
sizes (according to subsequent purposes) with a diamond cutter; (2) gold samples were
immersed into an ethanol/water solution (1:1 by volume) and ultrasonicated for 30
seconds to remove physically attached particles; (3) after drying with argon, gold wafers
were cleaned with atmospheric O2/Ar plasma [power of 100w, Ar flow set at 3 pm, O2
flow set at 10 sccm] for 20 passes to remove any remaining organic contaminants. After
these steps, the cleaned gold samples were ready for immersion in SAM solutions.
23
2.1.2 XPS analysis of SAMs
XPS can be used to characterize the quality of SAMs by collecting C 1s high
resolution spectra. The XPS instrument used in this research has a Kratos Analytical Axis
Ultra X-ray gun with photon energy of 1486.7eV from a monochromatic Al Ka source.[35]
The C1s peak deconvolutions of methyl, hydroxyl, carboxylic acid, carbonyl and alkene
terminated SAMs appear in Figure 2.1. The major peaks found in all three cases at a
binding energy of ~284.7eV (or 284.6 eV) correspond to C-C species. A small shoulder
is also present in each case at a binding energy of ~285.7eV (or 285.6eV), corresponding
to C-S species. Other C deconvoluted peaks are quite different for each SAM. The OH-
terminated SAM spectrum shown in Figure 2.1(b) has another shoulder at a binding
energy of ~286.4eV, corresponding to C species in C-OH. The COOH-terminated SAM
spectrum in Figure 2.1(c) separates a peak at ~289.3eV, representing the carbon species
in the COOH group; a shoulder at ~286.7eV is also observed on COOH SAM spectrum,
Table 2-1: Organo-thiols chemical information
Name of chemical Molecular
structure
Functional
group
Concentration
(mM)
1-Hexadecanethiol 99% HS-(CH2)15-CH3 Methyl 20
11-Merchapto-1-undecanol 99% HS-(CH2)11-OH Hydroxyl 20
12-Mercaptododecanoic acid
96%
HS-(CH2)11-
COOH
Carboxylic
Acid
20
3-Mercapto-2-butanone solution
10wt. % in triacetin
Carbonyl 20
2-Propnene-1-thiol technical
60% (GC)
HS-CH2-CH=CH2 Alkene 5
24
which cannot be identified yet. In Figure 2.1(c), C 1s peak of carbonyl SAM contains a
peak at ~287.2 eV, corresponding to C as in C=O species. Although C 1s peak of alkene
SAM should be deconvoluted into only two peaks at ~284.7 and 285.7eV, a third peak at
~287.8eV is also present, which may be due to the impurity of alkene SAM, or the
oxidization of unsaturated bonds.
Based on the analysis of XPS C 1s peak of various SAMs, functional groups have
been confirmed according to peak positions, though in some cases, such as carboxylic
acid and alkenes groups, certain side peak cannot be confirmed yet. To quantify each C
species on SAMs can also be realized by analyzing the peak areas, which will be
discussed in detail in Chapter 3.
Au-S-C2H2-(C1H2)13-CH3
288 287 286 285 284 283 282 281 Binding Energy (eV)
XPS
inte
nsity
(A.U
.)
CH3SAM C 1s Peak C1
C2 background
284.7
285.7
(a)
25
288 287 286 285 284 283 282 281
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
OH SAM C1s Peak C1
C2
C3 background
Au-S-C2H2-(C1H2)9-C3H2-OH
284.7
285.7286.4
293 292 291 290 289 288 287 286 285 284 283 282 281
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
COOH C 1s C1
C2
C3
C4
Background
Au-S-C2H2-(C1H2)9-C3H2-C4OOH
284.6
285.6286.66289.26
(b)
(c)
26
290 288 286 284 282
XPS
Inte
nsity
(A.U
.)
Binding energy (eV)
C=O SAM C 1s peak C1
C2
C3
background
Au-S-C2H(C1H3)-C3(=O)-C1H3284.6
285.6287.2
Figure 2-1: XPS C1s high resolution peak deconvolution analyses of SAMs.
290 289 288 287 286 285 284 283 282
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
C=C SAM C 1s peak
C1
C2 undentified C background
Au-S-C2H2-C1H=C1H2
284.7
285.7
287.8
(d)
(e)
27
2.1.3 PM-RAIRS analysis of SAMs
SAMs can also be characterized by IR techniques.[56,105,107-109] PM-RAIRS used in
this research with assistance from XPS and AES, studied the packing quality of SAMs
prepared on gold film. PM-RAIR spectra were recorded using a Nexus 670 spectrometer
equipped with a nitrogen cooled MCT (Mercury Cadmium Telluride) /A detector. The
incident beam from the IR source splitted into s-polarized and p-polarized light beams by
a polarizer and a photoelastic modulator, before going through the sample. Two spectra
were captured by the detector: the addition of s-polarized and p-polarized light, and the
difference between them. The ratio of the two spectra provided certain characteristics of
the samples. For PM-RAIRS tests, only CH3, OH and COOH terminated SAMs were
investigated; C=O and C=C terminated SAMs were not studied using PM-RAIRS,
because the main chains (containing 3 atoms for each case) of these two SAMs are short
and hardly well packed.
PM-RAIRS spectra of the SAMs prepared by immersion in SAM solutions,
provided courtesy of Aimee Tu, appear in Figure 2.2. Two peaks at the wave numbers of
2920 (2918) and 2850 (2848) cm-1 correspond to CH2 asymmetric and symmetric
stretching modes respectively, and observable in all of three SAMs. The CH3 terminated
SAM, shown in Figure 2.2(a), has a CH3 asymmetric stretching peak at 2958 cm-1 and a
symmetric stretching peak around 2885 cm-1 which is masked by the CH2 asymmetric and
symmetric stretching peaks. The spectrum of OH-terminated SAMs, shown in Figure
2.2(b), has a broad peak around 3380 cm-1 which corresponds to the OH stretching
vibration mode. The spectrum of COOH-terminated SAMs, shown in Figure 2.2(c), has a
28
peak at 1711 cm-1, corresponding to the COOH group. Based on PM-RAIRS data, the
packing quality of CH3, OH, and COOH terminated SAMs has been confirmed.
3000 2700 2400 2100 1800 1500
A.U
.
Wavenumber (cm-1)
C14
-CH3 SAM
2918
2848
29581471
(a). RM-RAIRS spectra for Au-S-(CH2)14-CH3
29
(b). RM-RAIRS spectra for Au-S-(CH2)11-OH
3600 3400 3200 3000 2800
A.U
.
Wavenumber (cm-1)
C11-OH SAM
3380
2920
2850
(c)RM-RAIRS spectra for Au-S-(CH2)11-COOH
3000 2700 2400 2100 1800 1500 1200
A.U
.
Wavenumber (cm-1)
C11
-COOH SAM2920
2850
1711
1458
1580
Figure 2-2: PM-RAIRS data for (a) CH3, (b) OH, and (c) COOH terminated SAM
30
2.2 Preparation of SAM patterned samples
The SAM samples represent a well-controlled surface to optimize reaction
conditions, to test reaction selectivity, and to calculate reaction conversion. For imaging
capabilities, patterned surfaces with more than one functional group species are needed.
Micro-contact printing is a widely-used technique to generate SAM patterns on gold
surfaces. Micro-contact printing is a soft-lithography technique that applies an
elastomeric patterned stamp with organothiol molecules onto the gold film surface, by
which, thiol molecules will transfer from the stamp to the gold surface by contact.[111-113]
Compared to conventional photolithography and other techniques, soft lithography is
straightforward, widely applied, low in cost, and reproducible.[111]
2.2.1 Preparation of stamps
The stamp material used was Poly(dimethylsiloxane) (PDMS) elastomers. PDMS
consists of an inorganic siloxane backbone with attached organic methyl groups, shown
in Figure 2.3.[114] PDMS has special properties that make it very popular in the soft
lithography field: (a) Its elasticity allows for conformal contact with the surface during
printing; (b) low surface free energy (21.6 dyn/cm) and chemical stability allow for the
molecules to be transferred without adherence to or reaction with PDMS; (c) thermal
stability and inertness towards humidity allow for prolonged storage, and (d) it has the
ability to be reused multiple times (up to 50 times).[111] Sylgard 184 PDMS, used in this
research , was a Dow Corning Company purchase and included a base and a curing agent.
The first step to make PDMS stamps was to mix the base and curing agents in a
plastic cup at a ratio of 10:1 by weight. A plastic spoon was used to mix for at least 10
31
minutes to make sure the mixing was complete. The mixed solution was originally
transparent and gradually turned milky-white, with air bubbles incorporated into the
solution. The second step was degassing the mixture by extracting the air by a desicator
connected to a vacuum system. This process took at least 1.5 hours to make sure the
solution was clear, transparent, uniform, and with few bubbles. After degassing, the
PDMS solution was poured onto a patterned, model substrate, or master mold, which was
a silicon wafer, fabricated by photolithography and reactive-ion etching techniques.[113]
Patterns on the substrate were 25 μm x 25 μm (area) x 7 μm (depth), shown in Figure
2.4. In the next step, the substrate, covered with PDMS, was degassed in the desicator for
another half an hour. Finally, the template covered with clear PDMS mixture was baked
in an oven at 65-70oC for 12-24 hours. After peeling, the cured stamp was ready to use.
Figure 2.5 is an optical microscopy image of a PDMS stamp surface with patterns.
Figure 2-3: PDMS molecular structure[114]
32
Prior to printing, PDMS stamps need a cleaning step to remove uncured
molecules and short chain oligmers left in the stamps; otherwise, these residues would
transfer to the gold surface by contact. The stamps were soaked in n-hexane (95%) liquid
for 1.5 hours and allowed to swell so that the short chain molecues left in the PDMS
stamp would diffuse into the hexane solution. The step, repeated two more times,
preceded placing the stamp in a oven at 70oC for 24 hours to evaporate the hexane and
allow the stamp to shrink to its original size. Then, the stamp was immersed in a
Figure 2-4: Procedures to make PDMS stamps[111]
Figure 2-5: Optical microscope image of PDMS stamp surface
7 μm depth
l = d = 25 μm
33
water/ethanol solution (1:1 by volume) and sonicated for 15 minutes to remove any
particulates. Finally, the stamp was dried with argon and pressed onto a clean silicon
wafer (using RCA cleaning) 2-3 times, so that the remaining residual monemers and short
chain oligmers (if not fully removed from the previous steps) would be transferred to the
silicon wafer. After all these cleaning steps, the stamp was cleaned and immersed into
SAM solutions.
Gold wafers were cut into pieces a little larger than the stamps so that during
printing, the whole stamp would have a good contact with the gold surface. The gold
pieces underwent the same cleaning process previously described.
2.2.2. Stamping
In the stamping process, described in Figure 2.6,[111] the clean gold-coated silicon
wafer was placed horizontally on a stable stage. The PDMS stamps were taken from
SAM solution, dried with argon and then carefully placed onto the gold surface. A 50
grams weight was placed on top of the stamp. After a certain time, the weight was
removed and the stamp was peeled from gold surface. The sample was immersed in the
second SAM solution immediately. COOH SAMs or OH SAMs were used as ink for
stamping while CH3 SAMs were used to back-fill the rest of the surface. The blank area
of gold which did not have contact with the stamp would be filled with CH3 SAMs.
Groups with OH or COOH surface patterns and groups with backfilled CH3 were thus
prepared.
34
2.2.3 Testing pattern quality
The characterization of SAMs by micro-contact printing has been studied using
scanning electron microscopy (SEM), a case is shown in Figure 2-7.[113, 115-117] The
printing process, described schematically in Figure 2-7(a) has the stamp pattern size
10μm by 10 μm; the ink for printing is 25mM 11-mercaptoundecanoic acid (MUDA).
Figure 2-7 (b) and (c) show the SEM images of SAM samples printed for 10 seconds and
10 minutes, respectively. In both cases, bright area should represent SAM patterns while
the darker area should correspond to the gold substrate without contact printing. SEM
images show that the printing time of 10-second gives a better edge than the 10-minute,
printing, indicating the 10-minute sequence may cause a diffusion of SAM molecules
into non-contact areas. Although SEM can provide an image of the surface, the image is
insufficient to show the packing or functionality of SAMs. Besides, SEM may damage
the SAMs by using electrons as the probe beam. In this study, in order to obtain a mixed
SAM surface with controlled patterns, two extremes should be avoided during printing
step: on the one hand, SAM molecules are not well transferred to the gold surface; on the
other hand, SAM molecules may diffuse into the non-contacting areas to the degree
Figure 2-6: Micro-contact printing procesure [111]
35
patterns disappear. To solve those two problems, PM-RAIRS and an optical microscope
were used.
2.2.3.1 PM-RAIRS test for SAM packing
As described earlier in this chapter, PM-RAIRS has been used to analyze the
quality of fully covered SAM surface, prepared by immersing the gold wafer in
Organothiol-ethanol solution, shown in Figure 2.2. Similarly, SAMs obtained by
stamping can also be characterized by PM-RAIRS, only on the assumption that, under the
same printing conditions (contact time, pressure, gold substrate, solution), SAMs printed
by a flat PDMS stamp are the same as those printed by a patterned PDMS stamp. Based
on this assumption, the printing conditions (especially printing time) can be optimized
using flat stamps. Figure 2.8 shows PM-RAIRS spactra using flat stamps with (a) a
COOH SAM solution, and (b) OH SAM solution as ink. The concentration of ink is the
same with the SAM solutions, listed in Table 2.1. For COOH SAM spectrum, a COOH
Figure 2-7: (A) Schematic stamping with MUDA onto gold surface. FESEM images of
pattern obtained after stamping for 10 seconds(B) and 10 minutes(C). [21]
36
stretching peak is present at 1713 cm-1, and two CH2 stretching peaks appear at 2923 cm-1
and 2852 cm-1, as shown in Figure 2.8(a). Only two CH2 stretching peaks appear at 2922
cm-1 and 2849 cm-1, observed on OH SAM spectrum, while an OH broad peak at about
3395cm-1 in Figure 2.2(b) is not obvious here. Comparing spectra that stand for different
printing times, 30 seconds and 60 seconds show better OH and COOH peaks, indicating
better packing of SAMs.
37
Figure 2-8: PM-RAIRS spectra for (a) COOH and (b) OH SAMs printing
3100 3050 3000 2950 2900 2850 2800 2750 2700
IR u
nits
wavenumber (λ -1)
10sec 30sec 60sec 1min 2min 3min 4min
PM-RAIRS test for printing COOH SAM on gold2923
2851
CH2 stretching
2960
CH3 stretching
1800 1770 1740 1710 1680 1650 1620
IR u
nits
wavenumber (λ -1)
1713 carbocilic acid
3100 3000 2900 2800 2700
IR u
nits
Wavenumber (λ-1)
10 sec 30 sec 60 sec 1 min 2 min 3 min 4 min
PM-RAIRS test for printing OH SAM on gold2922
2849
CH2 stretching
(b)
(a)
38
2.2.3.2 Optical microscopy images
Diffusion problems that occur on noncontacting areas during the printing process
should be taken into account. An easy way to check the pattern quality is to use a “water
pattern,” based on a water condensation mechanism. The surface should be prepared with
both hydrophilic and hydrophobic areas. The hydrophilic area is covered with COOH or
OH SAMs while the hydrophobic area is covered with CH3 SAMs. When the sample
with both areas is cooled in a humid enviroment, patterns of condensed water on
hydrophilic areas will appear.
Figure 2.9(a),(c) show the water pattern formed on the OH-pattern/CH3-backfilling
sample. Figure 2.9(b),(d) show the water pattern formed on the COOH-pattern/CH3-
backfilling sample. The printing time was 1 minute and the backfilling time was 30
minutes for both cases. In Figure 2.9(a),(b), some little water particles were observed in
the CH3-terminated area, which may be due to the diffusion of OH or COOH SAM
molecules onto the noncontacting area, or those particles were introduced accentally
during the condensation process. Other than those particles, most of these two surfaces
were covered with well-arranged water patterns with clear edges between hydrophilic and
hydrophobic areas, proving that the printing and immersion time are appropriate. Figure
2.10 shows water patterns on the surface stamped with CH3 SAMs and backfilled with
COOH SAMs. It was not easy to capture the water pattern picture of this surface, because
of surface tension. But Figure 2.10 confirmed the printing and immersion time (1minute
vs 30 minutes) as well.
39
Figure 2-9: Optical microscopy images of water pattern on OH SAM patterns with CH3
backfilling (a,c); and COOH SAM patterns with CH3 backfilling (b,d)
Figure 2-10: Optical Microscopy Images of CH3 SAM patterns with COOH backfilling.
50 μm 50 μm
100 μm100 μm
50 μm50 μm
(b)(a)
(c) (d)
40
2.2.3.3 SEM image
Figure 2.11 shows an SEM image of the patterned SAM surface (COOH pattern
with CH3 backfilling), corresponding to the water pattern image in Figure 2.9a. The
brighter area was covered with COOH SAMs while the darker area was covered with
CH3 SAMs. This image was taken while collecting AES data to obtain the chemical
information on the surface. Apparently the SAMs were destroyed by ESD, which Chapter
4 discusses in detail. Therefore, another method is needed to prepare model surfaces for
AES imaging.
Figure 2-11: SEM image of pattern sample surface.
41
2.3 Polymer thin film coated on silicon wafer
The other method to prepare a controlled carbonaceous surface is to spin-coat
polymer films on silicon wafers. The three model polymers, containing three typical
organic functional groups, appear in the list in Table 2.2.
2.3.1 Preparation of polymer thin films
All three polymers, purchased from Sigma-Aldrich, were used as obtained. PVA
dissolved completely in mili-Q water when heated to 70oC. PAA dissolved in mili-Q
water when thoroughly stirred. Polyvinylmethyl ketone (PVMK) dissolves easily in
chloroform(CHCl3). New silicon wafers were cut into pieces. (1.2cm x 1.2cm) and
ultrasonicated in a water/ethanol solution (1:1 by volume) to remove any physically
attached particles and then cleaned with RCA-1 solution to remove any organic
contaminants.
Polymers were spin-coated (4000 rpm, 30 secondes ) onto a silicon wafer using a
spin coater from Intergrated Technologies (Model P6204 4-1591). An Ellipso
Technology Elli-633 system ellipsometer (wavelength 628nm and incidence angle of 70o)
measured the thickness of polymer films. Optical microscopy provided the surface
Table 2-2: Three polymers used for reactions and their solvents
Polymer Molecular unit Solvent Functional
group
PVA [CH2CH(OH)]n 2%w/v in water R-OH
PAA [CH2CH(COOH)]n 2% w/v in water R-COOH
PVMK [CH2CH(COCH3)]n 1% w/v in chloroform RC(=O)R’
42
morphology. Figure 2.12 indicates the increase of polymer film thickness as a function of
concentrations of polymer solution. Figure 2.13 shows the optical microscopy images of
PVMK polymer surfaces on both bright and dark fields. Based on the literature[81,90] and
the experiment data shown in Figure 2.12, in order to prepare polymer films with a
thickness of 45-50nm, a 1%w/v PVMK solution in chloroform, a 2%w/v PVA in water,
and a 2%w/v PAA in water were used.
0.0 0.5 1.0 1.5 2.00
10
20
30
40
50
60
Film
Thi
ckne
ss(n
m)
Concentration (%w/v)
PVA in H2O PAA in H2O PVMK in CHCl3
Figure 2-12: Thickness of PVMK, PVA and PAA as a function of concentration
43
2.3.2 Making patterns on the polymer films
Argon/oxygen plasma cleaning can thoroughly remove the organic layer on the
surfaces. This is the same technique used to clean the gold wafer discussed earlier, and it
is also used to etch patterns on the polymer layers. For PVA and PAA films with 45-
50nm thickness, a minimum of 4 passes is necessary for thorough removal of polymer
films; for PVMK film with a similar thickness, 6 passes are necessary. The relationship
between film thickness and number of passes needed to remove the film is shown in
Figure 2.14.
Figure 2-13: Optical Microscopy images of PVMK thin film surface on both
bright and dark fields
50μm 50μm
44
A sheet of aluminum foil with 400μm~1mm diameter holes (not always in a
regular shape) was placed on top of the polymer thin film. The assembly went through an
Ar/O2 plasma, shown schematically in Figure 2.15. This process left the polymer film
with etched holes, exposing the underlying silicon wafer surface. Figure 2.16 shows an
0 1 2 3 4 5 6
0
10
20
30
40
50
Thic
knes
s (n
m)
Number of cleaning cycles
PVA PAA PVMA
Figure 2-14: Number of passes needed to remove film layers with O2/Ar plasma
Figure 2-15: Schematic O2/Ar plasma etching of Polymer film through the holes
on Al foil
Silicon waferPolymer thin film
O2/ Ar plasma
Al foil
45
SEM image of an etched PVA polymer film; the dark area corresponds to the PVA and
the light area corresponds to the blank silicon substrate. Chapter 4 contains more SEM
images of etched patterns.
2. 4 Summary
This chapter introduced two methods to prepare controlled model surfaces
containing organic functional groups. Immersion of clean gold wafer into SAM solutions
prepared uniform SAM surface. Spin-coating polymer solutions on silicon wafer
prepared model polymer films. These two uniform surfaces provided reaction
quantification and selectivity analysis in chapter 3.
Micro-contact printing technique prepared SAM surfaces with patterns, while
O2/Ar plasma cleaning technique etched patterns on polymer films. These pattern
surfaces proved XPS and AES imaging capability after derivatization in chapter 4.
Figure 2-16: Edge of pattern on polymer thin film
46
Chapter 3
Stoichiometry and Selectivity of Reactions
The main goal of this project is to combine derivatization reactions of surface
functional groups with surface chemical analysis and state-of-the-art imaging techniques
so that the spatial distribution and molecular concentrations of specific carbonaceous
functional groups can be studied. The initial step for realizing this goal is to establish a
library of derivatization reactions, each of which has specific selectivity towards a
functional group in the presence of other functional groups. This chapter discusses the
details of the stoichiometry, the conversion, and the selectivity of each derivatization
reaction as well as the reaction conditions and operations.
3.1 Preparation
SAMs with various functional groups, prepared on gold surfaces were used as
model surfaces to establish a library of derivatizing reactions. They are listed in Table 2.1
with names, molecular formulae, carbonaceous functional groups, and concentrations in
ethanol solution. SAMs containing 11~15 carbon atoms are usually 1.5 ~2.0nm thick
depending on the exact number of carbons in the main chain. XPS has an information
depth of 10 nm from the top surface. Thus, the Au 4f peaks were used as background and
reference for all XPS analysis of SAMs.
47
Derivatizing agents that will react with specific carbonaceous groups in this study
include (a) TFAA and TClAA tagging hydroxyl groups, (b) TFH tagging carbonyl
groups, (c) Ba(OH)2, zinc hydroxide/zinc carbonate mixture(Zn(OH)2/ZnCO3), cadmium
hydroxide (Cd(OH)2), toluidine blue, and TMAC tagging carboxylic acid groups, and (d)
OsO4 tagging alkene groups. All of these chemicals were purchased from Sigma-Aldrich.
TFAA, TClAA, TFH, and OsO4 were used as received for vapor phase reactions. BaOH2,
Zn (OH)2/ZnCO3, Cd(OH)2, toluidine blue, and TMAC were dissolved in mili-Q water
and used for liquid phase reactions.
Vapor phase reaction is the preferred derivatizing method because it has the least
possibility of physical contamination. The reaction in vapor phase was accomplished in a
250ml short glass jar, as shown in Figure 3.1. A 10ml beaker containing derivatizing
agent was kept separate from the samples in the jar. The jar was purged with argon gas
before starting the reaction and sealed during the reaction. For liquid phase reactions,
clean 20ml disposable scintillation vials were used to immerse the samples into the liquid
solution.
For conversion calculation purposes, a piece of gold covered with SAMs was split
into two pieces. One piece was kept in an Ar-purged 20 ml vial, while the other piece
underwent the corresponding reaction. Both of the SAM samples, before and after
reaction, were subjected to XPS analysis. By analyzing the XPS spectra, the raw atomic
percentage of specific elements were obtained and normalized with the Au peaks. The
data was further processed to calculate the reaction conversion based on individual
reaction stoichiometry. For selectivity purposes, gold pieces prepared with various SAMs
underwent the same reaction for parallel testing. In section 3.2 – 3.6 of this chapter,
48
derivatizing reactions aimed at each carbonaceous group will be discussed, individually,
including the reaction, stoichiometry, conversion, reproducibility, selectivity, and
compatibility.
3.2 Hydroxyl group (alcohol) reactions
The widely-used derivatizing reaction for hydroxyl groups is an esterification
reaction between the hydroxyl groups with TFAA in a vapor phase. (Reaction 3.1)[86-90]
Theoretically, three fluorine atoms are exchanged for each hydroxyl group after 100%
conversion. F is a distinguishing tag because of its high relative sensitivity factor
(RSF=1) in XPS analysis and its absence on most surfaces. Based on the same reaction
mechanism, TClAA can also be used to label hydroxyl groups as well. (Reaction 3.2)
Chlorine has a RSF of 0.85 in XPS analysis.
Figure 3-1: Schematic for vapor phase reaction
SAMsample
Beaker with chemicals
49
3.2.1 XPS analysis of TFAA test
XPS survey scans were used to collect the atomic percentages of C, O, and F. C
1s high resolution spectrum was collected to deconvolute different carbonaceous species.
C 1s, O 1s and F 1s peaks on OH SAM before and after TFAA reaction appear in Figure
3.2. Figure 3.2(a) exhibits the F 1s peak at a binding energy of 688.3 eV (blue) after
hydroxyl groups reacted with TFAA, while no F peak is observed before the reaction
(black). Figure 3.2(b) shows the O 1s peak of OH SAM spectrum, and Figure 3.2(c)
shows the O 1s peak of the OH SAM after TFAA reaction, which can be deconvoluted
into two peaks. An additional O species has been added to the SAMs on the surface by
the reaction, as seen in Reaction 3.1. Figure 3.2(d) shows the C 1s peak of the OH SAM,
which is deconvoluted into three C species corresponding to: C1-C, C2-S, and C3-O
species at binding energies of 284.7eV, 285.7eV, and 286.4eV, respectively. The ratio
under the area of each peak is 83:7:10, which approximately corresponds to the atomic
percentage of each C species of OH SAM. Figure 3.2(e) shows the C 1s peak
deconvolution of OH SAM after TFAA reaction. C1 and C2 are still assigned to C-C and
C-S species at binding energies of 284.7eV and 285.7eV, respectively. While the C3 peak
Au -S-(CH2)11-OH +
CF3-C-O-C-CF3
O O
==
O OCCl3-C-O-C-CCl3
==Au
-S-(CH2)11-O-C-CF3
O
=
CF3-C-OH
O+
=
-S-(CH2)11-O-C-CCl3
O
=
CCl3-C-OH
O
+
=A
u -S-(CH2)11-OH +
CF3-C-O-C-CF3
O O
==
CF3-C-O-C-CF3
O O
CF3-C-O-C-CF3
O O
==
O OCCl3-C-O-C-CCl3
==
CCl3-C-O-C-CCl3
==Au
-S-(CH2)11-O-C-CF3
O
=
-S-(CH2)11-O-C-CF3
O
=
CF3-C-OH
O+
=
CF3-C-OH
O
CF3-C-OH
O+
=
-S-(CH2)11-O-C-CCl3
O
=
-S-(CH2)11-O-C-CCl3
O
=
CCl3-C-OH
O
+
=
CCl3-C-OH
O
CCl3-C-OH
O
+
=
Reaction 3.1(top) and Reaction 3.2(bottom)
(3.1)
(3.2)
50
has shifted from a binding energy of 286.4 eV to a higher binding energy of 287.2 eV.
This suggests that the C-OH bond has been modified to a C3 species in C3-O-C=O. Also,
C4 and C5 peaks appear at 290.3eV and 293.5eV, indicating that C species in C=O and
CF3 species were introduced onto the SAM. The ratio of the C1:C2:C3:C4:C5 is about
73:5:7.5:7:7.5.
A problem was discovered when the ratio between different C 1s species were
calculated. According to the molecular formula, the theoretical ratio between C1, C2, and
C3 on OH SAM should be 9:1:1, while the experimental XPS data show a ratio of
8.3:0.7:1. Also the theoretical ratio between C1, C2, C3, C4 and C5 on OH SAM after
reaction should be 9:1:1:1:1, while the actual experimental XPS data indicate a ratio of
10:0.6:1:0.95:1. Apart from the error caused by peak fitting and approximations,
apparently the number of photoelectrons collected by the XPS detector decreases as the
carbon species is deeper from the top surface. In another words, the deeper the location of
the atom from the top surface, the smaller the fraction of electrons’ energy is collected by
the XPS detector. This well-known phenomenon is due to the inelastic mean free path
(IMFP) and is explained in further detail in the next section.
51
..
Figure 3-2: C 1s, O 1s and F1s peaks of OH SAM before and after TFAA test: (a) F
peak after test, compared to OH spectrum before test; (b) O 1s peak of OH SAM; (c) O
1s peak after test; (e) C 1s peak of OH SAM; and (e) C 1s peak after test.
C C C CCCCC
285.7
(d) C 1s peaks before TFAA test (e) C 1s peaks after TFAA test
694 692 690 688 686 684 682 680
OH SAM OH+TFAA
Inte
nsity
(A.U
.)
Binding Energy (eV)
536 534 532 530 528
Inte
nsity
(A.U
.)
Binding Energy (eV)
O peak of OH SAM
537 536 535 534 533 532 531 530
Inte
nsity
(A.U
.)
Binding Energy (eV)
O peak after OH-TFAA test
F 1s
O 1s O 1s
Au -S-(CH2)11-O-C-CF3
O
=
Au -S-(CH2)11-O-C-CF3
O
=Au -S-(CH2)11-OH
(a) F 1s peaks before and after
(b) (c)
52
3.2.2 Information depth and probability
In XPS, the x-ray can travel through 1000 nm into the the solid material.
However, the photoelectrons excited by the x-ray are only able to penetrate within ~10
nm. Even within the 10 nm depth, a certain number of photoelectrons lose energy through
inelastic collisions with atoms or molecules on their way towards the detector. Beer’s law
(Equation 3.1) explains the decrease in the photoelectron intensity as the probe depth
increases.[36] In Equation 3.1, λ represents IMFP, meaning the average distance an
electron travels without any energy loss; d is the depth of the atom located from the free
surface (top surface); Id and I0 are the intensity of the electrons contributing to the
photoelectron peak without energy loss and the intensity of the electrons that have been
excited by photon, respectively. Probability (P) (Equation 3.2) describes the probability
of the electrons penetrating through a solid material without losing energy. For organic
compouds, such as SAMs, Equation 3.3 has been developed empirically to calculate the
IMFP, where KE is the kinetic energy of the atom or molecule.[90] A schematic of the
structure of the SAMs appears in Figure 3.3. The main chain consists of CH2 units, so the
KE of CH2 calculates. The KE of CH2 equals the Al x-ray source energy minus C 1s
BE.[36] The distance between the target atom and the atom on the top surface, d, depends
on the number of carbons in the SAM. For SAMs with 11-15 atoms such as 1-
Hexadecanethiol, 11-Merchapto-1-undecanol, and 12-Mercaptododecanoic acid used in
this study, the thickness or depth is about 1.5~2.0 nm. Based on the thickness of SAMs
obtained from literature and the number of units of the main chain, the depth of each unit
can be calculated so that the contribution of each unit of the KE detected can be obtained
53
with Equation 3.2.[90] Table 3.1 lists the results, and Figure 3.3 provides a graphic
representation.
)/(0
λdd eII −= [3.1]
)/( λdd eP −= [3.2]
5.02 11.049 KEKE += −λ [3.3]
eVCAleVKE 1202)(6.284)(6.1486 =−= [3.4]
The correction for the probability of electrons being detected can be applied to
quantify the XPS data. This will correct the experimental results such that they are closer
to the theoretical values. For example, the ratio between C1-C, C2-S, and C3-OH from the
OH SAMs before reaction is 8.3:0.7:1, experimentally. After taking into account the
probability of the electron losing energy before being detected, the ratio becomes 9.6:1:1,
which is closer to the theoretical value of 9:1:1. Equations 3.5 describe the details of
these calculations, and Table 3.2 lists the results. The probability of C3-OH is taken as
being the second atom from the surface since hydrogen cannot be detected by XPS. The
probability of C2-S is taken as being the twelfth atom from the surface and as shown in
Table 3.1 will have a probability of 0.697. The correction, also applied to the C species
calculation of OH SAM sample after reaction, appearing in Table 3.3, indicates that the
ratio between various carbon species after the correction is much closer to the theoretical
value derived from the molecular structure of SAMs. The percentage of C-C species is a
little higher than the theoretical value in both cases. This may be due to the small area of
SAM detected where molecules may not be fully perpendicular to the surface but instead
are at a ~30o normal to the surface.
54
Table 3-1: Escape probability of a photoelectron from a specific atom in SAMs
In/Itop Percentage
in total
In/I top Percenta
ge in total
1st (top) 1 1 9th 0.76931 0.865280
2nd 0.967749 0.967749 10th 0.744499 0.851860
3rd 0.936538 0.952143 11th 0.720488 0.838723
4th 0.906334 0.936874 12th 0.697252 0.825862
5th 0.877103 0.921931 13th 0.674765 0.813270
6th 0.848816 0.907308 14th 0.653003 0.800942
7th 0.821441 0.892997 15th 0.631943 0.788871
8th 0.794948 0.878990 16th 0.611562 0.777050
Figure 3-3: Schematic of SAMs and the probability based on depth profile
0.0 0.5 1.0 1.5 2.0 2.5 3.00.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
Prob
abili
ty
Depth from the top (nm)
OHOHOH
OH
30o
λ = inelastic mean free path
P =Id
Id 0
= e − d j / λ
n1
n 2
∑dn
55
)......(697252.0)(..)......(838723.0)(
)....(967749.0)().....(
2
1
3
]/[]/2[]/1[
AuSCCPCCCCP
OHCCPeeeP dndd
−−=−−=
−=++= −−− λλλ
So that,
1:1:6.9)3(:)2(:)1(
03.1967749.0
1)(
04.1697252.0
7.0)(
89.9838723.0
3.8)(
3
2
1
≈
==
==
==
CICICI
CI
CI
CI
Table 3-2: Ratio of different carbon species of OH terminated SAM
XPS Atomic Percentage C- C C-OH C-S
C raw data 8.3 1.0 0.7
C corrected data 9.6 1.0 1.0
Theoretical value 9 1 1
Table 3-3: Ratio of different carbon species of OH terminated SAM after TFAA test
XPS Atomic Percentage C1-C C2 –S C3–OC=O C4=O C5F3
C raw data 7.2 0.6 1.0 1.0 1.0
P ( Id / I0 ) 0.77 0.65 0.91 0.97 1.0
C corrected data 9.4 1.0 1.1 1.0 1.0
Theoretical value 9 1 1 1 1
[3. 5]
56
3.2.3 TFAA test conversion and selectivity
XPS survey scans also provide the atomic percentages among various elements,
which can be used to calculate reaction conversions. For the OH SAMs reacted with
TFAA, only C 1s, O 1s and F 1s are used to calculate conversions since the amount of
other elements (Au, S) does not change with the reaction. The atomic percentages of C, O
and F of both OH SAM before reaction, and OH SAM after TFAA reaction, are listed in
Table 3.4. The corrected are listed in Table 3.5.
Correction:
For C11-OH, Pc=0.825862, Po=1；
For C11-O4-C3O3-C2F13, Pc=0.7721, Po= 0.9214, PF=1
Table 3-4: XPS raw data for C, O, and F atomic percentage for both OH SAM and after
TFAA reaction
XPS Atomic Percentage (raw data) %C %O %F
OH SAM 87.83 12.17 0
OH SAM reacted with TFAA 66.36 11.73 21.9
Table 3-5: XPS corrected data for C, O, and F atomic percentage for both OH SAM and
after TFAA reaction
XPS Atomic Percentage (corrected) %C %O %F
OH SAM 89.73 10.27 0
OH SAM reacted with TFAA 71.28 10.56 18.16
57
From Reaction 3.1 between TFAA and OH SAM, for each hydroxyl group three F
atoms, two C atoms and one O atom (6 atoms in total) will be added. So the atomic
percentage of F can be calculated according to Equation 3.6, where [Cini] and [Oini] are
the initial atomic percentages of C and O, respectively, on the SAM surface before
reaction. [OOHini] is the concentration of hydroxyl groups on OH SAM surface, and for
the OH SAM, [OOHini]=[Oini], since no other oxygen atom is present in the OH SAM
theoretically. ε is the reaction efficiency or conversion, which equals 1 for a complete
reaction. The initial concentrations of C and O are obtained from Table 3.5. The
theoretical conversion is calculated with 100% conversion from Equation 3.6. The actual
reaction conversion was calculated from Equation 3.7. Table 3.6 shows the result from
Equation 3.7 as well as two repeated tests.
[3.6]
%3.95%10006.1916.18%100
%%)(% =×=×=
ltheoretica
rxn
FFFε [3.7]
Besides the three conversion tests, parallel tests were conducted to prove the
selectivity of the TFAA reaction towards hydroxyl group. TFAA has been tested against
methyl SAMs, carboxylic acid SAMs, carbonyl SAMs, and alkene SAMs. After
Table 3-6: Conversion of F from TFAA Tests
Test 1 Test 2 Test 3 Average Standard
deviation
%F 95.3 % 79.6 % 80.1 % 85.0 % 8.9%
06.19100][6][][
][3% =×
++= OH
iniiniini
OHini
rxn OOCO
Fε
ε
58
normalizing all the samples with their gold peaks, the F 1s peaks were compared for
selectivity purposes as shown in Figure 3.4. The F 1s peak on the OH SAM sample is
distinguished from the other SAM samples. Although a small F 1 peak was picked up by
the C=C SAM, it is negligible compared to the F 1s peak picked up by the OH SAM
sample; thus, proving that TFAA is selective towards hydroxyl groups.
3.2.4 TClAA test
Since TClAA reaction with hydroxyl group is similar to the TFAA reaction, the
reaction between hydroxyl groups and TClAA is studied as a second derivatizing reaction
for hydroxyl groups. Cl 2p (RSF = 0.85) has a lower RSF than F 1s (RSF = 1). An
important reason to study Cl as a tag for hydroxyl groups is that F can thus be a tag for
carbonyl group (discussed in 3.4). Having a different tag for hydroxyl groups makes
possible the study of surfaces containing both hydroxyl and carbonyl groups.
694 692 690 688 686 684 682
SAM-CH3SAM-COOHSAM-C=OSAM-C=C
SAM-OH
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
Figure 3-4: Selectivity of TFAA towards OH group
59
Figure 3.5 shows the XPS C 1s, O 1s and Cl 2p peaks of OH SAM before and
after TClAA test. Figure 3.5(a) shows Cl 2p peaks with two spectroscopic states from
spin-orbit splitting into Cl 2p 1/2 and Cl 2p 3/2; the ratio of the area between 2p 1/2 and 2p
3/2 peaks is 1:2, which corresponds to the theoretical ratio calculated by 2j+1.
Theoretically, the 1/2 has an area of 2 and the 3/2 has an area of 4; thus the theoretical ratio
is 1:2 between the 1/2 and 3/2. Figure 3.5(b) and Figure 3.5(c) indicate the C 1s peaks of
the OH SAMs before and after TClAA test, respectively. After peak fitting, Figure 3.5(c)
shows the C species in C3-O, C4(=O)O, and C5Cl3 at 286.6, 289.1 and 289.8eV,
respectively. Figure 3.5(d) shows that O 1s has only one species before the TClAA test at
532.8eV. After the TClAA reaction, two O species appear at 532.8eV and 534eV, shown
in Figure 3.5(e). These two O species do not have the same area suggesting the reaction
conversion was not 100%.
60
Figure 3-5: C 1s, O 1s and Cl 2p peaks of OH SAM before and after TClAA test
(a) Cl peak after TClAA test
206 205 204 203 202 201 200 199 198 197
Inse
nsity
(A.U
.)
Binding Energy (eV)
Cl 2p peakCl 2p3/2Cl 2p1/2
292 290 288 286 284 282 280
XPS
Inte
nsity
Binding Energy (eV)
C1
C2
C3
C4
(b) C 1s for OH SAM before TClAA test (c) C 1s for OH SAM after TClAA test
536 534 532 530 528
Inte
nsity
(A.U
.)
Binding Energy (eV)
O peak of OH SAM
536 534 532 530 528
Inte
nsity
(A.U
.)
Binding Energy (eV)
O 1s peakO1O2
(e) O 1s for OH SAM after TClAA test(d) O 1s for OH SAM before TClAA test
292 290 288 286 284 282
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
C 1s peak C1
C2
C3
C4
C5
background
Au-S-C2H2-(C1H2)9-C3H2-O-C4(=O)-C5Cl3284.6
285.6
286.6289.1289.8
61
The XPS raw data for C, O and Cl atomic percentages is listed in Table 3.7. The
corrected data is shown in Table 3.8. Comparing the C:O ratio of OH SAM in Table 3.7
and Table 3.8, obviously after correction, the C:O ratio is 10.63:1, which is closer to the
theoretical value 11:1 than the raw data value, 8.75:1. This proves the correction for the
energy loss due to inelastic collision. The same calculation method used to calculate
TFAA reaction conversion can be used for TClAA reaction, shown as Equation 3.8 and
Equation 3.9. Three TClAA tests were conducted using the same reaction conditions, and
the results of these tests appear in Table 3.9. Compared to the TFAA test (conversion
85%), the TClAA test has a lower conversion of 48%, meaning that only half of the
hydroxyl groups were involved in the reaction. This may be due to the fact that the
reaction condition for the TClAA test has not been optimized, while those for the TFAA
test has been widely studied in the literature.[ 86-90] Selectivity test results, shown in
Figure 3.6, prove that TClAA reaction is selective towards hydroxyl groups rather than
methyl, carboxylic acid, and carbonyl groups.
Table 3-7: XPS raw data for C, O, and Cl atomic percentages for both OH SAM and
after TClAA reaction
Raw data % C % O % Cl
Before reaction 89.74 10.26 0
After reaction 75.46 13.07 11.47
62
Correction:
For C11-O1H, Pc=0.825862, Po=1；
for C11-O4-C3O3-C2Cl13, Pc=0.7721, Po= 0.9214, PCl=1
[3.8]
[3.9]
Table 3-8: XPS corrected data for C, O, and Cl atomic percentage for both OH SAM and
after TClAA reaction
Corrected % C % O % Cl 2p
Before reaction 91.4 8.6 0
After reaction 79.2 11.5 9.3
Table 3-9: Conversion of Cl after TClAA tests
Test 1 Test 2 Test 3 Average Standard
deviation
ε (Cl) 54.7% 53.4% 35.3% 48.0% 10.8
%7.54%10017
3.9)(
:
17100][6][][
][3%
:_
=×=
=×++
=
Cl
conversionOOC
OCl
ncalculatioltheoretica
OHoOHoo
OHo
ε
εε
63
3.3 Carboxylic acid group reactions
In the literature, to derivatize carboxylic acid groups, TFE has been widely used
in presence of DTBC and pyridine via a DDC peptide coupling mechanism, shown in
Reaction 3.3.[89,91-93] In this reaction, three F atoms attach to each carboxylic acid group
in a 100% reaction conversion. Proof exists that Reaction 3.3 is a selective derivatizing
reaction for carboxylic acid groups in the presence of other functional groups.[83,96]
Carboxylic acid groups undergo typical salt-formation reactions with metal ions,
such as Ba(OH2,[84,96,97] Zn(OH)2/ZnCO3, and Cd(OH)2. Carboxylic acids react with
cationic dyes, such as Toluidine blue, shown in Figure 3.7. Carboxylic acids also react
with ammonium ions such as TMAC (CH3)4N+Cl-). Instead of using F, Ba, Zn, Cd, and N
are used as probes. Besides, salt-formation reactions are simpler to conduct than the
reactions involving TFE.
210 208 206 204 202 200 198 196 194 192
OH CH3 COOH CO
Binding Energy (eV)
XPS
Inte
nsity
(A.U
.)
Figure 3-6: Selectivity of TClAA towards OH in presence of other functional groups.
64
3.3.1 Barium hydroxide reaction
Reaction stoichiometry of barium hydroxide with carboxylic acid occurs between
two extreme conditions: (1) two carboxylic acid groups react with one barium atom and
(2) one carboxylic acid group reacts with one barium hydroxide, as shown in Reaction
3.4(a) and (b), respectively. Theoretical barium percentage was predicted as a value
between the calculation results based on two reaction conditions, both using initial C and
O percentages in the COOH SAM. One set of data is shown to explain how to calculate
the reaction yield. Table 3.10 lists XPS raw data of C, O and Ba atomic percentages. The
corrected data appear in Table 3.11. Upon comparing the C:O ratio of COOH SAM in
both tables, the corrected value (5.3) is much closer to the theoretical value (6) than the
raw data (4.3).
Reaction 3.3.
Figure 3-7: Molecular structure of Toluidine Blue.
65
In the case of Reaction 3.4(a), for each oxygen atom, one quarter of barium will be
added by the reaction, theoretical value of barium and conversion calculations follow
Equation 3.10 ; in the case of Reaction 3.4(b), for each oxygen, one half of barium will
be added by the reaction, theoretical value of barium and conversion calculations follow
Equation 3.11. Three conducted tests provide an average conversion range between
53.6% and 95.5%, as shown in Table 3.12.
Correction:
For C11-C2O2O1H, Pc=0.81327, Po=0.98387；
For C11-C3O3O2Ba11/2, Pc=0.78704, Po= 0.92144, PBa=1
5.02)(21 COOBaROHBaCOOHR −→+−
(a)
+−−→+− ][)( 2 BaOHCOOROHBaCOOHR (b)
Reaction 3.4
Table 3-10: XPS raw data for C, O, and Ba for COOH SAMs and after Ba(OH)2 test
Raw data % C % O % Ba
Before reaction 81.33 18.67 0
After reaction 77.33 18.86 3.81
66
[3-10]
%3.45%100
87.611.3)(
87.6][][][
][5.0%
2
000
0
=×=
=++
=
Ba
OOCO
BaCOOHCOOH
COOH
ε [3-11]
Table 3-11: XPS corrected data of C, O, and Ba for COOH SAM and after Ba(OH)2 test
Corrected % C % O % Ba
Before reaction 84.05 15.95 0
After reaction 80.18 16.71 3.11
%8.81%10080.311.3)(
80.3][25.0][][
][25.0%
1
000
0
=×=
=++
=
Ba
OOCO
BaCOOHCOOH
COOH
ε
Table 3-12: Conversion of Ba in Ba(OH)2 tests
Test 1 Test 2 Test 3 Average Standard deviation
ε1(Ba) 81.8% 99.5% 105.2% 95.5% 12.2%
ε2(Ba) 45.3% 56.2% 59.4% 53.6% 7.4%
67
After reaction, Ba 3d 3/2 and Ba 3d 5/2 peaks appear in XPS spectra, as
shown in Figure 3.8. The distance between the two Ba 3d peaks is 15eV and the
ratio of two single peaks (3d3/2 to 3d5/2) is 2:3, which is in accord with the
theoretical value (2j+1). The Ba(OH)2 selectivity tests on various carbonaceous
groups appear in Figure 3.9, proving that Ba(OH)2 is selective towards the
COOH group rather than the CH3, C-OH, RC=OR’, and C=C groups.
Figure 3-8: Ba(OH)2 test on COOH.
805 800 795 790 785 780 775 770
COOH_SAM
COOH_Ba(OH)2
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
68
3.3.2 Other metal ions reactions
Barium is one of the labels for the COOH group since it has a very high XPS RSF
(Ba 3d RSF = 12.4). Similarly, as Zn and Cd have high RSFs, Zn(OH)2 and Cd(OH)2
have also been tested to react with COOH group. The XPS raw data of COOH SAM
before and after Zn(OH)2 test or after the Cd(OH)2 test appear in Table 3.13. Table 3.14
shows the corrected data. Equation 3.12 calculates the theoretical value of the atomic
percentage of Zn or Cd based on two extreme conditions. The conversion ranges of
Zn(OH)2 and Cd(OH)2 were calculated as well in Equation 3.13 and 3.14.. Table 3.15
shows the result of the three tests completed with Zn(OH)2. Compared to the Ba(OH)2
test, Zn(OH)2 and Cd(OH)2 tests have lower conversions, which may be due to the fact
810 805 800 795 790 785 780 775 770 765 760
COOH CH3 OH C=O C=C
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
Figure 3-9: Ba(OH)2 selectivity tests.
69
that these two chemicals (Zn(OH)2/ZnCO3 and Cd(OH)2 ) have very lower solubility than
Ba(OH)2 in water; the reaction does not extend to completion.
Table 3-13 : XPS raw data of C, O, and Zn(or Cd) for COOH SAM and after Zn(OH)2 or
Cd(OH)2 test
Raw data %C %O % Zn or Cd
COOH SAM 85.88 14.12 0
Zn test 81.80 15.67 2.53
Cd test 83.27 14.61 2.11
Table 3-14: XPS corrected data of C, O, and Zn(or Cd) for COOH SAM and after
Zn(OH)2 or Cd(OH)2 test
Corrected data % C % O % Zn or Cd
COOH SAM 88.04 11.96 0
Zn test 84.17 13.78 2.05
Cd test 85.48 12.81 1.71
70
%0.32%10034.571.1)(2
%0.59%10090.271.1)(
%4.38%10034.505.2)(
%7.70%10090.205.2)(
34.5100][][][
][5.0)(%
90.2100][25.0][][
][25.0)(%
1
2
1
000
0
000
0
=×=
=×=
=×=
=×=
=×++
=
=×++
=
Cd
Cd
Zn
Zn
OOCO
orCdZn
OOCO
orCdZn
COOHCOOH
COOH
COOHCOOH
COOH
ε
ε
ε
ε [3.13]
3.3.3 Cationic dyes and ammonium ions tests
Cationic dyes such as Toluidine blue and ammonium ions such as TMAC are also
used to react with COOH groups. Both of them use N as the probe. Due to the bulky
groups in Toluidine blue molecules, shown in Figure 3.7, steric hindrance can limit the
reaction conversion, which is ~36 % on average, shown in Table 3.16. Compared to
Toluidine blue, TMAC has a higher conversion (about 75%), since no steric hindrance
occurs for TMAC. Reaction 3.5 shows the reaction mechanism between TMAC and
Table 3-15: Conversion of Zn(OH)2 tests
Test 1 Test 2 Test 3 Average Standard deviation
ε1 (Zn) 70.7% 52.8% 56.6% 60.0% 9.4%
ε2 (Zn) 38.4% 29.7% 36.7% 34.9% 4.6%
[3.12]
[3.14]
71
carboxylic acid groups. Table 3.17 shows the raw XPS data for C, O and N, and Table
3.8 presents the corrected data. Conversion calculation of the (CH3)4N+Cl- - COOH test
uses Equation 3.16, and confirms that the reaction has a 75% conversion. However, the
same reaction has not been successfully repeated, which requires further investigation.
Correction:
For C11-C2O2O1H, Pc=0.81327, Po=0.98387；
For C11-C4O4O3N2(C1H3)4, Pc=0.8595, Po= 0.9214, PN=0.9677
HClCHNCOORClNCHCOOHR +−→+− +−−+
4343 )()(
Reaction 3.5
Table 3-16: Toluidine Blue reaction conversions
Test 1 Test 2 Test 3 Average Standard deviation
ε (N) 33.1% 35.9% 38.5% 35.8% 2.7%
Table 3-17: XPS raw data for COOH SAM and after TMAC test
Raw data %C %O %N
Before reaction 84.95 15.05 0
After reaction 81.01 14.95 4.04
72
[3.15]
[3.16]
Table 3.19 summarizes all the derivatizing reactions tested for carboxylic acid
groups in this study, along with their conversions. Ba(OH)2 is undoubtedly the best
derivatizing agent for carboxylic acid groups because of relatively high conversion and
reproducibility. Zn(OH)2 and Cd(OH)2 are still satisfactory, but further study to optimize
reaction conditions to achieve higher conversions is necessary. Toluidine Blue test has a
high reproducibility, but the average reaction conversion is relative low comparing to
other tests, due to the steric hindrance. TMAC has a high conversion, but more tests are
needed to confirm the reaction reproducibility.
Table 3-18: XPS corrected data for COOH SAM and after TMAC test
Corrected % C % O % N
Before reaction 87.22 12.78 0
After reaction 82.20 14.16 3.64
%21.75%10084.464.3
84.4100][5.2][][
][5.0%
:_
=×=
=×++
=
ε
εε
ConversionOOC
ON
ncalculatiolTheoretica
OHoOHoo
OHo
73
3.3.4 Compatibility test
For those surfaces with multiple functional groups, more than one reaction may
be applied to the surfaces, one-by-one, therefore, a compatibility issue needs to be
considered, especially for liquid phase reactions. For the Ba(OH)2 test, physical contact
with a metal ion base solution is unavoidable. The question is: will those SAMs, other
than COOH SAMs, still be able to proceed with their own derivatizing reactions after
Ba(OH)2 test? A compatibility test was conducted to answer this question by reacting
TFAA with OH SAMs. Four OH-SAMs samples were prepared: Sample A was kept an
unreacted OH-SAM sample; Sample B was immersed in Ba(OH)2 solution for 30 minutes
before the TFAA test; Sample C was rinsed with water after the TFAA test, and Sample
D went though the TFAA test only. The comparison between Samples B and D will
reflect the influence of the Ba(OH)2 test before the TFAA test. The comparison between
Table 3-19: List of chemicals used to tag COOH groups
Chemical probe tag element (XPS RSF) Conversion yield
COOH Ba(OH)2 Ba 3d (12.40) 54 ± 7 % ~96 ± 12 %
COOH Zn(OH)2 Zn 2p (4.75) 35 ± 4 % ~ 60 ± 9 %
COOH Cd(OH)2 Cd 3d (6.67) 32 ~59 %
COOH Toluidine Blue N 1s (0.49) 36 ± 3 %
COOH (CH3)4N+Cl- N 1s (0.49) 75 %
74
Samples C and D can determine whether or not water rinsing affects the TFAA test
results. The XPS C 1s, O 1s and F 1s high resolution peaks of those four samples are
shown in Figure. 3.10. Results indicate that F 1s, O 1s, and C 1s peaks are very similar
for all three cases, indicating that the Ba(OH)2 liquid phase test is compatible with the
TFAA reaction and water rinsing does not change the TFAA test result.
Figure 3-10: Ba(OH)2 solution and water compatibility tests on OH-TFAA reaction. (a) OH
SAM only, (b) Ba(OH)2 test before TFAA test, (c) water rinsing after TFAA test, and (d)
TFAA test only
692 690 688 686 636 534 532 530 294 291 288 285 282
Binding Energy (eV)
XPS
Inte
nsity
(A.U
.)
F 1s O 1s C 1s
d
c
b
a
75
3.4 Carbonyl group reactions
Unlike OH-SAM or COOH-SAM that have chain lengths of 11 or 12 carbon
atoms respectively, the carbonyl SAM (CH3-C(=O)CH(SH)CH3) has a very different
molecular structure, as shown in Figure 3.11. Instead of forming a layer of carbon chains
with normal tilting angles of about 30o like OH-SAM or COOH SAM, the C=O SAM has
an unpredictable structure on gold. From the XPS atomic percentage data of C=O SAM,
the C:O ratio is about 5.4, which is higher than the theoretical value of 4, obtained from
its molecular formula. The assumption is that the C atoms are lying on the gold surface,
and some O atoms are buried inside C atoms while other O atoms are exposed on the
surface.
Figure 3-11: Molecular structure of the carbonyl SAM. [106]
Figure 3-12: molecular structure of TFMPH [81,90]
76
Previous studies of the vapor phase derivatization of carbonyl groups have
established that fluorinated derivatives of hydrazines, such as TFH, is very reactive and
selective towards carbonyl groups.[81,88-92,96-101] The reaction stoichiometry of TFH and
carbonyl groups appears in Reaction 3.6. Equation 3.17 allows calculation of the
theoretical F atomic percentage from the initial carbon and oxygen atomic percentage of
the SAM surface. The results of three TFH conversion tests are listed in Table 3.20. It is
proved that TFH test has a high reaction conversion (86%). The selectivity test of TFH
towards carbonyl group is shown in Figure 3.13. As expected, the largest F 1s XPS peak
occurs for the carbonyl SAM sample after the TFH test, while no peak is apparent for
CH3 SAMs, OH SAMs or C=C SAMs. However, the F 1s peak is apparent for the COOH
SAMs sample after the TFH test. This may be due to the fact that some of the carboxylic
acids from COOH SAM are in an anhydride form which may react with TFH.
[3.17]
[3.18]
Reaction 3.6
16.24100][6][][
][3% =×++
=COoCOoo
COo
OOCOF
εε
%4.9416.2481.22%100
%%)( ==×=
ltheoretica
XPS
FFFε
77
Table 3-20: Carbonyl group reaction conversion
Test 1 Test 2 Test 3 Average Standard
deviation
% (F) 94.4% 60.8% 101.2% 85.5% 21.6%
696 694 692 690 688 686 684 682 680 678
SAM-CH3SAM-OHSAM-COOHSAM-C=C
SAM-C=O
XPS
Inte
nsity
(A.U
.)
Binding Energey (eV)
Figure 3-13: Selectivity of TFH towards carbonyl group
78
3.5 Alkene group reactions
The differentiation of sp2 unsaturated carbon, alkenes, from sp3 saturated carbon
species can be realized by the oxidization reaction with OSO4.[103,104] The vapor phase
reaction at room temperature between propenethiol SAM and OsO4 is described in
Reaction 3.7. The XPS analysis of the Os peaks is realized by separating Os 4d 3/2 and
4d5/2 peaks from C 1s peaks, shown in Figure 3.14. The Os 4d 3/2 peak at 296.0eV and 4d
5/2 at 280.6eV can be deconvoluted from the C 1s peak at 284.6eV. Although not a main
peak, the Os 4p3/2 peak can still be used with the Os 4d peaks to prove the reaction,
shown in Figure.3.15. Other Os peaks are not distinguished from the background so that
they cannot be used for analysis. For example, Os 4f and Os 5p peaks overlap with the
Au 5p peak at 54eV; Os 4p1/2 is buried within the Au 4p 3/2 peak at 546eV.
The approximated conversion was calculated differently from previous methods.
From Figure.3.16, the atomic percentage ratio between Os to C was deduced based on
XPS spectra of C1s / Os 4d peak area and RSF, shown in Equation 3.19. Equation 3.20
calculates the theoretical ratio, and Equation 3.21 provides the conversion.
Reaction 3.7.
79
%1.11%1009010_:
%%
1
4
1 ==⎟⎟⎠
⎞⎜⎜⎝
⎛xXPSfrom
COs
s
d
ε [3.19]
%3.33%10031:2 ==⎟⎟
⎠
⎞⎜⎜⎝
⎛xlTheoretica
nn
C
Osε , [3.20]
%3.33%100%3.33%1.11%100)(
2
1 =×=×=εε
ε sO [3.21]
The selectivity of OsO4 toward alkenes rather than other functional groups is
shown in Figure 3.17 for both Os 4d and Os 4p3/2 peaks. From the selectivity test result,
OsO4 is selective towards C=C rather than CH3 and COOH groups. However, Os has also
picked up on OH SAM and C=O SAM. No conclusion arises as to the reaction between
OH/C=O SAM and OsO4. More tests are needed to prove both the conversion and
selectivity of OsO4.
Figure 3-14: Os 4d peak on propene SAM before and after OsO4 test.
320 300 280 260 240 220
SAM-C=C reacted with OsO4
C=C terminated SAM
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
Os 4d 3/2 Os 4 d5/2
80
490 480 470 460 450
C=C terminated SAM
SAM-C=C reacted with OsO4
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
Figure 3-15: Os 4p 3/2 peak on propene SAM before and after OsO4 test
Figure 3-16: Conversion calculation based on C1s and Os 4d peaks deconvolution
310 305 300 295 290 285 280 275
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
Os 4d 3/2 Os 4d 5/2
C 1s
81
3. 6 Summary of SAMs reactions
Derivatizing reactions, as well as reaction conversion and selectivity, on OH,
COOH, C=O, and C=C functional groups have been summarized in Table 3.21. Further
studies are needed in order to complete this table, such as the conversion and selectivity
tests of OsO4 reaction. It is shown that TFAA/TClAA, Ba(OH)2 and TFH are good probes
for OH, COOH and C=O groups, respectively.
Figure 3-17: OsO4 selectivity tests on various groups surface
305 300 295 290 285 280 275
SAM-C=CSAM-CH3
SAM-OHSAM-COOHSAM-C=O
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)480 475 470 465 460
SAM-C=CSAM-CH3
SAM-OHSAM-COOHSAM-C=O
XPS
Inte
nsity
(A.U
.)
Binding Energy (eV)
C 1s
Os 4d 5/2
Os 4d 3/2
Os 4p 3/2
82
3.7 Quantification data for model polymers
The conversions of PVA (OH) -TFAA reaction, PVA (OH) -TClAA reaction and
PVMK(C=O) -TFH reaction have been calculated as well, based on the XPS data listed
in Table 3.22. The theoretical atomic percentage of F or Cl after each reaction, as well as
the conversion of each reaction are calculated using the same method with SAMs’
reactions, the results, shown in Table 3.23 indicate that all three tests have high reaction
conversions.
Table 3-21: Summary of derivatizing reactions
SAM
Derivatizing
agent
Probe
element
Conversion
yield Selective against
OH (F3CC=O)2O F 85 ± 9
OH (Cl3CC=O)2O Cl 48 ± 11
CH3, COOH, C=O,
NH2
COOH Ba(OH)2 Ba 54(±7) ~96(± 12)
COOH Zn(OH)2 Zn 35(±4) ~60(± 9)
COOH Cd(OH)2 Cd 32 ~ 59
COOH Toluidine Blue N 36 ± 3
CH3, COOH, OH
C=O, C=C
COOH (CH3)4N+Cl- N 75 (not tested)
C=O CF3CH2NHNH2 F 86 ± 21 CH3, OH, COOH,
C=C
C=C OsO4 Os 33% yield , against CH3 , COOH
need further tests
83
Table 3-22: Quantification data for model polymers
XPS data % C % O % F (or Cl)
PVA 66.54 33.46 0
PVA+TFAA 45.24 27.32 27.44
PVA+TClAA 48.87 22.48 28.65
PVMK 81.86 18.39 0
PVMK+TFH 57.72 3.10 23.99
Table 3-23: TFAA, TClAA and TFH test conversions
XPS data Theoretical value XPS data Conversion
%F after TFAA test 33.37 27.44 82.3%
%Cl after TCAA test 33.37 28.65 85.9%
%F after TFH test 26.2 23.99 91.6%
84
Chapter 4
Chemical Imaging
In the previous chapters, a library of derivatizing reactions targeting individual
organic functional groups has been established. These derivatizing reactions include
labeling hydroxyl groups with F or Cl, labeling carboxylic acid groups with Ba or Zn,
and labeling carbonyl groups with F. Based on these three functional groups, the
chemical imaging compatibility was tested on the model surfaces with one or two carbon
species. Two methods, introduced in Chapter 2, described preparation of model patterned
surfaces: (i) patterned SAMs with two organic groups, and (ii) patterned polymer thin
film. XPS and AES imaging techniques have been used for chemical imaging of different
elements. The best spatial resolution currently reported for XPS is ~10μm, which uses a
position-sensitive detector.[9] Unfortunately, the Kratos Axis Ultra XPS available at the
Material Research Institute (MRI) at the Pennsylvania State University was not able to
map the 25 μm x 25 μm square patterns. However, XPS was able to image the patterned
polymers in the length scale of 100μm. The AES system (WITecAlphaSNOM system) at
MRI has a field emission electron gun that provides a spatial resolution lower than 1μm.
4.1 AES imaging of SAMs
Initially, patterned SAM samples after derivatizing reactions were imaged with
scanning AES. Figure 4.1 is an SEM image of a COOH-patterned sample with OH-
backfilled SAMs. This sample underwent the TClAA derivatizing reaction for the OH
85
groups and the Ba(OH)2 derivatizing reaction for the COOH groups. Figure 4.2 shows
the AES spectra of the Ba peak inside the square and the C peak outside the square. Both
peaks are very small. The Ba peak is small because barium has a low Auger relative
sensitivity factor (RSF (Ba) = 0.2 at 10 keV). Cl has a high RSF (6.4), still the peak is
very small, which is due to ESD phenomena.
Figure 4-1: SEM image of a COOH-patterned, OH-backfilled SAM sample after TClAA
test and Ba(OH)2 tests
.
1
.
2
86
In order to record this phenomenon, executing a quick scan revealed a
discernable Cl peak in the spectrum. However after the second scan, the Cl peak
decreased fast and disappeared. The same phenomenon occurred to F tagged OH-SAM.
This is illustrated in Figure 4.3, where (a) shows the decrease of differentiated Cl peak
from the 1st scan to the 4th scan, and (b) shows the decrease of F peak from the 1st to the
3rd scan. Deductively, the disappearance of F and Cl is caused by the EDS. This is often
typical for CF3 or CCl3 terminated thiol SAMS on metal surfaces.[119] Due to this reason,
patterned SAMs samples can not be used for AES imaging. Thus, alternative patterned
polymer film samples were used.
Figure 4-2: AES spectra of two regions: (a) COOH SAM and (b) OH SAM after
TClAA and Ba(OH)2 reactions.
Cl
500 550 600
AES
inte
nsity
(a.u
.)
Kinetic energy (eV)
Ba(a)
(b)
50 100 150 200 250
AES
inte
nsity
, N(E
) (a.
u.)
Kinetic energy (eV)
87
4.2 XPS and Auger imaging for polymer films
Polymer film with hydroxyl, carboxylic acid, or carbonyl groups were spin-coated
on the silicon wafers and etched with oxygen/argon plasma through a mask. Table 2.2 in
chapter 2 has shown the name, molecular unit, functional group, and solvent used for
each polymer. Notably, since both PVA (OH) and PAA (COOH) dissolve in water,
derivatizing agents that react in water solution (metal ions) were not used for either of the
polymers. TFAA-PVA reaction, TClAA-PAA reaction and TFH-PVMK (C=O) reactions
are vapor phase reactions that can be used for all the three samples to test the XPS and
Figure 4-3: (a) Cl tagged on OH-SAM and (b) F tagged on OH SAM. Both peaks
decrease with the number of scans due to ESD
1600 650 700
AE
S in
tens
ity, N
(E) (
a.u.
)
KE (eV)100 200 300 400 500
AE
S in
tens
ity, d
N(E
)/dE
(a.u
.)
Kinetic energy (eV)
ClCl FFC
4th scan
1st scan
2nd scan
3rd scan
SS(a) (b)
88
scanning AES imaging capability. Table 4.1 lists a library of chemical imaging tests for
both XPS and Auger imaging. The F 1s and Auger peaks are shown in Figure 4.4. These
peak positions were used for mapping purposes. For XPS F 1s imaging, the first step was
to determine the binding energy of the F 1s peak in survey scan. In this case, F binding
energy was 687.6eV, as shown in Figure 4.4 (a). The second step was to choose the XPS
instrument imaging mode and define the imaging area (usually 450 x 450 μm) that will
integrate the intensity at the binding energy of 687.6eV . The contrast in the images arose
from the difference in F intensity. For Auger imaging, a survey was completed first, as
well, but instead of choosing only one peak position, many more (up to five) positions
were chosen to form the appropriate peak. For the SAM sample, a minimun of two points
were chosen to minimize the ESD. For polymer film, a three-point method denoted
Points 1, 2 and 3, as in Figure 4.4. The kinetic energies of the three points, input for the
Auger computer program, provided the imaging.
89
Figure 4-4: F 1s (a) and Auger (b) peaks
Table 4-1: Derivatization reactions for XPS imaging and AES imaging
Techniques Derivatization Reaction Test samples
OH polymer (PVA)
COOH polymer (PAA)
(F3CC=O)2O ~ OH reaction
F tag C=O polymer (PVMK)
OH polymer (PVA)
COOH polymer (PAA)
(Cl3CC=O)2O ~ OH reaction
Cl tag C=O polymer (PVMK)
OH polymer (PVA)
COOH polymer (PAA)
XPS imaging
and
Auger imaging
F3CCH2NHNH2 ~ C=O reaction
F tag C=O polymer (PVMK)
696 694 692 690 688 686 684 682 680 678
XPS
Inte
nsity
(A.U
.)
Binding Energey (eV)
F
710 700 690 680 670 660 650 640 630 620 610 600
AES
inte
nsity
, N(E
) (a.
u.)
Kinetic Energy (eV)
F 1
F 3
F 2(a)(b)
90
XPS imaging results, shown in Figure 4.5, include Figure 4.5(a), PVA, PAA, and
PVMK with patterns from the same TFAA vapor phase reaction. Both C 1s and F 1s
images were taken for all samples. All three samples have the bright and dark contrast, in
the C 1s images, which is due to the C intensity difference between the polymer region
(bright region) and etched silicon region (dark region). While for F 1s images, only the
PVA has an obvious bright and dark contrast, suggesting that F was only picked up by
the OH groups. Furthermore, this proves the selectivity of TFAA towards the OH group
rather than the COOH and C=O groups. In the F 1s imaging of COOH and C=O,
apparently little contrast corresponding with the C 1s imaging is present. This means a
little F may be present on the other two polymers. A common phenomenon described in
the literature is that the polymer will physically absorb a small amount of F.[81,90] A
conclusion can be drawn based on Figure 4.5(a): If an unknown surface is covered with
OH, COOH, or C=O group, TFAA will selectively identify OH groups and locate them.
Figure 4.5 (b) shows the C 1s and Cl 2p XPS imaging after reacting the polymers
with TClAA. Apparently, TClAA is selective towards PVA rather than PAA and PVMK.
From the Cl 2p images of COOH and C=O samples, a little Cl seems to be apparent on
the etched region, which is the silicon wafer. The reason for the presence of Cl on silicon
area still needs further study, but the speculation is that OH groups form on the silicon
wafer during the oxygen/argon plasma process in a humid environment, and TClAA tags
those OH groups. Figure 4.5(c) proves the selectivity of TFH towards C=O group rather
than COOH and OH groups. In comparison to the TFH selectivity test on SAMs where a
small fluorine peak appeared from the COOH SAM, fluorine signals are not present on
91
the COOH polymer sample. This indicates some difference may exist between the COOH
in the polymer and those in the COOH SAM solution.
Figure 4.6 shows the AES imaging results for the three selective reactions on OH,
COOH, and C=O patterned polymers listed in Table 4.2. The F and Cl Auger images are
shown on PVA samples in Figure 4.6(a) and Figure 4.6(b), respectively, proving once
again, that both TFAA and TClAA have selectivity towards OH groups rather than
COOH and C=O groups. TFH has good selectivity towards C=O groups rather than OH
and COOH groups, as shown in Figure 4.6(c). Interestingly, regular, spherical-shaped
smaller particles formed in the center of etching patterns of PVMK film, as in Figure
4.6(c). Further study focused on those small particles; SEM image, AES C, F and N
images were shown in Figure 4.6(d). Although determining how those smaller particles
formed has not yet occurred, those particles do show the higher-resolution imaging
capability of AES.
92
(a) C 1s and F 1s XPS imaging for OH, COOH and C=O SAMs after TFAA test
COOH C=O
Car
bon
1sFl
uorin
e 1s
212μm
OH
(b) C 1s and Cl 2p XPS imaging for OH, COOH and C=O SAMs after TClAA test
OH
93
(c) C 1s and F 1s XPS imaging for OH, COOH and C=O SAMs after TFH test
COOH OH C=O
Car
bon
1sFl
uorin
e 1s
212μm
Figure 4-5: XPS C 1s and F 1s imaging for three reactions in Table 4.2.
94
(a) C and F Auger imaging for OH, COOH and C=O SAMs after TFAA test
COOH OH C=OC
arbo
n 1s
Fluo
rine
1s
100μm
(b) C and Cl Auger imaging for OH, COOH and C=O SAMs after TClAA test COOH OH C=O
Car
bon
1sC
hlor
ine
2p
100μm
95
(c) C and F Auger imaging for OH, COOH and C=O SAMs after TFH test
(d) SEM image and Auger C, F, N imaging of a particle in (c)
Figure 4-6: Auger imaging for three reactions in Table 4.2.
96
Chapter 5
Conclusion and Future Work
In summary, this study establishes a library of chemical probe reactions to
derivatize OH, COOH, C=O and C=C functional groups. The research also presents
reaction stoichiometry and selectivity and confirms calculated average conversions with
the use of XPS. The most significant breakthrough of this study is the demonstration of
chemical imaging capability on controlled model surfaces with the use of XPS and AES.
The chemical imaging combined with derivatizing reactions can be applied to various
carbonaceous surfaces and investigate the location of organic functional groups.
However, more work may be needed in order to further develop this imaging tool for
carbonaceous surface analysis.
1. The reactions to derivatize COOH groups were all completed in water solutions,
but PVA(COOH) and PAA (OH) used in this study are soluble in water, which is why the
COOH tests with chemical imaging could not be accomplished with the these two
polymers. However, different polymers containing COOH other than PAA, such as PBA,
that do not dissolve in water can be used instead in further study, in order to prove
COOH-Ba(OH)2 reaction selectivity by imaging techniques.
2. The reaction of OsO4 with RCH=CH2 has only been tested once. The conversion
of this reaction is only 33% and the selectivity of CH=CH2 in presence of OH and C=O
needs further confirmation. Furthermore, because osmium peaks were obscured by, or
97
overlapped with, gold peaks, polymer samples, without gold’s influence, may be better
for testing this reaction.
3. Scanning Auger imaging has a very high spatial resolution.(<1μm) Based on that,
using the high resolution imaging capability should be an interesting topic for future
investigation. Possibly, research could include preparing polymer thin films with a
smaller scale mask. One possibility would be to use a Transmission Electron Microscopy
(TEM) grid with a mask of 20 nm by 20 nm.
4. R-NH2 groups are not common species found after tribology testing, but the
species is common in biological samples, such as proteins. The study of amine group
derivatizing reactions would be useful and applicable to life sciences.
5. When the COOH-patterned, OH-backfilled SAMs samples were imaged with
AES, an interesting phenomenon was uncovered. Apparently, nanoparticles containing
Zn and O were adsorbed only onto the COOH patterns after immersing the sample in
unfiltered Zn(OH)2/ZnCO3 solution for 30 minutes, shown in Figure 5.1. If the solution is
filtered with 200-μm-diameter pores, no particles were observed. This result may suggest
the feasibility of chemically-assisted nanoparticle adhesion.
6. The application of elemental tagging and mapping to tribo-test samples is a
major motivation for this research. Having confirmed the reactions and imaging
capabilities, the application for surfaces that undergo tribo-testing can be done. Films,
such as DLC have shown tribochemistry products around wear tracks after tribo-testing,
as shown in chapter 1. Mapping and imaging these products and surface species will give
further information as to the chemistry occurring at the surface. Successful mapping of
diamond-like carbon films could also lead to mapping of other high carbon content films
98
and materials.
C. AES spectra of three spots shown in (a), Zn and O peak was found only on particle (spot 1) solution.
Figure 5-1: SEM images and AES spectra of Nano-particles on COOH pattern
5 μm um
25 um 12
3
a. Large area SEM image on the patterned sample
b. Small area SEM image of one pattern square with three spots: (1)on the particle, (2)inside square but not on the particle, (3)outside square
200 400 600 800 1000
Inside square w/o particles
Particlesinside square
AE
S in
tens
ity,d
N(E
)/dE
(a.u
.)
Kinetic energy (eV)
Outside square
99
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