The Pennsylvania State University. The Graduate School. Department of Chemistry FUNDAMENTAL STUDIES OF MOLECULAR SECONDARY ION MASS

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1 The Pennsylvania State University The Graduate School Department of Chemistry FUNDAMENTAL STUDIES OF MOLECULAR SECONDARY ION MASS SPECTROMETRY IONIZATION PROBABILITY MEASURED WITH FEMTOSECOND, INFRARED LASER POST-IONIZATION A Dissertation in Chemistry by Nicholas James Popczun 2017 Nicholas James Popczun Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2017

2 The dissertation of Nicholas James Popczun was reviewed and approved* by the following: Nicholas Winograd Evan Pugh Professor of Chemistry Dissertation Advisor Chair of Committee Barbara J. Garrison Shapiro Professor of Chemistry Philip C. Bevilacqua Professor of Chemistry, Biochemistry and Molecular Biology Themistoklis Matsoukas Professor of Chemical Engineering Thomas E. Mallouk Evan Pugh Professor of Chemistry, Physics, Biochemistry and Molecular Biology Head of the Department of Chemistry *Signatures are on file in the Graduate School

3 iii ABSTRACT The work presented in this dissertation is focused on increasing the fundamental understanding of molecular secondary ion mass spectrometry (SIMS) ionization probability by measuring neutral molecule behavior with femtosecond, mid-infrared laser post-ionization (LPI). To accomplish this, a model system was designed with a homogeneous organic film comprised of coronene, a polycyclic hydrocarbon which provides substantial LPI signal. Careful consideration was given to signal lost to photofragmentation and undersampling of the sputtered plume that is contained within the extraction volume of the mass spectrometer. This study provided the first ionization probability for an organic compound measured directly by the relative secondary ions and sputtered neutral molecules using a strong-field ionization (SFI) ionization method. The measured value of ~10-3 is near the upper limit of previous estimations of ionization probability for organic molecules. The measurement method was refined, and then applied to a homogeneous guanine film, which produces protonated secondary ions. This measurement found the probability of protonation to occur to be on the order of 10-3, although with less uncertainty than that of the coronene. Finally, molecular depth profiles were obtained for SIMS and LPI signals as a function of primary ion fluence to determine the effect of ionization probability on the depth resolution of chemical interfaces. The interfaces chosen were organic/inorganic interfaces to limit chemical mixing. It is shown that approaching the inorganic chemical interface can enhance or suppress the ionization probability for the organic molecule, which can lead to artificially sharpened or broadened depths, respectively. Overall, the research described in this dissertation provides new methods for measuring ionization efficiency in SIMS in both absolute and relative terms, and will inform both innovation in the technique, as well as increase understanding of depth-dependent experiments.

4 iv TABLE OF CONTENTS List of Figures... vii List of Tables... xi Acknowledgements... xii Chapter 1 Introduction Secondary ion mass spectrometry (SIMS) Secondary ionization efficiency Molecular depth profiling and three-dimensional imaging Laser post-ionization Absorptive photoionization mechanisms Field ionization Thesis overview References Chapter 2 Experimental SIMS instrumentation Primary ion source and alignment optics Temperature-controlled sample stage Reflectron time-of-flight mass analyzer Microchannel plate detector Signal processing Laser system Oscillator Chirped pulse amplifier Optical parametric amplification Laser pulse and SIMS coupling Temporal coupling Spatial overlap optimization Sample preparation physical vapor deposition Crater characterization atomic force microscopy References Chapter 3 Quantification of molecular SIMS ionization probability of coronene Abstract Introduction Experimental methods Instrumentation Sample preparation Laser system Results and Discussion... 52

5 v Ionization probability vs. primary ion fluence Photofragmentation Sampling efficiency Secondary ionization probability Conclusions References Chapter 4 Ionization probability in molecular SIMS: protonation efficiency of sputtered guanine molecules studied by laser post-ionization Abstract Introduction Experimental Results and discussion Fluence dependence Photofragmentation Undersampling correction Measured neutral molecular guanine signal Ionization probability Conclusion References Chapter 5 Effect of SIMS ionization probability on depth resolution for organic/inorganic interfaces Abstract Introduction Experimental Results and discussion Guanine silicon interface Trehalose silicon interface Conclusions References Chapter 6 Conclusions and future directions Conclusions Future directions Appendix A Additional information for the optimization of parameters in chapters 3 and A.1 Effective sensitive volume A.2 Influence of the emission velocity distribution of the sputtered particles A.3 References Appendix B Supporting figures for chapter Appendix C Supporting figures for chapter

6 C.1 Depth scale calibration C.2 SIMS reference waterfall spectra C.3 References vi

7 vii LIST OF FIGURES Figure 1-1. Secondary ion mass spectrometry sputtering process. A primary ion (C 60 + ) bombards the sample surface, causing electrons, positive and negative ions, and neutral species to be ejected... 2 Figure 1-2. Mass spectrometry image of copper grid (red) on indium foil substrate (green).. 3 Figure 1-3. Side and top view of phase-separated aerosol particles using SIMS (left) and laser photoions (right). The aerosol particle consists of an ammonium sulfate core (green) a pimelic acid shell (magenta) on a silicon substrate (blue). The lack of organic signal in the SIMS image is due to severe ionization suppression by the salt core, referred to as matrix effects... 4 Figure 1-4. Example of depth profile application and measured signal on multilayered film consisting of Irganox 1098 and Irganox Figure 1-5. Visualization of molecular depth profiling characteristic values... 8 Figure 1-6. Absorptive photoionization mechanisms Figure 1-7. Strong field ionization using single active electron approximation Figure 1-8. Non-adiabatic multi-electron mechanism for strong-field ionization Figure 2-1. Schematic of the Bio-ToF instrument and ion time-of-flight path (purple), including key components and the sections in of this chapter in which they are discussed in detail Figure kev C 60 primary ion gun layout including focusing lenses (blue), mass and neutral filters (yellow), alignment optics (green) and beam scan plates (red) Figure 2-3. Normalized spatial distribution of gas phase water with reflectron voltage of 98% of extraction voltage Figure 2-4. Microchannel plate detector schematic including the grid used for blocking low mass photofragments, as well as the dual chevron arrangement designed to amplify current produced by secondary ions Figure 2-6. TOPAS-C HE beam path showing the beam path for the seed beam (cyan), pre-amplification stage pump beam (magenta), amplification stage 1 beam (green) and amplification stage 2 beam (red) Figure 2-7. Experimental timing diagram of LPI experiments. The laser pulse entering the sensitive volume of the experiment is the pulse following the pulse that triggers the experiment Figure 2-9. Photoionization volume in cylindrical coordinates showing the difference between the laser intensity at I/e and the radius of the photoionization volume for a saturation intensity of 3 x W/cm

8 Figure 3-1. A coronene depth profile (a) showing the exponential decrease commonly observed, followed by a period of constant decline for both LPI and SIMS signals. The LPI signal is 2.5 times the SIMS signal at the clean surface, and increases to 14.4 times the SIMS signal at 5.3 x ions/cm 2. At doses above 1.2 x ions/cm 2, the LPI signal remains times the SIMS signal (inset). The coronene ion fraction (b) normalized to the initial ion/neutral ratio shows an early decline, after which the fraction increases until it reaches a steady state of around an ion fluence of 1.2 x ions/cm 2 (shown in blue) Figure 3-2. Strong-field ionization spectrum of thermally evaporated coronene showing the molecular ion (M +, m/z 300, blue) and the characteristic fragment ion ([M-C 2 ] + m/z 276, red), as well as the signal attributed to the respective doubly- and triplycharged ions Figure 3-3. Laser post-ionization spectra of coronene molecules sputtered under static conditions. The ratio of single and multiply-charged molecular species (m/z 300) to the total signal observed is 5.1 x 10-2 for the LPI spectrum Figure 3-4. Sum of single and multiply-charged coronene as function of the natural log of peak laser intensity. The coronene saturation intensity was calculated to be 3.4 x W/cm Figure 3-5. Two-dimensional spatial distribution of sputtered neutral coronene, normalized from 0 to 1 on the pixel of optimal laser overlap. The plane of the figure is 38 to primary ion flight path, which originates from the negative horizontal area Figure 4-1. Molecular SIMS ([M+H] + at m/z 152) and LPI ([M] + at m/z 151) signal (a) and ratio between both signals (b) of guanine molecules sputtered under bombardment with 20 kev C 60 + ions as a function of primary ion fluence. The data were normalized to the value obtained for a pristine surface at zero fluence Figure 4-2. Mass spectrum of thermally evaporated (a) and sputtered (b) guanine for the determination of upper and lower limits for the photofragmentation branching ratio. The arrows indicate the molecular ion and dimer ion signals at m/z 151, respectively. The arrow at m/z 75.5 in (b) refers to the doubly charged molecular ion Figure 4-3. Proposed structures for the molecular photoion (a), photofragment at m/z 87 (b), and collision-induced fragments m/z 135 (c) and m/z 110 (d) Figure 4-4. Signal of laser post-ionized guanine molecules vs. natural log of the peak laser intensity. The asymptote intersects the laser intensity axis at the saturation intensity of about 7 x W/cm Figure 4-5. Measured signal of post-ionized sputtered neutral guanine molecules vs. lateral position of the ionizing laser beam. The laser was scanned in the plane perpendicular to the beam propagation along vertical and horizontal directions with respect to the sample surface. The axes are scaled with respect to the position for optimum detected signal, and the intensity scale has been normalized to the measured SIMS signal viii

9 ix Figure 4-6. Measured signal of photo-ionized of gas phase benzene molecules vs. position of the ionizing laser beam. The laser was scanned in the plane perpendicular to the beam propagation along vertical and horizontal directions with respect to the sample surface and the extraction volume. The axes are scaled the same as in Figure Figure 5-1. SIMS (a) and LPI (b) signal as a function of primary ion fluence for guanine film deposited on silicon substrate. Both SIMS and LPI signals for guanine are on the left scale, and silicon on the right Figure 5-2. Molecular SIMS [M+H] + (a) and LPI [M] 0 (b) signal measured across the guanine-silicon interface as a function of apparent depth. The depth scale has been calculated assuming a constant erosion rate as described in the text. The vertical lines denote the 84%, 50% and 16% levels of the signal variation observed across the interface Figure 5-3. Ratio of SIMS [M+H] + signal to LPI M 0 signal for molecular guanine as a function of depth. The vertical drop lines indicate the interface position as derived from the 50% points as described in the text Figure 5-4. Structure of the trehalose molecule (a) and characteristic fragment F (b) Figure 5-5. SIMS and LPI depth profiles of characteristic fragments of trehalose. The depth scale has been calculated assuming a constant erosion rate and may therefore be inaccurate beyond the film-substrate interface Figure 5-6. Ionization probability of different molecule specific fragment ions of trehalose as function of apparent depth. The grey depths show the average LPI interface width Figure 5-7. Section of LPI mass spectra recorded as a function of depth profile cycle number. The interface between the trehalose film and the silicon substrate is located around cycle # Figure A-1. Sketch of effective ion extraction volume ( sensitive volume ) for gas phase (b) and for sputtered (orange) species Figure A-2. Measured signal of intact post-ionized neutral guanine molecules M + at m/z 151 (closed symbols) and quasi-molecular secondary ion signal [M+2H] + (open symbols) vs. primary ion pulse length Figure A-3. Emission velocity distribution of In + secondary ions and post-ionized neutral In atoms emitted from a polycrystalline indium surface under bombardment with 5 kev Ar + ions (data taken from ref. 2) Figure B-1. Detailed view of [M-C 2 H n ] q+ (left column) and [M-H n ] q+ (right column) peak series for q = 1 (top row) and q = 2 (bottom row) observed in an LPI spectrum of coronene. Note that the doubly charged species have higher signal for the deprotonated species relative to the parent ion

10 x Figure B-2. SIMS spectra of coronene molecules sputtered under static conditions. The ratio of single molecular species (m/z 300) to the total signal observed is 0.97, indicating the collision-induced fragmentation is negligible assuming similar ionization probabilities for all species Figure B-3. Singly-charged xenon photoions as a function of the natural log of the peak laser intensity. The xenon saturation intensity of 1.2 x W/cm 2 was close to literature values as described in the main text Figure B-4. Negative coronene spectra sputtered with 20 kev C 60 + primary ions. The molecular coronene signal (m/z 300) is near the noise level of the experiment Figure C-1. SIMS (upper panels) and LPI (bottom panels) signal of molecular guanine and silicon tetramer as a function of depth using three different approaches to convert the applied primary ion fluence into eroded depth. The erosion rate was interpolated between the values determined for the organic film and the silicon substrate using a) weight factors calculated from the variation of the molecule specific guanine signal alone (Equation C-2); b) weight factors calculated from both signals using Equation C-4 and c) weight factors calculated from the silicon substrate signals alone (Equation C-3) Figure C-2. Relative ion fraction of guanine as a function of depth assuming a nonlinear erosion rate as calculated using Equation C-3 in the text. The drop lines show the interface location as evaluated from the midpoints of the SIMS and LPI signals, respectively Figure C-3. Section of SIMS mass spectra recorded as a function of depth profile cycle number in a SIMS depth profile of a trehalose film on silicon. The interface between the film and the substrate is located around cycle #100. Note the pronounced intensity maximum observed for m/z 67 at the interface

11 xi LIST OF TABLES Table C-1. SIMS and LPI depth widths for guanine and silicon employing different erosion rate equations

12 xii ACKNOWLEDGEMENTS The completion of my doctoral research is not only personal milestone in my life, but also a testament to the love and support that I have received from family, friends, and colleagues in achieving that goal. I would like to thank everyone to whom I will be forever grateful. First, I would like to thank my research advisor, Dr. Nicholas Winograd, for his support and guidance during my time at Penn State. Nick allowed me the freedom to explore my own research interests and to develop solutions to problems. His patience allowed me to grow a deeper understanding of mass spectrometry and the state-of-the-art laser system which I have performed my research on. I am fortunate to have had such an experience in the laboratory. I would also like to thank Dr. Barbara Garrison for her insight, as she planted the seed to pursue post-ionization, which blossomed to be the driving force of my doctoral research. Her approachability and wit made the transition to Pennsylvania more relaxed for both my wife and myself. I also thank my collaborator Dr. Andreas Wucher. Andreas provided a sounding board for my experimental designs, data interpretation, and general laser post-ionization queries. His assistance in my final years will put me forever in his debt. I also had the fortunate experience of working with a number of Winograduates and postdocs, each of which assisted me during my time here. In particular, I want to thank Dr. Andrew Kucher and Dr. Jordan Lerach for sharing their experience and knowledge of the Bio- ToF II instrument. Also, I thank Dr. Lars Breuer, who taught me a great deal about the electronic design and software programming of the instrument. I thank Dr. Kan Shen, who taught me to use the AFM, as well as helping brainstorm ideas for depth profiling post-ionization experiments. He will always be the Michelangelo of NSC. I similarly thank our Donatello, my fellow guardian of the last city, and technology wizard, Dr. Jay Tarolli. His ability and willingness to implement my suggestions when designing the ImagingSIMS software made data analysis intuitive and simple.

13 xiii He is also the most compassionate Jets fan I know, and for that I am equally grateful. I also want to thank the penultimate Winograduate, my dog-sitter, and NSC social chair Dr. Anna Bloom. She was a great friend that made navigating the first couple of years here at Penn State easier. I wish her and Jens Mueller all the best in the future, with the exception their chosen American football team. Give them back. I want to thank the rest of the friends I have made during my time here, who were always there to lend an ear, provide a break from life in the laboratory, or indulge my immature sense of humor. I thank Michael Sennett and Lauren Rajakovich for being my social buffers and beloved company during football season. It is your turn to get that PhD, buddy! I thank Chris Rumble, Brian Conway, and Michael Shadeck for the inane lunch conversations about the basically infinite remakes of ChronoTrigger, new innovations in gristle storage textiles, or teaching bears to read. I always walked away ready to reengage in my research. I thank Liz Brown and Chris Averill for their friendship and dedication to creating positive change. I also thank Chris Hoehling for making me commit to spending at least two hours a week outdoors. I also want to acknowledge Sean Sawyer for inspiring me to return to school, and Sergeant Mark Tiearney, Jr for his unwavering support. I want to thank my in-laws, Big Al and Sherry Surrena. Their support and pride helped steel my resolve to persevere when the going got rough. I thank my brother-in-law, Tony Surrena. His excitement about my research was always refreshing. All three of my in-laws made me feel like not only a part of their family, but also their entire community. I would like to say thank you to my brother, and fellow Nittany Lion, Dr. Eric Popczun. I was told as a teenager that he looked up to me, so I should set a good example. I say this so that the irony is not lost when I say that I found myself looking up to him, and following in his footsteps. I am glad that I had him to show me what I could (and should) be doing. I also thank

14 xiv him for hosting Sarah during prospective weekend, which made the decision to come to Penn State much easier. Finally, I want to thank Eric for being my Rock, Man. I also want to thank my parents, Jim and Betty Popczun. They always supported me, protected me when they could, and provided me all the opportunities to succeed. Despite my meandering path that eventually led to the completion of my doctoral research, I always felt they were behind me. In retrospect, I cannot thank them enough for their belief in me. Finally, I want to thank my beautiful and compassionate wife, Sarah Popczun. There is no greater joy that returning to her each night, and there is no greater motivation than to justify her faith in me. During our time at Penn State, Sarah has sacrificed much to support me, and I consider her contributions to the completion of my doctoral research to be integral and inseparable from my own. In that regard, I suppose I also owe Sarah a commendation. Congratulations, Little One! We did it!

15 1 Chapter 1 Introduction Mass spectrometry has become ubiquitous in laboratories across numerous scientific disciplines. The ability of mass spectrometry experiments to gain chemical information depends critically on the creation, separation, and detection of ionized atoms and molecules present in the sample. The research presented herein focuses specifically on molecular ion creation during a secondary ion mass spectrometry (SIMS) experiment for organic compounds, described in more detail in Section 1.1. To accomplish this goal, the SIMS ion signal is compared to the signal obtained from a complementary photoionization event, described in Section 1.2. Finally, Section 1.3 presents the motivation and direction for the research. 1.1 Secondary ion mass spectrometry (SIMS) A multitude of methods have been employed to generate ions for mass spectrometry experiments. Secondary ion mass spectrometry (SIMS) is a unique technique combining small probe size 1-3, high surface sensitivity 4-5, and the capability of detecting intact molecular ions 6. Briefly, a SIMS experiment consists of a primary ion bombarding the sample surface, from which electrons, positive and negative ions, and neutral species are ejected 7, as shown in Figure 1-1. Once ejected, the ionized components are then extracted to the mass analyzer, separated by massto-charge (m/z) ratio and detected. The relative intensities of the m/z ratios detected are output as a mass spectrum.

16 2 Figure 1-1. Secondary ion mass spectrometry sputtering process. A primary ion (C 60 + ) bombards the sample surface, causing electrons, positive and negative ions, and neutral species to be ejected This chemical information contained within the mass spectrum can also be assigned spatial components based on the location bombarded on the sample surface The surface chemistry can then be recreated by arranging the mass spectra as pixels based on location and designating color assignments to different mass ranges, referred to as a mass spectrometry image. A mass spectrometry image of a copper grid (red) placed on an indium foil (green) substrate is shown in Figure 1-2. One of the principle advantages SIMS analysis holds over similar mass spectrometry imaging (MSI) techniques is the submicron probe sizes available, which in principle allows SIMS images to achieve higher spatial resolution for sample surfaces compared to other techniques. Ultimately, however, the limit on spatial resolution for a chemical surface is not a consequence of probe size, but rather one of poor ionization efficiency.

17 3 125 m Figure 1-2. Mass spectrometry image of copper grid (red) on indium foil substrate (green) Secondary ionization efficiency equation 12, The secondary ion signal produced from a sample surface is described by the basic SIMS (1-1) where S m is the secondary ion signal, is the fractional mass concentration of species m in the sample surface, is the effective sampling time which includes primary pulse width and instrument transmission, is the primary ion current, is the total sputter yield, and is the positive ionization probability of species m. Assuming a homogeneous film, reduces to unity, and to ensure that each ionization event in the sample surface is pristine, a limit of ~ ions/cm 2 permits less than 1% of the sample surface to be bombarded. The areas to improve secondary ion signals, therefore, lay in parameters,, and. While current innovations in SIMS rely on improving all three of these parameters 13-20, the motivation of the research

18 4 contained in this work focuses on positive ionization probability,, an elusive figure that has been estimated to be anywhere from zero to 10-3 for organic molecules 21-22, and provides the most room for improvement. In addition to these low estimations, the ionization probability can also be effected by the local chemical environment, a phenomenon known as matrix effects These matrix effects can inhibit sputtering of ions from the surface, or enhance re-neutralization of ions near the sample surface area. An example can be seen in Figure 1-3. Figure 1-3. Side and top view of phase-separated aerosol particles using SIMS (left) and laser photoions (right). The aerosol particle consists of an ammonium sulfate core (green) a pimelic acid shell (magenta) on a silicon substrate (blue). The lack of organic signal in the SIMS image is due to severe ionization suppression by the salt core, referred to as matrix effects Estimation of is necessary due to its convolution with collision-induced damage produced during primary ion bombardment when measuring the secondary ion signal. Deconvolution requires chemical information from the neutral species sputtered from the sample surface. Instead, ionization efficiency is described by other means. One such description is secondary ion yield 16, 18-19, 25-27, a measure of secondary ions produced per primary ion impingement. The benefit of using secondary ion yield to describe the ionization efficiency is that

19 5 it is obtainable without information from the neutral component, and is focused on maximizing secondary ion production from the ~ ions/cm 2 fluence as a method of comparison for different primary ion identities. Evolution of new primary ion identities has provided an avenue for drastic improvements in SIMS analysis. The shift from atomic primary ions to polyatomic, and more recently, gas cluster ion beams (GCIBs) resulted in increased secondary ion yields, reduced the collisioninduced damage remaining in the sample surface or a combination of both , This reduction in remaining damage has also been critical in the development of molecular depth profiling Molecular depth profiling and three-dimensional imaging Molecular depth profiling has been successfully applied to a variety of organic molecules. 16, A successful molecular depth profile, as shown in Figure 1-4, is obtained when the collision-induced damage produced during primary ion bombardment reaches an equilibrium with the amount of damage removed by the sputtering process. Polyatomic primary ions deposit a majority of their energy at the sample surface, making SF 5, C 60, and large argon cluster primary 6, ions acceptable candidates for molecular depth profiling.

20 Figure 1-4. Example of depth profile application and measured signal on multilayered film consisting of Irganox 1098 and Irganox

21 7 For depth profiles obtained at a fresh sample surface, the signal as a function of primary ion fluence often begins with an exponential drop, as the collision-induced damage remaining in the surface exceeds the amount of damage removed. With additional primary ion fluence, the signal reaches the steady state, where the creation and removal of damage is in equilibrium. This signal level continues until a chemical interface is reached and the signal declines due to the change of concentration at the interface. An erosion model for molecular depth profiling was developed by Cheng et al. 37 to determine the parameters affecting the shape of the signal as a function of primary ion fluence. The initial exponential drop in signal is described as the disappearance cross section, eff, in the equation σ where Y is the sputter volume per primary ion, d is the altered layer depth and D is the area damaged by the primary ion from which produces no molecular signal. A visualization of this relationship is shown in Figure 1-5. The erosion model predicts that as the bulk sample replenishes the molecular component of the sputtered material. 37 It is therefore preferential to select primary ions that deposit a majority of their energy at the sample surface to reduce the altered layer depth. This behavior has been shown through molecular dynamic simulations for polyatomic primary ions that dissociate upon impingement, with each atom carrying a 41, proportional amount of the initial kinetic energy. (1-2)

22 8 Figure 1-5. Visualization of molecular depth profiling characteristic values 1.2 Laser post-ionization As previously stated in Section 1.1.1, poor ionization probability produces a limited number of secondary ions. One solution to overcome this inefficiency is to ionize the neutral component of the sputtered material after it has been ejected from the sample surface, referred to as post-ionization Along with the supplementary molecular signal obtained, by ionizing after ejection, the sputtering and ionization of the molecule are decoupled, which avoids the matrix effects described previously The post-ionization technique employed is laser post-ionization (LPI) for the experiments described in this dissertation by means of strong-field ionization (SFI).

23 Absorptive photoionization mechanisms Various absorptive photoionization techniques are available for application of LPI to a SIMS experiment, shown in Figure 1-6. The three major regimes are single photon ionization (SPI), resonance-enhanced multiphoton ionization (REMPI) and non-resonant multiphoton ionization (NRMPI), listed in order of increasing laser intensity required to achieve 50, photoionization. The photoionization mechanism utilized in SPI is the most straightforward, where a single photon of ultraviolet or synchrotron radiation exceeding the ionization potential of the molecule is absorbed. The benefit of this simple technique is that the intensity of radiation required is of the order of 10 5 W/cm 2, which is low relative to other photoionization techniques. The core impediment to a more universal adoption of SPI is that the molecular ionization potential must be less than the photon energy, which is not the case for many organic molecules when applying commercially-available UV radiation While it is possible to increase the photon energy by employing shorter wavelengths produced from synchrotron radiation, maintaining the power density becomes difficult and limits the LPI signal obtained. 60 Photoionization employing REMPI uses multiple photons to remove an electron by using an electronic excited state of the molecule as an intermediary step. The challenge of REMPI for means of LPI is that the photon energy must be tailored for a specific electronic transition in the molecule. This requires knowledge of the electronic structure of the molecule prior to the experiment. Additionally, some transitions may be affected by the sputtering process, which is known to increase the internal energy of the sputtered molecular species. For LPI experiments were these limitations have been accepted and accounted for, the REMPI mechanism is capable of ionizing only the molecule for which it has been tailored. 57 While ideal for homogeneous films

24 10 and a single component with low concentration in heterogeneous mixtures, these limitations inhibit implementation for multiple components in heterogeneous samples. One method around this limitation is to transition to the NRMPI regime. During a NRMPI experiment, multiple photons are absorbed simultaneously, each promoting the electron to a virtual state until the ionization potential is overcome. The virtual state is a short-lived state that is not a stable electronic state of the molecule. 62 For this reason, the 2-10 photons necessary for ionization of most organic molecules must be absorbed simultaneously, and the laser pulse must be on the femtosecond time scale. The large flux necessary for NRMPI consequently produces significant photofragmentation. As intensity increases, the NRMPI mechanism does not reach photoionization saturation, but instead transitions to a field ionization mechanism known as strong-field ionization (SFI) with reduced photofragmentation. 63 Figure 1-6. Absorptive photoionization mechanisms

25 Field ionization Keldysh parameter The transition from NRMPI to SFI photoionization mechanism has been described for atoms using the Keldysh parameter, γ, shown in 64 γ (1-3) where IP is the ionization potential, I is the laser power density in W/cm 2, and is the wavelength in m. For γ > 5, NRMPI dominates the photoionization process, and for γ < 0.5, SFI dominates. For values between these two points, the two ionization schemes are competing. From Equation 1-3, it can be seen that SFI can be favored by using laser parameters which increase the laser intensity or increase the wavelength of the photoionizing radiation Strong-field ionization During an SFI event, laser intensities in excess of W/cm 2 are applied to the molecule. At this intensity, the electric field of the laser is on the order of or exceeds the magnitude of the intra-molecular Coulomb field binding the electron to the molecule. The Keldysh parameter shown in Equation 1-3 uses a single active electron (SAE) approximation, which has been applied successfully to describe the photoionization of small molecules. 65 This approach is shown in Figure 1-7, where the electric field of the laser suppresses the potential well,

26 allowing for a single electron in the highest occupied molecular orbital (HOMO) to tunnel out, or to freely escape over the suppressed potential barrier. 12 Figure 1-7. Strong field ionization using single active electron approximation In contrast, non-adiabatic multi-electron (NME) provides a second description of SFI for molecular systems, shown in Figure 1-8. In an NME description, the electronic states are coupled to each other, and lead to photoionization and typically photofragmentation The half lasercycle probability of entering the quasi-continuum, P i, of NME is estimated by 68 ~ exp Δ 4 where 0 represents the energy separation between the ground and the onset of the quasicontinuum, is the dipole matrix element, ε the electric field strength, and ω L is the angular frequency of the electric field oscillations produced by the laser. From this relation, it can be seen that when 4 Δ, the non-adiabatic excitation is avoided and photofragmentation mitigated. (1-4)

27 13 Figure 1-8. Non-adiabatic multi-electron mechanism for strong-field ionization The SAE description provided in Equation (1-3) suggests that increasing photon wavelength should favor SFI behavior over absorptive behavior. It has been shown that photons with different wavelengths in the near to mid-infrared range provide similar photoionization efficiencies. It can be seen in Equation 1-4 that the wavelength of the photons should affect the signal, but this is not observed yet, indicating that SFI behavior is still not fully understood. 69 Despite this, SFI still provides the best opportunity for a universal photoionization of heterogeneous samples. 1.3 Thesis overview The work presented in this dissertation is focused on increasing the understanding of the ionization probability in a sputter event, and its role in molecular depth profiling. Direct comparison of SIMS and LPI signals in a single experiment are complex due to the various experimental parameters necessary for each analysis. Changes in their respective behavior as a

28 14 function of primary ion fluence or depth, however, provides insight that most SIMS instruments are not capable of producing. In Chapter 2, the experimental setup for the SIMS instrumentation and femtosecond laser system used in this dissertation are explained in detail, as well as considerations necessary for their coupling. Film preparation by physical vapor deposition (PVD) and spin-coating, as well as film characterization by atomic force microscopy (AFM) are also discussed. In Chapter 3, a method for the determination of the ionization probability for an organic molecule is developed and a value is presented for the organic molecule coronene. This method includes measuring the total integrated neutral component of the sputtered material through LPI, and comparing it to the SIMS signal produced in the same experiment. The value presented is the first such measured ionization probability for an organic compound, and provides critical insight into the fundamentals of SIMS ionization efficiency. In Chapter 4, the method for quantifying ionization probability described in Chapter 3 is further developed and improved. The method is then applied to an organic molecule known to favor secondary ion formation through protonation in contrast to coronene. The signal for the integrated neutral component is obtained through motor-driven movement of the laser focal lens while the sample is held at liquid nitrogen temperatures to minimize ambient gas interference. In general, this study confirms that there is opportunity for increasing molecular signal up to two orders of magnitude. In Chapter 5, laser post-ionization is employed to observe molecular signal at chemical interfaces during a molecular depth profile of an organic film. These signals are then contrasted with the SIMS signal obtained concurrently, which shows that chemical interfaces can elicit matrix effects on the organic SIMS signal altering the measured width of the interface in the depth profile. These variations come in the form of both enhancement and suppression leading to broadening or narrowing the measured interface width. This study shows that understanding the

29 15 behavior of ionization probability at such interfaces is crucial for accurate interpretation for applications such as 3D imaging. In Chapter 6, future directions for fundamental applications of laser post-ionization are discussed. Determination of the matrix effect of accrued damage on the ionization probability of homogeneous films, primary ion identities, and LPI mass spectrometry imaging with variable laser focal alignment are introduced and briefly discussed to demonstrate the insight LPI can provide to SIMS experiments. 1.4 References 1. Davies, N.; Weibel, D. E.; Blenkinsopp, P.; Lockyer, N.; Hill, R.; Vickerman, J. C., Development and Experimental Application of a Gold Liquid Metal Ion Source. Applied Surface Science 2003, , Winograd, N., The Magic of Cluster Sims. Analytical Chemistry 2005, 77, 142 A-149 A. 3. Toyoda, N.; Matsuo, J.; Aoki, T.; Yamada, I.; Fenner, D. B., Secondary Ion Mass Spectrometry with Gas Cluster Ion Beams. Applied Surface Science 2003, , Braun, R. M.; Beyder, A.; Xu, J.; Wood, M. C.; Ewing, A. G.; Winograd, N., Spatially Resolved Detection of Attomole Quantities of Organic Molecules Localized in Picoliter Vials Using Time-of-Flight Secondary Ion Mass Spectrometry. Analytical Chemistry 1999, 71, Kollmer, F., Cluster Primary Ion Bombardment of Organic Materials. Applied Surface Science 2004, , Postawa, Z.; Czerwinski, B.; Winograd, N.; Garrison, B. J., Microscopic Insights into the Sputtering of Thin Organic Films on Ag{111} Induced by C60 and Ga Bombardment. The Journal of Physical Chemistry B 2005, 109, Benninghoven, A., Beobachtung Von Oberflächenreaktionen Mit Der Statischen Methode Der Sekundärionen-Massenspektroskopie. I Die Methode. Surf Sci 1971, 28, Simko, S. J.; Bryan, S. R.; Griffis, D. P.; Murray, R. W.; Linton, R. W., Secondary Ion Imaging of Heterogeneous Organic Polymer Films. Analytical Chemistry 1985, 57, Gillen, G.; Simons, D. S.; Williams, P., Molecular Ion Imaging and Dynamic Secondary Ion Mass Spectrometry of Organic Compounds. Analytical Chemistry 1990, 62, Passarelli, M. K.; Winograd, N., Lipid Imaging with Time-of-Flight Secondary Ion Mass Spectrometry (Tof-Sims). Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 2011, 1811, Tian, H.; Wucher, A.; Winograd, N., Molecular Imaging of Biological Tissue Using Gas Cluster Ions. Surface and Interface Analysis 2014, 46, Vickerman, J. C.; Briggs, D., Tof-Sims: Materials Analysis by Mass Spectrometry; IM Publications: Chichester, UK, 2013.

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31 Development and Secondary Ion Yield Characteristics. Analytical Chemistry 2003, 75, Mahoney, C. M.; Roberson, S. V.; Gillen, G., Depth Profiling of 4-Acetamindophenol- Doped Poly(Lactic Acid) Films Using Cluster Secondary Ion Mass Spectrometry. Analytical Chemistry 2004, 76, Shard, A. G.; Green, F. M.; Brewer, P. J.; Seah, M. P.; Gilmore, I. S., Quantitative Molecular Depth Profiling of Organic Delta-Layers by C60 Ion Sputtering and Sims. The Journal of Physical Chemistry B 2008, 112, Shard, A. G.; Green, F. M.; Gilmore, I. S., C60 Ion Sputtering of Layered Organic Materials. Applied Surface Science 2008, 255, Zheng, L.; Wucher, A.; Winograd, N., Depth Resolution During C60+ Profiling of Multilayer Molecular Films. Analytical Chemistry 2008, 80, Cheng, J.; Winograd, N., Depth Profiling of Peptide Films with Tof-Sims and a C60 Probe. Analytical Chemistry 2005, 77, Cheng, J.; Wucher, A.; Winograd, N., Molecular Depth Profiling with Cluster Ion Beams. The Journal of Physical Chemistry B 2006, 110, Wucher, A., A Simple Erosion Dynamics Model for Molecular Sputter Depth Profiling. Surface and Interface Analysis 2008, 40, Garrison, B. J.; Delcorte, A.; Krantzman, K. D., Modeling Sputtering of Organic Molecules. Izv Akad Nauk Fiz+ 2002, 66, Delcorte, A.; Wehbe, N.; Bertrand, P.; Garrison, B. J., Sputtering of Organic Molecules by Clusters, with Focus on Fullerenes. Applied Surface Science 2008, 255, Rzeznik, L.; Paruch, R.; Garrison, B. J.; Postawa, Z., Sputtering of a Coarse-Grained Benzene and Ag(111) Crystals by Large Ar Clusters Effect of Impact Angle and Cohesive Energy. Surface and Interface Analysis 2013, 45, Garrison, B. J.; Ryan, K. E.; Russo, M. F.; Smiley, E. J.; Postawa, Z., Quadratic Friction Model for Cluster Bombardment of Molecular Solids. The Journal of Physical Chemistry C 2007, 111, Postawa, Z.; Czerwinski, B.; Szewczyk, M.; Smiley, E. J.; Winograd, N.; Garrison, B. J., Microscopic Insights into the Sputtering of Ag{111} Induced by C60 and Ga Bombardment. The Journal of Physical Chemistry B 2004, 108, Delcorte, A.; Garrison, B. J., Sputtering Polymers with Buckminsterfullerene Projectiles: A Coarse-Grain Molecular Dynamics Study. The Journal of Physical Chemistry C 2007, 111, Garrison, B. J.; Postawa, Z., Computational View of Surface Based Organic Mass Spectrometry. Mass Spectrometry Reviews 2008, 27, Czerwinski, B.; Rzeznik, L.; Paruch, R.; Garrison, B. J.; Postawa, Z., Effect of Impact Angle and Projectile Size on Sputtering Efficiency of Solid Benzene Investigated by Molecular Dynamics Simulations. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2011, 269, Garrison, B. J.; Paruch, R. J.; Postawa, Z., Combined Molecular Dynamics and Analytical Model for Repetitive Cluster Bombardment of Solids. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2013, 303, Kanski, M.; Garrison, B. J.; Postawa, Z., Effect of Oxygen Chemistry in Sputtering of Polymers. The Journal of Physical Chemistry Letters 2016, 7, Tehorst, M.; Möllers, R.; Niehuis, E.; Benninghoven, A., High-Spatial-Resolution Surface Imaging of Inorganic and Organic Structures by Multiphoton Post-Ionization of 17

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34 20 Chapter 2 Experimental Both secondary ion mass spectrometry (SIMS) and laser post-ionization (LPI) experiments begin with the creation of a sputter plume from the bombardment by an energetic primary ion. Once a plume of sputtered material has been emitted from the sample surface, the laser pulse intersects that plume and photoionizes the neutral material within the photoionization volume. This chapter will describe the experimental design for the SIMS experiment, the creation of a femtosecond pulse, and the optimization of temporal and spatial overlap of the pulse with the sputtered material. The chapter concludes with a description of sample preparation and characterization of sputter craters. 2.1 SIMS instrumentation The mass spectrometer utilized for LPI experiments, henceforth referred to as Bio-ToF, was designed for molecular imaging of surfaces. 1 This instrument, shown in Figure 2-1, consists of a 40 kev C + 60 primary ion source, a temperature-controlled sample stage, a reflectron style time-of-flight (ToF) mass spectrometer, a chevron-stack microchannel plate (MCP) detector with a 25 mm active area, post-acceleration, and transient digitizer card for signal processing. The Bio- ToF also includes a CaF 2 window to allow integration of the laser pulse for post-ionization experiments.

35 21 Figure 2-1. Schematic of the Bio-ToF instrument and ion time-of-flight path (purple), including key components and the sections in of this chapter in which they are discussed in detail The Bio-ToF operates at pressures < 10-9 torr to ensure a long mean-free path for detection sensitivity through the spectrometer, reduces the amount of contamination adsorption on the sample, and limits the signal from photoionization of gas molecules such as nitrogen, water, and carbon dioxide. The instrument has been modified to include a physical vapor deposition chamber, allowing for sample deposition and analysis without exposure to atmosphere. This addition allows for minimal contamination of the sample surface.

36 Primary ion source and alignment optics A schematic of the 40 kev C 60 primary ion source used on the Bio-ToF is shown in Figure 2-2. To create primary ions, C 60 powder is sublimed from a reservoir and ionized by electron bombardment. The C n+ 60 ions are then extracted from the primary ion source and a userselectable aperture restricts the beam diameter, which reduces the achievable focus of the source. While smaller apertures can produce smaller probe sizes for chemical imaging, the experiments performed in this work used a 300 m aperture, which allowed a sufficient C + 60 current to reach the sample. Figure kev C 60 primary ion gun layout including focusing lenses (blue), mass and neutral filters (yellow), alignment optics (green) and beam scan plates (red)

37 23 The primary ions next pass through a Wien filter, where orthogonal magnetic and electric fields filter the ions by velocity. This prevents multiply-charged C 60 primary ions from reaching the sample surface. To this point of the primary ion source and alignment, the primary ion current is continuous. After the Wien filter, a pair of pulse plates creates the primary ion pulses. One plate is held at ground while the second plate is held at ~300V to deflect the beam out of alignment. When the pulse is desired, both plates are held at ground potential for a period of time equal to the desired temporal pulse length. The primary ions then pass through a 2 bend, which serves to filter neutral molecules from reaching the sample. After the 2 bend, an Einzel lens collects and focuses the ions into a series of alignment plates. Once the primary ions have been aligned, they reach the scan plates, which are used to control the horizontal and vertical location of primary ion bombardment on the sample surface over the field-of-view (FOV) dictated by the user. Finally, a second Einzel lens is used to focus the beam at the sample surface and minimize the spot size Temperature-controlled sample stage Samples are attached to a copper block, and inserted into the temperature-controlled sample stage. The stage was designed to allow a sample to reach 100 K within 10 minutes using a pre-cooled stage. This is accomplished by running N 2 gas through copper gas lines submerged in a dewar filled with liquid N 2, then routing the cooled gas through the sample stage, referred to as a cold stage. This arrangement also serves to allow for heated gas to be routed through the sample stage to sublime organic samples. The sample stage is also responsible for ion extraction into the mass spectrometer. During a SIMS experiment, once the primary ion pulse has finished bombarding the sample, a voltage is applied to the sample stage while an annular ring at the mass spectrometer entrance is held at

38 24 ground potential. The electrical polarity of the voltage will determine whether positive or negative ions are extracted. Photoionization produces positive ions, so the experiments described in this work use a positive extraction voltage of ~2500V applied within nanoseconds using a fast HV switch Reflectron time-of-flight mass analyzer The voltage applied to the sample stage works in tandem with ion optics that extract ions into a flight tube where they transverse a given distance with a kinetic energy determined by both the extraction voltage and their spatial position within the extraction volume. The primary benefit of time-of-flight analysis is the capability for parallel separation and detection of ions of different masses. The separation is created by their velocities, which are measured as the time necessary to travel the length of the flight tube. The length of the flight tube and the spatial distribution of sputtered ions together determine the mass resolving power of the mass spectrometer. The reflectron is an ion mirror at an angle of 4 to reflect ions back to a detector positioned near the flight tube entrance. To accomplish this, the extraction optics focus the ions into the reflectron, which allows for the ions of the same mass, but different kinetic energies due to their spatial position at extraction, to penetrate the electric field with different depths. In turn, this elongates the effective flight time for ions with a high velocity relative to ions of the same mass but lower velocities. The reflectron refocuses the ions temporally at the detector, increasing the mass resolution. For signal optimization, the reflectron voltage is set to around 102% that of the extraction voltage, which ensures that ions created at the sample surface can reach the detector. Reducing the reflectron voltage less than the extraction voltage restricts the extraction volume, as shown in Figure 2-3. This reduction in the extraction volume is used to ensure that the

39 25 laser photoionization volume can overlap the entirety of the extraction volume of the mass spectrometer. Figure 2-3. Normalized spatial distribution of gas phase water with reflectron voltage of 98% of extraction voltage Microchannel plate detector The microchannel plate detector utilized by the Bio-ToF consists of a high transmission grid positioned over two stacked 40 mm chevron-stacked plates, which create an electron cascade when struck by a secondary ion, as shown Figure 2-4. The electrons are then collected, and the current produced is amplified, converted to a voltage, and delivered to the signal processing card on a PC.

40 26 Figure 2-4. Microchannel plate detector schematic including the grid used for blocking low mass photofragments, as well as the dual chevron arrangement designed to amplify current produced by secondary ions. During an LPI experiment, the amount of photoions created can temporarily reduce or exhaust the electron supply of the MCP. In this circumstance, a voltage in excess of the extraction voltage is applied to the high transmission grid, which deflects most, but not all, ions from detection. This grid voltage can be used to block specific masses from the spectrum, and be grounded within nanoseconds to permit the transmission of higher mass ions to the MCP. Secondary ions counts are typically low in SIMS experiments, allowing the high transmission grid to be held at ground potential throughout the experiment.

41 Signal processing Due to low SIMS ionization probability, it is unlikely that a single SIMS sputtering event creates more than one ion of any single mass. The signal processing hardware found in a SIMS experiment is typically a time-to-digital converter (TDC), which records the flight time needed from extraction to detection in nanosecond time bins, once the signal exceeds a set threshold. Due to the large number of ions created during an LPI experiment, the probability that multiple ions are created during a single sputtering event increases, and single bit counting is not sufficient to record multiple ions arriving at the detector concurrently. For this reason, the voltage from the MCP detector is processed by an 8-bit transient digitizer (TD) card on the Bio-ToF instrument, where the signal can range between 0-255, representing a voltage range of 500 mv. 2.2 Laser system The laser system used for post-ionization consists of an oscillator, a chirped-pulse dual amplification system, and an optical parametric amplifier (OPA), shown in Figure 2-5. Together, these three components constitute a Class IV laser system capable of producing 40 fs pulses of mid-infrared (IR) radiation, tunable from 1160 to 2580 nm, at 1 khz repetition rate with peak power densities up to W/cm 2 when focused by a 150 mm focal length lens.

42 Figure 2-5. Laser system layout, including master oscillator (red, Section 2.2.1), dual-stage, chirped amplification system (yellow, Section 2.2.2), and optical parametric amplifier (blue, Section 2.2.3). 28

43 Oscillator The commercially available Mantis Oscillator (Coherent, Santa Clara, CA) provides a mode-locked, 800 nm, 40 fs seed beam at a frequency of 80 MHz and 500 mw power. A continuous wave beam is produced by pumping a Ti: Sapphire crystal with 532 nm radiation produced by a diode laser within the Mantis enclosure. One of the mirrors is then moved to change the cavity length. This change in cavity length increases the beam power density, which causes a Kerr lens to form. A Kerr lens occurs when the electric field of the light changes the refractive index of the gain medium at the center of the pulse. The Gaussian distribution results in higher gain at the center of the gain medium, which results in preferential pumping of the modelocked pulse Chirped pulse amplifier The 800 nm, 40 fs modelocked seed beam is routed from the Mantis Oscillator to the commercially available Legend Elite Duo (Coherent, Santa Clara, CA) for dual stage, chirped pulse amplification. The amplification system consists of a stretcher, regenerative amplifier, single-pass amplifier, and compressor Stretcher The high intensities created in the amplification process are capable of damaging optics, so the beams are stretched temporally, or chirped, to the nanosecond scale. The peak power of each pulse is reduced from ~10 8 to ~10 3 W per pulse. This is accomplished by reflecting the pulse

44 30 off a diffraction grating, which spatially disperses the different frequencies creating the pulse. The path length within the stretcher differs for each frequency, with higher frequencies traveling a longer distance than lower frequencies. The frequencies are then recombined spatially, but due to the difference distances traveled, are dispersed temporally, resulting in a reduced peak power Regenerative amplifier The stretched pulses are then routed into a regenerative amplifier (RGA) cavity, consisting of a Ti: Sapphire crystal pumped by a 527 nm, 20.2 W beam produced by a neodymium-doped yttrium lithium fluoride (Nd:YLF) crystal. The RGA permits a single pulse to enter the cavity at 1 khz through the application of voltage on a Pockels cell placed in the cavity. This voltage allows the Pockels cell to act as a quarter waveplate, and causing the pulse in the cavity to maintain its P-polarization. It then travels through the cavity for five passes, increasing in power with each pass, as measured by a photodiode. After the final pass, voltage is applied to a second Pockels cell, which rotates the amplified pulse to S-polarization. This polarization allows the amplified pulse to be reflected out of the cavity by a Brewster window with a peak power of ~10 6 W per pulse. Generally, loss of output power for the entire system is created in the RGA cavity. Poor overlap between the pump beam and seed pulse can decrease the Legend Elite Duo output power by up to half. Careful realignment and cleaning of the pump routing mirror prior cavity and the reflecting mirror after the cavity can regain the lost power, with minor adjustments to the seed beam input. If the seed beam input must be adjusted, any components after the RGA must be realigned as well, including the optical parametric amplifier.

45 Single-pass amplifier Once outcoupled from the RGA cavity, the beam is guided into a periscope leading to the single-pass amplifier (SPA). The SPA consists of another Ti: Sapphire crystal pumped by a 527 nm, 30 W beam produced by a Nd:YLF crystal through which the seed beam is amplified to 10 7 W per pulse in one pass. The beam is then expanded with telescoping lenses before entering the compressor Compression The compressor is placed after the amplification stages, and is designed for temporal realignment of the pulse. A compressor grating disperses the incoming pulses spatially, with the lower frequencies travelling a longer distance than the higher frequencies. At the output of the Legend Elite Duo, the pulse width has returned to 40 fs with a peak power of W per pulse as it is routed to the optical parametric amplifier. The peak power created in the compressor section of the Legend Elite Duo system can create burns, particularly in humid climates. Regular monitoring of the compressor grating for dust particles or water deposits can prevent aberrations to beam shape at the output, although a careful stream of nanopure water followed by an even nitrogen gas stream can clean most deposits, if caught early Optical parametric amplification The optical parametric amplifier (OPA) consists of a preamplification stage and two amplification stages, shown in Figure 2.6, to produce pulses of up to 2.4 W with a beam waist of 8.2 mm. While the 800 nm pulses produced by the Legend Elite Duo amplification system can

46 create the conditions necessary for strong-field ionization of sputtered neutral molecules, the use of longer wavelengths has been found to cause less photofragmentation. 2-3 The TOPAS-C HE optical parametric amplifier (Light Conversion, Lithuania) converts the 800 nm, 10 mj pulses output by the Legend Elite Duo to mid-ir radiation between 1160 and 2580 nm. The conversion leads to the emittance of two different wavelengths from the non-linear optical medium. These wavelengths are called the signal and idler, and their wavelengths obey the law of conservation of energy (2-1)

47 Figure 2-6. TOPAS-C HE beam path showing the beam path for the seed beam (cyan), preamplification stage pump beam (magenta), amplification stage 1 beam (green) and amplification stage 2 beam (red). 33

48 34 Both wavelengths are created in the preamplification stage of the OPA, although only the signal is amplified at each subsequent stage, the idler beam is also created although it is dumped in the preamplification and first amplification stages. The only idler output originates from the second amplification stage. The 10 mj input beam is routed through beam splitters to provide pump beams for the three stages of the OPA as well as a seed beam. The preamplification stage consists of a 60 μj pump and a 15 μj seed beam, while the first amplification stage uses a 425 μj pump beam and the remaining 9.5 mj pumps the second amplification stage Preamplification stage The preamplification (PA) stage is responsible of the determination of the wavelength of the output beam. To accomplish this, the seed beam is routed through a pair of moveable mirrors, through a sapphire crystal to create a white light continuum (WLC) and into a lithium triborate (LBO) crystal. Here, the seed and pump beams overlap non-collinearly to create a signal beam at the desired wavelength through overlap of the temporally dispersed wavelengths of the WLC and at an angle to the crystal designed to promote phase-matching of the two beams. The noncollinearity of the pump and seed beam allows the pump to be dumped while allowing the signal through to the first amplification stage First amplification stage During the first amplification (A1) stage, the signal and pump beams overlap in an LBO crystal collinearly, allowing the signal to pass through to the second amplification stage while a dichroic mirror dumps the residual pump beam.

49 35 The A1 stage is the OPA stage where power attenuation is regulated. The low pump power allows temporal displacement to reduce the output power, while retaining the wavelength determined in the PA stage provided the crystal angle is properly set for phase-matching. The output beam of the OPA system is very sensitive to the spatial overlap of the pump and signal beam in the A1 stage, making that overlap a crucial parameter of the whole experiment Second amplification stage The second amplification (A2) stage both amplifies the signal and creates an idler beam for OPA output and employs a dichroic mirror to dump the residual pump beam. At the OPA exit, an interchangeable dichroic mirror reflects either the signal or the idler, leading to the instrumentation interface, while the beam that passes through the mirror is dumped. The sensitivity of the output beam profile to spatial overlap in the A2 stage is minimal due to the large size of the pump beam, although temporal overlap and crystal angle significantly influence the wavelengths of the emitted light and has therefore to be adjusted more carefully. 2.3 Laser pulse and SIMS coupling Performing laser post-ionization experiments requires both a temporal and spatial overlap of the laser pulse with the sputtered plume of neutral species created during a SIMS experiment. For an LPI experiment, the application of the extraction field with the arrival of the laser pulse to the sputtered material produces the maximum signal given a sufficiently long primary ion pulse. Spatially, an optimal position is located through careful adjustment of a laser focusing lens in vertical and horizontal axes, both of which are orthogonal to the direction of laser propagation.

50 36 Lens adjustments in the direction of laser propagation can increase the photoionization volume, as discussed in Section It should be noted that experiments operate at a repetition rate of 1 khz as a product of the Nd:YLF pump beams of the RGA and SPA chirped pulse amplifiers. While SIMS experiments can operate at higher speeds, the ability of the laser system to amplify the beam limits the LPI experimental repetition rate Temporal coupling To couple the laser pulse to a SIMS experiment, the timing of a SIMS experiment must first be optimized. Both the SIMS and LPI experiments use a BNC channel delay generator (Berkeley Nucleonics, San Rafael, CA) to synchronize the experimental timings, shown in Figure 2-7. Figure 2-7. Experimental timing diagram of LPI experiments. The laser pulse entering the sensitive volume of the experiment is the pulse following the pulse that triggers the experiment

51 SIMS experimental timing For a SIMS experiment, only three delays are used. These delays correspond to the grounding of the pulse plates (Delay C) of the primary ion source (Figure 2-2) to allow the primary ion beam to pass through to the sample stage, the application of positive voltage on the stage (Delay B), and the start of data acquisition (Delay F). Delay F and Delay B have been coupled, so that the acquisition timing always begins at the start of extraction. This setup ensures mass calibration of the final mass spectrum to be consistent for both SIMS and LPI experiments. The temporal difference between Delay B and Delay C is the sum of the flight time of the primary ion to reach the sample stage and the duration of the primary ion pulse length. Reducing this temporal difference can result in the extraction voltage being applied prematurely, and secondary ion creation after the extraction voltage is applied limits the mass and lateral resolution of the experiment. For SIMS experiments, a sub-μs pulse length provides sufficient mass resolution and secondary ions LPI experimental timings For an LPI experiment, the timing of the laser pulse must coincide with the creation of the sputter neutral plume. To accomplish this, the timing of the laser pulse arrival and the SIMS experiment need to be set relative to each other. A photodiode in the oscillator of the laser system provides an input trigger for a SDG Elite synchronization and delay generator (Coherent, Santa Clara, CA) used to control the laser timings and beam alignment. One of the outputs of the SDG is delayed 0.8 ms, which is then routed as an input trigger for the BNC-575 delay generator. Delay B is then set to match the travel time of the laser pulse from the oscillator output to the sputtered plume, plus an additional 0.2 ms. This results in the laser pulse intersecting the plume

52 38 being the pulse following the oscillator output pulse that triggered the remainder of the experiment. This arrangement is necessary due to the discrepancy of the flight time of the laser pulse (~2.5 μs) and the time of flight of 20 kev C + 60 primary ions (~ 5.6 μs). Delay C is then set to account for the primary ion flight time and pulse width from this time. For an LPI experiment, the primary ion pulse is typically set to 2000 ns, depending on the species of sputtered material. This allows the sensitive volume of the mass spectrometer fill with neutral species of all kinetic energies, shown in Figure 2-8. Figure 2-8. LPI signal as a function of primary ion pulse width. At approximately 2 μs, the signal saturates The final voltage introduced for LPI experiments is the detector grid timing (Delay H). The grid is programmable to block up to 3 mass ranges using TTL logic to combine chosen delay

53 39 times from the extraction. This permits gas phase molecules, such as water or nitrogen, to be blocked and prevent detector saturation Spatial overlap optimization Horizontal and vertical spatial optimization Once the laser pulse is properly positioned temporally, the beam then needs to be optimized spatially. The pulse is routed through a series of mirrors, through a 150 mm (at nm) BK-7 focusing lens, a CaF 2 window on the Bio-ToF instrument, and through the plume of sputtered material. To obtain laser intensity greater than W/cm 2, the beam is focused to a few tens of microns, as calculated by 2 where w 0 is the minimum beam waist, M 2 is the beam aberration (a value of 1.5 is used for the Legend Elite Duo system as measured by the manufacturer), F is the focal length of the lens, which varies by wavelength, λ is the wavelength of the light, and D is the input beam diameter at the total beam intensity times 1/e 2. The intensity at the minimum beam waist is given by (2-2) 2 (2-3)

54 40 where I 0 is the intensity at the minimum beam waist and P peak is the peak power of each pulse. While the intensity at any point in space of the laser profile can be described as a function of the distance from the minimum beam waist along the propagation direction of the beam, z, and the radial distance from the beam center, r, a distance known as Rayleigh range (z R in Equation 2-4) describes the axial distance from the minimum beam waist where the radial dependence of the intensity is negligible. (2-4) When the minimum beam waist is located at the center of the extraction field, the Rayleigh range is longer than the depth of the plume of sputtered material. Therefore, the photoionization volume can be treated as a cylinder, and optimization of the laser position is simply performed by moving the focusing lens vertically and horizontally until a maximum for the LPI signal is found Spatial optimization in the direction of beam propagation Optimization of the laser position orthogonal to the direction of beam propagation is straightforward, though optimization in the axial direction is more complicated. While an optimal position is possible to find in this direction, a mathematical approach explains and identifies the need for fine adjustments to the axial movement of the focal lens. The laser intensity as a function of the radial distance and axial distance from the minimum beam waist for points outside of the Rayleigh range is given by Equation 2-5.

55 41, 1 (2-5) For each sputtered particle, there is an associated saturation intensity. The saturation intensity is the intensity necessary to initiate barrier suppression. As radial and axial distances increase, the effective photoionization volume increases for some distance, but has a sharp decline. An example of the difference between effective beam radius and a laser profile radius is shown in Figure 2-9, using the saturation intensity (3.4 x W/cm 2 ) for coronene and an I/e laser profile for a 5 x W/cm 2 pulse typically used for experiments. Figure 2-9. Photoionization volume in cylindrical coordinates showing the difference between the laser intensity at I/e and the radius of the photoionization volume for a saturation intensity of 3 x W/cm 2

56 42 The red distance in 500 μm on either side axially from the minimum beam waist represents the depth the sputtered material fills, while the blue distance represents the Rayleigh range. It should be clear that by moving the focal lens 3.5 mm along the axis of beam propagation, the effective beam radius can be increased from 44 μm to 65 μm. When LPI conditions are used to supplement SIMS signal, this approach should always be utilized to produce maximum photoionized signal. For the measurements used in Chapters 3 and 4, the cylindrical treatment possible in the Rayleigh Range permits a more straightforward description of the photoionization volume, and is therefore preferred. 2.4 Sample preparation physical vapor deposition For sample preparation, a physical vapor deposition (PVD) chamber has been added to the Bio-ToF instrument. The chamber allows for the creation and investigation of samples under ultra-high vacuum (UHV) conditions without exposure to atmosphere. The PVD chamber was designed and built by former lab member David Willingham and consists of a translational arm, positioned orthogonal to the translational arm used to move samples from the preparation chamber into the sample stage. The PVD arm is equipped with a sample block holder capable of rotating 180 degrees so the substrates attached to the top of the block are positioned to face bottom of the chamber. The arm moves the block holder into contact with a stainless-steel block containing a quartz crystal microbalance (QCM). The stainless-steel block is cooled by liquid nitrogen-cooled N 2 gas, which in turn cools the block holder. Underneath the block holder, an alumina crucible is filled with the sample of interest. The crucible is wrapped in a coil of tungsten wire and heated resistively by an external power supply. This results in sublimation of the sample molecules. As the sample sublimes, it deposits on both

57 43 the QCM and the sample substrate. The QCM provides an estimate of the sample thickness during deposition, allowing film thicknesses to be tailored to the experimental needs. To expedite the process, and reduce water deposition on the sample surface, the sample stage is used to cool the sample block while a cooled QCM determines when a consistent deposit rate is reached. At that time, the sample block is moved from the stage, and moved to the PVD chamber within a minute. After the deposit is made, the block is moved back to the stage, and LPI and SIMS experiments can begin immediately. This method is used to minimize surface contamination on the sample. 2.5 Crater characterization atomic force microscopy To measure the volume of material removed during an LPI or SIMS experiment, atomic force microscopy (AFM) was performed with a Nanopics 2100 (KLA-Tencor, San Jose, CA). The instrument is capable of scanning over a 1000 x 1000 μm 2 area. For experiments in this work, the Nanopics 2100 was operated in contact mode, where the AFM tip scans the sample surface through physical contact. 2.6 References 1. Weibel, D.; Wong, S.; Lockyer, N.; Blenkinsopp, P.; Hill, R.; Vickerman, J. C., A C60 Primary Ion Beam System for Time of Flight Secondary Ion Mass Spectrometry: Its Development and Secondary Ion Yield Characteristics. Analytical Chemistry 2003, 75 (7), Willingham, D.; Kucher, A.; Winograd, N., Strong-field ionization of sputtered molecules for biomolecular imaging. Chemical Physics Letters 2009, 468 (4-6), Kucher, A.; Wucher, A.; Winograd, N., Strong Field Ionization of β-estradiol in the IR: Strategies To Optimize Molecular Postionization in Secondary Neutral Mass Spectrometry. The Journal of Physical Chemistry C 2014, 118 (44),

58 44 Chapter 3 Quantification of molecular SIMS ionization probability of coronene This chapter has been adapted from Popczun, N.J., Breuer, L., Wucher, A. Winograd, N., In the SIMS ionization probability of organic molecules. Journal of The American Society for Mass Spectrometry 2017, DOI: /s The first author performed all experiments. All authors performed data analysis and experimental design. 3.1 Abstract The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation and postionization techniques. The largest factor affecting secondary ion efficiency is believed to be the poor ionization probability ( ) of sputtered material, a value rarely measured directly, but estimated to be in some cases as low as Our lab has developed a method for the direct determination of in a SIMS experiment using laser post-ionization (LPI) to detect neutral molecular species in the sputtered plume for an organic compound. Here, we apply this method to coronene (C 24 H 12 ), a polyaromatic hydrocarbon that exhibits strong molecular signal during gas phase photoionization. A two-dimensional spatial distribution of sputtered neutral molecules is measured and presented. It is shown that the ionization probability of molecular coronene desorbed from a clean film under bombardment with 40 kev C 60 cluster projectiles is of the order of 10-3, with some remaining uncertainty arising from laser induced fragmentation and possible differences in the emission velocity distributions of neutral and ionized molecules. In general,

59 this work establishes a method to estimate the ionization efficiency of molecular species sputtered during a single bombardment event Introduction Secondary ion mass spectrometry (SIMS) utilizes charged primary ions to sputter material from a sample surface in the form of neutral species, electrons and positively and negatively charged ions. These secondary ions are then separated by mass-to-charge ratio and detected to elucidate the chemical composition of the sample. The introduction of polyatomic primary ion sources that distribute the kinetic energy of the primary ion near the surface has made it possible to acquire spatial and depth information of chemical distributions within heterogeneous organic samples. 1-8 The impediment to more universal adoption of SIMS for these purposes is the inefficiency observed in the conversion from a molecule present in the sample surface to a detectable secondary molecular ion. The positive secondary ion signal for species m is described by the basic SIMS equation (3-1) where S m is the measured positive secondary ion signal, is the fractional mass concentration of species m, is an effective sampling time which includes the instrument transmission, I p is the primary ion current, Y tot is the total sputter yield and is the positive ionization probability of species m. 9 It should be noted that I p is limited by the requirement of primary ion doses which impact less than 1% of the sample surface (static limit) when surface integrity is required, while is an intrinsic value of the sample, leaving η, Y tot, and α + as areas of opportunity for improving secondary ionization efficiency. Most innovations in SIMS focus on

60 46 improving instrument transmission and total sputter yield, and have only recently explored increasing the ionization probability Improvements in secondary ionization efficiency are commonly reported as secondary ion yields ( ), or the number of secondary ions detected per primary ion particle An alternative is to report the useful ion yield (UY), a value derived from the ratio of the secondary ions detected to the total molecular equivalents sputtered For molecular ions M +, the useful ion yield is the product of, and the percentage of molecules that are sputtered intact, while the secondary ion yield is the product of UY, and Y tot. Both secondary ion yield and useful ion yield provide indirect information about the relative values of different systems and are attainable without information from the molecular neutral component of the sputtered material. While the useful yield can be obtained through single ion counting and atomic force microscopy (AFM) of the sputtered crater, quantification of is difficult since the probability of a molecule to survive the desorption process is unknown. Therefore, experimental data regarding ionization probabilities of molecular species are rarely reported, and mostly for inorganic clusters sputtered from metal or semiconductor 26 surfaces when so. Increasing is critically important for expanding SIMS applications, as poor SIMS detection efficiency for organic molecules is generally attributed to low , 16, 22-24, A numeric value can be determined in principle by the direct measurement of the ionic and neutral molecule intensities. Laser post-ionization (LPI) can provide access to chemical information of the neutral component in the sputtered material Several different LPI techniques have been explored, including single-photon ionization (SPI), resonance enhanced multiphoton ionization (REMPI), non-resonant multiphoton ionization (NRMPI) and strong-field ionization (SFI) The low photon flux required for SPI allows a single pulse to sample the neutral component within the extraction volume of the spectrometer, but the accessible photon energies are insufficient to ionize most organic molecules. Our laboratory utilizes SFI since it is

61 47 capable of ionizing organic molecules and we have found that the deleterious effects of laserinduced photofragmentation are greatly reduced The goal of this study is to utilize LPI to estimate of an organic film derived directly from sputtered ionized and neutral molecular species. The molecule investigated is coronene (C 24 H 12 ), a planar, highly symmetrical polyaromatic hydrocarbon that exhibits a strong signal increase in LPI experiments relative to SIMS. To achieve our goal, the focused ionization laser is rastered in both the horizontal and vertical directions with respect to the investigated surface in order to sample the entire detectable plume of sputtered material under conditions where the postionization efficiency is saturated. From this series of LPI experiments, an integrated measure of sputtered neutral molecules within the acceptance volume of the mass spectrometer is obtained. Comparison of the SIMS signal with the respective integrated neutral molecular signal allows to estimate for the molecular ion M + of coronene. The method provides a measurement of the number density of neutral and ionized molecules M 0 and M + in the volume above the bombarded surface, which is integrated over the emission velocity distribution of the sputtered particles and limited in precision by the inability to separate sputtered neutral fragments that are photoionized from sputtered neutral molecules that undergo photofragmentation during the post-ionization process. Apart from possible differences between the emission velocity distributions of sputtered ions and neutrals, the ratio between the acquired secondary ion and neutral signals directly relates to the molecular ionization probability. The method also yields a visual representation of the spatial distribution of sputtered neutral molecules within the acceptance volume of the mass spectrometer, which can be used to improve post-ionization techniques.

62 Experimental Methods Instrumentation The time-of-flight (ToF) SIMS instrument used in these experiments has been described previously. 50 In brief, the instrument consists of a 40 kev C + 60 primary ion gun (Ionoptika IOG C60-40, Ionoptika Ltd., Southampton, UK) 51, a controllable temperature sample stage, a reflectron mass spectrometer, and a microchannel plate (MCP) detector equipped with a high transmission grid above the detector surface. A voltage in excess of the extraction potential is applied to the high transmission grid to prevent gain saturation from low mass photo-ionized fragments by blocking them from reaching the detector for all experiments with the exception of the sputtered photofragmentation branching ratio experiment. During the acquisition of a TOF spectrum, the grid is pulsed to ground potential within nanoseconds to allow ions above m/z 60 to reach the detector. The reflectron voltage was set at 2% less than the extraction field, thereby preventing ions starting directly at the surface from being reflected and detected. In connection with the time refocusing properties of the reflectron, this setting determines an effective ion extraction volume located above the surface, henceforth referred to as the sensitive volume, from which ions can be extracted and detected as described in detail elsewhere. 35 This volume then needs to be overlapped with the laser ionization volume in order to efficiently detect sputtered neutral species. For all experiments, the ionization laser and the ion extraction voltage were fired simultaneously within nanoseconds of the end of the primary pulse. As outlined in Appendix A and described in detail elsewhere 17, 35, the width of the primary ion pulse determines the lower limit of the velocity distribution integral which characterizes the measured signals. If this width is chosen long enough, particles of all relevant emission velocities are detected and the measured signal reaches a steady state value which does not increase with increasing pulse width any more.

63 49 A measurement of the pulse width dependence of the post-ionization signal is presented in Figure 2-8 of Chapter 2, which shows that a pulse width of 2000 ns is sufficient to ensure these conditions. Therefore, we chose to use this setting in order to minimize the amount of sputtered material which is not sampled by the pulsed TOF detection scheme. As described in detail elsewhere 17, 35, the signal measured under these conditions represents the number density of the emitted particles, which is integrated over their entire velocity distribution. Since the ionization probability is related to the flux of sputtered ionized and neutral particles rather than their number density, the ion/neutral ratio resulting from a comparison of measured secondary ion and neutral signals might in principle be influenced by differences between the emission velocity distributions of secondary neutrals and ions. 23 Unfortunately, reliable experimental data regarding the magnitude of this influence is scarce 52 and practically non-existent for molecular species. The quantity which is relevant in this context is the average inverse emission velocity of the sputtered particles, which can in principle be determined from a measurement of their emission velocity distribution. As described in Appendix A (Figure A-3 and surrounding text), a published experiment performed on sputtered indium atoms 53 finds the average inverse emission velocity of secondary ions and neutrals to differ by roughly a factor two, so that in this case the ionization probability appears to be underestimated by the number density ion/neutral ratio measurement. Unfortunately, a similar measurement as performed in ref. 53 is not easily possible for the sputtered molecules investigated here, since the detected molecular signals are too low to map the velocity distribution particularly of the secondary ions. The result obtained from the indium experiment, however, suggests that the influence of the flux-density correction is likely to be of the order of a factor two, which is a significant uncertainty but will not change the order of magnitude of the measured ionization probability.

64 Sample preparation Coronene films were prepared on 10 x 10 mm Si shards (Ted Pella Inc., Redding, CA) that had been ultrasonicated in hexane, isopropyl alcohol, methanol and water for 15 minutes per cycle. The shards were dried via N 2 stream, attached to the sample block with Cu tape and introduced to the preparatory chamber of the instrument. An additional chamber was added to the instrument for the purpose of physical vapor deposition (PVD) of films without exposure to atmosphere. The shards are cooled by passing N 2 gas through a copper tube submerged in a dewar containing liquid N 2. The cooled gas is then passed through a quartz crystal microbalance (QCM) in contact with the sample block. An aluminum oxide crucible containing coronene was heated resistively through a tungsten filament carrying 13 A while the silicon shards were positioned in the flux of the coronene sublimed from the crucible. Coronene films were deposited to thicknesses in excess of 200 nm, measured by the QCM Laser system Laser ionization of thermally evaporated and sputtered molecules was performed with a commercially available chirped pulse amplification laser system (Coherent Legend Elite Duo, Santa Clara, CA, USA), providing 40 fs pulses of 800 nm radiation at a repetition rate of 1 khz. The pulses are converted to mid-infrared radiation through an optical parametric amplifier (OPA) (Light Conversion TOPAS-C-HE, Vilnius, Lithuania), with wavelengths tunable from 1160 nm to 2580 nm. Experiments were performed at 1500 nm with a peak power of about 5 x W/cm 2 to ionize the thermally evaporated or sputtered neutral molecules. The laser beam is introduced into the analysis chamber via a CaF 2 window and directed parallel to the sample surface at an angle of 38 with respect to the primary ion beam. A 150 mm (at nm) BK-7 focusing lens

65 51 positioned outside the analysis chamber focuses the laser such that the beam waist coincides with the location of the sensitive volume. The lens was translated in both the horizontal and vertical directions perpendicular to the direction of beam propagation in order to determine the optimal overlap with the sputtered material. In some experiments, a slit aperture was inserted before the ion extraction optics of the TOF spectrometer in order to restrict the extension of the effective ionization volume along the laser beam propagation direction to the central 600 m within the Rayleigh range (~ 4 mm). Power attenuation of the laser beam was performed by increasing the temporal delay between the seed and pump pulses in the first amplification stage of the OPA. A power meter (Coherent Field Max II TO, Portland, OR) was used to measure the laser power as a 30 second average. The laser intensity in the focal volume was calibrated using xenon gas, which was introduced into the analysis chamber via a controllable leak valve and exhibits a well-known photoionization behavior as a function of the laser intensity. Depth profile experiments were performed by alternating between analytical cycles and sputter erosion cycles. Acquisition of spectra for raw LPI (laser and primary ion beam active), raw SIMS (only primary ion beam active), a gas phase background signal (GPBG) (only laser active) and a noise background signal (neither laser nor primary ion beam active) constitutes one analytical cycle. The effective SIMS signal is the difference between the raw SIMS signal and the noise signal, while the effective LPI signal is the raw LPI signal minus both the GPBG and SIMS signals. The analytical cycles consisted of 10,000 primary ion pulses with a pulsed primary ion beam of 25 pa current rastered across a field of view (FoV) of 150 x 150 m 2, while a sputter erosion cycle was carried out by switching the ion beam to dc for 3 seconds over a 400 x 400 m 2 raster area with an idle time of 10 seconds before the next analytical cycle began. An ion fraction depth profile is then plotted as a ratio of the effective molecular SIMS and LPI signals as a function of primary ion fluence.

66 52 In order to investigate the role of laser induced photofragmentation, gas phase experiments were performed on thermally evaporated coronene molecules. For that purpose, a clean coronene sample was heated by wrapping the copper tube normally supplying the N 2 cooling gas to the sample holder in heating tape. The laser ionized gas phase species were then extracted for separation by their mass-to-charge ratio and detected. At the beginning of each experiment, the position of the laser beam was optimized for maximum LPI signal. Due to the fact that the laser beam is tightly focused, the effective ionization volume is significantly smaller than the extension of the volume from which postionized neutral particles can in principle be extracted and detected. This volume, which will in the following be referred to as the "detectable plume", is determined by the overlap between the plume of - either sputtered or thermally desorbed - neutral molecules and the sensitive volume of the TOF spectrometer, with its dimension both along and perpendicular to the ion extraction axis being of the order of millimeters. Since the laser beam waist is of the order of several ten micrometers, the laser beam largely undersamples the detectable plume if kept at a fixed position. In order to investigate the magnitude of the undersampling, the laser focusing lens was translated in 100 m steps both horizontally and vertically with respect to the sample surface and LPI spectra were recorded as a function of the laser beam position until the signal vanished. To account for possible signal loss as the experiment proceeds, for instance due to variations in laser power, the signals were measured at the optimal laser position again at the end of each experiment. 3.4 Results and discussion The goal of this work is to establish a method to estimate the order of magnitude of for an organic molecule by comparing the secondary molecular ion signal to the integrated signal

67 53 of the respective neutral molecular species located in the same extraction volume through laser post-ionization. Besides the velocity distribution effect described above, there are three issues associated with this goal that require consideration. First, it has been shown that damage accrued by primary ion bombardment can cause changes in α + near the sample surface. 36 Therefore, the value of accumulated damage is determined and the primary ion fluence needed to generate a steady state is exceeded before beginning the α + experiment to ensure it is independent of transient effects. Next, the degree of photofragmentation caused by the laser post-ionization of sputtered molecular species must be accounted for. Then, the saturation intensity for strong-field photoionization of sputtered coronene must be determined, which defines the extension of the effective ionization volume sampled by the laser post-ionization as described in detail elsewhere. 24, 34 Finally, the undersampling effect described in section must be accounted for by scanning the laser through the effective plume of sputtered material, thereby determining the total molecular neutral signal Ionization probability vs. primary ion fluence Molecular LPI and SIMS depth profiles of coronene are presented in Figure 3-1a. Despite the difference in signal, both the LPI and SIMS signal follow a similar trend, exhibiting an exponential decay before reaching a state of constant degradation at a fluence of about 1 x C + 60 /cm 2, henceforth referred to as the critical dose and marked in blue in Figure 3-1. Beyond this primary ion fluence, both the LPI and SIMS signals exhibit a weak linear decrease as shown in the inset of Figure 3-1a. This decline can, for instance, be caused by a fluence-dependent erosion rate as found in many other organic films under bombardment with C 60 projectiles 54-56, a notion which is supported by similar rates of decline in the LPI (21.0% signal loss per C 60 /nm 2 ) and SIMS (20.7% signal loss per C 60 /nm 2 ) for primary ion fluences greater than the critical dose. 57 As

68 54 a consequence, we presume that the bombardment induced damage has reached a stationary level where the ion/neutral ratio has become independent of the primary ion fluence. To examine the influence of bombardment induced damage on, the ion/neutral ratio is presented as a function of primary ion fluence in Figure 3-1b. It is evident that the ionization probability is strongly influenced at the beginning of the depth profile, where it at first exhibits a rather strong initial decrease followed by a subsequent increase. This minimum in relative ionization probability corresponds to the difference in dose necessary to reach the steady state in the SIMS and LPI depth profiles, observable in Figure 3-1a. The relative change in is negative, indicating that the damage accrued with primary ion fluence suppresses SIMS ionization. While it is possible that the initially high value of is due to a surface contamination, we have found that surface contamination tends to reduce the ionization probability for 20 kev C + 60 primary ion bombardment of coronene and would expect similar behavior for 40 kev C + 60 primary ions. In any case, the ion/neutral ratio reaches a steady state at the critical ion fluence, confirming a stationary surface state with constant α + at ion fluences exceeding the critical fluence. In connection with the absolute value of the ion/neutral ratio in the steady-state region determined below, the normalized curve in Figure 3-1b can be used to quantitatively determine the fluence dependent variation of the ionization probability at the beginning of the depth profile, including its value at the virgin surface being explored under static conditions. While not further investigated here, this change in with bombardment induced variations in surface composition observed for homogeneous samples might allow anticipation of matrix effects which cause deviations from ideal behavior for heterogeneous samples. 58

69 Figure 3-1. A coronene depth profile (a) showing the exponential decrease commonly observed, followed by a period of constant decline for both LPI and SIMS signals. The LPI signal is 2.5 times the SIMS signal at the clean surface, and increases to 14.4 times the SIMS signal at 5.3 x ions/cm 2. At doses above 1.2 x ions/cm 2, the LPI signal remains times the SIMS signal (inset). The coronene ion fraction (b) normalized to the initial ion/neutral ratio shows an early decline, after which the fraction increases until it reaches a steady state of around an ion fluence of 1.2 x ions/cm 2 (shown in blue) 55

70 Photofragmentation The influence of photofragmentation can be described by the branching ratio,, which is defined as the probability of a neutral molecule interacting with the laser to be photoionized without being fragmented. This value introduces uncertainty into the measured ion/neutral ratio, since the LPI signal measured for the molecular ion may underestimate the actual number of neutral molecules interacting with the laser. The problem in quantifying the amount of photofragmentation is the difficulty to deconvolute the source of fragmentation observed during an LPI experiment. In an ideal post-ionization scenario, the laser would ionize a sputtered neutral molecule with no further laser-induced fragmentation. In this case, the branching ratio would be unity, and any detected fragment ions could be attributed solely to collision-induced fragmentation during the sputtering process. Even in that case, however, it is unlikely that all collision induced fragments will exhibit fragmentation-free photoionization with the same efficiency as the parent molecule. In addition to the variations in chemistry of the different species, it is known that the sputtering process can cause elevated internal energy in sputtered molecules, which in turn may lead to increased photofragmentation. 59 Laser post-ionization of sputtered neutral molecular species and collision-induced fragments is therefore likely to induce further fragmentation, thereby greatly complicating the measured spectrum. To characterize the loss of molecular coronene signal due to photofragmentation, upper and lower limits of the respective branching ratio were determined. To obtain the upper limit, a pristine coronene film was heated, and the laser was used to ionize the thermally evaporated gas phase coronene molecules. In that case, it is safe to assume that the neutral precursor prior to photoionization and fragmentation consists only of intact coronene molecules with negligible thermal internal energy. The mass spectrum of thermally evaporated coronene (Figure 3-2) is dominated by 6 major peaks at m/z 300, 276, 150, 138, 100 and 92, respectively. The signals at

71 57 m/z 300 and m/z 276 correspond to the molecular ion M + and a molecule specific fragment [M- C 2 ] + which arises from the coronene molecule having evaporated a carbon dimer after internal heating during the photoionization process. Both signals are also observed in a SIMS spectrum, which shows a series of peaks corresponding to the sequential loss of carbon atoms from sputtered molecular coronene. The remaining four signals appear at m/z values not observed in SIMS. Instead, they arise from multiply charged M q+ and [M-C 2 ] q+ ions with q = 2 and 3, respectively. A detailed view of the LPI spectrum, shown in Figure B-1 of Appendix B, confirms this notion, since the multiply-charged species exhibit similar isotope distributions and proton loss sequences as the singly-charged species. In order to determine the degree of photofragmentation, we therefore add the respective signals of all charge states and relate the resulting total [M] q+ signal to the sum of [M-H n ] q+, [M-C 2 H n ] q+ and all other signals appearing at m/z greater than m/z 151. The resulting branching ratio was found to be 0.53, indicating that about 53% of the thermally evaporated coronene molecules survive the SFI photoionization process intact, while the remaining 47% fragment due to the interaction with the laser, mainly by evaporative cooling via the loss of a carbon dimer.

72 58 Figure 3-2. Strong-field ionization spectrum of thermally evaporated coronene showing the molecular ion (M +, m/z 300, blue) and the characteristic fragment ion ([M-C 2 ] + m/z 276, red), as well as the signal attributed to the respective doubly- and triply-charged ions In order to investigate photofragmentation for sputtered species, we look at LPI spectra (Figure 3-3) which were obtained under static conditions, thereby ensuring that each primary ion impacts onto a virgin surface area. Note that the spectrum shown in Figure 3-3 was acquired with the blanking of small fragment signals as described in the experimental section being switched off in order to detect all relevant fragment signals of all masses. Here, the calculation of is more straightforward, since the signal of [M-C 2 H n ] + is small, rendering the contribution of multiplycharged ions of this fragment negligible. In contrast, the signal of doubly- and triply-charged

73 59 molecular ions at m/z 150 and 100 is still clearly discernible with roughly the same relative intensity as in Figure B-1 of Appendix B. In this case, the value of is simply determined by relating the summed [M] q+ signal to the total ion signal. As explained above, the measured spectrum reflects a convolution of laser induced photofragmentation and photoionization of intact molecules as well as pre-existing fragments that were produced in the course of the sputtering process. The resulting value of = 5 x 10-2 therefore represents a lower bound of the photoionization branching ratio, indicating that at least 5% of the sputtered Coronene molecules must survive the photoionization process intact. It should be noted, however, that this value is likely to overestimate the actual amount of photofragmentation undergone by a sputtered neutral Coronene molecule. In order to examine the role of collisional fragmentation induced by the sputtering process, we look at the corresponding SIMS spectrum measured under the same bombardment conditions (Figure B-2 of Appendix B). It is seen that this spectrum is dominated by the molecular ion peak group around m/z 300 and contains only small signals of low mass fragments. Assuming the ionization probability of all fragments to be similar, the data therefore indicate that the contribution of collision induced fragmentation to the LPI spectrum of Figure 3-3 should be rather low.

74 60 Figure 3-3. Laser post-ionization spectra of coronene molecules sputtered under static conditions. The ratio of single and multiply-charged molecular species (m/z 300) to the total signal observed is 5.1 x 10-2 for the LPI spectrum Sampling efficiency The material ejected from the sample surface during a sputtering experiment fills a greater volume than the focused laser pulse required for strong-field ionization can probe in a single experiment. It is therefore necessary to characterize the undersampling of the principally detectable sputtered material to quantitatively compare the measured post-ionization signal with that measured for the respective secondary ions. The volume probed by the laser depends on the

75 61 laser intensity and can be estimated from a simple barrier suppression photoionization model as described in detail elsewhere. 24 The model assumes the effective ionization volume to be defined by all points in space where the laser intensity exceeds the saturation intensity, I sat, which denotes the laser intensity needed to initiate barrier suppression ionization for a selected neutral species. 60 In general, the non-linear relationship between photoionization efficiency and laser intensity, along with the spatial variation of the laser intensity overlapped with the sensitive volume of the mass spectrometer, makes calculation of the effective ionization volume complicated. In order to reduce the complexity, a slit aperture is inserted to limit the sensitive volume to the central 600 m of the Rayleigh range in the laser propagation direction. This establishes so-called parallel beam conditions, where the laser intensity only depends on the radial coordinate perpendicular to the laser beam. If the laser intensity in the beam center, I 0, reaches the value of I sat, saturation of the photoionization efficiency occurs, first starting in the beam center and expanding towards larger volume with increasing I 0. In the limit of high laser intensity, i.e. when I 0 >> I sat,, the measured photoion signal follows a simple relationship according to 61 ln : (3-2) 61 where n is the number density of neutral molecules, l is the length of the ionization volume and R is the distance from the beam center where the laser intensity has fallen to I 0 /e. 60 The effective beam radius, R, is defined by the bracketed expression in Equation 3-2. A linear plot of the measured signal vs ln(i 0 ) therefore asymptotically follows a straight line with a slope equal to. Extrapolation of this line to the ln(i 0 ) axis identifies the saturation intensity, I sat 60, and the effective ionization volume is calculated as 24.

76 62 The laser intensity calibration was examined with xenon, the photoionization signal of which was obtained in parallel with coronene, shown in Figure B-3 of Appendix B. The experimentally measured I sat value of 1.2 x W/cm 2 for Xe + is close to the literature value of 1.1 x W/cm 2, 61 so that no additional correction was applied to the laser intensity. The sum of the singly- and multiply-charged coronene signals is then plotted as a function of ln(i 0 ), shown in Figure 3-4. By extrapolating the slope of the signal increase to the horizontal axis, the saturation intensity for the coronene molecule is found to be 3.4 x W/cm 2. Using a value of R = 27 m, calculated from the parameters of the unfocused beam, the effective beam radius at our setting of I 0 = 5 x W/cm 2 is calculated as R = 44 m. In order to examine the degree of undersampling, the signal measured with the laser adjusted to a certain position (typically the position delivering maximum LPI signal) must be compared to the integrated LPI signal obtained with the laser beam scanned across the entire detectable plume. With the scanning steps x and y in horizontal and vertical directions, the integral is approximated by the sum where the correction factor, x y (3-3) is applied in order to account for the fact that the laser samples a smaller volume than the voxel size. For the conditions of our experiment, the factor was found to be As a result, we find that the laser samples about 1.2% of the entire detectable plume of sputtered neutral molecules when adjusted to the position delivering optimum post-ionization signal. This value can be compared to the result of a similar study on indium atoms sputtered from a clean indium surface under bombardment with a

77 63 20 kev C + 60 ion beam. 24 In this experiment, which was performed using the same instrument as utilized here, it was found that the laser sampled a fraction of about 3% of the detectable plume of sputtered neutral indium atoms. Since the exact value of the undersampling factor depends on the saturation intensity, the difference between both values is not surprising. The results consistently show, however, that the fraction of principally detectable post-ionized neutral particles is on the percent level and could in principle be enhanced by about two orders of magnitude if a more intense laser would be available. Figure 3-4. Sum of single and multiply-charged coronene as function of the natural log of peak laser intensity. The coronene saturation intensity was calculated to be 3.4 x W/cm 2

78 Secondary ionization probability, In order to determine the ionization probability of a sputtered particle, it is important to note that the secondary ion spectrum measured in a SIMS experiment with delayed extraction as performed here samples all secondary ions which are present in the sensitive volume of the mass spectrometer at the time when the extraction field is switched on. For the case of the secondary ions, the experiment therefore samples the number density distribution integrated over the entire detectable plume. In principle, the spectrometer cannot distinguish between secondary ions and the corresponding photoions produced via photoionization of the respective neutral species. Therefore, if the post-ionization process would ensure that all detectable neutrals present in the sensitive volume are being ionized, the ionization probability could simply be determined from the signal ratio obtained without and with the post-ionization laser being fired. In the experiment performed here, however, the post-ionization laser is tightly focused and the undersampling effect described above must be properly accounted for. By scanning the laser through the sputtered material, we find the spatial number density distribution of post-ionized coronene molecules which is shown in Figure 3-5. This figure is presented as a two-dimensional representation of the detectable plume, with the xy scanning plane oriented at an angle of 38 with respect to the primary ion beam axis. The signal plotted in Figure 3-5 has been normalized to the maximum LPI signal obtained with the laser set to its optimal position. Apart from the velocity distribution correction mentioned above, the SIMS positive ionization probability is then given by the equation 1, (3-4)

79 65 where represents the signal of positive molecular ions, is the signal of post-ionized neutral molecular species measured at laser position (i,j) and is the signal of negative molecular ions. Since the negative molecular coronene signal sputtered by 20 kev C + 60 primary ions has been found to be much smaller than the total post-ionized neutral signal, shown in Figure B-4 of Appendix B, we expect similar behavior under 40 kev C + 60 primary ion bombardment and therefore have omitted M - from the calculation in Equation 3-4. The ratio of measured SIMS and LPI signals with the laser adjusted to its optimum position is 0.21, which is nearly identical to the ratio of the LPI and SIMS signals obtained from the depth profile. To calculate the true ion/neutral ratio, we sum the measured LPI signal over all 165 laser positions and apply the corrections shown in Equation 3-4. For a coronene surface pre-irradiated with a fluence of 40 kev C + 60 primary ions greater than the critical dose at room temperature, the resulting value of is between 2.5 x 10-3 and 2.6 x 10-4, depending on whether the upper or lower limit of the branching ratio is used. Note that this experiment was performed under steady state bombarding conditions, which result in damage at the sample surface that can enhance or suppress SIMS signal as seen in section A. From the normalized data in Figure 1b, one finds that the ionization probability of intact coronene molecules sputtered from a fresh sample surface is about a factor two higher. Given the further uncertainty regarding the velocity distribution correction, we therefore conclude that the ionization probability of intact coronene molecules sputtered from a bulk coronene film under bombardment with 40 kev C + 60 primary ions is of the order of This result agrees well with the outcome of a similar experiment reported for a similar coronene film bombarded by swift heavy ions 34, 62, where the emission process is governed by electronic rather than nuclear sputtering. In principle, the technique utilized here can be transferred to other organic molecules as well, thereby providing a method to estimate relevant ionization probabilities in molecular SIMS experiments. These values are of great interest

80 66 since they allow one to judge the degree of opportunity to improve the detection sensitivity in these experiments via an enhancement of the ionization probability. In that sense, what is important is the order of magnitude rather than the exact value of the ionization probability, so that the still existing ambiguity with respect to the influence of photofragmentation on one hand and possible emission velocity effects on the other hand are probably of minor importance. Nevertheless, we note that it would in principle be desirable to measure the velocity distributions of secondary ions and neutrals in the same experiment in order to account for the velocity effect. While this would be a rather straightforward task for the post-ionized neutrals, it remains extremely difficult if not impossible for the respective secondary ions. In the post-ionization experiment, the effective interaction volume is determined by the focused ionization laser, so that the emission velocity of the detected particles can easily be selected by the time delay between the laser pulse and a sufficiently short primary ion pulse. For the secondary ions, on the other hand, the interaction volume is determined by the entire sensitive volume of the mass spectrometer, so that the distance between the surface and the interaction volume must be significantly increased in order to achieve reasonable velocity resolution. While this has been accomplished for indium atoms that were sputtered using a 5 kev Ar + ion beam with several microamperes of beam current 53, it appears almost impossible for the relatively low molecular secondary ion signals obtained under C + 60 cluster ion bombardment with beam currents of the order of picoamperes. Nevertheless, the method described here provides a valuable tool for comparison of molecular ionization probabilities from various sample systems which could be used in conjunction with secondary ion yield and useful ion yield measurements to propel innovations towards enhancing the detection sensitivity in molecular SIMS.

81 67 Figure 3-5. Two-dimensional spatial distribution of sputtered neutral coronene, normalized from 0 to 1 on the pixel of optimal laser overlap. The plane of the figure is 38 to primary ion flight path, which originates from the negative horizontal area 3.5 Conclusions The ionization probability of sputtered coronene molecules observed in a SIMS experiment involving 40 kev C + 60 ion bombardment of a freshly prepared coronene film is estimated to be of the order of This result illuminates the magnitude by which low useful yields commonly observed in molecular SIMS experiments may be limited by poor ionization efficiency, and allows to judge prospects for possible future enhancements. More specifically, our data show that at least for the system investigated here - there is principal headroom to increase

82 68 the molecular secondary ion signal by at least two orders of magnitude using strategies targeted to enhance the ionization efficiency of the sputtered molecules. Moreover, the results presented here show that the ionization probability changes with increasing ion fluence due to bombardment induced variations of the chemical surface state. For a homogeneous coronene film, we find that a steady state is reached at an ion fluence around 1 x C + 60 /cm 2, where both the secondary ion and the post-ionized neutral signal of intact sputtered coronene molecules reach a plateau, corresponding to a constant ionization probability. The two dimensional spatial representation of the detectable plume illustrates the potential for improvement in post-ionization experiments. Currently, the laser post-ionization occurs in a single pass, with lens translation in the direction of laser propagation as the primary method for increasing the volume of the sputtered material which is probed by the laser. Adding additional laser passes through the sputtered material can increase the secondary neutral signal, and the two-dimensional spatial plot will be useful in guiding that development. The data also show that the post-ionization scheme applied here is in principle capable of enhancing the SIMS detection sensitivity by two or three orders of magnitude, provided a more powerful laser is used to sample the entire detectable plume of sputtered neutral particles. 3.6 References 1. Winograd, N., The Magic of Cluster SIMS. Analytical Chemistry 2005, 77 (7), 142 A- 149 A. 2. Postawa, Z.; Czerwinski, B.; Szewczyk, M.; Smiley, E. J.; Winograd, N.; Garrison, B. J., Enhancement of Sputtering Yields Due to C60 versus Ga Bombardment of Ag{111} As Explored by Molecular Dynamics Simulations. Analytical Chemistry 2003, 75 (17), Appelhans, A. D.; Delmore, J. E., Comparison of polyatomic and atomic primary beams for secondary ion mass spectrometry of organics. Analytical Chemistry 1989, 61 (10), Wucher, A.; Cheng, J.; Winograd, N., Protocols for Three-Dimensional Molecular Imaging Using Mass Spectrometry. Analytical Chemistry 2007, 79 (15), Xu, J.; Szakal, C. W.; Martin, S. E.; Peterson, B. R.; Wucher, A.; Winograd, N., Molecule-Specific Imaging with Mass Spectrometry and a Buckminsterfullerene Probe:

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87 73 Chapter 4 Ionization probability in molecular SIMS: protonation efficiency of sputtered guanine molecules studied by laser post-ionization This chapter has been adapted from Popczun, N.J., Breuer, L., Wucher, A. Winograd, N., Ionization probability in molecular SIMS: protonation efficiency of sputtered guanine molecules studied by laser post-ionization. Journal of Physical Chemistry C, 2017, in press, DOI: /acs.jpcc.7b The first author performed all experiments. All authors performed data analysis and experimental design. 4.1 Abstract The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation and postionization techniques. An important factor affecting the detection sensitivity in molecular SIMS and other desorption techniques as well is believed to be the poor ionization probability of a sputtered molecule, a value which is often assumed to be as low as 10-5 but at present is basically unknown. In order to estimate how much headroom there is for future developments toward strategies aimed at enhancing the ionization probability, we study the protonation efficiency of sputtered guanine molecules for formation of [M+H] + secondary ions using strong field laser post-ionization (LPI) to detect the corresponding neutral molecules. In order to allow a quantitative comparison of secondary ion and neutral yields, the post-ionization signal is corrected for undersampling of the principally detectable plume of sputtered neutral particles by the focused laser beam. It is shown that the protonation probability of molecular guanine desorbed from a clean film under bombardment with 20 kev C 60 cluster projectiles is of the order of x 10-3, with some remaining uncertainty arising from laser induced fragmentation and

88 74 possible differences in the emission velocity distributions of neutral and ionized molecules. Moreover, we find that the post-ionization signal can in principle be boosted by two orders of magnitude if a more powerful ionization laser is employed. 4.2 Introduction Secondary ion mass spectrometry (SIMS) is a powerful tool for chemical imaging due to the submicron spatial resolution and the ability to obtain molecular information during an experiment. 1-2 Molecular imaging of organic compounds has benefitted from increased sensitivity provided by the introduction of new primary ion projectiles such as metal, fullerene or gas clusters. Typically, these projectiles increase the sputter yield and reduce the collision-induced damage remaining in the sample surface, although the useful ion yield obtained particularly for molecular systems is generally still low. This situation is often attributed to a poor ionization efficiency of the sputtered molecules, thereby triggering the development of strategies to design chemically active cluster projectiles in order to enhance the ionization efficiency. For instance, it has been demonstrated that water cluster projectiles can in some cases significantly enhance useful molecular secondary ion yields at comparable total sputter yield with respect to rare gas cluster ion beams. 3-4 Using a different approach, our group has developed a strategy to dope reactive species into a rare gas cluster projectile in order to boost the chemical ionization efficiency. 5-6 In all cases, however, the measured useful yield, i.e., the number of detected molecular secondary ions divided by the total number of sputtered molecule equivalents, is still rather low, 6 an observation that suggests poor ionization efficiency limits the measured values. Many factors influence the value of the useful molecular ion yield. These factors include the ability of a molecule to survive the violent sputtering process without fragmentation, the probability of ionization during emission (including a possible re-neutralization of a molecular

89 75 secondary ion) and the instrumental collection and detection efficiency for the resulting secondary ion. To guide strategies for further improvement, it is helpful to investigate the role of each of these different contributing factors separately. Here, we focus on the determination of the ionization probability of a sputtered intact parent molecule in order to estimate how much headroom there is for future enhancements of molecular useful ion yields by strategies aimed at enhancing this quantity. In fact, such improvements are urgently needed particularly in imaging experiments, since as pixel and voxel sizes of two and three-dimensional chemical images decrease, the number of molecules contained within a voxel grow fewer, so conversion of these molecules to detected molecular ions is crucial for generating chemically-informative images. A quantitative determination of ionization probabilities in sputtering requires the simultaneous detection of secondary ions and their neutral counterparts under otherwise identical experimental conditions. Time of flight SIMS instruments equipped with laser post-ionization have been demonstrated to be well suited for such a task. 7-8 Using this methodology, quantitative estimates of absolute ionization probability values have been reported for inorganic metal or semiconductor atoms and clusters sputtered from the respective clean surfaces Recently, this method has also been applied to the study of organic molecules One of the fundamental problems here is that the post-ionization laser needs to be capable of efficient photoionization of a sputtered molecule without excessive photofragmentation. Basically, two strategies have proved successful in this respect. Single photon ionization, on one hand, may constitute a soft ionization mechanism 8, 23 but requires the photon energy to be above the ionization energy of the targeted molecule, a requirement which for most organic molecules is hard to fulfil with sufficiently high photon flux to allow efficient post-ionization. The strategy pursued in our lab, on the other hand, utilizes strong field photoionization in the near-infrared wavelength range, 8 which was shown to permit the intact ionization of many organic molecules Since this technique requires relatively high laser power densities in order

90 76 to be efficient, it can at present only be used in connection with tightly focused laser beams which sample only a small portion of the detectable plume of sputtered neutral particles. We have recently developed a method to correct for this undersampling effect by scanning the laser beam across the sensitive volume above the bombarded surface, i.e., the volume capable of ion extraction and detection in the mass spectrometer , 26 The resulting integrated post-ionization signal can then be directly compared with the respective secondary ion signal extracted from the same volume in order to deliver a quantitative estimate of the ionization probability. Respective data obtained for coronene molecules sputtered from a coronene film held at room temperature have delivered a probability for the formation of M + molecular ions of the order of In the present work, we apply the method to guanine as a biologically relevant molecule. Moreover, the sample is held at low temperature throughout the analysis in order to reduce the background arising from evaporated gas phase molecules. The results reveal a much more detailed representation of the detectable plume of sputtered neutral molecules, which is shown to deviate considerably from that measured for gas phase molecules. The ionization probability of the intact guanine molecules sputtered by 20 kev C + 60 primary ions is estimated to be of the order of x Experimental The time-of-flight (ToF) SIMS instrument used in these experiments has been described elsewhere. 27 In brief, the instrument employs a 40 kev C + 60 primary ion gun (Ionoptika IOG C60-40, Ionoptika Ltd., Southampton, UK) 28, a temperature controlled sample stage and a calcium fluoride (CaF 2 ) window to allow integration of radiation for laser ionization. Depth profiles were obtained by alternating a 20 kev C + 60 primary ion beam of 85 pa current between 5 second dc etch cycles at a field of view (FOV) of 250 x 250 m 2 and analytical cycles consisting of 10,000

91 primary ion pulses rastered over a FOV of 100 x 100 m 2. A primary ion pulse length of 2000 ns was used, which was shown to be long enough to ensure a stationary distribution of sputtered particles in the probed volume above the surface (see Figure A-1 in the supplemental material). 29 As described in detail elsewhere, 8 the signal measured under these conditions represents the number density of the emitted particles which is integrated over their entire velocity distribution. In order to restrict the sensitive volume of the time of flight mass spectrometer in the direction towards the sample surface, the reflectron voltage was set at 98% of the sample potential generating the ion extraction field, ensuring that ions originating from distances less than about 0.5 mm above the bombarded surface are excluded from detection. In addition, the time refocusing and ion optical properties restrict the sensitive volume in the directions towards the extraction optics and parallel to the surface, respectively, thereby allowing to observe postionized neutrals and secondary ions under otherwise identical experimental conditions as 7-8, 29 described in more detail previously. Laser ionization of thermally evaporated and sputtered molecules was performed with a commercially available chirped pulse amplification laser system (Coherent Legend Elite Duo, Santa Clara, CA, USA) and optical parametric amplifier (OPA) (Light Conversion TOPAS-C- HE, Vilnius, Lithuania), providing 1500 nm, 40 fs radiation, focused with a 150 mm (at nm) BK-7 lens positioned outside the analysis chamber to a peak power 4 x W/cm 2. At the beginning of each experiment, the position of the laser beam was optimized for maximum LPI signal. Guanine films were deposited on 10 x 10 mm Si shards (Ted Pella Inc.) to thicknesses of ~220 nm, measured by a quartz crystal microbalance (QCM). With the exception of the thermal desorption measurements, all experiments were performed with the sample kept at low temperature (~100 K) in order to reduce the signal background originating from gas phase molecules. 77

92 Results and discussion The goal of this work is to determine the α SIMS ionization probability for sputtered guanine molecules by quantitatively comparing the [M+H] + secondary ion signal and the M + photoion signal arising from laser post-ionization of neutral molecules M present in the sensitive volume of the TOF mass spectrometer. The method has been explained in great detail elsewhere. 22 In brief, the effect of a collision-induced chemical modification of the surface ("damage") on the ionization probability, the loss of neutral molecular signal from photofragmentation as well as the relationship between the effective photoionization volume and the extension of the sensitive volume must be characterized. For the latter, it has been shown that the focused laser employed in these experiments significantly undersamples the entire plume of principally detectable neutral molecules and must therefore be scanned across the plume with the signal being summed over the scan. 22, 26 The SIMS ionization probability can then be calculated according to signal, where 1,, (4-1) M is the positive ionization probability, S is the measured secondary positive ion 0 S i,j is the signal of post-ionized neutral molecules measured with the laser positioned at the scan position (i,j), S is the measured secondary negative ion signal, υ is a correction factor determined by the volumetric overlap of the effective photoionization volume sampled by the laser and the voxel size of the laser raster scan steps, and φ is the fraction of molecules that survive the photoionization process intact.

93 Fluence dependence The individual molecular SIMS and LPI signals are shown as a function of the primary ion fluence in Figure 4-1a. Both signals experience an exponential decay before both reaching steady state at a fluence of about 2.5 x ions/cm 2, henceforth referred to as the critical dose. The initial decay is due to accumulation of chemical damage and can be characterized using the erosion dynamics model The ratio of the steady state LPI signal to that measured at the surface before bombardment is 0.31, while the same ratio for the SIMS signal is It can also be seen that the LPI signal determines the critical dose, with the SIMS signal apparently reaching a steady state slightly before that of the post-ionized neutral molecules. These discrepancies demonstrate the action of the bombardment-induced chemical damage towards modifying the protonation probability of sputtered molecules. The relative variation of the ionization probability under prolonged ion bombardment can be found from the ratio between both signals shown in Figure 4-1a. The result is depicted in Figure 4-1b. The initial data point depicted at zero fluence was obtained under static conditions, i.e., with a fluence of about ions/cm 2 used to obtain a spectrum, which ensure that each primary ion impinges onto a previously unaltered part of the sample surface. The remaining data points were then normalized to this static value. The figure shows that the protonation probability of sputtered guanine molecules increases by about 20% with increasing primary ion fluence and reaches a steady state at the critical dose. This finding indicates an accumulative effect where the chemical modification of the surface produced by previous impacts apparently enhances the protonation efficiency, for instance by liberation of free protons. 32 The establishment of steady state conditions as shown in Figure 4-1 is in agreement with earlier studies performed on the same system. 33 It is essential, because a laser beam scan across the entire detectable plume of sputtered neutral molecules, as is needed to estimate the absolute

94 80 value of the ionization probability, requires 357 individual mass spectra to be recorded in succession. Steady state conditions ensure that the measured signal does not fluctuate during the acquisition of such a scan, for instance by a primary ion fluence-dependent sputter rate.

95 Figure 4-1. Molecular SIMS ([M+H] + at m/z 152) and LPI ([M] + at m/z 151) signal (a) and ratio between both signals (b) of guanine molecules sputtered under bombardment with 20 kev C 60 + ions as a function of primary ion fluence. The data were normalized to the value obtained for a pristine surface at zero fluence 81

96 Photofragmentation A mass spectrum of photoions obtained from thermally evaporated guanine molecules is shown in Figure 4-2a. In this case, it is fair to assume that the precursor prior to photoionization is just the intact neutral molecule with negligible thermal internal energy. For reasons explained below, the spectrum is only shown for the mass-to-charge range greater than m/z It is seen that in this range the spectrum is dominated by the molecular C 5 H 5 N 5 O + ion at m/z 151 along with a C 2 H 3 N 3 O + fragment at m/z 87, whose proposed structures are shown in Figure 4-3a and b, respectively. This fragment is formed by a cleavage between the two rings of the guanine molecule followed by addition of two hydrogen atoms to saturate the dangling bonds. In order to estimate the total photofragmentation probability of an intact guanine molecule according to Reaction 4-1. Photofragmentation of molecular species. we make the crude assumption that all fragments F i are photoionized and contribute to the measured spectrum with comparable efficiency. Since the sum of the fragment masses must equal the mass of the original parent molecule, it is sufficient to scan the spectrum in the m/z range between the half and full molecular mass. This procedure ensures that each detected photofragment must originate from a distinct, thermally-evaporated parent molecule and that each fragmentation Reaction 4-1 is therefore counted only once. Comparison of the molecular ion signal to the integrated total ion signal depicted in Figure 4-2a therefore allows to estimate a photofragmentation probability of about 85%, indicating that about 15% of the thermally evaporated guanine molecules survive the photoionization process intact. Since the sputtered molecules may contain substantial amounts of internal energy and are therefore probably more

97 83 prone to photofragmentation, this value constitutes a lower limit of the photofragmentation probability that will occur during an LPI experiment. We wish to note that the spectrum depicted in Figure 4-2a also includes the guanine dimer at m/z 302, indicating that there is a contribution of dimers in the evaporated flux. It is interesting to note that this signal also appears in the SIMS spectrum taken at the pristine sample surface, shown in Figure 4-2b, indicating that guanine dimers are also being generated in the more energetic sputtering process. In both cases, however, the signal is small compared to the monomer signal, so we neglect dimer formation in the determination of the fragmentation probability. In addition to the SIMS spectrum, Figure 4-2b shows an LPI spectrum obtained at the pristine sample surface. Note that this spectrum was measured with the low mass ion suppression described in the experimental section being switched off. Moreover, the background signal arising from photoionization of the residual gas was eliminated by subtracting the spectrum taken without the ion bombardment. To determine an upper limit for the photofragmentation that will occur during an LPI experiment, the molecular guanine signal observed in Figure 4-2b is compared to the sum of the total ion signal. This treatment assumes that only molecular guanine is sputtered from the sample surface, and that all signals observed at other mass-to-charge ratios are strictly due to photofragmentation, with each fragment arising from an unfragmented parent molecule. This way, an upper limit of 92% is estimated for the photofragmentation probability, leaving about 8% of the sputtered molecules intact. As explained above, however, these assumptions are likely to lead to a significant overestimation of the fragmentation probability since i) low mass fragments arising from the same fragmentation chain reaction may contribute multiple times and b) the signal contribution arising from photoionization of collision-induced neutral fragments produced in the sputter ejection process is neglected. From the SIMS spectrum, on the other hand, it is evident that there are collision-induced fragments at m/z 135 and m/z 110,

98 84 shown in Figure 4-3c and d, respectively, as well as some smaller fragments at mass-to-charge ratios less than m/z 60. The bracketing values for the photofragmentation probability of a sputtered intact guanine molecule determined above introduce a primary source of uncertainty of the order of a factor two in the ionization probability as calculated using Equation 4-1. Nevertheless, the data indicate that the branching ratio, i.e., the probability for a sputtered guanine molecule to survive the post-ionization process intact, amounts to approximately 10%.

99 Figure 4-2. Mass spectrum of thermally evaporated (a) and sputtered (b) guanine for the determination of upper and lower limits for the photofragmentation branching ratio. The arrows indicate the molecular ion and dimer ion signals at m/z 151, respectively. The arrow at m/z 75.5 in (b) refers to the doubly charged molecular ion 85

100 86 Figure 4-3. Proposed structures for the molecular photoion (a), photofragment at m/z 87 (b), and collision-induced fragments m/z 135 (c) and m/z 110 (d) Undersampling correction As noted above, the spatially-focused laser beam required for strong-field photoionization does not overlap the entirety of principally detectable sputtered neutral material in a single experiment. Therefore, the undersampling of the principally detectable plume of sputtered neutral molecules is characterized by scanning the laser beam horizontally and vertically with respect to the sample surface and repeating the experiment at different positions of the focal volume, thereby integrating the measured post-ionization signal. The integration process requires knowledge of the effective ionization volume sampled by the laser in a single

101 87 experiment, which is estimated by determining the laser intensity I sat required to saturate the 21, 24, 34 photoionization process. As described in detail elsewhere, the value of I sat is identified by plotting the photoion signal for the selected neutral component as a function of the natural log of the peak intensity, I 0, in the center of the laser beam. When I 0 >> I sat, this plot asymptotically follows a straight line describing the ionization volume expansion with increasing laser intensity, which can be extrapolated to the ln(i 0 ) axis to determine I sat. For the molecular guanine LPI signal, this is illustrated in Figure 4-4, yielding I sat = 6.7 x W/cm 2. The effective ionization volume is then defined by all points in space with laser intensity I I sat, delivering an effective ionization radius R described by 34 ln where R is the distance from the beam center where the laser intensity has fallen to I 0 /e and (4-2) R 2 denotes the cross section of the effective ionization volume in the direction perpendicular to the beam propagation. Using R = 27 m, calculated from the parameters of the unfocused beam, the effective radius at our setting of I 0 = 4 x W/cm 2 is calculated as R = 35.5 m. In order to determine the integrated post-ionization signal, the signal measured at each laser position is summed and a correction factor R 2 x y is applied to account for the difference between the volume effectively sampled by the laser and the voxel size given by the translation steps of Δx and Δy during the laser beam scan. For the experiments performed here, the factor was found to be = 0.40.

102 88 Figure 4-4. Signal of laser post-ionized guanine molecules vs. natural log of the peak laser intensity. The asymptote intersects the laser intensity axis at the saturation intensity of about 7 x W/cm Measured neutral molecular guanine signal As described above, the laser was scanned through the plume of principally detectable sputtered neutral molecules to create the two-dimensional image shown in Figure 4-5. The signal at each position was normalized to the SIMS signal, which was recorded with the post-ionization laser beam blocked. The resulting total signal of post-ionized neutral guanine molecules summed from all 357 laser positions was 109 times the SIMS signal. Comparing total integrated signal with the signal measured with the laser beam adjusted to the position delivering optimal LPI signal, one finds that under optimized conditions a single LPI experiment only samples about 1.1% of the entire detectable plume.

103 89 Figure 4-5. Measured signal of post-ionized sputtered neutral guanine molecules vs. lateral position of the ionizing laser beam. The laser was scanned in the plane perpendicular to the beam propagation along vertical and horizontal directions with respect to the sample surface. The axes are scaled with respect to the position for optimum detected signal, and the intensity scale has been normalized to the measured SIMS signal In previous applications of this technique to estimate the ionization probability of sputtered -estradiol 21 and coronene 22 molecules, the laser beam was vertically scanned only upwards from the optimal laser position, since the beam could not be moved closer to the sample without starting to ablate surface material. In the present work, the sensitive volume was moved farther away from the surface by slightly lowering the reflection voltage. Moreover, the experiment was performed with the sample held at low temperature, so that the density of gas phase molecules evaporated from the surface was greatly reduced. As a consequence, the entire detectable plume could be mapped without ablation of the sample surface, and particularly the

104 90 signal originating from sputtered molecules at laser positions located beneath the optimal position could be clearly identified. A laser scan with no primary ion bombardment was performed in order to map the sensitive volume for gas phase species as well. As an example, a plot of the signal recorded at m/z 78 under these conditions is presented in Figure 4-6. It is noteworthy that the sensitive volume for gas phase species is different from that for sputtered species. More specifically, we find maximum gas phase signal to originate from a laser position which is shifted by about 300 m above and 300 m in the direction of the primary ion flight path from that delivering maximum sputtered guanine signal. As explained in more detail in the supplemental material, we attribute this finding, which has been reported before, 21 to the emission velocity and angle distribution of the sputtered molecules along with the ion optical settings of the mass spectrometer.

105 91 Figure 4-6. Measured signal of photo-ionized of gas phase benzene molecules vs. position of the ionizing laser beam. The laser was scanned in the plane perpendicular to the beam propagation along vertical and horizontal directions with respect to the sample surface and the extraction volume. The axes are scaled the same as in Figure Ionization probability With the photofragmentation and undersampling characterized, the ion/neutral ratio within the sensitive volume of the mass spectrometer can be determined according to Equation 4-1. Since the SIMS signal measured for negative molecular ions is small, it is neglected in the following. Depending on whether the minimum or maximum estimate of the photofragmentation probability is used, this results in ion/neutral ratio values between 7.6 x 10-4 and 1.5 x 10-3 under steady state sputtering conditions. To interpret these values in terms of the ionization probability,

106 92 it is important to realize that the experiment performed here is sensitive to the number density of sputtered particles rather than their flux. The ionization probability, on the other hand, refers to the partial sputter yields of secondary ions and neutrals and, hence, reflects a flux ratio. If the emission velocity distributions of sputtered ions and neutrals both species were different, the conversion from measured density to flux would introduce a correction to the measured value of the ionization probability. A detailed discussion of the conversion along with an estimate of its possible influence is presented in the supplemental material (Figure A-3 and surrounding text), indicating that the number density ratio measured here may in principle lead to an underestimation of the ionization probability, with the magnitude of the effect being of the order of a factor two. Therefore, the uncertainty introduced by the velocity effect appears to be of similar magnitude as that introduced by the photofragmentation issue and therefore does not change the order of magnitude of the measured value. As a consequence, we conclude that the ionization probability, i.e. the probability for a sputtered intact guanine molecule to form a protonated [M+H] + secondary ion, is about x The protonation probability determined here for guanine agrees well with the estimate of the ionization probability of coronene molecules sputtered from a fresh coronene film determined under similar bombardment conditions. 22 Note that the coronene experiment was performed at room temperature, which lead to a significantly higher background signal originating from laser ionization of thermally desorbed molecules. Therefore, the high density of these species close to the surface did not allow the measurement of photoionized sputtered neutral molecules at laser positions located below the optimal position. In addition, the uncertainty introduced by the photofragmentation issue is improved nearly 5-fold with respect to that of the coronene experiment, providing a much smaller bracketing range for the determined ionization probability value.

107 Conclusion From the quantitative comparison of the molecular secondary ion signal with that obtained by post-ionization of the corresponding neutral precursor molecules, we arrive at a measured value of about x 10-3 for the protonation probability of sputtered guanine molecules under bombardment with 20 kev C + 60 ions. This value agrees well with the order of magnitude estimate published earlier for coronene molecules sputtered under similar bombardment conditions. It is of great interest since it allows to judge the degree of opportunity to improve the detection sensitivity of molecular SIMS experiments via an enhancement of the ionization efficiency. In that sense, what is important is the correct order of magnitude rather than the exact value of the ionization probability, so that the still existing ambiguity with respect to the influence of photofragmentation on one hand and possible emission velocity effects on the other hand is probably of minor importance. The data presented here indicate that there is headroom for improving the ionization efficiency of a sputtered intact molecule by two to three orders of magnitude as compared to 20 kev C + 60 bombardment. This information is important in order to guide new strategies to improve the sensitivity particularly in SIMS imaging experiments, for instance by designing new optimized, chemically active projectile ions. On the other hand, quantitation of the degree of undersampling in the laser post-ionization experiment indicates that the molecular post-ionization signal, which is at present comparable to the molecular SIMS signal, can in principle be boosted by two orders of magnitude provided a more intense ionization laser would be available, which could then be defocused to sample the entire detectable plume of sputtered neutral molecules while still maintaining saturation ionization conditions.

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110 96 Chapter 5 Effect of SIMS ionization probability on depth resolution for organic/inorganic interfaces This chapter has been adapted from Popczun, N.J., Breuer, L., Wucher, A. Winograd, N., Effect of SIMS ionization probability on depth resolution for organic/inorganic interfaces. Surface and Interface Analysis, 2017, DOI: /sia The first author performed all experiments. All authors performed data analysis and experimental design. 5.1 Abstract Secondary ion mass spectrometry (SIMS) relies on the fact that surface particles ejected from a solid surface are ionized under ion bombardment. By comparing the signal of molecular secondary ions desorbed from an organic film with that of the corresponding sputtered neutral precursor molecules, we investigate the variation of the molecular ionization probability when depth profiling through the film to the substrate interface. As a result, we find notable variations of the ionization probability both at the original surface and in the interface region, leading to a strong distortion of the measured SIMS depth profile. The experiments show that the effect can act in two ways, leading either to an apparent broadening or to an artificial sharpening of the observed film-substrate transition. As a consequence, we conclude that care must be taken when assessing interface location, width or depth resolution from a molecular SIMS depth profile.

111 Introduction Secondary ion mass spectrometry (SIMS) is a powerful tool for chemical imaging due to the submicron spatial resolution and the ability to obtain molecular information with great surface sensitivity. 1-3 Molecular imaging of organic compounds has benefitted from increased sensitivity provided by the introduction of new primary ion projectiles such as metal, fullerene or gas clusters. Moreover, these cluster ion beams allow the erosion of the sample surface without accumulating bombardment-induced chemical damage, which has opened the possibility of molecular sputter depth profiling. 4-5 These aspects greatly expand the versatility of the technique with respect to 3D imaging applications. A fundamental problem when characterizing multicomponent materials, however, regards the ionization efficiency of a sputtered molecule, a quantity which is at present largely unknown. Particularly when profiling across interfaces between two different components, variations of the chemical composition may be superimposed upon matrix dependent changes of the ionization probability, leading to great uncertainty when trying to quantify the measured SIMS data. 6-7 It is therefore highly desirable to collect information about possible variations of the ionization probability of a sputtered molecule when profiling through an interface. Unfortunately, experimental data of this kind are scarce. In order to unravel the ejection and ionization processes of a sputtered molecule, it is necessary to detect the molecular ion and its neutral precursor under otherwise identical experimental conditions, which requires post-ionization experiments with well characterized ionization efficiency. In our laboratory, we have developed a strategy to photoionize sputtered molecules via strong field photoionization in the near-infrared wavelength range. 8 This method has been shown to permit the intact ionization of many organic molecules In these experiments, the post-

112 98 ionization process is decoupled from the emission, so that sputtered neutral molecules are detected with constant efficiency regardless of the momentary surface chemistry. Comparing the mass resolved signal detected for a molecular secondary ion and its neutral counterpart therefore directly delivers information about the SIMS ionization probability. 8 We have used this methodology in the past to determine the formation of molecular secondary ions for a few organic molecules sputtered from a homogeneous film It was found that even when profiling through such a single component material, the ionization probability changes as a function of applied ion fluence due to the chemical surface modification induced by prolonged ion bombardment. Here, we focus on the influence of possible ionization efficiency changes when profiling through an interface between different layers. As exemplary cases, we study the film-substrate interface when depth profiling through a guanine and a trehalose film deposited on a silicon substrate. The results show that such changes may lead to strong distortions of a SIMS depth profile, a finding which bears significant implications with respect to the assessment of the interface position as well as interface width and depth resolution. 5.3 Experimental The time-of-flight (ToF) SIMS instrument used in these experiments has been described previously. 15 In brief, the instrument consists of a 40 kev C + 60 primary ion source (Ionoptika IOG C60-40, Ionoptika Ltd., Southampton, UK) 16, a temperature controllable sample stage, a reflectron mass spectrometer, and a microchannel plate (MCP) detector equipped with a high transmission grid above the detector surface, and a calcium fluoride (CaF 2 ) window to introduce a femtosecond laser beam for post-ionization. All experiments were performed with a liquid nitrogen-cooled sample stage, which was held at ground potential during the pulsed ion bombardment. Secondary ions and post-ionized neutral particles are extracted into the time-of-

113 99 flight (ToF) mass spectrometer by pulsing the stage to positive potential immediately after the end of the primary ion pulse. A voltage in excess of the extraction potential is applied to the high transmission grid in front of the MCP detector to prevent gain saturation from low mass photoionized fragments by blocking them from reaching the detector. During the acquisition of a ToF spectrum, the grid is pulsed to ground potential to allow only detection of ions above m/z 60. For all experiments, the primary ion pulse width was set to 2000 ns, which was found long enough so that the measured signals did not increase with a further increase of the pulse width, thereby ensuring that the probed number density of sputtered particles is integrated over the entire emission velocity distribution of the sputtered particles. 17 Post-ionization of sputtered neutral particles was performed with a commercially available chirped pulse amplification laser system (Coherent Legend Elite Duo, Santa Clara, CA, USA) coupled to an optical parametric amplifier (OPA) (Light Conversion TOPAS-C-HE, Vilnius, Lithuania), providing 40 fs pulses of 1500 nm radiation at a repetition rate of 1 khz. The beam is focused with a 150 mm (at nm) BK-7 lens positioned outside the analysis chamber to generate a peak intensity of 3 x W/cm 2 in the beam waist. The lens is moved in a motorcontrolled manner in order to steer the beam and overlap its waist with the plume of sputtered neutral particles within the sensitive volume of the mass spectrometer. Guanine films were prepared in situ by low temperature vapor deposition on 5 x 5 mm Si shards (Ted Pella Inc., Redding, CA, USA) previously ultrasonicated hexane, isopropyl alcohol, methanol and water for 15 minutes per solvent and dried via N 2 stream. The substrates were precooled to the deposition temperature (~ 100K) at the sample stage, then quickly transferred to a side chamber of the ToF instrument where the guanine films were deposited with the substrate held at low temperature, and then transferred to the pre-cooled sample stage for analysis without breaking the vacuum. Depth profiles of guanine were performed with a 20 kev C + 60 primary ion beam operated in alternating analytical and sputter erosion cycles, using fluences of 1 x 10 11

114 100 ions/cm 2 and 6 x ions/cm 2, respectively. Trehalose films were prepared ex situ by spincoating a 1 M aqueous solution on the Si shards at ~3000 rpm. Depth profiles of trehalose were performed with a 40 kev C + 60 primary ion beam at fluences of 3 x ions/cm 2 and 6 x ions/cm 2 for the analytical and erosion cycles, respectively. 5.4 Results and discussion Guanine silicon interface The molecule-specific signal of guanine observed in the SIMS spectra is the protonated [M+H] + molecule at m/z 152. Using LPI, one finds the molecular [M] + ion at m/z 151 which is generated by photoionization of the intact neutral guanine molecule M 0. The silicon substrate is represented by the Si + 4 tetramer ion at m/z 112 observed in both the SIMS and the LPI spectra. All three signals are plotted as a function of primary ion fluence in Figure 5-1. The molecular guanine signal shows an exponential decay for both ionized and neutral molecules as the fresh sample surface accumulates ion bombardment induced chemical damage. At a flux of 2.5 x ions/cm 2, an equilibrium is reached between the damage created by primary ion bombardment and damage removed by the sputtering process, leading to a steady state plateau of the measured signals. The ratio of the LPI signal measured under these conditions to that detected at the beginning of the depth profile provides the cleanup efficiency of the system, or the amount of damage removed per primary ion relative to the total sputter volume, as described elsewhere. 18 For the guanine sample bombarded with 20 kev C + 60, the cleanup efficiency determined from the LPI depth profile is 0.31, while the same ratio determined from the SIMS depth profile is An exponential fit of the initial signal decay performed for the LPI data set produces an altered

115 layer depth of 17 nm and damage cross section of 21 nm 2, while the same procedure applied to the SIMS data results in values of 12 nm and 23 nm 2, respectively. 101 Figure 5-1. SIMS (a) and LPI (b) signal as a function of primary ion fluence for guanine film deposited on silicon substrate. Both SIMS and LPI signals for guanine are on the left scale, and silicon on the right

116 102 After the steady state region, the guanine signal declines while the Si 4 + cluster ion signal rises, indicating that the interface between the organic film and the silicon substrate has been reached. This transition is shown in Figure 5-2 for both the LPI and SIMS depth profiles.

117 Figure 5-2. Molecular SIMS [M+H] + (a) and LPI [M] 0 (b) signal measured across the guaninesilicon interface as a function of apparent depth. The depth scale has been calculated assuming a constant erosion rate as described in the text. The vertical lines denote the 84%, 50% and 16% levels of the signal variation observed across the interface 103

118 104 In order to convert the applied ion fluence into eroded depth, the possible variation of the erosion rate across an interface must be accounted for. This is particularly important for an interface between an organic film and an inorganic substrate as investigated here, since it is well known that the sputter yield induced by C 60 impact onto a molecular film is significantly larger than that of the silicon substrate. The sputter yield volume of the guanine film was determined as Y M = 152 nm 3 by eroding a crater into the film and measuring its depth using atomic force microscopy (AFM). The silicon sputter yield under 40 kev C 60 bombardment, on the other hand, is known to be Y Si = 2.5 nm It has been argued how the transition between these values should be handled when eroding across a film-substrate interface. A possible approach to account for the erosion rate variation is by linear interpolation between the values measured for the film and the substrate, respectively, with weighing factors determined from either the molecule or the substrate signals. 18,20-22 Plots of the interface region using different versions of this non-linear depth axis calibration are included in the supplementary material. Here, we revert to the simpler approach by assuming a constant erosion rate until the film is removed, with the latter condition identified as the point where the silicon substrate signal has risen to its maximum value. Note that this oversimplified depth axis calibration will result in inaccurate values for the interface width and underestimation of the actual depth resolution. To improve the depth axis calibration across the interface, the fluence dependent variation of the erosion rate must be determined, for instance by eroding a wedge crater as described in detail elsewhere. 23 The focus of the present work, however, is not set on a quantitative assessment of interface widths and depth resolution, but rather to elucidate differences between these quantities as derived from secondary ion and neutral depth profiles, respectively. For that purpose, we feel that the simple linear depth scale calibration as applied here is sufficient and will in the following refer to it as the "apparent depth" scale. As shown in Figure 5-2a, the SIMS signals measured for the guanine-silicon interface are plotted as a function of apparent depth. In interpreting the observed signal variation, note that the

119 105 silicon signal is apparently convoluted with a signal arising from a known fragment of molecular guanine, so that the peak intensity measured at m/z 112 contains contributions from the film as well as the substrate. However, it is reasonable to assume that the guanine fragment signal follows a similar decay at the interface as observed for the molecular ion signal. Its contribution has therefore already fallen to negligible values when the silicon signal starts to rise. The beginning of the plot refers to the steady state region of the depth profile, where the molecular guanine SIMS signal remains constant. The apparent interface width is derived between points with signal levels of 84% and 16%, marked by vertical drop lines in Figure 5-2, and the location of the interface is identified as the point where the signal level has reached 50% with respect to either the steady state value for the molecular signal or the signal maximum for the substrate signal. Note that the interface location derived from both plotted signals significantly differs, with the silicon signal rising later than the decay of the molecular signal. This finding indicates the presence of an interlayer between the guanine film and the substrate. A detailed inspection of the mass spectra acquired in this region reveals the occurrence of oxygen containing silicon clusters such as a Si 2 O 2 in both the SIMS and the LPI profiles, providing strong indication for a silicon oxide or hydroxide interface layer. In spite of the different interface location, the apparent interface width determined from the guanine and substrate SIMS signals (~39 nm) is about the same. As shown in Figure 5-2b, the LPI signal for the guanine-silicon interface is plotted as a function of apparent depth. The LPI molecule signal remains at steady state conditions much longer than the corresponding SIMS signal, i.e. until ~625 nm as opposed to that of ~600 nm for the SIMS signal. The signal then declines sharply, reaching 84% and 16% levels at 633 and 654 nm, respectively, resulting in an apparent interface width of 21 nm. The LPI signal for the silicon tetramer begins to increase around 630 nm, reaches 16% and 84% of its maximum at 650 nm and 687 nm, respectively, producing an apparent interface width of 37 nm. While this value is similar

120 106 to that determined from the SIMS profiles, the interface deduced from the LPI guanine signal is significantly sharper. The difference between the information obtained from corresponding LPI and SIMS depth profiles must be attributed to the change in ionization probability of the sputtered particles when going through the interface. To elucidate the magnitude of this variation, the SIMS/LPI signal ratio for sputtered intact guanine molecules is presented as a function of apparent depth in Figure 5-3. In addition, the apparent interface position as evaluated from the SIMS and the LPI depth profile is included for reference. It is obvious that the protonation efficiency forming the [M+H] + secondary ion begins to decline at an apparent depth of ~ 605 nm. The fact that the LPI signal is constant indicates that the sputter yield does not change, unless the changes were coincidentally counterbalanced by a change in the emission velocity and angle distributions of the sputtered molecules. We feel that the latter is highly unlikely and, hence, assume that the erosion rate does not significantly change in that region. This means that the ionization probability is starting to become influenced already about 30 nm before the actual interface is reached, leading to an apparently poorer depth resolution in the SIMS profile. As a consequence, the apparent interface locations determined from the SIMS and LPI depth profiles differ by 18 nm, with the SIMS profile obviously indicating the interface too early. Overall, the ionization probability of the sputtered guanine molecules is reduced about three-fold upon going through the film-substrate interface. On the other hand, we find the ionization probability of sputtered silicon clusters representing the substrate material (data not shown) to remain constant throughout the interface. At this point, we can only speculate about the reason for the changes of the ionization efficiency when going through the interface. In principle, the velocity-integrated ionization probability measured here can be influenced by variations of the emission velocity distribution. 12 While this dependence has been discussed (and debated) mainly for inorganic materials and ejectees, we feel that it is an unlikely cause for changes in the chemical ionization mechanism

121 responsible for the formation of the quasi-molecular ions studied here. We therefore believe that the effects observed here are due to a change in the chemistry at the interface. 107 Figure 5-3. Ratio of SIMS [M+H] + signal to LPI M 0 signal for molecular guanine as a function of depth. The vertical drop lines indicate the interface position as derived from the 50% points as described in the text Trehalose silicon interface In the preceding section, an example was presented where suppression of the ionization efficiency when reaching the interface lead to an apparent broadening of the film-substrate interface width observed with SIMS. However, reaching a chemical interface is also capable of enhancing the ionization probability, as shown here for the case of a trehalose-silicon interface.

122 The structure of trehalose and a characteristic fragment detected in the mass spectra are shown in Figure 5-4. To obtain a true steady state region, the depth profile must be run at low temperature, as described in the experimental section. Since the trehalose samples were prepared ex-situ and had to be cooled after introduction into the vacuum system, a thin layer of adsorbed water ice is created on the sample surface. This ice layer must be removed at the beginning of the depth profile, thereby masking the initial variation of the signals as the steady state is approached. For this reason, the cleanup efficiency cannot be determined from the depth profiles measured here, 14, 16 but has been reported for this system many times before. 108 Figure 5-4. Structure of the trehalose molecule (a) and characteristic fragment F (b) In both the SIMS and LPI spectra recorded on trehalose, the molecular ion signals at m/z 343 ([M+H] +, SIMS) and 342 (M 0, LPI) observed under C 60 bombardment are usually very small. However, a molecule specific fragment at m/z 325 is readily detectable in both spectra, which corresponds to the parent trehalose molecule having lost an OH group. In the following, we

123 109 therefore investigate the ionization probability of this characteristic molecular fragment. The SIMS and LPI signals obtained at m/z 325 are shown in Figure 5-5 as a function of apparent depth along with the signals detected for other characteristic fragments at m/z 179, 145 and 131, respectively. The signals representing the silicon substrate are not shown, as they exhibit the same behavior as observed for the guanine/silicon interface. The average interface position as evaluated from the decay of the molecular signal was located at apparent depths of 328 nm for the SIMS and 325 nm for the LPI depth profiles, respectively, while the average value of the apparent interface width was 20 nm for the SIMS and 48 nm for the LPI depth profiles. Figure 5-5. SIMS and LPI depth profiles of characteristic fragments of trehalose. The depth scale has been calculated assuming a constant erosion rate and may therefore be inaccurate beyond the film-substrate interface

124 110 In this case, the LPI signal in each instance shows a characteristic decline in the signal when approaching the film-substrate interface, while the SIMS signal shows a prolonged steady state with even a slight increase before declining at the interface. From the SIMS/LPI signal ratio plotted in Figure 5-6, it is obvious that the effective ionization probability of a sputtered trehalose molecule must increase at the interface, with the magnitude of the effect being of the order of a factor two. About the reason for this increase we can only speculate. Figure 5-6. Ionization probability of different molecule specific fragment ions of trehalose as function of apparent depth. The grey depths show the average LPI interface width

125 111 Scrutiny of the mass spectra acquired at different cycles in the depth profile reveals a number of peaks that exhibit pronounced intensity maxima within the interface region. The intensity variation of these peaks is illustrated in Figure 5-7, which shows a section of the recorded LPI spectra as a function of the depth profile cycle number. It is seen that the signals recorded at m/z 62 and 63 clearly represent the trehalose film. The signal at m/z 68 contains two components, one representing an organic fragment of the trehalose film and the other one - detected at slightly lower mass - representing the inorganic Si 2 C cluster arising from the silicon substrate. The signals recorded at m/z also show this organic-inorganic mass transition, albeit with a maximum of the inorganic component at the interface. The interface maximum of the m/z 67 signal is observed in the SIMS spectrum as well, as shown in the supplemental information. Similar interface maxima are also observed at various other masses, all representing inorganic components such as Na as well as a number of Si x O y H z clusters. The occurrence of these signals clearly indicates a modified surface chemistry when profiling through the interface, which may be due to accrued collision-induced damage or a change in the pre-existing chemistry at the interface. This modified chemistry then acts to enhance the formation probability of the [M- OH] + ion. In contrast to the guanine molecules, the trehalose fragments experience an enhancement in ionization probability at the film-substrate interface, which, superimposed with the simultaneous reduction of the trehalose surface concentration, results in an apparently sharpened interface width.

126 112 Figure 5-7. Section of LPI mass spectra recorded as a function of depth profile cycle number. The interface between the trehalose film and the silicon substrate is located around cycle # Conclusions The results presented here indicate that care must be taken when assessing interface widths and depth resolution from molecular SIMS depth profiles. We show two exemplary cases where the ionization probability of molecules sputtered from an organic film deposited on an inorganic substrate is found to change notably while profiling through the film-substrate interface. The observed changes reflect a modified surface chemistry when approaching the interface. These changes may in part be induced by a change of the energetics within the collision cascade due to energy reflection at the hard inorganic substrate, or by the presence of interface layers between film and substrate. In any case, it is evident that the ionization probability is not only dependent upon the chemical identity of the sputtered molecule, but also is affected by the changing chemical environment when profiling through an interface.

127 113 It is shown that the effect may act in two ways. If the ionization probability of a molecule representing a particular sample component varies in the same way as its surface concentration, the interface observed in the SIMS depth profile appears to be broadened, as demonstrated here for a guanine film deposited on silicon. If, on the other hand, the ionization probability exhibits the opposite trend, i.e., increases with decreasing surface concentration (or vice versa), the interface observed in the SIMS depth profile may appear artificially sharpened or even exhibit apparent interface maxima, as exemplified here for the case of a trehalose film deposited on silicon. In both cases, the measured interface location and width are found to significantly deviate from the more realistic values evaluated from an LPI depth profile. For the guanine system investigated here, we show that the SIMS ionization probability of sputtered intact guanine molecules already becomes influenced at a distance of 30 nm before the actual interface is reached. It is interesting to note that this value is of the same order as the altered layer thickness, albeit by about a factor two larger, indicating that chemical modifications induced by an upcoming interface may in principle range even farther than the bombardment induced chemical damage accrued while eroding through a homogenous film. In future experiments, it will be interesting to see if this is a characteristic of the organic-inorganic interfaces studied here or applies for interfaces between different organic layers as well. In the latter case, one would expect significant ion bombardment induced interface mixing to occur, which may then lead to even stronger distortions of a SIMS depth profile in addition to the matrix effects studied here. In any case, it is clear that understanding the complex interplay between ion induced modification of the surface chemistry and its influence on the ionization probability of a sputtered molecule is paramount to understanding the complexities of SIMS depth profiling through chemical interfaces.

128 References 1. Winograd, N., The Magic of Cluster SIMS. Analytical Chemistry 2005, 77 (7), 142 A- 149 A. 2. Gillen, G.; Simons, D. S.; Williams, P., Molecular Ion Imaging and Dynamic Secondary Ion Mass Spectrometry of Organic Compounds. Analytical Chemistry 1990, 62 (19), Lockyer, N. P., Secondary Ion Mass Spectrometry Imaging of Biological Cells and Tissues. In Electron Microscopy: Methods and Protocols, 3rd Edition, Kuo, J., Ed. 2014; Vol. 1117, pp Shard, A. G.; Gilmore, I. S.; Wucher, A., Molecular depth profiling. In TOF-SIMS: Materials analysis by mass spectrometry, IM Publications and SurfaceSpectra: Chichester, 2013; pp Mahoney, C. M.; Wucher, A., Molecular Depth Profiling with Cluster Ion Beams. In Cluster Secondary Ion Mass Spectrometry, John Wiley & Sons, Inc.: 2013; pp Dowsett, M. G.; Kelly, J. H.; Rowlands, G.; Ormsby, T. J.; Guzmán, B.; Augustus, P.; Beanland, R., On determining accurate positions, separations, and internal profiles for delta layers. Applied Surface Science 2003, , Jiang, Z.-X.; Alkemade, P. F. A.; Algra, E.; Radelaar, S., High Depth Resolution SIMS Analysis with Low-energy Grazing O2+ Beams. Surface and Interface Analysis 1997, 25 (4), Wucher, A., Laser postionization - fundamentals. In TOF-SIMS: Materials analysis by mass spectrometry, 2 ed.; Vickerman, J. C.; Briggs, D., Eds. IM Publications and SurfaceSpectra: 2013; pp Kucher, A.; Jackson, L. M.; Lerach, J. O.; Bloom, A. N.; Popczun, N. J.; Wucher, A.; Winograd, N., Near Infrared (NIR) Strong Field Ionization and Imaging of C-60 Sputtered Molecules: Overcoming Matrix Effects and Improving Sensitivity. Analytical Chemistry 2014, 86 (17), Willingham, D.; Kucher, A.; Winograd, N., Strong-field ionization of sputtered molecules for biomolecular imaging. Chemical Physics Letters 2009, 468 (4-6), Karras, G.; Lockyer, N. P., Quantitative Surface Analysis of a Binary Drug Mixture- Suppression Effects in the Detection of Sputtered Ions and Post-Ionized Neutrals. J. Am. Soc. Mass Spectr. 2014, 25 (5), Popczun, N.; Breuer, L.; Wucher, A.; Winograd, N., On the SIMS ionization probability of sputtered organic molecules. Journal of the American Society of Mass Spectrometry 2017, in press. 13. Popczun, N.; Breuer, L.; Wucher, A.; Winograd, N., Ionization probability in molecular SIMS: protonation efficiency of sputtered guanine molecules studied by laser post-ionization. J. Phys. Chem. C 2017, submitted. 14. Kucher, A.; Wucher, A.; Winograd, N., Strong Field Ionization of beta-estradiol in the IR: Strategies To Optimize Molecular Postionization in Secondary Neutral Mass Spectrometry. J Phys Chem C 2014, 118 (44), Braun, R. M.; Blenkinsopp, P.; Mullock, S. J.; Corlett, C.; Willey, K. F.; Vickerman, J. C.; Winograd, N., Performance characteristics of a chemical imaging time-of-flight mass spectrometer. Rapid Communications in Mass Spectrometry 1998, 12 (18), Weibel, D.; Wong, S.; Lockyer, N.; Blenkinsopp, P.; Hill, R.; Vickerman, J. C., A C60 Primary Ion Beam System for Time of Flight Secondary Ion Mass Spectrometry: Its Development and Secondary Ion Yield Characteristics. Analytical Chemistry 2003, 75 (7),

129 17. Wucher, A., Laser Postionization: Fundamentals. In ToF-SIMS: Surface Analysis by mass spectrometry, Vickerman, J. C., Ed. IM Publications: Chicester, 2001; pp Cheng, J.; Wucher, A.; Winograd, N., Molecular Depth Profiling with Cluster Ion Beams. J. Phys. Chem. B 2006, 110 (16), Kozole, J.; Winograd, N., Controlling energy deposition during the C60+ bombardment of silicon: The effect of incident angle geometry. Appl. Surf. Sci. 2008, 255 (4), Wucher, A.; Cheng, J.; Winograd, N., Molecular depth profiling of trehalose using a C 60 cluster ion beam. Appl. Surf. Sci. 2008, 255 (4), Cheng, J.; Winograd, N., Molecular depth profiling of multilayer systems with cluster ion sources. Appl. Surf. Sci. 2006, 252, Wucher, A.; Cheng, J.; Winograd, N., Protocols for Three-Dimensional Molecular Imaging Using Mass Spectrometry. Anal. Chem. 2007, 79 (15), Mao, D.; Lu, C.; Winograd, N.; Wucher, A., Molecular depth profiling by wedged crater bevelling. Anal. Chem. 2011, 83, Hofmann, S., Sputter depth profile analysis of interfaces. Reports on Progress in Physics 1998, 61 (7), Hofmann, S.; Liu, Y.; Jian, W.; Kang, H. L.; Wang, J. Y., Depth resolution in sputter profiling revisited. Surface and Interface Analysis 2016, 48 (13), Standard Guide for Measuring Widths of Interfaces in Sputter Depth Profiling Using SIMS. ASTM International: Wucher, A., Formation of Atomic Secondary Ions in Sputtering. Appl. Surf. Sci. 2008, 255 (4), Wittmaack, K., Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding. Surf. Sci. Rep. 2013, 68 (1),

130 116 Chapter 6 Conclusions and future directions 6.1 Conclusions The purpose of this dissertation is to increase the fundamental understanding of how changes in the molecular SIMS ionization probability affect the interpretation of depth profiles and increasing our fundamental understanding of the probability of ionization in a SIMS sputter event. The initial focus of the dissertation was to eliminate the need for estimations when discussing SIMS ionization probability by establishing a method of quantification based on measurements of sputtered positive ions and neutral molecules. The measured ionization probability for the molecular ion in 40 kev C + 60 sputtering of 10-3 for a fresh coronene sample indicates there is room to improve this value up to three orders of magnitude. A second molecule, guanine, known to produce protonated SIMS ions was measured using an improved system consisting of automated laser focal lens movement, while the sample is at liquid nitrogen stage conditions. The measured ionization probability again was found to be of the order of 10-3, again indicating an opportunity for 1000-fold increases in signal. The similarity in these two values begets the question if all organic molecules will exhibit similar values, but this is merely speculation until the ionization probabilities of more molecules are characterized. With the methodology presented in this dissertation, the groundwork has been laid to build a library of molecular SIMS ionization probabilities, measured by direct comparison of secondary ion and secondary neutral particle signals under the same experimental conditions.

131 117 For the two molecules examined in this dissertation, the 10-3 value is higher than traditional estimates for positive ionization probability values compared to traditional estimates. This indicates that collision-induced damage is responsible for a non-trivial amount of loss of molecular species contained in the sample. By quantifying the ionization probability of films strictly from the molecular ions and neutral species, new primary ions can be identified and tailored to the needs of specific SIMS experiments. Another focus of this dissertation was to determine the effect changing SIMS ionization probability elicits on the depth resolution at chemical interfaces. Homogeneous organic films were deposited on inorganic substrates, and the relative ionization probability was monitored throughout the interfacial region during depth profiling. For the first system, consisting of a guanine layer on top of a silicon substrate, the SIMS ionization probability dropped for the organic molecule as the organic-inorganic interface was approached, creating an artificial broadening of the measured interfacial region. For the second system, consisting of a trehalose layer on top of a silicon substrate, the SIMS ionization probability was enhanced for characteristic organic fragments as the interface to the substrate was approached, creating an artificially sharpened depth resolution. Accurate reconstruction of chemical depth locations becomes critical as SIMS imaging moves into three dimensions. The data presented proves that the determination of the width of interfacial regions in organic SIMS is a more complex task than believed so far. The change of ionization probabilities at the interface strongly influences the ability to determine interfacial widths by increasing or decreasing the measured signal. These in general non-predictable changes in the measured signal lead to false determination of the width of interfacial regions. This effect can be compensated by the use of post-ionization as performed in this work.

132 Future directions A natural result of the ionization probability quantification performed in Chapters 3 and 4 is to improve the fraction of ionized material leaving the surface. A possible approach is to investigate the dependence of the ionization probability on the primary ion beam used. Currently, secondary ion yields, or the number of secondary ions per primary ion bombardment, is typically used to describe the differences in primary ion systems. This convention is necessary because direct comparison of different primary ion beams is difficult. This difficulty can be attributed to the different characteristics of sputtering, energy deposition, collision-induced fragmentation, and projectile deposition in the sample. The quantification method presented in this dissertation provides a new tool to measure and compare ionization efficiency for different primary ion sources. By examining model systems of interest, ion source manufacturers can tailor primary ions to maximize molecular SIMS ionization. Recently, interest in applying LPI protocols for overcoming matrix effects in 2- and 3- dimensional imaging has grown. From Figure 4-5, it can be seen that for a radius of < 100 μm surrounding the optimal laser position, the LPI signal is ~90% of that at the optimal laser position. At laser positions greater than 100 μm, the LPI signal drops ~50%. For point source investigations, like depth profiling experiments, the laser can remain in a static location throughout the experiment. To apply LPI protocols to imaging areas greater than 200 x 200 μm 2, imaging may suffer from what appears to be a gradient of concentrations at distances > 200 μm from the optimal laser position. It is therefore necessary to create a means to raster the laser focal lens dynamically to match the primary ion bombardment location on the sample surface. Finally, molecular SIMS ionization probability during a molecular depth profile was shown to change at chemical interfaces in Chapter 5. Applying a similar methodology to the transition between the signals at a fresh sample surface and signal from the film under steady

133 119 state conditions can be used to indicate the effect of accrued, collision-induced damage on the molecular SIMS ionization probability for homogeneous systems. By performing this characterization in this manner, the source of changes to the ionization probability is restricted to implantation of the primary ion and collision-induced damage remaining in the sample surface. These values, therefore, are matrix effects intrinsic to the primary ion and molecule itself. The ratio of the steady state signal (S SS ) to the initial signal (S 0 ) for LPI indicates the change in the sputtering of molecular species, and therefore the change in the concentration of molecular component at the sample surface. A similar S SS /S 0 ratio for SIMS would equal the LPI ratio if the accrued damage did not affect the molecular ionization probability. From Figures 3-1b, 4-1b, 5-3, and 5-6, it has been shown in this dissertation that it does. Division of the SIMS ratio by the LPI ratio gives the degree of ion enhancement or suppression as a percent relative to unity, which would indicate no effect on the molecular ionization probability. A library of these intrinsic matrix effects can be created, and once this database is robust, models and predictions for matrix effects in multi-component systems should be hypothesized, investigated, tested, and refined.

134 120 Appendix A This appendix contains additional information for the optimization of parameters in chapters 3 and 4 A.1 Effective sensitive volume The experiments performed here to map the sensitive volume of the mass spectrometer by scanning the post-ionization laser beam find different shapes of the sensitive volume for gas phase and sputtered neutral species. Based on detailed ion trajectory simulations, 1 we attribute this finding to different starting conditions of the ions upon extraction into the time-of-flight (TOF) mass spectrometer. It is well known that under oblique projectile incidence as employed here, the angular distribution of sputtered material may be slanted towards the direction of specular reflection with respect to the direction of the projectile impact. Moreover, sputtered particles are emitted with hyperthermal velocities, leading to non-negligible starting velocity of the resulting photoions upon extraction into the mass spectrometer. If the spectrometer is tuned for optimum post-ionization signal of sputtered particles, it will be set to extract ions from a volume which is slightly displaced from the ion optical axis as sketched in Figure A-1 in order to sample the volume with the highest number density of sputtered particles. With these settings, gas phase ions starting from the same volume will not be detected due to their negligible starting velocity. The sensitive volume for ions derived from photoionization of gas phase particles will therefore be displaced as shown in the sketch of Figure A-1.

135 121 Figure 0-1. Sketch of effective ion extraction volume ( sensitive volume ) for gas phase (b) and for sputtered (orange) species A.2 Influence of the emission velocity distribution of the sputtered particles Due to the pulsed extraction scheme applied in these experiments, the acquired signal samples the number density of sputtered particles which are present in the sensitive volume of the TOF-spectrometer at the time when the extraction field is switched on. If the primary pulse has a duration t p and the measurement is performed at a delay time t after the end of the primary ion pulse, The number density detected at a distance r away from the point of emission is given by

136 122, (0-1) where f v denotes the emission velocity distribution of the sputtered particles. The limits of the velocity integration in Equation (A-1) are given by vmax r t and vmin r t tp. If the measurement is performed at zero delay, the upper limit v max goes to infinity. For an infinitely long primary ion pulse, the lower limit v min approaches zero, which means that the integral is performed over the entire velocity distribution, thereby generating a stationary number density distribution of sputtered particles in the volume above the bombarded surface which decays roughly with 2 1 r. In the limit of short primary ion pulses, on the other hand, the observed density distribution directly maps the velocity distribution f v of the sputtered particles. Under these conditions, only particles of a specific emission velocity v r t are present at distance r from the emission spot. If the primary ion pulse width is gradually increased, one observes a transition between the two limiting cases, which manifests as an initial increase of the signal measured at each point r, followed by a turnover where the signal levels off and becomes constant. For the sputtered organic molecules investigated here, this dependence is shown in Figure A-2. The closed symbols represent the signal of post-ionized neutral guanine molecules measured at m/z 151 with the post-ionization laser being adjusted to the position delivering optimum signal, while the open symbols represent the quasi-molecular [M+2H] + secondary ion signal measured at m/z 153, which was chosen for display because there is no interference from post-ionized neutral molecules at that mass. Note that the displayed postionization signal is measured with a focused laser beam and therefore samples the number density

137 of neutral molecules in the center of the detectable plume of sputtered particles, while the SIMS signal is integrated over the entire detectable plume Signal (arb. units) Pulse width ( s) Figure 0-2. Measured signal of intact post-ionized neutral guanine molecules M + at m/z 151 (closed symbols) and quasi-molecular secondary ion signal [M+2H] + (open symbols) vs. primary ion pulse length It is clearly seen that both signals saturate at pulse widths exceeding 2 µs, thereby proving that the stationary state is reached. This is the reason why we chose to use this value in the present work in order to minimize the amount of sputtered material which is not sampled by the pulsed detection scheme and therefore wasted for analysis. By definition, the ionization probability, i.e. the probability of a sputtered particle X to form a secondary ion X +, is given by the ratio between the secondary ion yield partial sputter yield YX and the Y X. Since sputter yields characterize the flux of the emitted particles rather

138 124 than their number density, the measured TOF-MS signals must be corrected for possible differences between the emission velocity distributions of secondary ions and neutrals. For a particular emission velocity v, the flux contribution f v is related to the measured number density n v via f v n v v. With the sputter yield Y f v dv and the measured, it is clear that the measured signal must be divided by the signal S n v dv f v vdv average inverse emission velocity (0-2) in order to convert the measured number density into flux. In order to illustrate the possible influence of this correction, we refer to published experimental data on the emission velocity distribution of atomic secondary ions and post-ionized neutral atoms sputtered from an indium surface under 5 kev Ar + bombardment. 2 The velocity distributions extracted from the data presented in ref. 2 are shown in Figure A-3. The average inverse emission velocities v 1 calculated from these distributions are 7.3 µs/cm and 13.4 µs/cm for sputtered secondary In + ions and neutral In atoms, respectively. Therefore, the true ionization probability is underestimated by the number density ion/neutral ratio, with the magnitude of the effect being roughly a factor two. These data indicate that the velocity distribution effect will not change the order of magnitude of the measured ionization probability but may well influence its exact value.

139 125 1 normalized signal 0.1 SIMS SNMS emission velocity (cm/µs) Figure 0-3. Emission velocity distribution of In + secondary ions and post-ionized neutral In atoms emitted from a polycrystalline indium surface under bombardment with 5 kev Ar + ions (data taken from ref. 2) A.3 References 1. M. Herder, Masters Thesis, University of Duisburg-Essen, Mazarov, P.; Samartsev, A. V.; Wucher, A., Determination of Energy Dependent Ionization Probabilities of Sputtered Particles. Applied Surface Science 2006, 252,

140 126 Appendix B This appendix contains supporting figures for chapter 3 Figure B-1. Detailed view of [M-C 2 H n ] q+ (left column) and [M-H n ] q+ (right column) peak series for q = 1 (top row) and q = 2 (bottom row) observed in an LPI spectrum of coronene. Note that the doubly charged species have higher signal for the deprotonated species relative to the parent ion

141 Figure B-2. SIMS spectra of coronene molecules sputtered under static conditions. The ratio of single molecular species (m/z 300) to the total signal observed is 0.97, indicating the collisioninduced fragmentation is negligible assuming similar ionization probabilities for all species 127

142 Figure B-3. Singly-charged xenon photoions as a function of the natural log of the peak laser intensity. The xenon saturation intensity of 1.2 x W/cm 2 was close to literature values as described in the main text 128

143 Figure B-4. Negative coronene spectra sputtered with 20 kev C 60 + primary ions. The molecular coronene signal (m/z 300) is near the noise level of the experiment 129

144 130 Appendix C This appendix contains supporting figures for chapter 5 C.1 Depth scale calibration The erosion rate in the interface region is linearly interpolated between the values of the organic film and the silicon substrate. With Y and M Y Si denoting the sputter yield volume in the molecular overlayer and the silicon substrate, respectively, the depth interval eroded at a particular point (i) in the depth profile is calculated as With Δ Δ (C-1) where (i) S M and steady state region, respectively, and (ss) S M denote the molecular ion signal measured at point (i) and in the f is the fluence interval applied between subsequent points of the depth profile. Alternatively, the substrate signal can be used to calculate the weight factor according to 1-2 (C-2)

145 131 1 yielding A third alternative suggested in ref. 3 uses both signals to calculate the weight factors, (C-3) (C-4) Plots of the interface region shown in Figure 5-2 of Chapter 5 are presented in Figure C- 1, where the depth scale calibration was performed according to Equations C-2, C-3, and C-4, respectively. It is seen that now the interface appears to be compressed with respect to the plot in Figure 5-2, with, however, different degrees depending on which signal was used to interpolate the erosion rate. If the molecule signal is used (Equation C-2, Figure C-1a), we find interface widths of 28 nm and 8.0 nm as evaluated from the decline of the molecular SIMS and LPI signal, respectively. In contrast, the interface width evaluated from the rise of the substrate specific Si 4 cluster signal becomes very small (1.4 and 3.3 nm, respectively), reflecting the fact that the erosion rate calculated from the declined molecule signal has already become very small when the silicon signal starts to rise. If the erosion rate interpolation is based on the variation of the silicon substrate signal (Equation C-3, Figure C-1c), one obtains interface widths of 33 nm (SIMS) and 18 nm (LPI) from the guanine vs. 12 nm (SIMS) and 21 nm (LPI) from the substrate signal, respectively. Using the more sophisticated interpolation according to Equation C-4 (Figure C-1b), one finds interface width values of 33 nm (SIMS) and 15 nm (LPI) determined from the

146 132 guanine along with 2.0 nm (SIMS) and 6.5 nm (LPI) determined from the substrate signal variation. These values are arranged in Table C-1 for reference. While the values determined from the guanine signal decay are not very different from those obtained using the simple linear depth scale calibration employed in the main text, assuming a constant erosion rate across the entire interface, the interface width values determined from the substrate signal rise are significantly smaller, reflecting the fact that the erosion rate must slow down upon approaching the silicon substrate. Figure C-1. SIMS (upper panels) and LPI (bottom panels) signal of molecular guanine and silicon tetramer as a function of depth using three different approaches to convert the applied primary ion fluence into eroded depth. The erosion rate was interpolated between the values determined for the organic film and the silicon substrate using a) weight factors calculated from the variation of the molecule specific guanine signal alone (Equation C-2); b) weight factors calculated from both signals using Equation C-4 and c) weight factors calculated from the silicon substrate signals alone (Equation C-3)

147 133 Equation C-2 (Molecular signal) Equation C-3 (Weighted signals) Equation C-4 (Substrate signal) SIMS guanine (nm) SIMS silicon (nm) LPI guanine (nm) LPI guanine (nm) Table C-1. SIMS and LPI depth widths for guanine and silicon employing different erosion rate equations Figure C-2. Relative ion fraction of guanine as a function of depth assuming a nonlinear erosion rate as calculated using Equation C-3 in the text. The drop lines show the interface location as evaluated from the midpoints of the SIMS and LPI signals, respectively

148 134 C.2 SIMS reference waterfall spectra Figure C-3. Section of SIMS mass spectra recorded as a function of depth profile cycle number in a SIMS depth profile of a trehalose film on silicon. The interface between the film and the substrate is located around cycle #100. Note the pronounced intensity maximum observed for m/z 67 at the interface C.3 References 1. Cheng, J.; Winograd, N., Depth profiling of peptide films with TOF-SIMS and a C-60 probe. Anal. Chem. 2005, 77 (11), Wagner, M. S., Molecular depth profiling of multilayer polymer films using time-offlight secondary ion mass spectrometry. Anal. Chem. 2005, 77 (3), Wucher, A.; Cheng, J.; Winograd, N., Molecular Depth Profiling using a C 60 Cluster Beam: the Role of Impact Energy. J. Phys. Chem. C 2008, 112,