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Fragmentation of Organic Molecules Desorbed from a Surface using Secondary-Ion Mass Spectrometry Alger Pike Nicholas Winog...
Secondary-Ion Mass Spectrometry SIMS <ul><li>Imagine shooting a bullet into sand. </li></ul><ul><li>Shrink the bullet and ...
SIMS in Combinatorial Chemistry An optical image of a bead-holder specially fabricated for 60   m polystyrene beads (capa...
Why Study Fragmentation? <ul><li>To learn what factors contribute to fragmentation patterns seen in SIMS spectra </li></ul...
Types of Fragmentation 1) Direct Desorption 2) Desorb then Fragment 3) Ion-Beam Induced
The ARTOF-SIMS Machine
ARTOF-SIMS Sample Manipulator a) Azimuthal Rotation: Sample rotates like the hands of a clock, around the center of the cr...
Ion Trajectories
Simulation Parameters
Simulation Results
Simulation vs. Real
Machine Automation
Design Goals <ul><li>Easy to use Graphical User Interface (GUI) </li></ul><ul><ul><li>Most common controls on main window ...
Controllable Parameters
CD 3 S-Cu (100): The Model System 1) Chemisorption to a four-fold hollow 3) No domains 2) No tilt angle due to short R gro...
FCC (100) Surface 1) Red atom is an ejecting atom 2) Blue atoms are blocking atoms 3) SIMS yield decreases with blocking
Azimuthal Distribution of Cu(100) 50 0
1200 L CD 3 SH on Cu(100) High Mass
1200 L CD 3 SH on Cu (100) Low Mass
Overall Fragmentation of CD 3 SH (total fragments signal) (total monolayer signal) F =
Direct Desorption Fragmentation Low energy cascade that desorbs an ion which does not have enough energy to fragment.
Direct Desorption Fragmentation
Fragmentation After Desorption High energy cascade leads to desorbed species which have enough energy to further fragment.
Fragmentation After Desorption
Ion-Beam Induced Fragmentation The ion beam directly breaks a bond which causes desorption of the fragment into vacuum.
Ion-beam Induced Fragmentation (fragment signal) (total monolayer signal) C =
Two-Body Model Simulation
Ion Trajectories at 35 º Incidence Angle
Summary <ul><li>Specialized TOF-SIMS machine built </li></ul><ul><ul><li>Designed with computer to optimize parameters </l...
Acknowledgements <ul><li>People </li></ul><ul><ul><li>Nick Winograd </li></ul></ul><ul><ul><li>Barbara Garrison </li></ul>...
Further Evidence for Cu 2 SCD 3 +  Ejection <ul><li>No SCD 3 +  ions seen in SIMS </li></ul><ul><li>Small amounts of CuSCD...
Further Evidence for CD 3 +  Formation XSCD 3 +     XS + CD 3 +
Image Potential
Ion Profile Above Extraction Plate
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TOF-SIMS Machine and software.

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Transcript of "TOF-SIMS Machine and software."

  1. 1. Fragmentation of Organic Molecules Desorbed from a Surface using Secondary-Ion Mass Spectrometry Alger Pike Nicholas Winograd
  2. 2. Secondary-Ion Mass Spectrometry SIMS <ul><li>Imagine shooting a bullet into sand. </li></ul><ul><li>Shrink the bullet and sand to atomic scale. </li></ul>
  3. 3. SIMS in Combinatorial Chemistry An optical image of a bead-holder specially fabricated for 60  m polystyrene beads (capacity: 10,000 beads/cm 2 ) The TOF image of Sasrin-Biotin beads loaded into the bead-holder. The molecular mass of biotin 245.3 amu is shown in green. R. M. Braun, A. Beyder, J. Xu, M. C. Wood, A. G. Ewing and N. Winograd, Anal. Chem. 71, 3318 (1999).
  4. 4. Why Study Fragmentation? <ul><li>To learn what factors contribute to fragmentation patterns seen in SIMS spectra </li></ul><ul><li>To establish control over these factors in order to allow easier interpretation of spectra and assay of complex organic mixtures </li></ul><ul><li>To expand applications for imaging SIMS of organic molecules – i.e. screening combinatorial libraries </li></ul>
  5. 5. Types of Fragmentation 1) Direct Desorption 2) Desorb then Fragment 3) Ion-Beam Induced
  6. 6. The ARTOF-SIMS Machine
  7. 7. ARTOF-SIMS Sample Manipulator a) Azimuthal Rotation: Sample rotates like the hands of a clock, around the center of the crystal. b) Polar Rotation: Sample rotates like a revolving door, around the axis perpendicular to the azimuthal axis.
  8. 8. Ion Trajectories
  9. 9. Simulation Parameters
  10. 10. Simulation Results
  11. 11. Simulation vs. Real
  12. 12. Machine Automation
  13. 13. Design Goals <ul><li>Easy to use Graphical User Interface (GUI) </li></ul><ul><ul><li>Most common controls on main window </li></ul></ul><ul><ul><li>Redundancy for heavily used features </li></ul></ul><ul><li>High-speed data throughput </li></ul><ul><ul><li>Optimized I/O is ~100 times faster </li></ul></ul><ul><ul><li>Device driver allows application level I/O </li></ul></ul><ul><ul><li>real-time Windows NT/2000 </li></ul></ul><ul><ul><li>Interrupt driven / multithreaded code </li></ul></ul><ul><li>High level of automation </li></ul><ul><ul><li>“ Go button” ease of use </li></ul></ul>
  14. 14. Controllable Parameters
  15. 15. CD 3 S-Cu (100): The Model System 1) Chemisorption to a four-fold hollow 3) No domains 2) No tilt angle due to short R group 4) Simplified mass spectra Imanishi, S. Takenaka, T. Yokoyama, Y. Kitajima and T.Ohta J. PHYS. IV FRANCE 7 (1997)
  16. 16. FCC (100) Surface 1) Red atom is an ejecting atom 2) Blue atoms are blocking atoms 3) SIMS yield decreases with blocking
  17. 17. Azimuthal Distribution of Cu(100) 50 0
  18. 18. 1200 L CD 3 SH on Cu(100) High Mass
  19. 19. 1200 L CD 3 SH on Cu (100) Low Mass
  20. 20. Overall Fragmentation of CD 3 SH (total fragments signal) (total monolayer signal) F =
  21. 21. Direct Desorption Fragmentation Low energy cascade that desorbs an ion which does not have enough energy to fragment.
  22. 22. Direct Desorption Fragmentation
  23. 23. Fragmentation After Desorption High energy cascade leads to desorbed species which have enough energy to further fragment.
  24. 24. Fragmentation After Desorption
  25. 25. Ion-Beam Induced Fragmentation The ion beam directly breaks a bond which causes desorption of the fragment into vacuum.
  26. 26. Ion-beam Induced Fragmentation (fragment signal) (total monolayer signal) C =
  27. 27. Two-Body Model Simulation
  28. 28. Ion Trajectories at 35 º Incidence Angle
  29. 29. Summary <ul><li>Specialized TOF-SIMS machine built </li></ul><ul><ul><li>Designed with computer to optimize parameters </li></ul></ul><ul><ul><li>Fully automated: computer manages the system </li></ul></ul><ul><li>Fragmentation shows orientation effects </li></ul><ul><ul><li>CuM + yield is higher with normal primary ions </li></ul></ul><ul><ul><li>Primary ion interactions create fragmentation </li></ul></ul><ul><li>Three distinct fragmentation mechanisms </li></ul><ul><ul><li>Direct desorption of CuM + </li></ul></ul><ul><ul><li>CD 3 + metastable decay of high energy M + </li></ul></ul><ul><ul><li>C + and D + fragments created by primary ions </li></ul></ul>
  30. 30. Acknowledgements <ul><li>People </li></ul><ul><ul><li>Nick Winograd </li></ul></ul><ul><ul><li>Barbara Garrison </li></ul></ul><ul><ul><li>Winograd and Garrison Groups </li></ul></ul><ul><li>Money </li></ul><ul><ul><li>ONR, NIH, NSF </li></ul></ul>
  31. 31. Further Evidence for Cu 2 SCD 3 + Ejection <ul><li>No SCD 3 + ions seen in SIMS </li></ul><ul><li>Small amounts of CuSCD 3 + are seen </li></ul><ul><li>Cu 2 + itself is formed by recombination i.e. there are no ejected Cu dimers </li></ul><ul><li>Peak width of Cu 2 SCD 3 + is consistent with dimer formation not trimer </li></ul>
  32. 32. Further Evidence for CD 3 + Formation XSCD 3 +  XS + CD 3 +
  33. 33. Image Potential
  34. 34. Ion Profile Above Extraction Plate

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