Central Facilities
Procedure to Run 2D NMR COSY, NOESY, and HC-INEPT

I. Double-Quantum Filtered COSY
II. NOESY
III. H C 2D Correlation Experiment (2D HC INEPT)

I. Double-Quantum Filtered COSY

  1. Run a 1H Experiment First
  2. See 1D Procedures.
  3. Run with Narrowest possible sweep width
  4. run 1H experiment
  5. expand around spectrum
  6. click on spectrum with left button
  7. define left cursor with middle button
  8. define right cursor with middle button
  9. display will expand around the cursors.
  10. click "utilities", then "sw-sfo1"
  11. write down "sw" and "O1"
  12. click "return"
  13. type "rg"
  14. write down number
  15. DOT NOT CHANGE VALUE
  16. hit carrage return on keyboard
  17. type "dir" and choose "cosy"
  18. type "acqu" to go to acquisition window
  19. type "eda"
  20. You will see 2 columns of numbers: F2 and F1
  21. F2 is the directly detected dimension (normal 1D) (this is t2 in my notes)
  22. F1 is the indirectly detected dimension (this is t1 in my notes)
  23. You only need to change a few parameters
  24. TD in F2 column
  25. this is the number of points that will be collected in t2
  26. if this number is too large (like what is normally used in 1D H NMR) the data files will be too large for the computer to handle.
  27. try 1k -> 2k (k = 1024)
  28. TD in F1 column
  29. this is the number experiments performed in 2D or equivalently the number of points in t1.
  30. if this is too large, not only will the data set be too large to handle, the experiment will take a long time to do.
  31. try 512 -> 1k
  32. NS (number of scans). Needs to be a multiple of 8.
  33. DS (number of dummy scans: scans without acquistion used to create a steady state magnetization for the experiment) try 0, 2, or 4
  34. SW F1 and F2. (sweep widths for 1st and 2nd dimensions) enter the value determined in your 1D H NMR experiment (see above)
  35. rg (receiver gain) set to value used in 1D H NMR experiment (see above)
  36. O1 (center frequency of spectrum) You will need to scroll down a little to find this parameter. Use the value that you used in the 1D H NMR experiment (see above)
  37. click on "save"
  38. Other parameters
  39. D1 (recycle delay) set to (1-5)*T1 (longitudinal relaxation time)
  40. P1 (H 90 pulse) about 10us
  41. type "expt"
  42. This will give you the experiment time
  43. If the experiment will take too long, you can either change NS or TD{F1} (in eda)
  44. You should expect the experiment to take 3-12 hours.
  45. Type "zg" to run the experiment.
  46. Come back when the experiment is finished.
  47. Set up processing parameters. Type "edp".
  48. SI{F2} = TD{F2}
  49. SI{F1} = 2*TD{F1}
  50. wdw{F2} = wdw{F1} = GM
  51. To set lb and gb for F1 and F2
  52. use my defaults of lb = -1.0 and gb = 0.1
  53. or find good values for your experiment
  54. click "save"
  55. type "rser 1"
  56. click "process", then "manuel window adjust"
  57. will get a duel display
  58. Top: damped FID with window function
  59. Bottom: Fourier Transform of this FID
  60. click "gm"
  61. click "+" or "-" next to "lb" and "gb" to adjust the values
  62. adjust "lb" and "gb" until FID goes to zero at end and the spectrum looks good to you
  63. write down values of "lb" and "gb"
  64. click "return"
  65. Click "file", then "recall last", then "last 2D data set"
  66. type "edp"
  67. enter valuse of "lb" and "gb" into the proper fields
  68. click "save"
  69. type "xfb" to Fourier Transform both dimensions
  70. 2D spectrum will be displayed
  71. Phase 2D
  72. click "phase"
  73. click "row"
  74. Will now get cross hairs in 2D spectrum
  75. click on a peak with the middle mouse button
  76. click with right mouse button to remove cross hairs
  77. can change the chosen slice by clicking "+" and "-"
  78. when you have the slice that you want, click "mov:1"
  79. will move slice to window 1
  80. you can change the height of spectrum with "*2" and "/2" buttons below the "mov:1:2:3" buttons
  81. choose 2 other rows and move them to windows 2 and 3 with the "mov:2" and the "mov:3" buttons. Choose the to sample entire spectrum (peaks near both edges and in the middle)
  82. phase with "PH0" and "PH1" (remember that the peaks in this experiment are not all positive)
  83. click "column" and follow the same procedure (steps 2-4 above) to phase the columns.
  84. click "return", then "save and return"
    the program will ask: "start xfbp?" (perform phasing in both dimensions)
    click "OK"
  85. Plot 2D
  86. Define Plot Region
  87. click on the box (upper left of xwinnmr window)
  88. outline the region of interest
  89. hold right mouse button to draw box around peaks
  90. click right button to define region
  91. Define Intensity of Spectrum
  92. click "+/-" twice (until gauge on right side of xwinnmr window shows both red and purple region. This shows both positive and negative peaks)
  93. click on "*8", "/8", "*2", "/2" until the spectrum intensity is as you want it.
  94. Open "output", then "Define/Show Plot region", then "According to screen limits". Program will ask:
  95. "change levels?" answer "Y"
  96. "Please enter number of pos. levels" enter the number of positive levels that you want. try 5
  97. "Please enter number of neg. levels" enter the number of negative levels that you want. try 5
  98. "Display contours?" answer "N"
  99. To see what will be plotted
  100. type "view"
  101. quit view window by clicking on "quit"
  102. Plot by typing "plot"

II. NOESY

  1. Run a 1H Experiment First
  2. See 1D Procedures.
  3. Run with Narrowest possible sweep width
  4. run 1H experiment
  5. expand around spectrum
  6. click on spectrum with left button
  7. define left cursor with middle button
  8. define right cursor with middle button
  9. display will expand around the cursors.
  10. click "utilities", then "sw-sfo1"
  11. write down "sw" and "O1"
  12. click "return"
  13. type "rg"
  14. write down number
  15. DOT NOT CHANGE VALUE
  16. hit carrage return on keyboard
  17. type "dir" and choose "noesy"
  18. type "acqu" to go to acquisition window
  19. type "eda"
  20. You will see 2 columns of numbers: F2 and F1
  21. F2 is the directly detected dimension (normal 1D) (this is t2 in my notes)
  22. F1 is the indirectly detected dimension (this is t1 in my notes)
  23. You only need to change a few parameters
  24. TD in F2 column
  25. this is the number of points that will be collected in t2
  26. if this number is too large (like what is normally used in 1D H NMR) the data files will be too large for the computer to handle.
  27. try 1k -> 2k (k = 1024)
  28. TD in F1 column
  29. this is the number experiments performed in 2D or equivalently the number of points in t1.
  30. if this is too large, not only will the data set be too large to handle, the experiment will take a long time to do.
  31. try 512 -> 1k
  32. NS (number of scans). Needs to be a multiple of 8.
  33. DS (number of dummy scans: scans without acquistion used to create a steady state magnetization for the experiment) try 0, 2, or 4
  34. SW F1 and F2. (sweep widths for 1st and 2nd dimensions) enter the value determined in your 1D H NMR experiment (see above)
  35. rg (receiver gain) set to value used in 1D H NMR experiment (see above)
  36. O1 (center frequency of spectrum) You will need to scroll down a little to find this parameter. Use the value that you used in the 1D H NMR experiment (see above)
  37. click on "save"
  38. Other parameters
  39. D1 (recycle delay) set to (1-5)*T1 (longitudinal relaxation time)
  40. P1 (H 90 pulse) about 10us
  41. D8 (mixing time for cross relaxation) try (0.01->1.0)*T1 (longitudinal relaxation time) you might need to do a series of NOESY experiment as a function of D8
  42. type "expt"
  43. This will give you the experiment time
  44. If the experiment will take too long, you can either change NS or TD{F1} (in eda)
  45. You should expect the experiment to take 3-12 hours.
  46. Type "zg" to run the experiment.
  47. Come back when the experiment is finished.
  48. Set up processing parameters. type "edp"
  49. SI{F2} = TD{F2}
  50. SI{F1} = 2*TD{F1}
  51. wdw{F2} = wdw{F1} = GM
  52. To set lb and gb for F1 and F2
  53. use my defaults of lb = -1.0 and gb = 0.1
  54. or find good values for your experiment
  55. click "save"
  56. type "rser 1"
  57. click "process", then "manuel window adjust"
  58. will get a duel display
  59. Top: damped FID with window function
  60. Bottom: Fourier Transform of this FID
  61. click "gm"
  62. click "+" or "-" next to "lb" and "gb" to adjust the values
  63. adjust "lb" and "gb" until FID goes to zero at end and the spectrum looks good to you
  64. write down values of "lb" and "gb"
  65. click "return"
  66. Click "file", then "recall last", then "last 2D data set"
  67. type "edp"
  68. enter valuse of "lb" and "gb" into the proper fields
  69. click "save"
  70. type "xfb" to Fourier Transform both dimensions
  71. 2D spectrum will be displayed
  72. Phase 2D
  73. click "phase"
  74. click "row"
  75. Will now get cross hairs in 2D spectrum
  76. click on a peak with the middle mouse button
  77. click with right mouse button to remove cross hairs
  78. can change the chosen slice by clicking "+" and "-"
  79. when you have the slice that you want, click "mov:1"
  80. will move slice to window 1
  81. you can change the height of spectrum with "*2" and "/2" buttons below the "mov:1:2:3" buttons
  82. choose 2 other rows and move them to windows 2 and 3 withe the "mov:2" and "mov:3" buttons. Choose the slices to sample entire spectrum (peaks near both edges and in the middle)
  83. phase with "PH0" and "PH1" (remember that the peaks in this experiment are not all positive)
  84. click "column" and follow the same procedure (steps 2-4 above) to phase the columns.
  85. click "return", then "save and return"
    the program will ask: "start xfbp?" (perform phasing in both dimensions)
    click "OK"
  86. Plot 2D
  87. Define Plot Region
  88. click on the box (upper left of xwinnmr window)
  89. outline the region of interest
  90. hold right mouse button to draw box around peaks
  91. click right button to define region
  92. Define Intensity of Spectrum
  93. click "+/-" twice (until gauge on right side of xwinnmr window shows both red and purple region. This shows both positive and negative peaks)
  94. click on "*8", "/8", "*2", "/2" until the spectrum intensity is as you want it.
  95. Open "output", then "Define/Show Plot region", then "According to screen limits". Program will ask
  96. "change levels?" answer "Y"
  97. "Please enter number of pos. levels" enter the number of positive levels that you want. try 5
  98. "Please enter number of neg. levels" enter the number of negative levels that you want. try 5
  99. "Display contours?" answer "N"
  100. To see what will be plotted
  101. type "view"
  102. quit view window by clicking on "quit"
  103. Plot by typing "plot"

III. H C 2D Correlation Experiment (2D HC INEPT)

  1. Run a 1H and 13C Experiments First
  2. 1. See 1D Procedures.
  3. 2. Run with both spectra with the narrowest possible sweep widths
  4. run 1H experiment
  5. expand around spectrum
  6. click on spectrum with left button
  7. define left cursor with middle button
  8. define right cursor with middle button
  9. display will expand around the cursors.
  10. click "utilities", then "sw-sfo1"
  11. write down "sw" and "O1"
  12. click "return"
  13. repeat steps b and c with 13C experiment
  14. type "dir" and choose "HC_inept_2d"
  15. type "acqu" to go to acquisition window
  16. type "eda"
  17. You will see 2 columns of numbers: F2 and F1
  18. F2 is the directly detected dimension (normal 1D) (this is t2 in my notes)
  19. F1 is the indirectly detected dimension (this is t1 in my notes)
  20. You only need to change a few parameters
  21. TD in F2 column
  22. this is the number of points that will be collected in t2
  23. if this number is too large (like what is normally used in 1D H NMR) the data files will be too large for the computer to handle.
  24. try 1k -> 2k (k = 1024)
  25. TD in F1 column
  26. this is the number experiments performed in 2D or equivalently the number of points in t1.
  27. if this is too large, not only will the data set be too large to handle, the experiment will take a long time to do.
  28. try 512 -> 1k
  29. NS (number of scans). Needs to be a multiple of 16.
  30. DS (number of dummy scans: scans without acquistion used to create a steady state magnetization for the experiment) try 0, 2, or 4
  31. SW F1 and F2. (sweep widths for 1st and 2nd dimensions)
  32. SW{F2} = sweep width from your 13C NMR experiment (see above)
  33. SW{F1} = sweep width form your 1H NMR experiment (see above)
  34. O1 (center frequency of 13C spectrum) You will need to scroll down a little to find this parameter. Use the value that you used in the 13C experiment (see above)
  35. O2 (center frequency of 1H spectrum) You will need to scroll down a little to find this parameter. Use the value that you used in the 1H experiment (see above)
  36. click on "save"
  37. Other parameters
  38. D1 (recycle delay) set to (1-5)*T1 (longitudinal relaxation time)
  39. P1 (H 90 pulse) about 10us
  40. type "rga" to set receiver gain.
  41. type "expt"
  42. This will give you the experiment time
  43. If the experiment will take too long, you can either change NS or TD{F1} (in eda)
  44. You should expect the experiment to take 3-12 hours. THIS TENDS TO BE A LONG EXPERIMENT.
  45. Type "zg" to run the experiment.
  46. Come back when the experiment is finished.
  47. Set up processing parameters. type "edp"
  48. SI{F2} = TD{F2}
  49. SI{F1} = 2*TD{F1}
  50. wdw{F2} = EM wdw{F1} = GM
  51. To set lb and gb for F1 and F2
  52. use my defaults of
  53. for F2 lb = 5
  54. for F1 lb = -1.0 and gb = 0.1
  55. or find good values for the lb{F2}
  56. click "save"
  57. type "rser 1"
  58. click "process", then "manuel window adjust"
  59. will get a duel display
  60. Top: damped FID with window function
  61. Bottom: Fourier Transform of this FID
  62. click "em"
  63. click "+" or "-" next to "lb"" to adjust the values
  64. adjust "lb"" until FID goes to zero at end and the spectrum looks good to you
  65. write down values of "lb"
  66. click "return"
  67. Click "file", then "recall last", then "last 2D data set"
  68. type "edp"
  69. enter valuse of "lb"" into the proper fields
  70. click "save"
  71. to find values for lb{F1} and gb{f1} take a 1H spectrum with TD = TD{F1} and use the manuel window adjust to find good values. Enter the values in the proper fields in edp.
  72. type "xfb" to Fourier Transform both dimensions
  73. 2D spectrum will be displayed
  74. Phase 2D
  75. click "phase"
  76. click "row"
  77. Will now get cross hairs in 2D spectrum
  78. click on a peak with the middle mouse button
  79. click with right mouse button to remove cross hairs
  80. can change the chosen slice by clicking "+" and "-"
  81. when you have the slice that you want, click "mov:1"
  82. will move slice to window 1
  83. you can change the height of spectrum with "*2" and "/2" buttons below the "mov:1:2:3" buttons
  84. choose 2 other rows and move them to windows 2 and 3. Choose the slices to sample entire spectrum (peaks near both edges and in the middle)
  85. phase with "PH0" and "PH1" (remember that the peaks in this experiment are ALL POSITIVE)
  86. click "column" and follow the same procedure (steps 2-4 above) to phase the columns.
  87. click "return", then "save and return"
    the program will ask: "start xfbp?" (perform phasing in both dimensions)
    click "OK"
  88. Plot 2D
  89. Define Plot Region
  90. click on thebox (upper left of xwinnmr window)
  91. outline the region of interest
  92. hold right mouse button to draw box around peaks
  93. click right button to define region
  94. Define Intensity of Spectrum
  95. click "+/-" twice (until gauge on right side of xwinnmr window shows both red and purple region. This shows both positive and negative peaks)
  96. click on "*8", "/8", "*2", "/2" until the spectrum intensity is as you want it.
  97. Open "output", then "Define/Show Plot region", then "According to screen limits". Program will ask
  98. "change levels?" answer "Y"
  99. "Please enter number of pos. levels" enter the number of positive levels that you want. try 5
  100. "Please enter number of neg. levels" enter the number of negative levels that you want. use 0 (there should be no negative peaks in this experiment)
  101. "Display contours?" answer "N"
  102. To see what will be plotted
  103. type "view"
  104. quit view window by clicking on "quit"
  105. Plot by typing "plot"

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