Bruker AMX 500 MHz NMR

Transcription

1 Bruker AMX 500 MHz NMR Precautions: Be careful with metal objects in the room. Avoid taking your credit or ATM cards or watch too close to the magnet (approx. 10 feet). People with medical implants should not approach the magnet. You must be trained or certified by a staff member. The UXNMR software is run under Unix, on a Bruker X32 computer. The magnet strength is Tesla. Use of the mouse will be described as Click or Drag, using the Left, Middle or Right mouse button. The term Click by itself assumes use of the left mouse button. Acquisition: Turn up the brightness and contrast with the knobs at the bottom right of the monitor, then login. Type uxnmr to start the software. Middle Click lock d g on the lower right to display the lock signal. Insert the nmr tube in the spinner; use the depth gauge to adjust the nmr tube in the spinner. On the SCM keyboard, Press the Orange colored button, then Press LIFT OFF button to turn the lift air on. Put the sample on the column of air on top of the magnet. Press LIFT OFF button to lower the sample into the magnet. Press SPIN button to spin the sample. The light on the SPIN button should turn on. On the UXNMR software window type rsh bb. This will load the standard shim set onto the SCM keyboard. Check that the FINE button light is on. The deuterium sweep signal should be visible on the screen; if not: Press FIELD and adjust the field until the deuterium signal appears in the middle of the window. (Jan 2003 Field = 3044 for CDCl3, for Acetone-d6 Field = 3518). Press LOCK POWER on the SCM keyboard and set the value by turning the knob. (Assuming CDCl3 solvent, for Acetone-d6 use 10-15). Press LOCK GAIN and adjust the value between Press LOCK PHASE button and adjust the value to 213 (this value may change in the future). Press LOCK (the deuterium signal will disappear and the light on the SWEEP OFF button will turn on). The LOCK button light will blink. If the lock light continues blinking, press FIELD and slowly adjust the field until the lock light stops blinking and is continuously illuminated. SCM Keyboard

2 Y Now we will start shimming the magnet. If the lock level disappears off the top of the screen, Press LOCK POWER (or LOCK GAIN) and lower the value until the lock level is one to two grids below the top. Y Press Z and adjust the value in whichever direction increases the lock level. Y Once the Z value is optimized (i.e. the lock level is maximized) press Z2 and repeat the procedure. Y Once the Z2 value is optimized (i.e. the lock level is maximized) press Z3 and repeat the procedure. Y After optimizing Z3, go back to Z and re-optimize it. Repeat this cycle with Z, Z2 and Z3 until the lock level no longer increases. Y Press LOCK PHASE and adjust to maximize lock level. Y Press STANDBY. Y Type edc to set your experiment name (NAME), experiment number (EXPNO), processed data number (PROCNO), user name (USER), and disk unit (DU). Please use disk unit x. We have limited space on disk unit u, and if it becomes too full the computer response will slow down. Use your login name for your user name. Click SAVE to create the new data set and exit the edc window. Y Type rpar cdcl3. This will load the parameters for a proton spectrum with CDCl3 solvent. For d6-acetone solvent type rpar acetone; or for a carbon spectrum type rpar c13. Y Click Acqu button in the upper left corner to observe the real time FID acquisition. Y Type rga to have the system automatically adjust the receiver gain. Wait for the message rga : finished to appear at the bottom of the screen. Y Type zg and wait for the acquisition to finish. PROCESS: Y Type ef to perform the Fourier transform. Y To expand the spectrum, Left Click, the cursor will now trace the spectrum. Move to the left side of the expansion and Middle Click, and then move to the right side of the expansion and Middle Click. The expansion region between the two middle clicks will be displayed. Left Click again to exit this mode. This expansion mode does not work within other sub-windows (e.g. phasing, calibration, integration, etc.) because the mouse cursor is used for other functions. Y Click Hz/ppm to change the axis units between Hertz or ppm. The axis units determine units of input for prompts. Y To restore a full display of the spectra window Right Click <> >< r. Y Right Click 2 2 r. Then Left Click 8 8 s. This will set the vertical scaling prior to phasing. Y At the bottom of the screen Click phase to enter the phasing window.

3 Y Click Biggest. A dashed vertical line will appear on the spectrum at the biggest peak. Zero order phasing occurs at this line, by Middle Drag up or down over the spectral window. First order phasing is applied as a function of the distance from the vertical line, by Right Drag up or down over the spectral window. Y When finished phasing, to store the phasing changes and return to the main window Click Store in the upper left corner. Y To set a chemical shift reference first expand around the peak to be referenced. Then Click calib to enter the calibration window. Left Click in the spectral window, the cursor will now trace the spectrum. Move the cursor to the top of the reference peak, then Middle Click. A prompt will appear asking for input of the chemical shift value. To return to the main window Click Return on the upper menu bar. Y Click integ to enter the integration window. Adjustment of the integral bias and slope is easiest done on all the peaks at once. Otherwise, the slope and bias will have to be adjusted for each individual integral. Y Left Click in the spectral window, the cursor will now trace the spectrum. Y Move to the left side of the displayed peaks and Middle Click, and then move to the right side and Middle Click. A single integral curve will be displayed. Y Left Click within the integral curve to regain the mouse cursor and set the integral curve as the current integral. The current integral is denoted by a star * on the integral curve. Y With the mouse cursor over the spectral window Middle Drag up or down adjusts the bias. The slope is adjusted by Right Drag up or down. Y After adjustment of the bias and slop Click Del_Cur. The current integral curve will be deleted, but the bias and slope adjustments will be remembered. Y Now, define integrals for each spectral peak or multiplet. Left Click to trace the spectrum, then Middle Click on the left and right side of each peak. Finally, Left Click over the peak to be used for calibration, to regain the mouse cursor and set that integral curve as the current integral. Y With the current integral defined, Click Calib. A prompt will appear asking for input of the area of the integral. The areas of the other integrals are automatically recalculated. Y Click Write+Return to save the integral regions in the file intrng, and return to the main window. The intrng file is necessary for plotting. Y Use the mouse to expand the spectrum. Left Click DPl1 2 3 to define the plot region numerically. The current value of F1 (the left downfield edge of the plot region) is printed with a prompt for the new value. Then the current value of F2 (the right upfield edge of the plot region) is printed with a prompt for its new value. Finally, there is a prompt to answer the question, Change y-scaling of display according to PSCAL? Answer with y. Y To display the plot region at any time just Click PlotReg. Y Display the plot region, and adjust the vertical scaling (e.g. Right Click 2 2 r ). Click calib to enter the calibration window. Left Click MI MAXI. A horizontal line that is controlled by the mouse will appear on the screen, any peak above the line will be selected by peak picking, Left Click to set the horizontal line. Type pps to display a list of the peaks selected.

4 Y Type setti to open a window for typing the title. Type i to begin typing (insert text). Type text wanted. Use Backspace key to edit on the current line. Hit Esc key to finish typing. Type ZZ to exit edit window. If the window does not clear from screen, Click Clr to clear the screen. (For more instructions on editing look up the vi editor for Unix.) PLOT: Y Click edplot to enter the plot edit window. This window allows an interactive plotting setup. Y First Click A to set the paper size (8½ x 11 ). ( B is 11 x 17 ) Y A grid is displayed with boxes representing spectral window, title window and parameter window. These windows can be activated or deactivated by clicking in the corresponding fields below the grid, labeled Spec, Title and Param. Deactivated windows are marked Disabled. Y Click Spec on the menu on the right side under the edit-windows: label, to enable interactive modification of the spectral window. The window will now have 5 little boxes, one in the center and one in each corner. Left Drag the corner boxes to resize the window, and Left Drag the center box to reposition the window. Similarly modify the title or parameter windows by clicking on Title or Param. Y Click fix-wind when finished adjusting the windows. The spectral window will display the spectrum. The title and parameter windows are blank due to limited screen resolution. Y Three new fields will appear below the grid for integral curves (Integ), integral labels (Integ Labels) and peak labels (Peak Labels). Click in a field to activate or deactivate. Activated fields are marked Enabled, and deactivated fields are marked Disabled. Y Adjustments can now be made of the integral curves, integral labels and peak labels (if enabled). Y Left Drag plhei (or ilhei ) to adjust the height of the box for printing peak labels (or integral values). Y The integral curves can be adjusted with the buttons under edit-integrals: by Left Drag vmove, or vscal. Y The axis can be adjusted with the three buttons under edit axis:. Y Finally, the spectrum can be fine tuned if needed with the buttons under edit spectrum:. Usually the only necessary modification is Right Click <> >< r, to adjust the vertical scaling. Y Click Sto+plot to plot the spectrum. A message window noting the plot job submittal will appear after 5-15 seconds, Click on it to dismiss it. Click Return to exit the plot editing window and return to the main window. Y To eject the sample Press Spin on the SCM keyboard (to turn the spinner off). Press the orange button, then Press Lift. Pickup the sample, then Press Lift Off to turn the eject air off. Y Type exit. Answer OK when prompted to confirm EXIT. Type exit to logoff the UNIX login.

5 APPENDIX: Navigating the Window: Y There are two regions at the top and bottom of each window that have buttons that are manipulated with the mouse. A. The buttons at the top of the window either perform a single function, or provide a drop down menu. For the drop down menus the left mouse button has to be held down while moving over the selections. B. The buttons at the bottom are arranged in 3 rows and 10 columns. It is nicknamed the chocolate bar (think Hershey s). Each button can contain one, two or three commands. The commands are assigned to the left, middle or right mouse button. If the field for a button has just a single command it is executed with the left mouse button, or if there are two commands they are assigned to the left and middle mouse buttons. 1 Toggles: Some buttons are toggles that switch between two states with a click. Sometimes the two states are separated by a slash, e.g. Hz/ppm. a. With almost all the buttons it is apparent which are one, two or three commands. One important exception is the button y-axis. Left Click toggles on or off the y-axis display. Additionally, Middle Click toggles y scaling between units of cm or an absolute relative intensity. For peak picking to work the units need to be set to cm. 2 Dragging: Most of the commands are executed by just clicking on the button with the appropriate mouse button. But some of the commands involve dragging the mouse while holding down the appropriate mouse button. b. Example 1: is used to change the vertical position of the spectrum. The Left and Right mouse clicks move the spectrum up or down. The Middle mouse button when held down will drag the spectrum up or down. c. Example 2: 8 8 s is used to change the vertical scaling of the spectrum. Left and Middle mouse clicks increase or decrease the scaling by a factor of 8. Dragging with the Right mouse button allows interactive scaling of the spectrum. Y Multi-Windowing: Many commands pop open an input window on top of the main window. While one of these input windows is open you cannot access the main window. You have to complete any needed input and Select an item, or Click SAVE, QUIT,or CANCEL to exit the input window before you can continue. It looks like a multi-tasking multi-windowing environment, but it is not a full-fledged implementation. FILES: Y Directory Structure: Files are stored in a set directory structure. These are the same directories setup with the edc command, used to create new files. Y The first directory level used by the UXNMR software is the disk unit (DU), which corresponds to the disk partition(s) of the Unix operating system. For this instrument always use x; but there are two choices: u or x. Y The second level is the user name (USER), i.e. your login name. Y The third level is the file name (NAME), usually some name that represents the compound or experiment. This can be up to 14 letters and/or numbers. Y The fourth level is the experiment number (EXPNO). This is normally set to 1, but can be any number greater than or equal to 1. The actual raw data is stored at this level as well as the acquisition parameters.

6 Y The fifth level is the process number (PROCNO). The processed spectrum is stored here with processing parameters, title, integer results, and peak picking results. Spectra processed with different parameters can be stored under different process numbers. Y These levels refer to the directories used by the nmr software to work with the data. The actual Unix operating system directory structure is similar, but not identical. An example Unix directory structure for an UXNMR software file is: /x/data/user/nmr/name/1/pdata/1 i.e. /DU/data/USER/nmr/NAME/EXPNO/pdata/PROCNO Y Accessing the files within the UXNMR software is most easily done with the Browse graphical interface. Y Click and hold Data, drag down to Browse >, then drag to the right and select from the menu disk - disk names user - user names name - data set names exp - experiment number proc - processing number Y After making the selection a list of items at that level will be displayed. Click on the item desired, and then a list of items at the next level will be displayed. A selection must be made at each level, even if there is only one item at a given level, until you reach the bottom of the directory structure. Y To reverse direction within the file structure Click BACK at the bottom of the list. Y Type search to start another, different style, graphical interface. Y If you know the name and experiment number of a file you can type re name expno procno to read in the file, assuming the current file has the same USER and DU (disk unit). PARAMETERS: Y Adjusting parameters: There are two modes to make parameter changes. Y From the command line, if you know the name of the parameter just type it. After ENTER the current value of the parameter is displayed. If no change is desired, just hit ENTER again. To enter a new value just type it, the previous value will be erased as you start to type. Y There are two ways to display a menu with in which to modify parameters. Y Click and hold Param, drag down to Data/Acqu/Proc >, then drag to the right and select eda to modify acquisition parameters, or edp to modify processing parameters. There are other edit menus for specific functions. Y Alternatively, just type eda or edp to start the menus. Y Navigating these menus is straightforward. To change a parameter 1.) move the mouse cursor over the value, a white background will highlight the value, 2.) click on the value 3.) type in the new value (the previous value will be erased as you start to type) 4.) hit ENTER. Y Some menus extend beyond the current screen and can be scrolled up or down. There is a scroll bar on the right side of the menu. The unshaded box on the scroll bar represents the portion of the menu displayed. You can scroll by 1.) clicking in the shaded area below or above the

7 unshaded box, 2.) dragging the unshaded box, or 3.) clicking on the arrows at the top and bottom of the scroll bar. Y There are a large number of edit menus. Here is a list of the most useful: Y edc current file name Y edasp change nucleus, turn on/off decoupler Y ased acquisition parameters specific to the current pulse sequence Y eda acquisition parameters Y edp processing parameters Y edo output plot device Y edg plot parameters Y Following is a list of the most common parameters. Values are not listed since there are no universal values. Y ns number of scans (transients). Y ds dummy scans (pulses at the beginning to establish a spin state equilibrium). Y d1 relaxation delay time. Y p1 pulse width of transmitter (units of µ seconds). Y rg receiver gain (normally adjusted with the command rga). Y swp spectral window in units of ppm. Y sw spectral window in units of Hz. Y td number of time domain data points collected for the FID. Y si number of data points (size) for the processed read spectrum. Y lb line broadening factor applied with exponential multiplication of FID. Y sfo1 spectrometer (transmitter) frequency, the sum of bf1 and o1. Y bf1 base frequency of transmitter nucleus. Y o1 frequency offset. HELP: Y To access help just Click Help. The message HELP : Please enter or click command will appear at the bottom of the screen. If you know the name of a parameter or command, try typing it. This gives results 50% of the time. Otherwise, Click Help, then click on the menu to select the item for which you want help. If it is a submenu under one of the pull down menus, hold the mouse button down until you reach the desired submenu. HANGUPS: Y Occasionally the system will hangup. Make certain the software isn t waiting for a response from you. This is a 1991 vintage computer, so allow for slower processing and response. But if you are certain the software has hungup on you, try typing Ctrl-\ (i.e. hold down the Control key and type the back slash \ key). This resets the graphics processor, where most hangups occur. Type y when prompted, to restart the display.

8 Version 1.0 Chris Kojiro 2003 The Regents of The University of Michigan NMR Staff: Chris Kojiro Chemistry 3500A