Guide for the Bruker AV-III 400 MHz NMR Spectrometer using ICON NMR in Automation

Transcription

1 Guide for the Bruker AV-III 400 MHz NMR Spectrometer using ICON NMR in Automation Yun Qu, 08/08/2015 Before You Start: Your NMR tube must be at least 7 inches in length and must have a top that is neither broken nor cracked. If your tube is shorter than 7 inches, it will not be grabbed fully by the sample changer and may fall and break on the floor or on the top of the magnet. Tubes with chipped tops are weakened and may be broken by the sample pincers which grab the tube very firmly close to the top. Any tube shorter than 7 inches or with a chipped top is not allowed. Your NMR tube must not have any label (paper, tape, sticker etc...) attached to it. This will stop the sample pincher from working properly and may result in sample breakage and equipment damage. Tubes can be labeled on the glass or the cap with permanent marker. Any tube with an attached label submitted to the sample changer is not allowed. Sample tubes with screw caps or vacuum valves will not be handled by the sample changer. They will cause equipment damage. Approximate amount of middle-size compound (MW ~ 500) advisable for running following experiments: 1H NMR experiment - about 3-5 mg 31P NMR experiment - about 3-5 mg 13C NMR short run experiment - about mg 13C NMR long run experiment - about 6-10 mg ml of NMR solvent is appropriate for the right solvent level in NMR tube. Unsuitable solvent level can lead to a bad shimming result and horrible looking spectrum. Never lean or exert any force on the sample changer or magnet. This may cause a magnet quench resulting in many weeks of down time and hundreds of thousands of $$ being spent. Users are asked to report improper sample tubes to the NMR Facility staff immediately in order to avoid needless down time and equipment damage! Improper sample tubes are: sample tubes shorter than 7 inches sample tubes with chipped tops sample tubes with screw caps or vacuum valves sample tubes with attached labels sample tubes with inaccurate outer diameter, which does not fit perfectly the plastic spinner hole. The 400 NMR uses the Sample Xpress Automatic Sample Changer, and it is extremely important that you pay attention to the holder number containing your sample, and to only remove your samples from your holder number, from the sample rack. It is possible that someone might have samples in the rack with longer experiments submitted in the Night Queue. You must be sure to not disturb samples left by other users. Labeling your NMR tubes (on the glass or the cap with permanent marker.) is STRONGLY recommended. 1

2 Start: 1. Log-In to your User Account your User Name (PI) then enter password. After logging in to Work Station, click on the TopSpin icon 2. Start ICON NMR Type icona in the command line, then enter The IconNMR: Identify User pop up, click on ok Then IconNMR Password pop up, type in your account password, enter 3. Setup Experiment 1). Wipe-off your NMR tube with kimwipes (1), so that it is CLEAN. Take a Blue Sample spinner from the spinner box, and Insert your sample tube in the spinner (2). Set the sample depth using Bruker depth gauge (3). 2

3 2). Place your sample/samples in the holder position/positions carefully. Then, you are now ready to setup your experiment/experiments. Get to know the Icons Sample Holder position Data In your home File name Experiment # Double- sample holder # to setup experiment Select solvent Select experiment change parameter Type remark Double- sample holder # to add more experiments, Edit, Delete experiment Or highlight the # line, then click Submit, Cancel, Edit Click OK after changes Type in title, remark Then Click Set Title 3

4 3). Double-Click in the row of Holder #. The row will open up a. the Solvent Box, and a pull-down menu will appear, then select your solvent from the pulldown Menu. b. the Experiment Box, and a pull-down menu will appear, then select the experiment from the pulldown Menu. c. You can change basic parameters by clicking on the icon: this will bring up a dialog box in which you can change basic parameters: NS is the number of scans; D1 is the relaxation delay SW is the spectral width in PPM; O1P is the center of the spectrum If you want to change a parameter, click in the box, and enter the new value, then click [OK]. (If you change any parameter from the default, the icon will change to, this is normal) d. Click the box you will see the dialog box for you to add a Title or remark, then Click [Set Title] when everything is entered. e. Double-Check that everything in the row is correct, confirm that your sample is properly placed in the correctly numbered holder in the sample-change. For the first sample, click the, then the Start / Start button, The status indicator will turn green. Once green, it will insert your sample, tune the probe, lock on your solvent, shim, and proceed with your experiment. f. Add another experiment for the same sample: Select the row containing a previously defined experiment, and click the Add button. You may Submit the next experiment as soon as all of the information has been entered. The status indicator will turn yellow if other experiments are already running, or green if nothing is running ahead. lights no experiment Yellow light experiment in queue Red light experiment completed Green light expeiment in progress 4

5 4. Finish. After your samples are done, wait until the eject air turns off, removing your sample from the rack. Removing your sample too soon may crash the system. 5. Data Processing 1). the Start in the TopSpin Menu bar, then click on Open Dataset, your dir/files will appear select dir/file which you want to process, then click on Open 2). the Process in the TopSpin Menu bar, then click on Proc. Spectrum 3). Phase Correction. The simplest procedure is automatic phase correction which is implemented using the command apk. Or Adjust Phase for manual phase 5

6 4). Optimizing the Spectral width. To display a specific region of your spectrum hold the left mouse key and drag your mouse over the region of interest. If you want an exact chemical shift range, click on the Exact Zoom tab and specify the range you wish to display. For example, to display the region of the spectral window from 9 to -1 ppm, put 9 and -1 in the From and To fields, then click OK. 5). Manual Integration. Process, then Integrate. 6

7 Make sure the Define new peak picking range button is highlighted. Set the cursor line, starting at the left of the spectrum, to the left of the first peak to be integrated, click the left mouse button and drag the cursor line to the right of the peak, then release the mouse repeat this process to integrate all peaks of interest. to save the integration regions For set integral reference: a. Place the cursor within the integral label peak you wish to calibrate and press the right mouse button. b. Select calibrate Current Integral. c. Enter the desired value of the selected integral, then OK. d. the floppy disk icon to save the integrals. 7

8 6). Peak Picking. Peak picking can be performed interactively in the peak picking mode. A. Process, then Peak Pick button in the TopSpin Menu bar. B. Make sure the Define new peak picking range button is highlighted. C. Press and hold the left mouse button over the peaks of interest. A green highlight will form. D. Release the left mouse button. E. the floppy disk icon to save the peak pick. For set peak reference: a. Click Calib. Axis. b. Click the peak you wish to reference. c. Enter the desired chemical shift of the peak, then click OK.. d. the floppy disk icon to save the integrals. 6. Plotting To Plot, or Print your spectra, enter the command prnt. This will automatically print your spectra as displayed (what you see is what you get). You may also use the commands below if you want to change the look of your plot. plot : will start the Plot Editor, the interactive program for viewing or designing plot layouts. autoplot : will plot data according to Plot Editor layout (1D,2D), with the current limits and scaling. 7. Logout 1). Click Stop / yes then click File / Close AII to logout Icon NMR. 2). Click 3). Click Then click Then logout your account And 8