DISCLAIMER Brief IconNMR and Topspin 3.5 User Guide for Bruker NMR Spectrometers Avance IIIHD 400MHz NMR with Autosampler in Chemistry room 93 This document is intended to be a brief, bare-bones user s guide for NMR data collection using Bruker s IconNMR Automation software for the 400 MHz Avance-IIIHD Bruker NMR spectrometer located in Chem93 managed by the UC Davis NMR Facility. For detailed help with both routine and advanced NMR experiments, please consult Bruker s User Guides, which can be found within the Resources tab on our website, nmr.ucdavis.edu. CONVENSIONS Some user control will be done in Bruker s Topspin 3.5 interface. For Topspin interaction, keyboard input is shown as boldface type in this manual. Note that in TS the enter key must be used after the command is typed; this is assumed through-out this manual and enter key strokes are not given explicitly. Commands in TS are typed in on the TS command line near the bottom of the TS window; again this is assumed and will not generally be stated explicitly herein. LMB, MMB, and RMB are used to indicate actions of the left, middle, and right mouse button respectively. On a PC the mouse wheel acts as the MMB. Click, and double click refer to pressing the LMB. GENERAL PROCEDURE You will find that the general procedure for acquiring NMR data on all NMR spectrometers is essentially the same. IconNMR handles the majority of the tasks listed below. The general procedure is as follows: 1 Sample Preparation 2 Login and Startup 3 Setup Initial Parameters 4 Check/Edit Acquisition parameters 5 Insert Sample 6 Lock onto Solvent 7 Tune the Probe 8 Shim 9 Check Receiver Gain 10 Acquire 11 Process Data 12 Remove Sample 13 Logout, Sign Logbook
Experiment: Parameter Set: Instrument: Routine Proton NMR PROTON Chem Bruker 400 using IconNMR Sample Preparation 1. Dissolve your sample in an appropriate deuterated NMR solvent. Make sure there is no un-dissolved material. If there is, you will need to either centrifuge or filter your sample to remove crystals/debris. TIP: use a small amount of KimWipe in a Pasteur Pipette to quickly filter out any undissolved material 2. Transfer about 550-600 ul of solvent into a clean NMR tube. We recommend high-quality NMR tubes - rated 600 MHz or higher, but economy tubes will be OK for routine work at lower fields (400 MHz and below). Your sample height should be about 4-5 cm. Login and Startup 1. Log into your iconnmr user account. If a previous user is currently logged in, you will need to select Change User, then log into your account. NOTE: If your IconNMR account has not yet been created, please reach out to Bennett Addison: jbaddison@ucdavis.edu
Set Initial Parameters 1. Identify an empty holder in the BACS120 autosampler. We strongly recommend you use the holders in the inner ring: holders 1-60. 2. Place your sample into an available blue spinner, set depth using the depth gauge, and drop your sample off in the appropriate holder. Do NOT drop off your sample while the carousel or sample-arm is moving. Use inner ring: Inner ring is the lower numbers, outer ring higher numbers 3. Identify the matching holder in IconNMR menu and double-click to add an experiment. 4. Enter your details: Data Directory, Experiment Name, Experiment Number, Solvent, Experiment/Parameter Set. Experiment Number. The default is increments of 10 (10, 20, 30 ) for each sample/holder, or increments of 1 (10, 11, 12 ) if you are collecting multiple experiments on the same sample/holder. Experiment: Select your experiment from the dropdown list. If there is an experiment you would like to run but it is not on the list, contact Bennett. Directory: Your directory should be based on your PI. It is set automatically when you log in. Experiment Name. Users often include initials, lab notebook page, date, and any additional info if desired. Note do not use spaces, special characters, etc. Solvent: Select your solvent from the drop-down menu
Check/Edit Acquisition Parameters 1. If desired, hit the equals button to edit standard Proton acquisition parameters including number of scans, spectral width, acquisition time, offset frequency, etc. Note: The default acquisition parameters are good, but feel free to change them as desired. If you would like to change any other parameters not accessible in this list, you can select Parameters Edit All, which brings you to Topspin. You may need to do this for some 2D experiments. 2. Edit the title if desired. You can add any sample/experiment description in this text box. You may find it useful later for your bookkeeping. 3. Edit the Start Time if desired. The clock is set to 24 hr time. Note, if you set a start time between the hours of 8pm 8am (night-time queue), please make a reservation on the online scheduler. 11 pm Start Time 4. If you would like to also collect another experiment on this sample (e,g, C13CPD), you can highlight the current experiment and then hit the Add button. Another experiment will appear below with experiment number 11 and an empty experiment type. Select the appropriate experiment and edit acquisition parameters if necessary. Details are provided in later pages. Note: This is red only because a parameter (ns) has been changed
Submit your Experiment 1. When you are satisfied with all experiments and are ready to collect your data, highlight the appropriate experiment or holder directory, and hit the Submit icon. AUTOMATION PROCESSES: After hitting Submit, the autosampler will take over. The automation software will handle the following processes: Insert Sample, Tune the Probe, Lock onto Solvent, Shim, Check Receiver Gain, Acquire Data, Process Data, Remove Sample, Backup Data to Google Drive. Current Process If Flashing: in Progress If Green: Completed If Clear: Skipped or Not Completed
Data Processing 1. To look at your spectra, simply double-click on your completed experiment in the Preceding Experiments list. If data acquisition and processing is complete, you will see a checkmark under Acq and Proc by your experiment. When you double click, you will be sent to Topspin for spectral viewing. Identify your completed experiment and double-click. The list is ordered chronologically. Spectral Processing Commands and Tips: 1. Navigate to the Process tab, and hit Proc. Spectrum button. This will perform Fourier transform (efp), autophase your data (apk), and perform an automatic baseline correction (abs). 2. Click and drag to zoom in 3. Double-click or hit the Full View button to zoom out. 4. Use middle mouse scroll wheel to zoom up and down 5. Click and hold the Hand icon to shift the baseline up or down or side to side 6. Return to IconNMR when done processing / viewing spectrum
Logout Procedure: 1. When the autosampler has returned your sample to the holder, you can remove your sample and spinner. Caution: do NOT remove your sample while the carousel is moving, and do NOT reach across the center where the sensor is located. This is especially problematic when there is a sample currently in the magnet. Tripping the sensor with your hand may result in shutdown of the autosampler. If this happens, be sure to call Bennett or an NMR TA. 2. When you are done and no longer using your chosen holder, return to IconNMR, select your completed holder, and hit Delete. The holder should become available. 3. Sign the log book, including Date, Name/PI, Nucleus, Drop-Off Time, Pickup Time, and check if you have deleted your completed run in IconNMR.