PART 1A – Orientation, Safety, & Success
(~2 hrs)

Introductions

• Trainees and the facility manager introduce themselves to one another, discussing prior NMR experience
• Identification of research aims

Orientation

• Identification of all spectrometers and their lab locations, discussion of each instrument’s functions and top-level capabilities
• Mention of the EPR spectrometer, query for interest
• Identification of the support lab in Searle, equipped with fume hood, bench, sink, and eyewash station, enabling titrations and reaction initiation for kinetics studies

Safety

• Identification of exits, fire extinguishers, safety contact information posters, first aid kits, cleaning/spill supplies
• Review of PPE requirements (labcoats prohibited, safety glasses optional, gloves optional but only fresh)
• Lab-specific chemical safety
  • Response procedures for broken samples, including reporting procedure (send text or email to facility manager)
  • Requirement for use of secondary container for transporting samples
  • Introduction to the community craft table with safety flasks and decoration supplies
• Magnet safety – Cryogens (frostbite and suffocation hazards, quench identification and response, hazards of weekly nitrogen fills)
• Magnet safety – Magnetic field
  • Discussion of problematic/safe metals, risks of various medical devices/implants
  • Identification of 5-gauss radius safety limit and its significance
  • Caution about variability of 5-gauss radii in other facilities
• Identification of major spectrometer components (magnet, autosampler and components, console, computer, probe)
  • Special attention and procedures for handling samples broke in the carousel or magnet
  • Advice on when to press the emergency stop button on the autosampler
  • Discussion of when and how to report instrument problems and work with the manager to resolve them
  • Clear distinction between the console and computer buttons in case power cycling of one is required; clear identification of the “Do not ever touch this” cover on the magnet

Success with Sample Preparation

• Discussion of probe geometry and alignment of sample using sample depth gauge
  • Proper use of the depth gauge, proper handling of the spinner, and cleaning the sample
  • Importance of filling detection region with sample
  • Importance of excess material (0.6 mL); contrast with UV/Vis requirement; discussion of magnetic susceptibility
  • Hands-on practice inserting and aligning a normal sample
  • Hands-on practice realigning a sample with small volume
  • Tactile evaluation of spinner grip strength, then contrast with a too-loose spinner-sample interaction
    • Cautionary tale: the $10K+downtime consequences of a tube that is too loose
  • Discussion of suspended particles resulting in broad lines; relationship to magnetic susceptibility
• NMR tube selection (economy vs precision glass, MHz ratings); economics factors deciding whether to reuse NMR tubes
• Procedure for cleaning and drying NMR tubes, including Wilmad oven-drying guidelines
• Discussion of when to discard NMR tubes (scratched, chipped, bent, too narrow, too contaminated)
• Discussion of NMR tube CAP quality and economics
• Best practices for sample labeling
  • At least include initials
  • Acceptable: Sharpie on cap, Sharpie on upper part of tube, Lab tape securely wrapped around upper part of tube, Paint pen on cap
  • Unacceptable: Paint pen on tube, Sharpie or paint pen where it would contact the spinner
• NMR tube length requirements (< 8.75″ / 222 mm); cautionary discussion about bumping the red safety lever on the autosampler
  • J. Young tubes OK if they fit the length requirement
  • Regular tube sealed with electrical tape over cap often OK

Sample Management

• Never take samples that do not belong to you out of the lab. You may take your own samples at any time
• OK to move others’ samples from carousel to TOP SHELF racks next to magnet, ONLY IF the sample’s experiments are ALL marked “finished” in Icon software.
• CYCLE: Every week, the racks on the top shelf get moved down to the bottom shelf. Then the samples from the bottom shelf (which had been there for a week and some days on the top shelf) are considered ABANDONED and moved to the “TAKE ME” beaker.
• All samples in the TAKE ME beaker may be taken by any user who agrees to dispose of the contents properly.

Part 1B: Submitting samples
(~30 min)

• Orientation to the ICON-NMR interface in Bruker’s Topspin software
  • Login panel, importance of logging in, use of the “Next User” button
  • Upper part: For sample submission, able to delete entries
  • Lower part: Completed Samples, like a log
• Viewing completed spectra
  • Double-clicking on a completed spectrum in lower part of ICON – intended just for a quick check
  • DO NOT ANALYZE spectra on the spectrometer computer; permissions disabled for phasing, pick peaking, integrating
  • CAUTION: Do not close the Topspin window after viewing a spectrum! This shuts down all data acquisition.

Sample Submission columns, actions, best practices:

• “Holder” column: designates sample position in carousel
• “Status” column: Available, Finished, Queued, Running, Failed, AutoCalibrate
  • Use any “Available” position
  • Any sample with ALL experiments “Finished” may be converted to Available with the Delete button
  • Failed samples cannot be deleted, except by the admin. Their owners may return and fix whatever problem arose and try again.
  • Position #60, “AutoCalibrate”. is RESERVED for the admin and cannot be used by researchers. It is used for automatic weekly reshimming and performance checks.
  • Hands-on introduction to the AutoCalibrate sample, which MUST STAY IN THE CAROUSEL. It is in a unique orange spinner labeled “DO NOT MOVE”, is permanently sealed, bears a bar code, and the tube is glued to the orange spinner. Don’t touch it!
• “Name” and “Number”: Sample name and Spectrum number are described
  • File location location is identified, and Data structure is discussed: Freely-named sample folder with each spectrum assigned a numerically-named subfolder.
  • Best practices on sample naming, advocating adoption of a convention that will preserve order in a single folder containing hundreds or thousands of sample names. Recommended:
    • <initials><lab notebook number>-<page number>-<A/B/C…, 1/2/3…, or other identifiers>
    • <initials>YYMMDD_<A/B/C…, 1/2/3…, or other identifiers>
  • Default experiments number = 10. Can be changed if desired. Incremented automatically when experiments added to the sample.
• “Solvent” – Pull-down menu to select solvent
  • Default = CDCl3
  • Must choose a solvent in the list. If using a mixed solvent not in the list, choose the one with more deuterium
  • “No-D” deuterium-free samples are supported, but the user must choose either the protiated version of the solvent (e.g. C6H6 instead of C6D6) or “None”. Choosing “None” will provide a spectrum with unoptimized lineshape and requires manual referencing.
  • The facility manager welcomes new solvents to be added to the list, but the user must provide a sample of that solvent for calibration.
• “Experiment” – Pull-down menu to select experiment(s)
  • Default = PROTON8
  • Most common experiments at top of list: PROTON8, PROTON1, PARAMAG-1H, CARBON, CARBON-3.5hr
  • Discussion of PROTON8 experiment. 8 scans, 30 deg excitation in vector model, 36 sec total acquisition. Decent S/N and integral accuracy for typical sample (~5 mg of 150 MW material).
  • Contrast with PROTON1: 1 scan w/ 17 second relaxation delay D1, 90 deg excitation. Great for accurate integrals, plenty of S/N in one scan.
  • Discussion of relationship between S/N improvement and NS, number of scans.
  • Identification of the “=” button, which enables changing of parameter values. Discussion of meaning of NS, D1, O1P, SW, and AQ
  • Identification of the “Title” button, which enables addition of a meaningful comment/title to each spectrum, e.g. “1H 1D”, “13C 1D”
  • Adding an experiment, noting change in experiment number
  • Distinction between CARBON and CARBON-3.5hr: only parameter difference is NS, but longer one is nighttime-only
  • Discussion of usage rules, Day Queue / Night Queue, per-sample time limits, per-day & per-night time limits. Spelled out here:
    https://chemnmrlab.uchicago.edu/policies/#signup_rules
  • Identification of the Day/Night queue toggle button
  • Setup of common “SW-optimized” 2D experiments (COSY-opt, HSQC-opt, HMBC-opt, etc.). Requirement of PROTON8 experiment and pitfalls that cause failure. Identification of equivalent non-optimized “-manual” experiments in list.
  • Identification of heteronuclear experiments and nomenclature, e.g. difference between PHOSPHORUS and PHOSPHORUS_noHdec. See instrument pages for their available nuclei. https://chemnmrlab.uchicago.edu/instruments/
  • Identification of 1H-15N HSQC, HMBC
  • Identification of WATER experiment for automated solvent suppression of 90/10 H2O/D2O samples
  • Identification of PROTON_T1 experiment (and FLUORINE_T1 and PHOSPHORUS_T1 on 400-2). Discussion of the importance of measuring T1 for accurate quantitation. Tragedy avoidance: no one wants a situation where a manuscript reviewer asks whether quantitative conclusions are justified by 1H NMR integrations, and it turns out the D1+AQ settings were not long enough to provide high-quality integration.
• Assessing total experiment time. Discussion of extra steps in data acquisition that take time (sample changing, tuning, locking, shimming without going into detail about what those processes are). Identification of the current “Day” and “Night” queue totals and the more informative “Busy Until” time. Also identification of “Current” sample identifier.
• Clicking “Submit” to add experiments to the queue.
• Clicking “Cancel” and “Edit” to remove experiments from the queue and resubmit.
• Discussion of the “Copy” function.
• Importance of logging out by clicking “Next User” button. Avoids next user submitting samples in your account.

Queue Management – For Problem Recovery Only

• Build awareness of Start and Stop queue-control buttons.
• Only use when troubleshooting a stopped queue and in conversation with the facility manager. Not for ordinary use.
• Ignore the top row of software menu buttons. Those are admin-only.