The Liquids NMR facility is part of the Division of Chemistry and Chemical Engineering (CCE), and located in the Crellin sub-basement, Room B250. It is an open access facility used by researchers in CCE, as well as other divisions at Caltech, JPL, and some outside users. Below is a summary of the instruments in our facility; contact us for more information about our capabilities and how our lab can be accessed. Other magnetic resonance core facilities in CCE include the Solid State NMR Facility and the EPR Facility.
In order to comply with division guidelines for safely reopening facilities, please observe the updated instructions on how to access the Liquids NMR facility.
Initial access will be contactless where researchers drop off their NMR samples already loaded in capped sample tubes at a receiving station just inside the front door of Crellin Hall. Either David Vander Velde or one of the laboratory GLA's will pick them up from there, take them down to the lab, disinfect the samples, and load the majority of them into one of five automated instruments equipped with autosampler robots. A small fraction of the samples are likely to require manual spectrometer operation. After completion of experiments, lab personnel will return the sample tubes to the dropoff location for researchers to reclaim. Researchers are already accustomed to retrieving their raw data and opening it on their own computers using the site licensed MestReNova software. Additionally, lab personnel will be using some enhanced remote access software tools. As the instrument completes each new analysis, the researcher will be emailed a PDF plot of the results. Staff will also use a web browser based interface to the facility's two Bruker spectrometers to allow remote addition, editing, or deletion of experiments for samples already in the sample changer.
Technical details are outlined in an nmrusers listserv message sent June 5. Contact Dr. Vander Velde if you didn't receive this message.
Dr. David Vander Velde (email@example.com), Manager
Each spectrometer has a graduate laboratory assistant (GLA) who is responsible for user training and basic troubleshooting. The current GLA's are listed on the Instruments page.
NMR Facility Instrumentation Information
Webcal signup - reserve time for manually operated instruments in facility
See Dave for training on hg2. No desk phone at Hg2; call Hg3 Ext. 8602
Schedule: 24 hours/day - 30 minutes Weekend Schedule: n/a
FY2019 Internal Hourly rate: $12.36
300 MHz, 50 position SMS Autosampler
GLA: Nick Fastuca (firstname.lastname@example.org) Ext. 6061
Desk phone at Hg3: Ext. 8602
Schedule: Monday to Friday 8 AM - 10 PM, 30 minutes; Monday to Thursday 10 PM - 8 AM, 4 hours;
Friday 10 PM - 8 AM Monday, 8 hours
Signup required only for experiments more than 2 hours long.
FY2019 Internal Hourly rate: $15.45
400 MHz, VT (-80 - +130), multinuclear autotune, 12 position 7510 autosampler
See Dave for training on siena. Desk phone at Siena: Ext. 3014
Schedule: M-F 8 AM - 5 PM, 30 minutes; 5 PM - 8 AM unlimited
Weekend Schedule: 8 AM - 4 PM, 2 hours (sign up after 4 PM previous day); 4 PM - 8 AM, unlimited
FY2019 Internal Hourly rate: $17.51
400 MHz, multinuclear iProbe, 1H/19F, 31P-109Ag, VT (-150 - +150, 24 position sample changer).
See Dave for training on verona. Desk phone at verona: Ext. 8601
Schedule: Alternate days in automation mode and in manual mode. In automation mode, experiment limits set through ICON-NMR software. In manual mode, 24 hours, sign up less than 72 hours in advance, longer times available upon request.
FY2019 Internal Hourly rate: $18.54
600 MHz, VT, inverse probes (i.e. higher proton sensitivity)
5 mm Penta PFG probe (H,C,P,N,D) is default, VT range -20 - +80
5 mm HCN Triax probe (backup only), VT range 0 - +50
3 mm inverse broadband PFG probe, VT range -20 - +80
See Dave for training on fid. Desk phone at FID: Ext. 8601
Schedule: 48 hours, sign up less than 72 hours in advance; longer times available upon request.
Weekend Schedule: same
FY2019 Internal Hourly rate: $22.66
400 MHz, 60 position SampleXpress sample changer, cryoprobe (i.e. higher sensitivity)
5 mm Prodigy cryoprobe (H/multinuclear from 31P to 15N) is default, VT range 0 - +80
5 mm SMART probe(H, F/multinuclear from 31P to 103Rh), VT range -150 - +150
GLA: David Schuman (email@example.com) Ext. 4047
Schedule: Day queue, 9 am - 9 pm daily, 46 minute maximum per experiment, 2.5 hours maximum per person. Night queue, 9 pm - 9 am, no limits.
You only need to sign up for the night queue, to verify the instrument is not overbooked. The samples will be run in the order they are submitted to the queue, not necessarily the order shown on the webcal schedule. If you are worried about the stability of a sample, you do not have to put it in the sample changer at the time of submission; you can wait until just before the time the sample will run.
FY2019 Internal Hourly rate: $24.72
FY2019 NMR Facility Rates
About the NMR facility
The lab is open for visits or tours from the main door up to the yellow line in the floor tile. Past that line, there are areas around each NMR magnet where the stray magnetic field exceeds 5 gauss. These areas are marked on the floor with red and white striped tape. The high magnetic field areas should only be entered by authorized instrument users who have completed new user safety training (see below), and do not have cardiac pacemakers or other risk factors. Authorized users should not bring visitors with them inside any marked 5 gauss line.
Instrument users should receive training from a GLA before running any of the instruments. As part of the training, you will receive and complete a form acknowledging your understanding of the lab safety rules, and entering the PTA (Caltech internal accounting number) to which your NMR bills will be charged. The PTA will normally begin with your advisor's initials. The "PTA alias" which is a letter P followed by a 5-6 numbers is not valid. Return this completed form to the GLA or to Dave before using the instrument for the first time. If your PTA number changes, inform Dave what the new number is.
To request new user training, sign up on the white board just inside the NMR lab main door. You will also find a list of any currently scheduled training sessions there, and GLA contact information. If there isn't a training session already scheduled for the instrument you are interested in, the GLA should contact you to schedule one. We ask that users sign up for training on only one instrument at a time; otherwise, it can become very unclear what the sequence of training sessions is going to be. Also, we have found that new users progress faster if they get trained on one instrument, then practice until they gain competence before moving on to another instrument. There is one training for the automated instruments indy and fid--at the conclusion, you will get user accounts on both instruments.
At the time you sign up for your first training session, subscribe to the NMR users mailing list. This mailing list is how we inform users about instruments that are down, when they come back up, new software, lab policy changes, etc. You can subscribe here:
Each instrument has a specific signup/reservation/acceptable use policy. Those are summarized on the Instruments page, and the GLA will cover them during your training session. Instrument scheduling is done as needed on a Webcal schedule, for instance this one for siena (the others are analogous):
The instruments which should be scheduled on webcal at all times are fid, siena, and hg2. Verona should be scheduled on webcal on the days when it is in manual mode, or for the night queue. The automated instruments hg3, indy, florence, and verona on automation days are run under automation software and maintain their own first come, first served schedules. We only use the webcal schedules on those three instruments during the night queue, in order to make sure that the night queues do not get overbooked. During the day, do not sign up on webcal for those instruments. Webcal does not enforce any scheduling rules when reservations are made. The instrument automation software will enforce some, but not all, of the signup rules. Knowing and adhering to the signup rules is the responsibility of the user.
Each instrument has a written log book, where you should enter your initials and your advisor's initials, lab phone extension, starting and ending time, nuclei and solvent, and any problems you encountered.
If you have a problem with an instrument, and it is during business hours, attempt to contact Dave first and then the instrument GLA. After hours, you may call or look for the instrument GLA in their lab, but if you cannot reach them, send an email or text to them (also copy Dave on the email). The GLA's are not on call 24/7. If the problem means that the instrument is not usable, leave a note on the workstation saying the instrument is down. Exercise some judgment when you plan your experiments--e.g. if you will be attempting an experiment you have little familiarity with, don't do it in the middle of the night when it is very unlikely you can get any help.
We have a site license for the MestReNova NMR software, and encourage all lab users to install it on their own computers and become familiar with it. The principal way you can retrieve your data to process it or back it up on your own computer is through Windows read-only network drives, which also work with Apple software. Many users get their data from a global shared drive, although if you prefer, you can choose to exclude your data from this drive and have an individual password protected drive containing just your data. The drives are only accessible through the Caltech on campus network or VPN. In any case, we strongly recommend you make your own frequent backups of your important files, although we do back up all new data nightly to a central server, which is in turn doing a cloud backup.
NMR Facility FAQ's
The NMR Lab may have up to 3 copies of spectra that you save:
- On the host workstation of the spectrometer where it was originally acquired. Any data you save is immediately accessible on the network drive from that spectrometer (e.g. \\indy.caltech.edu\nmrdata)
- On our main lab server, mangia. Newly created data is copied from each spectrometer to mangia overnight. Consequently, data acquired today will not be visible on mangia until tomorrow.
- On the cloud backup made from mangia. It may take a few days for new spectra to get copied to the cloud backup.
See the page on retrieving data for instructions on accessing the network drives on the spectrometer hosts and on mangia. Individual users do not have access to the cloud backup.
The data you save on the spectrometer workstation will be there until one of two things happens:
- You leave Caltech and your account on the workstation is deleted.
- The computer breaks. The commonest cause of this is hard drive failure. Typical hard drives last 2-3 years in computers that are on all the time. We have a dozen or so computers in the lab, so hard drive failures occur multiple times per year. After a hard drive failure, we reload VnmrJ on a new drive, but not the old data. You can retrieve the old data from the mangia server.
The archives on mangia go back to 2007-2008 and we plan to maintain them indefinitely--we never purposely delete archived data from mangia. A small number of spectra may be missing from mangia. For instance, if a hard drive fails in the middle of the day, spectra acquired since the last overnight backup won't get copied to the server.
We strongly recommend that you make regular and frequent backups of all your research data and have multiple copies that you can access yourself. You might, for example, copy all your data weekly to your laptop and have automatic cloud backup software running on it. In the event of a major earthquake, the mangia server could be offline for an extended period; you might also lose access to your computer. But if you can access your research data, you might be able to work on writing papers or your thesis if you don't have a lab to work in.
For 1D spectra, it is almost always advantageous to use some exponential multiplication, aka line broadening. This means you are multiplying the raw data (the free induction decay, or fid) by a decaying exponential function. Since the fid is a decaying exponential (or sum of multiple decaying exponentials) to begin with, this does not change its basic shape. However, it can meaningfully improve the signal to noise of the processed spectrum. The front of the fid is dominated by signal, whereas the tail should be mostly noise (assuming the acquisition time is well matched to the expected linewidth of the peaks in your spectrum). The decaying exponential will have little effect on the front of the fid, but will truncate the noise present in the tail of the fid. We normally specify the decay rate of the decaying exponential by the amount it will add to the apparent linewidth of the peaks in the transformed spectrum, thus its common name "line broading."
The most effective signal to noise reduction will be obtained if the line broadening applied is equal to the natural linewidth of the peak. Of course, in a multiline spectrum, each peak can have a unique width. An easy way to find out the average linewidth of your spectrum is to open the Processing -> Apodization window in MestReNova (you may find the shortcut "w" helpful). The average value is given at the top of the apodization window. For 1H decoupled carbon spectra, or other spectra with little in the way of J-coupled fine structure, setting the line broadening to this value has little down side. However, for proton NMR, this value may make J-coupled multiplets less well resolved, and it may be better to take less noise reduction so as to preserve the multiplet structure. In MestReNova, it is easy to watch what happens as you change the amount of line broadening if you have the "Interactive" button checked in the apodization window. With a 3 button wheel mouse, roll the wheel up and down to change the line broadening, and watch what happens. A value of 0.2-0.3 Hz is typical for 1H spectra. Sometimes, broad carbon peaks (for instance quaternary aromatic carbons alpha to a nitrogen atom) will be nearly inobservable with the default line broadening of 0.5-1 Hz, but become easy to see with 5-10 Hz.
For 2D spectra, there will be an apodization function for each axis. It matters a lot whether the 2D data has been acquired in phase sensitive or magnitude mode. In phase sensitive mode, the spectrum can and should be phased so that peaks are purely up or purely down. 2D fid's are normally acquired in a very truncated form compared with 1D spectra, to keep 2D data files from being unreasonably large. The apodization should be chosen to make sure the truncated fid is smoothly tailed down to zero at the end to avoid severe truncation artifacts ("sinc wiggles") in the transformed spectra. A cosine squared function (or sine squared with a 90 degree phase shift) is a safe choice which should give an artifact free transform. Some people may prefer to give a moderate amount of resolution enhancement to a phase sensitive 2D spectrum by use of some gaussian function, linear prediction, or both. It may be a good idea to compare the effects of those apodization schemes with the cosine squared function to make sure you are not overdoing it with resolution enhancement. For magnitude mode 2D spectra, phasing is not possible because the lineshape will have a mixed absorption/dispersion character. To work around the problems this would cause, a magnitude calculation is performed by squaring the spectrum and then taking the positive square root. This solves the phasing problem, but in turn leads to loss of resolution. To work around that, a strong resolution enhancing apodization function is used. A typical choice would be a sine bell (half sine wave) function with a zero degree phase shift. This function zeroes out the beginning and the end of the fid, but enhances the middle section.
Most 2D spectra are either phase sensitive in both dimensions or magnitude mode in both dimensions. An exception is an HMBC, which is advantageously acquired as magnitude mode in the 1H direction (because phase sensitive is not possible there) and phase sensitive in the X nucleus direction. This gives much sharper, better resolved peaks along the X direction. However, your apodization and processing parameters should match the way the spectrum was acquired.
Varian 5 mm probes will most reliably shim to spec with about 700 microliters of solvent. Bruker 5 mm probes may do so with somewhat less, 550 microliters or so. If you have a limited amount of compound to work with, adding this much solvent may produce a dilute solution. Using less than the recommended amount of solvent will produce a more concentrated solution, but one that will require more effort to shim, and will not shim as well. If possible, the best option for using a reduced amount of solvent is to use a Shigemi tube. These can be filled with 275-300 microliters of solvent and still give good resolution. Shigemi tubes can be purchased for water/D2O, chloroform, methanol, and DMSO. If you decide to use a smaller volume in a regular NMR tube, carefully center the liquid in the tube around the center of the NMR probe. The center line in the probe is marked in each sample depth gauge. Even if the sample is well centered, a short sample will mean some compromise on the peak width or shape in the spectrum, and the shorter the sample is, the worse the spectrum will look even when it is optimized.
NMR Facility Documents
Training Documents (Note: Training documents are not a substitute for training by Facility staff or GLAs when using a new instrument!)
VnmrJ on the manual instruments siena and hg2
Florence - Bruker 400 with Prodigy cryoprobe
Automated 500 MHz NMR (Indy) and 300 (Hg3)
Daytona, manual 500 MHz NMR
Troubleshooting hints for the Inova and Mercury systems
"No-D" NMR (no deuterated solvent)
Quick deuterium NMR
Notes on chemical shift referencing methods
Notes on doing variable temperature experiments
Data Retrieval and Analysis
Using Caltech's MestReNova site license
Retrieving current data from the spectrometers and archived data from the server
How to get the highest sensitivity and best shimming on your sample
Text lists of archived spectra
Acknowledging federal grants to the Caltech NMR Facility