NMR

NMR

[[file:|frameless]]
Owner/Loaner	Pending
Make/Model	Varian EM-360A
Arrival Date	11/4/21
Usability	Yes
Contact	Pending
Where	1st Floor. Corner of lounge.
Authorization Needed	yes
Hackable	No
Estimated Value	$-999.00
Host Area	Science

Background

Er, what?

Yes. There are many, many types of spectroscopy. This ones involves magnets and radio frequencies, and can (potentially) tell you things about a liquid which is placed into a thin/tall glass tube. The principle under which it operates is the same as an MRI scanner; however, rather than making pictures, it makes squiggly lines. It is not a Gas Chromatograph, nor a Mass Spec, as a few have called it...

Unlike some other techniques which allow for elements to be looked at (ICP-MS, ICP-OES, XRF, etc.), this one is concerned with compounds and most commonly with Hydrogen or Carbon. It can be used to determine the structure of a compound and so lends itself to organic compounds. Only certain elements (or more accurately, certain isotopes of those elements) are NMR Active (meaning, in essence, they will behave like magnets), and it is through putting those into resonance that we can learn more about how they exist within a sample. The technique can be used to identify what something is, and also to quantify how much of various parts are present.

But Why?

• Because makerspace.
• Because when life calls and lets you know you can have a 600lb magnet, naturally, you say yes.
• Naturally one could argue this is highly specialized and potentially not relevant. So, really, why?
  • Well, it's an experiment. It might serve as a hands-on, gentle introduction to spectroscopy, science, analytical instrumentation, etc. We're pretty sure no makerspace in the world has put one of these inside of it, but given the right community and encouragement around it, maybe something interesting could happen.
  • Activities, applications, and maybe some classes are pending.
• While NMR makes a lot more sense with a grounding in organic chemistry (and thus potentially intimidating), it is worth pointing out that one could easily learn how to operate the instrument and get meaningful results if one has a specific application in mind. Quantification of ethanol in a sample could easily be performed with less than an hours time in initial training and no need for an organic chemistry background.

Getting Involved / Authorization

Do you know things about NMR or want to learn? Have interesting ideas on what we could use this for? Lets talk... We're still working out details on things like supplies (NMR tubes) and usage, however, the equipment is online, functional, and remotely accessible if you like.

Tech Specs

• 1.4 Tesla Permanent Magnet.
• Has the usual Hydrogen-1 (Proton) probe
• Has either a Carbon-13 Probe or Wideband Probe (not clear if it is in fact wideband).
• In spite of the EM360A being an extremely old instrument (c. late 1979 ish), it has been retrofitted with completely modern controls. This makes the instrument quite relevant even today. This "desk of knobs" with the "chart recorder" is replaced with a modern PC, allowing digital storage/capture and advanced pulse sequences involving Fourier-transforms.

Safety

There are no safety risks to the user with the machine itself. While the machine does use a relatively strong (1.4 Tesla Permanent Magnet), it is deep inside, very well shielded, and ultimately even the strongest of permanent magnets are still just magnets. There are superconducting, helium-cooled, electromagnet NMRs out there which deserve some serious respect, however, what we have is just a regular permanent magnet. It is tame, and best of all, maintenance free! Nevertheless, if you prefer notoriety, you can decorate the beige box with "Danger" stickers regarding pacemakers, credit cards, hip implants, etc. It will undoubtedly be the most decorated NMR on the planet as a result. Beige box could use some flare...

Since samples are loaded into thin glass tubes, the usual common sense in terms of handling glass is important. If you manage the epic failure of somehow shattering a tube inside of the instrument, well, it probably amounts to an interesting opportunity in terms of disassembly of a probe and so it wouldn't be the worst thing in the world. Heck, we might all learn something cool...

Improper operation of the NMR cannot damage the instrument, with the only real risk being poor or no spectra.

The instrument thus strikes a fairly wonderful balance of being pretty approachable.

Introductory Theory

NMR: Like many types of spectroscopy, NMR ultimately produces a squiggly line on a graph.
Breaking down the acronym, we have:

• Nuclear simply means we are concerned with the nucleus of the atoms we are interested in (so the protons and neutrons). In spite of sounding scary, ionizing radiation is not involved in this technique (which is the actually scary part when you hear the world nuclear).
• In essence, any atoms that have an odd number of protons or neutrons (or both) in their nucleus will behave like magnets. This is due to their 'spin'. Only some isotopes of some elements have this property. These are commonly referred to as "NMR active" (Common ones being Hydrogen-1 and Carbon-13).
• By exposing atoms to a magnetic field and RF of a given frequency, we can put them into resonance. This can be measured, and is the basis for the technique.

While the nucleus plays a fundamental role in this technique working at all, the configuration of the electrons of an atom in relation to other atoms does play a subtle but very important role in NMR -- an atom's configuration of electrons does influence how much an atom is diamagnetically shielded from the effects of RF.. We use this to our advantage because different electron configurations will resonate at slightly different frequencies. This allows us to discern between different ways a nucleus can exist within a sample.

So, in essence and in the most simple of cases with NMR:

• First one selects something NMR active to work with (Hydrogen-1 / Proton NMR being the most common).
• Ultimately the goal is to produce a spectrum.
  • The height on the Y-Axis predictably represents how much of something there is.
  • The X-Axis represents resonance at different frequencies (called chemical shift).
• If you are performing the typical Hydrogen-1 (Proton NMR) analysis of a sample, the peaks on the X-Axis represents different ways the electrons of a given Hydrogen within a compound are configured. For a simple compound where there is hydrogen in just one configuration (H2O / Water), you'd expect one peak. For Ethanol, CH3-CH2-OH, we'd expect three peaks.

One thing to note at this point is that the resonant frequency for a given NMR active nucleus is related to the strength of your NMR's magnetic field -- the stronger magnetic field, the greater resolution (sharper peaks) one can achieve.

You will often hear of people referring to the strength of their NMR in terms of MHz (as opposed to the strength of the magnetic field in Tesla). When this is the case, they are typically referring to the frequency of Hydrogen-1 at a given field strength. So, in our case, at 1.4 Tesla, you could say we have a 60MHz NMR. The implication, again, is that it operates at 60MHz when using the Hydrogen-1 probe. The resonant frequency is different if you are analyzing a different nucleus.

Because people have instruments of various field strengths, but would like to be able to compare data to eachother, the x-axis is not reported in frequency of Hz, but rather in a unit called ppm, which represents the chemical shift. PPM is simply the chemical shift in Hz divided by the NMR frequency and multiplied by 1,000,000. This standardizes the position of the resulting peaks across instruments, so something like water or vinegar will always shows peaks in the same ppm values regardless of the capabilities of an instrument.

Terminology

• NMR - Nuclear magnetic resonance
• NMR Sample Tube or 'Tube' - A thin glass tube (~5mm thick) and about 7" long. Your sample is placed into this tube.
• Sample Spinner - Before your NMR tube can be placed into the intrument's probe, the Sample Spinner (a white piece of plastic) needs to be placed around your NMR tube. This keeps the tube centered inside the probe (which has a much wider diameter than the your NMR sample tube).
• Probe - The detector of an NMR. Most commonly, this is Hydrogen-1, but probes for other isotopes exist. The probe is ultimately just a coil, but it is tuned to the isotope of interest. There are "wideband" probes that can be tuned to various isotopes as long as they are NMR active, though it should be noted that many isotopes will not enjoy the otherwise excellent signal-to-noise ratio that Hydrogen-1 is capable of producing.
• Proton NMR - What they really mean is NMR performed with a H-1 (Hydrogen-1) probe.
• C-13 NMR - NMR performed with a Carbon-13 probe.
• TMS - Tetramethylsilane Si(CH3)4 - A colorless liquid commonly used as a reference standard. The peak of TMS is used to set a reference of where zero is.
• Chemical Shift (PPM) - The unit of the x-axis is "chemical shift" in ppm. PPM is simply the chemical shift in Hz divided by the NMR frequency and multiplied by 1,000,000. This standardizes the position of the resulting peaks across instruments with different field strengths, so something like water or vinegar will always shows peaks in the same ppm values regardless of the capabilities of an instrument. This corresponds to the shift from the reference frequency from 0ppm.
• Upfield / Shielded / Lower Energy - Peaks occurring closer to 0ppm (near the right side of x-axis). They require less energy to bring them into resonance.
• Downfield / Deshielded / Higher Energy - Peaks further left on the x-axis (away from 0ppm), require more energy to bring them into resonance.
• Gyromagnetic Ratio or Gamma γ - This is a fundamental property of a given isotope. The higher this number, the more signal it produces in NMR. For Hydrogen-1 this is 42.58MHZ / Tesla. Hydrogen-1 has one of the higher Gyromagnetic Ratios and the presence of hydrogen in just about everything makes it one of the most commonly analyzed isotopes in NMR spectroscopy.
• Shim - NMR relies on having a very homogeneous magnetic field. "Shimming" the magnet refers to adjusting it, and this is achieved by electronic coils that fine-tune the magnetic field. The term comes from the old days when shimming was achieved mechanically by using pieces of thin metal (shim stock) to manually adust the magnetic field, up hill, both ways.
• Shunt - A mechanical adjustment which slightly increases or decreases the magnetic field, thus changing the "field offset" and moving the peaks left or right along the x-axis. As the magnetic field strength drifts through time and temperature, this might be necessary if the machine has not been used in a while. Performing this adjustment requires a brass, copper, or wooden flathead to turn a screw deep inside the instrument. Use of a typical iron-containing screwdriver will result in it distorting the field (making adjustment challenging), and it'll try to consume the screwdriver the whole time you are trying (it's not worth it). There should be a thin copper tube pinched flat on one side around the instrument for this purpose.
• CW - Continuous Wave. Before modern signal processing with Fourier Transforms, we had instruments which would do a sweep with increasing magnetic field. This was slow.
• FID - Free induction decay. This is a view of the raw signal before applying a Fourier transform to it.

History of NMR as a technique

• First generation instruments would use a constant RF frequency but ramp the magnetic field up slowly, and this is in fact what this unit did in its original form.
• Second generation instruments would keep the magnetic field constant but pulse the RF, covering the entire set of radio frequencies. Advances in computing and signal processing enabled Fourier transforms, and this is precisely what the retrofit to this instrument allows it to do.
• A great watch if you have an hour: Youtube: History of NMR / Keynote Chemistry

Operation

Overview

NMR uses thin (5mm diameter) glass tubes for samples. A sample needs to be liquid. Special solvents are often used to prepare a sample, but, direct analysis is possible. No harm in trying and seeing what happens. Advanced techniques might involved solvent suppression pulse sequences or deuterated solvents.

Hardware

• Your sample:
  • Placed into an NMR Tube: A thin and long glass tube that holds your sample.
  • Sample spinner: A white piece of plastic that goes around the NMR tube. This serves two purposes:
    • It keeps the sample centered in the instrument's probe
    • It allows the sample to the spun while inside the tube. (This is done with compressed air that is supplied to the NMR). Spinning allows for better spectra to be taken.
• The instrument:
  • Sample height gauge: There is a small hole on top of the unit toward the front. This is merely to set the height of the sample spinner against your NMR tube.
  • Lifing the top lid of the instrument, one will see a few things:
    • In the center, one sees the probe where the sample is inserted.
    • One will also see a button that uses compressed air to eject the sample upward when pressed.
    • There is also a switch that turns the sample spinner on and off, as well as an adjustment to change the spinning speed.

Running your first sample: Tap Water

• Find an NMR tube to use and fill it with plain water to somewhere between 1/3 to 1/2 the height of the tube.
• Find the sample spinner. It may be inside of the instrument's probe. Never have your face over the probe while ejecting the sample probe entrance -- air pressure is used to push the sample out of the instrument when the eject button. To eject, have your hand around the entrance to the probe and press the eject button inward slowly. The sample should gently rise upward and you should be able to retrieve it.
• Place your NMR tube filled with water into the sample spinner (the white piece of plastic that goes around the tube)
• The height of the tube inside the spinner should be set with the height gauge on the instrument.
• The tube can now be placed into the instrument. Hold the eject button partway and release it slowly to allow the tube to gently fall into the probe.
• Use the PNMR software to capture and observe the resulting spectrum.
  • Type GS and hit enter. You should see a small menu appear on the top-right and a peak should be produced. If you see a ringing wave instead, you are actually looking at the FID. Hit Control-S to switch to the spectrum.
• If the NMR has not been used in a long time, and you do not see a peak from your water sample, you may need to adjust the shunt mechanically.
  • You will need either a long brass flathead screwdriver or a long wooden tool to turn the screw deep inside the instrument (it should more very freely with almost no resistance).
  • Hit Control-K to get out of GS if you are in there. Type W1 and enter a large value (like 40,000) for the Spectrum Width. What this does is effectively zooms out quite a bit as the peak is likely "off screen" when using more common values like 1,000 for spectrum width. Type SI and set the value to 4096. This will reduce the time it takes to obtain a spectrum, allowing for easier interactive adjustment to happen.
  • Type GS and look for a peak. Turn the shunt counter-clockwise and you should see the peak move left. Clockwise to move right. With the water sample, you'll want it roughly in the center of the screen.
  • Once centered, you might want to have the electronic shimming routine do the rest of the fine tuning. Hit Control-K to get out of GS and type SHIM and hit enter. This will take a few minutes...

Operation / Background

• Unless performing more elaborate techniques, NMR spectra are generally a squiggly line.
  • Y-Axis is intensity. Simple enough. The taller a peak, the more of something there is. If you take the area underneath a peak and add it up (integrate it), you can now say something about how much of something exists and begin to quantify it.
  • X-Axis has quirks:
    • It technically represents the amount the frequency of whatever is being analyzed is shifted from the signal from Tetramethylsilane. TMS is a commonly used for calibration and whose single peak is defined to be 0ppm.
    • Also, 0 starts from the right side. Higher frequencies are to the left 0 on the X-Axis (Historical Quirks)
    • Technically, we are measuring how many Hertz higher something is than where the signal for TMS is.
    • In practice, we never refer to this in Hz because the amount of shift would depend on the strength of the NMR we have. Since it would be nice to sensibly compare data across different instruments, the amount of Hertz shift is divided by the frequency of the instrument. We call this value PPM. Do not confused the usages of "PPM" here for perhaps the more common use case in other techniques where one would be referring to concentration of a sample. In all cases, it stands for "Parts per million", but here it is important to remember ppm is the x-axis, which has more to do with what something is and not with how much there is.

Software

The software on the machine has two parts:

• PNMR: Used to run the hardware, acquire spectra. This program is very specific to the instrument we have, however, the commands used may be similar/familiar to users of other instruments, harkening back to the Unix days of these instruments and their command line commands.
• NUTS: Used to process/look at spectra. There are alternatives to NUTS -- it is merely what is bundled with this instrument but many other free and non-free tools exist. MNova is a common commercial software, and free tools include Spinworks and Topspin. You can even turn your FID into an audio file and "listen" to the sound of a sample. The possibilities here are endless, but starting with NUTS might not be a bad way to go unless you already have some other software you know.

PNMR (Acquiring Spectra)

While there is a graphical display of spectra, this is actually a command line tool. Common commands:

GS
ZG

Keystrokes:

Control-Q: Stop After next scan
Control-K: Stop immediately (this is useful to get out of GS quickly)
Control-S: Switch between FID and spectrum.
Up/Down arrows: Change vertical scaling

NUTS (Processing Spectra)

NUTS is a piece of software from Acorn NMR that is bundled with this NMR.

Understanding Spectra

Basic qualitative analysis can be performed by looking to see if peaks exist at a given ppm. Peaks can be a single, well-defined peak (singlet), but often exist with multiple peaks to either side (doublets, triplets, quartets and so on).

Examples of Common Spectra

Common Spectra
Water	4.9ppm Singlet
Acetone	1.79ppm Singlet
Ethanol	4.5ppm singlet 3.3ppm quartet 0.9ppm triplet
Acetic Acid (Vinegar)	11.1ppm singlet 1.6ppm singlet
Isopropanol	5.0ppm doublet 3.6ppm multiplet 0.8ppm doublet

Examples of Common Standards

Common Standards
Chemical Formula	Common Name	Purpose
EtC6H5	Ethylbenzene	SNR measurements
(CH3)4Si	TMS / Tetramethylsilane	Reference for 0ppm
CDCl3	Deuterated Chloroform	Most common solvent used in NMR
	Sodium Acetate C13

• Yep, there's no 'D' on the periodic table. When you see a 'D' in a chemical formula, it is Hydrogen-2 aka Deuterium. When this form of hydrogen is used in a compound, it is often referred to as being "Deuterated". This is a form in which the hydrogen atoms are replaced with a more rare (but stable) isotope of hydrogen. The reason for doing this is that this form of hydrogen is not "NMR Active". Normally, a strong hydrogen signal (from say, plain water) would overwhelm the incoming NMR signal, thus making it harder to see small peaks. Deuterated solvents are used because they are not NMR active and so would not contribute to the spectrum.

Peak Splitting / Multiplicity

When a given peak is a single, sharp peak, this is called a singlet or (s).

Quantification

Anasazi has a pretty good video library on how to use the NUTS software to process spectra.

• Guide to Processing 1H NMR data using NUTS Program

Functional Status / Service Log

Full turnup and test complete with H1 and C13 probes functional. Celebrations were had by drinking beer with the machine (beige box partaking as well), and relative quantification of ethanol vs water were undertaken with wobbly, but within an order-of-magnitude results. Further adventures planned... It probably works at a given point. Probably needs electronic shimming if it has been sitting for a while.

• Feburary 2023: Failed Switchmode PSU in the shim control box was replaced with a center-tap transformer and a self-designed +/-15V 7815/7915 linear PSU on an aluminum substrate PCB.
• As of March 2023, it still works.
• October 2023: Primary Hard Drive (32GB SSD failed.) Recovered onto some random hard drive with dddrescue. Instrument online again. Pending analysis of corrupted files via ddru_ntfsfindbad
• October 2024: Switchmode PSU in other giant box has failed. 4A main fuse blown and a capacitor on a PSU supplying +5V +/-15V has blown. A second power supply providing 28V in the same box has yet to be tested. Repairs pending.
• November 2024: Switchmode PSUs have had just about every capacitor replaced and some giant mosfet. Verified +5V, +-15V, and 28V present.