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{{Template:EquipmentPage
{{Template:EquipmentPage
|image = [[File:Varian_EM-360A.jpg]]
|owner = Pending
|owner = Pending
|hostarea = Science
|hostarea = Science
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[[Category:Science]]
[[Category:Science]]https://wiki.pumpingstationone.org/index.php?title=NMR&action=edit
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 [https://www.youtube.com/watch?v=9Gq3UEAiWio Gas Chromatograph], nor a Mass Spec, as a few have called it...
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 [https://www.youtube.com/watch?v=9Gq3UEAiWio 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.
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? ==
== But 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.
** 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.
** 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 ==
== Getting Involved / Authorization ==
* Has the usual Hydrogen-1 (Proton) probe
* Has the usual Hydrogen-1 (Proton) probe
* Has either a Carbon-13 Probe or Wideband Probe (not clear if it is in fact wideband).
* 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.
* 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 ==
== Safety ==
The instrument thus strikes a fairly wonderful balance of being pretty approachable.
The instrument thus strikes a fairly wonderful balance of being pretty approachable.
== Functional Status ==
== Functional Status / Service Log ==
Full turnup and test complete with H1 and C13 probes functional.
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.
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 <code>dddrescue</code>. Instrument online again. Pending analysis of corrupted files via <code>ddru_ntfsfindbad</code>
= Theory =
= Introductory Theory =
NMR:
NMR:
Like many types of spectroscopy, NMR ultimately produces a squiggly line on a graph.
Like many types of spectroscopy, NMR ultimately produces a squiggly line on a graph.
Taken a step further:<br>
Taken a step further:<br>
In spite of the nucleus being crucial to NMR in that the technique is only useful with certain configurations of the nucleus, [https://www.youtube.com/watch?v=TJhVotrZt9I 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 confiugrations will resonate at different frequencies.
In spite of the nucleus being crucial to NMR in that the technique is only useful with certain configurations of the nucleus, [https://www.youtube.com/watch?v=TJhVotrZt9I 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 different frequencies.
* Ultimately, you are producing a spectrum with NMR.
* Ultimately, you are producing a spectrum with NMR.
** If you are performing the typical Hydrogen-1 (Proton NMR) analysis of a sample, where these peaks are 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, [https://www.youtube.com/watch?v=CjII0Cg882U we'd expect three peaks].
** If you are performing the typical Hydrogen-1 (Proton NMR) analysis of a sample, where these peaks are 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, [https://www.youtube.com/watch?v=CjII0Cg882U we'd expect three peaks].
The stronger magnetic field, the greater resolution one can achieve. You will occasionally hear of people referring to the strength of the 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.
== Terminology ==
== Terminology ==
* 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.
* 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.
* 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 -
== History ==
== 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.
* 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.
* 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.
= Operation =
= Operation =
== Overview ==
== Overview ==
NMR uses thin 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.
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 ==
== Hardware ==
== Operation / Background ==
== Operation / Background ==
* Unless performing more elaborate techniques, NMR spectra are generally a squiggly line.
* Unless performing more elaborate techniques, NMR spectra are generally a squiggly line.
** Y-Axis is intensity. Simple enough.
** 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:
** X-Axis has quirks:
*** It technically represents the amount the frequency of whatever is being analyzed is shifted from the signal from TMS (which is used for calibration and whose single peak is considered 0).
*** It technically represents the amount the frequency of whatever is being analyzed is shifted from the signal from [https://en.wikipedia.org/wiki/Tetramethylsilane 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)
*** 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.
*** 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.
*** 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 =
= Software =
== PNMR ==
== PNMR (Acquiring Spectra) ==
While there is a graphical display of spectra, this is actually a command line tool. Common commands:
While there is a graphical display of spectra, this is actually a command line tool. Common commands:
<pre>
<pre>
ZG
ZG
</pre>
</pre>
Keystrokes:
<pre>
Control-Q: Stop After next scan
Control-K: Stop immediately
Control-S: Switch between FID and spectrum.
Up/Down arrows: Change vertical scaling
</pre>
== 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 ==
{| class="wikitable"
! colspan="2" | Common Spectra
|-
||Water || 4.9ppm Singlet
|-
||Acetone || 1.79ppm Singlet
|-
||Ethanol || 4.5ppm singlet<br>3.3ppm quartet<br>0.9ppm triplet
|-
||Acetic Acid<br>(Vinegar) || 11.1ppm singlet<br>1.6ppm singlet
|-
||Isopropanol || 5.0ppm doublet<br>3.6ppm multiplet<br>0.8ppm doublet
|}
== Examples of Common Standards ==
{| class="wikitable"
! colspan="3" | Common Standards
|-
! Chemical Formula || Common Name || Purpose
|-
|EtC<sub>6</sub>H<sub>5</sub> || Ethylbenzene || SNR measurements
|-
|(CH<sub>3</sub>)<sub>4</sub>Si || TMS / Tetramethylsilane || Reference for 0ppm
|-
|CDCl<sub>3</sub>|| 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 [https://en.wikipedia.org/wiki/Deuterium 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 [https://www.aiinmr.com/video-library video library] on how to use the NUTS software to process spectra.
* [https://www.aiinmr.com/guide-to-processing-1h-nmr-data-using-nuts-software/ Guide to Processing 1H NMR data using NUTS Program]
= In greater depth =
== C-13 Spectra ==
