NMR: Difference between revisions

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* 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.

* 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 Hydrogen-1 probe.

* 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.

* PPM - The unit "chemical shift" is ~~measured~~ in ~~when looking at~~ NMR ~~spectra (x-axis)~~. This corresponds to the shift from the reference frequency from 0ppm.

* 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 -

* 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 ==

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* 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).

** As you do this, you should see the peak move left ~~when turning counter-clockwise, and~~ right ~~when turning clockwise~~. ~~The goal is to keep~~ it in the center.

** 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.

** Once centered, you might want ~~to run the "shim" command~~ to have the electronic shimming routine do the rest of the fine tuning.

** 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 ==

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= Software =

The software has two parts:

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.

* 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.

* 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.

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<pre>

Control-Q: Stop After next scan

Control-K: Stop immediately

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

@@ Line 77: / Line 77: @@
 * 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.
+* 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 Hydrogen-1 probe.
+* 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.
-* PPM - The unit "chemical shift" is measured in when looking at NMR spectra (x-axis). This corresponds to the shift from the reference frequency from 0ppm.
+* 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 &gamma; -
+* Gyromagnetic Ratio or Gamma &gamma; - 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 ==
@@ Line 118: / Line 122: @@
 * 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).
-** As you do this, you should see the peak move left when turning counter-clockwise, and right when turning clockwise. The goal is to keep it in the center.
+** 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.
-** Once centered, you might want to run the "shim" command to have the electronic shimming routine do the rest of the fine tuning.
+** 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 ==
@@ Line 131: / Line 136: @@
 = Software =
-The software has two parts:
+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.
+* 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.
+* 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.
@@ Line 146: / Line 151: @@
 <pre>
 Control-Q: Stop After next scan
-Control-K: Stop immediately
+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