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  1. - Top - End - #1
    Bugbear in the Playground
     
    HalflingPirate

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    Default Spectroscopy: No idea how to read these graphs.

    IR spec: Just looks like squiggly lines to me. I can't read the squiggles.
    HNMR or mass spec: Can't tell the difference between these two. Also can't read them...


    Youtube videos have been completely unhelpful, my teacher is elusive and I can't even set up appointments with him, and the textbook is completely useless.

    I have no idea what to do.

    I don't even understand the terminology.
    Last edited by MonkeySage; 2019-02-19 at 05:01 PM.

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Examples, maybe?
    Time travels in divers paces with divers persons.
    As You Like It, III:ii:328

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    HalflingPirate

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    Default Re: Spectroscopy: No idea how to read these graphs.

    I can't actually show a picture but... well, here. What does this mean?

    "Parent ion is 120 with no M + 2 peaks"... To me... I know what an ion is, but the rest is gibberish.

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    gomipile's Avatar

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Here are a couple of good articles on that terminology with respect to mass spectrometry:

    https://www.chemguide.co.uk/analysis/masspec/mplus.html

    https://www.chemguide.co.uk/analysis...ec/mplus2.html

    An M+2 peak is the second peak when you get two peaks separated by two AMU. This happens when there are two isotopes of an element that differ by two neutrons, and those isotopes are common enough to show up in the mass spec.
    Quote Originally Posted by Harnel View Post
    where is the atropal? and does it have a listed LA?

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    PaladinGuy

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by gomipile View Post
    Here are a couple of good articles on that terminology with respect to mass spectrometry:

    https://www.chemguide.co.uk/analysis/masspec/mplus.html

    https://www.chemguide.co.uk/analysis...ec/mplus2.html

    An M+2 peak is the second peak when you get two peaks separated by two AMU. This happens when there are two isotopes of an element that differ by two neutrons, and those isotopes are common enough to show up in the mass spec.
    It should be in the notes. But roughly

    In Mass Spec, the X axis is the mass and the Y axis is the quantity. For each peak there should be a reasonable molecule or part molecule of that mass. So for Carbon-dioxide you'd expect peaks at 44 from CO2, 28ish from CO, 16 from O and 12 from C. You wouldn't expect a peak at 32 as there isn't a joined up bit of the atom that contains two oxygens without a carbon. Plus there'd be a few more complications [e.g. additional peaks as above due to isotopes and double ions].

    In Infra Red, the X axis is the energy and the Y axis is the quantity (for each peak/trough, depending on which way up the graph is) there has to be a bond of that energy.
    So for alcohol you'd expect a peak corresponding to each of C-H C-O O-H

    HNMR is totally different from mass spec, I'd say it's closer to Infra Red but instead of looking at the bond energies it's looking at the nucleus energies (which means each type of atom is seperated)
    Last edited by jayem; 2019-02-19 at 07:14 PM.

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    Default Re: Spectroscopy: No idea how to read these graphs.

    And in case it's not clear, all of the masses are in atomic mass units, meaning it's basically a count of all of the protons and neutrons in the molecule (since protons and neutrons each weigh very close to 1 AMU, and the electrons have negligible mass by comparison).
    Time travels in divers paces with divers persons.
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    Brother Oni's Avatar

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    Default Re: Spectroscopy: No idea how to read these graphs.

    To use an analogy for mass spec, you have an unknown item in a bag that disguises its physical shape.

    You then take a hammer and hit the bag repeatedly.

    The bag of bits is emptied out and you try to identify the original object, based on the pieces you have.

    This is essentially what mass spectrometry is - you have a compound which you smash to bits by ionising it, then based on the molecular mass of the fragments, you can get a reasonable idea of what the original compound was.

    Sometimes you have ambiguous results, which is why you have things like HNMR, which tells you about what type of bonds there are in a compound.

    As an example, a primary alcohol (eg propanol) and its equivalent secondary alcohol (eg propan-2-ol) would have the exact same fragmentation pattern on the mass spec, but their NMR patterns are different as the local environments for the carbon atoms are different:

    Spoiler: Propanol vs Propan-2-ol
    Show


    Propanol has three peaks as it has three environments (CH3, CH2 and CH2OH), while Propan-2-ol only has 2 (CH3 and CHOH).


    Meanwhile propanol and butanol would have similar NMR spectroscopy (butanol has an extra peak at ~33 ppm as the effect of the O atom is diluted on the second CH2 group), but the fragmentation pattern would be different (butanol has an extra fragment at 74 AMU and any fragment involving C and H would be larger in comparison to propanol)
    Last edited by Brother Oni; 2019-02-20 at 08:08 AM.

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by MonkeySage View Post
    I can't actually show a picture but... well, here. What does this mean?

    "Parent ion is 120 with no M + 2 peaks"... To me... I know what an ion is, but the rest is gibberish.
    120 is the molecular weight, generally somewhat rounded - so you can assume there are 120 (neutrons+protons) in the ion. The lack of M+2 (mass + 2) peaks also means that you aren't looking at any elements with common isotopes where one is 2 heavier than the other, which in an O-Chem class usually means that chlorine isn't making an appearance. Each individual peak corresponds to a particular element*, and the peak height tells you how many of each there are. Once you have the formula you can then put it together; isomers may require additional data.

    This additional data comes from IR and NMR, both of which respond to bonds. IR is basically just a case where you memorie what particular bonds look like in terms of where the bulges are and what they look like. Hydrogen NMR essentially measures shielding, which is basically just an extension of bond polarity. There's a molecular electron cloud which spends a lot more time in some places than others, and this effect does extend further than 1 bond, though it gets a lot less pronounced pretty quickly. As with mass spec the height** of the peaks corresponds to the number of things making it, here equivalent hydrogens. Note that you'll generally only see hydrogens attached to carbons, those directly attached to oxygen, nitrogen, etc. tend not to show up.

    *Which I can only say because there's no M+2 peak.
    **Technically area.
    I would really like to see a game made by Obryn, Kurald Galain, and Knaight from these forums.

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by Knaight View Post
    Each individual peak corresponds to a particular element*, and the peak height tells you how many of each there are.
    This depends on how aggressively ionised the compound was. If you've reduced it to its constituent elements and assuming a near 100% collection rate on the detector, the best you can get is an approximate ratio of each element to each other.

    Using the hammering the bag analogy, you've used a jackhammer to pound the item into a fine powder rather than using a claw hammer to leave variable sized bits.

    Ideally you want to break the compound up enough so that you get a mix of its constituent components (the elements alone and larger functional groups, like hydroxyl, phenyl, etc) and some of the original compound to give an absolute upper limit.

  10. - Top - End - #10
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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by Brother Oni View Post
    To use an analogy for mass spec, you have an unknown item in a bag that disguises its physical shape.

    You then take a hammer and hit the bag repeatedly.

    The bag of bits is emptied out and you try to identify the original object, based on the pieces you have.

    This is essentially what mass spectrometry is - you have a compound which you smash to bits by ionising it, then based on the molecular mass of the fragments, you can get a reasonable idea of what the original compound was.
    I am very disappointed that you missed the chance to use the analogy of a sack full of god-stuff and smashing it until the quiddities start leaking out.

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    ClericGuy

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    Post Re: Spectroscopy: No idea how to read these graphs.

    Ok I don't understand people that answer without really knowing the subject they should talk about. Anyway:

    IR

    Usually in x-axis you have the wavelength, and in y-axis the % transmittance, the "peak" begin at the top and the more they go down, the less is the transmittance (increased absorption of the radiation of that wavelength). The transmittance in the graph is linked by the variation of polarity in the molecule due to the movement of the bond(s) that absorb the radiation while the position of the "peak" is linked by the strength of the bond that absorb the radiation. Usually IR spectroscopy is useful to have an idea of what functional group are present in a organic molecule.

    Mass spectroscopy

    As someone else said in that case you "broke" the molecule in ions. In the graph you'll have in x-axis the mass/charge (m/z) ratio of the ion, and in y-axis the intensity of the signal (linked to the amount of ions formed with that specific m/z ratio). Usually you look (1) for the signal with the higher m/z (on the right), usually it is the molecular ion (M<sup>+</sup>) and gives the molecular weight of the compound and (2) for the stronger signals (the ones that go higher, so the more stable ions) and try to understand what kind of molecule could produce those fragments.

    H-NMR

    That is quite complex to explain, I try my best. Here in y-axis you have a value linked to the intensity of the signal and in x-axis a value that is the linked to the magnetic field around the hydrogen(s) that gives the signal. The position of the signal in the x-axis give you an idea of the chemical surrounding the hydrogen (aliphatic or aromatic, near a carbonyl group,...) while the integration of the intensity of the peaks is linked to the number of hydrogens that give the signal. Here also the shape of the signal is important: the number of peaks (N+1) that form a signal is linked by the number of hydrogen (N) that are bond to the near carbons.

    I hope that this help

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by Xyril View Post
    I am very disappointed that you missed the chance to use the analogy of a sack full of god-stuff and smashing it until the quiddities start leaking out.
    I'm not familiar with that reference. Source?

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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by Brother Oni View Post
    This depends on how aggressively ionised the compound was. If you've reduced it to its constituent elements and assuming a near 100% collection rate on the detector, the best you can get is an approximate ratio of each element to each other.
    True. There was a bit of an unstated "given the idealized graphs produced in introductory organic chemistry classes" to that; real data is of course messier.
    I would really like to see a game made by Obryn, Kurald Galain, and Knaight from these forums.

    I'm not joking one bit. I would buy the hell out of that.
    -- ChubbyRain

    Current Design Project: Legacy, a game of masters and apprentices for two players and a GM.

  14. - Top - End - #14
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    Default Re: Spectroscopy: No idea how to read these graphs.

    Quote Originally Posted by Brother Oni View Post
    I'm not familiar with that reference. Source?
    I don't want to spoil anything for you, so I'll just say it's something that comes up in some of the more recent strips (of Order of the Stick.)

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