How does this mass spectrometer work?

Well we put in a small sample of a substance that is in most cases comprised of one particular molecule into a mass spectrometer and it gives us a mass spectrum graph which we must interpret. How does this equipment work While in Chem 14c we might not be working directly with a mass spectrometer it is important to conceptually understand what occurs in the process of producing the reading we will interpret. 1) we introduce a sample to the spectrometer 2) this sample undergoes ionization, this is done by using an electron gun that shoots out electrons at the molecules ( not yet charged) then this interaction between the incoming electrons and the substance result in ionization. One important distinction is that it can result in ionization which produces a molecular ion which can be analyzed later by the detector or it can cause cleavage of one or more bonds which results in the production of fragment ions. These fragment ions are NOT molecular ions but are still charged and therefore can be detected by the detector. So all those little lines not the M, M+1 or M+2 are readings from other charged particles. This is a good time to introduce the base peak~ this is the ion which presents on the graph to have the highest relative abundance. So why isnt the molecular ion that derives from the original molecule we are interested always the base peak or the ion which has the highest abundance? Well in some cases a molecule can fragment more readily than others and therefore the fragments produced are not the molecular ion but product ions that in some cases are quite abundant in an easily fragmentable molecule. 3) Then the ions produces are passed through an accelerator which allows the positively charged particles to pass through to the electromagnet 4) this electromagnet then works to deflect ions or manipulate the flight path of the ions passing through, those ions with smaller m/z ratio are more likely to not make it to the detector and those with large m/z value will. This is one of the reasons we often see the base peak, or the peak with the highest relative abundance present as the M or molecular ion. But why not M+1 or M+2? Well remember a molecule is comprised of various atoms and those atoms have isotopes with natural abundance. As Aston discovered that there are stable isotopes of different elements the same concept applies in which the molecule can be comprised of different atoms which can have different molecular weights due to the different atoms that comprise them and the isotopes present. BUT we must recognize that there is also a natural abundance of these isotopes we must take into consideration. The M is representative of the molecular ion made of isotopes that are of the lowest molecular weight. Why? Well these are the most abundant as see in the table on page 99 of your course reader.

So now understanding the mass spectrometer, some good questions to consider... Why do we need a sample and not just a moecule? Well this process of spectrometry produces product ions which could be molecular ions or fragment ions and we cannot obtain an accurate reading if our one lil molecule never made it through the spectrometer, or if it only gave us a reading for one of the molecular ions of the molecule in question. So having multiple molecules of a substance allows for a graph that not only shows the M value but also the M+2, M+1 and also those fragment ions that are produced. While in chem 14c we dont analyze these fragment ions it could be applicable in other areas of chemistry as well.

Base Peak: ion peak with the highest relative abundance, often, but not always M see explanation above. Mass Spectrum Graphs: X axis: m/z: mass to charge ration, not simply the molecular weight as depicted by the periodic table Y axis: Relative ion abundance, the amount of that particular ion present in sample. M: What is it It is the molecular ion in question, usually has a high m/z value on the graph. This depicts the mass of the molecular ion comprised of the isotopes with the lowest molecular weight. M+1: This is the M value with one amu added. This indicates that there is likely to be an isotope which varies by 1 amu or by one neutron. We can see that these are commonly c (1.1% abundance) N ( .37%) and S (.76%) We will most commonly see C as it has the highest abundance
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How is this M+1 value used to determine presence of these atoms or the molecular formula of the molecular ion in question? Well since M+1 is most commonly an indicator of the presence of the isotope of carbon we can use this to determine an approximate amount of carbons in the formula. HOW to do this and not screw up the calculations: If we take the M+1 relative intensity/ 1.1% = approximate number of carbons When M is 100 on the y axis in the relative abundance then the M+1 value is already indicating the M+1 relative intensity but what if M doesnt have 100% relative abundance This equation could be useful (relative abundance of M +1)X (100) / ( relative abundance of M) = The intensity of M+1 as if the M value was 100 Then take this value and plug it into the equation above. Also recognize that there could be presence of the other atoms such as sulfur and nitrogen

present and one must take this into account before definitively deciding on a molecular formula. M+2 so what is M+2? Again it is one unit over from M+1 and two units over from M, It is representative of a molecular ion which differs by 2 amus and therefore has some isotope of an atom it is comprised of within it. For the purposes of this course these atoms could be SCl BrHow to determine presence? Compare the relative intensity of the M+2 line. Remember if M isnt 100 you must manipulate the M+2 value to give you the correct value simply take (M+2 relative abundance/ M relative abundance) X 100 = relative intensity of M+2 Presence by relative intensity of M+2 S - 4% Cl - 33% Br-100% Note: if two halogens are present in the formula then the relative intensities are added as the probability of having one of those halogens in the formula or sulfur differing by 2 amus compounds so 2 Cls would have a relative intensity of 66% about, obviously make sure it fits the mass that we expect the molecular ion to have.
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Challenge: Check this out! Divide the natural abundance of this isotope by the more abundant isotope and check those numbers. How do they correlate to the numbers above? This was based on a discussion board question If you are having issues understanding what all these relative ions, abundances, and natural abundances mean this should help!

Relative ion abundance: the abundance of a particular molecular ion We are interested in the M, M+1, and M+2 peaks Relative intensity: The intensity of one molecular ion, we should scale M to 100% if not already done But how to? And why? Well M has the highest relative molecular ion abundance of the peaks of the 3 highest molecular weights (depicted on the Y-axis) By scaling M to 100 % we can also scale each of the natural abundance percentages of isotopes depicted on page 99 of the think book to allow the M contributors to be the 100% and the rest of the isotopes scaled from there. This allows us to compare the M+1 line and M+2 line to M easily and correlate the percentages of each with the natural abundances percentages when scaled to let the M contributors have 100% and the others scaled from there.

Pretty much we want to scale everything equally easier to compare. Also DO NOT get confused relative intensity of each of the molecular ion lines (M, M+1, and M+2) will not correspond to the relative ion abundance depicted on the y axis unless M is scaled to 100% Also unless you scale the percentages of the natural abundances of isotopes so that the M contributors are 100 percent and you base the rest of the percentages off of that. You cant compare the natural abundance to the relative ion intensities directly I suggest: 1) Make sure M has 100% relative ion abundance on graph, if it doesnt scale it and the other M+1 and M+2 peaks so that this is the case. This can be done by (M+1 or M+2 /M) X 100 = relative intensity of M+1 or 2 when M is 100 2) Make sure the relative intensities you are comparing to the natural abundances of isotopes ( in order to determine presence) also allow M contributors to be the 100% abundance and from there scale the rest for easier comparison Since usually the most abundant isotope (for our purposes) are the ones with the lowest molecular mass and the M value depicts the molecular ion with the lowest molecular mass by scaling to 100% for M and then scaling M+2 and M+1 we can get an idea of the chances of an isotope or isotopes with higher molecular mass (1 amu for M+1 and 2amus for M+2) appearing. Sometimes more than one isotope is indicated on the M +1 orM+2 lines Like for M+1 we could have two or more M +1 contributors (see p 99) Or we could have two or more M+2 contributors present (see owls 3 answer) Surprisingly this is applicable for why we divide the M+1 relative intensity by 1.1% This might be an abstract concept but let me try to explain it this way lets use the example of C6H6 predicted relative intensity of M+1 is 6.66% See page 100 of the think book. But why? Well in this situation we have 6 carbon atoms, all of them could differ by 1 amu unit but they all cant differ at once that would be the M+6 line! But think if we have 6 carbon atoms and the abundance of that M+1 molecular ion line depends on just one little carbon in the formula differing by 1 amu unit the probability of this happening increases by 1.1% for each addition carbon because for 100 12Cs we have 1.1 13Cs!

Why? Well we still have 100 12Cs for 1.1 13C but as the formula has more carbons the chance of one of those carbons being an isotope increases and a molecular ion that is 1 amu heavier than the molecular ion comprised of the lowest mass isotopes (this is the M+1) has a greater relative intensity and greater possibility of occurring If there was magic in the world right (we are at Hogwarts or something) Taking this concept and I am going to go elementary school on you!

Before I go over this example try this. Divide C natural abundance percent by the 12C percent and then multiply by 100 This will get you 1.107% X 100 = 1.1 ish 98.893% ^ This part of the calculation yields a ratio that says for every .011123 13C we have 1 12C isotope. Then by multiplying by 100 we can deal with the number a bit better and then we can have the abundance ratio 1.1:100 Mull over this While you think lets try this trivial analogy:
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So we have these ducks they will help us understand the M+1/M value, what this value means, why we scale to 100, and why in the heck we divide by 1.1? We have ducks white ducks; skinny white ducks aka 12 C isotopes

For every 100 ducks Of Isotope of 12C

.1
We have 1.1 fatter (like the M+1 has 1.1 13C isotopes which are a little heavier) brown ducks.

Now lets say we have these groups of ducks we will create (like molecules ducks like to form groups) and in this case these groups will only have 1 duck differ at a time (we could have more like if we were talking about the M+2 isotope in which we could have 2 ducks carbons differing at a time but this is M+1 example) In this case we just need one of those ducks to differ at a time for it to be classified as the M+1 group if we have 6 ducks and each has a 1.1% chance of being brown and all we need is 1 to be brown in order to classify into the M+1 group. SOOOO we can say for every for every 100 times all the ducks are white (M) then 6.6 times one duck is brown (M+1)

This example considers a 6 carbon compound This example is very trivial but it might help a bit!