TBR Organic Chemistry Example 2.31

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CookieZine

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If a mass spectrometer reading indicates a signal at 80 amu and a signal roughly three times larger at 78 amu, then that the organic molecule likely contains:

A. a bromine atom
B. a chlorine atom
C. an amine group
D. an ester group

The mass spectrometer results for bromine would would show 2 peaks of roughly equal size separated by 2 amu while chlorine would 2 peaks in a 3:1 ratio separated by 2 amu. In the answer explanation they state that neither amine group nor an ester group would cause 2 signals 2 amu apart from one another and the ratio of the signals produced could not be 3:1. Where did they get this information from? Had I not just read a paragraph explaining the 1:1 and 3:1 ratios for bromine and chlorine I would not have been able to get this. Doesn't this require knowledge of how the radical cations would fragment?

From the AAMC Biological Sciences Content Outline:

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It does not seem necessary to know anything about fragmentation. TBR shows the mass spectroscopy graph for butanone and they list 4 peaks of interest one of which is the parent peak and another is the base peak. Why the other two peak values are given is not explained. I know it has to do with the fragmentation.

Can someone explain what the Y-axis means in a mass spectrometry graph?
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The peak at 44 m/z is 100. TBR lists the Y-axis as being relative intensity. What do we mean when we say that the peak at 44 m/z has a relative intensity of 100? How is the intensity measured? I know that mass spectrometry is used to measure the mass of organic compounds and that the charge on most of the cations is +1, which allows us to say that m/z is the mass of the compound. When looking at the graph is the peak at 44 amu both the parent peak (M+) and the base peak?

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What version of TBR do you have? I am trying to look this up and cannot find it nor do I remember learning this...
 
I have the 2013 edition.
Per usual, TBR goes into more detail than needed. The only peak worth understanding is the molecular ion peak (M+ peak); it's essentially the molecular weight of the compound (with the loss of 1 electron). Since an electron is ~1/2000 amu, it's loss has a very insignificant effect on the molecular weight. FYI - the Y-axis has to do with relative abundances/intensity. Being that the intensity is 100, then what that basically means is the molecule undergoes very little if any fragmentation. You could have deduced this though by looking at the graph for smaller peaks.

You definitely don't need to know anything about fragmentation patterns though. But if you were curious, in this scenario above, for Cl and Br it has to do with the different isotopes. Chlorine can be either of two chlorine isotopes: 35Cl and 37Cl. The molecular weight (average) on the periodic table is 35.5, which indicates we have more of the 35Cl isotope in nature - in fact, 3/4 as much. So on a mass spec, you'll see an M+ peak and a nearby peak that's smaller (M+2) peak simply because a few compounds have the larger isotope (the peak will be approx 1/4 in size). For Bromine (79Br and 81Br), it also exists in two isotope forms, however, those isotopes are in a 1:1 ratio, and so we anticipate an M+ and M+2 peak equal in size. It turns out having an odd molecular ion peak represents a compound with an odd number of nitrogens. Again, this is stuff not on the AAMC outline and definitely nothing you need to know. But if you were interested, hopefully that helps.
 
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