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Basics of Mass Spectroscopy the Roots of Mass Spectroscopy (MS)

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Basics of Mass Spectroscopy the Roots of Mass Spectroscopy (MS) Spectroscopy Beauchamp 1 Basics of Mass Spectroscopy The roots of mass spectroscopy (MS) trace back to the early part of the 20th century. In 1911 J.J. Thomson used a primitive form of MS to prove the existence of isotopes with neon-20 and neon- 22. Current, easy-to-use, table-top instruments of today are a very recent luxury. In less than a day, you could be running samples on a mass spectrometer. However, it would take you longer to learn the many intricacies of MS, something we cannot pursue in a book such as this. We will mainly look at electron impact mass spectrometry (EI) and briefly mention chemical ionization (CI) as they pertain to determining an organic structure. The technique of MS only requires very small amounts of sample (g-ng) for high quality data. For that reason, it is the preferred method to evaluate product structures in combinatorial chemistry, forensic laboratories and with complicated biological samples. Generally, in these situations, you have some indication of the structure(s) possible. MS can be coupled to separation techniques such as gas chromatography (GC) and high pressure liquid chromatography (HPLC) to make a combination technique (GC-MS and LC-MS). GC can separate components in relatively volatile mixtures and HPLC can separate components in relatively less volatile mixtures. There are also options for direct inlet of solid samples and sampling methods for high molecular weight biomolecules and polymers. But, these are beyond the scope of this book. MS is different from the other spectroscopies (UV-Vis, IR, NMR) in that absorption or emission of electromagnetic radiation is not used. Rather, the sample (molecule) is ionized by some method (often a high energy electron beam = electron impact = EI). An electron is knocked out of a bonding molecular orbital (MO), forming a radical cation. Dications and anions can also be formed, but we will not consider these possibilities. high EI mass spec RH+ energy RH 2 e- e- + radical cation The cations formed are accelerated in a high voltage field, focused and separated by mass to charge ratio (m/z or m/e) using a magnetic and/or electric fields. A detector indicates the intensity of each mass signal and the mass data (x axis) are plotted against this intensity (y axis) to produce a spectrum similar to that shown below. It is also possible that this same data can be printed in a tabulated, numerical form (shown in the side box). The most useful information from the MS is the molecular weight (the M+ peak), which can indicate what the formula is. The formula provides the degree of unsaturation, which gives important clues to the possible structures (rings and pi bonds). Fragment peaks that are detected provide hints as to the nature of the carbon skeleton, heteroatoms and functional groups present. The most abundant peak (largest) in the mass spectrum is called the base peak. It is assigned a value of 100% and all other detectable masses are indicated as a percent of the base peak. The molecular weight peak is called the mass peak or molecular ion peak or parent peak and symbolized with an M. Since this peak is a radical cation, it often also has a + or + . (plus sign and a dot) superscript as well. We will use M+. There is often ambiguity in the other fragment peaks because of high energy rearrangements that are possible. It is usually very difficult to assign a structure to a completely unknown molecule based solely on mass spectroscopy. But a mass spectrum can help provide a very important piece of the puzzle, the molecular weight. y:\files\classes\Spectroscopy Book home\1 Spectroscopy Workbook, latest MS full chapter.doc Spectroscopy Beauchamp 2 base peak = largest peak in MS spectrum = 100% peak, other peaks are reported as a percent of this peak molecular ion = M = M+ = M+ = parent peak Only specific isotopic masses are found in the molecular formula. We do not see “average” masses that are listed in the periodic table. Also present will be M+1, M+2, etc. peaks due to other isotopes. On low resolution MS these peaks can help decide what the molecular formula is. In the MS example below, some of the peaks are very ‘logical’ (57, 85 and 91 are logical) and some are less so (39, 41, 42, 51 and 55). It is also true that peaks that are ‘logical’ are sometimes small or completely missing (119). Many of the other peaks will be explainable with certain assumptions about fragmentations discussed later in this chapter. Tabulated Data 91 57 85 119 Mass percent O 1-phenyl-2-hexanone 27 6 C12H16O , MW = 176 28 2 29 24 57 85 = base peak 39 7 100 41 26 Many smaller 42 1 peaks are not 43 1 shown, but listed 50 1 in data table to 51 3 75 the left. 55 3 57 99 58 5 percent 60 1 relative 50 63 3 intensity 65 11 91 77 2 85 100 (base) 29 41 86 6 25 M+ 89 2 65 peak 90 2 27 176 91 36 39 58 86 92 92 6 0 176 7 = M+ 177 1 0 25 50 75 100 125 150 175 200 mass m = charge e Spectroscopy Beauchamp 3 Typical MS Instrument Features. The moving charged cations (R-H+) can be made to curve in their direction of flight in a magnetic or electric field. The amount of curvature is determined by the mass (m) of the ions as shown in the following equations (assuming the charge, e, is constant = +1). The magnetic field (B) and/or accelerator plate voltage (V) can be altered to cause each possible mass to impact the detector. The charged masses must survive about 10-6 to 10-5 seconds to make this journey to the detector. Often there is some rational feature to explain each peak’s special stability that allows it to last long enough to reach the detector, where it becomes part of the data we examine. We will look at some of these features later in this discussion. We will not discuss other possibilities, such as metastable ions or +2 and negatively charged ions. Our main goal in this book is interpretation. 2 2 m = B r m = mass e 2V e = charge (usually +1) B = size of magnetic field r = radius of curvature V = voltage on accelerator plate r mV 1 = e B Besides just seeing a positively charged mass at the detector, we must resolve it from nearby mass values. MS instruments can be either low resolution (LRMS) or high resolution (HRMS). Low resolution MS instruments can generally resolve single amu values as high as about 2000 amu’s (e.g. they can distinguish 300 amu from 301 amu). An atomic mass unit is defined as 1/12 the mass of a neutral carbon-12 atom (12C = 12.0000, by definition). High resolution MS instruments can resolve masses as close as the fourth decimal place (XXX.XXXX). With such accuracy, an exact molecular formula can be determined by a computer. A molecular formula can also be obtained from LRMS, y:\files\classes\Spectroscopy Book home\1 Spectroscopy Workbook, latest MS full chapter.doc Spectroscopy Beauchamp 4 through a slightly more involved procedure. HRMS instruments tend to be more expensive and less common. Exact Masses We need to be precise in our calculation of possible masses for each collection of atoms because the atoms in any cation hitting the detector are specific isotopes. The atomic weights listed in the periodic table are average weights based on the abundance and mass of all of the naturally occurring isotopes of each element. For example, the atomic weight of bromine in the periodic table is 79.9, even though there is no bromine isotope with a mass of 80. The 79.9 atomic weight is a result of an approximate 50/50 mixture of two stable isotopes of mass 78.9 and 80.9. Because of this complication, we will require data on the exact masses and the relative abundance of the common isotopes that we expect to encounter. Those most useful to us in organic chemistry and biochemistry are listed below. Average Element Atomic Weight Nuclides Exact Mass Relative Abundance* hydrogen 1.00797 1H 1.00783 100.0 2 H (D) 2.01410 0.015 carbon 12.01115 12C 12.00000 100.0 13 C 13.00336 1.11 nitrogen 14.0067 14N 14.00307 100.0 15 N 15.00011 0.37 oxygen 15.9994 16O 15.9949 100.0 17 O 16.9991 0.04 18 O 17.9992 0.20 fluorine 18.9984 19F 18.9984 100.0 silicon 28.086 28Si 27.9769 100.0 29 Si 28.9765 5.06 30 Si 29.9738 3.36 phosphorous 30.974 31P 30.9738 100.0 sulfur 32.064 32S 31.9721 100.0 33 S 32.9715 0.79 34 S 33.9679 4.43 chlorine 35,453 35Cl 34.9689 100.0 37 Cl 36.9659 31.98 bromine 79.909 79Br 78.9183 100.0 81 Br 80.9163 97.3 iodine 126.904 127I 126.9045 100.0 *The most abundant nuclide is assigned 100% and the others assigned a fractional percent of that value. Coincidently, in the examples listed in the table above with more than one isotope, the lowest mass isotope is the 100% isotope. Spectroscopy Beauchamp 5 Obtaining a molecular formula from a HRMS is relatively straight forward Each possible molecular mass is unique when calculated to 3-4 decimal places and computers can do the calculations for us.
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