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					 Chemistry 4631

Instrumental Analysis
      Lecture 20




                        Chem 4631
      Mass Spectrometry (MS)
Instrumentation
  Principle components:
  –   Inlet
  –   Ion source
  –   Mass analyzer
  –   Ion transducer
  –   Pumps
  –   Signal processor


                           Chem 4631
    Mass Spectrometry (MS)
Instrumentation
Pumps

Mass Specs operates in a vacuum.


Pumps - Rough pumps

Takes pressure down to ~10-2 torr



                                    Chem 4631
      Mass Spectrometry (MS)
Instrumentation
Pumps - Oil Diffusion Pump

Diffusion pump oil is boiled and vapor rises and condenses
  on chamber wall.

The first downward flow of oil vapor collides with gas from
  MS and compresses it in bottom of chamber.

Rough pump removes gases from bottom.

Inexpensive – but if rough pump fails oil vapor can
  contaminate MS.

                                                      Chem 4631
     Mass Spectrometry (MS)
Instrumentation
Pumps - Oil Diffusion Pump




                             Chem 4631
     Mass Spectrometry (MS)
Instrumentation
Pumps - Turbo Pump
Composed of a set of fans similar to a jet engine.
Alternate sets of blades rotate while others are
  stationary.
Blades turn at speeds over 20,000 revolutions per
  minute.
Molecules collide with the blades and are deflected
 downward and removed by rough pump.

Advantage – quick startup and shutdown.
Disadvantage – expensive.

                                               Chem 4631
    Mass Spectrometry (MS)
Instrumentation
Pumps - Turbo Pump




                         Chem 4631
      Mass Spectrometry (MS)
Applications of MS
  –   MW determination
  –   Isotope ratios
  –   Structural determination
  –   Compound identification
  –   Quantitative analysis




                                 Chem 4631
Mass Spectrometry (MS)




                     Chem 4631
     Mass Spectroscopy (MS)
MS Interpretation




                          Chem 4631
     Mass Spectroscopy (MS)
MS Interpretation




                          Chem 4631
      Mass Spectroscopy (MS)
  MS Interpretation

Atomic Masses and Isotopes

Atomic masses on the periodic table represent an
   average for all the naturally occurring isotopes.
   For example chlorine is a mixture of:
35Cl - 75.77%        and 37Cl - 24.23%

For MS the most abundant isotope is set to 100%
  and all other isotopes are normalized relative to
  the most abundant.


                                                Chem 4631
     Mass Spectroscopy (MS)
MS Interpretation




                          Chem 4631
   Mass Spectroscopy (MS)

MS Interpretation
 Isotope Classes

The A, A+1, and A+2 represent the types of
  isotopes present.

A - only a single isotope, i.e. F
A+1 - two isotopes, i.e. C and N
A+2 - at least two isotopes with the highest mass
  isotope being +2 from the lowest mass
  isotope, i.e. O, S, Cl, Br.


                                             Chem 4631
     Mass Spectroscopy (MS)
  MS Interpretation

Looking at other A+1 abundances, notice that
  nitrogen has a very small number, that is why we
  use the nitrogen rule.

For some A+2 elements, O also has a very small
  abundance, but sulfur is easier to see.

Cl and Br are A+2 elements and have relatively high
  abundances for the isotopes. So it is important to
  look at the patterns to identify Cl and Br
  containing compounds.
                                              Chem 4631
  Mass Spectroscopy (MS)
MS Interpretation.




                       Chem 4631
    Mass Spectroscopy (MS)
MS Interpretation




                         Chem 4631
    Mass Spectroscopy (MS)
MS Interpretation




                         Chem 4631
    Mass Spectroscopy (MS)
MS Interpretation




                         Chem 4631
    Mass Spectroscopy (MS)
MS Interpretation




                         Chem 4631
Mass Spectroscopy (MS)




                     Chem 4631
     Mass Spectroscopy (MS)
                    Definitions
Resolving power is defined as M/DM, where M is an
  m/z value and DM is the difference between M and
  the next highest m/z that can be distinguished
  from M.

Resolution is defined as DM/M, the inverse of
  resolving power. It is usually expressed as DM at
  M in parts-per-million units.

Sensitivity is the ability of the system to measure
  small quantities of materials. Most MS can detect
  less than 10-11 g of a compound.

                                              Chem 4631
     Mass Spectroscopy (MS)
                    Definitions

Scan Rate – typically 10 scans per second over the
  selected m/z range.

Scan range – the range of m/z values selected.

Mass range – the range of m/z over which data can
  be acquired.

Mass accuracy – typically 0.3 m/z units.



                                             Chem 4631
     Mass Spectroscopy (MS)
                    Definitions

Molecular Ions – the ion produced by removing an
 electron from the molecule.

Mass is equal to the sum of the atomic masses of
  the most abundant isotope of each element that
  makes up the molecule.

The peak with the highest m/z value may not be the
  molecular ion peak.

Ion addition reactions or isotopes can produce ions
  with higher m/z.
                                             Chem 4631
     Mass Spectroscopy (MS)
                    Definitions

Base peak – the most intense peak in the spectrum.
  Represent stable ions that retain much of the
  structure of the original compound. The mass
  spectrum is normalized to the base peak (0 –
  100).

Neutral fragment – does not appear in the spectrum,
  but its mass can be implied by the difference in
  mass between the molecular ion and the product
  ion.

Characteristic ions – ions produced for compound
  classes that guide interpretation.

                                             Chem 4631
  Mass Spectroscopy (MS)

Mass Spectrum

The pattern of ion intensities is characteristic
  (fingerprint) of the original molecule.




                                             Chem 4631
     Mass Spectroscopy (MS)
            Structural Interpretation
Rings Plus Double Bonds Rule
Knowing the number of rings (R) and double bonds
  (DB) in an ion can help to determine the structure.
The R+DB value can be calculated as follows:
R + DB = C – (H + X)/2 + N/2 + 1 (round down)
Where C, H, X, and N stand for the number of
   carbons, hydrogen, halogen, and nitrogen atoms
   in the ion.
Si is treated as a carbon and P as nitrogen.
Neither oxygen or sulfur are considered in the
   calculation.

                                                Chem 4631
     Mass Spectroscopy (MS)
              Structural Interpretation
Rings Plus Double Bonds Rule
Examples:

Ion Formula         Calculation
CH3COCH2+           R+DB = 3 – (5+0)/2 + 0/2 + 1 = 1.5
                    =1

C5H4NCl+            R+DB = 5 – (4-1)/2 + ½ + 1 = 4




                                                Chem 4631
     Mass Spectroscopy (MS)

           Structural Interpretation
Nitrogen Rule
Molecules that contain an odd number of nitrogen
 atoms have an odd nominal mass.

Molecules with no nitrogen atoms or an even
 number of nitrogen have an even nominal mass.




                                            Chem 4631
       Mass Spectroscopy (MS)
                   Structural Interpretation
Formation of Ions
Three factors determine which bond in a molecular ion will
  break and which ions will form:
-stability of the ions formed
cleavage often occurs at branching points to form a stable secondary
   or tertiary carbonium ion.
-relative bond strength
weak bonds such as those adjacent to hetero atoms are easily
  broken. This is called alpha cleavage and is common in esters,
  ketones, alcohols and amines.
-neutral fragment stability
cleavage to from a stable neutral molecule is preferred.


                                                            Chem 4631
      Mass Spectroscopy (MS)
            Structural Interpretation
Libraries
• NIST/EPA/NIH library contains about 130,000
  spectra with 10 million peaks.
• Wiley library contains about 233,000 with 8
  million peaks.
• There are other smaller libraries that specialize in
  certain kinds of compounds, i,e. drugs, poisons,
  pesticides, flavors, and fragrances.
• Of course manufacturers supply smaller
  databases with their instruments.


                                                Chem 4631
     Mass Spectroscopy (MS)
            Structural Interpretation
Libraries

Search routines – often use a presearch to compare
  8 most intense peaks in the unknown with 16
  intense peaks in each library spectrum.

This reduces the number of candidates, usually to
  about 100.

Ions are weighted for significance based on their
  intensity and mass, higher mass ions are
  considered more important.

                                              Chem 4631
       Mass Spectroscopy (MS)
                 Structural Interpretation

Libraries
Three figures of merit are calculated for each candidate:
   PURITY, FIT, and RFIT.
PURITY – a measure of similarity based on all ions in both the
   unknown and library spectrum. High purity is strong
   indication of a match.
FIT – ignores ions that are in the unknown but not the library
   spectrum and give high values even if contamination is
   present.
RFIT – ignores ions that are in library spectrum but not in the
   unknown, and will give high values even when the sample
   spectrum is weak.


                                                        Chem 4631
                Assignment
•   Read Chapter 11
•   Read Chapter 20
•   HW Chapter 20: 1-4, 7-10
•   HW Chapter 10: 1-4, 6, 8, 9
•   HW Chapter 10 due 3/22/10
•   Outline for Research paper due 3/12/10
•   Test II 3/26/10