Ms interpretation

1. MASS SPECTROMETRY INTERPRETATION BY K RAKESH GUPTA

2. INTERPRETATION * Mass of M + • - most abundant isotope masses of each element in the molecule * MS have unit mass resolution-atomic mass- nominal mass * M + • -identified as the ion with highest m/z ratio * But with caution- may be an impurity/ an isotope of M + • * Many compounds- no M + • - Low energy EI or CI for confirmn . * Base peak- Ion with greatest abundance-need not be M + • * Mass Spectrum- finger print of molecular structure * Computer data bases can be used to identify unknown compounds

3. Characteristics of Molecular Ions * Most compounds have an even molecular mass-exception is ‘N’ rule * Nitrogen rule: Compound with an odd number of ‘N’ –odd M + • * Compounds with even or zero number –even molecular mass * CH 4 (16), NH 3 (17), C 9 H 7 N (129), N 2 H 4 (32), C 27 H 46 O (386) * Nitrogen- odd valence and even mass M + • , the next highest mass fragment-loss of a neutral fragment Look for the ratio of M+. to M+2 peak- 3:1-Cl and 1:1 -Br

4. M- Ion 1 H 3-14 None 15 CH 3 16 O, NH 2 17 OH, NH 3 18 H 2 O 21-25 None 26 C 2 H 4 Reasonable Losses due to Fragmentation

5. C 6 H 12 O C 6 H 14 N MW → 100 100/13 = 7C+0 → C 7 H 16 1 O: C 7 H 16 -CH 4 +O MW → 99 odd! 99/13 = 7C → C 7 H 16 1 N: C 7 H 16 -CH 2 +N Nitrogen Rule

6. m/z 57 (100), m/z 43 (2), m/z 42 (2), m/z 41 (50), m/z 29 (45) CH 3 CH=CH-NH 2 (M +. m/z 57) m/z 42 (M-CH 3 ); m/z 41 (M-NH 2 ); m/z 43 (-14 units) Loss of CH 2 is rare and unlikely- so m/z 57 is not M +. It may be fragment ion- CH 3 -C(CH 3 ) 3 +.

7. Natural Abundances of the Isotopes C 13 , N 15 , S 33 - contribute to M+1; O 18 , S 34 Cl 35, Br 81 to M+2 CH 4 , M+1, 1.1%; C 2 H 6 - 2.2%

8. Mass and Relative Abundance of Organic Elements Elements containing only one isotopic form : Element Mass H(A) 1 F(A)    19 Elements containing two isotopic forms : Element Mass % Abundance Mass % Abundance C (A + 1) 12 100 13 1.10 O (A + 2) 16 100 18 0.20 Elements containing three isotopic forms : Element Mass % Abundance Mass % Abundance Mass % Abundance S (A + 2) 32 100 33 0.80 34 4.4 Si (A + 2) 28 100 29 5.10 30 3.4

9. Molecular Formula from Mass Spectra Inferences from graph : m/z Relative abundance (x) (y) 64 100.0 65     0.9 66     5.0 With the error limits, m/z Relative abundance (x) (y) 64 100.0 65     0.9 ± 0.20 66     5.0 ± 0.50 m/z Relative abundance S O 2 64 100.0 100.0 100.0 65     0.9 ± 0.20     0.8        0.08 66     5.0 ± 0.5     4.4        0.4 Conclusions : Presence of an sulfur atom and O 2 due to (A+2) pattern and from the peaks in the corresponding spectra.

10. (a+b) n ; a=3, b=1 for Cl; for Br a=2 and b=2

11. M+. Cl 35 , Br 79 ; =3x2=6 M+2 Cl 37 , Br 79 & Cl 35 , Br 81 = 8 M+4 Cl 37 , Br 81 =2

12. Mass spectral reactions: Unimolecular, competitive and consecutive Ions with wide range of internal energy ABCD + e -  ABCD + • + 2e ABCD + e -  A + • + BCD •  AB + + CD •  A + + B  AB • + CD +  C + + D (I)  AD + + BC • (II) ABCD + • + ABCD  [ ABCD ABCD ] +  ABCDA + (III) “Cool ions” appear as M + • (I) Simple cleavages (II) Rearrangements (III) ion-molecule reactions MS FRAGMENTATION OF HYPOTHETICAL MOLECULE

13. Abundance of ions depends on :  Stability of the +ve charge in the cation or +.  ion stabilization- e - sharing –hetero atoms nonbonding orbital CH 3 -C + =O  CH 3 -CO +  Resonance stabilization:CH 2 =CH-CH 2 +  + CH 2 -CH=CH 2  Stability of radical or neutral species  Steric arrangements of atoms or groups of atoms- favoring Rearrangements  Stevenson Rule: ABCD+.  A + + BCD • or A . + BCD + Radical of high IE, Ion of low IE  Loss of largest alkyl group-most abundance ion-exception C 2 H 5 CH(CH 3 ) -C 4 H 9 +  [ C 2 H 5 CH(CH 3 ) + ] > [ CH(CH 3 ) -C 4 H 9 + ] > [C 2 H 5 CH-C 4 H 9 + ] > [C 2 H 5 C(CH 3 ) -C 4 H 9 + ]

14. ---- C – C ---- ---- C + . C ---- + ---- C – Z ---- ---- C + . Z ---- + At heteroatom + . + . a to heteroatom ---- C - C – Z ---- C=Z + ---- C . + + . ---- C - C – Z ---- Z + . ---- C = C + + . Fragmentation process Cleavage of s bond

15. + . ---- HC – C – Z ---- ---- C=C + HZ + Retro Diels-alder + . + + . + . McLafferty + . Fragmentation process Cleavage of 2 s bond (rearrangements)

16. R R CH + < C + R R R R R” CH R’ Loss of Largest Subst. Is most favored Alkanes Intensity of M . + is Larger for linear chain than for branched compound Intensity of M . + decrease with Increasing M.W. (fatty acid is an exception) Cleavage is favored at branching  reflecting the Increased stability of the ion Stability order: CH 3 + < R-CH 2 + <

17. Molecular ion peaks are present, possibly with low intensity.  The fragmentation pattern contains clusters of peaks 14 mass units apart (which represent loss of (CH 2 ) n CH 3 ). Alkane

18. Illustration of first 3 rules (large MW)

19. MW=170 M . + is absent with heavy branching Fragmentation occur at branching: largest fragment loss Branched alkanes

20. Molecular ion is stronger than in previous sample

21. Molecular ion smaller than linear alkane Cleavage at branching is favored 43 (Branched alkane with Smaller MW)

22. Alkanes Cleavage Favored at branching Loss of Largest substituent Favored intensity of M . + is smaller with branching

23. Aromatic Rings, Double bond, Cyclic structures stabilize M . + Double bond favors Allylic Cleavage  Resonance – Stabilized Cation

24. Aromatic ring has stable M .+

25. Cycloalkane ring has stable M .+

26. + . + -R . + + . + . Saturated Rings lose a Alkyl Chain (case of branching) Unsaturated Rings  Retro-Diels-Alder

27. + . + . Retro Diels-Alder

28. -and -ionones-different spectra-position of db --ionone-RDA frgment m/z 136-abundant -ionone-RDA not favorable-unsubstituted olefin

29. -R . m/z 91 Aromatic Compounds Cleave in b  Resonance Stabilized Tropylium Tropylium ion

30. Tropylium ion

31. - [RCH 2 ]  - [R 2 ]  larger C-C Next to Heteroatom cleave leaving the charge on the Heteroatom

32. Esters lose a molecule of acid- similar to loss of H 2 O from alcs. Deuterium expts- ‘H’ comes from -position When -H not available- a ketene is eliminated Rearrangement reactions in OMS involve ‘H’ atom transfer

33. McLafferty Y  H, R, OH, NR2 Ion Stabilized by resonance - CH 2 =CH 2 Cleavage of small neutral molecules (CO 2 , CO, olefins, H 2 O ….) Result often from rearrangement

34. McLafferty Rearrangement: Involves - H migration to a d.b-6TS Requires- multiple bond. C=O, C=C, C=S, C=N, CC, CN and a - H Interatomic distance of 1.8 A between - H and acceptor Enol form is retained before fragmentation

35. Neutral species like H 2 O, NH 3 , ROH etc.-eliminated from ortho Disubstituted aromatic compounds- Ortho effect Differentiation of Ortho- from meta- and para- isomers

36. -Et  -29 Most intense peaks are often: m/z 41, 55, 69 Double Bond Stabilize M  + Double Bond favor Allylic cleavage CH 2 CH CH  + Et Et Me + CH 2 CH CH Et Me CH 2 CH CH + Et Me M  + = 112 m/z = 83

37. Alcohol An alcohol's molecular ion is small or non-existent.  Cleavage of the C-C bond next to the oxygen usually occurs.  A loss of H 2 O may occur as in the spectra below.

38. Alcohols

39. Phenol

40. Molecular ion is prominent 1) Cleavage in b of aromatic ring Rearrangement 2) C 5 H 5 -CO m/z 93 m/z 65 - CH 2 =CH 2 m/z 94 - R  Aromatic Ether

41. • + B CH 3 —CH 2 —O—CH 2 —CH 2 —CH 2 —CH 3 CH 3 —CH 2 —O + =CH 2 CH 3 —CH 2 —O —CH 2 + Cleavage of C-C next to Oxygen Loss of biggest fragment m/z 59 Aliphatic Ether

42. m/z 73 m/z 45 B CH 3 —CH 2 —CH —O —CH 2 —CH 3 CH 3 CH =O + —CH 2 CH 3 H — CH 2 Box rearr. CH =O + H CH 3 1- Cleavage of C-C next to Oxygen m/z 73 m/z 45 M ·+ 2- Cleavage of C-O bond: charge on alkyl Ether Rearrangement

43. Ether Fragmentation tends to occur alpha to the oxygen atom

44. Aldehyde Cleavage of bonds next to the aldehyde group results in the loss of hydrogen (molecular ion less 1) or the loss of CHO. Major fragmentation peaks result from cleavage of the C-C bonds adjacent to the carbonyl Ketone

45. Carboxylic Acid In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH (molecular ion less 45) are prominent due to cleavage of bonds next to C=O. Ester Fragments appear due to bond cleavage next to C=O (alkoxy group loss, -OR) and hydrogen rearrangements

46. Amide Primary amides show a base peak due to the McLafferty rearrangement Amine Molecular ion peak is an odd number.  Alpha-cleavage dominates aliphatic amines. The base peak is from the C-C cleavage adjacent to the C-N bond.

47. Halide The presence of chlorine or bromine atoms is usually recognizable from isotopic peaks