MASS SPECTROMETRY: BASIC EXPERIMENT

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1 Pavia MASS SPECTROMETRY: BASIC EXPERIMENT scienceaid.co.uk -e - Molecule Molecule +. Types of Ionization Electron Ionization, EI Chemical Ionization, CI Desorption Ionization Techniques Secondary Ion MS, SIMS Fast Atom Bombardment, FAB Matrix Assisted Laser Desorption Ionizaton, MALDI Electrospray Ionization, ESI

2 Electron Ionization en.wikipedia.org High vacuum e e - MW=142

3 ml Effect of electron energy on appearance of E.I spectra e + 2e 1-propanol (C 3 H 8 O, M = 60) 70 ev 20 ev 14 ev 11 ev Chemical Ionization Introduction of Ionizing reagent CH 4, NH 3, etc CH 5 + CH + 5 CH 4 M CH 4 CH 4 CH 5 + CH CH 4 4 vacuum CH 4 + e - CH e - CH CH 4 CH CH 3 CH 5 + (M+H) + + CH 4

4 MW=142 EI CH 4 (CH 3 ) 2 CHCH 3 Desorption Ionization Techniques: SIMS: secondary ion bombardment Xe: Fast AtomBombardment h : Matrix Assisted Laser Desorption Ionization The matrix can be many compounds (see list Fiqs 8.6 & 8.7). Very often the ion with the highest MW is M+matrix.

5 Electrospray Ionization (ESI) Used for very high molecular weight biological molecules because multiple charged species are formed. ESI mass spectrum of horse heart myoglobin (mass Da)

6 Mass Analyzers Magnetic sector scienceaid.co.uk Kinetic energy = 1 / 2 mv 2 = zv r = mv /zb m/z = B 2 r 2 /2V Double focusing Mass Spectrometer home.postech.ac.kr epa.gov

7 Quadrapole Mass Spectrometer Ion Trap Low MW < 1000 and unit mass resolution. Very compact and relatively cheap. Time of Flight (ToF) Detects all ions so this is very sensitive. Can be used for very high molecular weight. High resolution. When coupled to MALDI, ToF is excellent for biological samples

8 IONIZATION Pavia 8.8 Where does the electron come from? e e - FRAGMENTATION Pavia 8.8 Radical cations formed upon electron impact are unstable! Remember: You will only see positively charged species (cations and radical cations), not neutral radicals.

9 Fragmentation of Radical Cations Radical cations are very reactive species Radical cations are very unstable. Fragmentations are unimolecular chemical reactions. The relative stability of cations and radical cations can often be understood in terms of substitution patterns and resonance. Remember: Ease of formation of carbocations less stable more stable c.f. ease of S N 1 reactions of R-Hal, or E1 dehydration of ROH Alkyl groups are inductive electron donating substituents Allylic and benzylic cations are resonance stabilized

10 Spectral Database for Organic Compounds (SDBS) Alkanes Pavia 8.8 I hexane (C 6 H 14 ; M = 86) 43 M M M M base peak 57 small M 15 Linear Alkanes - Molecular ions fragment by cleavage of C-C bonds to give one cation and one radical 29 M M M M Peaks appear in clusters separated by 14 mass units.

11 Spectral Database for Organic Compounds (SDBS) with other fragments corresponding to 1 and 2 mass units fewer. Alkyl radical cations can lose a hydrogen atom (radical) to give a new cation radical, e.g.: 2-methylpentane (C 6 H 14 ; M = 86) 43 M M M M base peak 43 smaller

12 Spectral Database for Organic Compounds (SDBS) 29 M M M M methylpentane (C 6 H 14 ; M = 86) 57 M M M M base peak 57 even smaller

13 Spectral Database for Organic Compounds (SDBS) 29 M M M M M 43?! (Radical) Carbocations rearrange: 2,2-dimethylbutane (C 6 H 14 ; M = 86) 43 M M M M No!!

14 29 M M M M Branched alkanes give weaker M + ions, and stronger M 15 peaks. Which is which? (all C 6 H 14 ) hexane 2-methylpentane 2,2-dimethylbutane

15 Which is which? (all C 10 H 22 ; M = 142) 3,4-diethylhexane 3,3-dimethyloctane 5-methylnonane Summary: Alkanes For straight chain alkanes - Molecular ion peak is usually present but weak - Clusters of fragments appear spaced by m/z of 14, corresponding to CH 2 - The largest peak in each cluster corresponds to an alkyl radical cation, C n H 2n+1 - A peak for M CH 3 is often weak or absent - The intensity of lower m/z fragments is greater, with the intensities decreasing smoothly up to M C 2 H 5. Branched alkanes - Smaller molecular ion peak - More fragmentation at highly branched positions

16 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) Cycloalkanes cyclohexane (C 6 H 12 ; M = 84) 41 M M Pavia 8.8 J 69 M 15 base peak has even m/z M 28 strong!! methylcyclopentane (C 6 H 12 ; M = 84) 56 M M 43 84

17 Spectral Database for Organic Compounds (SDBS) Summary: Cycloalkanes 1. Relatively large molecular ion peak 2. Significant peak at M 28 (often the base peak) 3. M 15: from rearrangement Alkenes 1-hexene (C 6 H 12 ; M = 84) 41 M M 28 Pavia 8.8 K 84 strong M 43 base peak has even m/z M 28

18 Spectral Database for Organic Compounds (SDBS) Summary: Alkenes 1. Relatively strong ion 2. Strong peak arises from fragmentation to form a resonance stabilized allylic cation 3. Difficult to identify position of alkene since the double bond migrates easily. cyclohexene (C 6 H 10 ; M = 82) 54 M base peak has even m/z M 28?!

19 Retro-Diels-Alder Reaction limonene (C 10 H 16 ; M = 136) base peak has even m/z M 68

20 Spectral Database for Organic Compounds (SDBS) Which is which? (all C 8 H 16 ; M = 112) propylcyclopentane 2-ethyl-1-hexene 2,5-dimethyl-1-hexene Alkynes Pavia 8.8 L 1-hexyne (C 6 H 10 ; M = 82) M 1 82 M 1!!

21 Spectral Database for Organic Compounds (SDBS) Summary: Alkynes M 1 peak observed strong peak arises from fragmentation to form a resonance stabilized propargyl cation Aromatic Hydrocarbons toluene (C 7 H 8 ; M = 92) 91 M 1 92 Pavia 8.8 M strong m/z = 91

22 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) ethylbenzene (C 8 H 10 ; M = 106) 91 M strong m/z = 91 1-butylbenzene (C 10 H 14 ; M = 134) 91 M strong m/z = 91

23 Spectral Database for Organic Compounds (SDBS) -bromotoluene (C 7 H 7 Br, M = 170[ 79 Br]) 91 M M+2 strong m/z = 91 What are all those m/z = 91 for PhCH 2 X?

24 Spectral Database for Organic Compounds (SDBS) 1,4-diethylbenzene, M =134 Alcohols, Ethers and Amines Pavia 8.8 N,O,T 1-hexanol (C 6 H 14 O, M = 102) 56 M M M M M m/z = 31 Base peak m/z = even!! M 18??

25 Spectral Database for Organic Compounds (SDBS) Summary: Alcohols 1. Weak peak 2. -cleavage of an alkyl radical 3. Dehydration 4. Dehydration with loss of CH 2 =CH 2 2-hexanol (C 6 H 14 O, M = 102) 45 M M M M

26 Spectral Database for Organic Compounds (SDBS) Which is which? (all C 7 H 16 O; M = 116) heptanol 2,2-dimethyl-3- pentanol 3-ethyl-3-pentanol diisopropyl ether (C 6 H 14 O, M = 102) 45 M M

27 Spectral Database for Organic Compounds (SDBS) Summary: Ethers 1. -cleavage of alkyl radical 2. C-O bond cleavage dibutyl amine (C 8 H 19 N, M = 129) 86 M 43 The Nitrogen Rule: C,H,N,O,S molecules with an odd molecular mass must contain an odd number of nitrogen atoms 129

28 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) 1-methylheptylamine (C 8 H 19 N, M = 129) 44 M Which amine? 58 M

29 science.widener.edu/svb/massspec/ci.html Identify each compound There is one alcohol, one ether and one amine dipropylether 3,3-dimethyl-2-butanol triethylamine E.I and C.I of tri-n-butylamine C 12 H 27 N (MW = 185) C.I. (CH 4 )

30 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) Aldehydes and ketones Pavia 8.8 P-Q propanal (C 3 H 6 O, M = 58) 29 M M 1 2-butanone (C 4 H 8 O, M = 72) 43 M M 15 72

31 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) hexanal (C 6 H 12 O, M = 100) 44 M M hexanone (C 6 H 12 O, M = 100) 43 M M M M

32 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) benzaldehyde (C 7 H 6 O, M = 106) 77 M M acetophenone (C 8 H 8 O, M = 120) 77 M M

33 Summary: Aldehydes and Ketones 1. -cleavage: C C(=O) and C(=O)-H 2. McLafferty rearrangement for CH-C-C-C(=O) Which is which?

34 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) Which ketone? 105 M M Carboxylic acids and derivatives propanoic acid (C 3 H 6 O 2, M = 74) 29 M Pavia 8.8 R,S 45 M M M 1

35 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) butanoic acid (C 4 H 8 O 2, M = 88) 60 M M M M benzoic acid (C 7 H 6 O 2, M = 122) 77 M M

36 Spectral Database for Organic Compounds (SDBS) Summary: Carboxylic acids 1. M-1 2. Cleavage of OH 3. Cleavage of R-C(O) [CO 2 H]+, M = 45 R+ 4. McLafferty rearrangement for CH-C-C-C(=O)OH methyl acetate (C 3 H 6 O 2, M = 74) 43 M M 15 74

37 Spectral Database for Organic Compounds (SDBS) Summary: Esters 1. Cleavage of C(=O) OR 2. -cleavage of R-C(O) 3. McLafferty 4. Elimination to give RCO 2 H + alkene derives from R Which ester?

38 Spectral Database for Organic Compounds (SDBS) Identify each ester C 6 H 12 O 2 esters, MW = tert-butyl acetate CH 3 C(=O)OC(CH 3 ) Methyl pentanoate CH 3 CH 2 CH 2 CH 2 COOCH 3 57 Isopropyl propionate CH 3 CH 2 COOCH(CH 3 ) Halogen Containing Compounds Pavia 8.8 V 2-chloropropane (C 3 H 7 Cl, M = 78 [ 35 Cl]) 43 M M M+2

39 Spectral Database for Organic Compounds (SDBS) Spectral Database for Organic Compounds (SDBS) 1-chloropropane (C 3 H 7 Cl, M = 78 [ 35 Cl]) 42 M chloroheptane (C 7 H 15 Cl, M = 134 [ 35 Cl]) M+2

40 Spectral Database for Organic Compounds (SDBS) 2-bromopropane (C 3 H 7 Br, M =122 [ 79 Br]) 43 M Br M+2 Summary: Alkyl halides C-X bond cleavage -cleavage Dehydrohalogenation (-HX) Dehydrohalogenation with loss of an alkene

41 SUMMARY: SOME COMMON FRAGMENT PEAKS Pavia Appendix 12 Peak Fragment Interpretation lost M 1 H aldehydes, 3 alcohols, cyclic amines M 2 Multiple H 2 alcohols M 3 Multiple H 1 alcohols M 15 CH3 methyl groups M 17 HO alcohols, phenols, carboxylic acids M 18 H 2 O alcohols M 26 HC CH M 27 HC=CH 2 M 28 CH 2 =CH 2 cyclic alkanes, alkenes CH 3 CH 2 CH 2 C(=O)X [McLafferty rearr.] M 19,35/37,79/81 halogen M 15,29,43,57,71, alkyl M 31,45,59,73,87 alkoxy esters, ethers Peak Fragment Interpretation observed Pavia Appendix H 2 C C CH from alkyne propargyl cation + 41 H 2 C CH=CH 2 from terminal alkene allyl cation 42 H 2 C=C=NH 2 from 1 amine (R CH 2 NH 2 ) 43 H 2 C=C=OH from 1 alcohol C 6 H 5 + from substituted phenyl 91 C 7 H + 7 from C-substituted phenyl tropylium cation

42 Spectral Database for Organic Compounds (SDBS) Compound X revisited, yet again Analysis of fragmentation STRUCTURAL information 57 M Fragmentation: Structure contains: Georgia Tech Mass Spec Facility VG Instruments 70SE Two sector MS; high resolution and accurate mass measurement (< 5 ppm); equipped with a GC; ionization by EI or CI for analysis of low molecular mass (< 700 Da). FAB for much larger (< 5 kda) polar, non-volatile molecules. Applied Biosystems 4000 QTrap Hybrid quadrupole / linear ion trap tandem mass spectrometer; HPLC interfaced. Applied Biosystems 4700 Proteomics Analyzer Time-of-flight (TOF/TOF) MALDI. Molecular mass species up to 10 kda with low resolution, and high resolution and accurate mass measurement <10 kda. Micromass Quattro LC Low resolution, moderate mass accuracy triple quadrupole (QQQ) tandem MS; ionization via ESI and atmospheric pressure chemical ionization (APCI). Thermo Orbitrap Very high-resolution, very sensitive ESI instrument. Bruker ToF/ToF For imaging and proteomics, with a quadrupole ion trap. Interfaced with LC

43 NEVER ASK A MASS SPECTROMETRIST FOR JUST A MASS SPEC! 1. Always define the technique that you want. 2. Even Better, discuss the problem you are working on! Reporting MS Spectra in Papers and Progress Reports A MS (EI, 70 kv): molecular ion m/z 91 (tropilium, 100%), 205 (M-29, 64%), 234(, 35%), B C base peak 235 (M+1, 4.6%). D Fragments that help in structure determination M+1 peak (or others) that indicate something about molecular structure based on isotope distribution A B C D Ionization technique/method (e.g., EI, CI, FAB, MALDI). Mass Assignment of the peak to a particular ion Height of the peak relative to the base peak (100%)

44 Reporting HRMS Spectra in Papers and Progress Reports A HRMS (EI, 70 kv): m/z , 39%; Calc. for C 4 H 8 N 2 O, = 2 ppm. B C D E A B C D E Ionization technique/method (e.g., EI, CI, FAB, MALDI). Mass Height of the peak relative to the base peak (100%) Suggested formula The difference between the experimental value of molecular weight and the value calculated for the putative molecular formula, in ppm: = M exp M calc 10 6 /M exp WORK AS MANY PROBLEMS AS POSSIBLE! Pavia, chap 8 questions: 7 (a)-(x), 8, 9, 10, (a)-(f), 11, (a)-(g), 12 (a)-(c), 13, 14, 15 (a)-(b)

45 Problem sets based on M.S. alone Intensities of peaks are provided, you need to download free spectral visualization software to view actual spectra Determine the structures of the compounds for which the mass spectra and IR spectra are provided on the following slides. In some cases you might be able to identify a single compound. For others, a 1 H NMR would really help!! Compound A IR functional group fragmentation structure! Exact mass = C 7 H 14 O

46 Compound B IR functional group MS probably lets you identify the exact isomer C.I. Exact mass = C 7 H 16 O Compound C Quickly hone in on formula and 4 possible structures Exact mass = C 7 H 7 Br

47 Compound D Formula, IR a few possibilities MS probably might let you identify the exact isomer Exact mass = C 5 H 11 Br Compound E IR functional group McLafferty small number of possible structures! Exact mass = C 6 H 12 O

48 Compound F Small molecule! IR functional group structure! Exact mass = C 3 H 6 O 2 Compound G Only a few possibilities here Exact mass = C 4 H 11 N

49 Compound H Formula, IR structure! C.I. Exact mass = C 3 H 4 O Compound I Which functional groups contains N and O and have a distinctive set of IR peaks? C.I. Exact mass = C 3 H 7 NO 2

50 Compound J NMR would help here, but what can you tell about the structure based on IR and MS? Exact mass = C 8 H 10 O 2 Compound K What can you tell about the structre based on IR and MS? When do we get the NMR? Exact mass = C 8 H 10 O

51 Compound L functional group? m/z = 74 m/z = 71 structure! Exact mass = C 3 H 10 O 2 Compound P What N-containing functional group? Sites of unsaturation? 3 possible strucutres? Exact mass = C 6 H 4 ClNO 2

52 Compound Q You will need an NMR to solve this, but what do you know from the IR and MS? C.I. Exact mass = C 7 H 13 BrO 2 Compound R You will need an NMR to solve this, but what do you know from the IR and MS? Exact mass = C 6 H 10 O

53 Compound S You might only get a limited amiount of information from this data Exact mass = C 8 H 14 O Compound T McLafferty says? C.I. Exact mass = C 6 H 12 O 2

54 Compound U Data a few possible compounds Exact mass = C 6 H 4 Cl 2 O Compound V Data a few possible compounds Exact mass = C 8 H 10 O

55 Compound W C=O (low freq?); M-28; C 6 H 8 O How many possibilities? Exact mass = C 6 H 8 O

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