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Chem-805 Identification of organic and inorganic compounds by spectroscopy

Chem-805 Identification of organic and inorganic compounds by spectroscopy. Mass Spectrometry NMR Infrared. Mass Spectrometry. Simplest form of mass spectrometer performs 4 essential functions: (under vacuum 10 -6 mm Hg).

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Chem-805 Identification of organic and inorganic compounds by spectroscopy

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  1. Chem-805Identification of organic and inorganic compounds by spectroscopy Mass Spectrometry NMR Infrared

  2. Mass Spectrometry Simplest form of mass spectrometer performs 4 essential functions: (under vacuum 10-6 mm Hg) • It subjects vaporized molecules to bombardment by a stream of high-energy electrons, converting these molecules to ions • These ions are then accelerated in an electric field • The accelerated ions are then separated according to their mass-to-charge ratio in a magnetic or electric field • The ions that have a particular mass-to-charge ratio are then detected by a device that counts the number of ions striking it

  3. Mass Spectrometry: Introduction MS is concerned with the separation of matter according to atomic and molecular mass. With recent development and improvement of instrumentation and techniques it can be used in the analysis of organic compounds of molecular mass up to as high as 200,000 Daltons. MS uses magnetic and electric fields to exert forces on charged particles (ions) in a vacuum. Therefore, a compound must be charged or ionized to be analyzed by a mass spectrometer.

  4. Mass Spectrometry Atomic and molecular weight are expressed in Atomic Mass Unit (amu). The amu is based on a relative scale in which 12C is assigned exactly 12 amu. Also called dalton Each isotope has specific exact mass. MS is interested in exact mass up to 3-4 figures after decimal point (high resolution HR). Chemical atomic weight is the average weight taking into account the mass of each isotope and their natural abundance.

  5. Components of a mass spectrometer 10-5 to 10-8 Torr System Inlet Ion Source Mass Analyzer Detector Signal processor Vacuum System m/z

  7. MS : Ionization • Gas Phase: • Electron ionization (EI) • Chemical ionization (CI) • Field Ionization (FI) • Desorption • Field Desorption (FD) • Fast Atom Bombardment (FAB) • Secondary Ion Mass Spectrometry (SIMS) • Laser Desorption (LD) • Plasma Desorption (PD) • Thermal Desorption • Thermospray ionization (TS) • Electrospray (ES)

  8. Mass analyzers: Magnetic sector In Magnetic Field (H) an ion of charge z and mass m experiences centripal force Hzv (where v is the velocity of the ion). At the same time, any particle moving on a circle of radius r experiences centrifugal force of mv2/r When these two forces are equal the ion travel on a circle and Hzv = mv2/r m/z = Hr/v We could measure v, the velocity of the ion to determine the mass but this is very difficult experimentally

  9. Mass Spectrometer • If a molecule absorb an electron (creating a Negative Ion), It will be absorbed by the repeller plate • The repeller plate (Positively charged) directs the ions through a series of accelerating plates Kinetic Energy : • In Magnetic Field (H) ions describe a curved Path (r -> curvature) • Ions with reater m/e have larger curve • Instruments has fixed curve => only particules with correct m/e can reach detector • Magnetic field is varied to detect all ions 1 mv2 = eV2 m = H2 r2 e 2v r = mv eH

  10. Components of MS: MassAnalyzers Dispersion of the ions is based on mass-to-charge ratio Mass Analyzer There are several type of mass analyzers. • Magnetic sector • Electrostatic and Magnetic sector • Quadrupole MS filter • Ion trap analyzers • TOF – Time-of-Flight • FT-MS

  11. Components of MS: Detector, Vacuum Detector Convert the beam of ions in an electrical signal that can be processed, stored, displayed and recorded in many ways. Electron Multiplier (most commonly used) Other: Faraday cup Photographic plates Scintillation type Vacuum System MS require the high vacuum is maintained in all spectrometer components (except signal processing)

  12. Amplifying signal Continuous Dynode electron multiplier Provide high gain and nanosecond response time.

  13. CH3OH + e-CH3OH+ + 2e- [CH3OH]+ [CH2OH]++ H  Mass Spectrum Ionization: m/z 32 Molecular ion Fragmentation: m/z 31 CH3++ HO  CHO++ H2 m/z 15 m/z 29 B  Base Peak  100% Tabular presentation Bar graph presentation

  14. B+ Benzamide: EI M+ 77 44 - NH2 - CO C6H5C=O + C6H5+ m/z 105 m/z 77 105

  15. 3-methyl-6-i-PropylCyclohex-2-ene-1-one MW = 152 Isotopic cluster M, M+1, M+2

  16. Natural Abundance of a few elements Isotope Atomic weight Mass % Abundance 1H 1.008 1.00783 99.99 2H 2.01410 0.016 12C 12.011 12.0000 (std) 98.89 13C 13.00336 1.11 14N 14.0067 14.0031 99.64 15N 15.0001 0.36 16O 15.9994 15.9949 99.76 17O 16.9991 0.04 18O 17.9992 0.20

  17. Natural Abundance of a few elements Isotope Atomic weight Mass % Abundance 19F 18.998 18.9984 100.0 28Si 28.0855 27.9769 92.17 29Si 28.9765 4.71 30Si 29.9738 3.12 32S 32.066 31.9721 99.64 33S 32.9715 0.76 34S 33.9679 4.20 35Cl 35.4527 34.9689 75.77 37Cl 36.9659 24.23

  18. Natural Abundance of a few elements Isotope Atomic weight Mass % Abundance 31P 30.9738 30.9738 100.0 79Br 79.9094 78.9183 50.52 81Br 80.9163 49.48 126I 126.9045 126.9045 100.00 The Atomic weight: Average atomic weight of all isotopes with their natural abundances Atomic weight Br: [% 79Br x 78.9183] + [% 81Br x 80.9163] [50.52 x 78.9183] + [49.48 x 80.9163]= 79.9094

  19. Natural Abundance of a few elements

  20. M+ (molecular ion)  m/z Molecular formula M mass of the most abundant isotope e.g C7H7NO : 7 x 12C = 84 7 x 1H = 7 1 x 14N = 14 1 x 16O = 16 m/z  121 Isotope peaks: (% respect to M) M+1 due to (13C) or 15N (17O) or 2H are negligeable) %(M+1) = (1.1 * #C) + (.38 * #N) = 8.08 % %(M+2) = (1.1 * #C)2/200 + (.2 * #O) = 0.5% For C, H, N,O, F, P composition

  21. Molecular formula in general Molecular ion: Even Mass : can containC, H, O , halogen, even # N Odd Mass :can containC, H, O , halogen,odd # N Fragmentation ions: Even Mass : From even mass M+ comes from rearrangement or 2 bond breaking Odd Mass : From even mass M+ comes from single bond breaking even Mass:from Odd Mass M+ comes fromsingle bond breaking

  22. Molecular formula: RULE of 13 Consider CH unit  13 amu If we divide the mass by 13 we can establish easily possible formula: Example: Molecular ion=>152 152 / 13 = # carbons = 11 Mass = 12 * 11 = 132 therefore H = 152 – 132 = 20 Basic formula C11H20 If Oxygen is present : mass = 16 remove CH4 If Nitrogen is present : mass = 14 remove CH2 If one oxygen : C11H20– CH4+ O = C10H16O If second oxygen : C10H16 O– CH4+ O = C9H12O2 If third oxygen : C9H12 O2– CH4+ O = C8H8O3

  23. Molecular formula: RULE of 13 After establishing the basic formula with only Carbon/hydrogen, Other element can be introduced by substracting the proper hydrocarbon value 16O => CH4 14N => CH2 19F => CH7 1H12=> C 28Si => C2H4 31P => C2H7 32S => C2H8 35Cl => C2H11 79Br => C6H7 127I => C10H7

  24. Nitrogen rule Molecular ion=>26 Molecular ion=>27 odd! 26 / 13 = # carbons = 2 27 / 13 = # carbons = 2 Mass = 12 * 2 = 24 therefore H = 2 Basic formula C2H3 Basic formula C2H2 One NitrogenC2H3 - CH2 + N

  25. Nitrogen rule Molecular ion=>100 Molecular ion=>99 odd! 100 / 13 = # carbons = 7 Basic formula C7H16 Mass = 12 * 7 = 84 therefore H = 16 1 Nitrogen: C7H16 – CH2 + N Basic formula C7H16 C6H14 N 1 Oxygen: C7H16 - CH4 + O C6H12 O

  26. Calculating M+1 and M+2

  27. Isotope peaks Usually [M+2] peak is very small Except for: M M+1 M+2 Sulfur : 32S : 100 34S : 4.4 Silicon : 28Si: 100 29Si: 5.2 30Si : 3.35 Chlorine : 35Cl : 100 37Cl : 32.5 Bromine : 79Br : 100 81Br : 98

  28. Isotope peaks : CH3Br [12CH379Br]+ [12CH381Br]+ M - H [13CH379Br]+ [12CH279Br]+ [12CH281Br]+ [13CH381Br]+

  29. Bromine 79Br 81Br 79Br 81Br 2 intense peaks for the molecular ion, spaced by 2 daltons. 79Br and 81Br

  30. Chlorine 35Cl (P= .75) 37Cl (P= .25) Ratio 3:1 Probability : [M+] / [M + 2] = 0.75 / 0.25 = 3 / 1 100 : 33

  31. Calculation of isotope pattern: 2 Cl C2H235Cl2 1 Cl C2H235Cl 37Cl C2H237Cl35Cl C2H237Cl2 2 Cl P (2 35Cl) = (0.75 )2 = 0.563 P (35Cl 37Cl) + P (37Cl 35Cl ) = (0.75 ) (0.25 ) + (0.25 ) (0.75 ) = 0.375 P (2 37Cl) = (0.25 )2 = 0.063 [M+] / [M + 2] / [M + 4] = 100 / 66 / 11

  32. Calculation of isotope pattern: ClBr 35Cl => .7537Cl => .25 79Br => 51%81Br => 49% [RClBr]+ can exist as 4 isotopic forms: 35Cl 79Br M 0.75 x 0.51 = 38% 35Cl 81BrM+20.75 x 0.49= 37% 50% 37Cl 79Br M+20.25 x 0.51 = 13% 37Cl 81BrM+40.25 x 0.49= 12% At very high resolution, the 2 (M + 2) peaks can be distinguished (separated by 0.001 Dalton)

  33. Chlorine and Bromine The Molecular ionM+ is always the lowest mass peak in the ion cluster (regardless of it’s relative intensity)

  34. Isotopic abundances for Carbon containing compounds M+ => p(M) = p(n12C) = (0.989)n The probability of finding 1 13C among n carbons is: [M+1]+ => p(M+1) = p(n-1) 12C + 1 13C= n p[n-1] 12C x p(13C) = n(0.989)n-1(0.011) Relative ratio: [M+1]+ / [M+] =n(0.989)n-1(0.011) / (0.989)n =n (0.011) / (0.989) =n (0.0111) In percentage: n x 1.1 %

  35. Isotopic abundances for Carbon containing compounds When comparing calculated abundances with observed intensities: We see that the ratio is not identical: due to experimental error The relative abundance of the larger peaks are reproducible to ±10% For smaller peaks, relative intensity is larger Generally speaking, The size of the [M+1]+ ion can be used to figure out the number of carbons in a molecule For example, if molecular ion is observed at m/z 118 and the ion at m/z 119 has an intensity of about 9% There are probably 8 carbons(1.1% x 8 = 8.8% )

  36. Isotopic abundances for Carbon containing compounds Due to the relatively large error on peak intensity ( ±10%) determination of the number of carbons is sometime ambiguous For example: [M+1]+=> intensity22.5± 2.3% Range covers 20.2 to 24.8 => 20 ± 2 carbons

  37. Isotopic abundances for other common nuclei For 15N: [M+1]+ / [M]+ => n x 0.36% For 33S: [M+1]+ / [M]+ => n x 0.80% For 18O: [M+2]+ / [M]+ => n x 0.20% For 34S: [M+2]+ / [M]+ => n x 4.42%

  38. Calculating Peak Intensities from Isotopic abundances

  39. Isotopic abundances for Silicon Often observed is TMS compounds M+2 larger than usual Often observed either from GC column Or septum

  40. Isotopic abundances for Sulfur SO+ M+2 M+2 For 18O: [M+2]+ / [M]+ => n x 0.20% For 34S: [M+2]+ / [M]+ => n x 4.42% [M+2]+= 4.42 + (2 x 0.20) = 4.82%

  41. isotope pattern: 2 Cl (example) When there are many carbons, isotopic pattern for 13C adds up to chlorine pattern

  42. Steps in the Identification of Unknown • Identify Molecular ion M.+ • Determine Molecular Formula (odd / even mass) • Analyze heteroatom (M+1 and M+2 …) • S, Si, Cl, Br, …. • Use rule of 13 to determine # Carbons (M+1 and M+2 …) • Compare with 13C-NMR(# carbons) with APT experiment (J-MOD) ( # protons) • Compare with proton NMR ( # protons) • Identify base peak (note if even / odd) • One or two bond fragmentation • Test your conclusions: in lab make derivatives (TMS … or Na or K complexes  mass shift)

  43. Solving problems in MS • Try to identify the Molecular Ion ordecide if it is present (most critical step in solving a structure) • Check if [M+1]+ ion is too large to accommodate reasonable number of carbons. (the [M+1]+ ion might be the very small M+ instead!) • Determine the first loss from proposed molecular ion. Some loss are impossible (e.g 12, 14, 23 daltons) • Does the spectrum appear dirty? (lots of small peaks even at high mass) • If GC of the comopund Is available, compare retention time • Is the molecular weight even or odd? • An odd mass can be associated with an odd number of Nitrogen • An even mass means no Nitrogen or an even number of Nitrogen • This Rule is applicable only to Molecular ion and to odd-electron ions • Examine ion cluster for isotopic natural abundance (look for special heteroatom pattern). Try to calculate number of carbons

  44. Solving problems in MS • From the overall appearance: is it a fragile compound? Is it likely to be aromatic or aliphatic? • Look in the low mass ions. Do you see any clues of the family of compounds that you might be dealing with? • Make a list of suggested losses from the molecular ion and try to make a pattellsrn from them. • Look for intense odd-electron ions in the spectrum: this is almost impossible in compounds containing Nitrogen! These provides clues for rearrangements (retro Diels Alder, McLafferty…) • Speculate on the structure using all that information Index of Hydrogen deficiency CxHyNzOn Index = x – ½ y + ½ z+1

  45. Neutral losses and Ion series M-30 NO  (Nitro compounds), H2 CO  (anisoles) M-1 H M-15 CH3 M-16 O  (rare) , NH2  M-31 CH3O  M-17 OH , NH3(rare) M-32 CH3OH M-18 H2O M-35 Cl  M-19 F  M-36 HCl M-20 HF (very rare) M-42 CH2=C=O, CH2=CH-CH3 M-26 HCCH , CN M-43 CH3CO  , C3H7 M-27 HCN M-44 CO2 M-28 H2C=CH2 , CO M-45 CH3CH2O  , CO2H  M-29 CH3CH2  ,HCO 

  46. Neutral losses and Ion series Figuring out which peak is molecular ion can be supported by identifying what fragment is lost. There can be sometimes 2 consecutive loss: In steroid, M-33 is often observed: comes from the loss of Me and H2O The ions loss are only useful from molecular ion There is no fragment in organic compounds between M-1 and M-15 Loss of M-14 is never observed! Other gaps in mass loss are: between 21-25, 33-34, 37-41 Ionsin these areas should be viewed suspiciously: either compound is not pure or postulated molecular ion is wrong

  47. Neutral losses and Ion series Among the losses: most common are Loss of H, CH3 , H2O(from some oxygenated compounds), HCCH (from aromatic compounds), HCN (from aromatic compounds containing Nitrogen), CO and CH2=CH2(both at 28! Difficult to tell which one is lost) Ethyl radical (29) Methoxy radical (31) Cl and HCl (35, 36) Acetyl (43) accompanied by m/z 43 prominent and propyl (43) radical

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