CHEM 2041 FUNDAMENTAL ORGANIC CHEMISTRY II

1. CHEM 2041 FUNDAMENTAL ORGANIC CHEMISTRY II Second Semester Course By Dr. Barry Miburo

2. CPT 1. INFRARED SPECTROSCOPY & MASS SPECTROMETRY . Objectives: 1.�������� Describe and explain the basic principles and the operation of mass spectrometry (MS) and infrared spectroscopy (IR). 2.�������� Use MS and IR spectra to identify the structure or structural characteristics of organic compounds.

3. 1.1. Infrared Spectroscopy a. Introduction Demos: *Wave: �http://www.colorado.edu/physics/2000/waves_particles/waves.html * Electromagnetic waves & Frequencies: http://www.astronomynotes.com/light/s3.htm Electromagnetic (EM) radiation: synonym of EM wave Photons: components of an EM radiation

4. Electromagnetic Radiations (Continued) Features of electromagnetic radiations: * Wavelength (l): distance between 2 consecutive crests or troughs of one wave. * Period(p): the distance in time between 2 consecutive crests or troughs of one wave. * Frequency(n): the number of crests that pass by one point per second. Note: p = 1/n * Speed = speed of light (c) l = c x p = c / n * Energy: Energy carried by a radiation.

5. Electromagnetic Radiations (Continued 2) Electromagnetic energy: carried by electromagnetic particles (photons) Relation between the characteristics of a radiation. * l = cp = c/n * n = c/ l * E = hn = hc/ l Notes: * c = speed of light * h = Planck�s constant. Refer to CHEM 1211 textbook for additional information

6. Electromagnetic Radiations (Continued 3) Electromagnetic spectrum: http://images.google.com/imgres?imgurl=http://www.nasa.gov/centers/langley/images/content/114284main_EM_Spectrum500.jpg&imgrefurl=http://www.nasa.gov/centers/langley/science/FIRST.html&h=317&w=500&sz=67&tbnid=KDl_2eEm--FMJM:&tbnh=82&tbnw=130&prev=/images%3Fq%3Delectromagnetic%2Bspectrum%26um%3D1&start=2&sa=X&oi=images&ct=image&cd=2 Definition: range of all electromagnetic radiations.

7. b. Infrared absorption spectra Molecules absorb infrared radiation energy. Result: changes in the vibrations of their bonds. Illustrations of bond vibrations: http://www.cmbi.kun.nl/wetche/organic/vibr/ E:\Chapter_12\Present\Animations\IRStretchingandBending.htm IR Spectroscopic process: 1. Molecules are irradiated by IR photons from l = 2.5E-6 m to l = 2.5E-5 m. 2. Molecules absorb the IR energy and undergo bond vibrations. 3. Absorbed energy is detected by IR spectrometer. Instrument schematic image: irinstrmt12_04 �

8. IR absorption spectrum Definition: a graph that shows IR radiations absorbed by a molecule. Example: propane: http://webbook.nist.gov/cgi/cbook.cgi?Name=propane&Units=SI&cIR=on 2-propanol: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-propanol&Units=SI&cIR=on acetone:� http://webbook.nist.gov/cgi/cbook.cgi?Name=2-propanone&Units=SI&cIR=on

9. IR absorption spectrum (Continued) IR Spectra features: X axis: Top of chart: wavelength (l). Units: mm Bottom of chart : Wavenumber (n) = inverse of wavelength. Significance: number of waves / length unit. Units: reciprocal cm (rcm): cm- 1 Y axis: Transmittance: proportion of radiation that passes through. Range: 100% at top of chart, 0% at bottom. Absorbance: proportion of radiation that does not pass through. Range: 0% at top of chart, 100% at bottom. Example: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-propanone&Units=SI&cIR=on

10. c. Interpretation of infrared spectra. *1. Characteristic regions: From 4000 to 2500 rcm: N-H, C-H, O-H single bond stretching From 2500 to 2000 rcm: CC & CN triple bond stretching From 2000 to 1500 rcm: C=C, C=N, and C=O vibrations Below 1500rcm: fingerprint region. different for each molecule.

11. Noticeable peaks (from table 12-2, pg 531) Wave- Absorbing Features number���Substance 3300 Alcohol O-H Strong, broad Amine, amide N-H broad, with 1 or 2 spikes Alkynes ?C-H sharp, may be strong

12. Noticeable peaks (Continued) Wave- Absorbing Features number���Substance 3000 rcm Alkanes C-H Just below 3000 Alkenes =C-H Just above 3000 Carboxylic acid O-H very broad 2300 alkyne -C ?C- just below 2300 nitriles -C ?N- just above 2300

13. Noticeable peaks (Continued 2) Wave- Absorbing Features number���group 1710 rcm carbonyl C=O very strong Aldehydes ketones Esters around 1735 conjugated C=O around 1650 Examples: butanone http://webbook.nist.gov/cgi/cbook.cgi?ID=C78933&Units=SI&Type=IR-SPEC&Index=1#IR-SPEC Butanal: http://webbook.nist.gov/cgi/cbook.cgi?ID=C123728&Units=SI&Mask=80#IR-Spec

14. Noticeable peaks (Continued 2) Wave- Absorbing Features number���group 1660 Alkenes C=C conjugated C=C below 1660 Amides C=O Stronger than C=C Examples: 2-methylbutene: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-methylbutene&Units=SI&cIR=on propanamide http://webbook.nist.gov/cgi/cbook.cgi?Name=propanamide&Units=SI&cIR=on

15. d. Typical IR Spectra 1. Hydrocarbons Example 1: butane, represents alkanes http://webbook.nist.gov/cgi/cbook.cgi?ID=C106978&Units=SI&Type=IR-SPEC&Index=1#IR-SPEC * Strong peak around 2900 rcm: alkane C-H stretch * Peaks below 1450 rcm: fingerprint region

16. Hydrocarbons (Continued: Alkenes) Example 2: 2-methylbutene http://webbook.nist.gov/cgi/cbook.cgi?Name=2-methylbutene&Units=SI&cIR=on#IR-Spec * Sharp peak at 3100 rcm: =C-H stretch * Strong peak at 2980 rcm: -C-H stretch * Sharp peak at 1620 rcm: C=C stretch * Peaks below 1420 rcm: fingerprint region

17. Hydrocarbons (Continued: aromatic compounds) Example: http://webbook.nist.gov/cgi/cbook.cgi?ID=C108883&Units=SI&Type=IR-SPEC&Index=2#IR-SPEC * Above 3000 rcm: =C-H stretches * Around 1600 rcm: C=C stretches

18. Hydrocarbons (Continued: Alkynes) Example: 1-octyne http://webbook.nist.gov/cgi/cbook.cgi?ID=C629050&Units=SI&Type=IR-SPEC&Index=1#IR-SPEC * Around 3350 rcm: ?C-H stretch * Around 2100 rcm: C?C stretch * 1560 rcm & below: fingerprint region

19. *2. Alcohols Example: * 1-butanol: http://wps.prenhall.com/wps/media/objects/340/348272/Instructor_Resources/Chapter_12/Text_Images/FG12_09.JPG �Around 3310 rcm: OH strecth Around 2900 rcm: C-H stretch

20. Carboxylic Acids Example: Propanoic acid http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi * Around 3000 rcm: OH stretch mixed with C-H stretch * Around 1710 rcm: C=O stretch

21. Amines Example: Butanamine: primary amine, RNH2 http://webbook.nist.gov/cgi/cbook.cgi?ID=C109739&Units=SI&Type=IR-SPEC&Index=2#IR-SPEC Around 3300 rcm: N-H stretch. Two spikes for the 2 H�s on N Around 2900 rcm: C-H stretch

22. Amines (2) Example: secondary amine, R2NH 2: �http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi Around 3200 rcm: N-H stretch. One spike -> one H on N. Around 2900 rcm: C-H stretch

23. *3. Carbonyl Compounds General characteristic: C=O group Example: hexanal (aldehyde) http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi * Around 2700 rcm: C-H stretch characteristic of aldehydes * Around 1730 rcm: C=O stretch Note: conjugated C=O groups absorb at lower frequencies

24. Carbonyl Compounds (Esters & Conjugated Ketones ) Example: ethyl butanoate (ester) http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi * At 1739 rcm: C=O group stretching Example 2: 1-penten-3-one (conjugated ketone) http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi * At 1685 rcm: C=O stretch

25. 1.2. Mass Spectrometry (MS) Purpose: Determination of the structure of a compound by recombination of its fragments. Instrument used: mass spectrometer. Procedure: *Decomposition of a molecule into ionized fragments * Separation and identification of the resulting fragments.

26. a. MS: Fundamental Principles Most common type of mass spectrometers: electron ionization spectrometers. Image of MS instrument: http://wps.prenhall.com/wps/media/objects/340/348272/Instructor_Resources/Chapter_12/Text_Images/FG12_15.JPG� Operation process: * A molecule is bombarded by an electron beam. The molecule loses a bond electron to form an cation radical. * The cation-radical breaks down further into charged and neutral fragments. * The charged fragments are attracted into and deflected by the magnetic field in the MS. Angle of deflection: according to their masses and charges. * The position and abundance of the fragments in the detector part of the MS provides information about the mass & structure of the fragments.

27. Mass Spectrum Definition: a bar graph indicating the fragments generated and their abundance as peaks of different heights. * X Axis: m/z (m/e) = fragment mass related info * Y axis: Abundance = info about stability of the fragment. Parent peak or Molecular ion: due to cation from molecule - 1 electron. Base Peak: the tallest peak (given 100% intensity), due to the most stable fragment. Isotopic peaks: * due to presence of isotopes of C, H, O, N, ... in the sample molecule. * appear around the main peaks.

28. Mass Spectrum (Illustration) Example: 2-methylpentane http://wps.prenhall.com/wps/media/objects/340/348272/Instructor_Resources/Chapter_12/Text_Images/FG12_16.JPG� Molecular ion: m/z = 100 Base peak: m/z = 41 Other remarkable peaks: * m/z = 85 : M(+) � 15 * m/z = 57: m/z 85 - 28

29. b. MS fragmentation patterns of some functional groups General rule: most favored fragmentation routes are the ones that: * produce most stable cations * lose the most stable radicals. � b1. Alkanes Most visible losses: * ethyl radical, more stable than methyl radical * Ethene molecule Example: Hexane: http://webbook.nist.gov/cgi/cbook.cgi?Name=hexane&Units=SI&cMS=on

30. Hexane MS

31. Hexane MS (Continued)

32. Alkenes Most stable fragments: allylic cations Reason for stability: delocalization of the charge by resonance Example: 2-hexene http://webbook.nist.gov/cgi/cbook.cgi?Name=2-hexene&Units=SI&cMS=on

33. 2-Hexene MS

34. 2-Hexene MS (Continued)

35. b3.� Alcohols Two major fragmentation patterns a-cleavage: loss of a C-C bond nexte to the OH group. Result: a neutral radical and a O containing cation Dehydration: elimination of h2o. Result: a alkene radical cation + H2O. Notes: * Presence of a even numbered peak = Hint of loss of neutral molecule. * Loss of H2O is so frequent that M(+) peak of alcohols is low or absent. Example: 2-methylbutanol http://wps.prenhall.com/wps/media/objects/340/348272/Instructor_Resources/Chapter_12/Text_Images/FG12_21.JPG

36. Alcohols Fragmentation (Illustration)

37. Alcohol MS (2-methylbutanol)

38. b4. Amines Fragmentation General feature: odd MW Most common fragmentation pattern: alpha cleavage. Result: N-containing fragment with an even m/z Example: N-methyl-2-pronanamine http://webbook.nist.gov/cgi/cbook.cgi?ID=C4747211&Units=SI&Mask=200#Mass-Spec

39. MS of N-methyl-2-pronanamine

40. b5. Carbonyl compounds Major fragmentation patterns *1. McLafferty rearrangement Structural condition: minimum 3-C chain Next to the C=O group. MS Event: Transfer of the H 3 C's away from the O. Result: an alkene radical and O-containing fragment with an even m/z.�

41. McLafferty Rearrangement

42. *2. Alkyl-carbonyl cleavage General structure: R-CO-R� Bond breaks between the C=O group and the R group. Result: Acylium ion, R'-(C=O)(+) Example: 2-hexanone: http://webbook.nist.gov/cgi/cbook.cgi?ID=C591786&Units=SI&Mask=200#Mass-Spec�

43. Alkyl-carbonyl cleavage (in general)

44. MS of 2-Hexanone (Ketone)

45. b6. Carboxylic acids *1. Acyl-alkyl cleavage Bond breaks between C=O group and alkyl group. Result Acylium-type of ion *2. Alkyl loss to produce an allylic system in resonance with the two O atoms. *2. McLafferty rearrangement when possible Example: Hexanoic acid http://webbook.nist.gov/cgi/cbook.cgi?ID=C142621&Units=SI&Mask=200#Mass-Spec

46. Carboxylic Acids Example: hexanoic acid