CHEM 2041FUNDAMENTAL ORGANIC CHEMISTRY IISecond Semester Course

By

Dr. Barry Miburo

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.

1.1. Infrared Spectroscopya. IntroductionDemos:*Wave: http://www.colorado.edu/physics/2000/waves_particles/waves.html* Electromagnetic waves & Frequencies: http://www.astronomynotes.com/light/s3.htmElectromagnetic (EM) radiation: synonym of EM wave Photons: components of an EM radiation

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.

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/ lNotes: * c = speed of light* h = Plancks constant. Refer to CHEM 1211 textbook for additional information

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.

b. Infrared absorption spectraMolecules 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

IR absorption spectrumDefinition: a graph that shows IR radiations absorbed by a molecule.Example: propane: http://webbook.nist.gov/cgi/cbook.cgi?Name=propane&Units=SI&cIR=on2-propanol: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-propanol&Units=SI&cIR=onacetone: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-propanone&Units=SI&cIR=on

IR absorption spectrum (Continued)IR Spectra features:X axis: Top of chart: wavelength (l). Units: mmBottom of chart : Wavenumber (n) = inverse of wavelength. Significance: number of waves / length unit. Units: reciprocal cm (rcm): cm- 1Y 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

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

Noticeable peaks (from table 12-2, pg 531) Wave- Absorbing Features numberSubstance 3300Alcohol O-HStrong, broadAmine, amide N-Hbroad, with 1 or 2 spikesAlkynes C-Hsharp, may be strong

Noticeable peaks (Continued)Wave- Absorbing Features numberSubstance 3000 rcmAlkanes C-HJust below 3000Alkenes =C-HJust above 3000Carboxylic acidO-Hvery broad2300alkyne -C C-just below 2300nitriles -C N-just above 2300

Noticeable peaks (Continued 2)Wave- Absorbing Features numbergroup1710 rcmcarbonyl C=Overy strongAldehydes ketonesEstersaround 1735conjugated C=Oaround 1650Examples: butanonehttp://webbook.nist.gov/cgi/cbook.cgi?ID=C78933&Units=SI&Type=IR-SPEC&Index=1#IR-SPECButanal: http://webbook.nist.gov/cgi/cbook.cgi?ID=C123728&Units=SI&Mask=80#IR-Spec

Noticeable peaks (Continued 2)Wave- Absorbing Features numbergroup1660AlkenesC=Cconjugated C=C below 1660AmidesC=OStronger than C=CExamples: 2-methylbutene: http://webbook.nist.gov/cgi/cbook.cgi?Name=2-methylbutene&Units=SI&cIR=onpropanamidehttp://webbook.nist.gov/cgi/cbook.cgi?Name=propanamide&Units=SI&cIR=on

d. Typical IR Spectra1. HydrocarbonsExample 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

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

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

Hydrocarbons (Continued: Alkynes)Example: 1-octynehttp://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: CC stretch* 1560 rcm & below: fingerprint region

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

Carboxylic AcidsExample: Propanoic acidhttp://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

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

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

*3. Carbonyl CompoundsGeneral characteristic: C=O groupExample: 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 stretchNote: conjugated C=O groups absorb at lower frequencies

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 stretchingExample 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

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.

a. MS: Fundamental PrinciplesMost 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.JPGOperation 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.

Mass SpectrumDefinition: 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.

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

b. MS fragmentation patterns of some functional groupsGeneral rule: most favored fragmentation routes are the ones that:* produce most stable cations* lose the most stable radicals.b1. AlkanesMost 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

Hexane MS

Hexane MS (Continued)

AlkenesMost stable fragments: allylic cationsReason for stability: delocalization of the charge by resonanceExample: 2-hexene http://webbook.nist.gov/cgi/cbook.cgi?Name=2-hexene&Units=SI&cMS=on

2-Hexene MS

2-Hexene MS (Continued)

b3. AlcoholsTwo major fragmentation patternsa-cleavage: loss of a C-C bond nexte to the OH group. Result: a neutral radical and a O containing cationDehydration: 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-methylbutanolhttp://wps.prenhall.com/wps/media/objects/340/348272/Instructor_Resources/Chapter_12/Text_Images/FG12_21.JPG

Alcohols Fragmentation (Illustration)

Alcohol MS (2-methylbutanol)

b4. Amines FragmentationGeneral feature: odd MWMost common fragmentation pattern: alpha cleavage. Result: N-containing fragment with an even m/zExample: N-methyl-2-pronanaminehttp://webbook.nist.gov/cgi/cbook.cgi?ID=C4747211&Units=SI&Mask=200#Mass-Spec

MS of N-methyl-2-pronanamine

b5. Carbonyl compoundsMajor fragmentation patterns *1. McLafferty rearrangementStructural 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.

McLafferty Rearrangement

*2. Alkyl-carbonyl cleavageGeneral structure: R-CO-RBond 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

Alkyl-carbonyl cleavage (in general)

MS of 2-Hexanone (Ketone)

b6. Carboxylic acids*1. Acyl-alkyl cleavageBond 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 possibleExample: Hexanoic acidhttp://webbook.nist.gov/cgi/cbook.cgi?ID=C142621&Units=SI&Mask=200#Mass-Spec

Carboxylic Acids Example: hexanoic acid