Spectroscopy Techniques: Mass Spectrometry, Infrared, and Nuclear Magnetic Resonance - Pro, Study notes of Organic Chemistry

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Structure Determination: Mass Spectrometry and Infrared Spectroscopy Based on McMurry’s Organic Chemistry, 6th edition 2 Determining the Structure of an Organic Compound  The analysis of the outcome of a reaction requires that we know the full structure of the products as well as the reactants  In the 19th and early 20th centuries, structures were determined by synthesis and chemical degradation that related compounds to each other WG , Spectrometer _- Magnet _ CRT display Ionizing electron beam Detector Heated filament Sample inlet © 2004 Thomson/Brooks Cale 6 The Mass Spectrum  Plot mass of ions (m/z) (x-axis) versus the intensity of the signal (corresponding to the number of ions) (y-axis)  Tallest peak is base peak (100%) – Other peaks listed as the % of that peak  Peak that corresponds to the unfragmented radical cation is parent peak or molecular ion (M+) 7 MS Examples: Methane and Propane  Methane produces a parent peak (m/z = 16) and fragments of 15 and 14 (See Figure 12-2 a) 10 12.2 Interpreting Mass Spectra  Molecular weight from the mass of the molecular ion  Double-focusing instruments provide high- resolution “exact mass” – 0.0001 atomic mass units – distinguishing specific atoms  Example MW “72” is ambiguous: C5H12 and C4H8O but: – C5H12 72.0939 amu exact mass C4H8O 72.0575 amu exact mass – Result from fractional mass differences of atoms 16O = 15.99491, 12C = 12.0000, 1H = 1.00783 11 Other Mass Spectral Features  If parent ion not present due to electron bombardment causing breakdown, “softer” methods such as chemical ionization are used  Peaks above the molecular weight appear as a result of naturally occurring heavier isotopes in the sample – (M+1) from 13C that is randomly present 12 12.3 Interpreting Mass- Spectral Fragmentation Patterns  The way molecular ions break down can produce characteristic fragments that help in identification – Serves as a “fingerprint” for comparison with known materials in analysis (used in forensics) – Positive charge goes to fragments that best can stabilize it Hexane = 5 80- o q 3 604 S 2 4 2 407 2 +» 4 204 3 0 10 20 © Thomson - Brooks Cole i 40 il T 60 100 120 140 16 Practice Problem 12.2: methylcyclohexane or ethylcyclopentane? 17 Mass Spectral Cleavage Reactions of Alcohols  Alcohols undergo -cleavage (at the bond next to the C-OH) as well as loss of H-OH to give C=C Fragmentation of Ketones and Sauce hae ASG IF | __MeLafferty Cy iS Cc rearrangement : Y 'ie" SR : /\ O O I ais I RCH,* + + RCH, -- C—R’ cleavage C—R’ | © Thomson - Brooks 20 12.5 The Electromagnetic Spectrum Frequency (v) in Hz 102° 1018 1016 1014 1012 1019 T T T T T T T T T T ag ‘rays X rays t Infrared Microwaves | Radio waves @ | ! ! ! | ! ! ! 10-2 10-10 10-8 ! 11076 10-4 10°? & Wavelength (A) in m ee Oc Wavelength (A) in m ee Visible Oa 380 nm 500 nm 600 nm 700 nm 780 nm 3.8 x 1077 m 7.81077 m © Thomson - Brooks Cole Wavelength and Frequency |— Wavelength — i<—— 800 nm —— Violet light (v = 7.50 X 104 s~4) (v = 3.75 X 10!* gs") © 2004 Thomson/Srooks Cole 25 12.6 Infrared Spectroscopy of Organic Molecules  IR region is lower in photon energy than visible light (below red – produces heating as with a heat lamp)  2.5  106 m to 2.5  105 m region used by organic chemists for structural analysis  IR energy in a spectrum is usually measured as wavenumber (cm-1), the inverse of wavelength and proportional to frequency:  Wavenumber (cm-1) = 1/(cm)  Specific IR absorbed by organic molecule is related to its structure IR region and vicinity | Visible Near infrared Microwaves | | — : = 1 h 107° 10-4 107° 107” 107! (em) 4=2.5 x 1074 cm h=2.5 X 1072 cm = 2.5 um = 25 pm p = 4000 em7! ® = 400 cm7! © 2004 Thomson/Brooks Cale 27 Infrared Energy Modes  IR energy absorption corresponds to specific modes, corresponding to combinations of atomic movements, such as bending and stretching of bonds between groups of atoms called “normal modes”  Energy is characteristic of the atoms in the group and their bonding  Corresponds to molecular vibrations TABLE 12.1 Characteristic |R Absorptions of Some Functional Groups Functional group class Band position (em=) Intensity of absorption Alkanes, alkyl groups C—H Alkenes —C—H c=C Alleynes =C—H — (iC — Alkyl halides C—tl C—Br eS Alcohols O—H C—O Aromatics ap or 2850-2960 3020-3 100 1640-1680 3300 2100-2260 600-800 500-600 500 3400-3650 1050-1150 3030 Medium to strong Medium Medium Strong Medium Strong Strong Strong Strong, broad Strong Weak 2 0 Fy Amines N—H C—N Carbonyl compounds? cC=0 Carboxylic acids O—HE Nitriles CaN Nitro compounds NOg 1660-2000 1450-1600 3300-3500 1030-1230 1670-1780 2500-3100 2210-2260) 1540 “Carboxylic acids, esters, aldehydes, and ketones: Weak Medium Medium Medium Strong Strong, very broad Medium Strong  Transmittance (%) » 2 6 Sy 0 4000 3000 2600 2200 2000 Wavelength (zm) t 1800 1600 1400 1200 Wavenumber (em~') 1000 velength (um) B 8 10 CH,(CH ),CH, (CHy(CH,)gCH 3000 2600 2200 2000 1800 1600 1400 1200 Wavenumber (em~1) 1000 Wavelength (um) CHs(CH} 4000 3600 3000 2600 2200 2000 ©2004 Thomson - Brooks/Cole 1800 1600 1400 Wavenumber (em-1) 1200 1600 00 35 Differences in Infrared Absorptions  Molecules vibrate and rotate in normal modes, which are combinations of motions (relates to force constants)  Bond stretching dominates higher energy (frequency) modes 36 Differences in Infrared Absorptions  Light objects connected to heavy objects vibrate fastest (at higher frequencies): C-H, N-H, O-H  For two heavy atoms, stronger bond requires more energy (higher frequency): C  C, C  N > C=C, C=O, C=N > C-C, C-O, C- N, C-halogen 37 12.8 Infrared Spectra of Hydrocarbons  C-H, C-C, C=C, C  C have characteristic peaks ib) Wavelength (um) 25 3 4 5 6 7 8 8 10 12 14 16 20 24 c | Ly en | CH,(CHy),CH—=CHy Transmittance l | T T T T 4000 3500 300 260) 2200 2000 1800 1600 1400 1200 1000 A) 600 400 Wavenumber (em?!) kynes ©2004 Thomson - Brooks/Cole (e) Wavelength (um) 2.6 a 4 5 6 7 B 9 10 12 14 16 20 24 ] i 4 i i i {ol | i i 100 b= J —-= & a | | | | | | i 5 | : 60 é |__| i TI ‘ = — 0 ——F_ | z an | | | i | a | { ¥ L | | i E20 } |} CHs(CH)),C=CH —-\} . =p. | uJ 0 ' T T T T T 4000 2600 S000 2600 2200 2000 HOO LHDD 1400 1200 1000 Bi ‘60g 4000 Wavenumber (em!) 42 12.9 Infrared Spectra of Some Common Functional Groups  Spectroscopic behavior of functional groups is discussed in later chapters  Brief summaries presented here 45 IR: Aromatic Compounds  Weak C–H stretch at 3030 cm1  Weak absorptions 1660 - 2000 cm1 range  Medium-intensity absorptions 1450 to 1600 cm1 ea aT=Tab are lea ad -ral= Wavelength (um) 2.5 3 4 5 6 7 8 9 10 12 14 16 20 24 100 | | | | \ SS \ L \ \ l sca r) at mapa Ty I, raf an now A At “| = @ | | | : { l g 0 wet AA z 60> || | L | | @ | (\ ee iW | I I T 1 T ! T I T | I 4000 3500 3000 2600 2200 2000 1800 1600 1400 1200 1000 800 600 400 Wavenumber (cm—!) © 2004 Thomson/Brooks Cale 47 IR: Carbonyl Compounds  Strong, sharp C=O peak 1670 to 1780 cm1  Exact absorption characteristic of type of carbonyl compound – 1730 cm1 in saturated aldehydes – 1705 cm1 in aldehydes next to double bond or aromatic ring 50 C=O in Ketones  1715 cm1 in six-membered ring and acyclic ketones  1750 cm1 in 5-membered ring ketones  1690 cm1 in ketones next to a double bond or an aromatic ring 51 C=O in Esters  1735 cm1 in saturated esters  1715 cm1 in esters next to aromatic ring or a double bond 52 Chromatography: Purifying Organic Compounds  Chromatography : a process that separates compounds using adsorption and elution – Mixture is dissolved in a solvent (mobile phase) and placed into a glass column of adsorbent material (stationary phase) – Solvent or mixtures of solvents passed through – Compounds adsorb to different extents and desorb differently in response to appropriate solvent (elution) – Purified sample in solvent is collected from end of column – Can be done in liquid or gas mobile phase HPLC of Pesticide Mixture - Oxamyl . Methomy! . ANTU Aldicarb Carbofuran . Propoxur . Fluometuron . Diuron . Warfarin . Siduron . Methiocarb 3. Linuron . Mexacarbate 1 2 3 4, 5 6. 7 8 9 Start 1 7 8 9 10 11 12 #138 #14 Minutes © 2004 Thomson/Broaks Cole Prob. 12.39: Cyclohexane or Cyclohexene? Transmittance (%) 4000 3500 3000 2600 2200 2000 1800 1600 1400 1200 1000 Wavenumber (em~") Wavelength (um) 5 é 5 é 4000 3500 3000 2600 2200 2000 1800 1600 1400 1200 1000 Wavenumber (cm!) ©2004 Thomson - Brooks/Cole 800 56 Problem 12.48: Unknown hydrocarbon ) Relative abundance (% | lil ull T t T 60 80 Wavelength (um) E 8 9 10 12 14 1) L 1 i 1 L \ Cy) W\pren 80 | \_f\ a VV \ | | IVE \ ie | \f 60 40 - Transmittance (%) 20 oO T Tt t T t T 4000 3500 3000 2600 2200 2000 1800 1600 1400 1200 1000 Wavenumber (cm~") ©2004 Thomson - Brooks/Cole