1. Comments on homework
Lots of “Index of Hydrogen Deficiency” Math errors
Matching arrows with HR MS data & Molecular formulas
Following instructions:
-typed & chemdraw work
-Not applying rules for fragmentation
-Not providing mechanisms
Poor mechanism presentations (Review arrow pushing)
Some organizational problems in “presentation” of homework

2. Parent ion: m/z 150

3. 1.6 Match each of the exact masses to the following mass
spectra. (A–W) Note that two compounds have the
same exact mass, and you will need to consider the CI
mass spectrum when given: (a) , (b) ,
(c) , (d) , (e) , (f) ,
(g) , (h) , (i) , (j) ,
(k) , (l) , (m) , (n) ,
(o) , (p) , (q) , (r) ,
(s) , (t) , (u) , (v) ,
(w)

4. (r) =

5.
C5H11

6. C5H11Br
IHD = 0
Therefore it is a pentylbromide isomer
A propyl radical
[M –Br] or [M -79]
[M - 43]
[M - 29]
m/z 71 =
m/z 107 = C2H4Br+
m/z 121 = C3H6Br+

7. Fragmentation mechanisms must be consistent with valences of atoms
-radical & cation chemistry

8. Some helpful hints: Draw hydrogens in.
Use proper arrow pushing –exactly like in mechanisms.
Gas phase radical cations have plenty of energy to rearrange and fragment.

9. M-1
m/z 39, C3H3+
[M -17] or [M-OH] M
M+1

10. M-1
m/z 39, C3H3+
[M -17] or [M-OH] M

11. Chapter 2: Infrared Spectroscopy

12. Duality wave/particle of the light
Electromagnetic Energy: Light
E = hυ
h: Planck constant h = 6.626x10-34 J.s υ=c/λ
Duality wave/particle of the light

13. Infrared Spectroscopy
The vibrational IR extends from 2.5 x m (2.5 m) to 2.5 x m (25 m).
The frequency of IR radiation is commonly expressed in wavenumbers.
Wavenumber: The number of waves per centimeter, with units cm-1
Expressed in wavenumbers, the vibrational IR extends from 4000 cm-1 to 400 cm -1

14. Molecular vibrations
Fundamental stretching and bending vibrations for a methylene group.

15. Molecular Vibrations
Consider two covalently bonded atoms as two vibrating masses connected by a spring.
The total energy is proportional to the frequency of vibration; E = hn where h is Planck’s constant.
The frequency of a stretching vibration is given by an equation derived from Hooke’s law.
K = a force constant, which is a measure of bond strength, m = reduced mass of the two atoms, (m1m2)/(m1 + m2), where m is the mass of the atoms in amu.

16. Potential energy diagrams. Curve 1, harmonic oscillator
Potential energy diagrams. Curve 1, harmonic oscillator. Curve 2, anharmonic oscillator

17. Molecular Vibrations
From this equation, we see that the peak position of a stretching vibration
is proportional to the strength of the vibrating bond.
is inversely proportional the masses of the atoms connected by the bond.
The intensity of absorption depends primarily on the polarity of the vibrating bond.

19. i)   Stretching frequencies are higher than corresponding bending frequencies. (It is easier to bend a bond than to stretch or compress it.) ii)   Bonds to hydrogen have higher stretching frequencies than those to heavier atoms. iii)   Triple bonds have higher stretching frequencies than corresponding double bonds, which in turn have higher frequencies than single bonds.

21. Comparison Beetween Dispersion Spectrometer and FTIR
To separate IR light, a grating is used.
Detector
Grating
Slit
In order to measure an IR spectrum,
the dispersion Spectrometer takes
several minutes.
Also the detector receives only
a few % of the energy of
original light source.
Sample
To select the specified IR light,
A slit is used.
Light source
Fixed CCM
An interferogram is first made by the interferometer using IR light.
FTIR
In order to measure an IR spectrum,
FTIR takes only a few seconds.
Moreover, the detector receives
up to 50% of the energy of original
light source.
(much larger than the dispersion
spectrometer.)
Detector
B.S.
Sample
Moving CCM
The interferogram is calculated and transformed
into a spectrum using a Fourier Transform (FT).
IR Light source

22. Figure Single- and double-beam spectra of atmospheric water vapor and CO2. In the lower, single-beam trace, the absorption of atmospheric gases is apparent. The top, double-beam trace shows that the reference beam compensates nearly perfectly for this absorption and allows a stable 100% T baseline to be obtained. (From J. D. Ingle Jr. and S. R. Crouch, Spectrochemical Analysis, p Englewood Cliffs, NJ: Prentice-Hall, With permission.)

23. IR Source
 Sources of continuous radiation
 A hot material emits a continuum of radiation.
Blackbody (no envelope): intensity highest near 5000 cm-1;
about 100 times lower near 500 cm-1.
a) Nichrome coil heated electrically to 1100oC and a black oxide film forms.
Simple, robust, reliable, long lifetime.

24. Figure 16-4 Specpral distribution of energy from a Nernst glower operated at approximately 2200 K.

25. Mirror moves to create path difference between 2 beams
Interferometer produces plot of intensity vs time during 1 scan (interferogram).Interference of beams occurs from fixed and moving mirrors.
Mirror moves to create path difference between 2 beams
Transmits 50%, reflects 50%
At t=0, zero path difference between 2 beams for monochromatic radiation; constructive interference; maximum signal at detector.At a later time, path difference = /2; destructive interference; minimum signal. Later on, …. …maximum signal. So interferogram is a cosine wave.

26. Interference is a superpositioning of waves
FTIR seminar
Relationship between light source spectrum and the signal output from interferometer
Light source spectrum I
Signal output from interference wave Az
Monochromatic
light
Dichroic light
Continuous
spectrum light
Wavenumber u
Time t S I
SAz
Wavenumber u
Time t
I(t)
b (u) u
Time t
Wavenumber
All intensities are standardized.

27. Centreburst grows when more frequencies are present
One frequency
Three frequencies
Many frequencies

28. Peak width
When band is broader, interferogram wings decay faster: more frequencies give more chance of cancellation

29. Relation between spectrum and interferogram.
3 interferogram parameters important: A, P, T

30. Fourier Transform Time axis by FFT Wavenumber Single strength SB 4000
Wavenumber[cm-1]
400
Optical path difference [x]
(Interferogram)
(Single beam spectrum)
Time axis by FFT Wavenumber

33. End of scan from (i) white light source or (ii) centreburst
Schematic of steps in spectrum collection
End of scan from (i) white light source or (ii) centreburst
Background spectrum

34. This only comes from aliasing and can be prevented. 5. Resolution
Advantages of FT-instrument over dispersive one
Fellgett advantage
All frequencies are measured simultaneously. Typical scan times are only a few seconds.
2. Jacquinot advantage
The energy throughput is higher for any resolution, giving a higher signal:noise ratio.
3. Connes advantage
The laser wavelength is used as a reference for the calculation of band positions, and is precise.
4. Stray light
This only comes from aliasing and can be prevented.
5. Resolution
This is constant for the whole spectral range
6. Robustness
FT instruments only have 1 moving part

35. Instrument scanning Signal: noise ratio, S/N  (measurement time)0.5
S/N  (no. of scans)0.5
How many scans do I need to reduce the noise in 1 scan by a factor of 4?
Often 1 scan of sample is ratiod against 1 scan of (empty) background. In the ranges 70-35%T and 0-35%T normally the ratio of background:sample scans is increased to 1:2 and 1:4 respectively.
When the energy throughput is reduced by a factor of x for the sample spectrum, x times more scans are required.

36. Resolution

37. Sample preparation Methods
Transmission
Solids: KBr Pellet
Liquids: NaCl Plates
Quick press KBr pellet press

38. Instrumental Setup: Attenuated Total Reflectance (ATR) Technique
IR radiation passes through (IRE-internal reflection element) crystal and hits sample at a 45 degree angle
IRE made of high refractive index material (zinc selenide, diamond, germanium
Incident radiation penetrates into sample (~1 micrometer) where it can be absorbed
Attenuated radiation is reflected

39. Sample preparation Methods
ATR
Liquids and solids loaded directly onto crystal
Arm Applies pressure to solids for uniform contact with crystal
PSI can be controlled

40. Transmission vs. ATR ATR Advantages
High Quality Spectrum for qualitative analysis
Minimal sample preparation
Non destructive
Time efficient
Spectra not affected by sample thickness
Radiation penetrates only a few micrometers
Highly reproducible results
Wide variety of sample types
Threads, yarns, fabrics, fibers, pastes, powders, suspensions, polymers, rubbers

41. ATR forensic applications
Drug analysis
Fiber analysis
Paint chip analysis
Ink analysis
Paper analysis
Biological analysis

42. Spectra Comparison
Resulting peaks from ATR are very similar in intensity and wavelength to transmittance technique
Koulis, Cynthia, et. al. Comparison of Transmission and Internal Reflection Infrared Spectra of Cocaine. Journal of Forensic Sciences, 2001.

43. ATR Peak Shift Small variations in peak intensity and position occur:
Carbonyl band Absorption of cocaine shows ATR peak shift
Koulis, Cynthia, et. al. Comparison of Transmission and Internal Reflection Infrared Spectra of Cocaine. Journal of Forensic Sciences, 2001.

44. C-H Stretch occurs around 3000 cm-1
C-H Stretch occurs around 3000 cm-1. In alkanes (except strained ring compounds), sp3 C-H absorption always occurs at frequencies less than 3000 cm-1 ( cm-l).
Methylene groups have a characteristic bending absorption of approximately 1465 cm-1.
Methyl groups have a characteristic bending absorption of approximately 1375 cm-1.
The bending (rocking) motion associated with four or more CH2 groups in an open chain occurs at about 720 cm-1 (called a long-chain band).

45. =C-H Stretch for sp2 C-H occurs at values between 3100-3010 cm-1.
=C-H Out-of-plane (oop) bending occurs in the range cm-1.
Stretch occurs at cm-1; often conjugation moves C=C stretch to lower frequencies and increases the intensity. Symmetrically substituted bonds (e.g., 2,3-dimethyl-2-butene) do not absorb in the infrared (no dipole change). Symmetrically disubstituted (trans) double bonds are often vanishingly weak in absorption; cis are stronger.

48. Alkene isomers
=CH bend
=CH bend

49. Aromatics C–H stretch from 3100-3000 cm-1
overtones, weak, from cm-1
C–C stretch (in-ring) from cm-1
C–C stretch (in-ring) from cm-1
C–H "oop" from cm-1

50. Alkynes

53. Alcohols O–H stretch, hydrogen bonded 3500-3200 cm-1
C–O stretch cm-1 (s) 

55. http://www2. chemistry. msu

56. equatorial C-O absorption at 1068 is relatively stronger than the axial C-O absorption at 970

57. Carbonyls
Conjugation with a double bond or benzene ring lowers the stretching frequency.

58. Carbonyls
Changing an alkyl substituent of a ketone for an electron releasing or withdrawing group.
Stronger CO
Weaker CO
Incorporation of the carbonyl group in a small ring (5, 4 or 3-membered), raises the stretching frequency.

59. Carbonyls C-CO-C bond angle
Incorporation of the carbonyl group in a small ring (5, 4 or 3-membered), raises the stretching frequency & makes CO stronger.
120°
CO sigma bond becomes more s-orbital rich
108°
90°

60. 1715 cm1 in six-membered ring and acyclic ketones
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
1735 cm1 in saturated esters
1715 cm1 in esters next to aromatic ring or a double bond
C=O in Esters

63. Aldehydes H–C=O stretch 2830-2695 cm-1 C=O stretch:
aliphatic aldehydes cm-1
alpha, beta-unsaturated aldehydes cm-1 

64. Esters C=O stretch aliphatic from 1750-1735 cm-1
a,b-unsaturated from cm-1
C–O stretch from cm-1 

65. Esters

66. Amides

67. Carboxylic acids O–H stretch from 3300-2500 cm-1
C=O stretch from cm-1
C–O stretch from cm-1
O–H bend from and cm-1 

68. Carboxylate

69. Acid Anhydrides Two C=O and two C-O stre

70. Acid Anhydrides Two C=O and two C-O stre

71. Amines C-N stretching Aromatic amines 1200 to 1350 cm-1
C-N stretching
Aromatic amines 1200 to 1350 cm-1
Aliphatic amines 1000 to 1250 cm-1

72. Nitro compounds N–O asymmetric stretch from 1550-1475 cm-1
N–O symmetric stretch from cm-1 

73. Halogenated organics C–H wag (-CH2X) from 1300-1150 cm-1
C–X stretches (general) from cm-1
C–Cl stretch cm-1
C–Br stretch cm-1

74. Infrared-spectroscopical Polymer Identification
very strong ,
and
Modif.
Epoxies
Polycarbon-
ates
Alkyd-,
Polyesters,
Cellulose ether,
PVC(plasticized)
Polyvinyl
acetate,
PVC-copolymers
Cellulose
ester
Polyurethane
Acrylics,
Polyester
Phenol
derivatives,
Polystyrenes,
Arylsilicones,
Aryl-alkyl Silicone Copolymers
Polyamides,
amines
Nitrocellulose
cellophane
Cellophan,
Alkylcellulose,
PVA, PEO
PAN, PVC,
Polyvinylidene
chloride
POM
Alkylsilicone,
aliphatic hy
drocarbons,
Polytetra
fluorethylene
Thiokol
sharp
strong
1610 –1590,
1600 – 1580 and
All numbers have the meaning of wave numbers
and are given in cm-1
yes no
Infrared-spectroscopical Polymer Identification

75.
cm-1
cm-1
cm-1
modified epoxides, polycarbonate, Alkyd resins, polyester, cellulose ester, cellulose ether, PVC (plast),
PVAc, PVC-copolym., PU, acrylics
modified epoxides, polycarbonate, Alkyd resins, polyester, cellulose ester, cellulose ether, PVC (plast)
modified epoxies, polycarbonate
polycarbonate

76. Determination of a Layer Thickness
Intensity, arbitrary units
wave length
1/d= 2/n (1/l1 -1/l2)
n = number of minima between two maxima l1 and l2

77. Figure Infrared absorption spectrum of a thin polystyrene film recorded with a modern infrared spectrophotometer. Note that the abscissa scale changes at 2000 cm-1.
Usually wavenumber is used: directly proportional to energy;