Organic Spectroscopy 1 Michaelmas 2011

Lecture 5
Dr Rob Paton

[email protected]
http://paton.chem.ox.ac.uk
Organic Spectroscopy 1: Outline of Lectures 5-8
In lectures 5-6 of this course, aspects of Ultraviolet-visible and Infra red techniques will be introduced that are important in
assigning organic structures. Coverage of the underlying theory and instrumentation associated with each method will be kept
to a bare minimum since these aspects are covered elsewhere.

We will look at a variety of real spectra and learn to correlate distinguishing features in these spectra with functional groups.

UV-vis and IR spectroscopy provide direct experimental data to support of a number of the underlying concepts in organic
chemistry introduced last year, such as conjugation and the mesomeric effect. We will also take a moment to consider these
points.

O O
O O
N N

In lectures 7-8 we will go through worked examples to illustrate how to combine 13C and 1H NMR with UV-vis and IR spectra
to assign structures.

Digital copies of all handouts, problems and slides are available through the web: http://paton.chem.ox.ac.uk

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Organic Spectroscopy 1: Outline of Lectures 5-8
Further Reading:
Chemical Structure and Reactivity: an Integrated Approach – J. Keeler and P. D. Wothers, OUP (Chapter 11)
Introduction to Organic Spectroscopy - L. M. Harwood and T. D.W. Claridge, Oxford Chemistry Primers
Organic Chemistry – Clayden, Greeves, Warren and Wothers, OUP (Chapter 3)
Organic Spectroscopic Analysis – R. J. Anderson. D. J. Bendell and P. W. Groundwater, RSC
For more complete coverage including many more real examples of spectra, tables of spectroscopic data that will be useful in
structural elucidation, and worked examples consult the following:
Organic Structure Analysis – P. Crews, J. Rodriguez and M. Jaspers, OUP
Spectroscopic Methods in Organic Chemistry (6th edition) – D. H. Williams and I. Fleming, Mcgraw-Hill

A wealth of experimental spectra may be found on the internet, in openly accessible repositories. The following may be of
interest:
NMRshift DB - NMR database for organic structures: http://www.ebi.ac.uk/nmrshiftdb/

The Japanese Spectral Database for Organic Compounds (SDBS) has free access to IR, Raman, 1H and 13C NMR and MS data:
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

Sigma-Aldrich has IR, Raman and 1H and 13C NMR spectra for many of their commericially available compounds:
http://www.sigmaaldrich.com

Problems in structure, combining IR with 1H and 13C NMR courtesy of Prof Craig Merlic, UCLA:
http://www.chem.ucla.edu/~webspectra/

Past Paper Questions containing to NMR/IR/UV-vis spectroscopy:

NB Since 2011 Mass Spectrometry has been shifted to 1B
Part IA: 2004 (Q7), 2005 (Q2), 2006 (Q1), 2007 (Q8), 2008 (Q9), 2009 (Q1), 2010 (Q1), 2011 (Q7).
General Paper I: 1993 Q6, 2000 (Q1), 2001 (Q5) and 2004 (Q8)
General Paper II: 1991 (Q3, Q5), 1992 (Q8), 1993 (Q3), 1994 (Q1), 1995 (Q3), 1996 (Q7), 1997 (Q5), 1998, Q3), 1999
(Q6), 2000 (Q9), 2002 (Q1) and 2003 (Q3)
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The Electromagnetic Spectrum
By irradiating molecules at different frequencies, it is possible to gain different types of information about their structure,
since these frequencies bring into resonance various modes of molecular motion, or electronic or nuclear excitation. In modern
laboratories, NMR spectroscopy is the first choice method for gaining structural information, with Infrared (IR) and mass
spectroscopy (MS) techniques acting in a supporting capacity and UV spectra only being required in specialized circumstances
(e.g. analysis of specific compound classes such as polymers or porphyrins).

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The Electromagnetic Spectrum
 
Electronic States Vibrational energy levels Rotational energy levels Nuclear spin states

100000 - 25000 - 2500 -

80000 - 20000 - 2000 -

60000 - 15000 - 1500 -

0.01 cm-1
(400 MHz)
40000 - 10000 - 1000 -

20000 - 5000 - 500 -

0 0 0

(energies in wavenumbers, cm-1)

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UV-vis Spectroscopy
UV-vis is a form of absorption spectroscopy. Radiation in the UV-visible region of the EM spectrum is absorbed, causing an
electron to be excited to a higher energy level.

ΔE hν

ground state excited state

UV and visible spectra of organic compounds are associated with excitations of electrons from the ground state to an excited
state higher in energy. The transition occurs from a filled bonding or non-bonding orbital to a formerly empty antibonding
orbital.
The energy gap is proportional to the frequency of absorption, and so UV-vis spectroscopy is a source of bonding information
UV spectroscopy is most important in the structural analysis of compounds containing π-bonds, in particular conjugated
systems.

σ∗
4π∗

2π∗

3π∗

(750 kJ/mol) (500 kJ/mol)

(900 kJ/mol)
2π

1π

σ 1π

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UV-vis Spectroscopy

hypsos = height
bathos = depth

molar extinction coefficient, ε

hyper = above
hypo = below

200 400 600 800

wavelength, λ (nm)

600 300 200 150

Energy gap (kJ/mol)

Recording UV-vis spectra

The ultraviolet or visible spectrum is usually taken using a dilute solution of the sample in a glass or quartz tube, or cuvette.
Typically the sides of the cuvette are 1 cm, and the total volume is 2-3 cm3. UV or visible light is passed through the sample
and the intensity of the transmitted beam is recorded across the wavelength range of the instrument (I). First the intensity of
the light is recorded with pure solvent in the cuvette (I0) the absorbance due to the sample can then be computed as log10
(I0/I).

I0 I
light source * detector

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UV-vis Spectroscopy
The Beer-Lambert law states that the absorption of light by a given sample is proportional to the number of absorbing
molecules, and independent of the source intensity.

I0 and I are the intensities of the incident and transmitted light, respectively, l is the path length of the absorbing solution in cm
and c is the concentration in moles/litre. ε is the molar extinction coefficient in 1000 cm2 mol-1. log10 (I0/I) is called the
absorbance.

Example:
A 1.12 x 10-4 M solution of paranitroaniline, in a cuvette of path length 1cm, has a measured absorbance maximum of 1.55 at
227 nm. This means the intensity of the transmitted light is 101.55 = 35 times the intensity of the incident light.

The ε value for this absorption is:

This would be quoted as:

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UV-vis Spectroscopy
The solvent and vessels must be transparent in the range of interest.
cyclohexane
chloroform
95% ethanol
water
quartz
glass

150 170 190 210 230 wavelength (nm) 290 310 330 350

UV-vis absorptions of common functional groups:

σ*

n−π*
π*
conjugated π−π*

double bonds n (LP)

isolated π−π*

lone pairs (O, N, S) π

n−σ*
single bonds
σ−σ*
σ
150 170 190 210 230 wavelength (nm) 290 310 330 350

Vacuum UV UV

Functional groups such as polyenes and poly-ynes that give rise to diagnostic absorptions in the UV-vis region of the EM
spectrum are referred to as chromophores

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UV-vis Spectroscopy
Selection Rules and Intensity

Irradiation of organic compounds does not always give rise to excitations of electrons from any filled to unfilled orbital,
because there are rules based on symmetry governing which transitions are allowed. The intensity of absorption is related to
the “allowedness” of a particular transition

A chromophore with two double bonds conjugated together possesses a fully allowed transition, and has associated ε values of
about 10,000

Forbidden absorptions are in practice observed with weak absorptions, as the symmetry may be broken by a molecular
vibration or by unsymmetrical substitution.

allowed "forbidden"

π - π* n - π* π - π*
ε > 10,000 ε = 10 - 100 ε = 100 - 1000

The most important point to be made is that, in general:

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UV-vis Spectroscopy
Example: conjugated dienes:
Me Ph
Me Ph
n n
n λmax (nm) ε λmax (nm) ε
3 275 30,000 358 75,000
4 310 76,500 384 86,500
5 342 122,000 403 94,000
6 380 146,000 420 113,000
7 401 - 435 135,000
8 411 - -

The most important point to be made is that, in general:

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UV-vis Spectroscopy
Absorption maxima for substituted benzene rings (Ph-R)
R λmax (nm) ε λmax (nm) ε λmax (nm) ε
H 203.5 7,400 254 204 254 204
NH3 203 7,500 254 160 254 160
Me 206.5 7,000 261 225 261 225
I 207 7,000 257 700 257 700
Cl 209.5 7,400 263.5 190 263.5 190
Br 210 7,900 261 192 261 192
OH 210.5 6,200 270 1450 270 1450
OMe 217 6,400 269 1480 269 1480
SO2NH2 217.5 9,700 264.5 740 264.5 740
CN 224 13,000 271 1000 271 1000
CO2 224 8,700 268 560 268 560
CO2H 230 11,600 273 970 273 970
NH2 230 8,600 280 1430 280 1430
O 235 9,400 287 2600 287 2600
NHAc 238 10,500
COMe 245.5 9,800
CH=CH2 248 14,000 282 750 291 500
CHO 249.5 11,400
Ph 251.5 18,300
OPh 255 11,000 272 2000 278 1800
NO2 268.5 7,800
CH=CHCO2H 273 21,000
CH=CHPh 295.5 29,000

pH induced shifts: an acid induced blue (i.e. hypsochromic) shift

NH2 NH3
H

λmax 230 nm λmax 203 nm

NH2 NH2 NH2

H N
H

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 UV-vis Spectroscopy
pH induced shifts: a base induced red (i.e. bathochromic) shift
OH O

-H
λmax 210.5 nm λmax 235 nm

Effects of “complementary” EWG/EDG substituents

NH2 NO2

λmax 230 nm λmax 269 nm

ε 7800 ε 8600
NO2 NO2
NH2 NH2 H2N NO2 NH2 NH2 NO2
H2N NO2

O2N O2N O2N

λmax 229 nm
λmax 229 nm λmax 235λnm
max 235 nm λmax 375 nm375 nm
λmax λmax 260 nm
ε 14800 ε 14800 ε 16000 ε 16000 ε 16000
ε 16000 ε 1300

Acid base indicators: e.g phenolphthalein

λmax 231 nm (25,800) λmax 230 nm (25,800)
λmax 275 nm (4,200) λmax 553 nm (26,000)

HO O

OH

pKa 9.4
HO O HO O
O O

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UV-vis Spectroscopy
Carbonyls:
4π∗

2π∗ 2π∗

3π∗
2pO 2pO

2π

1π 1π

1π

O O

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UV-vis Spectroscopy
Predicting UV absorptions of conjugated dienes:
Alkyl substitution of a diene extends the chromophore through hyperconjugative interactions, causing a small red shift to
longer values for λmax.

The effect of alkyl substitution on open chain dienes and dienes in six-membered rings is approximately additive, so a few rules
(first formulated by R. B. Woodward in 1941) can be used to predict absorption. Woodward’s rules have since been refined as
a result of experience by Fieser.

Woodward’s rules may be applied to predict the absoroption of a diene that is either homoannular with both double bonds
contained in one ring or heteroannular with two double bonds distributed between two rings.

Woodward's rules for diene and triene absorption

Base value for parent s-trans diene (heteroannular) 214 nm
Base value for parent s-cis diene (homoannular) 253 nm

Increments for:
(a) each alkyl substituent or ring residue +5 nm
(b) exocyclic nature of any double bond +5 nm
(c) additional double bond extending conjugation +30 nm
(d) auxochrome:
-OAcyl +0 nm -OAcyl
-OAlkyl +6 nm -OAlkyl
-SAlkyl +30 nm - -SAlkyl
-Cl or -Br +5 nm -Cl or -Br
-NAlkyl +60 nm -NAlkyl

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UV-vis Spectroscopy
Example of applying the Woodward-Fieser rules:

Less empirical treatment… particle in a box: En = n2h2/8mL2

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UV-vis Spectroscopy
Rules for the principal band of substituted benzenes RC6H4OX
Parent chromophore: O
X R
X
alkyl or ring residue 246 nm
H 250 nm
OH or Oalkyl 230 nm

Increment for each substituent:

-alkyl/ring residue o, m +3 -Br o, m +2
-OH, OMe, OAlkyl p -OH, OMe, OAlkyl p +15
o, m o, m +10 -NH2 o, m +13
-O p +7 om p +58
o o -NHAc o, m +20
m m +25 o, m p +45
-Cl p +11 -NHMe p +73
o, m o, m +20 -NMe2 o, m +20
p p +78 p +85
0
+10
Example:

MeO

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UV-vis Spectroscopy
trans-stilbene and cis-stilbene

λmax 296 nm (ε 29,000) λmax 280 nm (ε 10,500)

2,4,6-trimethylacetophenone and para-methylacetophenone

O O

λmax 242 nm (ε 3,200) λmax 252 nm (ε 15,000)

Strain release in the hydrolysis of a dilactone produced from shelloic acid.

O O H O O H
H2O
H H
O OH
O O
H H OH

no strong absoprtion >210 nm λmax 227 nm (ε 5,500)

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 UV-vis Spectroscopy
Tomatoes are a deeper red than carrots. Given that the conjugated systems of β-carotene and lycopene are both eleven
double bonds conjugated together with a similar number of alkyl substituents, why might lycopene absorb at a longer
wavelength and with greater intensity?

β-carotene

lycopene

Dehydration of graphene oxide to grapheme (Chem. Mater. 2009, 21, 2950)

H+

H
OH

Expanding a porphyrin π-system (Org. Lett. 2008, 10, 3945)

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IR Spectroscopy

O O
Me
O O
H
Me H

H H
O
cortisone acetate

Electronic States Vibrational energy levels Rotational energy levels

100000 - 25000 - 2500 - E = h c / λ

80000 - 20000 - 2000 - i.e. C-H bonds absorb at around 3000 cm -1 :

6.63x10 -34 x 3x10 8 x 3000x10 2 x N a
60000 - 15000 - 1500 -
= 36 kJ/mol
40000 - 10000 - 1000 -

20000 - 5000 - 500 -

0 0 0

(energies in wavenumbers, cm-1)

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IR Spectroscopy
High-resolution IR spectrum of CO in the gas phase:

Transmission
2000 2050 2100 2150 2200 2250
wavenumber (cm-1)

Modelling a vibration: Hooke’s law (“as the extension, so the force”)

kf
m1 m2

oscillation
about COM
The frequency depends on the mass and the stiffness of the spring

When applying this model to a pair of bonded atoms, the force constant corresponds to the strength of the covalent bond.
Stronger bonds are harder to stretch.

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IR Spectroscopy
Unlike a mass hanging from a spring, when a diatomic molecule vibrates, both of the atoms move. We take this into account by
using the reduced mass for the system to compute the frequency of oscillation:

For a vibrating diatomic molecule, the frequency of vibration (expressed as a wavenumber, in cm-1) is given by:

When one of the two masses is considerably larger than the other, as in a X-H bond, this expression approximates to the
lighter of the two masses:

Due to the inverse relationship between reduced mass and frequency, the stretching frequencies for X-H bonds are
considerably greater than those for other bonds.

For atoms with similar masses, the stretching frequencies of triple bonds are greater than double bonds, which in turn are
greater than for single bonds. This is a consequence of force constants following the bond strengths.

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IR Spectroscopy
Compare the C-H region of the IR spectra of fluorobenzene and d5-fluorobenzene. 1H
1H F

1H 1H
1H

2D
2D F

2D 2D
2D

C-H - 3050 cm-1 C-D - 2280 cm-1

ν C-H/ν C-D = 1.34

reduced mass C-H: 1 x 12 / (1+ 12) 1

reduced mass C-D: 2 x 12 / (2+ 12) 2

ratio of C-H to C-D stretching frequency = = 1.4

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IR Spectroscopy
The complex vibrational motion of polyatomic molecules can be resolved into a series of simpler normal modes.
There are 3N – 6 (non-linear molecule) or 3N – 5 (linear molecule) normal modes.
bending mode symmetric stretching mode antisymmetric mode
Normal modes of sulfur dioxide, SO2: 519 cm-1 1151 cm-1 1361 cm-1

Different bends of a methylene group:

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IR Spectroscopy
Normal modes of carbon dioxide:
symmetric stretching mode antisymmetric mode

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IR Spectroscopy
It is helpful to divide the IR spectrum into regions:

Example: cyanoacetamide

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