Organic Spectroscopy

Introduction to Organic Spectroscopy

When talking about organic spectroscopy, we ask the questions:

 How is the structure of an organic compound determined?

 What are the different organic spectroscopic techniques and how can
we use this to characterize organic compounds?

Spectroscopy — the science that deals with interactions of various types of

radiation with matter, specifically electromagnetic radiation
Spectrometry — measurement of the intensity of radiation with an electronic
device

In most cases, these two terms are interchangeable but spectroscopy is often
referred as the techniques involving electromagnetic radiation

Spectroscopic Techniques

 Quantitative — used to determine the concentration of a particular

sample, e.g. UV Vis-Spectroscopy where we determine the
concentration by Beer-Lambert's Law

 Qualitative — used to determine the structure of an unknown compound

or characterize the compound in general

Uses of Spectroscopy

 Made structural elucidation easier

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  Widely used in the sciences, e.g. in drug discovery (isolating novel
compounds and determining their structures which could have valuable or
pharmacologically significant activities)

The Electromagnetic Spectrum

Ultraviolet Spectroscopy (UV)

UV Spectroscopy detects conjugated pi systems. Studies ultraviolet rays in the
electromagnetic spectrum

One of the most known use of UVVis is the determination of the concentration
of an unknown compound. Recalling Beers Law or Beer-Lambert's Law which
relates the absorbance (describes the amount of light absorbed by the sample)
to the molar absorptivity, length of sample, and concentration. This law is
primarily used for quantitative analysis. There is a linear relationship between
the absorption and concentration

Goal of Organic Spectroscopy: To determine the wavelength of maximum

absorption rather than the concentration using the Woodward Feiser Rule

Organic compounds may absorb UV radiation through conjugated pi system.

The basis for the absorption of the UV region is the transition of the electron
from the highest unoccupied molecular orbital to the lowest once UV is used

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 on the sample. A particular energy level based on the HUMOLUMO will have a
particular energy wavelength in which it would absorb light (which fall under
the UV region of the spectrum)

In general, ↑ conjugation, ↑ λmax

The energy absorbed is inversely proportional to the wavelength which means
the higher the wavelength, the lower the energy. If you increase the
conjugation, it increases the λmax meaning the gap between the HUMo and
the LUMO is lower

Terms in UV Spectroscopy

 Chromophores — primary absirbing species that contains the valence

electrons (the conjugated electrons for UVVis) with relatively low
excitation energies

Examples: conjugated dienes or polyenes, conjugated carbonyl

compounds or aromatic rings

 Auxochromes — functional group of atoms with nonbonded electrons

which may alter the wavelength and intensity of absorption; also
referred to as accessory subsitutents

 Bathochromic Shift or Red Shift — shift to longer wavelength and lower

frequency

 Hypsochromic Shift or Blue Shift — shift to shorter wavelength and

higher frequency

 Hyperchromic Shift — shift to higher value of molar absorptivity

 Hypochromic Shift — shift to lower molar absorptivity

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 Woodward Feiser Rule

To predict the wavelength of maximum absorption of various chemical

compounds, we use the Woodward Feiser Rule. At least 3 chromophore
systems would be used: 1 conjugated dienes, 2 conjugated enones, and 3
benzoyl derivatives. Each chromophore has a corresponding value and
whatever auxochromes attached also have a particular wavelength value

 Identify chromophores

 Identify auxochromes

 Add corresponding Values

Examples:

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 Terms in Conjugate Diene:

 Homoannular — double bonds on the same ring

 Heteroannular — double bonds on differint rings

 Acyclic — double bonds on a linear compound

 Exocyclic — double bonds outside and pointing at the ring system

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 *** The α carbon is the carbon next to the carbonyl carbon. The α and β
region would determine the different values of the auxochromes

Example:

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  First determine the base: acyclic 214

 Determine alkyl auxochromes: alkyl auxochrome at C3 5 and C4 5

 Calculate total = 224 nm

Example:

 Determine the base: clyclohexanone 215

 Determine auxochrome: extending conjugation 30, exocyclic to ring B

5, aliphatic auxochrom at β 5, 2 aliphatic auxochromes at δ 36

 Calculate total = 298 nm

Example:

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  Determine the base: aliphatic 246 with methyl CH3

 Determine auxochrome: 2 aliphatic auxochromes at ortho and meta

poistions 6

 Calculate total = 252 nm

Infrared Spectroscopy (IR)

IR Spectroscopy determines the different kinds of bonds in a compound which
eventually detects the functional groups present. Studies infrared in the
electromagnetic spectrum
The Infrared Region is the region of the electromagnetic spectrum which
covers the range just above the visible region, 780 nm, to apporixmately to
10−4 m. It lies between microwave to visible light
Types of Molecular Motions

 Translation — displacement of molecules from one point to another

 Rotation — circular motion of a particular atom or molecule about

an axis

 Vibrational — stretching or bending of bonds

In infrared spectroscopy, we focus on vibrational motion which has two types:

stretching and bending (or scissoring)

 Symmetric Stretching — bonds stretch in both direction

 Antisymmetric Stretching — bonds move in one direction

 In-plane Bending

 Out-of-plane Bending

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 Molecular vibrations happen at a quantized energy level and discrete energy.
This frequency is expressed in terms of wave number with the unit cm−1 . Each
bond would have a characterisitc wave number for its frequency

If infrared radiation is passed through a particular substance corresponding

to the vibration frequency, the molecule will absorb that radiation
Most functional groups have characteristics absorption bands in the
infrared region

The Infrared Spectra

*** The CO corresponds to the 1709 peak while HCH corresponds to the
2936 peak

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 Interpretation of Infrared Spectra

The fingerprint region are peaks from 500 to 1500 which are composed
of complex abroption and should not be used for interpretation. They
are only used when comparing two spectra (a standard and unknown
compound), if their fingerptints are the same then we can say they are
the same compound

Region with peaks at 1500 to 4000 cm−1 corresponds to a particular

functional group.

An IR spectra only answers if a certain functional group

present and ask if there are corresponding peaks

Short, strong bonds vibrate at a higher energy and frequency than long
weak bonds
Example, CC would be shorter and have higher energies and
frequencies than CC bond

Springs connecting small weights vibrate faster than springs connecting

large weights

Thus, CH, OH, and NH bonds have higher frequencies than CO or C
N bonds

Remember to not over interpret

The Functional Groups and the IR Spectra

 Alkanes — IR spectra would be fairly uninformative because most of the

organic compounds would likely contain CC bonds (which are found in
the fingerprint region) and CH bonds

 Alkenes — for vinylic CH bond is present at 3020 to 3100 while alkene
CC is at 1650

 Alkynes — show a C≡C stretching absorption at 2100 to 2260 while

terminal alkynes ≡CH stretches at 3300

 Aromatics — weak CH bond at 3030 which is difficult to locate; there are
also peaks at 1660 to 2000 for weak peaks and 1450 to 1600 for medium
intensity of CC

 Alcohols — have a characteristic band at 3400 to 3650 which are broad

and intense

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  Amines — relatively broader peak at around 3300 to 3500

Primary amines have "tooth" peaks which corresponds to the two

hydrogens of NH2

 Carbonyl Compounds — CO or acid derivatives (aldehydes, ketones,

carboxylic acid) with an intense sharp peak at 1670 to 1780

 Aldehydes — saturated aldehydes absorb at 1730 while the presence of a

double bond or aromatic ring would lower it to 1705

 Ketones — saturated open chains and six-membered cyclic ketones absorb

at 1715 while five membered cyclic ketones absorb at 1750, ketones next
to a double bond or aromatic ring absorbs at 1690

 Esters — absorb at 1735 while 1715 if next to a double bond or ring

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  Carboxylic Acids — absorb similar to esters with the additional OH stretch
seen at 3400 to 3600 but are less intense and broad than alcohol

 Amides — CO can be found around 1715 and expect a tooth-like peak (
NH2 ) for primary amides at 3200 to 3500 region due to hydrogen
bonding. Secondary amines have sharp single peaks

Examples:

 To solve IR problems, first calculate the degree of unsaturation:

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  Determine the functional groups present

 Draw structure

Nuclear Magnetic Resonance Spectroscopy (NMR)

NMR Spectroscopy basically describes or gives data to describe the CH or N
H framework depending on the nuclear technique. Studies radio waves in the
electromagnetic spectrum

The NMR Phenomenon

Most nuclei possess an intrinsic angular momentum, P, and any spinning

charged particle generates a magnetic field. If the mass number and atomic
number are both even, then l=0 and the nucleus has no spin. For each nucleus
with a spin, the number of allowed spin states can be quantized: nucleus with
l = 2l + 1

1H Proton NMR Spectra

 Number of Signals — number of chemically unique H's in the molecule

 Chemical Shift — type of hydrogens presents e.g. aromatic, vinyl,

aldehyde, alkyl, hydroxyl

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  Integration — number of each chemically unique H

 Spin-spin Splitting — determines the proximity of the protons to each

other

Determining the Number of Signals

 In CH3 CH2 CH2 CH3 , due to the symmetry of the molecule, we are only
expecting it to produce 2 signals rather than 4. The only difference is the
level of integration

 In benzene, all the hydrogens are equivalent = 1 signal

 In ⌬OCH3, the hydrogen in OCH3 gives out 1 signal and the ring
produces 3 signals because of its symmetry. A total of 4 signals

 For heptane, the number of unique protons are 4 and give out 4 signals

 In ethyl ethanoate, there is no symmetry and thus each hydrogen has a

different chemical environment producing 4 signals

 In CH3⌬CH3, we have 2 signals since the protons in the ring are all
similar due to the horizontal and vertical planes of symmetry

The Chemical Shift

The chemical shift or the variations in the positions of NMR absorptions arise
from electronic shielding and deshielding. The chemical shift (in ppm) is
independent of the spectrometer used

Chemical shift is affected by electron density around the nucleus. An increase

in electron density shields the nucleus resulting in an upfield shift and a
decrease in electron density deshields the nucleus in a downfield shift
More electronegative atoms deshield more and give larger shift values. The
additional of electronegative atoms cause an increase in chemical shift

The deshielding effect of an electronegative substituent decreases

with distance

Chemical Shift Ranges

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 Intensity of Signals: Integration

The amount of integral trace rises is proportional to the are of that peak

Spin-Spin Splitting

If the protons are bonded to the same proton, there would be no spin-spin
splitting since they are in the same chemical environment and are equivalent. If
they are nonequivalent (e.g. in an aliphatic ring), then there is spin-splitting

If the protons are bonded to adjacent carbons, spin-spin splitting is normally

observed

 The Doublet (↑↓)

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 The signal of Hb is split by the green proton resulting into a parallel and
anti parallel

 The Triplet

If a proton is coupled to two protons: ↑↑, ↓↓ or ↑↓

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 Example:

 The Quartet

A proton split by three protons: ↑↑↑, ↓↓↓, ↑↑↓, or ↑↓↓. The proton is
split into 1331

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 If a proton is split into n protons then the proton is split into
n+1

Examples:

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 Example: Propose a structure for the compound of molecular formula
C4 H10 O whose proton NMR structure follows: doublet-singlet-singlet-sextet
2116

 Determine degree of unsaturation DoU = 0 which means it is an alkene)

 Partial structure: HOCH2CHCH3CH3

C13 NMR

Carbon-12 does not usually have an NMR signal. Carbon-13 does but it is
difficult to obtain due to its limited abundance. This is used to determine the
number of carbons with one signal for each chemically unique carbon

 Doublet — the carbon is attached to one proton

 Triplet — attached to two protons

 Quartet - attached to three carbons

Mass Spectrometry (MS)

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 Mass Spectroscopy is used to determine the molecular mass and formula of an
organic compound. There is no electromagnetic spectrum interaction and uses
high energy electron to ionize the organic compound

Basic Principle: The sample is injected and vaporized. An electron beam

ionizes the sample and deflected towards the detector. If a sample is heavy,
it is least deflected by light samples are highly deflected
Steps in Mass Spectrometry

 Vaporization

 Ionization

 Sorting

 Detection

Background of Mass Spectrometry

Mass spectrometry uses high energy electrons to break a molecule into

fragments. Separation and analysis of the fragments provide information about
the molecular weight and structure

The impact of a stream of high energy electrons cause the molecule to lose an
electron and forms a radical cation which is then resolved by the magnetic
field in the instrument

If one of the ions are ejected, it is called the molecular ion which accounts for
the molecular weight

Only cations are detected by the instrument, MS does not detect

radicals

Molecular Ion is the radical cation corresponding to the mass of the original
molecule. It is usually the highest mass in the spectrum except for some
exceptions with specific isotopes or the absence of some molecular ion peaks

The resulting mass spectrum is a graph of the mass of each cation vs its
relative abundance

The base peak is the highest abundance but is not necessarily the molecular
ion peak

Fragmentation Pattern

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 Fragmentation patterns help in generating the formula of the compound. For
example, if the resulting molecular weight is odd then that would mean there is
an odd number of nitrogen in the compound

Another clue: Bromine] if there is an M and a M2 with peaks of

almost equal intensity and only a couple units apart

Another clue: Chlorine] if the M2 is 1/3 large as the M

Another clue: Sulfur] if there is an unusual large M compared to M2

Another clue: Iodine] if there is a large gap between I and M

Alkanes] have fragmentation splits of:

 Loss of methyl — M 15

 Loss of ethyl — M 29

 Loss of propyl — M 43

 Loss of butyl — M 57

Alkenes] typically form resonance stabilized allylic carbocations

Aromatics] fragment at the benzylic carbon, forming a resonance

stabilized benzylic carbocation (which rearranges to the tropylium ion
with m/z = 91 or a peak at benzene ring with m/z = 77

Alcohols] fragment easily resulting in very small or missing parent ion

peak because it's easy to lose the hydroxyl radical M 17 or water
M 18

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  Primary Alcohols usually have a prominent peak at m/z = 31
corresponding to H2 C = OH +
Amines] contain nitrogen meaning there is an odd M and will cleave
between the alpha and beta position

Ethers] cleave to form oxonium ion or carbocation

Aldehydes] fragmentation may form acylium ion M 1 and M 29
for R after fragmentation and loss of CHO

Ketones] has a loss of one of the R groups to form the acylium ion

Esters] common fragment is the loss of OR with a peak at M OR' or a

loss of R' peak at M R'

The Rule of Thirteen

Not all the peaks at mass spectrum should be interpreted. Only interpret M or
M2 if present and if there is a presence of bromine, chlorine, etc. Just get the
molecular weight and the fragmentation pattern
The Rule of Thirteen can be used to identify possible molecular formulas for an
unknown hydrocarbon, Cn Hm

Steps in The Rule of Thirteen

M+
 Divide M over 13 and get the integer only, n =
13
 While m = n + r where r is the remainder from step 1
Example:

The formula for a hydrocarbon with M106 can be found:

106
 n= = 8 with remainder 2
13
 Thus, m = 8 + 2 = 10

 The formula is: C8 H10

If a heteroatom is present...

 Use information from MS (bromine, iodine, etc.), IR (peaks) and NMR

 Subtract the mass of each heteroatom from the molecular weight

 Use the rule of thirteen

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 Example:

A compound with a molecular ion peak at m/2 = 102 has a strong peak at 1739
cm−1 in its IR spectrum. Determine its molecular formula
 Peak at 1739 = ester

 Subtract Os from 102 102 − 16(2) = 70

70
 Use Rule of Thirteen, n = = 5 remainder 5
13
 m = 5 + 5 = 10
 Formula: C5 H10 O2

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