Chapter 14: Determining the Structure of Organic Molecules
1. Mass Spectrometry
2. IR Spectroscopy
3. UV Visible Spectroscopy
Mass Spectrometry (Sec14.2)
Mass spectrometry helps to determine the molecular mass and the molecular formula of the compound with some structural
features.
An organic compound (M) is ionized (loss an e ) to a charged radical species, M+. (molecular ion). This charge radical ion
fragments into smaller radicals and cations, but only cations are accelerated further and detected by analyzer. filtered
Masses of positively charged species are determined by sending the ions (cations) through a magnetic field. The mass Atm,
spectrometer records a mass spectrum, which is a graph of the relative abundance of each fragment plotted against m/z value.
If we assume all the ions have a charge of +1, then the peaks give the mass ratio, and their heights give the proportion of
ions of different masses.
My 2 = 1 them
note:@not solved D E P T
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 1
Mass spectrum of pentane:
A. The peak with highest m/z value in the spectrum i.e., m/Z=72 is parent peak (molecular ion peak) This peak provides the
mass (in amu) of the compound with the lowest mass isotopes. because highest molar
B. The base peak (tallest) has the highest relative abundance.
mass
Fragment ion gives structural information about the original compound.
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 2
C. Isotope peaks results in formation of isotope cations.
M+1 peak is of importance for naturally occurring isotopes of carbon. tells # o f c in compound
10€
Naturally occurring carbon isotopic abundance
~ 99% 12C, ~ 1%; we ignore 14C
use
For
This helps to determine the number of carbons in compound.
1M¥,
anne
Molecule ion m/z Relative abundance
M 102 100% =#C
M +1 103 6.9%
When relative abundance of M = 100%, (Relative abundance of M+1/1.1%) gives approximate no of carbons in formula,
In above example, M+1 = 103
6.9/1.1 = 6.3; i.e., Number of carbons = 6
D. Isotope peak (M +2) is important for Cl, Br or S in the compound. -Peak height
Isotope Natural abundance Intensity (M:M+2)
35Cl : 37Cl 75.8 : 24.2 3:1
79Br : 81Br 50.7 : 49.3 1:1
32S : 34S 0.01 : 4.22 24 : 1
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 3
a Br
s
If the height of M and M+2 peak is almost same, then compound has one Br. If it is 3:1, then there is Cl in the compound.
-parent
Note: For Nitrogen if m/z for M is odd, then the molecular formula contain odd number of nitrogen atoms. If m/z for M is even,
then the molecular formula contain even number of nitrogen atoms(this #
includes 0).
Alkanes: Unbranched alkanes form series of fragments differing in 14 amu (CH2), whereas branched chain fragments at the
bond forming secondary or tertiary cations as base peak.
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 4
r n pentane → r t + A
→ i t
w i s e pentane
i t i s moststable carbecutin
→
i n neo-pentane
base peak w i l l show highly substituted C's
base peaki s a ten sans halide be electronegative groups destabilize
chargea t carbocations
Alkyl halides: Important peaks: M, M+2 peaks. The base peak is due to heterolytic cleavage between C & Br or C & Cl
( cleavage). Thus M-79 or M-35 are base peaks for connecting Br or Cl.
often
Different functional groups have characteristic fragmentation patterns
The presence of a functional group, particularly one having a heteroatom Y with non-bonding valence electrons (Y = N, O, S, X
etc.), can alter the fragmentation pattern of a compound. it is easier to remove (ionize) a non-bonding electron than one that is
part of a covalent bond.
The general fragmentation pattern for organic functional groups can be summarized as:
a. -cleavage This involved hetrolytic cleavage at bond to produce
resonance stabilized cations. Ketone molecular ion undergo -cleavage
is#→ i t
to form acylium ion.
i t →
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 5
.
b. Loss of neutral molecule: A cationic fragment formed from M+ can cleave
further by loss stable molecule, such as: CO, HCN, H2O, HCl, NO
c. Rearrangement A molecule containing a keto- -
cleavage with migration of -hydrogen forming enol radical cation
(resonance stabilized) is called McLafferty rearrangement.
_
Ketones:
Mass spectrum of 3-heptanone
cleavage: McLafferty Rearrangement:
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 6
Infrared Spectroscopy (sec14.3)
Infrared spectroscopy is used to identify functional groups in organic compounds.
IR spectroscopy or vibrational spectroscopy is based on the fact that bonds (and groups of bonds) vibrate at characteristic
frequencies and light of precisely those frequencies are absorbed (IR region) and increase the amplitude of vibration.
For a particular vibration to result into an absorption band it must change the dipole moment of the molecule.
This technique measures the amount of light absorbed or transmitted as a function of wavenumber.
tu
IR Spectra are typically plotted as % transmittance (% T) vs. wavenumber in cm 1 (Typically spans from 4000 cm--1to 500
cm 1). The position of absorption bands is reported in wave numbers (directly proportional to energy).
The wavenumbers at which an organic molecule absorbs radiation give information on functional groups present in the molecule.
a) Frequency (wavenumber) and Intensity of IR Absorption:
The atoms in a molecule are in constant motion.
The covalent bond between two atoms acts like a spring, allowing the
atoms to vibrate (stretch and bend) relative to each other.
Due to quantization of energy, covalent bonds can vibrate only at
certain allowed frequencies.
The position of an absorption band correlates with the type of chemical
bond.
Organic molecules contain many atoms, as a result there are many
stretching and bending absorption bands.
Stretching Vibration (higher frequency)
Bending Vibration (lower frequency)
stretchinggives m o r e info than bending
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 7
stronger bonds higher freqs
The
= or =
Where: k = force constant (measure of bond shift)
= reduced mass
= where mA, mB are mass of 2 atoms
i) Bond strength: stronger bonds vibrate at higher frequencies (i.e.,
: -C
C=O > C-O
H > =C(sp2) H > - C(sp3) H
Wave number (cm-1): 3300 3050 2900
iii) The position of absorption band is affected by resonance, electron donation, electron withdrawal and H-Bonding
More the single bond character due to resonance, lesser bond order lowers the frequency/wavenumber.
C-O absorption band shown for different compound:
resonance makes the doublebond
i..
lesslike a doublebend,like a
single bendpart oft h el i n e
s o m e r e single bend character
single bond character i s weakerand thus lower freq/higher u n e num
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 8
electron donating= lower freq//withdrawing = higher freq
Electron donating atom/groups) next to C=O group, shift the frequency on lower side and electron withdrawing groups
increases the frequency. holds
N ( t ) better thanO
iv) Masses of the bonded atoms the greater the mass, the lower the frequency (all other factors being equal).
C-H (3000 cm 1) > C-D (2100 cm 1) O-H (~3500 cm 1) > S-H (~2570 cm 1
b) Intensity of the Absorption depends on:
i) The change in dipole moment during vibration:
a. Vibration that causes a significant change in dipole moment of a chemical bond leads to strong absorption bands
(IR active vibrations)
b. Vibrations that result in no or very little change in dipole moment lead to weak or no absorption band.
Symmetrical bonds often exhibit weak or no absorption bands (IR inactive vibrations = no dipole moment due to
symmetry.
ii) The number of bonds of a given type -more the C- -H absorptions
iii) The absorption of O-H, N-H group in alcohols, carboxylic acids, amines does not usually appear as a sharp peak, instead
a broad band is observed because the vibration of O-H and N-H group is complicated due to hydrogen bonding.
iv) Intensities of the vibrations are referred as strong, medium, weak, broad, and sharp.
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 9
2 3 1 b e resonance increases
singlebend character
Try: 1. List the following compounds in order of decreasing of C=O absorption band
3<221
I 2 3
c
2. Circle the one which are IR inactive: a) 2-butyne b) 1-butyne c) 1,1, dichloroethane symmetrical alleyne
C-H, C-D, C-C, C-Cl, C-Br
Interpretation of IR Spectra:
In general, the IR spectrum can be split into four regions for interpretation:
4000 2500 cm-1 : Absorption of single bonds formed by hydrogen and
other elements e.g., C H, O H, N H
2300 2000 cm-1 : Absorption of triple bonds e.g.,
2000 1500 cm-1 : Absorption of double bonds e.g., C=C, C=O
1500 600 cm-1: Absorption of single bonds C C, C O, C N
/
This region often consists of many different, complicated bands. This part
of the spectrum is unique to each compound and is often called the
fingerprint region. It is rarely used for identification of particular functional
groups.
Table 14.5
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 10
Sample IR Spectra:
Alkane, Alkene
C-H ~ 2 7 0 - 3 0 0 0
c@1640
=L-it@zero
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 11
CEC ← 2200→ CE N
Alkyne
The alkyne C C signal is much weaker
and is just below 2200 cm-1
E l - H @3300
2200t 33002 CEC-H
Nitriles:
C N absorbs just above 2200 cm-1 (med strong)
Benzonitrile
Ar@Moo-Iboo
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 12
Alcohol:
broadottband
~ 3500
Amines: strong signal
absorption
R-NHL
R-NHR weak signal
absorption
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 13
Focus o n carbonyls
strong E -O band - 1 7 2 0
Carbonyls:
Carbonyl stretches are generally strong:
Conjugation shifts all carbonyls to lower frequencies.
Ring strain shifts carbonyls to higher frequencies.
Aldehydes:
aldehydeshare R-R-H
extra absorption
a t 2720-2820
Ketones:
R-E-R
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 14
Carboxylic Acids:
R-E-O-H
R-Eto-R
Esters
Amides:
R-E-NRz
Textbook problems: 14.5 14.25; except: 10, 11
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 15
Carbonyl shifts
bond,indicating carbonylgroup
1 7c o - 1 7 5 0 13 G o
RkoI t broad O - H band
= very
deep C - O band@1250
reor =
RRH = band @2720-2820
n o extra
band
per =
RINHa = N - H band@33c o
1. Assign correct IR to the following compounds
Eat
Ee (
a
[Link]
Hpeaksunsaturated
small C-
✓ A
¥
carbonyl
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 16
dudehyde
13
@ carbonyl
2. Provide a structure that is consistent with the data below:
Cathy
C9H7Cl
IR (cm 1):
1H NMR
Ar, DEAR
3050, 2950, 2220, 1620 hi,,§ax2k=2o-8=1%26
in ppm): 7.8 (2H, d), 7.2 (2H, d), 2.1 (3H, s)
6>4 = A r
f 'hop-it
13C NMR ( in ppm): 140, 132, 125, 122, 88, 83, 18
'A r
21ft
signals-_symmetry
¥E¥Eii¥¥÷÷.at.
Ha
Hb
H,
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 17
e 3. C5H10O Draw the structures of the compound from given IR, 13C NMR, and 1H NMR
H
H#yo H
' C H3
kHz
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 18
4 Predict the molecular formula and possible
structures for the unknown compound based
on mass spec and IR information given.
notarbonyl (co = - a m u )
7 2
M a n u i s m a ss
SanscarbonyffGHonly) ¥ 1720
44-(12×3)=8.'. 034860
(saturated) 44
no extrapeakat 2720-2820
so not aldehyde
72
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 19
UV-vis Spectroscopy
UV-vis spectroscopy provides useful information about unsaturated and conjugated systems. J c Mo's
UV/visible light energy causes an electronic transition between HOMO and LUMO. UV (190nm-400nm) and visible
radiations(400nm-800nm) have enough energy to cause electronic transition from n and .nonbonding → yet
J l → # *
Degree of absorption depends on:
1. Frequency of light 3. Path length of cell
2. Concentration of sample 4. Probability of transition
Intensity of absorption can be expressed in terms of the extinction coefficient and the greater the value, the more is the
probability of absorption. higherEthigherpfebsorption)
In general, we may distinguish bonding type MO ( ,non-bonding type (n) lone pair MO, and anti-bonding type MO (
O E
too
high# X - F - too high
A schematic illustration of six (6) transitions between three types of occupied MO ( , n) and two types of unoccupied MO
( *, *).
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 20
*
n → at i s lever energy than t o→ *
Depending on the functional groups, organic molecules may undergo several possible transitions which can be placed in the
increasing order of their energies viz. n <n . Since all these transitions require fixed
amount of energy (quantized), an ultraviolet or visible spectrum of a compound would consist of one or more well defined peaks,
each corresponding to the transfer of an electron from one electronic level to another.
The spectral information is given as a list of the values of max, with molar absorptivity of each
value of max.
In the case of simple carbonyl compounds, irrespective whether they are conjugated or not,
two types of transitions may be observed: the low energy (longer wavelength) n and the
higher energy (shorter wavelength) as illustrated:
UV spectra of acetone (CH3COCH3, has two absorption bonds, one n and other .
The max is the wavelength at which the absorbance band has its maximum absorbance.
*. *.
max at 195 nm is for max at 274nm is for n
Absorption bands are different in sizes because of difference in molar absorptivity at the two
different wavelengths.
Comparison of energy difference of some pi systems
In conjugated systems, lower the E (more the conjugation), higher is max.
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 21
The effect of conjugation on the electronic transitions of unsaturated hydrocarbons.
Functional Group
max (nm)
C=C
C=C-C=C
C=C-C=C-C=C
The wavelength shift towards larger values i.e., -
conjugative interaction. X increases w/morei t bends
The max increases by 30 40 nm for each double bond extending the conjugated
system.
The alkyl group substitution on double bond also causes absorption to occur at longer wavelength. For example,
In molecules with extended pi systems, the HOMO-LUMO energy gap becomes so small that Color absorbed Color seen
absorption occurs in the visible rather than the UV region of the electromagnetic spectrum. The Violet Yellow
color of the substance is subtractive color. As we move from UV to Visible, the first color in the Blue Orange
spectrum is violet. If violet is subtracted from white, the color we see is yellow. Green Red
Yellow Violet
Example: subtractivecolor = s e e opposite o f absorbedi t Orange Blue
Beta-carotene, with its system of 11 conjugated double bonds, absorbs light with wavelengths in the blue region of the visible
spectrum while allowing other visible wavelengths mainly those in the red-yellow region - to be transmitted. This is why carrots
are orange.
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 22
more R → higher k
more conjugation → higherX
Try:
Q1 Identify the lowest energy transition and rank the given compounds in order of increasing max
4
\ 2 3
12243 L 4
at>X yet
I" z s 1 carbonyl: d of n→ y e →
z
2 only has a → I t , carbonyl has 0 :
O
Q2 Acetone has electrons transitions at
that corresponds to the max shown.
max = 280 nm ( = 15) and max = 190 nm ( = 1100). State the electronic transitions
Chapter 14: Determining the Structure of Organic Molecules (KSethi) Page 23
abserptron band o f C - O a t lover w e r e #
#OH,#OH
m k i n w i n t h
÷.÷÷÷÷÷i÷÷÷ which h a s
G o
higher w a v e # f o r
band?
1µA
#H
Mass Spectrometry
Mass spec is based upon carbocation stability
a molecule 13 ionized and allowed to split into smaller parts, a n d a
mass spectrometer measures how often each type o f piece appears
fragments are groupedby mdar m a s s and their abundance is
measured and reported o n the Y-axis
o f t h e parent molecule a n d the
right most peak 13 the molar mass
highest peak is the base peak -
most stable carbocation
peaks a r e named i n relative terms, w i t h the parent peak being (m),
fragments being(M-omass),a n d isotope peaks being (MH)o r l i n t2 )
namelpositionadistancefromM
predict the most stable carbonh e n b y comparing masses of M and base peak
to s e e w h a t stayed and what broke off
MH peaks g i v e information about #C's i n the parent (P.3)
abundance
when relative abundance o f M B leo% , divide the relative
o f M H b y l .1 t o g e t a n approximate number o f C i n the molecule
M t 2 peaks gire information about Br, d , a n d S in the parent(P.3 -4)
here,the relative intensity (height) 13 m o r e important
a Br means the M t 2 peak i s roughly similar t o M
a 4 Means the M t z peak i s roughly 'gr d of M
an 5 means the M t 2 peak i s much smaller than M
Fo r N : i f the m a s s of M i s odd, i t contains a n odd number o f N atoms
contains a n even n u m b e r (includes
i f the mass o f M B even, i t a)
o f N atoms
Cleavage patterns (carbocation stability) (P. 5-6)
non-bending electrons a r e easier t o r e m o v e them covalent e -
x . cleavage i s heterolytic bend breaking t h a t creates resonance-stabilized
fragments
stable, neutral molecules l i k e CAo r Huo c a n leave i n iced fragments,meaning
they a r e likely not included o n the b a s e peak
Mclatterty Rearrangement i s cyclic rearrangement/p-cleavage o f a
molecule w i t h a Iulo group which also involves a r-hydrogen money
t o form an end with the'0 o f the ketene
note: ketenes c a n do both d - cleavage a n d McLafferty rearrangement
I R spectroscopy
molecule i n constant motion, a n d covalent bonds a c t a s springs
Atoms in a a r e
a n d they
Governedby Hooke's l a w - s t r o n g e r bonds increase frequency
resonance a t a double bond, such a s w i t h a n ester, increases the
single band character o f t h a t bond w e a k e r bond
stronger bonds= higher frequency further l e f t
=
w e a ke r bonds= lower frequency = further right
the e n e r g y g a p btwn T L a n d a * i s O E
e n e rg y in the form o f U v o r visible light i s absorbed b y
an electron,pushing A past O E
O E is largerf o r smaller T c systems
longer w e r e lengths o f light = lower e n e r g y
therefore? oE&fmq&
larger T c system= smallero E = longerwavelength loverfreq =
smaller J u system higher0 E shorterwavelength higherfreq
= = =
adding a conjugated a bond adds 3e - 4 0 n m
therefore, high X = high#conjugated t o
bonds