Identification of Unknown

Compounds
1
Steps in the Identification of Unknown
Identify Molecular ion M
.
+
Determine Molecular Formula (odd / even mass)
Analyze heteroatom(M+1 and M+2 )
S, Si, Cl, Br, .
Use rule of 13 to determine # Carbons (M+1 and M+2 )
Compare with
13
C-NMR (# carbons) with APT experiment (J-MOD)
( # protons)
Compare with proton NMR ( # protons)
Identify base peak (note if even / odd)
One or two bond fragmentation
Test your conclusions: in lab make derivatives (TMS or Na or K
complexes mass shift)
2
Solving problems in MS
Try to identify the Molecular Ion or decide if it is present (most
critical step in solving a structure)
Check if [M+1]
+
ion is too large to accommodate reasonable number of
carbons. (the [M+1]
+
ion might be the very small M
+
instead!)
Determine the first loss from proposed molecular ion. Some loss are
impossible (e.g 12, 14, 23 daltons)
Does the spectrum appear dirty? (lots of small peaks even at high mass)
If GC of the comopund Is available, compare retention time
Is the molecular weight even or odd?
An odd mass can be associated with an odd number of Nitrogen
An even mass means no Nitrogen or an even number of Nitrogen
This Rule is applicable only to Molecular ion and to odd-electron ions
Examine ion cluster for isotopic natural abundance (look for
special heteroatom pattern). Try to calculate number of carbons
3
Solving problems in MS
From the overall appearance: is it a fragile compound?
Is it likely to be aromatic or aliphatic?
Look in the low mass ions. Do you see any clues of the family of
compounds that you might be dealing with?
Make a list of suggested losses from the molecular ion and try to
make a pattellsrn from them.
Look for intense odd-electron ions in the spectrum: this is almost
impossible in compounds containing Nitrogen! These provides
clues for rearrangements (retro Diels Alder, McLafferty)
Speculate on the structure using all that information
Index of Hydrogen deficiency/Degree of Unsaturation (DU)
C
x
H
y
N
z
O
n
Index = x y + z +1
4
Index of Hydrogen deficiency
Nitrogen rule
M
+
even even # of N 0, 2, 4,
M
+
odd odd # of N 1, 3, 5,
Index = C H/2 X/2 + N/2 + 1
e.g. C
7
H
7
NO Index = 7 - 3.5 + 0.5 + 1 = 5
Hydrogen deficiency can be unsaturation (multiple bonds)
or cyclic structure
I=4 (3 DB + cycle)
R-CN
I=2
I=2 (1 DB + cycle)
5
Neutral losses and Ion series
M-1 H

M-15 CH
3

M-16 O

(rare) , NH
2

M-17 OH

, NH
3
(rare)
M-18 H
2
O
M-19 F

M-20 HF (very rare)

M-26 HCCH , CN
M-27 HCN
M-28 H
2
C=CH
2
, CO
M-29 CH
3
CH
2

, HCO

M-30 NO

(Nitro compounds),
H
2
CO

(anisoles)
M-31 CH
3
O

M-32 CH
3
OH
M-35 Cl

M-36 HCl
M-42 CH
2
=C=O, CH
2
=CH-CH
3
M-43 CH
3
CO

, C
3
H
7

M-44 CO
2
M-45 CH
3
CH
2
O

, CO
2
H

6
Neutral losses and Ion series
Figuring out which peak is molecular ion can be supported by identifying what fragment is lost.
There can be sometimes 2 consecutive loss:
In steroid, M-33 is often observed: comes from the loss of Me and H
2
O
The ions loss are only useful from molecular ion
There is no fragment in organic compounds between M-1 and M-15
Loss of M-14 is never observed!
Other gaps in mass loss are: between 21-25, 33-34, 37-41
Ions in these areas should be viewed suspiciously: either compound is not pure or postulated
molecular ion is wrong
7
Neutral losses and Ion series
Among the losses: most common are
Loss of H

, CH
3

, H
2
O(from some oxygenated compounds),
HCCH (from aromatic compounds),
HCN (from aromatic compounds containing Nitrogen),
CO and CH
2
=CH
2
(both at 28! Difficult to tell which one is lost)
Ethyl radical (29)
Methoxy radical (31)
Cl and HCl (35, 36)
Acetyl (43) accompanied by m/z 43 prominent and propyl (43) radical
8
Neutral losses and Ion series
Among the losses: most common are
Loss of H

, CH
3

, H
2
O(from some oxygenated compounds),
HCCH (from aromatic compounds),
HCN (from aromatic compounds containing Nitrogen),
CO and CH
2
=CH
2
(both at 28! Difficult to tell which one is lost)
Ethyl radical (29)
Methoxy radical (31)
Cl and HCl (35, 36)
Acetyl (43) accompanied by m/z 43 prominent and propyl (43) radical
9
Generally, with only three pieces of data
1) empirical formula (or % composition)
2) infrared spectrum
3) NMR spectrum
a chemist can often figure out the complete
structure of an unknown molecule.
SPECTROSCOPY IS A POWERFUL TOOL
10
FORMULA
Gives the relative numbers of C and H
and other atoms
INFRARED SPECTRUM
Reveals the types of bonds that are present.
NMR SPECTRUM
Reveals the enviroment of each hydrogen
and the relative numbers of each type.
EACH TECHNIQUE YIELDS VALUABLE DATA
11
Typical Infrared Absorption
Regions
C-Cl
2.5 4 5 5.5 6.1 6.5 15.4
4000 2500 2000 1800 1650 1550 650
FREQUENCY (cm
-1
)
WAVELENGTH (mm)
O-H C-H
N-H
C=O C=N
Very
few
bands
C=C
C-Cl
C-O
C-N
C-C
X=C=Y
(C,O,N,S)
C N
C C
N=O N=O
*
12
How to Use an Infrared Spectrum
Molecular formula:
Check for carbonyl:
Check for O-H, N-H
Check for triple bonds
Check for C=C, benzene rings
calculate index of hydrogen deficiency
note any shift from 1715 cm
-1
1)
2)
3)
4)
5)
13
How to Use an Infrared Spectrum
Look below 1550 cm
-1
;
Go back over spectrum for refinements;
check the C-H region for aldehydes
and for peaks above 3000 cm
-1
CONTINUED
check for C-O and
(alkenes and terminal alkynes)
6)
nitro
7)
14
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
15
C=O present ?
2 C=O Peaks
OH present ?
OH present ?
NH present ?
NH present ?
C-O present ?
C-O present ?
CHO present ?
C=N present ?
C=C present ?
C=C present ?
anhydride
acid
amide
ester
aldehyde
ketone
alcohol
amine
ether
nitrile
alkyne
alkene
aromatic
NO
2
present ? nitro cpds
C-X present ? halides
(benzene ?)
YES
YES
NO
YES
NO
=
=
16
17
NMR Correlation Chart
12 11 10 9 8 7 6 5 4 3 2 1 0
-OH -NH
CH
2
F
CH
2
Cl
CH
2
Br
CH
2
I
CH
2
O
CH
2
NO
2
CH
2
Ar
CH
2
NR
2
CH
2
S
C C-H
C=C-CH
2
CH
2
-C-
O
C-CH-C
C
C-CH
2
-C
C-CH
3
RCOOH RCHO
C=C
H
TMS
H CHCl
3
,
d (ppm)
DOWNFIELD UPFIELD
DESHIELDED SHIELDED
Ranges can be defined for different general types of protons.
This chart is general, the next slide is more definite. 18
19
Aldehydes
Ketones
Acids Amides
Esters Anhydrides
Aromatic ring
carbons
Unsaturated
carbon - sp
2
Alkyne
carbons - sp
Saturated carbon - sp
3
electronegativity effects
Saturated carbon - sp
3
no electronegativity effects
C=O
C=O
C=C
C C
200 150 100 50 0
200 150 100 50 0
8 - 30
15 - 55
20 - 60
40 - 80
35 - 80
25 - 65
65 - 90
100 - 150
110 - 175
155 - 185
185 - 220
Correlation chart for
13
C Chemical Shifts (ppm)
C-O
C-Cl
C-Br
R
3
CH R
4
C
R-CH
2
-R
R-CH
3
RANGE
/
20
Problem 1: C
3
H
5
BrO
2
, MW = 152
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 3 (5+1)/2 + 1
= 1
21
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
22
23
Problem 1: C
3
H
5
BrO
2
, MW = 152
NMR Correlation Chart
12 11 10 9 8 7 6 5 4 3 2 1 0
-OH -NH
CH
2
F
CH
2
Cl
CH
2
Br
CH
2
I
CH
2
O
CH
2
NO
2
CH
2
Ar
CH
2
NR
2
CH
2
S
C C-H
C=C-CH
2
CH
2
-C-
O
C-CH-C
C
C-CH
2
-C
C-CH
3
RCOOH RCHO
C=C
H
TMS
H CHCl
3
,
d (ppm)
DOWNFIELD UPFIELD
DESHIELDED SHIELDED
Ranges can be defined for different general types of protons.
This chart is general, the next slide is more definite. 24
Aldehydes
Ketones
Acids Amides
Esters Anhydrides
Aromatic ring
carbons
Unsaturated
carbon - sp
2
Alkyne
carbons - sp
Saturated carbon - sp
3
electronegativity effects
Saturated carbon - sp
3
no electronegativity effects
C=O
C=O
C=C
C C
200 150 100 50 0
200 150 100 50 0
8 - 30
15 - 55
20 - 60
40 - 80
35 - 80
25 - 65
65 - 90
100 - 150
110 - 175
155 - 185
185 - 220
Correlation chart for
13
C Chemical Shifts (ppm)
C-O
C-Cl
C-Br
R
3
CH R
4
C
R-CH
2
-R
R-CH
3
RANGE
/
25
ChemNMR
1
H Estimation
3.57
2.73
11.0
Br
O
OH
Estimation quality is indicated by color: good, medium, rough
0 2 4 6 8 10 12
PPM
26
27
28
Problem 2: C
8
H
14
O
4,
MW = 174
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 8 14/2 + 1
= 2
29
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
30
31
Problem 2: C
8
H
14
O
4,
MW = 174
ChemNMR
1
H Estimation
0.82 3.39
2.47
2.47
1.06
1.06
O
O
Estimation quality is indicated by color: good, medium, rough
0 1 2 3 4
PPM
32
Problem 3: C
9
H
12,
MW = 120
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 9 12/2 + 1
= 4
33
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
34
35
Problem 3: C
9
H
12,
MW = 120
NMR Correlation Chart
12 11 10 9 8 7 6 5 4 3 2 1 0
-OH -NH
CH
2
F
CH
2
Cl
CH
2
Br
CH
2
I
CH
2
O
CH
2
NO
2
CH
2
Ar
CH
2
NR
2
CH
2
S
C C-H
C=C-CH
2
CH
2
-C-
O
C-CH-C
C
C-CH
2
-C
C-CH
3
RCOOH RCHO
C=C
H
TMS
H CHCl
3
,
d (ppm)
DOWNFIELD UPFIELD
DESHIELDED SHIELDED
Ranges can be defined for different general types of protons.
This chart is general, the next slide is more definite. 36
Aldehydes
Ketones
Acids Amides
Esters Anhydrides
Aromatic ring
carbons
Unsaturated
carbon - sp
2
Alkyne
carbons - sp
Saturated carbon - sp
3
electronegativity effects
Saturated carbon - sp
3
no electronegativity effects
C=O
C=O
C=C
C C
200 150 100 50 0
200 150 100 50 0
8 - 30
15 - 55
20 - 60
40 - 80
35 - 80
25 - 65
65 - 90
100 - 150
110 - 175
155 - 185
185 - 220
Correlation chart for
13
C Chemical Shifts (ppm)
C-O
C-Cl
C-Br
R
3
CH R
4
C
R-CH
2
-R
R-CH
3
RANGE
/
37
38
Problem 4: C
7
H
13
Br
,
MW = 176
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 7 (13+1)/2 + 1
= 1
39
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
40
41
Problem 4: C
7
H
13
Br
,
MW = 176
42
Problem 5: C
5
H
8
O
,
MW = 84
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 5 8/2 + 1
= 2
43
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
44
45
Problem 5: C
5
H
8
O
,
MW = 84
ChemNMR
1
H Estimation
4.00
1.90
1.90
4.60
6.40
O
Estimation quality is indicated by color: good, medium, rough
0 1 2 3 4 5 6 7
PPM
46
Problem 6: C
9
H
13
NO
,
MW = 151
C
x
H
y
N
z
O
n
Index (DU) = x y + z +1
= 9 13/2 + 1/2 + 1
= 4
47
acid
THE MINIMUM YOU NEED TO KNOW
OH 3600
NH 3400
CH 3000
C N 2250
C C 2150
C=O 1715
C=C 1650
C-O 1100
3300 3100 2900 2850
2750
3000
1800 1735 1725 1715 1710 1690
=C-H -C-H
-CHO
C-H
ketone ester acid
chloride
aldehyde
amide
anhydride : 1810 and 1760
CH
2
and CH
3
bend : 1465 and 1365
BASE VALUES
Know also the effects of H-bonding, conjugation and ring size.
benzene C=C : between 1400 and 1600
EXPANDED CH
EXPANDED C=O
48
49
Problem 6: C
9
H
13
NO
,
MW = 151
ChemNMR
1
H Estimation
7.37
7.27
7.37
7.30
7.30
3.09
3.94;3.69
3.06;2.81
3.65
5.11
OH
NH
2
Estimation quality is indicated by color: good, medium, rough
0 1 2 3 4 5 6 7 8
PPM
50