Solving Unknown Structures Using NMR

1
Solving Unknown Structures Using NMR
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
2
Six Simple Steps for Successful Structure Solution

• Get molecular formula. Use combustion analysis,
  mass spectrum and/or 13C NMR spectrum. Calculate
  double bond equivalents.
• Determine functional groups from IR, 1H and 13C
  NMR
• Compare 1H integrals to number of Hs in the MF.
• Determine coupling constants (Js) for all
  multiplets.
• Use information from 3. and 4. to construct spin
  systems (substructures)
• Assemble substructures in all possible ways,
  taking account of dbe and functional groups. Make
  sure the integrals and coupling patterns agree
  with the proposed structure.

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SOLUTION
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
3
USING 1H NMR DATA UNKNOWN B

• A compound shows an M. in the EIMS at 154 m/z
• Further fragments are at 121, 93, 71, 55 and 39
  m/z
• The IR shows bands at 3400 cm-1 (broad) 1450
  cm-1
• Use the 1H and 13C data to determine the
  structure of the
• compound

Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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13C NMR DATA UNKNOWN B
t
t
t
q
q
d
d
q
s
s
A B C D E
F GHI J
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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MOLECULAR FORMULA DETERMINATION UNKNOWN B
s d t q
A C
D F I
G H J
B E
(C)2 (CH)2 (CH2)3 (CH3)3 C10H17
137 Da
The M. appears at 154 m/z, so there is a mass
difference of 17 Da ( OH)
Therefore molecular formula C10H18O (2 dbe)
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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1H NMR DATA UNKNOWN B
Integrals
ONLY 17 H!
5H
3H
3H
3H
2H
H
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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SUBSTRUCTURES UNKNOWN B
dC 112 t, 146 d dH 5.00 dd, 5.15 dd, 5.85 dd
dC 125 d, 132 s dH 5.05 t Me groups at dH 1.5
dC 73 s dH 1.05 s
MF C10H18O !
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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WORKING STRUCTURES UNKNOWN B
A Ha should be ddt
B Ha should be ddt
C Ha should be dd
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
9
MASS SPECTRAL FRAGMENTATION UNKNOWN B
Fragments at 121, 93, 71, 55 and 39 m/z
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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USING MASS SPECTRAL DATA UNKNOWN G

• A compound shows an M. in the EIMS at 128 m/z
• Further fragments are at 99, 83, 72 and 57 m/z
• The IR shows bands at 1680 cm-1 (strong)
• bands at 1400 - 1500 cm-1
• Use the 1H and 13C NMR and MS data to determine
• the structure of the compound

Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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13C NMR DATA UNKNOWN G
t
t
q
d
d
d
t
A B C D
E FG
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
12
MOLECULAR FORMULA DETERMINATION UNKNOWN G
s d t q
A B C
D E F
G
(C)0 (CH)3 (CH2)3 (CH3)1 C7H12
96 Da
The M. appears at 128 m/z, so there is a mass
difference of 32 Da ( O2)
Therefore molecular formula C7H12O2 (2 dbe)
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
13
1H NMR DATA UNKNOWN G
Integrals
12 H Total
3H
2H
H
H
H
H
H
H
H
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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SUBSTRUCTURES UNKNOWN G
dC 96 d dH 4.9 t
dC 140 d, 101 d dH 6.15 d, 4.70 m
dC 64 t
4 Oxygens in substructures but only 2 in MF
MF C7H12O2 !
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
15
WORKING STRUCTURES UNKNOWN G
13C Shift additivity data
MS Fragmentation
Retro Diels-Alder
Fragments are at 99, 83, 72 and 57 m/z
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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USING COSY DATA UNKNOWN H

• A compound shows an M H in the FAB MS at 132
  m/z
• MW 131 (Odd) therefore odd number of nitrogens
• A further fragment is at 86 m/z
• The IR shows bands at 3400cm-1 (broad) 1640
  cm-1 (broad)
• Use the NMR data to determine the structure of
  the compound

Organic Structure Analysis, Crews, Rodriguez and
Jaspars
17
13C NMR DATA UNKNOWN H
d
t
t
d
s
A
B C D E
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
18
MOLECULAR FORMULA DETERMINATION UNKNOWN H
s d t q
B C
D E
A
(C)1 (CH)2 (CH2)2 (CH3)0 C5H6
66 Da
The MW is 131, so there is a mass difference of
65 Da ( NO3H3)
Therefore molecular formula C6H9NO3 (2 dbe)
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
19
1H NMR DATA UNKNOWN H
Integrals
D2O so no XH (OH, NH)
ONLY 6 H!
H
H
H
H
2H
b c d d
e e
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
20
SUBSTRUCTURES UNKNOWN H
dC 176 s IR band at 3400
dC 70 d dH 4.6 m
dC 60 d dH 3.9 m
MF C5H9NO3 !
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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1H 1H COSY NMR SPECTRUM UNKNOWN H
b c d d e
e
d-e
c-e/e
e-e
b-e/e
d-d
b-d/d
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
22
1H 1H COSY NMR DATA UNKNOWN H
c-e/e
b-e/e
b-d/d
Also 4-bond correlation d-e Diastereotopic pairs
d-d and e-e
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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SUBTRUCTURES UNKNOWN H
MF C5H9NO3
Working structures
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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ASSIGNING NMR DATA TO A KNOWN STRUCTURE GUAIAZULEN
E
Expect
(C)5
(CH)6
(CH2)0
(CH3)4
MF C15H18
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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13C NMR DATA GUAIAZULENE
(C)5 (CH)6 (CH2)0 (CH3)4 C15H18
qq LM
d J
d H
d K
ddd EFG
q N
q O
s B
s D
s I
s A
s C
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HSQC NMR DATA GUAIAZULENE
n
o
lm
k
O
O
N
LM
N
LM
K
K
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HSQC NMR DATA GUAIAZULENE
g
e
f
h
j
J
J
H
H
G
G
F
F
E
E
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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1H NMR DATA GUAIAZULENE
Label spectrum according to HSQC
3H m
3H l
3H o
3H n
H g
H e
H f
H j
H h
H k
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
We will need expansions
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
g e f j
h
HI G F CDE B A
I-g
I-j
G-f
F-g
C-h
D-j
D-e
C-g
B-h
A-f
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
g e f j
h
O N LM K
N-h
K-g
K-f
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
n o
lm
LM-lm
K-lm
I-o
H-n
C-n
D-o
B-lm
A-n
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
Carbon Proton
A f, n
B h, l/m
C g, h, n
D e, j, o
E
F g
G f
H n
I g, j, o
J
K f, g, l/m
L m
M l
N h
O
Obvious assignments
N/O
F/H
J/E
H/F
E/J
M
O/N
K
L
1H-1H COSY data indicates that e and j are
adjacent (J(e-j) 4 Hz) as are f and h (J(f-h)
11 Hz)
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
Carbon Proton
A f, n
B h, l/m
C g, h, n
D e, j, o
E
F g
G f
H n
I g, j, o
J
K f, g, l/m
L m
M l
N h
O
N/O
H
J/E
F
E/J
G
M
O/N
K
L
Signal for f is a dd long-range coupling to
remaining proton g
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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HMBC NMR DATA GUAIAZULENE
Carbon Proton
A f, n
B h, l/m
C g, h, n
D e, j, o
E
F g
G f
H n
I g, j, o
J
K f, g, l/m
L m
M l
N h
O
N
A
H
J/E
C
F
E/J
B
G
M
O
K
L
HMBC data cant decide positions of E, J
HMBC data cant decide positions of D, I
How do we decide?
Organic Structure Analysis, Crews, Rodriguez and
Jaspars
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FINALISING THE ASSIGNMENTS GUAIAZULENE
NOE
N
A
H
J
C
F
E
I
D
B
G
M
O
K
L
puts it in a similar environment to C (136 ppm)
Placing D (134 ppm) here
This puts I (125 ppm) here
Organic Structure Analysis, Crews, Rodriguez and
Jaspars