Solving Unknown Structures Using NMR

Organic Structure Analysis, Crews, Rodriguez and Jaspars

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.

Organic Structure Analysis, Crews, Rodriguez and Jaspars

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

13C

NMR DATA UNKNOWN B

t q t q q s

t d d

B C

GHI J

Organic Structure Analysis, Crews, Rodriguez and Jaspars

MOLECULAR FORMULA DETERMINATION UNKNOWN B

s B E d A C t D F I q G H J

(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

1H

NMR DATA UNKNOWN B

Integrals: ONLY 17 H! 5H 3H 3H 2H

3H
H

Organic Structure Analysis, Crews, Rodriguez and Jaspars

SUBSTRUCTURES UNKNOWN B
CH3 H H3C

dC 125 d, 132 s dH 5.05 t & Me groups at dH 1.5

H H H

dC 112 t, 146 d dH 5.00 dd, 5.15 dd, 5.85 dd

H3C

OH

dC 73 s dH 1.05 s

D'

MF = C10H18O !
Organic Structure Analysis, Crews, Rodriguez and Jaspars

WORKING STRUCTURES UNKNOWN B

Ha

A Ha should be ddt
OH Ha

OH

B Ha should be ddt
Ha

C Ha should be dd
OH

Organic Structure Analysis, Crews, Rodriguez and Jaspars

MASS SPECTRAL FRAGMENTATION UNKNOWN B

Ha mass spectral fragmentation O+ H OH m/z 99

H +O

Fragments at: 121, 93, 71, 55 and 39 m/z

2

OH Ha mass spectral fragmentation m/z 113 O+

Ha

m/z 85
mass spectral fragmentation

OH

+O H m/z 71

Organic Structure Analysis, Crews, Rodriguez and Jaspars

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

13C

NMR DATA UNKNOWN G

t t q

dd

B C

E FG

Organic Structure Analysis, Crews, Rodriguez and Jaspars

MOLECULAR FORMULA DETERMINATION UNKNOWN G

s d A B C t D E F q 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

1H

NMR DATA UNKNOWN G

Integrals: 12 H Total

3H
H H H 2H H H HH

Organic Structure Analysis, Crews, Rodriguez and Jaspars

SUBSTRUCTURES UNKNOWN G
H H O
O

dC 140 d, 101 d dH 6.15 d, 4.70 m

H O

dC 96 d dH 4.9 t

H H

dC 64 t

Me

4 Oxygens in substructures but only 2 in MF

MF = C7H12O2 !
Organic Structure Analysis, Crews, Rodriguez and Jaspars

13C

Shift additivity data

O O
62 20* 36*

WORKING STRUCTURES UNKNOWN G

O
15
O O + O

26

O
64 10*

O
64

15

MS Fragmentation

m/z 83 O O+.

Retro Diels-Alder
O O O m/z 56 +. O

m/z 99
+.

m/z 72

Fragments are at 99, 83, 72 and 57 m/z

Organic Structure Analysis, Crews, Rodriguez and Jaspars

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

13C

NMR DATA UNKNOWN H

d t

t d s

A
Organic Structure Analysis, Crews, Rodriguez and Jaspars

B CD

MOLECULAR FORMULA DETERMINATION UNKNOWN H

s A d B C t D E q

(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

1H

NMR DATA UNKNOWN H

Integrals: D2O so no XH (OH, NH) ONLY 6 H! H H 2H H H

d d

Organic Structure Analysis, Crews, Rodriguez and Jaspars

SUBSTRUCTURES UNKNOWN H
O OH

dC 176 s IR band at 3400

OH

dC 70 d dH 4.6 m

dC 60 d dH 3.9 m

H N D E

MF = C5H9NO3 !
Organic Structure Analysis, Crews, Rodriguez and Jaspars

1H

1H COSY NMR SPECTRUM UNKNOWN H

c c-e/e d d d-e e e

e-e

b-e/e

b-d/d

d-d

Organic Structure Analysis, Crews, Rodriguez and Jaspars

1H

1H COSY NMR DATA UNKNOWN H

OH b

e'

d'

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

SUBTRUCTURES UNKNOWN H
c OH b

O H N OH

e' d

d'

MF = C5H9NO3 Working structures:

H Hc N COOH
12 % NOE

H H N c COOH
NO NOE

HO H b 1

HO H b 2

Organic Structure Analysis, Crews, Rodriguez and Jaspars

ASSIGNING NMR DATA TO A KNOWN STRUCTURE GUAIAZULENE

15 10 9 8 14 7 6 11 13 12 2 1 3 4 5

Expect: (C)5

(CH)6 (CH2)0 (CH3)4

MF = C15H18
Organic Structure Analysis, Crews, Rodriguez and Jaspars

NMR DATA GUAIAZULENE

(C)5 + (CH)6 + (CH2)0 + (CH3)4 = C15H18
ddd EFG d H d J d K q N ss s BD A s C s I q O qq LM

13C

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HSQC NMR DATA GUAIAZULENE

no k O N K lm O N LM LM K

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HSQC NMR DATA GUAIAZULENE

g e f j h

H G E

H G E

Organic Structure Analysis, Crews, Rodriguez and Jaspars

DATA GUAIAZULENE Label spectrum according to HSQC:

3H n 3H o 3H l 3H m

1H NMR

H g

HHHH ef j h

H k

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

We will need expansions:

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

g e f j h

I-g

I-j

HI

F-g C-g

G-f D-e A-f

D-j

C-h B-h

G F CDE B A

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

g e f j h

N-h

N LM

K-g

K-f

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

n o lm

LM-lm K-lm

H-n I-o C-n A-n

D-o

B-lm

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

Carbon A B C D E F G H I J g f n g, j, o Proton f, n h, l/m g, h, n e, j, o

Obvious assignments: N/O J/E E/J F/H H/F

O/N L
1H-1H

K
L M N O

f, g, l/m
m l h

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

HMBC NMR DATA GUAIAZULENE

Carbon A B C D E F G H I J g f n g, j, o Proton f, n h, l/m g, h, n e, j, o

N/O J/E E/J G O/N L Signal for f is a dd long-range coupling to remaining proton g K H F

K
L M N O

f, g, l/m
m l h

Organic Structure Analysis, Crews, Rodriguez and Jaspars

HMBC NMR DATA GUAIAZULENE

Carbon A B C D E F G H I J g f n g, j, o Proton f, n h, l/m g, h, n e, j, o

N J/E E/J G O L HMBC data cant decide positions of E, J HMBC data cant decide positions of D, I How do we decide? B K C

H F

K
L M N O

f, g, l/m
m l h

Organic Structure Analysis, Crews, Rodriguez and Jaspars

FINALISING THE ASSIGNMENTS GUAIAZULENE NOE

N J E I O L
Placing D (134 ppm) here puts it in a similar environment to C (136 ppm) This puts I (125 ppm) here

H F

B K M

Organic Structure Analysis, Crews, Rodriguez and Jaspars