ESSENTIAL NMR EXPERIMENTS FOR EVERY
ORGANIC CHEMIST
A presentation by Dr. M. Sales
in the Laboratories of
Prof. A. B. Charette
10 January 2005
General Outline
1. Introduction to information that can be obtained from NMR spectroscopy
2. A Diels-Alder adduct is used as an example to illustrate
The various NMR experiments that can be obtained
2.1-2.3 Examples of C,H (heteronuclear) correlation experiments
2.4, 2.5 and 2.10 Examples of H,H (homonuclear) correlation experiments
2.6-2.9 Examples of NOE and chemical exchange experiments
3. A brief application of experiments on a precursor substrate
4. Recommended resources for a detailed INTRODUCTION to NMR Theory and Application
Problems, problems
Question
Design
Question
substrate, reagents
molar equivalents
rxn time, rxn temperature
Design
Execution
reaction-setup
order of addition
of reagents
Execution
Process
reaction workup
purification
Process
identify product/s
ratio of products
relative
configuration
scalar coupling
dipolar coupling (NOE or
chemical exchange)
Appropriate 1D / 2D NMR
expt
signal to noise ratio
Resolution
Fourier transforms
Window functions
Zerofilling
Analysis
Result
Answer
The complexity of the questions asked is
only limited by the ability to analyze the
'complex' results.
1. What information can NMR spectroscopy provide
Structural Theory
NMR equivalent
Qualitative composition
Choice of nucleus / isotope
Quantitative composition
Signal intensities / integration
Functional groups
Chemical shifts
Connectivity
J (scalar) couplings
Spatial relationship of atoms
NOE (distance)
J couplings (dihedral angle)
Dynamics
Chemical exchange, lineshape
broadening
1.1 Functional group information from Chemical Shift
1.2 Connectivity information from scalar coupling
1J
2J
H C
HC
HC,
3J
H
HC
H
C
2J
HH and
2J
3J
5J
HH ,
HMQC
(Heteronuclear
Multiple Quantum
Coherence)
3J
HH,
HH……
H
HH
4J
C
HH,
C
H
H
H
H
C
H
H
C
H
H
HMBC
(Heteronuclear
Multiple Bond
Correlation)
2D COSY
(Correlation
SpectroscopY)
Homodecoupling,
1D selective COSY
2D TOCSY (TOtal
Correlation
SpectroscopY)
1D selective TOCSY
1.3 Spatial Relationships of atoms from scalar
couplings
The Karplus equation
relates 3JHH with the
dihedral angle.
3J
HH values are obtained
from routine H NMR
spectra and
homodecoupling
experiments.
C. Altona et al
Magn. Res. Chem.
1994, 32, 670
O
H
O
O
OMOM
4a
4
8a
O
OH
Coupling constant analysis
assigns the 4,4a-syn/anti
relationship
OH
3"
3
4
1'
S
N
OMOM
N
S
S
4a
S
O
4
H
4,4a-syn
N
O
R
O
216
N
H
J4-4a = 3-4 Hz
4"
S
215
8a
O
H
O
O
OMOM
4a
4
8a
S
4,4a-anti
O
H
O
S
S
217
8a
4a
4
H
O
R
J4-4a = 8-11 Hz
1.4 Spatial Relationships of atoms from NOE
H
CO2CH3
H
N
H
o
CO2CH3
150-170 C
Bz
Bz
N
H
H
H3CO2C
NOE
Bz
Typical usage of NOE relationships in literature to
assign relative stereochemistry
Arakawa, Y. et al
Chem. Pharm. Bull.
2003, 51, 1015-1020
1.5 Investigation of Dynamic processes by
observation of Chemical Exchange
2.9ppm
CH3
Line-broadening and coalescence of signals are routine methods to
investigate Dynamics in moleculer systems. However, 1D and 2D
EXSY (EXchange SpectroscopY) methods can indicate chemical
exchange before line broadening occurs
2.8ppm
CH3
O
CH3
N
H
CH3
2.8ppm
CH3
Perrin, C. L. and
Dwyer T. J.
Chem. Rev.
1990, 90, 935-967
2.9ppm
CH3
2D EXSY of N,N-dimethylformamide
2. DA derivative used in NMR study
O
Diels-Alder
N
Ph
+
N
O
N
Ph
N
O
O
Functioal
Group
Interconversion
Ph
N
OBn
O
O
OBn
O
DA derivative
Examples of the following NMR experiments of the DA derivative will be
presented :
13C
NMR
DEPT
HMQC
HMBC
1H
NMR
2D COSY
2D TOCSY
2D NOESY
1D NOE
2D ROESY
homodecoupling
1D selective COSY
1D EXSY
2.1 C-13 and DEPT
7
O
Ph
1
N
8
4
3
6
5 2'
CH2
CH
2"
CH3
OBn
1'
2
OBn
1"
methine
methylene
methyl
doublet (d)
triplet (t)
quartet (q)
The d,t and q refers to the 13C multiplicity with respect to
C31 H33 N O3
couplings from attached (geminal) protons.
7
CO
180
170
160
150
140
130
120
110
100
90
80
70
60
50
40
30
20
10
7
O
Ph
1
N
8
4
5 2'
2"
OBn
1'
3
4xAr
d
2.1 C-13 and DEPT
6
2
Ar = one aromatic carbon
# = 2xAr
d
OBn
1"
C31 H33 N O3
#
#
* = Ar
#
d
2 x Ar
s
#
4
d
Ar
s
3
d
*
*
*
2 x Ar
d
139
138
137
136
135
134
133
132
131
130
129
128
127
126
7
O
Ph
1
N
8
4
3
6
5 2'
2.1 C-13 and DEPT
2"
OBn
1'
2
OBn
1"
C31 H33 N O3
2”
6
1’
2
5
7
2’
1”
2 x CH2Ph
70
60
50
40
30
20
2.2 HMQC
7
O
Ph
1
N
8
4
3
6
5 2'
2"
OBn
1'
2
4
3
2
5 1’ 2’
OBn
1"
H
C
1”
2”
7
O
Ph
1
N
8
4
2.2 HMQC
6
5 2'
3
2"
OBn
1'
2
1”
OBn
1"
2”
H
C
o-Ar
1’
5
2’
3
4
2
6
2.3 HMBC
7
O
Ph
1
N
8
6
5 2'
4
2"
OBn
1'
3
2
OBn
1"
H
C
H
C
C
C
D
C
A
C
Regions A, B, C and
D are expanded on
next slide.
B
7
O
Ph
1
N
8
4
2.3 HMBC
6
5 2'
2"
OBn
1'
3
o-Ar (Bn)
2
OBn
Unambiguous assignment of ortho-Ar to the
benzylic moeity attached to C-1”.
1"
H
C
C
6
CO
H
C
2
CH2Ph (1”)
C
C
CH2Ph (2”)
Region B
Region A
C-1”
C-2’
CH2Ph
(1”)
C-5
2”
2”
C-2”
CH2Ph
(2”)
CH2Ph
(1”)
C-1’
1”
1”
C-2
CH2Ph
(2”)
2”
2”
Region C Unambiguous assignment of both CH2Ph is
achieved from analysis of HMBC spectrum
C-6
Region D
1”
1”
2.4 COSY
7
O
Ph
6
1
N
8
5 2'
4
3
7
2"
OBn
1'
2
OBn
1"
5
H
H
H
H
6
2
3
4
2.4 COSY
7
O
Ph
1
N
8
4
2
6
5 2'
2
2"
OBn
1’
1"
5
H
H
1’
5
OBn
1'
3
6
H
H
6
2
2.4 COSY
7
O
Ph
1
N
8
4
6
2’
5 2'
OBn
1'
3
2"
2
1’
OBn
1"
1”
H
H
H
H
2”
2”
1”
2.4.1 Spin system deduced from COSY
6(4.18)
7(1.27)
2"(3.35)
7
O
Ph
1
N
8
4
3
4(6.37)
5(2.92)
2'(2.49)
6
5 2'
2"(3.17)
2"
OBn
1'
2
OBn
1"
1"(3.39)
3(6.28)
geminal J (2 bond coupling)
according to HMQC
vicinal J (3 bond coupling)
2(4.56)
1'(2.56)
1"(2.96)
2.5 Homodecoupling
Reference
(Irradiate 9 ppm)
2 (4.56 ppm)
2.6, 5.5 Hz
4 (6.37 ppm)
decoupled
(Irradiate 6.37 ppm)
6.8
6.6
6.4
6.2
6.0
5.8
5.6
5.4
5.2
5.0
4.8
4.6
4.4
4.2
7
O
Ph
1
N
8
4
3
reference
J 2-4 = 0.5 Hz
6
5 2'
2"
OBn
1'
2
OBn
1"
J 2-3 = 5.5 Hz
J 2-1’ = 2.6 Hz
decoupled
4.60
4.55
4.50
4.45
2.5 Homodecoupling
Reference
(Irradiate 9 ppm)
7
O
Ph
1
N
8
6
5 2'
4
3
2"
OBn
1'
2
3 (6.28 ppm)
OBn
1’ (2.56 pm)
2 (4.56 ppm)
1.5, 7 Hz
4.7, 9.5, 10 Hz
1"
Decoupled
(Irradiate 4.56 ppm)
6.6
6.4
6.2
6.0
5.8
5.6
5.4
5.2
5.0
4.8
4.6
4.4
J 2-3 = 5.5 Hz
J 1’-2 = 2.6 Hz
J 3-5 = 1.5 Hz
J 3-4 = 7 Hz
J 1’-1” = 4.7 Hz
J 1’-1” = 9.5 Hz
J 1’-2’ = 10 Hz
6.45
6.40
6.35
6.30
6.25
2.70
2.65
4.2
4.0
3.8
3.6
3.4
3.2
3.0
2.8
2.6
2.4
2.2
reference
decoupled
2.60
2.55
2.50
2.45
2.5.1 Analysis of coupling constants
6(4.18)
6.1 Hz
6.5 Hz
O
Ph
1
N
8
4
3
4(6.37)
1.8 Hz
5(2.92)
6
8.5 Hz
2
2"(3.17)
2"
OBn
1'
8.9 Hz
2'(2.49)
1.5 Hz
5 2'
2"(3.35)
5.8 Hz
1.8 Hz
7
7(1.27)
7 Hz
10 Hz
OBn
1"
1"(3.39)
0.5 Hz
4.7 Hz
3(6.28)
4 possible relative
configurations where
dihedral angle between
HC-1’ and HC-2’ is = 0 º.
(J 1’-2’= 10 Hz)
5.5 Hz
2(4.56)
O
Ph
N
1"(2.96)
O
N
OBn
Ph
O
N
OBn
A
9.5 Hz
1'(2.56)
10 Hz
O
Ph
2.6 Hz
OBn
OBn
B
OBn
Ph
N
OBn
C
D
OBn
OBn
2.6 2D NOESY
O
Ph
7
6
1
N
8
3
5
4
3
1’ 2’
4
6
2'
1'
2"
2
1"
7
5
OBn
1’ 2’
OBn
Integration of NOE crosspeaks :
Reference = Diagonal of protons 1’ and 2’
Integrate for 2.00
4
3
6
5
7
-1% NOE
-4% NOE
-3% NOE
2.6.1 Assignment of benzylic protons with the aid of
NOE crosspeaks
Note: No scalar couplings
between 1” or 2” to any of the
benzylic were observed in
the COSY or homodecoupling
experiments. Therefore
NOE/dipolar interactions are
used to assign benzylic protons
O
Ph
7
1’/2’-2
-4%
6
2”
1”
5
1’ 2’
1’/2’-6
-7%
5
4
3
2
1” 2”
6
1
N
8
CH2Ph CH2Ph
2'
1'
2
1"
2"
OBn
OBn
CH2Ph
(1”)
CH2Ph
(2”)
Note: The combined NOE
between 1’,2’-6
of -7% offers further
support for assigned
relative configuration
1”-CH2Ph
-3%
2”-CH2Ph
-3%
1”-CH2Ph
-2%
2”-CH2Ph
-3%
5-6
-5%
1”-2
-2%
2.6.2 Chemical exchange crosspeaks observed in 2-D
NOESY
O
O
N
N
Z
OBn
OBn
OBn
E
OBn
E/Z isomerism
of 3o amide
2.6.2 Chemical exchange crosspeaks observed in 2-D
NOESY
2
2
(Z)
These expansions of the 2-D NOESY spectrum
clearly indicate that the crosspeaks correlate the
proton resonances of the major conformer (E) to
those of the minor conformer (Z).
This establsihes the identity of the minor species in
the H NMR spectrum as a conformer of the major
compound and not a contaminant.
(E)
2
(E)
2
(Z)
7
(E)
7 (Z)
7
(Z)
6
(E)
2” (E)
2” (Z)
7 (E)
6 (Z)
6 (E)
6
(Z)
2”
(Z)
2”
(E)
2.6.3 Further support for the assigment of o-Ar (Bn) via
analysis of NOE crosspeaks
O
N
H
H
-0.5%
OBn
O
H
H
H -1% and -1.5%
CH2Ph
(1”)
2
o-Ar
(PhCON)
region expanded
-0.5%
-1%
-1.5%
O
Ph
7
8
2.7 1D NOE
6
1
N
5
4
3
2'
1'
2
1"
2"
OBn
OBn
7
4
1.5%
3
0.5%
6
4%
5
3%
4
Irradiation
Frequency =
5
8%
2
3%
3
40%
7
(Z)
3
4
34%
7.0
6.5
2
9%
6.0
5.5
5.0
5
5%
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
O
Ph
7
8
2.8 2D ROESY
6
1
N
5
4
3
2'
1'
2
1"
2"
OBn
OBn
n0 = Larmor frequency of precessing proton
nucleus
tc = correlation time which is dependant on solvent
viscosity and moleculer weight
Imax/Io represents relative maximum crosspeak signal intensity
2D NOESY
tc →  maximum 20%, the case for small molecules
tc → 0 maximum 50%, the case for proteins
o x tc = 0 the crosspeak intensitiy = 0
2D ROESY
tc → 0 maximum 20%
tc →  maximum 34%
Useful for molecules of intermediate molecule weight
O
Ph
7
6
1
N
8
3
2.8 2D ROESY
5
4
2'
1'
2
1"
2"
OBn
OBn
4
Chemical exchange
crosspeaks observed in 2D
ROESY
ROE crosspeaks detected between methyl
proton 7 to protons 4 and 3 support
assigned relative configuration
3
7
E
7
Z
7
0.15 % ROE
0.3 % ROE
Integration of NOE crosspeaks :
Reference = Diagonal of protons 1’ and 2’
Integrate for 2.00
7
E
7
Z
O
Ph
7
6
1
N
8
2.9 TOCSY
5
4
2'
1'
3
2"
2
1"
OBn
1” 2” 5
1” 1’ 2’
2”
OBn
B
A
H
H
H
H
regions A and B
are expanded on
next slide
H
O
Ph
7
1
N
8
2.9 TOCSY
6
5
4
3
2'
1'
2"
2
1"
1” 2”
H
OBn
H
H
H
OBn
2”
H
1”
5
4
1’ 2’
7
1’
2’
1’ 2’
5
1”
1” 5
2”
1” 2”
2”
1”
2”
2
Region A
Region B
3
2.10 1D EXSY experiment
1D EXSY (EXchange SpectroscopY) uses the same pulse sequence as the 1D NOESY
except that the mixing time has been optimised to observe chemical exchange.
Reference
(1H NMR)
O
Ph
7
6
1
N
8
5
4
3
2'
1'
2
1"
2"
OBn
Expt 1
(1D EXSY)
OBn
2
(Z)
Irradiation
Frequency =
2
(E)
Expt 2
(1D EXSY)
7
(E)
8.0
7.5
7.0
6.5
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
7
(Z)
1.0
0.5
3.1 Chemical exchange
I
N
Ph
N
MeI
I
N
N
O
N
7
Ph
6
5
N
OH-
N
4
OBn
3
OBn
2
Z
OBn
OBn
OBn
E
OBn
OBn
OBn
H NMR revealed two conformers Z : E in ratio 1 : 2
7
(E)
4 (E), 4 (Z)
2
(E)
3
(Z)
9.0
8.5
8.0
7.5
7.0
6.5
3
(E)
6.0
7
(Z)
2
(Z)
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
3.2 1D selective COSY used for assignment of proton
resonances
7
1 6
N 5
N
I
4 (E), 4 (Z)
4
3
2
Z
H
H
2
(E)
OBn
3
(Z)
OBn
H
7
(E)
3
(E)
2
(Z)
7
(Z)
H
3
(Z)
2
(Z)
Irradiation
Frequency =
2
(E)
3
(E)
9.0
8.5
8.0
7.5
7.0
6.5
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
3.3 1D EXSY experiment
I
7
1 6
N 5
N
4
3
2
Z
OBn
OBn
These 1D EXSY
experiments
provide evidence
that the two
species observed
in the H NMR
spectrum are
conformers.
3
(Z)
3
(E)
3
(Z)
3
(E)
Irradiation
Frequency =
2
(Z)
2
(E)
7
(E)
9.0
8.5
8.0
7.5
7.0
6.5
6.0
5.5
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
7
(Z)
1.0
0.5
4. Recommended resources for a detailed
INTRODUCTION to NMR Theory and Application
H. Friebolin
Basic One- and Two-Dimensional NMR Sectroscopy
3rd Edition 1998 Wiley-VCH
Croasmun W. R., Carlson R. M. K.
Two-Dimensional NMR Spectroscopy – Applications for Chemists and Biochemists
2nd Edition 1994 VCH Publishers
Sanders J. K. M. and Hunter B. K.
Modern NMR spectroscopy – A Guide for Chemists
2nd Edition 1993 Oxford University Press
Derome A. E.
Modern NMR techniques for chemistry research
1st Edition 1987 Pergamon press
Braun S., Kalinowski H.-O., Berger S.
150 and More Basc NMR Experiments – A Practical Course
2nd Edition 1998 Wiley VCH Publishers