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Arts and Tricks on Structure Elucidation

of Natural Compounds
(Spectra Reading and Methodology)

General Methodology
Sometimes needs H-H COSY, HMQC

Identifying
Identify Skeleton
Identifying
Skeleton
Skeleton
Identifying
IdentifyingFunctional
Functional
Groups
Groups

Formulating
FormulatingStructures
Structures
(Including
(Includingthose
thosealternative
alternative
structures)
structures)

H & 13C NMR, IR and UV spectra


13
C NMR: APT/DEPT
1

HMQC
HMBC

NOESY

Complete
Complete
Structure
Structure

Check
CheckChemical
Chemical
Abstract
Abstract
New

Confirmation
Confirmation
Structure
Structure
(ONE)
(ONE)
Determining
Determining
Stereochemistr
Stereochemistr
y

Known

Literature

Confirmation
Confirmation
Structure
Structure

by
bycomparison
comparisonof
ofspectral
spectraland
and
physical
data
physical data

Complete
Complete
Structure
Structure

Step One: Identifying Basic Skeleton


This is the most crucial step: establishing a working hypothesis
Knowledge
Knowledgeof
ofChemical
Chemical
Structures
Structuresof
ofNatural
NaturalCompounds
Compounds
(in
(inthe
theGenus)
Genus)

Aromatic or aliphatic ?
Alkaloids or non-alkaloids ?
Aliphatic = Terpenoids
Aromatic = Flavonoids,
Stilbenes, 2-Arylbenzofuran,
Coumarins, etc
Aromatic + Aliphatic =
Lignans, Flavones, Prenylated
aromatic compounds

13
1
Analysis
Analysis 13CCand
and 1HHNMR
NMRSpectra
Spectra

Number of carbons
Number of aromatic/alkene carbons
Carbonyl carbon(s)
Number of alkyl carbons: C, CH, CH2 and CH3
Signals of alcohol/eter
Characteristic proton signal(s): such as methoxyl, aldehyde,
and hydroxyl, acetyl group

Basic
Basic
Skeleton
Skeleton

Step One: Identifying Basic Skeleton


Some typical structures of aromatic compounds

Characteristics:
blue: symmetrical
Number of carbons
Containing substituted phenyl group 1H NMR spectrum
13

C NMR spectrum (APT experiment)

red: unsymmetrical

Step One: Identifying Basic Skeleton


Some typical structures of non-aromatic compounds: terpenoids

Characteristics:
Number of carbons
Number of methyl groups
13

H NMR spectrum

C NMR spectrum (DEPT experiments must be carried out)

Step One: Identifying Basic Skeleton

Transformation of terpenoid structures to their respective basic skele

the best way to look


at the functional
group is from carbon
spectrum:
13
C NMR + DEPT or
APT

Step One: Identifying Basic Skeleton


Rule for basic
skeleton
transformation

Functional groups observed

Origin in the basic


skeleton

-CH3 (alkyl)

-CH3

-CH2OH (primary alcohol/ether)


-CH=O (aldehyde)
-COOH (carboxylic acid)
=CH2 (double bond methylene)
=CH-O- (furan ring)
-CH2 (alkyl)

-CH2

-CH-O (secondary alcohol/ether)


-C=O (keton)
=CH (vinyl)
-CH (alkyl)

-CH

-C-O (tertiary alcohol/ether)


=C-q
-Cq (alkyl)

-Cq

Step One: First Inspection

aromatics or alkenes depend on the coupling constants


strong coupling (roof effect)
impurities

acetoned6

aromatic/alkene

alkyl

CH2 ?

EXAMPLE 1

Step One: Identifying Basic Skeleton (Example


1) A compound was isolated from methanol extract of a species of Intsia
(Leguminosae)
Background:
Below are the compounds isolated from Intsia

Step One: Identifying Basic Skeleton (Example


1) Carbon spectrum (APT)
2 benzene
rings

12 C-sp2 (aromatic)

3 C-sp3 (alkyl)

Step Two: Identifying Functional Groups and Formulating Structure


(Example 1)
From carbon spectrum (APT)

2C

2C

OH

OH

4 oxyaryl carbons
(oxygen functional groups
attached to benzene rings)

2C

Step Two: Identifying Functional Groups and Formulating Structure


(Example
From 1H1)
NMR spectrum
4 phenolic -OH
2 -OH

6 aromatic =CH

Basic skeleton:

NO

-OH

-OH

no correlation
In HMQC spectrum

YES

alcohol -OH
-CH-O

4H of alkyl group

Step Two: Identifying Functional Groups and Formulating Structure


(Example
From 1H1)
NMR spectrum

Step Three: Confirming Structure (Example 1)


HMBC spectrum

CH2

ruled out

=C

=CH

confirmed
=CH-O

EXAMPLE 2

Step One: Identifying Basic Skeleton (Example


2) A compound was isolated from acetone extract of a species of Eremophila
(Myoporaceae)
Background:
A number of compounds isolated from Eremophila include
sesquiterpenes and
diterpenes, examples are:

Step One: Identifying Basic Skeleton (Example


2) 13C NMR and DEPT 135 spectra of the compound
3 -CH3

functional groups
2 -CH

=CH
=C

C=O

C=O

=CH
=CH

=CH-O
=CH-O

4 -CH2

basic skeleton

Step Two: Identifying Functional Groups and Formulating Structure


(Example
2)
13
C NMR and DEPT 135 spectra of the compound
basic skeleton

O
O

A
X
O

+ conjugated -C=O
O

O
O

B
X

O
O

+ C=O

O
O

four possible
structures A-D

O
O

D
X
O

=CH

3 signals of
methyl doublets

=C

C=O

C=O

=CH
=CH

-CH-CH3
the methine-C
are away from
the carbonyl

-CH2

**

Step Three: Confirming Structure (Example 2)

EXAMPLE 3

Step One: Identifying Basic Skeleton (Example


3) A compound was isolated from Scoparia

C=O

CH 2
CH 2

CH 2-OH

C-OH

CH-OH

=CH

=CH

APT and DEPT 135 spectra of the compound

C=O

CH 2
CH 2

CH 2-OH

C-OH

CH-OH

=CH

O=C-CH=CH

=CH

Step Two: Identifying Functional Groups and Formulating Structure


(Example
3) spectrum:
From 13C NMR

Step Two: Identifying Functional Groups and Formulating Structure


(Example 3)
From 1H NMR spectrum:
d
10.6
H-3

H-2
d
10.6

H2-5
H-6
H2-8
H2-7

OH

Step Two: Identifying Functional Groups and Formulating Structure


(Example 3)
Support from 1H-1H COSY spectrum:
H-3
H-2

H-6

H2-8

H2-5 H2-7

Step Three: Confirmation of the Structure (Example 3)


HMBC spectrum:
H-3
H2-7

C-5

C-8
C-1
C-6

C-2

HMBC (1H 13C)

Conclusion:
A methodology for structure elucidation of natural compounds,
based on basic skeleton, is proposed.
Proposed structure is formulated mainly using 1-D NMR spectra.
Carbon spectra are used to identify the basic skeleton; while both
proton and carbon spectra are used to put the substituents. 2-D
NMR spectra used in this stage only to clarify the structural identity
of signals.
2-D NMR spectra are used to confirm the proposed structure,
especially for new compounds.