Using 2D NMR Strategy Organic Structure Analysis, Crews, Rodriguez and Jaspars.

Using 2D NMR

Strategy

Organic Structure Analysis, Crews, Rodriguez and Jaspars


Molecularformula

Functionalgroups

Substructures

Very secure3D molecular

structure

MS, NMR

NMR, IR

UV

NMR

X-RAY

UnsaturationNumber(UN)

Working 2D

structures

List of working

2D structures

Reasonable3D molecular

structure

New 2Dmolecularstructure

NMR

ORD Totalsynthesis Molecular

modeling

Knownmolecularstructure

Dereplicate by MF

Dereplicate

Draw all isomers

NMR, MS, IR, UV

by structure

Purecompound

THE PROCESS OF STRUCTURE ELUCIDATION


C10H18OUnknownAnalysis

Determine molecularformula

OH

H

IR/1H NMR/Tests

Determinefunctionalgroups

OH

H

1H NMR/IR

Assemble completelist of substructures

All substructures add up to molecular formula

3

OH OH Combine substructuresin all possible ways

Three possible structureswith correct MF and dbe(There are many more)

OH

OH

Use NMR evidence torule out or confirmstructures

Chosen structureconfirm using data tables


13C spectrum/DEPT-135

Low Resolution MS

m/z 335 [M+H]+

APT Formula C20H29

High Resolution MS

m/z 335.2222 [M+H]+

Molecular Formula C20H30O4

Crystal Unit Cell Dimensions

DATABASE

Substructures

1D NMR Spectra 2D NMR Spectra

DEREPLICATION:The process of rapidlydiscovering whethera compound haspreviously been reported.


Get 13C NMR spectrum

get multiplicities

STRATEGY BASED ON C-C CONNECTIVITY

Get 2D INADEQUATE Make C-C map

Get 13C-1H correlation spectrum

(HSQC)

Get one bond 13C-1H correlations

assign 1H resonances

Bridge heteroatoms

using long range 13C-1H correlation spectrum

(eg HMBC) or using nOe data

Generate 2D structure

• Based on 13C-13C correlations – 1/10 000 chance• Need large amounts of sample• Sample must have high solubility• Need long acquisition times (>24 h)• Correlations across heteroatoms not possible – these must be

determined using HMBC data• Gives no information about C-H correlations – need to get

HSQC data to assign protons• BUT: If possible to use INADEQUATE, connectivity information

is unambiguous (unlike HMBC)

STRATEGY BASED ON C-C CONNECTIVITY PROBLEMS



STRATEGY BASED ON C-C CONNECTIVITYEXAMPLE13C axis

(ppm)

Double quantum axis (Hz)

A

B

C

D

E

F

A-B

A-D

D-C

C-EF-B


STRATEGY BASED ON C-C CONNECTIVITYEXAMPLE

F B A D C E

Gives topology of molecule

Chemical shift information gives:

F

B

A

D

C

E

OH


STRATEGY BASED ON C-C CONNECTIVITYREAL EXAMPLE

A-B

A-I

A-K

D-CB-E

B-F E-C

D-GF-D

D-JC-N

G-H

E-ME-L

I-JH-N

G-O



Data: A-B, A-I, A-K, B-E, B-F, E-C, E-L, E-M, C-D, C-N, N-H, H-G, G-D, G-O, D-F, D-J, J-I

A

K

B

I

F

E

ML

C

D

NH

G

O JOH

CEDROL


STRATEGY BASED ON C-H CONNECTIVITY

H

C C

HHSQCHSQC &

H

C C

H

1H-1H COSY

C C

H

C C C

HSQC &H

C C C

HMBC

C C C

HMBC data is ambiguous (2 or 3 bond correlations – impossible to tell which)


STRATEGY BASED ON C-H CONNECTIVITY

Get 1H, 13C NMR spectra

get multiplicities and integrals

Get one bond 13C-1H correlations

assign 1H resonances to 13C resonancesGet 1H-1H correlation data (eg COSY)

Check assignment of diastereotopic protonsusing COSY and HMQC

Assemble substructures using COSY data

Get long range 13C-1H correlation spectrum

(eg HMBC)Combine substructures into

all possible working structures

Check all working structures for consistencywith 2D NMR data

2D structure

Get 13C-1H correlation spectrum (eg HSQC)


STRATEGY BASED ON C-H CONNECTIVITY – DEPT DATA

CCH2

CH, CH3

CHCH CH

CH2

CH3 CH3

ABC

D(C)0 + (CH)3 + (CH2)1 + (CH3)2 = C6H11 = 83

EF

LRMS = 100 m/z so add OH MF = C6H12O

C

Label from leftto right in capitals

A B C D E F


STRATEGY BASED ON C-H CONNECTIVITY – HSQC DATA

A B C D E F C

ab

c

d’d

ef

label protons in lower case letters

diastereotopicprotons



ATOM C (ppm) DEPT H (ppm)

A 131 CH 5.5

B 124 CH 5.2

C 68 CH 4.0

D 42 CH2 3.0

2.5

E 23 CH3 1.5

F 17 CH3 1.2









diastereotopic protons


STRATEGY BASED ON C-H CONNECTIVITY – COSY DATA

ab

c

d

d'

ef

a b c d d' e f

Vicinal (3 bond)

Geminal (2 bond)

4 bondDiagonal

a-b

a-d/d’

b-fc-e

And many more…



ATOM C (ppm) DEPT H (ppm) COSY (HH)

A 131 CH 5.5 b, c, d/d’, f

B 124 CH 5.2 a, d/d’, f

C 68 CH 4.0 a, d/d’, e

D 42 CH2 3.0

2.5

a, b, c, d, e

E 23 CH3 1.5 c, d/d’

F 17 CH3 1.2 a, b



diagonal

r

r




STRATEGY BASED ON C-H CONNECTIVITY – COSY DATAHSQC suggests diastereotopic protons:3.08/2.44 ppm1.86/2.07 ppm

OK?


STRATEGY BASED ON C-H CONNECTIVITY – HMBC DATA

A B C D E F

ab

c

d

d'

ef

C

H

B-a C-a

A-b

D-c

And many more…



ATOM C (ppm) DEPT H (ppm) COSY (HH) HMBC (CH)

A 131 CH 5.5 b, c, d/d’, f b, c, d, f

B 124 CH 5.2 a, d/d’, f a, d, f

C 68 CH 4.0 a, d/d’, e a, d, e

D 42 CH2 3.0

2.5

a, b, c, d, e a, b, c, e

E 23 CH3 1.5 c, d/d’ c, d

F 17 CH3 1.2 a, b a, b








STRATEGY BASED ON C-H CONNECTIVITYRETROSPECTIVE CHECKING

Pieces:

A

H

B

H

C

OH

H

D

HH

E

H H

H

F

H H

H

C 131 C 124 C 68 C 42 C 23 C 17

H 5.5 H 5.2H 4.0

H 3.0H 2.5

H 1.5 H 1.2

Possibilities:

F

A

B

C

D

E

OH

F

B

A

C

D

E

OH

E

B

A

C

D

F

OH

E

A

B

C

D

F

OH

F

D

A

B

C

E

OH

E

D

B

A

C

E

OH

E

D

A

B

C

E

OH

F

D

B

A

C

E

OH

F

A

B

D

C

E

OH

E

B

A

D

C

F

OH

E

A

B

D

C

F

OH

F

B

A

D

C

E

OH

Combinatorialexplosion



MeF

B

A

D

C

MeE

OH

Hb

Ha

Hd Hd'

Hc

HMBC data (C-C-H & C-C-C-H) from C H

And similarly for COSY data


PROSPECTIVE CHECKING

Pieces: A

H

B

H

C

OH

H

D

HH

E

H H

H

F

H H

H

C 131 C 124 C 68 C 42 C 23 C 17

H 5.5 H 5.2H 4.0

H 3.0H 2.5

H 1.5 H 1.2

A B

Reason: only 2 sp2 C's

A B

F

HMBC: F-a, F-b, A-f, B-f

A B

F

DHMBC: D-a, D-b, A-d, B-d

A B

F

DC

OH

HMBC: C-d, C-a, D-c, A-cA B

F

DC

E

OH

HMBC: E-c, E-d, C-e, C-d


COMPARISON OF C-H AND C-C STRATEGIES

C-C Strategy C-H Strategy

Experiment Time Experiment Time1H NMR < 1 min 1H NMR 1 min13C NMR < 1 min 13C NMR 1 – 4 h

DEPT 135 < 1 min DEPT 135 1 – 4 h

HSQC nt=1, ni=256 15 min HSQC nt=4, ni=256 1 h

HMBC nt=1, ni=512 15 min HMBC nt=4, ni=512 1 h

NOESY nt=4, ni=256 1 h NOESY nt=4, ni=256 1 h

INADEQUATE 24 h COSY nt=1, ni=256 15 min

Total time ~26 h 6 – 12 h

Sample conc 6 M 10 – 100 mM


EXERCISE 1. For a simple organic compound the mass spectrum shows a molecular ion at m/z 98. The following data has been obtained from various 1D and 2D NMR experiments. Using this information determine the structure of the molecule in question and rationalise the 2D NMR data given.

Atom dC (ppm) dH (ppm) 1H - 1H COSY

(3 bond only)

1H 13C Long range

(2 - 3 bonds)

A 218 s - - A-b, A-c, A-d, A-e

B 47 t 1.8 dd b-d B-c, B-d, B-e, B-f

C 38 t 2.3 m c-e C-b, C-d, C-e

D 32 d 1.5 m d-b, d-e, d-f D-b, D-c, D-e, D-f

E 31 t 2.2 m e-c, e-d E-b, E-c, E-d, E-f

F 20 q 1.1 d f-d F-b, F-d, F-e


EXERCISE 2. For a simple organic compound the mass spectrum shows a molecular ion at m/z 114. The following data has been obtained from various 1D and 2D NMR experiments. Using this information determine the structure of the molecule in question and rationalise the 2D NMR data given.

An additional peak is present in the 1H NMR at 11.6 ppm (bs).

Atom dC (ppm) dH (ppm) 1H - 1H COSY

(3 bond only)

1H 13C Long range

(2 - 3 bonds)

A 178 s - - A-d, A-b

B 136 d 5.7 m b-c, b-d B-d, B-c, B-e

C 118 d 5.5 m c-b, c-e C-b, C-d, C-e, C-f

D 38 t 3.0 d d-b D-b, D-c

E 25 t 2.1 m e-c, e-f E-b, E-c, E-f

F 13 q 1.0 t f-e F-c, F-e


SELECTIVE 1D - TOCSY

Spin-lock90o

(selective)

Preparation DetectionMixing

J. Mag. Res. 1989, 85, 1-14. J. Mag. Res. 1989, 81, 186-190


SELECTIVE 1D – TOCSYSUBSPECTRA

8 7 6 5 4 3 2 1 ppm

NNH

N

O

ON S

O

OMe

8 7 6 5 4 3 2 1 ppm


OOH

HOH

HHO

H

H

Mystery Compound:

Eunicellin



Data: A-B, A-I, A-K, B-E, B-F, E-C, E-L, E-M, C-D, C-N, N-H, H-G, G-D, G-O, D-F, D-J, J-I



Pieces:

A

H

B

H

C

OH

H

D

HH

E

H H

H

F

H H

H

C 131 C 124 C 68 C 42 C 23 C 17

H 5.5 H 5.2H 4.0

H 3.0H 2.5

H 1.5 H 1.2

Possibilities:

F

A

B

C

D

E

OH

F

B

A

C

D

E

OH

E

B

A

C

D

F

OH

E

A

B

C

D

F

OH

F

D

A

B

C

E

OH

E

D

B

A

C

E

OH

E

D

A

B

C

E

OH

F

D

B

A

C

E

OH

F

A

B

D

C

E

OH

E

B

A

D

C

F

OH

E

A

B

D

C

F

OH

F

B

A

D

C

E

OH

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Using 2D NMR Strategy Organic Structure Analysis, Crews, Rodriguez and Jaspars.

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