Common NMR Method for Structure Elucidation of Organic Molecule

8/13/2019 Common NMR Method for Structure Elucidation of Organic Molecule

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Structure Elucidation with NuclearStructure Elucidation with Nuclear

Magnetic Resonance (NMR)Magnetic Resonance (NMR)

This was prepared from any material downloaded from internet.


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NMRspectrum Structure

Chem. ShiftJ CouplingPeak Int.

NOECorrelationH HC H O

OOH

O

CH3

O

H

OH

OH

OH

CH2OH

COOCH2

1

2

3

4

5

6

7

8

9

10

1''

2''3''

4''

5'' 6''

1'

2'3'

4'

5'

6'

7''

Applications:

Sample quality control for Synthetic works. Elucidation of chemical structures.

Getting functional group, bonding, dynamics, kinetics and

chemical exchange information of molecules. 3D structures of the molecules.

NMR Applications in Chemistry


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Connections through spaceConnections through spacedipolar couplingdipolar coupling1D1D2D NOESY2D NOESYROESY, HOESY(HSQCROESY, HOESY(HSQC--NOESY)NOESY)usageusage connecting spin systemsconnecting spin systems structure determinationstructure determination

Connections through bondsConnections through bondsspinspin--spin couplingspin couplingHomonuclearHomonuclear 1D1D2D2D 11HH--11H COSY, DQFH COSY, DQF--COSY, TOCSYCOSY, TOCSY

usageusagespin system assignmentspin system assignmentHeteronuclearHeteronuclear

Direct (detectDirect (detect 1313C):C): APT, DEPT, HETCORAPT, DEPT, HETCOR

Inverse (detectInverse (detect11H):H): HMQC, HSQC, HMBC, HSQCHMQC, HSQC, HMBC, HSQC--COSY,COSY,

HSQCHSQC--TOCSY, HMQCTOCSY, HMQC--TOCSYTOCSY

usageusageassigningassigning heteronucleiheteronucleiconnecting spin systemsconnecting spin systems

Some common NMR experiments:Some common NMR experiments:


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COSY spectrum is used for determining the connectivities

between protons on the basis of geminal and vicinal couplings.Disadvantage: bulky dispersive diagonal peaks.

C C H

HH

Vicinal

Geminal

2D COSY2D COSY HomonuclearHomonuclear ShiftShift COCOrrelationrrelation SSpectroscoppectroscopYY

t1 AQ

The basic COSY (x=45 or 90) pulse sequence

90 xt2


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ppm

1.01.52.02.53.03.5 ppm

1.0

1.5

2.0

2.5

3.0

3.5

Current Data ParametersNAME butcosyEXPNO 1PROCNO 1

F2 - Acquisition ParametersDate_ 20001102

Time 8.04INSTRUM DRX500PROBHD 5 mm TBI 1H/PULPROG cosygpTD 1024SOLVENT CDCl3

NS 1DS 16SWH 2185.315 HzFIDRES 2.134096 Hz

AQ 0.2345700 secRG 40.3DW 228.800 usecDE 6.00 usecTE 288.0 K

D0 0.00000300 secD1 1.60000002 secD13 0.00000300 secD16 0.00010000 secIN0 0.00045765 sec

============ CHANNEL f1 =============NUC1 1HP0 3.00 usecP1 6.00 usecPL1 -4.00 dBSFO1 500.1310815 MHz

============ GRADIENT CHANNEL ========GPNAM1 sine.100

GPNAM2 sine.100GPX1 0.00 %GPX2 0.00 %GPY1 0.00 %GPY2 0.00 %GPZ1 10.00 %GPZ2 10.00 %P16 1000.00 usec

F1 - Acquisition parametersND0 1TD 256SFO1 500.1311 MHzFIDRES 8.535453 HzSW 4.369 ppmFnMODE undefined

F2 - Processing parametersSI 2048SF 500.1300144 MHz

WDW QSINESSB 0LB 0.00 HzGB 0PC 0.20

F1 - Processing parametersSI 1024

MC2 QFSF 500.1300144 MHz

WDW QSINE

SSB 0LB 0.00 HzGB 0

11 22 33 44

11

22

33

44

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

11--2222--33

33--44

2D Gradient COSY2D Gradient COSY--4545


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2D2D DQFDQFCOSYCOSY((DDoubleouble--QQuantumuantum FFilterediltered COSYCOSY))

90 90 90

t

1 t

2

allow J coupling constant measurementsallow J coupling constant measurements

observing crossobserving cross--peaks close to diagonalpeaks close to diagonal

But lower sensitivity (~40%) of COSY expt.But lower sensitivity (~40%) of COSY expt.


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ppm

3.63.84.04.24.44.64.85.05.25.45.65.86.06.2 ppm

3.6

3.8

4.0

4.2

4.4

4.6

4.8

5.0

5.2

5.4

5.6

5.8

6.0

6.2

Current Data ParametersNAME gbc35dqfEXPNO 2PROCNO 1


Time 4.01INSTRUM DRX500PROBHD 5 mm TBI 1H/PULPROG cosydfetgp.2TD 4096SOLVENT Pyr


AQ 0.5359376 secRG 512DW 130.800 usecDE 6.00 usecTE 288.0 KD0 0.00000300 secD1 1.60000002 sec

D11 0.03000000 secD16 0.00010000 secDELTA 0.00110300 secDELTA1 0.00110800 secIN0 0.00026161 secl3 256



GPNAM2 sine.100GPNAM3 sine.100GPX1 0.00 %GPX2 0.00 %GPX3 0.00 %GPY1 0.00 %GPY2 0.00 %GPY3 0.00 %GPZ1 30.00 %GPZ2 10.00 %GPZ3 50.00 %P16 1000.00 usec

F1 - Acquisition parametersND0 1TD 512SFO1 500.1318 MHz

FIDRES 7.465717 HzSW 7.643 ppmFnMODE undefined


WDW SINESSB 2LB 0.00 HzGB 0PC 0.20


MC2 echo-antiechoSF 500.1300038 MHz

WDW SINESSB 2LB 0.00 HzGB 0

2D Gradient DQF2D Gradient DQF--COSYCOSY


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33J=8.00HzJ=8.00Hz


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TOCSYTOCSY ((TOTOtaltal CCorrelationorrelation SSpectroscoppectroscopYY) or) or

HOHAHAHOHAHA((HoHomonuclearmonuclear HaHartmanrtman--HaHahn Spectroscopy)hn Spectroscopy)

t1 MLEV17 AQ

Pulse sequence for a TOCSY spectrum.

Different mixing time gives different degree of relay ofDifferent mixing time gives different degree of relay of

correlation. At small mixing time, TOCSY spectrum is similar tocorrelation. At small mixing time, TOCSY spectrum is similar toCOSY spectrum. At long mixing time, gives total correlation.COSY spectrum. At long mixing time, gives total correlation.

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

COSYCOSY RLRL--COSYCOSY TOCSYTOCSY

mixing timemixing timet2

2D G di TOCSY2D G di t TOCSY


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ppm

1.01.52.02.53.03.5 ppm

1.0

1.5

2.0

2.5

3.0

3.5

Current Data ParametersNAME buttoc10EXPNO 1PROCNO 1

F2 - Acquisition ParametersDate_ 20001102Time 4.14INSTRUM DRX500

PROBHD 5 mm TBI 1H/PULPROG mlevetgpTD 1024SOLVENT CDCl3


AQ 0.2345700 secRG 16DW 228.800 usecDE 6.00 usecTE 300.0 KD0 0.00000300 secD1 1.79999995 secD9 0.01000000 secD11 0.03000000 sec

D16 0.00010000 secDELTA 0.00109943 secDELTA1 0.00110800 secFACTOR1 0IN0 0.00045765 secl1 0l3 128SCALEF 6

============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.33 usecP6 29.00 usecP7 58.00 usecP17 2500.00 usecPL1 -4.00 dB

PL10 10.00 dBSFO1 500.1310815 MHz

============ GRADIENT CHANNEL ========GPNAM1 sine.100GPNAM2 sine.100GPX1 0.00 %GPX2 0.00 %GPY1 0.00 %GPY2 0.00 %GPZ1 30.00 %GPZ2 30.00 %P16 1000.00 usec







HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

2D Gradient TOCSY,2D Gradient TOCSY, mixing time=10ms

Same as COSY spectrumSame as COSY spectrum

11 22 33 44

11

22

33

44

11--2222--33

33--44

2D G di t TOCSY2D G di t TOCSY


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ppm

1.01.52.02.53.03.5 ppm

1.0

1.5

2.0

2.5

3.0

3.5



PROBHD 5 mm TBI 1H/PULPROG mlevetgpTD 1024SOLVENT CDCl3




============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.33 usecP6 29.00 usecP7 58.00 usecP17 2500.00 usecPL1 -4.00 dB

PL10 10.00 dBSFO1 500.1310815 MHz








2D Gradient TOCSY,2D Gradient TOCSY, mixing time=20ms11 22 33 44

11

22

33

44

11--22

22--33

33--44

11--33

22--44

Same as RLSame as RLCOSYCOSYHO C

H1

H

C C C

H2

H

H3

H

H4

H

H

2D G di t TOCSY2D G di t TOCSY


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ppm

1.01.52.02.53.03.5 ppm

1.0

1.5

2.0

2.5

3.0

3.5


F2 - Acquisition ParametersDate_ 20001101Time 16.43INSTRUM DRX500PROBHD 5 mm TBI 1H/PULPROG mlevetgpTD 1024SOLVENT CDCl3




============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.33 usecP6 29.00 usecP7 58.00 usecP17 2500.00 usecPL1 -4.00 dBPL10 10.00 dBSFO1 500.1310815 MHz


F1 - Acquisition parametersND0 1TD 256

SFO1 500.1311 MHzFIDRES 8.535453 HzSW 4.369 ppm





WDW QSINESSB 4LB 0.00 Hz

GB 0

2D Gradient TOCSY,2D Gradient TOCSY, mixing time=50ms11 22 33 44

11

22

33

44

11--22

22--33

33--44

11--33

22--4411--44

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

Total CorrelationTotal Correlation


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DEPT: Distortionless Enhancement by Polarization Transfer

Heteronuclear expt.Detection: 13C

Distinguish

CH, CH2, CH3

By suitable combination of

=45, 90 & 135 spectra

All CHs

Only CH

CH & CH3up

CH2 down


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HETCORHETCOR ((HetHeteronucleareronuclear chemical shiftchemical shift corcorrelation,relation, 11HH -- 1313C COSY)C COSY)

13C

1H t1 1 2

The standard pulse sequence forThe standard pulse sequence for 1313CC--detecteddetected11HH--1313C chemical shift correlation.C chemical shift correlation.

AQt2

1H decoupling

Removing JCH splittings

*But Inverse experiment has the following Advantages:

increase sensitivity of detecting the less sensitive nuclei

1H is in the direct detection dimension => larger np =>better resolution


15/27

HSQCHSQC ((HHeteronucleareteronuclear SSingleingle QQuantumuantum CCoherence)oherence)

AQ

1H

13C /2 /2 GARP-1t1 /2 /2

Pulse sequence for 1H-detected 1H-13C

correlation through single-quantum coherence

HSQC can give considerably better 13C resolution and sensitivity

than HMQC for CH2 groups of natural products

HMQC has simpler pulse sequence and it is more robust and easierto perform.

13C decouplingRemoving JCH splittings

HMQCHMQC ((HHeteronucleareteronuclear MMultipleultiple QQuantumuantum CCoherence)oherence)

t2


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ppm

1.01.52.02.53.03.5 ppm

10

15

20

25

30

35

40

45

50

55

60

65

Current Data ParametersNAME buthsqcEXPNO 1PROCNO 1


PROBHD 5 mm TBI 1H/PULPROG invietgpsiTD 1024SOLVENT CDCl3


AQ 0.2345700 secRG 2298.8DW 228.800 usecDE 6.00 usecTE 300.0 KD0 0.00000300 secD1 2.00000000 secD4 0.00170000 secD11 0.03000000 secD13 0.00000300 sec

D16 0.00010000 secD24 0.00090000 secDELTA 0.00116720 secDELTA1 0.00110700 secIN0 0.00003600 secl3 256

============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP28 2500.00 usecPL1 -4.00 dBSFO1 500.1310815 MHz

============ CHANNEL f2 =============CPDPRG2 garp

NUC2 13CP3 17.70 usec

P4 35.40 usecPCPD2 89.00 usecPL2 -1.00 dBPL12 13.00 dBSFO2 125.7633722 MHz






MC2 echo-antiecho

SF 125.7577969 MHzWDW SINESSB 2LB 0.00 HzGB 0

HO C

H1

HC C C

H2

H

H3

H

H4

HH

11 22 33 44

11

22

33

44

HSQC spectrum: HHSQC spectrum: H--C correlatedC correlated

(HMQC and HETCOR spectra look similar)(HMQC and HETCOR spectra look similar)

C-d

imension

HH--dimensiondimension


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HSQCHSQC--TOCSYTOCSY

AQ

1H

13C /2 /2 GARP-1t1 /2 /2

Pulse sequence forPulse sequence for 11HH--detected HSQCdetected HSQC--TOCSY experimentTOCSY experimentthrough singlethrough single--quantum coherence.quantum coherence.

Longer mixing time gives longer extend of spinLonger mixing time gives longer extend of spin--spinspincorrelations.correlations.

SLy

MLEV17

SLy

mixing timemixing time

G di HSQCG di HSQC TOCSY( i i i 10 )TOCSY( i i i 10 )


18/27

ppm

1.01.52.02.53.03.5 ppm

10

15

20

25

30

35

40

45

50

55

60

65

Current Data ParametersNAME buthsto10EXPNO 1PROCNO 1

F2 - Acquisition ParametersDate_ 20001101Time 18.31INSTRUM DRX500PROBHD 5 mm TBI 1H/

PULPROG invietgsmlTD 1024SOLVENT CDCl3


AQ 0.2343412 secRG 2048DW 228.800 usecDE 6.00 usecTE 300.0 KCNST0 2.0000000D0 0.00000300 secD1 1.79999995 secD4 0.00170000 secD11 0.03000000 secD12 0.00002000 sec

D13 0.00000300 secD16 0.00010000 secd20 0.00111720 secd21 0.00110700 secIN0 0.00003600 secL1 3l3 128

============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.34 usecP6 29.00 usecP7 58.00 usecP17 2500.00 usecP28 2000.00 usecPL1 -4.00 dBPL10 10.00 dBSFO1 500.1310815 MHz


NUC2 13CP3 15.70 usecP4 31.40 usecPCPD2 89.00 usecPL2 -2.00 dBPL12 13.00 dB

SFO2 125.7633722 MHz

============ GRADIENT CHANNEL ========P16 1000.00 usec







WDW SINE

SSB 2LB 0.00 HzGB 0

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

Same asSame as HSQCHSQCCOSYCOSY spectrumspectrum

Gradient HSQCGradient HSQC--TOCSY(mixing time=10ms)TOCSY(mixing time=10ms)

11 22 33 44

11

22

33

44

11--11

11--22

22--11

HH--dimensiondimension

C-d

imension

G di t HSQCG di t HSQC TOCSY( i i ti 20 )TOCSY( i i ti 20 )


19/27

ppm

1.01.52.02.53.03.5 ppm

10

15

20

25

30

35

40

45

50

55

60

65







============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.34 usecP6 29.00 usecP7 58.00 usec

P17 2500.00 usecP28 2000.00 usecPL1 -4.00 dB

PL10 10.00 dBSFO1 500.1310815 MHz


NUC2 13CP3 15.70 usecP4 31.40 usecPCPD2 89.00 usecPL2 -2.00 dBPL12 13.00 dBSFO2 125.7633722 MHz


F1 - Acquisition parametersND0 2TD 256SFO1 125.7634 MHzFIDRES 54.253471 HzSW 110.437 ppm





WDW SINE

SSB 2LB 0.00 HzGB 0

11 22 33 44

11

22

33

44

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H


11--22

22--1111--11

11--33

33--11

C-d

imension

HH

--dimensiondimension

G di t HSQCG di t HSQC TOCSY( i i ti 80 )TOCSY( i i ti 80 )


20/27

ppm

1.01.52.02.53.03.5 ppm

10

15

20

25

30

35

40

45

50

55

60

65







============ CHANNEL f1 =============NUC1 1HP1 5.60 usecP2 11.20 usecP5 19.34 usecP6 29.00 usecP7 58.00 usec

P17 2500.00 usecP28 2000.00 usecPL1 -4.00 dBPL10 10.00 dBSFO1 500.1310815 MHz


NUC2 13CP3 15.70 usecP4 31.40 usecPCPD2 89.00 usecPL2 -2.00 dBPL12 13.00 dBSFO2 125.7633722 MHz








WDW SINE

SSB 2LB 0.00 HzGB 0

HO C

H1

H

C C C

H2

H

H3

H

H4

H

H

11 22 33 44

11

22

33

44


11--22

22--1111--11

11--33

33--11

11--44

44--11

C-d

imension

HH


HMBCHMBC ((HH t leteronuclear MM lti lultiple BB dond CC l ti S t )orrelation Spectroscopy)


21/27

HMBCHMBC ((HHeteronucleareteronuclear MMultipleultiple--BBondond CCorrelation Spectroscopy)orrelation Spectroscopy)

13

C

1H t1AQ

C2, C3 and C4: Quaternary or protonated carbons X: O, N

C1 C2 C3 C4

H1

C1

X C2

C3

H1

Pulse sequence for HMBCPulse sequence for HMBC

Long range connections or connections between spin systemsLong range connections or connections between spin systems

Gradient HMBCGradient HMBC


22/27

ppm

3.54.04.55.05.56.06.57.07.58.0 ppm

30

40

50

60

70

80

90

100

110

120

130

140

150

160

Current Data ParametersNAME cfyhmbcEXPNO 1PROCNO 1


PULPROG inv4gplrndTD 1024SOLVENT CDCl3


AQ 0.1488800 secRG 11585.2DW 145.200 usecDE 6.00 usecTE 300.0 KD0 0.00000300 secD1 1.50000000 secD6 0.07000000 secD13 0.00000300 secD16 0.00050000 sec

IN0 0.00002380 sec


============ CHANNEL f2 =============NUC2 13CP3 15.70 usecPL2 -2.00 dBSFO2 125.7693867 MHz

============ GRADIENT CHANNEL ========GPNAM1 sine.100GPNAM2 sine.100

GPNAM3 sine.100GPX1 0.00 %

GPX2 0.00 %GPX3 0.00 %GPY1 0.00 %GPY2 0.00 %GPY3 0.00 %GPZ1 50.00 %GPZ2 30.00 %GPZ3 40.10 %P16 1000.00 usec

F1 - Acquisition parametersND0 2TD 256SFO1 125.7694 MHzFIDRES 82.064079 Hz

SW 167.039 ppmFnMODE undefined




MC2 QFSF 125.7577961 MHz

WDW QSINE

SSB 0LB 0.00 HzGB 0

N

N N

N

O

O

CH3

CH3

H3C

H

1

3

5

2

8

76

4

Gradient HMBCGradient HMBC

11

2233

55

11

44

33

22

55

66

77

88

33--44

33--5522--66

22--77

11--77

11--88

HH


C-dimens

ion


23/27

2D2D NOESYNOESY ((NNuclearuclear OOverhauserverhauser EEnhancementsnhancements SSpectroscoppectroscopYY))

t1 m AQ

The NOESY pulse sequence.

C ~ C

Ha HbVC*r-6, r


24/27

ppm

3.54.04.55.05.56.06.57.07.5 ppm

3.5

4.0

4.5

5.0

5.5

6.0

6.5

7.0

7.5

8.0

Current Data ParametersNAME cfynoesyEXPNO 1PROCNO 1


Time 8.53INSTRUM DRX500PROBHD 5 mm TBI 1H/PULPROG noesygptpTD 1024SOLVENT CDCl3


AQ 0.1488800 secRG 64DW 145.200 usecDE 6.00 usecTE 288.0 KD0 0.00000300 secD1 1.60000002 secD8 0.40000001 secD16 0.00010000 secd20 0.19890000 secIN0 0.00014520 sec



GPNAM2 sine.100GPX1 0.00 %GPX2 0.00 %GPY1 0.00 %GPY2 0.00 %GPZ1 40.00 %GPZ2 -40.00 %P16 1000.00 usec

F1 - Acquisition parametersND0 2TD 256SFO1 500.1326 MHzFIDRES 13.451274 HzSW 6.885 ppm

FnMODE undefined




MC2 TPPISF 500.1300144 MHz

WDW SINE

SSB 2LB 0.00 HzGB 0

N

N N

N

O

O

CH3

CH3

H3CH

1

3

5

2

8

76

4

33--CH3, 5CH3, 5--HH

Gradient NOESYGradient NOESY


25/27

NOESYNOESY

gives sequentialgives sequential

assignment of peptidesassignment of peptides

2

3

1

2 3

CH2

C2N C

H

N

O

H

C C

H

CH2O

N

H

C

CH2

C

H

OH

O

1 321


26/27

Spin-lock

90

t1

t2

mixing timemixing time

2D ROESY pulse program2D ROESY pulse program

For small molecule NOE can be very small or zeroROESY can be used in place of NOESY experiment. ROE

intensity is also related to the H-H distances.


27/27

Structure Determination ProceduresStructure Determination Procedures

1D1D 11H &H & 1313C & DEPT (+MSC & DEPT (+MSIRIRbasic chemical structure orbasic chemical structure orfunctional groups informationfunctional groups information

EstablishEstablish

1313

CC--

11

H connections by thru bond JH connections by thru bond JCHCH couplingscouplingsHMQCHMQCHSQCHSQCHSQCHSQC--TOCSY experimentsTOCSY experiments

EstablishEstablish 11HH--11H connection (spin systems or partial piecesH connection (spin systems or partial piecesDecoupledDecoupled 11

H, 1D TOCSY, 2DH, 1D TOCSY, 2D 11

HH

--11

H COSY, TOCSYH COSY, TOCSY

exptsexpts

.

.

usually starts with wellusually starts with well--resolvedresolved 11H signalsH signalsLong range connectionsLong range connectionsconnecting spin systems & assigningconnecting spin systems & assigning

quaternary carbonquaternary carbon1D NOESY & 2D HMBC, NOESY, ROESY experiments1D NOESY & 2D HMBC, NOESY, ROESY experiments

3D structure or conformation determination3D structure or conformation determination

1D NOESY & 2D NOESY, ROESY, (HSQC)1D NOESY & 2D NOESY, ROESY, (HSQC)--NOESYNOESY exptsexpts..

Documents

Common NMR Method for Structure Elucidation of Organic Molecule