1. Stereochemical determination
Advanced Spectroscopy 2015/2016
Stereochemical determination
Professor Dan Stærk
Natural Products Research
Department of Drug Design & Pharmacology
Faculty of Health and Medical Sciences
University of Copenhagen
Open door policy –> you are always welcome to come and ask questions (or send me an )

2. Topics for today Brush up of isomerism/stereochemistry
Advanced Spectroscopy 2015/2016
Topics for today
Brush up of isomerism/stereochemistry
Constitional isomers (Functional isomers, positional isomers)
Stereoisomers (enantiomers, diastereomers)
Relative and absolute stereochemistry
R/S-nomenclature
a and b nomenclature
D/L nomenclature
NOE-experiments – strengths and limits
Mosher’s methods
Questions related to all aspects of NMR
Work with exam project

3. Constitutional isomerism versus stereoisomerism
Advanced Spectroscopy 2015/2016
Constitutional isomerism versus stereoisomerism 2 4 1 3 2 4 4 1 3 2 2 1 3 1 3 4

4. Different constitutional isomers
Advanced Spectroscopy 2015/2016
Different constitutional isomers
Different 1H and 13C NMR spectra
Functional isomers
Positional isomers

5. Advanced Spectroscopy 2015/2016
Stereoisomers

6. Overview stereoisomers
Advanced Spectroscopy 2015/2016
Overview stereoisomers
Identical spectra?
Discriminable?
Identical spectra?
Discriminable?
Identical spectra?
Discriminable?
Identical spectra?
Discriminable?

7. Absolute stereochemistry – sequence rules
Advanced Spectroscopy 2015/2016
Absolute stereochemistry – sequence rules
Identify the four substituents attached to the chiral carbon atom
The group/atom with highest atom number is given highest priority (i.e., labelled 1); the group/atom with second-highest atom number is given second-highest priority (i.e., labelled 2); etc.
If two or more atoms have the same atom number, the next groups/atoms are considered!!!!
Example:
Substituent Priority
-CHO 2
-OH 1
-CH2OH 3
-H 4

8. Absolute stereochemistry – R/S nomenclature
Advanced Spectroscopy 2015/2016
Absolute stereochemistry – R/S nomenclature
Chiral center(s) named R/S according to Cahn-Ingolf-Prelog sequence rules
Draw molecule with lowest prioritized group backwards
Write priority for remaining substituents
Configuration either R- (Rectus, right-hand) or S- (sinister, left-hand)
(S)-glyceraldehyde
(R)-glyceraldehyde

9. Stereochemical nomenclature – a/b nomenclature
Advanced Spectroscopy 2015/2016
Stereochemical nomenclature – a/b nomenclature
For many natural products containing ring systems, the a/b nomenclature is frequently used
Skeleton considered as being in the plane (although this is not the case)
Substituents below the plane are a
Substituents obove the plane are b a b b a
Betulinic acid
IUPAC name: (3β)-3-Hydroxy-lup-20(29)-en-28-oic acid

10. Stereochemical nomenclature – exercise
Advanced Spectroscopy 2015/2016
Stereochemical nomenclature – exercise
What is the absolute stereochemistry of C3 and C17? Can the stereoisomer with inverse configuration in all chiral centers be discriminated from the below structure with NMR? 17 3
Betulinic acid

11. Stereochemical nomenclature – a/b nomenclature
Advanced Spectroscopy 2015/2016
Stereochemical nomenclature – a/b nomenclature
a/b also used for describing stereochemistry of anomeric carbon in ring-closed carbohydrates – ‘easy-to-use’ rule for D-carbohydrates:
OH (or OR for glycosides) below the plane: a
OH (or OR for glycosides) above the plane: b

12. Stereochemical nomenclature – exercise
Advanced Spectroscopy 2015/2016
Stereochemical nomenclature – exercise
Draw the below structures using correct chair conformations and orientations of substituents – and explain if/how NMR can be used to identify the absolute stereochemistry of C-1

13. Stereochemistry – naturally occurring carbohydrates
Advanced Spectroscopy 2015/2016
Stereochemistry – naturally occurring carbohydrates
Naturally occuring carbobydrates are D-isomers – and we can therefore conclude that:
H-5 is always positioned axial for D-hexopyranosides
Orientation of H-1 and H-3 on same side gives strong NOE due to their 1,3-diaxial relationship
Orientation of H-1 can be determined based on the above and/or the coupling pattern to H-2
Jax,eq
Jax,ax

14. NOE – nuclear Overhauser effect
Advanced Spectroscopy 2015/2016
NOE – nuclear Overhauser effect
The nuclear Overhauser effect (NOE) is an incoherent process in which two nuclear spins “cross-relax” through dipole-dipole interaction. This cross relaxation causes changes in one spin through perturbations of the other spin. The NOE is dependent on many factors. The major factors are rotational correlation time and internuclear distance. In principle the intensity of the NOE is proportional to r -6 where r is the distance between the 2 spins.
Steady state NOE – only applicable for molecules that tumble ‘rapidly’ in solution
Transient NOE – applicable to both small and large molecules
ROE – Always positive and applicable to all sizes of molecules
Tau c –avarage time taken for the molecule to rotate through 1 radian.
Important information obtained from NOE-based experiments –
but learn the limitations as seen in the following examples!!!

15. NOE difference spectrum
Advanced Spectroscopy 2015/2016
NOE difference spectrum
Requires a stable sample environment
Prone to difference artefacts
Manually intensive setup

16. NOE difference spectrum
Advanced Spectroscopy 2015/2016
NOE difference spectrum
NOE-enhanced spectrum
- non-enhanced spectrum
NOE difference spectrum
non-enhanced spectrum
Can this experiment be used for establishing
the absolute stereochemistry of this molecule???

17. NOE difference spectra
Advanced Spectroscopy 2015/2016
NOE difference spectra
Can this experiment be used for establishing
the absolute stereochemistry of this molecule???

18. Mosher’s Method – distinguish enantiomers by NMR
Advanced Spectroscopy 2015/2016
Mosher’s Method – distinguish enantiomers by NMR
Chiral molecule with unknown stereochemistry -> R or S-konfiguration???
(must possess functional group, e.g., hydroxy group)
(?)-substrate
Chiral auxillary reagent that reacts with chiral substrate
(R)-Aux and (S)-Aux
Chem. Rev. 104, 17, 2004

19. Mosher Method – distinguish enantiomers by NMR
Advanced Spectroscopy 2015/2016
Mosher Method – distinguish enantiomers by NMR
Chiral Solvating Agents (CSA)
Chiral environment
Weak linkages
add (R)-Aux
(?)-substrate-(R)-Aux
(?)-substrate
(?)-substrate-(S)-Aux
add (S)-Aux
Covalent linkages
Transformation to diastereomers
Chiral Derivatizing Agents (CDA)
Chem. Rev. 104, 17, 2004

20. Procedure for assignment after use of CDA (Mosher method)
Advanced Spectroscopy 2015/2016
Procedure for assignment after use of CDA (Mosher method)
Chem. Rev. 104, 17, 2004

21. Structural features of Chemical Derivatizing Agents (CDA’s)
Advanced Spectroscopy 2015/2016
Structural features of Chemical Derivatizing Agents (CDA’s)
Carboxylic acid
Hydroxy group
Amine group
Other…
Group linking covalently to the substrate
Polar group
Group inducing magnetic anisotropy
Aromatic ring
Carbonyl group
Other…
EXAMPLE:
(R)-MTPA
Chem. Rev. 104, 17, 2004

22. Common CDA’s and monofunctional substrates
Advanced Spectroscopy 2015/2016
Common CDA’s and monofunctional substrates
Chiral derivatizing agents
Monofunctional substrates
Chem. Rev. 104, 17, 2004

23. Rationale for the shielding L1/L2 of CDA’s
Advanced Spectroscopy 2015/2016
Rationale for the shielding L1/L2 of CDA’s
Chem. Rev. 104, 17, 2004

24. Exercise – determine the absolute configuration of pentanol
Advanced Spectroscopy 2015/2016
Exercise – determine the absolute configuration of pentanol
Chem. Rev. 104, 17, 2004

25. Topics for today Brush up of isomerism/stereochemistry
Advanced Spectroscopy 2015/2016
Topics for today
Brush up of isomerism/stereochemistry
Constitional isomers (Functional isomers, positional isomers)
Stereoisomers (enantiomers, diastereomers)
Relative and absolute stereochemistry
R/S-nomenclature
a and b nomenclature
D/L nomenclature
NOE-experiments – strengths and limits
Mosher methods
Questions related to all aspects of NMR
Work with exam project