Structure elucidation by NMR and computer-assisted structure generation of bi- and tri-cyclic products derived from electrocyclic rearrangements in biomimetic synthesis

1
Structure elucidation by NMR and
computer-assisted structure generation of bi- and
tri-cyclic products derived from electrocyclic
rearrangements in biomimetic synthesis Barbara
Odell, Tim D.W. Claridge, John E. Moses,
Sebastian Bruckner, Jack E. Baldwin The Dyson
Perrins Laboratory, Department of Chemistry,
University of Oxford, OX1 3QY, UK,
Barbara.Odell_at_chem.ox.ac.uk
THE NMR STRUCTURAL ASSIGNMENT PROBLEM
INTRODUCTION

• The process of assigning unique structures
  consistent with 1H,1H and 1H, 13C correlation
  data proved to be unusually challenging for these
  systems due to four principle features
•   the general lack of vicinal proton-proton
  couplings
• the ambiguity introduced by 2JCH, 3JCH, 4JCH and
  even 5JCH correlations in HMBC experiments of
  these extended conjugated systems
• the potential variety and complexity of
  structures which may, in principle, result from
  the electrocyclisations
• the time required for data analysis and
  identification of candidate structures
• In general when seeking unknown structures, there
  may be several candidates consistent with the
  available NMR data, but the spectroscopist may
  only consider one or perhaps a smaller subset of
  them. Identifying functional groups and smaller
  fragments is not usually a problem. Connecting
  them together is where the difficulties can
  arise.
• Hence, we wished to employ a computer program
  which would utilize knowledge of the functional
  groups together with correlations from 2D NMR
  data to produce all viable structures consistent
  with the input data in a short time. The
  development of expert systems (ES) or
  Computer-Assisted Structure Elucidation (CASE)
  programs has flourished over recent years3-9
  StrucEluc3, X-PERT4, RASTR (STREC)5, COCON6,7,
  and LSD8,9. We chose to examine the Nuzillard
  program Logic for Structure Determination or
  LSD . This is made freely available by Jean-Marc
  Nuzillard and is reasonably user-friendly in
  terms of data input which consists of 1D 13C,
  COSY, HMQC/HSQC and HMBC data.

Biomimetic synthesis of natural products is a
well established area of chemistry with
applications to the pharmaceutical industry. Two
areas of interest to the Baldwin group at Oxford
University are i) the crispatene family of
compounds1 (I) which are believed be mild
cytotoxic agents and ii) the SNF4435C and
SNF4435D family2 of hexasubstituted bicyclo
immunosupressants2 (II) isolated from the culture
broth of a strain of Steptomyces spectabilis.
Although very diverse in structure, it is
believed that both classes of compound are
originally derived from biosynthetic
transformations involving propionate and acetate.
One interesting aspect is that these proposed
biosynthetic schemes are believed to involve
polyene intermediates. This prompted the Baldwin
group to consider using polyenes as precursors in
chemical transformations using thermal,
photochemical and heterogeneous catalysis as
possible routes to biologically active
molecules. Extensive 1D and 2D NMR analysis of
the resulting products was employed to elucidate
the structures of the rearranged products. The
complexities we encountered in determining
unambiguous structures led us to consider the
application of Computer-Assisted Structure
Elucidation (CASE) programs in this task.
Example 2 Photochemical and Thermal
Rearrangements of the all-(E) Tetraene
Thermal Tricyclic core with observed nOes
Example 1 Photochemical Rearrangement of the
all-(E) Pentaene
Photochemical Cyclised product crispatene core
with observed nOes Intermediate 1st
isomerisation product
1H and 13C NMR spectra for the cyclisation
product note the scarcity of proton resonances
and couplings
HMBC of the cyclisation product
Starting tetraene
traces of impurities S starting tetraene
I isomerisation intermediate
The unusual tricyclic core suggested by NMR via
LSD and nOes for the thermal rearrangement was
subsequently confirmed by crystallographic
analysis of a suitable derivative, which also
proved the absolute stereochemistry (stereo view
shown).
Crystal structure of the tetraene showing steric
clash of adjacent methyl groups- a driving force
for isomerisation
The round circles on the HMBC spectrum indicate
4JCH (blue, H15 to C19) and 5JCH (red, H23 to
C22).
LSD input file for the cyclisation product The
file format is an edited example of the LSD input
file for this compound.
LSD output file for the cyclisation product
Summary scheme for the all-(E) Tetraene
 
Conclusions The work reported here shows that the
LSD Computer-Assisted Structure Elucidation
(CASE) program is a powerful tool for utilizing
1D and 2D NMR data to generate chemical
structures with viable connectivities. In cases
such as the examples shown above, where
long-range heteronuclear 1H-13C NMR correlations
are too complex to provide rapid solutions to
the assignment problem, we discovered that the
LSD ELIM command was very useful for overcoming
assignment discrepancies arising from ambiguities
over very long-range correlations (ngt3). We
would recommend that use of such structure
generation programs be augmented by additional
nOe studies to cross-check the proposed
structures and to yield stereochemical data.
Together they from an integrated approach to 3D
chemical structure elucidation yielding
consistent structural and stereochemical
assignments for the molecule in question.
  COSY 9 11 Define COSY correlations
(2/3J) COSY 10 12 COSY 14 20 COSY 3 13   HMBC 1
3 Define HMBC correlations ( 13C-1H) HMBC
1 13 HMBC 1 14 . . HMBC 22 23 HMBC 23 5 HMBC 23
3   BOND 4 11 Define known bonding
patterns eg within esters, aromatic rings
or other known fragments BOND 4 12
. BOND 14 26 BOND 14 20   EXIT Terminate
file
sb1311 File identity   DISP 1 Define output
format HIST 1 Display progress during
structure generation ELIM 2 5 Define
eliminations for nJCH gt 3   MULT 1 C 2
0 Define atom numbers, type, hybridisation
multiplicity eg 13C from DEPT, APT MULT 22
C 3 3 MULT 23 C 3 3 MULT 24 X 3 0 Define
heteroatoms or dummy groups eg NO2 MULT 25 O 2
0 MULT 26 O 3 0   VALE X 1 Define valence of
dummy groups   HMQC 3 3 Define HMQC
connectivities HMQC 5 5
The ELIM command allows the user to define any
number of HMBC correlations that may arise over
more than 3-bonds. Thus ELIM 2 5 allows
structures to be generated that can have up to 2
correlations arising over 4 or 5 bonds. This is
useful when no structures can be generated
assuming n 3 for all nJCH.
LSD program suggests a crispatene core solution
for the cyclisation product
References 1 J E Moses , J E Baldwin, R Marquez,
R Adlington, T D W Claridge and B Odell Organic
Letters Vol 5 No 5 2003 661-663. 2 J E Moses , J
E Baldwin, R Marquez, R Adlington and A R Cowley
Organic Letters Vol 4 No 21 2002 3731-3734. 3 K A
Blinov, D Carlson, M E Elyashberg, G Martin E R
Martirosian, S Molodtsov and A J Williams Magn
Reson Chem, 2003, 41, 399-372. 4 M E Elyashberg,
E R Martirosian, Y Z Karasev, H Thiele and H
Somberg Anal.Chim. Acta 1997, Vol 337,265. 5.M E
Elyashberg, VV Serov, E R Martirosian, L A
Zlatina, YZ Karasev, V N Koldashov, Y Y
Yampolskiy. J. Mol. Struct. 1991, Vol 230, 191. 6
T Lindel , J Junker, M Köck. Eur. J. Org. Chem.
1999 Vol 3 579. 7M Köck, J Junker, W Maier, M
Will, T. Lindel Eur. J. Org. Chem. 1999 3 573. 8
J-M Nuzillard and G Massiot Tetrahedron 1991 Vol
47 3655. 9 S V Ley, K Doherty, J-M Nuzillard
and G Massiot Tetrahedron 1994 Vol 42 12267.
Acknowledgements We would like to thank Dr.
Jean-Marc Nuzillard of the University of Reims,
France, for making his LSD program available to
us and for helpful discussions. We also thank Mr
Charles Baker-Glenn for his valuable assistance
in the preparation of this poster.
Spectra for the various products analysed were
recorded on a Bruker DRX500 spectrometer
equipped with a triple resonance inverse probe, a
Bruker AMX500 spectrometer equipped with a
broadband probe, and/or a Bruker DPX400 equipped
with an inverse probe. The LSD program was run on
a Silicon Graphics O2 workstation. Details of the
LSD program can be obtained from
http//www.univ-reims.fr/Labos/UPRESA6013/GNOSIE/L
SD/