Conformational and structural analysis of a ter-cyclopentane scaffold for molecular recognition

Article abstract of DOI:10.1002/ejoc.200600807

Well-defined oligomers of cycloalkanes comprise a relatively unstudied class of organic compounds, and may have general utility in the development of receptors for biologically relevant molecules. We have investigated the solution structure of a ter-cyclo

Full text of DOI:10.1002/ejoc.200600807

FULL PAPER
DOI: 10.1002/ejoc.200600807
Conformational and Structural Analysis of a ter-Cyclopentane Scaffold for
Molecular Recognition
Peter C. Gareiss,[a] Prakash B. Palde,[a] Robert D. Hubbard,[b][‡] and
Benjamin L. Miller*[a,c,d]
Keywords: Molecular modeling / Molecular recognition / Conformational analysis
Well-defined oligomers of cycloalkanes comprise a relatively
unstudied class of organic compounds, and may have gene-
ral utility in the development of receptors for biologically rel-
evant molecules. We have investigated the solution structure
tended rigid conformation, with inter-ring torsion angles
preferentially at 180°. These experiments demonstrate that
conformational hypotheses developed in the course of
designing ter-cyclopentane scaffolds for lipid A recognition
of a ter-cyclopentane member of this class by molecular mod- are accurate, and furthermore provide support to the broader
eling and by NMR spectroscopy. We find that the molecular use of this class of compounds as scaffolds in molecular re-
ensembles derived from conformational searches incorporat- cognition.
ing NMR-derived restraints are in excellent qualitative
agreement with unrestrained molecular mechanics confor-
(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim,
mation searches. The ter-cyclopentane scaffold adopts an ex-
Germany, 2007)
106305 (3)[11] (versions of 1 in which l = m = n = 0) are
essentially the only naturally occurring members of this
group of compounds incorporating more than two rings,
and their interesting biological activity and novel structure
have driven an extensive effort in the synthetic com-
munity.[12] Second, oligocycloalkanes appeared to provide a
new set of structural motifs for conformational design. We
anticipated that other oligocycloalkanes would have intrin-
sic interest as novel materials, requiring development of new
synthetic methodology. Ultimately, oligocycloalkanes were
envisioned to serve as potential scaffolds for the construc-
tion of new molecular recognition systems (Figure 1).
Introduction
Organic chemistry has a rich tradition of employing con-
formational restraint in the design and synthesis of novel
molecules. From early observations of the conformational
bias of substituted cyclohexanes,[1] to more recent efforts
in “conformational design” by Still,[2] Hoffmann,[3,4] and
others,[5–7] consideration of conformational bias allows for
the generation of complex organic structures with predicta-
ble three-dimensional solution structures. In turn, this con-
formational predictability can be a strategy-level design ele-
ment in the development of molecules targeting a specific
biological function.
As part of a general program directed towards the identi-
fication of novel receptors for carbohydrates and carbo-
hydrate derivatives, we initiated a study of the synthesis and
properties of substituted, stereoregular oligocycloalkanes
(1). Such compounds seemed interesting at the outset for
several reasons. First, relatively few examples of this struc-
tural class have been described in the literature.[8,9] The olig-
ocyclopropane natural products FR-900848 (2)[10] and U-
[a] Department of Biochemistry and Biophysics, University of
Rochester,
Rochester, New York, USA
[b] Department of Chemistry, University of Rochester,
Rochester, New York, USA
[c] Department of Dermatology, University of Rochester,
Rochester, New York, USA
[d] The Center for Future Health, University of Rochester,
Rochester, New York, USA
Figure 1. Examples of stereoregular oligocycloalkanes.
As we have reported previously,[13] our study of the syn-
thesis and properties of oligocycloalkanes began with the
design and synthesis of the ter-cyclopentane derivative 4.
[‡] Current address: Abbott Laboratories, Abbott Park, Illinois,
USA
Supporting information for this article is available on the
WWW under http://www.eurjoc.org or from the author.
Eur. J. Org. Chem. 2007, 53–61
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
53

B. L. Miller, P. C. Gareiss, P. B. Palde, R. D. Hubbard
FULL PAPER
This molecule binds lipid A, the component of bacterial steric repulsion by the methyl groups in the anti conformer
lipopolysaccharide believed to be responsible for most cases destabilizes this structure. Dihedral angle drive calculations
of Gram-(–) bacterial sepsis,[14] with an affinity rivaling that employing a number of different force fields implemented in
of lipid A-binding natural products such as the topical anti- the Maestro/Macromodel molecular mechanics package[22]
biotic polymyxin B.[15] In addition, compound 4 proved indicate that all are able to reproduce this behavior both in
useful as the recognition component of a label-free optical the gas phase and when continuum solvation terms (GB/
sensor for Gram-(–) bacteria.[16] Our design of 4 as a lipid SA water or chloroform)[23] are included in the calculation
A receptor was primarily based on molecular mechanics (data not shown).
calculations. To more clearly understand the molecular re-
Next, we calculated the energies for the anti and gauche
cognition process, and lend information to the future devel- conformers of 1-(cyclopentyl)cyclopentane, starting from
opment of new receptors for lipid A and other glycoconju- an envelope–envelope[24–26] conformer in which each cy-
gates, it was necessary to experimentally validate the com- clopentyl is an equatorial substituent of the other. We antic-
putational models. Herein, we present the conformational ipated that the geometric constraints of the cyclopentane
analysis, synthesis, and solution NMR structures of the rings would force inter-ring bond angles to open sufficiently
tetra-alcohol ter-cyclopentane derivative 5 (Figure 2). Grat- to allow the “intuitive ranking” of conformers to hold true.
ifyingly, we demonstrate a strong correlation between con- Indeed, this is what we observed for all force fields in both
formational biases predicted by molecular mechanics and the gas phase and GB/SA solvent (water or CHCl3)
experimentally determined solution structures for ter-cyclo- (Table 1). It is unsurprising that Amber* and OPLS* pro-
pentanes.
duce ∆E(gauche – anti) slightly different from the other
force fields, because the parameterization of these force
Table 1. Calculated steric energies (kcal/mol) for gauche and anti
conformers of 1-(cyclopentyl)cyclopentane with various force fields
and gas phase or GB/SA solvent (water or CHCl3).
Gas Phase
Figure 2. Structure of the lipid A binding tetra-tryptophan ter-cy-
clopentane derivative 4, and the tetra-alcohol ter-cyclopentane syn-
thetic precursor, 5.
Force Field gauche
anti
∆E
MM2*
MM3*
Amber*
OPLS*
MMFFs*
24.1
38.4
21.1
18.8
17.4
22.2
36.5
19.6
16.7
16.7
1.9
1.9
1.5
2.1
1.7
Our initial molecular modeling efforts focused on simple
dihedral angle drives in order to map out the conforma-
tional preferences of oligocyclopentanes. Because parame-
terization varies from force field to force field, this also af-
forded us an opportunity to examine whether there were
any force field-based differences in the potential energy sur-
face. To provide a benchmark for comparison, we began
with the well-studied compound 2,3-dimethylbutane. One
might predict based on a simple “back of the envelope”
drawing of Newman projections that the anti structure
would be lower in energy than the two degenerate gauche
conformers. However, both high-level computational and
experimental studies have indicated that these conformers
are essentially isoenergetic.[17–21] This is presumably because
GB/SA CHCl3
MM2*
MM3*
Amber*
OPLS*
MMFFs*
18.2
32.5
15.2
12.8
11.5
16.7
30.5
13.6
10.7
9.7
1.5
2.0
1.5
2.1
1.8
GB/SA H2O
MM2*
26.5
40.8
22.9
21.1
19.7
25.1
38.9
21.3
19.0
18.0
1.4
1.9
1.6
2.1
1.7
MM3*
Amber*
OPLS*
MMFFs*
54
www.eurjoc.org
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2007, 53–61

ter-Cyclopentane Scaffold for Molecular Recognition
FULL PAPER
fields is primarily biopolymer-directed. As with all molecu- formers for 6 were found to be on the order of 5.4 kcal/
lar mechanics calculations, it is the differences in energy mol. Interestingly, although the potential energy surface for
between conformations that are important and not their ab- 7 is similar to that calculated for 6, it is not identical.
solute values.
Rather, a slight asymmetry is observed, with one anti,-
Introduction of a third cyclopentane ring at the 3-posi- gauche conformation predicted to lie just 0.2 kcal/mol in
tion reduces the level of symmetry in the molecule [vs. 1- energy higher than the global energy minimum (anti,anti).
(cyclopentyl)cyclopentane], and we were interested in de- Barriers to conformational interconversion for 7 are also
termining the structural impact of this, as well as additional asymmetric, varying from 4 to 6.3 kcal/mol. While the ob-
substitution. We concentrated on the meso isomer (or 1,3- served asymmetry may be in part an artifact of the way the
cis), primarily for reasons of synthetic accessibility, but also dihedral angle drive calculation is run (i.e., no pseudorota-
because it appeared more suitable as a scaffold for the de- tion of cyclopentane rings is allowed, and thus the calcula-
velopment of receptor molecules. The all-envelope confor- tion yields a somewhat unrealistic view of the potential en-
mation was chosen for dihedral angle analysis of cis-(1,3- ergy surface), the non-symmetrical substitution of the cy-
dicyclopentyl)cyclopentane (6), with cyclopentyl substitu- clopentane rings is almost certainly a contributor as well.
ents of the central cyclopentane ring in 6 placed pseudo- Taken together, these data suggested that although ter-cy-
equatorially (Figure 3). For the hexamethyl-substituted ter- clopentane scaffolds have some conformational flexibility,
cyclopentane 7, methyl-substituted rings twist out of the there is a significant energetic preference for the anti,anti
envelope conformation in order to minimize steric repul- conformer. Substitution of the core scaffold changes the po-
sion. Results of the two dihedral angle drive calculations tential energy surface somewhat, allowing the gauche,anti
are shown in Figure 4. In each case, the lowest energy con- conformer to nearly match the anti,anti conformer. Of
former was found to be that with both inter-ring torsion course, we anticipate that further substitution of the scaf-
angles anti, with a 1.9 kcal/mol difference in energy separat- fold for utility as a functional receptor could potentially
ing the lowest energy conformer from the next-lowest alter the conformational ensemble, either enhancing or re-
(gauche) for 6. Barriers between neighboring gauche con- ducing the degree to which the all-anti conformer is favored.
Figure 3. Starting conformations for ter-cyclopentane (6, left) and hexamethyl ter-cyclopentane (7, right) dihedral angle drives. Only
protons flanking the critical torsion angles are shown.
Figure 4. Dihedral angle drive for 6 and 7. Legend indicates relative energy in kcal/mol.
Eur. J. Org. Chem. 2007, 53–61
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
55

B. L. Miller, P. C. Gareiss, P. B. Palde, R. D. Hubbard
FULL PAPER
Scheme 1. (a) KMnO4 on CuSO4, CH2Cl2, room temp., 12 h; (b) KOtBu, THF, 0 °C to room temp. 2 h, then –78 °C, 10, 10 h (61% over
2 steps); (c) (CH3)3Al (0.05 equiv.), AlCl3 (0.5 equiv.), cyclopentadiene (10 equiv.), CH2Cl2, 4 °C, 18 h (15%); (d) LiAlH4 (6 equiv.), THF,
room temp., 24 h (51%); (e) benzoyl chloride (3.6 equiv.), Et3N (4 equiv.), CH2Cl2, room temp., 3 h (35%); (f) O3, CH2Cl2/CH3OH (1:1),
–78 °C, 15 min., then NaBH4 (20 equiv.), 4 h (89%).
Synthesis
The optimized route currently used to synthesize the ter-
cave/concave–convex diastereomers of the cycloadduct 12
was obtained in 70% yield. Final purification of the con-
vex–convex diastereomer was accomplished in 15% yield by
reverse phase (C18) preparatory HPLC.
Reduction of diastereomerically pure 12 with LiAlH4 in
THF followed by double benzoylation provided 14 in mod-
erate yield (18% over the two steps). Subsequent ozonolysis
in a 1:1 MeOH/CH2Cl2 solution at –78 °C and reductive
workup with NaBH4 (–78 °C to room temperature) cleanly
provided tetrol 5 as a faint yellow oil in 89% yield. Our
choice of benzoyl derivatization prior to ozonolysis was
governed in part by synthetic accessibility; previous
attempts at bis-silylation were unsuccessful.
cyclopentane scaffolds is shown in Scheme 1. The synthesis
of 5 begins with oxidative cleavage of norbornene (8) to
afford cyclopentane-1,3-dialdehyde (9). While the synthesis
of 9 from 8 has been well precedented, the reported yields
were low (40–50%) and in our hands were not amenable to
large-scale synthesis (Ͼ3 g). After surveying a broad range
of oxidants (including ozonolysis, wet permanganate and
alumina,[27] and a two-step Sharpless dihydroxylation[28]
/
oxidative cleavage procedure), we found a procedure em-
ploying KMnO4 adsorbed on copper sulfate[29] to be repro-
ducibly high-yielding (essentially quantitative) and scalable.
Conversion of the dialdehyde 9 to the bis(α,β-unsatu-
rated ester) 11 was accomplished by a bidirectional Horner–
Wadsworth–Emmons reaction employing the phosphonate
10.[30] By analogy to previous observations by Kishi,[31] we
NMR Spectra of Tetra-Alcohol 5 in CD3OD
With the tetra-alcohol 5 in hand, we were ready to begin
chose diisopropyl phosphonate in order to improve the E:Z solution NMR analysis. The one-dimensional H and 13C
selectivity, while the phenethyl ester was solely selected to spectra, while too complex by themselves to allow full as-
simplify chromatographic detection of the product. To a signment, provided useful information about the structure
solution of the phosphonate 10 in THF was added potas- of 5 in CD3OD at room temperature. First, integration of
sium tert-butoxide. Cannulation of the yellow anion into a peaks revealed an upfield multiplet corresponding to a sin-
THF solution of the di-aldehyde 9 at –78 °C, followed by gle proton. By simple geometry, this must correspond to
warming the reaction to 4 °C, and stirring at this tempera- one of the diastereotopic protons on the central ring, at the
ture for 18 h afforded the desired product 11 in 61% yield, meso plane of symmetry. This observation was crucial to
1
and E,E:E,Z selectivity of at least 20:1.
assigning the rest of the protons on the molecule. Comple-
With 11 in hand, we were ready to perform the bi-direc- tion of the assignment of the ter-cyclopentane ring core of
tional Diels–Alder reaction, using a Lewis acid catalyst we 5 was accomplished following acquisition of a full suite of
had previously examined in the context of a “unidirec- 1H-1H (DQF-COSY and NOESY) and 1H-13C (HSQC)
tional” model system.[31] The bis-dienophile 11 was dis- spectra (Table 2). Analysis of the DQF-COSY experiment
solved into CH2Cl2, and cooled to 0 °C. The solution was allowed for extraction of a critical torsional angle restraint:
treated with Me3Al (0.05 equiv.) and AlCl3 (0.5 equiv.) at the crosspeak connecting H1, H1ЈЈ and H1Ј, H3Ј showed a
0 °C. Cyclopentadiene (10 equiv.) was added to the reac- coupling constant of 14 Hz (at an acquired digital resolu-
tion; the reaction was then warmed to 4 °C and stirred for tion of 2.9 Hz/point, or 1.47 Hz/point following pro-
18 h. After standard work-up and flash chromatography, a cessing). From the Karplus relationship,[32,33] this is consis-
mixture of the endo–endo convex–convex and convex–con- tent with a dihedral angle of 180 °. Studies of other com-
56
www.eurjoc.org
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2007, 53–61

ter-Cyclopentane Scaffold for Molecular Recognition
FULL PAPER
pounds described in the literature also support this as- sents an unfortunate degradation in the precision of the
sertion. For example, Roush and co-workers report a coup- output conformational ensemble, because differences in
ling constant of 11.5 Hz for 15, a rigid bicyclic structure NOE peak volumes are clearly visible for these proton pairs
used as an intermediate in their studies towards the total in the NOESY spectra. However, it was also unavoidable,
synthesis of FR182877.[34]
because at this stage we are not able to individually assign
these protons with confidence. NOE peaks are not observed
between benzoate ring protons and the core ter-cyclopen-
tane, indicating that these moieties are extended away from
the core structure.
Table 2. NMR assignments and structure numbering for 5 (derived
from the HSQC spectrum).
Position
13C (ppm)
1H (ppm)
1,1ЈЈ
2,2ЈЈ
3,3ЈЈ
4,4ЈЈ
5,5ЈЈ
1Ј,3Ј
2Ј
4Ј,5Ј
6,6ЈЈ
7,7ЈЈ
8,8ЈЈ
50.6
44.8
45.4
34.3
47.8
46.7
38.7
30.5
67.0
63.7
67.5
1.52
2.3
2.2
2.2, 1.9
1.97
1.97
Figure 5. Distance restraints derived from the NOESY spectrum of
5 in CD3OD.
2.15, 0.92
1.91, 1.27
4.28, 4.16
3.58, 3.70
3.58, 3.39
Figure 6. Hypothetical alternative NOE assignments for the 5,5ЈЈ–
3,3ЈЈ crosspeak.
Structure Calculations for 5
Peak volumes from the 300-ms NOESY spectrum were
inspected in order to generate set of strong
a
The 32 unique NOE distance restraints and the two in-
(1.75 ÅϮ0.75 Å), medium (3.00 ÅϮ0.5 Å) and weak ter-ring torsional restraints were used as the basis for re-
(4.25Ϯ0.75 Å) distance restraints.[35] A total of 16 unique strained conformational analysis of 5. The Monte–Carlo
non-vicinal restraints were observed; accounting for sym- multiple minimum (MCMM) method implemented in
metry, these translated into 32 unique distance restraints in Macromodel 7.2 was employed to generate 10,000 conform-
the structure calculation (Figure 5). In assigning distance ers. Structures were minimized using the Merck molecular
restraints, we made the assumption that where two possible mechanics force field (MMFFs) and the generalized Born/
assignments could be made for symmetry-related protons, solvent accessible surface (GB/SA) continuum solvation
geometric considerations would dictate that the restraint model for water. While the similarity in rank ordering of
pair with the shorter apparent distance was more likely. For dicyclopentane conformers for different force fields de-
example, one could assign the NOE constraint from the scribed above suggests that any of the commonly available
symmetry-related pair of protons 5,5ЈЈ to 3,3ЈЈ as an inter- force fields would suffice for our purposes, we chose to
ring distance (Figure 6, a) or as an intra-ring restraint (Fig- move forward with the MMFFs force field because of its
ure 6, b). While a conformation is conceivable that would reported high accuracy for conformational energies across
allow for the inter-ring distance to be shorter than the intra- a broad range of structural types.[36] Torsional bonds varied
ring distance, this would preclude a 180° torsional angle for and ring closure bonds are indicated in Figure 7. Structures
at least one of the 1,1ЈЈ–1Ј,3Ј angles. Thus, the restraint was falling within a 50 kJ/mol (12.5 kcal/mol) energy window
assigned as shown in Figure 6 (b). For diastereotopic pro- were retained, and rank-ordered according to energy. For
ton pairs (those α to ester oxygen atoms, in this case), iden- comparison, identical conformation searches were per-
tical restraints were assigned to both protons. This repre- formed without the torsional restraints, and without the
Eur. J. Org. Chem. 2007, 53–61
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
57

B. L. Miller, P. C. Gareiss, P. B. Palde, R. D. Hubbard
FULL PAPER
distance and torsional restraints. An analogous computa-
tional protocol has been applied by Smith and co-workers
in the analysis of a β-turn peptidomimetic[37] and (+)-dis-
codermolide,[38] and by Paterson and co-workers towards
the solution structural determination of laulimalide.[39]
Results
Figure 8 shows an overlay of the 10 lowest energy output
structures from the conformational analysis of 5 without,
with distance, and with distance and torsional NMR-de-
rived restraints. Incorporation of NMR distance restraints
clearly reduces the conformational degrees of freedom fall-
ing within the designated potential energy window, al-
though the lack of observed NOEs to benzoate side chains
means the position of these groups is not precisely defined.
None of the low-energy structures were found to have any
NOE violations. As expected, application of the strong di-
hedral angle restraint to the inter-ring torsion results in all
of the output structures of 5 adopting the anti/anti inter-
ring geometry. Additionally, the incorporation of this tor-
sional restraint to the distance restrained analysis greatly
enhances the convergence of conformations occupying the
potential energy window. This is in excellent qualitative
agreement with the lowest-energy structure obtained by un-
restrained conformational analysis. The lowest energy
Figure 7. Torsional bonds varied (black lines) and ring closures
(dotted lines) in restrained and unrestrained conformational analy-
sis of 5.
Figure 8. Wall-eyed stereoview of the overlay of the first 10 lowest energy output structures from conformation searches (MCMM,
MMFFs, GB/SA H2O) for 5 in the absence of NMR-derived restraints (top, lowest 0.4 kcal/mol of output structures), in the presence of
only NMR-derived distance restraints (middle, lowest 1.4 kcal/mol of output structures), and in the presences of both NMR-derived
distance and torsional restraints (bottom, lowest 3.0 kcal/mol of output structures). This figure was generated with Maestro.[14]
58
www.eurjoc.org
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2007, 53–61

ter-Cyclopentane Scaffold for Molecular Recognition
FULL PAPER
Cyclopentane-1,3-dicarbaldehyde (9): Norbornene (5.0 g) was dis-
solved in 170 mL CH2Cl2 in a 250-mL round-bottom flask.
KMnO4 (54 g) and CuSO4·5H2O (27 g) was ground to a fine pow-
der using a mortar and pestle. This fine powder (76 g) was placed
in a 1000-mL round-bottom flask equipped with an overhead stir-
rer. H2O (2.5 mL) and CH2Cl2 (100 mL) were added, and stirring
was started. After 5 min, the solution of norbornene in CH2Cl2
was added. After an additional 10 min of stirring, tBuOH (12 mL)
was added, and this mixture stirred for 12 h at room temperature.
At this point, TLC of the reaction mixture showed complete con-
sumption of starting material. The slurry was filtered through Ce-
lite, dried with Na2SO4, filtered, and reduced in vacuo. Because of
the volatility of the compound, care must be taken at this stage
to prevent product loss. Compound 9 was obtained in essentially
quantitative yield, and exhibited spectral characteristics identical
to literature reports.
NMR-derived structure features a central cyclopentane in
the envelope conformation, with the two substituent cyclo-
pentanes in a pseudoequatorial orientation.
Conclusions
While determination of a single lowest-energy conforma-
tion by NMR is complicated by solution phase dynamics,
detailed structural information about low energy conforma-
tions is readily obtainable. In this study, comparison of the
ensemble of the 10 lowest energy structures, in addition to
the highest and lowest energy conformers, reveals the rigid
behavior of the core ter-cyclopentane scaffold in solution.
As we have demonstrated elsewhere, the ter-cyclopentane
scaffold has promise as a new structural motif for molecular
recognition and biosensing. The experimental and compu-
tational analysis presented here serves to confirm our initial
hypotheses regarding the likely solution conformation of cis
1,3-ter-cyclopentanes as rigid easily derivatizable molecular
recognition scaffolds, with significant agreement between
conformational analyses with and without application of
experimentally derived distance and torsional restraints.
The work described herein proves the utility of ter-cyclo-
pentanes as molecular recognition scaffolds, and provides a
foundation for moving forward with additional structural
studies.
Bis-α,β-unsaturated Ester 11: The Phenethyl diisopropyl phos-
phonate 10 (62.8 g, 191.4 mmol) was dissolved to a concentration
of 0.5  in THF at 0 °C, and allowed to stand at that temperature
30 min to ensure thermal equilibration. Addition of potassium tert-
butoxide (20.06 g, 178.78 mmol) to the phosphonate solution re-
sulted in a canary yellow reaction color. After stirring for 20 min
at 0 °C, or until the entire base had dissolved in the reaction mix-
ture, the reaction was warmed to room temp. and stirred for an
additional 2 h. Concurrently, the aldehyde 9 (10.72 g, 85.1 mmol)
was dissolved into 2.0  THF, and cooled to –78 °C for 30 min.
The yellow potassium anion of 10 was added by a cannula to the
aldehyde solution over 1.5 h. After addition of the anion was com-
plete, the reaction was maintained at –78 °C for 10 h with monitor-
ing by TLC. The reaction was quenched with water (400 mL), and
the resulting layers were separated. The aqueous layer was ex-
tracted with diethyl ether (4ϫ250 mL). The organics were pooled
and washed with a brine solution, dried with Na2SO4, filtered, and
reduced in vacuo to give a yellow oil. Purification of the yellow
residue by flash chromatography (silica, 80:20 to 60:40 hexanes/di-
ethyl ether) afforded 11 as a pale yellow oil (21.7 g, 61% yield,
E,E:E,Z Ͼ20:1).
Experimental Section
General Experimental Details: All nonaqueous reactions were con-
ducted in flame-dried glassware under N2, and were stirred with a
teflon-coated magnetic stir bar, unless otherwise stated. Air-sensi-
tive reagents and solutions were transferred through syringe (unless
otherwise stated) and were introduced to the reaction vessel
through a rubber septum. Room temperature (r.t.) refers to ambi-
ent temperature, which is approximately 22 °C. Unless otherwise
stated, temperatures other than r.t. denote the temperature of the
cooling/heating bath. All distillations were performed under N2, or
at reduced pressure using a water aspirator (15–30 Torr), or vac-
uum pump (1 Torr).
Compound 11: 1H NMR (400 MHz, CDCl3): δ = 7.32–7.35 (m, 4
3
H), 7.24–7.27 (m, 6 H), 6.93 (apparent dd, JH,H = 8, 16 Hz, 2 H),
3
3
5.80 (apparent dd, JH,H = 1, 16 Hz, 2 H), 4.37 (t, JH,H = 7 Hz, 4
3
H), 3.0 (t, JH,H = 7 Hz, 4 H), 2.71–2.82 (m, 2 H), 2.04–2.10 (m, 1
3
H), 1.91–2.01 (m, 1 H), 1.76 (t, JH,H = 8 Hz, 1 H), 1.37–1.62 (m,
2 H), 1.29–1.37 (m, 1 H) ppm. 13C NMR (75 MHz, CDCl3): δ =
166.5, 155.5, 152.2, 137.8, 128.8, 128.4, 126.5, 119.7, 119.6, 64.7,
42.6, 41.3, 38.9, 37.6, 35.1, 32.1, 31.1 ppm. FTIR (thin film, from
Reagent-grade solvents were used without further purification for
all extractions and work-up procedures. Double distilled water was
used for all aqueous reactions, work-ups, and for the preparation
of all aqueous solutions. Reaction solvents were dried and purified
according to standard procedures by distillation under N2 from an
appropriate drying agent, or by purification through a Glas-Col
solvent drying system. Cyclopentadiene was cracked at 140 °C, and
stored indefinitely at –80 °C.
CDCl ): ν = 3060, 3026, 2951, 1714, 1650, 1496, 1453, 1149,
˜
3
984 cm–1. HRMS Calculated for C27H31O4 [M + H] 419.2222;
found 419.2224.
Diels–Alder Adduct 12: Dienophile 11 (20 g, 47.7 mmol) was dis-
solved to a concentration of 0.3  in CH2Cl2. The resulting solu-
tion was cooled to 0 °C for 15 min. Addition of Me3Al (1.19 mL,
2.39 mmol, 2.0  in hexanes) yielded slight gas evolution, which
Proton NMR spectra were obtained with a Bruker Avance 400
(400 MHz), Avance 500 (500 MHz) or
a Varian Inova-500 dissipated upon stirring at 0 °C for an additional 10 min. To the
(500 MHz) instrument at 25 °C. Carbon NMR spectra were ac-
quired with an Avance 400 (101 MHz), or with a Varian Inova-500
(126 MHz). Chemical shifts are reported in ppm (δ) relative to the
appropriate deuterated solvent. Infrared (IR) spectra were recorded
with a Perkin–Elmer 1610 FT-IR spectrophotometer and are re-
ported in wavenumbers (cm–1) with a polystyrene standard. High
resolution mass spectrometry (HRMS) was performed at the
yellow solution was added AlCl3 (23.8 mL, 23.85 mmol, 1.0  in
CH3NO2) and the reaction was stirred an additional 5 min at 0 °C.
Cyclopentadiene (31.4 g, 477 mmol, 4.0  in CH2Cl2) was added to
the colorless solution by an addition funnel dropwise over 30 min.
The reaction was warmed to 4 °C, and allowed to stir at 4 °C for
12 h. The reaction was quenched with pyridine (20 mL), the reac-
tion was quickly warmed to room temp. The resulting thick white
national mass spectrometry facility at the University of California, slurry was filtered through silica (300 mL), and washed with Et2O
Riverside, California.
(5ϫ100 mL). The organics were reduced in vacuo. Azeotropic re-
Eur. J. Org. Chem. 2007, 53–61
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
59

B. L. Miller, P. C. Gareiss, P. B. Palde, R. D. Hubbard
FULL PAPER
moval of the pyridine and CH3NO2 was accomplished by treatment
1717, 1451, 1313, 1271, 1175, 1110, 1069, 1026, 710 cm–1. HRMS
with heptane (4ϫ50 mL) and rotary evaporation, affording a yel- Calculated for C35H38O4 (M+) 522.2770; found 522.2752.
low residue. Purification by flash chromatography (silica, 95:5, hex-
Tetra-Alcohol 5: The di-benzoate 14 (15 mg, 0.028 mmol) was dis-
anes/Et2O) afforded a mixture of the endo–endo convex–convex and
solved to a concentration of 0.1  in a solution of 1:1 CH2Cl2/
convex–concave/concave–convex diastereomers of the cycloadduct
MeOH, and cooled to –78 °C for 10 min. Next, O3 was bubbled
through the solution, until the reaction mixture became deep blue
in color (10 min). O3 treatment was continued for an additional
35 min. O3 bubbling was then discontinued, and began bubbling
O2, to remove excess O3. Once the blue color dissipated, the reac-
tion was warmed to 0 °C for 10 min. NaBH4 (14.8 g, 0.402 mmol)
was added yielding slight gas evolution and the vessel was allowed
to slowly warm to room temp. over 30 min. The reaction was
stirred for 4 h at room temp. then quenched with 10% aq. HCl
(0.4 mL). The contents were diluted with ethyl acetate, and the lay-
ers were separated. The aqueous layer was extracted with ethyl ace-
tate (4ϫ1 mL). The organic extracts were combined and washed
sequentially with water (1 mL), satd. aq. Na2CO3 (1 mL), and satd.
aq. NaCl (1 mL). The organics were dried with Na2SO4, filtered,
and reduced in vacuo to afford an opaque solid 5 (15 mg, 89%
yield) as a clear oil.
12 in 70% yield. The mixture was brought up in DMSO (0.1 parts),
then diluted with CH3OH (3 parts) and CH3CN (1 part). The con-
vex–convex diastereomer was separated in 15% yield by reverse
phase (C18) preparatory HPLC with a 92% CH3CN, 8% H2O,
0.1% TFA isocratic method with approximately a 15% yield of the
desired convex-convex product.
1
Compound 12: H NMR (400 MHz CDCl3): δ = 7.35–7.22 (m, 10
H), 6.26–6.24 (m, 2 H), 5.87–5.84 (m, 2 H) 4.27–4.14 (m, 4 H),
3
3.09 (s, 2 H) 2.93–2.89 (t, JH,H = 6 Hz, 3 H), 2.67 (s, 2 H) 2.54–
3
2.52 (t, JH,H = 4 Hz, 2 H), 1.94–1.88 (m, 3 H), 1.76–1.70 (m, 2
H), 1.63–1.59 (m, 2 H), 1.54 (s, 1 H), 1.52 (s, 1 H), 1.43–1.34 (m,
3
5 H), 1.13–1.06 (q, JH,H = 12 Hz, 1 H) ppm. 13C NMR (75 MHz
CDCl3): δ = 30.7, 34.9, 38.8, 45.6, 46.1, 46.3, 46.4, 49.4, 50.0, 64.6,
126.4, 128.4, 128.9, 133.3, 137.9, 138.5, 174.5 ppm. FTIR (thin
film, from CDCl ): ν = 3061, 3026, 2940, 2867, 1731, 1454, 1331,
˜
3
1261, 1167, 1116, 1015, 698 (cm–1). HRMS Calculated for
1
3
Compound 5: H NMR (400 MHz CD3OD): δ = 7.96 (d, JH,H
=
6.8 Hz, 4 H), 7.53–7.51 (m, 2 H), 7.42 (t, 3JH,H = 8 Hz, 4 H), 4.30–
4.26 (m, 2 H), 4.18–4.14 (m, 2 H), 3.71–3.69 (m, 2 H) 3.63–3.58
(m, 4 H), 3.39 (m, 2 H) 2.34–2.23 (m, 4 H), 1.98–1.95 (m, 7 H),
C37H43O4 [M + H] 551.3161 found 551.3177.
Reduction of 12 to 13: LiAlH4 (79.8 mg, 2.1 mmol) was added to
12 (116 mg, 0.21 mmol) in 2 mL THF, at room temp. with slight
gas evolution. The reaction stirred for 24 h at room temp., then
was quenched sequentially with water (0.5 mL) and 10% NaOH
aq. solution (0.5 mL), and diluted with 10 mL THF. The reaction
formed a white precipitate and was stirred for 2 h at room temp.
The reaction contents were filtered through Celite (400 mL), and
the pad was washed with diethyl ether (5ϫ100 mL). The filtrate
was dried with Na2SO4, filtered and reduced in vacuo to give a
yellow oil. Purification of the oil by flash chromatography (silica,
66:34 hexanes/ethyl acetate) afforded the diol (34 mg, 51% yield).
3
1.77–1.74 (m, 2 H), 1.53 (t, JH,H = 6 Hz, 2 H), 1.36–1.26 (m, 7
H), 0.94–0.86 (m, 2 H) ppm. 13C NMR (75 MHz CD3OD): δ =
168.2, 134.2, 131.6, 130.6, 129.6, 67.5, 67.0, 63.7, 50.6, 47.8, 46.7,
45.4, 44.8, 38.7, 34.3, 30.5 ppm. FTIR (thin film, from CD OD): ν
˜
3
= 3323, 2923, 2361, 1716, 1450, 1276, 1114, 1070, 1026, 712 cm–1.
HRMS Calculated for C35H47O8 [M
595.3263.
+ H] 595.3270 found
Experimental Procedures for 2D NMR Sample Preparation and
Data Acquisition: The tetra-alcohol 5 (15 mg, 0.025 mmol) was dis-
solved into 0.3 mL of CD3OD, that had been dried by treating with
4-Å molecular sieves, to afford a 8.3 m solution. The solution was
transferred to an NMR tube, under N2. N2 was bubbled through
the solution for 10 min, to remove dissolved O2. All 2D NMR ex-
periments were performed with a Bruker Avance-500. A constant
temperature of 25 °C was used for all experiments. DQF-COSY
spectra were acquired with a sweep width of 12.0 ppm in both di-
mensions, and a digital resolution of 2.9 Hz/point in F2 and
11.7 Hz/point in F1. Zerofilling in both dimensions during pro-
Compound 13: 1H NMR (400 MHz CDCl3): δ = 6.17 (s, 2 H), 6.02
3
(s, 2 H), 3.52–3.47 (m, 2 H), 3.14 (t, JH,H = 10 Hz, 2 H), 2.90 (s,
3
2 H), 2.56 (s, 2 H), 1.87 (d, JH,H = 6 Hz, 4 H), 1.73–1.70 (m, 5
3
H), 1.48–1.40, (m, 5 H), 1.25–1.19 (m, 6 H), 0.741 (q, JH,H
=
12 Hz, 1 H), 0.56 (m, 2 H) ppm. 13C NMR (75 MHz CDCl3): δ =
30.9, 39.9, 43.7, 45.7, 46.0, 46.1, 48.6, 49.1, 66.5, 133.2, 138.1 ppm.
FTIR (thin film, from CDCl ): ν = 3213, 2960, 2360, 1012,
˜
3
725 cm–1. HRMS Calculated for C21H31O2 [M + H] 315.2324
found 315.2316.
cessing provided
a final digital resolution of 1.47 Hz/point.
Di-benzoate 14: The di-alcohol derived from reduction of 13
(34 mg, 0.11 mmol) was slurried into CH2Cl2 at room temp. to pro-
vide a 0.2  solution. Sequential addition of benzoyl chloride
(55 mg, 0.38 mmol), and Et3N (0.06 mL, 0.432 mmol) at room
temp. to the slurry caused the reaction to become yellow and
homogeneous. After stirring for 24 h at room temp. TLC analysis
showed consumption of starting material. The reaction was
quenched with water (0.5 mL), and dried to yield a white solid.
Purification of the oil by flash chromatography (silica, 95:5 hex-
anes/diethyl ether) yielded 14 (15 mg, 18% yield) as a colorless oil.
NOESY spectra were acquired using a sweep width of 10.00 ppm
in each dimension, and a mixing time of 300 ms. HSQC spectra
were acquired with sweep widths of 10 ppm in F2 (1H) and
220 ppm in F1 (13C). Data processing was performed using Mes-
tReC[40] on a Windows PC, with 90 degree sinebell-squared apodiz-
ation functions applied in each dimension during processing.
Supporting Information (see also the footnote on the first page of
this article): Spectral information and all 2D NMR experiments
(21 pages).
Compound 14: 1H NMR (400 MHz CDCl3): δ = 8.03–8.01 (m, 4
3
3
H), 7.52 (t, JH,H = 8 Hz, 2 H), 7.39 (t, JH,H = 8 Hz, 4 H), 6.24–
Acknowledgments
3
6.22 (m, 2 H), 6.05–6.03 (m, 2 H), 4.2 (apparent d of d, JH,H
4.8 Hz, JH,H = 6.4 Hz, 4 H), 3.77 (t, JH,H = 10 Hz, 2 H), 2.92 (s,
=
3
3
Funding by NIH-NIGMS (R01-GM-062825-03) and DHHS-PHS
2 H), 2.60 (s, 2 H) 2.26–2.12 (m, 3 H), 1.94–1.88 (m, 2 H), 1.82– (2T32AR007472-16) is gratefully acknowledged.
1.75 (m, 2 H), 1.55 (s, 1 H), 1.51–1.41 (m, 4 H), 1.31–1.25 (m, 7
3
3
H), 0.92–0.82 (m, 3 H) 0.74 (apparent d of d, JH,H = 4 Hz, JH,H
= 10 Hz, 2 H) ppm. 13C NMR (75 MHz, CDCl3): δ = 166.4, 138.3,
133.5, 132.6, 129.6, 128.2, 68.2, 49.2, 46.2, 46.0, 45.8, 45.0, 44.2,
[1] F. R. Jensen, C. H. Bushweller, J. Am. Chem. Soc. 1969, 91,
5774.
[2] M. T. Burger, A. Armstrong, F. Guarnieri, D. Q. McDonald,
W. C. Still, J. Am. Chem. Soc. 1994, 116, 3593–3594.
39.7, 30.9, 30.7 ppm. FTIR (thin film, from CDCl ): ν = 2963,
˜
3
60
www.eurjoc.org
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2007, 53–61

ter-Cyclopentane Scaffold for Molecular Recognition
FULL PAPER
[3] T. Brandl, R. W. Hoffmann, Eur. J. Org. Chem. 2004, 4373–
4378.
[4] T. Trieselmann, R. W. Hoffmann, K. Menzel, Eur. J. Org.
Chem. 2002, 1292–1304.
[5] A subset of work in this area includes: a) R. E. Taylor, Y. Chen,
G. M. Galvin, P. K. Pappa, Org. Biomol. Chem. 2004, 2, 127–
132.
[6] H. B. Lee, M. C. Zaccaro, M. Pattarawarapan, S. Roy, H. U.
Saragovi, K. Burgess, J. Org. Chem. 2004, 69, 701–713.
[7] J. D. Sadowsky, M. A. Schmitt, H.-S. Lee, N. Umezawa, S.
Wang, Y. Tomita, S. H. Gellman, J. Am. Chem. Soc. 2005, 127,
11966–11968.
[8] For an early synthesis of the parent ter-cyclopentane hydro-
carbon, see:J. v. Braun, J. Reitz-Kopp, Ber. Dtsch. Chem. Ges.
1941, 74, 1105–1110.
[9] A more recent synthesis of polycyclohexylcyclohexanes may be
found in: I. Columbus, R. E. Hoffman, S. E. Biali, J. Am.
Chem. Soc. 1996, 118, 6890–6896.
[10] M. Yoshida, M. Ezaki, M. Hashimoto, M. Yamashita, N. Shig-
ematsu, H. Okuhara, M. Kohsaka, K. Horikoshi, J. Antibiot.
1990, 43, 748.
[11] M. S. Kuo, R. J. Zielinski, J. I. Cialdella, C. K. Marschke, M. J.
Dupuis, G. P. Li, D. A. Kloosterman, C. H. Spilman, V. P.
Marshall, J. Am. Chem. Soc. 1995, 117, 10629.
[12] For lead references, see: J. Pietruszka, Chem. Rev. 2003, 103,
1051–1070.
[19]
[20]
D. H. Wertz, N. L. Allinger, Tetrahedron 1974, 30, 1579.
L. Lunazzi, D. Macciantelli, F. Bernardi, K. U. Ingold, J. Am.
Chem. Soc. 1977, 99, 4573.
R. H. Boyd, J. Am. Chem. Soc. 1975, 97, 5353.
Macromodel 7.2; Schroedinger, Inc.
W. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am.
Chem. Soc. 1990, 112, 6127.
J. E. Kilpatrick, K. S. Pitzer, R. Spitzer, J. Am. Chem. Soc.
1947, 69, 2483–2488.
F. V. Brutche Jr., T. Roberts, S. J. Barr, N. Pearson, J. Am.
Chem. Soc. 1959, 81, 4915–4920.
F. V. Brutcher Jr., W. Bauer Jr., J. Am. Chem. Soc. 1962, 84,
2233–2236.
D. G. Lee, T. Chen, Z. Wang, J. Org. Chem. 1993, 58, 2918–
2919.
H. Becker, M. A. Soler, K. B. Sharpless, Tetrahedron 1995, 51,
1345–1376.
S. Göksu, R. Altundas, Y. Sütbeyaz, Synth. Commun. 2000, 30,
1615.
[21]
[22]
[23]
[24]
[25]
[26]
[27]
[28]
[29]
[30] R. D. Hubbard, B. L. Miller, J. Org. Chem. 1998, 63, 4143.
[31] H. Nagaoka, Y. Kishi, Tetrahedron 1981, 37, 3873–3888.
[32] M. Karplus, J. Am. Chem. Soc. 1963, 85, 2870.
[33] C. A. G. Hassnoot, F. A. A. M. De Leeuw, C. Altona, Tetrahe-
dron 1980, 36, 2783.
[34] J. L. Methot, W. R. Roush, Org. Lett. 2003, 5, 4223–4226.
[35] M. Williamson, T. Havel, K. Wüthrich, J. Mol. Biol. 1985, 182,
295–315.
[13] R. D. Hubbard, S. R. Horner, B. L. Miller, J. Am. Chem. Soc.
2001, 123, 5810–5811.
[14] C. R. H. Raetz, Annu. Rev. Biochem. 1990, 59, 129–170.
[15] D. C. Morrison, D. M. Jacobs, Immunochemistry 1976, 13,
813–818.
[16] S. Chan, S. R. Horner, B. L. Miller, P. M. Fauchet, J. Am.
Chem. Soc. 2001, 123, 11797–11798.
[36] T. A. Halgren, J. Comput. Chem. 1999, 20, 730–748.
[37] A. B. Smith III, W. Wang, P. A. Sprengeler, R. Hirschmann, J.
Am. Chem. Soc. 2000, 122, 11037–11038.
[38] A. B. Smith III, M. J. LaMarche, M. Falcone-Hindley, Org.
Lett. 2001, 3, 695–698.
[17] U. Burkert, N. L. Allinger, “Molecular Mechanics” (ACS
Monograph 177), American Chemical Society, Washington,
D. C., 1982, p. 87.
[18] W. Ritter, W. Hull, H.-J. Cantow, Tetrahedron Lett. 1978, 19,
3093.
[39] I. Paterson, D. Menche, R. Britton, A. E. Håkansson, M. A.
Silva-Martínez, Tetrahedron Lett. 2005, 46, 3677–3682.
[40] MestReC, Mestrelab Research Company, http://www.mestrec.co.
Received: September 15, 2006
Published Online: November 13, 2006
Eur. J. Org. Chem. 2007, 53–61
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
61