Synthesis and conformational study of water-soluble, rigid, rodlike oligopiperidines

Article abstract of DOI:10.1002/anie.200502991

An oligomeric backbone of piperidine rings can be synthesized by solution or solid-phase synthesis. These oligomers adopt well-defined, rodlike structures with all the piperidine residues in chair conformations (see picture) both in solution (D₂O, CD₃OD) and the solid state. (Figure Presented).

Full text of DOI:10.1002/anie.200502991

Communications
Molecular Rods
DOI: 10.1002/anie.200502991
Synthesis and Conformational Study of Water-
Soluble, Rigid, Rodlike Oligopiperidines**
Vincent Semetey, Demetri Moustakas, and
George M. Whitesides*
Herein, we describe the preparation of oligopiperidines as a
new family of water-soluble, rigid oligomers. The design of
molecules with nanometer dimensions, defined shapes, and
physical properties (solubility, conductivity, etc.) is a matter of
considerable interest in macromolecular chemistry.[1,2]
“Molecular rods” are rigid, linear macromolecules that
constitute promising materials for applications in nanotech-
nology, such as spacers, wires, and construction elements.[3]
The poor water solubility of many current examples of
molecular rods[1,4] limit their applications, particularly in
biology. Only a few bio-oligomers exhibit a rigid-rod struc-
ture,[2c] of which oligoprolines, which have been considered
the most rigid,[5] have been used as spacers in biochemistry.[6]
The structure of these compounds is, however, still a subject
of discussion. Levins and Schafmeister reported the synthesis
of a water-soluble molecular rod based on fused diketopiper-
azine oligomers starting from a complex building block.[7]
We hypothesized that an oligomeric backbone of piper-
idine rings would be a rigid rod, with the piperidine moieties
adopting chair conformations in aqueous solution.[8] We have
developed a synthesis of representative members of this class
of molecules and investigated their conformations in polar
solvents, including deuterated water. We are particularly
interested in the possibility that they might serve as extended,
[*] Dr. V. Semetey, Dr. D. Moustakas, Prof. G. M. Whitesides
Department ofChemistry and Chemical Biology
Harvard University
12 Oxford Street, Cambridge, MA 02138 (USA)
Fax: (+1)617-495-9857
E-mail: gwhitesides@gmwgroup.harvard.edu
[**] This work was supported by the NIH (Grant GM30367). V.S.
acknowledges La Ligue contre le Cancer for a postdoctoral fellow-
ship. Initial design ofthis project was carried out by Dr. Val
Martichonok.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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water-soluble linkers or scaffolds for the oligovalent display
of ligands.
Scheme 1 outlines the strategy used to synthesize the
oligopiperidines in solution. In this strategy, elongation is
bonyl) on a 50-mmol scale. After deprotection with 20%
piperidine in dimethylformamide (DMF), the resin was
allowed to react with the N-Fmoc-protected isonipecotic
acid in the presence of benzotriazolyl-N-oxy-tris(dimethyla-
mino)phosphonium (BOP reagent)
and the Hunig base to afford 9. We
assembled building blocks to form
the molecular rod by using a sequen-
tial procedure: deprotection, reduc-
tive amination with Fmoc-4-piperi-
done, and capping with acetic anhy-
dride. The resin was then washed
and dried prior to treatment with
trifluoroacetic acid (TFA)/H2O
(95:5) for 2 h. HPLC purification
on a C18 column and lyophilization
afforded pure oligopiperidines 10
and 11.
The structure of 7 was investi-
gated by 1D and 2D NMR spectros-
copy in CD3OD. This solvent was
used because it produced a larger
dispersion of chemical shifts than
solvents such as CDCl3 or D2O. The
spin systems of all four piperidine
residues were unambiguously iden-
tified from COSY experiments. The
Scheme 1. Solution-phase synthesis oftetrapiperidine 7. a) Na2CO3, CbzCl; b) 1,4-dioxa-8-aza-spiro-
[4.5]decane (3), NaBH(OAc)3, 1,2-dichloroethane; c) Pd/C, H2, EtOH; d) concentrated HCl, 08C to
room temperature, 20 min; e) NaBH(OAc)3, 1,2-dichloroethane.
based on iterative reductive amination. We protected the
commercially available 4,4-piperidinediol hydrochloride (1)
with a benzyloxycarbonyl (Cbz) group to obtain 2. This
compound was allowed to react with 1,4-dioxa-8-aza-spiro-
[4.5]decane (3) in the presence of triacetoxyborohydride to
afford piperidinopiperidin-4-one 4 diprotected with a cyclic
ketal and a Cbz group.[9] Compound 4 led to two further
intermediates. Its catalytic hydrogenation yielded compound
5, and treatment of which with a concentrated aqueous HCl
solution afforded compound 6. Reductive amination of 5 and
6 yielded the tetramer derivative 7.
sequence was assigned on the basis of NOESY experiments
(mixing time = 400 ms) and was deduced from the strong
NOE interaction connectivities between piperidine rings.
Analysis of 1D spectra recorded between 273 and 323 K at
10 K increments revealed that the coupling values are only
weakly affected by temperature changes; we infer that a
single conformation dominates over this range of temper-
1
ature. In the H NMR spectrum recorded at room temper-
ature, in CD3OD, and at 500 MHz (Figure 1), the axial and
equatorial protons of the piperidine rings B, C, and D (H5,
H6, H8, H9, H11, and H12) are discernible. The eight ring
protons (H2 and H3) of the piperidine ring A appear as two
triplets at d = 2.66 and 1.71 ppm; this observation indicates
that the axial and equatorial positions in this ring exchange
rapidly on the NMR time scale through combined nitrogen
inversion and chair–chair inversion. Rings B–D all
display approximately the same series of signals
with 1) a triplet of triplets for H4, H7, and H10, all
in axial positions and 2) significant chemical-shift
differences (0.4 < Ddae
We used solid-phase techniques to synthesize oligopiper-
idines up to ten units in length (Scheme 2). Solid-phase
synthesis of oligopiperidine was performed on preloaded
Fmoc-b-Ala Wang resin 8 (Fmoc = 9-fluorenylmethoxycar-
< 1.4 ppm) between the axial and the equatorial
sites of each methylene group with the axial proton
at higher field. These characteristics provide strong
evidence that all of these rings have the same chair
conformation.[10] The chemical-shift difference
between H12a and H12e in ring D is accentuated
by the location of H12e in the shielding zone of the
Cbz group.
NOESY experiments at 298 K with a mixing
time of 400 ms yielded additional information
about the three-dimensional structure of the
tetrapiperidine 7. Several inter- and intraresidue
Scheme 2. General procedure for the solid-phase synthesis of oligopiperidine.
a) Fmoc-isonipecotic acid, BOP, NEt(iPr)2 in DMF; b) 20% piperidine in DMF,
20 min; c) Fmoc-4-piperidone, NaBH(OAc)3 in 1,2-dichloroethane, 2”60 min;
d) acetic anhydride, NEt(iPr)2, CH2Cl2; e) TFA/H2O (95:5).
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Communications
Figure 3. ORTEP diagram ofthe crystal structure of 7 (50% thermal
ellipsoids; protons are omitted for clarity). Selected distances [Š] and
torsion angles [8]: N5-N6 4.273, N6-N7 4.339, N7-N8 4.357; C48-N6-
C41-C40 178.6(5), C53-N7-C46-C45 179.9(5), C58-N8-C51-C50
179.9(5).
Figure 1. 1H NMR spectrum (500 MHz) oftetrapiperidine derivative 7
in CD3OD.
NOE interactions were extracted and are consistent with the
presence of a rodlike conformation (Figure 2). Intraresidue
NOE interactions confirmed the existence of a chair geom-
etry in piperidine rings. Interresidue NOE interactions
Molecular dynamics (MD) simulations on the oligomer 7
were performed at 300, 350, and 400 K to characterize the
conformational ensemble of the oligopiperidine as a function
of increasing temperature. For each temperature, the system
was equilibrated for 10 ps using a 2-fs time step, during which
time the temperature was ramped from 0 K to the final system
temperature (300, 350, or 400 K). Production simulations
were run for 1 ns using a 2-fs time step. Snapshots of the
system were written out every ten steps to insure that fine
details of the system were observed. To determine how linear
the geometry of the molecule remained during each simu-
lation, two metrics were used. The first is the length of the
major axis, defined as the distance between two carbon atoms
at the opposite ends of the molecule (Table 1), which was
Figure 2. Intra- and interresidue NOE interactions found between two
piperidine units.
revealed: 1) a linear structure with each piperidine unit in
an equatorial position and 2) the existence of several con-
Table 1: Statistics ofthe major-axis length (measured rfom the carbon
atoms labeled A and B) distributions of 7 observed in three MD
simulations.
À
formations of the N C bond between each piperidine unit
that are probably the three minimum-energy staggered
conformations of this bond.[11] The same characteristic NOE
interactions were found with a small model molecule,
methylpiperidinopiperidine (see the Supporting Informa-
1
tion). The H NMR spectra of 7 and methylpiperidinopiper-
idine (see the Supporting Information) in deuterated water
exhibit approximately the same characteristic pattern of
signals as that in CD3OD, with significant chemical-shift
differences between axial and equatorial protons from the
same methylene group; these characteristics indicate the
presence of a unique structure in methanol and water. IR
analysis of the oligopiperidine 7 in CDCl3 and the Bohlmann
band at 2814 cmÀ1 (see the Supporting Information) provide
further evidence in favor of an extended structure in which
the piperidine rings are in equatorial positions.[10a] Collec-
tively, these data strongly suggest that 7 adopts a well-defined
rodlike structure in solution.
The slow evaporation of a solution of 7 in deuterated
methanol yielded crystals of the unprotected base suitable for
X-ray structural determination.[12] The unit cell contains two
tetrapiperidine 7 molecules. The conformations of these two
molecules differ in the arrangement of their Cbz groups. Their
ORTEP representations clearly reveal linear rodlike struc-
tures (Figure 3). The molecules each consist of four piperidine
rings in chair conformations. All piperidine segments occupy
the equatorial position on each connected ring and are
separated by approximately 4.3 Š.
Temperature [K]
Mean length [Š]
Standard deviation
300
350
400
15.0
14.9
14.9
0.4
0.7
0.9
measured for each snapshot in each MD trajectory. The
second is the major axis angle, formed by the previously
defined major-axis carbon atoms and a central nitrogen atom
in the molecule (see the Supporting Information). These two
values characterize the overall geometry of the molecule
during the simulations, thus describing its tolerance for
stretching, compressing, and bending. The distributions of
the oligopiperidine lengths remain fairly invariant across all
three temperatures simulated (Table 1), thus indicating that
the linear geometry of this molecule, and its corresponding
ability to resist stretching and compressing, is stable across a
large range of temperatures.
Furthermore, the values of the major-axis angles indicate
that the molecule remains very extended through simulations
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[12]Crystal data: C 30H46N4O4, Mr = 526.71 gmolÀ1, colorless needle,
at all three temperatures. At higher temperature simulations,
the distribution of the major axis angle values has an
increased mean and a decreased variance. This implies that
as the temperature increases, the oligopiperidine structure
tends to bend less and remain slightly more fully extended.
Altogether, these data demonstrate that these oligopiperidine
molecules adopt a stable linear conformation. Visual inspec-
tion of the simulation trajectories confirms that the molecule
retains an extended structure throughout the entire simula-
crystal size: 0.10 ” 0.08 ” 0.04 mm3, a = 9.1261(14), b =
11.4111(17), c = 105.305(16) Š, a = 90, b = 90, g = 908, V=
10966(3) Š3, T= 193(2) K, orthorhombic, space group Pbca,
Z = 16, 1calcd = 1.276 MgmÀ3. Crystallographic data were col-
lected using a Bruker SMART CCD (charge-coupled device)
based diffractometer equipped with an Oxford Cryostream low-
temperature apparatus operating at 193 K, l = 0.71073 Š. 32596
measured reflections, 5102 unique (Rint = 0.0505), the structure
was solved by direct methods and refined by full matrix least
squares on F2 for all data to R1 = 0.0850 (I > 2s(I)) and wR2 =
0.1729 (I > 2s(I)). CCDC 263974 contains the supplementary
crystallographic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
À
tion. Although rotations about the C N bonds occur, these
rotations result in only small deviations around the linear
geometry of the molecule.
This report describes a simple, inexpensive, and widely
accessible method for the preparation of rigid, rodlike
oligopiperidines with a defined length of up to ten units
(4.3 nm length). This oligomeric system does not require
control of the stereochemistry at the Cg position of the
piperidine ring, but rather allows the molecule to equilibrate
into the proper conformations. Because of their structure, we
expect these molecules to be more resistant to proteolysis
than polyprolines. These well-defined, water-soluble mole-
cules may provide access to materials with well-defined
structures (e.g., rigid linkers, construction elements, etc.).
Received: August 22, 2005
Published online: December 12, 2005
Keywords: molecular dynamics · molecular rods ·
.
NMR spectroscopy · oligomers · structure elucidation
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