The synthesis of functionalized nanoscale molecular rods of defined length

Article abstract of DOI:10.1021/ja0293958

We report a synthetic approach to spiro-ladder oligomers of defined length and structure that form water-soluble molecular rods. We describe the synthesis of a chiral molecular building block 1 and its assembly on solid support to form flexible chains that were then rigidified by the parallel formation of several diketopiperazine rings. Two molecular rods approximately 15 and 25 A in length were synthesized containing three and five monomers, respectively. The molecular rods were easily functionalized on both ends and were shown to have high water solubility, making them compatible with biological buffers. These molecules may find use as scaffolds for the display of ligands in chemical-biology applications and as spacers and construction materials for nanoscience applications. Copyright

Full text of DOI:10.1021/ja0293958

Published on Web 03/29/2003
The Synthesis of Functionalized Nanoscale Molecular Rods of Defined Length
Christopher G. Levins and Christian E. Schafmeister*
Department of Chemistry, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15260
Received November 19, 2002; E-mail: meister@pitt.edu
The development of systematic approaches to the synthesis of
nanometer scale molecules of discrete size, shape, and mechanical
properties is a long-term goal of macromolecular chemistry.1-10
Molecular rods are macromolecules that have many exciting
potential applications in nanoscale science as spacers, wires, and
construction elements; yet as Michl’s authoritative review11 points
out, the poor solubility of many current examples of molecular rods
is the primary obstacle to their study and application. We have
developed a synthetic approach to water-soluble molecular rods
that are of defined length and contain multiple chiral centers. These
molecules can be easily synthesized and functionalized on both
ends. We present here the synthesis of a prototype molecular
building block 1 and demonstrate the solid-phase synthesis of two
molecular rods 2 and 3 containing three and five monomers,
respectively. Molecular mechanics was used to predict the confor-
mation of the scaffold 2, and the prediction was confirmed by 2D
NMR analysis.
Our prototype building block 1 was synthesized on a 1.8 g scale
from inexpensive, commercially available trans-4-hydroxy-L-proline
4 in nine steps with an overall yield of 25% (Scheme 1). The
synthesis uses a Bucherer-Bergs reaction12 to install a quaternary
stereocenter with a diastereoselectivity of 5:1.13 Using a single
chromatographic column, we isolated 16.5 g of pure diastereomer
5a from a 20 g mixture of 5a and 5b. The intermediate 5a leads to
the differentially protected bis amino acid 1.
We assembled three building blocks to form the molecular rod
2 using sequential solid-phase synthesis on a 46 µmol scale (Scheme
2). Each building block was activated as the 1-hydroxy-7-azaben-
zotriazole (HOAt) ester,14 and quantitative coupling to the previous
building block was achieved in less than 10 min, a surprising result
given the apparent hindered nature of the nucleophile. After three
monomers were coupled, the oligomer was functionalized with a
tyrosine residue to facilitate characterization. The flexible oligomer
8 was cleaved from the resin, and high-performance liquid
chromatography with mass spectrometry (HPLC-MS) analysis
revealed a single peak with the expected m/z ratio of 1061.2 (M +
H+). The carboxybenzyl (Cbz) groups were then removed by
hydrogenolysis to form 9. The flexible oligomer 9 was converted
into the rigidified scaffold 2 through the parallel formation of two
diketopiperazine15 rings by exposure to 20% piperidine/DMF over
48 h at 4 °C.16 The product 2 precipitated from the 20% piperidine
solution, and filtration was used to recover 5 mg (∼15% yield based
on resin loading). HPLC-MS analysis of this material reveals a
single peak with the expected m/z ratio of 595.2 (M + H+) for 2.
The scaffold 2 is soluble in water to more than 5 mg/mL and stable
in neutral and acidic aqueous solution at room temperature for
weeks.
Scheme 1 . Synthesis of Monomer 1a
a Reagents and conditions: (a) (i) TMS-Cl, NEt(iPr)2, CH2Cl2, reflux;
(ii) Cbz-Cl, 0 °C to room temperature. (b) Jones reagent, acetone, 20 °C.
(c) Isobutylene, H2SO4 (cat.), CH2Cl2, room temperature. (d) (i) (NH4)2CO3,
KCN, 1:1 DMF/H2O, 60 °C, sealed tube; (ii) silica gel chromatography,
99:1 CH2Cl2/MeOH. (e) (Boc)2O, DMAP, THF, room temperature. (f) KOH,
1:1 H2O/THF, room temperature. (g) (i) TMS-Cl, NEt(iPr)2, CH2Cl2, reflux;
(ii) Fmoc-Cl, 0 °C to room temperature. (h) (i) MeOH, DCC, DMAP,
CH2Cl2, 0 °C to room temperature; (ii) silica gel chromatography 2:1 EtOAc/
hexanes. (i) CF3CO2H/CH2Cl2.
Scheme 2. Synthesis of Scaffold 2a
a Reagents and conditions: (a) 20% piperidine/DMF, 40 min, room temperature. (b) Two times 2 equiv of 1-OAt ester, 4 equiv of NEt(iPr)2, 20%
CH2Cl2/DMF, 60 min, room temperature. (c) 3 equiv of N-R-Fmoc-O-tert-butyl-L-Tyr-OAt ester, 6 equiv of NEt(iPr)2, 20% CH2Cl2/DMF, 60 min, room
temperature. (d) 20% piperidine/DMF, 120 min, room temperature. (e) 95% CF3CO2H/2.5% (iPr)3SiH/2.5% H2O, 120 min, room temperature. (f) H2 (∼1
atm), 10% Pd/carbon, 7:2:1 MeOH/H2O/AcOH, 60 min, room temperature. (g) 20% piperidine/DMF, 48 h, 4 °C.
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10.1021/ja0293958 CCC: $25.00 © 2003 American Chemical Society

C O M M U N I C A T I O N S
C, D, E, F and the folded tyrosine conformation are identical. The
differences between the five conformations involve combinations
of rotamers around the C2-C3 bond, rotamers around the tyrosine
OH bond, and two envelope conformations of ring A. The 2D
ROESY spectra display cross-peaks consistent with those from the
predicted rigid B-F ring system. The NMR data are more consistent
with ring A existing predominately in the single envelope confor-
mation depicted in Figure 2 based upon a strong cross-peak between
4HR and 10H and a weak or nonexistent cross-peak between 4Hâ
and 10H.
We have demonstrated the synthesis of two nanoscale molecular
rods using a novel building block approach. The synthesis takes
place in two phases: a flexible chain is first assembled through
amide coupling on solid support, and then the scaffold is rigidified
by the selective formation of a second set of amide bonds. We
have also demonstrated that the three-mer scaffold has a rodlike
three-dimensional structure. The scaffolds were rapidly assembled
using solid-phase synthesis and were easily functionalized on either
of their two ends. Among molecular rods, these scaffolds exhibit
the rare property of water solubility,11 making them compatible
with biological buffers. Because of their fused ring structure, we
expect them to be more inflexible than spacers such as poly-proline
helices.19,20 This synthetic approach may also be extended to
incorporate other building blocks to construct more complex shapes
and ultimately functional macromolecules.
Figure 1. The chemical structure of scaffold 3. Modeling indicates that
the spiro-fused ring structure forms a narrow left-handed helical rod with
approximately four residues per turn and a pitch of ∼20 Å. Inset: the C18
reverse phase HPLC chromatogram of the unpurified ether precipitated
product containing 3 (0-20% MeCN/H2O, 0.1% TFA).
Acknowledgment. We thank the Research Corporation and the
Camille and Henry Dreyfus New Faculty Awards program for
financial support. Additional funds were provided by the University
of Pittsburgh. The authors thank Blake Hill for valuable discussions.
Supporting Information Available: Synthesis and characterization
of 1, 2, and 3. HPLC-MS and 2D NMR data for 2 and HPLC-MS data
for 3 (PDF). This material is available free of charge via the Internet
at http://pubs.acs.org.
Figure 2. A stereoimage of the predicted third lowest energy conformer
of scaffold 2 most consistent with NMR data. The arrows indicate that strong
and medium ROESY cross-peaks are seen between the indicated pairs of
protons. The molecule forms a molecular rod about 1.5 nm in length.
References
To demonstrate the generality of this synthetic approach, the five-
mer scaffold 3 (Figure 1) was synthesized in a fashion similar to
that of scaffold 2. The resin (49 mg, 31.4 umol loading) was first
charged with an Fmoc-protected tyrosine residue, and then five
cycles of coupling using monomer 1 were performed. Roughly 13
mg of resin was removed and subjected to cleavage conditions.
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in the five lowest energy minima (Figure 2). A superposition of
these predicted lowest energy conformations reveals that rings B,
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