Ni(II)-mediated self-assembly of artificial β-dipeptides forming a macrocyclic tetranuclear complex with interior spaces for in-line molecular arrangement

Article abstract of DOI:10.1021/ja8009555

Metal-mediated self-assembly of bioinspired molecular building blocks shows promise as an excellent strategy to provide well-defined metal arrays and nanoscopic metallo-architectures in a programmable way. Herein, we report Ni(II)-mediated self-assembly of artificial β-dipeptides (1) which were prepared from a newly designed β-amino acid bearing a propanediamine ligand as the side chain. The β-dipeptide (1) has thus two sets of ligands, that is, each building block serves as a tridentate ligand with a bidentate propanediamine unit and an amide carbonyl group. Both C- and N-terminal tridentate ligands in 1 bind to two Ni(II) ions independently, and consequently, four β-dipeptides are circularly arranged in a head-to-tail fashion to form a macrocyclic tetranuclear Ni(II) complex, Ni₄1₄(ClO₄)₈(H₂O)₁₀. The cyclic structure was determined by X-ray analysis and ESI-TOF mass spectrometry. The resulting unique twisted-boat structure allows the formation of isolated spaces for in-line hydrogen-bonded arrangement of water and anion molecules within a hole and two grooves rich in hydrogen bonding groups. Copyright

Full text of DOI:10.1021/ja8009555

Published on Web 04/09/2008
Ni(II)-Mediated Self-Assembly of Artificial ꢀ-Dipeptides
Forming a Macrocyclic Tetranuclear Complex with Interior
Spaces for In-Line Molecular Arrangement
Ryosuke Miyake,† Shohei Tashiro,† Motoo Shiro,‡ Kentaro Tanaka,†,§ and
Mitsuhiko Shionoya*,†
Department of Chemistry, Graduate School of Science, The UniVersity of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan, Rigaku Corporation, 3-9-12 Matsubaracho,
Akishima, Tokyo 196-8666, Japan, and Department of Chemistry, Graduate School of Science,
Nagoya UniVersity, Furo-cho Chikusa-ku, Nagoya, Aichi 464-8602, Japan
Received February 7, 2008; E-mail: shionoya@chem.s.u-tokyo.ac.jp
Metal-mediated self-assembly has been recognized as an
excellent strategy to build up well-defined molecular architectures
with an isolated, functional nanospace.1,2 To date, a large number
of excellent examples of self-assembled macrocyclic molecules
have been reported.2–5 Internal spaces of these molecules have their
unique shape and volume and thereby provide a variety of functions
such as molecular recognition4 and specific chemical reactions.5
However, to construct more sophisticated molecular functions,
systematically, chemically easy-to-modify building blocks are
required. In this respect, our group has focused on biorelated
molecular building blocks such as amino acids and nucleosides
because they can be easily modified in a way that their structure,
number, and sequence are controlled.6 For instance, amino acids
that have a metal binding site at the side chains7 could provide
functional oligopeptides bearing a repeated sequence of metal-ligand
and amide functionalities. Therefore, metal-mediated assemblage
of such functional building blocks would generate unique structural
frameworks and spaces. Herein, we report a well-defined mac-
rocyclic tetranuclear Ni(II) complex with four artificial ꢀ-dipeptides
1 (Figure 1). The unique twisted-boat structure allows the formation
of interior spaces for in-line arrangement of water and anion
molecules.
Figure 1. Schematic representation of the formation of a macrocyclic
tetranuclear complex, Ni414(ClO4)8(H2O)10, from a ꢀ-dipeptide 1 and
Ni(ClO4)2 ·6H2O. Metal binding sites of the N-terminal and the C-terminal
sides of the ꢀ-dipeptide 1 are colored blue and red, respectively. In the
center circle, the coordination mode of the Ni(II) center is indicated. The
figure in the circle shows a Λ-fac configuration.
The ꢀ-dipeptide 1 consists of two artificial ꢀ-amino acids
with a propanediamine ligand at the side chain, thereby pro-
viding two tridentate ligands with two amide carbonyl groups.
The dipeptide 1 was prepared starting from N-protected 2,2-
bis(tert-butoxycarbonylaminomethyl)-3-phthalimidopropanoic
acid8 as its trifluoroacetic acid salts. The subsequent coupling
reaction of this building block was carried out under microwave
irradiation to obtain the dipeptide 1·(CF3CO2H)4 in 36% overall
yield (for the details, see Supporting Information).
Figure 2. (a) Molecular structure of [Ni414]8+ with 50% thermal ellipsoids
viewed from the side of the top groove. Only one enantiomer is shown: Λ-∆-
Λ-∆ for Ni(1)-Ni(2)-Ni(1′)-Ni(2′). It is notable that the peptide direction
from the N- to the C-terminal portions is counterclockwise in this view. The
dashed lines represent hydrogen bonds. (b) An outline drawing showing a
twisted-boat structure with a hole and two grooves. A dashed red circle and
two gray half-cylinders represent a hole and two grooves, respectively.
The reaction of dipeptide 1 · (CF3CO2H)4 with Ni(ClO4)2 ·
6H2O in a 1:1 ratio in the presence of 4 equiv of diisopropyl-
ethylamine in EtOH at 50 °C for 3 h produced a pale purple
powder, which was recrystallized from water to obtain
Ni414(ClO4)8(H2O)10 in 38% yield as purple block crystals
suitable for X-ray diffraction analysis.9 In the resulting molecular
structure, four Ni(II) ions and four dipeptides 1 are connected
in a head-to-tail manner. An N-terminal tridentate ligand of one
dipeptide is connected with a C-terminal tridentate ligand of
another dipeptide to complete an octahedral Ni(II) center, and
the two oxygen donor atoms of their amide groups are placed
in the cis position (Figure 1). The cyclic structure of the Ni(II)
complex has a crystallographically imposed C2 symmetry with
one-half of the molecule being in the asymmetric unit (Figure
2a). As shown in the conceptual diagram of the Ni(II) complex
with a twisted-boat structure (Figure 2b), four Ni(II) centers
are positioned at the apexes of a distorted tetrahedron. There
are two crystallographically different Ni(II) centers, Ni(1) and
Ni(2), due to different coordination bond lengths around each
Ni(II) center (see Supporting Information), and each Ni(II)
center adopts a different configuration (Λ-fac or ∆-fac).10
Therefore, this complex is chiral, and one set of enantiomeric
tetranuclear Ni(II) complexes coexists in the crystal to form a
racemate. When viewed from the top groove side of an
enantiomer shown in Figure 2a, the direction of the peptide
framework from the N- to the C-terminal portions is counter-
† The University of Tokyo.
‡ Rigaku Corporation.
§ Nagoya University.
9
5646 J. AM. CHEM. SOC. 2008, 130, 5646–5647
10.1021/ja8009555 CCC: $40.75
2008 American Chemical Society

C O M M U N I C A T I O N S
new way of a precise molecular arrangement within isolated
spaces. In a preliminary study, we found that the ꢀ-dipeptide 1
forms a cyclic trinuclear Zn(II) complex. In addition to the type
of metals, controlling the number, sequence, and structural
frameworks of amino acid residues in the peptide ligand would
develop new approaches to designable peptide-based molecular
architectures with novel functions directed toward molecular
recognition, transport, and transformation.
Acknowledgment. This study was supported by the Global
COE Program for Chemistry Innovation, a Grant-in-Aid for
Scientific Research (S) to M.S. (Grant No. 16105001) from the
Ministry of Education, Culture, Sports, Science and Technology
of Japan.
-
Figure 3. Encapsulated H2O and ClO4 molecules in the hole and the
-
two grooves. (a) In-line arrangement of H2O and ClO4 molecules along
the central hole with a side view of the packing structure of the macrocyclic
-
Ni(II) complex. Some H2O and ClO4 molecules included in the two
-
Supporting Information Available: Experimental procedures,
additional structural data, and spectral data of Ni414(ClO4)8(H2O)10
complex. This material is available free of charge via the Internet
at http://pubs.acs.org.
grooves are omitted for clarity. (b) In-line arrangement of H2O and ClO4
molecules within the top and bottom grooves. H2O molecules are shown
without hydrogen atoms.
clockwise. The distances of the neighboring Ni(II) · · ·Ni(II) ions
are 8.14 Å (Ni(1)-Ni(2)) and 7.90 Å (Ni(2)-Ni(1′)). In the
peptide framework, amide groups support the macrocyclic
structure by six hydrogen bonds in the internal space of the
macrocyclic structure in the Ni(II) complex (Figure 2a).
The uniquely folded, twisted-boat structure allows the space
formation of two half-cylinder-shaped grooves and a central hole
along the c axis with a diameter of ca. 2 Å within the Ni(II)
complex, as drawn in Figure 2b. Four H2O molecules and five
ClO4- anions are encapsulated into these internal spaces. Of these
included guest molecules, two H2O and one ClO4- molecules are
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aligned in the order of H2O-H2O-ClO4 along the 2-fold axis
through the central hole (Figure 3a).11 The central H2O molecule
is doubly hydrogen bonded with the macrocyclic framework (Table
S1). It is also notable that the central H2O molecule is very close
to the terminal H2O molecule with an extremely short O · · ·O
distance of 2.58 Å, which is shorter than that seen in the Ih type of
ice crystal (ca. 2.7 Å).12 In the crystal packing structure, the holes
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along the 2-fold axis to form a channel, and therefore, the
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intermolecularly hydrogen bonded with one terminal H2O molecule
of the neighboring Ni(II) complex (Figure 3a). Such an in-line
molecular arrangement of H2O and ClO4– molecules was also found
in the top and bottom grooves, which are nearly vertical to the
hole forming the channel (Figure 2b). In the top groove, one H2O
-
and two ClO4 molecules are aligned in the order of
ClO4--H2O-ClO4-, while in the bottom groove, two H2O and
-
three ClO4
molecules are aligned in the order of
(8) Heinoen, P.; Rosenberg, J.; Lonnberg, H. Eur. J. Org. Chem. 2000, 3647.
(9) Crystal data for complex Ni414(ClO4)8(H2O)10: C48H128Cl8N28Ni4O54, Fw
) 2480.12, orthorhombic, space group Pba2, a ) 21.5700(8), b )
ClO4--H2O-ClO4--H2O-ClO4-. The terminal H2O and ClO4-
molecules in the central hole are identical to the central H2O
molecule in the top groove and the central ClO4- molecule in the
bottom groove, respectively.
22.1013(8), c ) 10.0759(3) Å, V ) 4803.4(3) Å3, Z ) 2, µ ) 1.109 cm-1
,
F(000) ) 2584.00, λ ) 0.71075 Å, GOF ) 1.092, R1 ) 0.0705 (I > 2F(I)),
wR2 ) 0.2274 (for all data) (for details, see Supporting Information). CCDC
673136 contains the supplementary crystallographic data for this paper.
These data can be obtained free of charge via www.ccdc.cam.ac.uk/
data_request/cif.
The electrospray ionization time-of-flight (ESI-TOF) mass
spectrum of the macrocyclic Ni(II) complex in CH3CN showed
prominent signals of Ni414 species at m/z 474.1 ([Ni414-
(ClO4)4]4+) and 665.0 ([Ni414(ClO4)5]3+) (Figure S8), indicating
that the macrocyclic tetranuclear Ni(II) complex exists in solution.
In summary, we synthesized a macrocyclic tetranuclear Ni(II)
complex of an artificial ꢀ-dipeptide 1 which possesses two sets
of tridendate ligands. Its cyclic twisted-boat structure provides
well-defined isolated spaces for in-line molecular arrangement
of water and anion molecules. Such an approach would open a
(10) The assignment of the absolute configurations was determined based on
the arrangement of the two sets of propanediamine units at each Ni(II)
center.
-
(11) In a preliminary study, the kind of counteranions (BF4-, PF6-, CF3SO3
)
was not found to affect the macrocyclic structure. However, for instance,
in the crystal which was obtained from a mixture of Ni414(ClO4)8(H2O)10
and NaBF4 salts in water, three H2O molecules were found aligned in the
hole. The effects of counteranion will be reported elsewhere.
(12) Ludwig, R. Angew. Chem., Int. Ed. 2001, 40, 1808.
(13) One enatiomeric Ni(II) complex is homogeneously stacked.
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