Helical pores self-assembled from homochiral dendritic dipeptides based on L-Tyr and nonpolar α-amino acids

Article abstract of DOI:10.1021/ja071088k

The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH ₂-Boc-L-Tyr-X-OMe where X = Gly, L-Val, L-Leu, L-lle, L-Phe, and L-Pro is reported. Their self-assembly in bulk and in solution and the structural and retrostructural analysis of their pe

Full text of DOI:10.1021/ja071088k

Published on Web 04/13/2007
Helical Pores Self-Assembled from Homochiral Dendritic
Dipeptides Based on L-Tyr and Nonpolar r-Amino Acids
Virgil Percec,*, Andr e´ s E. Dulcey, Mihai Peterca, Peter Adelman,†
†
†
†,‡
†
‡
‡
Ritika Samant, Venkatachalapathy S. K. Balagurusamy, and Paul A. Heiney
Contribution from the Roy and Diana Vagelos Laboratories, Department of Chemistry,
UniVersity of PennsylVania, Philadelphia, PennsylVania 19104-6323, and Department of Physics
and Astronomy, UniVersity of PennsylVania, Philadelphia, PennsylVania 19104-6396
Received February 14, 2007; E-mail: percec@sas.upenn.edu
Abstract: The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH -Boc-L-Tyr-X-OMe where X ) Gly,
2
L-Val, L-Leu, L-Ile, L-Phe, and L-Pro is reported. Their self-assembly in bulk and in solution and the structural
and retrostructural analysis of their periodic assemblies were compared to those of the previously reported
and currently reinvestigated dendritic dipeptides with X ) L-Ala. All dendritic dipeptides containing as X
nonpolar R-amino acids self-assemble into helical porous columns. The substituent of X programs the
structure of the helical pore and the resulting periodic array, in spite of the fact that its molar mass represents
only between 0.05 and 4.77% from the molar mass of the dendritic dipeptide. In addition to the various
2-D columnar lattices, the dendritic dipeptides based on L-Ala, L-Leu, and L-Phe self-organize into 3-D
hexagonal columnar crystals while those based on L-Val and L-Ile into an unknown columnar crystal. The
principles via which the aliphatic and aromatic substituents of X program the structure of the helical pores
indicate synthetic pathways to helical pores with bioinspired functions based on artificial nonpolar R-amino
acids.
Introduction
fluid membrane environment and in the solid state. However,
with few exceptions, porous protein mimics do not assemble
9
Natural porous proteins function as viral helical coats,1
into periodically ordered structures that are stable in solution
and in the solid state. This behavior limits their structural
analysis by combinations of solution and solid-state comple-
mentary techniques. Recently, our laboratory elaborated a new
strategy to helical porous protein mimics that is based on the
transmembrane channels responsible for ion regulation and
transport, molecular recognition and response, and energy
2
3
4
5
transduction, antibiotics, antimicrobials, and toxins. Remod-
eled porous proteins are used for reversible encapsulation of
molecules6 and in stochastic sensing.7 Integral membrane
10
self-assembly of amphiphilic dendritic dipeptides. The internal
structure and stability of the porous structure self-assembled
from dendritic dipeptides are programmed by the stereochem-
proteins, including those functioning as transmembrane channels,
exist in very low natural abundance, and since they form three-
dimensional functional structures only in the membrane envi-
ronment, their crystallization had limited success. Therefore,
the molecular details of their structure and function are not well
(
8) (a) Nolte, R. J. M.; van Beijnen, A. J. M.; Neevel, J. G.; Zwikker, J. W.;
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2
,3
understood. Simple synthetic assemblies that mimic the
structure and function of transmembrane channels are expected
to contribute to the understanding of the structure and function
of the more complex natural proteins. Strategies for the synthesis
and assembly of porous or tubular supramolecular structures
8
have been elaborated. Natural porous proteins are stable in the
†
Department of Chemistry.
Department of Physics and Astronomy.
‡
(
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A. Philos. Trans. R. Soc. London, Ser. B 1999, 354, 531-535.
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Khazanovich, N. Nature 1993, 366, 324-327. (b) Petitjean, A.; Cuccia,
L. A.; Lehn, J.-M.; Nierengarten, H.; Schmutz, M. Angew. Chem., Int. Ed.
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Chem.sEur. J. 1999, 5, 3471-3481. (d) Schmitt, J.-L.; Stadler, A.-M.;
Kyritsakas, N.; Lehn, J.-M. HelV. Chim. Acta 2003, 86, 1598-1624. (e)
Schmitt, J.-L.; Lehn, J.-M. HelV. Chim. Acta 2003, 86, 3417-3426.
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(
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J. AM. CHEM. SOC. 2007, 129, 5992-6002
10.1021/ja071088k CCC: $37.00 © 2007 American Chemical Society

Helical Pores Self-Assembled from Dendritic Dipeptides
A R T I C L E S
Scheme 1. Synthesis of Dendritic Dipeptides (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe, X ) Gly (14), L-Val (15), L-Leu (16), L-Ile (17), L-Phe
18), L-Pro (19)
(
istry11a and protective groups11b of the dipeptide, by the number
of methylenic units from the alkyl groups of the dendron,
and L-Pro, were investigated. The results of this study are
reported and compared with that of the dendritic dipeptide with
1
1c
1
0,11
and by the primary structure of the dendron attached to the
dipeptide.1 These experiments provided some of the molec-
ular principles required to program the self-assembly of helical
pores from dendritic dipeptides. This cooperative self-assembly
X ) L-Ala which was studied previously
and was reinves-
1d,e
tigated here.
Results and Discussion
11,12
process involves allosteric regulation.
In all previous studies
Synthesis of Dendritic Dipeptides (4-3,4-3,5)12G2-CH2-
Boc-L-Tyr-X-OMe with X ) Gly, L-Val, L-Leu, L-Ile, L-Phe,
and L-Pro. The dipeptides Boc-L-Tyr-Gly-OMe (7), Boc-L-Tyr-
L-Val-OMe (8), Boc-L-Tyr-L-Leu-OMe (9), Boc-L-Tyr-L-Ile-
OMe (10), Boc-L-Tyr-L-Phe-OMe (11), and Boc-L-Tyr-L-Pro-
OMe (12) were synthesized from Boc N-protected L-Tyr with
the hydrochloride of the methyl ester of the nonpolar R-amino
acids Gly (1), L-Val (2), L-Leu (3), L-Ile (4), L-Phe (5), and
L-Pro (6) in the presence of 2-chloro-4,5-dimethoxy-1,3,5-
the dendritic dipeptide was constructed from Boc-Tyr-Ala-OMe
dipeptide containing various combinations of Tyr and Ala
1
0,11a
11b
stereochemistry,
architectures.
different protective groups, and dendron
1
1c-e
In order to assess the scope, limitations, and
generality of this self-assembly strategy, the synthesis, self-
assembly, structural and retrostructural analysis of the dendritic
dipeptides (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe, in which
X are all nonpolar R-amino acids Gly, L-Val, L-Leu, L-Ile, L-Phe,
1
0,13
triazene (CDMT)
/N-methylmorpholine (NMM) in EtOAc
(
11) (a) Percec, V.; Dulcey, A. E.; Peterca, M.; Ilies, M.; Ladislaw, J.; Rosen,
at 23 °C (Scheme 1). All dipeptides were obtained in 60 to
70% yield after purification by column chromatography (SiO2/
gradient 2-4% MeOH in CHCl3). The dendritic dipeptides (4-
3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe (14-19) were synthe-
B. M.; Edlund, U.; Heiney, P. A. Angew. Chem., Int. Ed. 2005, 44, 6516-
6
521. (b) Percec, V.; Dulcey, A. E.; Peterca, M.; Ilies, M.; Sienkowska,
M. J.; Heiney, P. A. J. Am. Chem. Soc. 2005, 127, 17902-17909. (c) Percec,
V.; Dulcey, A. E.; Peterca, M.; Ilies, M.; Nummelin, S.; Sienkowska, M.
J.; Heiney, P. A. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 2518-2523. (d)
Percec, V.; Dulcey, A. E.; Peterca, M.; Ilies, M.; Miura, Y.; Edlund, U.;
Heiney, P. A. Aust. J. Chem. 2005, 58, 472-482. (e) Peterca, M.; Percec,
V.; Dulcey, A. E.; Nummelin, S.; Korey, S.; Ilies, M.; Heiney, P. A. J.
Am. Chem. Soc. 2006, 128, 6713-6720.
14
sized by Mitsunobu etherification of the benzyl alcohol group
of the second generation dendritic alcohol (4-3,4-3,5)12G2-CH2-
(
12) (a) Monod, J.; Changeux, J.-P.; Jacob, F. J. Mol. Biol. 1963, 6, 306-329.
(b) Perutz, M. Mechanisms of CooperatiVity and Allosteric Regulation in
(13) Kronin, J. S.; Ginah, F. O.; Murray, A. R.; Copp, J. D. Synth. Commun.
1996, 26, 3491-3494.
(14) Mitsunobu, O. Synthesis 1981, 1-28.
Proteins; Cambridge University Press: Cambridge, U.K., 1990. (c) Evans,
P. R. Curr. Opin. Struct. Biol. 1991, 1, 773-779.
J. AM. CHEM. SOC.
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VOL. 129, NO. 18, 2007 5993

A R T I C L E S
Percec et al.
Figure 1. DSC traces of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe. The structure of R-amino acid X from dipeptide, the phases, the transition temperatures
k
(
in °C), and the corresponding enthalpy changes (in kcal/mol, in brackets) are indicated; g ) glassy; Φh, hexagonal columnar liquid crystal phase; Φh ,
k
k
hexagonal columnar crystal phase; Φx , unknown columnar crystal phase; Φr-c, centered rectangular columnar liquid crystal phase. Φh phases separated by
endo or exo peaks exhibit different degrees of crystallinity and/or column and pore diameter.
OH15 with the hydroxyphenyl group of the dipeptides 7-12,
respectively. All dendritic dipeptides, with higher purities than
of the periodic arrays and their enthalpy changes were deter-
mined by DSC and are summarized in Table 1. Their structure
was assigned by XRD. For comparison, the DSC of (4-3,4-
99% (HPLC), were obtained in 30 to 50% yield after purification
by flash column chromatography (SiO2/gradient 2-4% MeOH
in CHCl3). Additional details for the synthesis and structural
analysis of the dipeptides and dendritic dipeptides by a
combination of 500 MHz H NMR, 125 MHz C NMR, HPLC,
MALDI-TOF, and elemental analysis are available in the
Supporting Information and in its Tables ST1 and ST2. The
CH2Cl2 solution of pure dendritic dipeptides was precipitated
in CH3OH, and the compounds were dried before being
subjected to structural analysis.
Structural Analysis in the Solid State by Differential
Scanning Calorimetry and Small-Angle X-ray Diffraction.
The as-prepared samples of all dendritic dipeptides are already
self-assembled into porous supramolecular columns that are self-
organized into various periodic columnar arrays. The structural
analysis of these periodic arrays was performed by a combina-
tion of differential scanning calorimetry (DSC) and powder
small-angle X-ray diffraction (XRD) experiments. Figure 1
illustrates the first heating and cooling and the second heating
scans of all (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe. The struc-
ture of the second R-amino acid from the dipeptide, X, is
marked on the left side of each DSC scan. The phase transitions
3,5)12G2-CH -Boc-L-Tyr-L-Ala-OMe is also included in
Figure 1.
2
A brief inspection of the data from Figure 1 reveals that the
structure of the substituent of the second R-amino acid from
the dipeptide determines the structure and the stability of the
periodic arrays assembled from dendritic dipeptides. This is a
remarkable result when we consider that the substituent of the
second R-amino acid contributes only 0.05% for Gly, 0.8% for
L-Ala, 2.31% for L-Val, 3.04% for L-Leu and L-Ile, 4.77% for
L-Phe, and 2.26% for L-Pro from the overall molecular mass of
the dendritic dipeptide. Moreover, based on the order of the
periodic array self-organized from the supramolecular columns,
the structure of the substituent of the second R-amino acid from
the dipeptide divides them in four groups. (1) Dendritic
dipeptides that produce only 2-D hexagonal columnar (Φh)
liquid crystalline periodic arrays. This group comprises dipep-
tides that contain as the second R-amino acid Gly, L-Ala, and
L-Pro. (2) Dendritic dipeptides that generate a biphasic mixture
1
13
made out of the Φh and an unknown yet columnar crystal phase
k
(
Φx ). Only the dipeptide containing L-Val exhibits this behavior
in the first heating scan. In subsequent heating and cooling scans
this dendritic dipeptide behaves similarly to group (1). (3)
Dendritic dipeptides that display a hexagonal columnar crystal
(
15) (a) Percec, V.; Cho, W.-D.; Ungar, G.; Yeardley, D. J. P. J. Am. Chem.
Soc. 2001, 123, 1302-1315. (b) Percec, V.; Mitchell, C. M.; Cho, W.-D.;
Uchida, S.; Glodde, M.; Ungar, G.; Zeng, X.; Liu, Y.; Balagurusamy, V.
S. K.; Heiney, P. A. J. Am. Chem. Soc. 2004, 126, 6078-6094.
k
k
phase (Φh ) or the Φx and a monotropic Φh phase. This group
5994 J. AM. CHEM. SOC.
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Helical Pores Self-Assembled from Dendritic Dipeptides
A R T I C L E S
Table 1. Thermal Transitions of
(4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe
thermal transitions (
°
C) and the corresponding
a
enthalpy changes (kcal/mol)
X
heating
cooling
b
101 (5.6) ic
Gly
Φ
Φ
Φ
Φ
h,g 55 Φ
h
i 98 (5.6) Φ
h
h
47 Φh,g
h,g 54 Φ
h,g 53 Φ
h,g 55 Φ
90 °C, 180 min] Φ
r-c,g 58 Φ
r-c,g 57 Φ
80 °C, 40 min] Φ
71 (2.2) Φ
66 (-1.6) Φ
90 °C, 30 min] Φ
h
101 (5.8) i
96 (5.7) i
96 (5.9) i
L-Ala
h
h
i 93 (5.7) Φ
i 83 (5.8) Φ
i 79 (5.0) Φ
i 76 (5.4) Φ
49 Φh,g
k d
[
h
105 (13.1)
e
k
L-Val
L-Leu
L-Ile
Φ
Φ
[
Φ
Φ
[
h
87 (2.2) Φ
x
100 (2.6) i
h
h
h
51 Φr-c,g
66 (3.1) Φ
45 Φh,g
h
87 (6.0) i
k f
x
99 (12.8)
k
k
k
k
h
h
107 (15.3) i
h
k
h
h
108 (18.6) i
k
x
108 (17.5)
k
Φ
Φ
h,g 49 Φ
h,g 48 Φ
h
77 (-0.9) Φ
80 (4.6) 84 (-6.2) Φ 99 +
x
x
104 (6.7) i
k
h
1
04 (9.3) i
k
[
90 °C, 30 min] Φ
67 (-5.4) Φ
102 (1.1) 105 (-2.0) Φ
110 °C, 30 min] Φ
h,g 44 Φ
h,g 47 Φ
x
104 (12.9)
121 (17.7) i
k
k
k
k
L-Phe
L-Pro
a
Φ
Φ
[
Φ
Φ
h
h
i 82 (14.7) Φ
h
k
h
h
121 (15.9) i
120 (16.7)
k
Figure 3. Stack of small-angle powder XRD of (4-3,4-3,5)12G2-CH2-
Boc-L-Tyr-X-OMe in various hexagonal columnar lattices. The structure
of R-aminoacid X from dipeptide, the temperatures, the lattices, and the
assignment of d-spacings are indicated. Φh, hexagonal columnar liquid
h
h
74 (4.9) i
74 (4.9) i
h
i 69 (4.7) Φ 41 Φh,g
h
k
crystal phase; Φh , hexagonal columnar crystal phase.
First line: data from the first heating and cooling scans. Second
line: data from the second heating (after the first cooling). Third line: data
from the first heating after annealing at the temperature and for the
b
time indicated in brackets before the transition. Φh, hexagonal columnar
c
d
k
phase; g, glassy. i, isotropic. Φh , hexagonal columnar crystal phase.
e
f
k
Φr-c, centered rectangular columnar phase. Φx , unknown columnar
crystal phase.
Figure 4. Wide-angle XRD of oriented fibers of (4-3,4-3,5)12G2-CH2-
Boc-L-Tyr-X-OMe in various columnar hexagonal phases. The structure
of R-amino acid X from dipeptide, recording temperature, and phase are
indicated. The nomenclature of phases is identical to that in Figure 1. i, 4.6
Å short-range helical feature; (10) peak of the Φh phase; m, high order
k
(
hk0) reflections of the Φh,g and Φh phases; l, 4.6 Å average column stratum
Figure 2. Heating DSC scans of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe
after the sample was annealed at the temperature and for the time indicated.
The gray squares indicate the annealing period and temperature. The
enthalpy associated with the isotropisation transition increased as compared
with the as-prepared samples (Figure 1). The structure of R-amino acid X
of the dipeptide is indicated. Φh, hexagonal columnar liquid crystal phase;
thickness; t, dendron tilt feature (48 ( 9°); e, 4.6 Å diffuse equatorial feature;
k, 5.0 Å stacking distance along the column axis, correlation length is ∼94
k
Å (∼19 layers); j, (hkl) reflections of Φh phase.
decreases as the molar mass of the substituent increases. There
is a small temperature difference between L-Leu and L-Ile,
although their substituents have equal molar mass but are
constitutional isomers. L-Pro provides an inversion in this trend
that is determined, as it will be discussed later, by the presence
of a tertiary rather than a secondary amide in its structure. This
decreases the number of the H-bonds from the inner part of the
pore. While the above dependence would intuitively be expected,
k
k
Φh , hexagonal columnar crystal phase; Φx , unknown columnar crystal
phase.
includes L-Leu and L-Ile. (4) Dendritic dipeptides that, regardless
k
of the thermal history of the sample, exhibit only a Φh phase.
This is the case of the dendritic dipeptide containing L-Phe.
The role of the substituent of the second R-amino acid of the
dipeptide on the thermal stability of its periodic array will be
discussed by considering the dependence of the transition
temperature from isotropic liquid to the Φh phase on the molar
mass of the substituent. This dependence follows the trend Gly
k
k
the dependence of the melting temperature of the Φh and Φx
phases on the size of the substituent is, at least at first sight,
unexpected. The following trend is observed in this case: L-Phe
(91/121) > L-Leu (57/107) > L-Ile (57/104) > L-Val (43/100),
where the ratio between parantheses is the same as that above.
The higher the molar mass of the substituent, the higher the
melting temperature of its corresponding periodic array. In
addition, the dendritic dipeptides with low molar mass substit-
(1/98) > L-Ala (15/93) > L-Val (43/83) > L-Leu (57/79) >
L-Ile (57/76) > L-Pro (42/69), where the ratio between paran-
theses refers to the molar mass of the substituent/transition
temperature (in °C). In general, the transition temperature
J. AM. CHEM. SOC.
9
VOL. 129, NO. 18, 2007 5995

A R T I C L E S
Percec et al.
Figure 5. CD spectra (1.6 × 10-4 m in cyclohexane) of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe. The structure of the R-aminoacid X from the dipeptide
and the temperature range are indicated. The insets illustrate the dependence of molecular ellipticity on temperature at a given wavelength. Tm is the middle
point of the S shape dependence of the molecular ellipticity on temperature.
k
Table 2. Structural and Retrostructural Analysis of the Φh, Φh , and Φr-c Lattices of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe
d
d
d
10a/A10c
20b/A20c
40b/A40c
d
d
d
11a/A11c
11b/A11c
22b/A22c
d
d
d
20a/A20c
31b/A31c
51b/A51c
d
d
d
21a/A21c
02b/A02c
42b/A42c
d
Fe (g/cm3)
µf
tg (Å)
R′h (deg)
X
T (°
C)
X
a
)
D
col (Å)
Dpore (Å)
Gly
L-Val
90
70
Φh
63.9/46.9
67.8/40.3
76.0/16.3
36.7/24.8
38.9/28.0
67.6/20.0
33.7/14.1
38.1/34.9
36.9/20.9
31.8/27.8
40.7/26.1
31.8/22.8
34.0/28.4
42.1/12.3
28.3/4.2
33.7/20.2
32.0/16.7
27.9/17.8
35.4/26.4
24.1/5.4
25.7/3.3
38.0/15.1
26.9/4.3
25.1/5.7
73.6 ( 0.4
78.3 ( 0.4
92.6 ( 0.6
75.9 ( 0.5
77.3 ( 0.4
74.0 ( 0.4
63.5 ( 0.4
81.4 ( 0.4
11.7 ( 0.8
14.2 ( 1.2k
15.3 ( 2.4
1.01
1.03
11.0
11.4
4.6
4.6
32.7
31.6
Φh
i
j
50
Φr-c
l
37.7/12.4
12.5 ( 1.9
L-Leu
L -Ile
L -Phe
L- Pro
85
75
65
25
Φhk
Φh
Φh
Φh
66.8/44.9
63.9/55.3
55.0/46.4
70.4/39.8
10.1 ( 1.6
12.4 ( 1.8
9.4 ( 0.8
15.1 ( 1.6
1.02
1.02
1.11
1.0
11.2
11.2
9.1
4.9
4.6
5.0
4.6
32.1
32.1
39.6
30.5
k
20.2/8.0
26.8/7.7
11.8
a ,b
c
d-spacings of the Φh and Φr-c phase, respectively (in Å). Peak amplitude scaled to the sum of the observed diffraction peaks (in arbitrary units).
d
e
f
Lattice parameter of Φh, a ) 2〈d100〉/
stratum µ ) (
x
3, 〈d100〉 ) (d100 +
x
3d110 +
x
4d200 +
x
7d210)/4. Experimental density at 22 °C. Number of dendrons per column
2
23
-1
g
x
3NAD tF)/2M, where NA ) 6.0220455 × 10 mol (Avogadro’s number), M is the molecular weight of the dendrons, and t is the average
h
i
height of the column stratum, calculated from the XRD of the oriented fibers as features k or l from Figures 4 and 10. R′ ) 2π/µ; Dcol along the long a
j
(along b)
(along a)
(along b)
and short b axis, Dcol
) b ) 75.9 Å, Dcol
) ꢀDcol
where ꢀ ) 1.2 ) is the fitted ellipticity ratio (see Supporting Information Figures SF7,
k
l
SF8 and Table ST3); Dpore along the a and b axis.
uents do not crystallize or, as it will be discussed later, crystallize
very slow. This trend is opposite to that observed for the
transition from the isotropic to Φh phase. The hypothesis for
the second trend is that large nonpolar substituents like those
of L-Val, L-Leu, L-Ile mediate a higher rate of crystallization,
most probably due to their hydrophobic character, while in the
case of the aromatic substituent of L-Phe it is due to π-π
stacking. This hypothesis will be discussed in one of the next
subchapters. In order to address the role of the substituent on
crystallization, all dendritic dipeptides were annealed at various
5996 J. AM. CHEM. SOC.
9
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Helical Pores Self-Assembled from Dendritic Dipeptides
A R T I C L E S
Figure 6. Cross sections of the molecular models of helical supramolecular pores assembled from (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe constructed
with the aid of XRD data from Table 2. The structure of R-aminoacid X from dipeptide, phases, temperatures, Dcol, and Dpore are indicated. Color code:
-
CH3 from the protective group of Tyr, blue; -CH3 of the methylester of the second R-amino acid, white; C, gray; O, red; N-H, green.
temperatures, both in the Φh phase and in the isotropic liquid.
Figure 2 illustrates the main results of these experiments. Only
the dendritic dipeptides based on Gly and L-Pro do not
crystallize. The dendritic dipeptides based on L-Ala, L-Val,
L-Leu, L-Ile, and L-Phe form Φh and Φx phases, respectively.
Details of their structural analysis will be presented in a different
subchapter. The lowest rate of crystallization was observed in
the case of dendritic dipeptide based on L-Ala, followed by
L-Val, L-Ile, L-Leu, and L-Phe.
lowest Dpore. An explanation of this trend will be provided in a
different subchapter.
Structural Analysis of Oriented Fibers by Small- and
Wide-Angle XRD. The combined small- and wide-angle XRD
data recorded from the oriented fibers of (4-3,4-3,5)12G2-CH2-
Boc-L-Tyr-X-OMe with X ) Gly, L-Val, L-Leu, L-Ile, L-Phe,
and L-Pro together with the assignment of the diffraction peaks
are shown in Figures 4, SF4, and SF6. The X shape of i
diffraction indicates that the columns obtained from X ) Gly,
L-Val, L-Leu, L-Ile, and L-Pro exhibit a short-range helical
structure. In the case of X ) L-Phe the i diffraction is most
probably overlapped by the intense j and k diffractions. The
average thickness of the column stratum is determined from
diffractions l and k and is summarized as value t in Table 2.
The dendron tilt (t) is most visible in the case of L-Val.
The helical structure of the supramolecular columns is also
supported by circular dichroism (CD) experiments that will be
discussed later for the case of X ) Gly, L-Val, L-Leu, L-Ile,
and L-Phe and compared with the CD experiments reported for
k
k
The powder small-angle XRD of all dendritic dipeptides
k
recorded at the indicated temperature in Φh and Φh phases are
shown in Figure 3. The enhanced amplitude of their (11), (20),
1
0,11
and (21) peaks provides an indication for a porous column.
The diameter of the pore (Dpore) was calculated by the
reconstruction of the XRD peak positions and intensities using
the electron density of the dendritic dipeptide and considering
a three-phase intracolumnar model consisting of regions of
aliphatic, aromatic together with dipeptide, and a hollow center,
by using the method reported previously (Figures SF7 and
1
0,11e
10
SF8).
The column diameter (Dcol) and Dpore calculated as
L-Ala.
1
mentioned above are summarized in Table 2 together with the
XRD data used for their calculation and the experimental
densities (F). It is interesting to observe that there is an unusual
correlation between Dpore and the size of the second R-amino
acid substituent. Gly that has H as the substituent provides a
smaller Dpore than those of L-Val, L-Ile, and L-Pro that have
larger substituents. L-Leu and L-Phe that have a methylene group
between a phenyl and isopropyl group, respectively, have the
Self-Assembly in Solution. A combination of 500 MHz H
NMR, CD, and UV spectroscopies was used to study the self-
1
0,11
assembly in the solvophobic solvent cyclohexane.
Here we
will discuss the analysis by CD (Figures 5, SF1 and SF2). The
achiral dendritic alcohols (4-3,4-3,5)nG2-CH2OH that are
precursors to the dendritic dipeptides self-assemble into racemic
11c
helical columns. Therefore, the stereochemistry of the dipep-
tide only selects the twist sense of the racemic supramolecular
J. AM. CHEM. SOC.
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A R T I C L E S
Percec et al.
Figure 7. One layer of the top view of the helical supramolecular pores assembled from (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe. The structure of R-aminoacid
X from the dipeptide, the number of dendritic dipeptides (µ) forming the cross section, and Dpore are indicated. Color code: -CH3 from the protective group
of Tyr, blue; -CH3 of the methylester of the second R-amino acid, white; C, gray; O, red; N-H, green.
helix.10,11 Additional examples of racemic helical supramolecular
dipeptides based on X ) L-Val and L-Ile exhibit similar Cotton
16
dendrimers assembled from achiral dendrons are known. This
self-assembly process relates to examples in which a stereocenter
effects, and their CD spectra are almost identical to that of (4-
1
1c
3,4-3,5)6G2-CH -Boc-L-Tyr-L-Ala-OMe. The CD of X )
2
17
selects the twist sense of a racemic helical structure and agrees
L-Leu resembles that of X ) L-Phe. These two pairs of similar
18a
with the principles elaborated by Green, although the de-
tailedmechanism is under elucidation.1 The assembly of the
helical supramolecular structures in the solvophobic solvent
cyclohexane was analyzed by CD (Figures 5, SF1, and SF2)
and UV (Figures SF1 and SF2).1
CD spectra show that related R-amino acid substituents (Scheme
1) induce similar conformations of the dendron in the supramo-
lecular structure. The CD of X ) Gly shows inversion of all
Cotton effects with λ < 260 nm when compared to the CD of
X ) L-Leu. All these trends demonstrate the role of the
substituent of X on the conformation of the dendron in the self-
assembled structure and support the allosteric regulation mech-
8b,c
0,11
For comparison, the CD of the dendritic dipeptide with X )
L-Ala is also included in Figure 5. The molecular solutions of
all dendritic dipeptides show a positive Cotton effect at 230
nm (Figures SF1 and SF2). On cooling, self-assembly takes
12
11a-c
anism advanced previously.
The similarity between the
CD pairs L-Val, L-Ile and L-Leu, L-Phe correlates with that of
their phase behavior in the solid state (Figure 1). The supramo-
lecular structures with large hydrophobic substituents are also
more stable in solution (see Tm in Figure 5). Gly provides an
exception from this trend. This dependence is also in line with
that observed in the solid state (Figure 1). L-Pro does not
assemble into a helical structure in the range of temperature
investigated in Figure 5. This is also expected, since it displays
a much less stable structure in the solid state (Figure 1), and
therefore, in solution the helical structure must form at lower
temperatures.
place and Cotton effects associated with the aromatic part of
the dendrons1
0,11
are observed. The CD spectra of dendritic
(
16) (a) Kwon, Y. K.; Chvalun, S.; Schneider, A.-I.; Blackwell, J.; Percec, V.;
Heck, J. A. Macromolecules 1994, 27, 6129-6132. (b) Kwon, Y. K.;
Chvalun, S. N.; Blackwell, J.; Percec, V.; Heck, J. A. Macromolecules
1
995, 28, 1552-1558. (c) Percec, V.; Glodde, M.; Bera, T. K.; Miura, Y.;
Shiyanovskaya, I.; Singer, K. D.; Balagurusamy, V. S. K.; Heiney, P. A.;
Schnell, I.; Rapp, A.; Spiess, H.-W.; Hudson, S. D.; Duan, H. Nature 2002,
4
19, 384-387. (d) Percec, V.; Glodde, M.; Peterca, M.; Rapp, A.; Schnell,
I.; Spiess, H. W.; Bera, T. K.; Miura, Y.; Balagurusamy, V. S. K.; Aqad,
E.; Heiney, P. A. Chem.sEur. J. 2006, 12, 6298-6314. (e) Percec, V.;
Peterca, M.; Sienkowska, M. J.; Ilies, M. A.; Aqad, E.; Smidrkal, J.; Heiney,
P. A. J. Am. Chem. Soc. 2006, 128, 3324-3334.
(
17) (a) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem.
ReV. 2001, 101, 3893-4012. (b) Brunsveld, L.; Zhang, H.; Glasbeek, M.;
Vekemans, J. A. J. M.; Meijer, E. W. J. Am. Chem. Soc. 2000, 122, 6175-
Structural and Retrostructural Analysis of the Supramo-
lecular Pores. In addition to Dcol and Dpore calculated from
small-angle XRD experiments, Table 2 summarizes the number
of dendrons (µ) forming a column cross section of average
height (t) determined from wide-angle XRDs on oriented fibers
6
182. (c) Percec, V.; Rudick, J. G.; Peterca, M.; Wagner, M.; Obata, M.;
Mitchell, C. M.; Cho, W.-D.; Balagurusamy, V. S. K.; Heiney, P. A. J.
Am. Chem. Soc. 2005, 127, 15257-15264. (d) Jin, W. I.; Fukushima, T.;
Niki, M.; Kosaka, A. I.; Ishii, N. I.; Aida, T. Proc. Natl. Acad. Sci. U.S.A.
2
005, 102, 10801-10806.
(
18) (a) Green, M. M.; Park, J.-W.; Sato, T. I.; Teramoto, A. I.; Lifson, S.;
Selinger, R. L. B.; Selinger, J. V. Angew. Chem., Int. Ed. 1999, 38, 3139-
(l and k in Figures 4, SF4, and SF6) and the experimental
3
154. (b) Jonkheijm, P.; van der Schoot, P.; Schenning, A. P. H. J.; Meijer,
10,11,15,16e
densities (F).
These data were used to generate the
E. W. Science 2006, 313, 80-83. (c) Percec, V.; Ungar, G.; Peterca, M.
1
0,11
Science 2006, 313, 55-56.
molecular models shown in Figure 6.
These models dem-
5998 J. AM. CHEM. SOC.
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Helical Pores Self-Assembled from Dendritic Dipeptides
A R T I C L E S
Figure 8. Conformation of the dipeptides in the helical supramolecular pores assembled from (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe (data from Figures
6
and 7; L-Val in Φh phase). The structure of R-aminoacid X from dipeptide and the structure of the dendritic dipeptides are indicated. Color code: -CH3
from the protective group of Tyr, blue; -CH3 of the methylester of the second R-amino acid, white; C, gray; O, red; N-H, green.
Figure 9. Alternative conformation of the dendritic dipeptide in the helical
supramolecular pores assembled from (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-L-
Phe-OMe: one column stratum top view (a), pore cross section (b), detail
of the dipeptide conformation (c), and detail of the H-bonding network
(length in Å) (d).
onstrate that larger hydrophobic substituents cover the inner part
of the pore more efficiently than Gly. Most probably this is
responsible for their contribution to the stabilization of the 3-D
structure and the enhanced tendency toward crystallization.
Extremely interesting is the case of L-Phe that, according to
this model, generates a helical π-π stack of phenyl groups
located in the inner part of the pore. The top views of a single
layer of these supramolecular columns from Figure 6 are shown
in Figures 7 and SF11. The conformation of the individual
Figure 10. Heating DSC traces of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe
with (a) X ) L-Ala and (b) X ) L-Val. Both in (a) and (b) the top DSC
traces represent second heating scans of the as-prepared samples, while
the subsequent DSC traces illustrate heating scans after the sample was
annealed at the mentioned temperature, for the indicated time; the bottom
DSC traces show heating scans after the final annealed sample was cooled
from the isotropic state.
dipeptides from the supramolecular structures from Figure 6
are illustrated in Figure 8 together with an alternative model
J. AM. CHEM. SOC.
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A R T I C L E S
Percec et al.
Figure 11. Combined small- and wide-angle XRD patterns of oriented fibers of (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe obtained after annealing at
the indicated temperatures for 1 h or as marked (columns a and c). The structure of R-amino acid X from dipeptide is indicated. The phase notations are
as those in Figure 1. Small-angle XRD patterns of the same oriented fibers collected before and after annealing at the indicated temperatures for 1 h
or as marked (columns b and d). Meridional q-plots for X ) L-Ala demonstrating crystallization during annealing as indicated by the k1, k2, k3 sharp
peaks (e). In all structures k ) 5.0 Å represents stacking registry along the column axis; e, diffuse equatorial feature; (10), (11), (20), (21), (hk0) reflections
k
of the Φh phase; j, (hkl) reflections of Φh phase; m, higher order (hk0) reflections of the Φh phase. For X ) L-Val the correlation length of the wide
k
angle meridional k feature (∼80 Å) has the same order as the ΦX lattice diffraction peak (∼76 Å at 85 °C) calculated from the shown small angle
pattern.
for the case of L-Phe. In all cases, except for L-Phe where two
models are possible, the substituent of the R-amino acid is in
the inner part of the pore, and this explains its contribution to
the pore structure and stability. The dependence of Dpore on µ
and on the projection of the solid angle of the dendron (R′)
suggests, as observed previously,1 that as R′ decreases, µ and
Dpore increase. Two conformers are shown in Figure 8 for L-Phe.
The left one is for the model from Figures 6 and 7. The right
one is for the model from Figure 9 in which the phenyl of L-Phe
forms a π-π stack with the phenyloxy group of L-Tyr in the
outer part of the pore. This model is favored since it facilitates
aromatic-aromatic rather than aromatic-aliphatic interactions.
This model also explains the lower Dcol self-assembled from
this dendritic dipeptide (Table 2). Additional support for this
model and elaboration of novel functional architectural motifs
based on it will be reported.
Crystalline phases with hexagonal symmetry are expected
to provide porous structures stable up to their melting temper-
ature. Therefore, the crystallization of all dendritic dipeptides
was investigated in Φh and in isotropic melt (Figures SF9,
SF10, SF12-SF14). Figure 10 shows the annealing of X )
L-Ala and L-Val in their Φh phase and the analysis of the
crystallization process by DSC. The dendritic dipeptide with X
) L-Ala requires 3 h of annealing at 95 °C for complete
1b,c
k
transformation of the Φh phase into Φh (Figures 10 and 11).
Shorter annealing time produces a biphasic mixture containing
k
Φh and Φh phases. However, the columnar hexagonal symmetry
is maintained in the crystal state. The same annealing process
for the case of X ) L-Val induces a complete crystallization
after 40 min at 80 °C. However, the crystal phase maintains a
k
columnar structure (Φx ) that was not yet elucidated (Figures
10 and 11).
k
Crystalline Supramolecular Pores and Their Impact on
Pore Stability. In previous experiments the supramolecular
The same Φx phase was obtained in the case of X ) L-Ile
(Figure 10). L-Phe and L-Leu crystallize in a Φh phase. This
k
pores forming Φh phases were stable below their glass transition
Due to molecular motion in the Φh
phase, above Tg, Dpore is temperature dependent. However,
crystallization process can be induced also by annealing in the
isotropic liquid (Figure SF 14). However, the crystal phase is
less ordered when crystallization is induced in the isotropic melt.
Regardless of the annealing temperature, the dendritic dipeptides
based on Gly and L-Pro do not crystallize.
temperature (Tg).1
1a,b
supramolecular pores forming Φh phases with intracolumnar
io
11b
order (Φh ) are stable up to the isotropization temperature.
6000 J. AM. CHEM. SOC.
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Helical Pores Self-Assembled from Dendritic Dipeptides
A R T I C L E S
Figure 13. In-layer (double arrows) and interlayer (single arrows)
H-bonding networks of the (4-3,4-3,5)12G2-CH2-Boc-L-Tyr-X-OMe. The
structure of X and H-bonding lengths (Å) are indicated. Four dipeptides
from two interdigitated layers of the channel are shown. For simplicity,
only the H-bonded hydrogen atoms are shown; the 4-phenyloxy group of
L-Tyr is not shown. Color code: O, red; NH, green; each of the four
dipeptides has its C atoms colored differently. For the case of X ) L-Phe
the model is from Figures 6, 7.
by other intermolecular interactions. The bulky substituent of
L-Phe eliminates four interlayer and one in-layer H-bonds.
However, by contrast with the case of L-Pro, in the L-Phe case
the π-π interactions created by its phenyl substituent overcome
the reduced number of H-bonds and even enhance the tendency
toward crystallization. The large and flexible alkyl substituents
also facilitate the crystallization process. These trends will be
exploited in the design of novel artificial R-amino acids that
are expected to provide even more powerful pore stabilization
strategies and new bioinspired pore functions.
Figure 12. Dependence of (a) Dcol and (b) Dpore on the temperature for
the helical porous columns assembled from (4-3,4-3,5)12G2-CH2-Boc-L-
Tyr-X-OMe. The structure of X is indicated. For X ) L-Val below 50 °C,
the Dcol and Dpore of the Φr-c phase are shown as calculated along the long
a (circles) and short b (triangles) axis of the Φr-c, respectively. For X )
L-Ala the annealing was done in the Φh phase at 90 °C for 4 h.
The dependence of Dcol and Dpore on temperature was
investigated both before and after crystallization for the case
Conclusions
k
of L-Ala, in the Φh and Φr-c phases for L-Val, in the Φh phases
for L-Phe and L-Leu, and in the Φh phase for the case of Gly
and L-Pro (Figures 12, SF9, and SF10).
In the Φh phase Dpore is not dependent on temperature up to
Tg, while in the Φhk phase Dpore is stable up to the melting
temperature. In the 2-D Φh phase the stability of Dpore is
The synthesis of dendritic dipeptides (4-3,4-3,5)12G2-CH2-
Boc-L-Tyr-X-OMe where X ) Gly, L-Val, L-Leu, L-Ile, L-Phe,
and L-Pro and their self-assembly in solution and in bulk are
reported. The structural and retrostructural analysis of the
supramolecular helical pores self-assembled from these dendritic
dipeptides was compared with that of the reinvestigated dendritic
determined by the intracolumnar order that includes the network
of H-bonds of the interdigitated dipeptides.1
0,11
In the current
dipeptide with X ) L-Ala that was reported previously.
10,11a-c
case the substituent of X influences the number of the inter-
peptide H-bonds and provides additional and complementary
intermolecular interactions such as hydrophobicity in the case
of alkyl substituents and π-π stacking in the case of aryl
substituents.
All dendritic dipeptides were shown to self-assemble into helical
pores that self-organize for the case of Gly and L-Pro into 2-D
Φh and Φr-c lattices, for the case of L-Ala, L-Leu, and L-Phe
k
into 2-D Φh and 3-D Φh lattices, and for the case of L-Val and
k
L-Ile into 2-D Φh and Φr-c and in 3-D Φx lattices. These
The H-bonding structures for two pairs of interdigitated
dendritic dipeptides provide the first examples of supramolecular
helical pores that self-organize into crystal lattices. This result
is important both for practical applications and for access to a
more detailed structural analysis by XRD. In 2-D lattices, Dpore
is stable only up to the glass transition temperature while, in
3-D crystals, it is stable up to the melting point. Unexpectedly,
the smaller substituents of X provide more stable 2-D arrays,
while the larger substituents facilitate crystallization via a
hydrophobic process in the case of aliphatic substituents and
1
0,11
peptides
are shown in Figure 13 for the case of X ) Gly,
L-Val, L-Leu, L-Ile, L-Phe, and L-Pro. In the case of X ) Gly,
L-Val, L-Leu, and L-Ile there are four in-layer and five interlayer
H-bonds. In the case of L-Pro the tertiary peptide facilitates only
two in-layer and two interlayer H-bonds. In addition, the bulky
and conformationally restricted cyclic substituent of L-Pro
explains the low thermal stability of its supramolecular pore
since the reduced number of H-bonds is not counterbalanced
J. AM. CHEM. SOC.
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A R T I C L E S
Percec et al.
respectively via π-π interactions in the case of aromatic sub-
stituents. Larger substituents provide higher melting tempera-
tures of crystal phases, while smaller substituents provide higher
isotropization temperatures of columnar liquid crystal phases.
This study complements the previous investigations on the role
and, therefore, expand the scope and limitations of self-
assembling dendrons in the design of complex functional
matter.
2
0
Acknowledgment. Financial support by the National Science
Foundation (DMR-0548559 and DMR-0520020) and P. Roy
Vagelos Chair at Penn, and discussions with Professor G. Ungar
of Sheffield University, U.K. are gratefully acknowledged.
11a
11b
of dipeptide stereochemistry, protective groups, dendron
architecture and its alkyl groups1
1c-e
and provides the molecular
principles required to design new biologically inspired func-
1
0
Supporting Information Available: Experimental section
containing materials, techniques, and synthesis with structural
and retrostructural analysis. This material is available free of
charge via the Internet at http://pubs.acs.org.
tions with the aid of artificial nonpolar R-amino acids. Since
these supramolecular helical pores represent dendronized su-
pramolecular polymers, it is expected that this concept can be
17c,19
extended to self-organizable dendronized covalent polymers
JA071088K
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A.; Ungar, G.; Yeardley, D. J. P. J. Am. Chem. Soc. 1998, 120, 8619-
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