Peptide dendrimers with designer core for directed self-assembly

Article abstract of DOI:10.1016/j.tet.2015.09.043

A series of designer peptide dendrimers with urea and urea-triazole cores were synthesized. Urea cored dendrimers assembled into fibrillar morphology, while dendrimers with urea-triazole core assembled into vesicular morphology. The core-dependent self-as

Full text of DOI:10.1016/j.tet.2015.09.043

Accepted Manuscript
Peptide dendrimers with designer core for directed self-assembly
Ram P. Verma, Ashutosh Shandilya, V. Haridas
PII:
S0040-4020(15)30071-5
10.1016/j.tet.2015.09.043
TET 27140
DOI:
Reference:
To appear in: Tetrahedron
Received Date: 29 July 2015
Revised Date: 18 September 2015
Accepted Date: 21 September 2015
Please cite this article as: Verma RP, Shandilya A, Haridas V, Peptide dendrimers with designer core for
directed self-assembly, Tetrahedron (2015), doi: 10.1016/j.tet.2015.09.043.
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Peptide dendrimers with designer core for directed self-assembly
Ram P. Verma, Ashutosh Shandilya and V. Haridas*
1

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Tetrahedron
journal homepage: www.elsevier.com
Peptide dendrimers with designer core for directed self-assembly
Ram P. Verma, Ashutosh Shandilya and V. Haridas*
Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
A series of designer peptide dendrimers with urea and urea-triazole cores were
synthesized. Urea cored dendrimers assembled into fibrillar morphology, while
dendrimers with urea-triazole core assembled into vesicular morphology. The core-
dependent self-assembly behaviour is studied by ultramicroscopy, X-ray crystallography
and supported by molecular dynamics simulation.
Available online
2010 Elsevier Ltd. All rights reserved.
Keywords:
Peptide
Dendrimer
Click reaction
Triazole
Urea
1. Introduction
Peptide dendrimers serve as models for proteins and therefore
have innumerable possibilities for applications in the area of biology
and nanotechnology. Peptide dendrimers are particularly attractive
because of the use of amino acid building blocks and their potential
to self-assemble due to the presence of several peptide bonds in their
structure. The synthesis and purification of peptide dendrimers are
difficult due to the presence of a large number of functional groups
on their surface and their branched architecture. The challenges
involved in the synthesis and their several applications make peptide
dendrimers, very interesting candidates for the chemists. Over the
last two decades, there have been significant developments in the
area of functional dendrimers.1-3 The design of functional dendrimers
is a challenge, since the central core and surface functional groups
are of critical in determining the topology and properties of these
branched molecules.4-5 Apart from this, the stitching of two large
peptide fragments without racemization using a clean reaction poss a
challenge.6-7
Here, in this paper, we report the urea and urea-triazole as central
cores in the design of self-assembling peptide dendrimers. We
envisioned that a carbonyl unit is one of the smallest structural entity
that can be used for linking two peptide dendrons through their N-
termini. The resultant linkage of dendrons through N-terminals by a
carbonyl unit results in a urea core which has additional benefits,
__________________________________________________
Corresponding author: Tel. 91-011-26591380, e-mail address:
h_haridas@hotmail.com, haridasv@iitd.ac.in
Figure 1: (a) Extended hydrogen bonding present in urea-type
molecules (b) Cartoon representation of the synthesis of urea cored
peptide dendrimers.
such as strong intrinsic self-assembly and anionic guest binding
properties.8-9 The urea linkage can arrange the dendrimers in a
supramolecular arrangement as a result of the urea α-type hydrogen
bonding pattern (Fig. 1a).10 Hence urea unit is one of the minimal
and benign structural entities that can be envisaged as a central core
for the design of self-assembling dendrimers.
In the second design, we introduced a urea-triazole unit with the
notion that it will induce a curvature to the overall assembly (Fig.
3a). The hydrogen bonding ability of urea along with the pentagonal
shape of triazole will induce a unique self-assembling pattern.
Cycloaddition of azides and alkynes in the presence of Cu(I) salt to
give triazoles is an effective synthetic strategy with several
applications.11
2

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Scheme 1. Synthesis of first generation urea cored dendrimers S3a-e.
Scheme 3. (a) Cartoon representation of synthesis of urea-triazole
cored peptide dendrimers, (b) synthesis of first (ST14) and second
(ST15-ST18) generation urea-triazole cored peptide dendrimers.
In the next step, we have undertaken the synthesis of urea-triazole
cored peptide dendrimers. Dialkyne units on both sides of urea were
introduced by reacting propargyl amine with triphosgene to generate
urea-based dialkyne S3f. In order to equip dendrons for the dipolar
cycloaddition reaction, an azide group was attached to the N-
terminus of the dendron. The N-terminal benzyloxycarbonyl group
(Z) of S5a, S5b and S8 was deprotected using H2/Pd/C and coupled
to azidoacetyl chloride to generate the dendrons S7a, S7b and S10 in
~70 % yield (Scheme 2). Urea cored dialkyne S3f was reacted with
dendrons equiped with azide to generate a series of urea-triazole
cored dendrimers ST14-ST18 (Scheme 3).
Higher generation dendrimer ST18 was synthesized to demonstrate
the versatility of this approach (Scheme 3). The reaction of H2N-
Glu.(Glu.diOMe)(Glu.diOMe) with 5-azidomethylbenzene-1,3-
dicarbonyldichloride afforded the dendron carrying an azide
functionality S12 (Scheme S1, Supplementary data).12 This S12
upon reaction dialkyne afforded ST18. The post reaction work up
afforded reasonably pure compounds and further purification was
done by passing the compounds through small silica gel column to
afford pure dendrimers.
Scheme 2. Synthesis of dendrons S7a-b, S10 and second generation
urea dendrimers S6a-b.
2. Results and Discussion
We envisioned that the peptide dendrimers with a urea core will
assemble as a result of urea-type hydrogen bonds that may lead to
fibrillar morphology.13 Dendrimers with urea and urea-triazole cores
were evaluated for their self-assembling properties by X-ray
crystallography and various ultramicroscopic techniques like
Scanning Electron Microscopy (SEM), Transmission Electron
Microscopy (TEM) and Atomic Force Microscopy (AFM) (Figs. 2-4
and Figs. S1-S5, Supplementary data). The X-ray structures revealed
that S3a, S3b and S3e form supramolecular arrays as a result of
intermolecular hydrogen bonding between the urea core (Table S1,
Supplementary data). The first generation dendrimers (S3a, S3b and
S3e) were crystallized from 1:1 CHCl3+EtOAc at room temperature
(Tables S2-S4, Supplementary data). X-ray structures revealed that
the molecules are arranged in a contiguous sheet assembly held
together by six-membered hydrogen bonded ring between the urea
COs and NHs (Figs. S2-S5, Supplementary data).
The first generation urea-based dendrimers were synthesized by
reacting several C-protected amino acids with triphosgene in
dichloromethane (Scheme 1). Compounds S3a-e (Scheme 1) were
obtained in ~ 60-64 % yield by reacting the corresponding amino
acid methyl esters with triphosgene. Glutamic acid and aspartic acid
are good choices for the synthesis of peptide dendrimers because
these residues have additional carboxylic acid group in its structure;
hence, can act as branching units.6 The Nα Z-Glu/Asp acids S4a/S4b
were reacted with the dimethyl esters of Asp/Glu to produce
dendrons with four methyl esters on the surface S5a/S5b (Scheme 2).
In the similar way, Asp-Leu based dendron S8 was also synthesized.
Deprotection of dendrons S5a-b using Pd/C/H2 followed by
treatment with triphosgene yielded urea cored dendrimers (S6a-b) in
~ 68-70 % yield (Scheme 2). The bidirectional linking ability, easy
reaction and atom economy are attributes of this reaction.
3

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b
d
f
a
c
e
a
b
c
d
Figure 3: (a) SEM image of gel from S6a (b) FE-SEM image of gel
from S6b, Inset shows photograph of the gel from S6b in (7.2 mM of
S6b chloroform: hexane, 6:4) in an inverted tube (c) TEM image of
gel from S6b (d) AFM image in tapping mode of gel made from
S6b.
In the next step, we turned our attention to urea-triazole based
dendrimers. The first generation dendrimer ST14, the second
generation dendrimers ST15-16, the leucine containing dendrimer
ST17 and structurally more complex ST18 were designed and
synthesized. SEM, AFM and TEM images of both lower and higher
generation Asp/Glu dendrimers ST14-17 showed vesicular assembly
in CHCl3+MeOH (Fig. 4 and Fig. S1b-e Supplementary data). The
diameters of the vesicles are in the range of 0.5-2.0 µm. Dendrimer
S18 was insoluble in CHCl3+MeOH, hence ultramicroscopy was not
recorded.
Figure 2: SEM images of (a) S3a (b) S3b (c) S3c (d) S3e (e) S6a
and (f) S6b.
Initially, urea cored first generation dendrimers S3a-e were studied
using ultramicroscopy. SEM images of S3a-d showed tape-like self-
assembly, while S3e showed rigid flat-tape morphology in
CHCl3+MeOH (Fig. 2a-c, 2d and Fig. S1a, Supplementary data). The
widths of individual tapes were in the range of ~ 1-10 µm. Self-
assembly of dendrimers of varying size were investigated in order to
study the effect of molecular size and shape on the self-assembling
pattern.14 The long tape-like structure observed in the first generation
dendrimers (S3a-e) might be arising due to intermolecular
association of molecules from hydrogen bonds. X-ray
crystallographic analysis also revealed an extended assembly. The
higher generation urea cored dendrimers (S6a-b) revealed different
morphological features compared to first generation dendrimers.
Interestingly, higher generation dendrimers (S6a-b) showed fibers ~
300-500 nm which were bundled together to form a flower-like
morphology in CHCl3+MeOH (Fig. 2e-f). Higher generation
dendrimers S6a and S6b showed fibrillar, but flower like assembly,
and is attributed to the fact that the bulky dendron on both sides of
the core may sterically disallow extended arrangement as observed in
the lower generation dendrimers (Fig. 2e-f).
(b)
(a)
We also envisioned that dendrimers with a self-assembling core
might gelate organic solvents due to their large size, surface area and
hydrogen bonding capabilities.15 Gels are promising materials for
several biomedical applications.16 Dendritic gels can be used for
controlled release of molecules, hence useful in drug delivery
applications.Therefore, all the urea cored dendrimers were screened
for gelation in organic solvents. It was found that the second
generation dendrimers S6a and S6b both showed gelation in organic
solvents. It is noteworthy that peptide dendrimers S6a-b displayed
gelling properties, when hexane was slowly added to homogeneous
solutions of S6a and S6b in chloroform separately. Gelation ability
of the dendrimers was tested in various solvents by the vial inversion
method (Fig. 3b, inset, Table S5, Supplementary data). The gels of
S6a-b were examined by SEM, TEM and AFM. The organgels from
S6a-b have fibrous morphologies with fibers wound around each
other to form entangled ribbon networks with fibers having widths
mostly in the range of ~ 0.2-1.0 µm. The fibrous morphology is
evident from TEM, AFM and SEM images (Fig. 3a-d).
Figure 4: (a) SEM image of ST14 (b) SEM images of ST17.
Molecular Dynamics (MD) simulations using Amber (ff99SB) force
field were performed on these dendrimers to rationalize the observed
self-assembly behavior.17 In order to carefully analyze the factors
responsible for the unique core-dependent self-assembly, we first
investigated the conformation of the core units. The results of
molecular modeling revealed that the urea cored and urea-triazole
cored dendrimers adopted different conformations (Fig. S6-S7,
Supplementary data). The urea cored dendrimers S3b and S6b
adopted an extended conformation (Figs. S6a-b and S7a,
Supplementary data), while the urea-triazole cored dendrimers ST14
and ST16 showed a turn conformation (Figs. S6c-d and S7b,
Supplementary data).
An 80 Å cubic box, containing approximately 4000 solvent
molecules (CHCl3 + MeOH) and 300 urea cored molecules S3b were
randomly placed. After heating, 10 ns of equilibration, and 90 ns of
production run resulted in several small and large clusters of these
4

molecules. The simulation clearly
assembled into ordered structures instead of disordered aggregates.
that dendrimers
(s, 4H), 3.68 (s, 6H), 3.76 (s, 6H), 4.51 (br s, 2H), 5.63 (d, 2H, J =
revealedACCEPTED MANUSCRIPT
4.2 Hz); 13C NMR (CDCl3, 75 MHz) δ 27.9, 29.9, 51.7, 52.3, 52.4,
156.8, 173.4, 173.5; IR (KBr): 3282, 3148, 3049, 2955, 1739, 1647,
1594, 1439, 1407, 1217, 1175, 1050 cm-1; HRMS: Calcd for
C15H24N2O9Na m/z 399.1380, found m/z 399.1386.
o
S3c.Yield: 60 %. mp: 58-62 C; [α]D = + 10.00 (c 0.20, CHCl3); ¹H
NMR (CDCl3, 300 MHz,) δ 0.93 (m, 12H), 1.44-1.73 (m, 6H), 3.73
(s, 6H), 4.45-4.52 (m, 2H), 5.07 (d, 2H, J = 7.5 Hz); 13C NMR
(CDCl3, 75 MHz) δ 22.0, 22.8, 24.7, 42.2, 51.5, 52.2, 156.9, 174.9;
IR (KBr): 3357, 3136, 2960, 2874, 1754, 1713, 1626, 1575, 1443,
1374, 1277, 1245, 1172, 1097, 1027 cm-1; HRMS: Calcd for
C15H29N2O5 m/z 317.2076, found m/z 317.2108.
o
S3d. Yield: 66 %. mp: 186-190 C; ¹H NMR (CDCl3, 300 MHz) δ
2.99 (d, 4H, J = 5.7 Hz), 3.62 (s, 6H), 4.80 (q, 2H, J = 13.9 Hz), 5.45
(d, 2H, J = 7.8 Hz), 7.07 (d, 4H, J = 6.6 Hz), 7.17-7.27 (m, 6H); IR
(KBr): 3322, 2959, 1741, 1698, 1654, 1533, 1439, 1358, 1319,
1259, 1174, 1020 cm-1; HRMS: Calcd for C21H24N2O5Na m/z
407.1577, found m/z 407.1572.
Figure 5: The vesicular assembly of urea-triazole cored dendrimer
ST14 (front view). The fully formed vesicle is presented. The red
color represents oxygen, the blue nitrogen and green carbon
backbone.
o
S3e. Yield: 64 %. mp: 186-190 C; [α]D = + 07.69 (c 0.10, CHCl3).
¹H NMR (CDCl3, 300 MHz) δ 1.39 (d, 6H, J = 7.2 Hz), 3.77 (s, 6H),
4.44-4.54 (m, 2H), 5.36 (d, 2H, J = 7.5 Hz); 13C NMR (CDCl3, 75
MHz) δ 25.5, 52.4, 56.0, 156.0, 176.9; IR (KBr): 3368, 3336, 2989,
2954, 1738, 1643, 1563, 1466, 1435, 1388, 1293, 1219, 1152 cm-1;
HRMS: Calcd for C9H16N2O5Na m/z 255.0957, found m/z 255.0955.
The extended conformation of urea cored molecules facilitated the
fibrillar assembly (Fig. S8, Supplementary data). On the other hand
the urea-triazole cored molecule ST14 adopted turn architecture,
which further assembled to vesicles with the solvent molecules
(mostly MeOH) inside. In a similar way, 400 urea-triazole cored
dendrimers ST14 were fixed inside 100 Å cubic box and were
arranged in such a way that nonpolar groups interacted with
chloroform and hydrophilic groups interacted with methanol.
Interestingly, complete and incomplete vesicles were apparent after
100 ns of MD simulations (Fig. 5 and S9, Supplementary data).
4.2 Synthesis of dialkyne S3f
A solution of propargyl amine (10 mL, 0.15 mmol) in dry
dicholoromethane was added drop-wise to a stirred solution of
triphosgene (0.016 g, 0.056 mmol) in two phase solution of dry
CH2Cl2 (20 mL) and saturated solution of NaHCO3 (40 mL). After 5
min. of stirring, a solution of propargyl amine (10 mL, 0.15 mmol)
was added further in to the reactiom mixture and stirred for
additional 4 h. The organic phase was then washed with water, dried
with anhydrous Na2SO4 and evaporated to give crude product, which
was purified by column chromatography.Yield: 46 %. mp: 186-188
oC; ¹H NMR (300 MHz, DMSO-d6): δ 3.05 (br s, 2H), 3.79 (br d,
4H), 6.35 (br s, 2H); 13C NMR (DMSO-d6,75 MHz): δ 28.8, 72.5,
82.3, 156.9; IR (KBr): 3324, 3149, 3010, 2923, 2117, 1618, 1426,
1357, 1297, 1256, 1062 cm-1; HRMS: Calcd for C7H9N2O m/z
137.0715, found m/z 137.0710.
3. Conclusions
We have designed and synthesized a variety of urea and urea-
triazole cored dendrimers. Our investigations revealed that the
dendrimer core can inculcate unique self-assembly patterns to the
dendrimers. Urea-based dendrimers showed fibrous morphology and
gelling properties, while urea-triazole based dendrimers displayed a
vesicular assembly. Ultra microscopy and X-ray structure analysis
provided connvincing evidences and MD simulations supported the
experimental findings. The studies presented in this paper points to
the fact that core unit has a profound role on self-assembly, hence
designer cores will be a new paradigm for the dendrimer design.
4.3 Synthesis of dendrons
4.3.1 Synthesis of S5a. To a well-stirred and ice-cooled solution of
Z-Aspartic acid S4a (1.50 g, 5.62 mmol) in 70 mL dry CH2Cl2 was
added N-hydroxysuccinimide (1.42 g, 12.35 mmol), DCC (2.54 g,
12.35 mmol), Asp.diOMe.HCl (2.44 g, 14.02 mmol), NEt3 (1.7 mL,
12.35 mmol). After stirring for 24 h at RT, the reaction mixture was
filtered. The residue was washed with CH2Cl2 (4 X 20 mL) and the
combined filtrates were washed sequentially with 2 N H2SO4, water
and 5 % aqueous NaHCO3 solution. The organic layer was dried over
anhydrous Na2SO4 and evaporated in vacuo to afford 2.90 g of S5a.
4. Experimental Section
4.1 General method of synthesis of urea derivatives of amino
acids: S3a-e
A solution of amino acid methyl ester (2.00 mmol) in dry
dicholoromethane was added drop-wise to a stirred solution of
triphosgene (0.74 mmol) in two phase solution of dry CH2Cl2 (20
mL) and saturated solution of NaHCO3 (40 mL). After 5 min. of
stirring, a solution of aminoacid methyl ester (2.00 mmol) was added
further in to the reactiom mixture and stirred for additional 4 h. The
organic phase was then washed with water, dried with anhydrous
Na2SO4 and evaporated to give crude product, which was purified by
column chromatography. S3a. Yield: 62 %. mp: 95-96 oC; [α]D = +
57.64 (c 0.085, CHCl3); ¹H NMR (CDCl3, 300 MHz) δ 2.84 (dd, 2H,
J = 17.4, 4.5 Hz), 3.04 (dd, 2H, J = 17.4, 4.5 Hz), 3.70 (s, 6H), 3.75
(s, 6H), 4.74-4.80 (m, 2H), 5.59 (d, 2H, J = 8.4 Hz); 13C NMR
(CDCl3, 75 MHz) δ 36.9, 49.3, 51.9, 52.7, 156.5, 171.7, 172.1; IR
(KBr): 3372, 3003, 2961, 1734, 1631, 1554, 1447, 1355, 1301,
1216, 1160 cm-1; HRMS: Calcd for C13H20N2O9Na m/z 371.1067,
found m/z 371.1070.
1
Yield: 93 %. H NMR (CDCl3, 300 MHz)2.55-3.30 (m, 6H), 3.68
(s, 6H), 3.73 (s, 6H), 4.62 (br, 1H), 4.80-4.85 (m, 2H), 5.12 (s, 2H),
6.29 (d, 1H, J = 7.8 Hz), 6.90 (d, 1H, J = 8.4 Hz), 7.35 (s, 5H), 7.64
(d, 1H, J = 7.8 Hz); IR (KBr): 3307, 3084, 2955, 2854, 1739, 1698,
1648, 1545, 1438, 1366, 1300 cm-1; HRMS calcd for C24H31N3O12Na
m/z 576.1805, found m/z 576.1793.
4.3.2 Synthesis of S5b. To a well-stirred and ice-cooled solution of
Z-Glutamic acid S4b (1.7 g, 5.75 mmol), N-hydroxysuccinimide
(1.45 g, 12.65 mmol) and DCC (2.61 g, 12.65mmol) in dry CH2Cl2
(100 mL) was added a solution of H2N-Glu.OMe.HCl (2.68 g, 12.65
mmol), NEt3 (1.7 mL, 13.31 mmol). After stirring for 24 h at RT, the
reaction mixture was filtered. The residue was washed with CH2Cl2
(4 × 20 mL) and the combined filtrates were washed sequentially
o
S3b.Yield: 62 %. mp: 110-112 C; [α]D = + 52.24 (c 0.080, CHCl3);
¹H NMR (CDCl3, 300 MHz) δ 1.96 (br s, 2H), 2.16 (br s, 2H), 2.42
5

with 2 N H2SO4, water and 5 % aqueous NaHCO3. The organic layer
3291, 3076, 2953, 1740, 1646, 1546, 1442, 1384, 1246, 1172 cm-1;
HRMS calcd for C33H48N6O21H m/z 865.2951, found m/z 865.2934.
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was dried over anhydrous Na2SO4, evaporated in vacuo and the
crude product was chromatographed on a column of silica gel using
EtOAc/hexane as eluents to afford the dendron S5b. Yield: 75 %.
4.4.2 Synthesis of S6b. To an ice-cooled solution of Z-Glu-
(Glu.diOMe)Glu.diOMe S5b (1.0 g, 1.68 mmol) in 20 mL of dry
MeOH was admixed with 10 % Pd/C, (peptide/catalyst 1:0.5 w/w),
and H2 was bubbled through the reaction mixture for 2 h. After
completion of the reaction, the solution was filtered, and the filtrate
was evaporated. The residue obtained was dissolved in dry
dichloromethane. The solution was cooled in an ice-bath and NEt3 (~
0.1 mL) was added and divided into two equal parts. One part (0.38
g, 0.84 mmol) was added drop wise to the stirring solution of
triphosgene (0.08 g, 0.31 mmol) in mixture of CH2Cl2 (20 mL) and
saturated solution of NaHCO3 (40 mL). A solution of second part
(0.38 g, 0.84 mmol) was added in the reactiom mixture and stirred it
for additional 4 h. The organic phase was then washed with water,
dried with anhydrous Na2SO4 and evaporated to give crude product.
The solid obtained was directly loaded in column and purified by
silica gel column chromatography using EtOAc/hexane to give the
o
mp: 116-118 C; [α]D = -40.4 (c 0.5, MeOH); ¹H NMR (CDCl3, 300
MHz) δ 1.80-2.10 (br s, 3H), 2.10-2.35 (m, 3H), 2.35-2.51 (br m,
6H), 3.68 (s, 3H), 3.69 (s, 3H), 3.77 (s, 3H), 3.79 (s, 3H), 4.06 (br
1H), 4.60-4.85 (br m, 2H), 5.08 (s, 2H), 5.33 (d, 1H, J = 5.4 Hz),
7.34 (s, 5H), 7.67 (d, 1H, J = 7.8 Hz), 8.03 (d, 1H, J = 7.8 Hz); IR
(KBr): 3301, 3059, 2953, 1737, 1693, 1652, 1536, 1440, 1387, 1334,
1276, 1250, 1215, 1176, 1055, 1000 cm-1; HRMS calcd for
C27H37N3O12Na m/z 618.2264, found m/z 618.2273.
4.3.3 Synthesis of S8. To a well-stirred and ice-cooled solution of Z-
Aspartic acid S4a (1.6 g, 5.99 mmol), N-hydroxysuccinimide (1.72
g, 14.97 mmol) and DCC (3.09 g, 14.97 mmol) in dry CH2Cl2 (20
mL) was added a dichloromethane solution of H2N-Leu.OMe.HCl
(2.72 g, 14.97 mmol) and NEt3 (2.1 mL, 14.97 mmol). After stirring
for 24 h at RT, the reaction mixture was filtered. The residue was
washed with CH2Cl2 (4 × 20 mL) and the combined filtrates were
washed sequentially with 2 N H2SO4, water and 5 % aqueous
NaHCO3. The organic layer was dried over anhydrous Na2SO4,
evaporated in vacuo and the crude product was chromatographed on
a column of silica gel using EtOAc/hexane as eluents to afford the
dendron S8. Yield: 94 %. mp: 143-144 oC; [α]D = -40.4 (c 0.5,
MeOH); ¹H NMR (CDCl3, 300 MHz) δ 0.90 (m, 12H), 1.57 (m, 6H),
2.63 (dd, 1H, J = 15.3, 7.0 Hz), 2.87 (br d, 1H), 3.70 (s, 3H), 3.71 (s,
3H), 4.55 (m, 3H), 5.11 (s, 2H), 6.40 (d, 1H, J = 7.2 Hz), 6.71 (d, 1H,
J = 7.5 Hz), 7.31 (m, 6H); 13C NMR (CDCl3, 75 MHz,)  21.6, 21.7,
22.6, 22.7, 24.7, 33.8, 38.0, 40.7, 41.0, 50.9, 51.0, 51.4, 52.1, 52.2,
67.0, 127.9, 128.0, 128.4, 136.1, 156.0, 170.6, 170.8, 173.2, 173.5;
IR (KBr): 3298, 3076, 2956, 2878, 1740, 1702, 1653, 1542, 1441,
1362, 1257, 1141 cm-1; HRMS calcd for C26H39N3O8Na m/z
544.2635, found m/z 544.2636.
o
urea product. Yield: 68 %. mp: 184-186 C; ¹H NMR (CDCl3, 300
MHz) δ 1.90-2.08 (br m, 6H), 2.12-2.33 (br m, 6H), 2.37-2.57 (m,
12H), 3.67 (s, 6H), 3.68 (s, 6H), 3.75 (s, 6H), 3.78 (s, 6H), 4.18-4.30
(m, 2H), 4.57-4.61 (m, 2H), 4.68-4.72 (m, 2H), 5.73 (d, 2H, J = 7.8
Hz), 7.68 (d, 4H, J = 8.4 Hz); IR (KBr): 3346, 3283, 2956, 1735,
1687, 1614, 1535, 1445, 1395, 1202, 1133 cm-1; HRMS calcd for
C39H60N6O21H m/z 949.3890, found m/z 949.3889.
4.5 Synthesis of azide linked dendrons
4.5.1 Synthesis of N3-Asp-(Asp.diOMe)Asp.diOMe S7a. To an ice-
cooled solution of Z-Asp-(Asp.diOMe)Asp.diOMe S5a (0.221 g,
0.41 mmol) in 10 mL of dry MeOH was admixed with 10 % Pd/C,
(peptide/catalyst 1:0.5 w/w), and H2 was bubbled through the
reaction mixture for 1.5 h. After completion of the reaction, the
solution was filtered, and the filtrate was evaporated. The residue
obtained was dissolved in dry dichloromethane. The solution was
cooled in an ice-bath and NEt3 (0.057 mL, 0.41 mmol) was added,
followed by the slow addition of azidoacetyl chloride (0.048 g, 0.41
mmol) over a period of 0.5 h. The reaction mixture was left stirred at
room temperature for 12 h. The solvent was removed in vacuo, the
solid obtained was dissolved in ethyl acetate (50 mL), washed, with
2 N H2SO4, water and 5 % aqueous NaHCO3 solution. The organic
layer was dried over anhydrous Na2SO4, evaporated and purified by
silica gel column chromatography using EtOAc/hexane to give the
desired product S7a. Yield: 72 %. mp: 135-136 oC; 1H NMR
(CDCl3, 300 MHz)2.60-3.20 (m, 6H), 3.70 (s, 6H), 3.75 (s, 3H),
3.76 (s, 3H), 4.02 (s, 2H), 4.82 (m, 3H), 6.85 (d, 1H, J = 7.4 Hz),
7.65 (d, 1H, J = 7.5 Hz), 7.87 (d, 1H, J = 7.0 Hz); IR (KBr): 3310,
2959, 2854, 2111, 1741, 1666, 1644, 1536, 1436, 1373, 1281 cm-1;
HRMS calcd for C18H27N6O11 m/z 503.1738, found m/z 503.1732.
4.3.4 Synthesis of S9. To an ice-cooled solution of Z-
Asp.(Leu.OMe).Leu.OMe S8 (0.65 g, 1.24 mmol) in 10 mL of dry
MeOH was admixed with 10 % Pd/C, (peptide/catalyst 1:0.25 w/w),
and H2 was bubbled through the reaction mixture for 1.5 h. After
completion of the reaction, the solution was filtered, and the filtrate
was evaporated to yield 0.442
g
of the NH2-Asp
(Leu.OMe)Leu.OMe S9. Yield: 92 %. ¹H NMR (CDCl3, 300 MHz) δ
0.95 (m, 12H), 1.58 (m, 6H), 1.91 (m, 2H), 2.51 (dd, 1H, J = 14.7,
7.5 Hz), 2.75 (dd, 1H, J = 14.5, 4.4 Hz), 3.73 (s, 6H), 4.53 (m, 2H),
4.58 (m, 1H) 6.99 (br d, 1H), 7.84 (d, 1H, J = 8.4 Hz); IR (KBr):
3324, 3188, 3077, 2960, 1752, 1679, 1525, 1443, 1375, 1313, 1242
cm-1; HRMS calcd for C18H33N3O6K m/z 426.2006, found m/z
426.2007.
4.4 Synthesis of urea cored dendrimers
4.4.1 Synthesis of S6a. To an ice-cooled solution of Z-Asp-
(Asp.diOMe)Asp.diOMe S5a (1.0 g, 1.87 mmol) in 20 mL of dry
MeOH was admixed with 10 % Pd/C, (peptide/catalyst 1:0.5 w/w),
and H2 was bubbled through the reaction mixture for 2 h. After
completion of the reaction, the solution was filtered, and the filtrate
was evaporated. The residue obtained was dissolved in dry
dichloromethane. The solution was cooled in an ice-bath and NEt3 (~
0.1 ml) was added and divided into two equivalent parts. One part
(0.39 g, 0.93 mmol) was added drop wise to the stirring solution of
triphosgene (0.09 g, 0.33 mmol) in a mixture of CH2Cl2 (20 mL) and
saturated solution of NaHCO3 (40 mL). The second part (0.39 g,
0.93 mmol) was added in the reaction mixture after 5 min. and
stirred it for additional 4 h. The organic phase was then washed with
water, dried with anhydrous Na2SO4 and evaporated to give crude
product. The solid obtained was purified by silica gel column
chromatography using EtOAc/hexane to give the urea product.
4.5.2 Synthesis of N3-Glu-(Glu.diOMe)Glu.diOMe S7b. To an ice-
cooled solution of Z-Glu-(Glu.diOMe)Glu.diOMe S5b (1.72 g, 2.8
mmol) in 20 mL of dry MeOH was admixed with 10 % Pd/C,
(peptide/catalyst 1:0.5 w/w), and H2 was bubbled through the
reaction mixture for 1.5 h. After completion of the reaction, the
solution was filtered, and the filtrate was evaporated. The residue
obtained was dissolved in dry dichloromethane. The solution was
cooled in an ice-bath and NEt3 (0.39 mL, 2.8 mmol) was added,
followed by the slow addition of azidoacetyl chloride (0.33 g, 2.80
mmol) over a period of 0.5 h. The reaction mixture was left stirred at
room temperature for 12 h. The solvent was removed in vacuo, the
solid obtained was dissolved in ethyl acetate (50 mL), washed, with
2 N H2SO4, water, and 5 % aqueous NaHCO3 solution. The organic
layer was dried over anhydrous Na2SO4, evaporated and purified by
silica gel column chromatography using EtOAc/hexane to give the
desired peptide dendron S7b. Yield: 72 %. mp: 138-140 oC; []D =
+
o
1
Yield: 70 %. mp: 148-150 C; ¹H NMR (CDCl3, 300 MHz) δ 1.95-
2.41 (m, 12H), 3.67 (s, 12H), 3.75 (s, 12H), 4.50 (br m, 2H), 4.68 (br
m, 4H), 5.37 (d, 2H, J = 6.0 Hz), 7.68 (d, 4H, J = 6.0 Hz); IR (KBr):
09.70 (c 0.268, CHCl3); H NMR (CDCl3, 300 MHz) 1.85-2.20
(m, 3H), 2.20-2.38 (br m, 3H), 2.38-2.65 (br m, 6H), 3.68 (s, 3H),
3.69 (s, 3H), 3.78 (s, 6H), 3.92 (s, 2H), 4.29 (br m, 1H), 4.67-4.74
6

(br m, 2H), 6.83 (d, 1H, J = 6.8 Hz), 7.65 (d, 1H, J = 8.7 Hz), 8.07
(d, 1H, J = 8.4 Hz); 13C NMR (CDCl3, 75 MHz) 26.5, 26.6, 28.8,
29.9, 30.2, 31.9, 51.4, 51.6, 51.7, 51.8, 51.9, 52.2, 52.8, 52.9, 166.3,
171.1, 172.5, 172.8, 173.9, 174.0; IR (KBr): 3289, 3073, 2956, 2104,
1735, 1645, 1545, 1440, 1385, 1212, 1173, 1123, 1070, 983 cm-1;
HRMS calcd for C21H32N6O11Na m/z 567.2027, found m/z 567.2028.
silica gel column chromatography using EtOAc/hexane to give the
desired product N3Glu.OMe2 S13. Yield: 82 %. H NMR (CDCl3,
ACCEPTED MANUSCRIPT
1
300 MHz) 2.03-2.46 (m, 4H), 3.70 (s, 3H), 3.78 (s, 3H), 4.01 (s,
2H), 4.62-4.69 (m, 1H), 6.98 (br s, 1H); 13C NMR (CDCl3, 75 MHz,)
 27.0, 29.9, 51.6, 51.9, 52.4, 52.6, 166.8, 171.7, 173.1; IR (KBr):
3347, 2955, 2925, 2854, 2110, 1739, 1670, 1533, 1441, 1374, 1210
cm-1; HRMS calcd for C9H14N4O5Na m/z 281.0856, found m/z
281.0860.
4.5.3 Synthesis of N3-Asp(Leu.OMe)2 S10. To an ice-cooled solution
of Z-Asp-(Leu.OMe)Leu.OMe S8 (0.7 g, 1.34 mmol) in 10 mL of
dry MeOH was admixed with 10 % Pd/C, (peptide/catalyst 1:0.5
w/w), and H2 was bubbled through the reaction mixture for 1.5 h.
After completion of the reaction, the solution was filtered, and the
filtrate was evaporated. The residue obtained was dissolved in dry
dichloromethane. The solution was cooled in an ice-bath and NEt3
(0.19 mL, 1.34 mmol) was added, followed by the slow addition of
azidoacetyl chloride (0.16 g, 1.34 mmol) over a period of 0.5 h. The
reaction mixture was left stirred at room temperature for 12 h. The
solvent was removed in vacuo, the solid obtained was dissolved in
ethyl acetate (50 mL), washed, with 2 N H2SO4, water, and 5 %
aqueous NaHCO3 solution. The organic layer was dried over
anhydrous Na2SO4, evaporated and purified by silica gel column
chromatography using EtOAc/hexane to give the desired product
S10. Yield: 72 %. mp: 94-95 oC; []D = +09.70 (c 0.268, CHCl3); ¹H
NMR (CDCl3, 300 MHz) δ 0.92 (t, 12H, J = 6.3 Hz), 1.54-1.72 (m,
6H), 2.64 (dd, 1H, J = 15, 7.5 Hz), 2.87 (dd, 1H, J = 15, 7.5 Hz),
3.72 (s, 3H), 3.73 (s, 3H), 4.00 (m, 2H), 4.50-4.62 (m, 2H), 4.47-4.82
(br m, 1H), 6.87 (d, 1H, J = 7.2 Hz), 7.64 (d, 1H, J = 7.5 Hz), 7.89
(d, 1H, J = 7.2 Hz); 13C NMR (CDCl3, 75 MHz) 21.5, 21.7, 22.7,
24.8, 37.9, 39.6, 39.9, 40.2, 40.4, 40.9, 49.6, 51.0, 51.2, 52.3, 52.4,
167.0, 170.3, 170.6, 173.3, 173.5; IR (KBr): 3289, 3079, 2959, 2873,
2104, 1746, 1647, 1549, 1437, 1369, 1249, 1209, 1154, 1021 cm-1;
HRMS calcd for C20H34N6O7Na m/z 493.2387, found m/z 493.2381.
4.6 Synthesis of urea-triazole cored dendrimers
4.6.1 Synthesis of ST14. To an ice-cooled solution of dialkyne S3f
(0.03 g, 0.22 mmol) in 20 mL of dry acetonitrile under argon
atmosphere was added diisopropylethylamine (0.038 mL, 0.22
mmol), N3-Glu.OMe2 S13 (0.113 g, 0.44 mmol) and CuI (0.004 g,
0.022 mmol). The reaction mixture was stirred under argon
atmosphere for 17 h. The reaction mixture was evaporated, the solid
thus obtained was washed with 0.2 N H2SO4, water, NH4Cl / NH4OH
(9:1) solution and finally with water. The residue obtained was dried
and crystallized from a mixture of chloroform and methanol to give
the symmetrical dendrimer ST14. Yield: 70 %. mp: 184-186 C; H
NMR (DMSO-d6, 300 MHz) 1.88-2.23 (m, 8H), 3.56 (s, 6H), 3.61
(s, 6H), 4.32 (br s, 6H), 5.23 (s, 4H), 6.56 (d, 2H, J = 6.3 Hz), 7.87
(s, 2H), 8.24 (d, 2H, J = 5.7 Hz); IR (KBr): 3324, 3071, 2956, 2855,
1738, 1664, 1538, 1442, 1376, 1212 cm-1; HRMS calcd for
C25H36N10O11Na m/z 675.2463, found m/z 675.2449.
o
1
4.6.2 Synthesis of ST15. To an ice-cooled solution of dialkyne S3f
(0.015 g, 0.11 mmol) in 20 mL of dry acetonitrile under argon
atmosphere was added diisopropylethylamine (0.019 mL, 0.11
mmol), N3-Asp-(Asp.diOMe)Asp.diOMe S7a (0.11 g, 0.22 mmol)
and CuI (0.002 g, 0.011 mmol). The reaction mixture was stirred
under argon atmosphere for 17 h. The reaction mixture was
evaporated, the solid thus obtained was washed with 0.2 N H2SO4,
water, NH4Cl / NH4OH (9:1) solution and finally with water. The
residue obtained was dried and crystallized from a mixture of
chloroform and methanol to give symmetrical dendrimer ST15.
4.5.4 Synthesis of N3-Ar-(Glu-(Glu.diOMe)Glu.diOMe)2 S12. To an
ice-cooled solution of Z-Glu-(Glu.diOMe)Glu.diOMe S5b (1.72 g,
2.8 mmol) in 20 mL of dry MeOH was admixed with 10 % Pd/C,
(peptide/catalyst 1:0.5 w/w), and H2 was bubbled through the
reaction mixture for 1.5 h. After completion of the reaction, the
solution was filtered, and the filtrate was evaporated. The residue
obtained was dissolved in dry dichloromethane. The solution was
cooled in an ice-bath and NEt3 (0.39 mL, 2.8 mmol) was added,
followed by the slow addition of 5-(azidomethyl) benzene-1,3-
dicarbonyl dichloride (0.359 g, 1.40 mmol) over a period of 0.5 h.
The reaction mixture was left stirred at room temperature for 24 h.
The solvent was removed in vacuo, the solid obtained was dissolved
in ethyl acetate (50 mL), washed, with 2 N H2SO4, water, and 5 %
aqueous NaHCO3 solution. The organic layer was dried over
anhydrous Na2SO4, evaporated and purified by silica gel column
chromatography using EtOAc/hexane to give the desired dendron
N3-Ar-(Glu-(Glu.diOMe)Glu.diOMe)2 S12. Yield: 64 %. mp: 160-
o
1
Yield: 67 %. mp: 202-204 C; []D = - 11.21 (c 0.106, MeOH); H
NMR (DMSO-d6, 300 MHz) 2.55-2.88 (br m, 12H), 3.60 (s, 12H),
3.62 (s, 12H), 4.26 (br s, 4H), 4.55-4.70 (br m, 6H), 5.00-5.20 (br m,
4H), 6.42 (br s, 2H), 7.83 (s, 2H), 8.46 (br s, 4H ), 8.57 (d, 2H, J =
5.7 Hz); 13C NMR (CDCl3, 75 MHz) 35.2, 36.7, 48.0,
48.1, 49.0, 50.8, 51.2, 51.7, 123.4, 145.2, 157.2, 164.8, 168.4, 169.9,
170.0, 170.4, 170.6 ; IR (KBr): 3286, 3086, 2955, 1734, 1652, 1552,
1439, 1370, 1298, 1226, 1173, 1052 cm-1; HRMS calcd for
C43H60N14O23Na m/z 1163.3848, found m/z 1163.3807.
4.6.3 Synthesis of ST16. To an ice-cooled solution of dialkyne S3f
(0.015 g, 0.11 mmol) in 20 mL of dry acetonitrile under argon
atmosphere was added diisopropylethylamine (0.019 mL, 0.11
mmol), N3-Glu-(Glu.diOMe)Glu.diOMe S7b (0.119 g, 0.22 mmol)
and CuI (0.002 g, 0.011 mmol). The reaction mixture was stirred
under Ar atmosphere for 17 h. The reaction mixture was evaporated,
the solid thus obtained was washed with 0.2 N H2SO4, water, NH4Cl /
NH4OH (9:1) solution and finally with water. The residue obtained
was dried and crystallized from a mixture of chloroform and
methanol to give symmetrical dendrimer ST16. Yield: 65 %. mp:
180-182 oC; []D = - 30.15 (c 0.126, MeOH); 1H NMR (DMSO-d6,
300 MHz) 1.61-2.00 (br m, 12H), 2.07-2.20 (br m, 4H), 2.27-2.36
(br m, 8H), 3.51 (s, 12H), 3.56 (s, 12H), 4.14-4.32 (br m, 10H), 5.06
(s, 4H), 6.31-6.40 (br m, 2H), 7.70 (s, 2H), 8.21 (d, 2H, J = 7.8 Hz),
8.39 (d, 2H, J = 7.8 Hz), 8.49 (d, 2H, J = 7.5 Hz); 13C NMR (DMSO-
d6, 75 MHz) 26.4, 26.5, 28.8, 30.1, 30.2, 31.7, 35.5, 51.7, 52.0,
52.5, 52.6, 124.6, 146.2, 158.3, 166.0, 171.7, 172.3, 172.5, 172.9,
173.2; IR (KBr): 3295, 2926, 2855, 1739, 1646, 1542, 1442, 1380,
1214, 1173 cm-1; HRMS calcd for C49H72N14O23Na m/z 1247.4792,
found m/z 1247.4796.
o
1
161 C; H NMR (CDCl3, 300 MHz)1.90-2.17 (br m, 6H), 2.17-
2.34 (br m, 6H), 2.41-2.67 (br m, 12H), 3.65 (s, 6H), 3.68 (s, 6H),
3.76 (s, 12H), 4.40 (s, 2H), 4.48-4.61 (br m, 2H), 4.62-4.83 (br m,
4H), 7.51-7.75 (m, 4H), 7.88 (s, 2H), 8.09 (br m, 2H), 8.17 (s, 1H);
13C NMR (CDCl3, 75 MHz) 26.6, 28.3, 29.7, 30.1, 30.2,
32.1, 33.9, 49.1, 51.6, 51.7, 51.8, 52.8, 52.9, 53.0, 53.9, 125.2, 130.1,
134.3, 136.7, 165.7, 172.0, 172.8, 172.9, 173.0, 173.8, 173.9; IR
(KBr): 3294, 3076, 2955, 2091, 1738, 1642, 1545, 1441, 1384, 1212,
1171 cm-1; HRMS calcd for C47H65N9O22Na m/z 1130.4136, found
m/z 1130. 4147.
4.5.5 Synthesis of N3-Glu.di.OMe S13. NH2-Glu.di.OMe.HCl (0.500
g, 2.36 mmol) was dissolved in 10 mL dicholomethane. The solution
was cooled in an ice-bath and NEt3 (1.8 mL, 11.8 mmol) was added,
followed by the slow addition of azidoacetyl chloride (0.28 g, 2.36
mmol) over a period of 0.5 h. The reaction mixture was left stirred at
room temperature for 12 h. The solvent was removed in vacuo, the
solid obtained was dissolved in ethyl acetate (50 mL), washed, with
2 N H2SO4, water, and 5 % aqueous NaHCO3 solution. The organic
layer was dried over anhydrous Na2SO4, evaporated and purified by
4.6.4 Synthesis of ST17. To an ice-cooled solution of dialkyne S3f
(0.015 g, 0.11 mmol) in 20 mL of dry acetonitrile under argon
7

5. (a) Newkom, G. R.; Moorefield, C. N.; Baker, G. R.; Saunders,
atmosphere was added diisopropylethylamine A(0C.01C9EmPLT, E0.D11 MANMU. SJ.C; GRroIsPsmTan, S. H. Angew. Chem. Int. Ed. Engl. 1991, 31,
mmol), N3-Asp-(Leu.OMe)Leu.OMe S10 (0.103 g, 0.16 mmol) and
1178 –1180; (b) Roush, W. M.; Michael, A.; David, A.; Harris,
J. J. Org. Chem. 1985, 50, 2004-2006.
CuI (0.002 g, 0.011 mmol). The reaction mixture was stirred under
Ar atmosphere for 17 h. The reaction mixture was evaporated, the
solid thus obtained was washed with 0.2 N H2SO4, water, NH4Cl /
NH4OH (9:1) solution and finally with water. The residue obtained
was dried and crystallized from a mixture of chloroform and
methanol to give symmetrical dendrimer ST17. Yield: 65 %. mp:
196-198 oC; []D = - 30.15 (c 0.126, MeOH); 1H NMR (DMSO-d6,
300 MHz)0.75-0.96 (br m, 24H), 1.18-1.30 (br m, 4H), 1.42-1.72
(br m, 8H), 2.53 (br m, 4H), 3.61 (s, 6H), 3.64 (s, 6H), 4.27 (br s,
8H), 4.57 (br m, 2H) 4.95-5.21 (br m, 4H), 6.54 (br s, 2H), 7.83 (d,
2H, J = 8.4 Hz), 8.30 (d, 4H, J = 7.8 Hz), 8.57 (d, 2H, J = 7.2 Hz); IR
(KBr): 3296, 2958, 1742, 1649, 1548, 1462, 1233, 1125 cm-1; HRMS
calcd for C47H76N14O15Na m/z 1099.5507, found m/z 1099.5504.
6. (a) Haridas, V.; Sharma, Y. K.; Sahu, S.; Verma, R. P.;
Sadanandan, S.; Kacheshwar, B. G. Tetrahedron 2011, 67,
1873-1884; (b) Franc, G.; Kakkar, A. Chem. commun., 2008,
5267-5276; (c) Meldal, M.; Torne, C. W. Chem. Rev. 2008,
108, 2952-3015; (d) Haridas, V.; Lal, K.; Sharma, Y. K.
Tetrahedron Lett. 2007, 48, 4719-4722; (e) Antoni, P.; Nystrom,
D.; Hawker, C. J.; Hulta, A.; Malkoch, M. Chem. Commun.,
2007, 2249-2251; (f) Bock, V. D.; Hiemstra, H.; van
Maarseveen, J. H. Eur. J. Org. Chem. 2006, 51-68; (g) Opsteen,
J. A.; Hest, J. C. M. V. Chem. Commun. 2005, 57-59; (h) Wu,
P.; Feldman, A. K.; Nugent, A. K.; Hawker, C. J.; Scheel, A.;
Voit, B.; Pyun, J.; Frechet, J. M. J. Sharpless, K. B.; Fokin, V.
V. Angew. Chem. Int. Ed., 2004, 43, 3928-3932; (i) Twyman, L.
J.; Beezer, A. E.; Mitchell, J. C. Tetrahedron Lett. 1994, 35,
4423-4424.
7. (a) Wong, V.; Zimmerman, S. C. Chem. Commun., 2013, 49,
1679-1695; (b) Baal, I. V.; Malda, H.; Synowsky, S. A.; van
Dongen, J. L. J.; Hackeng, T. M.; Merkx, M.; Meijer, E. W.
Angew. Chem. Int. Ed., 2005, 44, 5052-5057.
8. (a) Park, C.; Lee, J.; Kim, C. Chem. Commun., 2011, 47, 12042-
12056; (b) Amendola, V.; Fabbrizzi, L.; Mosca, L. Chem. Soc.
Rev., 2010, 39, 3889–3915; (c) Steed, J. W. Chem. Soc. Rev.,
2010, 39, 3686-3699.(d) Ko, H. S.; Park, C.; Lee, S. M.; Song,
H. H.; Kim, H. Chem. Mater. 2004, 16, 3872-3876; (d)
Newkome, G. R.; Moorefield, C. N.; Baker, G. R.; Behera, R.
K.; Escamillia, G. H.; Saunders, M.J. Angew. Chem. Int. Ed.,
1992, 31, 917-919; (e) Kim, C.; Kim, T. K.; Chang, Y. J. Am.
Chem. Soc. 2001, 123, 5586-5587.
4.6.5 Synthesis of ST18. To an ice-cooled solution of dialkyne S3f
(0.010 g, 0.07 mmol) in 20 mL of dry acetonitrile under argon
atmosphere was added diisopropylethylamine (0.012 mL, 0.07
mmol), N3-Ar-(Glu-(Glu.diOMe)Glu.diOMe)2 S12 (0.155 g, 0.14
mmol) and CuI (0.001 g, 0.0053 mmol). The reaction mixture was
stirred under Ar atmosphere for 24 h. The reaction mixture was
evaporated, the solid thus obtained was washed with 0.2 N H2SO4,
water, NH4Cl /NH4OH (9:1) solution and finally with water. The
residue obtained was dried and crystallized from a mixture of
chloroform and methanol to give dendrimer ST18. Yield: 43 %. mp:
o
1
160-161 C; H NMR (DMSO-d6, 300 MHz) 1.75-2.12 (m, 24H),
2.21-2.45 (m, 24H), 3.57 (s, 24H), 3.59 (s, 24H), 4.08-4.37 (br m,
12H), 4.44-4.58 (br m, 4H), 5.65 (br s, 4H), 6.40 (br s , 2H), 7.80 (d,
5H, J = 7.2 Hz), 8.29 (br m, 7H), 8.44 (d, 4H, J = 6.3 Hz), 8.64 (d,
4H, J = 6.0 Hz); IR (KBr): 3316, 2926, 2854, 1737, 1650, 1540,
1442, 1376, 1213 cm-1; HRMS calcd for C101H138N20O45Na m/z
2350.4147, found [M/2+Na]+ 1198.4463.
9. (a) Shimizu, L. S.; Salpage, S. R.; Korous, A. A. Acc. Chem.
Res. 2014, 47, 2116-2127; (b Yang, J.; Dewal, M. B.;
Sobransingh, D.; Smith, M. D.; Xu, Y.; Shimizu, L. S. J. Org.
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T. J. Am. Chem. Soc. 2002, 124, 9356-9357.
10. (a) Meazza, L.; Foster, J. A.; Fuke, K.; Metrangolo, P.;
Resnati, G.; Steed, J. W. Nat. Chem., 2013, 5, 42-45; (b) Zhao,
X.; Chang, Y. L.; Fowler, F. W.; Lauher, J. W. J. Am. Chem.
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11. (a) Zhang, H-L.; Zang, Yi.; Xie, Juan.; Li, Jia.; Chen, G-R.; He,
X-P.; Tian, H. Sci. Rep. 2014, 4, 5513; (b) Deng, Q.; He, X-P.;
Shi, H-W.; Chen, B-Q.; Liu, G. Tang, Y.; Long, Y-T.; Chen, G-
R.; Chen, K. Ind. Eng. Chem. Res. 2012, 51, 7160−7169; (c)
Rostovtsevi, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B.
Angew. Chem., Int. Ed. 2002, 41, 2596–2599.
Acknowledgements
This work was supported by DST-New Delhi. We thank DST -FIST
for mass spectral and single crystal XRD facilities at IITD. We thank
Department of Textile Technology, Department of Physics and NRF
IIT-Delhi for SEM images, AFM images and TEM studies
respectively. We also thank Prof. B. Jayaram, IITD for the help in
MD simulation. RPV thanks Council of Scientific & Industrial
Research (CSIR) New Delhi for the fellowship and Oil and Natural
Gas Corporation (ONGC) for the support.
12. Haridas, V.; Sharma, Y. K.; Naik, S. Eur. J. Org. Chem., 2009,
10, 1570-1577.
13. Schön, E-V.; Marques-Lopez, E.; Herrera, R. P.; Aleman, C.;
Diaz, D. D. Chem. Eur. J. 2014, 20, 10720-10731.
14. Hirst, A. R.; Huang, B.; Castelletto, V.; Hamley, I. W.; Smith, D.
K. Chem. Eur. J. 2007, 13, 2180-2188.
15. (a) Feng, Y.; He, Y-M.; Fan, Q-H. Chem. Asian J., 2014, 9,
1724-1750; (b) Haridas, V.; Sharma, Y. K.; Creasey, R.; Sahu,
S.; Gibson, C. T. Voelcker, N. H. New J. Chem., 2011, 35, 303-
309; (c) Ji, Y.; Luo, Y. F.; Jia, X. R.; Chen, E. Q.; Huang,Y.;
Ye, C.; Wang, B. B.; Zhou, Q. F. Wei, Y. Angew. Chem. Int.
Ed. 2005, 44, 6025-6029. (d) Newkome, G. R.; Baker, G. R.;
Arai, S.; Saunders, M. J.; Russo, P. S.; Theriot, K. J.;
Moorefield, C. N.; Rogers, L. E.; Miller, J. E.; Lieux, T. R.;
Murray, M. E.; Phillips, B.; Pascal, L. J. Am. Chem. Soc. 1990,
112, 8458-8465.
Supplementary data
1H NMR, 13C NMR, and HRMS of all new compounds.
Supplementary data related to this article can be found online at
doi:xxxxxxxxxxxxx
References and notes
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Albericio, F. Chem. Rev. 2005, 105, 1663−1681; (b)
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L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.;
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Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.;
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S.; Kovalenko, A.; Kollman, P. A. (2012), AMBER 12,
University of California, San Francisco.
8

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SUPPLEMENTARY INFORMATION
Peptide dendrimers with designer core for directed self-assembly
Ram. P. Verma, Ashutosh Shandilya and V. Haridas,*
Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016,
India
Table of Contents
1. General experimental section and scheme
2. NMR and mass spectral data
3. Ultramicroscopic studies
4. X-ray crystallographic data
5. Gelation study
S2-S4
S5-S23
S24-S24
S24-S29
S30
6. Molecular dynamics studies
7. References
S31-S35
S36
S1

ACCEPTED MANUSCRIPT
Experimental section
(a) Synthesis and characterization
All reagents were used without further purification. All solvents employed in the
reactions were distilled or dried from appropriate drying agents prior to use. All amino
acids used were of L-configuration. Progress of reactions was monitored by thin layer
chromatography (TLC). Purification of compounds was done by silica gel column
chromatography. Silica gel G (Merck) was used for TLC and silica gels with 100-200
mesh was used for column chromatography. Melting points were recorded on a Fisher-
Scientific melting point apparatus and were uncorrected. Optical rotations were measured
with a Rudolph Research Analytical Autopol® V Polarimeter; where concentrations are
given in gram/100 mL. IR spectra were recorded on a Nicolet, Protégé 460 spectrometer
1
as KBr pellets. H NMR spectra were recorded on Brucker-DPX-300 spectrometer using
tetramethylsilane as an internal standard. Coupling constants are in Hz and the 1H NMR
data are reported as s (singlet), d (doublet), br (broad), t (triplet) and m (multiplet), dd (double
doublet). High Resolution mass spectra (HRMS) were recorded in Bruker MicrO-TOF-QII
model and AB Sciex, 1011273/A model using ESI technique. MD simulations were
performed on 320 processors SUN Microsystems clusters at Supercomputing Facility
(SCFBio) at IIT Delhi.
(b) Gelation Study
The dendrimer was dissolved in a more polar solvent and the less polar solvent was added to
initiate the gel formation. The gel formation is assessed by the tube inversion method.
S2

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(c) Preparation of gel from S6a-b
In a typical procedure, 20 mg of S6a-b was dissolved in 0.3 mL chloroform and added 0.2 mL
hexane to get the gel.
Microscopic studies
(d) Scanning Electron Microscopy (SEM)
A 10 ꢀl aliquot of the sample solution was applied on a sticky carbon tape and it was then coated
with ~ 10 nm of gold. SEM images were recorded using a CARL ZEISS EVO 50 SEM.
(e) Field Emission-Scanning Electron Microscopy (FE-SEM)
A 10ꢀl aliquot of the sample solution was put on a fresh piece of glass, which is attached to a
stub via carbon tape. The sample was dried at room temperature and coated with ~10nm
of gold. Samples were analyzed using FEI Quanta 3D FEG High resolution scanning
electron microscope combined with High-current ion column with Ga liquid-metal ion
source.
(f) Atomic Force Microscopy (AFM)
Bruker Dimension Icon atomic force microscope was used for imaging. Tapping mode is
used for the analysis. About 10 ꢀl aliquot of the sample solution was transferred onto a freshly
cleaved mica and allowed to dry and imaged using AFM.
(g) High Resolution-Transmission Electron Microscopy (HR-TEM)
Samples for HR-TEM were prepared by dissolving the compound in 1:1 methanol and
chloroform mixture. A 2 ꢀl aliquot of the sample solution was placed on a 200 mesh
copper grid. It was then stained with 2 % phosphotungstate in water for 2 min. and the
S3

ACCEPTED MANUSCRIPT
excess fluid was removed using a filter paper and samples were viewed using a
TECHNAI G2 (20STWIN) electron microscope.
(a) MeOH/H2SO4; (b) 1 equiv. of NaOH; (c) BH3.Me2S; (d) SOCl2, reflux; (e) NaN3; (f) 2M
NaOH; (g) SOCl2, reflux (h) Dry NEt3, NH2Glu3OMe4
S4

ACCEPTED MANUSCRIPT
O
O
O
MeO
MeO
O
OMe
OMe
N
N
H
H
O
1H NMR (CDCl3, 300 MHz) spectrum of S3a
O
O
O
O
MeO
O
O
OMe
MeO
MeO
OMe
OMe
N
H
N
H
MeO
OMe
O
O
O
O
N
H
N
H
(M+K)+
(MH)+
(2M+Na)+
(2M+K)+
ESI-MS of compound S3a
S5

ACCEPTED MANUSCRIPT
MeO
MeO
O
O
OMe
OMe
O
N
N
H
H
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S3b
(M+Na)+
MeO
MeO
O
O
OMe
OMe
(M+K)+
O
N
N
H
H
O
O
(2M+Na)+
ESI-MS of compound S3b
S6

ACCEPTED MANUSCRIPT
O
MeO
OMe
N
H
N
H
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S3c
O
MeO
OMe
N
N
H
H
O
O
ESI-MS of compound S3c
S7

ACCEPTED MANUSCRIPT
O
H3CO
OCH3
N
H
N
H
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S3d
O
H3CO
OCH3
N
H
N
H
O
O
ESI-MS of compound S3d
S8

ACCEPTED MANUSCRIPT
1H NMR (CDCl3, 300 MHz) spectrum of S3e
O
MeO
OMe
N
N
H
H
O
O
ESI-MS of compound S3e
S9

ACCEPTED MANUSCRIPT
O
N
N
H
H
1H NMR (DMSO-d6, 300 MHz) spectrum of S3f
O
N
N
H
H
ESI-MS of compound S3f
S10

ACCEPTED MANUSCRIPT
O
OMe
O
OMe
N
O
H
O
O
H
O
N
H
N
OMe
OMe
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S5a
O
OMe
OMe
O
N
H
O
O
O
H
O
N
H
N
OMe
OMe
O
O
S11

ACCEPTED MANUSCRIPT
ESI-MS of compound S5a
1H NMR (CDCl3, 300 MHz) spectrum of S5b
OMe
O
OMe
O
NH
O
O
O
H
N
N
H
O
OMe
OMe
O
O
S12

ACCEPTED MANUSCRIPT
ESI-MS of compound S5b
O
O
MeO
MeO
OMe
O
O
O
O
OMe
N
H
N
H
O
O
O
O
O
H
H
N
N
N
N
H
H
MeO
MeO
OMe
OMe
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S6a
S13

ACCEPTED MANUSCRIPT
ESI-MS of compound S6a
OM e
O M e
OM e
H N
O
O
OM e
O
O
O
O
O
NH
O
O
H
N
H
N
MeO
N
N
OM e
OM e
H
H
O
O
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S6b
OMe
OMe
O
O
M eO
MeO
O
OMe
OMe
OMe
O
O
OMe
O
O
O
HN
HN
O
O
NH
N H
O
O
O
O
O
O
O
H
H
O
H
N
N
H
N
N
MeO
MeO
OM e
N
H
H
N
N
O
O
N
OMe
H
H
O
O
O
O
O Me
O
O
OMe
ESI-MS of compound S6b
S14

ACCEPTED MANUSCRIPT
1H NMR (CDCl3, 300 MHz) spectrum of S7a
O
OMe
O
OMe
N
O
H
O
N
H
3
O
N
N
H
OMe
OMe
O
O
ESI-MS of compound S7a
S15

ACCEPTED MANUSCRIPT
MeO
MeO
NH
O
O
O
O
O
H
N
N3
OMe
OMe
N
H
O
O
1H NMR (CDCl3, 300 MHz) spectrum of S7b
OMe
(M+Na)+
O
OMe
O
O
NH
O
O
H
N3
N
N
H
OMe
OMe
O
O
(M/2+Na)+
ESI-MS of compound S7b
S16

ACCEPTED MANUSCRIPT
O
O
OMe
OMe
N
H
O
O
O
N3
H
N
N
H
1H NMR (CDCl3, 300 MHz) spectrum of S10
(M+Na)+
O
OMe
N
O
O
O
H
N
H
3
N
H
N
OMe
O
ESI-MS of compound S10
S17

ACCEPTED MANUSCRIPT
OMe
O
OMe
OMe
HN
O
OMe
O
O
O
O
O
NH
O
O
O
H
N
H
N
MeO
MeO
N
H
N
H
OMe
OMe
O
O
O
O
N3
1H NMR (CDCl3, 300 MHz) spectrum of S12
ESI-MS of compound S12
S18

ACCEPTED MANUSCRIPT
O
OMe
OMe
O
MeO
MeO
O
N
O
N
O
N
N
N
N
N
N
N
N
H
H
H
H
O
O
1H NMR (DMSO-d6, 300 MHz) spectrum of ST14
O
OMe
OMe
O
MeO
MeO
O
N
O
N
O
N
N
N
N
N
N
N
N
H
H
H
H
O
O
ESI-MS of compound ST14
S19

ACCEPTED MANUSCRIPT
O
O
OM e
MeO
M eO
O
O
O Me
O
N
H
N
N
O
N
O
H
N
N
O
O
O
O
N
N
N
N
H
H
N
H
H
N
H
N
N
H
OM e
O Me
M eO
M eO
O
O
O
O
1H NMR (DMSO-d6, 300 MHz) spectrum of ST15
(M+Na)+
(M/2+Na)+
O
O
OMe
OMe
MeO
MeO
O
O
O
N
H
N
H
N
O
N
O
N
N
O
O
O
O
N
N
N
N
H
N
H
N
H
H
N
H
N
H
OMe
OMe
MeO
MeO
O
O
O
O
ESI-MS of compound ST15
S20

ACCEPTED MANUSCRIPT
MeO
MeO
O
OMe
OMe
O
O
O
HN
NH
O
O
O
O
O
N
O
N
O
N
N
N
N
H
H
N
N
N
N
H
H
N
H
N
H
MeO
MeO
OMe
OMe
O
O
O
O
1H NMR (DMSO-d6, 300 MHz) spectrum of ST16
ESI-MS of compound ST16
S21