Synthesis, characterization, and anti-bacterial efficacy of some novel cyclophane amide

Article abstract of DOI:10.1016/j.bmc.2006.07.020

Synthesis of macrocyclic di, tetra- and hexaamides with aza and oxy linkages has been achieved and the inhibitory activity of cyclophane amides against human pathogenic bacteria well documented.

Full text of DOI:10.1016/j.bmc.2006.07.020

Bioorganic & Medicinal Chemistry 14 (2006) 7458–7467
Synthesis, characterization, and anti-bacterial efficacy of some
novel cyclophane amide
Perumal Rajakumar,a,* A. Mohammed Abdul Rasheed,a P. M. Balub and K. Murugesanb
aDepartment of Organic Chemistry, University of Madras, Guindy Campus, Chennai 600 025, India
bCenter for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 600 025, India
Received 29 May 2006; revised 3 July 2006; accepted 7 July 2006
Available online 1 August 2006
Abstract—Synthesis of macrocyclic di, tetra- and hexaamides with aza and oxy linkages has been achieved and the inhibitory
activity of cyclophane amides against human pathogenic bacteria well documented.
ꢀ 2006 Elsevier Ltd. All rights reserved.
1. Introduction
amides.21 Synthesize of macrocyclic hexaamides and
their bonding properties with peptides has been also
reported.22 The self-assembly of acyclic peptides and
hence their ability to form b-sheet structures has been
demonstrated.23,24 Adamantane based systems also
form double-helical cyclic structures.25 Cyclic peptide26
with open pores is useful as transport vehicles for bio-
logically important ions27 or neutral molecules.28 The
increased anti-bacterial and anti-fungal activity of cop-
per complexes of macrocyclic compounds than the
uncomplexed macro cyclic compounds has been report-
ed.29 Tetra aza macrocyclic complexes have been
screened for their biological activity.30 Hence it is of
interest to synthesize and study the anti-bacterial activ-
ity of some novel cyclophane amides. We wish to report
the synthesize of cyclophane amides 7–11, 13–16, 17, 18,
and 21 and the anti-bacterial efficacy of some of the cyc-
lophane amides against Escherichia coli, Staphylococcus
aureus, Streptococcus faecalis, and Proteus vulgaris
bacteria.
The increasing interest in the synthesis of aza crown
compounds due to their important diverse application
in supramolecular chemistry1–5 stimulates the imagina-
tive skill of synthetic chemists. Various changes have
been made to the basic crown ether structure in order
to enhance the selectivity of the ligands and the stability
of complexes formed with both metal and organic cat-
ions and to use them as models of protein–metal binding
sites in biological systems,6–8 synthetic ionophores, ther-
apeutic reagents in chelate therapy, cyclic antibiotics,9 to
study host–guest interactions10 and in catalysis.11 Some
of these modifications involve the substitution of the
ligand polyether oxygen donor atoms by sulfur
and/or nitrogen atoms.12 Other substitution involved
the insertion of functional groups viz., amides, esters
in the ring.13–16 Recognition of the importance of
macrocyclic compounds has led to considerable effort
being invested in developing reliable inexpensive
synthetic routes to these compounds.
The biphenyl based cyclic amides have been reported for
anion complexation.17 Cyclic tetraamide receptors hav-
ing barbiturate binding domain were reported.18 Supra-
molecular amides are also used as molecular receptors19
and in molecular recognition20 of biologically interact-
ing substrates including anti-HIV active macrocyclic
2. Results and discussion
Diacid chlorides 1–5 were prepared by the reaction of
the corresponding dicarboxylic acid and thionyl chloride
and used for the synthesize of cyclophane amides.
Diamide 6 required for the synthesize of cyclophane
amide was obtained in 60% yield by the reaction of
diphenic acid chloride 4 with 2.1 equiv of N-phenyl eth-
ylene diamine (NPEDA) in presence of triethyl amine in
methylene chloride (Scheme 1).
Keywords: Cyclophane tetraamide; Ion transportation; Host–guest
interaction.
*
Corresponding author. Tel.: +91 4422 351 269; fax: +91 44 223
52494; e-mail: perumalrajakumar@hotmail.com
0968-0896/$ - see front matter ꢀ 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2006.07.020

P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
7459
Cl
O
O
Cl
O
O
O
Cl
Cl
O
O
O
O
Me
Me
O
O
Cl
O
O
O
ClOC
COCl
N
Cl
Cl
Cl
1
2
4
5
3
Diamide 6 in the 1H NMR spectrum displayed
–NCH2CH2N– protons as multiplet at d 2.87–3.50,
and a broad singlet at d 4.30 for –NHPh proton in addi-
tion to the aromatic protons at d 6.45–7.45 and the
amide proton at d 9.90 as a broad singlet. The structure
of the diamide 6 was confirmed based on spectral and
analytical data.
–NCH2CH2N– protons as a multiplet at d 3.18–3.72,
–OCH2 protons as an AB quartet at d 5.00 and 5.17 with
J = 13.2 Hz and the amide protons as a broad singlet at d
8.26 in addition to the aromatic protons. In 13C NMR
spectrum, two aromatic methyl carbons appeared at d
19.8, –NCH2CH2N–, –OCH2 and carbonyl carbon ap-
peared at d 38.6, 47.9, 68.7, and 170.4, respectively, in
addition to the aromatic carbons. Further the structures
of the cyclophane amide 8 was confirmed by the appear-
ance of the molecular ion at m/z 848. Similarly the struc-
ture of the cyclophane amides 7, 9, 10, and 11 were
thoroughly characterized by spectral and analytical data.
Cyclophane amide 7 showed carbonyl stretching frequen-
cy at 1677 cmÀ1 in IR spectrum. The reason for the higher
value compared to other cyclophane amides is possibly
due to the attachment of the carbonyl group to the meth-
ylene group, where as in the other cyclophane amide it is
attached to the aromatic ring. The structure of cyclo-
phane tetraamide 10 was also confirmed by XRD.
Reaction of the diamide 6 with diacid chlorides 1–5 in
the presence of triethyl amine under high dilution condi-
tion at reflux in chloroform gave cyclophane tetraamides
7–11 in 33–40% yield (Scheme 2).
Cyclophane amide 8 in 1H NMR spectrum displayed the
aromatic methyl protons as a singlet at d 2.36,
Cl
O
i
HN
NH
O
Cl
OO
With a view to synthesize cyclophane amides of smaller
cavity, dichloro compound 12 was prepared by the reac-
tion of OPDA with two equivalents of chloro acetyl
chloride in the presence of TEA in methylene chloride.
Reaction of the dichloro compound 12 with various
6
Ph NH
HN Ph
4
Scheme 1. Reagents and condition: (i) 2.1 equiv of NPEDA, TEA,
CH2Cl2, rt, 1 h.

7460
P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
i
Cyclophane
amide
HN
NH
1 - 5
Diacid chloride
+
OO
7 - 11
6
Ph NH
HN Ph
HN
N
NH
N
OO
HN
NH
N
HN
NH
N
OO
O
O
O
O
OO
N
O
O
N
O
O
O
O
O
O
H3C
CH3
9
8
7
33%
40%
35%
HN
N
NH
N
HN
NH
OO
OO
N
OO
N
O
N
O
10
11
35%
37%
Scheme 2. Reagents and condition: (i) TEA, chloroform, reflux, 6 h.
dihydroxy benzene derivatives viz., catechol, 2,6-dihy-
droxy acetophenone, 2,4-dihydroxy acetophenone, and
2,5-dihydroxy acetophenone in the presence of anhy-
drous potassium carbonate and KI in acetonitrile under
reflux for 12 h gave cyclophane diamides 13–16 in 40–
45% yield (Scheme 3).
O
Cl
Cyclophane
amide
NH
NH
NH2
NH2
i
a-d
13-16
ii
Cl
O
12
a = catechol, b = 2,6-dihydroxy acetophenone, c = 2,4-dihydroxy acetophenone,
d = 2,5-dihydroxy acetophenone,
O
O
O
O
O
O
O
O
O
O
Ac
O
O
NH
Ac
NH
NH
NH
NH
NH
Ac
O
O
NH
HN
O
O
14
40%
15
43%
13
45%
16
43%
Scheme 3. Reagents and condition: (i) 2.1 equiv of chloro acetylchloride, TEA, CH2Cl2; (ii) K2CO3, Kl, CH3CN, reflux, 12 h.

P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
7461
Figure 1. Energy minimization of cyclophane amide 14. Heat of
formation of cyclophane amide 14 is À0.8023 kcal/mol.
In the 1H NMR spectrum diamide 15 displayed the
–COCH3 protons as a singlet at d 2.54, –OCH2 pro-
tons as two singlets at d 4.33 and 5.11 and NH pro-
tons as two singlets at d 10.72 and 12.56 in addition
to the aromatic protons. In the 13C NMR spectrum,
methyl and methylene carbons appeared at d 26.6
and 65.7 and the carbonyl carbons appeared at d
163.8, 164.2, and 166.2 in addition to the aromatic
carbons. In the mass spectrum the molecular ion ap-
peared at m/z 340. Thus, the structure of cyclophane
15 was confirmed based on spectral and analytical
data. Similarly structures of the cyclophane 13, 14,
Figure 2. Energy minimization of cyclophane amide 18. Heat of
formation of cyclophane amide 18 is 5.5746 kcal/mol.
and 16 was also characterized by spectral and analyt-
ical data.
Structure of the cyclophane 14 would be interesting with
the possibility of acetyl group oriented in the cavity due
Cyclophane amide
a / b
HN
NH
17 / 18
i
OO
Ph NH
HN Ph
6
Me
Cl
Cl
b =
a =
Br
Br
Me
HN
N
NH
OO
N
N
NH
HN
N
O
O
Me
Me
17
18
40%
35%
Scheme 4. Reagents and condition: (i) K2CO3, CH3CN, reflux, 24 h.

7462
P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
O
H
N
O
Ph
O
HN
NH
H
N
Cl
O
i
19
HN
O
O
Ph
N
ii
O
Cl
Ph
H
H
N
N
N
HN
Cl
O
Ph
O
O
19
Ph
N
O
NH
Ph
O
20
21
62%
15%
Scheme 5. Reagents and condition: (i) 3.1 equiv of NPEDA, TEA, CH2Cl2, rt, 1 h; (ii) TEA, CHCl3, reflux, 6 h.
to the hydrogen bonding with the NH group. Hence
energy minimization (MM2) calculations were carried
out on the cyclophane amide 14, which reveals that
the acetyl group is projecting out of the cavity (Fig. 1).
Such preferred orientation could be due to the smaller
cavity, which pushes the acetyl group out of the cavity.
Triamide 20 was reacted with 1,3,5-benzene tricarboxyl-
ic acid chloride 19 in presence of TEA under very high
dilution conditions at reflux for 6 h to give bicyclic
hexaamide 21 in 15% yield (Scheme 5). Hexaamide 21
in pure form was insoluble in usual NMR solvents;
hence NMR spectrum could not be recorded. However,
cyclophane 21 in FAB mass spectrum showed the
molecular ion at m/z 720.
In order to synthesize cyclophane amides with aza link-
ages, the diamide 6 was reacted with 4,5-bis (chloro-
methyl) o-xylene and 1,3-bis (4-bromomethyl phenyl)
benzene in presence of anhyd K2CO3 in acetonitrile un-
der reflux for 24 h to give cyclophane diamides 17 and
18 in 35% and 40% yield, respectively (Scheme 4).
The 3D structure of the cyclophane amide 21 would be
interesting and there is a possibility for a cylindrical cav-
ity with the two trisubstituted aromatic rings as spacer
units. However, when MO calculation (MM2) was car-
Cyclophane 17 in the 1H NMR spectrum displayed aro-
matic methyl protons atd 2.15, –NCH2CH2N– protons
as a multiplet at d 3.11–3.89, –NCH2 protons at d 4.49
and amide protons as a broad singlet at d 8.04 in addi-
tion to the aromatic protons. In the 13C NMR spectrum,
the aromatic methyl carbons, –NCH2CH2N– carbons,
–NCH2 carbons and carbonyl carbon appeared at d
19.5, 38.9, 49.8, 51.3, and 170.0 in addition to the aro-
matic carbons and in the mass spectrum the molecular
ion appeared at m/z 608. Similarly cyclophane 18 was
also characterized by spectral and analytical data.
The presence of m-terphenyl group should increase the
cavity size if the cyclophane amide 18 is really rigid.
Hence MO calculation (MM2) was carried out on cyclo-
phane amide 18. However, the molecule adopted con-
cave nature and the biphenyl unit is twisted due to the
strain caused by the presence of large m-terphenyl group
(Fig. 2).
With a view to synthesize bicyclic hexaamide 21, 1,3,5-
benzene tricarboxylic acid chloride 19 was reacted with
three equivalents of N-phenyl ethylene diamine in pres-
ence of TEA in methylene dichloride to give triamide 20
1
in 62% yield. In H NMR spectrum, triamide 20 dis-
played –NCH2CH2N– protons as multiplet at d 3.22–
3.46, aromatic protons of the tricarbonyl benzene ring
as a singlet at d 8.44 and the amide protons appeared
as a broad singlet at d 8.82 in addition to the aromatic
protons. In mass spectrum the triamide 20 displayed
the molecular ion at m/z 564.
Figure 3. Energy minimization of bicyclic amide 21. Heat of formation
of bicyclic amide 21 is À3.1345 kcal/mol.

P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
7463
ried out on cyclophane 21, it revealed that the two aro-
matic spaces are nearly perpendicular to each other.
This shows that the molecule is not rigid and the dimen-
sion of the cavity is totally controlled by the groups
present in the pillar units [CONPhCH2CH2NHCO]
(Fig. 3).
[MIC] for cyclophane amide 17 is more than 50 lg/mL
against S. aureus, it did not inhibit the growth. Cyclo-
phane amides 8 and 21 exhibited significant activity to-
wards S. aureus. All cyclophane amides inhibited the
growth of St. faecalis except for cyclophane amide 17
at a concentration of 50 lg/mL, since the minimum
inhibitory concentration for cyclophane amide 17 is
more than 50 lg/mL against St. faecalis. Cyclophane
Similarly attempts were made to synthesize triamide 24
from diamine 23 which was synthesized by the reaction
of a-chloroacetanilide with 2-aminothiophenol in
methanolic KOH at rt for 4 h and subsequent reduction
of the resulting amide compound 22 with sodium boro-
hydride (excess) in presence of acetic acid in THF at re-
Table 1. Inhibition effects of cyclophane amides on the growth of
Escherichia coli
Cyclophane
Zone of inhibition (mm)
1
flux for 6 h in 48% overall yield. Compound 22 in H
50 lg/mL
100 lg/mL
150 lg/mL
NMR spectrum displayed –SCH2 and –NH2 protons
at d 3.60 and 4.60 and the amide –NH protons appeared
at d 9.20 in addition to aromatic protons. Diamine 23 in
1H NMR spectrum displayed –SCH2 protons as a triplet
at d 3.00 with J = 4.2 Hz and –NCH2 protons as multi-
plet at d 3.30, in addition to aromatic protons at d 6.30
to 7.40. The –NH2 and –NH protons appeared as broad
singlet at d 4.10. Reaction of 1,3,5-benzene tricarboxylic
acid chloride 19 with 3.1 equivalents of diamine 23 in
presence of TEA in methylene dichloride gave complex
reaction mixture and did not yield precyclophane 24
(Scheme 6).
7
8
10
11
9
12
13
11
10
11
8
14
14
12
12
12
10
11
13
10
9
13
15
16
17
18
21
8
8
7
8
10
12
9
11
8
Table 2. Inhibition effects of cyclophane amides on the growth of
Staphylococcus aureus
Cyclophane
Zone of inhibition (mm)
2.1. Anti-bacterial activity
50 lg/mL
100 lg/mL
150 lg/mL
The bactericidal activity of the cyclophane amides 7–9,
13, 15–18, and 21 was assayed against E. coli, S. aureus,
St. faecalis, and P. vulgaris by disc diffusion method. All
cyclophane amides inhibited the growth of E. coli.
Cyclophane amides 7 and 8 exhibited significant activity
towards E. coli. All cyclophane amides inhibited the
growth of S. aureus except for cyclophane amide 17 at
a concentration of 50 lg/mL of dimethylsulfoxide
(DMSO). Since the minimum inhibitory concentration
7
8
7
12
7
9
14
8
11
15
10
11
11
9
9
13
15
16
17
18
21
8
9
7
9
7
8
—
10
10
7
9
12
12
13
14
Cl
HN
HN
O
SH
O
NH
i
ii
+
S
NH2
S
NH2
NH2
23
60%
22
80%
H
N
S
HN
O
19
iii
H
N
O
HN
S
NH
O
S
NH
24
Scheme 6. Reagents and conditions: (i) KOH, MeOH, rt, 4 h; (ii) NaBH4, AcOH, THF, reflux, 6 h; (iii) TEA, CH2Cl2, rt, 1 h.

7464
P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
Table 3. Inhibition effects of cyclophane amides on the growth of
Streptococcus faecalis
spectra were recorded using JEOL DX-303 mass
spectrometer and FAB MS spectra were recorded using
JEOL SX 102/DA-6000 mass spectrometer using a
m-nitro benzyl alcohol (NBA) matrix. Melting points
were recorded with Gallenkamp melting point appara-
tus. Pre-coated silica gel plates from Merck were used
for TLC. Column chromatography was carried out
using silica gel (60–120 mesh) purchased from Acme.
Cyclophane
Zone of inhibition (mm)
50 lg/mL
100 lg/mL
150 lg/mL
7
8
7
8
9
10
7
10
12
9
9
6
13
15
16
17
18
21
7
8
9
8
10
9
11
12
10
14
8
4.2. General procedure for the preparation of diamide 6
and triamide 20
8
—
12
6
9
13
7
Diphenic acid chloride 4 (1.5 mmol)/1,3,5-benzene tri-
carboxylic acid chloride 19 (1.0 mmol) in methylene
chloride (10 mL) was added to a mixture of N-phenyl
ethylene diamine (3.0 mmol), TEA (3.0 mmol) in meth-
ylene chloride (30 mL) for 1 h at room temperature after
which the reaction mixture was washed with water and
dried over anhyd MgSO4. After removing the solvent
under vacuum, the residue was chromatographed over
SiO2 to give diamide 6/triamide 20.
Table 4. Inhibition effects of cyclophane amides on the growth of
Proteus vulgaris
Cyclophane
Zone of inhibition (mm)
50 lg/mL
100 lg/mL
150 lg/mL
7
8
10
12
11
8
12
14
12
9
13
15
13
10
8
4.2.1. Diamide 6. Yield: 60% (430 mg); mp 180–183 ꢁC;
eluent for column chromatography: CHCl3/MeOH
9
13
15
16
17
18
21
1
(99:1); H NMR: (400 MHz, CDCl3) d 2.87–3.50 (m,
—
9
7
8H), 4.30 (br s, 2H), 6.45–7.45 (m, 18H), 9.90 (br s,
2H); IR (KBr, cmÀ1): 3342, 2944, 1664, 1530; MS
(EI): m/z: 478; Elemental Anal. calcd for C30H30N4O2:
C, 75.30; H, 6.27; N, 11.7. Found: C, 75.27; H, 6.11;
N, 11.6.
10
8
11
9
—
9
11
8
12
10
7
18 exhibited significant activity towards St. faecalis. All
cyclophane amides inhibited the growth of P. vulgaris
except for cyclophane amides 15 and 17 at a concentra-
tion of 50 lg/mL, since the MIC for cyclophane amides
15 and 17 is more than 50 lg/mL against P. vulgaris.
Cyclophane 8 exhibited significant activity towards P.
vulgaris. The standard antibiotic disc (Streptomycin
10 lg/ disc) inhibited the growth of E. coli by 12 mm,
S. aureus by 15 mm, St. faecalis by 13 mm and P. vulga-
ris by 12 mm, respectively. The diameter of inhibition
zone for each concentration against all the test bacteria
is depicted in Tables 1–4.
4.2.2. Triamide 20. Yield: 62% (350 mg); mp 198–201 ꢁC;
eluent for column chromatography: CHCl3/MeOH
(19:1); 1H NMR: (400 MHz, DMSO-d6) d 3.22–3.46
(m, 12H), 5.70 (br s, 3H), 6.50–7.08 (m, 15H), 8.44 (s,
3H), 8.82 (br s, 3H); IR (KBr, cmÀ1): 3342, 2944,
1654,1521; MS (EI): m/z: 564; Elemental Anal. calcd
for C33H36N6O3: C, 70.19; H, 6.43; N, 14.8. Found: C,
70.22; H, 6.32; N, 14.6.
4.3. General procedure for the synthesize of cyclophane
tetraamides 7–11
A solution of the diacid chloride (0.5 mmol) in dry chlo-
roform (100 mL) and a solution of the diamine
(0.5 mmol) and triethyl amine (1.1 mmol) in dry chloro-
form (100 mL) were simultaneously added dropwise
during 6 h to a well-stirred solution of chloroform
(500 mL) at reflux. After the addition was complete,
the reaction mixture was refluxed for another 6 h. The
solvent was removed at reduced pressure and the residue
obtained was then dissolved in chloroform (300 mL),
washed with water (2· 100 mL) to remove the triethyl-
ammonium chloride and dried over magnesium sulfate.
Removal of the chloroform gave the cyclophane as a
crude material, which was purified by column chroma-
tography (SiO2) with suitable eluting solvent as men-
tioned under each cyclophane.
3. Conclusion
In conclusion, cyclophane diamides, cyclophane tetraa-
mides, and bicyclic hexaamide have been synthesized,
characterized and the bactericidal activity of the cyclo-
phane amides 7–9, 13, 15–18, and 21 was assayed
against E. coli, S. aureus, St. faecalis, and P. vulgaris
by disc diffusion method. Cyclophane amides 7, 8, and
18 could be used as potential compounds to ward-off
the diseases caused by these bacteria.
4. Experimental
4.1. General directions
4.3.1. Cyclophane tetraamide 7. Yield: 35% (117 mg); mp
207–210 ꢁC; eluent for column chromatography: CHCl3/
MeOH (99:1); 1H NMR: (400 MHz, CDCl3) d 2.98–4.70
(m, 8H), 4.08 and 4.53 (ABq, 4H, J = 14.1 Hz), 6.64–
1
All H NMR and 13C NMR were recorded in CDCl3
and DMSO-d6 with JEOL Model: GSX 400. EI-MS

P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
7465
7.67 (m, 22H), 7.87 (br s, 2H); 13C NMR: (100.4 MHz,
CDCl3) d 38.7, 47.9, 66.5, 122.8, 128.1, 128.6, 129.0,
129.6, 130.2, 134.4, 177.9; IR (KBr, cmÀ1): 3253, 1677,
1594; FAB MS (M+): m/z: 668; Elemental Anal. calcd
for C40H36N4O6: C, 71.84; H, 5.43; N, 8.38. Found: C,
71.75; H, 5.59; N, 8.33.
4.4.1. Cyclophane amide 13. Yield: 45% (47 mg); mp
220–222 ꢁC; eluent for column chromatography:
CHCl3/MeOH (99:1); H NMR: (400 MHz, DMSO-d6)
d 4.76 (s, 4H), 7.04–7.63 (m, 8H), 9.71 (s, 2H); IR
(KBr, cmÀ1): 3058, 1640, 1593; MS (EI): m/z: 208; Ele-
mental Anal. calcd for C16H14N2O4: C, 64.42; H, 4.69;
N, 9.39. Found: C, 64.48; H, 4.68; N, 9.38.
1
4.3.2. Cyclophane tetraamide 8. Yield: 40% (170 mg); mp
194–197 ꢁC; eluent for column chromatography: CHCl3/
4.4.2. Cyclophane amide 14. Yield: 40% (68 mg); mp
218–220 ꢁC; eluent for column chromatography:
CHCl3/MeOH (99:1); H NMR: (400 MHz, DMSO-d6)
d 2.58 (s, 3H), 5.01 (s, 4H), 6.47–7.81 (m, 7H), 10.72
(s, 2H); IR (KBr, cmÀ1): 3023, 2787, 1740,1669, 1581;
MS (EI): m/z: 340 Elemental Anal. calcd for
C18H16N2O5: C, 63.52; H, 4.74; N, 8.23. Found: C,
63.54; H, 4.77; N, 8.22.
1
MeOH (99:1); H NMR: (400 MHz, CDCl3) d 2.36 (s,
1
6H), 3.18–3.72 (m, 8H), 5.00 and 5.17(ABq, 4H,
J = 13.2 Hz), 6.50–7.84 (m, 28H), 8.26 (br s, 2H); 13C
NMR: (100.4 MHz, CDCl3) d 19.8, 38.6, 47.9, 68.7,
111.8, 120.6, 127.1,127.4, 127.7, 127.8, 128.1, 129.1,
129.4, 129.7, 129.8, 130.2, 132.1, 135.9, 136.8, 140.4,
141.6, 154.1, 170.4; IR (KBr, cmÀ1): 3253, 1655, 1593;
FAB MS (M+): m/z: 848; Elemental Anal. calcd for
C54H48N4O6: C, 76.39; H, 5.70; N, 6.60. Found: C,
76.55; H, 5.59; N, 6.53.
4.4.3. Cyclophane amide 15. Yield: 43% (73 mg); mp
208–210 ꢁC; eluent for column chromatography:
CHCl3/MeOH (99:1); H NMR: (400 MHz, DMSO-d6)
1
4.3.3. Cyclophane tetraamide 9. Yield: 33% (135 mg); mp
260–263 ꢁC; eluent for column chromatography: CHCl3/
MeOH (99:1); 1H NMR: (400 MHz, CDCl3) d 3.28–4.02
(m, 8H), 5.01 and 5.15 (ABq, 4H, J = 12.4 Hz), 6.80–
7.51 (m, 30H), 7.98 (br s, 2H); 13C NMR: (100.4 MHz,
CDCl3) d 39.6, 48.2, 70.0, 112.5, 121.0, 126.5, 127.1,
127.3, 127.5, 127.6, 127.9, 128.9, 129.7, 130.6, 136.1,
136.9, 1396.5, 142.4, 154.7, 170.4; IR (KBr, cmÀ1):
3222, 1640, 1595; FAB MS (M+): m/z: 820; Elemental
Anal. calcd for C52H44N4O6: C, 76.08; H, 5.40; N,
6.82. Found: C, 76.25; H, 5.50; N, 6.53.
d 2.54 (s, 3H), 4.33 (s, 2H), 5.11(s, 2H), 6.47–7.81 (m,
7H), 10.72 (s, 1H), 12.56 (s, 1H); 13C NMR:
(100.4 MHz, DMSO-d6) d 26.6, 65.7, 101.5, 107.5,
114.0, 116.3, 122.2, 123.5, 125.4, 133.1, 163.8, 164.2,
166.2; IR (KBr, cmÀ1): 3020, 2777, 1745,1663, 1591;
MS (EI): m/z: 340; Elemental Anal. calcd for
C18H16N2O5: C, 63.52; H, 4.74; N, 8.23. Found: C,
63.55; H, 4.75; N, 8.46.
4.4.4. Cyclophane amide 16. Yield: 43% (73 mg); mp
214–216 ꢁC; eluent for column chromatography:
CHCl3/MeOH (99:1); H NMR: (400 MHz, DMSO-d6)
1
4.3.4. Cyclophane tetraamide 10. Yield: 37% (127 mg);
mp 274–276 ꢁC; eluent for column chromatography:
d 2.55 (s, 3H), 4.34 (s, 2H), 5.10 (s, 2H), 6.48–7.64 (m,
7H), 10.72 (s, 1H), 11.89 (s, 1H); 13C NMR:
(100.4 MHz, DMSO-d6) d 22.0, 66.3, 95.4, 102.9,
109.9, 113.8,116.4, 122.2, 123.5, 125.5, 134.1, 158.0,
160.2, 166.4; IR (KBr, cmÀ1): 3020, 2902,
1726,1672,1620,1542; MS (EI): m/z: 340; Elemental
Anal. calcd for C18H16N2O5: C, 63.52; H, 4.74; N,
8.23. Found: C, 63.54; H, 4.73; N, 8.42.
1
CHCl3/MeOH (99:1); H NMR: (400 MHz, CDCl3) d
2.93–3.91 (m, 8H), 6.85–8.04 (m, 26H), 8.65 (br s, 2H);
13C NMR: (100.4 MHz, CDCl3) d 39.9, 41.0, 48.2,
48.6, 106.1, 126.6, 126.8, 127.4, 127.8, 127.9, 128.6,
129.0, 129.5, 130.1, 130.3, 131.2, 131.7, 136.3, 142.8,
164.7, 170.4; IR (KBr, cmÀ1): 3284, 1636, 1593; FAB
MS (M+): m/z: 684; Elemental Anal. calcd for
C44H36N4O4: C, 77.17; H, 5.30; N, 8.18. Found: 77.25;
H, 5.40; N, 8.53.
4.5. General procedure for the preparation of cyclophane
amides 17–18 by N-alkylation
4.3.5. Cyclophane tetraamide 11. Yield: 35% (127 mg);
mp 240–242 ꢁC; eluent for column chromatography:
A mixture of dihalo compound (0.5 mmol), diamide 6
(0.5 mmol), anhydrous potassium carbonate (2.0 mmol),
two crystals of KI and acetonitrile (600 mL) was re-
fluxed for 24 h. The reaction mixture was filtered and
the solvent was evaporated under vacuum. The crude
cyclophane amide was purified by column
chromatography.
1
CHCl3/MeOH (99:1); H NMR: (400 MHz, CDCl3) d
3.06–4.50 (m, 8H), 6.79–7.82 (m, 21H), 8.74 (br s, 2H);
IR (KBr, cmÀ1): 3058, 1640, 1593; FAB MS (M+): m/
z: 609; Elemental Anal. calcd for C37H31N5O4: C,
72.89; H, 5.13; N, 11.5. Found: C, 72.81; H, 5.16; N,
11.3.
4.5.1. Cyclophane amide 17. Yield: 35% (107 mg); mp
230–232 ꢁC; eluent for column chromatography:
4.4. General procedure for the preparation of cyclophane
amides 13–16 by O-alkylation
1
CHCl3/MeOH (99:1); H NMR: (400 MHz, CDCl3) d
2.15 (s, 6H), 3.11–3.89 (m, 8H), 4.49 (s, 4H), 6.70–7.41
(m, 20H), 8.04 (br s, 2H); 13C NMR: (100.4 MHz,
CDCl3) d 19.5, 38.9, 49.8, 51.3, 112.8, 117.2, 126.9,
127.6, 127.9, 128.3, 128.6, 129.3, 129.6, 132.9, 133.2,
135.2, 139.6, 145.0, 148.7, 170.0; IR (KBr, cmÀ1):
3311, 1636, 1578; FAB MS: m/z: 608; Elemental Anal.
calcd for C40H40N4O2: C, 78.92; H, 6.62; N, 9.20.
Found: C, 78.68; H, 6.48; N, 9.41.
A mixture of dichloro compound (0.5 mmol), dihydroxy
compound (0.5 mmol), anhydrous potassium carbonate
(2.0 mmol), two crystals of KI and acetonitrile (600 mL)
was refluxed for 12 h. The reaction mixture was filtered
and the solvent was evaporated under vacuum. The
crude cyclophane amide was purified by column
chromatography.

7466
P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
4.5.2. Cyclophane amide 18. Yield: 40% (107 mg); mp
188–190 ꢁC; eluent for column chromatography:
sulfate. After removing ether, the residue was chromato-
graphed over SiO2 to give diamine 23 as a clear liquid.
1
CHCl3/MeOH (99:1); H NMR: (400 MHz, CDCl3) d
3.23–3.47 (m, 8H), 4.45 (s, 4H), 6.68–7.64 (m, 30H),
8.24 (br s, 2H); 13C NMR: (100.4 MHz, CDCl3) d 37.0,
49.7, 53.3, 112.4, 112.5, 125.8, 126.6, 127.0, 127.3, 127.7,
129.0, 129.2, 129.3, 129.4, 139.7, 141.2, 170.3; IR (KBr,
cmÀ1): 3247, 1640, 1597, 1503. FAB MS: m/z: 732; Ele-
mental Anal. calcd for C50H44N4O2: C, 81.94; H, 6.05;
N, 7.65. Found: C, 81.68; H, 6.18; N, 7.41.
4.8.1. Diamine 23. Yield: 60% (3.1 g); eluent for column
chromatography: hexane/CHCl3 (1:1); 1H NMR:
(90 MHz, CDCl3) d 3.00 (t, 2H, J = 4.2 Hz), 3.30 (m,
2H), 4.10 (br s, 3H), 6.30–7.40 (m, 9H); IR (KBr,
cmÀ1): 3332, 2934, 1664, 1521; MS (EI): m/z: 244; Ele-
mental Anal. calcd for C14H16N2S: C, 68.81; H, 6.60;
N, 11.4. Found: C, 68.77; H, 6.41; N, 11.5.
4.6. General procedure for the synthesize of bicyclic
hexaamide 21
4.9. Anti-bacterial assay method
The disc diffusion assay was used to determine the anti-
bacterial activity of the test compounds using
E. coli, P. vulgaris (Gram negative) and S. aureus, St.
faecalis (Gram positive) as the test bacteria. Various
concentrations of cyclophane amides 7–9, 13, 15–18
and 21 were prepared by dissolving 50 lg, 100 lg and
150 lg in 1 mL of dimethylsulfoxide (DMSO). The syn-
thetic compounds were loaded into the filter paper disc
in different concentration [50 lg, 100 lg, 150 lg]; the
discs were air-dried. Base plates were prepared by
pouring 10 mL of Nutrient agar (NA) into the sterile
Petri plates and allowed to set. The bacteria were sub-
cultured in nutrient broth from which 100 lL of cell
suspension was taken and its OD was adjusted to
0.5, after which this was spread as a thin film over
the nutrient agar plates. Then the loaded filter paper
discs were placed on the surface of nutrient agar plates.
The plates were incubated at 37 ꢁC for 24 h and inhibi-
tion zone was thus measured. DMSO (150 lL) loaded
filter paper disc was used as negative control. The stan-
dard antibiotic disc (streptomycin 10 lg/disc) was used
as positive control.
A solution of the 1,3,5-benzene tricarboxylic acid
chloride (0.5 mmol) in dry chloroform (100 mL) and a
solution of the diamine (0.5 mmol) and triethyl amine
(1.6 mmol) in dry chloroform (100 mL) were simulta-
neously added dropwise during 6 h to a well-stirred solu-
tion of chloroform (500 mL) at reflux. After the addition
was complete, the reaction mixture was refluxed for
another 6 h. The solvent was removed at reduced pres-
sure and the residue obtained was then dissolved in chlo-
roform (300 mL), washed with water (2· 100 mL) to
remove the triethylammonium chloride and dried over
magnesium sulfate. Removal of the chloroform gave
the cyclophane as a crude material, which was purified
by column chromatography (SiO2).
4.6.1. Bicyclic hexaamide 21. Yield: 15% (54 mg); mp
>300 ꢁC; eluent for column chromatography: CHCl3/
MeOH (19:1); IR (KBr, cmÀ1): 3324, 1665, 1598; FAB
MS: m/z: 720; Elemental Anal. calcd for C42H36N6O6:
C, 69.99; H, 5.03; N, 11.6. Found: C, 69.91; H, 5.06;
N, 11.4.
4.7. General procedure for the synthesize of compound 22
Acknowledgments
To a solution of KOH (19.7 mmol) in methanol (40 mL)
was added 2-aminothiophenol (19.2 mmol) followed by
monohalide (15.0 mmol) at 30 ꢁC with stirring. After
stirring for 4 h, the solid obtained was filtered with suc-
tion, washed with methanol (25 mL) and then with
water (50 mL) and dried with suction to give pure com-
pound 22.
P.R. and A.R. thank CSIR, New Delhi, for financial
assistance, UGC SAP for providing facility to the
Department, SAIF, IIT, Chennai, for NMR spectra,
RSIC, CDRI, Lucknow, for FAB MS.
References and notes
4.7.1. Compound 22. Yield: 80% (3.1 g); mp 178–180 ꢁC;
1H NMR: (90 MHz, CDCl3) d 3.60 (s, 2H), 4.60 (br s,
2H) 6.40 7.60 (m, 9H), 9.20 (br s, 1H); IR (KBr,
cmÀ1): 3332, 2934, 1664, 1521; MS (EI): m/z: 258; Ele-
mental Anal. calcd for C14H14N2OS: C, 65.09; H, 5.46;
N, 10.8. Found: C, 65.27; H, 5.31; N, 10.7.
1. Ulrich, L. Liebigs Ann. Chem. 1987, 11, 949.
2. Dirk, L.; Rainer, A. J. B.; Helmar, G. Liebigs Ann. 1994,
1, 199.
3. Jingsong, Y.; Xiaoqi, Y.; Changlu, L.; Rugang, X. Synth.
Commun. 1999, 29, 2447.
4. Thomas, R. W.; Yuan, F.; Cynthia, J. B. J. Org. Chem.
1989, 54, 1584.
5. Yukito, M.; Junichi, K.; Hiroaki, T. J. Chem. Soc., Chem.
Commun. 1985, 753.
6. Hosseini, M. W.; Lehn, J. M.; Duff, S. R.; Gu, K.; Mertes,
M. P. J. Org. Chem. 1987, 52, 1662.
7. Lehn, J. M. Science (Washington, DC) 1985, 227, 849.
8. Yohannes, P. G.; Mertes, M. P.; Mertes, K. B. J. Am.
Chem. Soc. 1985, 107, 8288.
4.8. General procedure for the synthesize of diamine 23
To a mixture of compound 22 (1 g, 4.0 mmol) and sodi-
um borohydride (10 g, excess) in THF (50 mL) was add-
ed glacial acetic acid (6 mL) at reflux for 6 h. After 6 h of
reflux, the reaction mixture was cooled and quenched
with ice water (200 mL). The organic layer was extracted
with ether (4· 25 mL). The ether extracts were washed
with water (2· 25 mL) and dried over anhydrous sodium
9. Dobler, M. In Comprehensive Supramolecular Chemistry;
Gokul, G. W., Ed.; Pergamon: New York, 1996; 1, p 267.

P. Rajakumar et al. / Bioorg. Med. Chem. 14 (2006) 7458–7467
7467
10. Bradshaw, J. S.; Izatt, R. M.; Bordunov, A. V.; Zhu, C.
Y.; Hathway, J. K.. In Comprehensive Supramolecular
Chemistry; Gokel, G. W., Ed.; Pergamon: New York,
1996; 1, p 35.
11. Weber, E.; Vogtle, F.. In Comprehensive Supramolecular
Chemistry; Vogtle, F., Ed.; Pergamon: New York, 1996; 2,.
12. Weber, E. Kontakte (Merck) 1983, 38.
13. Fujita, T.; Lehn, J. M. Tetrahedron Lett. 1988, 29,
1709.
21. (a) Jhaumeer-Laulloo, B. S.; Witvrouw, M. Ind. J. Chem.
2000, 39B, 842; (b) Jhaumeer-Laulloo, B. S. Asian J.
Chem. 2000, 12, 775.
22. Eun, J. J.; Soo, Y. S. Bull. Kor. Chem. Soc. 2002, 23,
1483.
23. Ranganathan, D.; Haridas, V.; Kuru, S.; Nagaraj, R.
J. Am. Chem. Soc. 1999, 121, 7156.
24. Karle, I. L.; Ranganathan, D.; Haridas, V. J. Am. Chem.
Soc. 1998, 120, 6903.
14. Irie, S.; Yamamoto, M.; Kishikawa, K.; Kohmoto, S.;
Yamada, K. Synthesize 1995, 1179.
25. Ranganathan, D.; Haridas, V.; Nagaraj, R.; Karle, I. L.
J. Org. Chem. 2000, 65, 4415.
15. Roelens, S. J. Org. Chem. 1992, 57, 1472.
16. Chen, G.; Lean, J. T.; Alcala, M.; Mallouk, T. E. J. Org.
Chem. 2001, 66, 3027.
17. Costero, A. M.; Banuls, M. J.; Aurell, M. J.; Ward, M. D.;
Argent, S. Tetrahedron 2004, 60, 9471.
26. Vogtle, F.; Dunnwald, T.; Schmidt, T. Acc. Chem. Res.
1996, 29, 451.
27. (a) Rajakumar, P.; Rasheed, A. M. A. Tetrahedron 2005,
61, 5351; (b) Hiromi, K.; Toyoshi, K. Tetrahedron 1987,
43, 4519.
18. Brian, R.; Unai, E.; Troels, S. J. Chem. Soc. Perkin Trans.
2002, 1, 1723.
28. Bruce, H. R.; Andrew, D. H. J. Chem. Soc., Chem.
Commun. 1987, 171.
19. Christopher, A. H.; Duncan, H. P. Angew. Chem. Int. Ed.
Engl. 1992, 31, 792.
29. Sulekh, C.; Sangeetika, T.; Shalini, T. Transit. Metal
Chem. 2004, 29, 925.
20. Kyu, C. S.; Donna, V. E.; Erkang, F.; Andrew, D. H.
J. Am. Chem. Soc. 1991, 113, 7640.
30. Ashu, C.; Saurabh, D.; Ratan, S.; Singh, R. V. J. Ind.
Chem. Soc. 2002, 79, 371.