Structure and conformational analysis of a macrocyclic ligand: [24, 26-DIOXO-3,6,14,17-tetraazapentacyclo (21.0.11,19.1 3,6.18,12.114,17)Hexacosan-1(23),8(25),9,11,19, 21-hexaene]

Article abstract of DOI:10.1080/15421400390223149

24,26-Dioxo-3,6,14,17-tetraazapentacyclo((21.0.1^1,19.1 ^3,6.1^8,12.1^14,17)hexacosan-1(23),8(25),9,11,19, 21-hexaene, C₂₂H₂₄N₄O₂ FW=376.45, monoclinic, P2₁/n,a = 11.144(2) A, b = 6.395(1) A, c = 13.562(3) A, β = 95.81(1)°, V= 961.5(3) A³, Z =2, D_col = 1.300 Mg/m³, μ = 0.685 mm^-1, F(000)=400, λ (CuKα) = 1.5418 A final R1 and wR2 are 0.0409 and 0.1547, respectively. The macro ligand consists of two phenyl rings and two five-membered rings forming the walls of the central cavity which has roughly a square cross-section. The orientation of the phenyl ring is antiperiplanar and approximately perpendicular to the diazacyclopentanone ring which adopts envelope conformation. The molecules are stabilized by C-H ... O and C-H ... π types of intermolecular interactions in addition to van der Waals forces.

Full text of DOI:10.1080/15421400390223149

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STRUCTURE AND
CONFORMATIONAL ANALYSIS
OF A MACROCYCLIC LIGAND:
[24, 26-DIOXO-3,6,14,17-
TETRAAZAPENTACYCLO
(21.0.1 1,19 .1 3,6 .1 8,12 .1
14,17 )HEXACOSAN-1(23),8(25),9,1
HEXAENE]
S. M. Malathy Sony a , M. Kuppayee a , M. N.
Ponnuswamy a , V. Murali b & P. Rajakumar b
a Department of Crystallography and Biophysics ,
University of Madras , Guindy Campus, Chennai, 600
025, India
b Department of Organic Chemistry , University of
Madras , Guindy Campus, Chennai, 600 025, India
Published online: 18 Oct 2010.
To cite this article: S. M. Malathy Sony , M. Kuppayee , M. N. Ponnuswamy , V.
Murali & P. Rajakumar (2003) STRUCTURE AND CONFORMATIONAL ANALYSIS OF A
MACROCYCLIC LIGAND: [24, 26-DIOXO-3,6,14,17-TETRAAZAPENTACYCLO (21.0.1
1,19 .1 3,6 .1 8,12 .1 14,17 )HEXACOSAN-1(23),8(25),9,11,19,21-HEXAENE], Molecular
Crystals and Liquid Crystals, 399:1, 85-92, DOI: 10.1080/15421400390223149
To link to this article: http://dx.doi.org/10.1080/15421400390223149
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Mol. Cryst. Liq. Cryst., Vol. 399, pp. 85–92, 2003
Copyright # Taylor & Francis Inc.
ISSN: 1542-1406 print/1563-5287 online
DOI: 10.1080/15421400390223149
STRUCTURE AND CONFORMATIONAL
ANALYSIS OF A MACROCYCLIC LIGAND:
[24, 26-DIOXO-3,6,14,17-TETRAAZAPENTACYCLO
(21.0.11,19.13,6.18,12.114,17)HEXACOSAN-
1(23),8(25),9,11,19,21-HEXAENE]{
S. M. Malathy Sony, M. Kuppayee and M. N. Ponnuswamy*
Department of Crystallography and Biophysics,
University of Madras, Guindy Campus,
Chennai-600 025, India
V. Murali and P. Rajakumar
Department of Organic Chemistry,
University of Madras, Guindy Campus,
Chennai-600 025, India
24,26-Dioxo-3,6,14,17-tetraazapentacyclo((21.0.11,19.13,6.18,12.114,17) hexacosan-
1(23),8(25),9,11,19,21-hexaene,
C22H24N4O2,
FW ¼ 376.45,
monoclinic,
P21/n,a ¼ 11.144(2) A, b ¼ 6.395(1) A, c ¼ 13.562(3) A, b ¼ 95.81(1)ꢀ, V ¼
˚
˚
˚
3
961.5(3) A , Z ¼ 2, Dcol ¼ 1.300 Mg/m3, m ¼ 0.685 mm-1, F(000) ¼ 400,
l
˚
˚
(CuKa) ¼ 1.5418 A final R1 and wR2 are 0.0409 and 0.1547, respectively. The
macro ligand consists of two phenyl rings and two five-membered rings forming
the walls of the central cavity which has roughly a square cross-section. The
orientation of the phenyl ring is antiperiplanar and approximately perpendi-
cular to the diazacyclopentanone ring which adopts envelope conformation.
The molecules are stabilized by C-H . . . O and C-H . . . p types of intermolecular
interactions in addition to van der Waals forces.
Keywords: macro ligand; diazacyclopentanone; crystal structure; conformation; hydrogen
bonding
INTRODUCTION
Macrocyclic ligands are closed system compounds containing a minimum of
nine atoms with at least three donor atoms [1]. They are two types: The
{The CDB Reference Number: CCDC200293
*Corresponding author.
85

86
S. M. Malathy Sony et al.
first type are those systems which chiefly contain nitrogen, sulphur,
phosphorus, and arsenic as donors and which tend to have considerable
affinity for transition and other heavy metals but form less stable com-
plexes with ions of the alkali and alkaline earth metals. The second type
consists of a large group of cyclic compounds incorporating numbers of
ether functions as donors. Such crown polyethers show strong complexing
ability towards alkali and alkaline earth ions, but their tendency to coor-
dinate to transition metal ions is less.
There are a number of factors affecting the formation and thermo-
dynamic stabilities of these ion-macrocycle complexes, and thus there exist
unusual opportunities for the synthesis of macrocyclic molecules which
exhibit a high degree of selectivity in metal binding. Their hydrophobic
exteriors allow them to solubilize ionic substances in nonaqueous solvents
and in membrane media [2].
Macrocylic ligands are used as models for protein-metal binding sites in
a substantial array of metalloproteins in biological systems—as synthetic
ionophores, as models to study the magnetic exchange phenomenon, as
therapeutic reagents in chelate therapy for the treatment of metal intox-
ication, as cyclic antibiotics actions to specific metal complexation, and to
the guest-host interactions and in catalysis [3].
Macrocyclic ligands have been used successfully for diverse processes
such as separation of ions by transport through artificial and natural
membranes, liquid-liquid or solid-solid phase transfer reactions, dissolution
in apolar solvents of metal and organic salts, preparation of ionselective
electrodes, isotope separation, and in the understanding of some natural
processes through mimicry of metalloenzymes.
Compounds containing nitrogen donor atoms have been used as models
to explain metal ion–macrocycle reactions in biological systems [4]. The
azacyclophanes show high substrate specificity due to their intrinsic geo-
metrical requirements for host-guest interactions, which give them the
potential to be the superior enzyme models [4]. Due to the above said
importance, the macrocylic ligand [24,26-dioxo-3,6,14,17-tetraazapenta-
cyclo (21.0.11,19.13,6.18,12.114,17)hexacosan-1(23), 8(25),9,11,19,21-hexaene],
which possesses both the nitrogen and the ether group, was structurally
characterized.
EXPERIMENTAL
Synthesis
Equal moles of ethylene diamine and urea were refluxed for 3 h and allowed
to cool. The product imidazoline-2-one was crystallized from benzene. A
fresh N-bromo succinimide was added to m-xylene in CCl4. This mixture

Structure of a Dioxotetraazacyclophane
87
SCHEME 1 Synthetic route for the macro ligand.
was refluxed and added few milligrams of benzoyl peroxide, which was
then cooled and the precipitate obtained was washed. A solution of diazone
(in THF) was added to a suspension of sodium hydride (in THF), refluxed,
and cooled. The dibromide (in THF) solution was added to the reaction
mixture periodically at nitrogen atmosphere in room temperature. This
mixture was refluxed for 16 h and cooled. Dilute hydrochloric acid was
added to the mixture and the precipitate was washed with water. The
cyclophane was recrystallized from methylene chloride (Scheme 1).
X-Ray Data Collection
Transparent parallelopiped-shaped crystal of dimension 0.36
0.2260.28 mm was chosen for the intensity data collection on an Enraf-
Nonius CAD-4 diffractometer with graphite monochromated CuKa
˚
(l ¼ 1.5418 A) radiation. Accurate unit cell parameters were obtained from
25 reflections in the range 15 ꢁ y ꢁ 25ꢀ from least-squares refinement. The
intensities were measured to a maximum y of 72.37ꢀ by o/2y scan
mode. Three standard reflections monitored for every hundred reflections

88
S. M. Malathy Sony et al.
for intensity check showed little or no decay ( < 1%) throughout data
collection. Out of 1973 (Rint ¼ 0.0183) independent reflections collected,
1813 reflections with I ꢂ 2s(I) were used for structure analysis. The
intensities were corrected for Lorentz and polarization effects.
Structure Solution and Refinement
The structure was solved by direct methods using the program SHELXS97
[5] and was refined on F2 by full-matrix least-squares procedures using the
program SHELXL97 [6]. The nonhydrogen atoms were refined aniso-
tropically and all the hydrogens were identified from the difference Fourier
map. The final cycle of refinement converged to R1 ¼ 0.0409 and
wR2 ¼ 0.1547 for the observed reflections. The geometrical calculations
and the figures were done by using the programs PLATON [7] and ZORTEP
[8]. The crystal data and the other relevant parameters are given in Table 1.
The atomic coordinates with their equivalent isotropic displacement fac-
tors for nonhydrogen atoms are presented in Table 2.
TABLE 1 Crystal Data
Empirical formula
Formula weight
C22H24N4O2
376.45
293(2) K
˚
1.5418 A
Monoclinic, P21/n
Temperature
Wavelength
Crystal system, space group
Unit cell dimensions
˚
11.144(2) A
a
˚
6.395(1) A
b
˚
13.562(3) A
c
ꢀ
Volume
95.81(1)ꢀ
961.5(3) A
3
˚
Z, Calculated density
Absorption coefficient
F(000)
2, 1.300 Mg/m3
0.685 mmꢃ1
400
Theta range for data collection
Index ranges
5.41 to 72.37ꢀ
0 ꢁ h ꢁ 13
0 ꢁ k ꢁ 7
ꢃ16 ꢁ 1 ꢁ 16
Reflections collected/unique
Completeness to y ¼ 72.37
Refinement method
1973/1813 [R(int) ¼ 0.0183]
95.5%
Full-matrix least-squares on F2
1813/0/176
1.113
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [1 > 2s(I)]
R indices (all data)
Extinction coefficient
R1 ¼ 0.0409, wR2 ¼ 0.1547
R1 ¼ 0.0530, wR2 ¼ 0.1665
0.053(5)
ꢃ3
˚
Largest diff. peak and hole
0.217 and ꢃ0.216e. A

Structure of a Dioxotetraazacyclophane
89
TABLE 2 Atomic Coordinates (6104) and Equivalent Isotropic Displacement
2
3
˚
Parameters (A 610 ) Involving Nonhydrogen Atoms
Atom
x
y
z
*U(eq)
C1
C2
8236(2)
10593(2)
9516(1)
8861(2)
7811(2)
7892(1)
7038(2)
7091(2)
6045(2)
6083(2)
7172(2)
8903(2)
9202(1)
8182(2)
7735(3)
1979(4)
2341(3)
721(4)
6422(1)
2920(2)
3402(1)
3842(2)
4215(2)
3794(1)
3897(1)
4924(1)
5275(2)
6197(2)
6765(2)
3328(1)
2912(1)
5506(1)
52(1)
64(1)
61(1)
69(1)
67(1)
56(1)
59(1)
50(1)
61(1)
68(1)
62(1)
47(1)
69(1)
50(1)}
N3
C4
C5
N6
1876(4)
3925(2)
5558(4)
6514(3)
7232(3)
8164(4)
8419(3)
4170(3)
5751(2)
6770(3)
C7
C8
C9
C10
C11
C12
O13
C14
*U(eq) ¼ (1/3)Si Sj ai*aj* ai.aj
FIGURE 1 ZORTEP plot of the macro ligand showing the thermal displacement
ellipsoids at 30% probability level.

90
S. M. Malathy Sony et al.
FIGURE 2 Packing of the molecules viewed down b-axis (dotted lines indicate the
hydrogen bonds).
DISCUSSION
The perspective view of the molecule is shown in Figure 1. Only one half
molecule is present in the asymmetric unit, and the unit cell has two
molecules. The half of the molecule is related to the other half through its
inversion center. The macro ligand consists of two phenyl rings and two five
membered rings forming the walls of the central cavity. The bond lengths
around this macrocyclic ring structure are comparable with the literature
values [9,10].
The molecule has roughly a square cross-section, and the size of the
2
˚
cavity is approximately 4.9665.16 A measured between two parallel

Structure of a Dioxotetraazacyclophane
91
TABLE 3 Possible Nonbonded Interactions (Hydrogen Bonds)
< (DHA)ꢀ
˚
d(D-H)A
˚
d(D . . . A)A
˚
d(H . . . A)A
Donor-H . . . Acceptor
C10 ꢃH10 . . . O13i
C5 ꢃH5B . . . O13ii
C4 ꢃH4A . . . O13iii
C7 ꢃH7A . . . Cgiv
0.99(3)
1.03(3)
1.06(3)
1.00(2)
3.357(3)
3.544(3)
3.454(3)
3.777(1)
2.50(3)
2.84(2)
2.65(3)
3.03(1)
144(2)
126(2)
132(2)
132(1)
Cg, Centroid of the diazacyclopentanone ring.
Equivalent positions: i), xꢃ1/2, ꢃyþ1/2, þzþ1/2; ii), ꢃxþ1/2þ1, þyꢃ1/2, ꢃzþ1/2; iii), x,
þyꢃ1, þz; iv), 3/2ꢃx, 1/2þy, 1/2ꢃz.
atoms of the molecule. Any metal ion introduced may be caught in the
cavity of this macro ligand. Normally the orientations of the phenyl rings
can be described as synperiplanar, synclinal, antiperiplanar, and anticlinal
depending on the dihedral angle about the bond connecting the two rings
or angle between the planes [11]. In this molecule the orientation of the
phenyl rings is antiperiplanar as can be seen from the angle between the
planes [180.0(1)ꢀ].
The diazacyclopentanone ring adopts envelope conformation with C4
˚
atom deviating from the best plane by 0.152(2) A. This is also confirmed by
the asymmetry parameters which stand out to be q2 ¼ 0.0943 and
j2 ¼ 40.40 [12]. The phenyl ring is planar and approximately perpendicular
to the diazacyclopentanone ring with the orientation angle of 89.19(9)ꢀ.
The C10 atom in the phenyl ring forms C-H . . . O type of intermolecular
hydrogen bond with O13 atom of the diazacyclopentanone ring, and the C7
atom makes C-H . . . p intermolecular interaction with the phenyl ring.
These interactions pack the molecule in the crystal in such a way that they
are arranged in a linear polymer fashion (Fig. 2). Other than this the
molecules are also stabilized by many C-H . . . O type of intermolecular
interactions in addition to van der Waals forces (Table 3).
REFERENCES
[1] Lindoy, L. F. (1989). The Chemistry of Macrocyclic Ligand Complexes, Cambridge
University Press: Cambridge.
[2] Christensen, J. J., Eatough, D. J., & Izatt, R. M. (1974). Chem. Rev., 74, 351.
[3] Alexander, V. (1995). Chem. Rev., 95, 273.
[4] Izatt, R. M., Bradshaw, J. S., Nielsen, S. A., Lamb, J. D., & Christensen, J. J. (1985). Chem.
Rev., 85, 271.
[5] Sheldrick, G. M. (1997). SHELXS97. Program For The Solution of Crystal Structure,
University of Gottingen: Germany.
[6] Sheldrick, G. M. (1997). SHELXL-97. Program For the Crystal Structure Refinement,
University of Gottingen: Germany.

92
S. M. Malathy Sony et al.
[7] Spek, A. L. (1998). PLATON. A Multipurpose Crystallographic Tool, Utrecht Uni-
versity: Utrecht, The Netherlands.
[8] Zsolani, L. (1997). ZORTEP. Program for Crystal Structure Illustration, University of
Heidelberg: Germany.
[9] Forman, J. E., Marsh, R. E., Schaefer, W. P., & Dougherty, D. E. (1993). Acta. Cryst., B49,
892.
[10] Askawa, M., Ashton, P. R., Brown, C. L., Fyfe, M. C. T., Menzer, S., Pashini, D., Scheuer, C.,
Spencer, N., Stoddart, J. F., White, A. J. P., & Williams, D. J. (1997). J. Chem. Eur., 7,
1136.
[11] Klyne, W. & Prelog, V. (1960). Experientia, 16, 521.
[12] Cremer, D. & Pople, J. A., J. Am. Chem. Soc., 97, 1354.