Clathrate solvates of tetrakis(4-methoxycarbonylphenyl)porphyrin and its zinc(II)-pyridine complex, in which the porphyrin host structures are stabilized by porphyrin-porphyrin stacking and C-H...O attractions

Article abstract of DOI:10.1107/S010827010600641X

Tetrakis(4-methoxycarbonylphenyl)porphyrin, or tetramethyl 4,4′,4″,4?-porphyrin-5,10,15,20-tetrabenzoate, crystallizes as a nitrobenzene 1.9-solvate, C₅₂H₃₈N₄O ₈·1.9C₆H₅NO₂, (I).

Full text of DOI:10.1107/S010827010600641X

metal-organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
nation polymerization (Goldberg, 2005). In this study, we
characterize the supramolecular organization of the title
compounds, (I) (the free base porphyrin) and (II) (its zinc
pyridine complex), which have not been reported before, and
describe examples of their clathration behaviour. In relation
to the basic tetraphenylporphyrin clathrate host (Byrn et al.,
1993), these two compounds have slightly extended arms,
bearing an additional methoxycarbonyl group on the para
positions of the four phenyl substituents, and thus an increased
propensity, due to their elongated arms, for the formation of
solvates and clathrates (Krishna Kumar et al., 1998). The two
structures were analysed at ca 110 K.
ISSN 0108-2701
Clathrate solvates of tetrakis(4-
methoxycarbonylphenyl)porphyrin
and its zinc(II)±pyridine complex, in
which the porphyrin host structures
are stabilized by porphyrin±porphyrin
stacking and CÐHÁ Á ÁO attractions
Sankar Muniappan, Sophia Liptsman and Israel Goldberg*
School of Chemistry, Sackler Faculty of Exact Sciences, Tel-Aviv University,
Ramat-Aviv, 69978 Tel-Aviv, Israel
Correspondence e-mail: goldberg@post.tau.ac.il
Received 13 February 2006
Accepted 21 February 2006
Online 18 March 2006
Compound (I) crystallizes as a nitrobenzene disolvate
(Fig. 1), with the porphyrin species located on crystallographic
centres of inversion. The macrocyclic core 24-membered ring
Ê
is planar to within Æ0.053 A, except for atom N21, which
Tetrakis(4-methoxycarbonylphenyl)porphyrin, or tetramethyl
4,40,400,4000-porphyrin-5,10,15,20-tetrabenzoate, crystallizes as a
nitrobenzene 1.9-solvate, C52H38N4O8Á1.9C6H5NO2, (I). The
solvent molecules are contained in extended channels which
propagate through the host lattice between parallel screw/
glide-related columns of offset-stacked porphyrin entities.
Side packing of these columns involves ꢀ±ꢀ interactions
between the methoxycarbonylphenyl residues. Molecules of
the porphyrin host lie on crystallographic inversion centres.
The zinc(II)±pyridine derivative pyridine(tetramethyl 4,40,-
400,4000-porphyrin-5,10,15,20-tetrabenzoato)zinc(II), [Zn(C52-
H36N4O8)(C5H5N)], (II), is a square-pyramidal ®ve-coordinate
complex with pyridine as an apical ligand, which crystallizes as
a chloroform±pyridine solvate. The metalloporphyrin±pyri-
dine units form an open layered arrangement, occluding the
non-coordinated solvent moieties within the intralayer inter-
porphyrin voids. Within such arrays, the host porphyrin
molecules are in contact with one another through the
peripheral methoxycarbonyl substituents. The crystal packing
consists of a bilayered arrangement of inversion-related
porphyrin layers, with the axial ligands mutually penetrating
into the voids of neighbouring arrays and tight offset stacking
of these bilayers.
Ê
deviates by 0.118 (2) A from this plane. The four aryl substi-
tuents are oriented roughly perpendicular to the macrocycle in
a typical manner, the dihedral angle between their mean
planes and that of the macrocycle being 60.80 (3)ꢀ for the
C25±C30 group and 69.96 (5)ꢀ for the C35±C40 group.
Moreover, at every site, the methoxycarbonyl fragments are
nearly coplanar with the corresponding aromatic ring to which
they are bound, the dihedral angles between their mean planes
being only 8.8 (1) and 5.7 (1)ꢀ. The two inner pyrrole N-bound
H atoms are disordered between the four N-atom sites.
Comment
Tetraarylporphyrins and -metalloporphyrins are extremely
versatile host scaffolds for the formation of crystalline inclu-
sion compounds with a large number of guest species (Byrn et
al., 1993; Krishna Kumar et al., 1998; Goldberg, 2005). This
involves genuine lattice clathrates (without speci®c bonds
between the porphyrin hosts; Byrn et al., 1993), as well as
structures wherein functionalized porphyrins are interlinked
in two or three dimensions by hydrogen bonding of coordi-
Figure 1
The molecular structure of (I), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 50% probability level at ca
110 K. The porphyrin molecules are located on centres of inversion at
(
x, 1 y, 1 z). H atoms have been omitted.
m140 # 2006 International Union of Crystallography
DOI: 10.1107/S010827010600641X Acta Cryst. (2006). C62, m140±m143

metal-organic compounds
The crystal structure of (I) can be best described as
consisting of offset-stacked porphyrin columns aligned
parallel to the b axis of the crystal (Fig. 2). The mean distance
between the planes of successive porphyrin macrocycles is
ments of adjacent molecules related by the glide/screw
Ê
symmetry of about 3.7 A. Some relatively short intermolecular
CÐHÁ Á ÁO contacts, which may represent attractive inter-
actions, are listed in Table 1. These involve host±host contacts
within as well as between the porphyrin columns, and a
porphyrin±nitrobenzene contact.
The molecular structure of (II) is shown in Fig. 4. Note that
the O63±C64 methoxy substituent exhibits orientational
disorder. Compound (II) represents a square-pyramidal ®ve-
coordinate complex of the porphyrin species, with the inner
Ê
4.15 (5) A. Sideways, the columns are arranged in an
approximate square-grid array. The porphyrin molecules in a
given column are tilted by about 45ꢀ with respect to the
stacking axis (Fig. 3). This intermolecular organization is
associated with the presence of channel voids between the
porphyrin columns, which are accommodated by the nitro-
benzene guest components. The latter are aligned perpendi-
cular to the channel axis, exhibiting antiparallel orientation
between successive species in every channel [related by
Ê
pyrrole N atoms deviating alternately Æ0.021 (1) A from their
Ê
mean plane. The central Zn ion is displaced by 0.340 (1) A
from this N4 plane towards the axial ligand, imparting a domed
1
2
1
2
inversion at (12 x,
y
,
z)]. As shown in Fig. 3, the
porphyrin columns are arranged in a herring-bone fashion,
and their side packing is characterized by stacking interactions
between partly overlapping methoxycarbonylphenyl frag-
Figure 4
The molecular structure of host (II), showing its domed shape and the
atom-labelling scheme. Displacement ellipsoids are drawn at the 40%
probability level at ca 110 K. Note the orientational disorder of the C61±
C64 methoxycarbonyl group (primed atoms).
Figure 2
The crystal packing of (I), viewed approximately down the b axis. Note
the offset-stacked arrangement of the porphyrin molecules that form the
host lattice and the antiparallel arrangement of the nitrobenzene solvent
incorporated within the channel voids. H atoms have been omitted. N and
O atoms are denoted by shaded circles.
Figure 3
Figure 5
A perspective side view of three neighbouring porphyrin columns of (I)
related to one another by the glide/screw symmetry, showing the herring-
bone organization and the stacking interaction between the methoxy-
carbonyl fragments of adjacent columns (see Comment). H atoms have
been omitted for clarity. N and O atoms are denoted by shaded circles.
A
stereoview of the crystal packing of host molecules in (II)
(approximately down a), showing their layered organization edge-on
and the tight packing of the offset-stacked layers along the c axis. Zn, N
and O atoms are denoted by shaded circles. H atoms have been omitted.
ꢁ
Acta Cryst. (2006). C62, m140±m143
Muniappan et al.
C52H38N4O8Á1.904C6H5NO2 and [Zn(C52H36N4O8)(C5H5N)] m141

metal-organic compounds
structure to the metalloporphyrin entity. This is a character-
istic of many ®ve-coordinate complexes of metallated tetra-
arylporphyrins with a single axial ligand [184 hits; Cambridge
Structural Database (CSD), Version 5.27, November 2005
update; Allen, 2002; Lipstman et al., 2006; Lipstman &
Goldberg, 2006]. Otherwise, the intramolecular conforma-
tional features of (II) are similar to those observed in (I).
Thus, the dihedral angles between the mean planes of the
phenyl substituents and the plane of the four pyrrole N atoms
are 67.8 (1), 58.4 (1), 85.4 (1) and 82.1 (1)ꢀ, respectively, for
the C25±C30, C35±C40, C45±C50 and C55±C60 rings. The
mean planes of the corresponding methoxycarbonyl fragments
deviate only slightly from coplanarity with their adjacent
benzene rings, as indicated by the dihedral angles between the
respective phenyl and methoxycarbonyl residues of (in the
same order as above) 5.4 (3), 10.2 (3), 7.0 (3) and 7.0 (5)/
15.4 (4)ꢀ.
ecules. A given node of the open square-grid porphyrin array
is a contact point for the methoxycarbonyl groups of four
different molecules, which are related to one another by a
lattice translation along a or b. Inversion-related layers pack in
a lock-and-key mode, by inserting the axial ligands of one
layer into, and partly occupying, half of the interporphyrin
voids of a neighbouring layer (Fig. 5). The remaining void
space in these layers, and the other half of the interporphyrin
voids in every layer, is accommodated in a disordered manner
and with partial occupancies by molecules of the pyridine and
chloroform solvents. The approximate positions of the solvent
moieties are illustrated in Fig. 6. The bilayer domains thus
formed also stack in an offset manner in order to optimize van
der Waals interactions, by placing the aryl substituents of one
bilayer close to the concave porphyrin surfaces of adjacent
bilayers (Fig. 5).
The above-described porphyrin supramolecular organiza-
tion and solvent clathration features are consistent with earlier
observations in related tetraarylporphyrin materials, which
lack speci®c hydrogen-bonding or coordination interactions
between the porphyrin units [Byrn et al., 1993; Krishna Kumar
et al., 1998; CSD, 457 hits (Allen, 2002)].
The molecules of (II) are arranged in the crystal in a square-
layered fashion approximately perpendicular to the c axis.
Adjacent units in a layer contact one another in all four
directions through the peripheral cis-related methoxycarbonyl
fragments. The corresponding non-bonding contacts between
the carbonyl O atoms of one porphyrin to the methyl C atoms
0
Ê
are O32Á Á ÁC64(x 1, y, z) = 3.356 (5) A and O32Á Á ÁC64 (x 1,
Ê
Ê
1, z) = 3.621 (5) A,
y, z) = 3.141 (6) A, O42Á Á ÁC44(x, y
Experimental
Ê
O52Á Á ÁC44(x + 1, y, z) = 4.425 (5) A and O62Á Á ÁC54(x, y + 1,
Compound (I) was synthesized using the Lindsey method (Lindsey et
al., 1987) by condensation of pyrrole with 4-(methoxycarbon-
yl)benzaldehyde. The crude product was puri®ed by silica-gel
column chromatography using 2% acetone in chloroform as eluent.
Compound (I) was metallated with zinc(II) by reacting (I) (50 mg,
0.06 mmol) with zinc(II) bis(acetate) (133 mg, 0.06 mmol) in
methanol (120 ml), affording the metalloporphyrin derivative, zinc-
(I). The products were con®rmed by 1H NMR and UV±vis (in
tetrahydrofuran) spectra. Diffraction-quality crystals of (I) were
obtained by dissolving 5 mg (0.006 mmol) of the compound in a
minimal amount of chloroform and a few drops of nitrobenzene,
followed by slow evaporation over two weeks. Single crystals of (II)
were prepared by dissolving zinc-(I) (6 mg, 0.0065 mmol) in a small
amount (10 ml) of a chloroform±pyridine mixture (9:1 v/v) with a few
drops of nitrobenzene, followed by slow evaporation in air for 10 d.
Ê
z) = 3.143 (5) A. Additional intermolecular CÐH(phenyl)Á Á Á
O(carbonyl) weak hydrogen-bond type attractions between
neighbouring porphyrin species are also observed (Table 1).
Such supramolecular organization is associated with the
creation of void space between neighbouring porphyrin mol-
Compound (I)
Crystal data
3
C52H38N4O8Á1.904C6H5NO2
Dx = 1.347 Mg m
Mo Kꢂ radiation
Cell parameters from 5804
re¯ections
Mr = 1081.27
Monoclinic, C2=c
Ê
a = 32.6249 (8) A
Figure 6
b = 7.0657 (2) A
ꢃ = 1.4±28.2ꢀ
ꢄ = 0.09 mm
T = 110 (2) K
Ê
1
A face-on view of two overlapping layers in (II), in the form of a crystal
structure projection down the c axis (a horizontal and b vertical). The
upper layer is shown in a space-®lling mode, which also illustrates the
attractive contacts between the terminal methoxycarbonyl groups of
neighbouring porphyrin molecules. The lower porphyrin layer is
represented by a stick framework (except for the Zn ions, which are
denoted by small spheres). Note that the axial ligands of the lower
porphyrin layer penetrate into one set of interporphyrin voids in the
upper porphyrin layer. The approximate sites of the solvent molecules in
the voids of the upper layer (as derived from the conventional
re®nement) are represented by discrete spheres; pyridine is represented
by the larger spheres and chloroform by the smaller spheres.
Ê
c = 23.5160 (8) A
ꢁ = 100.2918 (9)ꢀ
3
Ê
V = 5333.6 (3) A
Z = 4
Prism, purple
0.35 Â 0.20 Â 0.15 mm
Data collection
Nonius KappaCCD area-detector
diffractometer
1ꢀ ' scans
20139 measured re¯ections
6404 independent re¯ections
3904 re¯ections with I > 2ꢅ(I)
Rint = 0.054
ꢃmax = 28.2ꢀ
h = 41 ! 42
k = 9 ! 9
l = 30 ! 30
ꢁ
m142 Muniappan et al. C52H38N4O8Á1.904C6H5NO2 and [Zn(C52H36N4O8)(C5H5N)]
Acta Cryst. (2006). C62, m140±m143

metal-organic compounds
Re®nement
O63±C64 fragment and 0.541 (8) for the O630±C640 fragment. The
structure of (II) was then re®ned as a 1:3 twin. It was found to contain
pyridine and chloroform solvent, which could not be modelled reli-
ably. Conventional re®nement converged at R = 0.088, showing
recognisable frameworks of the solvent species with partial occu-
pancies at well de®ned sites, but with very high anisotropic displa-
cement parameters for the corresponding atoms and with distorted
geometries. Correspondingly, it was preferable to subtract the
contribution of this solvent from the diffraction data using the
SQUEEZE procedure in PLATON (Spek, 2003). The modi®ed
calculations coverged smoothly at a considerably lower R factor,
resulting in a structural model of good precision for the porphyrin
lattice, as discussed in this paper. Standard re®nement calculations of
the entire structure in this case served to locate the guest components
in the lattice. The solvent-accessible voids were estimated to be 31%
of the crystal volume. The residual electron-density count was
assessed as 202 electrons per unit cell, which is consistent with
approximately two molecules of pyridine and two molecules of
chloroform.
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.057
wR(F2) = 0.158
S = 1.02
6404 re¯ections
374 parameters
H-atom parameters constrained
w = 1/[ꢅ2(Fo2) + (0.0865P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢅ)max < 0.001
3
Ê
Áꢆmax = 0.30 e A
3
Ê
0.31 e A
Áꢆmin
=
Compound (II)
Crystal data
[Zn(C52H36N4O8)(C5H5N)]
Mr = 989.32
Orthorhombic, P212121
a = 17.4965 (4) A
b = 18.2617 (2) A
c = 19.0558 (4) A
Ê
V = 6088.6 (2) A
Z = 4
Dx = 1.079 Mg m
Mo Kꢂ radiation
Cell parameters from 7893
re¯ections
ꢃ = 1.4±28.3ꢀ
ꢄ = 0.45 mm
T = 110 (2) K
Ê
Ê
Ê
1
3
Prism, purple
0.45 Â 0.40 Â 0.30 mm
3
Data collection
For both compounds, data collection: COLLECT (Nonius, 1999);
cell re®nement: DENZO (Otwinowski & Minor, 1997); data reduc-
tion: DENZO; program(s) used to solve structure: SIR97 (Altomare
et al., 1994); program(s) used to re®ne structure: SHELXL97 (Shel-
drick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson,
1996) and MERCURY (Bruno et al., 2002); software used to prepare
material for publication: SHELXL97.
Nonius KappaCCD area-detector
diffractometer
1ꢀ ' and ! scans
52179 measured re¯ections
14686 independent re¯ections
9268 re¯ections with I > 2ꢅ(I)
Rint = 0.085
ꢃmax = 28.2ꢀ
h = 23 ! 23
k = 24 ! 24
l = 25 ! 25
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.053
wR(F2) = 0.131
S = 0.90
14686 re¯ections
w = 1/[ꢅ2(Fo2) + (0.0727P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢅ)max = 0.001
This research was supported in part by the Israel Science
Foundation (grant No. 254/04).
3
Ê
Áꢆmax = 0.32 e A
3
Ê
0.40 e A
Áꢆmin
=
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: GD3004). Services for accessing these data are
described at the back of the journal.
649 parameters
H-atom parameters constrained
Absolute structure: Flack (1983),
with 6502 Friedel pairs
Flack parameter: 0.259 (9)
Table 1
ꢀ
Ê
Apparent CÐHÁ Á ÁO interactions (A, ).
References
Allen, F. H. (2002). Acta Cryst. B58, 380±388.
Compound
Contact
CÐH
HÁ Á ÁO
CÁ Á ÁO
CÐHÁ Á ÁO
Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C.,
Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.
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Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389±397.
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Ridge National Laboratory, Tennessee, USA.
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Terzis, A. & Strouse, C. E. (1993). J. Am. Chem. Soc. 115, 9480±9497.
Flack, H. D. (1983). Acta Cryst. A39, 876±881.
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37, 541±552.
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A. M. (1987). J. Org. Chem. 52, 827±836.
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Nonius (1999). COLLECT. Nonius BV, Delft, The Netherlands.
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Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M.
Sweet, pp. 307±326. New York: Academic Press.
(I)
(I)
(I)
(I)
(II)
(II)
C2ÐH2Á Á ÁO43i
0.95
0.95
0.95
0.95
0.95
0.95
2.45
2.30
2.51
2.43
2.40
2.49
3.357 (2)
3.197 (2)
3.296 (3)
3.233 (3)
3.293 (4)
3.418 (4)
160
157
141
143
147
164
C7ÐH7Á Á ÁO32ii
C30ÐH30Á Á ÁO53iii
C40ÐH40Á Á ÁO42iv
C36ÐH36Á Á ÁO62v
C46ÐH46Á Á ÁO32vi
1
1
1
1
1
1
Symmetry codes: (i) x; y; 2 z; (ii) 2 x; 2 y; z; (iii) 2 x; 2 ‡ y; 2 z; (iv) x, 1 ‡ y, z;
1
1
1
1
(v) 1 x; y ‡ 2; 2 z; (vi) 2 ‡ x; 2 y; z.
The H atoms were located in calculated positions and constrained
to ride on their parent atoms, with CÐH distances in the range 0.95±
Ê
0.98 A and with Uiso(H) = 1.2 or 1.5Ueq(C). The positional disorder of
the pyrrole H atoms in (I) is characterized by occupancy factors of
0.42 (3) and 0.58 (3) for atoms H21 and H22, respectively. Molecules
of the nitrobenzene guest occluded in the channels of (I) were re®ned
to have an occupancy of 0.95 at each site. The O63±C64 methoxy
group in (II) reveals orientational disorder, which was reasonably
well characterized. The relative occupancies are 0.459 (8) for the
È
Sheldrick, G. M. (1997). SHELXL97. University of Gottingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
ꢁ
Acta Cryst. (2006). C62, m140±m143
Muniappan et al.
C52H38N4O8Á1.904C6H5NO2 and [Zn(C52H36N4O8)(C5H5N)] m143