Nine N-aryl-2-chloronicotinamides: Supramolecular structures in one, two and three dimensions

Article abstract of DOI:10.1107/S0108768106015497

Structures are reported here for eight further substituted N-aryl-2-chloronicotinamides, 2-ClC₅H₃NCONHC ₆H₄X-4′. When X = H, compound (I) (C ₁₂H₉ClN₂O), the molecules are linked

Full text of DOI:10.1107/S0108768106015497

research papers
Acta Crystallographica Section B
Structural
Nine N-aryl-2-chloronicotinamides: supramolecular
Science
structures in one, two and three dimensions
ISSN 0108-7681
Silvia Cuffini,a Christopher
Glidewell,b* John N. Low,c
Aline G. de Oliveira,d
Marcus V. N. de Souza,d
Thatyana R. A. Vasconcelos,d
Solange M. S. V. Wardelld and
James L. Wardelle
Structures are reported here for eight further substituted N-
2-ClC5H3NCONHC6H4X-40.
Received 28 January 2006
Accepted 27 April 2006
aryl-2-chloronicotinamides,
When X = H, compound (I) (C12H9ClN2O), the molecules
are linked into sheets by N—Hꢀ ꢀ ꢀN, C—Hꢀ ꢀ ꢀꢀ(pyridyl) and
C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds. For X = CH3, compound
0
ꢀ
(II) (C13H11ClN2O, triclinic P1 with Z = 2), the molecules are
linked into sheets by N—Hꢀ ꢀ ꢀO, C—Hꢀ ꢀ ꢀO and C—
Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds. Compound (III), where X =
F, crystallizes as a monohydrate (C12H8ClFN2OꢀH2O) and
sheets are formed by N—Hꢀ ꢀ ꢀO, O—Hꢀ ꢀ ꢀO and O—Hꢀ ꢀ ꢀN
hydrogen bonds and aromatic ꢀꢀ ꢀ ꢀꢀ stacking interactions.
Crystals of compound (IV), where X = Cl (C12H8Cl2N2O,
monoclinic P21 with Z0 = 4) exhibit inversion twinning: the
molecules are linked by N—Hꢀ ꢀ ꢀO hydrogen bonds into four
independent chains, linked in pairs by C—Hꢀ ꢀ ꢀꢀ(arene)
a
ˆ
´
ˆ
Agencia Cordoba Ciencia-Unidad Ceprocor,
Cordoba, Argentina, bSchool of Chemistry,
´
University of St Andrews, St Andrews, Fife KY16
9ST, Scotland, cDepartment of Chemistry,
University of Aberdeen, Meston Walk, Old
Aberdeen AB24 3UE, Scotland, dFunda¸cao
˜
Oswaldo Cruz, Far Manguinhos, Rua Sizenando
Nabuco, 100 Manguinhos, 21041-250 Rio de
hydrogen bonds. When
X
=
Br, compound (V)
e
´
Janeiro-RJ, Brazil, and Instituto de Quımica,
(C12H8BrClN2O), the molecules are linked into sheets by
N—Hꢀ ꢀ ꢀO and C—Hꢀ ꢀ ꢀN hydrogen bonds, while in
compound (VI), where X = I (C12H8ClIN2O), the molecules
are linked into a three-dimensional framework by N—Hꢀ ꢀ ꢀO
´
ˆ
Departamento de Quımica Inorganica, Univer-
sidade Federal do Rio de Janeiro, CP 68563,
21945-970 Rio de Janeiro-RJ, Brazil
and
C—Hꢀ ꢀ ꢀꢀ(arene)
hydrogen
bonds
and
an
Correspondence e-mail: cg@st-andrews.ac.uk
iodoꢀ ꢀ ꢀN(pyridyl) interaction. For X = CH3O, compound
(VII) (C13H11ClN2O2), the molecules are linked into chains by
a single N—Hꢀ ꢀ ꢀO hydrogen bond. Compound (VIII)
0
ꢀ
(C13H8ClN3O, triclinic P1 with Z = 2), where X = CN, forms
a complex three-dimensional framework by N—Hꢀ ꢀ ꢀN, C—
Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀO hydrogen bonds and two independent
aromatic ꢀꢀ ꢀ ꢀꢀ stacking interactions.
1. Introduction
Nicotinic acid (pyridine-3-carboxylic acid) and nicotinamide
(niacinamide, pyridine-3-carboxamide) are two of the prin-
cipal members of the B-vitamin complex. Niacin, nicotinamide
and nicotinic acid have identical vitamin activities, but they
have very different pharmacological activities. Nicotinamide,
via its major metabolite nicotinamide adenine dinucleotide, is
involved in a wide range of biological processes including the
production of energy, the synthesis of fatty acids, cholesterol
and steroids, signal transduction, and the maintenance of the
integrity of the genome. Nicotinic acid in pharmacological
doses is used as an antihyperlipidemic agent: it also causes
vasodilation of cutaneous blood vessels. Nicotinamide has
been investigated as an agent for the prevention or delay of
the onset of type 1 diabetes mellitus. It also has anti-oxidant,
anti-inflammatory and anti-carcinogenic activities, and has
putative activity against osteoarthritis and granuloma annu-
lare. We have made a study of the properties and activities of
substituted derivatives, 2-chloro-N-(4-X-phenyl)nicotina-
# 2006 International Union of Crystallography
Printed in Great Britain – all rights reserved
Acta Cryst. (2006). B62, 651–665
doi:10.1107/S0108768106015497 651

research papers
2.2. Data collection, structure solution and refinement
mides, and here we report the structures and supramolecular
arrangements of nine examples having X = H (I), Me (II), F
(III), Cl (IV), Br (V), I (VI), OMe (VII) and CN (VIII), and
including the recently reported analogue with X = NO2, (IX)
(de Souza et al., 2005).
Here we report the molecular and supramolecular struc-
tures of eight closely related N-aryl-2-chloronicotinamides, 2-
ClC5H3NCONHC6H4X-40, whose crystallization character-
istics prove to be all different, even within the halogen-
substituted subset, (III)–(VI), and whose supramolecular
structures all prove to be different, with no two utilizing the
same combination of direction-specific intermolecular inter-
actions.
Details of cell data, data collection and structure solution
and refinement are summarized in Table 1 (Bruker, 2004;
Cernik et al., 1997; Ferguson, 1999; McArdle, 2003; Otwi-
nowski & Minor, 1997; Sheldrick, 1997a,b, 2003; Hooft, 1999).
The space groups for (I), (IV), (V), VI) and (VII) were all
assigned uniquely from the systematic absences: crystals of
(II), (III) and (VIII) are triclinic, and for each the space group
ꢀ
P1 was selected, and confirmed by the successful structure
analysis. The structures were all solved by direct methods
using SHELXS97 (Sheldrick, 1997a) and refined on F2 with all
data using SHELXL97 (Sheldrick, 1997b). A weighting
scheme based upon P = [Fo2 + 2Fc2]/3 was employed in order to
reduce statistical bias (Wilson, 1976). All H atoms were
located from difference maps and all were included in the
refinements as riding atoms, with distances C—H 0.95 and N—
˚
H 0.88 A, and with Uiso(H) = 1.2Ueq(C,N). For (V) and (VII),
the correct enantiomorph was selected using the Flack para-
meter (Flack, 1983): the final values were 0.031 (7) and
ꢂ0.05 (7), respectively. For (IV), where the crystals were all of
very poor quality, the Flack parameter 0.54 (11) indicated
inversion twinning.
Supramolecular analyses were made and the diagrams were
prepared with the aid of PLATON (Spek, 2003). Figs. 1–30
show the independent components of (I)–(VIII) and aspects
of their supramolecular structures. Selected torsional angles
are given in Table 2 and details of the hydrogen bonding are in
Table 3.1
3. Results and discussion
3.1. Crystallization characteristics
Compounds (II) and (VIII) both crystallize with Z0 = 2,
while (IV) has Z0= 4; similarly, the 4-nitrophenyl derivative
(IX) crystallizes with Z0 = 2 (de Souza et al., 2005). Of the
compounds (I)–(VIII) reported here, the 4-fluorophenyl
derivative is unique in crystallizing as a monohydrate,
although the 2-nitrophenyl analogue reported recently (de
Souza et al., 2005) also crystallizes as a stoichiometric mono-
hydrate.
2. Experimental
2.1. Synthesis
Samples of (I)–(VIII) were prepared by reaction of equi-
molar quantities of 2-chloronicotinoyl chloride and the
appropriate substituted aniline in tetrahydrofuran solution at
ambient temperature in the presence of a catalytic quantity of
triethylamine. After stirring for 8 h, the reaction mixtures
were neutralized with saturated aqueous sodium hydrogen-
carbonate solution and the resulting aqueous mixtures were
extracted with ethyl acetate (2 ꢁ 30 cm3). For each prepara-
tion, the organic extracts were combined, dried over anhy-
drous sodium sulfate, and then concentrated under reduced
pressure. Chromatography on silica, using hexane:ethyl
acetate gradients (up to 50% ethyl acetate), then yielded the
pure products, with yields in the range 80–90%. Crystals of (I),
(II) and (IV)–(VIII) suitable for single-crystal X-ray diffrac-
tion were grown from solution in ethanol, and crystals of (III)
were grown from an aqueous solution: m.p.s: (I) 395–397 K,
(II) 432–433 K, (III) 366–367 K, (IV) 421–422 K, (V) 399–
400 K, (VI) 448–450 K, (VII) 383–384 K and (VIII) 445–
446 K.
3.2. Molecular conformations
In each of compounds (I)–(VIII), as well as in (IX) (de
Souza et al., 2005), the central C—C—N—C spacer unit is
nearly planar, as shown by the torsional angles for this unit
which are all close to 180ꢃ, ranging between 170.0 (3) and
ꢂ173.4 (2)ꢃ (Table 2). However, the aryl ring is often mark-
edly twisted out of this plane, particularly in (II), (IV), (V),
(VI) and (VII), while the chloropyridyl is always twisted well
away from the plane of the central spacer, being nearly
orthogonal to this plane in (II), (VI), (VIII) and (IX). An
alternative way to consider the overall conformations is by
1 Supplementary data for this paper are available from the IUCr electronic
archives (Reference: BM5033). Services for accessing these data are described
at the back of the journal.
ꢄ
652 Silvia Cuffini et al.
Nine N-aryl-2-chloronicotinamides
Acta Cryst. (2006). B62, 651–665

research papers
Table 1
Experimental details.
(I)
(II)
(III)
(IV)
Crystal data
Chemical formula
Mr
Cell setting, space group
Temperature (K)
˚
a, b, c (A)
C12H9ClN2O
232.66
Orthorhombic, Pccn
120 (2)
13.2296 (6), 21.0744 (10),
7.6898 (16)
90, 90, 90
C13H11ClN2O
246.69
ꢀ
Triclinic, P1
120 (2)
9.6824 (6), 11.3082 (7),
11.5139 (7)
77.453 (2), 73.445 (2), 87.978
(2)
1179.07 (13)
4
1.390
Synchrotron,
ꢄ = 0.67510 A
C12H8ClFN2OꢀH2O
C12H8Cl2N2O
267.10
Monoclinic, P21
120 (2)
5.0855 (8), 28.982 (8),
15.607 (4)
90, 90.37 (2), 90
268.67
Triclinic, P1
ꢀ
120 (2)
6.8033 (4), 8.1303 (3),
11.5356 (6)
84.032 (3), 84.297 (2), 69.569
(3)
593.32 (5)
2
1.504
Mo Kꢁ
ꢁ, ꢂ, ꢃ (ꢃ)
3
˚
V (A )
2144.0 (5)
8
1.442
2300.2 (9)
8
1.543
Z
Dx (Mg mꢂ3
Radiation type
)
Mo Kꢁ
Mo Kꢁ
˚
No. of reflections for cell
parameters
2446
6881
2720
9787
ꢅ range (ꢃ)
3.1–27.5
0.33
2.1–28.8
0.31
3.3–27.8
0.33
3.0–27.5
0.55
ꢆ (mmꢂ1
)
Crystal form, colour
Crystal size (mm)
Needle, colourless
0.24 ꢁ 0.09 ꢁ 0.02
Needle, colourless
0.10 ꢁ 0.02 ꢁ 0.02
Plate, colourless
0.18 ꢁ 0.16 ꢁ 0.03
Plate, colourless
0.28 ꢁ 0.07 ꢁ 0.03
Data collection
Diffractometer
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.943
0.993
17 837, 2446, 1724
Bruker SMART APEX2
CCD diffractometer
Fine-slice ! scans
Multi-scan
0.970
0.994
12 982, 6881, 5217
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.933
0.990
12 303, 2720, 1943
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.862
0.984
24 726, 9787, 6370
Data collection method
Absorption correction
Tmin
Tmax
No. of measured, indepen-
dent and observed
reflections
Criterion for observed
reflections
Rint
ꢅmax (ꢃ)
I > 2ꢈ(I)
I > 2ꢈ(I)
I > 2ꢈ(I)
I > 2ꢈ(I)
0.104
27.5
0.022
28.8
0.052
27.8
0.053
27.5
Range of h, k, l
ꢂ16 ) h ) 17
ꢂ27 ) k ) 27
ꢂ9 ) l ) 9
ꢂ13 ) h ) 13
ꢂ16 ) k ) 16
ꢂ16 ) l ) 16
ꢂ8 ) h ) 8
ꢂ9 ) k ) 10
ꢂ14 ) l ) 14
ꢂ6 ) h ) 6
ꢂ37 ) k ) 37
ꢂ20 ) l ) 20
Refinement
Refinement on
F2
0.059, 0.129, 1.07
2446
145
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0479P)2 +
1.6007P], where P = (Fo2
2Fc2)/3
F2
0.044, 0.124, 1.02
6881
309
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0648P)2 +
0.3225P], where P = (Fo2
2Fc2)/3
F2
0.044, 0.113, 1.05
2720
163
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0536P)2 +
0.1705P], where P = (Fo2
2Fc2)/3
F2
0.069, 0.169, 1.04
9787
254
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0454P)2 +
5.774P], where P = (Fo2
2Fc2)/3
R[F2 > 2ꢈ(F2)], wR(F2), S
No. of reflections
No. of parameters
H-atom treatment
Weighting scheme
+
+
+
+
(Á/ꢈ)max
Áꢉmax, Áꢉmin (e A
Absolute structure
0.001
0.28, ꢂ0.28
0.001
0.43, ꢂ0.30
<0.0001
0.26, ꢂ0.29
0.001
0.79, ꢂ0.54
ꢂ3
˚
)
–
–
–
Flack (1983), 4396 Friedel
pairs
0.54 (11)
Flack parameter
–
–
–
(V)
(VI)
(VII)
(VIII)
Crystal data
Chemical formula
Mr
Cell setting, space group
Temperature (K)
˚
a, b, c (A)
C12H8BrClN2O
311.56
Orthorhombic, P212121
120 (2)
4.8810 (2), 13.3448 (2),
18.3974 (3)
90, 90, 90
C12H8ClIN2O
358.55
Orthorhombic, Pbca
120 (2)
10.6597 (2), 25.9833 (3),
9.2044 (6)
90, 90, 90
C13H11ClN2O2
262.69
Orthorhombic, P212121
120 (2)
4.8536 (2), 11.8437 (4),
21.0612 (7)
90, 90, 90
C13H8ClN3O
257.67
ꢀ
Triclinic, P1
120 (2)
7.2885 (3), 7.7607 (3),
20.8849 (9)
96.456 (2), 92.913 (2), 91.810
ꢁ, ꢂ, ꢃ (ꢃ)
(2)
3
˚
V (A )
Z
1198.33 (6)
4
1.727
2549.38 (18)
8
1.868
1210.69 (6)
4
1.441
1171.49 (8)
4
1.461
Dx (Mg mꢂ3
Radiation type
)
Mo Kꢁ
Mo Kꢁ
Mo Kꢁ
Mo Kꢁ
ꢄ
Acta Cryst. (2006). B62, 651–665
Silvia Cuffini et al.
Nine N-aryl-2-chloronicotinamides 653

research papers
Table 1 (continued)
(V)
(VI)
2909
(VII)
2661
(VIII)
5365
No. of reflections for cell
parameters
2736
ꢅ range (ꢃ)
3.0–27.5
3.64
3.0–27.5
2.71
3.6–27.5
0.31
2.9–27.6
0.32
ꢆ (mmꢂ1
)
Crystal form, colour
Crystal size (mm)
Block, colourless
0.16 ꢁ 0.16 ꢁ 0.16
Plate, colourless
0.33 ꢁ 0.18 ꢁ 0.07
Block, colourless
0.34 ꢁ 0.22 ꢁ 0.12
Block, colourless
0.40 ꢁ 0.10 ꢁ 0.10
Data collection
Diffractometer
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.558
0.558
36 201, 2736, 2597
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.469
0.833
19 649, 2909, 2314
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.921
0.964
7884, 2661, 2184
Bruker–Nonius 95 mm CCD
camera on ꢇ goniostat
’ and ! scans
Multi-scan
0.899
0.969
21 639, 5365, 3760
Data collection method
Absorption correction
Tmin
Tmax
No. of measured, indepen-
dent and observed
reflections
Criterion for observed
reflections
Rint
ꢅmax (ꢃ)
I > 2ꢈ(I)
I > 2ꢈ(I)
I > 2ꢈ(I)
I > 2ꢈ(I)
0.047
27.5
0.038
27.5
0.040
27.5
0.060
27.6
Range of h, k, l
ꢂ6 ) h ) 6
ꢂ17 ) k ) 17
ꢂ23 ) l ) 23
ꢂ13 ) h ) 13
ꢂ32 ) k ) 33
ꢂ11 ) l ) 11
ꢂ5 ) h ) 6
ꢂ15 ) k ) 11
ꢂ21 ) l ) 27
ꢂ9 ) h ) 9
ꢂ10 ) k ) 10
ꢂ27 ) l ) 26
Refinement
Refinement on
F2
0.023, 0.060, 1.07
2736
154
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0339P)2 +
0.2964P], where P = (Fo2
2Fc2)/3
F2
0.023, 0.056, 1.04
2909
154
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.026P)2 +
0.5926P], where P = (Fo2
2Fc2)/3
F2
F2
0.059, 0.171, 1.06
5365
325
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0844P)2 +
1.0407P], where P = (Fo2
2Fc2)/3
R[F2 > 2ꢈ(F2)], wR(F2), S
No. of reflections
No. of parameters
H-atom treatment
Weighting scheme
0.042, 0.104, 1.04
2661
164
Constrained to parent site
w = 1/[ꢈ2(Fo2) + (0.0579P)2],
where P = (Fo2 + 2Fc2)/3
+
+
+
(Á/ꢈ)max
Áꢉmax, Áꢉmin (e A
Absolute structure
0.001
0.43, ꢂ0.52
0.005
0.39, ꢂ0.78
<0.0001
<0.0001
0.74, ꢂ0.35
ꢂ3
˚
)
0.24, ꢂ0.35
Flack (1983), 1013 Friedel
pairs
ꢂ0.05 (7)
Flack (1983), 1098 Friedel
pairs
0.031 (7)
–
–
Flack parameter
–
–
3.3. Supramolecular structures
means of the dihedral angle denoted Á between the two rings
of each molecule, also shown in Table 2. It is striking to note
the relationships between the conformations of the four
independent molecules in (IV), shown particularly clearly by
the dihedral angles Á: molecules 1 and 2, containing N21 and
N41 respectively, are close to being enantiomorphs, as are
molecules 3 and 4 containing N61 and N81. However, the
relationships between molecules 1 and 3, and between mole-
cules 2 and 4 is that of diastereoisomers. The wide range of the
dihedral angles Á in (I)–(IX), varying from 10.2 (2)ꢃ in (VII)
to 89.4 (2)ꢃ in molecule 2 of (VIII), indicates that the intra-
molecular barriers to rotation about the C—C bonds
connecting the rings to the central spacer unit are rather
readily overcome by the intermolecular forces, in particular by
the direction-specific hydrogen bonds. In this way the
observed conformations are an indirect reflection of the action
of the hydrogen bonds, just as the detailed supramolecular
aggregation patterns are a direct reflection of the action of the
hydrogen bonds. The bond lengths and angles present no
unusual features.
3.3.1. Compound (I). In the unsubstituted parent
compound, (I) (Fig. 1), the molecules are linked into sheets by
a combination of N—Hꢀ ꢀ ꢀN, C—Hꢀ ꢀ ꢀꢀ(pyridyl) and C—
Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds, but N—Hꢀ ꢀ ꢀO hydrogen
bonds are absent (Table 3). The formation of the sheets is most
conveniently analysed and described in terms of the chains
formed by the N—Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀꢀ(pyridyl) hydrogen
bonds, and the linkage of the chains by the C—Hꢀ ꢀ ꢀꢀ(arene)
hydrogen bonds.
The amidic N21 atom in the molecule at (x; y; z) acts as a
hydrogen-bond donor to the pyridyl N11 atom in the molecule
1
at (12 ꢂ x; y; ꢂ þ z), thus forming a C(7) (Bernstein et al.,
2
1995) chain running parallel to the [001] direction and
generated by the c glide plane at x = 0.25. This chain is rein-
forced by the —Hꢀ ꢀ ꢀꢀ(pyridyl) hydrogen bond, where the C16
atom in the molecule at (x; y; z) acts as a donor to the pyridyl
ring in the molecule at (21 ꢂ x; y; 12 þ z), thus forming a [001]
chain of rings generated by the c glide plane at y = 0.25 (Fig. 2).
ꢄ
654 Silvia Cuffini et al.
Nine N-aryl-2-chloronicotinamides
Acta Cryst. (2006). B62, 651–665

research papers
Table 2
linked into a chain of edge-fused rings by a single,
nearly linear C—Hꢀ ꢀ ꢀO hydrogen bond, where the
pyridyl C35 atom in molecule 2 at (x; y; z) acts as a
hydrogen-bond donor to the O1 atom in molecule 1
at (1 ꢂ x; 1 ꢂ y; 1 ꢂ z). Propagation by translation
and inversion of these three hydrogen bonds, two of
the N—Hꢀ ꢀ ꢀO type and one of the C—Hꢀ ꢀ ꢀO type,
generates a chain of centrosymmetric, edge-fused
rings along (x; 12 ; 21), with R24ð16Þ rings centred at
(n; 12 ; 21) (n = zero or integer) and R44ð20Þ rings
Selected torsional and dihedral angles (ꢃ).
C13—C17—N21—C21
C12—C13—C17—N21
C17—N21—C21—C22
Á†
(I)
178.8 (2)
ꢂ56.2 (4)
ꢂ171.8 (2)
48.2 (2)
(II)
175.30 (13)
175.77 (13)‡
ꢂ99.53 (16)
ꢂ141.82 (15)
59.8 (2)
62.9 (2)
ꢂ103.14 (16)†
166.05 (14)†
(III)
171.39 (18)
130.5 (2)
174.60 (18)
62.6 (2)
1
2
centred at (n þ ; 12 ; 21) (n = zero or integer; Fig. 7).
(IV)
There are two C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds
in the structure of (II) (Table 3): one, having the C34
atom as the donor, lies within the [100] chain of rings,
but the other, having C14 as the donor, links the
[100] chains into sheets. The C14 atom in molecule 1
at (x; y; z) lies in the chain along (x; 12 ; 21): this atom
acts as a donor to the phenyl ring C41–C46 in
molecule 2 at (1 ꢂ x; 2 ꢂ y; ꢂz), which lies in the
175.0 (6)
ꢂ176.7 (6)‡
173.9 (6)‡
ꢂ176.9 (6)‡
135.5 (8)
ꢂ137.9 (8)†
134.4 (8)†
ꢂ138.0 (8)†
149.0 (6)
ꢂ148.6 (5)†
ꢂ141.9 (6)†
144.9 (5)†
78.2 (3)
77.8 (3)
12.4 (3)
11.5 (3)
(V)
178.86 (17)
51.3 (3)
ꢂ77.3 (2)
ꢂ134.5 (2)
143.6 (2)
ꢂ135.9 (2)
141.0 (2)
17.2 (2)
35.4 (2)
10.2 (2)
(VI)
172.75 (19)
1
chain along (x; 32 ; ꢂ ). Propagation by inversion of
2
(VII)
ꢂ179.41 (18)
this C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bond then links
[100] chains into a (011) sheet (Fig. 8). There are no
direction-specific interactions between adjacent
sheets.
(VIII)
170.3 (3)
ꢂ174.2 (3)‡
ꢂ73.7 (4)
ꢂ163.6 (3)
60.9 (2)
89.4 (3)
90.9 (3)†
177.8 (3)†
3.3.3. Compound (III). The 4-fluorophenyl deri-
vative crystallizes as a monohydrate, compound
(III), and in the selected asymmetric unit (Fig. 9) the
two components are linked by an N—Hꢀ ꢀ ꢀO
hydrogen bond: this utilization of the N—H donor
site immediately precludes the formation of the
characteristic amidic C(4) chain. Instead the mole-
cules are linked into chains of edge-fused rings by a
combination of O—Hꢀ ꢀ ꢀO and O—Hꢀ ꢀ ꢀN hydrogen
bonds (Table 3), and these chains are linked into
sheets by a single aromatic ꢀꢀ ꢀ ꢀꢀ stacking interac-
tion.
(IX)§
173.29 (19)
ꢂ173.4 (2)‡
78.1 (3)
ꢂ71.5 (3)†
ꢂ179.8 (2)
73.3 (2)
73.6 (3)
173.6 (2)†
† Á is the dihedral angle between the two rings in each independent molecule. ‡ In molecule 2 of
(II), (IV), (VIII) and (IX) the relevant atom sequence is C32—C33—C37—N41—C41—C42; in
molecules 3 and 4 of (IV) the relevant atom sequences are C52—C53—C57—N61—C61—C62 and
C72—C73—C77—N81—C81—C82, respectively (see Figs. 5, 12 and 25). § Data from de Souza et al.
(2005).
Four chains of this type pass though each unit cell, two each in
the domains 0.25 < y < 0.75 and ꢂ0.25 < y < 0.25, and within
each domain, one chain is generated by the c glide plane at
0.25, and the other, antiparallel to the first, is generated by the
c glide plane at y = 0.75. A simple centrosymmetric motif
serves to link the antiparallel pairs of [001] chains in each
domain to form sheets. The C15 atom in the molecule at
(x; y; z), which is part of a chain generated by the glide plane
at x = 0.25, acts as a hydrogen-bond donor to the phenyl ring in
the molecule at (1 ꢂ x; 1 ꢂ y; 1 ꢂ z), which is part of a chain
generated by the glide plane at x = 0.75 (Fig. 3). Propagation
of this interaction then links all the chains in a given domain of
y into a (010) sheet (Fig. 4): two sheets, related to one another
by the twofold rotation axes parallel to [001], pass through
each unit cell, but there are no direction-specific interactions
between adjacent sheets.
3.3.2. Compound (II). In the 4-methylphenyl derivative (II),
where Z0 = 2 (Fig. 5), the molecules are linked by two inde-
pendent N—Hꢀ ꢀ ꢀO hydrogen bonds (Table 3) into C22ð8Þ
chains (Fig. 6): it is convenient to refer to molecules containing
atoms O1 and O3 as 1 and 2, respectively. Two antiparallel
C22ð8Þ chains pass through each unit cell and these chains are
Figure 1
The molecule of (I) showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
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Table 3
Hydrogen-bond parameters (A, ).
The water atom O2 at (x; y; z) acts as a hydrogen-bond
donor, via H2B, to the amidic atom O1 at (ꢂ1 þ x; y; z), thus
generating by translation a C22ð6Þ chain running parallel to the
ꢃ
˚
D—Hꢀ ꢀ ꢀA
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
(I)
N21—H21ꢀ ꢀ ꢀN11i
C15—H15ꢀ ꢀ ꢀCg1ii†
C16—H16ꢀ ꢀ ꢀCg2iii‡
2.25
2.89
2.87
3.101 (3)
3.535 (3)
3.464 (3)
164
126
121
(II)
N21—H21ꢀ ꢀ ꢀO3
N41—H41ꢀ ꢀ ꢀO1iv
C35—H35ꢀ ꢀ ꢀO1ii
C14—H14ꢀ ꢀ ꢀCg3v§
C34—H34ꢀ ꢀ ꢀCg2ii‡
1.96
1.99
2.48
2.69
2.63
2.827 (2)
2.847 (2)
3.424 (2)
3.398 (2)
3.398 (2)
170
163
174
132
138
(III)
N21—H21ꢀ ꢀ ꢀO2
O2—H2Aꢀ ꢀ ꢀN11vi
O2—H2Bꢀ ꢀ ꢀO1iv
1.91
1.97
1.95
2.837 (2)
2.887 (2)
2.780 (2)
179
161
173
(IV)
N21—H21ꢀ ꢀ ꢀO1iv
N41—H41ꢀ ꢀ ꢀO3iv
N61—H61ꢀ ꢀ ꢀO5vii
N81—H81ꢀ ꢀ ꢀO7vii
C26—H26ꢀ ꢀ ꢀCg5}
C46—H46ꢀ ꢀ ꢀCg4††
2.11
2.00
2.11
2.00
2.76
2.75
2.88
2.87
2.925 (8)
2.833 (8)
2.925 (8)
2.841 (8)
3.444 (8)
3.448 (8)
3.588 (8)
3.579 (8)
153
157
153
159
130
131
132
132
C62—H62ꢀ ꢀ ꢀCg3vii
§
C82—H82ꢀ ꢀ ꢀCg2vii
‡
(V)
N21—H21ꢀ ꢀ ꢀO1iv
2.03
2.56
2.825 (2)
3.405 (3)
169
148
C22—H22ꢀ ꢀ ꢀN11viii
Figure 2
(VI)
N21—H21ꢀ ꢀ ꢀO1ix
Part of the crystal structure of (I) showing the formation of a hydrogen-
bonded chain of rings along [001]. For the sake of clarity, the H atoms not
involved in the motifs shown have been omitted. The atoms marked with
an asterisk (*), a hash (#) or a dollar sign ($) are at the symmetry
2.01
2.65
2.853 (2)
3.404 (2)
160
137
C15—H15ꢀ ꢀ ꢀCg2x‡
(VII)
N21—H21ꢀ ꢀ ꢀO1ii
positions (12 ꢂ x; y ꢂ þ z), (21 ꢂ x; y; 12 þ z) and (x; y; ꢂ1 þ z), respec-
1
2
1.92
2.785 (2)
168
tively.
(VIII)
N21—H21ꢀ ꢀ ꢀN44
N41—H41ꢀ ꢀ ꢀN24xi
C14—H14ꢀ ꢀ ꢀO11xii
C15—H15ꢀ ꢀ ꢀO11ii
C25—H25ꢀ ꢀ ꢀN11xiii
C34—H34ꢀ ꢀ ꢀO31xiv
C35—H35ꢀ ꢀ ꢀO31ii
C45—H45ꢀ ꢀ ꢀN31xiii
2.15
2.10
2.49
2.60
2.52
2.53
2.45
2.53
3.006 (4)
2.978 (4)
3.334 (4)
3.507 (4)
3.348 (4)
3.327 (4)
3.366 (4)
3.300 (4)
164
173
148
160
146
142
161
138
1
2
1
2
1
2
Symmetry codes: (i) ꢂ x; y; ꢂ þ z; (ii) 1 ꢂ x; 1 ꢂ y; 1 ꢂ z; (iii) ꢂ x; y; 12 þ z; (iv)
ꢂ1 þ x; y; z; (v) 1 ꢂ x; 2 ꢂ y; ꢂz; (vi) 1 ꢂ x; 2 ꢂ y; 1 ꢂ z; (vii) 1 þ x; y; z; (viii)
ꢂx; 12 þ y; 12 ꢂ z; (ix) x; 21 ꢂ y; 12 þ z; (x) ꢂ þ x; 12 ꢂ y; 1 ꢂ z; (xi) ꢂ2 þ x; 1 þ y; z; (xii)
1
2
1 ꢂ x; ꢂy; 1 ꢂ z; (xiii) 1 þ x; ꢂ1 þ y; z; (xiv) ꢂ1 ꢂ x; 1 ꢂ y; ꢂz. † Cg1 is the centroid
of ring N11, C12–C16. ‡ Cg2 is the centroid of ring C21–C26. § Cg3 is the centroid of
ring C41–C46. } Cg5 is the centroid of ring C81–C86. †† Cg4 is the centroid of ring
C61–C66.
[100] direction. An antiparallel pair of these C22ð6Þ chains is
linked by the N—Hꢀ ꢀ ꢀO hydrogen bond: the O2 atom at
(x; y; z) acts as a donor, via H2A, to the pyridyl N11 atom at
(1 ꢂ x; 2 ꢂ y; 1 ꢂ z), thus generating a centrosymmetric
R44ð16Þ ring, centred at (21 ; 1; 12). The combination of all the
hydrogen bonds then generates, by translation and inversion, a
chain of edge-fused R44ð16Þ rings along (x; 1; 21) (Fig. 10). There
are two types of ring within this chain and both are centro-
symmetric: those having amidic O atoms as two of the
acceptor sites are centred at (n; 1; 12) (n = zero or integer), and
Figure 3
Part of the crystal structure of (I) showing the centrosymmetric ring built
from C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds, which link the [001] chains into
(010) sheets. For the sake of clarity, the H atoms not involved in the motif
shown have been omitted. The atom marked with an asterisk (*) is at the
symmetry position (1 ꢂ x; 1 ꢂ y; 1 ꢂ z).
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ꢀ
those having water O atoms as two of the acceptor sites are
centred at (n þ ; 1; 21) (n = zero or integer).
[011] chain (Fig. 11), which links the chains of rings into a
(011) sheet.
1
2
The pyridyl rings in the amide molecules at (x; y; z) and
(1 ꢂ x; 1 ꢂ y; 2 ꢂ z) are strictly parallel with an interplanar
3.3.4. Compound (IV). We comment here only briefly on
the supramolecular aggregation of the 4-chlorophenyl
compound (IV). This compound crystallizes in the non-
centrosymmetric space group P21 with Z0 = 4 (Fig. 12), but the
crystal quality was extremely poor, with extensive twinning.
Nonetheless, the main features of the structure are clear
enough: each of the four independent molecules forms a C(4)
chain by translation along [100], built from N—Hꢀ ꢀ ꢀO
hydrogen bonds (Fig. 13), and these chains are linked in pairs
by the C—Hꢀ ꢀ ꢀ ꢀ(arene) hydrogen bonds (Table 3).
˚
spacing of 3.352 (2) A; the ring-centroid separation is
˚
˚
3.618 (2) A, corresponding to a nearly ideal ring offset of
1.362 (2) A. These two amide molecules form parts of the
chains of fused rings along (x; 1; 12) and (x; 0; 23), so that
propagation by inversion of this stacking interaction forms a
Figure 4
Stereoview of part of the crystal structure of (I), showing a hydrogen-
bonded (010) sheet. For the sake of clarity, the H atoms not involved in
the motifs shown have been omitted.
Figure 6
Part of the crystal structure of (II), showing the formation of a C22ð8Þ chain
along [100]. For the sake of clarity, the H atoms bonded to C atoms have
been omitted. The atoms marked with an asterisk (*) or a hash (#) are at
the symmetry positions (ꢂ1 þ x; y; z) and (1 þ x; y; z), respectively.
Figure 7
Figure 5
Stereoview of part of the crystal structure of (II) showing the formation
of a chain of edge fused R24ð16Þ and R44ð20Þ rings along [100]. For the sake
of clarity, the H atoms not involved in the motifs shown have been
omitted.
The two independent molecules of (II) showing the atom-labelling
scheme and the N—Hꢀ ꢀ ꢀO hydrogen bond within the asymmetric unit.
Displacement ellipsoids are drawn at the 30% probability level.
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the 21 screw axis along (0; y; 14) (Fig. 16). The combination of
the [100] and [010] chains then generates a (001) sheet in the
form of a (4,4) net built from a single type of R44ð22Þ ring (Fig.
3.3.5. Compound (V). In the 4-bromophenyl compound (V)
(Fig. 14), the molecules are linked into isolated sheets by a
combination of one N—Hꢀ ꢀ ꢀO and one C—Hꢀ ꢀ ꢀN hydrogen
bond (Table 3). The amidic N21 atom in the molecule at
(x; y; z) acts as a hydrogen-bond donor to the amidic O1 in the
molecule at (ꢂ1 þ x; y; z), so generating by translation a C(4)
chain running parallel to the [100] direction (Fig. 15). Four
chains of this type pass through each unit cell, two in each of
the domains 0 < z < 0.5 and 0.5 < z < 1.0, and within each of
these domains the chains are linked into sheets by a single C—
Hꢀ ꢀ ꢀN hydrogen bond. The aryl C22 atom in the molecule at
(x; y; z) acts as a hydrogen-bond donor to the pyridyl N11
atom in the molecule at (ꢂx; 12 þ y; 21 ꢂ z), so forming a C(8)
chain running parallel to the [010] direction, and generated by
Figure 10
Part of the crystal structure of (III) showing the formation of a hydrogen-
bonded chain of edge-fused rings along [100]. For the sake of clarity, the
H atoms bonded to C atoms have been omitted. The atoms marked with
an asterisk (*), a hash (#) or a dollar sign ($) are at the symmetry
positions (1 ꢂ x; 2 ꢂ y; 1 ꢂ z), (ꢂ1 þ x; y; z) and (ꢂx; 2 ꢂ y; 1 ꢂ z),
respectively.
Figure 8
Stereoview of part of the crystal structure of (II) showing the linking, by
means of a single C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bond, of the [100] chains of
rings into a (011) sheet. For the sake of clarity, the H atoms not involved
in the motifs shown have been omitted.
Figure 11
Stereoview of part of the crystal structure of (III) showing the
centrosymmetric ꢀ-stacking interaction which links the [100] chains into
(011) sheets. For the sake of clarity, the H atoms bonded to C atoms have
been omitted.
Figure 9
The molecular components of (III) showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level.
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Figure 12
The four independent molecules of (IV) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. The atom
labelling for the other three molecules and the conformational differences between the molecules are defined in Table 2.
17). Two sheets of this type pass through each unit cell,
generated by screw axes at y = 0.25 and y = 0.75, respectively,
but there are no direction-specific interactions between adja-
cent sheets: in particular, aromatic ꢀꢀ ꢀ ꢀꢀ stacking interactions
and C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds are absent.
3.3.6. Compound (VI). The molecules of the 4-iodophenyl
compound (VI) (Fig. 18) are linked into sheets by a combi-
nation of one N—Hꢀ ꢀ ꢀO hydrogen bond and one C—
Hꢀ ꢀ ꢀꢀ(arene) hydrogen bond (Table 3) and these sheets are
themselves linked by a single iodoꢀ ꢀ ꢀN(pyridyl) interaction.
The N21 atom in the molecule at (x; y; z) acts as a hydrogen-
bond donor to the O1 atom in the molecule at (x; 12 ꢂ y; 21 þ z),
so forming a C(4) chain running parallel to the [001] direction,
and generated by the c-glide plane at y = 0.25 (Fig. 19). In
addition, the pyridyl C15 atom in the molecule at (x; y; z) acts
as a hydrogen-bond donor to the aryl ring C21—C26 in the
Figure 13
Stereoview of part of the crystal structure of (IV) showing the formation
of four independent C(4) chains along [100]. For the sake of clarity, the H
atoms bonded to C atoms have been omitted.
1
molecule at (ꢂ þ x; 12 ꢂ y; 1 ꢂ z), so forming a chain running
2
parallel to the [100] direction and generated by the 21 screw
axis along (x; 14 ; 21) (Fig. 20). The combination of these two
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hydrogen-bonded motifs then generates a (010) sheet (Fig.
21): two sheets of this type pass through each unit cell, in the
domains ꢂ0.02 < y < 0.52 and 0.48 < y < 1.02. The sole
direction-specific interaction between adjacent sheets is an
iodoꢀ ꢀ ꢀN(pyridyl) interaction, somewhat analogous electro-
nically to an iodoꢀ ꢀ ꢀnitro interaction: the I24 atom in the
molecule at (x; y; z) forms a short contact with the pyridyl N11
atom in the molecule at (32 ꢂ x; 12 þ y; z), with dimensions
manner all the (010) sheets are linked into a continuous three-
dimensional array.
3.3.7. Compound (VII). The supramolecular aggregation of
the 4-methoxyphenyl derivative, compound (VII) (Fig. 23), is
exceptionally simple. A single N—Hꢀ ꢀ ꢀO hydrogen bond
(Table 3) links the molecules into C(4) chains generated by
translation (Fig. 24). Four chain of this type pass through each
unit cell, but there are no direction-specific interactions
between adjacent chains: in particular, C—Hꢀ ꢀ ꢀꢀ(arene)
i
i
ꢃ
˚
Iꢀ ꢀ ꢀN 3.116 (2) A, C—Iꢀ ꢀ ꢀN 167.5 (2) [symmetry code (i)
ꢂ x; 12 þ y; z]. This interaction thus forms a C(10) chain
3
2
(Starbuck et al., 1999) running parallel to the [010] direction
and generated by a b-glide plane at y = 0.75 (Fig. 22): in this
Figure 14
The molecule of (V) showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
Figure 16
Part of the crystal structure of (V) showing the formation of a hydrogen-
bonded C(8) chain along [010]. For the sake of clarity, the H atoms not
involved in the motif shown have been omitted. The atoms marked with
an asterisk (*) or
(ꢂx; 12 þ y; 12 ꢂ z) and (ꢂx; ꢂ þ y; 12 ꢂ z), respectively.
a hash (#) are at the symmetry positions
1
2
Figure 15
Part of the crystal structure of (V) showing the formation of a hydrogen-
bonded C(4) chain along [100]. For the sake of clarity, the H atoms
bonded to C atoms have been omitted. The atoms marked with an
asterisk (*) or a hash (#) are at the symmetry positions (ꢂ1 þ x; y; z) and
(1 þ x; y; z), respectively.
Figure 17
Stereoview of part of the crystal structure of (V) showing the formation
of a hydrogen-bonded (001) sheet of R44ð22Þ rings. For the sake of clarity,
the H atoms not involved in the motifs shown have been omitted.
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hydrogen bonds and aromatic ꢀꢀ ꢀ ꢀꢀ stacking interactions are
both absent.
3.3.8. Compound (VIII). The structure of the 4-cyanophenyl
compound (VIII) (Fig. 25) contains N—Hꢀ ꢀ ꢀN, C—Hꢀ ꢀ ꢀN and
C—Hꢀ ꢀ ꢀO hydrogen bonds (Table 3), as well as aromatic
ꢀꢀ ꢀ ꢀꢀ stacking interactions; the resulting three-dimensional
structure is of considerable complexity, although it is readily
analysed in terms of its constituent one-dimensional sub-
structures. Within the asymmetric unit, the amido N21 atom
acts as a hydrogen-bond donor to the cyano N44 atom: simi-
larly, the amido atom N41 at (x; y; z) acts as a donor to the
cyano N24 atom at (ꢂ2 þ x; 1 þ y; z), so generating by
2
ꢀ
translation a C2ð16Þ chain running parallel to the [210] direc-
Figure 18
The molecule of (VI) showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
Figure 21
Stereoview of part of the crystal structure of (VI) showing the formation
of a hydrogen-bonded (010) sheet. For the sake of clarity, the H atoms not
involved in the motifs shown have been omitted.
Figure 19
Part of the crystal structure of (VI) showing the formation of a hydrogen-
bonded C(4) chain along [001]. For the sake of clarity, the H atoms
bonded to C atoms have been omitted. The atoms marked with an
asterisk (*) or a hash (#) are at the symmetry positions (x; 12 ꢂ y; 21 þ z)
1
and (x; 12 ꢂ y; ꢂ þ z), respectively.
2
Figure 22
Figure 20
Part of the crystal structure of (VI) showing the formation of an
iodoꢀ ꢀ ꢀN(pyridyl) chain along [010]. For the sake of clarity, the H atoms
have been omitted. The atoms marked with an asterisk (*) or a hash (#)
Part of the crystal structure of (VI) showing the formation of a hydrogen-
bonded chain along [100]. For the sake of clarity, the H atoms not
involved in the motif shown have been omitted. The atoms marked with
1
are at the symmetry positions (32 ꢂ x; 21 þ y; z) and (23 ꢂ x; ꢂ þ y; z),
an asterisk (*) or
1
a hash (#) are at the symmetry positions
2
(ꢂ þ x; 12 ꢂ y; 1 ꢂ z) and (21 þ x; 12 ꢂ y; 1 ꢂ z), respectively.
respectively.
2
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tion (Fig. 26). In contrast to the simple chain generated by the
hard hydrogen bonds, the soft hydrogen bonds generate both
molecular ladders and chains of rings (Bernstein et al., 1995).
Atoms C15 and C35 in the bimolecular aggregate at (x; y; z)
act as hydrogen-bond donors respectively to atoms O11 and
O31 in the aggregate at (ꢂ1 þ x; y; z). The individual C—
Hꢀ ꢀ ꢀO hydrogen bonds each generate by translation a C(6)
chain along [100] and, together with the N—Hꢀ ꢀ ꢀN hydrogen
bond within the bimolecular aggregate, they generate a chain
of edge-fused R44ð32Þ rings (Fig. 27). Alternatively, this motif
can be regarded as a molecular ladder, in which the C(6)
chains form the uprights, and N—Hꢀ ꢀ ꢀN hydrogen bonds form
part of each rung.
In a similar way, the C25 and C45 atoms in the bimolecular
aggregate at (x; y; z) act as hydrogen-bond donors respec-
tively to pyridyl atoms N11 and N31 in the aggregate at
(1 þ x; ꢂ1 þ y; z). The individual C—Hꢀ ꢀ ꢀN hydrogen bonds
ꢀ
each generate by translation a C(9) chain along [110] and
together with the N—Hꢀ ꢀ ꢀN hydrogen bond within the
bimolecular aggregate they generate a chain of edge-fused
R44ð28Þ rings (Fig. 28). As before, this motif can be regarded as
a molecular ladder, with the C(9) chains now forming the
uprights and with the N—Hꢀ ꢀ ꢀN hydrogen bonds in the rungs.
Finally, atoms C14 and C34 at (x; y; z) acts as hydrogen-
bond donors respectively to atoms O11 at (1 ꢂ x; ꢂy; 1 ꢂ z)
and O31 at (ꢂ1 ꢂ x; 1 ꢂ y; ꢂz), so generating two distinct
R22ð10Þ rings, both centrosymmetric, and centred respectively
Figure 23
The molecule of (VII) showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
Figure 25
The two independent molecules of (VIII) showing the atom-labelling
scheme and the N—Hꢀ ꢀ ꢀN hydrogen bond within the asymmetric unit.
Displacement ellipsoids are drawn at the 30% probability level.
Figure 24
Part of the crystal structure of (VII) showing the formation of a
hydrogen-bonded C(4) chain along [100]. For the sake of clarity, the H
atoms bonded to C atoms have been omitted. The atoms marked with an
asterisk (*) or a hash (#) are at the symmetry positions (ꢂ1 þ x; y; z) and
(1 þ x; y; z), respectively.
Figure 26
Stereoview of part of the crystal structure of (VIII) showing the
2
ꢀ
formation of a C2ð16Þ chain along [210] built from N—Hꢀ ꢀ ꢀN hydrogen
bonds. For the sake of clarity, the H atoms bonded to C atoms have been
omitted.
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662 Silvia Cuffini et al.
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1
2
1
2
at (12 ; 0; 12) and (ꢂ ; 12 ; 0). The combination of these two rings,
and (ꢂ ; 1; 0), respectively, and their combination thus
ꢀ
generates a second [211] substructure (Fig. 30). The combi-
together with the N—Hꢀ ꢀ ꢀN hydrogen bond within the
ꢀ
ꢀ
ꢀ
asymmetric unit, then generates by inversion a chain of rings
ꢀ
running parallel to the [211] direction (Fig. 29). This chain, in
nation of chains along [100], [110], [210] and [211] suffices to
generate a continuous three-dimensional framework struc-
ture.
turn, is reinforced by a combination of two ꢀꢀ ꢀ ꢀꢀ stacking
interactions. The pyridyl rings containing N11 in the molecules
are (x; y; z) and (1 ꢂ x; 1 ꢂ y; 1 ꢂ z) and are parallel with an
3.3.9. Compound (IX). The structure of the 4-nitrophenyl
analogue (IX) has recently been described (de Souza et al.,
2005) and here we briefly summarize its supramolecular
behaviour. Compound (IX) crystallizes in the space group
P21/n with Z0 = 2, and the molecules are linked by two inde-
pendent N—Hꢀ ꢀ ꢀN hydrogen bonds into C22ð12Þ chains in
which the two independent molecules alternate: however, the
amidic N—Hꢀ ꢀ ꢀO hydrogen bonds which characterize (II)–
(VIII), although not (I), are absent from the structure of (IX).
3.3.10. General comments on the structures. Although the
approximately isosteric requirements of methyl and chloro
substituents on aryl rings often lead to the isomorphism of
corresponding pairs of compounds, the unit-cell dimension
and Z0 values (Table 1) for (II) (X = CH3) and (IV) (X = Cl)
here are entirely distinct. Likewise, the four 4-halogenophenyl
derivatives (III)–(VI) all crystallize in different space groups,
one triclinic, two monoclinic and one orthorhombic. In
contrast to this, we have recently observed:
˚
interplanar spacing of 3.426 (2) A; the ring-centroid separa-
˚
tion is 3.589 (2) A, corresponding to a ring offset of
˚
1.069 (2) A; similarly, the pyridyl rings containing N31 in the
molecules at (x; y; z) and (ꢂ1 ꢂ x; 2 ꢂ y; ꢂz) have an inter-
˚
planar spacing of 3.334 (2) A, with a ring-centroid separation
˚
˚
of 3.658 (2) A and ring offset of 1.505 (2) A. These two
interactions are centred across the inversion centres at (12 ; 21 ; 21)
(i) that the 4-substituted anilinium 2-carboxy-4-nitro-
benzoates [4-XC6H4NH3]+ꢀ[C8H4NO6]ꢂ, for X = H, Cl, Br and
I, are all isomorphous and approximately isostructural
(Glidewell et al., 2005);
(ii) that a series of cyclopenta[g]pyrazolo[1,5-a]pyrimidines
carrying 4-methylphenyl, 4-chlorophenyl or 4-bromophenyl
substituents are all strictly isostructural (Portilla et al., 2005);
and
Figure 27
Stereoview of part of the crystal structure of (VIII) showing the
formation of a chain of edge-fused R44ð32Þ rings along [100] built from N—
Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀO hydrogen bonds. For the sake of clarity, the H
atoms bonded to C atoms, but not involved in the motif shown, have been
omitted.
Figure 28
Stereoview of part of the crystal structure of (VIII) showing the
Figure 29
Stereoview of part of the crystal structure of (VIII) showing the
4
ꢀ
formation of a chain of edge-fused R4ð28Þ rings along [110] built from N—
2
ꢀ
Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀN hydrogen bonds. For the sake of clarity, the H
atoms bonded to C atoms, but not involved in the motif shown, have been
omitted.
formation of a chain of R2ð10Þ rings along [211] built from N—Hꢀ ꢀ ꢀN and
C—Hꢀ ꢀ ꢀO hydrogen bonds. For the sake of clarity, the H atoms bonded to
C atoms, but not involved in the motif shown, have been omitted.
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(iii) that a pair of benzo[f]pyrazolo[3,4-b]quinolines
carrying 4-chlorophenyl or 4-bromophenyl substituents are
also strictly isostructural (Serrano et al., 2005a,b).
As the single substituent in the aryl ring is varied within the
series (I)–(IX), so too are the direction-specific intermolecular
interactions which are manifested in the supramolecular
structures. A very common supramolecular motif found in the
crystal structures of simple amides is the formation of simple
C(4) chains built from N—Hꢀ ꢀ ꢀO hydrogen bonds, with
corresponding C22ð8Þ chains in some cases where Z0 = 2. Such
chains occur in (II), where the chain is of C22ð8Þ type; in (IV),
where there are four independent C(4) chains, and in (V), (VI)
and (VII), each of which forms a single C(4) chain. It is
striking how readily this motif can be disrupted when alter-
native hydrogen-bond acceptor sites are available, so that the
amidic N—H donor has a pyridyl N acceptor in each of (I),
(VIII) and (IX), while in (III) the water O atom acts as the
acceptor to form the amidic N—H bond (Table 3). Despite the
acceptor role for the pyridyl N atom manifested in (I), (VIII)
and (IX), this potential acceptor is completely inactive in each
of (II), (IV) and (VI), while in (III) and (V) this site acts as the
acceptor in O—Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀN hydrogen bonds,
respectively. No obvious pattern of behaviour can be
discerned here and any attempt to rationalize such behaviour
would necessarily be largely, if not entirely, speculative: in this
connection, it should perhaps be emphasized that the inter-
molecular forces involved here are all fairly weak and soft, and
not readily susceptible to quantitative modelling.
For (IV), where X = Cl, (VII) where X = OMe and (IX)
where X = NO2 (de Souza et al., 2005), the supramolecular
structures are all one-dimensional, with isolated chains built
from N—Hꢀ ꢀ ꢀO hydrogen bonds in (VII), similar chains
linked in pairs by C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds in (IV),
and chains built from N—Hꢀ ꢀ ꢀN hydrogen bonds in (IX).
Compounds (IV) and (IX) differ further in that (IV), where
Z0 = 4, contains four independent chains, each containing a
single molecular type, whereas (IX), where Z0 = 2, contains a
single chain where the two independent molecules alternate.
The structures of compounds (I), where X = H, (II), where
X = Me, (III), where X = F, and (V), where X = Br, are all two-
dimensional. N—Hꢀ ꢀ ꢀN hydrogen bonds are present only in
the structure of (I); C—Hꢀ ꢀ ꢀO and C—Hꢀ ꢀ ꢀꢀ(arene)
hydrogen bonds are present only in the structure of (II); O—
Hꢀ ꢀ ꢀO and O—Hꢀ ꢀ ꢀN hydrogen bonds, and aromatic ꢀꢀ ꢀ ꢀꢀ
stacking interactions are present only in the structure of (III);
and C—Hꢀ ꢀ ꢀN hydrogen bonds are present only in the
structure of (V). For the two compounds with three-dimen-
sional supramolecular structures, there are no direction-
specific intermolecular interactions in common: the structure
of (VI), where X = I, is built from N—Hꢀ ꢀ ꢀO and C—
Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds, and iodoꢀ ꢀ ꢀpyridyl interac-
tions, while the structure of (VIII), where X = CN, is built from
N—Hꢀ ꢀ ꢀN, C—Hꢀ ꢀ ꢀN and C—Hꢀ ꢀ ꢀO hydrogen bonds.
3.3.11. Compounds closely related to (I)–(IX). Here we
briefly comment on the supramolecular structures of some
closely related compounds, including two isomers (X) and
(XI) of (IX) (de Souza et al., 2005), and (XII)–(XV) retrieved
from the Cambridge Structural Database (CSD; Allen, 2002).
In (X), the only N—Hꢀ ꢀ ꢀO hydrogen bond is intramole-
cular, so that again the formation of a C(4) chain has readily
been prevented: the molecules of (X) are linked into chains of
centrosymmetric edge-fused R22ð14Þ and R44ð24Þ rings by two
independent C—Hꢀ ꢀ ꢀ.O hydrogen bonds, while the pyridyl N
atom is inactive as an acceptor. In the isomeric compound
Figure 30
Stereoview of part of the crystal structure of (VIII) showing the
formation of a ꢀ-stacked chain along [211]. For the sake of clarity, the H
atoms have been omitted.
ꢀ
ꢄ
664 Silvia Cuffini et al.
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(XI), which unexpectedly crystallizes as a stoichiometric
monohydrate just like compound (III), the amidic N—H bond
acts as a hydrogen-bond donor to the water molecule, and
these bimolecular aggregates are linked by a combination of
O—Hꢀ ꢀ ꢀN and O—Hꢀ ꢀ ꢀO hydrogen bonds to form a chain of
edge-fused rings containing two different types of R44ð16Þ ring.
Thus, despite the different composition and constitutions of
(III) and (XI), their supramolecular aggregation patterns
show a considerable degree of similarity.
Daresbury SRS Station 9.8, for which we thank the EPSRC-
funded synchrotron crystallography service and Professor W.
Clegg. JLW and SMSVW thank CNPq and FAPERJ for
financial support.
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Gdaniec et al., 1979), which may be regarded as the parent
compound for this whole series, forms simple C(4) chains built
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`
(XV) (CSD code ZIKWEX; Pepe et al., 1995), where the
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Nine N-aryl-2-chloronicotinamides 665