N-H...N(pyridyl) and N-H...O(urea) hydrogen bonding and molecular conformation of N-aryl-N′-pyridylureas

Article abstract of DOI:10.1016/j.molstruc.2010.01.030

Analysis of N-Ar-N′-4-pyridylureas (Ar = 4-X-phenyl, 4-py) crystal structures shows a gradual transition from urea...pyridyl N-H...N hydrogen bond in bifurcated synthon of R₂¹ (6) graph set (X = H, Me, Cl) to single N-H...O and N-H...N hydrogen bonds in X = Br, I to urea N-H...O tape synthon (R₂¹ (6) graph set) in N-phenyl-N′-tetrafluoropyridylurea. Thus the two extremes of urea pyridyl N-H...N synthon in N,N′-di(4-pyridyl) urea, N-H...O tape characteristic of diphenyl urea together with an in-between state are now visualized as snap shots in the solid-state. Most remarkably, molecular conformations too show a transition: the diaryl urea molecule is in the twisted metastable conformation in N-H...O tape structures, it is coplanar in the flat stable conformation for N-H...N structures, and one NH is in-plane while the other is oriented slightly outwards in the intermediate N-H...O and N-H...N hydrogen-bonded structure of N-4-Br-phenyl-N′-4-pyridylurea. Subtle and yet observable one-to-one molecular conformation to crystal structure systematic effects are analyzed. A one-dimensional zigzag chain in the crystal structure of N,N′-di(4-pyridyl) urea is consistent with the hydrogen bonding model for organic gelators.

Full text of DOI:10.1016/j.molstruc.2010.01.030

Journal of Molecular Structure 968 (2010) 99–107
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
N–H. . .N(pyridyl) and N–H. . .O(urea) hydrogen bonding and molecular
conformation of N-aryl-N0-pyridylureas
*
Sreekanth K. Chandran, Naba K. Nath, Suryanarayan Cherukuvada, Ashwini Nangia
School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
a r t i c l e i n f o
a b s t r a c t
Analysis of N-Ar-N0-4-pyridylureas (Ar = 4-X-phenyl, 4-py) crystal structures shows a gradual transition
from urea. . .pyridyl N–H. . .N hydrogen bond in bifurcated synthon of R12 (6) graph set (X = H, Me, Cl) to
single N–H. . .O and N–H. . .N hydrogen bonds in X = Br, I to urea N–H. . .O tape synthon (R12 (6) graph
set) in N-phenyl-N0-tetrafluoropyridylurea. Thus the two extremes of urea pyridyl N–H. . .N synthon in
N,N0-di(4-pyridyl) urea, N–H. . .O tape characteristic of diphenyl urea together with an in-between state
are now visualized as snap shots in the solid-state. Most remarkably, molecular conformations too show a
transition: the diaryl urea molecule is in the twisted metastable conformation in N–H. . .O tape structures,
it is coplanar in the flat stable conformation for N–H. . .N structures, and one NH is in-plane while the
other is oriented slightly outwards in the intermediate N–H. . .O and N–H. . .N hydrogen-bonded structure
of N-4-Br-phenyl-N0-4-pyridylurea. Subtle and yet observable one-to-one molecular conformation to
crystal structure systematic effects are analyzed. A one-dimensional zigzag chain in the crystal structure
of N,N0-di(4-pyridyl) urea is consistent with the hydrogen bonding model for organic gelators.
Ó 2010 Elsevier B.V. All rights reserved.
Article history:
Received 22 November 2009
Accepted 15 January 2010
Available online 20 January 2010
Keywords:
Hydrogen bond
Conformation
Pyridyl urea
Supramolecular synthon
Graph set
Gelation
1. Introduction
Me, Cl, Br, I, OH) along with the crystal structure of hydrogelator
N,N0-di(4-pyridyl)urea [6,7].
Pyridyl ureas are important in crystal engineering as diverse
structural scaffolds for the organized self-assembly of cocrystals
[1–3], as gelators [4–7], anion recognition and bonding [8–10],
molecular capsules [11–13], and metal–organic frameworks
[14,15]. Hydrogen bonding patterns in crystal structures of pyridyl
ureas [16,17] may be summarized as: (1) urea–pyridyl N–H. . .Npy
hydrogen bonding is quite common in contrast to the well known
urea N–H. . .O tape; (2) recurrence of intramolecular C–H. . .O inter-
action in a planar aryl-pyridyl urea conformation; and (3) binding
of urea NH donors to solvent, anion or cocrystal former species (see
Fig. 1). The occasional occurrence of urea NH. . .O tape was ascribed
2. Results and discussion
2.1. Crystal structures
The starting compounds were prepared and characterized as re-
ported recently [9]. Single crystals were obtained by slow crystal-
lization of the compound from common solvents (see Section 4).
We did not encounter polymorphism in this family of structures
during routine experiments, and neither is a polymorph pair re-
ported for pyridyl ureas to our knowledge.
to specific intermolecular interactions. For example, additional
p-
The crystal structure of N,N0-di(4-pyridyl)urea 1 was deter-
mined to compare perturbation in urea hydrogen bonding motifs
by replacing one X-phenyl with pyridyl ring. There are two mol-
ecules in the asymmetric unit (space group P21/c) of 1; both
molecules have a flat conformation that is stabilized by intramo-
lecular C–H. . .O interaction (2.19–2.26 Å). A one-dimensional zig-
zag chain is formed along [0 0 1] by two symmetry-independent
molecules via bifurcated N–H. . .N hydrogen bonds (2.08, 2.16,
2.01, 2.51 Å) (Fig. 3) in a supramolecular synthon [20] of R12 (6)
graph set notation [21]. Even though one solvate (GASMUJ), se-
ven salts (DIGBUR, DIGCAY, DIGCEC, GASNAQ, KAZVAJ, KAZVEN,
PAQLID) and ten metal coordination structures of dipyridylurea
(EKEJAF, LISDIB, VIMZAT, VINBOK, LISDEX, NAVWEN, SEQGEB,
SEQGIF, SEQGOL, SEQGUR) are reported in the Cambridge Struc-
stacking in naphthyl-pyridyl bis-urea gave a urea tape structure
whereas phenyl-pyridyl bis-urea showed N–H. . .N interaction
[17]. In short, the expected motif in pyridyl ureas is a bifurcated
or single N–H. . .Npy interaction of a planar molecular conforma-
tion. Similar structural trends were observed in diaryl ureas con-
taining an electron-withdrawing phenyl ring instead of pyridyl,
e.g. nitrophenyl [18] or cyanophenyl [19]. We report in this paper
a transition from N–H. . .N pyridyl to N–H. . .O urea hydrogen bond-
ing in N-4-X-phenyl-N0-4-pyridylureas (Fig. 2, substituent X = H,
* Corresponding author. Tel.: +91 40 23011338.
E-mail address: ashwini.nangia@gmail.com (A. Nangia).
0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2010.01.030

100
S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
O
O
O
O
N
H
N
H
N
H
N
H
N
H
N
H
O
O
O
O
N
H
N
H
solvent
urea-solvent
urea-carboxylate
R1 (6) synthon
R2 (8) synthon
2
2
O
O
N
H
N
H
N
H
N
H
N
H
N
H
urea N-H...O tape
R1 (6) synthon
2
N
N
O
N
N
H
H
O
X
N
urea-pyridyl
2
urea-pyridyl
& urea-urea
D motif
N
N
H
R1 (6) synthon
H
intramolecular C-H...O
S(6) synthon
Fig. 1. Hydrogen bonding in aryl-pyridyl ureas represented as supramolecular synthons and graph sets.
F
X
O
N
O
N
N
F
O
N
N
H
N
H
N
H
N
H
N
H
N
H
F
F
1
2 X = H
4 X = Cl
3 X = Me
5 X = Br
7 X = OH
8
6 X =
I
Fig. 2. Crystal structures of aryl-pyridyl ureas analyzed.
Fig. 3. Bifurcated N–H. . .N hydrogen bonds in R12 (6) motif connect dipyridylurea molecules 1 to form one-dimensional zigzag chain along [0 0 1]. The urea oxygen engages in
intramolecular C–H. . .O interactions. Symmetry-independent molecules are shaded differently.

S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
101
Fig. 4. (a) Bifurcated urea–pyridyl N–H. . .N hydrogen bonds in chlorophenyl pyridylurea 4. (b) Molecular layers formed by N–H. . .N and C–H. . .O hydrogen bonds are 3.59 Å
apart.
Fig. 5. Urea N–H. . .N and N–H. . .O hydrogen bonds in bromo- and iodophenyl pyridylurea 5 and 6 (a and b). Because of bulky iodine atom, three molecules of 6 (b) cannot
come as close to each other as those of 5. Zigzag tape of N–H. . .N and linear tape of N–H. . .O bonded molecules (c and d).

102
S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
tural Database [22] (CSD refcodes are listed), crystal structure of
pure 1 is surprisingly absent. Crystallization of single crystals of a
gelator molecule is very difficult because gel formation occurs
from most solvents. A plausible reason for more than one mole-
cule in the asymmetric unit of 1 could be that it has a packing
problem. Difficult to crystallize molecules often tend to crystal-
lize with Z0 > 1 [23]. While studying the hydrogelator property
of 1, Dastidar [6] reported single crystal structure of an ethylene
glycol hydrate but were unsuccessful in crystallizing its pure
form. Shinkai and Reinhoudt [24] groups proposed a model for
Fig. 6. Urea–hydroxyl N–H. . .O hydrogen bonding in hydroxyphenyl pyridylurea 7 instead of an anticipated urea tape.
Fig. 7. Hirshfeld contour and fingerprint plots of chlorophenyl pyridylurea 4. Note the bifurcated pyridyl N acceptor (red zones) which makes R12 (6) synthon with urea NH
donors. The spikes in N. . .H and O. . .H fingerprint plots (di, de ꢀ 1.2, 0.8; 1.3, 1.0 Å) are of intermolecular N–H. . .N and intramolecular C–H. . .O synthons. (For interpretation of
color mentioned in this figure, the reader is referred to the web version of this article.)

S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
103
gelation ability of carbohydrates in which 1D hydrogen-bonded
network is a required structural motif in organogelators. The
presence of zigzag chains in 1 gives a rationalization for its excel-
lent gelating behavior [6,7].
intramolecular C–H. . .O hydrogen bonds, thereby reducing its abil-
ity to make intermolecular N–H. . .O hydrogen bonds [16]. Cl being
more electronegative than Br and I makes the C–H hydrogen more
acidic leading to a planar conformation in 4 and an intermolecular
C–H. . .O contact (2.34 Å, 151.8°) compared to N–H. . .O and C–
H. . .O hydrogen bonds in 5 and 6. Both N–H. . .O and C–H. . .O
hydrogen bonds are shorter in 5 (2.16 Å, 137.3°; 2.43 Å, 148.3°)
compared to 6 (2.29 Å, 134.8°; 2.50 Å, 149.0°) but N–H. . .N dis-
tance is similar (2.09, 2.11 Å).
Noting that a dihydrate of 4-tolyl-3-pyridylurea (3-pyridyl iso-
mer of 3) has the urea tape synthon (whereas 3 has urea–pyridyl
bonding) [17] because the pyridyl N now engages in O–H. . .N
hydrogen bonding with water, we analyzed the crystal structure
of 4-hydroxyphenyl pyridylurea 7 to find out if the phenol OH do-
nor will play the role of H2O (Fig. 6). Disappointingly, NH donors
bond with hydroxyl O instead of urea. The urea O engages in inter-
molecular C–H. . .O interactions from a phenyl donor (ꢀ2.7 Å).
N-4-Fluorophenyl-N0-4-pyridylurea gave very poor quality sin-
gle crystals upon crystallization from various solvents. X-ray reflec-
tions on a poor quality crystal did not give a good enough data set
for structure solution from monoclinic unit cell parameters of
Crystal structures of phenyl, tolyl and chlorophenyl pyridylu-
reas 2, 3, 4 are similar. Tolyl pyridylurea crystals in our experi-
ments match with the reported monoclinic structure of 3 [17].
Molecules in the crystal lattice are organized via N–H. . .N hydro-
gen bond R12 (6) synthon. There are additional intermolecular C–
H. . .O interactions with urea oxygen (see crystal structure of 4 in
Fig. 4). A difference between crystal structure 1 vs. 2–4 (crystal
structure of 2 [25] and 4 [26]) is that while R12 (6) motif is pres-
ent in all of them, the molecules lie in a layer in 2–4 (NH donors
lie in the same plane as the pyridyl acceptor) whereas in 1 the
acceptor pyridyl ring is roughly orthogonal to urea NH donors
(like in tetragonal urea structure). Bromo- and iodophenyl pyr-
idylureas 5 and 6 show a transition from urea–pyridyl towards
urea–urea hydrogen bonding: one of the NH donors bonds to
pyridyl N and the other to urea O on two sides of a donor mol-
ecule (Fig. 5).
The strength of N–H. . .O hydrogen bond depends on the induc-
tive effect of phenyl and pyridyl rings. Strong electron-withdraw-
ing groups make the C–H donor more acidic for stronger
a = 9.698(9) Å, b = 20.217(17) Å, c = 22.11(2) Å,
a = 87.681(19)°,
b = 90°,
c
= 90°, V = 4331(7) Å3.
Fig. 8. Hirshfeld contour and fingerprint plots of bromophenyl pyridylurea 5. Note the single pyridyl N acceptor red zone which makes N–H. . .N hydrogen bond with urea.
The N–H. . .O hydrogen bond is not shown in this view because it is oriented away. Now N. . .H and O. . .H distance plots have spikes at similar distances (di, de ꢀ 1.2, 0.8; 1.2,
0.9 Å) in fingerprint plots. (For interpretation of color mentioned in this figure, the reader is referred to the web version of this article.)

104
S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
2.2. Hirshfeld plots
bonding in these three types of structures is made clear in the cap-
tions of Figs. 7–9. In effect, bromophenyl pyridylurea is an interme-
diate structure with one N–H. . .N and one N–H. . .O hydrogen bond,
lying in between the bifurcated R12 (6) synthons of N–H. . .N and N–
H. . .O hydrogen bonds present in 4 and 8, respectively. The absence
of red zone in fingerprint plot indicates that very short interactions
in these urea structures are absent.
Hirshfeld surface analysis [27–29] is a quantitative approach for
analyzing intermolecular interactions in crystal structures. Small
differences between polymorphs or between crystal structures in
a family of compounds are represented as 3D molecular surface
contours and 2D fingerprint plots of intermolecular interactions.
Hirshfeld surface defines the contour of shape occupied by a mol-
ecule in the crystal structure. The contour surrounds the molecule
as a van der Waals surface, which in turn will have near neighbor
molecules. Fingerprint plots show the distance of a point on the
surface to the nearest nucleus (atom) inside (di) and outside (de)
the mean surface (wA(r) = 0.5). Since the van der Waals radii of
atoms differ, contact distances di and de may be normalized to give
dnorm [30]. Now distances shorter than vdW radii sum to moderate
and longer than vdW sum are represented as red through white to
blue color in fingerprint plots and contour surfaces. Thus visual
representation of electrostatic potential (hydrogen bond donors/
acceptors) and intermolecular interactions (short, moderate, long)
in a crystal structure is given by Hirshfeld surfaces and contours.
Hirshfeld contours and fingerprint plots of a urea structure hav-
ing bifurcated N–H. . .N R12 (6) synthon (e.g. chlorophenyl pyridylu-
rea 4), combination of N–H. . .N and N–H. . .O hydrogen bonds as in
bromophenyl pyridylurea 5, and urea N–H. . .O R12 (6) tape in phe-
nyl tetrafluoropyridylurea 8 (CSD refcode TAPRAD [31]) were
drawn in CrystalExplorer 2.1 [32]. The difference in hydrogen
Apart from hydrogen bonding,
p-stacking is important for phe-
nyl and pyridyl groups. -Stacking is visualized in the shape index.
p
Specific types of intermolecular interaction display characteristic
patterns on the shape index surface and contacting regions of the
surface are naturally mapped in complementary colors. Hydrogen
bonds appear as a red concave region on the surface around the
acceptor atom and a complementary blue convex region around
the hydrogen bond donor (see Figs. S1-S3 for shape index maps
of Hirshfeld surfaces 4, 5, and 8).
p-Stacking appears as red and
blue complementary region triangles on phenyl rings that overlay
over one another. Shape index plots in Fig. 10 indicate aryl stacking
in chlorophenyl pyridylurea 4 and phenyl tetrafluoropyridylurea 8
but not in bromophenyl pyridylurea 5.
2.3. Conformational analysis
Hydrogen bonding in diaryl ureas is related to molecular con-
formation. Planar conformations engage in urea. . .pyridyl, ur-
ea. . .nitro or urea. . .carboxylate hydrogen bonding [16–18]. A
Fig. 9. Hirshfeld contour and fingerprint plots of phenyl tetrafluoropyridylurea 8. The pyridyl N is no longer a hydrogen bond acceptor. Urea NH donors make the linear tape
via R12 (6) synthon. O. . .H fingerprint spike is at di, de ꢀ 1.1, 0.8 Å but N. . .H distance is long.

S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
105
reason for this is that the intramolecular C–H. . .O interactions of
activated aryl groups (e.g. EWG-phenyl, pyridyl, etc.) weaken the
urea O for intermolecular H bonding. In contrast, twisted urea con-
formations make the linear tape N–H. . .O synthon (Fig. 1). The en-
ergy difference between planar (stable) and twisted (metastable)
diaryl urea conformations observed in crystal structures is
<3 kcal/mol [18]. Bromophenyl pyridylurea is an interesting inter-
mediate solid-state structure in which one urea NH is coplanar
with the phenyl ring and the other NH is twisted out of the pyridyl
plane (Fig. 11). What is most remarkable is that the near coplanar
Fig. 10. Hirshfeld shape index of chlorophenyl pyridylurea 4 (a) and phenyl tetrafluoropyridylurea 8 (c) have red and blue triangular patches indicating p-stacking whereas
bromophenyl pyridylurea 5 (b) has no aryl overlay but C–H. . .O interactions are seen. (For interpretation of color mentioned in this figure, the reader is referred to the web
version of this article.)

106
S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
Table 2
Hydrogen bond in structures 1, 5, 6, 7.
Interaction
HꢁꢁꢁA/
DꢁꢁꢁA/ Å
hD–
HꢁꢁꢁA/
°
Symmetry code
Å
1
N2–H2. . .N5
N3–H3. . .N5
N6–H6. . .N1
N7–H7. . .N1
C2–H2A. . .O1a
C8–H8. . .O1a
C13–H13. . .O2a
C19–H19. . .O2a
C20–H20. . .O2
2.08
2.16
2.01
2.51
2.19
2.21
2.26
2.24
2.40
3.030(3) 156.4 1 ꢂ x, 1 ꢂ y, 1 ꢂ z
3.054(3) 146.1 1 ꢂ x, 1 ꢂ y, 1 ꢂ z
2.961(3) 155.9 1 ꢂ x, ꢂ 1/2 + y, 1/2 ꢂ z
3.357(3) 140.7 1 ꢂ x, ꢂ1/2 + y, 1/2 ꢂ z
2.850(3) 117.0
2.868(3) 117.0
2.909(3) 116.4
2.890(3) 116.6
3.429(3) 159.2 ꢂx, 3 ꢂ y, 1 ꢂ z
5
N2–H2. . .O1
N3–H3. . .N1
C2–H2A. . .O1a
C8–H8. . .O1a
C9–H9. . .O1
2.16
2.09
2.30
2.29
2.43
2.982(5) 137.3 ꢂ1 + x, y, z
2.974(6) 145.5 ꢂ1/2 + x, 3/2 ꢂ y, ꢂ1/2 + z
2.868(6) 110.8
2.892(5) 113.1
3.398(6) 148.3 3 ꢂ x, 2 ꢂ y, 2 ꢂ z
6
N2–H2. . .O1
N3–H3. . .N1
C9–H9. . .O1
C2–H2A. . .O1a
C8–H8. . .O1a
2.29
2.11
2.50
2.29
2.33
3.088(3) 134.8 1 + x, y, z
3.014(4) 147.7 1/2 + x, 1/2 ꢂ y, 1/2 + z
3.482(3) 149.0 ꢂx, ꢂy, 1 ꢂ z
2.874(4) 111.9
2.911(3) 111.7
7
O2–H1. . .N1
N3–H3. . .O2
C8–H8. . .O1a
1.65
1.95
2.30
2.629(3) 171.1 x, y, 1 + z
2.959(3) 176.6 ꢂ1/2 + x, 1/2 ꢂ y, ꢂ1/2 + z
2.873(3) 111.2
a
Intramolecular interaction.
Fig. 11. Conformation of urea molecule in the crystal structure. (a) Chlorophenyl
pyridylurea 4 resides in a flat planar conformation such that diaryl groups flank the
urea NH donors and C@O acceptor. (b) In the twisted conformation of phenyl
tetrafluoropyridylurea 8, the urea functional group is oriented out of the aromatic
plane. (c) Bromophenyl pyridylurea 5 is an intermediate case wherein one NH is
somewhat coplanar with the aryl group and the other is twisted out. Phenyl–NH
and pyridyl–NH dihedral angles are 5, 9° (4), 20, 31° (8) and 9, 22° (5).
NH engages in N–H. . .N hydrogen bond whereas the twisted out-
of-plane NH donor makes N–H. . .O hydrogen bond. There is a
one-to-one correlation between the molecular conformation of
diaryl urea and its hydrogen bond synthon in the crystal structure.
Whereas planar and twisted diarylurea conformations leading to
non-urea (metastable) and urea tape (stable) synthons is reported
[16–18], we show in this paper an intermediate case of hydrogen
bonding and molecular conformation crystallized in the solid-
state. Such a subtle difference in molecular conformation leading
to a different crystal structure is useful to understand synthon for-
mation and polymorphism [33,34].
Table 1
Crystallographic dataa and structure refinement parameters.
Compound
1
5
6
7
Chemical
formula
Formula
weight
C11 H10 N4
O
214.23
C12 H10 Br
N3 O
292.14
C12 H10 I N3 C12 H11 N3
O
O2
339.13
229.24
Crystal system Monoclinic
Monoclinic
P21/n
Monoclinic
P21/n
Monoclinic
P21/n
Space group
P21/c
T/K
a/Å
b/Å
c/Å
298
100
298
298
3. Conclusions
16.767(3)
5.6296(9)
21.863(3)
90
94.653(2)
90
4.8451(10)
20.242(4)
11.537(2)
90
93.490(3)
90
4.8894(8)
20.721(3)
11.7942(18)
90
92.749(2)
90
11.132(3)
7.1864(18)
13.504(3)
90
107.969(4)
90
The outcome of crystallization is a balance or compensation be-
tween intramolecular (molecular conformation) and intermolecu-
lar (crystal lattice) energy factors [35]. Since a similar situation
holds true in diaryl/dipyridyl/aryl-pyridyl urea crystal structures,
crystallization of a molecular conformation between the planar
and twisted conformers provides valuable information to study
systematic effects in this family of crystal structures. A one-dimen-
sional motif in the crystal structure of dipyridylurea explains the
gelating property of these materials.
a
/°
b/°
c/°
Z
8
4
4
4
V/Å3
2057.0(6)
1.384
0.095
1129.4(4)
1.718
3.625
1193.5(3)
1.887
2.670
1027.6(4)
1.482
0.105
Dcalc/g cmꢂ3
l
/mmꢂ1
Reflns
collected
Unique reflns
Observed
reflns
R1[I > 2
wR2 [all]
Goodness-of-
fit
14863
7043
10770
3976
2851
4026
1706
2213
2080
2339
1469
2028
4. Experimental
r(I)]
0.0680
0.1265
1.157
0.0525
0.1314
1.004
0.0285
0.0651
1.111
0.0509
0.1143
1.032
4.1. Synthesis
Diffractometer SMART-
APEX CCD
SMART-
APEX CCD
SMART-APEX SMART-
CCD APEX CCD
4.1.1. N,N0-di(4-pyridyl)urea (1)
Isonicotinic acid hydrazide (3 mmol, 410 mg) was dissolved in
10 ml 25% aq. HCl at 0 °C and NaNO2 (5 mmol, 350 mg) dissolved
in 5 mL ice cold water was added to it with stirring. Stirring was
continued for 1 h, maintaining the temperature below 5 °C. The
solution was neutralized by adding solid Na2CO3 and extracted
a
Crystal data for 2, 3, 4 and 8 are already reported. 2 [25]: space group P21/a,
a = 12.55 Å, b = 11.86 Å, c = 7.29 Å, b = 93.2°, V = 1085 Å3. 3 [17]: space group P21/n,
a = 6.97 Å, b = 12.73 Å, c = 12.67 Å, b = 95.8°, V = 1119 Å3. 4 [26]: space group P21/n,
a = 7.00 Å, b = 12.81 Å, c = 12.52 Å, b = 94.3°, V = 1120 Å3. 8 [31]: P21/n, a = 7.59 Å,
b = 24.31 Å, c = 6.29 Å, b = 96.4°, V = 1155 Å3.

S.K. Chandran et al. / Journal of Molecular Structure 968 (2010) 99–107
107
with toluene. The organic extracts were dried over Na2SO4 and fil-
Appendix A. Supplementary data
tered. 4-aminopyridine (3 mmol, 282 mg) was added to the filtrate
and refluxed for 6 h. The precipitate was filtered and dried to afford
1 in 70% yield.
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.molstruc.2010.01.030.
All other aryl-pyridyl ureas were prepared similarly and charac-
terized by their satisfactory 1H NMR (400 MHz) and IR spectra and
melting points. Melting point of compounds 5, 6 and 7 could not be
determined because they decompose on heating.
References
[1] M.C. Etter, Z. Urbakzyk-Lipkowska, M. Zia-Ebrahimi, T.W. Panunto, J. Am.
Chem. Soc. 112 (1990) 8415.
[2] J.J. Kane, R.-F. Liao, J.W. Lauher, F.W. Fowler, J. Am. Chem. Soc. 117 (1995)
12003.
ꢃ N,N0-di(4-pyridyl)urea (1):
[3] T.L. Nguyen, F.W. Fowler, J.W. Lauher, J. Am. Chem. Soc. 123 (2001) 11057.
[4] L. Applegarth, N. Clark, A.C. Richardson, A.D.M. Parker, I. Radosavljevic-Evans,
A.E. Goeta, J.A.K. Howard, J.W. Steed, Chem. Commun. (2005) 5423.
[5] J. Esch, F. Schoonbeek, M. Loos, H. Kooijman, A.L. Spek, R.M. Kellogg, B.L.
Feringa, Chem. Eur. J. 5 (1999) 937.
[6] D.K. Kumar, D.A. Jose, A. Das, P. Dastidar, Chem. Commun. (2005) 4059.
[7] N.N. Adarsh, D.K. Kumar, P. Dastidar, Tetrahedron 63 (2007) 7386.
[8] C.E. Stanley, N. Clarke, K.M. Anderson, J.A. Elder, J.T. Lenthall, J.W. Steed, Chem.
Commun. (2006) 3199.
[9] S.K. Chandran, R. Thakuria, A. Nangia, CrystEngComm 10 (2008) 1891.
[10] R. Custelcean, P. Remy, P.V. Bonnesen, D. Jiang, B.A. Moyer, Angew. Chem. Int.
Ed. 47 (2008) 1866.
[11] Y.L. Cho, D.M. Rudkevich, J. Rebek Jr., J. Am. Chem. Soc. 122 (2000) 9868.
[12] R.K. Castellano, J. Rebek Jr., J. Am. Chem. Soc. 120 (1998) 3657.
[13] M. Alajarín, A. Pastor, R.-Á. Orenes, J.W. Steed, J. Org. Chem. 67 (2002) 7091.
[14] N.N. Adarsh, D.K. Kumar, P. Dastidar, CrystEngComm 10 (2008) 1565.
[15] R. Custelcean, B.A. Moyer, B.P. Hay, Chem. Commun. (2005) 5971.
[16] L.S. Reddy, S. Basavoju, V.R. Vangala, A. Nangia, Cryst. Growth Des. 6 (2006)
161.
[17] P. Byrne, D.R. Turner, G.O. Lloyd, N. Clarke, J.W. Steed, Cryst. Growth Des. 8
(2008) 3335.
[18] L.S. Reddy, S.K. Chandran, S. George, N.J. Babu, A. Nangia, Cryst. Growth Des. 7
(2007) 2675.
[19] R. Custelcean, B.A. Moyer, V.S. Bryantsev, B.P. Hay, Cryst. Growth Des. 6 (2006)
555.
[20] G.R. Desiraju, Angew. Chem. Int. Ed. Engl. 34 (1995) 2311.
[21] J. Bernstein, R.E. Davis, L. Shimoni, N.-L. Chang, Angew. Chem. Int. Ed. Engl. 34
(1995) 1555.
ꢃ IR (KBr): 3402, 3012, 1739, 1639, 1586, 1518, 1423, 828,
527 cmꢂ1
.
ꢃ
1H NMR (DMSO-d6): 7.46 (4H, d, J 4), 8.40 (4H, d, J 4), 9.32 (2H, s).
ꢃ mp 218–220 °C.
ꢃ N-4-bromophenyl-N0-4-pyridylurea (5):
ꢃ IR (KBr): 3327, 3040, 1928, 1695, 1589, 669, 646, 555 cmꢂ1
.
ꢃ
1H NMR (DMSO-d6): 7.38 (2H, d, J 8), 7.40 (2H, d, J 4), 7.41 (2H, d,
J 6), 8.35 (2H, d, J 4), 8.80 (1H, s), 8.96 (1H, s).
ꢃ N-4-iodophenyl-N0-4-pyridylurea (6):
ꢃ IR (KBr): 3329, 1930, 1693, 1541, 509 cmꢂ1
.
ꢃ
1H NMR (DMSO-d6): 7.29 (2H, d, J 8), 7.39 (2H, d, J 6), 7.56 (2H, d,
J 8), 8.31 (2H, d, J 4), 8.76 (1H, s), 8.92 (1H, s).
ꢃ N-4-hydroxyphenyl-N0-4-pyridylurea (7):
ꢃ IR (KBr): 3352, 3294, 3105, 1652, 1536, 1516, 1415, 827,
516 cmꢂ1
.
ꢃ
1H NMR (DMSO-d6): 6.75 (2H, d, J 8), 7.53 (2H, d, J 8), 7.83 (2H, d,
J 6), 8.75 (2H, d, J 6), 9.34 (1H, s), 10.27 (1H, s).
ꢃ N-4-fluorophenyl-N0-4-pyridylurea:
ꢃ IR (KBr): 3306, 3069, 1927, 1738, 1697, 1593, 1296, 995 cmꢂ1
.
ꢃ
1H NMR (CD3OD): 7.06 (2H, t, J 8), 7.45 (2H, dd, J 8,5), 7.57 (2H, d,
J 6), 8.32 (2H, d, J 6). NHs exchange in solvent.
ꢃ mp 207–209 °C.
[22] Cambridge Structural Database, ver. 5.30, ConQuest 1.11, November 2008
release, Sep 2009 update. Available from: <www.ccdc.cam.ac.uk>.
[23] J.W. Steed, CrystEngComm 5 (2003) 169.
[24] R. Luboradzki, O. Gronwald, M. Ikeda, S. Shinkai, D.N. Reinhoudt, Tetrahedron
56 (2000) 9595.
[25] K. Yamaguchi, K. Shudo, J. Agric. Food Chem. 39 (1991) 793.
[26] P. Le Magueres, L. Ouahab, A. Hocquet, J. Fournier, Acta Crystallogr. C 50 (1994)
1507.
Compound 1 was crystallized from ethyl acetate and com-
pounds 5–7 were crystallized from methanol to afford diffraction
quality crystals.
4.2. Crystallography
[27] M.A. Spackman, D. Jayatilaka, CrystEngComm 11 (2009) 19.
[28] J.J. McKinnon, D. Jayatilaka, M.A. Spackman, Chem. Commun. (2007) 3814.
[29] J.J. McKinnon, M.A. Spackman, A.S. Mitchell, Acta Crystallogr. B 60 (2004) 627.
X-ray reflections for all compounds were collected on Bruker
SMART APEX CCD equipped with graphite monochromator and
diꢂr
v
dw
deꢂrvdw
r dw
[30] dnorm
¼
þ
.
v
dw
v
[31] K. Yamagruchi, G. Matsumura, N. Haga, K. Shudo, Acta Crystallogr. C 48 (1992)
Mo-K
a fine-focus sealed tube (k = 0.71073 Å). Data integration
559.
[32] S.K. Wolff, D.J. Grimwood, J.J. McKinnon, D. Jayatilaka, M.A. Spackman,
CrystalExplorer 2.1, University of Western Australia, Perth, 2007,
hirshfeldsurface.net/CrystalExplorer.
[33] A. Nangia, Acc. Chem. Res. 41 (2008) 595.
[34] M. Rafilovich, J. Bernstein, R.K. Harris, D.C. Apperley, P.G. Karamertzanis, S.L.
Price, Cryst. Growth Des. 5 (2005) 2197.
[35] L. Yu, S.M. Reutzel-Edens, C.A. Mitchell, Org. Process Res. Dev. 4 (2000) 396.
[36] SAINT, Version 6.45/8/6/03, Bruker AXS.
[37] G.M. Sheldrick, SADABS, Program for Empirical Absorption Correction of Area
Detector Data, University of Göttingen, Germany, 1997.
[38] G.M. Sheldrick, SHELXS-97 and SHELXL-97, Programs for the Solution and
Refinement of Crystal Structures, University of Göttingen, Germany, 1997.
was done using SAINT [36]. Intensities for absorption were cor-
rected using SADABS [37]. Structure solution and refinement were
carried out using Bruker SHELX-TL [38]. Hydrogen atoms were re-
fined isotropically and heavy atoms were refined anisotropically.
N–H and O–H hydrogens were located from difference electron
density map and C–H hydrogens were fixed using HFIX command
in SHELX. Crystallographic data are summarized in Table 1 and
hydrogen bond parameters are listed in Table 2. CCDC Nos.
748,552–748,555 contain the crystallographic data for this paper,
which can be obtained free of charge via http://www.ccdc.cam.a-
c.uk/conts/retrieving.html.
Acknowledgements
We thank the CSIR (Project No. 01(2079)/06/EMR-II) for re-
search funding. S. K.C., N.K.N. and S.C. thank CSIR, UGC and ICMR
for fellowship. CCD X-ray diffractometer is funded by DST (IRPHA).