A bis-urea naphthalene macrocycle displaying two crystal structures with parallel ureas

Article abstract of DOI:10.1039/c1ce05207a

Herein we synthesized a bis-urea macrocycle from 2,7-dimethylnaphthalene that displays an unusual parallel urea conformation. The naphthalenes also adopt a bowl shape over the anticipated parallel planar orientation. Crystallization of the macrocycle from different solvent systems affords two solvated forms. 1·DMSO·(H₂O)₂ has an extended columnar structure where parallel macrocycles are linked by intervening hydrogen bonded water molecules. In 1·(MeOH)₂ direct hydrogen-bonds link the macrocycles into chains, which hydrogen-bond with methanol molecules to form a layered structure.

Full text of DOI:10.1039/c1ce05207a

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A bis-urea naphthalene macrocycle displaying two crystal structures with
parallel ureas†
*
Michael F. Geer, Mark D. Smith and Linda S. Shimizu
Received 16th February 2011, Accepted 2nd April 2011
DOI: 10.1039/c1ce05207a
bonds to form chains,4 sheets,5 gels,6 and polymers.7 Our bis-urea
macrocycles consist of two ureas conjoined by ‘‘C’’-shaped spacer
groups.8 The spacer groups were chosen to enforce planar orienta-
tions that are beneficial for stacking. Typically, bis-urea macrocycles
assembled into columns with the ureas adopting an anti-parallel
arrangement of the ureas in a macrocycle presumably to minimize
dipole interactions.9 A naphthalene spacer unit was investigated to
probe the effect of extending the aryl–aryl moiety in the spacer group
on the structure and on its subsequent assembly.
Herein we synthesized a bis-urea macrocycle from 2,7-dime-
thylnaphthalene that displays an unusual parallel urea conforma-
tion. The naphthalenes also adopt a bowl shape over the anticipated
parallel planar orientation. Crystallization of the macrocycle from
different solvent systems affords two solvated forms. 1$DMSO$
(H2O)2 has an extended columnar structure where parallel macro-
cycles are linked by intervening hydrogen bonded water molecules.
In 1$(MeOH)2 direct hydrogen-bonds link the macrocycles into
chains, which hydrogen-bond with methanol molecules to form
a layered structure.
The naphthalene bis-urea macrocycle 1 was synthesized in three
steps similar to previous reports.8 Commercial 2,7-dimethylnaph-
thalene was brominated under radical conditions to give the required
dibromide, which was subsequently cyclized with tert-butyl func-
tionalized triazinanone to yield the protected macrocycle (Fig. 1). The
protected macrocycle crystallized through slow evaporation of a 0.1
mg mLꢀ1 EtOAc : MeOH solution (9 : 1 by volume) resulting in
a colorless needle crystal suitable for X-ray diffraction. The crystal
structure revealed the desired solvent-free macrocycle. The extended
structure shows the centrosymmetric macrocycle monomers aligned
in a herringbone arrangement (Fig. 2). The naphthalene shelves of the
monomer adopt a flat parallel planar arrangement tilted 25ꢁ from the
plane of the macrocycle with the ureas oriented anti-parallel (Fig. 2,
inset). This is the typically observed conformation for bis-urea
macrocycles and was assumed to be beneficial for columnar
assembly.3,8–10 Since the protected macrocycle 2 crystallized in the
expected conformation, we proceeded to deprotect the ureas.
The triazinanone protecting groups were removed by treatment
with 20% acidic diethanol amine solution resulting in free ureas.
Introduction
The bulk morphology of materials is important in many aspects of
pharmaceuticals because of its impact on a compound’s stability and
solubility.1 In this aspect, it is important for chemists to understand
the factors that contribute to or govern the crystal structure and to try
to correlate the effect of the structure on properties.2 Previously, we
have reported on the synthesis and assembly of robust columnar
structures formed through self-assembly of bis-urea macrocycles.3
The lowest energy conformations of the macrocycle, as predicted by
gas phase calculations, together with the preferred anti-parallel
arrangement of the ureas and the propensity for aryl–aryl stacking
appear to govern their assembly into columnar structures regardless
of crystallization conditions. Herein, we report the synthesis of a new
bis-urea macrocycle that contains 2,7-dimethylnaphthalene spacer
units. This macrocycle displayed two structures that disregard the
paradigm typically observed for the assembly of bis-urea macrocycles
that usually favors the ureas adopting an anti-parallel alignment.
Separate crystallization techniques afford distinct structures that
displayed an unusual parallel arrangement of the ureas.
Results and discussion
Ureas, particularly N,N0-disubstituted ureas, are reliable supramo-
lecular building blocks that interact with strong 3-centered hydrogen
Fig. 1 Schematic synthesis of naphthalene macrocycle. Reagents and
conditions: (a) NaH, 5-tert-butyl tetrahydro-1,3,5-triazin-2(1H)-one,
THF (2, 15%), (b) 20% diethanolammonium chloride aqueous solution in
methanol (1, 97%). Typically, bis-urea macrocycles adopt an anti-parallel
orientation of the ureas shown above.
University of South Carolina, Department of Chemistry and Biochemistry,
Columbia, SC, 29208, USA. E-mail: shimizul@chem.sc.edu; Fax: +803-
777-9521; Tel: +803-777-2066
† CCDC reference numbers [813391–813393]. For crystallographic data
in CIF or other electronic format see DOI: 10.1039/c1ce05207a
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H-bonding sites and by one DMSO molecule (Fig. 3C). The water
molecule to the left side of Fig. 3C hydrogen bonds with both
nitrogens of the macrocycle above (N/O distances ¼ 2.934(3) and
ꢀ
ꢀ
3.000(3) A) and the oxygen below (O/O ¼ 2.749(3) A). This water is
also hydrogen bonded to the centrally located DMSO molecule (O/
ꢀ
O ¼ 2.756(3) A). The opposite water molecule hydrogen bonds
ꢀ
with one nitrogen of the macrocycle above (N/O ¼ 3.025(3) A), to
ꢀ
an oxygen of the macrocycle below (O/O ¼ 2.777(3) A), and
to a macrocycle carbonyl from a neighboring column (O/O ¼
ꢀ
3.053(3) A). This expanded columnar structure gives an average
ꢀ
distance between macrocycles of 5.3 A (from urea N to urea O). This
gives an extended columnar structure.
In comparison, most macrocyclic bis-ureas crystallize with an anti-
parallel arrangement of the urea groups.10 It is presumably preferred
to minimize the dipole interactions.3,8–10 In addition, the ureas typi-
cally prefer narcissistic self-assembly with any solvent typically
incorporated inside or outside of the columns.3,11 For example, the
previously reported meta-xylene 3 adopts an anti-parallel arrange-
ment of ureas (Fig. 4A) and assembles into columns via the 3-centered
8
ꢀ
urea–urea self-association (Fig. 4C). This gives a spacing of 4.614 A
between the urea groups.8 In comparison, the parallel aligned ureas of
naphthalene 1 (Fig. 4B) forgo the typical urea self-association in favor
of an extended structure via intervening water molecules (Fig. 3C).
Fig. 2 Crystal packing of the macrocycle displaying the herringbone
arrangement of the naphthalene moieties (hydrogens omitted for clarity).
(Inset) Crystal structure of single protected macrocycle crystallized from
EtOAc/MeOH solution showing the antiparallel urea and parallel planar
naphthalene shelves.
ꢀ
The spacing between ureas in 1 is 2.3 A longer than in the meta-xylene
macrocycles.8
The observed parallel arrangement of the ureas in naphthalene
macrocycle 1 was not observed in its protected precursor 2, which
adopted the normal anti-parallel alignment. This suggests the urea
groups in 1 have some ability to rotate. The naphthalene moieties
were arranged in a bowl shape that is oriented toward the electron
rich carbonyls instead of the parallel planar orientation that was
observed with m-xylene macrocycle (Fig. 4).8 In addition to the
unusual conformation of the macrocycle, the crystal structure
suggests ring strain as indicated by a decrease in the bond angle
between the methyl connector of the naphthalene and the ureas from
the ideal 120ꢁ to 115ꢁ and a 6ꢁ tilting of the ureas from perpendicular
to the plane of the macrocycle (Fig. 5).
The macrocycle was crystallized from a 1 mg mLꢀ1 solution of
DMSO and water to form clear colorless rhombic crystals suitable
for X-ray analysis (Fig. 3A). The X-ray structure showed the
expected macrocycle, but in an unexpected orientation and assembly.
The macrocycle 1 crystallized into a columnar structure inter-
penetrated by two independent water molecules occupying the urea
Fig. 3 SEM and crystal structure of macrocycle from DMSO/water
solution (some hydrogens have been omitted for clarity). (A) SEM image
of the cubic crystal (bar ¼ 100 mm). (B) Single macrocycle showing
parallel orientation of the ureas. (C) Single column of macrocycle
showing the H-bonding (blue lines) between the water, the ureas and
DMSO molecule.
Fig. 4 Comparison of previously reported meta-xylene macrocycle8 and
naphthalene macrocycle. (A) m-Xylenes are in parallel planar arrange-
ment with the ureas in anti-parallel to minimize dipole interaction.8 (B)
The naphthalenes are in a bowl shape turned toward the carbonyl groups
of the ureas that are oriented parallel to each other. (C) The m-xylene
assembles into columns via 3-centered urea–urea hydrogen bonds.8
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ꢀ
groups of the neighboring macrocycle urea (N/O ¼ 2.826(2) A).
The hydrogen bonded chains of macrocycle were separated by
disordered methanol molecules with an average distance between
ꢀ
macrocycle of 5.4 A. The MeOH molecules are hydrogen bonded to
the NH groups and carbonyl oxygens that are not H-bonded to
ꢀ
adjacent ureas (N/O ¼ 3.053(3) and 3.077(4) A and O/O distances
ꢀ
in the range 2.692(3)–2.806(4) A). Once removed from the mother
liquor the crystals desolvate beyond X-ray quality.
Experimental
All chemicals were used as received from commercial sources. NMR
were performed on Varian 300 and 400 MHz NMR.
Synthesis of naphthalene bis-urea macrocycle (1)
Fig. 5 Naphthalene macrocycle 1. (A) Macrocycle shows a bowl shape
orientation of the Naphthalene spacers. (B) Angle between the naph-
thalene and urea is strained to 115ꢁ from ideal 120ꢁ. (C) Side view of
macrocycle shows a 6ꢁ tilt of the ureas from perpendicular to the plane of
the macrocycle.
Bis(2,7-bromomethyl)
naphthalene.
N-Bromosuccinimide
(32 mmol, 5.7 g) and 2,7-dimethylnaphthalene (16 mmol, 2.5 g) were
dissolved in CCl4 (40 mL). Azobisisobutyronitrile (AIBN) (5%,
0.80 mmol, 0.131 g) was added, and the reaction mixture was heated
to 80 ꢁC for 18 h. Upon completion, the reaction mixture was cooled
to room temperature and the precipitate was filtered off and
rinsed with dichloromethane. The filtrate was evaporated in vacuo
and the product was purified via column chromatography (8 : 2
hexanes : dichloromethane) to afford a pale yellow powder (4.56 g,
90%), mp 150–152 ꢁC. 1H-NMR (300 MHz, CDCl3): d 7.82 (d, J ¼
8.8 Hz, 4H), 7.52 (d, J ¼ 8.5 Hz, 2H), 4.65 (s, 4H). 13C-NMR
(100 MHz, CDCl3): d 135.84, 128.60, 127.88, 127.51, 33.73. Direct
probe EIMS (m/z): 314 (calc. for C12H10Br2: 314.02).
Given the unexpected conformation observed, we next set out to
observe the assembly of this macrocycle from a series of other
solvents including acetonitrile, benzene, DMSO, and methanol.
Microcrystals from methanol and benzene were not suitable for
X-ray analysis. X-Ray quality hourglass shaped single crystals were
obtained by vapor diffusion of a 1 mg mLꢀ1 solution of DMSO by
MeOH (Fig. 6A). The macrocycle crystallized along with two
disordered methanol molecules (Fig. 6C). No DMSO molecules were
present. The macrocycle retains the bowl-shaped arrangement of the
naphthalenes and the parallel oriented ureas, similar to the DMSO/
water crystal (Fig. 6B). The monomers crystallized with an overall
lamellar structure consisting of chains of macrocycles directly
hydrogen bonded to one another in an offset, tilted fashion (Fig. 6C).
The carbonyl of one urea forms hydrogen bonds to the two NH
Protected naphthalene macrocycle (2). A 60% suspension of
sodium hydride in mineral oil (7.5 mmol NaH, 0.300 g) and 5-tert-
butyl tetrahydro-1,3,5-triazin-2(1H)-one (2.5 mmol, 0.39 g) were
added to freshly distilled THF and heated at reflux for 1 h. The
solution was cooled to room temperature, and a solution of dibro-
mide (2.5 mmol, 0.79 g) in 100 mL THF was added dropwise over 1
h. The reaction mixture was heated to reflux for 48 h and then cooled
to room temperature and neutralized with 20 mL 1 N HCl and 80 mL
distilled water. The mixture was reduced in vacuo to ꢂ100 mL and
extracted with methylene chloride (3 ꢃ 100 mL). The organic layer
was rinsed with brine and dried over anhydrous magnesium sulfate.
The product was isolated by column chromatography (95 : 5
EtOAc : MeOH) to yield a white crystalline powder (118.4 mg, 15%).
1H-NMR (400 MHz, CDCl3): d 7.87 (s, 4H), 7.79 (d, J ¼ 8.2 Hz, 4H),
7.27 (d, J ¼ 8.6 Hz, 4H), 5.88 (d, J ¼ 16.2 Hz, 4H), 4.47 (d, J ¼ 11.5
Hz, 4H), 4.22 (d, J ¼ 11.7 Hz, 4H), 3.84 (d, J ¼ 16.4 Hz, 4H), 1.20 (s,
18H). 13C-NMR (100 MHz, CDCl3): d 155.89, 136.05, 134.01, 131.96,
127.98, 125.42, 124.42, 63.05, 54.14, 49.37, 28.60. TOF ESI-MS: m/z
619 (100%) [M + H]+ (calc. for C38H46N6O2: 618.81).
Deprotection of (2) to yield naphthalene macrocycle (1). Pro-
tected macrocycle 2 (100 mg) was added to an aqueous solution of
20% diethanol amine (pH z 2) and MeOH (1 : 1 by volume) and
heated at reflux overnight. After cooling, the reaction mixture was
neutralized with 10 mL of 1 N HCl and 10 mL of water. The resulting
precipitate was filtered off and rinsed with 1 N HCl (3 ꢃ 10 mL) and
water (3 ꢃ 10 mL) yielding a white crystalline powder (68 mg, 97%).
1H-NMR (300 MHz, d6-DMSO): d 7.83 (d, J ¼ 8.5 Hz, 4H), 7.74 (s,
4H), 7.32 (d, J ¼ 8.2 Hz, 4H), 6.84 (s, 4H). 13C-NMR (100 MHz,
Fig. 6 Image of crystal and single crystal structure of 1 from MeOH/
DMSO solution: (A) optical microscope image of one of the abundant
‘‘hourglass’’ twin crystals at 11.5ꢃ magnification. The dataset was
obtained by cleaving such a twin to obtain a single crystal; (B) single
macrocycle showing the approximate positions of the disordered MeOH
molecules; (C) crystal packing displaying the lamellar packing of the
macrocycles and the MeOH.
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d6-DMSO): d 158.14, 139.74, 139.57, 133.16, 130.90, 127.50, 124.77,
one molecule, which is located on a crystallographic inversion center
(Table 1).
42.38.
1$(MeOH)2. The compound crystallizes in the triclinic system.
ꢁ
The space group P1 (no. 2) was confirmed by the successful solution
Crystallization of naphthalene macrocycle
Method 1. A dilute solution of 1 in DMSO (1 mg mLꢀ1) was
prepared and then diluted again with distilled water (1 : 1 ratio sol-
ution : water by volume). The resulting solution was drop cast onto
a glass slide and allowed to evaporate in atmospheric conditions to
yield colorless crystals.
and refinement of the structure. The asymmetric unit consists of one
cycle and two independent methanol molecules of crystallization.
Both methanol molecules are disordered over two roughly equally
populated positions, and were refined isotropically with C–O
ꢀ
distances restrained to 1.45(2) A. Reasonable positions for the four
methanolic protons were located in difference maps. Their coordi-
ꢀ
Method 2. A solution of 1 in DMSO (1 mg mLꢀ1) was prepared
and placed into a 3 mL scintillation vial and the vial was placed into
a pint size jar preloaded with 20 mL methanol. This vapor chamber
was allowed to sit in the dark for 2 weeks resulting in colorless
crystals. Removal of the crystal from the mother liquor caused them
to desolvate.
nates were adjusted to O–H ¼ 0.85 A and they were included as
riding atoms with Uiso,H ¼ 1.5Uiso,O. Their positions should be
regarded as approximate.
1$DMSO$(H2O)2. The compound crystallizes in the space group
P21/c. The asymmetric unit consists of one macrocycle molecule, one
DMSO molecule and two water molecules.
X-Ray crystallography
X-Ray intensity data were measured at 150(2) K or 100(2) K (both
Conclusions
forms of 1) using a Bruker SMART APEX diffractometer equipped
ꢀ
with Mo Ka radiation (l ¼ 0.71073 A). Raw area detector data
Herein we have synthesized a novel bis-urea macrocycle that utilizes
2,7-dimethylnaphthalene. Crystallization of macrocycle 1 resulted in
a distinct conformer with unusual parallel urea orientation and bowl
shaped monomer. This conformation goes against the expectations
set forth by previous studies in bis-urea macrocycles, resulting in an
apparent overall dipole of the monomer. This macrocycle also yielded
two differently solvated crystal structures from two separate crys-
tallization techniques. The first is an extended columnar structure
with water interdigitating the macrocycles. Interestingly, this struc-
ture has the parallel ureas all aligned in the same direction giving the
single column an overall dipole moment that is balanced by the
neighboring columns. The second crystal structure displays lamellar
packing of the macrocycle with MeOH. These extended structures
bring up an important conformational question. Is the parallel urea
frame reduction was performed with the SAINT+ program.12 Direct
methods structure solution, difference Fourier calculations and full-
matrix least-squares refinement against F2 were performed with the
SHELXTL suite of programs.13 All non-disordered non-hydrogen
atoms were refined with anisotropic displacement parameters.
Hydrogen atoms bonded to carbon were placed in geometrically
idealized positions and included as riding atoms. Urea and water
hydrogens were located in difference maps and refined isotropically
with their N–H and O–H distances restrained to be approximately
equal to those of the same type.
Protected naphthalene macrocycle (2). The compound crystal-
lizes in the space group P21/n. The asymmetric unit consists of half of
Table 1 Crystal data and refinement data for protected macrocycle (2), and the two crystal structures of bis-urea naphthalene macrocycle (1$DMSO$
(H2O)2 and 1$(MeOH)2)
2
1$DMSO$(H2O)2
1$(MeOH)2
Empirical formula
Formula weight
T/K
C38H46N6O2
618.81
150(2)
C28H34N4O5S
538.65
100(2)
C28H32N4O4
488.58
100(2)
Crystal system
Space group
Monoclinic
P21/n
8.8432(11)
18.133(2)
10.7628(13)
90
111.470(3)
90
1606.1(3)
2
1.280
0.081
664
12 794
0.0976
0.806
0.0413
0.0696
0.139/ꢀ0.143
Monoclinic
P21/c
7.1366(4)
10.9517(6)
33.5506(18)
90
94.278(1)
90
2614.9(2)
4
1.368
0.171
1144
26 330
0.1011
0.826
0.0418
0.0748
0.331/ꢀ0.318
Triclinic
ꢁ
P1
ꢀ
a/A
6.9772(4)
10.5977(6)
17.1780(9)
93.904(1)
90.3930(1)
104.4030(1)
1227.03(12)
2
1.322
0.090
520
12 870
ꢀ
b/A
ꢀ
c/A
a/ꢁ
b/ꢁ
g/ꢁ
V/A
Z
3
ꢀ
Dc/Mg mꢀ3
m/mmꢀ1
F(000)
Reflections collected
Rint
0.0532
0.911
0.0397
0.1005
GOF on F2
R1 [I > 2s(I)]
wR2 (all data)
ꢀ3
ꢀ
Drmin,max/e A
0.179/ꢀ0.196
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orientation responsible for the affinity of the ureas with water over
the typical urea self-association or are other factors responsible such
as ring strain, sterics or the bowl shaped conformation? We are
currently investigating larger extended aromatic spacers to probe
their properties and see if the parallel urea orientation can be more
widely stabilized in crystalline structures. Understanding the inter-
actions that govern the crystal structures will invariably result in
better understanding of crystallization and synthetic methods and
concurrently a cost saving in the synthetic and pharmaceutical
industry.
Acknowledgements
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Commun., 2001, 1592.
The authors gratefully acknowledge support for this work from the
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