Synthesis and crystal structure of a new diphenylglycoluril derivative

Article abstract of DOI:10.1007/s10870-010-9977-2

The title compound has been synthesized by alkylation of diphenylglycoluril with o-xylylenedihalides followed by Sonogashira cross-coupling reaction. The yielded product 2 was investigated with X-ray crystallographic, NMR, EI-MS, and IR techniques. The cr

Full text of DOI:10.1007/s10870-010-9977-2

J Chem Crystallogr (2011) 41:791–795
DOI 10.1007/s10870-010-9977-2
ORIGINAL PAPER
Synthesis and Crystal Structure of a New Diphenylglycoluril
Derivative
•
Yan Chen Nengfang She Anxin Wu
•
Received: 24 May 2009 / Accepted: 31 December 2010 / Published online: 19 January 2011
Ó Springer Science+Business Media, LLC 2011
Abstract The title compound has been synthesized by
alkylation of diphenylglycoluril with o-xylylenedihalides
followed by Sonogashira cross-coupling reaction. The yiel-
ded product 2 was investigated with X-ray crystallographic,
NMR, EI-MS, and IR techniques. The crystal belongs to a
triclinic system, space group P-1 with unit cell parameters
H-bonded tapes by exclusive heterochiral recognition
processes [16]. These results have suggested that glycoluril
derivatives have significant potential as a building block in
studies of crystal engineering.
˚
˚
˚
a = 10.5057(8) A, b = 12.6915(9) A, c = 13.3426(10) A,
a = 83.8540(10)o, b = 87.9360(10)o, c = 75.5700(10)o,
Experimental
3
˚
V = 1712.9(2) A , Z = 2, Dc = 1.322, Mr = 681.59, l =
General Methods
0.232 mm-1, F(000) = 708, R1 = 0.0586 and wR2 = 0.1470.
Melting point was determined with XT4A micromelting
point apparatus and was uncorrected. NMR Spectra were
measured on Plus-400 instruments operating at 400 MHz
for 1H and 100 MHz for 13C. MS was measured on a
Finnigan Trace MS spectrometer. IR was recorded on a
PE-983 infrared spectrometer as KBr pellet with absorption
in cm-1. The Diphenylglycoluril and 2,3-bis(bromo-
methyl)-1-4-dibromo-benzene were prepared according to
the methods reported [17, 18]. DMSO was dried and dis-
tilled under N2 over calcium hydride (CaH2) before use.
Potassium tert-butoxide and phenylacetylene were com-
mercially available from Acros Organics, and other chem-
icals were used as received without further purification.
Keywords Diphenylglycoluril Á Crystal structure Á
Dimeric aggregates Á Hydrogen bond Á p–p stacking
Introduction
Glycoluril recently has become an important building
block for supramolecular chemistry [1–11]. Many of
supramolcular systems are based on glycoluril, making use
of its molecular curvature and self-complementary
H-bonded ureid moiety. Rebek have previously used the
H-bonded potential of glycoluril itself to design the self-
assembly molecule encapsules [12–14] and engineer the
formation of H-bonded tapes in the crystal [15]. Our groups
have also reported glycoluril derivatives to form linear
Synthesis of the Title Compound
Scheme 1 shows the synthetic route for the title compound
2. Diphenylglycoluril was alkylated with 2,3-bis(bromo-
methyl)-1-4-dibromo-benzene using t-BuOK as base in
anhydrous DMSO to give intermediate 1 in 30% yield. The
coupling reaction between 1 and phenylacetylene was
readily accomplished using Pd(PPh3Cl2)2 and CuI as cat-
alysts in the presence of Et3N in DMF at 100 °C, and the
expected compound 2 was obtained. The structure of 2 was
Y. Chen Á N. She (&) Á A. Wu
Key Laboratory of Pesticide and Chemical Biology, Ministry
of Education, College of Chemistry, Central China Normal
University, Wuhan 430079, People’s Republic of China
e-mail: nfshe@mail.ccnu.edu.cn
1
confirmed by H NMR, 13C NMR, MS and IR.
123

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J Chem Crystallogr (2011) 41:791–795
Scheme 1 Synthetic route for
the preparation of the title
compound
Compound 1
X-ray Crystal Structure Determination
Diphenylglycoluril (2.94 g, 10 mmol) was dissolved in
anhydrous DMSO (40 mL) under argon, and t-BuOK
(4.48 g, 40 mmol) was added. After the reaction was stirred
for 1 min, 2,3-bis(bromomethyl)-1-4-dibromo-benzene
(0.84 g, 2 mmol) was added in one portion and stirring was
continued for 3 h. The reaction mixture was poured into
0.1 N HCl (1 L) and extracted with EtOAc (3 9 400 mL).
The extracts were washed with brine and dried over anhy-
drous MgSO4. After filtration and rotary evaporation, the
residue was purified by flash chromatography (SiO2,
CHCl3/MeOH = 50:1) to give 1 (0.33 g, 30%) as a white
solid. M.p. [ 300 °C. TLC (CHCl3/MeOH = 50:1) Rf
0.48. IR (KBr, cm-1): 3569w, 34089w, 3264w, 3066w,
Crystals suitable for X-ray structure determination were
obtained via slow evaporation of its solution in dichloride
methane. Crystal data were collected with Mo Ka radiation
˚
(k = 0.71073 A) on a BRUKER SMART APEX-CCD
Table 1 Crystal data and structure refinement of 2
CCDC No.
666025
Empirical formula
Formula weight
Temperature (K)
C41H30Cl2N4O2
681.59
292(2)
˚
Wavelength (A)
0.71073
Triclinic
P-1
Crystal system
Space group
1
1722 s, 1691 s, 1466 s, 1324w, 1161w, 974w, 779w. H
˚
a = 10.5057(8) A
NMR (400 MHz, CDCl3): d 7.35–7.07 (m, 12H), 5.84 (s,
2H), 5.64 (d, J = 16.0, 2H), 4.05 (d, J = 16.0, 2H). 13C
NMR (100 MHz, CDCl3): d 158.6, 138.1, 136.4, 133.8,
133.1, 129.2, 129.0, 128.9, 128.1, 127.8, 127.1, 124.0, 87.8,
78.8, 44.4. EI-MS: m/z 558 (2, [M ? H]?), 104 (100).
Unit cell dimensions
˚
b = 12.6915(9) A
˚
c = 13.3426(10) A
a = 83.8540(10)o
b = 87.9360(10)o
c = 75.5700(10)o
1712.9(2)
3
˚
Compound 2
Volume (A )
Z
2
Density (calculated) (mg/m3)
Absorption coefficient (mm-1
F000
1.3222
To a solution of Pd(PPh3)2Cl2 (36 mg, 0.05 mmol), CuI
(19 mg, 0.10 mmol) and compound 1 (279 mg, 0.50 mmol)
in freshly distilled Et3N (15 mL) and DMF (25 mL) under Ar
atmosphere at room temperature, were added phenylethyn-
ylene (204 mg, 2 mmol). The mixture was warmed to 110 °C
for 12 h (monitored by TLC), and then the solvent was
removed under reduced pressure. The solid residue was
purifiedbyflashchromatography(SiO2, CHCl3–MeOH,50:1)
to give 2 (218 mg, 0.365 mmol, 73%) as a white solid.
M.p. [ 300 °C. TLC (CHCl3/MeOH = 30:1) Rf 0.48. IR
(KBr, cm-1): 3375w, 3062w, 1705 s, 1457 s, 1428 m,
1363w, 757 m, 691 m. 1H NMR (400 MHz, CDCl3): d
7.64–7.03 (m, 22H), 5.92 (s, 2H), 5.83 (d, J = 16.0, 2H),
4.05(d, J = 16.0, 2H). 13C NMR (100 MHz, CDCl3):d 158.8,
138.8, 136.5, 133.3, 131.7, 131.4, 129.0, 128.8, 128.7, 128.5,
128.3,128.1,127.9,127.1,123.6,123.0,95.1, 88.3, 87.3, 77.3,
42.1. MS(ESI): m/z 597 ([M ? H]?), 619 ([M ? Na]?).
)
0.232
708
h range for data collection, Deg
1.67–27.00
Index ranges
-13 B h B 13
-16 B k B 16
-17 B l B 16
17830
Reflections collected
Independent reflections
Absorption correction
Refinement method
7391[R(int) = 0.0610]
Multiscan
Full-matrix least-squares on F2
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I [ 2r(I)]
R indices (all data)
7391/8/476
0.963
R1 = 0.0586, wR2 = 0.1470
R1 = 0.0933, wR2 = 0.1657
Largest diff. Peak and hole, e (A-3) 0.225 and -0.371
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J Chem Crystallogr (2011) 41:791–795
793
diffractometer with a w–x scan mode. A total of 17830
reflections were collected in the range of 1.67 \ h \ 27.00°
at room temperature, and 7391 were independent (Rint =
0.0610), of which 4592 observed reflections with
I [ 2r(I) were used in the structure determination and
refinements. Lattice determination and data collection were
carried out using SMART version 5.625 software. Date
reduction and absorption corrections were performed with
SAINT version 6.45 and SADABS version 2.03, respec-
tively [19]. Structure solution and refinement were made by
SHELXTL version 6.14 software package [20]. The non-
hydrogen atoms were refined anisotropically, and the
hydrogen atoms were generated geometrically with C–H
bond distances of 0.93–0.97 according to criteria described
in the SHELXTL manual. They were included in the
refinement with Uiso(H) = 1.2Ueq(C). The final full-matrix
˚
Table 2 Selected bond lengths (A) and angles (°) for 2
C(1)–C(2)
1.365(3)
1.372(4)
1.434(3)
1.192(3)
1.508(3)
1.364(3)
1.378(3)
1.469(2)
1.452(2)
1.213(2)
1.354(3)
1.385(3)
1.225(2)
1.441(2)
1.449(3)
1.373(3)
1.703(7)
C(2)–C(1)–C(6)
120.1(2)
C(2)–C(3)
N(2)–C(27)–C(34)
C(3)–C(4)–C(5)
99.97(14)
119.8(2)
C(6)–C(7)
C(7)–C(8)
C(8)–C(7)–C(6)
177.4(2)
C(10)–C(23)
C(11)–C(13)
C(17)–C(18)
C(23)–N(1)
C(24)–N(2)
C(25)–O(1)
C(25)–N(3)
C(25)–N(1)
C(26)–O(2)
C(34)–N(4)
C(34)–N(3)
C(37)–C(38)
C(41)–Cl(1)
C(7)–C(8)–C(9)
173.1(2)
C(11)–C(9)–C(8)
C(10)–C(9)–C(8)
C(12)–C(10)–C(9)
C(10)–C(12)–C(24)
C(12)–C(14)–C(15)
C(16)–C(15)–C(14)
C(15)–C(16)–C(17)
N(1)–C(23)–C(10)
N(2)–C(24)–C(12)
N(3)–C(25)–N(1)
O(2)–C(26)–N(2)
N(2)–C(26)–N(4)
118.01(18)
121.73(18)
119.34(17)
121.24(17)
122.00(18)
175.6(2)
179.7(3)
115.06(15)
113.84(15)
107.43(17)
125.87(19)
107.99(16)
Table 3 Selected torsion angles (o) for non-hydrogen atoms
Fig. 1 Crystalline structure of compound 2 and solvent molecules
C6–C1–C2–C3
C1–C2–C3–C4
-0.5(5)
N4–C34–C35–
C40
-159.29(19)
-28.1(3)
1.2(5)
N3–C34–C35–
C40
C4–C5–C6–C7
C2–C1–C6–C5
C10–C9–C11–C13
-178.2(2)
57.6(5)
-2.9(3)
0.2(3)
O1–C25–N1–C27
N3–C25–N1–C27
O2–C26–N2–C24
N4–C26–N2–C24
-168.74(18)
12.2(2)
-1.7(3)
C24–C12–C14–
C15
177.17(3)
C14–C15–C16–
C17
-82(51)
N4–C26–N2–C27
8.2(2)
C15–C16–C17–
C22
91(51)
C12–C24–N2–
C26
114.1(2)
-77.9(2)
103.24(18)
-19.5(2)
-66.1(2)
171.14(15)
N1–C27–C28–C33
N2–C27–C28–C33
C28–C27–C34–N4
N1–C27–C34–N3
N2–C27–C34–N3
-158.38(18)
-30.5(2)
-98.14(18)
20.89(17)
-94.20(16)
C12–C24–N2–
C27
C28–C27–N2–
C26
C34–C27–N2–
C26
C28–C27–N2–
C24
C34–C27–N2–
C24
N4–C34–C35–C36
N3–C34–C35–C36
25.1(3)
O2–C26–N4–C34
N2–C26–N4–C34
-172.2(2)
Fig. 2 Part of the crystal structure of 2, showed the formation of the
dimeric aggregates via hydrogen bond interactions
156.3(2)
8.9(2)
123

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J Chem Crystallogr (2011) 41:791–795
Fig. 3 The packing
arrangement viewed down the
a-axis. Hydrogen bonds are
shown by dashed lines
least-square refinement on F2 converged with R1 = 0.0586
and wR2 = 0.1470 for 4592 observed reflections
[I C 2r(I)]. The crystallographic data obtained and experi-
mental details employed were summarized in Table 1.
in the sidewall of two molecules is almost parallel, which
is favorable for the edge face phenyl embraces p–p
interactions between the dimeric structures (Fig. 3). The
distance between the planes of the two sidewall benzene
˚
rings is 3.63 A.
Results and Discussion
Supplementary Material
Selected bond distances and bond angles are listed in
Table 2. Selected torsion angle are given in Table 3. An
ORTEP view of the molecule with the atomic numbering
(thermal ellipsoids drawn at 30% probability) is shown in
Fig. 1.
CCDC-666025 contains the supplementary crystallo-
graphic data for this article. These data can be obtained free
of charge at www.ccdc.cam.ac.uk/conts/retrieving.html or
from the Cambridge Crystallographic Data Centre
(CCDC), 12 Union Road, Cambridge CB2 1EZ, UK; fax:
?44(0)1223-336033; e-mail: deposit@ccdc.cam.ac.uk.
The compound has a well-defined geometry due to the
rigidity that the fused rings confer on the molecule. The
bond distances and bond angles of the title compound are
in good agreement with the corresponding values obtained
in case of related glycoluril derivatives [21–23]. The angle
between the mean planes defined by the five-membered
rings is 111.3°. The distance between two carbonyl oxygen
Acknowledgments The authors would like to express their thanks
to Xianggao Meng for performing the x-ray crystallographic mea-
surements and gratefully acknowledge the financial support of this
work by the National Natural Science Foundation of China (Grant
Number 20902035).
˚
atoms (O1–O2) of the glycoluril moiety is 5.72 A. Inter-
estingly, both ethynyls are tortuose with torsion angles of
173.1° and 175.6°. The phenyl ring C (C9–C14) of the
sidewall and phenyl ring D (C1–C6) of the side chain is not
coplanar with a dihedral angle of 23.5°. The phenyl ring C
(C9–C14) is twisted with respect to ring E (C17–C22)
making a dihedral angle of 33.4°.
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