Synthesis and crystal structure of a novel molecular clip from diphenylglycoluril and phthalhydrazide

Article abstract of DOI:10.3184/030823410X12674504959007

A novel molecular clip from diphenylglycoluril and phthalhydrazide has been synthesised. Its structure and conformation was confirmed by single crystal X-ray diffraction.

Full text of DOI:10.3184/030823410X12674504959007

JOURNAL OF CHEMICAL RESEARCH 2010
RESEARCH PAPER 145
MARCH, 145–146
Synthesis and crystal structure of a novel molecular clip from
diphenylglycoluril and phthalhydrazide
Hu Sheng-Lia,b*, Wang Zhi-Guoc and Sun Wen-Binga
aDepartment of Chemical and Enviromental Engineering, Hubei Normal University, Huangshi 435002, P. R. China
bHubei Key Laboratory of Pollutant Analysis & ReuseTechnology, Huangshi 435002, P. R. China
cSchool of Chemical and Materials Engineering, Huangshi Institude ofTechnology, Huangshi 435003, P. R. China
A novel molecular clip from diphenylglycoluril and phthalhydrazide has been synthesised. Its structure and
conformation was confirmed by single crystal X-ray diffraction.
Keywords: diphenylglycoluril, phthalhydrazide, molecular clip
Natural receptors play a fundamental role in molecular recog-
nition, catalysis, and transport processes. Artificial receptors
have been developed to mimic these functions.1,2 The rigid
concave shape of glycoluril makes it a versatile building block
to construct various supramolecular structures, such as mole-
cule capsules,3 molecule clips,4 and the cucurbit[n]uril family
of macrocycles.5 Glycoluril-based clips with a preorganised
cleft and rigid aromatic arms have been proved to be effective
receptors for hydroxybenzene derivatives,6,7metal ions,8–10 and
anions.11 In order to expand the range of possible guest struc-
ture, we report here the synthesis and X-ray structure of a new
molecular clip from diphenylglycoluril and phthalhydrazide.
The title molecule clip 4 was prepared by reacting the
glycoluril cyclic ether 2 with phthalhydrazide 3 using MeSO3H
as an acid and solvent at 80 °C (Scheme 1). It was character-
Crystals of 4 were obtained by slow evaporation of solution
in chloroform–methanol mixtures. The structure analysis
showed that in the crystal, the asymmetric unit contained
two independent molecules A and B (Fig. 1). There were some
small differences in their structures and conformations.
In molecule A, the distance between the carbonyl oxygens
(O2–O3) of the glycoluril ring amounts to 5.363 Å, the dihedral
angle between two phenyl rings of the sidewalls is 35.74°,
and the distance between the centroids of two phenyl rings of
the sidewalls is 6.766 Å; In molecule B, the distance between
the carbonyl oxygens (O –O6) of the glycoluril ring amounts
to 5.415 Å, the dihedral5angle between two phenyl rings of
the sidewalls is 34.14°, and the distance between the centroids
of two phenyl rings of the sidewalls is 6.593 Å. As can be seen
compound 4 is similar to Nolte's molecular clips,12,13 but has
a deeper cavity. Hence molecule 4 is a potential synthetic
receptor for some neutral molecules through π-π stacking and
hydrogen bond interactions. Moreover, because compound 4
has more N and O atoms in its U-shaped cavity than the pre-
vious molecular clips,14 it is also a potential synthetic receptor
for metal ions.
1
ised by its NMR spectra. The H NMR spectrum of 4 in
DMSO-d6 shows two pairs of well-defined doublets with equal
intensity for the protons of methylene at δ = 6.62 ppm (J = 15.2
Hz) and δ = 4.72 ppm (J = 15.2 Hz), indicating that molecule
possess good symmetry and the four bridging methylene have
the same chemical environment. The IR and MS for the prod-
uct are in good agreement with the title compound. In addition,
its structure and conformation was confirmed by single crystal
X-ray diffraction, as shown in Fig. 1.
In conclusion, a new clip molecule from diphenylglycoluril
and phthalhydrazide was synthesised. Its structure and confor-
mation was also confirmed by single crystal X-ray diffraction.
Further studies on its molecular recognition are in progress.
Scheme 1 Synthesis of clip molecule 4.
* Correspondent. E-mail: hushengli168@126.com

146 JOURNAL OF CHEMICAL RESEARCH 2010
Fig. 1 The crystal structure of 4. solvent molecules omitted for clarity.
R1 = 0.0613, wR2 = 0.1433 [W = 1 / [σ2(F 2) + (0.0880P)2 + 0.0000P]
Experimental
o
where P = (Fo2 + 2Fc2)/3, (∆/σ)max = 0.000, S = 0.899, (∆ρ)max = 0.598,
(∆ρ) = 0.462 e/ Å3. All calculations were performed on a PC with
SHEmLinXS-97 program. Crystal data: C74 H Cl N O12, M = 1572.03,
Triclinic, space group P-1, a = 14.1307(5142), 6b 1=6 14.6268(12), c =
17.9728(15) Å, α = 87.514(2)°, β = 73.552(2)°, γ = 76.403(2)°, V =
3461.8(5)Å3, Z = 2, Dc = 1.508g cm−3, µ = 0.327mm−1. The data have
been deposited as CCDC 279807 which contains the supplementary
crystallographic information for this paper. 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 CB21EZ, UK; fax: +44(0)1223-336033; e-mail:
deposit@ccdc.cam.ac.uk.
General
All reagents obtained from commercial sources were of AR grade.
The melting point was determined with an XT4A micromelting point
apparatus and was uncorrected. The H NMR spectra were recorded
on a Mercury Plus-400 spectrometer with TMS as internal reference
and DMSO-d6 as solvent. IR spectra were recorded on a Perkin−Elmer
PE−983 IR spectrometer as KBr pellets with absorption in cm−1. MS
were obtained with Finnigan Trace MS instrument using EI method.
Elemental analyses were carried out on a Vario EL III instrument.
1
Synthesis
Diphenyl glycoluril 115 and cyclic ether 216 were prepared as the
literature method.
Preparation of molecular clip 4: Anh. MeSO H (10 mL) was added
to a flask containing phthalhydrazide 3 (0.36g3, 2.74 mmol), and the
mixture was stirred at 80 °C until homogeneous. Compound 2 (0.52g,
1.37 mmol) was added in one portion and the flask was sealed and
heated at 80 °C for 3 h. The reaction mixture was allowed to cool and
then poured into water (100 mL). The pale precipitate was collected
by filtration through a medium fritted funnel and washed with water
(50 mL) and dried under vacuum. Flash chromatography (MeOH/
CHCl3, 1: 20) gave compound 4 (0.59g, yield: 65%) as a white solid.
M.p. >300 °C. IR (KBr): 3025, 2924, 1741, 1650, 1608, 1452, 1429,
This work is supported by the National Natural Science
Foundation of China (Grant No. 20872042).
Received 21 February 2010; accepted 25 February 2010
Paper 101015 doi: 10.3184/030823410X12674504959007
Published online: 24 March 2010
References
1
2
J.-M. Lehn, Supramolecular chemistry, VCH: Weinheim, 1995.
J.W. Steed and J.L. Atwood, Supramolecular chemistry, Wiley, New York,
2000.
1
1298, 1130cm−1. H NMR (400 MHz, DMSO-d6): δ 8.11–8.08 (m,
4H, ArH), 7.95–7.92 (m, 4H, ArH), 7.23–7.17 (m, 10H, ArH), 6.62
(d, J = 15.2, 4H, NCH2N), 4.72 (d, J = 15.2, 4H, NCH2N). EI-MS:
m/z = 668 [M + 2H]2+. Anal. Calcd for C36H N O6 (666.2): C, 64.86;
H, 3.93; N, 16.81; Found: C, 64.70; H, 3.85;26N,816.71%.
3
4
J. Jr. Rebek, Angew.Chem., Int. Ed., 2005, 44, 2068.
A.E. Rowan, J.A.A.W. Elemans and R.J.M.Nolte, Acc. Chem. Res., 1999,
32, 995.
J.W. Lee, S. Samal, N. Selvapalam, H.-J. Kim and K. Kim, Acc.Chem.Res.,
2003, 36, 621.
J.N.H. Reek, A.H. Priem, H. Engelkamp, A.E. Rowan, J.A.A.W. Elemans
and R.J.M. Nolte, J. Am. Chem. Soc., 1997, 119, 9956.
B.-H. Zhou, L.-P. Cao and A.-X. Wu, J. Chem. Res., 2009, 440.
S.-L. Hu, S. Wang, Y.-T. Li, L.-P. Cao and A.-X. Wu, J. Chem. Res., 2009,
32.
5
6
X-ray diffraction study of 4
Crystals were obtained by slow evaporation from chloroform–
methanol solution (20:1 v/v). A colourless crystal of the title com-
pound 4 having approximate dimensions of 0.30mm × 0.20 mm ×
0.10mm was mounted on a glass fibre in a random orientation at
292(2) K. The determination of unit cell and the data collection were
performed with MoKα radiation (λ = 0.71073 Å) on a Bruker Smart
APEX-CCD diffactometer with a ψ–ω scan mode. A total of 36637
reflections were collected in the range of 1.18 < θ < 26.00° at room
temperature, and 13537 were independent (Rint = 0.0691), of which
6751 observed reflections with I > 2σ(I) were used in the structure
determination and refinements. The structure was solved by direct
methods using the SHELXS-97 program and expanded by Fourier
technique. The non-hydrogen atoms were refined anisotropically, and
the location of the hydrogen atoms were determined by a theoretical
calculation. A full-matrix least-squares refinement gave the final
7
8
9
S. Wang, N.-F. She and A.-X. Wu, J. Chem. Res., 2009, 265.
10 S.-L. Hu, G.-D. Yin, Y.-Z. Wang and A.-X. Wu, Can. J. Chem., 2008, 86,
691.
11 J. Kang and J. Kim, Tetrahedron Lett., 2005, 46, 1759.
12 R.P. Sijbesma, S.S. Wijmengand and R.J.M. Nolte, J.Am. Chem. Soc.,
1992, 114, 9807.
13 J.N.H. Reek, J.A.A.W. E1emans and R.J.M. Nolte, J. Org. Chem., 1997,
62, 2234.
14 S.-L. Hu, N.-F. She, G.-D.Yin, H.-Z. Guo, A.-X. Wu and C.-L. Yang,
Tetrahedron Lett., 2007, 48, 1591.
15 A.R. Butler and E. Leitch, J. Chem. Soc., Perkin Trans., II 1980, 103.
16 F.G.M. Niele and R.J.M. Nolte, J. Am. Chem. Soc., 1988, 110, 172.

Copyright of Journal of Chemical Research is the property of Science Reviews 2000 Ltd. and its content may
not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written
permission. However, users may print, download, or email articles for individual use.