Synthesis and crystal structure of 1,3-Bis[2-(pyrrol-2-carbonyloxy)ethoxy] Benzene

Article abstract of DOI:10.1007/s10870-010-9810-y

A new compound, 1,3-bis[2-(pyrrol-2-carbonyloxy)ethoxy]benzene (1), was synthesized and characterized by X-ray diffraction. The crystal is monoclinic, space group P2₁/c with a = 6.3571(7), b = 11.0416(11), c = 28.156(3) A, b = 92.821(2), V = 19

Full text of DOI:10.1007/s10870-010-9810-y

J Chem Crystallogr (2010) 40:1142–1145
DOI 10.1007/s10870-010-9810-y
ORIGINAL PAPER
Synthesis and Crystal Structure of 1,3-Bis[2-(pyrrol-2-
carbonyloxy)ethoxy]Benzene
•
•
•
Shipeng Sun Li Dong Jianhua Guo
Zhenming Yin
Received: 30 November 2009 / Accepted: 20 May 2010 / Published online: 15 June 2010
Ó Springer Science+Business Media, LLC 2010
Abstract A new compound, 1,3-bis[2-(pyrrol-2-carbon-
yloxy)ethoxy]benzene (1), was synthesized and character-
ized by X-ray diffraction. The crystal is monoclinic, space
recently [11, 12]. For instance, Sessler et al. [13] have
reported that some ferrocene-based pyrrole-2-carboxylates
form one-dimensional chain via pair of N–H_O hydrogen
bonds. Branda and coworkers [14] found that 2,20-dipyrr-
olyl ketone self-assembles via hydrogen bonding into
supramolecular helices. Lightner and cowokers [15] later
reported that 2,20-dipyrrylethanedione self-assembles via
hydrogen bonding into supramolecular ribbons. Recently
Maeda et al. [16] have fabricated micro- and nanometer-
scale porous, fibrous, and sheet architectures from supra-
molecular assemblies of dipyrrolyl diketones through
hydrogen bonds. We have studied the solid state structures
of some pyrrole-2-carboxylate compounds in our earlier
works [17, 18], and demonstrated that the pyrrole-2-car-
boxylate has good perspective on application to crystal
engineering. In the present study, we report the synthesis
and crystal structure of a new compound, 1,3-bis[2-(pyrrol-
2-carbonyloxy)ethoxy]benzene (1), which forms a two-
dimensional structure through helical catemeric hydrogen
bonding motif rather than the frequently observed dimeric
hydrogen bonding motif.
group P21/c with a = 6.3571(7), b = 11.0416(11), c =
3
˚
˚
28.156(3) A, b = 92.821(2), V = 1974.0(4) A , Z = 4,
Dc = 1.293 g/cm3, F(000) = 808, l = 0.097 mm-1. The
final R = 0.0395 and wR = 0.0927 for 3478 observed
reflections with I [ 2 r(I), and R = 0.0660 and wR =
0.1058 for all reflections. The title compound assembles into
2-D structure through a catemer type N–H_O hydrogen
bonding motif and further forms 3-D structure through
C–HꢀꢀꢀO hydrogen bonds.
Keywords 1,3-Bis[2-(pyrrol-2-carbonyloxy)ethoxy]
benzene ꢀ Synthesis ꢀ Crystal structure ꢀ Hydrogen bonding
motif
Introduction
Pyrrole-based compounds are frequently observed as hosts
for neutral molecules [1–3] and anionic species [4–9] for
its ability to form hydrogen bonds. 2-Carbonyl substituted
pyrrole possesses one hydrogen bond donor (N–Hpyrrole
)
Experimental
and one acceptor (C=O), which was found preferring to
form centrosymmetric dimers with a pair of N–H_O
hydrogen bonds (Scheme 1) [10]. Thus, using a-carbonyl-
functionalized pyrrole moieties as building blocks to create
hydrogen bonded aggregates has received some attention
General
1H NMR spectra were recorded in DMSO-d6, with TMS as
internal standard, on a BRUKER AV-400 MHz spec-
trometer. Mass spectra were obtained on an AEIMS-50/PS
30 mass spectrometer. Elemental analyses were performed
on a Perkin-Elmer 240 elemental analyzer. Melting points
(mp) were recorded on an electro-thermal digital melting
point apparatus and uncorrected. 2-Trichloroacetylpyrrole
was prepared according to literature procedures [19].
S. Sun ꢀ L. Dong ꢀ J. Guo ꢀ Z. Yin (&)
Tianjin Key Laboratory of Structure and Performance
for Functional Molecule, College of Chemistry,
Tianjin Normal Uinversity, Tianjin 300387, China
e-mail: tjyinzm@yahoo.com.cn; yinzm@eyou.com
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J Chem Crystallogr (2010) 40:1142–1145
1143
Table 1 Crystal data of compounds 1
O
O
N
N
O
O
CCDC deposit no.
Empirical formula
Formula weight
756384
20H20N2O6
H
H
O
O
1
C
384.38
293
Temperature (K)
Wavelength
N
N
O
O
O
O
H
O
H
HN
˚
O
O
0.71073 A
Monoclinic, P21/c
0.24 9 0.20 9 0.18
6.3571(7)
11.0416(11)
28.156(3)
90
O
H
H
N
Crystal system, space group
Crystal size (mm)
NH
O
O
N
O
O
˚
a (A)
Scheme 1 Diagram of dimeric R22 (10) hydrogen bonding motif (left)
and catemeric type motif (right) of pyrrole-2-carboxylate
˚
b (A)
˚
c (A)
a (°)
b (°)
c (°)
1,3-bis(hydroxyethoxy)benzene were commercial available
and used without further purification.
92.821(2)
90
3
˚
V (A )
1974.0(4)
4
Synthesis of Compound 1
Z
Dcalc. (g/cm3)
Absorption coefficient (mm-1
F(000)
1.293
A mixture of 1,3-Bis(hydroxyethoxy)benzene (198 mg,
1 mmol), 2-trichloroacetylpyrrole (633 mg, 3 mmol), tri-
ethylamine (0.5 mL), and acetonitrile (20 mL) was stirred
at the refluxing temperature for 20 h. After the solution was
allowed to cool to room temperature, the solvent was
removed under the reduced pressure and the residue
was purified by column chromatography on silica gel using
ethyl acetate/petroleum ether (v:v = 1:2) as eluent,
affording 242 mg compounds 1, white powder, yield 63%,
m.p. = 124 °C. 1H NMR (400 MHz, Methanol-d4): d 4.27
(t, 4H, J = 4.2 Hz, –CH2–), 4.56 (t, 4H, J = 4.2 Hz,
–CH2–), 6.20 (s, 2H, PyCH), 6.55 -6.62(m, 3H, PhCH),
6.90 (s, 2H, PyCH), 6.98 (s, 2H, PyCH), 7.17–9.20 (m, 1H,
PhCH) ppm; 13C NMR (100 MHz, Methanol-d4): d 63.7,
67.3, 102.8, 108.4, 110.8, 117.0, 123.2, 124.9, 131.1,
161.4, 162.6 ppm; ESI–MS: 385(M ? 1?). Elemental
analysis: C20H21N3O4: Calcd: C, 62.49; H, 5.24; N, 7.29.
Found: C, 62.21; H, 5.44; N, 7.05.
)
0.097
808
Range for data collection
Limiting indices
1.98 to 25.03
-7 B h B 7, -13 B k B 11, -
33 B l B 33
Reflections collected/unique
Refinement method
10486/3478 [R(int) = 0.0326]
Full-matrix least-squares on F2
R1 = 0.0395, wR2 = 0.0927
R1 = 0.0660, wR2 = 0.1058
1.042
Final R indices [I [ 2r(I)]
R indices (all data)
Goodness of fit F2
Extinction coefficient
0.0075 (11)
Largest different peak and hole 0.141 and -0.138
-3
˚
(e A
)
DFT Calculation
The catemer hydrogen bonding motif linked 1ꢀ1 dimer and
its two monomers units were cut out as the calculation
models from the crystal of 1. All hydrogen atoms were
included in the models. Single point energies of the
monomers and dimer were calculated at the B3LYP/6-
31G* level by using the Gaussian 98 program [22]. The
energies of the hydrogen bonds was computed as the dif-
ference in the single point energies between the 1ꢀ1 dimer
and its two monomers [23].
X-Ray Crystallography
The single crystal of compound 1 suitable for X-ray crys-
tallography study was grown by slowly evaporating its
MeOH solution. The diffraction data were measured on a
BRUKER SMART APEX II CCD diffractometer with Mo
˚
Ka radiation (k = 0.71073 A) by x scan mode at 293(2) K.
All data were corrected by semi-empirical method using
SADABS program. The program SAINT [20] was used for
integration of the diffraction profiles. The structure was
solved by the direct methods using SHELXS program of
the SHELXL-97 package and refined with SHELXL [21].
The final refinement was performed by full matrix least-
squares methods with anisotropic thermal parameters for
all non-hydrogen atoms on F2. Crystallographic data and
refinement parameters of the three crystals were summa-
rized in Table 1.
Results and Discussion
The molecular structure of compound 1 is shown in Fig. 1
which shows a C type conformation. In the structure, both
the pyrrole-2-carboxylate moieties adopt syn conformation,
with the carbonyl group arranged syn to its adjacent pyrrole
NH. The angles between the benzene ring and the two
pyrrole rings are 57.6° and 76.7°, respectively. The angle
123

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J Chem Crystallogr (2010) 40:1142–1145
Table 2 Hydrogen bonds parameters in crystals of 1
˚
˚
D–H_A
D–H
H_A (A)
D_A (A)
\D–H_A (°)
N1–H1_O6i
N2–H2_O1ii
C3–H3_O3iii
0.86
0.86
0.93
2.06
2.11
2.56
2.843 (2)
2.947 (2)
3.494 (2)
152
164
177
Symmetry code: (i) x, -y ? 3/2, z - 1/2; (ii) x ? 1, -y ? 3/2,
z ? 1/2; (iii) 2 - x, 1/2 ? y, ‘ - z
structure through C3–H3_O3 hydrogen bonds (Fig. 2a, c).
The parameters of the hydrogen bonds were listed in
Table 2.
DFT calculation reveals that the energies of the hydro-
gen bonds N1–H1_O6 and N2–H2_O1 are 7.1 and
5.7 kcal/mol, respectively. It is a well agreement with
previous result that the N–H_O hydrogen bonds in the
catemeric motif is more stable than that in the R22(10) type
motif. Calculations with PLATON [30] revealed that the
available volume for solvent is 4.5% of per unit cell in the
crystal of compound 1. It is also consistent with previous
presumption that the catemeric hydrogen bonding motif of
pyrrole-2-carboxylate always companies with loose crystal
packing.
Fig. 1 ORTEP view of compound 1; showing 30% probability
displacement ellipsoids with atom numbering
between the two pyrrole rings is 71.6°. The torsion angles
of O2–C6–C7–O3 and O4–C14–C15–O5 are 69.4° and
79.6°, respectively.
Molecules of 1 formed 2-D structure through a helical
catemeric hydrogen bonding motif which consists of
alternate N1–H1_O6 and N2–H2_O1 hydrogen bonds
(Fig. 2b). In terms of Etter’s graph-set formalism, this kind
of hydrogen bonds motif can be described as an C22(10)
system [24]. This kind of hydrogen bonding motif is quite
different with previous results in which the dimeric R22(10)
type motif is frequently observed (Scheme 1) [16, 25–28].
Few case of the catemeric hydrogen bonding motif has
been reported in crystals of pyrrole-2-carboxylate com-
pounds. However, they belong to C(5) system [17, 29]. The
2-D layer structures were held together to form 3-D
Conclusions
In conclusion, a new bis-pyrrole-2-carboxylate compound
was synthesized and its crystal structure was characterized
by X-ray crystallography. In the crystal, the pyrrole-2-
carboxylate moieties involve into a new helical catemeric
Fig. 2 Crystal packing diagram
(b), catemer N–H_O hydrogen
bonding motif (b) and C–H_O
hydrogen bonding (c) in the
crystal of compound 1
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J Chem Crystallogr (2010) 40:1142–1145
1145
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Crystallographic data for structural analysis have been
deposited with the Cambridge Crystallographic Data Cen-
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obtained free of charge on application to CCDC, 12 Union
Road, Cambridge CB2 1EZ, UK (Fax: ?44 1223 336 033;
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