Self-assembly of pyrrole-2-carboxylates: Substituent effect on the synthon conversion

Article abstract of DOI:10.1016/j.molstruc.2009.10.004

The substituent effect on the solid state self-assemblies of three pyrrole-2-carboxylate compounds, 2-4, with N-H?O hydrogen bonds have been studied by X-ray crystallography. Although just one group different in structure, the self-assemblies of 2-4 varie

Full text of DOI:10.1016/j.molstruc.2009.10.004

Journal of Molecular Structure 938 (2009) 322–327
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Self-assembly of pyrrole-2-carboxylates: Substituent effect
on the synthon conversion
a
b,
Yimei Cui a, Zhenming Yin a,b, , Li Dong , Jiaqi He
*
*
a College of Chemistry and Life Science, Tianjin Key Laboratory of Structure and Performance for Functional Molecule, Tianjin Normal Uinversity, Tianjin 300387, China
b Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
a r t i c l e i n f o
a b s t r a c t
Article history:
The substituent effect on the solid state self-assemblies of three pyrrole-2-carboxylate compounds, 2–4,
with N–HÁ Á ÁO hydrogen bonds have been studied by X-ray crystallography. Although just one group dif-
ferent in structure, the self-assemblies of 2–4 varied greatly. The phenyl substituted compound 2 assem-
bled into corrugated tape structure through a R22(10) type dimer synthon and the benzyl substituted
compound 3 assembled into 2-D layer structure through a C(5) type catemer synthon, whereas the butyl
substituted compound 4 assembled into 2-D layer through both type synthons.
Received 8 September 2009
Received in revised form 30 September 2009
Accepted 2 October 2009
Available online 12 October 2009
Keywords:
Ó 2009 Elsevier B.V. All rights reserved.
Crystal engineering
Synthon conversion
Pyrrole-2-carboxylate
1. Introduction
carboxylate, from dimer to catemer, was found with the steric hin-
drance increasing.
The study of synthetic assemblies linked by intermolecular non-
covalent interaction such as hydrogen bonding could lead both to
the creation of new structures with well-defined geometries and
providing insights into biological processes [1]. Varying the overall
macroscopic functional properties of a particular system by small
alterations in molecular structure is of particular appeal in this
field [2]. Pyrrole-based compounds are frequently observed as
hosts for neutral molecules [3] and anionic species [4]. Meantime,
2. Experimental
2.1. General
1H NMR spectra were recorded in DMSO-d6, with TMS as inter-
nal standard, on a BRUKER AV-400 MHz spectrometer. Mass spec-
tra were recorded on an AEIMS-50/PS 30 mass spectrometer.
Analyses of C, H and N were determined on a Perkin–Elmer 240
elemental analyzer. Melting points (mp) were recorded on an elec-
tro-thermal digital melting point apparatus and uncorrected. 2-Tri-
chloroacetylpyrrole was prepared according to literature
procedures [9]. N-phenyldiethanolamine, N-benzyldiethanolamine
and N-n-butyldiethanolamine were commercial available and used
without further purification.
the use of
a-carbonyl-functionalized pyrrole moieties as building
blocks to create hydrogen bonded self-assembled aggregates has
received some attention recently [5]. For example, Sessler and
coworkers [6] have reported that some ferrocene-based pyrrole-
2-carboxylates can self-assemble into one-dimensional chain via
pair of N–HÁ Á ÁO hydrogen bonds. Maeda and coworkers [7] have
fabricated micro- and nanometer-scale porous, fibrous, and sheet
architectures from supramolecular assemblies of dipyrrolyl dike-
tones through hydrogen bonds. In previous work [8], we have stud-
ied the robust synthon between two pyrrole-2-carboxylate
moieties in the crystal structure of compound 1 (Scheme 1). Here-
in, we reported the solid state self-assemblies of another three pyr-
role-2-carboxylate compounds, 2–4. In solid state, all the three
compounds self-assembled through hydrogen bonds and the pyr-
role-2-carboxylate moieties in 2–4 involved into two kinds of syn-
2.2. Preparation of compounds 2–4
Diethanolamine (1 mmol), 2-trichloroacetylpyrrole (3 mmol)
and triethylamine (0.5 mL) were added to acetonitrile (20 mL),
and then the mixture was refluxed for 16 h. The solution was evap-
orated under reduced pressure and the residue was purified by col-
umn chromatography on silica gel with ethyl acetate/petroleum
ether (v:v = 1:2), affording the compounds.
thons.
A phenomenon of synthon conversion of pyrrole-2-
Compound 2, white powder, 67%, m.p. = 135 °C. 1H NMR
(400 MHz, DMSO-d6): d 3.67 (t, 4H, J = 5.6 Hz, –CH2–), 4.26 (t, 4H,
J = 5.6 Hz, –CH2–), 6.09 (s, 2H, PyCH), 6.56 (t, 1H, J = 7.2 Hz, PhCH),
* Corresponding authors. Tel.: +86 22 2354 1675 (Z. Yin).
E-mail address: tjyinzm@yahoo.com.cn (Z. Yin).
0022-2860/$ - see front matter Ó 2009 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2009.10.004

Y. Cui et al. / Journal of Molecular Structure 938 (2009) 322–327
323
O
1, R=
N
NH
H
O
O
OH
OH
COCCl3
N
H
O
O
2, R=
3, R=
R
N
R
N
Et3N, CH3CN
O
NH
4, R= -n-C4H9
Scheme 1.
6.71 (s, 2H, PyCH), 6.80 (d, 1H, J = 8.4 Hz, PhCH), 6.96 (s, 2H, PyCH),
7.10 (t, 2H, J = 7.2 Hz, PhCH), 11.85 (s, 2H, PyNH); 13C NMR
(100 MHz, DMSO-d6): d 49.1, 60.9, 109.6, 111.7, 115.2, 116.0,
121.6, 124.3, 129.2, 147.1, 160.4; ESI-MS: 368(M+1+). Elemental
analysis: C20H21N3O4: Calcd: C, 65.38; H, 5.76; N, 11.44. Found:
C, 65.11; H, 6.01; N, 11.59.
crystal 3 and the catemer C and synthon I in crystal 4 were also cal-
culated using the same procedure.
2.5. Scanning electron microscopy studies
SEM images were obtained with a LX30W/TMP scanning elec-
tron microscope at acceleration voltages of 20 kV. The samples
were prepared by dropping a small amount of ethyl acetate solu-
tion of 2–4 onto a silicon plate and evaporating the solvent.
Compound 3, white powder, 60%, m.p. = 92 °C. 1H NMR-
(400 MHz, d ppm, DMSO-d6) : d 2.83 (t, 4H, J = 5.2 Hz, –CH2–),
3.73 (s, 2H, –CH2–), 4.25 (t, 4H, J = 5.2 Hz, –CH2–), 6.14 (s, 2H,
PyCH), 6.74 (s, 2H, PyCH), 7.00 (s, 2H, PyCH), 7.19–7.30 (m, 5H,
PhCH), 11.83 (s, 1H, PyNH); 13C NMR (100 MHz, DMSO-d6): d
51.9, 58.3, 64.5, 109.4, 114.9, 121.6, 123.9, 126.7, 128.0, 128.3,
139.3, 160.3; ESI-MS: 382(M+1+). Elemental analysis: C21H23N3-
O4: Calcd: C, 66.13; H, 6.08; N, 11.02. Found: C, 66.27; H, 6.11; N,
10.78.
3. Results and discussion
3.1. Crystal structures of 2–4
Compound 4, white powder, 65%, m.p. = 60 °C. 1H NMR-
(400 MHz, d ppm, CDCl3) : d 0.88 (t, 3H, J = 7.5 Hz, –CH3), 1.25–
1.48 (m, 4H, –CH2CH2–), 2.59 (t, 2H, J = 7.5 Hz, –CH2–), 2.91 (t,
4H, J = 6 Hz, –CH2–), 4.35 (t, 4H, J = 6 Hz, –CH2–), 6.23–6.25 (m,
2H, PyCH), 6.91–6.95 (m, 4H, PyCH), 9.62 (s, 1H, PyNH); 13C NMR
(100 MHz, CDCl3): d 14.0, 20.4, 29.6, 53.1, 55.0, 62.7, 110.4,
115.6, 122.6, 123.1, 161.2; ESI-MS: 348(M+1+). Elemental analysis:
C18H25N3O4: Calcd: C, 62.23; H, 7.25; N, 12.10. Found: C, 62.33; H,
6.99; N, 12.17.
The molecular structures of 2–4 were shown in Fig. 1, respec-
tively. In the three structures, all the pyrrole-2-carboxylate moie-
ties adopt syn conformation, with the carbonyl group arranged
syn to its adjacent pyrrole NH. In the crystal of compound 2, each
molecule 2 connected with its two neighbors through a pair of
N–HÁ Á ÁO hydrogen bonds and then formed into one-dimensional
corrugated tape (Fig. 2). The parameters of the hydrogen bonds
were listed in Table 2. In terms of Etter’s graph-set formalism, this
pair of hydrogen bonds motif can be described as an R22(10) sys-
tem [14], which has been frequently observed in the crystal struc-
tures of pyrrole-2-carboxylate compounds [8,15]. Different from
previous results, however, the R22(10) motif in crystal of com-
pound 2 is unsymmetrical.
2.3. X-ray crystallography
The single crystal of compound 2 suitable for X-ray crystallog-
raphy studies was grown by slowly evaporating its MeOH solution.
Crystals of compounds 3 and 4 were obtained by the diffusion of
petroleum ether to the ethyl acetate solution of compounds 3
and 4, respectively. The diffraction data were measured on a BRU-
In the crystal of compound 3, the molecules adopt a convergent
conformation which may ascribe to the intramolecular C–HÁ Á ÁO
KER SMART APEX II CCD diffractometer with Mo K
a radiation
Table 1
(k = 0.71073 Å) by scan mode at 293(2) K. All data were cor-
x
Crystal data of compounds 2–4.
rected by semi-empirical method using SADABS program. The pro-
gram SAINT [10] was used for integration of the diffraction profiles.
The structure was solved by the direct methods using SHELXS pro-
gram of the SHELXL-97 package and refined with SHELXL [11]. The
final refinement was performed by full matrix least-squares meth-
ods with anisotropic thermal parameters for all non-hydrogen
atoms on F2. Crystallographic data and refinement parameters of
the three crystals were summarized in Table 1.
Crystals
2
3
4
CCDC No.
725706
C20H21N3O4
367.40
Monoclinic
P2(1)/n
13.057(4)
8.138(3)
17.660(6)
90
94.412(5)
90
1870.8(11)
4
1.304
0.092
9840
3296
0.0387/0.0828
0.0702/0.0959
1.006
725704
C21H23N3O4
381.42
Monoclinic
P2(1)
11.735(5)
6.212(3)
14.612(6)
90
100.797(7)
90
1046.4(7)
2
1.211
0.085
5411
725705
C18H25N3O4
347.41
Monoclinic
P2(1)/n
17.060(7)
6.159(3)
18.485(8)
90
103.062(7)
90
1892.1(14)
4
1.220
0.087
9196
3347
0.0367/0.0947
0.0527/0.1055
1.010
Empirical formula
Formula weight
Crystal system
Space group
a (Å)
b (Å)
c (Å)
a
(°)
2.4. DFT calculation
b (°)
c
(°)
V (Å3)
R22(10) hydrogen bonding motif (synthon I) linked 2Á2 dimer
and its two monomers units were cut out as the calculation models
from the crystal of 2. 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 pro-
gram [12]. The energies of the synthon I in crystal 2 was computed
as the difference in the single point energies between the 2Á2 dimer
and its two monomers [13]. The energies of the catemer A and B in
Z
Dcalc (g/cm3)
l
(mmÀ1
)
Total reflections
Unique reflections
R1/wR2 [I > 2
3390
r(I)]
0.0337/0.0787
0.0409/0.0831
1.026
R1/wR2 (all data)
Go F on F2

324
Y. Cui et al. / Journal of Molecular Structure 938 (2009) 322–327
Fig. 1. ORTEP view of compound 2 (a), 3 (b) and 4 (c); showing 30% probability displacement ellipsoids with atom numbering.
hydrogen bond (C12–H12Á Á ÁO1, 2.57 Å, 3.43 Å, 153°). Molecules of
3 assembled into 2-D structure through two types helical catemer
hydrogen bonding motifs (Fig. 3). The catemer A consisted of N1–
H1Á Á ÁO1 hydrogen bonds and the catemer B consisted of N2–
H2Á Á ÁO3 hydrogen bonds. The parameters of the two hydrogen
bonds were also listed in Table 2.

Y. Cui et al. / Journal of Molecular Structure 938 (2009) 322–327
325
Fig. 2. Self-assembly of compound 2 with dimeric N–HÁ Á ÁO hydrogen bonding motif.
Table 2
3.2. Comparison of the hydrogen bond synthons in crystal structures of
2–4
Hydrogen bonds parameters in crystals of 2–4.
Compounds
D–HÁ Á ÁA
DÁ Á ÁA (Å)
HÁ Á ÁA (Å)
\D–HÁ Á ÁA (deg)
In the three crystal structures, the hydrogen bonding synthons
in which pyrrole-2-carboxylate moieties involved are R22(10) type
dimer (synthon I, Scheme 2) and C(5) type helical catemer (syn-
thon II, Scheme 2). The two kinds of hydrogen bonding motifs
are reminiscent of the hydrogen bonding dimer and catemer of car-
boxylic acid [16], oxime [17] and pyrazole [17–18] compounds. In
the crystals of compound 2 and 3, just one kind synthon was ob-
served, synthon I and synthon II, respectively. In the crystal of
compound 4, both kinds synthon were found. Obviously, the differ-
ent synthon resulted from the different substituent groups on
nitrogen atom in molecules of 2–4. The change of substituent
groups from phenyl in 2 to benzyl in 3 and butyl in 4 caused the
sp2 hybrid to sp3 hybrid of the nitrogen atom and consequent steric
hindrance increasing. Similar substituent effects on the formation
of dimer and catemer of carboxylic acid have been reported by
Desiraju [19]. The coexistence of synthon I and II in the crystal of
compound 4 should ascribed to that butyl group is smaller than
2
N2–H2Á Á ÁO3i
N3–H3Á Á ÁO1ii
N1–H1Á Á ÁO1iii
N2–H2Á Á ÁO3iv
N1–H1Á Á ÁO2v
N2–H2Á Á ÁO3vi
3.094
2.805
2.919
2.903
2.831
2.921
2.278
2.005
2.118
2.054
2.010
2.125
158
154
155
169
159
154
3
4
Symmetry code i: x + 1/2, Ày + 1/2, z À 1/2; ii: x À 1/2, Ày + 1/2, z + 1/2; iii: Àx,
y À 1/2, Àz; iv: Àx, y À 1/2, Àz + 1; v: Àx, Ày + 2, Àz; vi: Àx À 1/2, y + 1/2, Àz + 1/2.
In the solid state, the compound 4, which also adopt a convergent
conformation due to the intramolecular C–HÁ Á ÁO hydrogen bond
(C3–H3Á Á ÁO3, 2.55 Å, 3.40 Å, 152°), has the similar conformation to
compound 3. Molecules of 4 assembled into 1-D chain through a
hydrogen bonding catemer C which consisted of N2–H2Á Á ÁO3 hydro-
gen bonds. The chains form 2-D layer structure with the contribu-
tion of a symmetrical R22(10) hydrogen bonding motif (Fig. 4).
Fig. 3. Self-assembly of compound 3 with helical catemeric N–HÁ Á ÁO hydrogen bonding motifs.

326
Y. Cui et al. / Journal of Molecular Structure 938 (2009) 322–327
Fig. 4. Self-assembly of compound 4 with helical catemeric N–HÁ Á ÁO hydrogen bonding motifs and dimeric hydrogen bonding motifs.
Scheme 2. Diagram of synthon I (left) and synthon II (right).
benzyl group. It should be the transition structure of steric hin-
drance effects on the synthon conversion.
Self-assembled nanoscale structures of 2–4 were fabricated by
the deposition of target compounds from a saturated solution onto
clean substrates. Scanning electron microscopy (SEM) studies re-
vealed that distinct morphologies were formed. As shown in
Fig. 5, compounds 2 and 4 generated nanorod and block, respec-
tively, while compound 3 formed porous structure. It is consistent
with above X-ray structures and PLATON calculation results that
the catemer synthon cause the loose packing of molecules.
The hydrogen bond energy of synthon I and synthon II were cal-
culated to evaluate their strength by using DFT calculations. The
calculated energy of synthon I is about 9.8 kcal/mol for which ob-
served in the crystal of compound 2 and 11.9 kcal/mol for which
observed in the crystal of compound 4. The energies of catemers
A, B and C are 6.5, 7.0 and 6.6 kcal/mol, respectively. It means that
the hydrogen bonds in the catemer synthon is more stable than
that in the dimer synthon. Calculations with PLATON [20] revealed
that the available volume for solvent is 6.7% of per unit cell in the
crystal 3 and none in the crystal 2. It indicates that the catemer
synthon is geometry disadvantaged which cause loose packing of
the pyrrole-2-carboxylate compounds [21].
4. Conclusions
In conclusion, three structural similar pyrrole-2-carboxylate
compounds 2–4, just different in one substituent group, were syn-
Fig. 5. SEM images of (a) 2, (b) 3 and (c) 4.

Y. Cui et al. / Journal of Molecular Structure 938 (2009) 322–327
327
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thesized and their crystal structures were characterized by X-ray
crystallography. In the three crystals, the pyrrole-2-carboxylate
moieties involve into two kinds of synthons, R22(10) type dimer
and C(5) type catemer. DFT calculation rationalized that the cate-
mer synthon is energy more stable but is geometry disadvantaged.
Most importantly, a phenomenon of synthon conversion of pyr-
role-2-carboxylate, from dimer to catemer, was found with the ste-
ric hindrance increasing of the substituted groups and which
caused distinct assemblies of 2–4. This observation would be help-
ful to obtain desired supramolecular structures by purposefully
controlling the molecular structure of pyrrole-2-carboxylate com-
pounds and demonstrated that the pyrrole-2-carboxylate has good
perspective on application to crystal engineering.
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