A new hydrogen-bonding motif with constituents bearing donor and acceptor sites 7 ? apart

Article abstract of DOI:10.1515/znb-2005-0710

Aryl substituted dipyrromethanes [di(pyrrol-2-yl)-phenyl-methanes] with hydrogen acceptor substituents R in para position of the aryl ring [R = CO ₂Me, CO₂H, CONH(iPr) and NH₂] located 7 ? apart from the hydrogen donor pyr

Full text of DOI:10.1515/znb-2005-0710

A New Hydrogen-Bonding Motif with Constituents Bearing Donor
˚
and Acceptor Sites 7 A Apart
Katja Heinze and Anja Reinhart
Anorganisch-Chemisches Institut der Universita¨t Heidelberg, Im Neuenheimer Feld 270,
D-69120 Heidelberg, Germany
Reprint requests to K. Heinze. E-mail: katja.heinze@urz.uni-heidelberg.de
Z. Naturforsch. 60b, 758 – 762 (2005); received April 1, 2005
Aryl substituted dipyrromethanes [di(pyrrol-2-yl)-phenyl-methanes] with hydrogen acceptor sub-
˚
stituents R in para position of the aryl ring [R = CO2Me, CO2H, CONH(iPr) and NH2] located 7 A
apart from the hydrogen donor pyrrole nitrogen atom are shown to self-assemble in the solid state via
hydrogen bonds to form rings or chains.
Key words: Dipyrromethanes, Self-Assembly, Hydrogen Bonds, Bidentate Ligands, DFT
Introduction
Dipyrromethane derivatives are useful starting ma-
terials for the preparation of porphyrines [1] and
coordination compounds [2, 3]. However, the use
of (substituted phenyl)dipyrromethanes (Scheme 1)
as building blocks (synthons [4]) in supramolecular
chemistry and crystal engineering has not yet been
explored. Indeed there have been only few struc-
tural reports on (substituted phenyl)dipyrromethanes:
the parent compound with R = H [5], mesityl
dipyrromethane [5], a bis(dipyrromethane) [6] and (ni-
trophenyl)dipyrromethane (R = NO2) [7]. Only in the
latter case the substitutent R is involved in hydrogen
bonding to one of the acidic pyrrole hydrogen atoms
while in some other cases weak N-H···π(pyrrole) inter-
actions have been found in the solid state [6, 8].
We report herein the crystal structures of four (sub-
stituted phenyl)dipyrromethanes with potential hydro-
gen acceptor groups R = CO2Me (1), CO2H (2),
CONH(iPr) (3), NH2 (4) in para position of the phenyl
ring (Scheme 1).
Scheme 1.
Fig. 1. View of the molecular structures of 1 – 4 along the
aliphatic C8-H bond as found in the crystal lattice, number-
ing of relevant atoms and intramolecular distances of the hy-
drogen donor and acceptor atoms.
Results and Discussion
Dipyrromethanes 1, 2 and 4 were prepared from the
corresponding aromatic aldehyde and pyrrole in the
presence of trifluoroacetic acid according to literature
procedures [5], the amide 3 was formed by reaction of
the acid 2 with iPrNH2.
drogen bonds to the para substituent of a neighbouring
molecule to form dimers (1 – 3) or helical chains (4)
(Table 1, Fig. 2) [9]. The number of atoms separating
the hydrogen donor and acceptor sites is seven atoms
In the crystal structures of 1 – 4 (Fig. 1) the pyrrole for 1–3 and six atoms for 4 (Fig. 1 and 2). The in-
hydrogen atom at N1 is identified to be involved in hy- tramolecular distance of the hydrogen atom donor and
c
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K. Heinze – A. Reinhart · A New Hydrogen-Bonding Motif with Constituents
759
◦
˚
Table 1. Selected bond lengths (A) and angles ( ) of 1, 2, 3,
4 and the DFT optimised structure of di(pyrrol-2-yl)-phenyl-
methane.
1
2(×H2O)
3
4
DFT
A = O1 A = O1 A = O1 A = N3
N1···A’
2.917
169.2
7.3
2.970
170.9
7.1
2.832
171.8
7.1
2.989
160.2
6.8
–
–
–
N1-H9···A’
N1···A
C4-C8-C9-N1
C4-C8-C13-N2
−35.7
−41.7
−40.5
−70.6
88.5
155.5 164.4
125.1
146.3
152.4
Scheme 2.
Fig. 2. View of the ring and chain motifs found in the crystal
structures of 1 – 4.
Fig. 3. DFT optimised geometries of (1)2 in single-bonded
and double-bonded arrangements.
˚
acceptor atoms amounts to 7 A which is among the
boxylic acid dimer formation and amide dimerisation.
Even the water molecule present in the crystal lattice of
2 does not disturb the dimer formation but instead links
the dimers by OH···OH·2··O hydrogen bonds to form a
double strand [9].
largest found in supramolecular synthons for hydrogen
bonding motifs [10, 11] (cf. the donor acceptor distance
in the common carboxylic acids or amides amounts to
˚
only 2.2 – 2.3 A). The large intramolecular distances
between donor and acceptor sites and the angles N1-
C8-A of 92 – 102◦ (A = O1, N3) allow for the forma-
tion of small ellipsoid channels of approximately 8 –
In contrast to typical synthons (e.g. A or carboxylic
acids) the dipyrromethanes 1 – 4 are flexible and thus
non-preorganised for self-assembly. In order to gain
some insight into the flexibility of dipyrromethanes
the gas phase minimum geometry of the parent unsub-
stituted dipyrromethane was determined by means of
DFT calculations (B3LYP, 6-31G+(d,p) basis set). The
largest conformational difference between the calcu-
lated gas phase geometry and the solid state structures
involves the hydrogen bonded pyrrole ring. The tor-
sional angle C4-C8-C9-N1 differs by 124– 159◦ while
the orientation of the second pyrrole ring (C4-C8-C13-
N2) differs by only 9 – 39◦ (Table 1, Fig. 2). Thus the
˚
˚
10 A×3.7 A (atom-to-atom distance) running through
the crystals along the short a-axis (1: 5.65; 2: 5.87; 3:
5.66; 4: 6.18 A).
˚
Scheme 2 schematically depicts the hydrogen bond-
ing motifs observed for 1 – 4 in the crystal lattice:
dimeric ring motifs with graph set R22(20) [12] for 1 –
3 and a catena motif of graph set C(9) [12] for 4 [meso-
(4-nitrophenyl)dipyrromethane [7] forms a chain of
graph set C(10)]. The largest ring motif A [R22(20)]
with a very high probability of formation according to
a statistical analysis [11] is also shown for comparison.
The probability of ring or catena formation of accep- rather flexible orientation of the pyrrole rings has to
tor substituted dipyrromethanes is at present difficult to be adjusted for self-assembly. However, the energy re-
estimate due to the lack of sufficient crystal data. How- quired for ring rotation is small and can easily be com-
ever, from the available data it appears that the mo- pensated for by the formation of hydrogen bonds. One
tifs formed by 1 – 4 can successfully compete with car- hydrogen bond suffices to force two dipyrromethanes
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760
K. Heinze – A. Reinhart · A New Hydrogen-Bonding Motif with Constituents
Table 2. X-ray crystallograph-
ic data for 1, 2, 3 and 4.
1
2•H2O
3
4
Formula
Molecular mass
C17H16N2O2
280.32
C16H16N2O3
284.31
C19H21N3O
307.39
C15H15N3
237.30
a
R1 : I > 2σ(I); b Rw: all data.
Crystal dimension / mm 0.20×0.10×0.03 0.10×0.10×0.01 0.40×0.30×0.10 0.05×0.04×0.02
Crystal system
triclinic
P1 (2)
triclinic
triclinic
P1 (2)
orthorhombic
P212121 (19)
6.177(1)
7.737(2)
26.002(5)
90.0(0)
90.0(0)
90.0(0)
1242.7(4)
4
¯
¯
¯
Space group (no.)
P1 (2)
˚
a [A]
5.648(1)
7.623(2)
16.337(3)
96.56(3)
95.27(3)
95.58(3)
691.7(2)
2
5.869(1)
7.527(2)
16.204(3)
79.40(3)
86.32(3)
81.73(3)
695.8(2)
2
5.655(2)
10.990(2)
13.243(3)
85.67(3)
80.36(3)
87.49(3)
808.7(3)
2
˚
b [A]
˚
c [A]
α [◦]
β [◦]
γ [◦]
3
˚
Cell volume [A ]
Molecular units per cell
µ [mm−1
]
0.090
0.095
1.357
0.080
1.262
0.077
1.268
Density (calcd) [g cm−3] 1.346
T [K]
200
200
200
200
Scan range (2Θ)
2.5 – 55.1
5.1 – 54.8
50
3.7 – 59.9
6
3.1 – 55.0
60
Scan speed / sec frame−1 16
Measured reflections
Unique reflections
4313
2934
4636
3104
6364
4529
2856
2831
Obs. reflections (I ≥ 2σ)2215
1479
210
0.42/−0.27
2906
292
0.35/−0.33
2359
224
0.18/−0.21
Parameters refined
Max. of residual
196
0.37/−0.36
−3
˚
electron density [e A
Agreement factorsa,b
(F2 refinement)
]
R1 = 8.2%
R1 = 8.2%
Rw = 21.3%
R1 = 8.1%
Rw = 24.4%
R1 = 5.2%
Rw = 13.7%
Rw = 27.4%
into the correct conformation according to DFT calcu- Computational method
lations (B3LYP, 3-21G∗ basis set) of (1)2 in a single-
Density functional calculations were carried out with the
Gaussian03/DFT [13] series of programs. The B3LYP for-
mulation of density functional theory was used employing
the 6-31G+(d,p) and 3-21G∗ basis sets, respectively [13].
Harmonic vibrational frequencies and infrared intensities
were calculated by numerical second derivatives using an-
alytically calculated first derivatives.
bonded arrangement and (1)2 in the experimentally
determined and DFT optimised double-bonded ring
structure (Fig. 3).
Thus suitably substituted (substituted phenyl)dipyr-
romethanes are useful synthons for the construction of
hydrogen-bonded supramolecular systems – in spite of
˚
the facts that donor and acceptor sites are 7 A apart and
that their relative orientation is quite flexible.
Crystallographic structure determinations
The measurements were carried out on an Enraf-Nonius
Kappa CCD diffractometer using graphite monochromated
Mo-Kα radiation. The data were processed using the stan-
dard Nonius software [14]. All calculations were performed
using the SHELXT PLUS software package. Structures were
solved using direct or Patterson methods with the SHELXS-
97 program and refined with the SHELXL-97 program [15].
Graphical handling of the structural data during refinement
was performed using XMPA [16] and WinRay [17]. Atomic
coordinates and anisotropic thermal parameters of the non-
hydrogen atoms were refined by full-matrix least-squares
calculations.
Experimental Section
Unless noted otherwise, all manipulations were carried
out under argon by means of standard Schlenk techniques.
All solvents were dried by standard methods and distilled
under argon prior to use. All other reagents were used as re-
ceived from commercial sources.
NMR: Bruker Avance DPX 200 at 200.15 MHz (1H),
50.323 MHz (13C) at 303 K; chemical shifts (δ) in ppm with
respect to residual solvent peaks as internal standards: CDCl3
(1H: δ = 7.24; 13C: δ = 77.0); CD2Cl2 (1H: δ = 5.32; 13C:
δ = 53.5); [D6]-acetone (1H: δ = 2.04; 13C: δ = 29.8). –
IR spectra were recorded on a BioRad Excalibur FTS 3000
Crystallographic data for the structures have been de-
spectrometer using CsI disks. – Mass spectra were recorded posited with Cambridge Crystallographic Data Centre,
on a Finnigan MAT 8400 spectrometer. – Elemental analy- CCDC-258022 – CCDC-258025. Copies of the data can
ses were performed by the microanalytical laboratory of the be obtained free of charge on application to the Direc-
Organic Chemistry Department, University of Heidelberg.
tor, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK
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K. Heinze – A. Reinhart · A New Hydrogen-Bonding Motif with Constituents
Table 3. Analytical data of 1, 2, 3 and 4 (atom numbering according to Scheme 1).
761
1
164
2
164
3
110
4
62
M. p. [◦C]
IR (CsI) [cm−1
]
3350 (NH, s),
1700 (C=O, s)
3550 (NH, OH, s),
3350 (NH, OH, s),
1680 (C=O, s)
b
3346 (NH, s),
3226 (NH, s),
1650 (C=O, s)
c
3400 – 3310 (NH, s),
3200 (NH, m),
1250 (CN, s)
b
1H NMR
H1
a
8.15 (br.s)
8.00 (br.s)
9.74 (br.s)
7.95 (br.s)
6.68 – 6.75 (m)
6.19 (dd, J = 3.1; 2.7 Hz)
5.90 – 6.00 (m)
5.41 (s)
7.04 (d, J = 8.3 Hz)
6.68 (d, J = 8.3 Hz)
H2
6.77 (dd, J = 2.7; 1.6 Hz) 6.76 (dd, J = 2.7; 1.4 Hz) 7.71 (dd, J = 2.7; 1.6 Hz)
6.17 (dd, J = 2.7; 2.7 Hz) 6.22 (dd, J = 3.1; 2.7 Hz) 6.02 (dd, J = 2.7; 2.7 Hz)
5.90 – 5.95 (m)
5.59 (s)
7.35 (d, J = 8.2 Hz)
8.02 (d, J = 8.2 Hz)
H3
H4
5.90 – 6.00 (m)
5.59 (s)
7.37 (d, J = 8.3 Hz)
8.10 (d, J = 8.3 Hz)
–
5.74 – 5.82 (m)
5.53 (s)
7.28 (d, J = 8.0 Hz)
7.80 (d, J = 8.0 Hz)
1.25 (d, J = 6.7 Hz, CH3); 3.7 (br.s, NH2)
4.15 – 4.35 (m, CH);
H6
H8
H9
other hydrogen atoms 3.94 (s, CH3)
7.42 (br.s., NH)
1
a
b
c
b
13C{ H} NMR
C2
117.9
108.9
107.7
148.7
44.4
131.8
128.8
130.2
118.0
109.1
108.0
148.8
44.5
131.9
128.4
131.0
117.7
107.9
107.1
147.1
44.3
134.0
128.8
127.4
115.8
108.8
107.4
133.6
43.8
132.5
129.8
120.0
145.0
–
C3
C4
C5
C6
C7
C8
C9
C10
129.0
52.4 (CH3);
167.0 (CO2Me)
129.0
171.7 (CO2H)
133.2
other carbon atoms
22.4 (CH3);
42.0 (CH);
166.1 (CON)
MS (EI, 70 eV):
m/z (%)
280 (100) [M+], 214 (50) 266 (100) [M+], 200 (34) 307 (100) [M+], 241 (46)
237 (100) [M+], 170 (35)
[M+-pyrrole], 145 (32)
[M+-C6H6N]
[M+-pyrrole], 145 (72)
[M+-C8H7O2]
[M+-pyrrole], 145 (52)
[M+-C7H5O2]
[M+-pyrrole], 145 (97)
[M+-C11H13NO]
HR-MS (EI) calcd.
found
280.1212
280.1194
266.1055
266.1035
307.1785
307.1662
237.1266
237.1247
a
In CD2Cl2; b in CDCl3; c in [D6]-acetone.
(Fax: int.code+(1223)336-033; e-mail for inquiry: fileserv@ calcd. C 67.59, H 5.67, N 9.85; found C 67.87, H 5.66,
ccdc.cam.ac.uk).
N 9.95.
Synthesis of 3
Synthesis of 1, 2 and 4
The acid 2 was activated with 1-hydroxybenzotriazole
(1 eq) in the presence of 1,3-dicyclohexylcarbodiimide (1 eq)
for 12 h and treated with 1.1 equivalents of isopropylamine
in CH2Cl2 for 12 h at room temperature. After removal of
the solvent and recrystallisation from ethanol/water (10:1) 3
was obtained in 90% yield.
Following the general procedure of Lindsey et al. [5] a
mixture of pyrrole, the corresponding aldehyde and trifluo-
roacetic acid (50:1:0.004) was stirred at room temperature
for 10 min. 0.1 M NaOH and ethyl acetate were added,
and the layers were separated. The aqueous layer was acid-
ified with diluted HCl and extracted again with ethyl ac-
etate. The combined organic layers were washed with brine,
dried over Na2SO4 and concentrated to remove the ex-
cess pyrrole. Column chromatography [silica, CH2Cl2/ethyl
acetate (3:1)], washing with water and recrystallisation
Analytical data of 1 – 4 are summarised in Table 3.
Acknowledgements
This work was supported by the Deutsche Forschungsge-
from ethanol/water (10:1) afforded the pure dipyrromethanes meinschaft and the Fonds der Chemischen Industrie. The per-
in 95% (1), 75% (2•H2O) and 50% (4) yield, respec- manent, generous support from Prof. Dr. G. Huttner is grate-
tively. The presence of one water molecule in 2•H2O fully acknowledged. We thank Simone Leingang for prepar-
was confirmed by elemental analysis for C16H16N2O3: ative assistance.
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762
K. Heinze – A. Reinhart · A New Hydrogen-Bonding Motif with Constituents
[1] P. D. Rao, S. Dhanalekshmi, B. J. Littler, J. S. Lindsey,
gar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi,
G. Scalmani, N. Rega, G. A. Petersson, H. Nakat-
suji, M. Hada, M. Ehara, K. Toyota, R. Fukuda,
J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda,
O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox,
H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo,
R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin,
R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala,
K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannen-
berg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels,
M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck,
K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui,
A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Ste-
fanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi,
R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y.
Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,
B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and
J. A. Pople, Gaussian, Inc., Pittsburgh PA (2003).
[14] R. Hooft, Collect, Data Collection Software, Nonius,
The Netherlands (1998); http://www.nonius.com.
[15] G. M. Sheldrick, SHELXS-97, Program for Crys-
tal Structure Solution, University of Go¨ttingen, Ger-
many (1997); http://www.shelx.uni-ac.gwdg.de/shelx/
index.html; G. M. Sheldrick, SHELXL-97, Program
for Crystal Structure Refinement, University of
Go¨ttingen, Germany (1997); http://www.shelx.uni-ac.
gwdg.de/shelx/index.html; International Tables for X-
ray Crystallography, Vol. 4, Kynoch Press, Birming-
ham (1974).
J. Org. Chem. 65, 7323 (2000).
[2] S. R. Halper, M. R. Malachowski, H. M. Delaney, S. M.
Cohen, Inorg. Chem. 43, 1242 (2004).
[3] S. R. Halper, S. M. Cohen, Chem. Eur. J. 9, 4661
(2003).
[4] G. R. Desiraju, Angew. Chem. 107, 2541 (1995);
Angew. Chem. Int. Ed. Engl. 34, 2311 (1995).
[5] B. J. Littler, M. A. Miller, C.-H. Hung, R. W. Wagner,
D. F. O’Shea, P. D. Boyle, J. S. Lindsey, J. Org. Chem.
64, 1391 (1999).
[6] V. Bennis, J. F. Gallagher, Acta Crystallogr. C54, 130
(1998).
[7] G. K. Patra, Y. Diskin-Posner, I. Goldberg, Acta Crys-
tallogr. E58, o530 (2002).
[8] J. F. Gallagher, E. Moriarty, Acta Crystallogr. C55,
1079 (1999). [9]
[9] In the lattice of 2•H2O the water molecule con-
nects the dimers along the crystallographic a-axis to
form columns of dimers through O2-H···OW and OW-
H···O1’ ·h··ydrogen bonds with O2-OW = 2.583(4) A
˚
˚
and OW O1 = 2.774(5) A.
[10] T. Steiner, Angew. Chem. 114, 50 (2002); Angew.
Chem. Int. Ed. 41, 48 (2002).
[11] F. H. Allen, W. D. S. Motherwell, P. R. Raithby, G. P.
Shieldsa, R. Taylor, New. J. Chem. 25 (1999).
[12] Rxy(n): The superscript x denotes the number of hydro-
gen acceptors, the subscript y the number of hydrogen
donors and n the ring size. C(n) denotes a chain with
n atoms in the repeating unit. J. Bernstein, R. E. Davis,
L. Shimoni and N.-L. Chang, Angew. Chem. 107, 1689
(1995); Angew. Chem. Int. Ed. Engl. 34, 1555 (1995).
[13] Gaussian 03, Revision B.03, M. J. Frisch, G. W.
Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb,
J. R. Cheeseman, J. A. Montgomery, (Jr.), T. Vreven,
K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyen-
[16] L. Zsolnai and G. Huttner, XPMA, University of
Heidelberg, Germany (1998); http://www.rzuser.uni-
heidelberg.de/∼il1/laszlo/xpm.html.
[17] R. Soltek and G. Huttner, WinRay, University
of Heidelberg, Germany (1999); http://www.uni-
heidelberg.de/institute/fak12/AC/huttner/frame/frame
soft.html.
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