Crystal structures of some N-substituted 2,5-dimethylpyrrole derivatives

Article abstract of DOI:10.1515/znb-2010-0511

The crystal and molecular structures of five di-(2,5-dimethylpyrrole) and one tri-(2,5-dimethylpyrrole) derivatives have been determined. These compounds were synthesized from the respective diamino derivatives and hexane-2,5-dione in direct and simple reactions. The molecular packings are largely based on C-H?π interactions.

Full text of DOI:10.1515/znb-2010-0511

Crystal Structures of Some N-substituted 2,5-Dimethylpyrrole Derivatives
Peter G. Jonesa, Piotr Kus´b, Mariusz Łannikb, and Violetta Kozikb
a Institut fu¨r Anorganische und Analytische Chemie, Technische Universita¨t Braunschweig,
Postfach 3329, 38023 Braunschweig, Germany
b Department of Chemistry, University of Silesia, 9, Szkolna Street, 40-006 Katowice, Poland
Reprint requests to P. Kus´. E-mail: pkus@ich.us.edu.pl
Z. Naturforsch. 2010, 65b, 611 – 616; received January 4, 2010
The crystal and molecular structures of five di-(2,5-dimethylpyrrole) and one tri-(2,5-dimethyl-
pyrrole) derivatives have been determined. These compounds were synthesized from the respective
diamino derivatives and hexane-2,5-dione in direct and simple reactions. The molecular packings are
largely based on C–H···π interactions.
Key words: N-Pyrrole Derivatives, 2,5-Dimethylpyrrole, Solid-state Structure
Introduction
Hexane-2,5-dione has been found as a urinary
metabolite of n-hexane. It was identified as a 2,5-di-
methylpyrrole derivative obtained from the reaction
of a urine sample hydrolyzed with hydrochloric acid
and then neutralized [1]. Bis-(2,5-dimethylpyrrol-1-yl)
compounds were synthesized from hexane-2,5-dione
and amines in ethanol or benzene solutions [2] and
examined by electron spin resonance spectroscopy in
fluid solutions [3].
Fig. 1a. The molecule of compound 1 in the crystal. Only the
asymmetric unit is numbered. Displacement ellipsoids corre-
˚
spond to 50 % probability levels. Selected bond lengths (A)
and angles (deg): N1–C2 1.382(1), N1–C5 1.385(1), N1–C6
1.454(1); C2–N1–C5 109.85(6), C2–N1–C6 124.91(6), C5–
N1–C6 125.24(6).
Fig. 1b. Packing diagram of compound 1 showing the
HMe···π interactions (thick dashed lines) in the region z ≈ 1.
tion procedures (details in Experimental Section)
yielded crystals suitable for X-ray diffraction analysis.
In our experiments to synthesize bis-(2,5-dimeth-
ylpyrrol-1-yl) compounds we used a procedure with-
out solvents as described in [4]. In the Paal-Knorr
synthesis, hexane-2,5-dione is cyclocondensed with
α,ω-diaminoalkanes producing N-substituted 2,5-
Results
The surprising aspect of the synthetic work is
dimethylpyrroles. Simple separation and crystalliza- compound 6, which was obtained from triethylenete-
c
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P. G. Jones et al. · Crystal Structures of N-substituted 2,5-Dimethylpyrrole Derivatives
Fig. 2a. The two independent molecules of compound 2
in the crystal. Displacement ellipsoids correspond to 50 %
˚
probability levels. Selected bond lengths (A), angles and
torsion angles (deg) (values for both molecules are given):
N1–C2 1.384, 1.382(1), N1–C5 1.387, 1.386(1), N1–C14
1.459, 1.460(1), N2–N8 1.381, 1.382(1), N2–C11 1.383,
1.383(1), N2–C16 1.455, 1.460(1); C2–N1–C5 109.41(8),
109.48(7), C2–N1–C14 125.31(8), 124.41(8), C5–N1–C14
125.00(8), 126.04(8), C8–N2–C11 109.72(7), 109.66(8),
C8–N2–C16 124.59(8), 125.19(8), C11–N2–C16 125.67(8),
125.15(8); N1–C14–C15–C16 175.3(1), 60.8(1), C14–C15–
C16–N2 162.8(1), 178.1(1).
Fig. 2b. Packing diagram of compound 2 showing the
HMe···π interactions (thick dashed lines). View direction
¯
perpendicular to (10 2). Left: pairs of molecule 1; right: pairs
of molecule 2; center: connection between molecule 1 and 2.
The molecular structures of compounds 1 – 6 are
presented in Figs. 1a – 6, with corresponding pack-
ing diagrams (excluding 6, see below) in Figs.
1b – 5b. Compounds 1 and 3 crystallize with im-
posed inversion symmetry, as did the related com-
pound 2,2ꢀ,5,5ꢀ-tetramethyl-1,1ꢀ-(hexane-1,6-diyl)-di-
1H-pyrrole [5], which has a (CH2)6 bridge between
the dimethylpyrrole units; the other compounds dis-
play no crystallographic symmetry. The central bridg-
ing chains show an extended conformation, and the
rings are perpendicular to the bridges (interplanar an-
gles 85◦ and 89◦, respectively). Of the two independent
molecules of compound 2, one molecule (unprimed
atoms) has approximate twofold symmetry (r. m. s. de-
tramine [2,2ꢀ-ethylene-di-imino-bis(ethylamine)]. The
1H NMR and 13C NMR spectra for 6 are simple. The
1H NMR spectrum shows the pyrrole 3- and 4-protons
at 5.78 ppm, two singlets for the two CH2 group pro-
tons at 3.75 and 2.76 ppm, and a singlet at 2.26 ppm
for the CH3 protons. The 13C NMR spectrum displays
signals for two pyrrole carbons at 127.3 and 105.7 ppm
and only three signals for aliphatic carbons at 55.9,
42.5 and 12.7 ppm. The mass spectrum shows a peak
at m/z = 381 [M+H]+. The above results confirmed
that the expected compound 7 had not formed, and that
the product is symmetrical. Single crystals of the com-
pound were grown from methanol solution, and the
crystal structure analysis of compound 6 confirmed the
proposed structure.
˚
viation 0.27 A) with antiperiplanar (ap) conformations
about the bridge bonds, whereas the other has an ap
geometry about C15ꢀ–C16ꢀ but +sc about C14ꢀ–C15ꢀ.
Compound 4 has twofold symmetry to a good approxi-
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P. G. Jones et al. · Crystal Structures of N-substituted 2,5-Dimethylpyrrole Derivatives
613
Fig. 3a. The molecule of compound 3 in the crystal. Only the
asymmetric unit is numbered. Displacement ellipsoids cor-
respond to 50 % probability levels. Selected bond lengths
˚
(A), angles and torsion angles (deg): N1–C2 1.382(1),
N1–C5 1.382(1), N1–C6 1.461(1); C2–N1–C5 109.34(7),
C2–N1–C6 125.38(7), C5–N1–C6 125.26(7); N1–C6–C7–
C7#1 177.5(1).
Fig. 4b. Packing diagram of compound 4 (layer structure)
1
3
showing the H···π interactions in the region x ≈ /4, z ≈ /4.
¯
View direction perpendicular to (1 02). The slightly longer
Hbridge···π interactions are shown as thin, other H···π in-
teractions as thick dashed lines. Note the pairs of HMe···π
interactions around inversion centers (same horizontal level
as the axis labels O, b, c).
Fig. 3b. Packing diagram of compound 3 showing the
HMe···π interactions (thick dashed lines) in the region
1
y ≈ /2.
Fig. 5a. The molecule of compound 5 in the crystal. Dis-
placement ellipsoids correspond to 30 % probability lev-
˚
els. Selected bond lengths (A), angles and torsion an-
gles (deg): N1–C2 1.388(2), N1–C5 1.380(2), N1–C8
1.462(2), N2–C9 1.463(2), N2–C10 1.461(2), N3–C11
1.458(2), N3–C12 1.379(2), N3–C15 1.386(2); C2–N1–C5
109.3(1), C2–N1–C8 124.4(2), C5–N1–C8 126.2(1), C9–
N2–C10 112.5(1), C12–N3–C15 109.8(1), C11–N3–C12
124.7(1), C11–N3–C15 125.4(1); N1–C8–C9–N2 −66.9(2),
C8–C9–N2–C10 169.9(1), C9–N2–C10–C11 82.7(2), N2–
C10–C11–N3 −172.2(1).
Fig. 4a. The molecule of compound 4 in the crystal. Dis-
placement ellipsoids correspond to 50 % probability lev-
˚
els. Selected bond lengths (A), angles and torsion angles
(deg): N1–C2 1.377(1), N1–C5 1.378(1), N1–C14 1.453(1),
N2–C8 1.377(1), N2–C11 1.379(1), N2–C18 1.456(1);
C2–N1–C5 109.5(1), C2–N1–C14 124.7(1), C5–N1–C14
125.7(1), C8–N2–C11 109.7(1), C8–N2–C18 126.0(1),
C11–N2–C18 124.3(1); N1–C14–C15–C16 177.5(1), C14–
C15–C16–C17 68.3(1), C15–C16–C17–C18 65.8(1), C16–
C17–C18–N2 171.5(1).
has a conformationally asymmetric bridge, with ap
geometry about C9–N2 and C10–C11 but −ac, +sc
geometries about C8–C9 and N2–C10, respectively.
Compound 6 has formal threefold symmetry accord-
ing to the chemical formula, but the (CH2)2 bridges
show different conformations; ap about C11–C12 and
C21–22 and −ac about C1–C2. Bond lengths and an-
gles may be regarded as normal. Selected molecular
dimensions are given explicitly in the Figure captions.
˚
mation (r. m. s. deviation 0.09 A); in the central bridge,
the conformation is ap about C14–C15 and C17–C18
but +sc about C15–C16 and C16–C17. Compound 5
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P. G. Jones et al. · Crystal Structures of N-substituted 2,5-Dimethylpyrrole Derivatives
Table 1. Details of X–H···π interactions (X = C, N)a.
˚
˚
Compound
Interaction X–H···π
X–H (A)
1.08
1.08
H···π (A)
X–H···π (deg)
Symmetry operator
1
1
C8–H8B··· Cg
2.74
2.69
129
153
− /2 +x, 11/2 −y, −z
1
C8–H8C··· Cg
C13–H13B··· Cg2
C7ꢀ–H7ꢀ3···Cg1ꢀ
C7–H7B··· Cg2ꢀ
/2 +x, 11/2 −y, −z
2
1.08
1.08
1.08
2.76
2.75
2.61
137
150
152
2−x, 1−y, 1−z
−x, 1−y, −z
x, 1+y, z
3
4
C8–H8A··· Cg
C6–H6C··· Cg1
C10–H10··· Cg2
C15–H15B··· Cg2
C6–H6C··· Cg1
C14–H14··· Cg1
C10–H10B··· Cg3
N2–H2···Cg3
C8–H8A··· Cg3
C22–H22B··· Cg3
C7–H7A··· Cg4
C12–H12A··· Cg4
1.08
2.57
145
1−x, 1−y, −z
1.08
1.08
1.08
2.58
2.72
2.89
149
147
142
−x, −y, 1−z
1−x, 1/2 +y, 11/2 −z
x, −1+y, z
5
1.08
1.08
1.08
0.92
2.79
2.45
2.85
3.12
146
157
116
127
1−x, 1−y, 2−z
1−x, 1−y, 1−z
1−x, 1−y, 1−z
1−x, 1−y, 1−z
1
6
1.08
1.08
1.08
1.08
2.72
2.70
2.74
2.88
127
108
155
122
−x, − /2 +y, 1/2 −z
x, 11/2 −y, 1/2 +z
1−x, 1−y, 1−z
1
x, 11/2 −y, − /2 +z
a
Cg = center of gravity; Cgn refers to the ring with nitrogen Nn.
Fig. 5b. Packing diagram of compound 5 showing the H···π interactions (dashed lines) in one chain of dimers parallel to the
z axis. One complete dimer is shown in the center of the Figure. The bifurcated interactions (see text) are indicated by open
dashed bonds. View direction approximately parallel to the y axis.
Fig. 6. The molecule of compound 6 in the crystal. Displacement el-
lipsoids correspond to 50 % probability levels. Selected bond lengths
˚
(A), angles and torsion angles (deg): N1–C11 1.457(1), N1–C21
1.458(1), N1–C1 1.463(1), N2–C6 1.384(1), N2–C3 1.384(1), N2–C2
1.457(1), N3–C13 1.381(1), N3–C16 1.384(1), N3–C12 1.459(1),
N4–C23 1.382(1), N4–C26 1.382(1), N4–C22 1.456(1); C11–N1–
C21 115.6(3), C11–N1–C1 115.4(1), C21–N1–C1 113.8(1), C6–N2–
C3 109.3(1), C6–N2–C2 125.2(1), C3–N2–C2 125.5(1), C13–N3–C16
109.5(1), C13–N3–C12 125.2(1), C16–N3–C12 125.2(1), C23–N4–
C26 109.8(1), C23–N4–C22 124.9(1), C26–N4–C22 125.3(1); N1–
C1–C2–N2 −55.1(1), N1–C11–C12–N3 178.6(1), N1–C21–C22–N4
169.4(1).
¯
The molecular packing may, at least for compounds group (C8). Compound 2 forms layers parallel to (102)
1 – 5, be analyzed in terms of C–H···π interactions, via three HMe···π interactions; two of these link pairs
leading to simple structural motifs. Details of these of molecules around inversion centers, whereas the
˚
are given in Table 1 (C–H normalized to 1.08 A). Per- third links the two independent molecules by transla-
haps surprisingly, there are no C–H···N or (for 5) N– tion. For 3, the packing is even simpler; one HMe···π
H···N interactions. Compound 1 forms thick layers of interaction links the molecules pairwise across inver-
molecules parallel to the xy plane at z ≈ 0, 1, etc., via sion centers to form chains parallel to the z axis. Com-
¯
two HMe···π interactions involving the same methyl pound 4 forms a layer structure parallel to (1 02) via
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P. G. Jones et al. · Crystal Structures of N-substituted 2,5-Dimethylpyrrole Derivatives
Table 2. Crystallographic data for compounds 1 – 6.
615
1
2
3
4
5
6
Formula
Mr
Temperature, K
Crystal size, mm3
Crystal habit
C14H20N2
244.37
100(2)
C15H22N2
230.35
100(2)
C16H24N2
216.32
103(2)
C17H26N2
258.40
100(2)
C16H25N3
259.39
103(2)
C24H36N4
380.57
100(2)
0.35×0.35×0.20 0.40×0.40×0.15 0.25×0.20×0.20
0.40×0.15×0.10 0.25×0.15×0.04 0.12×0.10×0.08
colorless tablet
pale amber tablet colorless, irregular colorless prism
colorless tablet
colorless block
CuKα , 1.54184
monoclinic
P21/c
15.3186(3)
11.2875(2)
13.7255(3)
90
113.464(3)
90
2177.01(7)
4
˚
Radiation; λ, A
MoKα , 0.71073 MoKα , 0.71073 MoKα , 0.71073
orthorhombic
Pbca
7.1105(3)
11.1252(4)
15.5341(5)
90
90
90
MoKα , 0.71073 CuKα , 1.54184
monoclinic
P21/c
16.716(3)
6.3370(8)
14.687(2)
90
95.691(14)
90
Crystal system
Space group
triclinic
P1
monoclinic
P21/n
7.5885(3)
10.6339(4)
8.9323(3)
90
95.547(4)
90
717.42(6)
2
monoclinic
P21/n
14.6518(6)
7.5930(4)
14.9042(8)
90
114.941(6)
90
1503.47(13)
4
¯
˚
a, A
8.9056(3)
11.2538(3)
14.1242(5)
76.970(3)
87.353(3)
80.910(3)
1361.70(8)
4
˚
b, A
˚
c, A
α, deg
β, deg
γ, deg
3
˚
Volume, A
1228.84(8)
4
1.17
1548.1(4)
4
1.11
Z
Dcalc., g cm−3
F(000), e
1.12
504
1.13
268
1.15
568
1.16
832
472
568
2 θmax, deg
Refl. coll. / indep.
Rint
60
60
60
57.4
14990 / 3932
0.047
98.1
176
0.040
0.078
0.81
0.16 / −0.17
142
141
24661 / 1774
0.024
98.6
75
0.036
69679 / 7856
0.034
98.6
27585 / 2099
0.031
100.0
84
0.037
0.105
1.09
0.30 / −0.21
12802 / 2759
0.033
35946 / 4095
0.019
Completeness, %
Ref. parameters
R1 [I ≥ 2 σ(I)]
wR2 (all refl.)
97.8 to 135◦
180
99.7 to 135◦
259
315
0.0387
0.0998
0.93
0.28 / −0.22
0.045
0.115
1.08
0.17 / −0.18
0.034
0.086
1.03
0.22 / −0.26
0.113
Goodness-of-fit on F2 1.11
−3
˚
∆ρ (max / min), e A
0.36 / −0.24
three H···π interactions involving one methyl, one cal shifts are reported in ppm downfield from TMS. ESI mass
spectra were recorded on a Varian MS 500 instrument using
a flow injection system.
pyrrole and one bridge hydrogen atom. The central
feature of compound 5 is the formation of inversion-
symmetric dimers. An initial inspection showed only
an Hpyrrole···π interaction linking both molecules of
the dimer, but a closer analysis has revealed a bifur-
cated interaction from the central NH and one bridge
H to the centroid of the opposite molecule; the individ-
ual interactions are necessarily longer and have nar-
rower angles than single H···π contacts. The dimers
are linked by HMe···π interactions across further in-
version centers leading to chains of molecules parallel
to the z axis. Neighboring chains lie in planes paral-
General procedure for the synthesis of 2,5-dimethylpyrrole
derivatives 1 – 6
The amine (0.1 mole) and hexane-2,5-dione (0.2 mole)
were heated under reflux for 1 – 2 h. The reaction mix-
ture was then cooled to room temperature and poured into
a cooled mixture of water (50 mL) and concentrated hy-
drochloric acid (5 mL). The precipitate was collected by
suction filtration, washed with cold water, and recrystal-
lized from methanol. The products were obtained as color-
less crystals but darkened to pale yellowish-brown after a
few days in air. Colorless single crystals of 1 and 4 – 6 from
methanol, 2 and 3 from ethanol solutions were obtained by
slow evaporation.
1
lel to the yz plane at x ≈ /2. For compound 6, four
interactions may be tentatively identified, but three
have narrow angles. The combined packing is three-
dimensional and less clearly defined than that of the
other structures.
2,2ꢀ,5,5ꢀ-Tetramethyl-1,1ꢀ-ethylene-di-1H-pyrrole (1):
M. p. 144 – 146 ◦C. – 1H NMR (CDCl3): δ = 5.77 (bs, 4H),
4.00 (s, 4H), 2.03 (s, 12H). – 13C NMR (CDCl3): δ = 127.7,
105.9, 44.0, 12.0. – MS ((+)-ESI): m/z = 217 [M+H]+.
2,2ꢀ,5,5ꢀ-Tetramethyl-1,1ꢀ-(propane-1,3-diyl)di-1H-pyr-
Experimental Section
Commercial samples of amines were used without fur- role (2): M. p. 80 – 81 ◦C. – 1H NMR (CDCl3): δ = 5.79 (s,
ther purification. The purity of the amines was monitored by 4H), 3.77 (t, 4H), 2.19 (s, 12H), 1.96 (q, 2H). – 13C NMR
1H and 13C NMR spectroscopy. NMR spectra were obtained (CDCl3): δ = 127.2, 105.6, 40.7, 32.2, 12.4. – MS ((+)-ESI):
with a 400 MHz Bruker spectrometer in CDCl3, and chemi- m/z = 461 [2M+H]+.
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P. G. Jones et al. · Crystal Structures of N-substituted 2,5-Dimethylpyrrole Derivatives
2,2ꢀ,5,5ꢀ-Tetramethyl-1,1ꢀ-(butane-1,4-diyl)di-1H-pyrrole
X-Ray structure determinations
◦
(3): M. p. 160 – 162 C. – 1H NMR (CDCl3): δ = 5.77 (s,
4H), 3.73 (t, 4H), 2.21 (s, 12H), 1.66 (q, 4H). – 13C NMR
(CDCl3): δ = 127.3, 105.3, 43.3, 28.4, 12.6. – MS ((+)-ESI):
m/z = 489 [2M+H]+.
Numerical details are presented in Table 2. Crystals were
mounted in inert oil and transferred to the cold gas stream
of the diffractometer (various Oxford Diffraction area de-
tectors). Absorption corrections were performed for CuKα
data only, using the multi-scan method. Structures were re-
fined anisotropically on F2 using the program SHELXL-97
[6]. Hydrogen atoms of NH groups (compound 4) were re-
fined freely; other hydrogens were included using a riding
model or idealized rigid methyl groups. All methyl hydro-
gens were clearly visible in difference syntheses, an impor-
tant precondition for the discussion of weak hydrogen bonds
involving these atoms.
CCDC 759296 (1), 766996 (2), 759297 (3), 759298 (4),
759299 (5), 759300 (6) contain the supplementary crystal-
lographic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Center via www.ccdc.cam.ac.uk/data request/cif.
2,2ꢀ,5,5ꢀ-Tetramethyl-1,1ꢀ-(pentane-1,5-diyl)di-1H-pyr-
◦
role (4): M. p. 60 – 62 C. – 1H NMR (CDCl3): δ = 5.80
(s, 4H), 3.75 (t, 4H), 2.24 (s, 12H), 1.68 (q, 4H), 1.43 (q,
2H). – 13C NMR (CDCl3): δ = 127.4, 105.2, 43.5, 30.9, 24.5,
12.6. – MS ((+)-ESI): m/z = 259 [M+H]+.
2,2ꢀ,5,5ꢀ-Tetramethyl-1,1ꢀ-(3-aza-pentane-1,5-diyl)di-
1H-pyrrole (5): M. p. 84 – 85 ◦C. – 1H NMR (CDCl3):
δ = 5.79 (s, 4H), 3.87 (t, 4H), 2.81 (t, 4H), 2.26 (s,
12H). – 13C NMR (CDCl3): δ = 127.7, 105.5, 50.1,
43.9, 12.7. – MS ((+)-ESI): m/z = 260 [M+H]+, 519
[2M+H]+.
Tris{2[1-(2,5-dimethyl-1H-pyrrolyl)]ethyl}amine (6): M. p.
◦
114 – 116 C. – 1H NMR (CDCl3): δ = 5.78 (s, 6H), 3.75
(bs, 6H), 2.76 (bs, 6H), 2.24 (s, 18H). – 13C NMR (CDCl3):
δ = 127.3, 105.7, 55.9, 42.5, 12.7. – MS ((+)-ESI): m/z = 381
[M+H]+.
[5] A. C. Santos, M. Ramos Silva, P. V. Monsanto,
A. Matos Beja, A. J. F. N. Sobral, Acta Crystallogr.
2009, E65, o1594.
[6] G. M. Sheldrick, SHELXL-97, Program for the Refine-
ment of Crystal Structures, University of Go¨ttingen,
Go¨ttingen (Germany) 1997. See also: G. M. Sheldrick,
Acta Crystallogr. 2008, A64, 112 – 122.
[1] O. Masana, I. Tomoko, T. Toyohiro, Int. Arch. Occup.
Environ. Health, 1991, 62, 561 – 568.
[2] W. S. Bishop, J. Am. Chem. Soc. 1945, 67, 2261 – 2262.
[3] D. V. Avila, A. G. Davies, J. Chem. Soc. Perkin Trans. 2
1991, 1111 – 1118.
[4] L. F. Tietze, T. Eicher, U. Diederichsen, A. Speicher, in:
Reactions and Syntheses in the Organic Chemistry Lab-
oratory, Wiley-VCH, Weinheim, 2007, p. 392.
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