Mohammed A E Shaibah1, Hemmige S Yathirajan1, S Madan Kumar2, Kullaiah Byrappa3, Christopher Glidewell4. 1. Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysuru 570 006, India. 2. Department of Studies in Chemistry, Mangalore University, Mangalagangotri 574 199, India. 3. Materials Science Center, NCHS Building, University of Mysore, Manasagangotri, Mysuru 570 006, India. 4. School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, UK.
Abstract
The N,N-di-methyl-ethylamminium unit in N,N-dimethyl-[2-(2,2-diphen-yl)-2-prop-2-ynyloxyacet-oxy]ethyl-amine, C21H23NO3 (I), is disordered over two sets of atomic sites having occupancies of 0.880 (3) and 0. 120 (3), but there are no direction-specific inter-actions between the mol-ecules of (I). The cation in N,N-dimethyl-[2-(2,2-diphen-yl)-2-prop-2-ynyloxyacet-oxy]ethyl-ammonium 2,4,6-tri-nitro-phenolate (picrate), C21H24NO3+·C6H2N3O7- (II), shows a similar type of disorder, with occupancies of 0.654 (11) and 0.346 (11), although the overall conformation of the cation in (II) is different from that in the neutral (I). The component ions are are linked by an almost planar three-centre N-H⋯(O)2 hydrogen bond, and the ion pairs are further linked by a combination of three C-H⋯O hydrogen bonds to form sheets. Comparisons are made with some related structures.
The N,N-di-methyl-ethylamminium unit in N,N-dimethyl-[2-(2,2-diphen-yl)-2-prop-2-ynyloxyacet-oxy]ethyl-amine, C21H23NO3 (I), is disordered over two sets of atomic sites having occupancies of 0.880 (3) and 0. 120 (3), but there are no direction-specific inter-actions between the mol-ecules of (I). The cation in N,N-dimethyl-[2-(2,2-diphen-yl)-2-prop-2-ynyloxyacet-oxy]ethyl-ammonium 2,4,6-tri-nitro-phenolate (picrate), C21H24NO3+·C6H2N3O7- (II), shows a similar type of disorder, with occupancies of 0.654 (11) and 0.346 (11), although the overall conformation of the cation in (II) is different from that in the neutral (I). The component ions are are linked by an almost planar three-centre N-H⋯(O)2 hydrogen bond, and the ion pairs are further linked by a combination of three C-H⋯O hydrogen bonds to form sheets. Comparisons are made with some related structures.
N,N-dimethyl-[2-(2,2-diphenyl)-2-prop-2-ynyloxyacetoxy]ethylamine (pargeverine) is an established anti-spasmodic drug (Mishra et al., 2010 ▸). Although crystal structures have been reported (Bindya et al., 2007 ▸; Harrison, Bindya et al., 2007 ▸; Harrison, Sreevidya et al., 2007 ▸; Swamy et al., 2007 ▸; Yathirajan et al., 2007 ▸; Jasinski et al., 2009 ▸) for a number of related compounds that exhibit a range of pharmacological activities (e.g. Matsushima et al., 1997 ▸), the structure of pargeverine itself has not yet been reported. Here we report the structure of the neutral compound (I) and its 2,4,6-trinitrophenolate (picrate) salt (II).
Structural commentary
In the neutral compound (I) (Fig. 1 ▸) the methylaminoethyl fragment is disordered over two sets of atomic sites with occupancies of 0.880 (3) for the major disorder component comprising the atomic sites C2,C1,N1,C111 and C112, and 0.120 (3) for the minor component, comprising the atomic sites C22,C21,N21,C211 and C212. The atomic sites in the two disorder components exhibit an approximately mirror-image relationship, as shown by the corresponding pairs of torsional angles, thus: O11—C2—C1—N1 = 59.5 (5)° and O11—C22—C21—N21 = −57 (3)°, C2—C1—N1—C111 = 68.9 (4)° and C22—C21—N21—C211 = −56 (2)°, and C2—C1—N1—C112 = −167.3 (4)° and C22—C21—N21—C212 = −180 (2)°. Exact, though nonetheless non-crystallographic symmetry, would require that the corresponding torsional angles have identical magnitudes, but opposite signs. An unexpected feature of this conformational disorder is the close proximity of the two sites N1 and N21, which are separated by only 0.182 (18) Å.
Figure 1
The molecular structure of compound (I) showing the atom-labelling scheme and the disorder. Displacement ellipsoids are drawn at the 30% probability level, and the minor disorder component is drawn with broken lines.
In the cation of the picrate salt (II) (Fig. 2 ▸), the same fragment is disordered, again over two sets of atomic sites, but now with occupancies of 0.654 (11) and 0.346 (11). The physical separation of the two sets of atomic sites is, in general, rather less in (II) than in (I), but the overall conformation of the cation in (II) is different from that of the neutral compound (I). This is well illustrated by the values of the torsion angles O12—C11—C12—O13, 157.8 (2)° in (I) and 13.1 (2)° in (II), and C11—O11—C2—C1 − 123.1 (4)° in (I) and 172.8 (4)° in (II), resulting in very different locations for the disordered fragment relative to the fragment Ph2COCH2CCH (cf. Figs. 1 ▸ and 2 ▸).
Figure 2
The ionic components of compound (II) showing the atom-labelling scheme and the disorder. Displacement ellipsoids are drawn at the 30% probability level, and the minor disorder component is drawn with broken lines.
The C—O distance in the picrate anion in (II), 1.2486 (17) Å, is short for its type [mean value (Allen et al., 1987 ▸) 1.362 Å, lower quartile value 1.353 Å]; the C—N distances in this anion, in the range 1.445 (2)–1.459 (2) Å, all fall below the mean value of 1.468 Å for bonds of this type. In addition, the C31—C32 and C31—C36 distances are 1.445 (2) and 1.439 (2) Å, respectively, whereas the other four C—C distances in this ring lie in the range 1.367 (2)–1.385 (2) Å with a mean value of 1.375 Å. These observations point to significant contributions to the electronic structure of this anion of polarized forms in which the negative charge is delocalized from the phenolic O atom into the ring and thence onto the nitro groups as recently noted (Sagar et al., 2017 ▸).
Supramolecular features
Despite the abundance of potential hydrogen-bond donors and acceptors in (I), with the C—H bonds of the aryl rings and the alkynyl unit as potential donors, and the amino N atom, the carbonyl O atom, two aryl rings and the triple bond of the alkynyl function as potential acceptors, there are in fact, no hydrogen bonds of any kind in the crystal structure of (I): nor are there any aromatic π–π stacking interactions, so that the structure consists of essentially isolated molecules making only van der Waals-type contacts with one another.Both disorder components of the cation in (II) are linked to the anion within the selected asymmetric unit via a near planar, but markedly asymmetric three-centre N-H⋯(O)2 charge-assisted (Gilli et al., 1994 ▸) hydrogen bond (Table 1 ▸), which forms an (6) motif. The resulting ion pairs are further linked by three C—H⋯O hydrogen bonds into complex sheets: however, the straightforward identification of two simple one-dimensional sub-structures (Ferguson et al., 1998a
▸,b
▸; Gregson et al., 2000 ▸) leads to a simple analysis of the sheet formation. In the simpler of the two sub-structures, the C—H⋯O hydrogen bond involving an aryl C—H unit links ion pairs related by translation along [100] into a (12) chain (Fig. 3 ▸). In the second sub-structure, the cooperative effect of two C—H⋯O hydrogen bonds, both involving CH2 groups, generates a chain parallel to [10] containing alternating (6) and (11) rings (Fig. 4 ▸). The combination of these two chain motifs generates a sheet lying parallel to (001) in the domain 0.5 < z < 1.0: a second such sheet, related to the first by inversion, lies in the domain 0 < z < 0.5, but there are no direction-specific interactions between adjacent sheets.
Table 1
Hydrogen-bond geometry (Å, °) for (II)
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
N1—H1⋯O31
0.98
1.72
2.633 (7)
153
N1—H1⋯O37
0.98
2.33
3.010 (7)
126
N21—H21⋯O31
0.98
1.77
2.697 (14)
157
N21—H21⋯O37
0.98
2.34
2.944 (14)
120
C2—H2B⋯O33i
0.97
2.56
3.338 (9)
137
C14—H14B⋯O32i
0.97
2.52
3.407 (2)
153
C135—H135⋯O31ii
0.93
2.58
3.485 (2)
165
Symmetry codes: (i) ; (ii) .
Figure 3
Part of the crystal structure of compound (II) showing the formation of a hydrogen-bonded chain running parallel to [100]. For the sake of clarity, only the major disorder component of the cation is shown and the H atoms not involved in the motif shown have been omitted. The atoms marked with an asterisk (*) and a hash (#) are at the symmetry positions (−1 + x, y, z) and (1 + x, y, z), respectively.
Figure 4
Part of the crystal structure of compound (II) showing the formation of a hydrogen-bonded chain of rings running parallel to [10]. For the sake of clarity, only the major disorder component of the cation is shown and the H atoms bonded to the C atoms which are not involved in the motif shown have been omitted. The atoms marked with an asterisk (*) and a hash (#)are at the symmetry positions (1 + x, −1 + y, z) and (−1 + x, 1 + y, z), respectively.
Database survey
In the (2R,3R)-(hydrogentartrate) salt (III) (Glidewell et al., 2017 ▸), the cation is fully ordered, unlike that in the picrate (II) and the conformation of the cation closely resembles that of the neutral molecule (I).The anions are linked by three O—H⋯O hydrogen bonds to form sheets lying parallel to (001) and containing equal numbers of (7) and (21) rings (Fig. 5 ▸). Within this sheet, the anions related by translation along [100] are linked by a very short and nearly linear O—H⋯O hydrogen bond, although the H atom is nonetheless off-centre; O⋯Oi 2.461 (7) Å; O—H⋯Oi 167 (9)°, O—H 1.12 (1) Å, H⋯Oi 1.35 (10) Å [symmetry code: (i) 1 + x, y, z]. The cations are linked to this sheet by a three-centre N—O⋯(O)2 hydrogen bond and they are disposed to either side of the sheet (Fig. 6 ▸).
Figure 5
Part of the crystal structure of compound (III) showing the formation of a hydrogen-bonded sheet of anions parallel to (001). The original atomic coordinates (Glidewell et al., 2017 ▸) have been used and, for the sake of clarity, the H atoms bonded to C atoms have been omitted.
Figure 6
A projection down [100] of part of the crystal structure of compound (III) showing the disposition of the cations bonded to both faces of the anion sheet. For the sake of clarity, the H atoms bonded to C atoms have been omitted.
4-(2,2-Diphenyl-2-propoxyacetoxy)-1-methylpiperidin-1-ium picrate (propiverinium picrate) (IV) is closely related to compound (II), differing in containing a saturated alkoxy substituent and having an N-methyl piperidinium unit in place of the N,N-dimethylethylammonium unit in (II). The component anions in (IV) are linked (Jasinski et al., 2009 ▸) by the same type of hydrogen-bonded (6) ring as seen in (II) but there are no structurally significant interactions between adjacent ion pairs in (IV).
Synthesis and crystallization
A sample of compound (I) was a gift from RL Fine Chem, Pvt. Ltd., Bengaluru, India, and it was recrystallized from methanol solution by slow evaporation at room temperature, m.p. 347–351 K. For the preparation of compound (II), equimolar quantities (0.30 mmol) of (I) and picric acid were dissolved in hot methanol and the solution was held at 333 K for 0.5 h, with magnetic stirring throughout. The solution was then allowed to cool slowly to room temperature, giving crystals of (II) suitable for single-crystal X-ray diffraction. m.p. 386–389 K.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. It was apparent from an early stage in the refinements that in both (I) and (II) the dimethylaminoethyl portion was disordered over two sets of atomic sites having different occupancies in each case, and corresponding to different conformations. For the minor conformation of each compound, the bonded distances and the 1,3-non-bonded distances were restrained to be the same as the corresponding distances in the major conformer, subject to s.u.s of 0.005 and 0.01 Å, respectively: in addition, the anisotropic displacement parameters for corresponding pairs of atomic sites occupying essentially the same physical space were constrained to be equal. All H atoms, other than those in the minor disordercomponents, were located in difference maps, and then treated as riding atoms in geometrically idealized position, with distances C—H 0.93 Å (aromatic and alkyne), 0.96 Å (CH3) or 0.97 Å (CH2) and N—H 0.98 Å, with U
iso(H) = kU
eq(carrier), where k = 1.5 for the methyl groups, which were permitted to rotate but not to tilt, and 1.2 for all other H atoms. The H atoms in the minor disordercomponents were included in calculated positions using the same procedure. When the refinement of the atomiccoordinates for the H atoms bonded to N atoms in (II) was attempted, the resulting N—H distances were 1.04 (4) and 0.82 (8) Å: accordingly, the riding model was preferred. Two low-angle reflections which had been attenuated by the beam stop, (020) for (I) and (002) for (II), were omitted from the final refinements. Subject to these conditions, the occupancies of the disordercomponents were 0.880 (3) and 0.120 (3) in (I) and 0.654 (11) and 0.346 (11) in (II). In the final analyses of variance for (I) there was a large value, 22.969, of K = [mean(F
o
2)/mean(F
c
2)] for the group of 518 very weak reflections having F
c/F
c(max) in the range 0.000 < F
c/F
c(max) < 0.004, and for (II) a value of K = 9.509 for the group of 789 very weak reflections having F
c/F
c(max) in the range 0.000 < F
c/F
c(max) < 0.006.
Table 2
Experimental details
(I)
(II)
Crystal data
Chemical formula
C21H23NO3
C21H24NO3·C6H2N3O7
Mr
337.40
566.52
Crystal system, space group
Monoclinic, P21/n
Triclinic, P
Temperature (K)
296
296
a, b, c (Å)
9.2545 (9), 21.7246 (19), 9.4531 (9)
7.5208 (3), 8.3919 (3), 22.2282 (7)
α, β, γ (°)
90, 94.763 (9), 90
85.099 (3), 84.294 (3), 75.117 (3)
V (Å3)
1894.0 (3)
1346.51 (9)
Z
4
2
Radiation type
Mo Kα
Mo Kα
μ (mm−1)
0.08
0.11
Crystal size (mm)
0.30 × 0.24 × 0.23
0.23 × 0.21 × 0.21
Data collection
Diffractometer
Rigaku Saturn724
Rigaku Saturn724
Absorption correction
Multi-scan (SADABS; Sheldrick,2003 ▸)
Multi-scan (SADABS; Sheldrick,2003 ▸)
Tmin, Tmax
0.956, 0.982
0.949, 0.978
No. of measured, independent and observed [I > 2σ(I)] reflections
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.053
H-atom parameters constrained
wR(F2) = 0.136
w = 1/[σ2(Fo2) + (0.0499P)2 + 0.2103P] where P = (Fo2 + 2Fc2)/3
S = 1.05
(Δ/σ)max = 0.001
7547 reflections
Δρmax = 0.27 e Å−3
390 parameters
Δρmin = −0.22 e Å−3
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.