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Afobazole {systematic name: 2-[2-(morpholin-4-yl)ethylsulfanyl]-1H-benzimidazole} is a new anxiolytic drug and Actins, Auzins & Petkune [(2012). Eur. Patent EP10163962] described four polymorphic modifications. In the present study, the crystal structures of two monoclinic polymorphs, 5-ethoxy-2-[2-(morpholin-4-ium-4-yl)ethylsulfanyl]-1H-benzimidazol-3-ium dichloride, C15H23N3O2S2+·2Cl-, (II) and (IV), have been established from laboratory powder diffraction data. The crystal packing and conformation of the dications in (II) and (IV) are different. In (II), there are channels in the [001] direction, which offer atmospheric water molecules an easy way of penetrating into the crystal structure, thus explaining the higher hygroscopicity of (II) compared with (IV).
Supporting information
CCDC references: 934582; 934583
Samples of (II) and (IV) were prepared in polycrystalline form by JSC Grindeks
(Riga, Latvia) according to the procedure of Actins et al.
(2012).
Thermogravimetric analysis was performed on 8–10 mg samples with an
EXSTAR6000 TG/DTA 6300 analyser (Seiko, Japan) using open sample pans (5 mm;
P/N SS000E030) in an air atmosphere at a heating rate of 10 K min-1 over the
temperature range 303–393 K.
The X-ray powder diffraction data were collected using a Huber G670 Guinier
camera (Cu Kα1 radiation, λ = 1.54059 Å) equipped with an
imaging-plate detector. The monoclinic unit-cell dimensions for both
polymorphs were determined using three indexing programs: TREOR90
(Werner et al., 1985), ITO (Visser, 1969) and
AUTOX
(Zlokazov, 1992, 1995). Based on systematic extinctions, the
space group for
both (II) and (IV) was determined to be P21/c. The unit-cell
parameters and space groups were further tested using a Pawley fit (Pawley,
1981) and confirmed by crystal structure solution. The powder pattern
of (IV)
contains four very weak peaks (d spacings = 15.629, 15.278, 14.453 and
5.694 Å) from other polymorphic forms of afobazole.
The crystal structures were solved using the simulated annealing technique
(Zhukov et al., 2001). The Cambridge Structural Database
(Version 5.33;
Allen, 2002) contains no structures with the
5-ethoxy-2-(2-morpholinoethylthio)benzimidazole fragment. Therefore, the
initial molecular model was obtained in the course of density functional
theory (DFT) calculations in vacuo using the quantum-chemical program
PRIRODA (Laikov, 1997, 2004, 2005; Laikov &
Ustynyuk, 2005), employing
the generalized-gradient approximation (GGA) and the PBE exchange-correlation
function (Perdew et al., 1996). In simulated annealing runs
(without H
atoms), the total number of varied degrees of freedom (DOF) for (II) and (IV)
was 18, i.e. nine translational (for two anions and one cation), three
orientational and six torsional for the cation. The solutions found were
fitted using the program MRIA (Zlokazov & Chernyshev, 1992) in
bond-restrained Rietveld refinements using a split-type pseudo-Voigt
peak-profile function (Toraya, 1986). In the refinement of (IV), the
anisotropic line broadening was taken into account with the use of nine
variables (Popa, 1998) and the March–Dollase (Dollase, 1986)
formalism was
used for correction of the preferred orientation in the [001] direction.
Restraints were applied to the intramolecular bond lengths and contacts (<2.8 Å); the strength of the restraints was a function of interatomic separation
and, for intramolecular bond lengths, corresponded to an r.m.s. deviation 0.02 Å. Additional restraints were applied to the planarity of the benzimidazole
fragment with the attached atoms, with the maximum allowed deviation from the
mean plane being 0.03 Å. All non-H atoms were refined isotropically. H atoms
were positioned geometrically (C—H = 0.93–0.97 Å and N—H = 0.86–0.91 Å) and not refined. The diffraction profiles for both polymorphs after the
final bond-restrained Rietveld refinements are shown in Fig. 5.
For both compounds, data collection: G670 Imaging-Plate Guinier Camera Software (Huber, 2002); cell refinement: MRIA (Zlokazov & Chernyshev, 1992); data reduction: G670 Imaging-Plate Guinier Camera Software (Huber, 2002); program(s) used to solve structure: simulated annealing (Zhukov et al., 2001); program(s) used to refine structure: MRIA (Zlokazov & Chernyshev, 1992); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: MRIA (Zlokazov & Chernyshev, 1992) and SHELXL97 (Sheldrick, 2008).
(II) 5-Ethoxy-2-[2-(morpholin-4-ium-4-yl)ethylsulfanyl]-1
H-benzimidazol-3-ium
dichloride
top
Crystal data top
C15H23N3O2S2+·2Cl− | F(000) = 800 |
Mr = 380.33 | Dx = 1.322 Mg m−3 |
Monoclinic, P21/c | Melting point: 473 K |
Hall symbol: -P 2ybc | Cu Kα1 radiation, λ = 1.54059 Å |
a = 14.4952 (15) Å | µ = 4.17 mm−1 |
b = 16.5419 (19) Å | T = 298 K |
c = 7.9715 (8) Å | Particle morphology: no specific habit |
β = 90.858 (15)° | white |
V = 1911.2 (4) Å3 | flat sheet, 15 × 1 mm |
Z = 4 | Specimen preparation: Prepared at 298 K and 101 kPa |
Data collection top
Huber G670 Guinier camera diffractometer | Data collection mode: transmission |
Radiation source: line-focus sealed tube | Scan method: continuous |
Curved germanium(111) monochromator | 2θmin = 4.00°, 2θmax = 76.00°, 2θstep = 0.01° |
Specimen mounting: thin layer in the specimen holder of the camera | |
Refinement top
Refinement on Inet | Profile function: split-type pseudo-Voigt (Toraya, 1986) |
Least-squares matrix: full with fixed elements per cycle | 127 parameters |
Rp = 0.019 | 68 restraints |
Rwp = 0.022 | 0 constraints |
Rexp = 0.013 | H-atom parameters not refined |
RBragg = 0.059 | Weighting scheme based on measured s.u.'s |
χ2 = 2.870 | (Δ/σ)max = 0.003 |
7201 data points | Background function: Chebyshev polynomial up to the 5th order |
Excluded region(s): none | Preferred orientation correction: none |
Crystal data top
C15H23N3O2S2+·2Cl− | V = 1911.2 (4) Å3 |
Mr = 380.33 | Z = 4 |
Monoclinic, P21/c | Cu Kα1 radiation, λ = 1.54059 Å |
a = 14.4952 (15) Å | µ = 4.17 mm−1 |
b = 16.5419 (19) Å | T = 298 K |
c = 7.9715 (8) Å | flat sheet, 15 × 1 mm |
β = 90.858 (15)° | |
Data collection top
Huber G670 Guinier camera diffractometer | Scan method: continuous |
Specimen mounting: thin layer in the specimen holder of the camera | 2θmin = 4.00°, 2θmax = 76.00°, 2θstep = 0.01° |
Data collection mode: transmission | |
Refinement top
Rp = 0.019 | 7201 data points |
Rwp = 0.022 | 127 parameters |
Rexp = 0.013 | 68 restraints |
RBragg = 0.059 | H-atom parameters not refined |
χ2 = 2.870 | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.7461 (7) | 0.6121 (7) | 0.4652 (14) | 0.063 (5)* | |
H1 | 0.7658 | 0.5638 | 0.4481 | 0.076* | |
C2 | 0.6643 (10) | 0.6304 (8) | 0.5351 (17) | 0.061 (7)* | |
N3 | 0.6580 (8) | 0.7131 (7) | 0.5384 (14) | 0.059 (5)* | |
H3 | 0.6126 | 0.7400 | 0.5788 | 0.071* | |
C4 | 0.7628 (10) | 0.8279 (10) | 0.4499 (18) | 0.070 (7)* | |
H4 | 0.7268 | 0.8704 | 0.4880 | 0.084* | |
C5 | 0.8488 (11) | 0.8408 (8) | 0.370 (2) | 0.067 (6)* | |
C6 | 0.9048 (11) | 0.7742 (9) | 0.3214 (19) | 0.067 (7)* | |
H6 | 0.9597 | 0.7846 | 0.2667 | 0.080* | |
C7 | 0.8805 (11) | 0.6946 (9) | 0.3518 (19) | 0.070 (6)* | |
H7 | 0.9193 | 0.6519 | 0.3254 | 0.084* | |
C8 | 0.7940 (10) | 0.6819 (9) | 0.4248 (16) | 0.057 (6)* | |
C9 | 0.7361 (10) | 0.7474 (10) | 0.467 (2) | 0.074 (6)* | |
O10 | 0.8822 (6) | 0.9136 (5) | 0.3406 (11) | 0.054 (4)* | |
C11 | 0.9669 (10) | 0.9267 (9) | 0.2491 (18) | 0.061 (6)* | |
H11A | 0.9644 | 0.8987 | 0.1421 | 0.073* | |
H11B | 1.0196 | 0.9069 | 0.3132 | 0.073* | |
C12 | 0.9743 (11) | 1.0180 (9) | 0.2224 (17) | 0.069 (7)* | |
H12A | 1.0295 | 1.0299 | 0.1619 | 0.104* | |
H12B | 0.9766 | 1.0447 | 0.3292 | 0.104* | |
H12C | 0.9216 | 1.0367 | 0.1592 | 0.104* | |
S13 | 0.5883 (3) | 0.5626 (2) | 0.6276 (5) | 0.053 (2)* | |
C14 | 0.4898 (11) | 0.6262 (9) | 0.6950 (18) | 0.066 (6)* | |
H14A | 0.5112 | 0.6774 | 0.7406 | 0.079* | |
H14B | 0.4475 | 0.6366 | 0.6022 | 0.079* | |
C15 | 0.4433 (10) | 0.5741 (9) | 0.8325 (18) | 0.069 (7)* | |
H15A | 0.4379 | 0.5187 | 0.7941 | 0.083* | |
H15B | 0.4813 | 0.5745 | 0.9337 | 0.083* | |
N16 | 0.3487 (8) | 0.6070 (7) | 0.8707 (14) | 0.059 (5)* | |
H16 | 0.3102 | 0.5922 | 0.7849 | 0.071* | |
C17 | 0.3482 (11) | 0.6998 (9) | 0.879 (2) | 0.075 (6)* | |
H17A | 0.3932 | 0.7181 | 0.9624 | 0.090* | |
H17B | 0.3649 | 0.7221 | 0.7715 | 0.090* | |
C18 | 0.2532 (10) | 0.7292 (9) | 0.9263 (19) | 0.071 (7)* | |
H18A | 0.2547 | 0.7875 | 0.9389 | 0.086* | |
H18B | 0.2101 | 0.7165 | 0.8358 | 0.086* | |
O19 | 0.2213 (6) | 0.6943 (6) | 1.0765 (10) | 0.058 (4)* | |
C20 | 0.2146 (10) | 0.6087 (10) | 1.0605 (17) | 0.069 (6)* | |
H20A | 0.1734 | 0.5953 | 0.9675 | 0.083* | |
H20B | 0.1891 | 0.5861 | 1.1620 | 0.083* | |
C21 | 0.3101 (10) | 0.5720 (8) | 1.0300 (18) | 0.066 (7)* | |
H21A | 0.3511 | 0.5841 | 1.1240 | 0.079* | |
H21B | 0.3051 | 0.5137 | 1.0199 | 0.079* | |
Cl1 | 0.2325 (3) | 0.5693 (2) | 0.5691 (5) | 0.0539 (18)* | |
Cl2 | 0.5306 (3) | 0.8426 (2) | 0.6990 (5) | 0.0601 (19)* | |
Geometric parameters (Å, º) top
N1—C2 | 1.352 (18) | C12—H12C | 0.96 |
N1—C8 | 1.388 (19) | S13—C14 | 1.859 (16) |
N1—H1 | 0.86 | C14—C15 | 1.56 (2) |
C2—N3 | 1.372 (18) | C14—H14A | 0.97 |
C2—S13 | 1.743 (14) | C14—H14B | 0.97 |
N3—C9 | 1.396 (19) | C15—N16 | 1.510 (19) |
N3—H3 | 0.86 | C15—H15A | 0.97 |
C4—C9 | 1.39 (2) | C15—H15B | 0.97 |
C4—C5 | 1.42 (2) | N16—C21 | 1.510 (18) |
C4—H4 | 0.93 | N16—C17 | 1.537 (18) |
C5—O10 | 1.321 (17) | N16—H16 | 0.91 |
C5—C6 | 1.43 (2) | C17—C18 | 1.51 (2) |
C6—C7 | 1.38 (2) | C17—H17A | 0.97 |
C6—H6 | 0.93 | C17—H17B | 0.97 |
C7—C8 | 1.41 (2) | C18—O19 | 1.414 (17) |
C7—H7 | 0.93 | C18—H18A | 0.97 |
C8—C9 | 1.41 (2) | C18—H18B | 0.97 |
O10—C11 | 1.438 (17) | O19—C20 | 1.424 (19) |
C11—C12 | 1.53 (2) | C20—C21 | 1.53 (2) |
C11—H11A | 0.97 | C20—H20A | 0.97 |
C11—H11B | 0.97 | C20—H20B | 0.97 |
C12—H12A | 0.96 | C21—H21A | 0.97 |
C12—H12B | 0.96 | C21—H21B | 0.97 |
| | | |
C2—N1—C8 | 110.8 (12) | C15—C14—H14A | 111.1 |
C2—N1—H1 | 124.6 | S13—C14—H14A | 111.1 |
C8—N1—H1 | 124.6 | C15—C14—H14B | 111.0 |
N1—C2—N3 | 106.9 (12) | S13—C14—H14B | 111.0 |
N1—C2—S13 | 126.5 (11) | H14A—C14—H14B | 109.0 |
N3—C2—S13 | 126.2 (11) | N16—C15—C14 | 110.3 (12) |
C2—N3—C9 | 110.0 (12) | N16—C15—H15A | 109.6 |
C2—N3—H3 | 124.9 | C14—C15—H15A | 109.6 |
C9—N3—H3 | 125.0 | N16—C15—H15B | 109.6 |
C9—C4—C5 | 115.7 (14) | C14—C15—H15B | 109.6 |
C9—C4—H4 | 122.1 | H15A—C15—H15B | 108.1 |
C5—C4—H4 | 122.2 | C21—N16—C15 | 112.4 (11) |
O10—C5—C4 | 122.9 (13) | C21—N16—C17 | 110.1 (11) |
O10—C5—C6 | 116.3 (13) | C15—N16—C17 | 111.9 (11) |
C4—C5—C6 | 120.8 (13) | C21—N16—H16 | 107.4 |
C7—C6—C5 | 122.6 (14) | C15—N16—H16 | 107.4 |
C7—C6—H6 | 118.7 | C17—N16—H16 | 107.4 |
C5—C6—H6 | 118.7 | C18—C17—N16 | 109.7 (12) |
C6—C7—C8 | 116.5 (14) | C18—C17—H17A | 109.7 |
C6—C7—H7 | 121.8 | N16—C17—H17A | 109.7 |
C8—C7—H7 | 121.7 | C18—C17—H17B | 109.8 |
N1—C8—C7 | 132.3 (13) | N16—C17—H17B | 109.7 |
N1—C8—C9 | 106.4 (12) | H17A—C17—H17B | 108.3 |
C7—C8—C9 | 121.3 (14) | O19—C18—C17 | 112.9 (12) |
C4—C9—N3 | 131.0 (14) | O19—C18—H18A | 109.0 |
C4—C9—C8 | 122.8 (14) | C17—C18—H18A | 109.0 |
N3—C9—C8 | 105.9 (13) | O19—C18—H18B | 109.1 |
C5—O10—C11 | 122.7 (11) | C17—C18—H18B | 109.1 |
O10—C11—C12 | 106.2 (11) | H18A—C18—H18B | 107.7 |
O10—C11—H11A | 110.4 | C18—O19—C20 | 110.7 (10) |
C12—C11—H11A | 110.5 | O19—C20—C21 | 110.3 (12) |
O10—C11—H11B | 110.4 | O19—C20—H20A | 109.6 |
C12—C11—H11B | 110.5 | C21—C20—H20A | 109.6 |
H11A—C11—H11B | 108.7 | O19—C20—H20B | 109.6 |
C11—C12—H12A | 109.5 | C21—C20—H20B | 109.6 |
C11—C12—H12B | 109.5 | H20A—C20—H20B | 108.1 |
H12A—C12—H12B | 109.5 | N16—C21—C20 | 109.1 (11) |
C11—C12—H12C | 109.5 | N16—C21—H21A | 109.8 |
H12A—C12—H12C | 109.4 | C20—C21—H21A | 109.9 |
H12B—C12—H12C | 109.4 | N16—C21—H21B | 109.8 |
C2—S13—C14 | 104.5 (7) | C20—C21—H21B | 109.9 |
C15—C14—S13 | 103.5 (10) | H21A—C21—H21B | 108.3 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1i | 0.86 | 2.21 | 3.030 (12) | 160 |
N3—H3···Cl2 | 0.86 | 2.29 | 3.116 (12) | 161 |
N16—H16···Cl1 | 0.91 | 2.08 | 2.981 (12) | 172 |
C15—H15B···Cl2ii | 0.97 | 2.61 | 3.453 (15) | 145 |
C18—H18A···Cl1ii | 0.97 | 2.61 | 3.536 (15) | 160 |
C18—H18B···O19iii | 0.97 | 2.55 | 3.091 (17) | 115 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2; (iii) x, −y+3/2, z−1/2. |
(IV) 5-Ethoxy-2-[2-(morpholin-4-ium-4-yl)ethylsulfanyl]-1
H-benzimidazol-3-ium
dichloride
top
Crystal data top
C15H23N3O2S2+·2Cl− | F(000) = 800 |
Mr = 380.33 | Dx = 1.373 Mg m−3 |
Monoclinic, P21/c | Melting point: 482 K |
Hall symbol: -P 2ybc | Cu Kα1 radiation, λ = 1.54059 Å |
a = 9.7910 (11) Å | µ = 4.33 mm−1 |
b = 18.2689 (19) Å | T = 298 K |
c = 10.5687 (12) Å | Particle morphology: prism |
β = 103.225 (17)° | white |
V = 1840.3 (4) Å3 | flat sheet, 15 × 1 mm |
Z = 4 | Specimen preparation: Prepared at 298 K and 101 kPa |
Data collection top
Huber G670 Guinier camera diffractometer | Data collection mode: transmission |
Radiation source: line-focus sealed tube | Scan method: continuous |
Curved germanium(111) monochromator | 2θmin = 4.00°, 2θmax = 76.00°, 2θstep = 0.01° |
Specimen mounting: thin layer in the specimen holder of the camera | |
Refinement top
Refinement on Inet | Profile function: split-type pseudo-Voigt (Toraya, 1986); anisotropic line-broadening has
been
taken into account with nine varied parameters (Popa, 1998) |
Least-squares matrix: full with fixed elements per cycle | 137 parameters |
Rp = 0.023 | 68 restraints |
Rwp = 0.030 | 0 constraints |
Rexp = 0.012 | H-atom parameters not refined |
RBragg = 0.053 | Weighting scheme based on measured s.u.'s |
χ2 = 6.513 | (Δ/σ)max = 0.001 |
7201 data points | Background function: Chebyshev polynomial up to the 5th order |
Excluded region(s): none | Preferred orientation correction: March–Dollase (Dollase, 1986); direction of preferred orientation
[001],
texture parameter r = 0.970(12) |
Crystal data top
C15H23N3O2S2+·2Cl− | V = 1840.3 (4) Å3 |
Mr = 380.33 | Z = 4 |
Monoclinic, P21/c | Cu Kα1 radiation, λ = 1.54059 Å |
a = 9.7910 (11) Å | µ = 4.33 mm−1 |
b = 18.2689 (19) Å | T = 298 K |
c = 10.5687 (12) Å | flat sheet, 15 × 1 mm |
β = 103.225 (17)° | |
Data collection top
Huber G670 Guinier camera diffractometer | Scan method: continuous |
Specimen mounting: thin layer in the specimen holder of the camera | 2θmin = 4.00°, 2θmax = 76.00°, 2θstep = 0.01° |
Data collection mode: transmission | |
Refinement top
Rp = 0.023 | 7201 data points |
Rwp = 0.030 | 137 parameters |
Rexp = 0.012 | 68 restraints |
RBragg = 0.053 | H-atom parameters not refined |
χ2 = 6.513 | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.9781 (8) | 0.4679 (4) | 0.1534 (7) | 0.053 (3)* | |
H1 | 1.0252 | 0.4454 | 0.1059 | 0.064* | |
C2 | 0.8381 (10) | 0.4637 (5) | 0.1390 (8) | 0.059 (4)* | |
N3 | 0.8032 (8) | 0.5117 (4) | 0.2275 (7) | 0.056 (3)* | |
H3 | 0.7189 | 0.5218 | 0.2328 | 0.067* | |
C4 | 0.9415 (10) | 0.5916 (5) | 0.4103 (9) | 0.058 (4)* | |
H4 | 0.8670 | 0.6094 | 0.4424 | 0.070* | |
C5 | 1.0811 (10) | 0.6130 (5) | 0.4622 (9) | 0.062 (4)* | |
C6 | 1.1900 (10) | 0.5847 (5) | 0.4070 (9) | 0.057 (4)* | |
H6 | 1.2807 | 0.6011 | 0.4423 | 0.068* | |
C7 | 1.1737 (10) | 0.5362 (5) | 0.3081 (9) | 0.063 (4)* | |
H7 | 1.2490 | 0.5190 | 0.2767 | 0.076* | |
C8 | 1.0347 (10) | 0.5137 (5) | 0.2559 (9) | 0.057 (3)* | |
C9 | 0.9220 (10) | 0.5410 (5) | 0.3057 (9) | 0.056 (4)* | |
O10 | 1.1213 (6) | 0.6614 (3) | 0.5621 (5) | 0.046 (2)* | |
C11 | 1.0126 (10) | 0.7106 (5) | 0.5916 (8) | 0.056 (3)* | |
H11A | 0.9413 | 0.6832 | 0.6217 | 0.067* | |
H11B | 0.9683 | 0.7393 | 0.5160 | 0.067* | |
C12 | 1.0966 (10) | 0.7592 (5) | 0.6990 (9) | 0.060 (3)* | |
H12A | 1.0349 | 0.7938 | 0.7257 | 0.090* | |
H12B | 1.1673 | 0.7850 | 0.6670 | 0.090* | |
H12C | 1.1406 | 0.7294 | 0.7718 | 0.090* | |
S13 | 0.7215 (3) | 0.42270 (14) | 0.0146 (2) | 0.0510 (10)* | |
C14 | 0.5594 (10) | 0.4127 (5) | 0.0751 (9) | 0.063 (4)* | |
H14A | 0.5508 | 0.4518 | 0.1349 | 0.076* | |
H14B | 0.4768 | 0.4125 | 0.0039 | 0.076* | |
C15 | 0.5808 (10) | 0.3356 (5) | 0.1471 (9) | 0.065 (4)* | |
H15A | 0.5826 | 0.2963 | 0.0857 | 0.078* | |
H15B | 0.6678 | 0.3348 | 0.2131 | 0.078* | |
N16 | 0.4543 (8) | 0.3275 (4) | 0.2089 (7) | 0.062 (3)* | |
H16 | 0.3777 | 0.3445 | 0.1505 | 0.074* | |
C17 | 0.4721 (10) | 0.3743 (5) | 0.3303 (9) | 0.063 (3)* | |
H17A | 0.5588 | 0.3614 | 0.3912 | 0.076* | |
H17B | 0.4769 | 0.4255 | 0.3077 | 0.076* | |
C18 | 0.3493 (10) | 0.3620 (5) | 0.3923 (9) | 0.057 (3)* | |
H18A | 0.3618 | 0.3910 | 0.4710 | 0.068* | |
H18B | 0.2634 | 0.3779 | 0.3332 | 0.068* | |
O19 | 0.3379 (6) | 0.2867 (3) | 0.4230 (5) | 0.048 (2)* | |
C20 | 0.3036 (9) | 0.2454 (5) | 0.3042 (9) | 0.056 (3)* | |
H20A | 0.2192 | 0.2651 | 0.2477 | 0.067* | |
H20B | 0.2860 | 0.1948 | 0.3229 | 0.067* | |
C21 | 0.4272 (10) | 0.2498 (5) | 0.2354 (9) | 0.057 (3)* | |
H21A | 0.5105 | 0.2283 | 0.2903 | 0.068* | |
H21B | 0.4042 | 0.2226 | 0.1545 | 0.068* | |
Cl1 | 0.1768 (3) | 0.37260 (14) | 0.0310 (2) | 0.0500 (9)* | |
Cl2 | 0.5313 (3) | 0.56770 (14) | 0.2831 (2) | 0.0470 (9)* | |
Geometric parameters (Å, º) top
N1—C2 | 1.346 (12) | C12—H12C | 0.96 |
N1—C8 | 1.381 (11) | S13—C14 | 1.851 (11) |
N1—H1 | 0.86 | C14—C15 | 1.592 (13) |
C2—N3 | 1.381 (12) | C14—H14A | 0.97 |
C2—S13 | 1.705 (9) | C14—H14B | 0.97 |
N3—C9 | 1.372 (11) | C15—N16 | 1.533 (14) |
N3—H3 | 0.86 | C15—H15A | 0.97 |
C4—C5 | 1.407 (13) | C15—H15B | 0.97 |
C4—C9 | 1.420 (13) | N16—C21 | 1.483 (12) |
C4—H4 | 0.93 | N16—C17 | 1.518 (12) |
C5—O10 | 1.364 (11) | N16—H16 | 0.91 |
C5—C6 | 1.425 (15) | C17—C18 | 1.512 (15) |
C6—C7 | 1.352 (13) | C17—H17A | 0.97 |
C6—H6 | 0.93 | C17—H17B | 0.97 |
C7—C8 | 1.408 (13) | C18—O19 | 1.424 (11) |
C7—H7 | 0.93 | C18—H18A | 0.97 |
C8—C9 | 1.417 (15) | C18—H18B | 0.97 |
O10—C11 | 1.480 (12) | O19—C20 | 1.437 (10) |
C11—C12 | 1.525 (12) | C20—C21 | 1.550 (14) |
C11—H11A | 0.97 | C20—H20A | 0.97 |
C11—H11B | 0.97 | C20—H20B | 0.97 |
C12—H12A | 0.96 | C21—H21A | 0.97 |
C12—H12B | 0.96 | C21—H21B | 0.97 |
| | | |
C2—N1—C8 | 109.8 (8) | C15—C14—H14A | 111.2 |
C2—N1—H1 | 125.1 | S13—C14—H14A | 111.2 |
C8—N1—H1 | 125.1 | C15—C14—H14B | 111.2 |
N1—C2—N3 | 106.9 (7) | S13—C14—H14B | 111.2 |
N1—C2—S13 | 126.7 (8) | H14A—C14—H14B | 109.1 |
N3—C2—S13 | 125.1 (7) | N16—C15—C14 | 105.0 (7) |
C9—N3—C2 | 110.4 (8) | N16—C15—H15A | 110.8 |
C9—N3—H3 | 124.8 | C14—C15—H15A | 110.7 |
C2—N3—H3 | 124.8 | N16—C15—H15B | 110.8 |
C5—C4—C9 | 115.5 (9) | C14—C15—H15B | 110.7 |
C5—C4—H4 | 122.3 | H15A—C15—H15B | 108.8 |
C9—C4—H4 | 122.3 | C21—N16—C17 | 111.7 (7) |
O10—C5—C4 | 124.4 (9) | C21—N16—C15 | 111.7 (7) |
O10—C5—C6 | 116.2 (8) | C17—N16—C15 | 111.0 (7) |
C4—C5—C6 | 119.4 (8) | C21—N16—H16 | 107.4 |
C7—C6—C5 | 126.0 (9) | C17—N16—H16 | 107.4 |
C7—C6—H6 | 117.0 | C15—N16—H16 | 107.4 |
C5—C6—H6 | 117.0 | C18—C17—N16 | 109.5 (7) |
C6—C7—C8 | 115.3 (10) | C18—C17—H17A | 109.7 |
C6—C7—H7 | 122.4 | N16—C17—H17A | 109.8 |
C8—C7—H7 | 122.4 | C18—C17—H17B | 109.8 |
N1—C8—C7 | 131.5 (9) | N16—C17—H17B | 109.8 |
N1—C8—C9 | 107.3 (8) | H17A—C17—H17B | 108.2 |
C7—C8—C9 | 121.1 (9) | O19—C18—C17 | 110.7 (8) |
N3—C9—C8 | 105.3 (8) | O19—C18—H18A | 109.5 |
N3—C9—C4 | 131.9 (9) | C17—C18—H18A | 109.5 |
C8—C9—C4 | 122.7 (8) | O19—C18—H18B | 109.5 |
C5—O10—C11 | 117.6 (6) | C17—C18—H18B | 109.5 |
O10—C11—C12 | 102.7 (7) | H18A—C18—H18B | 108.1 |
O10—C11—H11A | 111.2 | C18—O19—C20 | 108.9 (6) |
C12—C11—H11A | 111.2 | O19—C20—C21 | 109.3 (7) |
O10—C11—H11B | 111.3 | O19—C20—H20A | 109.8 |
C12—C11—H11B | 111.3 | C21—C20—H20A | 109.8 |
H11A—C11—H11B | 109.1 | O19—C20—H20B | 109.9 |
C11—C12—H12A | 109.5 | C21—C20—H20B | 109.8 |
C11—C12—H12B | 109.5 | H20A—C20—H20B | 108.2 |
H12A—C12—H12B | 109.5 | N16—C21—C20 | 109.3 (8) |
C11—C12—H12C | 109.5 | N16—C21—H21A | 109.8 |
H12A—C12—H12C | 109.4 | C20—C21—H21A | 109.8 |
H12B—C12—H12C | 109.5 | N16—C21—H21B | 109.8 |
C2—S13—C14 | 104.7 (5) | C20—C21—H21B | 109.8 |
C15—C14—S13 | 102.9 (6) | H21A—C21—H21B | 108.3 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1i | 0.86 | 2.26 | 3.104 (8) | 165 |
N3—H3···Cl2 | 0.86 | 2.19 | 3.032 (8) | 165 |
N16—H16···Cl1 | 0.91 | 2.14 | 3.043 (8) | 171 |
C14—H14A···Cl2 | 0.97 | 2.67 | 3.634 (10) | 176 |
C17—H17B···Cl2 | 0.97 | 2.68 | 3.633 (10) | 169 |
C18—H18A···Cl2ii | 0.97 | 2.68 | 3.599 (9) | 160 |
C21—H21B···O19iii | 0.97 | 2.39 | 3.285 (11) | 153 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+1; (iii) x, −y+1/2, z−1/2. |
Experimental details
| (II) | (IV) |
Crystal data |
Chemical formula | C15H23N3O2S2+·2Cl− | C15H23N3O2S2+·2Cl− |
Mr | 380.33 | 380.33 |
Crystal system, space group | Monoclinic, P21/c | Monoclinic, P21/c |
Temperature (K) | 298 | 298 |
a, b, c (Å) | 14.4952 (15), 16.5419 (19), 7.9715 (8) | 9.7910 (11), 18.2689 (19), 10.5687 (12) |
β (°) | 90.858 (15) | 103.225 (17) |
V (Å3) | 1911.2 (4) | 1840.3 (4) |
Z | 4 | 4 |
Radiation type | Cu Kα1, λ = 1.54059 Å | Cu Kα1, λ = 1.54059 Å |
µ (mm−1) | 4.17 | 4.33 |
Specimen shape, size (mm) | Flat sheet, 15 × 1 | Flat sheet, 15 × 1 |
|
Data collection |
Diffractometer | Huber G670 Guinier camera diffractometer | Huber G670 Guinier camera diffractometer |
Specimen mounting | Thin layer in the specimen holder of the camera | Thin layer in the specimen holder of the camera |
Data collection mode | Transmission | Transmission |
Scan method | Continuous | Continuous |
2θ values (°) | 2θmin = 4.00 2θmax = 76.00 2θstep = 0.01 | 2θmin = 4.00 2θmax = 76.00 2θstep = 0.01 |
|
Refinement |
R factors and goodness of fit | Rp = 0.019, Rwp = 0.022, Rexp = 0.013, RBragg = 0.059, χ2 = 2.870 | Rp = 0.023, Rwp = 0.030, Rexp = 0.012, RBragg = 0.053, χ2 = 6.513 |
No. of data points | 7201 | 7201 |
No. of parameters | 127 | 137 |
No. of restraints | 68 | 68 |
H-atom treatment | H-atom parameters not refined | H-atom parameters not refined |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1i | 0.86 | 2.21 | 3.030 (12) | 160 |
N3—H3···Cl2 | 0.86 | 2.29 | 3.116 (12) | 161 |
N16—H16···Cl1 | 0.91 | 2.08 | 2.981 (12) | 172 |
C15—H15B···Cl2ii | 0.97 | 2.61 | 3.453 (15) | 145 |
C18—H18A···Cl1ii | 0.97 | 2.61 | 3.536 (15) | 160 |
C18—H18B···O19iii | 0.97 | 2.55 | 3.091 (17) | 115 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2; (iii) x, −y+3/2, z−1/2. |
Hydrogen-bond geometry (Å, º) for (IV) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···Cl1i | 0.86 | 2.26 | 3.104 (8) | 165 |
N3—H3···Cl2 | 0.86 | 2.19 | 3.032 (8) | 165 |
N16—H16···Cl1 | 0.91 | 2.14 | 3.043 (8) | 171 |
C14—H14A···Cl2 | 0.97 | 2.67 | 3.634 (10) | 176 |
C17—H17B···Cl2 | 0.97 | 2.68 | 3.633 (10) | 169 |
C18—H18A···Cl2ii | 0.97 | 2.68 | 3.599 (9) | 160 |
C21—H21B···O19iii | 0.97 | 2.39 | 3.285 (11) | 153 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+1; (iii) x, −y+1/2, z−1/2. |
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Afobazole {systematic name: 5-ethoxy-2-[2-(morpholin-4-ium-4-yl)ethylsulfanyl]-1H-benzimidazol-3-ium dichloride} is a new drug belonging to the class of 2-mercaptobenzimidazole derivatives. Afobazole exhibits pronounced anxiolytic action that is not accompanied by the side effects typical of tranquilizers of the benzodiazepine series. It does not produce sedative (calming), hypnotic and myorelaxant effects, and is still under intensive study (Cuevas et al., 2011a,b; Reutova et al., 2010). Clinical trials have shown afobazole to be well tolerated and reasonably effective for the treatment of anxiety, although its mechanism of action remains poorly defined. The physicochemical properties of afobazole have been studied and methods for its standardization developed (Milkina et al., 2006), but no published crystal structures were found in the Cambride Structural Database (CSD, Version 5.33; Allen, 2002). Recently, four polymorphic modifications of afobazole [(I), (II), (III) and (IV)] were reported by Actins et al. (2012). Herein, we report the crystal structures of the polymorphic salts (II) and (IV) determined from laboratory powder diffraction data.
The asymmetric units of (II) and (IV) are shown in Fig. 1. In both polymorphs, the geometry of the cation is normal and the morpholine ring has a chair conformation. However, the overall conformations of the cation in (II) and (IV) are different, as can be seen from Figs. 1 and 2. The crystal packings of (II) and (IV) are also different. In (II), classical intermolecular N—H···Cl hydrogen bonds (Table 1) link two cations and four anions into an electroneutral centrosymmetric unit (Fig. 3, top) and weak C—H···O interactions (Table 1) consolidate the crystal packing further. In (IV), intermolecular N—H···Cl hydrogen bonds (Table 2) link cations related by translation along the a axis and anions into electroneutral chains (Fig. 3, bottom), which are further held together by weak C—H···O interactions (Table 2).
Thermogravimetric analysis (TGA) shows that (IV) is stable at a relative humidity of 55 (3)% and T = 295 K over a period of 8 h, while (II) is hygroscopic, exhibiting a weight increase of 2.4% after 2 h exposure under the same conditions. However, the water content in the studied sample of (II), estimated by Karl Fischer titration, suggested no more than one water molecule per ten formula units of afobazole. These ambiguous data, along with the observed difference of 18 Å3 in the asymmetric unit-cell volumes of (II) and (IV), necessitated a check for the possible presence of solvent water in (II). In the crystal structure of (II), PLATON (Spek, 2009) detects solvent-accessible voids of 12 Å3 centred at (0.08, 0.81, 0.99). Atom OW was placed in the centre of the void, with an initial occupancy of 0.5 and a Uiso value fixed at 0.1 Å-2, and refined. The atomic coordinates and occupancy factor of atom OW refined to (0.08, 0.80, 1.09) and 0.1 (2), respectively, with insignificant improvements in the R factors, which allows us to consider the investigated sample of form (II) as anhydrous. On the other hand, atom OW in the refined position has a reasonable environment and forms hydrogen bonds with atoms O19 (OW···O19 = 2.73 Å) and Cl1 [OW···Cl1(x, -y + 3/2, z + 1/2) = 3.10 Å], thus showing the position where an atmospheric water molecule could be docked without rearrangement of the crystal structure. Interestingly, the voids found by PLATON in (II) form sinuous channels in the [001] direction (Fig. 4), which offer water molecules an easy way of penetrating into the crystal structure.
In conclusion, we can state that crystal-packing features are responsible for the high hygroscopicity of (II) and therefore afobazole form (IV) is superior for prolonged storage.