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The crystal structure of diaquabis(omeprazolate)magnesium dihydrate (DABOMD) in the solid state has been determined using single-crystal X-ray diffraction. Single crystals of DABOMD were obtained by slow crystallization in ethanol with water used as an antisolvent. The crystal structure shows a dihydrated salt comprising a magnesium cation coordinating two omeprazolate anions and two water molecules (W1) that are strongly bound to magnesium. In addition, two further water molecules (W2) are more weakly hydrogen-bonded to the pyridine nitrogen atom of each omeprazolate anion. The crystal structure was utilized to estimate key material properties for DABOMD, including crystal habit and mechanical properties, which are required for improved understanding and prediction of the behaviour of particles during pharmaceutical processing such as milling. The results from the material properties calculations indicate that DABOMD exhibits a hexagonal morphology and consists of a flat slip plane through the (100) face. It can be classed as a soft material based on elastic constant calculation and exhibits a two-dimensional hydrogen-bonding framework. Based on the crystal structure, habit and mechanical properties, it is anticipated that DABOMD will experience large disorder accompanied by plastic deformation during milling.
Supporting information
CCDC reference: 1920020
Data collection: CrysAlis PRO 1.171.39.43c (Rigaku OD, 2018); cell refinement: CrysAlis PRO 1.171.39.43c (Rigaku OD, 2018); data reduction: CrysAlis PRO 1.171.39.43c (Rigaku OD, 2018); program(s) used to solve structure: ShelXT (Sheldrick, 2015); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: Olex2 (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 (Dolomanov et al., 2009).
Crystal data top
C34H40MgN6O8S2·2H2O | F(000) = 828 |
Mr = 785.18 | Dx = 1.389 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 17.475 (9) Å | Cell parameters from 455 reflections |
b = 8.051 (2) Å | θ = 6.2–68.5° |
c = 14.190 (5) Å | µ = 1.99 mm−1 |
β = 109.91 (5)° | T = 120 K |
V = 1877.1 (14) Å3 | Plate, colourless |
Z = 2 | 0.11 × 0.03 × 0.01 mm |
Data collection top
SuperNova, Dual, Cu at home/near, Atlas diffractometer | 3546 independent reflections |
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source | 1689 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.166 |
Detector resolution: 5.3095 pixels mm-1 | θmax = 73.6°, θmin = 5.4° |
ω scans | h = −15→21 |
Absorption correction: gaussian CrysAlisPro 1.171.39.43c (Rigaku Oxford Diffraction, 2018)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm. | k = −9→9 |
Tmin = 0.812, Tmax = 1.000 | l = −15→17 |
8269 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.150 | H-atom parameters constrained |
wR(F2) = 0.416 | w = 1/[σ2(Fo2) + (0.2P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
3546 reflections | Δρmax = 1.71 e Å−3 |
249 parameters | Δρmin = −0.66 e Å−3 |
216 restraints | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S1 | 0.58530 (16) | 0.6073 (3) | 0.72447 (16) | 0.0288 (6) | |
Mg1 | 0.5000 | 0.5000 | 0.5000 | 0.0305 (11) | |
O1 | 0.5987 (5) | 0.5499 (9) | 0.6294 (5) | 0.0350 (16) | |
O2 | 0.1453 (6) | 0.8220 (14) | 0.6272 (7) | 0.062 (2) | |
O3 | 0.8991 (6) | 0.8318 (12) | 0.9725 (8) | 0.064 (2) | |
O4 | 0.5015 (5) | 0.7391 (8) | 0.4444 (5) | 0.0348 (16) | |
H4A | 0.4719 | 0.7436 | 0.3810 | 0.052* | |
H4B | 0.5500 | 0.7651 | 0.4445 | 0.052* | |
N1 | 0.4341 (5) | 0.6023 (10) | 0.5913 (5) | 0.0285 (15) | |
N2 | 0.4408 (5) | 0.7129 (10) | 0.7408 (6) | 0.0314 (16) | |
N3 | 0.7275 (6) | 0.9068 (11) | 0.6906 (6) | 0.0390 (19) | |
C1 | 0.3565 (7) | 0.6506 (13) | 0.5844 (8) | 0.035 (2) | |
C2 | 0.2826 (7) | 0.6417 (13) | 0.5067 (8) | 0.040 (2) | |
H2 | 0.2793 | 0.5968 | 0.4450 | 0.048* | |
C3 | 0.2135 (7) | 0.7016 (15) | 0.5230 (9) | 0.044 (2) | |
H3 | 0.1633 | 0.6969 | 0.4717 | 0.053* | |
C4 | 0.2190 (7) | 0.7703 (14) | 0.6182 (9) | 0.041 (2) | |
C5 | 0.2908 (7) | 0.7750 (14) | 0.6939 (8) | 0.040 (2) | |
H5 | 0.2931 | 0.8171 | 0.7559 | 0.048* | |
C6 | 0.3617 (7) | 0.7175 (12) | 0.6806 (7) | 0.0332 (19) | |
C7 | 0.1475 (10) | 0.893 (2) | 0.7219 (11) | 0.067 (4) | |
H7A | 0.0945 | 0.9351 | 0.7157 | 0.100* | |
H7B | 0.1861 | 0.9828 | 0.7396 | 0.100* | |
H7C | 0.1632 | 0.8097 | 0.7731 | 0.100* | |
C8 | 0.4778 (6) | 0.6396 (11) | 0.6839 (6) | 0.0272 (17) | |
C9 | 0.6156 (6) | 0.8249 (12) | 0.7413 (7) | 0.0304 (19) | |
H9A | 0.5871 | 0.8857 | 0.6804 | 0.036* | |
H9B | 0.5999 | 0.8718 | 0.7951 | 0.036* | |
C10 | 0.7054 (7) | 0.8450 (12) | 0.7656 (8) | 0.0337 (19) | |
C11 | 0.7619 (7) | 0.8097 (13) | 0.8603 (8) | 0.041 (2) | |
C12 | 0.8433 (8) | 0.8488 (15) | 0.8786 (10) | 0.049 (2) | |
C13 | 0.8676 (8) | 0.9129 (18) | 0.8006 (10) | 0.055 (3) | |
C14 | 0.8074 (7) | 0.9366 (15) | 0.7102 (9) | 0.045 (2) | |
H14 | 0.8229 | 0.9766 | 0.6578 | 0.054* | |
C15 | 0.7374 (9) | 0.7365 (16) | 0.9439 (9) | 0.050 (3) | |
H15A | 0.6870 | 0.7853 | 0.9429 | 0.075* | |
H15B | 0.7789 | 0.7593 | 1.0071 | 0.075* | |
H15C | 0.7307 | 0.6186 | 0.9348 | 0.075* | |
C16 | 0.9366 (11) | 0.673 (2) | 0.9940 (16) | 0.093 (6) | |
H16A | 0.9532 | 0.6382 | 0.9392 | 0.140* | |
H16B | 0.8985 | 0.5942 | 1.0032 | 0.140* | |
H16C | 0.9833 | 0.6793 | 1.0540 | 0.140* | |
C17 | 0.9564 (9) | 0.956 (3) | 0.8180 (13) | 0.080 (5) | |
H17A | 0.9882 | 0.8564 | 0.8291 | 0.120* | |
H17B | 0.9767 | 1.0272 | 0.8756 | 0.120* | |
H17C | 0.9603 | 1.0129 | 0.7602 | 0.120* | |
O5 | 0.6036 (6) | 0.9976 (10) | 0.5097 (6) | 0.0449 (19) | |
H5A | 0.5792 | 1.0495 | 0.5434 | 0.067* | |
H5B | 0.6528 | 0.9918 | 0.5485 | 0.067* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0526 (13) | 0.0191 (11) | 0.0168 (10) | −0.0003 (9) | 0.0145 (9) | −0.0002 (8) |
Mg1 | 0.061 (3) | 0.018 (2) | 0.0162 (19) | −0.0011 (18) | 0.018 (2) | −0.0021 (15) |
O1 | 0.057 (4) | 0.028 (4) | 0.022 (3) | 0.002 (3) | 0.017 (3) | −0.006 (2) |
O2 | 0.075 (5) | 0.058 (6) | 0.057 (5) | 0.003 (4) | 0.029 (4) | −0.005 (4) |
O3 | 0.075 (5) | 0.040 (5) | 0.062 (5) | −0.001 (4) | 0.005 (4) | −0.001 (4) |
O4 | 0.066 (5) | 0.016 (3) | 0.028 (3) | −0.005 (3) | 0.023 (3) | 0.002 (2) |
N1 | 0.055 (4) | 0.015 (3) | 0.016 (3) | 0.000 (3) | 0.014 (3) | 0.004 (2) |
N2 | 0.057 (4) | 0.018 (4) | 0.022 (3) | −0.004 (3) | 0.018 (3) | −0.001 (3) |
N3 | 0.064 (4) | 0.024 (4) | 0.032 (4) | −0.006 (3) | 0.020 (3) | −0.006 (3) |
C1 | 0.052 (4) | 0.022 (5) | 0.030 (4) | 0.000 (3) | 0.014 (3) | 0.000 (3) |
C2 | 0.058 (4) | 0.021 (5) | 0.038 (4) | −0.003 (3) | 0.012 (4) | 0.007 (4) |
C3 | 0.053 (5) | 0.034 (6) | 0.040 (5) | −0.003 (4) | 0.007 (4) | 0.001 (4) |
C4 | 0.053 (4) | 0.025 (5) | 0.041 (4) | −0.002 (3) | 0.013 (4) | 0.003 (4) |
C5 | 0.057 (4) | 0.028 (5) | 0.037 (4) | −0.005 (3) | 0.019 (3) | 0.000 (4) |
C6 | 0.056 (4) | 0.020 (4) | 0.026 (4) | −0.004 (3) | 0.017 (3) | 0.000 (3) |
C7 | 0.081 (9) | 0.063 (9) | 0.063 (7) | 0.006 (7) | 0.034 (7) | −0.010 (6) |
C8 | 0.055 (4) | 0.014 (4) | 0.016 (3) | −0.001 (3) | 0.016 (3) | 0.003 (3) |
C9 | 0.056 (4) | 0.013 (4) | 0.020 (4) | −0.003 (3) | 0.010 (4) | −0.006 (3) |
C10 | 0.055 (4) | 0.017 (4) | 0.031 (4) | −0.002 (3) | 0.016 (3) | −0.004 (3) |
C11 | 0.063 (4) | 0.022 (5) | 0.034 (4) | 0.000 (3) | 0.012 (3) | −0.002 (3) |
C12 | 0.062 (5) | 0.029 (5) | 0.053 (5) | 0.000 (4) | 0.014 (4) | −0.003 (4) |
C13 | 0.059 (5) | 0.048 (7) | 0.055 (5) | −0.009 (4) | 0.016 (4) | −0.006 (4) |
C14 | 0.062 (5) | 0.032 (6) | 0.045 (5) | −0.010 (4) | 0.022 (4) | −0.011 (4) |
C15 | 0.080 (8) | 0.036 (6) | 0.032 (5) | −0.008 (5) | 0.016 (5) | 0.000 (4) |
C16 | 0.098 (11) | 0.047 (7) | 0.102 (13) | 0.010 (7) | −0.006 (10) | 0.007 (7) |
C17 | 0.065 (6) | 0.100 (14) | 0.074 (9) | −0.019 (6) | 0.023 (6) | −0.015 (9) |
O5 | 0.073 (5) | 0.028 (4) | 0.037 (4) | −0.002 (4) | 0.024 (4) | −0.004 (3) |
Geometric parameters (Å, º) top
S1—O1 | 1.518 (7) | C4—C5 | 1.347 (16) |
S1—C8 | 1.786 (11) | C5—H5 | 0.9300 |
S1—C9 | 1.822 (10) | C5—C6 | 1.396 (16) |
Mg1—O1i | 2.086 (7) | C7—H7A | 0.9600 |
Mg1—O1 | 2.086 (7) | C7—H7B | 0.9600 |
Mg1—O4i | 2.084 (7) | C7—H7C | 0.9600 |
Mg1—O4 | 2.084 (7) | C9—H9A | 0.9700 |
Mg1—N1i | 2.168 (8) | C9—H9B | 0.9700 |
Mg1—N1 | 2.168 (8) | C9—C10 | 1.497 (15) |
O2—C4 | 1.400 (15) | C10—C11 | 1.398 (15) |
O2—C7 | 1.450 (16) | C11—C12 | 1.394 (17) |
O3—C12 | 1.364 (16) | C11—C15 | 1.511 (16) |
O3—C16 | 1.421 (19) | C12—C13 | 1.410 (19) |
O4—H4A | 0.8729 | C13—C14 | 1.367 (19) |
O4—H4B | 0.8732 | C13—C17 | 1.528 (19) |
N1—C1 | 1.381 (14) | C14—H14 | 0.9300 |
N1—C8 | 1.310 (12) | C15—H15A | 0.9600 |
N2—C6 | 1.355 (14) | C15—H15B | 0.9600 |
N2—C8 | 1.333 (12) | C15—H15C | 0.9600 |
N3—C10 | 1.345 (14) | C16—H16A | 0.9600 |
N3—C14 | 1.350 (15) | C16—H16B | 0.9600 |
C1—C2 | 1.385 (16) | C16—H16C | 0.9600 |
C1—C6 | 1.442 (13) | C17—H17A | 0.9600 |
C2—H2 | 0.9300 | C17—H17B | 0.9600 |
C2—C3 | 1.392 (17) | C17—H17C | 0.9600 |
C3—H3 | 0.9300 | O5—H5A | 0.8500 |
C3—C4 | 1.433 (16) | O5—H5B | 0.8498 |
| | | |
O1—S1—C8 | 102.8 (4) | O2—C7—H7B | 109.5 |
O1—S1—C9 | 106.4 (4) | O2—C7—H7C | 109.5 |
C8—S1—C9 | 97.4 (5) | H7A—C7—H7B | 109.5 |
O1—Mg1—O1i | 180.0 | H7A—C7—H7C | 109.5 |
O1i—Mg1—N1i | 81.3 (3) | H7B—C7—H7C | 109.5 |
O1i—Mg1—N1 | 98.7 (3) | N1—C8—S1 | 118.7 (7) |
O1—Mg1—N1 | 81.3 (3) | N1—C8—N2 | 118.2 (9) |
O1—Mg1—N1i | 98.7 (3) | N2—C8—S1 | 122.9 (7) |
O4i—Mg1—O1 | 87.6 (3) | S1—C9—H9A | 109.3 |
O4i—Mg1—O1i | 92.4 (3) | S1—C9—H9B | 109.3 |
O4—Mg1—O1i | 87.6 (3) | H9A—C9—H9B | 108.0 |
O4—Mg1—O1 | 92.4 (3) | C10—C9—S1 | 111.7 (7) |
O4i—Mg1—O4 | 180.0 (5) | C10—C9—H9A | 109.3 |
O4i—Mg1—N1i | 87.3 (3) | C10—C9—H9B | 109.3 |
O4—Mg1—N1i | 92.7 (3) | N3—C10—C9 | 114.7 (9) |
O4—Mg1—N1 | 87.3 (3) | N3—C10—C11 | 122.5 (10) |
O4i—Mg1—N1 | 92.7 (3) | C11—C10—C9 | 122.7 (9) |
N1i—Mg1—N1 | 180.0 | C10—C11—C15 | 122.5 (11) |
S1—O1—Mg1 | 120.6 (4) | C12—C11—C10 | 118.3 (11) |
C4—O2—C7 | 117.9 (11) | C12—C11—C15 | 119.1 (11) |
C12—O3—C16 | 115.1 (12) | O3—C12—C11 | 120.3 (12) |
Mg1—O4—H4A | 110.4 | O3—C12—C13 | 119.9 (12) |
Mg1—O4—H4B | 111.0 | C11—C12—C13 | 119.8 (12) |
H4A—O4—H4B | 103.0 | C12—C13—C17 | 121.2 (13) |
C1—N1—Mg1 | 140.6 (6) | C14—C13—C12 | 116.6 (12) |
C8—N1—Mg1 | 116.1 (7) | C14—C13—C17 | 122.3 (13) |
C8—N1—C1 | 103.3 (8) | N3—C14—C13 | 125.4 (12) |
C8—N2—C6 | 103.3 (8) | N3—C14—H14 | 117.3 |
C10—N3—C14 | 117.3 (10) | C13—C14—H14 | 117.3 |
N1—C1—C2 | 131.9 (10) | C11—C15—H15A | 109.5 |
N1—C1—C6 | 107.1 (9) | C11—C15—H15B | 109.5 |
C2—C1—C6 | 121.0 (10) | C11—C15—H15C | 109.5 |
C1—C2—H2 | 120.8 | H15A—C15—H15B | 109.5 |
C1—C2—C3 | 118.4 (11) | H15A—C15—H15C | 109.5 |
C3—C2—H2 | 120.8 | H15B—C15—H15C | 109.5 |
C2—C3—H3 | 119.7 | O3—C16—H16A | 109.5 |
C2—C3—C4 | 120.5 (11) | O3—C16—H16B | 109.5 |
C4—C3—H3 | 119.7 | O3—C16—H16C | 109.5 |
O2—C4—C3 | 115.6 (10) | H16A—C16—H16B | 109.5 |
C5—C4—O2 | 123.7 (11) | H16A—C16—H16C | 109.5 |
C5—C4—C3 | 120.5 (11) | H16B—C16—H16C | 109.5 |
C4—C5—H5 | 119.6 | C13—C17—H17A | 109.5 |
C4—C5—C6 | 120.8 (11) | C13—C17—H17B | 109.5 |
C6—C5—H5 | 119.6 | C13—C17—H17C | 109.5 |
N2—C6—C1 | 108.0 (9) | H17A—C17—H17B | 109.5 |
N2—C6—C5 | 133.3 (9) | H17A—C17—H17C | 109.5 |
C5—C6—C1 | 118.7 (10) | H17B—C17—H17C | 109.5 |
O2—C7—H7A | 109.5 | H5A—O5—H5B | 104.5 |
Symmetry code: (i) −x+1, −y+1, −z+1. |
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