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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2024 Jan 31;80(Pt 2):223–227. doi: 10.1107/S2056989024000835

Crystal structure and Hirshfeld surface analysis of 4-(2-chloro­eth­yl)-5-methyl-1,2-di­hydro­pyrazol-3-one

Farid N Naghiyev a, Victor N Khrustalev b,c, Mehmet Akkurt d, Evgeny A Dukhnovsky b, Ajaya Bhattarai e,*, Ali N Khalilov f,a, İbrahim G Mamedov a
Editor: X Haog
PMCID: PMC10848985  PMID: 38333121

In the crystal, mol­ecular pairs form dimers through N—H⋯O hydrogen bonds. These dimers are linked into ribbons parallel to the (100) plane by further N—H⋯O hydrogen bonds. In addition, π–π and C—Cl⋯π inter­actions between the ribbons form layers parallel to the (100) plane.

Keywords: crystal structure, hydrogen bonds, dimers, pyrazole ring, Hirshfeld surface analysis

Abstract

In the crystal of the title compound, C6H9ClN2O, mol­ecular pairs form dimers with an R 2 2(8) motif through N—H⋯O hydrogen bonds. These dimers are connect into ribbons parallel to the (100) plane with R 4 4(10) motifs by N—H⋯O hydrogen bonds along the c-axis direction. In addition, π–π [centroid-to-centroid distance = 3.4635 (9) Å] and C—Cl⋯π inter­actions between the ribbons form layers parallel to the (100) plane. The three-dimensional consolidation of the crystal structure is also ensured by Cl⋯H and Cl⋯Cl inter­actions between these layers. According to a Hirshfeld surface study, H⋯H (43.3%), Cl⋯H/H⋯Cl (22.1%) and O⋯H/H⋯O (18.7%) inter­actions are the most significant contributors to the crystal packing.

1. Chemical context

Nitro­gen-based heterocyclic compounds are an important branch of organic chemistry. These systems have received increasing attention over the past two decades. Synthetic chemistry is growing extensively with recently developed heterocyclic systems for various research and commercial purposes (Maharramov et al., 2021, 2022; Erenler et al., 2022; Akkurt et al., 2023). These systems have found wide applications in diverse branches of chemistry, including the chemistry of coordination compounds (Gurbanov et al., 2021; Mahmoudi et al., 2021), drug development (Donmez & Turkyılmaz, 2022; Askerova, 2022) and material science (Velásquez et al., 2019; Afkhami et al., 2019). The pyrazole motif is the most widespread five-membered heteroaromatic ring system in nitro­gen heterocycles. It is an essential structural motif present in many natural bioactive mol­ecules such as l-α-amino-β-(pyrazolyl-N)-propanoic acid, withasomnine, pyrazofurin, pyrazofurin B, formycin, formycin B, oxoformycin B, nostocine A, fluviols (A, B, C, D and E), pyrazole-3(5)-carb­oxy­lic acid, 4-Methyl pyrazole-3(5)-carb­oxy­lic acid, 3-n-nonyl­pyrazole (Khalilov et al., 2022; Kumar et al., 2013; Sobhi & Faisal, 2023). The pyrazole ring incorporating derivatives with various biological activities (Singh et al., 2023), such as anti­convulsant, anti­diabetic, anti-inflammatory, anti­oxidant, anti­cancer, anti­tubercular, anti­ulcer activities and other properties has been reviewed recently (Fig. 1).

Figure 1.

Figure 1

The biological activities of compounds incorporating the pyrazole motif.

On the other hand, the incorporation of various pharmacophore groups in a pyrazole scaffold has led to the development of best-selling drugs such as ibrutinib, ruxolitinib, axitinib, niraparib and baricitinib (Atalay et al., 2022; Alam, 2023). Thus, in the framework of our studies in heterocyclic chemistry (Naghiyev et al., 2020, 2021, 2022), we herein report the crystal structure and Hirshfeld surface analysis of the title compound, 4-(2-chloro­eth­yl)-5-methyl-1,2-di­hydro­pyrazol-3-one, for which the proposed reaction mechanism is shown in Fig. 2. 1.

Figure 2.

Figure 2

The proposed reaction mechanism for the formation of the title compound.

2. Structural commentary

In the title compound (Fig. 3), the pyrazoline ring (N1/N2/C3–C5) has an essentially planar conformation [maximum deviation = 0.006 (1) Å for N1]. The C3—C4—C7—C8 and C4—C7—C8—Cl1 torsion angles are 105.67 (19) and 172.38 (11)°, respectively. The geometric parameters of the title compound are normal and comparable to those of related compounds given in the Database survey section.

Figure 3.

Figure 3

The mol­ecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features and Hirshfeld surface analysis

In the crystal, mol­ecular pairs form dimers with an Inline graphic (8) motif (Bernstein et al., 1995) through N—H⋯O hydrogen bonds (Table 1 and Fig. 4). These dimers are also connected into ribbons parallel to the (100) plane by forming N—H⋯O hydrogen bonds with Inline graphic (10) motifs along the c-axis direction (Figs. 5 and 6). In addition, π–π [Cg1⋯Cg1i = 3.4635 (9) Å, slippage = 0.511 Å; symmetry code: (i) − x, 1 − y, 1 − z; Cg1 is a centroid of the pyrazole ring (N1/N2/C3–C5)] and C—Cl⋯π [C8—Cl1⋯Cg1ii: C8—Cl1 = 1.8040 (18) Å, Cl1⋯Cg1ii = 3.8386 (8) Å, C8—Cl1⋯Cg1ii = 84.57 (6)°; symmetry code: (ii) x, Inline graphic  − y, Inline graphic  + z] inter­actions between the ribbons form layers parallel to the (100) plane. The three-dimensional consolidation of the crystal structure is also ensured by the Cl⋯H and Cl⋯Cl inter­actions [(C8)Cl1⋯H6B iii = 3.12 (3) Å, C8—Cl1⋯H6B iii = 135.3 (6)° and (C8)Cl1⋯Cl1iv = 3.5071 (7) Å, C8—Cl1⋯Cl1iv = 161.79 (7)°; symmetry codes: (iii) 1 − x, Inline graphic  + y, Inline graphic  − z; (iv) 1 − x, 1 − y, 2 − z] between these layers (Table 2; Fig. 7).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1i 0.88 (3) 1.81 (3) 2.6861 (18) 174 (2)
N2—H2⋯O1ii 0.92 (3) 1.75 (3) 2.6772 (17) 177 (2)

Symmetry codes: (i) Inline graphic ; (ii) Inline graphic .

Figure 4.

Figure 4

View of the N—H⋯O hydrogen bonds of the title compound down the a-axis.

Figure 5.

Figure 5

View of the N—H⋯O hydrogen bonds of the title compound down the b-axis.

Figure 6.

Figure 6

View of the N—H⋯O hydrogen bonds of the title compound down the c-axis.

Table 2. Summary of short inter­atomic contacts (Å) in the title compound.

Cl1⋯H6B 3.12 1 − x, Inline graphic  + y, Inline graphic  − z
Cl1⋯Cl1 3.51 1 − x, 1 − y, 2 − z
H1⋯O1 1.80 x, 2 − y, 1 − z
H6C⋯O1 2.89 x, 1 − y, 1 − z
O1⋯H2 1.76 x, Inline graphic  − y, Inline graphic  + z
H6A⋯H7B 2.60 x, Inline graphic  − y, − Inline graphic  + z

Figure 7.

Figure 7

View of the π-π- and C—Cl⋯π inter­actions of the title compound down the b-axis.

To qu­antify the inter­molecular inter­actions in the crystal, two-dimensional fingerprint plots and Hirshfeld surfaces were produced using Crystal Explorer 17.5 (Spackman et al., 2021). Fig. 8 shows the mapping of the Hirshfeld surfaces over d norm in the range −0.7296 (red) to +1.3271 (blue) a.u. The inter­actions given in Tables 1 and 2 play a key role in the mol­ecular packing of the title compound. H⋯H is the most significant inter­atomic contact because it contributes the most to the crystal packing (43.3%, Fig. 9 b). Other significant contributions are made by Cl⋯H/H⋯Cl (22.1%, Fig. 9 c) and O⋯H/H⋯O (18.7%, Fig. 9 d) inter­actions. The following inter­actions make minor contributions: Cl⋯C/C⋯Cl (2.4%), C⋯H/H⋯C (2.6%), N⋯H/H⋯N (4.3%), N⋯C/C⋯N (3.4%), Cl⋯N/N⋯Cl (0.7%), and C⋯C (0.7%).

Figure 8.

Figure 8

(a) Front and (b) back sides of the three-dimensional Hirshfeld surface of the title compound mapped over d norm, with a fixed colour scale of −0.7296 to +1.3271 a.u.

Figure 9.

Figure 9

The two-dimensional fingerprint plots of the title compound, showing (a) all inter­actions, and delineated into (b) H⋯H, (c) Cl⋯H/H⋯Cl and (d) O⋯H/H⋯O inter­actions. [d e and d i represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (inter­nal) the surface, respectively].

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.43, last update November 2022; Groom et al., 2016) for the central five-membered ring 2,3-di­hydro-1H-pyrazole yielded six compounds related to the title compound, viz. 3-methyl-5-(3-methyl­phen­oxy)-1-phenyl-1H-pyrazole-4-carb­aldehyde (CSD refcode TERZAV; Archana, et al., 2022), N-{3-cyano-1-[2,6-di­chloro-4-(tri­fluoro­meth­yl)phen­yl]-4-(ethyl­sulf­an­yl)-1H-pyrazol-5-yl}-2,2,2-tri­fluoro­acetamide (FERPOL; Priyanka et al., 2022), 4-[3-(4-hy­droxy­phen­yl)-4,5-di­hydro-1H-pyrazol-5-yl]-2-meth­oxy­phenol monohydrate (KOXGAI; Duong Khanh et al., 2019), 5-chloro-N 1-(5-phenyl-1H-pyrazol-3-yl)benzene-1,2-di­amine (CAXZUZ; Yartsev et al., 2017), 5-(butyl­amino)-3-methyl-1-(pyridin-2-yl)-1H-pyrazole-4-carbaldehyde (EYEHEX; Macías et al., 2016) and 5-amino-1-(2-chloro­phen­yl)-1H-pyrazole-4-carbo­nitrile (AFIJOP; Lin et al., 2007).

The mol­ecular packing of TERZAV features aromatic π–π stacking and weak C—H⋯π inter­actions. In the crystal of FERPOL, strong N—H⋯O hydrogen bonds link the mol­ecules into chains that extend parallel to the a-axis. In the crystal of KOXGAI, the mol­ecules are connected into chains running in the b-axis direction by O—H⋯N hydrogen bonding. Parallel chains inter­act through N—H⋯O hydrogen bonds and π–π stacking of the tris­ubstituted phenyl rings. In the crystal of CAXZUZ, the A and B mol­ecules are linked by two pairs of N—H⋯N hydrogen bonds, forming AB dimers. These are further linked by a fifth N—H⋯N hydrogen bond, forming tetra­mer-like units that stack along the a-axis direction, forming columns, which are in turn linked by C—H⋯π inter­actions, forming layers parallel to the ac plane. The supra­molecular structure of EYEHEX assembly has a three-dimensional arrangement controlled mainly by weak C—H⋯O and C—H⋯π inter­actions. The crystal structure of AFIJOP is consolidated by two N—H⋯N hydrogen bonds.

5. Synthesis and crystallization

Aceto­acetic ether (7.7 mmol), di­chloro­ethane (7.7 mmol) and hydrazine hydrate (15.4 mmol) were dissolved in 40 ml of ethanol and the reaction mixture was refluxed for 4 h. Then the reaction mixture was cooled to room temperature with the formation of white crystals. The crystals were separated by filtration and recrystallized from an ethanol–water mixture (m.p. 499–500 K, yield 78%).

1H NMR (300 MHz, DMSO-d 6, ppm.): 2.06 (s, 3H, CH3); 2.64 (t, 2H, CH2, H-H J 2 = 7.2); 3.49 (s, 2H, 2NH); 3.58 (t, 2H, ClCH2, H-H J 2 = 7.2). 13C NMR (75 MHz, DMSO-d 6, ppm.): 10.28 (CH3), 26.02 (CH2), 44.91 (CH2Cl), 97.63 (C tert. =), 160.12 (HN—C tert. =), 162.34 (N—C=O).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. The C-bound H atoms were placed in calculated positions (0.95–0.99 Å) and refined as riding with U iso(H) = 1.2 or 1.5U eq(C). The N-bound H atoms were located in a difference map and freely refined.

Table 3. Experimental details.

Crystal data
Chemical formula C6H9ClN2O
M r 160.60
Crystal system, space group Monoclinic, P21/c
Temperature (K) 100
a, b, c (Å) 9.8420 (2), 6.9145 (2), 11.1807 (2)
β (°) 93.618 (2)
V3) 759.36 (3)
Z 4
Radiation type Cu Kα
μ (mm−1) 3.92
Crystal size (mm) 0.20 × 0.12 × 0.06
 
Data collection
Diffractometer XtaLAB Synergy, Dualflex, HyPix
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2022)
T min, T max 0.513, 0.750
No. of measured, independent and observed [I > 2σ(I)] reflections 6642, 1532, 1467
R int 0.027
(sin θ/λ)max−1) 0.633
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.036, 0.097, 1.05
No. of reflections 1532
No. of parameters 127
H-atom treatment All H-atom parameters refined
Δρmax, Δρmin (e Å−3) 0.28, −0.41

Computer programs: CrysAlis PRO (Rigaku OD, 2022), SHELXT (Sheldrick, 2015a ), SHELXL (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012) and PLATON (Spek, 2020).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989024000835/nx2004sup1.cif

e-80-00223-sup1.cif (219.1KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989024000835/nx2004Isup2.hkl

e-80-00223-Isup2.hkl (123.7KB, hkl)

Supporting information file. DOI: 10.1107/S2056989024000835/nx2004Isup3.cml

CCDC reference: 2327646

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

Authors contributions are as follows. Conceptualization, IGM, ANK and EAD; methodology, AB and MA; investigation, VNK and FNN; writing (original draft), MA, AB and ANK; writing (review and editing of the manuscript), MA and ANK; visualization, MA, IGM and FNN; funding acquisition, VNK, AB and FNN; resources, AB, VNK and MA; supervision, MA and ANK.

supplementary crystallographic information

Crystal data

C6H9ClN2O F(000) = 336
Mr = 160.60 Dx = 1.405 Mg m3
Monoclinic, P21/c Cu Kα radiation, λ = 1.54184 Å
a = 9.8420 (2) Å Cell parameters from 4592 reflections
b = 6.9145 (2) Å θ = 4.5–77.6°
c = 11.1807 (2) Å µ = 3.92 mm1
β = 93.618 (2)° T = 100 K
V = 759.36 (3) Å3 Prism, colourless
Z = 4 0.20 × 0.12 × 0.06 mm

Data collection

XtaLAB Synergy, Dualflex, HyPix diffractometer 1467 reflections with I > 2σ(I)
Radiation source: micro-focus sealed X-ray tube Rint = 0.027
ω scans θmax = 77.5°, θmin = 4.5°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2022) h = −12→12
Tmin = 0.513, Tmax = 0.750 k = −8→7
6642 measured reflections l = −14→8
1532 independent reflections

Refinement

Refinement on F2 Primary atom site location: difference Fourier map
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036 Hydrogen site location: difference Fourier map
wR(F2) = 0.097 All H-atom parameters refined
S = 1.05 w = 1/[σ2(Fo2) + (0.0501P)2 + 0.606P] where P = (Fo2 + 2Fc2)/3
1532 reflections (Δ/σ)max = 0.001
127 parameters Δρmax = 0.28 e Å3
0 restraints Δρmin = −0.41 e Å3

Special details

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)

x y z Uiso*/Ueq
Cl1 0.45324 (5) 0.61848 (7) 0.86496 (4) 0.03447 (18)
O1 0.06705 (13) 0.89161 (17) 0.64445 (10) 0.0231 (3)
N1 0.05777 (14) 0.7905 (2) 0.44644 (12) 0.0197 (3)
H1 0.013 (3) 0.890 (4) 0.413 (2) 0.040 (7)*
N2 0.11129 (14) 0.6437 (2) 0.38217 (12) 0.0195 (3)
H2 0.096 (2) 0.636 (3) 0.300 (2) 0.038 (6)*
C3 0.18687 (16) 0.5302 (2) 0.45765 (14) 0.0189 (3)
C4 0.18362 (16) 0.6035 (2) 0.57245 (14) 0.0181 (3)
C5 0.10154 (16) 0.7717 (2) 0.56311 (13) 0.0188 (3)
C6 0.2560 (2) 0.3553 (3) 0.41307 (16) 0.0254 (4)
H6A 0.282 (3) 0.372 (4) 0.331 (3) 0.058 (8)*
H6B 0.338 (3) 0.328 (5) 0.458 (3) 0.065 (9)*
H6C 0.205 (3) 0.250 (5) 0.414 (3) 0.066 (9)*
C7 0.25721 (17) 0.5342 (2) 0.68559 (14) 0.0205 (3)
H7A 0.194 (2) 0.527 (3) 0.7508 (18) 0.021 (5)*
H7B 0.295 (2) 0.406 (3) 0.676 (2) 0.029 (5)*
C8 0.37260 (18) 0.6724 (3) 0.71941 (16) 0.0254 (4)
H8A 0.340 (2) 0.807 (4) 0.724 (2) 0.031 (6)*
H8B 0.443 (2) 0.665 (4) 0.664 (2) 0.037 (6)*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Cl1 0.0401 (3) 0.0366 (3) 0.0249 (3) 0.00431 (18) −0.01242 (19) −0.00157 (17)
O1 0.0374 (7) 0.0209 (6) 0.0110 (5) 0.0082 (5) 0.0007 (5) −0.0010 (4)
N1 0.0297 (7) 0.0180 (7) 0.0114 (6) 0.0045 (5) 0.0008 (5) −0.0006 (5)
N2 0.0278 (7) 0.0194 (7) 0.0115 (7) 0.0026 (5) 0.0013 (5) −0.0028 (5)
C3 0.0237 (7) 0.0179 (7) 0.0153 (7) −0.0011 (6) 0.0027 (6) 0.0008 (6)
C4 0.0238 (7) 0.0177 (7) 0.0128 (7) 0.0008 (6) 0.0024 (6) 0.0017 (6)
C5 0.0273 (8) 0.0183 (7) 0.0110 (7) −0.0002 (6) 0.0023 (6) 0.0003 (6)
C6 0.0333 (9) 0.0233 (8) 0.0198 (9) 0.0057 (7) 0.0033 (7) −0.0036 (7)
C7 0.0280 (8) 0.0192 (8) 0.0144 (8) 0.0036 (6) 0.0015 (6) 0.0016 (6)
C8 0.0264 (8) 0.0315 (9) 0.0180 (8) 0.0006 (7) −0.0019 (6) 0.0029 (7)

Geometric parameters (Å, º)

Cl1—C8 1.8040 (18) C4—C7 1.496 (2)
O1—C5 1.2920 (19) C6—H6A 0.97 (3)
N1—C5 1.354 (2) C6—H6B 0.95 (3)
N1—N2 1.3685 (19) C6—H6C 0.88 (3)
N1—H1 0.88 (3) C7—C8 1.514 (2)
N2—C3 1.342 (2) C7—H7A 0.99 (2)
N2—H2 0.92 (3) C7—H7B 0.97 (2)
C3—C4 1.382 (2) C8—H8A 0.99 (2)
C3—C6 1.489 (2) C8—H8B 0.95 (2)
C4—C5 1.416 (2)
C5—N1—N2 108.95 (13) H6A—C6—H6B 105 (2)
C5—N1—H1 126.8 (17) C3—C6—H6C 113 (2)
N2—N1—H1 123.6 (17) H6A—C6—H6C 107 (3)
C3—N2—N1 108.66 (13) H6B—C6—H6C 107 (3)
C3—N2—H2 129.9 (15) C4—C7—C8 108.91 (14)
N1—N2—H2 121.4 (15) C4—C7—H7A 110.2 (12)
N2—C3—C4 108.96 (14) C8—C7—H7A 110.3 (12)
N2—C3—C6 120.74 (15) C4—C7—H7B 111.5 (13)
C4—C3—C6 130.29 (15) C8—C7—H7B 108.6 (13)
C3—C4—C5 106.22 (14) H7A—C7—H7B 107.3 (18)
C3—C4—C7 128.97 (15) C7—C8—Cl1 112.04 (12)
C5—C4—C7 124.69 (14) C7—C8—H8A 111.5 (13)
O1—C5—N1 122.31 (15) Cl1—C8—H8A 105.7 (13)
O1—C5—C4 130.49 (14) C7—C8—H8B 111.5 (15)
N1—C5—C4 107.19 (13) Cl1—C8—H8B 106.1 (15)
C3—C6—H6A 111.6 (17) H8A—C8—H8B 109.7 (19)
C3—C6—H6B 111.9 (19)
C5—N1—N2—C3 0.98 (18) N2—N1—C5—C4 −1.24 (18)
N1—N2—C3—C4 −0.30 (18) C3—C4—C5—O1 179.99 (17)
N1—N2—C3—C6 178.79 (15) C7—C4—C5—O1 −3.7 (3)
N2—C3—C4—C5 −0.45 (18) C3—C4—C5—N1 1.04 (18)
C6—C3—C4—C5 −179.43 (17) C7—C4—C5—N1 177.36 (15)
N2—C3—C4—C7 −176.56 (16) C3—C4—C7—C8 105.67 (19)
C6—C3—C4—C7 4.5 (3) C5—C4—C7—C8 −69.8 (2)
N2—N1—C5—O1 179.70 (15) C4—C7—C8—Cl1 172.38 (11)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
N1—H1···O1i 0.88 (3) 1.81 (3) 2.6861 (18) 174 (2)
N2—H2···O1ii 0.92 (3) 1.75 (3) 2.6772 (17) 177 (2)

Symmetry codes: (i) −x, −y+2, −z+1; (ii) x, −y+3/2, z−1/2.

Funding Statement

This paper was supported by Baku State University and the RUDN University Strategic Academic Leadership Program.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989024000835/nx2004sup1.cif

e-80-00223-sup1.cif (219.1KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989024000835/nx2004Isup2.hkl

e-80-00223-Isup2.hkl (123.7KB, hkl)

Supporting information file. DOI: 10.1107/S2056989024000835/nx2004Isup3.cml

CCDC reference: 2327646

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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