Synthesis and structure of clozapine N-oxide hemi(hydro­chloride): an infinite hydrogen-bonded poly[n]catenane

The recrystallization of clozapine N-oxide hydro­chloride from a range of solvents leads to the loss of half an equivalent of HCl and the formation of single crystals of a hydrogen-bond-linked poly[n]catenane of clozapine N-oxide hemi­hydro­chloride.

Key indicators

• Single-crystal synchrotron study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.049
• wR factor = 0.138
• Data-to-parameter ratio = 25.5

checkCIF/PLATON results

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Alert level A
DIFF019_ALERT_1_A  _diffrn_standards_number is missing
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Author Response: Rapid collection Synchrotron

DIFF020_ALERT_1_A  _diffrn_standards_interval_count and
            _diffrn_standards_interval_time are missing. Number of measurements
            between standards or time (min) between standards.

Author Response: Rapid collection Synchrotron

DIFF022_ALERT_1_A  _diffrn_standards_decay_% is missing
            Percentage decrease in standards intensity.

Author Response: Rapid collection Synchrotron

Alert level C
PLAT303_ALERT_2_C Full Occupancy Atom H1A       with # Connections       2.00 Check
PLAT480_ALERT_4_C Long H...A H-Bond Reported H15A     ..O1       .       2.64 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H15B     ..CL1      .       2.91 Ang.
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600         20 Report
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....         11 Note
PLAT918_ALERT_3_C Reflection(s) with I(obs) much Smaller I(calc) .          2 Check

Alert level G
ABSMU01_ALERT_1_G  Calculation of _exptl_absorpt_correction_mu
                not performed for this radiation type.
PLAT042_ALERT_1_G Calc. and Reported MoietyFormula Strings  Differ     Please Check
PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT  Unusually Large      11.46 Why ?
PLAT304_ALERT_4_G Non-Integer Number of Atoms in ..... (Resd  2  )       0.50 Check
PLAT605_ALERT_4_G Largest Solvent Accessible VOID in the Structure        483 A   3  
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600        845 Note
PLAT933_ALERT_2_G Number of HKL-OMIT Records in Embedded .res File          3 Note
PLAT952_ALERT_5_G Calculated (ThMax) and CIF-Reported Lmax Differ.          2 Units
PLAT958_ALERT_1_G Calculated (ThMax) and Actual (FCF) Lmax Differ.          2 Units
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          8 Info

   3 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   6 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  10 ALERT level G = General information/check it is not something unexpected

   6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   4 ALERT type 2 Indicator that the structure model may be wrong or deficient
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   5 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check


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PUBL024_ALERT_1_A The number of authors is greater than 5.
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Computing details

Data collection: AS QEGUI; cell refinement: XDS (Kabsch, 1993); data reduction: XDS (Kabsch, 1993); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: WinGX (Farrugia, 2012).

8-Chloro-11-(4-methyl-1-piperazinyl)-5H-dibenzo[b,e][1,4]diazepine N-oxide hemi(hydrochloride)

Crystal data

2C18H19ClN4O·HCl	Dx = 1.230 Mg m^−3
Mr = 722.10	Synchrotron radiation, λ = 0.710757 Å
Tetragonal, I4/m	Cell parameters from 5908 reflections
a = 17.305 (2) Å	θ = 1.4–31.8°
c = 26.040 (5) Å	µ = 0.28 mm^−1
V = 7798 (3) Å^3	T = 100 K
Z = 8	Block, yellow
F(000) = 3024	0.06 × 0.05 × 0.04 mm

Data collection

ADSC Quantum 210r diffractometer	5096 reflections with I > 2σ(I)
Radiation source: MX1 Beamline Australian Synchrotron	Rint = 0.049
Silicon Double Crystal monochromator	θmax = 31.8°, θmin = 1.4°
ω Scan scans	h = −25→25
66433 measured reflections	k = −25→25
5901 independent reflections	l = −36→36

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.049	w = 1/[σ^2(Fo^2) + (0.0661P)^2 + 11.4576P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.138	(Δ/σ)max = 0.001
S = 1.03	Δρmax = 0.81 e Å^−3
5901 reflections	Δρmin = −0.49 e Å^−3
231 parameters	Extinction correction: SHELXL2016/6 (Sheldrick 2015b), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0069 (5)

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.13932 (3)	0.04426 (2)	0.37292 (2)	0.03680 (13)
Cl2	0.16534 (4)	0.44691 (3)	0.500000	0.03563 (15)
O1	0.02559 (6)	0.43450 (7)	0.13599 (5)	0.0285 (2)
N3	0.17304 (7)	0.39022 (7)	0.21729 (5)	0.0225 (2)
N2	0.15846 (7)	0.30145 (7)	0.28157 (5)	0.0228 (2)
N1	0.18161 (8)	0.38441 (8)	0.37970 (5)	0.0261 (3)
N4	0.10378 (8)	0.43810 (8)	0.12165 (5)	0.0248 (3)
C1	0.23713 (9)	0.42470 (8)	0.35074 (6)	0.0242 (3)
C7	0.18814 (8)	0.36630 (8)	0.26780 (5)	0.0216 (3)
C2	0.24220 (8)	0.41696 (8)	0.29712 (6)	0.0228 (3)
C10	0.15645 (9)	0.18517 (9)	0.32919 (6)	0.0252 (3)
H10	0.150809	0.159189	0.298148	0.030*
C14	0.14157 (9)	0.46872 (8)	0.21112 (6)	0.0239 (3)
H14A	0.170572	0.504443	0.232387	0.029*
H14B	0.088144	0.469610	0.222369	0.029*
C9	0.16811 (8)	0.26540 (8)	0.32932 (6)	0.0228 (3)
C16	0.13708 (9)	0.35868 (9)	0.12884 (6)	0.0254 (3)
H16A	0.190585	0.358444	0.117741	0.030*
H16B	0.108830	0.322118	0.107741	0.030*
C15	0.14617 (9)	0.49399 (8)	0.15559 (6)	0.0245 (3)
H15A	0.123725	0.545067	0.152003	0.029*
H15B	0.199875	0.496810	0.145089	0.029*
C3	0.29823 (9)	0.46033 (9)	0.27067 (6)	0.0256 (3)
H3	0.302804	0.454729	0.235282	0.031*
C11	0.15328 (9)	0.14442 (9)	0.37477 (6)	0.0291 (3)
C5	0.33991 (10)	0.52005 (10)	0.34901 (7)	0.0317 (3)
H5	0.371497	0.554918	0.366272	0.038*
C8	0.17647 (9)	0.30343 (9)	0.37683 (6)	0.0253 (3)
C17	0.13260 (9)	0.33393 (8)	0.18470 (5)	0.0237 (3)
H17A	0.078931	0.330314	0.195175	0.028*
H17B	0.156037	0.283374	0.188721	0.028*
C6	0.28604 (9)	0.47695 (10)	0.37606 (6)	0.0291 (3)
H6	0.282259	0.482756	0.411475	0.035*
C4	0.34685 (9)	0.51128 (9)	0.29616 (7)	0.0294 (3)
H4	0.383731	0.539293	0.278039	0.035*
C13	0.17144 (12)	0.26047 (10)	0.42216 (6)	0.0352 (4)
H13	0.176053	0.285737	0.453531	0.042*
C12	0.15973 (11)	0.18114 (10)	0.42162 (7)	0.0361 (4)
H12	0.156323	0.153376	0.452117	0.043*
C18	0.10927 (11)	0.46237 (11)	0.06669 (6)	0.0345 (4)
H18A	0.079973	0.427372	0.045739	0.052*
H18B	0.162386	0.461630	0.056060	0.052*
H18C	0.088990	0.513702	0.062973	0.052*
H1	0.1789 (13)	0.3988 (13)	0.4114 (9)	0.037 (6)*
H1A	0.000000	0.500000	0.1357 (17)	0.077 (14)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0421 (2)	0.02417 (19)	0.0442 (2)	0.00136 (15)	0.01026 (17)	0.00663 (15)
Cl2	0.0513 (4)	0.0331 (3)	0.0224 (2)	0.0004 (2)	0.000	0.000
O1	0.0225 (5)	0.0313 (6)	0.0318 (6)	−0.0003 (4)	−0.0012 (4)	0.0007 (4)
N3	0.0265 (6)	0.0200 (5)	0.0210 (5)	−0.0002 (4)	−0.0015 (4)	−0.0017 (4)
N2	0.0234 (6)	0.0225 (5)	0.0224 (5)	0.0017 (4)	0.0001 (4)	−0.0013 (4)
N1	0.0321 (7)	0.0252 (6)	0.0211 (6)	0.0006 (5)	0.0007 (5)	−0.0034 (4)
N4	0.0263 (6)	0.0271 (6)	0.0210 (6)	−0.0012 (5)	0.0007 (4)	−0.0003 (4)
C1	0.0234 (6)	0.0237 (6)	0.0256 (7)	0.0024 (5)	−0.0024 (5)	−0.0013 (5)
C7	0.0216 (6)	0.0219 (6)	0.0214 (6)	0.0025 (5)	0.0000 (5)	−0.0024 (5)
C2	0.0219 (6)	0.0214 (6)	0.0249 (6)	0.0018 (5)	−0.0018 (5)	−0.0015 (5)
C10	0.0234 (6)	0.0241 (7)	0.0282 (7)	0.0020 (5)	0.0025 (5)	0.0007 (5)
C14	0.0272 (7)	0.0211 (6)	0.0233 (6)	0.0015 (5)	−0.0014 (5)	−0.0014 (5)
C9	0.0203 (6)	0.0236 (6)	0.0246 (6)	0.0021 (5)	0.0006 (5)	0.0006 (5)
C16	0.0286 (7)	0.0256 (7)	0.0220 (6)	−0.0001 (6)	0.0009 (5)	−0.0028 (5)
C15	0.0264 (7)	0.0228 (6)	0.0241 (6)	−0.0020 (5)	−0.0011 (5)	0.0003 (5)
C3	0.0239 (6)	0.0236 (6)	0.0293 (7)	0.0010 (5)	0.0000 (5)	−0.0010 (5)
C11	0.0286 (7)	0.0238 (7)	0.0349 (8)	0.0030 (6)	0.0051 (6)	0.0046 (6)
C5	0.0275 (7)	0.0284 (7)	0.0392 (9)	−0.0019 (6)	−0.0071 (6)	−0.0053 (6)
C8	0.0258 (7)	0.0257 (7)	0.0245 (7)	0.0022 (5)	−0.0009 (5)	0.0001 (5)
C17	0.0275 (7)	0.0230 (6)	0.0205 (6)	−0.0010 (5)	−0.0005 (5)	−0.0027 (5)
C6	0.0294 (7)	0.0304 (7)	0.0274 (7)	0.0016 (6)	−0.0056 (6)	−0.0055 (6)
C4	0.0233 (7)	0.0262 (7)	0.0387 (8)	−0.0019 (5)	−0.0006 (6)	−0.0014 (6)
C13	0.0494 (10)	0.0340 (8)	0.0224 (7)	0.0029 (7)	−0.0001 (7)	0.0013 (6)
C12	0.0477 (10)	0.0327 (8)	0.0279 (8)	0.0034 (7)	0.0032 (7)	0.0070 (6)
C18	0.0464 (9)	0.0368 (8)	0.0203 (7)	−0.0016 (7)	0.0000 (6)	0.0033 (6)

Geometric parameters (Å, º)

Cl1—C11	1.7506 (17)	C9—C8	1.409 (2)
O1—N4	1.4051 (17)	C16—C17	1.518 (2)
O1—H1A	1.2169 (12)	C16—H16A	0.9700
N3—C7	1.4035 (18)	C16—H16B	0.9700
N3—C17	1.4692 (18)	C15—H15A	0.9700
N3—C14	1.4723 (18)	C15—H15B	0.9700
N2—C7	1.2852 (19)	C3—C4	1.388 (2)
N2—C9	1.4012 (19)	C3—H3	0.9300
N1—C1	1.406 (2)	C11—C12	1.380 (2)
N1—C8	1.406 (2)	C5—C6	1.386 (2)
N1—H1	0.86 (2)	C5—C4	1.390 (2)
N4—C18	1.494 (2)	C5—H5	0.9300
N4—C15	1.5016 (19)	C8—C13	1.398 (2)
N4—C16	1.502 (2)	C17—H17A	0.9700
C1—C6	1.403 (2)	C17—H17B	0.9700
C1—C2	1.405 (2)	C6—H6	0.9300
C7—C2	1.492 (2)	C4—H4	0.9300
C2—C3	1.406 (2)	C13—C12	1.388 (3)
C10—C11	1.382 (2)	C13—H13	0.9300
C10—C9	1.403 (2)	C12—H12	0.9300
C10—H10	0.9300	C18—H18A	0.9600
C14—C15	1.513 (2)	C18—H18B	0.9600
C14—H14A	0.9700	C18—H18C	0.9600
C14—H14B	0.9700
N4—O1—H1A	107.9 (6)	N4—C15—H15A	109.5
C7—N3—C17	115.75 (12)	C14—C15—H15A	109.5
C7—N3—C14	116.31 (11)	N4—C15—H15B	109.5
C17—N3—C14	111.87 (11)	C14—C15—H15B	109.5
C7—N2—C9	126.07 (13)	H15A—C15—H15B	108.1
C1—N1—C8	120.58 (13)	C4—C3—C2	121.53 (15)
C1—N1—H1	114.0 (15)	C4—C3—H3	119.2
C8—N1—H1	109.5 (15)	C2—C3—H3	119.2
O1—N4—C18	109.17 (12)	C12—C11—C10	121.41 (15)
O1—N4—C15	110.03 (11)	C12—C11—Cl1	119.43 (13)
C18—N4—C15	110.59 (12)	C10—C11—Cl1	119.16 (13)
O1—N4—C16	107.20 (11)	C6—C5—C4	120.17 (15)
C18—N4—C16	110.61 (12)	C6—C5—H5	119.9
C15—N4—C16	109.18 (12)	C4—C5—H5	119.9
C6—C1—C2	119.37 (14)	C13—C8—N1	119.28 (14)
C6—C1—N1	118.67 (14)	C13—C8—C9	119.13 (15)
C2—C1—N1	121.88 (13)	N1—C8—C9	121.24 (13)
N2—C7—N3	116.40 (13)	N3—C17—C16	110.00 (12)
N2—C7—C2	128.37 (13)	N3—C17—H17A	109.7
N3—C7—C2	115.03 (12)	C16—C17—H17A	109.7
C1—C2—C3	118.60 (14)	N3—C17—H17B	109.7
C1—C2—C7	121.68 (13)	C16—C17—H17B	109.7
C3—C2—C7	119.68 (13)	H17A—C17—H17B	108.2
C11—C10—C9	120.58 (14)	C5—C6—C1	120.92 (15)
C11—C10—H10	119.7	C5—C6—H6	119.5
C9—C10—H10	119.7	C1—C6—H6	119.5
N3—C14—C15	110.58 (12)	C3—C4—C5	119.38 (15)
N3—C14—H14A	109.5	C3—C4—H4	120.3
C15—C14—H14A	109.5	C5—C4—H4	120.3
N3—C14—H14B	109.5	C12—C13—C8	121.79 (16)
C15—C14—H14B	109.5	C12—C13—H13	119.1
H14A—C14—H14B	108.1	C8—C13—H13	119.1
N2—C9—C10	114.92 (13)	C11—C12—C13	118.44 (15)
N2—C9—C8	125.70 (13)	C11—C12—H12	120.8
C10—C9—C8	118.63 (13)	C13—C12—H12	120.8
N4—C16—C17	110.97 (12)	N4—C18—H18A	109.5
N4—C16—H16A	109.4	N4—C18—H18B	109.5
C17—C16—H16A	109.4	H18A—C18—H18B	109.5
N4—C16—H16B	109.4	N4—C18—H18C	109.5
C17—C16—H16B	109.4	H18A—C18—H18C	109.5
H16A—C16—H16B	108.0	H18B—C18—H18C	109.5
N4—C15—C14	110.53 (12)
C8—N1—C1—C6	−127.64 (15)	C18—N4—C15—C14	−179.16 (13)
C8—N1—C1—C2	55.7 (2)	C16—N4—C15—C14	−57.23 (15)
C9—N2—C7—N3	177.72 (13)	N3—C14—C15—N4	57.38 (16)
C9—N2—C7—C2	3.2 (2)	C1—C2—C3—C4	−1.4 (2)
C17—N3—C7—N2	−6.69 (19)	C7—C2—C3—C4	176.48 (14)
C14—N3—C7—N2	127.72 (14)	C9—C10—C11—C12	1.4 (2)
C17—N3—C7—C2	168.54 (12)	C9—C10—C11—Cl1	−179.55 (11)
C14—N3—C7—C2	−57.05 (17)	C1—N1—C8—C13	132.81 (16)
C6—C1—C2—C3	2.0 (2)	C1—N1—C8—C9	−54.0 (2)
N1—C1—C2—C3	178.72 (13)	N2—C9—C8—C13	168.37 (15)
C6—C1—C2—C7	−175.82 (13)	C10—C9—C8—C13	−1.2 (2)
N1—C1—C2—C7	0.9 (2)	N2—C9—C8—N1	−4.9 (2)
N2—C7—C2—C1	−35.2 (2)	C10—C9—C8—N1	−174.45 (14)
N3—C7—C2—C1	150.21 (14)	C7—N3—C17—C16	−166.50 (12)
N2—C7—C2—C3	146.92 (15)	C14—N3—C17—C16	57.13 (16)
N3—C7—C2—C3	−27.63 (19)	N4—C16—C17—N3	−57.28 (16)
C7—N3—C14—C15	166.35 (12)	C4—C5—C6—C1	−0.8 (2)
C17—N3—C14—C15	−57.55 (16)	C2—C1—C6—C5	−1.0 (2)
C7—N2—C9—C10	−156.61 (14)	N1—C1—C6—C5	−177.76 (15)
C7—N2—C9—C8	33.5 (2)	C2—C3—C4—C5	−0.3 (2)
C11—C10—C9—N2	−170.69 (14)	C6—C5—C4—C3	1.4 (2)
C11—C10—C9—C8	0.0 (2)	N1—C8—C13—C12	174.49 (17)
O1—N4—C16—C17	−61.75 (15)	C9—C8—C13—C12	1.1 (3)
C18—N4—C16—C17	179.32 (13)	C10—C11—C12—C13	−1.5 (3)
C15—N4—C16—C17	57.41 (16)	Cl1—C11—C12—C13	179.46 (14)
O1—N4—C15—C14	60.16 (15)	C8—C13—C12—C11	0.2 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O1^i	1.22 (1)	1.22 (1)	2.434 (2)	179 (4)
N1—H1···Cl2	0.86 (2)	2.46 (2)	3.3259 (14)	176 (2)
C15—H15A···O1^i	0.97	2.64	3.2598 (19)	122
C15—H15A···N1^ii	0.97	2.51	3.416 (2)	156
C15—H15B···Cl1^iii	0.97	2.91	3.8431 (17)	162

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