Crystal structure, Hirshfeld surface analysis and energy framework calculation of the first oxoanion salt containing 1,3-cyclo­hexa­nebis(methyl­ammonium): [3-(aza­niumylmeth­yl)cyclo­hex­yl]methanaminium dinitrate

Chebbi, H.; Mezrigui, S.; Ben Jomaa, M.; Zid, M.F.

doi:10.1107/S2056989018008381

Crystal structure, Hirshfeld surface analysis and energy framework calculation of the first oxoanion salt containing 1,3-cyclohexanebis(methylammonium): [3-(azaniumylmethyl)cyclohexyl]methanaminium dinitrate

H. Chebbi, S. Mezrigui, M. Ben Jomaa and M. F. Zid

In the organic cation of the title salt, the cyclohexane ring is in chair conformation with the two methylammonium substituents in the equatorial positions. The crystal structure features extensive hydrogen-bonding interactions.

Keywords: oxoanion salt; crystal structure; organic dinitrate; Hirshfeld surface; fingerprint plots; energy framework.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989018008381/xu5926sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S2056989018008381/xu5926Isup2.hkl Contains datablock I
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989018008381/xu5926Isup3.cml Supplementary material

CCDC reference: 1847743

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.005 Å
R factor = 0.062
wR factor = 0.173
Data-to-parameter ratio = 15.9

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT026_ALERT_3_B Ratio Observed / Unique Reflections (too) Low ..        33% Check

Author Response: ...The crystal of limited quality does not diffract X-ray well and hence the numbers of observed reflections are rather low.


Alert level C
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of         N3 Check
PLAT242_ALERT_2_C Low    'MainMol' Ueq as Compared to Neighbors of         N4 Check
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............      0.005 Ang.
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1 Note
              C8 H20 N2
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......     25.184 Check
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.209 Check
PLAT978_ALERT_2_C Number C-C Bonds with Positive Residual Density.          0 Info

Alert level G
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT790_ALERT_4_G Centre of Gravity not Within Unit Cell: Resd.  #          3 Note
              N O3
PLAT793_ALERT_4_G Model has Chirality at C1          (Centro SPGR)          R Verify
PLAT793_ALERT_4_G Model has Chirality at C3          (Centro SPGR)          S Verify
PLAT951_ALERT_5_G Calculated (ThMax) and CIF-Reported Kmax Differ           2 Units
PLAT952_ALERT_5_G Calculated (ThMax) and CIF-Reported Lmax Differ          -2 Units
PLAT954_ALERT_1_G Reported (CIF) and Actual (FCF) Kmax Differ by .          2 Units
PLAT955_ALERT_1_G Reported (CIF) and Actual (FCF) Lmax Differ by .          2 Units

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

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

Computing details top

Data collection: CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); cell refinement: CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2006) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).

[3-(Azaniumylmethyl)cyclohexyl]methanaminium dinitrate top

Crystal data top

C₈H₂₀N₂²⁺·2NO₃⁻	D_x = 1.299 Mg m⁻³
M_r = 268.28	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 25 reflections
a = 10.475 (4) Å	θ = 11–15°
b = 16.884 (4) Å	µ = 0.11 mm⁻¹
c = 15.514 (2) Å	T = 293 K
V = 2743.8 (13) Å³	Plate, colorless
Z = 8	0.52 × 0.40 × 0.15 mm
F(000) = 1152

Data collection top

Enraf–Nonius CAD-4 diffractometer	991 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.036
Graphite monochromator	θ_max = 27.0°, θ_min = 2.4°
ω/2θ scans	h = −13→2
Absorption correction: ψ scan (North et al., 1968)	k = −1→19
T_min = 0.946, T_max = 1.000	l = −1→21
3798 measured reflections	2 standard reflections every 120 reflections
2980 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.062	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.173	w = 1/[σ²(F_o²) + (0.063P)²] where P = (F_o² + 2F_c²)/3
S = 0.98	(Δ/σ)_max < 0.001
2980 reflections	Δρ_max = 0.17 e Å⁻³
187 parameters	Δρ_min = −0.13 e Å⁻³

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.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > 2sigma(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.5381 (5)	0.0463 (2)	0.6598 (3)	0.0659 (10)
H1A	0.601 (4)	0.058 (2)	0.694 (3)	0.081 (16)*
H1B	0.550 (3)	0.080 (2)	0.611 (2)	0.085 (13)*
H1C	0.471 (4)	0.059 (3)	0.690 (3)	0.096 (19)*
N2	0.4634 (5)	−0.1776 (3)	1.0032 (3)	0.0674 (10)
H2D	0.534 (4)	−0.178 (3)	1.016 (3)	0.081 (19)*
H2E	0.431 (4)	−0.155 (2)	1.057 (3)	0.098 (15)*
H2F	0.426 (5)	−0.230 (3)	1.002 (3)	0.16 (2)*
C1	0.5681 (4)	−0.0935 (2)	0.7032 (2)	0.0606 (10)
H1	0.6549	−0.0819	0.7232	0.073*
C2	0.4800 (4)	−0.0856 (2)	0.7804 (2)	0.0652 (11)
H2A	0.4832	−0.0316	0.8016	0.078*
H2B	0.3930	−0.0965	0.7626	0.078*
C3	0.5166 (4)	−0.1416 (2)	0.8520 (2)	0.0601 (10)
H3	0.6037	−0.1279	0.8695	0.072*
C4	0.5197 (4)	−0.2269 (2)	0.8201 (2)	0.0652 (11)
H4A	0.5512	−0.2610	0.8657	0.078*
H4B	0.4338	−0.2437	0.8058	0.078*
C5	0.6040 (4)	−0.2355 (2)	0.7419 (2)	0.0784 (12)
H5A	0.6920	−0.2259	0.7583	0.094*
H5B	0.5979	−0.2893	0.7204	0.094*
C6	0.5673 (4)	−0.1791 (2)	0.6718 (2)	0.0741 (12)
H6A	0.4826	−0.1923	0.6510	0.089*
H6B	0.6264	−0.1845	0.6241	0.089*
C7	0.5393 (4)	−0.0372 (2)	0.6311 (2)	0.0701 (11)
H7A	0.6030	−0.0436	0.5862	0.084*
H7B	0.4568	−0.0503	0.6066	0.084*
C8	0.4321 (4)	−0.1278 (2)	0.9289 (2)	0.0710 (11)
H8A	0.4386	−0.0727	0.9458	0.085*
H8B	0.3442	−0.1377	0.9123	0.085*
N3	0.2781 (4)	−0.09045 (18)	0.1598 (2)	0.0718 (9)
O1	0.2195 (3)	−0.10116 (18)	0.0922 (2)	0.1032 (11)
O2	0.2248 (3)	−0.06216 (17)	0.22373 (18)	0.0826 (9)
O3	0.3922 (3)	−0.1097 (2)	0.16492 (19)	0.1031 (11)
N4	0.7872 (4)	−0.1535 (2)	0.0224 (2)	0.0685 (9)
O4	0.7259 (3)	−0.09475 (18)	0.0414 (3)	0.1171 (12)
O5	0.9065 (3)	−0.15214 (15)	0.02450 (17)	0.0747 (8)
O6	0.7335 (3)	−0.21487 (18)	0.0004 (2)	0.1000 (11)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.070 (3)	0.063 (3)	0.065 (2)	−0.009 (2)	0.001 (3)	0.010 (2)
N2	0.071 (3)	0.078 (3)	0.054 (2)	0.000 (2)	0.001 (2)	0.0046 (19)
C1	0.064 (3)	0.059 (2)	0.058 (2)	−0.004 (2)	0.004 (2)	−0.001 (2)
C2	0.073 (3)	0.056 (2)	0.066 (2)	0.009 (2)	0.005 (2)	0.0013 (19)
C3	0.062 (2)	0.058 (2)	0.060 (2)	0.005 (2)	0.000 (2)	0.009 (2)
C4	0.072 (3)	0.054 (2)	0.069 (2)	0.003 (2)	0.000 (2)	0.0053 (19)
C5	0.098 (3)	0.058 (2)	0.080 (3)	0.013 (2)	0.011 (3)	−0.001 (2)
C6	0.091 (3)	0.062 (2)	0.070 (3)	0.003 (2)	0.016 (2)	0.000 (2)
C7	0.084 (3)	0.063 (3)	0.063 (2)	0.000 (2)	0.007 (2)	0.000 (2)
C8	0.076 (3)	0.071 (2)	0.066 (2)	0.012 (2)	0.007 (2)	0.007 (2)
N3	0.074 (3)	0.068 (2)	0.074 (3)	0.001 (2)	0.005 (2)	−0.0120 (19)
O1	0.092 (2)	0.140 (3)	0.078 (2)	0.009 (2)	−0.0104 (19)	−0.0334 (19)
O2	0.081 (2)	0.0903 (19)	0.0764 (18)	0.0065 (17)	0.0102 (17)	−0.0262 (16)
O3	0.074 (2)	0.140 (3)	0.096 (2)	0.028 (2)	−0.0052 (19)	−0.033 (2)
N4	0.070 (3)	0.075 (2)	0.060 (2)	−0.003 (2)	−0.016 (2)	0.0003 (19)
O4	0.091 (2)	0.095 (2)	0.165 (3)	0.024 (2)	−0.026 (2)	−0.042 (2)
O5	0.071 (2)	0.082 (2)	0.0709 (18)	−0.0077 (16)	−0.0064 (16)	−0.0090 (14)
O6	0.084 (2)	0.0728 (17)	0.143 (3)	−0.0103 (17)	−0.033 (2)	−0.0060 (18)

Geometric parameters (Å, º) top

N1—C7	1.479 (5)	C4—C5	1.507 (5)
N1—H1A	0.87 (4)	C4—H4A	0.9700
N1—H1B	0.95 (4)	C4—H4B	0.9700
N1—H1C	0.87 (5)	C5—C6	1.496 (5)
N2—C8	1.464 (5)	C5—H5A	0.9700
N2—H2D	0.77 (4)	C5—H5B	0.9700
N2—H2E	0.99 (4)	C6—H6A	0.9700
N2—H2F	0.96 (6)	C6—H6B	0.9700
C1—C7	1.499 (5)	C7—H7A	0.9700
C1—C2	1.518 (5)	C7—H7B	0.9700
C1—C6	1.524 (5)	C8—H8A	0.9700
C1—H1	0.9800	C8—H8B	0.9700
C2—C3	1.508 (4)	N3—O1	1.229 (4)
C2—H2A	0.9700	N3—O2	1.234 (4)
C2—H2B	0.9700	N3—O3	1.241 (4)
C3—C8	1.503 (5)	N4—O4	1.218 (4)
C3—C4	1.523 (5)	N4—O6	1.227 (4)
C3—H3	0.9800	N4—O5	1.250 (4)

C7—N1—H1A	113 (3)	C5—C4—H4B	109.3
C7—N1—H1B	109 (2)	C3—C4—H4B	109.3
H1A—N1—H1B	104 (3)	H4A—C4—H4B	108.0
C7—N1—H1C	114 (3)	C6—C5—C4	111.9 (3)
H1A—N1—H1C	103 (4)	C6—C5—H5A	109.2
H1B—N1—H1C	113 (4)	C4—C5—H5A	109.2
C8—N2—H2D	115 (3)	C6—C5—H5B	109.2
C8—N2—H2E	112 (2)	C4—C5—H5B	109.2
H2D—N2—H2E	96 (4)	H5A—C5—H5B	107.9
C8—N2—H2F	114 (3)	C5—C6—C1	111.7 (3)
H2D—N2—H2F	113 (5)	C5—C6—H6A	109.3
H2E—N2—H2F	104 (4)	C1—C6—H6A	109.3
C7—C1—C2	114.3 (3)	C5—C6—H6B	109.3
C7—C1—C6	111.2 (3)	C1—C6—H6B	109.3
C2—C1—C6	109.4 (3)	H6A—C6—H6B	107.9
C7—C1—H1	107.2	N1—C7—C1	112.4 (3)
C2—C1—H1	107.2	N1—C7—H7A	109.1
C6—C1—H1	107.2	C1—C7—H7A	109.1
C3—C2—C1	111.9 (3)	N1—C7—H7B	109.1
C3—C2—H2A	109.2	C1—C7—H7B	109.1
C1—C2—H2A	109.2	H7A—C7—H7B	107.9
C3—C2—H2B	109.2	N2—C8—C3	113.8 (3)
C1—C2—H2B	109.2	N2—C8—H8A	108.8
H2A—C2—H2B	107.9	C3—C8—H8A	108.8
C8—C3—C2	109.8 (3)	N2—C8—H8B	108.8
C8—C3—C4	114.6 (3)	C3—C8—H8B	108.8
C2—C3—C4	111.0 (3)	H8A—C8—H8B	107.7
C8—C3—H3	107.0	O1—N3—O2	121.1 (4)
C2—C3—H3	107.0	O1—N3—O3	119.8 (4)
C4—C3—H3	107.0	O2—N3—O3	119.1 (4)
C5—C4—C3	111.5 (3)	O4—N4—O6	120.9 (4)
C5—C4—H4A	109.3	O4—N4—O5	120.3 (4)
C3—C4—H4A	109.3	O6—N4—O5	118.8 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2ⁱ	0.87 (4)	2.22 (4)	3.084 (6)	169 (4)
N1—H1A···O3ⁱ	0.87 (4)	2.36 (4)	3.013 (5)	132 (3)
N1—H1B···O4ⁱⁱ	0.95 (4)	2.59 (4)	3.187 (6)	121 (3)
N1—H1B···O5ⁱⁱ	0.95 (4)	1.87 (4)	2.818 (5)	172 (3)
N1—H1C···O2ⁱⁱⁱ	0.87 (5)	2.12 (5)	2.939 (6)	157 (4)
N2—H2D···O4^iv	0.77 (4)	2.48 (4)	3.142 (6)	145 (4)
N2—H2D···O6^iv	0.77 (4)	2.19 (4)	2.899 (6)	153 (4)
N2—H2E···O1^iv	0.99 (4)	2.46 (4)	3.178 (6)	130 (3)
N2—H2E···O3^iv	0.99 (4)	1.88 (4)	2.858 (5)	173 (4)
N2—H2F···O5^v	0.96 (6)	2.05 (6)	2.967 (5)	159 (5)
N2—H2F···O6^v	0.96 (6)	2.23 (6)	3.016 (6)	139 (4)

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

Interaction energies. top

N refers to the number of molecules with an R molecular centroid-to-centroid distance (Å). Energies are in kJ mol^-1.

N	Symop	R	E'_ele	E'_pol	E'_dis	E'_rep	E_tot
2	-x, -y + 1/2, z + 1/2	8.51	-63.9	-50.6	-6.3	5.4	-107.1
1	-x, -y, -z	9.69	32.1	-42.9	-4.6	1.8	-0.7
2	x, y + 1/2, -z + 1/2	8.86	0.0	-53.8	0.0	0.0	-39.8
2	x + 1/2, -y + 1/2, z	5.33	-23.1	-75.4	-20.1	14.1	-89.0
1	x + 1/2, -y + 1/2, z	5.60	-21.5	-50.6	-6.3	2.1	-64.4
1	x + 1/2, -y + 1/2, z	5.77	11.3	-14.6	-0.5	0.0	0.7
1	x + 1/2, -y + 1/2, z	5.33	-44.5	-18.9	-0.8	0.0	-61.8
1	-x, -y, -z	7.97	-128.4	-53.8	-4.3	0.2	-179.2
1	-x, -y, -z	6.43	-9.8	-18.9	-0.8	0.0	-25.0

Scale factors used to determine E_tot: k_ele = 1.057, k_pol = 0.740, k_dis = 0.871, k_rep = 0.618 (Mackenzie et al., 2017).

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Crystal structure, Hirshfeld surface analysis and energy framework calculation of the first oxoanion salt containing 1,3-cyclo­hexa­nebis(methyl­ammonium): [3-(aza­niumylmeth­yl)cyclo­hex­yl]methanaminium dinitrate

Supporting information

Key indicators

checkCIF/PLATON results

Crystal structure, Hirshfeld surface analysis and energy framework calculation of the first oxoanion salt containing 1,3-cyclohexanebis(methylammonium): [3-(azaniumylmethyl)cyclohexyl]methanaminium dinitrate