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Acta Crystallogr Sect E Struct Rep Online. 2008 May 1; 64(Pt 5): o878.
Published online 2008 April 23. doi:  10.1107/S1600536808010519
PMCID: PMC2961261

(S)-2-Methylpiperazinediium dichloride 0.42-hydrate

Abstract

The cations and anions of the chiral title compound, C5H14N2 2+·2Cl·0.42H2O, are linked by N—H(...)Cl hydrogen bonds into chains propagating in [100], which contain R 4 2(14) loops.

Related literature

For crystal structures containing the same chiral cation, see: Muller et al. (2005 [triangle]); Tuel et al. (2002 [triangle]). For background on graph theory, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o878-scheme1.jpg

Experimental

Crystal data

  • C5H14N2 2+·2Cl·0.42H2O
  • M r = 180.65
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o878-efi1.jpg
  • a = 5.7548 (2) Å
  • b = 11.6176 (4) Å
  • c = 6.9248 (2) Å
  • β = 105.7599 (16)°
  • V = 445.57 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.66 mm−1
  • T = 120 (2) K
  • 0.10 × 0.08 × 0.02 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 5193 measured reflections
  • 1999 independent reflections
  • 1952 reflections with I > 2σ(I)
  • R int = 0.071

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.110
  • S = 1.05
  • 1999 reflections
  • 93 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.93 e Å−3
  • Δρmin = −0.23 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 929 Friedel pairs
  • Flack parameter: 0.04 (9)

Data collection: COLLECT (Nonius, 1998 [triangle]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO (Otwinowski & Minor, 1997 [triangle]), SCALEPACK and SORTAV (Blessing, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808010519/ng2428sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808010519/ng2428Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

I thank the EPSRC National Crystallography Service (University of Southampton) for the data collection.

supplementary crystallographic information

Comment

The title compound, (I), is a chiral molecular salt, in which the organic species has accepted two protons from the hydrochloric acid. The geometrical parameters of the C5H14N22+ dication (Fig. 1) are similar to those of the same speies in other structures (Muller et al., 2005; Tuel et al., 2002) and its six-membered ring is a typical chair. The C4 stereogenic centre has S configuration and the pendant C5 methyl group occupies an equatorial position with respect to the ring.

In the crystal of (I), the cations and anions are linked by N—H···Cl hydrogen bonds (Table 1) into chains propagating in [100], with two chloride ions bridging each dication, as shown in Fig 2. In terms of graph theory (Bernstein et al., 1995), R42(14) loops arise from this connectivity.

The O1 water molecule is partially occupied in the crystal of (I), although there is no obvious crystallographic reason (e.g. symmetry generated close contacts) as to why this should be the case. Based on short O···Cl contacts of less than 3.5 Å, the water molecule probably participates in O—H···Cl hydrogen bonds thereby helping to crosslink the [100] chains, but the water H atoms could not be found or placed unambiguously in the present study.

Experimental

Equimolar quantities of 0.1 M aqueous (S)-2-methylpiperazine and 0.1 M aqueous hydrochloric acid were mixed, leading to a clear solution. Colourless plates of (I) grew as the water slowly evaporated.

Refinement

When refined with full occpancy, atom O1 showed an excessively large Uiso value of 0.15 Å2. Its fractional site occupancy was refined and rapidly converged to 0.420 (11) with a more reasonable Uiso value and improvement in fit. Its Uij values were subsequently refined and converged without difficulty. Its presumed attached H atoms could not be located from difference maps in the present study. Attempts at geometrical placement were ambiguous, as there are several possible O···Cl contacts that might correspond to O—H···Cl hydrogen bonds.

The other hydrogen atoms were geometrically placed (C—H = 0.95–0.99 Å, N—H = 0.92 Å) and refined as riding with Uiso(H) = 1.2Ueq(C,N) or 1.5Ueq(methyl C). The methyl group was allowed to rotate, but not tip, to best fit the electron density.

The highest difference peak is 0.73Å from H1.

Figures

Fig. 1.
View of the molecular structure of (I) showing 50% displacement ellipsoids (arbitrary spheres for the H atoms). Hydrogen bonds are indicated by double-dashed lines.
Fig. 2.
Fragement of a [100] hydrogen bonded chain of cations and anions in the crystal of (I). The carbon-bound H atoms are omitted for clarity. Symmetry code suffixes: (*) x - 1, y, z; (#) x + 1, y, z.

Crystal data

C5H14N22+·2Cl·0.42H2OF000 = 192
Mr = 180.65Dx = 1.346 Mg m3
Monoclinic, P21Mo Kα radiation λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 2691 reflections
a = 5.7548 (2) Åθ = 2.9–27.5º
b = 11.6176 (4) ŵ = 0.66 mm1
c = 6.9248 (2) ÅT = 120 (2) K
β = 105.7599 (16)ºPlate, colourless
V = 445.57 (3) Å30.10 × 0.08 × 0.02 mm
Z = 2

Data collection

Nonius KappaCCD diffractometer1952 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.071
Monochromator: graphiteθmax = 27.5º
T = 120(2) Kθmin = 3.1º
ω and [var phi] scansh = −7→7
Absorption correction: nonek = −14→15
5193 measured reflectionsl = −8→9
1999 independent reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.042  w = 1/[σ2(Fo2) + (0.0558P)2 + 0.1729P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.110(Δ/σ)max < 0.001
S = 1.06Δρmax = 0.93 e Å3
1999 reflectionsΔρmin = −0.22 e Å3
93 parametersExtinction correction: none
1 restraintAbsolute structure: Flack (1983), 929 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.04 (9)
Secondary atom site location: difference Fourier map

Special details

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.
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 > σ(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)

xyzUiso*/UeqOcc. (<1)
N10.7382 (4)−0.00043 (19)0.4593 (3)0.0150 (4)
H10.6241−0.01300.52780.018*
H20.8880−0.01250.54680.018*
N20.4376 (4)0.06003 (19)0.0680 (3)0.0171 (5)
H30.55040.0729−0.00160.020*
H40.28690.0723−0.01810.020*
C10.7209 (4)0.1215 (3)0.3871 (4)0.0181 (5)
H50.85090.13720.32200.022*
H60.74180.17450.50250.022*
C20.4781 (5)0.1420 (2)0.2391 (4)0.0190 (5)
H70.34900.13240.30760.023*
H80.47030.22190.18810.023*
C30.4563 (5)−0.0617 (2)0.1406 (4)0.0176 (5)
H90.4345−0.11460.02490.021*
H100.3263−0.07740.20580.021*
C40.7000 (5)−0.0841 (2)0.2891 (4)0.0164 (5)
H110.8297−0.07290.21970.020*
C50.7142 (6)−0.2064 (3)0.3697 (5)0.0228 (6)
H120.8577−0.21430.48390.034*
H130.7248−0.26050.26390.034*
H140.5694−0.22320.41330.034*
Cl10.88946 (10)0.12630 (6)−0.08251 (9)0.02299 (18)
Cl21.28588 (11)−0.04977 (5)0.61677 (10)0.02002 (17)
O10.1426 (11)0.3549 (5)0.1162 (10)0.039 (2)0.420 (11)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0128 (10)0.0182 (10)0.0123 (11)0.0011 (7)0.0003 (8)0.0017 (8)
N20.0175 (10)0.0190 (11)0.0128 (11)0.0002 (8)0.0010 (9)0.0012 (8)
C10.0173 (12)0.0148 (12)0.0210 (13)−0.0016 (11)0.0033 (10)−0.0015 (13)
C20.0188 (11)0.0174 (12)0.0204 (12)0.0027 (9)0.0048 (9)0.0000 (10)
C30.0206 (12)0.0166 (12)0.0139 (12)0.0009 (10)0.0017 (10)−0.0010 (10)
C40.0180 (11)0.0165 (11)0.0146 (12)0.0031 (9)0.0042 (9)−0.0003 (9)
C50.0228 (15)0.0182 (14)0.0241 (17)0.0033 (10)0.0008 (13)0.0022 (11)
Cl10.0175 (3)0.0339 (4)0.0176 (3)0.0027 (3)0.0048 (2)0.0015 (3)
Cl20.0129 (3)0.0300 (3)0.0166 (3)−0.0009 (2)0.0031 (2)−0.0016 (3)
O10.042 (4)0.027 (4)0.050 (4)0.004 (2)0.017 (3)0.003 (3)

Geometric parameters (Å, °)

N1—C11.497 (4)C2—H70.9900
N1—C41.497 (3)C2—H80.9900
N1—H10.9200C3—C41.519 (4)
N1—H20.9200C3—H90.9900
N2—C21.488 (3)C3—H100.9900
N2—C31.495 (3)C4—C51.521 (4)
N2—H30.9200C4—H111.0000
N2—H40.9200C5—H120.9800
C1—C21.510 (3)C5—H130.9800
C1—H50.9900C5—H140.9800
C1—H60.9900
C1—N1—C4111.7 (2)N2—C2—H8109.5
C1—N1—H1109.3C1—C2—H8109.5
C4—N1—H1109.3H7—C2—H8108.1
C1—N1—H2109.3N2—C3—C4111.0 (2)
C4—N1—H2109.3N2—C3—H9109.4
H1—N1—H2107.9C4—C3—H9109.4
C2—N2—C3110.9 (2)N2—C3—H10109.4
C2—N2—H3109.5C4—C3—H10109.4
C3—N2—H3109.5H9—C3—H10108.0
C2—N2—H4109.5N1—C4—C3109.5 (2)
C3—N2—H4109.5N1—C4—C5109.6 (2)
H3—N2—H4108.1C3—C4—C5110.8 (2)
N1—C1—C2110.0 (2)N1—C4—H11109.0
N1—C1—H5109.7C3—C4—H11109.0
C2—C1—H5109.7C5—C4—H11109.0
N1—C1—H6109.7C4—C5—H12109.5
C2—C1—H6109.7C4—C5—H13109.5
H5—C1—H6108.2H12—C5—H13109.5
N2—C2—C1110.8 (2)C4—C5—H14109.5
N2—C2—H7109.5H12—C5—H14109.5
C1—C2—H7109.5H13—C5—H14109.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H2···Cl20.922.253.096 (2)153
N1—H1···Cl2i0.922.243.136 (2)166
N2—H3···Cl10.922.263.149 (2)163
N2—H4···Cl1i0.922.303.137 (2)152

Symmetry codes: (i) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2428).

References

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  • Blessing, R. H. (1995). Acta Cryst. A51, 33–38. [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Muller, E. A., Cannon, R. J., Sarjeant, A. N., Ok, K. M., Halasyamani, P. S. & Norquist, A. J. (2005). Cryst. Growth Des.5, 1913–1917..
  • Nonius (1998). COLLECT . Nonius BV, Delft, The Netherlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter, Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Tuel, A., Gramlich, V. & Ch. Baerlocher, Ch. (2002). Micropor. Mesopor. Mater.56, 119–130.

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