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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2011 Mar 2;67(Pt 4):m392. doi: 10.1107/S1600536811007033

Dibromido[(1R,2R,N 1 S)-N-(pyridin-2-ylmeth­yl)cyclo­hexane-1,2-diamine-κ3 N,N′,N′′]cadmium

Run-Ting Yin a, Zhe Cao a, Lin Cheng a,*
PMCID: PMC3099840  PMID: 21753928

Abstract

In the title compound, [CdBr2(C12H19N3)], the CdII atom is coordinated by the three N atoms of the (1R,2R)-N-(pyridin-2-ylmeth­yl)cyclo­hexane-1,2-diamine ligand and a bromide ion in the basal plane, and by a second bromide in the apical position. The coordination environment can be described as distorted square pyramidal. The coordination of the enanti­o­pure ligand to the metal atom renders the central N atom chiral with an S configuration, so the complex is enanti­omerically pure and corresponds to the S,R,R diastereoisomer. In the crystal, the mol­ecules are linked via weak N—H⋯Br hydrogen bonds into a chain parallel to the b axis.

Related literature

For related structures, see: Gou et al. (2010 ▶). For non-linear optical properties of chiral coordination polymers, see: He et al. (2010 ▶).graphic file with name e-67-0m392-scheme1.jpg

Experimental

Crystal data

  • [CdBr2(C12H19N3)]

  • M r = 477.52

  • Orthorhombic, Inline graphic

  • a = 8.7153 (16) Å

  • b = 9.1978 (17) Å

  • c = 19.759 (4) Å

  • V = 1583.9 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 6.41 mm−1

  • T = 173 K

  • 0.12 × 0.09 × 0.08 mm

Data collection

  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2008 ▶) T min = 0.513, T max = 0.628

  • 9389 measured reflections

  • 3048 independent reflections

  • 2348 reflections with I > 2σ(I)

  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033

  • wR(F 2) = 0.052

  • S = 0.96

  • 3048 reflections

  • 163 parameters

  • H-atom parameters constrained

  • Δρmax = 0.49 e Å−3

  • Δρmin = −0.48 e Å−3

  • Absolute structure: Flack (1983 ▶), 1244 Friedel pairs

  • Flack parameter: 0.049 (11)

Data collection: SMART (Bruker, 2000 ▶); cell refinement: SAINT-Plus (Bruker, 2000 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 ▶), ORTEP-3 for Windows (Farrugia, 1997 ▶) and PLATON (Spek, 2009 ▶); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811007033/dn2658sup1.cif

e-67-0m392-sup1.cif (17.2KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811007033/dn2658Isup2.hkl

e-67-0m392-Isup2.hkl (149.6KB, hkl)

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

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

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N3—H3B⋯Br2i 0.92 2.89 3.750 (5) 156
N3—H3C⋯Br1ii 0.92 2.59 3.498 (5) 168

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

Acknowledgments

The authors thank the Program for Young Excellent Talents in Southeast University for financial support.

supplementary crystallographic information

Comment

Recently, rational design and synthesis of chiral coordination polymers have been of great interests due to their potential utility in enantiomerically selective catalysis and separations, second-order nonlinearoptical (NLO) applications and luminescence (He et al., 2010). A simple and effective design route for such polymers is to appropriately organize the metal ions into ordered architectures by use of chiral ligands. Herein, we report a new chiral complex, Zn(pcd)Br2 (pcd = (1R,2R)-N1-(pyridin-2-ylmethyl)cyclohexane -1,2-diamine), with a enantiomerically pure pcd ligand.

The title compound is a mononuclear complex, in which the coordination environment of CdII ion can be described as distorted square-pyramidal, being surrounded by one tridentate ligand and two bromine anions (Fig. 1).

The molecules are linked to each other, via weak N—H···Br hydrogen bonds, into a one-dimensional hydrogen bonding network developping parallel to the b axis (Table 1, Fig. 2).

Experimental

(1R,2R)-N1-(pyridin-2-ylmethyl)cyclohexane -1,2-diamine (0.041 g, 0.2 mmol) dissolved in water (8 ml) was added to a methanol solution (10 ml) of CdBr2 (0.054 g, 0.2 mmol). The mixture solution was stirred for 1 h at room temperature and then filtered. The filtrate was allowed to evaporate slowly at room temperature. After 2 weeks, yellow block crystals were obtained in 32.5% yield (0.031 g).

Refinement

All H atoms were fixed geometrically and treated as riding with C—H = 0.93–0.97 Å and N—H = 0.92–0.93 Å with Uiso(H) = 1.2 Ueq(C or N) and Uiso(H) = 1.5 Ueq(O).

Figures

Fig. 1.

Fig. 1.

View of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.

Fig. 2.

Fig. 2.

Partial packing view showing the chain developping parallel to the b axis. H atoms not involved in hydrogen bondings have been omitted for clarity. H bonds are shown as dashed lines. [Symmetry codes: (i) -x+1, y-1/2, -z+1/2; (ii) -x+1, y+1/2, -z+1/2]

Crystal data

[CdBr2(C12H19N3)] F(000) = 920
Mr = 477.52 Dx = 2.003 Mg m−3
Orthorhombic, P212121 Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab Cell parameters from 792 reflections
a = 8.7153 (16) Å θ = 2.5–28.0°
b = 9.1978 (17) Å µ = 6.41 mm−1
c = 19.759 (4) Å T = 173 K
V = 1583.9 (5) Å3 Block, yellow
Z = 4 0.12 × 0.09 × 0.08 mm

Data collection

Bruker SMART APEX CCD diffractometer 3048 independent reflections
Radiation source: fine-focus sealed tube 2348 reflections with I > 2σ(I)
graphite Rint = 0.048
φ and ω scans θmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 2008) h = −10→9
Tmin = 0.513, Tmax = 0.628 k = −11→10
9389 measured reflections l = −23→22

Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033 H-atom parameters constrained
wR(F2) = 0.052 w = 1/[σ2(Fo2) + (0.0014P)2 + 0.1P] where P = (Fo2 + 2Fc2)/3
S = 0.96 (Δ/σ)max < 0.001
3048 reflections Δρmax = 0.49 e Å−3
163 parameters Δρmin = −0.47 e Å−3
0 restraints Absolute structure: Flack (1983), 1244 Friedel pairs
Primary atom site location: structure-invariant direct methods Flack parameter: 0.049 (11)

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)

x y z Uiso*/Ueq
Cd1 0.24783 (5) 0.10173 (5) 0.207493 (18) 0.03280 (11)
Br1 0.29207 (7) −0.17278 (7) 0.18146 (3) 0.04158 (18)
Br2 0.35856 (7) 0.29959 (7) 0.13039 (3) 0.04411 (18)
C1 −0.0384 (8) 0.1320 (7) 0.0949 (3) 0.052 (2)
H1A 0.0404 0.1650 0.0654 0.062*
C2 −0.1845 (8) 0.1196 (8) 0.0697 (3) 0.062 (2)
H2A −0.2071 0.1427 0.0239 0.075*
C3 −0.2968 (8) 0.0725 (8) 0.1131 (4) 0.065 (2)
H3A −0.3993 0.0630 0.0973 0.077*
C4 −0.2620 (8) 0.0390 (7) 0.1792 (3) 0.0499 (16)
H4A −0.3396 0.0064 0.2094 0.060*
C5 −0.1119 (7) 0.0538 (6) 0.2009 (3) 0.0353 (15)
C6 −0.0630 (6) 0.0155 (7) 0.2716 (3) 0.0373 (16)
H6A −0.1516 0.0257 0.3026 0.045*
H6B −0.0290 −0.0872 0.2728 0.045*
C7 0.1349 (6) 0.0623 (6) 0.3592 (3) 0.0336 (15)
H7A 0.1528 −0.0449 0.3564 0.040*
C8 0.0343 (7) 0.0913 (8) 0.4213 (3) 0.0448 (18)
H8A 0.0029 0.1947 0.4214 0.054*
H8B −0.0599 0.0314 0.4181 0.054*
C9 0.1152 (7) 0.0572 (7) 0.4877 (3) 0.0508 (19)
H9A 0.0488 0.0868 0.5260 0.061*
H9B 0.1323 −0.0490 0.4911 0.061*
C10 0.2669 (8) 0.1347 (7) 0.4929 (3) 0.0550 (19)
H10A 0.3191 0.1056 0.5353 0.066*
H10B 0.2492 0.2410 0.4946 0.066*
C11 0.3695 (7) 0.0987 (8) 0.4326 (3) 0.0499 (18)
H11A 0.4665 0.1542 0.4362 0.060*
H11B 0.3950 −0.0062 0.4333 0.060*
C12 0.2901 (6) 0.1360 (6) 0.3664 (2) 0.0339 (15)
H12A 0.2723 0.2434 0.3659 0.041*
N1 −0.0014 (5) 0.0998 (6) 0.1591 (2) 0.0377 (13)
N2 0.0625 (4) 0.1095 (6) 0.2950 (2) 0.0313 (12)
H2B 0.0265 0.2041 0.2997 0.038*
N3 0.3872 (5) 0.0999 (6) 0.3071 (2) 0.0366 (12)
H3B 0.4298 0.0093 0.3132 0.044*
H3C 0.4659 0.1662 0.3040 0.044*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Cd1 0.0323 (2) 0.0391 (3) 0.02707 (19) −0.0016 (3) 0.0035 (2) 0.0018 (2)
Br1 0.0462 (4) 0.0380 (4) 0.0405 (3) 0.0053 (3) −0.0043 (3) 0.0000 (3)
Br2 0.0478 (4) 0.0428 (4) 0.0418 (3) −0.0031 (4) 0.0129 (3) 0.0066 (3)
C1 0.056 (5) 0.061 (6) 0.039 (4) 0.011 (4) −0.004 (3) −0.001 (4)
C2 0.070 (5) 0.064 (6) 0.053 (4) 0.018 (5) −0.020 (4) −0.008 (4)
C3 0.047 (5) 0.070 (6) 0.076 (5) 0.013 (4) −0.023 (4) −0.036 (5)
C4 0.036 (4) 0.052 (4) 0.061 (4) 0.001 (4) 0.001 (4) −0.020 (3)
C5 0.029 (4) 0.031 (4) 0.046 (4) 0.006 (3) 0.002 (3) −0.011 (3)
C6 0.034 (4) 0.039 (4) 0.039 (4) −0.005 (3) 0.006 (3) −0.004 (3)
C7 0.036 (4) 0.033 (4) 0.032 (3) −0.004 (3) 0.004 (3) 0.002 (3)
C8 0.051 (4) 0.048 (5) 0.035 (3) −0.002 (4) 0.010 (3) −0.004 (4)
C9 0.067 (5) 0.053 (5) 0.032 (4) −0.004 (4) 0.017 (4) 0.000 (3)
C10 0.072 (5) 0.064 (5) 0.029 (3) −0.001 (5) −0.008 (4) −0.005 (3)
C11 0.051 (4) 0.059 (5) 0.040 (4) −0.001 (4) −0.002 (3) 0.001 (4)
C12 0.041 (4) 0.033 (4) 0.028 (3) −0.001 (3) 0.005 (3) −0.009 (3)
N1 0.041 (3) 0.039 (3) 0.034 (3) 0.010 (3) 0.001 (2) −0.003 (3)
N2 0.032 (3) 0.029 (3) 0.032 (3) −0.006 (2) −0.001 (2) −0.003 (3)
N3 0.034 (3) 0.043 (3) 0.032 (3) −0.005 (3) 0.001 (2) −0.003 (3)

Geometric parameters (Å, °)

Cd1—N3 2.313 (4) C7—C12 1.520 (7)
Cd1—N2 2.366 (4) C7—C8 1.532 (7)
Cd1—N1 2.373 (5) C7—H7A 1.0000
Cd1—Br2 2.5621 (8) C8—C9 1.522 (7)
Cd1—Br1 2.6054 (9) C8—H8A 0.9900
C1—N1 1.342 (7) C8—H8B 0.9900
C1—C2 1.372 (8) C9—C10 1.506 (8)
C1—H1A 0.9500 C9—H9A 0.9900
C2—C3 1.370 (9) C9—H9B 0.9900
C2—H2A 0.9500 C10—C11 1.526 (7)
C3—C4 1.377 (8) C10—H10A 0.9900
C3—H3A 0.9500 C10—H10B 0.9900
C4—C5 1.383 (8) C11—C12 1.520 (7)
C4—H4A 0.9500 C11—H11A 0.9900
C5—N1 1.338 (7) C11—H11B 0.9900
C5—C6 1.502 (7) C12—N3 1.483 (6)
C6—N2 1.468 (7) C12—H12A 1.0000
C6—H6A 0.9900 N2—H2B 0.9300
C6—H6B 0.9900 N3—H3B 0.9200
C7—N2 1.483 (6) N3—H3C 0.9200
N3—Cd1—N2 74.77 (15) C7—C8—H8B 109.0
N3—Cd1—N1 145.44 (16) H8A—C8—H8B 107.8
N2—Cd1—N1 70.73 (15) C10—C9—C8 111.6 (5)
N3—Cd1—Br2 108.26 (12) C10—C9—H9A 109.3
N2—Cd1—Br2 132.07 (13) C8—C9—H9A 109.3
N1—Cd1—Br2 96.34 (13) C10—C9—H9B 109.3
N3—Cd1—Br1 94.77 (13) C8—C9—H9B 109.3
N2—Cd1—Br1 105.92 (12) H9A—C9—H9B 108.0
N1—Cd1—Br1 92.79 (13) C9—C10—C11 111.0 (5)
Br2—Cd1—Br1 121.01 (3) C9—C10—H10A 109.4
N1—C1—C2 123.2 (7) C11—C10—H10A 109.4
N1—C1—H1A 118.4 C9—C10—H10B 109.4
C2—C1—H1A 118.4 C11—C10—H10B 109.4
C3—C2—C1 117.6 (6) H10A—C10—H10B 108.0
C3—C2—H2A 121.2 C12—C11—C10 110.9 (5)
C1—C2—H2A 121.2 C12—C11—H11A 109.5
C2—C3—C4 120.5 (6) C10—C11—H11A 109.5
C2—C3—H3A 119.8 C12—C11—H11B 109.5
C4—C3—H3A 119.8 C10—C11—H11B 109.5
C3—C4—C5 118.7 (6) H11A—C11—H11B 108.1
C3—C4—H4A 120.7 N3—C12—C11 111.7 (4)
C5—C4—H4A 120.7 N3—C12—C7 109.5 (4)
N1—C5—C4 121.4 (6) C11—C12—C7 112.7 (5)
N1—C5—C6 116.4 (5) N3—C12—H12A 107.6
C4—C5—C6 122.2 (6) C11—C12—H12A 107.6
N2—C6—C5 111.4 (5) C7—C12—H12A 107.6
N2—C6—H6A 109.3 C5—N1—C1 118.7 (5)
C5—C6—H6A 109.3 C5—N1—Cd1 114.3 (4)
N2—C6—H6B 109.3 C1—N1—Cd1 126.8 (4)
C5—C6—H6B 109.3 C6—N2—C7 114.4 (4)
H6A—C6—H6B 108.0 C6—N2—Cd1 105.1 (3)
N2—C7—C12 109.1 (4) C7—N2—Cd1 109.1 (3)
N2—C7—C8 113.1 (4) C6—N2—H2B 109.4
C12—C7—C8 110.9 (5) C7—N2—H2B 109.4
N2—C7—H7A 107.8 Cd1—N2—H2B 109.4
C12—C7—H7A 107.8 C12—N3—Cd1 111.8 (3)
C8—C7—H7A 107.8 C12—N3—H3B 109.3
C9—C8—C7 112.9 (5) Cd1—N3—H3B 109.3
C9—C8—H8A 109.0 C12—N3—H3C 109.3
C7—C8—H8A 109.0 Cd1—N3—H3C 109.3
C9—C8—H8B 109.0 H3B—N3—H3C 107.9

Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
N3—H3B···Br2i 0.92 2.89 3.750 (5) 156
N3—H3C···Br1ii 0.92 2.59 3.498 (5) 168

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2658).

References

  1. Bruker (2000). SMART and SAINT-Plus Bruker AXS Inc., Madison, Wisconsin, USA.
  2. Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.
  3. Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.
  4. Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  5. Gou, S. H. & Tong, T. F. (2010). Faming Zhuanli Shenqing (P. R. China), p. 16.
  6. He, R., Song, H. H., Wei, Z., Zhang, J. J. & Gao, Y. Z. (2010). J. Solid State Chem. 183, 2021–2026.
  7. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
  8. Spek, A. L. (2009). Acta Cryst. D65, 148–155. [DOI] [PMC free article] [PubMed]

Associated Data

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

Supplementary Materials

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811007033/dn2658sup1.cif

e-67-0m392-sup1.cif (17.2KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811007033/dn2658Isup2.hkl

e-67-0m392-Isup2.hkl (149.6KB, hkl)

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


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