A hydrated complex of DL-alanine with cadmium chloride

In the title complex, catena-poly­[[[dicadmium(II)]-μ-DL-alanine-di-μ-chloro] monohydrate], {[CdCl₂(C₃H₇NO₂)]·H₂O}_n, the DL-alanine mol­ecules exist in the zwitterionic form. The Cd atoms lie on inversion centers and are coordinated by four Cl atoms and two carboxyl O atoms, forming a distorted octahedral environment. These octahedra are linked through Cl—Cl edges and are bridged by the carboxyl groups of the alanine residues, forming a one-dimensional polymer chain that extends along [100].

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.005 Å
• H-atom completeness 78%
• R factor = 0.048
• wR factor = 0.133
• Data-to-parameter ratio = 16.4

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT052_ALERT_1_A (Proper) Absorption Correction Method Missing           ?
PLAT306_ALERT_2_A Isolated Oxygen Atom (H-atoms Missing ?) .....           O3

Alert level C
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings    Differ ..          ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ..          ?
PLAT057_ALERT_3_C Correction for Absorption Required   RT(exp) =       1.14
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing).          ?
PLAT431_ALERT_2_C Short Inter HL..A Contact:Cl1     .. O3      =       3.23 Ang.
PLAT431_ALERT_2_C Short Inter HL..A Contact:Cl2     .. O3      =       3.17 Ang.
PLAT764_ALERT_4_C Overcomplete CIF Bond list Detected (Rep/Expd)       1.18 Ratio

Alert level G
FORMU01_ALERT_2_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and the formula from the _atom_site* data.
            Atom count from _chemical_formula_sum:C3 H9 Cd1 Cl2 N1 O3
            Atom count from the _atom_site data:  C3 H7 Cd1 Cl2 N1 O3
CELLZ01_ALERT_1_G Difference between formula and atom_site contents detected.
CELLZ01_ALERT_1_G WARNING: H atoms missing from atom site list. Is this intentional?
           From the CIF: _cell_formula_units_Z    4
           From the CIF: _chemical_formula_sum  C3 H9 Cd Cl2 N O3
           TEST: Compare cell contents of formula and atom_site data

           atom    Z*formula  cif sites diff
           C         12.00     12.00    0.00
           H         36.00     28.00    8.00
           Cd         4.00      4.00    0.00
           Cl         8.00      8.00    0.00
           N          4.00      4.00    0.00
           O         12.00     12.00    0.00

   2 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   7 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   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
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

---

S1. Comment

Halagenocadmium–amino acid complexes are intersting, as cadmium is a naturally occurring metallic element, chemically similar to zinc. Cadmium is found to occur naturally in at least one protein, metallothionein (Kagi & Vallee, 1960). A precise determination of the crystal structure of DL-alanine itself was recently carried out in our laboratory (Subha Nandhini et al., 2001). The present study reports the crystal struture of a complex of DL-alanine with cadmium chloride, namely catena-poly[[[dicadmium(II)]-µ-DL-alanine-di-µ-chloro] monohydrate], (I). The crystal structures of complexes of cadmium chloride with glycine (Thulasidhass & Mohana Rao, 1980), L-proline (Yukawa et al., 1983) and hydroxy-L-proline (Yukawa et al., 1982), L-alanine (Schaffers & Keszler, 1993), sarcosine (Krishnakumar et al., 1996) and β-alanine (Subha Nandhini et al., 2002) have already been reported.

The DL-alanine molecules exist as zwitterions. The torsion angles involving C1—C2 bond [−3.4 (4), 177.7 (3), −125.2 (3) and 55.9 (4)°; see Table 1] observed in (I) are distinctly different from those observed in DL-alanine [16.3 (2), −164.0 (2), −105.7 (2) and 74.0 (2)°; Subha Nandhini et al., 2001]. The conformation of the alanine molecule about the N—C bond corresponds to the staggered ethane-type.

In the crystal structures of the majority of the complexes, the Cd atom has a tetrahedral coordination (Bürgi, 1973; Liptrot, 1974). In (I), both Cd atoms lie on inversion centers and coordinate with four Cl atoms and two carboxyl O atoms, forming distorted octahedra. The four Cl atoms which coordinate to a Cd atom form a square plane. These square planes extend along the shorter axis, a. The dihedral angle between adjacent square planes is 34.8 (1)°. These square planes are spanned by the carboxyl O atoms, which complete the coordination around the Cd atom. These polyhedra fuse directly by sharing Cl–Cl edges, forming one-dimensional polymeric chains in the [100] direction. The water O atom does not participate in coordination with cadmium. The metal–ligand coordination observed in this structure is remarkably similar to those observed in the crystal structures of complexes of CdCl₂ with L-alanine, L-proline, hydroxy L-proline and β-alanine, and distinctly different from glycine–CdCl₂ and sarcosine–CdCl₂.

Selected interatomic distances are listed in Table 1. The mean Cd—Cl distance, 2.61 (1) Å, is in agreement with the corresponding distances reported in the structures of complexes of CdCl₂ with β-alanine [2.619 (5) Å], L-alanine [2.61 (1) Å], L-proline [2.615 (3) Å], 4-hydroxy-L-proline [2.620 (2) Å], glycine [2.543 (6) Å] and sarcosine [2.589 (1) Å]. The Cd—Cl distances also agree well with those observed in other simple organic complexes of CdCl₂, viz. 2.60 (1) and 2.65 (1) Å for CdCl₂·4H₂O (Lelingy & Monier, 1979) and CdCl₂ dipyridine (Paulus, 1969), respectively. The Cd—Cl distances reported for CdCl₂ diimidazole (Flook et al., 1973), viz. 2.706 (2) and 2.731 (2) Å, are longer compared to those in the present structure.

The crystal structure of (I) is illustrated in Fig. 2 and the hydrogen bonds that stablize it are listed in Table 2. There are no direct interactions between the alanine molecules. The adjacent polymeric chains are interconnected through N—H···O and N—H···Cl hydrogen bonds. The water O3 atom is involved in short contacts with Cl1 [3.234 (3) Å], Cl2ⁱ [3.166 (3) Å] and O2ⁱⁱ [3.030 (4) Å] [symmetry codes: (i) x, 1/2 − y, z − 1/2; (ii) 1 + x, y, z].

S2. Experimental

Colourless single crystals of the title complex were grown as transparent plates, using a mixture of water and acetone, containing DL-alanine and cadmium chloride in a stoichiometric ratio.

S3. Refinement

H atoms were placed at calculated positions and were allowed to ride on their respective parent atoms, with C—H = 0.97 or 0.98 Å and N—H = 0.89 Å. No satisfactory H-atom positions were found for the water O atom. Hence, the structure was refined without them. The highest peaks in the final difference map were located at distances less than 0.92 Å from the Cd atoms.

Computing details

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1999) and ORTEPIII (Johnson & Burnett, 1996); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. An ORTEPIII (Johnson & Burnett, 1996) view of title complex, showing part of the polymeric chain and the atom-numbering scheme for the contents of the asymmetric unit. The displacement ellipsoids are shown at 50% probability level.
	Fig. 2. Packing of the molecules in the unit cell, viewed down the b axis.

catena-poly[[[dicadmium(II)]-µ-DL-alanine-di-µ-chloro] monohydrate]

Crystal data

[CdCl2(C3H7NO2)]·H2O	F(000) = 560
Mr = 290.42	Dx = 2.289 Mg m^−3 Dm = 2.29 Mg m^−3 Dm measured by flotation in a mixture of carbon tetrachloride and bromoform
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 7.1190 (15) Å	θ = 19–32°
b = 14.408 (3) Å	µ = 3.18 mm^−1
c = 8.6396 (13) Å	T = 293 K
β = 107.98 (2)°	Transparent plate, colourless
V = 842.9 (3) Å^3	0.18 × 0.12 × 0.10 mm
Z = 4

Data collection

Enraf-Nonius sealed tube diffractometer	1469 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.095
Graphite monochromator	θmax = 25.3°, θmin = 2.8°
ω–2θ scans	h = −8→8
Absorption correction: ψ scan (North et al., 1968)	k = 0→17
Tmin = 0.639, Tmax = 0.728	l = −9→10
1797 measured reflections	2 standard reflections every 60 min
1541 independent reflections	intensity decay: 0.1%

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.048	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.134	H-atom parameters constrained
S = 1.15	w = 1/[σ^2(Fo^2) + (0.096P)^2 + 1.0634P] where P = (Fo^2 + 2Fc^2)/3
1541 reflections	(Δ/σ)max < 0.001
94 parameters	Δρmax = 2.57 e Å^−3
0 restraints	Δρmin = −2.89 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
Cd1	0.5000	0.0000	1.0000	0.0067 (3)
Cd2	1.0000	0.0000	1.0000	0.0088 (3)
Cl1	0.66360 (12)	0.01708 (7)	0.76270 (10)	0.0129 (3)
Cl2	0.82562 (11)	0.05798 (6)	1.20109 (10)	0.0154 (3)
O3	0.6809 (4)	0.2414 (2)	0.7618 (4)	0.0311 (7)
O1	0.3931 (4)	0.14897 (17)	0.9765 (3)	0.0183 (6)
O2	0.0712 (4)	0.15519 (17)	0.9545 (3)	0.0198 (6)
N1	0.4428 (5)	0.3237 (2)	0.9441 (4)	0.0222 (7)
H1A	0.4861	0.2908	0.8748	0.033*
H1B	0.5206	0.3137	1.0452	0.033*
H1C	0.4445	0.3838	0.9206	0.033*
C1	0.2340 (5)	0.1899 (2)	0.9571 (4)	0.0131 (7)
C2	0.2358 (5)	0.2949 (2)	0.9300 (4)	0.0155 (7)
H2	0.1513	0.3085	0.8193	0.019*
C3	0.1636 (6)	0.3507 (3)	1.0470 (4)	0.0229 (8)
H3A	0.1692	0.4156	1.0235	0.034*
H3B	0.2456	0.3385	1.1562	0.034*
H3C	0.0297	0.3337	1.0362	0.034*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cd1	0.0062 (4)	0.0051 (4)	0.0085 (4)	0.00054 (10)	0.0019 (3)	−0.00156 (10)
Cd2	0.0081 (4)	0.0095 (4)	0.0102 (4)	−0.00016 (10)	0.0048 (3)	−0.00043 (11)
Cl1	0.0168 (5)	0.0155 (5)	0.0059 (5)	0.0004 (3)	0.0026 (3)	0.0003 (3)
Cl2	0.0135 (5)	0.0212 (5)	0.0108 (5)	−0.0029 (3)	0.0026 (3)	−0.0099 (3)
O3	0.0320 (16)	0.0233 (16)	0.0347 (16)	−0.0006 (12)	0.0054 (13)	0.0129 (12)
O1	0.0198 (13)	0.0076 (11)	0.0258 (14)	0.0025 (10)	0.0043 (11)	0.0021 (10)
O2	0.0179 (13)	0.0109 (12)	0.0312 (15)	−0.0024 (10)	0.0084 (11)	0.0042 (11)
N1	0.0283 (17)	0.0109 (14)	0.0268 (18)	−0.0018 (13)	0.0077 (15)	0.0037 (13)
C1	0.0215 (18)	0.0128 (17)	0.0047 (14)	0.0021 (14)	0.0033 (11)	0.0012 (13)
C2	0.0221 (17)	0.0135 (17)	0.0082 (16)	−0.0004 (13)	0.0007 (13)	0.0005 (13)
C3	0.037 (2)	0.0177 (18)	0.0142 (18)	0.0069 (16)	0.0087 (16)	−0.0024 (15)

Geometric parameters (Å, º)

Cd1—O1	2.265 (2)	O1—C1	1.241 (4)
Cd1—O1^i	2.265 (2)	O2—C1	1.256 (4)
Cd1—Cl2	2.5697 (10)	O2—Cd2^iv	2.352 (3)
Cd1—Cl2^i	2.5697 (10)	N1—C2	1.500 (5)
Cd1—Cl1	2.6635 (9)	N1—H1A	0.89
Cd1—Cl1^i	2.6635 (9)	N1—H1B	0.89
Cd2—O2^i	2.352 (3)	N1—H1C	0.89
Cd2—O2^ii	2.352 (3)	C1—C2	1.532 (5)
Cd2—Cl2	2.5669 (8)	C2—C3	1.501 (5)
Cd2—Cl2^iii	2.5669 (8)	C2—H2	0.98
Cd2—Cl1	2.6397 (11)	C3—H3A	0.96
Cd2—Cl1^iii	2.6397 (11)	C3—H3B	0.96
Cl1—Cd2^iii	2.6397 (11)	C3—H3C	0.96
Cl2—Cd2^iii	2.5669 (8)
O1—Cd1—O1^i	180.0	Cl2—Cd2—Cl1^iii	90.98 (3)
O1—Cd1—Cl2	87.73 (7)	Cl2^iii—Cd2—Cl1^iii	89.02 (3)
O1^i—Cd1—Cl2	92.27 (7)	Cl1—Cd2—Cl1^iii	180.0
O1—Cd1—Cl2^i	92.27 (7)	C1—O1—Cd1	136.8 (2)
O1^i—Cd1—Cl2^i	87.73 (7)	C1—O2—Cd2^iv	128.3 (2)
Cl2—Cd1—Cl2^i	180.0	C2—N1—H1A	109.5
O1—Cd1—Cl1	93.33 (7)	C2—N1—H1B	109.5
O1^i—Cd1—Cl1	86.67 (7)	H1A—N1—H1B	109.5
Cl2—Cd1—Cl1	88.44 (3)	C2—N1—H1C	109.5
Cl2^i—Cd1—Cl1	91.56 (3)	H1A—N1—H1C	109.5
O1—Cd1—Cl1^i	86.67 (7)	H1B—N1—H1C	109.5
O1^i—Cd1—Cl1^i	93.33 (7)	O1—C1—O2	127.7 (3)
Cl2—Cd1—Cl1^i	91.56 (3)	O1—C1—C2	116.1 (3)
Cl2^i—Cd1—Cl1^i	88.44 (3)	O2—C1—C2	116.2 (3)
Cl1—Cd1—Cl1^i	180.0	N1—C2—C3	109.2 (3)
O2^i—Cd2—O2^ii	180.0	N1—C2—C1	108.4 (3)
O2^i—Cd2—Cl2	91.27 (7)	C3—C2—C1	113.9 (3)
O2^ii—Cd2—Cl2	88.73 (7)	N1—C2—H2	108.4
O2^i—Cd2—Cl2^iii	88.73 (7)	C3—C2—H2	108.4
O2^ii—Cd2—Cl2^iii	91.27 (7)	C1—C2—H2	108.4
Cl2—Cd2—Cl2^iii	180.0	C2—C3—H3A	109.5
O2^i—Cd2—Cl1	91.59 (7)	C2—C3—H3B	109.5
O2^ii—Cd2—Cl1	88.41 (7)	H3A—C3—H3B	109.5
Cl2—Cd2—Cl1	89.02 (3)	C2—C3—H3C	109.5
Cl2^iii—Cd2—Cl1	90.98 (3)	H3A—C3—H3C	109.5
O2^i—Cd2—Cl1^iii	88.41 (7)	H3B—C3—H3C	109.5
O2^ii—Cd2—Cl1^iii	91.59 (7)
O2^i—Cd2—Cl1—Cd1	67.44 (7)	O1—Cd1—Cl2—Cd2	−117.78 (7)
O2^ii—Cd2—Cl1—Cd1	−112.56 (7)	O1^i—Cd1—Cl2—Cd2	62.22 (7)
Cl2—Cd2—Cl1—Cd1	−23.80 (2)	Cl1—Cd1—Cl2—Cd2	−24.39 (3)
Cl2^iii—Cd2—Cl1—Cd1	156.20 (2)	Cl1^i—Cd1—Cl2—Cd2	155.61 (3)
O1—Cd1—Cl1—Cd2^iii	111.42 (7)	Cl2—Cd1—O1—C1	−145.1 (3)
O1^i—Cd1—Cl1—Cd2^iii	−68.58 (7)	Cl2^i—Cd1—O1—C1	34.9 (3)
Cl2—Cd1—Cl1—Cd2	23.78 (2)	Cl1—Cd1—O1—C1	126.6 (3)
Cl2^i—Cd1—Cl1—Cd2	−156.22 (2)	Cl1^i—Cd1—O1—C1	−53.4 (3)
O2^i—Cd2—Cl2—Cd1	−66.96 (7)	Cd1—O1—C1—O2	5.2 (6)
O2^ii—Cd2—Cl2—Cd1	113.04 (7)	Cd1—O1—C1—C2	−173.6 (2)
Cl1—Cd2—Cl2—Cd1	24.62 (3)	Cd2^iv—O2—C1—O1	3.9 (6)
Cl1^iii—Cd2—Cl2—Cd1	−155.38 (3)	Cd2^iv—O2—C1—C2	−177.3 (2)
O1—Cd1—Cl2—Cd2^iii	−117.78 (7)	O1—C1—C2—N1	−3.4 (4)
O1^i—Cd1—Cl2—Cd2^iii	62.22 (7)	O2—C1—C2—N1	177.7 (3)
Cl1—Cd1—Cl2—Cd2^iii	−24.39 (3)	O1—C1—C2—C3	−125.2 (3)
Cl1^i—Cd1—Cl2—Cd2^iii	155.61 (3)	O2—C1—C2—C3	55.9 (4)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O3	0.89	2.05	2.900 (5)	158
N1—H1B···O3^v	0.89	2.03	2.901 (5)	166
N1—H1C···Cl1^vi	0.89	2.46	3.270 (3)	152

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