supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

Acta Cryst. (2009). E65, m89    [ doi:10.1107/S1600536808042141 ]

Aqua(iminodiacetato-[kappa]3O,N,O')(1,10-phenanthroline-[kappa]2N,N')zinc(II) sesquihydrate

H. L. Ng, C. H. Ng and S. W. Ng

Abstract top

The iminodiacetate dianion in the title compound, [Zn(C4H5NO4)(C12H8N2)(H2O)]·1.5H2O, chelates to the ZnII center with its N and two O atoms. The metal atom is also chelated by the N-heterocycle and coordinated by one water molecule, leading to a distorted octahedral environment. The dianion, and coordinated and uncoordinated water molecules interact through O-H...O hydrogen bonds, generating a three-dimensional network. One of the two uncoordinated water molecules has half-site occupancy. The crystal studied was a non-merohedral twin with a 15% twin component.

Related literature top

For the structure of zinc bis[iminodiacetate(1-)] tetrahydrate, see: Sinkha et al. (1975). For the dihydrated adenine adduct of zinc iminodiacetate, see: Morel et al. (2003). For the use of PLATON in de-twinning diffraction data, see: Spek (2003).

Experimental top

An methanol solution of zinc(II) nitrate hexahydrate (0.30 g, 1 mmol) and 1,10-phenanthroline (0.20 g, 1 mmol) was mixed with an aqueous solution of iminodiacetic acid (0.14 g, 1 mmol) and sodium hydroxide (0.08 g, 2 mmol). The mixture was briefly heated. The cool solution yielded a white solid. This was recrystallized from a water-methanol mixture to give colorless crystals.

Refinement top

Carbon- and nitrogen-bound hydrogen atoms were placed at calculated positions (C–H 0.95–0.98 Å, N–H 0.88 Å) and were treated as riding on their parent atoms, with U(H) set to 1.2 times Ueq(C or N). The water H-atoms were placed in chemically-sensible positions on the basis of hydrogen bonding, but were not refined; their temperature factors were tied by a factor of 1.5.

For the three phenanthroline groups, the central six-membered ring was refined as a rigid hexagon of 1.39 Å sides. The temperature factors of the carbon atoms of this fused-ring system were restrained to be nearly isotropic.

The O3w atom gave a large temperature factor when allowed to refined at full occupancy. The occupancy could be refined, and this refined to nearly 0.5. As such, the occupancy was then fixed as exactly 0.5. This water molecule was within hydrogen bonding distance of only one other acceptor atom.

The structure is a non-merohedral twin. PLATON (Spek, 2003) was used to de-twin the structure. The twin component refined to 15%; the inclusion of the twin law lowered the R index from 6.4%. More importantly, it improved the weighting scheme. The final difference Fourier map was now diffuse, with the largest peak of slighly over 1 e Å-3 in the vicinity of C12.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: pubCIF (Westrip, 2009).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of Zn(H2O)(C4H5NO4)(C12H8N2).1.5H2O at the 70% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius. The O3w water molecule, which lies on a general position, has 0.5 occupancy.
Aqua(iminodiacetato-κ3O,N,O')(1,10-phenanthroline- κ2N,N')zinc(II) sesquihydrate top
Crystal data top
[Zn(C4H5NO4)(C12H8N2)(H2O)]·1.5H2OZ = 2
Mr = 421.70F(000) = 434
Triclinic, P1Dx = 1.736 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.5989 (1) ÅCell parameters from 6223 reflections
b = 10.6440 (1) Åθ = 2.5–28.3°
c = 11.5456 (2) ŵ = 1.57 mm−1
α = 95.156 (1)°T = 100 K
β = 91.845 (1)°Block, colorless
γ = 92.190 (1)°0.35 × 0.25 × 0.15 mm
V = 806.56 (2) Å3
Data collection top
Bruker SMART APEX
diffractometer		3640 independent reflections
Radiation source: fine-focus sealed tube3455 reflections with I > 2σ(I)
graphiteRint = 0.025
ω scansθmax = 27.5°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −8→8
Tmin = 0.610, Tmax = 0.799k = −13→13
7242 measured reflectionsl = −14→14
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.146H-atom parameters constrained
S = 1.22 w = 1/[σ2(Fo2) + (0.0241P)2 + 4.8628P]
where P = (Fo2 + 2Fc2)/3
3640 reflections(Δ/σ)max = 0.001
233 parametersΔρmax = 1.01 e Å−3
72 restraintsΔρmin = −0.88 e Å−3
Crystal data top
[Zn(C4H5NO4)(C12H8N2)(H2O)]·1.5H2Oγ = 92.190 (1)°
Mr = 421.70V = 806.56 (2) Å3
Triclinic, P1Z = 2
a = 6.5989 (1) ÅMo Kα radiation
b = 10.6440 (1) ŵ = 1.57 mm−1
c = 11.5456 (2) ÅT = 100 K
α = 95.156 (1)°0.35 × 0.25 × 0.15 mm
β = 91.845 (1)°
Data collection top
Bruker SMART APEX
diffractometer		3640 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		3455 reflections with I > 2σ(I)
Tmin = 0.610, Tmax = 0.799Rint = 0.025
7242 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.146Δρmax = 1.01 e Å−3
S = 1.22Δρmin = −0.88 e Å−3
3640 reflectionsAbsolute structure: ?
233 parametersFlack parameter: ?
72 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Zn10.30260 (7)0.63033 (5)0.84683 (4)0.01073 (15)
O1−0.0016 (5)0.7036 (3)0.8533 (3)0.0154 (6)
O2−0.1646 (5)0.8841 (3)0.8519 (4)0.0242 (8)
O30.3125 (5)0.6228 (3)1.0256 (3)0.0137 (6)
O40.3975 (5)0.7409 (3)1.1911 (3)0.0168 (7)
O1W0.6167 (5)0.5782 (3)0.8460 (3)0.0137 (6)
H110.69020.63760.87950.021*
H120.62940.51310.88120.021*
O2W0.5864 (6)1.0151 (3)0.7055 (3)0.0270 (8)
H210.66010.97370.74750.040*
H220.58861.09020.73490.040*
O3W0.7199 (12)1.0113 (7)0.4793 (7)0.0287 (16)0.50
H310.67051.01150.54550.043*0.50
H320.78701.07900.47400.043*0.50
N10.3717 (6)0.8255 (3)0.8921 (3)0.0155 (8)
H10.47350.84960.85070.019*
N20.1966 (5)0.4443 (4)0.7994 (3)0.0142 (7)
N30.3044 (5)0.6254 (4)0.6611 (3)0.0157 (7)
C1−0.0062 (7)0.8228 (4)0.8568 (4)0.0153 (8)
C20.1934 (7)0.8985 (4)0.8650 (5)0.0207 (10)
H2A0.21370.93490.79010.025*
H2B0.18490.96960.92590.025*
C30.4372 (7)0.8367 (4)1.0155 (4)0.0178 (9)
H3A0.38110.91411.05380.021*
H3B0.58690.84781.02060.021*
C40.3754 (6)0.7252 (4)1.0842 (4)0.0127 (8)
C50.1390 (6)0.3577 (4)0.8671 (4)0.0149 (8)
H50.13550.38020.94850.018*
C60.0828 (7)0.2336 (5)0.8242 (5)0.0200 (9)
H60.04240.17350.87600.024*
C70.0864 (7)0.1993 (5)0.7068 (4)0.0198 (9)
H70.05040.11510.67680.024*
C90.1991 (4)0.4127 (3)0.67929 (18)0.0146 (8)
C80.1450 (5)0.2916 (2)0.6299 (2)0.0186 (9)
C100.1399 (5)0.2654 (2)0.5097 (3)0.0265 (11)
H100.10290.18270.47590.032*
C110.1889 (5)0.3603 (3)0.43886 (18)0.0271 (11)
H11A0.18540.34230.35670.032*
C120.2430 (5)0.4813 (3)0.4883 (2)0.0213 (10)
C130.2481 (4)0.5075 (2)0.6085 (2)0.0168 (9)
C140.2936 (7)0.5828 (6)0.4185 (4)0.0254 (11)
H140.29120.56830.33600.030*
C150.3446 (7)0.6986 (5)0.4710 (4)0.0220 (10)
H150.37650.76680.42620.026*
C160.3497 (7)0.7169 (5)0.5941 (4)0.0209 (10)
H160.38740.79850.63040.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn10.0119 (2)0.0110 (2)0.0096 (2)0.00101 (17)0.00101 (17)0.00212 (17)
O10.0118 (14)0.0139 (14)0.0205 (16)−0.0007 (11)0.0005 (12)0.0029 (12)
O20.0160 (16)0.0179 (16)0.040 (2)0.0051 (13)0.0028 (15)0.0070 (15)
O30.0180 (15)0.0111 (14)0.0121 (15)0.0005 (12)0.0027 (12)0.0010 (11)
O40.0199 (16)0.0168 (15)0.0137 (15)0.0026 (12)−0.0020 (12)0.0013 (12)
O1W0.0139 (14)0.0114 (14)0.0162 (15)−0.0003 (11)−0.0003 (12)0.0035 (12)
O2W0.036 (2)0.0172 (17)0.0267 (19)0.0008 (15)−0.0018 (16)−0.0029 (14)
O3W0.038 (4)0.023 (4)0.026 (4)0.005 (3)0.006 (3)0.003 (3)
N10.0130 (18)0.0134 (17)0.021 (2)0.0021 (14)0.0008 (14)0.0051 (14)
N20.0089 (16)0.0159 (18)0.0175 (19)0.0032 (13)−0.0017 (14)−0.0013 (14)
N30.0078 (16)0.027 (2)0.0135 (18)0.0044 (14)0.0017 (13)0.0069 (15)
C10.014 (2)0.017 (2)0.016 (2)0.0014 (16)0.0028 (16)0.0052 (17)
C20.013 (2)0.014 (2)0.037 (3)0.0018 (16)0.0014 (19)0.0100 (19)
C30.023 (2)0.0123 (19)0.018 (2)−0.0015 (17)0.0011 (18)−0.0002 (16)
C40.0091 (18)0.0126 (19)0.017 (2)0.0027 (15)0.0023 (15)0.0016 (16)
C50.0088 (18)0.019 (2)0.016 (2)0.0008 (15)−0.0006 (15)−0.0006 (16)
C60.016 (2)0.018 (2)0.027 (2)0.0023 (17)0.0023 (18)0.0038 (18)
C70.014 (2)0.019 (2)0.025 (2)0.0023 (17)−0.0019 (18)−0.0068 (18)
C90.0073 (18)0.024 (2)0.013 (2)0.0044 (16)0.0002 (15)0.0001 (17)
C80.0083 (19)0.024 (2)0.023 (2)0.0015 (16)0.0000 (16)−0.0039 (18)
C100.011 (2)0.042 (3)0.024 (2)0.004 (2)−0.0026 (18)−0.012 (2)
C110.013 (2)0.050 (3)0.016 (2)0.005 (2)−0.0006 (17)−0.006 (2)
C120.0075 (18)0.041 (3)0.016 (2)0.0062 (18)0.0046 (16)0.0011 (19)
C130.0101 (19)0.026 (2)0.015 (2)0.0059 (17)0.0009 (15)0.0034 (17)
C140.014 (2)0.053 (3)0.010 (2)0.010 (2)0.0018 (17)0.008 (2)
C150.012 (2)0.042 (3)0.016 (2)0.0095 (19)0.0052 (16)0.015 (2)
C160.013 (2)0.033 (3)0.018 (2)0.0052 (18)0.0019 (17)0.0109 (19)
Geometric parameters (Å, °) top
Zn1—O32.072 (3)C2—H2B0.9900
Zn1—N22.093 (4)C3—C41.535 (6)
Zn1—N12.124 (4)C3—H3A0.9900
Zn1—N32.141 (4)C3—H3B0.9900
Zn1—O1W2.166 (3)C5—C61.401 (6)
Zn1—O12.182 (3)C5—H50.9500
O1—C11.267 (5)C6—C71.373 (7)
O2—C11.255 (5)C6—H60.9500
O3—C41.278 (5)C7—C81.433 (6)
O4—C41.233 (6)C7—H70.9500
O1W—H110.8399C9—C81.3900
O1W—H120.8400C9—C131.3900
O2W—H210.8400C8—C101.3900
O2W—H220.8400C10—C111.3900
O3W—H310.8401C10—H100.9500
O3W—H320.8399C11—C121.3900
N1—C31.469 (6)C11—H11A0.9500
N1—C21.475 (6)C12—C131.3900
N1—H10.8800C12—C141.440 (6)
N2—C51.315 (6)C14—C151.350 (8)
N2—C91.398 (4)C14—H140.9500
N3—C161.329 (6)C15—C161.415 (7)
N3—C131.376 (5)C15—H150.9500
C1—C21.513 (6)C16—H160.9500
C2—H2A0.9900
O3—Zn1—N298.01 (14)N1—C3—H3A108.3
O3—Zn1—N183.15 (14)C4—C3—H3A108.3
N2—Zn1—N1172.78 (14)N1—C3—H3B108.3
O3—Zn1—N3175.75 (14)C4—C3—H3B108.3
N2—Zn1—N379.24 (16)H3A—C3—H3B107.4
N1—Zn1—N399.99 (16)O4—C4—O3125.7 (4)
O3—Zn1—O1W88.31 (12)O4—C4—C3117.1 (4)
N2—Zn1—O1W92.50 (13)O3—C4—C3117.2 (4)
N1—Zn1—O1W94.66 (13)N2—C5—C6122.7 (4)
N3—Zn1—O1W88.57 (13)N2—C5—H5118.6
O3—Zn1—O190.74 (12)C6—C5—H5118.6
N2—Zn1—O193.69 (13)C7—C6—C5119.5 (5)
N1—Zn1—O179.15 (13)C7—C6—H6120.3
N3—Zn1—O192.67 (13)C5—C6—H6120.3
O1W—Zn1—O1173.81 (12)C6—C7—C8119.5 (4)
C1—O1—Zn1114.4 (3)C6—C7—H7120.3
C4—O3—Zn1114.8 (3)C8—C7—H7120.3
Zn1—O1W—H11109.5C8—C9—C13120.0
Zn1—O1W—H12109.4C8—C9—N2121.7 (2)
H11—O1W—H12109.5C13—C9—N2118.2 (2)
H21—O2W—H22108.3C10—C8—C9120.0
H31—O3W—H32110.0C10—C8—C7122.4 (3)
C3—N1—C2114.7 (4)C9—C8—C7117.5 (3)
C3—N1—Zn1105.8 (3)C8—C10—C11120.0
C2—N1—Zn1109.4 (3)C8—C10—H10120.0
C3—N1—H1108.9C11—C10—H10120.0
C2—N1—H1108.9C12—C11—C10120.0
Zn1—N1—H1108.9C12—C11—H11A120.0
C5—N2—C9119.1 (4)C10—C11—H11A120.0
C5—N2—Zn1128.5 (3)C13—C12—C11120.0
C9—N2—Zn1112.3 (3)C13—C12—C14118.0 (3)
C16—N3—C13118.5 (4)C11—C12—C14122.0 (3)
C16—N3—Zn1129.7 (4)N3—C13—C12121.9 (2)
C13—N3—Zn1111.8 (2)N3—C13—C9118.1 (2)
O2—C1—O1125.1 (4)C12—C13—C9120.0
O2—C1—C2116.7 (4)C15—C14—C12119.5 (4)
O1—C1—C2118.3 (4)C15—C14—H14120.2
N1—C2—C1114.4 (4)C12—C14—H14120.2
N1—C2—H2A108.7C14—C15—C16119.0 (5)
C1—C2—H2A108.7C14—C15—H15120.5
N1—C2—H2B108.7C16—C15—H15120.5
C1—C2—H2B108.7N3—C16—C15123.0 (5)
H2A—C2—H2B107.6N3—C16—H16118.5
N1—C3—C4115.9 (4)C15—C16—H16118.5
O3—Zn1—O1—C195.8 (3)Zn1—O3—C4—C3−1.0 (5)
N2—Zn1—O1—C1−166.1 (3)N1—C3—C4—O4−167.9 (4)
N1—Zn1—O1—C112.9 (3)N1—C3—C4—O314.5 (6)
N3—Zn1—O1—C1−86.8 (3)C9—N2—C5—C61.0 (6)
N2—Zn1—O3—C4179.4 (3)Zn1—N2—C5—C6−175.9 (3)
N1—Zn1—O3—C4−7.8 (3)N2—C5—C6—C7−0.2 (7)
O1W—Zn1—O3—C487.1 (3)C5—C6—C7—C8−0.9 (7)
O1—Zn1—O3—C4−86.8 (3)C5—N2—C9—C8−0.8 (5)
O3—Zn1—N1—C314.2 (3)Zn1—N2—C9—C8176.55 (15)
N3—Zn1—N1—C3−162.9 (3)C5—N2—C9—C13176.0 (3)
O1W—Zn1—N1—C3−73.6 (3)Zn1—N2—C9—C13−6.6 (3)
O1—Zn1—N1—C3106.2 (3)C13—C9—C8—C100.0
O3—Zn1—N1—C2−110.0 (3)N2—C9—C8—C10176.8 (3)
N3—Zn1—N1—C272.9 (3)C13—C9—C8—C7−177.0 (3)
O1W—Zn1—N1—C2162.3 (3)N2—C9—C8—C7−0.2 (4)
O1—Zn1—N1—C2−17.9 (3)C6—C7—C8—C10−175.9 (3)
O3—Zn1—N2—C55.3 (4)C6—C7—C8—C91.0 (5)
N3—Zn1—N2—C5−178.0 (4)C9—C8—C10—C110.0
O1W—Zn1—N2—C594.0 (4)C7—C8—C10—C11176.9 (3)
O1—Zn1—N2—C5−85.9 (4)C8—C10—C11—C120.0
O3—Zn1—N2—C9−171.7 (2)C10—C11—C12—C130.0
N3—Zn1—N2—C95.0 (2)C10—C11—C12—C14−179.6 (3)
O1W—Zn1—N2—C9−83.1 (3)C16—N3—C13—C121.8 (5)
O1—Zn1—N2—C997.0 (3)Zn1—N3—C13—C12−178.48 (15)
N2—Zn1—N3—C16176.8 (4)C16—N3—C13—C9−179.4 (3)
N1—Zn1—N3—C164.1 (4)Zn1—N3—C13—C90.3 (3)
O1W—Zn1—N3—C16−90.4 (4)C11—C12—C13—N3178.8 (3)
O1—Zn1—N3—C1683.5 (4)C14—C12—C13—N3−1.6 (4)
N2—Zn1—N3—C13−2.9 (2)C11—C12—C13—C90.0
N1—Zn1—N3—C13−175.6 (2)C14—C12—C13—C9179.6 (3)
O1W—Zn1—N3—C1389.9 (3)C8—C9—C13—N3−178.8 (3)
O1—Zn1—N3—C13−96.2 (3)N2—C9—C13—N34.2 (3)
Zn1—O1—C1—O2174.2 (4)C8—C9—C13—C120.0
Zn1—O1—C1—C2−4.4 (5)N2—C9—C13—C12−176.9 (3)
C3—N1—C2—C1−97.2 (5)C13—C12—C14—C150.2 (5)
Zn1—N1—C2—C121.6 (5)C11—C12—C14—C15179.8 (3)
O2—C1—C2—N1169.4 (4)C12—C14—C15—C160.9 (7)
O1—C1—C2—N1−11.9 (7)C13—N3—C16—C15−0.6 (6)
C2—N1—C3—C4101.9 (4)Zn1—N3—C16—C15179.8 (3)
Zn1—N1—C3—C4−18.9 (4)C14—C15—C16—N3−0.8 (7)
Zn1—O3—C4—O4−178.3 (3)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2w0.882.643.388 (5)143
O1w—H11···O1i0.842.172.801 (4)132
O1w—H12···O3ii0.841.922.757 (4)172
O2w—H21···O2i0.841.982.815 (5)177
O2w—H22···O4iii0.841.922.756 (5)177
O3w—H31···O2w0.841.942.780 (9)174
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+2; (iii) −x+1, −y+2, −z+2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1w—H11···O1i0.842.172.801 (4)132
O1w—H12···O3ii0.841.922.757 (4)172
O2w—H21···O2i0.841.982.815 (5)177
O2w—H22···O4iii0.841.922.756 (5)177
O3w—H31···O2w0.841.942.780 (9)174
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+2; (iii) −x+1, −y+2, −z+2.
Acknowledgements top

We thank Universiti Tunku Abdul Rahman and the University of Malaya for supporting this study.

references
References top

Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.

Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Morel, C., Choquesillo-Lazarte, D., Alarcón-Payer, C., González-Pérez, J. M., Castiñeiras, A. & Niclós-Gutiérrez, J. (2003). Inorg. Chem. Commun. 11, 1354–1357.

Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Sinkha, U.-Ch., Kramarenko, F. G., Polynova, T. N., Porai-Koshits, M. A. & Mitrofanova, N. D. (1975). Zh. Strukt. Khim. 16, 144–145.

Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

Westrip, S. P. (2009). publCIF. In preparation.