supplementary materials


hy2612 scheme

Acta Cryst. (2013). E69, m99-m100    [ doi:10.1107/S160053681300069X ]

(2-Amino-7-methyl-4-oxidopteridine-6-carboxylato-[kappa]3O4,N5,O6)aqua(ethane-1,2-diamine-[kappa]2N,N')nickel(II) dihydrate

S. S. Baisya and P. S. Roy

Abstract top

The NiII atom in the title complex, [Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2O, is six-coordinated in a distorted octahedral geometry by a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxylate (pterin) ligand, a bidentate ancillary ethane-1,2-diamine (en) ligand and a water molecule. The pterin ligand forms two chelate rings. The en and pterin ligands are arranged nearly orthogonally [dihedral angle between the mean plane of the en molecule and the pterin ring = 77.1 (1)°]. N-H...O, O-H...N and O-H...O hydrogen bonds link the complex molecules and lattice water molecules into a three-dimensional network. [pi]-[pi] interactions are observed between the pyrazine and pyrimidine rings [centroid-centroid distance = 3.437 (2) Å].

Comment top

The importance of pterins in several classes of metalloenzymes has catalysed symbiotic developments of their coordination chemistry (Basu & Burgmayer, 2011; Burgmayer, 1998; Fitzpatrick, 2003; Fukuzumi & Kojima, 2008; Kaim et al., 1999). A SciFinder search reveals the existence of only one structurally characterized nickel(II)–pterin complex (Crispini et al., 2005), thereby highlighting the urgency of development in this direction. The present endeavour is concerned with the title complex, possessing both a tridentate pterin ligand and a σ-donor ligand like en. The six-coordinated NiII atom shows departure from a regular octahedral geometry with respect to both bond lengths and angles (Fig. 1). The equatorial plane is formed by the two N atoms (N1, N2) of en, the pyrazine ring N atom (N3) of the pterin ligand and the aqua O atom (O6). The axial positions are occupied by the two pterin O atoms (O1 and O3), with the latter one forming the longest axial bond [2.327 (2) Å]. One important factor causing distortion from regular octahedral geometry is that this pterin ligand forms two five-membered chelate rings with small bite angles [76.31 (9) and 77.20 (10)°], instead of only one per pterin ligand for the earlier case (Crispini et al., 2005). A perusal of the charge balance of this complex indicates that this pterin ligand acts as a binegative tridentate ONO-donor. A near orthogonal disposition of the en ligand and pterin chelate ring is observed, which helps to minimize the steric repulsion. Of the three axes, least deviation from linearity is observed in the N3—Ni1—N2 direction [177.56 (11)°], where the highest electron density is concentrated [Ni1—N3 = 1.976 (2), Ni1—N2 = 2.065 (3) Å]. It represents the unique combination of a σ-donor atom N2 (en) and the N3 atom of the redox noninnocent pterin ligand from the opposite directions of the NiII centre (d8), with possible assistance from the π-donating phenolate and carboxylate O atoms (Kohzuma et al., 1988). Again, location of the pyrazine ring N atom (N3) in the equatorial plane is consistent with the earlier observations on related copper complexes (Odani et al., 1992).

Although the exocyclic bond length data of the pyrazine ring, e.g. C3—C9 [1.527 (4) Å] and C4—C10 [1.503 (4) Å] reflect only limited conjugation with the pyrazine ring π system, the corresponding bond length data of the pyrimidine ring, C7—O3 [1.267 (3) Å] and C6—N7 [1.349 (4) Å] merit attention. Small deviations, e.g. 2.02° and 1.37° of the C7/N6/C6 and C5/N5/C6 segments respectively, with respect to the C6—N7 multiple bond, indicate near planarity for the pyrimidine ring. So it can participate in the electron-shuffling process by the pterin unit from the pyrazine ring N4 to the C7-carbonyl group, as per literature suggestion (Beddoes et al., 1993; Russell et al., 1992). Formation of the Ni1—O3 bond assists this process.

In the crystal, the complex molecules and lattice water molecules are linked by intermolecular N—H···O, O—H···N and O—H···O hydrogen bonds (Table 1) into a three-dimensional network. The lattice water molecules are decisive for the crystal packing (Figure 2).

Related literature top

For the importance of pterin in metalloenzymes, see: Basu & Burgmayer (2011); Burgmayer (1998); Fitzpatrick (2003); Fukuzumi & Kojima (2008); Kaim et al. (1999). For the structure of related nickel complex, see: Crispini et al. (2005). For structures of related copper complexes, see: Odani et al. (1992). For the electron-shuffling ability of the pterin unit as well as its donor groups and the affect on the geometric parameters of related complexes, see: Beddoes et al. (1993); Kohzuma et al. (1988); Russell et al. (1992). For the synthesis of the pterin ligand, see: Wittle et al. (1947). For refinement of H atoms, see: Cooper et al. (2010).

Experimental top

2-Amino-4-hydroxy-7-methylpteridine-6-carboxylic acid sesquihydrate (C8H7N5O3.1.5H2O) was obtained by published procedure (Wittle et al., 1947). The title complex was prepared by the slow addition of an aqueous alkaline solution (NaOH: 44 mg, 1.1 mmol) of the pterin ligand (124 mg, 0.5 mmol) to a well stirred warm (323 K; paraffin oil bath) aqueous reaction mixture containing NiSO4.7H2O (140 mg, 0.5 mmol) and 1,2-ethanediamine (36 mg, 0.6 mmol) under subdued light; final volume was 35 ml. The pH value was adjusted to 9.2 and the stirring was continued for 3 h. Upon standing, the reaction medium deposited yellow-brown crystals after 2 days, which were suitable for single-crystal X-ray diffraction (yield: 30%). Analytically pure compound could be obtained by filtration, repeated washing with small quantities of water and drying in vacuo over silica gel. Analysis, calculated for C10H19N7NiO6: C 30.70, H 4.89, N 25.06%; found: C 30.51, H 5.11, N 24.55%.

Refinement top

H atoms were all located in a difference map, but those attached to C atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on bond lengths and angles to regularize their geometry (C—H = 0.93–0.98, N—H = 0.86–0.89, O—H = 0.82 Å) and with Uiso(H) = 1.2–1.5Ueq(parent atom), after which the positions were refined with riding constraints (Cooper et al., 2010).

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: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 40% probability level. Lattice water molecules are omitted for clarity.
[Figure 2] Fig. 2. The crystal packing diagram of the title compound, viewed along the c axis. Dotted lines indicate hydrogen bonds.
(2-Amino-7-methyl-4-oxidopteridine-6-carboxylato- κ3O4,N5,O6)aqua(ethane-1,2-diamine- κ2N,N')nickel(II) dihydrate top
Crystal data top
[Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2OF(000) = 816
Mr = 392.01Dx = 1.675 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8393 reflections
a = 10.406 (4) Åθ = 2.0–28.2°
b = 14.323 (5) ŵ = 1.29 mm1
c = 10.450 (4) ÅT = 293 K
β = 93.294 (6)°Plate, brown
V = 1554.9 (10) Å30.49 × 0.38 × 0.28 mm
Z = 4
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2760 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
φ & ω scansθmax = 28.2°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1313
Tmin = 0.56, Tmax = 0.70k = 1815
8393 measured reflectionsl = 1113
3488 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.135 Method = Modified Sheldrick w = 1/[σ2(F2) + (0.09P)2 + 1.95P],
where P = (max(Fo2,0) + 2Fc2)/3
S = 0.92(Δ/σ)max = 0.001
3488 reflectionsΔρmax = 1.12 e Å3
217 parametersΔρmin = 0.84 e Å3
0 restraints
Crystal data top
[Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2OV = 1554.9 (10) Å3
Mr = 392.01Z = 4
Monoclinic, P21/cMo Kα radiation
a = 10.406 (4) ŵ = 1.29 mm1
b = 14.323 (5) ÅT = 293 K
c = 10.450 (4) Å0.49 × 0.38 × 0.28 mm
β = 93.294 (6)°
Data collection top
Bruker Kappa APEXII CCD
diffractometer
3488 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
2760 reflections with I > 2σ(I)
Tmin = 0.56, Tmax = 0.70Rint = 0.035
8393 measured reflectionsθmax = 28.2°
Refinement top
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.135Δρmax = 1.12 e Å3
S = 0.92Δρmin = 0.84 e Å3
3488 reflectionsAbsolute structure: ?
217 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier, J. & Glazer, A.M., 1986. J. Appl. Cryst. 105–107) with a nominal stability of 0.1 K.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Ni10.33168 (3)0.37414 (3)0.40998 (3)0.0270
O10.2677 (2)0.35342 (17)0.2158 (2)0.0355
C90.1450 (3)0.3461 (2)0.1944 (3)0.0297
O20.0914 (2)0.3290 (2)0.0880 (2)0.0430
C30.0659 (3)0.3591 (2)0.3117 (3)0.0255
N30.1423 (2)0.37361 (17)0.4173 (2)0.0245
C80.0909 (3)0.3850 (2)0.5295 (3)0.0236
C50.0427 (3)0.3859 (2)0.5402 (3)0.0248
N40.1228 (2)0.37363 (19)0.4340 (2)0.0282
C40.0692 (3)0.3588 (2)0.3213 (3)0.0279
C100.1616 (3)0.3442 (3)0.2074 (3)0.0400
H1110.16530.28100.18530.0637*
H1130.13530.37680.13260.0631*
H1120.24770.36440.22570.0629*
N50.0930 (2)0.39909 (19)0.6560 (2)0.0285
C60.0042 (3)0.4045 (2)0.7565 (3)0.0290
N60.1283 (2)0.4046 (2)0.7564 (2)0.0310
C70.1792 (3)0.3970 (2)0.6422 (3)0.0268
O30.2995 (2)0.39847 (18)0.6257 (2)0.0369
N70.0522 (3)0.4136 (3)0.8732 (3)0.0489
O60.3383 (2)0.51989 (16)0.3730 (2)0.0341
H1820.28330.56260.37350.0551*
H1810.38890.52300.31560.0554*
N10.3513 (3)0.2334 (2)0.4537 (3)0.0343
C10.4854 (4)0.2201 (3)0.5050 (4)0.0463
C20.5735 (3)0.2713 (3)0.4201 (4)0.0475
N20.5298 (3)0.36927 (19)0.4057 (3)0.0343
H2210.55590.38880.33260.0516*
H2220.56300.39940.46910.0520*
H2110.66260.27050.45600.0603*
H2120.57060.23940.33830.0606*
H2020.50960.15460.51230.0585*
H2010.49100.24820.59080.0590*
H1920.29660.21950.51350.0560*
H1910.33710.20060.38170.0561*
O40.5313 (3)0.5259 (3)0.2007 (3)0.0699
H2310.59470.54990.23950.1050*
H2320.57490.51890.13840.1048*
O50.2936 (3)0.4894 (2)0.0008 (3)0.0646
H2410.31130.53700.04130.1023*
H2420.30590.45420.06220.1021*
H1710.00410.42060.94330.0500*
H1720.13060.44160.89770.0500*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ni10.0198 (2)0.0344 (2)0.0270 (2)0.00059 (15)0.00148 (14)0.00027 (15)
O10.0291 (12)0.0516 (15)0.0262 (11)0.0017 (10)0.0057 (9)0.0032 (10)
C90.0317 (16)0.0329 (16)0.0248 (14)0.0026 (12)0.0035 (12)0.0003 (12)
O20.0388 (13)0.0651 (17)0.0246 (11)0.0035 (12)0.0024 (9)0.0070 (11)
C30.0270 (15)0.0261 (15)0.0230 (13)0.0008 (11)0.0010 (11)0.0025 (11)
N30.0232 (12)0.0270 (12)0.0234 (12)0.0004 (9)0.0012 (9)0.0012 (9)
C80.0213 (13)0.0270 (15)0.0225 (13)0.0001 (11)0.0002 (10)0.0002 (11)
C50.0243 (14)0.0264 (15)0.0236 (13)0.0007 (11)0.0010 (11)0.0007 (11)
N40.0210 (12)0.0360 (14)0.0273 (12)0.0003 (10)0.0011 (9)0.0011 (10)
C40.0254 (14)0.0316 (16)0.0261 (14)0.0005 (11)0.0026 (11)0.0014 (12)
C100.0275 (16)0.062 (2)0.0293 (16)0.0013 (15)0.0087 (13)0.0057 (15)
N50.0222 (12)0.0391 (15)0.0242 (12)0.0033 (10)0.0026 (9)0.0006 (10)
C60.0281 (15)0.0344 (16)0.0245 (14)0.0061 (12)0.0006 (11)0.0019 (12)
N60.0258 (13)0.0416 (15)0.0252 (12)0.0018 (11)0.0016 (10)0.0017 (11)
C70.0233 (14)0.0311 (16)0.0255 (14)0.0000 (11)0.0018 (11)0.0014 (12)
O30.0213 (11)0.0557 (15)0.0332 (12)0.0005 (10)0.0013 (9)0.0076 (10)
N70.0346 (16)0.090 (3)0.0223 (13)0.0139 (16)0.0031 (11)0.0031 (15)
O60.0233 (10)0.0379 (13)0.0413 (12)0.0031 (9)0.0028 (9)0.0008 (10)
N10.0297 (14)0.0376 (15)0.0361 (14)0.0018 (11)0.0058 (11)0.0034 (12)
C10.042 (2)0.047 (2)0.049 (2)0.0061 (16)0.0049 (16)0.0111 (17)
C20.0299 (18)0.047 (2)0.065 (2)0.0032 (15)0.0009 (17)0.0042 (19)
N20.0263 (13)0.0369 (15)0.0396 (15)0.0014 (11)0.0009 (11)0.0022 (12)
O40.0535 (18)0.117 (3)0.0386 (15)0.0370 (18)0.0034 (13)0.0002 (16)
O50.065 (2)0.0592 (19)0.071 (2)0.0075 (15)0.0150 (16)0.0168 (16)
Geometric parameters (Å, º) top
Ni1—O12.120 (2)C6—N71.350 (4)
Ni1—N31.977 (3)N6—C71.338 (4)
Ni1—O32.324 (2)C7—O31.273 (4)
Ni1—O62.125 (2)N7—H1710.917
Ni1—N12.075 (3)N7—H1720.958
Ni1—N22.066 (3)O6—H1820.838
O1—C91.288 (4)O6—H1810.821
C9—O21.239 (4)N1—C11.478 (5)
C9—C31.527 (4)N1—H1920.892
C3—N31.339 (4)N1—H1910.892
C3—C41.416 (4)C1—C21.503 (5)
N3—C81.326 (4)C1—H2020.974
C8—C51.401 (4)C1—H2010.981
C8—C71.461 (4)C2—N21.479 (5)
C5—N41.361 (4)C2—H2110.980
C5—N51.359 (4)C2—H2120.969
N4—C41.349 (4)N2—H2210.872
C4—C101.501 (4)N2—H2220.847
C10—H1110.934O4—H2310.828
C10—H1130.965O4—H2320.821
C10—H1120.970O5—H2410.827
N5—C61.361 (4)O5—H2420.833
C6—N61.378 (4)
O1—Ni1—N377.16 (10)C5—N5—C6114.6 (2)
O1—Ni1—O3153.46 (8)N5—C6—N6129.4 (3)
N3—Ni1—O376.30 (9)N5—C6—N7115.6 (3)
O1—Ni1—O688.57 (10)N6—C6—N7115.0 (3)
N3—Ni1—O693.08 (9)C6—N6—C7116.6 (2)
O3—Ni1—O692.13 (9)C8—C7—N6117.7 (3)
O1—Ni1—N195.53 (11)C8—C7—O3118.1 (3)
N3—Ni1—N194.21 (11)N6—C7—O3124.2 (3)
O3—Ni1—N187.12 (10)Ni1—O3—C7109.05 (19)
O6—Ni1—N1172.28 (9)C6—N7—H171118.7
O1—Ni1—N2103.50 (11)C6—N7—H172130.3
N3—Ni1—N2177.63 (11)H171—N7—H172104.8
O3—Ni1—N2103.04 (10)Ni1—O6—H182133.3
O6—Ni1—N289.22 (10)Ni1—O6—H181102.4
N1—Ni1—N283.47 (11)H182—O6—H181115.6
Ni1—O1—C9115.57 (18)Ni1—N1—C1106.5 (2)
O1—C9—O2124.2 (3)Ni1—N1—H192108.2
O1—C9—C3115.1 (3)C1—N1—H192110.2
O2—C9—C3120.6 (3)Ni1—N1—H191108.4
C9—C3—N3111.1 (3)C1—N1—H191110.2
C9—C3—C4129.8 (3)H192—N1—H191113.2
N3—C3—C4119.1 (3)N1—C1—C2108.6 (3)
C3—N3—Ni1120.9 (2)N1—C1—H202112.7
C3—N3—C8119.9 (3)C2—C1—H202110.7
Ni1—N3—C8119.15 (19)N1—C1—H201106.5
N3—C8—C5121.6 (3)C2—C1—H201109.5
N3—C8—C7117.4 (3)H202—C1—H201108.8
C5—C8—C7121.0 (3)C1—C2—N2109.2 (3)
C8—C5—N4119.9 (3)C1—C2—H211111.3
C8—C5—N5120.5 (3)N2—C2—H211109.2
N4—C5—N5119.6 (3)C1—C2—H212107.6
C5—N4—C4117.9 (3)N2—C2—H212111.4
C3—C4—N4121.6 (3)H211—C2—H212108.2
C3—C4—C10122.6 (3)C2—N2—Ni1109.3 (2)
N4—C4—C10115.9 (3)C2—N2—H221106.5
C4—C10—H111110.4Ni1—N2—H221111.7
C4—C10—H113112.1C2—N2—H222107.1
H111—C10—H113106.2Ni1—N2—H222109.2
C4—C10—H112111.0H221—N2—H222112.9
H111—C10—H112108.2H231—O4—H23288.8
H113—C10—H112108.8H241—O5—H24293.4
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H192···O1i0.892.393.175 (4)147
N1—H192···O2i0.892.423.243 (4)154
N2—H221···O40.872.403.103 (5)137
N2—H222···O6ii0.852.223.064 (4)176
N7—H171···O2iii0.922.162.890 (4)136
N7—H172···O5iv0.962.293.225 (5)167
O4—H231···O3ii0.831.892.683 (4)160
O4—H232···O5v0.822.042.858 (5)171
O5—H242···O10.832.213.010 (4)160
O6—H181···O40.821.962.774 (4)171
O6—H182···N5iv0.842.062.805 (3)148
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x+1, y+1, z+1; (iii) x, y, z+1; (iv) x, y+1, z+1; (v) x+1, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H192···O1i0.892.393.175 (4)147
N1—H192···O2i0.892.423.243 (4)154
N2—H221···O40.872.403.103 (5)137
N2—H222···O6ii0.852.223.064 (4)176
N7—H171···O2iii0.922.162.890 (4)136
N7—H172···O5iv0.962.293.225 (5)167
O4—H231···O3ii0.831.892.683 (4)160
O4—H232···O5v0.822.042.858 (5)171
O5—H242···O10.832.213.010 (4)160
O6—H181···O40.821.962.774 (4)171
O6—H182···N5iv0.842.062.805 (3)148
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x+1, y+1, z+1; (iii) x, y, z+1; (iv) x, y+1, z+1; (v) x+1, y+1, z.
Acknowledgements top

The authors are grateful to the UGC, New Delhi, for financial assistance (SAP–DRS program). Thanks are due to the CSMCRI, Bhavnagar, Gujrat, India, for the X-ray structural data and elemental analysis data, and the University of North Bengal for infrastructure.

references
References top

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