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Crystal structure of (2-amino-7-methyl-4-oxido­pteridine-6-carboxyl­ato-κ3O4,N5,O6)aqua­(1,10-phenanthroline-κ2N,N′)copper(II) trihydrate

aDepartment of Chemistry, University of North Bengal, Siliguri 734 013, India
*Correspondence e-mail: psrnbu@gmail.com

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 24 September 2014; accepted 9 October 2014; online 18 October 2014)

In the title compound, [Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2O, the CuII cation is O,N,O′-chelated by the 2-amino-7-methyl-4-oxidopteridine-6-carboxyl­ate anion and N,N′-chelated by the 1,10-phenanthroline (phen) ligand. A water mol­ecule further coordinates to the CuII cation to complete the elongated distorted octa­hedral coordination geometry. In the mol­ecule, the pteridine ring system is essentially planar [maximum deviation = 0.055 (4) Å], and its mean plane is nearly perpendicular to the phen ring system [dihedral angle = 85.97 (3)°]. In the crystal, N—H⋯O, O—H⋯N and O—H⋯·O hydrogen bonds, as well as weak C—H⋯O hydrogen bonds and C—H⋯π inter­actions, link the complex mol­ecules and lattice water mol­ecules into a three-dimensional supra­molecular architecture. Extensive ππ stacking between nearly parallel aromatic rings of adjacent mol­ecules are also observed, the centroid-to-centroid distances being 3.352 (2), 3.546 (3), 3.706 (3) and 3.744 (3) Å.

1. Chemical context

The ubiquitous presence of pterins in nature including several classes of metalloenzymes, has catalysed developments of their coordination chemistry (Basu & Burgmayer, 2011[Basu, P. & Burgmayer, S. J. N. (2011). Coord. Chem. Rev. 255, 1016-1038.]; Burgmayer, 1998[Burgmayer, S. J. N. (1998). Struct. Bond. 92, 67-119.]; Dix & Benkovic, 1988[Dix, T. A. & Benkovic, S. J. (1988). Acc. Chem. Res. 21, 101-107.]; Erlandsen et al., 2000[Erlandsen, H., Bjørgo, E., Flatmark, T. & Stevens, R. C. (2000). Biochemistry, 39, 2208-2217.]; Fitzpatrick, 2003[Fitzpatrick, P. F. (2003). Biochemistry, 42, 14083-14091.]). Literature survey reveals the paucity of structurally characterized CuII complexes involving tridentate pterin coordination (Kohzuma et al., 1989[Kohzuma, T., Masuda, H. & Yamauchi, O. (1989). J. Am. Chem. Soc. 111, 3431-3433.]). The present work is concerned with the title complex, possessing both a tridentate pterin ligand and a π-acidic ligand like phen.

[Scheme 1]

2. Structural commentary

The hexa­coordinated CuII atom is located in an axially elongated distorted octa­hedron (Fig. 1[link] and Table 1[link]). The equatorial plane is formed by the two N atoms of phen, the pyrazine ring N atom of the pterin ligand and the aqua O atom. The axial positions are occupied by the two pterin O atoms, with the former one forming the longest axial bond [2.384 (3) Å]. Apart from the characteristic Jahn–Teller effect, another reason for distortion from a regular octa­hedral geometry is that the pterin ligand forms two five-membered chelate rings with small bite angles [76.47 (10) and 74.66 (11)°]. Consideration of the charge balance of this complex indicates that this pterin ligand acts as a binegative tridentate O,N,O′-donor. A near orthogonal disposition of the phen ligand and pterin chelate ring helps to minimize the steric repulsion. Of the three axes, the least deviation from linearity is observed in the O4—Cu1—N2 direction [174.45 (13)°]. Location of the pyrazine ring N atom (N6) in the equatorial plane is in agreement with earlier observations on related copper and cobalt complexes (Baisya et al., 2013[Baisya, S. S., Sen, S. & Roy, P. S. (2013). Acta Cryst. E69, m70-m71.]; Odani et al., 1992[Odani, A., Masuda, H., Inukai, K. & Yamauchi, O. (1992). J. Am. Chem. Soc. 114, 6294-6300.]); the Cu1—N6 bond length [1.999 (3) Å] is the shortest one in this case.

Table 1
Selected bond lengths (Å)

Cu1—N1 2.002 (3) Cu1—O1 2.384 (3)
Cu1—N2 2.037 (3) Cu1—O2 2.304 (3)
Cu1—N6 1.999 (3) Cu1—O4 2.019 (3)
[Figure 1]
Figure 1
The mol­ecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level.

The multiple bond character of the O1—C13 bond [1.237 (4) Å] may be elucidated in the light of Joule's hypothesis (Beddoes et al., 1993[Beddoes, R. L., Russell, J. R., Garner, C. D. & Joule, J. A. (1993). Acta Cryst. C49, 1649-1652.]; Russell et al., 1992[Russell, J. R., Garner, C. D. & Joule, J. A. (1992). J. Chem. Soc. Perkin Trans. 1, pp. 1245-1249.]), suggesting electron-density withdrawal from the pyrazine ring N5 by the pyrimidine ring C13 carbonyl group through mesomeric inter­action. Formation of the O1—Cu1 bond assists this electron flow towards atom O1, with possible participation of the electron-rich N7—C14 [1.327 (5) Å] bond in this process.

3. Supra­molecular features

In the crystal, inter­molecular N—H⋯·O, O—H⋯·N and O—H⋯O hydrogen bonds (Table 2[link]) link the complex mol­ecules and lattice water mol­ecules into a layer parallel to (001) (Fig. 2[link]). Inter­molecular weak C—H⋯O hydrogen bonds and C—H⋯π inter­actions are also observed in the crystal. In addition, ππ stacking between nearly parallel pterin ring systems of adjacent mol­ecules occurs in the crystal structure, the centroid–centroid distance being 3.352 (2) Å (Fig. 3[link]). Again, the nearly parallel phen rings of adjacent mol­ecules also display ππ stacking inter­actions with centroids distances of 3.546 (3), 3.706 (3) and 3.744 (3) Å. These inter­molecular inter­actions link the mol­ecules into a three-dimensional supra­molecular architecture.

Table 2
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the N3/N4/C13–C16 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H4C⋯O5 0.82 (3) 1.92 (3) 2.722 (4) 169 (5)
O4—H4D⋯N4i 0.81 (3) 2.26 (3) 3.038 (4) 161 (5)
O5—H5C⋯O6 0.82 (3) 1.96 (4) 2.748 (5) 162 (4)
O5—H5D⋯N4ii 0.82 (5) 2.07 (5) 2.891 (5) 176 (3)
O6—H6C⋯O2 0.82 (3) 2.23 (3) 2.921 (4) 141 (5)
O6—H6C⋯O3 0.82 (3) 2.25 (4) 3.029 (4) 158 (5)
O7—H7C⋯O6 0.82 (2) 2.24 (3) 2.965 (6) 148 (5)
O7—H7D⋯O1iii 0.81 (5) 2.16 (4) 2.943 (6) 162 (5)
N7—H7E⋯O5i 0.85 (5) 2.17 (4) 2.998 (6) 162 (4)
N7—H7F⋯O3iv 0.86 (4) 2.14 (5) 2.908 (5) 148 (4)
C1—H1⋯O3v 0.93 2.47 3.175 (6) 133
C10—H10⋯O1vi 0.93 2.54 3.406 (5) 155
C12—H12⋯O7vii 0.93 2.57 3.343 (7) 140
C6—H6⋯Cgvi 0.93 2.82 3.740 (5) 173
Symmetry codes: (i) -x+2, -y+2, -z+2; (ii) x, y-1, z; (iii) x-1, y-1, z; (iv) x+1, y+1, z; (v) x+1, y, z; (vi) -x+2, -y+2, -z+1; (vii) x, y+1, z.
[Figure 2]
Figure 2
The crystal packing diagram of the title compound, viewed along the a axis. Hydrogen bonds (dotted lines) assist the formation of a layer structure parallel to (001).
[Figure 3]
Figure 3
A mol­ecular packing diagram highlighting ππ stacking inter­actions between neighbouring phen–phen and pterin–pterin rings.

4. Database survey

The crystal structures of copper(II) complexes chelated by the pterin-6-carboxyl­ate anion have been reported by Kohzuma et al. (1989[Kohzuma, T., Masuda, H. & Yamauchi, O. (1989). J. Am. Chem. Soc. 111, 3431-3433.]) and Funahashi et al. (1999[Funahashi, Y., Kato, C. & Yamauchi, O. (1999). Bull. Chem. Soc. Jpn, 72, 415-424.]). In both complexes, the CuII atom has the elongated distorted octa­hedral coordination geometry.

5. Synthesis and crystallization

2-Amino-4-hy­droxy-7-methyl­pteridine-6-carb­oxy­lic acid sesquihydrate (C8H7N5O3·1.5H2O) was obtained by a published procedure (Wittle et al., 1947[Wittle, E. L., O'Dell, B. L., Vandenbelt, J. M. & Pfiffner, J. J. (1947). J. Am. Chem. Soc. 69, 1786-1792.]). The title complex could be obtained by two different methods; the crystals obtained by method B have been used for the present structural study. The X-ray structural data of the crystals synthesized by method A, are available from the Cambridge Crystallographic Data Center (CCDC deposition No. 985054).

Method A. The title complex was synthesized by bubbling ­oxy­gen into an aqueous reaction mixture (50 ml) containing Cu(NO3)2·3H2O (30 mg, 0.125 mmol), 1,10-phenanthroline monohydrate (25 mg, 0.125 mmol) and pterin (31 mg, 0.125 mmol) dissolved in NaOH (11 mg, 0.275 mmol) for 60 h at 310–312 K under subdued light; additional NaOH solution was added for adjusting the initial pH at 10.5. Within a short while the initial bright-green solution turned hazy blue due to the presence of a fine white precipitate which gradually disappeared substanti­ally. The final blue solution was slightly hazy. Upon storage under aerobic conditions for one week the clear blue solution yielded green crystals, suitable for X-ray structure determination. Analysis calculated for C20H21CuN7O7: C 44.90, H 3.93, N 18.33%; found: C 44.38, H 4.06, N 17.65%. ESIMS data: the mol­ecular ion peak [M + 2H]+ appeared at 536.4 (relative abundance = 41.2%); the [M − 4H2O − 3H]+ peak was observed at 459.2 (relative abundance = 100%), indicating stability of the desolvated ternary species arising from the title complex.

Method B. Using NaBH4 reduction in equimolar proportion of the original complex (obtained by Method A) and subsequent aerial reoxidation of the reduced complex to the present crystals merits attention due to the involvement of intricate redox chemistry. The NaBH4 treatment (Beddoes et al., 1993[Beddoes, R. L., Russell, J. R., Garner, C. D. & Joule, J. A. (1993). Acta Cryst. C49, 1649-1652.]; Russell et al., 1992[Russell, J. R., Garner, C. D. & Joule, J. A. (1992). J. Chem. Soc. Perkin Trans. 1, pp. 1245-1249.]) leads to the formation of a dark-brown compound in solution, which could be isolated in the solid state and characterized (microanalysis, ESIMS, 2DNMR, etc.,) to be Na2[Cu2I(L′)2(phen)(H2O)4]·2H2O, where L′ is the 7,8-di­hydro form of the present pterin ligand anion (C8H5N5O3) (Burgmayer, 1998[Burgmayer, S. J. N. (1998). Struct. Bond. 92, 67-119.]); it is able to convert bromo­benzene into 4-bromo­phenol in the presence of ­oxy­gen (Baisya & Roy, unpublished results). However, in the absence of any substrate (e.g. bromo­benzene; Dix & Benkovic, 1988[Dix, T. A. & Benkovic, S. J. (1988). Acc. Chem. Res. 21, 101-107.]), aerial oxidation reconverts the reduced compound to the title complex (Method B).

Although the title compound could be obtained by two alternative methods, the present structural data obtained using the crystals from Method B, represent better accuracy [R = 0.057 and wR(F2)= 0.135] as compared to the other one [R = 0.113 and wR(F2) = 0.279].

Cyclic voltammetry data of this complex indicate an E°′ value of −0.68 V; now using an E°′ value of −0.80 V for NaBH4 in neutral medium (Chatenet et al., 2006[Chatenet, M., Micoud, F., Roche, I. & Chainet, E. (2006). Electrochim. Acta, 51, 5459-5467.]; Celikkan et al., 2007[Celikkan, H., Sahin, M., Aksu, M. L. & Nejat Veziroğlu, T. (2007). Int. J. Hydrogen Energy, 32, 588-593.]), an Ecell value (Ecell = E1E2; Segel, 1976[Segel, I. H. (1976). Biochemical Calculations, 2nd ed., pp. 172-179. New York: John Wiley & Sons.]) of 0.12 V is obtained for the CuII → CuI reduction in the title complex; it is within the range of Ecell value (0.033 V) for the FeIII–tetra­hydro­biopterin reduction in phenyl­alanine hy­droxy­lase (Hagedoorn et al., 2001[Hagedoorn, P. L., Schmidt, P. P., Andersson, K. K., Hagen, W. R., Flatmark, T. & Martínez, A. (2001). J. Biol. Chem. 276, 22850-22856.]; Gorren et al., 2001[Gorren, A. C. F., Kungl, A. J., Schmidt, K., Werner, E. R. & Mayer, B. (2001). Nitric Oxide: Biol. Chem. 5, 176-186.]). The dark-brown reduced complex (as above) shows an E°′ value of −0.67 V (cyclic voltammetry); using an E°′ value of 0.70 V for the O2/H2O2 couple, an Ecell value of 1.37 V is obtained, indicating facile aerial oxidation. Now using an E°′ value of 0.19 V for the chelated pterin ligand (oxidized/aromatic; Eberlein et al., 1984[Eberlein, G., Bruice, T. C., Lazarus, R. A., Henrie, R. & Benkovic, S. J. (1984). J. Am. Chem. Soc. 106, 7916-7924.]), synchronization of its reduction or oxidation with the above redox process may be rationalized. Actually, for pterin-containing metalloenzymes the redox processes at the metal centres could be linked to the changes in the pterin ring oxidation level (Burgmayer, 1998[Burgmayer, S. J. N. (1998). Struct. Bond. 92, 67-119.]; Erlandsen et al., 2000[Erlandsen, H., Bjørgo, E., Flatmark, T. & Stevens, R. C. (2000). Biochemistry, 39, 2208-2217.]).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. H atoms attached to N and O atoms were located in a difference Fourier map and refined with distance constraints of N—H = 0.86 (1) Å and O—H = 0.82 (1) Å. H atoms attached to C atoms were positioned geometrically, with C—H = 0.93–0.96 Å, and refined in riding mode. For all atoms, Uiso(H) = 1.2–1.5Ueq(C,N,O).

Table 3
Experimental details

Crystal data
Chemical formula [Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2O
Mr 534.98
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 273
a, b, c (Å) 8.5399 (17), 10.038 (2), 13.601 (3)
α, β, γ (°) 97.292 (3), 94.587 (3), 110.999 (3)
V3) 1069.8 (4)
Z 2
Radiation type Mo Kα
μ (mm−1) 1.08
Crystal size (mm) 0.20 × 0.05 × 0.03
 
Data collection
Diffractometer Bruker Kappa APEXII
Absorption correction Multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.813, 0.968
No. of measured, independent and observed [I > 2σ(I)] reflections 8227, 4134, 3590
Rint 0.024
(sin θ/λ)max−1) 0.617
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.136, 1.15
No. of reflections 4134
No. of parameters 349
No. of restraints 10
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.66, −0.31
Computer programs: APEX2 and SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]) and CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.]).

Supporting information


Chemical context top

The ubiquitous presence of pterins in nature including several classes of metalloenzymes, has catalysed developments of their coordination chemistry (Basu & Burgmayer, 2011; Burgmayer, 1998; Dix & Benkovic, 1988; Erlandsen et al., 2000; Fitzpatrick, 2003). Literature survey reveals the paucity of structurally characterized CuII complexes involving tridentate pterin coordination (Kohzuma et al., 1989). The present work is concerned with the title complex, possessing both a tridentate pterin ligand and a π-acidic ligand like phen.

Structural commentary top

The hexacoordinated CuII atom is located in an axially elongated distorted o­cta­hedron (Fig. 1 and Table 1). The equatorial plane is formed by the two N atoms of phen, the pyrazine ring N atom of the pterin ligand and the aqua O atom. The axial positions are occupied by the two pterin O atoms, with the former one forming the longest axial bond [2.384 (3) Å]. One reason for distortion from regular o­cta­hedral geometry is that the pterin ligand forms two five-membered chelate rings with small bite angles [76.47 (10) and 74.66 (11)°]. A consideration of the charge balance of this complex indicates that this pterin ligand acts as a binegative tridentate O,N,O'-donor. A near orthogonal disposition of the phen ligand and pterin chelate ring, helps to minimize the steric repulsion. Of the three axes, least deviation from linearity is observed in the O4—Cu1–N2 direction [174.45 (13)°]. Location of the pyrazine ring N atom (N6) in the equatorial plane is in agreement with the earlier observations on related copper and cobalt complexes (Baisya et al., 2013; Odani et al., 1992); the Cu1—N6 bond distance [1.999 (3) Å] is the shortest one in this case.

The multiple bond character of the O1—C13 bond [1.237 (4) Å] may be elucidated in the light of Joule's hypothesis (Beddoes et al., 1993; Russell et al., 1992), suggesting electron-density withdrawal from the pyrazine ring N5 by the pyrimidine ring C13 carbonyl group through mesomeric inter­action. Formation of the O1—Cu1 bond assists this electron flow towards atom O1, with possible participation of the electron-rich N7—C14 [1.327 (5) Å] bond in this process.

Supra­molecular features top

In the crystal, inter­molecular classic N—H···.O, O—H···.N and O—H···O hydrogen bonds (Table 2) link the complex molecules and lattice water molecules into a layer parallel to (001) (Fig. 2). Inter­molecular weak C—H···O hydrogen bonds and C—H···π inter­actions are also observed in the crystal. In addition, ππ stacking between nearly parallel pterin ring systems of adjacent molecules occurs in the crystal structure, centroids distance being 3.352 (2) Å (Fig. 3). Again the nearly parallel phen rings of adjacent molecules also display ππ stacking inter­actions with centroids distances of 3.546 (3), 3.706 (3) and 3.744 (3) Å. These inter­molecular inter­actions link the molecules into a three-dimensional supra­molecular architecture.

Database survey top

The crystal structures of the copper(II) complexes chelated by the pterin-6-carboxyl­ate anion have been reported by Kohzuma et al. (1989) and Funahashi et al. (1999). In both complexes, the Cu atom has the elongated distorted o­cta­hedral coordination geometry.

Synthesis and crystallization top

2-Amino-4-hy­droxy-7-methyl­pteridine-6-carb­oxy­lic acid sesquihydrate (C8H7N5O3.1.5H2O) was obtained by a published procedure (Wittle et al., 1947). The title complex could be obtained by two different methods; the crystals obtained by method B have been used for the present structural study. The X-ray structural data of the crystals synthesized by method A, are available from the Cambridge Crystallographic Data Center (CCDC deposition No. 985054).

Method A. The title complex was synthesized by bubbling di­oxy­gen into an aqueous reaction mixture (50 ml) containing Cu(NO3)2.3H2O (30 mg, 0.125 mmol), 1,10-phenanthroline monohydrate (25 mg, 0.125 mmol) and pterin (31 mg, 0.125 mmol) dissolved in NaOH (11 mg, 0.275 mmol) for 60 h at 310–312 K under subdued light; additional NaOH solution was added for adjusting the initial pH at 10.5. Within a short while the initial bright-green solution turned hazy blue due to the presence of a fine white precipitate which gradually disappeared substanti­ally. The final blue solution was slightly hazy. Upon storage under aerobic conditions for one week the clear blue solution yielded green crystals, suitable for X-ray structure determination. Analysis calculated for C20H21CuN7O7: C 44.90, H 3.93, N 18.33%; found: C 44.38, H 4.06, N 17.65%. ESIMS data: the molecular ion peak [M + 2H]+ appeared at 536.4 (relative abundance = 41.2%); the [M - 4H2O - 3H]+ peak was observed at 459.2 (relative abundance = 100%), indicating stability of the desolvated ternary species arising from the title complex.

Method B. Using NaBH4 reduction of the original complex (obtained by Method A) and subsequent aerial reoxidation of the reduced complex to the present crystals merits attention due to the involvement of intricate redox chemistry. The NaBH4 treatment (Beddoes et al., 1993; Russell et al., 1992) leads to the formation of a dark-brown compound in solution, which could be isolated in the solid state and characterized (microanalysis, ESIMS, 2DNMR, etc.,) to be Na2[Cu2I(L')2(phen)(H2O)4].2H2O, where L' is the 7,8-di­hydro form of the present pterin ligand anion (C8H5N5O3) (Burgmayer, 1998); it is able to convert bromo­benzene into 4-bromo­phenol in the presence of di­oxy­gen (Baisya & Roy, unpublished results). However in the absence of any substrate (e.g. bromo­benzene; Dix & Benkovic, 1988), aerial oxidation reconverts the reduced compound to the title complex (Method B).

Although the title compound could be obtained by two alternative methods, the present structural data obtained using the crystals from Method B, represent better accuracy [R = 0.057 and wR(F2)= 0.135] as compared to the other one [R = 0.113 and wR(F2) = 0.279].

Cyclic voltammetry data of this complex indicates an E°' value of -0.68 V; now using an E°' value of -0.80 V for NaBH4 in neutral medium (Chatenet et al., 2006; Celikkan et al., 2007), an Ecell value (Ecell = E1 - E2; Segel, 1976) of 0.12 V is obtained for the CuII CuI reduction in the title complex; it is within the range of Ecell value (0.033 V) for the FeIII–tetra­hydro­biopterin reduction in phenyl­alanine hy­droxy­lase (Hagedoorn et al., 2001; Gorren et al., 2001). The dark-brown reduced complex (as above) shows an E°' value of -0.67 V (cyclic voltammetry); using an E°' value of 0.70 V for the O2/H2O2 couple, an Ecell value of 1.37 V is obtained, indicating facile aerial oxidation. Now using an E°' value of 0.19 V for the chelated pterin ligand (oxidized/aromatic; Eberlein et al., 1984), synchronization of its reduction or oxidation with the above redox process may be rationalized. Actually, for pterin-containing metalloenzymes the redox processes at the metal centres could be linked to the changes in the pterin ring oxidation level (Burgmayer, 1998; Erlandsen et al., 2000).

Refinement top

H atoms attached to N and O atoms were located in a difference Fourier map and refined with distance constraints of N—H = 0.86 (1) Å and O—H = 0.82 (1) Å. H atoms attached to C atoms were positioned geometrically, with C—H = 0.93–0.96 Å, and refined in riding mode. For all atoms, Uiso(H) = 1.2–1.5Ueq(C,N,O).

Related literature top

For related literature, see: Baisya et al. (2013); Basu & Burgmayer (2011); Beddoes et al. (1993); Burgmayer (1998); Celikkan et al. (2007); Chatenet et al. (2006); Dix & Benkovic (1988); Eberlein et al. (1984); Erlandsen et al. (2000); Fitzpatrick (2003); Funahashi et al. (1999); Gorren et al. (2001); Hagedoorn et al. (2001); Kohzuma et al. (1989); Odani et al. (1992); Russell et al. (1992); Segel (1976); Wittle et al. (1947).

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
The molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level.

The crystal packing diagram of the title compound, viewed along the a axis. Hydrogen bonds (dotted lines) assist the formation of a layer structure parallel to (001).

A molecular packing diagram highlighting ππ stacking interactions between neighbouring phen–phen and pterin–pterin rings.
(2-Amino-7-methyl-4-oxidopteridine-6-carboxylato-κ3O4,N5,O6)aqua(1,10-phenanthroline-κ2N,N')copper(II) trihydrate top
Crystal data top
[Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2OZ = 2
Mr = 534.98F(000) = 550
Triclinic, P1Dx = 1.661 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5399 (17) ÅCell parameters from 4804 reflections
b = 10.038 (2) Åθ = 3.0–29.0°
c = 13.601 (3) ŵ = 1.08 mm1
α = 97.292 (3)°T = 273 K
β = 94.587 (3)°Needle, green
γ = 110.999 (3)°0.20 × 0.05 × 0.03 mm
V = 1069.8 (4) Å3
Data collection top
Bruker Kappa APEXII
diffractometer
4134 independent reflections
Radiation source: fine-focus sealed tube3590 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ϕ & ω scansθmax = 26.0°, θmin = 1.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 1010
Tmin = 0.813, Tmax = 0.968k = 1212
8227 measured reflectionsl = 1616
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)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.15 w = 1/[σ2(Fo2) + (0.052P)2 + 1.8801P]
where P = (Fo2 + 2Fc2)/3
4134 reflections(Δ/σ)max = 0.001
349 parametersΔρmax = 0.66 e Å3
10 restraintsΔρmin = 0.31 e Å3
Crystal data top
[Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2Oγ = 110.999 (3)°
Mr = 534.98V = 1069.8 (4) Å3
Triclinic, P1Z = 2
a = 8.5399 (17) ÅMo Kα radiation
b = 10.038 (2) ŵ = 1.08 mm1
c = 13.601 (3) ÅT = 273 K
α = 97.292 (3)°0.20 × 0.05 × 0.03 mm
β = 94.587 (3)°
Data collection top
Bruker Kappa APEXII
diffractometer
4134 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
3590 reflections with I > 2σ(I)
Tmin = 0.813, Tmax = 0.968Rint = 0.024
8227 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.05110 restraints
wR(F2) = 0.136H atoms treated by a mixture of independent and constrained refinement
S = 1.15Δρmax = 0.66 e Å3
4134 reflectionsΔρmin = 0.31 e Å3
349 parameters
Special details top

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

Cosier, J. & Glazer, A. M., 1986. J. Appl. Cryst. 105–107.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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) top
xyzUiso*/Ueq
Cu10.96752 (6)0.72720 (5)0.73038 (3)0.02733 (16)
O11.1883 (3)0.9602 (3)0.7732 (2)0.0353 (7)
O20.6970 (4)0.5696 (3)0.7379 (2)0.0402 (7)
O30.4778 (4)0.5558 (3)0.8185 (3)0.0463 (8)
O41.0500 (4)0.6534 (3)0.8475 (2)0.0356 (7)
O50.8413 (4)0.4056 (3)0.9019 (3)0.0425 (7)
O60.5380 (4)0.2754 (3)0.7786 (3)0.0496 (8)
O70.5000 (6)0.0210 (5)0.6878 (5)0.0974 (17)
N11.1082 (4)0.6636 (3)0.6383 (2)0.0288 (7)
N20.8823 (4)0.7835 (4)0.6039 (2)0.0296 (7)
N31.2193 (4)1.1811 (3)0.8566 (2)0.0309 (7)
N40.9983 (4)1.2067 (3)0.9516 (2)0.0303 (7)
N50.7502 (4)1.0056 (4)0.9482 (3)0.0330 (8)
N60.8684 (4)0.8399 (3)0.8203 (2)0.0247 (7)
N71.2417 (5)1.3974 (4)0.9441 (3)0.0410 (9)
C11.2221 (5)0.6068 (5)0.6587 (3)0.0360 (9)
H11.23740.58460.72230.043*
C21.3205 (6)0.5790 (5)0.5872 (4)0.0454 (11)
H21.40110.54030.60390.054*
C31.2988 (6)0.6084 (5)0.4932 (4)0.0450 (11)
H31.36170.58710.44520.054*
C41.1804 (5)0.6712 (5)0.4691 (3)0.0374 (10)
C51.1463 (6)0.7074 (6)0.3733 (3)0.0502 (12)
H51.20720.69120.32240.060*
C61.0283 (7)0.7643 (5)0.3551 (3)0.0485 (12)
H61.00840.78550.29180.058*
C70.9651 (5)0.7606 (4)0.5263 (3)0.0291 (8)
C81.0885 (5)0.6975 (4)0.5453 (3)0.0295 (8)
C90.9327 (6)0.7929 (5)0.4312 (3)0.0384 (10)
C100.8072 (6)0.8508 (5)0.4183 (3)0.0449 (11)
H100.78110.87410.35660.054*
C110.7228 (6)0.8730 (5)0.4962 (4)0.0459 (11)
H110.63860.91060.48770.055*
C120.7642 (5)0.8386 (5)0.5887 (3)0.0376 (10)
H120.70700.85500.64150.045*
C131.1328 (5)1.0386 (4)0.8256 (3)0.0275 (8)
C141.1494 (5)1.2573 (4)0.9168 (3)0.0298 (8)
C150.9039 (5)1.0639 (4)0.9189 (3)0.0276 (8)
C160.9640 (5)0.9774 (4)0.8548 (3)0.0245 (8)
C170.6568 (5)0.8674 (4)0.9142 (3)0.0330 (9)
C180.7141 (5)0.7807 (4)0.8461 (3)0.0274 (8)
C190.6205 (5)0.6222 (4)0.7984 (3)0.0316 (9)
C200.4884 (6)0.8090 (5)0.9510 (4)0.0537 (13)
H20A0.48740.87221.01000.081*
H20B0.46950.71430.96660.081*
H20C0.40060.80320.90000.081*
H4C0.984 (5)0.575 (3)0.856 (4)0.050*
H4D1.062 (6)0.702 (5)0.9021 (19)0.050*
H5C0.750 (3)0.351 (4)0.871 (3)0.046 (15)*
H5D0.882 (6)0.346 (4)0.915 (4)0.054 (16)*
H6C0.540 (6)0.358 (2)0.778 (4)0.050*
H6D0.448 (3)0.215 (4)0.750 (3)0.050*
H7C0.548 (6)0.0668 (15)0.705 (4)0.050*
H7D0.415 (4)0.043 (6)0.715 (4)0.050*
H7E1.204 (6)1.455 (4)0.977 (3)0.050*
H7F1.338 (3)1.442 (5)0.926 (4)0.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0323 (3)0.0302 (3)0.0238 (3)0.0159 (2)0.00750 (18)0.00499 (18)
O10.0324 (15)0.0302 (15)0.0431 (17)0.0104 (12)0.0163 (13)0.0017 (12)
O20.0420 (17)0.0321 (16)0.0416 (17)0.0097 (13)0.0077 (14)0.0001 (13)
O30.0329 (16)0.0410 (18)0.055 (2)0.0011 (14)0.0115 (14)0.0083 (15)
O40.0413 (17)0.0350 (17)0.0323 (16)0.0151 (14)0.0047 (13)0.0092 (13)
O50.0405 (19)0.0339 (18)0.053 (2)0.0139 (15)0.0021 (16)0.0098 (15)
O60.0364 (17)0.0333 (17)0.076 (3)0.0082 (14)0.0124 (17)0.0077 (17)
O70.073 (3)0.065 (3)0.155 (5)0.025 (3)0.057 (3)0.004 (3)
N10.0300 (17)0.0279 (17)0.0277 (17)0.0113 (14)0.0037 (13)0.0000 (13)
N20.0300 (17)0.0322 (18)0.0267 (17)0.0114 (14)0.0043 (13)0.0058 (13)
N30.0299 (17)0.0273 (17)0.0348 (18)0.0083 (14)0.0109 (14)0.0058 (14)
N40.0328 (18)0.0244 (16)0.0339 (18)0.0108 (14)0.0080 (14)0.0029 (13)
N50.0303 (18)0.0308 (18)0.040 (2)0.0128 (15)0.0123 (15)0.0034 (15)
N60.0257 (16)0.0248 (16)0.0249 (16)0.0090 (13)0.0077 (13)0.0069 (12)
N70.039 (2)0.0264 (19)0.050 (2)0.0044 (16)0.0169 (18)0.0010 (16)
C10.035 (2)0.036 (2)0.037 (2)0.0165 (19)0.0012 (18)0.0006 (18)
C20.038 (2)0.046 (3)0.053 (3)0.022 (2)0.004 (2)0.005 (2)
C30.038 (2)0.046 (3)0.046 (3)0.013 (2)0.013 (2)0.006 (2)
C40.036 (2)0.034 (2)0.037 (2)0.0077 (18)0.0114 (18)0.0016 (17)
C50.054 (3)0.060 (3)0.033 (2)0.016 (3)0.018 (2)0.002 (2)
C60.062 (3)0.053 (3)0.029 (2)0.016 (2)0.011 (2)0.013 (2)
C70.029 (2)0.0248 (19)0.029 (2)0.0055 (16)0.0053 (16)0.0025 (15)
C80.030 (2)0.027 (2)0.026 (2)0.0059 (16)0.0054 (16)0.0001 (15)
C90.041 (2)0.036 (2)0.032 (2)0.0060 (19)0.0026 (18)0.0075 (18)
C100.048 (3)0.050 (3)0.035 (2)0.014 (2)0.000 (2)0.018 (2)
C110.038 (2)0.050 (3)0.052 (3)0.017 (2)0.000 (2)0.017 (2)
C120.038 (2)0.040 (2)0.039 (2)0.019 (2)0.0067 (19)0.0082 (19)
C130.029 (2)0.030 (2)0.0250 (19)0.0112 (16)0.0066 (15)0.0077 (15)
C140.032 (2)0.0254 (19)0.031 (2)0.0090 (16)0.0032 (16)0.0052 (16)
C150.027 (2)0.0265 (19)0.029 (2)0.0104 (16)0.0052 (15)0.0047 (15)
C160.0288 (19)0.0242 (19)0.0216 (18)0.0105 (16)0.0056 (15)0.0044 (14)
C170.027 (2)0.034 (2)0.039 (2)0.0114 (17)0.0088 (17)0.0074 (17)
C180.0260 (19)0.029 (2)0.028 (2)0.0110 (16)0.0049 (15)0.0076 (15)
C190.031 (2)0.031 (2)0.031 (2)0.0085 (17)0.0003 (17)0.0091 (16)
C200.036 (3)0.045 (3)0.076 (4)0.009 (2)0.026 (2)0.001 (2)
Geometric parameters (Å, º) top
Cu1—N12.002 (3)N7—H7E0.856 (10)
Cu1—N22.037 (3)N7—H7F0.854 (11)
Cu1—N61.999 (3)C1—C21.400 (6)
Cu1—O12.384 (3)C1—H10.9300
Cu1—O22.304 (3)C2—C31.361 (7)
Cu1—O42.019 (3)C2—H20.9300
O1—C131.237 (5)C3—C41.408 (7)
O2—C191.267 (5)C3—H30.9300
O3—C191.234 (5)C4—C81.404 (6)
O4—H4C0.819 (10)C4—C51.432 (7)
O4—H4D0.812 (10)C5—C61.346 (7)
O5—H5C0.819 (10)C5—H50.9300
O5—H5D0.820 (10)C6—C91.430 (7)
O6—H6C0.823 (10)C6—H60.9300
O6—H6D0.817 (10)C7—C91.403 (6)
O7—H7C0.819 (10)C7—C81.433 (6)
O7—H7D0.815 (10)C9—C101.400 (6)
N1—C11.321 (5)C10—C111.367 (7)
N1—C81.363 (5)C10—H100.9300
N2—C121.328 (5)C11—C121.398 (6)
N2—C71.357 (5)C11—H110.9300
N3—C131.345 (5)C12—H120.9300
N3—C141.364 (5)C13—C161.460 (5)
N4—C141.355 (5)C15—C161.405 (5)
N4—C151.363 (5)C17—C181.425 (6)
N5—C171.326 (5)C17—C201.499 (6)
N5—C151.348 (5)C18—C191.528 (5)
N6—C161.326 (5)C20—H20A0.9600
N6—C181.333 (5)C20—H20B0.9600
N7—C141.327 (5)C20—H20C0.9600
N6—Cu1—N1165.66 (13)C6—C5—H5119.2
N6—Cu1—O491.01 (12)C4—C5—H5119.2
N1—Cu1—O493.79 (13)C5—C6—C9121.4 (4)
N6—Cu1—N293.79 (13)C5—C6—H6119.3
N1—Cu1—N282.20 (13)C9—C6—H6119.3
O4—Cu1—N2174.45 (13)N2—C7—C9123.3 (4)
N6—Cu1—O274.74 (11)N2—C7—C8116.3 (3)
N1—Cu1—O2118.84 (12)C9—C7—C8120.4 (4)
O4—Cu1—O288.62 (12)N1—C8—C4123.1 (4)
N2—Cu1—O289.98 (12)N1—C8—C7117.1 (3)
N6—Cu1—O176.45 (11)C4—C8—C7119.8 (4)
N1—Cu1—O189.79 (11)C10—C9—C7116.7 (4)
O4—Cu1—O193.07 (12)C10—C9—C6125.0 (4)
N2—Cu1—O190.74 (12)C7—C9—C6118.3 (4)
O2—Cu1—O1151.17 (10)C11—C10—C9120.1 (4)
C13—O1—Cu1107.2 (2)C11—C10—H10120.0
C19—O2—Cu1113.0 (3)C9—C10—H10120.0
Cu1—O4—H4C114 (4)C10—C11—C12119.4 (4)
Cu1—O4—H4D116 (4)C10—C11—H11120.3
H4C—O4—H4D101 (5)C12—C11—H11120.3
H5C—O5—H5D100 (5)N2—C12—C11122.4 (4)
H6C—O6—H6D111 (5)N2—C12—H12118.8
H7C—O7—H7D106 (5)C11—C12—H12118.8
C1—N1—C8118.7 (3)O1—C13—N3123.3 (3)
C1—N1—Cu1128.8 (3)O1—C13—C16119.8 (3)
C8—N1—Cu1112.3 (3)N3—C13—C16116.9 (3)
C12—N2—C7118.2 (3)N7—C14—N4116.9 (4)
C12—N2—Cu1129.9 (3)N7—C14—N3115.4 (4)
C7—N2—Cu1111.9 (3)N4—C14—N3127.6 (3)
C13—N3—C14118.8 (3)N5—C15—N4119.1 (3)
C14—N4—C15115.3 (3)N5—C15—C16119.8 (3)
C17—N5—C15119.0 (3)N4—C15—C16121.0 (3)
C16—N6—C18120.8 (3)N6—C16—C15120.5 (3)
C16—N6—Cu1117.0 (2)N6—C16—C13119.4 (3)
C18—N6—Cu1122.2 (3)C15—C16—C13120.1 (3)
C14—N7—H7E122 (4)N5—C17—C18121.4 (3)
C14—N7—H7F125 (3)N5—C17—C20116.2 (4)
H7E—N7—H7F112 (5)C18—C17—C20122.4 (4)
N1—C1—C2121.7 (4)N6—C18—C17118.3 (3)
N1—C1—H1119.2N6—C18—C19114.0 (3)
C2—C1—H1119.2C17—C18—C19127.7 (3)
C3—C2—C1120.3 (4)O3—C19—O2124.7 (4)
C3—C2—H2119.9O3—C19—C18119.5 (4)
C1—C2—H2119.9O2—C19—C18115.8 (3)
C2—C3—C4119.6 (4)C17—C20—H20A109.5
C2—C3—H3120.2C17—C20—H20B109.5
C4—C3—H3120.2H20A—C20—H20B109.5
C8—C4—C3116.6 (4)C17—C20—H20C109.5
C8—C4—C5118.5 (4)H20A—C20—H20C109.5
C3—C4—C5124.9 (4)H20B—C20—H20C109.5
C6—C5—C4121.6 (4)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the N3/N4/C13–C16 ring.
D—H···AD—HH···AD···AD—H···A
O4—H4C···O50.82 (3)1.92 (3)2.722 (4)169 (5)
O4—H4D···N4i0.81 (3)2.26 (3)3.038 (4)161 (5)
O5—H5C···O60.82 (3)1.96 (4)2.748 (5)162 (4)
O5—H5D···N4ii0.82 (5)2.07 (5)2.891 (5)176 (3)
O6—H6C···O20.82 (3)2.23 (3)2.921 (4)141 (5)
O6—H6C···O30.82 (3)2.25 (4)3.029 (4)158 (5)
O7—H7C···O60.82 (2)2.24 (3)2.965 (6)148 (5)
O7—H7D···O1iii0.81 (5)2.16 (4)2.943 (6)162 (5)
N7—H7E···O5i0.85 (5)2.17 (4)2.998 (6)162 (4)
N7—H7F···O3iv0.86 (4)2.14 (5)2.908 (5)148 (4)
C1—H1···O3v0.932.473.175 (6)133
C10—H10···O1vi0.932.543.406 (5)155
C12—H12···O7vii0.932.573.343 (7)140
C6—H6···Cgvi0.932.823.740 (5)173
Symmetry codes: (i) x+2, y+2, z+2; (ii) x, y1, z; (iii) x1, y1, z; (iv) x+1, y+1, z; (v) x+1, y, z; (vi) x+2, y+2, z+1; (vii) x, y+1, z.
Selected bond lengths (Å) top
Cu1—N12.002 (3)Cu1—O12.384 (3)
Cu1—N22.037 (3)Cu1—O22.304 (3)
Cu1—N61.999 (3)Cu1—O42.019 (3)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the N3/N4/C13–C16 ring.
D—H···AD—HH···AD···AD—H···A
O4—H4C···O50.82 (3)1.92 (3)2.722 (4)169 (5)
O4—H4D···N4i0.81 (3)2.26 (3)3.038 (4)161 (5)
O5—H5C···O60.82 (3)1.96 (4)2.748 (5)162 (4)
O5—H5D···N4ii0.82 (5)2.07 (5)2.891 (5)176 (3)
O6—H6C···O20.82 (3)2.23 (3)2.921 (4)141 (5)
O6—H6C···O30.82 (3)2.25 (4)3.029 (4)158 (5)
O7—H7C···O60.82 (2)2.24 (3)2.965 (6)148 (5)
O7—H7D···O1iii0.81 (5)2.16 (4)2.943 (6)162 (5)
N7—H7E···O5i0.85 (5)2.17 (4)2.998 (6)162 (4)
N7—H7F···O3iv0.86 (4)2.14 (5)2.908 (5)148 (4)
C1—H1···O3v0.932.473.175 (6)133
C10—H10···O1vi0.932.543.406 (5)155
C12—H12···O7vii0.932.573.343 (7)140
C6—H6···Cgvi0.932.823.740 (5)173
Symmetry codes: (i) x+2, y+2, z+2; (ii) x, y1, z; (iii) x1, y1, z; (iv) x+1, y+1, z; (v) x+1, y, z; (vi) x+2, y+2, z+1; (vii) x, y+1, z.

Experimental details

Crystal data
Chemical formula[Cu(C8H5N5O3)(C12H8N2)(H2O)]·3H2O
Mr534.98
Crystal system, space groupTriclinic, P1
Temperature (K)273
a, b, c (Å)8.5399 (17), 10.038 (2), 13.601 (3)
α, β, γ (°)97.292 (3), 94.587 (3), 110.999 (3)
V3)1069.8 (4)
Z2
Radiation typeMo Kα
µ (mm1)1.08
Crystal size (mm)0.20 × 0.05 × 0.03
Data collection
DiffractometerBruker Kappa APEXII
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.813, 0.968
No. of measured, independent and
observed [I > 2σ(I)] reflections
8227, 4134, 3590
Rint0.024
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.136, 1.15
No. of reflections4134
No. of parameters349
No. of restraints10
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.66, 0.31

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

 

Acknowledgements

The authors express their gratitude to UGC, New Delhi, for financial assistance (SAP–DRS program). Thanks are due to CSMCRI, Bhavnagar, India, for the X-ray structural and microanalytical data. ESIMS data have been obtained from the SAIF, CDRI, Lucknow. Infrastructural support of University of North Bengal is duly acknowledged. Cyclic voltammetric data have been recorded by Professor J. P. Naskar, Jadavpur University, Kolkata, India.

References

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