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

Baisya, S.S.; Roy, P.S.

doi:10.1107/S1600536814022302

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Volume 70| Part 11| November 2014| Pages 348-351

doi:10.1107/S1600536814022302

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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

Siddhartha S. Baisya ^a and Parag S. Roy ^a ^*

^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 Cu^II 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 Cu^II 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 π–π 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.

Keywords: pterin; copper; π–π stacking; crystal structure.

CCDC reference: 1028413

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 ; Burgmayer, 1998 ; Dix & Benkovic, 1988 ; Erlandsen et al., 2000 ; Fitzpatrick, 2003 ). Literature survey reveals the paucity of structurally characterized Cu^II 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.

2. Structural commentary

The hexacoordinated Cu^II 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]. 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 ; Odani et al., 1992 ); 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
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 ; 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.

3. Supramolecular features

In the crystal, intermolecular 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, π–π 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). Again, the nearly parallel phen rings of adjacent molecules also display π–π 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	D⋯A	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⋯O3^iv	0.86 (4)	2.14 (5)	2.908 (5)	148 (4)
C1—H1⋯O3^v	0.93	2.47	3.175 (6)	133
C10—H10⋯O1^vi	0.93	2.54	3.406 (5)	155
C12—H12⋯O7^vii	0.93	2.57	3.343 (7)	140
C6—H6⋯Cg^vi	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
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
A molecular packing diagram highlighting π–π 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) and Funahashi et al. (1999 ). In both complexes, the Cu^II 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 ). 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; 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[Cu₂^I(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 oxygen (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 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 ; Celikkan et al., 2007 ), an E_cell value (E_cell = E₁ − E₂; Segel, 1976 ) of 0.12 V is obtained for the Cu^II → Cu^I reduction in the title complex; it is within the range of E_cell value (0.033 V) for the Fe^III–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 E_cell 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).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. 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, U_iso(H) = 1.2–1.5U_eq(C,N,O).

Table 3
Experimental details

Crystal data
Chemical formula	[Cu(C₈H₅N₅O₃)(C₁₂H₈N₂)(H₂O)]·3H₂O
M_r	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)
V (Å³)	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 )
T_min, T_max	0.813, 0.968
No. of measured, independent and observed [I > 2σ(I)] reflections	8227, 4134, 3590
R_int	0.024
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.66, −0.31
Computer programs: APEX2 and SAINT (Bruker, 2007 ), SHELXS97 (Sheldrick, 2008 ), CRYSTALS (Betteridge et al., 2003 ) and CAMERON (Watkin et al., 1996 ).

Supporting information

CCDC reference: 1028413

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536814022302/xu5822sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814022302/xu5822Isup2.hkl

checkCIF report

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 Cu^II 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 Cu^II 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, π–π 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 π–π 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[Cu₂^I(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).

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 E_cell value (E_cell = E₁ - E₂; Segel, 1976) of 0.12 V is obtained for the Cu^II → Cu^I reduction in the title complex; it is within the range of E_cell value (0.033 V) for the Fe^III–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 E_cell 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, U_iso(H) = 1.2–1.5U_eq(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 π–π 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)]·3H₂O	Z = 2
M_r = 534.98	F(000) = 550
Triclinic, P1	D_x = 1.661 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 8.5399 (17) Å	Cell parameters from 4804 reflections
b = 10.038 (2) Å	θ = 3.0–29.0°
c = 13.601 (3) Å	µ = 1.08 mm⁻¹
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 tube	3590 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
ϕ & ω scans	θ_max = 26.0°, θ_min = 1.5°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −10→10
T_min = 0.813, T_max = 0.968	k = −12→12
8227 measured reflections	l = −16→16

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.051	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.136	H atoms treated by a mixture of independent and constrained refinement
S = 1.15	w = 1/[σ²(F_o²) + (0.052P)² + 1.8801P] where P = (F_o² + 2F_c²)/3
4134 reflections	(Δ/σ)_max = 0.001
349 parameters	Δρ_max = 0.66 e Å⁻³
10 restraints	Δρ_min = −0.31 e Å⁻³

Crystal data top

[Cu(C₈H₅N₅O₃)(C₁₂H₈N₂)(H₂O)]·3H₂O	γ = 110.999 (3)°
M_r = 534.98	V = 1069.8 (4) Å³
Triclinic, P1	Z = 2
a = 8.5399 (17) Å	Mo Kα radiation
b = 10.038 (2) Å	µ = 1.08 mm⁻¹
c = 13.601 (3) Å	T = 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)
T_min = 0.813, T_max = 0.968	R_int = 0.024
8227 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.051	10 restraints
wR(F²) = 0.136	H atoms treated by a mixture of independent and constrained refinement
S = 1.15	Δρ_max = 0.66 e Å⁻³
4134 reflections	Δρ_min = −0.31 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Cu1	0.96752 (6)	0.72720 (5)	0.73038 (3)	0.02733 (16)
O1	1.1883 (3)	0.9602 (3)	0.7732 (2)	0.0353 (7)
O2	0.6970 (4)	0.5696 (3)	0.7379 (2)	0.0402 (7)
O3	0.4778 (4)	0.5558 (3)	0.8185 (3)	0.0463 (8)
O4	1.0500 (4)	0.6534 (3)	0.8475 (2)	0.0356 (7)
O5	0.8413 (4)	0.4056 (3)	0.9019 (3)	0.0425 (7)
O6	0.5380 (4)	0.2754 (3)	0.7786 (3)	0.0496 (8)
O7	0.5000 (6)	−0.0210 (5)	0.6878 (5)	0.0974 (17)
N1	1.1082 (4)	0.6636 (3)	0.6383 (2)	0.0288 (7)
N2	0.8823 (4)	0.7835 (4)	0.6039 (2)	0.0296 (7)
N3	1.2193 (4)	1.1811 (3)	0.8566 (2)	0.0309 (7)
N4	0.9983 (4)	1.2067 (3)	0.9516 (2)	0.0303 (7)
N5	0.7502 (4)	1.0056 (4)	0.9482 (3)	0.0330 (8)
N6	0.8684 (4)	0.8399 (3)	0.8203 (2)	0.0247 (7)
N7	1.2417 (5)	1.3974 (4)	0.9441 (3)	0.0410 (9)
C1	1.2221 (5)	0.6068 (5)	0.6587 (3)	0.0360 (9)
H1	1.2374	0.5846	0.7223	0.043*
C2	1.3205 (6)	0.5790 (5)	0.5872 (4)	0.0454 (11)
H2	1.4011	0.5403	0.6039	0.054*
C3	1.2988 (6)	0.6084 (5)	0.4932 (4)	0.0450 (11)
H3	1.3617	0.5871	0.4452	0.054*
C4	1.1804 (5)	0.6712 (5)	0.4691 (3)	0.0374 (10)
C5	1.1463 (6)	0.7074 (6)	0.3733 (3)	0.0502 (12)
H5	1.2072	0.6912	0.3224	0.060*
C6	1.0283 (7)	0.7643 (5)	0.3551 (3)	0.0485 (12)
H6	1.0084	0.7855	0.2918	0.058*
C7	0.9651 (5)	0.7606 (4)	0.5263 (3)	0.0291 (8)
C8	1.0885 (5)	0.6975 (4)	0.5453 (3)	0.0295 (8)
C9	0.9327 (6)	0.7929 (5)	0.4312 (3)	0.0384 (10)
C10	0.8072 (6)	0.8508 (5)	0.4183 (3)	0.0449 (11)
H10	0.7811	0.8741	0.3566	0.054*
C11	0.7228 (6)	0.8730 (5)	0.4962 (4)	0.0459 (11)
H11	0.6386	0.9106	0.4877	0.055*
C12	0.7642 (5)	0.8386 (5)	0.5887 (3)	0.0376 (10)
H12	0.7070	0.8550	0.6415	0.045*
C13	1.1328 (5)	1.0386 (4)	0.8256 (3)	0.0275 (8)
C14	1.1494 (5)	1.2573 (4)	0.9168 (3)	0.0298 (8)
C15	0.9039 (5)	1.0639 (4)	0.9189 (3)	0.0276 (8)
C16	0.9640 (5)	0.9774 (4)	0.8548 (3)	0.0245 (8)
C17	0.6568 (5)	0.8674 (4)	0.9142 (3)	0.0330 (9)
C18	0.7141 (5)	0.7807 (4)	0.8461 (3)	0.0274 (8)
C19	0.6205 (5)	0.6222 (4)	0.7984 (3)	0.0316 (9)
C20	0.4884 (6)	0.8090 (5)	0.9510 (4)	0.0537 (13)
H20A	0.4874	0.8722	1.0100	0.081*
H20B	0.4695	0.7143	0.9666	0.081*
H20C	0.4006	0.8032	0.9000	0.081*
H4C	0.984 (5)	0.575 (3)	0.856 (4)	0.050*
H4D	1.062 (6)	0.702 (5)	0.9021 (19)	0.050*
H5C	0.750 (3)	0.351 (4)	0.871 (3)	0.046 (15)*
H5D	0.882 (6)	0.346 (4)	0.915 (4)	0.054 (16)*
H6C	0.540 (6)	0.358 (2)	0.778 (4)	0.050*
H6D	0.448 (3)	0.215 (4)	0.750 (3)	0.050*
H7C	0.548 (6)	0.0668 (15)	0.705 (4)	0.050*
H7D	0.415 (4)	−0.043 (6)	0.715 (4)	0.050*
H7E	1.204 (6)	1.455 (4)	0.977 (3)	0.050*
H7F	1.338 (3)	1.442 (5)	0.926 (4)	0.050*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cu1	0.0323 (3)	0.0302 (3)	0.0238 (3)	0.0159 (2)	0.00750 (18)	0.00499 (18)
O1	0.0324 (15)	0.0302 (15)	0.0431 (17)	0.0104 (12)	0.0163 (13)	0.0017 (12)
O2	0.0420 (17)	0.0321 (16)	0.0416 (17)	0.0097 (13)	0.0077 (14)	0.0001 (13)
O3	0.0329 (16)	0.0410 (18)	0.055 (2)	0.0011 (14)	0.0115 (14)	0.0083 (15)
O4	0.0413 (17)	0.0350 (17)	0.0323 (16)	0.0151 (14)	0.0047 (13)	0.0092 (13)
O5	0.0405 (19)	0.0339 (18)	0.053 (2)	0.0139 (15)	0.0021 (16)	0.0098 (15)
O6	0.0364 (17)	0.0333 (17)	0.076 (3)	0.0082 (14)	0.0124 (17)	0.0077 (17)
O7	0.073 (3)	0.065 (3)	0.155 (5)	0.025 (3)	0.057 (3)	−0.004 (3)
N1	0.0300 (17)	0.0279 (17)	0.0277 (17)	0.0113 (14)	0.0037 (13)	0.0000 (13)
N2	0.0300 (17)	0.0322 (18)	0.0267 (17)	0.0114 (14)	0.0043 (13)	0.0058 (13)
N3	0.0299 (17)	0.0273 (17)	0.0348 (18)	0.0083 (14)	0.0109 (14)	0.0058 (14)
N4	0.0328 (18)	0.0244 (16)	0.0339 (18)	0.0108 (14)	0.0080 (14)	0.0029 (13)
N5	0.0303 (18)	0.0308 (18)	0.040 (2)	0.0128 (15)	0.0123 (15)	0.0034 (15)
N6	0.0257 (16)	0.0248 (16)	0.0249 (16)	0.0090 (13)	0.0077 (13)	0.0069 (12)
N7	0.039 (2)	0.0264 (19)	0.050 (2)	0.0044 (16)	0.0169 (18)	−0.0010 (16)
C1	0.035 (2)	0.036 (2)	0.037 (2)	0.0165 (19)	0.0012 (18)	−0.0006 (18)
C2	0.038 (2)	0.046 (3)	0.053 (3)	0.022 (2)	0.004 (2)	−0.005 (2)
C3	0.038 (2)	0.046 (3)	0.046 (3)	0.013 (2)	0.013 (2)	−0.006 (2)
C4	0.036 (2)	0.034 (2)	0.037 (2)	0.0077 (18)	0.0114 (18)	−0.0016 (17)
C5	0.054 (3)	0.060 (3)	0.033 (2)	0.016 (3)	0.018 (2)	0.002 (2)
C6	0.062 (3)	0.053 (3)	0.029 (2)	0.016 (2)	0.011 (2)	0.013 (2)
C7	0.029 (2)	0.0248 (19)	0.029 (2)	0.0055 (16)	0.0053 (16)	0.0025 (15)
C8	0.030 (2)	0.027 (2)	0.026 (2)	0.0059 (16)	0.0054 (16)	−0.0001 (15)
C9	0.041 (2)	0.036 (2)	0.032 (2)	0.0060 (19)	0.0026 (18)	0.0075 (18)
C10	0.048 (3)	0.050 (3)	0.035 (2)	0.014 (2)	0.000 (2)	0.018 (2)
C11	0.038 (2)	0.050 (3)	0.052 (3)	0.017 (2)	0.000 (2)	0.017 (2)
C12	0.038 (2)	0.040 (2)	0.039 (2)	0.019 (2)	0.0067 (19)	0.0082 (19)
C13	0.029 (2)	0.030 (2)	0.0250 (19)	0.0112 (16)	0.0066 (15)	0.0077 (15)
C14	0.032 (2)	0.0254 (19)	0.031 (2)	0.0090 (16)	0.0032 (16)	0.0052 (16)
C15	0.027 (2)	0.0265 (19)	0.029 (2)	0.0104 (16)	0.0052 (15)	0.0047 (15)
C16	0.0288 (19)	0.0242 (19)	0.0216 (18)	0.0105 (16)	0.0056 (15)	0.0044 (14)
C17	0.027 (2)	0.034 (2)	0.039 (2)	0.0114 (17)	0.0088 (17)	0.0074 (17)
C18	0.0260 (19)	0.029 (2)	0.028 (2)	0.0110 (16)	0.0049 (15)	0.0076 (15)
C19	0.031 (2)	0.031 (2)	0.031 (2)	0.0085 (17)	0.0003 (17)	0.0091 (16)
C20	0.036 (3)	0.045 (3)	0.076 (4)	0.009 (2)	0.026 (2)	−0.001 (2)

Geometric parameters (Å, º) top

Cu1—N1	2.002 (3)	N7—H7E	0.856 (10)
Cu1—N2	2.037 (3)	N7—H7F	0.854 (11)
Cu1—N6	1.999 (3)	C1—C2	1.400 (6)
Cu1—O1	2.384 (3)	C1—H1	0.9300
Cu1—O2	2.304 (3)	C2—C3	1.361 (7)
Cu1—O4	2.019 (3)	C2—H2	0.9300
O1—C13	1.237 (5)	C3—C4	1.408 (7)
O2—C19	1.267 (5)	C3—H3	0.9300
O3—C19	1.234 (5)	C4—C8	1.404 (6)
O4—H4C	0.819 (10)	C4—C5	1.432 (7)
O4—H4D	0.812 (10)	C5—C6	1.346 (7)
O5—H5C	0.819 (10)	C5—H5	0.9300
O5—H5D	0.820 (10)	C6—C9	1.430 (7)
O6—H6C	0.823 (10)	C6—H6	0.9300
O6—H6D	0.817 (10)	C7—C9	1.403 (6)
O7—H7C	0.819 (10)	C7—C8	1.433 (6)
O7—H7D	0.815 (10)	C9—C10	1.400 (6)
N1—C1	1.321 (5)	C10—C11	1.367 (7)
N1—C8	1.363 (5)	C10—H10	0.9300
N2—C12	1.328 (5)	C11—C12	1.398 (6)
N2—C7	1.357 (5)	C11—H11	0.9300
N3—C13	1.345 (5)	C12—H12	0.9300
N3—C14	1.364 (5)	C13—C16	1.460 (5)
N4—C14	1.355 (5)	C15—C16	1.405 (5)
N4—C15	1.363 (5)	C17—C18	1.425 (6)
N5—C17	1.326 (5)	C17—C20	1.499 (6)
N5—C15	1.348 (5)	C18—C19	1.528 (5)
N6—C16	1.326 (5)	C20—H20A	0.9600
N6—C18	1.333 (5)	C20—H20B	0.9600
N7—C14	1.327 (5)	C20—H20C	0.9600

N6—Cu1—N1	165.66 (13)	C6—C5—H5	119.2
N6—Cu1—O4	91.01 (12)	C4—C5—H5	119.2
N1—Cu1—O4	93.79 (13)	C5—C6—C9	121.4 (4)
N6—Cu1—N2	93.79 (13)	C5—C6—H6	119.3
N1—Cu1—N2	82.20 (13)	C9—C6—H6	119.3
O4—Cu1—N2	174.45 (13)	N2—C7—C9	123.3 (4)
N6—Cu1—O2	74.74 (11)	N2—C7—C8	116.3 (3)
N1—Cu1—O2	118.84 (12)	C9—C7—C8	120.4 (4)
O4—Cu1—O2	88.62 (12)	N1—C8—C4	123.1 (4)
N2—Cu1—O2	89.98 (12)	N1—C8—C7	117.1 (3)
N6—Cu1—O1	76.45 (11)	C4—C8—C7	119.8 (4)
N1—Cu1—O1	89.79 (11)	C10—C9—C7	116.7 (4)
O4—Cu1—O1	93.07 (12)	C10—C9—C6	125.0 (4)
N2—Cu1—O1	90.74 (12)	C7—C9—C6	118.3 (4)
O2—Cu1—O1	151.17 (10)	C11—C10—C9	120.1 (4)
C13—O1—Cu1	107.2 (2)	C11—C10—H10	120.0
C19—O2—Cu1	113.0 (3)	C9—C10—H10	120.0
Cu1—O4—H4C	114 (4)	C10—C11—C12	119.4 (4)
Cu1—O4—H4D	116 (4)	C10—C11—H11	120.3
H4C—O4—H4D	101 (5)	C12—C11—H11	120.3
H5C—O5—H5D	100 (5)	N2—C12—C11	122.4 (4)
H6C—O6—H6D	111 (5)	N2—C12—H12	118.8
H7C—O7—H7D	106 (5)	C11—C12—H12	118.8
C1—N1—C8	118.7 (3)	O1—C13—N3	123.3 (3)
C1—N1—Cu1	128.8 (3)	O1—C13—C16	119.8 (3)
C8—N1—Cu1	112.3 (3)	N3—C13—C16	116.9 (3)
C12—N2—C7	118.2 (3)	N7—C14—N4	116.9 (4)
C12—N2—Cu1	129.9 (3)	N7—C14—N3	115.4 (4)
C7—N2—Cu1	111.9 (3)	N4—C14—N3	127.6 (3)
C13—N3—C14	118.8 (3)	N5—C15—N4	119.1 (3)
C14—N4—C15	115.3 (3)	N5—C15—C16	119.8 (3)
C17—N5—C15	119.0 (3)	N4—C15—C16	121.0 (3)
C16—N6—C18	120.8 (3)	N6—C16—C15	120.5 (3)
C16—N6—Cu1	117.0 (2)	N6—C16—C13	119.4 (3)
C18—N6—Cu1	122.2 (3)	C15—C16—C13	120.1 (3)
C14—N7—H7E	122 (4)	N5—C17—C18	121.4 (3)
C14—N7—H7F	125 (3)	N5—C17—C20	116.2 (4)
H7E—N7—H7F	112 (5)	C18—C17—C20	122.4 (4)
N1—C1—C2	121.7 (4)	N6—C18—C17	118.3 (3)
N1—C1—H1	119.2	N6—C18—C19	114.0 (3)
C2—C1—H1	119.2	C17—C18—C19	127.7 (3)
C3—C2—C1	120.3 (4)	O3—C19—O2	124.7 (4)
C3—C2—H2	119.9	O3—C19—C18	119.5 (4)
C1—C2—H2	119.9	O2—C19—C18	115.8 (3)
C2—C3—C4	119.6 (4)	C17—C20—H20A	109.5
C2—C3—H3	120.2	C17—C20—H20B	109.5
C4—C3—H3	120.2	H20A—C20—H20B	109.5
C8—C4—C3	116.6 (4)	C17—C20—H20C	109.5
C8—C4—C5	118.5 (4)	H20A—C20—H20C	109.5
C3—C4—C5	124.9 (4)	H20B—C20—H20C	109.5
C6—C5—C4	121.6 (4)

Hydrogen-bond geometry (Å, º) top

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

D—H···A	D—H	H···A	D···A	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···O3^iv	0.86 (4)	2.14 (5)	2.908 (5)	148 (4)
C1—H1···O3^v	0.93	2.47	3.175 (6)	133
C10—H10···O1^vi	0.93	2.54	3.406 (5)	155
C12—H12···O7^vii	0.93	2.57	3.343 (7)	140
C6—H6···Cg^vi	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.

Selected bond lengths (Å) top

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)

Hydrogen-bond geometry (Å, º) top

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

D—H···A	D—H	H···A	D···A	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···O3^iv	0.86 (4)	2.14 (5)	2.908 (5)	148 (4)
C1—H1···O3^v	0.93	2.47	3.175 (6)	133
C10—H10···O1^vi	0.93	2.54	3.406 (5)	155
C12—H12···O7^vii	0.93	2.57	3.343 (7)	140
C6—H6···Cg^vi	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.

Experimental details

Crystal data
Chemical formula	[Cu(C₈H₅N₅O₃)(C₁₂H₈N₂)(H₂O)]·3H₂O
M_r	534.98
Crystal system, space group	Triclinic, 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)
V (Å³)	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 diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2001)
T_min, T_max	0.813, 0.968
No. of measured, independent and observed [I > 2σ(I)] reflections	8227, 4134, 3590
R_int	0.024
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	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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Volume 70| Part 11| November 2014| Pages 348-351

doi:10.1107/S1600536814022302

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