Aqua­(di-2-pyridylamine-[kappa]²N,N')(malonato-[kappa]²O,O')copper(II) monohydrate

In the structure of the title complex, [Cu(C₃H₂O₄)(C₁₀H₈N₃)(H₂O)]·H₂O or [Cu(mal)(dpyam)(H₂O)]·H₂O, where mal is malonate and dpyam is di-2-pyridylamine, the Cu^II atom displays square-pyramidal geometry, being coordinated by two N atoms from the dpyam ligand, two O atoms from the mal group and one O atom of a water ligand. The complex mol­ecules are linked to form a three-dimensional network by hydrogen-bonding inter­actions between coordinated/uncoordinated water mol­ecules and the uncoordinated malonate N and O atoms of neighboring mol­ecules.

S1. Comment

There has been considerable interest in the design and syntheses of transition metal complexes with the malonate ligand in coordination chemistry, owing to the fact that this type of complex has potential application in molecular-based magnets (Rodriguez-Martín et al., 2001). The malonate dianion generally exhibits bidentate, tridentate or tetradentate coordination modes (Shen et al., 2000). Although some complexes containing mixed malonate and nitrogen-donor ligands have been synthesized and characterized, complexes containing mixed malonate (mal) and di-2-pyridylamine (dpyam) ligands have never been reported. To the best of our knowledge, there are only four reports on structures with malonate/nitrogen-donor ligands, such as phen (1,10-phenanthroline), bpy (2,2'-bipyridyl) and bpym (2,2'-bipyrimidine), namely [Cu(phen)(mal)(H₂O)]·1.5H₂O, (II) (Kwik et al., 1986), [Cu(bpym)(mal)(H₂O)]·H₂O, (III) (Rodriguez-Martín et al., 2001), [Cu(bpy)(mal)(H₂O)]·H₂O, (IV) (Suresh & Bhadbhade, 1997), and [Cu(bpy)(mal)(H₂O)]·H₂O, (V) (Shen et al., 2000). The first three compounds exhibit mononuclear structures, while the last compound involves a dinuclear unit. In this paper, we report the crystal structure of [Cu(dpyam)(mal)(H₂O)]·H₂O, (I), in which the three-dimensional network is formed by hydrogen bonds. The ligand dpyam has been selected primarily because of the fact that it also has an NH hydrogen-bond donor function that might form one-, two- or three-dimensional supramolecular architectures. The structure of complex (I) consists of neutral mononuclear [Cu(dpyam)(mal)(H₂O)] units (see Fig. 1) and crystallization water molecules. The Cu atom exhibits a slightly distorted square–pyramidal environment, the geometric τ value (Addison et al., 1984) being only 0.045. The Cu^II ion is bonded to two dpyam N atoms and two carboxylate O atoms from the malonate ligand in the basal plane, and to a water molecule in the apical position (Table 1 and Fig. 1). The Cu atom is displaced by 0.257 (1) Å from the mean basal plane towards the apical position. In the Cu unit, the dihedral angle between the N1/Cu1/N2 and O1/Cu1/O2 planes is 21.3°. The dpyam ligands are not planar, with a dihedral angle of 22.9°. Other related examples of the malonate are compounds (II)–(V). In each of these, the Cu^II atom exhibits a slightly distorted square–pyramidal geometry, with τ values of 0.057 for (II), 0.006 for (III), 0.061 for (IV) and 0.040 for (V).

The electronic reflectance spectrum of (I) involves two bands at 15 800 and 11 000 cm⁻¹, this spectral character of the compound is consistent with the distorted square–pyramidal geometry with τ = 0.045. The transitions may be assigned as the d_z² → d_x²-_y² transition for the low-energy peak and the d_xz ≈ d_yz → d_x²-_y² transition for the high-energy peak. The electronic spectrum of (I) is similar to that found in a complex with similar Cu^II environment, compound (V) (15 400 and 11 000 cm⁻¹). The IR spectrum of (I) exhibits several characteristic strong bands at 1670–1600 cm⁻¹, which are attributed to C═O stretching modes. The complex molecules are linked to form a three-dimensional network by hydrogen-bonding interactions between the NH group of the dpyam group and the uncoordinated water molecule, and between the coordinated water molecule and the uncoordinated malonate O atoms (Table 2 and Fig. 2). All available hydrogen-bonding donors take part in hydrogen bonds.

S2. Experimental

A warming solution containing copper(II) acetate monohydrate (0.181 g, 1.0 mmol) in water (10 ml) was added to a warming solution of di-2-pyridylamine (0.171 g, 1.0 mmol) in methanol (15 ml), and then the solid of malonic acid disodium salt monohydrate (0.084 g, 0.5 mmol) was added. The green solution was slowly evaporated at room temperature. After several days, blue–green crystals were formed. The crystals were filtered off, washed with mother liquor and air-dried.

S3. Refinement

H atoms bonded to water O atoms were visible in a difference map and were refined with a DFIX (SHELXTL; Sheldrick, 2000b) restraint [O—H = 0.90 (1) Å]. H atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H distances of 0.93–0.97 Å and an N—H distance of 0.86 Å [U_iso(H) = 1.2U_eq(C,N)].

Computing details

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2000b); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The molecular structure of (I), with 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. The packing of (I), with hydrogen bonds indicated by dashed lines, showing the three-dimensional structure.

Aqua(di-2-pyridylamine-κ²N,N')(malonato-κ²O,O')copper(II) monohydrate

Crystal data

[Cu(C3H2O4)(C10H8N3)(H2O)]·H2O	Z = 2
Mr = 372.82	F(000) = 382
Triclinic, P1	Dx = 1.695 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.2409 (1) Å	Cell parameters from 3443 reflections
b = 9.6351 (2) Å	θ = 1.9–30.4°
c = 11.43800 (1) Å	µ = 1.53 mm^−1
α = 87.815 (1)°	T = 293 K
β = 71.700 (1)°	Plate, blue–green
γ = 74.844 (1)°	0.33 × 0.32 × 0.10 mm
V = 730.46 (2) Å^3

Data collection

Siemens SMART CCD area-detector diffractometer	4432 independent reflections
Radiation source: fine-focus sealed tube	3443 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.018
ω scans	θmax = 30.4°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2000a)	h = −9→10
Tmin = 0.599, Tmax = 0.858	k = −11→13
5409 measured reflections	l = −16→16

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.101	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0652P)^2 + 0.0267P] where P = (Fo^2 + 2Fc^2)/3
3945 reflections	(Δ/σ)max = 0.001
224 parameters	Δρmax = 0.37 e Å^−3
4 restraints	Δρmin = −0.53 e Å^−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cu	0.32750 (3)	0.72392 (2)	0.26124 (2)	0.02562 (9)
O1	0.3253 (3)	0.68233 (19)	0.09718 (14)	0.0381 (4)
O2	0.0799 (2)	0.66796 (18)	0.33730 (14)	0.0364 (3)
O3	0.2227 (3)	0.5950 (2)	−0.03979 (15)	0.0435 (4)
O4	−0.1659 (3)	0.5697 (2)	0.34784 (16)	0.0437 (4)
O5	0.5461 (2)	0.50946 (16)	0.27038 (14)	0.0300 (3)
O6	0.3125 (3)	0.3190 (2)	0.40014 (19)	0.0540 (5)
N1	0.5275 (3)	0.83725 (18)	0.18613 (16)	0.0283 (3)
N2	0.2880 (3)	0.81266 (18)	0.42481 (16)	0.0272 (3)
N3	0.3603 (3)	1.02676 (18)	0.33734 (17)	0.0317 (4)
H5	0.3158	1.1189	0.3471	0.038*
C1	0.6765 (3)	0.7858 (2)	0.0790 (2)	0.0360 (4)
H1	0.7045	0.6893	0.0553	0.043*
C2	0.7869 (4)	0.8690 (3)	0.0046 (2)	0.0415 (5)
H2	0.8915	0.8293	−0.0663	0.050*
C3	0.7389 (4)	1.0153 (3)	0.0376 (2)	0.0394 (5)
H3	0.8047	1.0760	−0.0145	0.047*
C4	0.5945 (3)	1.0685 (2)	0.1471 (2)	0.0341 (4)
H4	0.5630	1.1653	0.1711	0.041*
C5	0.4939 (3)	0.9747 (2)	0.22312 (19)	0.0268 (4)
C6	0.2886 (3)	0.9497 (2)	0.43851 (18)	0.0265 (4)
C7	0.2116 (3)	1.0219 (2)	0.5553 (2)	0.0356 (4)
H7	0.2103	1.1179	0.5634	0.043*
C8	0.1385 (4)	0.9486 (3)	0.6567 (2)	0.0405 (5)
H8	0.0843	0.9954	0.7343	0.049*
C9	0.1452 (4)	0.8037 (3)	0.6437 (2)	0.0407 (5)
H9	0.1005	0.7514	0.7120	0.049*
C10	0.2197 (3)	0.7412 (2)	0.5272 (2)	0.0348 (4)
H10	0.2239	0.6450	0.5175	0.042*
C11	0.2282 (3)	0.6048 (2)	0.06699 (18)	0.0290 (4)
C12	0.1167 (4)	0.5167 (2)	0.1642 (2)	0.0343 (4)
H12A	0.0222	0.4870	0.1328	0.041*
H12B	0.2141	0.4300	0.1738	0.041*
C13	0.0018 (3)	0.5899 (2)	0.29054 (18)	0.0293 (4)
H14	0.617 (4)	0.469 (3)	0.1958 (17)	0.033 (7)*
H13	0.632 (4)	0.526 (4)	0.300 (3)	0.063 (10)*
H16	0.383 (5)	0.378 (4)	0.358 (3)	0.074 (11)*
H15	0.259 (5)	0.353 (4)	0.478 (2)	0.073 (11)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu	0.02937 (14)	0.02235 (13)	0.02621 (13)	−0.01086 (9)	−0.00663 (9)	−0.00120 (8)
O1	0.0500 (9)	0.0443 (9)	0.0288 (7)	−0.0263 (8)	−0.0138 (7)	0.0058 (6)
O2	0.0319 (7)	0.0420 (9)	0.0342 (8)	−0.0180 (6)	−0.0001 (6)	−0.0135 (6)
O3	0.0455 (9)	0.0584 (11)	0.0277 (8)	−0.0166 (8)	−0.0096 (7)	−0.0075 (7)
O4	0.0378 (8)	0.0635 (11)	0.0357 (8)	−0.0300 (8)	−0.0059 (7)	−0.0021 (8)
O5	0.0287 (7)	0.0304 (7)	0.0292 (7)	−0.0072 (6)	−0.0069 (6)	−0.0004 (6)
O6	0.0710 (13)	0.0345 (9)	0.0466 (10)	−0.0264 (9)	0.0063 (9)	−0.0085 (8)
N1	0.0313 (8)	0.0240 (8)	0.0294 (8)	−0.0107 (6)	−0.0064 (7)	0.0004 (6)
N2	0.0302 (8)	0.0246 (8)	0.0282 (8)	−0.0085 (6)	−0.0095 (6)	−0.0014 (6)
N3	0.0351 (9)	0.0186 (7)	0.0383 (9)	−0.0083 (6)	−0.0058 (7)	−0.0020 (6)
C1	0.0392 (11)	0.0313 (10)	0.0341 (10)	−0.0123 (9)	−0.0038 (9)	−0.0032 (8)
C2	0.0394 (12)	0.0446 (13)	0.0347 (11)	−0.0146 (10)	−0.0007 (9)	0.0022 (9)
C3	0.0388 (11)	0.0403 (12)	0.0432 (12)	−0.0194 (10)	−0.0126 (10)	0.0137 (10)
C4	0.0364 (10)	0.0245 (9)	0.0439 (12)	−0.0128 (8)	−0.0131 (9)	0.0076 (8)
C5	0.0259 (8)	0.0225 (8)	0.0344 (10)	−0.0079 (7)	−0.0116 (7)	0.0012 (7)
C6	0.0245 (8)	0.0231 (9)	0.0322 (9)	−0.0048 (7)	−0.0098 (7)	−0.0039 (7)
C7	0.0343 (10)	0.0326 (10)	0.0372 (11)	−0.0054 (8)	−0.0088 (9)	−0.0101 (8)
C8	0.0390 (11)	0.0469 (13)	0.0312 (10)	−0.0046 (10)	−0.0093 (9)	−0.0089 (9)
C9	0.0454 (12)	0.0437 (13)	0.0288 (10)	−0.0095 (10)	−0.0078 (9)	0.0040 (9)
C10	0.0425 (11)	0.0290 (10)	0.0337 (10)	−0.0119 (9)	−0.0116 (9)	0.0040 (8)
C11	0.0293 (9)	0.0287 (9)	0.0271 (9)	−0.0052 (7)	−0.0077 (7)	−0.0034 (7)
C12	0.0416 (11)	0.0296 (10)	0.0323 (10)	−0.0160 (8)	−0.0061 (9)	−0.0067 (8)
C13	0.0300 (9)	0.0300 (9)	0.0283 (9)	−0.0109 (8)	−0.0071 (8)	−0.0010 (7)

Geometric parameters (Å, º)

Cu—O2	1.9368 (15)	C1—C2	1.364 (3)
Cu—O1	1.9396 (15)	C1—H1	0.9300
Cu—N2	1.9929 (16)	C2—C3	1.397 (4)
Cu—N1	2.0002 (17)	C2—H2	0.9300
Cu—O5	2.2722 (15)	C3—C4	1.368 (3)
O1—C11	1.272 (2)	C3—H3	0.9300
O2—C13	1.271 (2)	C4—C5	1.411 (3)
O3—C11	1.243 (3)	C4—H4	0.9300
O4—C13	1.247 (3)	C6—C7	1.407 (3)
O5—H14	0.887 (17)	C7—C8	1.368 (4)
O5—H13	0.848 (18)	C7—H7	0.9300
O6—H16	0.89 (4)	C8—C9	1.397 (4)
O6—H15	0.887 (18)	C8—H8	0.9300
N1—C5	1.342 (2)	C9—C10	1.368 (3)
N1—C1	1.359 (3)	C9—H9	0.9300
N2—C6	1.337 (2)	C10—H10	0.9300
N2—C10	1.357 (3)	C11—C12	1.527 (3)
N3—C5	1.377 (3)	C12—C13	1.515 (3)
N3—C6	1.385 (3)	C12—H12A	0.9700
N3—H5	0.8600	C12—H12B	0.9700
O2—Cu—O1	91.84 (7)	C3—C4—C5	119.1 (2)
O2—Cu—N2	87.37 (7)	C3—C4—H4	120.5
O1—Cu—N2	166.18 (7)	C5—C4—H4	120.5
O2—Cu—N1	163.51 (7)	N1—C5—N3	120.26 (17)
O1—Cu—N1	88.80 (7)	N1—C5—C4	121.22 (19)
N2—Cu—N1	88.10 (7)	N3—C5—C4	118.53 (18)
O2—Cu—O5	97.62 (7)	N2—C6—N3	120.91 (17)
O1—Cu—O5	94.39 (7)	N2—C6—C7	121.38 (19)
N2—Cu—O5	99.39 (6)	N3—C6—C7	117.69 (18)
N1—Cu—O5	98.76 (6)	C8—C7—C6	118.9 (2)
C11—O1—Cu	127.75 (14)	C8—C7—H7	120.6
C13—O2—Cu	128.12 (13)	C6—C7—H7	120.6
Cu—O5—H14	111.7 (17)	C7—C8—C9	120.1 (2)
Cu—O5—H13	108 (2)	C7—C8—H8	120.0
H14—O5—H13	105 (3)	C9—C8—H8	120.0
H16—O6—H15	108 (3)	C10—C9—C8	117.7 (2)
C5—N1—C1	118.31 (18)	C10—C9—H9	121.1
C5—N1—Cu	121.30 (14)	C8—C9—H9	121.1
C1—N1—Cu	118.83 (13)	N2—C10—C9	123.3 (2)
C6—N2—C10	118.53 (17)	N2—C10—H10	118.3
C6—N2—Cu	121.98 (14)	C9—C10—H10	118.3
C10—N2—Cu	118.19 (14)	O3—C11—O1	122.8 (2)
C5—N3—C6	128.29 (17)	O3—C11—C12	117.79 (19)
C5—N3—H5	115.9	O1—C11—C12	119.42 (17)
C6—N3—H5	115.9	C13—C12—C11	116.74 (17)
N1—C1—C2	123.1 (2)	C13—C12—H12A	108.1
N1—C1—H1	118.4	C11—C12—H12A	108.1
C2—C1—H1	118.4	C13—C12—H12B	108.1
C1—C2—C3	118.4 (2)	C11—C12—H12B	108.1
C1—C2—H2	120.8	H12A—C12—H12B	107.3
C3—C2—H2	120.8	O4—C13—O2	121.28 (19)
C4—C3—C2	119.5 (2)	O4—C13—C12	119.25 (18)
C4—C3—H3	120.3	O2—C13—C12	119.45 (17)
C2—C3—H3	120.3
O2—Cu—O1—C11	−18.7 (2)	C1—N1—C5—N3	−172.77 (19)
N2—Cu—O1—C11	−105.1 (3)	Cu—N1—C5—N3	21.7 (3)
N1—Cu—O1—C11	177.81 (19)	C1—N1—C5—C4	6.9 (3)
O5—Cu—O1—C11	79.11 (19)	Cu—N1—C5—C4	−158.71 (16)
O1—Cu—O2—C13	19.8 (2)	C6—N3—C5—N1	19.1 (3)
N2—Cu—O2—C13	−174.0 (2)	C6—N3—C5—C4	−160.5 (2)
N1—Cu—O2—C13	111.8 (3)	C3—C4—C5—N1	−4.7 (3)
O5—Cu—O2—C13	−74.8 (2)	C3—C4—C5—N3	175.0 (2)
O2—Cu—N1—C5	33.0 (3)	C10—N2—C6—N3	178.72 (19)
O1—Cu—N1—C5	125.44 (16)	Cu—N2—C6—N3	−14.5 (3)
N2—Cu—N1—C5	−41.09 (16)	C10—N2—C6—C7	−3.0 (3)
O5—Cu—N1—C5	−140.30 (16)	Cu—N2—C6—C7	163.74 (15)
O2—Cu—N1—C1	−132.5 (2)	C5—N3—C6—N2	−23.3 (3)
O1—Cu—N1—C1	−40.05 (17)	C5—N3—C6—C7	158.4 (2)
N2—Cu—N1—C1	153.42 (17)	N2—C6—C7—C8	1.3 (3)
O5—Cu—N1—C1	54.21 (17)	N3—C6—C7—C8	179.6 (2)
O2—Cu—N2—C6	−126.71 (16)	C6—C7—C8—C9	1.4 (3)
O1—Cu—N2—C6	−39.7 (4)	C7—C8—C9—C10	−2.3 (4)
N1—Cu—N2—C6	37.43 (16)	C6—N2—C10—C9	2.2 (3)
O5—Cu—N2—C6	136.00 (15)	Cu—N2—C10—C9	−165.11 (19)
O2—Cu—N2—C10	40.09 (17)	C8—C9—C10—N2	0.5 (4)
O1—Cu—N2—C10	127.1 (3)	Cu—O1—C11—O3	173.39 (17)
N1—Cu—N2—C10	−155.77 (17)	Cu—O1—C11—C12	−8.0 (3)
O5—Cu—N2—C10	−57.20 (16)	O3—C11—C12—C13	−139.3 (2)
C5—N1—C1—C2	−3.2 (3)	O1—C11—C12—C13	42.0 (3)
Cu—N1—C1—C2	162.7 (2)	Cu—O2—C13—O4	−175.46 (17)
N1—C1—C2—C3	−2.7 (4)	Cu—O2—C13—C12	6.1 (3)
C1—C2—C3—C4	4.9 (4)	C11—C12—C13—O4	140.6 (2)
C2—C3—C4—C5	−1.4 (3)	C11—C12—C13—O2	−41.0 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H5···O6^i	0.86	2.04	2.836 (3)	155
O5—H13···O4^ii	0.85 (3)	1.86 (3)	2.702 (3)	173 (2)
O5—H14···O3^iii	0.89 (2)	1.82 (2)	2.706 (2)	173 (2)
O6—H15···O4^iv	0.89 (2)	2.00 (2)	2.885 (3)	174 (2)
O6—H16···O5	0.89 (4)	1.99 (4)	2.874 (3)	177 (2)

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