Aqua[bis(pyrimidin-2-yl-κN)amine](carbonato-κ²O,O′)copper(II) dihydrate

The title mononuclear complex, [Cu(CO₃)(C₈H₇N₅)(H₂O)]·2H₂O, was obtained by fixation of CO₂ by a mixture of copper(II) tetra­fluoro­borate and the ligand bis­(pyrimidin-2-yl)­amine in ethanol/water. The Cu^II ion of the complex has a distorted square-pyramidal environment, with a basal plane formed by two N atoms of the ligand and two chelating O atoms of the carbonate group, while the apical position is occupied by the O atom of the coordinating water mol­ecule. In the solid state, hydrogen-bonding interactions are dominant, the most unusual being the Watson–Crick-type coplanar ligand pairing through two N—H...N bonds. Lattice water mol­ecules also participate in hydrogen bonding.

S1. Comment

The title compound was obtained in our ongoing research into ligands which can act as a trap for CO₂ by the insertion of atmospheric CO₂ into coordination compounds. Insertion reactions of CO₂ into metal-ligand bonds are not uncommon, and in the past few years many review papers have been published on the subject (Gibson, 1999; Walther et al., 1999; Yin & Moss, 1999). Several dinuclear copper(II) compounds have been synthesized by means of fixation of CO₂ from air (Nishida et al., 1999; Kitajima et al., 1993; Kruger et al., 1995; Youngme et al., 2000). In order to build and control larger aggregates, we have started a research programme in which the ligands used also act as hydrogen-bond donors or acceptors.

The recently developed ligand bis(pyrimidin-2-yl)amine (abbreviated to dipm; Yao et al., 2000) is a prototype, as it may form Watson-Crick-type hydrogen bonds, as already shown in the literature with the first-generation ligand 2-aminopyrimidine (van Albada, Quiroz-Castro et al., 2000; van Albada, Smeets et al., 2000). Continuing this work, we present here the crystal stucture of the title complex, (I). \sch

Structural analysis of (I) shows a neutral [Cu(dipm)(CO₃)(H₂O)] unit and two non-coordinating water molecules. The Cu^II anion has a distorted square-pyramidal environment, with a basal plane formed by two N atoms of the dipm ligand and two O atoms of the carbonato group [basal Cu—N/O distances vary from 1.9410 (16) to 1.9852 (17) Å]. The apical position is occupied by the O atom of the coordinating water molecule at a distance of 2.3004 (18) Å.

The distortion from square-pyramidal geometry can be best expressed with the parameter τ (for five-coordinate complexes, τ describes the relative amount of trigonality; τ = 0 for square pyramidal and τ = 1 for trigonal bipyramidal; Addison et al., 1984), and in this case τ = 0.045, representing a very small distortion from square pyramidal and indicating a d_x2-y2 orbital ground state.

The aromatic ring-ring stacking interactions between neighbouring bipyrimidine rings, which help to stabilize the lattice structure, are characterized by a centroid-centroid distance of 3.592(?)Å Please provide s.u. on this distance.

The Cu geometry in (I) is related to that in [Cu(dpyam)(CO₃)(H₂O)]·2H₂O (dpyam is di-2-pyridylamine; Akhter et al., 1991). In the latter structure, the distortion is slightly larger (τ = 0.097).

Compound (I) has an additional hydrogen-bonding feature which generates dinuclear units: the amino N atom forms a Watson-Crick-type hydrogen bond with the neighbouring ring N atom [N1···N123 2.979 (3) Å] (Fig.2). Additional hydrogen-bonding contacts occur between the O atom of the axial water molecule and the non-coordinating O atoms of a neighbouring carbonato anion and a lattice water molecule [O1···O5 3.018 (3), O1···O6 2.841 (3) Å (a bifurcated hydrogen bond) and O1···O2 2.933 (3) Å]. The lattice water molecules form hydrogen bonds with neighbouring carbonato anions and uncoordinated water molecules, the O···O distances varying from 2.785 (3) to 2.960 (4) Å.

The IR spectrum of (I) clearly shows the out-of-plane mode of the CO₃ dianion, with a medium to strong band at 807 cm^-1, and this matches well with the bands observed in the literature (van Albada, Mutikainen et al., 2000; Youngme et al., 2000) for chelating carbonato ligands.

S2. Experimental

The dipm ligand was synthesized using the literature method of Yao et al. (2000). Metal salts and solvents were sourced commercially and were used without further purification. Copper(II) tetrafluoroborate (?.?? mg, 1.3 mmol) and dipm (?.?? mg, 1.3 mmol) were each dissolved in ethanol/water (1:1, 10 ml) and the solutions mixed carefully together. A few drops of 2 M sodium hydroxide solution were then added gradually, so that no precipitate was formed and pH ≈ 5. The mixture was filtered to remove any solid particles and was then placed in a desiccator under a CO₂ atmosphere generated from solid CO₂ (van Albada, Mutikainen et al., 2000), and after a period of a few weeks to one month, long blue needles of (I) separated. The crystals were filtered off and washed with ethanol. Attempts to synthesize the compounds by the addition of sodium carbonate or potassium carbonate were unsuccessful. Satisfactory elemental analyses were obtained. A crystal was selected for the X-ray measurements and mounted on a glass fibre using the oil-drop method (Kottke & Stalke, 1993). Please give masses of reagents used above.

S3. Refinement

Please check these details Water H atoms were picked from a difference map and refined using restraints for the O—H and H···H distances of 0.83 (1) and 1.34 (1) Å, respectively. Other H atoms were introduced in calculated positions and refined with fixed geometry with respect to their carrier atoms, at distances of 0.88 and 0.95 Å for N—H and C—H, respectively. For all H atoms, U_iso(H) = 1.2U_eq(carrier atom).

Computing details

Data collection: CAD-4 Software (Nonius, 1998); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1995) and PLATON?; software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. A view of the molecule of (I) with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii. The lattice water molecules have been omitted for clarity.
	Fig. 2. A plot showing a fragment of the hydrogen-bonded network in (I).

Aqua[bis(pyrimidin-2-yl-κN)amine](carbonato-κ²O,O')copper(II) dihydrate

Crystal data

[Cu(C8H7N5)(CO3)(H2O)]·2H2O	F(000) = 716
Mr = 350.78	Dx = 1.838 Mg m^−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54178 Å
a = 5.8520 (12) Å	Cell parameters from 25 reflections
b = 12.897 (3) Å	θ = 12–27°
c = 16.801 (3) Å	µ = 2.83 mm^−1
β = 90.87 (3)°	T = 193 K
V = 1267.9 (4) Å^3	Column, blue
Z = 4	0.40 × 0.25 × 0.25 mm

Data collection

Enraf-Nonius CAD-4 diffractometer	2079 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.041
Graphite monochromator	θmax = 65.0°, θmin = 4.3°
ω/2θ scans	h = −6→6
Absorption correction: ψ-scan (North et al., 1968)	k = −15→15
Tmin = 0.400, Tmax = 0.493	l = −19→19
2955 measured reflections	3 standard reflections every 200 reflections
2144 independent reflections	intensity decay: 0.0%

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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0754P)^2 + 1.1584P] where P = (Fo^2 + 2Fc^2)/3
2144 reflections	(Δ/σ)max = 0.001
208 parameters	Δρmax = 0.52 e Å^−3
0 restraints	Δρmin = −0.33 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. The intensity data were corrected for Lorentz and polarization effects and for absorption. All nonhydrogen atoms were refined anisotropically.

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

	x	y	z	Uiso*/Ueq
Cu1	0.35416 (5)	0.38080 (2)	0.171674 (18)	0.01520 (17)
N111	0.3810 (3)	0.32871 (15)	0.06179 (11)	0.0171 (4)
C112	0.5540 (4)	0.35070 (18)	0.01255 (13)	0.0165 (5)
N113	0.5843 (4)	0.30800 (16)	−0.05875 (12)	0.0211 (4)
C114	0.4333 (4)	0.2366 (2)	−0.08194 (15)	0.0237 (5)
H11B	0.4515	0.2043	−0.1323	0.028*
C115	0.2501 (4)	0.2076 (2)	−0.03531 (15)	0.0240 (5)
H11C	0.1441	0.1562	−0.0526	0.029*
C116	0.2290 (4)	0.25626 (19)	0.03647 (15)	0.0214 (5)
H11D	0.1044	0.2388	0.0695	0.026*
N1	0.7196 (3)	0.42252 (15)	0.03229 (11)	0.0181 (4)
H1	0.8218	0.4320	−0.0049	0.022*
N121	0.6128 (3)	0.47737 (14)	0.16102 (11)	0.0152 (4)
C122	0.7550 (4)	0.48205 (17)	0.09914 (13)	0.0155 (5)
N123	0.9398 (3)	0.54366 (15)	0.09508 (11)	0.0176 (4)
C124	0.9850 (4)	0.60329 (18)	0.15832 (15)	0.0199 (5)
H12C	1.1149	0.6474	0.1574	0.024*
C125	0.8504 (4)	0.60323 (19)	0.22492 (15)	0.0208 (5)
H12D	0.8853	0.6457	0.2697	0.025*
C126	0.6630 (4)	0.53878 (18)	0.22355 (13)	0.0183 (5)
H12E	0.5658	0.5376	0.2683	0.022*
C1	0.0550 (4)	0.36856 (17)	0.26314 (14)	0.0174 (5)
O4	0.2387 (3)	0.42356 (13)	0.27722 (9)	0.0196 (4)
O5	0.0527 (3)	0.32572 (13)	0.19326 (10)	0.0191 (4)
O6	−0.1036 (3)	0.35672 (14)	0.31162 (10)	0.0235 (4)
O1	0.5747 (3)	0.24475 (14)	0.21689 (11)	0.0253 (4)
H11	0.685 (3)	0.275 (2)	0.2393 (16)	0.030*
H12	0.623 (5)	0.210 (2)	0.1792 (13)	0.030*
O2	0.6791 (4)	0.07989 (17)	0.10284 (12)	0.0367 (5)
H21	0.729 (6)	0.076 (3)	0.0569 (9)	0.044*
H22	0.733 (6)	0.0297 (19)	0.1281 (16)	0.044*
O3	0.7592 (4)	0.0221 (2)	−0.06045 (14)	0.0507 (6)
H32	0.803 (6)	0.060 (3)	−0.0975 (16)	0.061*
H31	0.643 (5)	−0.008 (3)	−0.077 (2)	0.061*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cu1	0.0142 (2)	0.0161 (2)	0.0153 (2)	−0.00217 (11)	0.00032 (15)	−0.00093 (11)
N111	0.0173 (10)	0.0168 (10)	0.0173 (9)	−0.0025 (7)	−0.0021 (7)	0.0000 (8)
C112	0.0176 (11)	0.0130 (10)	0.0187 (11)	0.0009 (9)	−0.0010 (9)	0.0026 (9)
N113	0.0246 (11)	0.0206 (11)	0.0180 (10)	−0.0042 (8)	0.0007 (8)	−0.0036 (8)
C114	0.0302 (13)	0.0230 (13)	0.0179 (12)	−0.0040 (10)	−0.0019 (10)	−0.0034 (10)
C115	0.0275 (13)	0.0221 (13)	0.0224 (12)	−0.0084 (10)	−0.0044 (10)	−0.0032 (10)
C116	0.0197 (12)	0.0215 (12)	0.0231 (12)	−0.0050 (9)	−0.0007 (9)	0.0007 (10)
N1	0.0190 (10)	0.0197 (11)	0.0156 (10)	−0.0057 (8)	0.0040 (7)	−0.0038 (8)
N121	0.0167 (9)	0.0122 (9)	0.0168 (9)	0.0019 (7)	−0.0006 (7)	0.0001 (7)
C122	0.0163 (11)	0.0117 (10)	0.0185 (11)	0.0019 (8)	−0.0014 (9)	0.0000 (8)
N123	0.0198 (10)	0.0134 (9)	0.0197 (10)	−0.0031 (8)	0.0010 (8)	−0.0024 (8)
C124	0.0219 (12)	0.0162 (11)	0.0216 (12)	−0.0027 (9)	−0.0010 (9)	−0.0012 (9)
C125	0.0246 (13)	0.0164 (12)	0.0214 (13)	−0.0012 (9)	−0.0002 (10)	−0.0034 (9)
C126	0.0211 (12)	0.0165 (12)	0.0173 (11)	0.0021 (9)	0.0021 (9)	−0.0010 (9)
C1	0.0157 (12)	0.0127 (11)	0.0237 (12)	0.0045 (8)	−0.0019 (9)	0.0040 (9)
O4	0.0172 (8)	0.0219 (9)	0.0196 (8)	−0.0010 (7)	0.0015 (6)	−0.0014 (7)
O5	0.0155 (8)	0.0214 (9)	0.0203 (8)	−0.0023 (6)	−0.0003 (6)	0.0002 (7)
O6	0.0200 (9)	0.0261 (9)	0.0245 (9)	0.0010 (7)	0.0049 (7)	0.0039 (7)
O1	0.0191 (9)	0.0217 (9)	0.0348 (11)	−0.0022 (7)	−0.0050 (7)	0.0032 (7)
O2	0.0438 (12)	0.0353 (12)	0.0311 (11)	0.0082 (9)	0.0018 (9)	0.0030 (9)
O3	0.0495 (14)	0.0605 (16)	0.0421 (13)	−0.0113 (12)	−0.0032 (10)	0.0212 (11)

Geometric parameters (Å, º)

Cu1—O1	2.3004 (18)	N121—C126	1.345 (3)
Cu1—O4	1.9852 (17)	N121—C122	1.343 (3)
Cu1—O5	1.9410 (16)	C122—N123	1.345 (3)
Cu1—N111	1.973 (2)	N123—C124	1.335 (3)
Cu1—N121	1.971 (2)	C124—C125	1.378 (4)
Cu1—C1	2.352 (3)	C124—H12C	0.9500
N111—C112	1.347 (3)	C125—C126	1.376 (4)
N111—C116	1.354 (3)	C125—H12D	0.9500
C112—N113	1.333 (3)	C126—H12E	0.9500
C112—N1	1.377 (3)	C1—O6	1.253 (3)
N113—C114	1.330 (3)	C1—O5	1.298 (3)
C114—C115	1.389 (4)	C1—O4	1.307 (3)
C114—H11B	0.9500	O1—H11	0.836 (10)
C115—C116	1.367 (4)	O1—H12	0.832 (10)
C115—H11C	0.9500	O2—H21	0.830 (10)
C116—H11D	0.9500	O2—H22	0.833 (10)
N1—C122	1.373 (3)	O3—H32	0.834 (10)
N1—H1	0.8800	O3—H31	0.831 (10)
O1—Cu1—O4	96.53 (7)	C122—N1—H1	114.0
O1—Cu1—O5	99.56 (7)	C112—N1—H1	114.0
O1—Cu1—N111	89.84 (8)	C126—N121—C122	116.6 (2)
O1—Cu1—N121	94.83 (7)	C126—N121—Cu1	117.40 (16)
O4—Cu1—O5	67.19 (7)	C122—N121—Cu1	125.77 (16)
O4—Cu1—N111	164.43 (7)	N121—C122—N123	125.0 (2)
O4—Cu1—N121	100.25 (8)	N121—C122—N1	121.4 (2)
O5—Cu1—N111	97.79 (8)	N123—C122—N1	113.6 (2)
O5—Cu1—N121	161.79 (8)	C124—N123—C122	116.7 (2)
N111—Cu1—N121	93.33 (8)	N123—C124—C125	122.5 (2)
O5—Cu1—C1	33.47 (8)	N123—C124—H12C	118.8
N121—Cu1—C1	133.02 (8)	C125—C124—H12C	118.8
N111—Cu1—C1	131.22 (8)	C126—C125—C124	116.9 (2)
O4—Cu1—C1	33.74 (8)	C126—C125—H12D	121.6
O1—Cu1—C1	98.77 (7)	C124—C125—H12D	121.6
C112—N111—C116	116.6 (2)	N121—C126—C125	122.2 (2)
C112—N111—Cu1	125.03 (16)	N121—C126—H12E	118.9
C116—N111—Cu1	117.89 (16)	C125—C126—H12E	118.9
N113—C112—N111	125.2 (2)	O6—C1—O5	122.6 (2)
N113—C112—N1	113.0 (2)	O6—C1—O4	124.3 (2)
N111—C112—N1	121.7 (2)	O5—C1—O4	113.1 (2)
C112—N113—C114	116.9 (2)	O6—C1—Cu1	176.85 (17)
N113—C114—C115	122.4 (2)	O5—C1—Cu1	55.59 (11)
N113—C114—H11B	118.8	O4—C1—Cu1	57.53 (11)
C115—C114—H11B	118.8	C1—O4—Cu1	88.73 (14)
C116—C115—C114	117.1 (2)	C1—O5—Cu1	90.94 (14)
C116—C115—H11C	121.5	Cu1—O1—H11	103 (2)
C114—C115—H11C	121.5	Cu1—O1—H12	111 (2)
N111—C116—C115	121.8 (2)	H11—O1—H12	109 (2)
N111—C116—H11D	119.1	H21—O2—H22	107 (2)
C115—C116—H11D	119.1	H32—O3—H31	106 (2)
C122—N1—C112	132.0 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N123^i	0.88	2.10	2.979 (3)	179
O1—H11···O5^ii	0.84 (3)	2.39 (3)	3.017 (3)	132 (2)
O1—H11···O6^ii	0.84 (3)	2.02 (3)	2.841 (3)	167 (3)
O1—H12···O2	0.83 (3)	2.14 (3)	2.933 (3)	160 (3)
O2—H21···O3	0.83 (3)	2.10 (3)	2.888 (3)	159 (4)
O2—H22···O4^iii	0.83 (3)	2.10 (3)	2.886 (3)	156 (3)
O3—H31···O2^iv	0.83 (3)	2.14 (3)	2.960 (3)	171 (4)
O3—H32···O6^v	0.83 (3)	1.95 (4)	2.785 (4)	177 (4)

Symmetry codes: (i) −x+2, −y+1, −z; (ii) x+1, y, z; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+1, −y, −z; (v) x+1, −y+1/2, z−1/2.