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Acta Cryst. (2007). E63, m1598    [ doi:10.1107/S1600536807021605 ]

A redetermination of (N9-adenine-[kappa]N)aqua[glycylglycinato(2-)-[kappa]3N,N',O]copper(II)

M. P. Brandi-Blanco, B. Dumet-Fernandes, J. M. González-Pérez and D. Choquesillo-Lazarte

Abstract top

In the title complex, [Cu(C4H6N2O3)(C5H5N5)(H2O)], the CuII atom is five-coordinated in a square-pyramidal geometry by a tridentate glycylglycinate ligand (glygly), an N atom from an adenine ligand (Hade) and a water molecule in the apical position. The Hade coordination is reinforced by an intramolecular hydrogen-bonding interaction. A much lower precision structure has already been determined using intensities collected by the film method [Tomita, Izumo & Fujiwara (1973). Biochem. Biophys. Res. Commun. 54, 96-99].

Comment top

The molecular structure of the title compound, (I) (Fig.1), has been reported previously (Tomita et al., 1973) but the prescision of the current structure determination is vastly improved. The CuII ion exhibits a square base pyramidal 4 + 1 coordination, τ parameter 0.26 (Addison et al., 1984). An intra-molecular interligand H-bonding interaction, namely N—H(glygly)···N3(Hade), reinforces the Cu—N9(Hade) coordination bond, thus contributing to the molecular recognition pattern between the Cu-dipeptide chelate and the adenine, which retains its dissociable H atom on N7. In the crystal structure, molecules are linked through N—H···N, N—H···O and O—H···O hydrogen bonds, forming a three-dimensional network (Fig. 2).

Related literature top

The reported molecular recognition mode was not described previously (Tomita et al., 1973). In constrast, it has long been known that in the closely related [Cu(glygly)(9Meade)(H2O)].4H2O (Kistenmacher et al., 1976), the Cu—N(9Meade) bond is reinforced by one Namine—H···O(apical/aqua) intramolecular bond, but there is not a direct glygly-9-methyladenine intramolecular interligand interaction. For related literature, see: Addison et al. (1984).

Experimental top

To a solution resulting from the reaction of Cu2CO3(OH)2 (0.5 mmol) in 90 ml of water, an aqueous solution (60 ml) of the base pair adenine:thymine (1 mmol of each base) was added. The evaporation at r.t. yields crystals of the new mixed-ligand complex [CuII(C4H6N2O3)(C5H5N5)(H2O)]. The same compound was also obtained using the free base adenine instead of the complementary pair.

Refinement top

Aqua and amine H atoms were located in a difference map and refined as riding, in their as-found positions. Other H atoms were positioned geometrically and treated as riding with C—H = 0.95–0.99 Å. All Uiso(H) values were constrained to be 1.2 times Ueq of the carrier atom. The highest peak in the final difference Fourier of 0.99 e Å-3 is 0.97Å from Cu1 and the deepest hole of -1.40 e Å-3 is 0.96Å from Cu1

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as spheres of arbitrary radii. The dashed line indicates an intramolecular hydrogen bond.
[Figure 2] Fig. 2. A view, along the a axis, of the molecular packing of (I). The intermolecular hydrogen bonds are shown as dashed lines.
(N9-adenine-κN)aqua[glycylglycinato(2-)-\ κ3N,N',O]copper(II) top
Crystal data top
[Cu(C4H6N2O3)(C5H5N5)(H2O)]Z = 2
Mr = 346.80F(000) = 354
Triclinic, P1Dx = 1.828 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.919 (3) ÅCell parameters from 806 reflections
b = 7.617 (3) Åθ = 2.7–28.5°
c = 12.060 (5) ŵ = 1.76 mm−1
α = 93.213 (7)°T = 273 K
β = 94.640 (6)°Plate, blue
γ = 94.614 (7)°0.33 × 0.13 × 0.08 mm
V = 630.2 (5) Å3
Data collection top
Bruker SMART 1000
diffractometer		2566 independent reflections
Radiation source: fine-focus sealed tube1816 reflections with I > 2σ(I)
graphiteRint = 0.068
ω scansθmax = 26.4°, θmin = 1.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)		h = −8→8
Tmin = 0.594, Tmax = 0.872k = −9→9
6720 measured reflectionsl = 0→15
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)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.166H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.087P)2]
where P = (Fo2 + 2Fc2)/3
2566 reflections(Δ/σ)max = 0.001
190 parametersΔρmax = 0.99 e Å−3
0 restraintsΔρmin = −1.40 e Å−3
Crystal data top
[Cu(C4H6N2O3)(C5H5N5)(H2O)]γ = 94.614 (7)°
Mr = 346.80V = 630.2 (5) Å3
Triclinic, P1Z = 2
a = 6.919 (3) ÅMo Kα radiation
b = 7.617 (3) ŵ = 1.76 mm−1
c = 12.060 (5) ÅT = 273 K
α = 93.213 (7)°0.33 × 0.13 × 0.08 mm
β = 94.640 (6)°
Data collection top
Bruker SMART 1000
diffractometer		2566 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2004)		1816 reflections with I > 2σ(I)
Tmin = 0.594, Tmax = 0.872Rint = 0.068
6720 measured reflectionsθmax = 26.4°
Refinement top
R[F2 > 2σ(F2)] = 0.059H-atom parameters constrained
wR(F2) = 0.166Δρmax = 0.99 e Å−3
S = 1.04Δρmin = −1.40 e Å−3
2566 reflectionsAbsolute structure: ?
190 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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 (Å2) top
xyzUiso*/Ueq
Cu10.36815 (9)0.28116 (9)0.21733 (5)0.0320 (3)
N1−0.3262 (6)0.0393 (6)0.3990 (3)0.0308 (10)
C2−0.2523 (8)0.0108 (8)0.3017 (4)0.0337 (13)
H2−0.3304−0.06270.24900.040*
N3−0.0810 (6)0.0733 (6)0.2693 (3)0.0336 (11)
C40.0252 (7)0.1750 (7)0.3516 (4)0.0244 (10)
C5−0.0351 (7)0.2129 (7)0.4549 (4)0.0255 (11)
C6−0.2217 (7)0.1437 (7)0.4798 (4)0.0282 (11)
N6−0.3000 (7)0.1763 (7)0.5760 (4)0.0415 (12)
H6A−0.24660.23360.63630.050*
H6B−0.39540.11020.59820.050*
N70.1150 (6)0.3158 (6)0.5138 (3)0.0313 (10)
H70.10340.35820.58420.038*
C80.2554 (8)0.3370 (7)0.4460 (4)0.0345 (13)
H80.37330.40290.46640.041*
N90.2114 (6)0.2550 (6)0.3458 (3)0.0295 (10)
N110.5310 (6)0.2917 (6)0.0976 (3)0.0334 (11)
C110.7143 (8)0.3996 (7)0.1182 (4)0.0324 (12)
H11A0.71870.49400.06750.039*
H11B0.82180.32850.10640.039*
C120.7302 (7)0.4758 (7)0.2375 (4)0.0297 (11)
O110.5924 (5)0.4369 (5)0.2984 (3)0.0368 (9)
O120.8795 (5)0.5740 (5)0.2714 (3)0.0413 (10)
C210.4650 (8)0.2204 (7)−0.0009 (4)0.0335 (13)
O130.5490 (6)0.2262 (5)−0.0904 (3)0.0445 (11)
C220.2650 (8)0.1224 (8)−0.0016 (4)0.0400 (14)
H22A0.16730.1927−0.03470.048*
H22B0.26060.0119−0.04620.048*
N120.2224 (7)0.0868 (6)0.1136 (4)0.0387 (12)
H12A0.09820.07170.11810.046*
H12B0.2639−0.01050.13580.046*
O10.1997 (7)0.5145 (7)0.1604 (5)0.0747 (17)
H1A0.19430.58300.21590.090*
H1B0.23920.58030.11380.090*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0182 (4)0.0414 (5)0.0332 (4)−0.0137 (3)0.0056 (2)−0.0064 (3)
N10.018 (2)0.038 (3)0.034 (2)−0.0133 (19)0.0031 (17)0.0008 (19)
C20.021 (3)0.045 (3)0.031 (3)−0.014 (2)−0.001 (2)−0.004 (2)
N30.021 (2)0.045 (3)0.030 (2)−0.018 (2)0.0017 (17)−0.0037 (19)
C40.016 (2)0.026 (3)0.029 (2)−0.008 (2)−0.0010 (18)0.001 (2)
C50.014 (2)0.030 (3)0.031 (3)−0.007 (2)−0.0001 (18)0.003 (2)
C60.019 (3)0.037 (3)0.029 (2)−0.004 (2)0.0048 (19)0.007 (2)
N60.030 (3)0.061 (3)0.030 (2)−0.018 (2)0.0086 (19)−0.005 (2)
N70.021 (2)0.037 (3)0.032 (2)−0.015 (2)−0.0001 (17)−0.0038 (18)
C80.024 (3)0.041 (3)0.037 (3)−0.011 (2)0.005 (2)0.001 (2)
N90.015 (2)0.038 (3)0.033 (2)−0.0133 (19)0.0028 (17)−0.0002 (18)
N110.022 (2)0.043 (3)0.032 (2)−0.016 (2)0.0040 (18)−0.0038 (19)
C110.021 (3)0.044 (3)0.030 (3)−0.011 (2)0.005 (2)−0.004 (2)
C120.019 (3)0.037 (3)0.032 (3)−0.004 (2)0.004 (2)−0.004 (2)
O110.0220 (19)0.054 (3)0.0317 (19)−0.0125 (17)0.0090 (15)−0.0059 (17)
O120.025 (2)0.055 (3)0.038 (2)−0.0212 (19)0.0083 (16)−0.0134 (18)
C210.025 (3)0.039 (3)0.033 (3)−0.012 (2)0.001 (2)−0.006 (2)
O130.038 (2)0.057 (3)0.034 (2)−0.019 (2)0.0083 (17)−0.0069 (18)
C220.024 (3)0.049 (4)0.041 (3)−0.017 (3)−0.001 (2)−0.009 (3)
N120.025 (2)0.044 (3)0.044 (3)−0.014 (2)0.010 (2)−0.010 (2)
O10.043 (3)0.084 (4)0.107 (4)0.012 (3)0.033 (3)0.044 (3)
Geometric parameters (Å, °) top
Cu1—N111.903 (4)C8—N91.330 (7)
Cu1—N91.972 (4)C8—H80.9300
Cu1—O112.024 (4)N11—C211.310 (7)
Cu1—N122.030 (4)N11—C111.451 (6)
Cu1—O12.309 (5)C11—C121.513 (7)
N1—C21.331 (6)C11—H11A0.9700
N1—C61.346 (7)C11—H11B0.9700
C2—N31.337 (6)C12—O121.252 (6)
C2—H20.9300C12—O111.276 (6)
N3—C41.352 (6)C21—O131.268 (6)
C4—C51.369 (6)C21—C221.518 (7)
C4—N91.389 (6)C22—N121.479 (7)
C5—N71.373 (6)C22—H22A0.9700
C5—C61.416 (6)C22—H22B0.9700
C6—N61.339 (6)N12—H12A0.8640
N6—H6A0.8669N12—H12B0.8644
N6—H6B0.8663O1—H1A0.8305
N7—C81.326 (6)O1—H1B0.8219
N7—H70.9031
N11—Cu1—N9175.42 (19)C8—N9—Cu1125.0 (3)
N11—Cu1—O1182.58 (16)C4—N9—Cu1130.4 (3)
N9—Cu1—O1196.86 (15)C21—N11—C11123.2 (4)
N11—Cu1—N1281.47 (18)C21—N11—Cu1119.5 (4)
N9—Cu1—N1298.07 (17)C11—N11—Cu1116.8 (3)
O11—Cu1—N12159.99 (17)N11—C11—C12108.1 (4)
N11—Cu1—O193.39 (19)N11—C11—H11A110.1
N9—Cu1—O191.19 (17)C12—C11—H11A110.1
O11—Cu1—O194.36 (19)N11—C11—H11B110.1
N12—Cu1—O198.6 (2)C12—C11—H11B110.1
C2—N1—C6119.2 (4)H11A—C11—H11B108.4
N1—C2—N3128.9 (5)O12—C12—O11123.4 (5)
N1—C2—H2115.6O12—C12—C11117.8 (4)
N3—C2—H2115.6O11—C12—C11118.8 (5)
C2—N3—C4111.7 (4)C12—O11—Cu1113.6 (3)
N3—C4—C5124.6 (4)O13—C21—N11127.3 (5)
N3—C4—N9126.0 (4)O13—C21—C22119.7 (5)
C5—C4—N9109.4 (4)N11—C21—C22113.0 (4)
C4—C5—N7106.5 (4)N12—C22—C21109.9 (4)
C4—C5—C6119.2 (5)N12—C22—H22A109.7
N7—C5—C6134.3 (5)C21—C22—H22A109.7
N6—C6—N1118.7 (5)N12—C22—H22B109.7
N6—C6—C5124.9 (5)C21—C22—H22B109.7
N1—C6—C5116.4 (4)H22A—C22—H22B108.2
C6—N6—H6A128.6C22—N12—Cu1107.8 (3)
C6—N6—H6B123.3C22—N12—H12A110.4
H6A—N6—H6B104.3Cu1—N12—H12A116.1
C8—N7—C5106.7 (4)C22—N12—H12B113.6
C8—N7—H7132.5Cu1—N12—H12B105.5
C5—N7—H7120.8H12A—N12—H12B103.5
N7—C8—N9113.5 (5)Cu1—O1—H1A107.6
N7—C8—H8123.3Cu1—O1—H1B121.9
N9—C8—H8123.3H1A—O1—H1B103.0
C8—N9—C4104.0 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1B···O13i0.822.042.740 (6)143
O1—H1A···O12ii0.832.332.735 (6)111
N12—H12B···O13iii0.862.242.978 (7)143
N12—H12A···N30.862.292.927 (6)131
N7—H7···O12iv0.901.782.674 (5)170
N6—H6B···N1v0.872.162.996 (6)162
Symmetry codes: (i) −x+1, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y, −z; (iv) −x+1, −y+1, −z+1; (v) −x−1, −y, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1B···O13i0.822.042.740 (6)143
O1—H1A···O12ii0.832.332.735 (6)111
N12—H12B···O13iii0.862.242.978 (7)143
N12—H12A···N30.862.292.927 (6)131
N7—H7···O12iv0.901.782.674 (5)170
N6—H6B···N1v0.872.162.996 (6)162
Symmetry codes: (i) −x+1, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y, −z; (iv) −x+1, −y+1, −z+1; (v) −x−1, −y, −z+1.
Acknowledgements top

Financial support from ERDF-EC, MEC Spain (Project CTQ2006–15329-C02–02/BQU) are gratefully acknowledged. DCh-L thanks CSIC-EU for an I3P postdoctoral research contract.

references
References top

Addison, A. W., Rao, T. N., Reedijk, J., van Rijn, J. & Verschoor, G. C. (1984). J. Chem. Soc. Dalton Trans. pp. 1349–1356.

Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Kistenmacher, T. J., Marzilli, L. G. & Szalda, D. J. (1976). Acta Cryst. B32, 186–193.

Sheldrick, G. M. (2001). SHELXTL. Version 5.0. Bruker AXS Inc., Madison, Wisconsin, USA.

Sheldrick, G. M. (2004). SADABS. University of Göttingen, Germany.

Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

Tomita, K., Izuno, T. & Fujiwara, T. (1973). Biochem. Biophys. Res. Commun. 54, 96–99.

Westrip, S. P. (2007). publCIF. In preparation.