Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807021605/lh2382sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807021605/lh2382Isup2.hkl |
CCDC reference: 650543
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.
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
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).
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).
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).
[Cu(C4H6N2O3)(C5H5N5)(H2O)] | Z = 2 |
Mr = 346.80 | F(000) = 354 |
Triclinic, P1 | Dx = 1.828 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.919 (3) Å | Cell parameters from 806 reflections |
b = 7.617 (3) Å | θ = 2.7–28.5° |
c = 12.060 (5) Å | µ = 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 |
Bruker SMART 1000 diffractometer | 2566 independent reflections |
Radiation source: fine-focus sealed tube | 1816 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.068 |
ω scans | θmax = 26.4°, θmin = 1.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2004) | h = −8→8 |
Tmin = 0.594, Tmax = 0.872 | k = −9→9 |
6720 measured reflections | l = 0→15 |
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)] = 0.059 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.166 | H-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 parameters | Δρmax = 0.99 e Å−3 |
0 restraints | Δρmin = −1.41 e Å−3 |
[Cu(C4H6N2O3)(C5H5N5)(H2O)] | γ = 94.614 (7)° |
Mr = 346.80 | V = 630.2 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.919 (3) Å | Mo Kα radiation |
b = 7.617 (3) Å | µ = 1.76 mm−1 |
c = 12.060 (5) Å | T = 273 K |
α = 93.213 (7)° | 0.33 × 0.13 × 0.08 mm |
β = 94.640 (6)° |
Bruker SMART 1000 diffractometer | 2566 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2004) | 1816 reflections with I > 2σ(I) |
Tmin = 0.594, Tmax = 0.872 | Rint = 0.068 |
6720 measured reflections |
R[F2 > 2σ(F2)] = 0.059 | 0 restraints |
wR(F2) = 0.166 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.99 e Å−3 |
2566 reflections | Δρmin = −1.41 e Å−3 |
190 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cu1 | 0.36815 (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 | −0.0627 | 0.2490 | 0.040* | |
N3 | −0.0810 (6) | 0.0733 (6) | 0.2693 (3) | 0.0336 (11) | |
C4 | 0.0252 (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 | −0.2466 | 0.2336 | 0.6363 | 0.050* | |
H6B | −0.3954 | 0.1102 | 0.5982 | 0.050* | |
N7 | 0.1150 (6) | 0.3158 (6) | 0.5138 (3) | 0.0313 (10) | |
H7 | 0.1034 | 0.3582 | 0.5842 | 0.038* | |
C8 | 0.2554 (8) | 0.3370 (7) | 0.4460 (4) | 0.0345 (13) | |
H8 | 0.3733 | 0.4029 | 0.4664 | 0.041* | |
N9 | 0.2114 (6) | 0.2550 (6) | 0.3458 (3) | 0.0295 (10) | |
N11 | 0.5310 (6) | 0.2917 (6) | 0.0976 (3) | 0.0334 (11) | |
C11 | 0.7143 (8) | 0.3996 (7) | 0.1182 (4) | 0.0324 (12) | |
H11A | 0.7187 | 0.4940 | 0.0675 | 0.039* | |
H11B | 0.8218 | 0.3285 | 0.1064 | 0.039* | |
C12 | 0.7302 (7) | 0.4758 (7) | 0.2375 (4) | 0.0297 (11) | |
O11 | 0.5924 (5) | 0.4369 (5) | 0.2984 (3) | 0.0368 (9) | |
O12 | 0.8795 (5) | 0.5740 (5) | 0.2714 (3) | 0.0413 (10) | |
C21 | 0.4650 (8) | 0.2204 (7) | −0.0009 (4) | 0.0335 (13) | |
O13 | 0.5490 (6) | 0.2262 (5) | −0.0904 (3) | 0.0445 (11) | |
C22 | 0.2650 (8) | 0.1224 (8) | −0.0016 (4) | 0.0400 (14) | |
H22A | 0.1673 | 0.1927 | −0.0347 | 0.048* | |
H22B | 0.2606 | 0.0119 | −0.0462 | 0.048* | |
N12 | 0.2224 (7) | 0.0868 (6) | 0.1136 (4) | 0.0387 (12) | |
H12A | 0.0982 | 0.0717 | 0.1181 | 0.046* | |
H12B | 0.2639 | −0.0105 | 0.1358 | 0.046* | |
O1 | 0.1997 (7) | 0.5145 (7) | 0.1604 (5) | 0.0747 (17) | |
H1A | 0.1943 | 0.5830 | 0.2159 | 0.090* | |
H1B | 0.2392 | 0.5803 | 0.1138 | 0.090* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.0182 (4) | 0.0414 (5) | 0.0332 (4) | −0.0137 (3) | 0.0056 (2) | −0.0064 (3) |
N1 | 0.018 (2) | 0.038 (3) | 0.034 (2) | −0.0133 (19) | 0.0031 (17) | 0.0008 (19) |
C2 | 0.021 (3) | 0.045 (3) | 0.031 (3) | −0.014 (2) | −0.001 (2) | −0.004 (2) |
N3 | 0.021 (2) | 0.045 (3) | 0.030 (2) | −0.018 (2) | 0.0017 (17) | −0.0037 (19) |
C4 | 0.016 (2) | 0.026 (3) | 0.029 (2) | −0.008 (2) | −0.0010 (18) | 0.001 (2) |
C5 | 0.014 (2) | 0.030 (3) | 0.031 (3) | −0.007 (2) | −0.0001 (18) | 0.003 (2) |
C6 | 0.019 (3) | 0.037 (3) | 0.029 (2) | −0.004 (2) | 0.0048 (19) | 0.007 (2) |
N6 | 0.030 (3) | 0.061 (3) | 0.030 (2) | −0.018 (2) | 0.0086 (19) | −0.005 (2) |
N7 | 0.021 (2) | 0.037 (3) | 0.032 (2) | −0.015 (2) | −0.0001 (17) | −0.0038 (18) |
C8 | 0.024 (3) | 0.041 (3) | 0.037 (3) | −0.011 (2) | 0.005 (2) | 0.001 (2) |
N9 | 0.015 (2) | 0.038 (3) | 0.033 (2) | −0.0133 (19) | 0.0028 (17) | −0.0002 (18) |
N11 | 0.022 (2) | 0.043 (3) | 0.032 (2) | −0.016 (2) | 0.0040 (18) | −0.0038 (19) |
C11 | 0.021 (3) | 0.044 (3) | 0.030 (3) | −0.011 (2) | 0.005 (2) | −0.004 (2) |
C12 | 0.019 (3) | 0.037 (3) | 0.032 (3) | −0.004 (2) | 0.004 (2) | −0.004 (2) |
O11 | 0.0220 (19) | 0.054 (3) | 0.0317 (19) | −0.0125 (17) | 0.0090 (15) | −0.0059 (17) |
O12 | 0.025 (2) | 0.055 (3) | 0.038 (2) | −0.0212 (19) | 0.0083 (16) | −0.0134 (18) |
C21 | 0.025 (3) | 0.039 (3) | 0.033 (3) | −0.012 (2) | 0.001 (2) | −0.006 (2) |
O13 | 0.038 (2) | 0.057 (3) | 0.034 (2) | −0.019 (2) | 0.0083 (17) | −0.0069 (18) |
C22 | 0.024 (3) | 0.049 (4) | 0.041 (3) | −0.017 (3) | −0.001 (2) | −0.009 (3) |
N12 | 0.025 (2) | 0.044 (3) | 0.044 (3) | −0.014 (2) | 0.010 (2) | −0.010 (2) |
O1 | 0.043 (3) | 0.084 (4) | 0.107 (4) | 0.012 (3) | 0.033 (3) | 0.044 (3) |
Cu1—N11 | 1.903 (4) | C8—N9 | 1.330 (7) |
Cu1—N9 | 1.972 (4) | C8—H8 | 0.9300 |
Cu1—O11 | 2.024 (4) | N11—C21 | 1.310 (7) |
Cu1—N12 | 2.030 (4) | N11—C11 | 1.451 (6) |
Cu1—O1 | 2.309 (5) | C11—C12 | 1.513 (7) |
N1—C2 | 1.331 (6) | C11—H11A | 0.9700 |
N1—C6 | 1.346 (7) | C11—H11B | 0.9700 |
C2—N3 | 1.337 (6) | C12—O12 | 1.252 (6) |
C2—H2 | 0.9300 | C12—O11 | 1.276 (6) |
N3—C4 | 1.352 (6) | C21—O13 | 1.268 (6) |
C4—C5 | 1.369 (6) | C21—C22 | 1.518 (7) |
C4—N9 | 1.389 (6) | C22—N12 | 1.479 (7) |
C5—N7 | 1.373 (6) | C22—H22A | 0.9700 |
C5—C6 | 1.416 (6) | C22—H22B | 0.9700 |
C6—N6 | 1.339 (6) | N12—H12A | 0.8640 |
N6—H6A | 0.8669 | N12—H12B | 0.8644 |
N6—H6B | 0.8663 | O1—H1A | 0.8305 |
N7—C8 | 1.326 (6) | O1—H1B | 0.8219 |
N7—H7 | 0.9031 | ||
N11—Cu1—N9 | 175.42 (19) | C8—N9—Cu1 | 125.0 (3) |
N11—Cu1—O11 | 82.58 (16) | C4—N9—Cu1 | 130.4 (3) |
N9—Cu1—O11 | 96.86 (15) | C21—N11—C11 | 123.2 (4) |
N11—Cu1—N12 | 81.47 (18) | C21—N11—Cu1 | 119.5 (4) |
N9—Cu1—N12 | 98.07 (17) | C11—N11—Cu1 | 116.8 (3) |
O11—Cu1—N12 | 159.99 (17) | N11—C11—C12 | 108.1 (4) |
N11—Cu1—O1 | 93.39 (19) | N11—C11—H11A | 110.1 |
N9—Cu1—O1 | 91.19 (17) | C12—C11—H11A | 110.1 |
O11—Cu1—O1 | 94.36 (19) | N11—C11—H11B | 110.1 |
N12—Cu1—O1 | 98.6 (2) | C12—C11—H11B | 110.1 |
C2—N1—C6 | 119.2 (4) | H11A—C11—H11B | 108.4 |
N1—C2—N3 | 128.9 (5) | O12—C12—O11 | 123.4 (5) |
N1—C2—H2 | 115.6 | O12—C12—C11 | 117.8 (4) |
N3—C2—H2 | 115.6 | O11—C12—C11 | 118.8 (5) |
C2—N3—C4 | 111.7 (4) | C12—O11—Cu1 | 113.6 (3) |
N3—C4—C5 | 124.6 (4) | O13—C21—N11 | 127.3 (5) |
N3—C4—N9 | 126.0 (4) | O13—C21—C22 | 119.7 (5) |
C5—C4—N9 | 109.4 (4) | N11—C21—C22 | 113.0 (4) |
C4—C5—N7 | 106.5 (4) | N12—C22—C21 | 109.9 (4) |
C4—C5—C6 | 119.2 (5) | N12—C22—H22A | 109.7 |
N7—C5—C6 | 134.3 (5) | C21—C22—H22A | 109.7 |
N6—C6—N1 | 118.7 (5) | N12—C22—H22B | 109.7 |
N6—C6—C5 | 124.9 (5) | C21—C22—H22B | 109.7 |
N1—C6—C5 | 116.4 (4) | H22A—C22—H22B | 108.2 |
C6—N6—H6A | 128.6 | C22—N12—Cu1 | 107.8 (3) |
C6—N6—H6B | 123.3 | C22—N12—H12A | 110.4 |
H6A—N6—H6B | 104.3 | Cu1—N12—H12A | 116.1 |
C8—N7—C5 | 106.7 (4) | C22—N12—H12B | 113.6 |
C8—N7—H7 | 132.5 | Cu1—N12—H12B | 105.5 |
C5—N7—H7 | 120.8 | H12A—N12—H12B | 103.5 |
N7—C8—N9 | 113.5 (5) | Cu1—O1—H1A | 107.6 |
N7—C8—H8 | 123.3 | Cu1—O1—H1B | 121.9 |
N9—C8—H8 | 123.3 | H1A—O1—H1B | 103.0 |
C8—N9—C4 | 104.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1B···O13i | 0.82 | 2.04 | 2.740 (6) | 143 |
O1—H1A···O12ii | 0.83 | 2.33 | 2.735 (6) | 111 |
N12—H12B···O13iii | 0.86 | 2.24 | 2.978 (7) | 143 |
N12—H12A···N3 | 0.86 | 2.29 | 2.927 (6) | 131 |
N7—H7···O12iv | 0.90 | 1.78 | 2.674 (5) | 170 |
N6—H6B···N1v | 0.87 | 2.16 | 2.996 (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. |
Experimental details
Crystal data | |
Chemical formula | [Cu(C4H6N2O3)(C5H5N5)(H2O)] |
Mr | 346.80 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 273 |
a, b, c (Å) | 6.919 (3), 7.617 (3), 12.060 (5) |
α, β, γ (°) | 93.213 (7), 94.640 (6), 94.614 (7) |
V (Å3) | 630.2 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.76 |
Crystal size (mm) | 0.33 × 0.13 × 0.08 |
Data collection | |
Diffractometer | Bruker SMART 1000 |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2004) |
Tmin, Tmax | 0.594, 0.872 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6720, 2566, 1816 |
Rint | 0.068 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.166, 1.04 |
No. of reflections | 2566 |
No. of parameters | 190 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.99, −1.41 |
Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SAINT, SHELXTL (Sheldrick, 2001), SHELXTL, PLATON (Spek, 2003), publCIF (Westrip, 2007).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1B···O13i | 0.82 | 2.04 | 2.740 (6) | 142.6 |
O1—H1A···O12ii | 0.83 | 2.33 | 2.735 (6) | 110.9 |
N12—H12B···O13iii | 0.86 | 2.24 | 2.978 (7) | 142.9 |
N12—H12A···N3 | 0.86 | 2.29 | 2.927 (6) | 130.9 |
N7—H7···O12iv | 0.90 | 1.78 | 2.674 (5) | 169.8 |
N6—H6B···N1v | 0.87 | 2.16 | 2.996 (6) | 161.6 |
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. |
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).