metal-organic compounds
Diaquabis(L-serinato)copper(II) 0.1-hydrate at 120 K
aDepartamento de Química, Pontificia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente 225, Gávea, 22453-999 Rio de Janeiro, RJ, Brazil, bDepartamento de Química Inorgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil, and cDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
*Correspondence e-mail: j.skakle@abdn.ac.uk
The title compound, [Cu(C3H6NO3)2(H2O)2]·0.1H2O, is isostructural with the nickel analogue. The octahedral CuII ion lies on a twofold axis, with cis chelating O,N-serine groups and trans aqua ligands. Small amounts of a solvent water molecule form hydrogen bonds to link the molecules along the [010] direction, while a number of strong hydrogen bonds combine to form sheets in the (110) plane.
Comment
As part of our continuing study of Cu complexes with amino acids (Felcman & de Miranda, 1997; de Miranda & Felcman, 2001; de Miranda et al., 2002; Felcman et al., 2003), we have isolated and characterized the diaquabis(L-serinato)copper(II) complex, (1), from an aqueous reaction mixture containing (L)-serine (ser), guanidinoacetic acid (gaa) and CuII (1:1:1). Crystals of (1) were obtained after several months. No crystalline complex containing gaa, either alone or in a mixed complex with ser, appeared in a similar time. van der Helm & Franks (1969) reported the structure of the unhydrated complex, [bis(L-serinato)copper(II)], (2), obtained from CuII and (L)-serine in methanol containing a little water.
Complex (1), isostructural with the analogous nickel complex, diaquabis(L-serinato)nickel(II) hydrate, (3), (van der Helm & Hossain, 1969), has an octahedrally coordinated CuII ion with cis chelating O,N-ser groups and trans aqua ligands (Fig. 1). A similar cis arrangement of ser units arises in square-pyramidal (2), in which a carboxylate O atom, from an adjacent molecule, occupies the apical position. A distant O atom is sited 3.632 (6) Å from Cu trans to the apical ligand in (2), but this can at most be considered only a very weak interaction. Comparison of the serine–Cu bond lengths in (2) [Cu—O 1.952 (5) and 1.970 (5) Å; Cu—N 1.975 (6) and 1.988 (6) Å] and in (1) (Table 1) indicates that the weaker interactions occur in the higher coordinate complex, (1). The serine chelate rings in (1) have envelope conformations with flaps at the N atoms. The CuII ion and the four serine binding atoms are essentially co-planar.
Small amounts of additional water molecules are present in both (1) and (3). The PLATON; Spek, 2003) confirm its presence.
and structure of (1) are notably different from those of the unhydrated compound, (2), and although only a very small amount of water was found to be present in (1), both the hydrogen-bonding scheme (see below) and the availability of space (The non-isolation of any gaa-containing complex from the reaction mixture probably reflects more their solubility in the reaction media than their non-formation. A number of Cu–gaa complexes have been isolated, including tetrakis(μ-guanidinoacetic acid-κ2O:O′)bis[nitrato-κO)copper], [Cu2(NO3)2(gaa)4], (4) (de Miranda et al., 2002), {aqua[μ-(N′-carboxylatomethylguanidino)oxidoacetato](μ-guanidinoacetic acid)dicopper(II)} nitrate dihydrate, [Cu2(oag)(gaa)(H2O)]NO3·2H2O, (5) (Felcman et al., 2003), and [CuCl2(gaa)2] (Silva et al., 2001]. Compounds (4) and (5) were obtained from reaction mixtures containing gaa and CuII, both in the presence and absence of another amino acid, namely aspartine. Furthermore, mixed Cu–L-serine complexes, e.g. with glycine, have been reported (D'yakon et al., 1991).
The solvent water molecule forms hydrogen bonds (Table 2) with the O atom of the aqua ligand in the main molecule (Fig. 2), leading to chains along [010]. Together with the other strong hydrogen bonds (Table 2), these form sheets in the (110) plane (Fig. 2).
Experimental
To a hot solution (333 K) of guanidinoacetic acid (0.3513 g, 3 mmol) and serine (0.3153, 3 mmol) in deionized water (100 ml) was slowly added a solution of copper(II) nitrate (0.7248 g, 3 mmol) in deionized water (5 ml). The reaction mixture was stirred at 333 K for 8 h, cooled slowly to 277 K, and the pH adjusted to 6.0 with KOH (3 M). The white precipitate which formed was filtered off and the filtrate was stored in a covered vessel. Thin blue plate-like crystals began to be formed after the fifth month and were collected after six months, washed with absolute ethanol and dried at 323 K.
Crystal data
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Data collection
Refinement
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C2, Cm and C2/m as possible space groups; C2 was selected and confirmed by the subsequent structure analysis. In this atoms Cu1 and O5W of the low-occupancy solvent water molecule (see below) lie on crystallographic twofold axes. Therefore, the comprises, in addition to these two atoms, one of each of a complete serinate and aqua ligand and a single H atom of the solvent water molecule. The small amount of solvent water was clearly identified from the difference map. During the structure solution, and prior to the location of the water molecule, the difference map revealed two electron-density peaks close to one another, which suggested disorder of the water over two sites. However, the two positions could not be refined simultaneously and indeed, once one O atom was refined, the peak in the difference map corresponding to the `second site' disappeared. Approximate positions for the H atoms of the aqua ligand and of the low-occupancy solvent water molecule were then obtained from difference maps and modified to provide acceptable O—H distances (0.81–0.82 Å) and H—O—H angles (103°). Owing to correlation with the isotropic displacement parameter, the occupancy of the solvent water molecule could only be established by trial and error. The value of 0.10 finally chosen was such as to provide a reasonable value for the freely refined isotropic displacement parameter of the O atom (O5W). All other H atoms were placed in calculated positions, with X—H distances of 0.99 (CH2), 1.00 (aliphatic CH), 0.92 (NH2) or 0.84 Å (OH). The torsion angle of the OH group was also refined. All H atoms were refined, finally, with a riding model, with Uiso(H) = 1.2Ueq(C,N) or 1.5Ueq(O).
permittedData collection: COLLECT (Nonius, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL-X (McArdle, 1994, 2005) and SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: OSCAIL-X and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: CIFTAB (Sheldrick, 1997).
Supporting information
https://doi.org/10.1107/S1600536805035221/bt6774sup1.cif
contains datablocks global, 1. DOI:Structure factors: contains datablock 1. DOI: https://doi.org/10.1107/S1600536805035221/bt67741sup2.hkl
Data collection: COLLECT (Nonius, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 1994, 2005) and SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: CIFTAB (Sheldrick, 1997).[Cu(C3H6NO3)2(H2O)2]·0.1H2O | F(000) = 320 |
Mr = 309.55 | Dx = 1.837 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2y | Cell parameters from 673 reflections |
a = 7.5866 (2) Å | θ = 2.9–27.5° |
b = 8.5684 (2) Å | µ = 1.99 mm−1 |
c = 8.8257 (2) Å | T = 120 K |
β = 102.7701 (15)° | Plate, pale blue |
V = 559.52 (2) Å3 | 0.40 × 0.30 × 0.08 mm |
Z = 2 |
Bruker Nonius KappaCCD area-detector diffractometer | 1220 independent reflections |
Radiation source: Bruker Nonius FR591 rotating anode | 1214 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.026 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 4.0° |
φ and ω scans | h = −7→9 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −10→11 |
Tmin = 0.666, Tmax = 0.853 | l = −11→10 |
3347 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: geom and difmap |
R[F2 > 2σ(F2)] = 0.019 | H-atom parameters constrained |
wR(F2) = 0.053 | w = 1/[σ2(Fo2) + (0.0104P)2 + 0.5389P] where P = (Fo2 + 2Fc2)/3 |
S = 1.10 | (Δ/σ)max < 0.001 |
1220 reflections | Δρmax = 0.29 e Å−3 |
81 parameters | Δρmin = −0.44 e Å−3 |
1 restraint | Absolute structure: Flack (1983), with 536 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.071 (12) |
Experimental. Although determined using DIRAX, the cell is refined during data reduction DIRAX refs: Duisenberg AJM, J. Appl. Cryst. 1992 25 92–96 and Duisenberg AJM, Hooft RWW, Schreurs AMM, Droon J.: J. Appl. Cryst. 2000 33 893–898 |
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 | Occ. (<1) | |
Cu1 | 0.5000 | 0.5000 | 0.0000 | 0.00801 (11) | |
O1 | 0.3839 (3) | 0.3345 (2) | 0.1111 (2) | 0.0070 (4) | |
O2 | 0.2506 (2) | 0.2929 (2) | 0.30727 (18) | 0.0105 (3) | |
O3 | 0.2453 (3) | 0.7763 (2) | 0.38982 (18) | 0.0150 (4) | |
H3 | 0.2571 | 0.7839 | 0.4864 | 0.022* | |
N1 | 0.3790 (3) | 0.6455 (3) | 0.1359 (3) | 0.0061 (5) | |
H1A | 0.4516 | 0.7304 | 0.1686 | 0.007* | |
H1B | 0.2695 | 0.6807 | 0.0794 | 0.007* | |
C1 | 0.3257 (3) | 0.3816 (3) | 0.2255 (3) | 0.0066 (4) | |
C2 | 0.3529 (3) | 0.5539 (3) | 0.2706 (3) | 0.0057 (4) | |
H2 | 0.4682 | 0.5609 | 0.3512 | 0.007* | |
C3 | 0.2045 (3) | 0.6195 (3) | 0.3435 (3) | 0.0107 (4) | |
H3A | 0.0871 | 0.6151 | 0.2674 | 0.013* | |
H3B | 0.1945 | 0.5558 | 0.4349 | 0.013* | |
O4 | 0.73885 (15) | 0.5018 (3) | 0.17483 (13) | 0.0081 (3) | |
H4A | 0.7519 | 0.4420 | 0.2483 | 0.012* | |
H4B | 0.7402 | 0.5867 | 0.2162 | 0.012* | |
O5W | 0.5000 | 0.947 (3) | 0.0000 | 0.014 (5)* | 0.10 |
H5 | 0.5356 | 1.0067 | −0.0597 | 0.020* | 0.10 |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.01260 (16) | 0.00605 (17) | 0.00643 (17) | 0.000 | 0.00435 (11) | 0.000 |
O1 | 0.0129 (9) | 0.0053 (9) | 0.0040 (8) | −0.0007 (7) | 0.0044 (7) | −0.0013 (7) |
O2 | 0.0204 (9) | 0.0067 (8) | 0.0070 (8) | −0.0030 (7) | 0.0087 (7) | 0.0006 (7) |
O3 | 0.0377 (11) | 0.0045 (8) | 0.0054 (8) | −0.0004 (7) | 0.0105 (7) | −0.0013 (7) |
N1 | 0.0111 (11) | 0.0018 (10) | 0.0065 (11) | 0.0000 (8) | 0.0044 (8) | 0.0003 (8) |
C1 | 0.0097 (10) | 0.0029 (11) | 0.0065 (11) | 0.0003 (9) | 0.0004 (9) | −0.0002 (9) |
C2 | 0.0107 (10) | 0.0044 (11) | 0.0032 (10) | −0.0005 (8) | 0.0042 (8) | 0.0005 (8) |
C3 | 0.0184 (12) | 0.0048 (10) | 0.0117 (11) | −0.0002 (9) | 0.0095 (9) | −0.0008 (9) |
O4 | 0.0133 (6) | 0.0046 (6) | 0.0063 (6) | −0.0016 (11) | 0.0020 (5) | 0.0009 (11) |
Cu1—O1i | 2.032 (2) | N1—H1A | 0.9200 |
Cu1—O1 | 2.032 (2) | N1—H1B | 0.9200 |
Cu1—N1 | 2.079 (2) | C1—C2 | 1.531 (4) |
Cu1—N1i | 2.079 (2) | C2—C3 | 1.522 (3) |
Cu1—O4i | 2.1044 (11) | C2—H2 | 1.0000 |
Cu1—O4 | 2.1044 (11) | C3—H3A | 0.9900 |
O1—C1 | 1.255 (3) | C3—H3B | 0.9900 |
O2—C1 | 1.267 (3) | O4—H4A | 0.8154 |
O3—C3 | 1.419 (3) | O4—H4B | 0.8126 |
O3—H3 | 0.8400 | O5W—H5i | 0.8209 |
N1—C2 | 1.474 (3) | O5W—H5 | 0.8209 |
O1—Cu1—O1i | 91.50 (11) | Cu1—N1—H1B | 110.2 |
O1i—Cu1—N1 | 172.11 (9) | H1A—N1—H1B | 108.5 |
O1—Cu1—N1i | 172.11 (9) | O1—C1—O2 | 123.2 (2) |
O1—Cu1—N1 | 81.16 (7) | O1—C1—C2 | 117.9 (2) |
O1i—Cu1—N1i | 81.16 (7) | O2—C1—C2 | 118.8 (2) |
N1—Cu1—N1i | 106.31 (13) | N1—C2—C3 | 112.8 (2) |
O1—Cu1—O4 | 92.65 (8) | N1—C2—C1 | 109.8 (2) |
O1i—Cu1—O4i | 92.65 (8) | C3—C2—C1 | 113.3 (2) |
O1i—Cu1—O4 | 87.95 (8) | N1—C2—H2 | 106.8 |
O1—Cu1—O4i | 87.95 (8) | C3—C2—H2 | 106.8 |
N1i—Cu1—O4 | 89.99 (8) | C1—C2—H2 | 106.8 |
N1—Cu1—O4i | 89.99 (8) | O3—C3—C2 | 109.65 (19) |
N1—Cu1—O4 | 89.49 (8) | O3—C3—H3A | 109.7 |
N1i—Cu1—O4i | 89.49 (8) | C2—C3—H3A | 109.7 |
O4—Cu1—O4i | 179.14 (14) | O3—C3—H3B | 109.7 |
C1—O1—Cu1 | 115.53 (18) | C2—C3—H3B | 109.7 |
C3—O3—H3 | 109.5 | H3A—C3—H3B | 108.2 |
C2—N1—Cu1 | 107.53 (16) | Cu1—O4—H4A | 120.8 |
C2—N1—H1A | 110.2 | Cu1—O4—H4B | 105.1 |
Cu1—N1—H1A | 110.2 | H4A—O4—H4B | 102.5 |
C2—N1—H1B | 110.2 | H5i—O5W—H5 | 103.1 |
O1i—Cu1—O1—C1 | 164.3 (2) | Cu1—O1—C1—C2 | −1.7 (3) |
N1—Cu1—O1—C1 | −12.74 (15) | Cu1—N1—C2—C3 | −157.24 (16) |
O4i—Cu1—O1—C1 | −103.05 (19) | Cu1—N1—C2—C1 | −29.8 (2) |
O4—Cu1—O1—C1 | 76.33 (19) | O1—C1—C2—N1 | 22.2 (3) |
O1—Cu1—N1—C2 | 23.48 (14) | O2—C1—C2—N1 | −159.7 (2) |
N1i—Cu1—N1—C2 | −159.1 (2) | O1—C1—C2—C3 | 149.4 (2) |
O4i—Cu1—N1—C2 | 111.40 (17) | O2—C1—C2—C3 | −32.6 (3) |
O4—Cu1—N1—C2 | −69.28 (17) | N1—C2—C3—O3 | −57.8 (3) |
Cu1—O1—C1—O2 | −179.65 (16) | C1—C2—C3—O3 | 176.65 (18) |
Symmetry code: (i) −x+1, y, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O2ii | 0.92 | 2.39 | 3.154 (3) | 141 |
N1—H1B···O1iii | 0.92 | 2.25 | 3.071 (2) | 149 |
O3—H3···O2iv | 0.84 | 1.84 | 2.671 (2) | 172 |
O4—H4A···O3v | 0.82 | 1.90 | 2.701 (3) | 168 |
O4—H4B···O2ii | 0.81 | 1.94 | 2.747 (3) | 177 |
O5W—H5···O4vi | 0.82 | 2.18 | 2.807 (4) | 134 |
Symmetry codes: (ii) x+1/2, y+1/2, z; (iii) −x+1/2, y+1/2, −z; (iv) −x+1/2, y+1/2, −z+1; (v) x+1/2, y−1/2, z; (vi) −x+3/2, y+1/2, −z. |
Acknowledgements
The authors thank CNPq and FAPERJ, Brazil, for support, and the EPSRC X-ray Crystallographic Service, University of Southampton, UK, for the data collection. In addition, we acknowledge the help and advice of J. L. Wardell.
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