Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010903128X/fg3106sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S010827010903128X/fg3106IIsup2.hkl |
CCDC reference: 749688
Compound (I) was synthesized by the literature method (Comba et al., 1991). X-ray quality crystals of (II) were grown by slow diffusion of methanol into a solution of (I) in distilled water at room temperature over a period of 3 d.
All H atoms of the metal complex of (II) were clearly visible in difference maps and then allowed for as riding atoms, with N—H = 0.93, methylene C—H = 0.99 and methyl C—H = 0.98 Å, and with Uiso(H) = 1.2Ueq(N or C) for methylene C, or 1.5Ueq(C) for methyl C. The water/methanol hydroxy H atom was included at the position found in the difference map.
Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and WinGX (Farrugia, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999).
[Cu(C8H13N3O6)]·0.45CH4O·0.55H2O | F(000) = 684 |
Mr = 335.08 | Dx = 1.750 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 4693 reflections |
a = 13.0407 (16) Å | θ = 3.9–28.5° |
b = 8.0578 (15) Å | µ = 1.76 mm−1 |
c = 13.383 (2) Å | T = 200 K |
β = 115.726 (16)° | Rectangular, blue-purple |
V = 1266.9 (3) Å3 | 0.55 × 0.45 × 0.38 mm |
Z = 4 |
Oxford Xcalibur2 diffractometer | 2974 independent reflections |
Radiation source: fine-focus sealed tube | 2401 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
Detector resolution: 8.4190 pixels mm-1 | θmax = 28.7°, θmin = 3.9° |
ω scans | h = −16→17 |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm] | k = −10→10 |
Tmin = 0.387, Tmax = 0.511 | l = −17→17 |
13298 measured reflections |
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)] = 0.027 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.085 | H-atom parameters constrained |
S = 1.15 | w = 1/[σ2(Fo2) + (0.0483P)2 + 0.234P] where P = (Fo2 + 2Fc2)/3 |
2974 reflections | (Δ/σ)max = 0.001 |
186 parameters | Δρmax = 0.44 e Å−3 |
0 restraints | Δρmin = −0.37 e Å−3 |
[Cu(C8H13N3O6)]·0.45CH4O·0.55H2O | V = 1266.9 (3) Å3 |
Mr = 335.08 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 13.0407 (16) Å | µ = 1.76 mm−1 |
b = 8.0578 (15) Å | T = 200 K |
c = 13.383 (2) Å | 0.55 × 0.45 × 0.38 mm |
β = 115.726 (16)° |
Oxford Xcalibur2 diffractometer | 2974 independent reflections |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm] | 2401 reflections with I > 2σ(I) |
Tmin = 0.387, Tmax = 0.511 | Rint = 0.023 |
13298 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | 0 restraints |
wR(F2) = 0.085 | H-atom parameters constrained |
S = 1.15 | Δρmax = 0.44 e Å−3 |
2974 reflections | Δρmin = −0.37 e Å−3 |
186 parameters |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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. Final difference Fourier synthesis cycles located both a methanol and a water solvate molecule clearly hydrogen-bonded to carboxylate oxygen O4. Various models were tested to effect stable refinement of the solvent molecules. The most suitable treatment had the fractionally occupied methanol and water atoms O1S and H1S located at the same lattice sites summing up to unit occupancy. The methyl group of the methanol solvent molecule, in contrast, had an occupancy factor of 0.45, in effect requiring (I) to be a mixed water/methanol solvate of 0.55/0.45 fractional composition. No restraints were necessary to achieve refinement convergence with this approach. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Cu1 | 0.572812 (19) | 0.43953 (3) | 0.135407 (19) | 0.01577 (10) | |
O1 | 0.54400 (12) | 0.30903 (18) | 0.00358 (11) | 0.0181 (3) | |
O2 | 0.42778 (12) | 0.11413 (19) | −0.10515 (12) | 0.0212 (3) | |
O3 | 0.71071 (12) | 0.54406 (17) | 0.13960 (11) | 0.0171 (3) | |
O4 | 0.84447 (12) | 0.72833 (19) | 0.23393 (11) | 0.0201 (3) | |
O5 | 0.26376 (19) | 0.6346 (3) | 0.1131 (2) | 0.0643 (7) | |
O6 | 0.38471 (18) | 0.8069 (3) | 0.2256 (2) | 0.0604 (6) | |
N1 | 0.41743 (15) | 0.3628 (2) | 0.10928 (14) | 0.0184 (4) | |
H101 | 0.3655 | 0.4330 | 0.0562 | 0.022* | |
N2 | 0.59049 (14) | 0.6078 (2) | 0.25097 (14) | 0.0171 (4) | |
H102 | 0.5539 | 0.7034 | 0.2136 | 0.020* | |
N3 | 0.34979 (17) | 0.6656 (3) | 0.19686 (19) | 0.0363 (5) | |
C1 | 0.46187 (17) | 0.2030 (2) | −0.02231 (16) | 0.0171 (4) | |
C2 | 0.40542 (18) | 0.1970 (3) | 0.05647 (17) | 0.0206 (4) | |
H2A | 0.3239 | 0.1684 | 0.0149 | 0.025* | |
H2B | 0.4423 | 0.1113 | 0.1140 | 0.025* | |
C3 | 0.38875 (19) | 0.3608 (3) | 0.20433 (19) | 0.0245 (5) | |
H3A | 0.4309 | 0.2688 | 0.2544 | 0.029* | |
H3B | 0.3065 | 0.3370 | 0.1766 | 0.029* | |
C4 | 0.4155 (2) | 0.5213 (3) | 0.2714 (2) | 0.0266 (5) | |
C5 | 0.54229 (19) | 0.5677 (3) | 0.32878 (18) | 0.0221 (5) | |
H5A | 0.5520 | 0.6646 | 0.3776 | 0.027* | |
H5B | 0.5854 | 0.4740 | 0.3762 | 0.027* | |
C6 | 0.71369 (17) | 0.6473 (3) | 0.30783 (17) | 0.0185 (4) | |
H6A | 0.7536 | 0.5653 | 0.3673 | 0.022* | |
H6B | 0.7250 | 0.7590 | 0.3418 | 0.022* | |
C7 | 0.76104 (17) | 0.6420 (3) | 0.22209 (16) | 0.0158 (4) | |
C8 | 0.3708 (2) | 0.5061 (4) | 0.3597 (2) | 0.0414 (7) | |
H8A | 0.4087 | 0.4132 | 0.4093 | 0.062* | |
H8B | 0.2885 | 0.4863 | 0.3235 | 0.062* | |
H8C | 0.3865 | 0.6091 | 0.4028 | 0.062* | |
O1S | 0.8891 (2) | 0.6816 (3) | 0.04747 (19) | 0.0572 (6) | |
C1S | 0.9499 (6) | 0.5456 (8) | 0.0491 (7) | 0.057 (2) | 0.45 |
H1S | 0.867 (4) | 0.657 (5) | 0.105 (3) | 0.098 (14)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cu1 | 0.01401 (14) | 0.01581 (16) | 0.01615 (15) | −0.00174 (9) | 0.00529 (10) | −0.00397 (10) |
O1 | 0.0184 (7) | 0.0165 (8) | 0.0167 (7) | −0.0011 (6) | 0.0052 (6) | −0.0022 (6) |
O2 | 0.0248 (8) | 0.0147 (7) | 0.0182 (7) | 0.0001 (6) | 0.0038 (6) | −0.0036 (6) |
O3 | 0.0173 (7) | 0.0160 (8) | 0.0177 (7) | −0.0013 (5) | 0.0074 (6) | −0.0026 (6) |
O4 | 0.0177 (7) | 0.0207 (8) | 0.0215 (7) | −0.0047 (6) | 0.0083 (6) | −0.0027 (6) |
O5 | 0.0446 (13) | 0.0572 (15) | 0.0644 (15) | 0.0176 (11) | −0.0013 (11) | −0.0135 (12) |
O6 | 0.0419 (12) | 0.0342 (12) | 0.0938 (17) | 0.0070 (9) | 0.0189 (12) | −0.0060 (12) |
N1 | 0.0179 (9) | 0.0172 (9) | 0.0179 (9) | −0.0001 (7) | 0.0057 (7) | −0.0032 (7) |
N2 | 0.0153 (8) | 0.0168 (9) | 0.0182 (9) | −0.0003 (7) | 0.0064 (7) | −0.0011 (7) |
N3 | 0.0236 (11) | 0.0364 (14) | 0.0494 (14) | 0.0046 (9) | 0.0164 (10) | −0.0110 (11) |
C1 | 0.0173 (9) | 0.0115 (10) | 0.0171 (10) | 0.0062 (7) | 0.0024 (8) | 0.0021 (8) |
C2 | 0.0207 (10) | 0.0170 (11) | 0.0217 (10) | −0.0030 (8) | 0.0070 (9) | −0.0034 (9) |
C3 | 0.0212 (11) | 0.0283 (13) | 0.0263 (12) | −0.0066 (9) | 0.0125 (9) | −0.0056 (10) |
C4 | 0.0231 (11) | 0.0288 (13) | 0.0319 (13) | −0.0030 (9) | 0.0158 (10) | −0.0075 (10) |
C5 | 0.0226 (11) | 0.0248 (12) | 0.0216 (11) | −0.0040 (9) | 0.0121 (9) | −0.0066 (9) |
C6 | 0.0170 (10) | 0.0193 (12) | 0.0163 (10) | −0.0033 (8) | 0.0047 (8) | −0.0033 (8) |
C7 | 0.0157 (10) | 0.0136 (10) | 0.0158 (10) | 0.0038 (8) | 0.0047 (8) | 0.0017 (8) |
C8 | 0.0372 (15) | 0.0543 (17) | 0.0455 (16) | −0.0201 (13) | 0.0299 (13) | −0.0218 (14) |
O1S | 0.0716 (16) | 0.0622 (15) | 0.0548 (13) | 0.0033 (12) | 0.0432 (13) | 0.0057 (12) |
C1S | 0.043 (4) | 0.039 (4) | 0.078 (5) | 0.009 (3) | 0.018 (4) | −0.018 (4) |
Cu1—O1 | 1.9453 (14) | N3—C4 | 1.529 (3) |
Cu1—O1i | 2.7247 (15) | C1—C2 | 1.526 (3) |
Cu1—O3 | 1.9644 (14) | C2—H2A | 0.9900 |
Cu1—N2 | 1.9934 (18) | C2—H2B | 0.9900 |
Cu1—N1 | 1.9988 (18) | C3—C4 | 1.526 (3) |
Cu1—O4ii | 2.3410 (15) | C3—H3A | 0.9900 |
O1—C1 | 1.294 (2) | C3—H3B | 0.9900 |
O2—C1 | 1.229 (2) | C4—C8 | 1.534 (3) |
O3—C7 | 1.282 (2) | C4—C5 | 1.536 (3) |
O4—C7 | 1.242 (2) | C5—H5A | 0.9900 |
O4—Cu1iii | 2.3410 (15) | C5—H5B | 0.9900 |
O5—N3 | 1.219 (3) | C6—C7 | 1.521 (3) |
O6—N3 | 1.225 (3) | C6—H6A | 0.9900 |
N1—C3 | 1.474 (3) | C6—H6B | 0.9900 |
N1—C2 | 1.487 (3) | C8—H8A | 0.9800 |
N1—H101 | 0.9300 | C8—H8B | 0.9800 |
N2—C5 | 1.467 (3) | C8—H8C | 0.9800 |
N2—C6 | 1.483 (3) | O1S—C1S | 1.347 (7) |
N2—H102 | 0.9300 | O1S—H1S | 0.95 (5) |
O1—Cu1—O3 | 94.11 (6) | H2A—C2—H2B | 108.4 |
O1—Cu1—N2 | 169.44 (7) | N1—C3—C4 | 114.78 (18) |
O1—Cu1—N1 | 83.80 (7) | N1—C3—H3A | 108.6 |
O1—Cu1—O4ii | 97.44 (6) | C4—C3—H3A | 108.6 |
O3—Cu1—N1 | 169.60 (7) | N1—C3—H3B | 108.6 |
O3—Cu1—N2 | 83.69 (6) | C4—C3—H3B | 108.6 |
O3—Cu1—O4ii | 99.85 (6) | H3A—C3—H3B | 107.5 |
N1—Cu1—O4ii | 90.53 (6) | C3—C4—N3 | 109.92 (19) |
N2—Cu1—N1 | 96.50 (7) | C3—C4—C8 | 108.6 (2) |
N2—Cu1—O4ii | 93.11 (7) | N3—C4—C8 | 105.7 (2) |
C1—O1—Cu1 | 114.29 (13) | C3—C4—C5 | 114.99 (19) |
C7—O3—Cu1 | 114.13 (13) | N3—C4—C5 | 108.54 (19) |
C7—O4—Cu1iii | 126.62 (13) | C8—C4—C5 | 108.71 (19) |
C3—N1—C2 | 112.73 (17) | N2—C5—C4 | 113.46 (18) |
C3—N1—Cu1 | 118.05 (13) | N2—C5—H5A | 108.9 |
C2—N1—Cu1 | 104.51 (13) | C4—C5—H5A | 108.9 |
C3—N1—H101 | 107.0 | N2—C5—H5B | 108.9 |
C2—N1—H101 | 107.0 | C4—C5—H5B | 108.9 |
Cu1—N1—H101 | 107.0 | H5A—C5—H5B | 107.7 |
C5—N2—C6 | 112.67 (16) | N2—C6—C7 | 108.10 (16) |
C5—N2—Cu1 | 117.40 (13) | N2—C6—H6A | 110.1 |
C6—N2—Cu1 | 106.19 (12) | C7—C6—H6A | 110.1 |
C5—N2—H102 | 106.7 | N2—C6—H6B | 110.1 |
C6—N2—H102 | 106.7 | C7—C6—H6B | 110.1 |
Cu1—N2—H102 | 106.7 | H6A—C6—H6B | 108.4 |
O5—N3—O6 | 123.2 (2) | O4—C7—O3 | 123.19 (19) |
O5—N3—C4 | 118.4 (2) | O4—C7—C6 | 120.51 (18) |
O6—N3—C4 | 118.4 (2) | O3—C7—C6 | 116.30 (17) |
O2—C1—O1 | 124.0 (2) | C4—C8—H8A | 109.5 |
O2—C1—C2 | 120.71 (19) | C4—C8—H8B | 109.5 |
O1—C1—C2 | 115.28 (17) | H8A—C8—H8B | 109.5 |
N1—C2—C1 | 108.49 (17) | C4—C8—H8C | 109.5 |
N1—C2—H2A | 110.0 | H8A—C8—H8C | 109.5 |
C1—C2—H2A | 110.0 | H8B—C8—H8C | 109.5 |
N1—C2—H2B | 110.0 | C1S—O1S—H1S | 102 (3) |
C1—C2—H2B | 110.0 | ||
O3—Cu1—O1—C1 | 172.87 (13) | Cu1—N1—C2—C1 | −37.89 (18) |
N2—Cu1—O1—C1 | −109.6 (3) | O2—C1—C2—N1 | −150.80 (18) |
N1—Cu1—O1—C1 | −17.36 (13) | O1—C1—C2—N1 | 27.6 (2) |
O4ii—Cu1—O1—C1 | 72.36 (13) | C2—N1—C3—C4 | 171.79 (18) |
O1—Cu1—O3—C7 | −177.83 (13) | Cu1—N1—C3—C4 | 49.7 (2) |
N2—Cu1—O3—C7 | 12.54 (14) | N1—C3—C4—N3 | 59.5 (2) |
N1—Cu1—O3—C7 | 104.2 (4) | N1—C3—C4—C8 | 174.6 (2) |
O4ii—Cu1—O3—C7 | −79.54 (14) | N1—C3—C4—C5 | −63.4 (3) |
O1—Cu1—N1—C3 | 156.77 (16) | O5—N3—C4—C3 | 23.1 (3) |
O3—Cu1—N1—C3 | −124.3 (3) | O6—N3—C4—C3 | −158.6 (2) |
N2—Cu1—N1—C3 | −33.85 (16) | O5—N3—C4—C8 | −93.9 (3) |
O4ii—Cu1—N1—C3 | 59.35 (16) | O6—N3—C4—C8 | 84.5 (3) |
O1—Cu1—N1—C2 | 30.60 (12) | O5—N3—C4—C5 | 149.7 (2) |
O3—Cu1—N1—C2 | 109.5 (4) | O6—N3—C4—C5 | −32.0 (3) |
N2—Cu1—N1—C2 | −160.02 (13) | C6—N2—C5—C4 | −178.27 (18) |
O4ii—Cu1—N1—C2 | −66.82 (12) | Cu1—N2—C5—C4 | −54.4 (2) |
O1—Cu1—N2—C5 | 127.4 (3) | C3—C4—C5—N2 | 65.9 (3) |
O3—Cu1—N2—C5 | −154.09 (16) | N3—C4—C5—N2 | −57.7 (2) |
N1—Cu1—N2—C5 | 36.38 (16) | C8—C4—C5—N2 | −172.2 (2) |
O4ii—Cu1—N2—C5 | −54.51 (15) | C5—N2—C6—C7 | 165.38 (17) |
O1—Cu1—N2—C6 | −105.5 (3) | Cu1—N2—C6—C7 | 35.54 (18) |
O3—Cu1—N2—C6 | −27.03 (13) | Cu1iii—O4—C7—O3 | 170.26 (13) |
N1—Cu1—N2—C6 | 163.44 (13) | Cu1iii—O4—C7—C6 | −10.3 (3) |
O4ii—Cu1—N2—C6 | 72.55 (13) | Cu1—O3—C7—O4 | −174.49 (15) |
Cu1—O1—C1—O2 | 176.88 (15) | Cu1—O3—C7—C6 | 6.0 (2) |
Cu1—O1—C1—C2 | −1.5 (2) | N2—C6—C7—O4 | 151.78 (19) |
C3—N1—C2—C1 | −167.32 (16) | N2—C6—C7—O3 | −28.7 (2) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, y−1/2, −z+1/2; (iii) −x+3/2, y+1/2, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1S—H1S···O4 | 0.95 | 1.96 | 2.823 (3) | 163 |
N1—H101···O5 | 0.93 | 2.42 | 2.984 (3) | 119 |
N1—H101···O3i | 0.93 | 2.37 | 3.101 (3) | 135 |
N2—H102···O6 | 0.93 | 2.43 | 3.017 (3) | 121 |
N2—H102···O2i | 0.93 | 2.15 | 2.912 (3) | 138 |
Symmetry code: (i) −x+1, −y+1, −z. |
Experimental details
Crystal data | |
Chemical formula | [Cu(C8H13N3O6)]·0.45CH4O·0.55H2O |
Mr | 335.08 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 200 |
a, b, c (Å) | 13.0407 (16), 8.0578 (15), 13.383 (2) |
β (°) | 115.726 (16) |
V (Å3) | 1266.9 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 1.76 |
Crystal size (mm) | 0.55 × 0.45 × 0.38 |
Data collection | |
Diffractometer | Oxford Xcalibur2 diffractometer |
Absorption correction | Multi-scan [CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm] |
Tmin, Tmax | 0.387, 0.511 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13298, 2974, 2401 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.675 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.085, 1.15 |
No. of reflections | 2974 |
No. of parameters | 186 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.44, −0.37 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and WinGX (Farrugia, 1999), WinGX (Farrugia, 1999).
Cu1—O1 | 1.9453 (14) | Cu1—N2 | 1.9934 (18) |
Cu1—O1i | 2.7247 (15) | Cu1—N1 | 1.9988 (18) |
Cu1—O3 | 1.9644 (14) | Cu1—O4ii | 2.3410 (15) |
O1—Cu1—O3 | 94.11 (6) | O3—Cu1—N2 | 83.69 (6) |
O1—Cu1—N2 | 169.44 (7) | O3—Cu1—O4ii | 99.85 (6) |
O1—Cu1—N1 | 83.80 (7) | N1—Cu1—O4ii | 90.53 (6) |
O1—Cu1—O4ii | 97.44 (6) | N2—Cu1—N1 | 96.50 (7) |
O3—Cu1—N1 | 169.60 (7) | N2—Cu1—O4ii | 93.11 (7) |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, y−1/2, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1S—H1S···O4 | 0.95 | 1.96 | 2.823 (3) | 163 |
N1—H101···O5 | 0.93 | 2.42 | 2.984 (3) | 119 |
N1—H101···O3i | 0.93 | 2.37 | 3.101 (3) | 135 |
N2—H102···O6 | 0.93 | 2.43 | 3.017 (3) | 121 |
N2—H102···O2i | 0.93 | 2.15 | 2.912 (3) | 138 |
Symmetry code: (i) −x+1, −y+1, −z. |
The reaction of CuII ions in methanol with two molar equivalents of an amino acid such as glycine (HL) in the presence of a base affords the nominally square-planar chelate CuL2. The geometric isomer with cis amino groups is pre-organized for N,N-chelate ring formation (i.e. ring closure) in the presence of excess formaldehyde, one molar equivalent of a diprotic carbon nucleophile such as nitroethane, and excess base. This elegant template reaction, which links the cis metal-bound NH2 groups with a three-carbon bridge, was developed by Comba and co-workers 23 years ago (Comba et al., 1986) and then extended sometime later to include compound (I) and its derivatives (Comba et al., 1991). More recent synthetic efforts by others with the same type of system have employed diethylmalonate as the carbon diacid for ring closure (Supriya et al., 2007). The reduced ligand (in which the nitro group is converted into an amino group) has also been condensed with aldehydes to form Schiff base analogues of (I) with pendant non-coordinating base groups (Villanueva et al., 1998).
The structure of (I) crystallized from water has an unsolvated crystal structure (orthorhombic, P212121) and has been reported previously (Comba et al., 1991). In (I), the CuII ion is weakly bound to the carboxylate O atom of an adjacent molecule to form an infinite one-dimensional coordination polymer in which the five-coordinate mononuclear repeat units are linked by long axial Cu—O bonds (2.60 Å). Although nominally five-coordinate, the coordination geometry at the CuII ion is closer to being square-planar than square-pyramidal, due to the in-plane location of the metal ion relative to the ligand donor atoms (Comba et al., 1991). In the present study, we report the structure of compound (II), the monoclinic water/methanol solvate of (I). In (II), the copper chelate forms a novel MOF extended structure based upon a half-solvated two-dimensional rhombus net of Ci-symmetry dimeric repeats. The markedly different extended structure of the material described here leads to significant structural differences for the metal centre that clearly reflect supramolecular control of the molecular geometry of the copper chelate.
The molecular structure of (II), i.e. the symmetry-unique monomer unit of the Ci-symmetry coordination dimer, is shown in Fig. 1. The CuII ion exhibits the expected four-coordinate geometry within the tetradentate chelate. The equatorial Cu—O and Cu—N distances average 1.955 (14) and 1.996 (4) Å, respectively. The mean Cu—O distance is within the normal range expected for terminal carboxylates bound to CuII [1.96 (2) Å; Orpen et al., 1989]. It is, however, noteworthy that the Cu1—O1 distance is significantly shorter than the Cu1—O3 distance (Table 1), presumably because atom O1 is involved in bridging the two CuII ions of the dimeric structure (see below). Although the average equatorial Cu—O distance is normal, the mean Cu—N distance is compressed by the chelate ring and is thus shorter than that of a standard secondary amine bound to CuII [2.03 (3) Å; Orpen et al., 1989]. The four ligand donor atoms lie exactly on the best-fit (least-squares) mean plane, with the CuII ion displaced by 0.179 (1) Å out of this plane in the direction opposite to that of the two N—H group bond vectors. Consequently, and in contrast with the orthorhombic structure of (I) reported earlier (Comba et al., 1991), the coordination geometry of the CuII ion in (II) is closest to being square-pyramidal if one considers all dative covalent bonds < 2.5 Å in length to the CuII ion (see below).
That said, consideration of all metal–ligand interactions (first coordination sphere) less than the sum of the van der Waals radii of the pairwise interacting atoms (O···Cu 2.92 Å, O···N 2.95 Å; Bondi, 1964) suggests that the coordination geometry of each CuII centre is best described as a distorted octahedron with a significant axial displacement of the metal ion away from the Cu2O2 dimer core towards the closest axially coordinated (bridging) carboxylate O atom. The axial Cu—O distances of (II) are therefore markedly different, with the intra-dimer distance [Cu1—O1i = 2.7247 (15) Å] significantly longer than the inter-dimer distance [Cu—O4iv = 2.3410 (15)Å], and both are considerably longer than the equatorial Cu—O bonds [symmetry codes: (i) 1 - x, 1 - y, -z; (iv) 3/2 - x, -1/2 + y, 1/2 - z]. Interestingly, the equatorial Cu—O and Cu—N distances of the present monoclinic structure, (II), are some 0.03 and 0.01 Å longer, respectively, than those of the orthorhombic crystalline form, (I) (Comba et al., 1991). This clearly reflects the bond elongation required to support the out-of-plane displacement of the CuII ion in (II) and, ultimately, the markedly different extended structures of the two materials.
One intriguing hallmark of the molecular conformation of (I) [(II)?] is the approximate chair conformation of the six-membered chelate ring, in which the nitro group and amino group H atoms are positioned on the same side of the ring. (The ring-closing reaction could produce the alternative configurational isomer at C4 with the C8 methyl group axial, but does not.) Several noteworthy intramolecular hydrogen bonds appear to result from this particular chelate ring conformation (Table 2). More specifically, the nitro group O atoms (O5 and O6) are neatly hydrogen-bonded and thus `tethered' to the closest amino group H atoms (H101 and H102). This may have some impact on transition-state geometries during the ring-closing reaction and certainly has some directional influence on thermal libration of the nitro group, as evidenced by the similar principal axes of displacement for the two O atoms. (The O-atom displacements are predominantly towards the amino group H atoms, as opposed to a more isotropic electron-density distribution which might be expected if rotational motion about the C4—N3 axis were favoured to a greater extent.) Perhaps more significant from the standpoint of conformational stability is the fact that the amino group H atoms of one chelate ring within the Ci-symmetry dimer are hydrogen-bonded to the closest carboxylate group O atoms of the second chelate. These hydrogen bonds clearly complement the structural stability associated with the Cu2O2 core of the dimer. On the whole, the six-membered chelate ring is somewhat flattened in the region of the CuII ion, such that the chelate-ring geometry tends towards being partly half-chair-like in conformation. This ring-flattening effect is highlighted by the fact that the CuII ion and the opposite C atom, C4, are displaced from the six-atom chelate ring mean plane (defined by atoms Cu1/N1/C3–C5/N2) by 0.127 (2) and 0.264 (2) Å, respectively.
The unit-cell packing shown in Fig. 3(a) clearly reveals the infinite two-dimensional network structure (or MOF architecture) of compound (II). As evidenced by the distinct arrangement of the Ci-symmetry Cu2O2 dimer units in the structure, chains of interconnected dimers run parallel to, and include, the [110] plane. Furthermore, these chains are linked obliquely to adjacent chains via bridging Cu—O bonds, giving rise to a second series of parallel chains of interconnected dimers running parallel to, and including, the [110] plane. In effect, the two-dimensional coordination framework creates a `diamondoid' or rhombus-like two-dimensional net. This net lies in the [202] plane and, together with its translational repeats, generates parallel stacks of rather unusual metal–organic sheets in the crystal structure. The distance between parallel metal–organic sheets, e.g. that between the [202] and [202] planes, is 11.18 (1) Å.
The interesting layered crystal structure of (I) [(II)?], with a reasonably large nanometre-scale interlayer separation, creates solvent-accessible voids of 166 Å3 in the crystal structure. Upon closer inspection (PLATON; Spek, 2009), these voids comprise two 83 Å3 voids centred at (1/2, 0.0, 1/2) and (0.0, 1/2, 1.0). The cavities are just large enough to accommodate methanol molecules (molecular volume ~71 Å3) or water molecules (molecular volume ~ 30 Å3), and compound (I) was, not surprisingly, isolated as the mixed water/methanol solvate, (II), with a fractional composition ratio (from electron-density maxima) of 0.55/0.45 (Fig. 3b). The methanol and water O atoms are located at the same coordinates in the structure and the hydroxyl groups of both solvents are clearly hydrogen-bonded to the bridging carboxylate group atoms O4 (Table 2). Although the unit-occupancy solvent atom H1S was cleanly located in a difference Fourier map, the remaining water H atom and the H atoms belonging to the methyl group of the methanol solvate molecule were not located and were omitted from the structural model during refinement. A full unit-occupancy methanol molecule can not be accommodated, as the methanol methyl C atom is too close [2.343 (3) Å] to the inversion-related methyl C atom at (2 - x, 1 - y, -z).
Finally, other somewhat more simple CuII coordination compounds based on 4,4'-bipyridine linking ligands have been described with two-dimensional MOF sheet-like structures that form clathrates with small molecules such as CO2 (Kondo et al., 2006). This particular material exhibited reversible sorption/desorption of the guest molecules with varying CO2 partial pressure. Given the increasing likelihood that MOFs may become the materials of choice for gas-storage applications (Czaja et al., 2009), we attempted to desolvate the crystal of (II), i.e. (I).0.55H2O.0.45CH3OH, used for X-ray data collection. This crystal was neatly glued to the glass microfibre through only a very small area of the largest crystal face, thereby exposing >90% of the crystal surface to the atmosphere. Furthermore, the crystal faces were clean and uncovered by inert mounting oil. The glass-mounted crystal was warmed and maintained at 358 K in a thermal convection oven for 3 d. However, complete desolvation was not observed under the conditions tested (as judged from a post-warming X-ray data set), possibly due to the tight solvent-binding cavities, and to hydrogen-bonding between the solvent guests and the rigid host MOF.