Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270199016145/qb0158sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270199016145/qb0158Isup2.hkl |
CCDC reference: 140852
The ligand N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxo-pyrimidin-2-yl)glycine was prepared according to the method previously reported (Low et al., 1997). Complex (I) was obtained from aqueous solution at pH ca 6.2, MgCl2 (3 mmol) was dissolved in KCl 0.5 M (25 ml) and added to a solution of the potassium salt of the ligand (1 mmol) in the minimum amount of water (20 ml). A violet crystalline precipitate appeared and was filtered off and washed with water, ethanol and diethyl ether and stored under an anhydrous environment. Analysis, calculated for C14H32MgN10O16: C 27.08, H 5.01, N 22.08%; found C 26.66, H 5.15, N 21.99%.
Molecule (I) crystallized in the triclinic system; space group P1 assumed and confirmed by the analysis. H atoms were treated as riding atoms with C—H 0.98 to 0.99 Å, N—H 0.88 Å, The water of crystallization O—H distance was set by DFIX to 0.82 Å after location of the H atoms on a difference Fourier map.
Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997b); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
[Mg(H2O)6](C7H8N5O4)2·2H2O | Z = 1 |
Mr = 620.81 | F(000) = 326 |
Triclinic, P1 | Dx = 1.593 Mg m−3 |
a = 7.3152 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 7.5917 (4) Å | Cell parameters from 2947 reflections |
c = 12.3024 (6) Å | θ = 1.7–27.5° |
α = 86.661 (3)° | µ = 0.16 mm−1 |
β = 73.172 (3)° | T = 150 K |
γ = 81.79 (3)° | Block, pink |
V = 647.15 (5) Å3 | 0.25 × 0.25 × 0.25 mm |
Kappa-CCD diffractometer | 2947 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 2428 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.034 |
ϕ scans and ω scans with κ offsets | θmax = 27.5°, θmin = 1.7° |
Absorption correction: multi-scan SORTAV (Blessing, 1995, 1997) | h = −9→8 |
Tmin = 0.960, Tmax = 0.960 | k = −9→7 |
8396 measured reflections | l = −15→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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0622P)2 + 0.0773P] where P = (Fo2 + 2Fc2)/3 |
2947 reflections | (Δ/σ)max = 0.001 |
212 parameters | Δρmax = 0.35 e Å−3 |
8 restraints | Δρmin = −0.28 e Å−3 |
[Mg(H2O)6](C7H8N5O4)2·2H2O | γ = 81.79 (3)° |
Mr = 620.81 | V = 647.15 (5) Å3 |
Triclinic, P1 | Z = 1 |
a = 7.3152 (3) Å | Mo Kα radiation |
b = 7.5917 (4) Å | µ = 0.16 mm−1 |
c = 12.3024 (6) Å | T = 150 K |
α = 86.661 (3)° | 0.25 × 0.25 × 0.25 mm |
β = 73.172 (3)° |
Kappa-CCD diffractometer | 2947 independent reflections |
Absorption correction: multi-scan SORTAV (Blessing, 1995, 1997) | 2428 reflections with I > 2σ(I) |
Tmin = 0.960, Tmax = 0.960 | Rint = 0.034 |
8396 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 8 restraints |
wR(F2) = 0.110 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.35 e Å−3 |
2947 reflections | Δρmin = −0.28 e Å−3 |
212 parameters |
Experimental. Kappa CCD diffractometer using the following programs. Collect: Data collection software (Hooft, 1998) [Hooft, R. (1998). Nonius B·V., Delft, The Netherlands], is a graphical user interface written by Enraf–Nonius which encompasses the following programs. DENZO (Otwinowski & Minor, 1997) and indexing and data collection software package and a scaling package, SCALEPACK both of which programs are produced by the company HKL. Absorption corrections are performed by the SORTAV package, (Blessing, 1995, 1997) within the maXus suite of programs, (Mackay et al., 1998) [Mackay, S., Gilmore, C·J., Edwards, C., Tremayne, M., Stewart, N. & Shankland, K. (1998). maXus. University of Glasgow, Scotland, UK, Nonius BV, Delft, The Netherlands and MacScience Co. Ltd, Yokohama, Japan]. High redundancy data were used in the scaling program hence the 'multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file. Low temperature data were collected using an Oxford Cryosystems cryostream (Cosier & Glazer, 1986) [Cosier, J. and Glazer, A·M., J. Appl. Cryst., (1986), 19, 105–107]. |
x | y | z | Uiso*/Ueq | ||
Mg1 | 0.5000 | 0.5000 | 0.0000 | 0.01627 (17) | |
N1 | 0.78085 (16) | 0.11420 (16) | −0.62695 (10) | 0.0188 (3) | |
C2 | 0.67248 (19) | 0.08331 (18) | −0.69121 (11) | 0.0168 (3) | |
N2 | 0.75512 (16) | −0.00192 (16) | −0.78824 (10) | 0.0191 (3) | |
C21 | 0.96153 (19) | −0.05176 (19) | −0.83161 (12) | 0.0198 (3) | |
C22 | 1.06469 (19) | 0.09140 (18) | −0.90801 (11) | 0.0180 (3) | |
O21 | 1.23336 (13) | 0.03862 (13) | −0.96815 (8) | 0.0217 (2) | |
O22 | 0.98289 (14) | 0.24691 (13) | −0.90725 (9) | 0.0236 (2) | |
N3 | 0.47488 (16) | 0.13152 (15) | −0.66389 (9) | 0.0173 (3) | |
C3 | 0.3669 (2) | 0.0914 (2) | −0.74119 (12) | 0.0223 (3) | |
C4 | 0.37696 (19) | 0.22715 (18) | −0.56642 (11) | 0.0174 (3) | |
O4 | 0.20384 (13) | 0.27875 (14) | −0.54719 (8) | 0.0235 (2) | |
C5 | 0.49109 (18) | 0.25797 (18) | −0.49232 (11) | 0.0170 (3) | |
N5 | 0.39075 (17) | 0.34517 (16) | −0.39674 (9) | 0.0207 (3) | |
O5 | 0.48429 (15) | 0.37789 (15) | −0.32857 (8) | 0.0264 (3) | |
C6 | 0.69615 (19) | 0.19867 (18) | −0.52866 (11) | 0.0173 (3) | |
N6 | 0.80611 (17) | 0.22707 (18) | −0.46561 (10) | 0.0233 (3) | |
O1W | 0.48312 (14) | 0.75553 (13) | 0.04960 (9) | 0.0209 (2) | |
O2W | 0.38321 (14) | 0.58082 (14) | −0.13439 (8) | 0.0207 (2) | |
O3W | 0.22033 (14) | 0.49424 (14) | 0.09946 (8) | 0.0216 (2) | |
O4W | 0.04467 (15) | 0.55360 (15) | 0.32194 (9) | 0.0277 (3) | |
H2 | 0.6810 | −0.0293 | −0.8280 | 0.023* | |
H21A | 0.9865 | −0.1626 | −0.8752 | 0.024* | |
H21B | 1.0163 | −0.0772 | −0.7667 | 0.024* | |
H3A | 0.4057 | 0.1605 | −0.8120 | 0.033* | |
H3B | 0.2286 | 0.1228 | −0.7053 | 0.033* | |
H3C | 0.3944 | −0.0359 | −0.7579 | 0.033* | |
H6A | 0.9308 | 0.1911 | −0.4884 | 0.028* | |
H6B | 0.7551 | 0.2821 | −0.4006 | 0.028* | |
H1W1 | 0.3901 (17) | 0.8291 (18) | 0.0481 (14) | 0.025* | |
H2W1 | 0.5794 (16) | 0.807 (2) | 0.0271 (14) | 0.025* | |
H1W2 | 0.2740 (12) | 0.636 (2) | −0.1242 (14) | 0.025* | |
H2W2 | 0.403 (2) | 0.5187 (19) | −0.1901 (10) | 0.025* | |
H1W3 | 0.176 (2) | 0.518 (2) | 0.1669 (6) | 0.026* | |
H2W3 | 0.152 (2) | 0.4240 (18) | 0.0882 (15) | 0.026* | |
H1W4 | 0.079 (3) | 0.4754 (19) | 0.3635 (13) | 0.033* | |
H2W4 | −0.0682 (11) | 0.594 (2) | 0.3509 (15) | 0.033* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Mg1 | 0.0169 (3) | 0.0143 (3) | 0.0163 (3) | −0.0011 (2) | −0.0030 (2) | −0.0006 (2) |
N1 | 0.0168 (5) | 0.0218 (6) | 0.0175 (6) | −0.0029 (5) | −0.0044 (5) | −0.0010 (5) |
C2 | 0.0183 (7) | 0.0149 (6) | 0.0172 (6) | −0.0046 (5) | −0.0048 (5) | 0.0027 (5) |
N2 | 0.0178 (6) | 0.0231 (6) | 0.0168 (6) | −0.0031 (5) | −0.0047 (5) | −0.0032 (5) |
C21 | 0.0189 (7) | 0.0182 (7) | 0.0204 (7) | 0.0004 (5) | −0.0033 (5) | −0.0025 (5) |
C22 | 0.0179 (6) | 0.0186 (7) | 0.0193 (6) | −0.0007 (6) | −0.0080 (5) | −0.0051 (5) |
O21 | 0.0166 (5) | 0.0210 (5) | 0.0262 (5) | −0.0023 (4) | −0.0038 (4) | −0.0020 (4) |
O22 | 0.0191 (5) | 0.0176 (5) | 0.0328 (6) | 0.0005 (4) | −0.0063 (4) | −0.0024 (4) |
N3 | 0.0163 (6) | 0.0203 (6) | 0.0161 (6) | −0.0042 (5) | −0.0050 (5) | −0.0003 (5) |
C3 | 0.0212 (7) | 0.0287 (8) | 0.0201 (7) | −0.0055 (6) | −0.0092 (6) | −0.0016 (6) |
C4 | 0.0165 (6) | 0.0172 (7) | 0.0170 (6) | −0.0040 (5) | −0.0022 (5) | 0.0029 (5) |
O4 | 0.0148 (5) | 0.0310 (6) | 0.0233 (5) | −0.0006 (4) | −0.0042 (4) | −0.0022 (4) |
C5 | 0.0165 (6) | 0.0166 (7) | 0.0168 (6) | −0.0037 (5) | −0.0024 (5) | 0.0006 (5) |
N5 | 0.0219 (6) | 0.0221 (6) | 0.0176 (6) | −0.0033 (5) | −0.0048 (5) | −0.0009 (5) |
O5 | 0.0265 (5) | 0.0340 (6) | 0.0199 (5) | −0.0031 (5) | −0.0073 (4) | −0.0077 (4) |
C6 | 0.0173 (6) | 0.0178 (7) | 0.0167 (6) | −0.0047 (5) | −0.0041 (5) | 0.0021 (5) |
N6 | 0.0163 (6) | 0.0331 (7) | 0.0207 (6) | −0.0037 (5) | −0.0043 (5) | −0.0052 (5) |
O1W | 0.0178 (5) | 0.0161 (5) | 0.0271 (5) | −0.0009 (4) | −0.0040 (4) | −0.0016 (4) |
O2W | 0.0202 (5) | 0.0221 (5) | 0.0183 (5) | 0.0034 (4) | −0.0057 (4) | −0.0031 (4) |
O3W | 0.0196 (5) | 0.0251 (6) | 0.0185 (5) | −0.0060 (4) | −0.0005 (4) | −0.0046 (4) |
O4W | 0.0245 (5) | 0.0334 (6) | 0.0205 (5) | 0.0015 (5) | −0.0015 (4) | −0.0017 (4) |
Mg1—O1W | 2.0437 (10) | C21—C22 | 1.529 (2) |
Mg1—O1Wi | 2.0437 (10) | C22—O22 | 1.2442 (17) |
Mg1—O3W | 2.0626 (10) | C22—O21 | 1.2630 (16) |
Mg1—O3Wi | 2.0626 (10) | N3—C4 | 1.3905 (18) |
Mg1—O2Wi | 2.0952 (10) | N3—C3 | 1.4694 (18) |
Mg1—O2W | 2.0952 (10) | C4—O4 | 1.2283 (16) |
N1—C2 | 1.3213 (18) | C4—C5 | 1.4506 (19) |
N1—C6 | 1.3418 (18) | C5—N5 | 1.3461 (18) |
C2—N2 | 1.3302 (18) | C5—C6 | 1.4474 (18) |
C2—N3 | 1.3850 (17) | N5—O5 | 1.2799 (16) |
N2—C21 | 1.4497 (17) | C6—N6 | 1.3135 (18) |
O1W—Mg1—O1Wi | 180.0 | C2—N2—C21 | 123.12 (12) |
O1W—Mg1—O3W | 88.91 (5) | N2—C21—C22 | 113.46 (11) |
O1Wi—Mg1—O3W | 91.09 (5) | O22—C22—O21 | 124.75 (14) |
O1W—Mg1—O3Wi | 91.09 (5) | O22—C22—C21 | 120.23 (12) |
O1Wi—Mg1—O3Wi | 88.91 (5) | O21—C22—C21 | 115.02 (12) |
O3W—Mg1—O3Wi | 180.0 | C2—N3—C4 | 120.76 (12) |
O1W—Mg1—O2Wi | 87.09 (4) | C2—N3—C3 | 120.32 (11) |
O1Wi—Mg1—O2Wi | 92.91 (4) | C4—N3—C3 | 118.82 (11) |
O3W—Mg1—O2Wi | 93.30 (4) | O4—C4—N3 | 119.95 (13) |
O3Wi—Mg1—O2Wi | 86.70 (4) | O4—C4—C5 | 124.08 (12) |
O1W—Mg1—O2W | 92.91 (4) | N3—C4—C5 | 115.97 (11) |
O1Wi—Mg1—O2W | 87.09 (4) | N5—C5—C6 | 127.21 (13) |
O3W—Mg1—O2W | 86.70 (4) | N5—C5—C4 | 114.51 (11) |
O3Wi—Mg1—O2W | 93.30 (4) | C6—C5—C4 | 118.25 (12) |
O2Wi—Mg1—O2W | 180.0 | O5—N5—C5 | 117.33 (11) |
C2—N1—C6 | 118.60 (12) | N6—C6—N1 | 117.69 (12) |
N1—C2—N2 | 118.96 (12) | N6—C6—C5 | 120.47 (12) |
N1—C2—N3 | 124.39 (12) | N1—C6—C5 | 121.84 (12) |
N2—C2—N3 | 116.65 (12) | ||
C6—N1—C2—N2 | −179.34 (12) | C3—N3—C4—C5 | 178.38 (12) |
C6—N1—C2—N3 | −0.4 (2) | O4—C4—C5—N5 | 1.8 (2) |
N1—C2—N2—C21 | −4.7 (2) | N3—C4—C5—N5 | −177.69 (12) |
N3—C2—N2—C21 | 176.30 (12) | O4—C4—C5—C6 | −176.46 (13) |
C2—N2—C21—C22 | −89.68 (16) | N3—C4—C5—C6 | 4.07 (18) |
N2—C21—C22—O22 | 16.58 (18) | C6—C5—N5—O5 | −1.2 (2) |
N2—C21—C22—O21 | −163.98 (11) | C4—C5—N5—O5 | −179.27 (11) |
N1—C2—N3—C4 | 3.5 (2) | C2—N1—C6—N6 | 179.55 (12) |
N2—C2—N3—C4 | −177.47 (11) | C2—N1—C6—C5 | −0.7 (2) |
N1—C2—N3—C3 | 179.93 (12) | N5—C5—C6—N6 | 0.5 (2) |
N2—C2—N3—C3 | −1.08 (19) | C4—C5—C6—N6 | 178.51 (12) |
C2—N3—C4—O4 | 175.32 (12) | N5—C5—C6—N1 | −179.23 (13) |
C3—N3—C4—O4 | −1.11 (19) | C4—C5—C6—N1 | −1.2 (2) |
C2—N3—C4—C5 | −5.18 (18) |
Symmetry code: (i) −x+1, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O21ii | 0.88 | 2.41 | 3.003 (2) | 125 |
N6—H6A···O4iii | 0.88 | 2.11 | 2.866 (2) | 144 |
N6—H6B···O5 | 0.88 | 1.97 | 2.618 (2) | 130 |
N6—H6B···O4Wi | 0.88 | 2.47 | 3.011 (4) | 120 |
O1W—H11W···O21iv | 0.82 | 1.86 | 2.6569 (1) | 163 |
O2W—H12W···O22v | 0.82 | 1.90 | 2.7256 (2) | 177 |
O3W—H13W···O4W | 0.82 | 1.89 | 2.6995 (1) | 171 |
O4W—H14W···O4vi | 0.82 | 2.07 | 2.8812 (2) | 172 |
O1W—H21W···O21vii | 0.82 | 1.89 | 2.6995 (1) | 169 |
O2W—H22W···O5 | 0.82 | 1.96 | 2.7764 (1) | 172 |
O3W—H23W···O22viii | 0.82 | 1.94 | 2.7535 (2) | 168 |
O4W—H24W···O4ix | 0.82 | 2.52 | 3.0721 (2) | 126 |
O4W—H24W···N5ix | 0.82 | 2.25 | 3.0447 (2) | 164 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+2, −y, −z−2; (iii) x+1, y, z; (iv) x−1, y+1, z+1; (v) −x+1, −y+1, −z−1; (vi) x, y, z+1; (vii) −x+2, −y+1, −z−1; (viii) x−1, y, z+1; (ix) −x, −y+1, −z. |
Experimental details
Crystal data | |
Chemical formula | [Mg(H2O)6](C7H8N5O4)2·2H2O |
Mr | 620.81 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 150 |
a, b, c (Å) | 7.3152 (3), 7.5917 (4), 12.3024 (6) |
α, β, γ (°) | 86.661 (3), 73.172 (3), 81.79 (3) |
V (Å3) | 647.15 (5) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 0.16 |
Crystal size (mm) | 0.25 × 0.25 × 0.25 |
Data collection | |
Diffractometer | Kappa-CCD diffractometer |
Absorption correction | Multi-scan SORTAV (Blessing, 1995, 1997) |
Tmin, Tmax | 0.960, 0.960 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8396, 2947, 2428 |
Rint | 0.034 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.110, 1.06 |
No. of reflections | 2947 |
No. of parameters | 212 |
No. of restraints | 8 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.28 |
Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 1997a), SHELXL97 (Sheldrick, 1997b), SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
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The title compound, hexaaquamagnesium(II) bis[N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)glycinate] dihydrate, (I), continues our study of the reactivity of metal ions with N-protected amino acids. These reactions occur in several biological processes (Bonamartini Corradi, 1992). This type of compound shows great versatility in the formation of hydrogen-bonded complexes as a result of the presence of numerous hydrogen-bond donor and acceptor groups. Divalent magnesium ions shows a rich coordination ability to low-molecular weight metabolites, nucleic acid derivatives, and carrier ligands and in all cases, water molecules of coordination are involved in the binding interactions (Cowan, 1995). In this case, the Mg ion sits on a crystallographic centre of symmetry and is coordinated to six water molecules (three unique and three symmetry related); the anion is not coordinated to the Mg cation. Examination of the structure with PLATON (Spek, 1999) showed that there were no solvent-accessible voids in the crystal lattice.