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The analysis of the title compound, [Mg(H2O)6](C7H8N5O4)2·2H2O, continues our study of the reactivity of metal ions with N-protected amino acids. The Mg ion lies on an inversion centre with Mg-O 2.0437 (10)-2.0952 (10) Å. The [Mg(H2O)6]2+cations, anions and water mol­ecules are linked by an extensive hydrogen-bond network.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270199016145/qb0158sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270199016145/qb0158Isup2.hkl
Contains datablock I

CCDC reference: 140852

Comment top

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.

Experimental top

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%.

Refinement top

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.

Computing details top

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).

Hexaaquomagnesium(II) di[N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxo- pyrimidin-2-yl)glycinate] dihydrate top
Crystal data top
[Mg(H2O)6](C7H8N5O4)2·2H2OZ = 1
Mr = 620.81F(000) = 326
Triclinic, P1Dx = 1.593 Mg m3
a = 7.3152 (3) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.5917 (4) ÅCell parameters from 2947 reflections
c = 12.3024 (6) Åθ = 1.7–27.5°
α = 86.661 (3)°µ = 0.16 mm1
β = 73.172 (3)°T = 150 K
γ = 81.79 (3)°Block, pink
V = 647.15 (5) Å30.25 × 0.25 × 0.25 mm
Data collection top
Kappa-CCD
diffractometer
2947 independent reflections
Radiation source: fine-focus sealed X-ray tube2428 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
ϕ scans and ω scans with κ offsetsθmax = 27.5°, θmin = 1.7°
Absorption correction: multi-scan
SORTAV (Blessing, 1995, 1997)
h = 98
Tmin = 0.960, Tmax = 0.960k = 97
8396 measured reflectionsl = 1515
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)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0622P)2 + 0.0773P]
where P = (Fo2 + 2Fc2)/3
2947 reflections(Δ/σ)max = 0.001
212 parametersΔρmax = 0.35 e Å3
8 restraintsΔρmin = 0.28 e Å3
Crystal data top
[Mg(H2O)6](C7H8N5O4)2·2H2Oγ = 81.79 (3)°
Mr = 620.81V = 647.15 (5) Å3
Triclinic, P1Z = 1
a = 7.3152 (3) ÅMo Kα radiation
b = 7.5917 (4) ŵ = 0.16 mm1
c = 12.3024 (6) ÅT = 150 K
α = 86.661 (3)°0.25 × 0.25 × 0.25 mm
β = 73.172 (3)°
Data collection top
Kappa-CCD
diffractometer
2947 independent reflections
Absorption correction: multi-scan
SORTAV (Blessing, 1995, 1997)
2428 reflections with I > 2σ(I)
Tmin = 0.960, Tmax = 0.960Rint = 0.034
8396 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0388 restraints
wR(F2) = 0.110H-atom parameters constrained
S = 1.06Δρmax = 0.35 e Å3
2947 reflectionsΔρmin = 0.28 e Å3
212 parameters
Special details top

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].

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Mg10.50000.50000.00000.01627 (17)
N10.78085 (16)0.11420 (16)0.62695 (10)0.0188 (3)
C20.67248 (19)0.08331 (18)0.69121 (11)0.0168 (3)
N20.75512 (16)0.00192 (16)0.78824 (10)0.0191 (3)
C210.96153 (19)0.05176 (19)0.83161 (12)0.0198 (3)
C221.06469 (19)0.09140 (18)0.90801 (11)0.0180 (3)
O211.23336 (13)0.03862 (13)0.96815 (8)0.0217 (2)
O220.98289 (14)0.24691 (13)0.90725 (9)0.0236 (2)
N30.47488 (16)0.13152 (15)0.66389 (9)0.0173 (3)
C30.3669 (2)0.0914 (2)0.74119 (12)0.0223 (3)
C40.37696 (19)0.22715 (18)0.56642 (11)0.0174 (3)
O40.20384 (13)0.27875 (14)0.54719 (8)0.0235 (2)
C50.49109 (18)0.25797 (18)0.49232 (11)0.0170 (3)
N50.39075 (17)0.34517 (16)0.39674 (9)0.0207 (3)
O50.48429 (15)0.37789 (15)0.32857 (8)0.0264 (3)
C60.69615 (19)0.19867 (18)0.52866 (11)0.0173 (3)
N60.80611 (17)0.22707 (18)0.46561 (10)0.0233 (3)
O1W0.48312 (14)0.75553 (13)0.04960 (9)0.0209 (2)
O2W0.38321 (14)0.58082 (14)0.13439 (8)0.0207 (2)
O3W0.22033 (14)0.49424 (14)0.09946 (8)0.0216 (2)
O4W0.04467 (15)0.55360 (15)0.32194 (9)0.0277 (3)
H20.68100.02930.82800.023*
H21A0.98650.16260.87520.024*
H21B1.01630.07720.76670.024*
H3A0.40570.16050.81200.033*
H3B0.22860.12280.70530.033*
H3C0.39440.03590.75790.033*
H6A0.93080.19110.48840.028*
H6B0.75510.28210.40060.028*
H1W10.3901 (17)0.8291 (18)0.0481 (14)0.025*
H2W10.5794 (16)0.807 (2)0.0271 (14)0.025*
H1W20.2740 (12)0.636 (2)0.1242 (14)0.025*
H2W20.403 (2)0.5187 (19)0.1901 (10)0.025*
H1W30.176 (2)0.518 (2)0.1669 (6)0.026*
H2W30.152 (2)0.4240 (18)0.0882 (15)0.026*
H1W40.079 (3)0.4754 (19)0.3635 (13)0.033*
H2W40.0682 (11)0.594 (2)0.3509 (15)0.033*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Mg10.0169 (3)0.0143 (3)0.0163 (3)0.0011 (2)0.0030 (2)0.0006 (2)
N10.0168 (5)0.0218 (6)0.0175 (6)0.0029 (5)0.0044 (5)0.0010 (5)
C20.0183 (7)0.0149 (6)0.0172 (6)0.0046 (5)0.0048 (5)0.0027 (5)
N20.0178 (6)0.0231 (6)0.0168 (6)0.0031 (5)0.0047 (5)0.0032 (5)
C210.0189 (7)0.0182 (7)0.0204 (7)0.0004 (5)0.0033 (5)0.0025 (5)
C220.0179 (6)0.0186 (7)0.0193 (6)0.0007 (6)0.0080 (5)0.0051 (5)
O210.0166 (5)0.0210 (5)0.0262 (5)0.0023 (4)0.0038 (4)0.0020 (4)
O220.0191 (5)0.0176 (5)0.0328 (6)0.0005 (4)0.0063 (4)0.0024 (4)
N30.0163 (6)0.0203 (6)0.0161 (6)0.0042 (5)0.0050 (5)0.0003 (5)
C30.0212 (7)0.0287 (8)0.0201 (7)0.0055 (6)0.0092 (6)0.0016 (6)
C40.0165 (6)0.0172 (7)0.0170 (6)0.0040 (5)0.0022 (5)0.0029 (5)
O40.0148 (5)0.0310 (6)0.0233 (5)0.0006 (4)0.0042 (4)0.0022 (4)
C50.0165 (6)0.0166 (7)0.0168 (6)0.0037 (5)0.0024 (5)0.0006 (5)
N50.0219 (6)0.0221 (6)0.0176 (6)0.0033 (5)0.0048 (5)0.0009 (5)
O50.0265 (5)0.0340 (6)0.0199 (5)0.0031 (5)0.0073 (4)0.0077 (4)
C60.0173 (6)0.0178 (7)0.0167 (6)0.0047 (5)0.0041 (5)0.0021 (5)
N60.0163 (6)0.0331 (7)0.0207 (6)0.0037 (5)0.0043 (5)0.0052 (5)
O1W0.0178 (5)0.0161 (5)0.0271 (5)0.0009 (4)0.0040 (4)0.0016 (4)
O2W0.0202 (5)0.0221 (5)0.0183 (5)0.0034 (4)0.0057 (4)0.0031 (4)
O3W0.0196 (5)0.0251 (6)0.0185 (5)0.0060 (4)0.0005 (4)0.0046 (4)
O4W0.0245 (5)0.0334 (6)0.0205 (5)0.0015 (5)0.0015 (4)0.0017 (4)
Geometric parameters (Å, º) top
Mg1—O1W2.0437 (10)C21—C221.529 (2)
Mg1—O1Wi2.0437 (10)C22—O221.2442 (17)
Mg1—O3W2.0626 (10)C22—O211.2630 (16)
Mg1—O3Wi2.0626 (10)N3—C41.3905 (18)
Mg1—O2Wi2.0952 (10)N3—C31.4694 (18)
Mg1—O2W2.0952 (10)C4—O41.2283 (16)
N1—C21.3213 (18)C4—C51.4506 (19)
N1—C61.3418 (18)C5—N51.3461 (18)
C2—N21.3302 (18)C5—C61.4474 (18)
C2—N31.3850 (17)N5—O51.2799 (16)
N2—C211.4497 (17)C6—N61.3135 (18)
O1W—Mg1—O1Wi180.0C2—N2—C21123.12 (12)
O1W—Mg1—O3W88.91 (5)N2—C21—C22113.46 (11)
O1Wi—Mg1—O3W91.09 (5)O22—C22—O21124.75 (14)
O1W—Mg1—O3Wi91.09 (5)O22—C22—C21120.23 (12)
O1Wi—Mg1—O3Wi88.91 (5)O21—C22—C21115.02 (12)
O3W—Mg1—O3Wi180.0C2—N3—C4120.76 (12)
O1W—Mg1—O2Wi87.09 (4)C2—N3—C3120.32 (11)
O1Wi—Mg1—O2Wi92.91 (4)C4—N3—C3118.82 (11)
O3W—Mg1—O2Wi93.30 (4)O4—C4—N3119.95 (13)
O3Wi—Mg1—O2Wi86.70 (4)O4—C4—C5124.08 (12)
O1W—Mg1—O2W92.91 (4)N3—C4—C5115.97 (11)
O1Wi—Mg1—O2W87.09 (4)N5—C5—C6127.21 (13)
O3W—Mg1—O2W86.70 (4)N5—C5—C4114.51 (11)
O3Wi—Mg1—O2W93.30 (4)C6—C5—C4118.25 (12)
O2Wi—Mg1—O2W180.0O5—N5—C5117.33 (11)
C2—N1—C6118.60 (12)N6—C6—N1117.69 (12)
N1—C2—N2118.96 (12)N6—C6—C5120.47 (12)
N1—C2—N3124.39 (12)N1—C6—C5121.84 (12)
N2—C2—N3116.65 (12)
C6—N1—C2—N2179.34 (12)C3—N3—C4—C5178.38 (12)
C6—N1—C2—N30.4 (2)O4—C4—C5—N51.8 (2)
N1—C2—N2—C214.7 (2)N3—C4—C5—N5177.69 (12)
N3—C2—N2—C21176.30 (12)O4—C4—C5—C6176.46 (13)
C2—N2—C21—C2289.68 (16)N3—C4—C5—C64.07 (18)
N2—C21—C22—O2216.58 (18)C6—C5—N5—O51.2 (2)
N2—C21—C22—O21163.98 (11)C4—C5—N5—O5179.27 (11)
N1—C2—N3—C43.5 (2)C2—N1—C6—N6179.55 (12)
N2—C2—N3—C4177.47 (11)C2—N1—C6—C50.7 (2)
N1—C2—N3—C3179.93 (12)N5—C5—C6—N60.5 (2)
N2—C2—N3—C31.08 (19)C4—C5—C6—N6178.51 (12)
C2—N3—C4—O4175.32 (12)N5—C5—C6—N1179.23 (13)
C3—N3—C4—O41.11 (19)C4—C5—C6—N11.2 (2)
C2—N3—C4—C55.18 (18)
Symmetry code: (i) x+1, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···O21ii0.882.413.003 (2)125
N6—H6A···O4iii0.882.112.866 (2)144
N6—H6B···O50.881.972.618 (2)130
N6—H6B···O4Wi0.882.473.011 (4)120
O1W—H11W···O21iv0.821.862.6569 (1)163
O2W—H12W···O22v0.821.902.7256 (2)177
O3W—H13W···O4W0.821.892.6995 (1)171
O4W—H14W···O4vi0.822.072.8812 (2)172
O1W—H21W···O21vii0.821.892.6995 (1)169
O2W—H22W···O50.821.962.7764 (1)172
O3W—H23W···O22viii0.821.942.7535 (2)168
O4W—H24W···O4ix0.822.523.0721 (2)126
O4W—H24W···N5ix0.822.253.0447 (2)164
Symmetry codes: (i) x+1, y+1, z; (ii) x+2, y, z2; (iii) x+1, y, z; (iv) x1, y+1, z+1; (v) x+1, y+1, z1; (vi) x, y, z+1; (vii) x+2, y+1, z1; (viii) x1, y, z+1; (ix) x, y+1, z.

Experimental details

Crystal data
Chemical formula[Mg(H2O)6](C7H8N5O4)2·2H2O
Mr620.81
Crystal system, space groupTriclinic, 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)
V3)647.15 (5)
Z1
Radiation typeMo Kα
µ (mm1)0.16
Crystal size (mm)0.25 × 0.25 × 0.25
Data collection
DiffractometerKappa-CCD
diffractometer
Absorption correctionMulti-scan
SORTAV (Blessing, 1995, 1997)
Tmin, Tmax0.960, 0.960
No. of measured, independent and
observed [I > 2σ(I)] reflections
8396, 2947, 2428
Rint0.034
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.110, 1.06
No. of reflections2947
No. of parameters212
No. of restraints8
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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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