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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2655–o2656.
Published online 2009 October 7. doi:  10.1107/S1600536809039968
PMCID: PMC2971361

Diammonium 1,1′,3,3′-tetra­methyl-2,2′,4,4′,6,6′-hexa­oxoperhydro-5,5′-bipyrimidine-5,5′-diide monohydrate

Abstract

In the title hydrated salt, 2NH4 +·C12H12N4O6 2−·H2O, the two hexa­hydro­pyrimidine rings in the dianion are inclined to one another at a dihedral angle of 62.76 (5)°. In the crystal structure, the anions and water mol­ecules are linked into sheets parallel to the bc plane by inter­molecular O—H(...)O hydrogen bonds and sustained by C—H(...)O contacts. The linking of the anions and water mol­ecules with the cations by N—H(...)O hydrogen bonds creates a three-dimensional extended network. The crystal structure is further stabilized by very weak C—H(...)π inter­actions.

Related literature

For general background to and applications of barbituric acid derivatives, see: Negwer (2001 [triangle]). For related structures, see: Rezende et al. (2005 [triangle]); da Silva et al. (2005 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2655-scheme1.jpg

Experimental

Crystal data

  • 2NH4 +·C12H12N4O6 2−·H2O
  • M r = 362.36
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2655-efi1.jpg
  • a = 8.5345 (1) Å
  • b = 12.1579 (2) Å
  • c = 7.7482 (1) Å
  • β = 100.595 (1)°
  • V = 790.26 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 100 K
  • 0.46 × 0.24 × 0.20 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.945, T max = 0.975
  • 15091 measured reflections
  • 3387 independent reflections
  • 3237 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.029
  • wR(F 2) = 0.083
  • S = 1.05
  • 3387 reflections
  • 270 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809039968/tk2548sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809039968/tk2548Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

HKF and JHG thank Universiti Sains Malaysia (USM) for a Research University Golden Goose Grant (No. 1001/PFIZIK/811012). JHG thanks USM for the award of a USM Fellowship. VV is grateful to DST-India for funding through the Young Scientist Scheme (Fast Track Proposal).

supplementary crystallographic information

Comment

Barbituric acid derivatives show high hypnotic and sedative activity (Negwer, 2001).

The asymmetric unit of the title hydrated salt (I, Fig. 1) contains two ammonium cations, a 1,1',3,3'-tetramethyl-2,2',4,4',6,6'-hexaoxooctahydro-1H, 1'H-5,5'-bipyrimidine-5,5'-diide dianion and a water molecule. Two protons transfer from the C4 and C5 atoms to the ammonia molecules resulted in the formation of salts. The dianion is built up from one dimethylbarbiturate anion connected to the other one through the Csp3—Csp3 (C4—C5) bond. The two hexahydropyrimidine rings are essentially planar, with maximum deviations of 0.036 (1) Å for atom C1 and 0.018 (1) Å for atom N3, respectively, for rings with atom sequence C1/N1/C2/N2/C3/C4 and C5/C6/N3/C7/N4/C8. These two rings are inclined to one another at a dihedral angle of 62.76 (5)°. The bond lengths and angles are comparable to those found in related structures (Rezende et al., 2005; da Silva et al., 2005).

The crystal structure of (I) is mainly stabilized by a network of N—H···O, and O—H···O hydrogen bonds as well as C—H···O and C—H···π contacts. Each ammonium H-atom participates in intermolecular hydrogen bonds. In the crystal structure (Fig. 2), the anions and water molecules are linked into sheets parallel to the bc plane by O—H···O hydrogen bonds and sustained by C—H···O contacts (Table 1). The ammonium cations act as bridges between the anions and water molecules via N—H···O hydrogen bonds (Table 1) to create a three-dimensional extended network. The crystal structure is further stabilized by weak intermolecular C10—H10C···Cg1 interactions (Table 1).

Experimental

A solution of 1,3-dimethylbarbituric acid was refluxed in acetonitrile at 363 K for 2 h (monitored by TLC). After completion of the reaction, excess of solvent was distilled off. The solid product obtained was washed with mixture of ether and acetone, and dried. The purity of the crude product was checked through TLC and recrystallized using chloroform and benzene mixture. M.p. 515–517 K.

Refinement

The H-atoms bound to atoms N5, N6 and O1W were located from the difference Fourier map and allowed to refine freely. The other H-atoms were placed in calculated positions, with C—H = 0.96 Å, Uiso = 1.5Ueq(C). Rotating models were used for the methyl groups. In the absence of significant anomalous dispersion, 2042 Friedel pairs were merged for the final refinement.

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids for non-H atoms and the atom-numbering scheme.
Fig. 2.
The crystal structure of (I) viewed along the b axis, showing the three-dimensional network. H atoms not involved in intermolecular interactions (dashed lines) have been omitted for clarity.

Crystal data

2NH4+·C12H12N4O62·H2OF(000) = 384
Mr = 362.36Dx = 1.523 Mg m3
Monoclinic, PcMo Kα radiation, λ = 0.71073 Å
Hall symbol: P -2ycCell parameters from 9975 reflections
a = 8.5345 (1) Åθ = 3.0–34.6°
b = 12.1579 (2) ŵ = 0.13 mm1
c = 7.7482 (1) ÅT = 100 K
β = 100.595 (1)°Block, yellow
V = 790.26 (2) Å30.46 × 0.24 × 0.20 mm
Z = 2

Data collection

Bruker SMART APEXII CCD area-detector diffractometer3387 independent reflections
Radiation source: fine-focus sealed tube3237 reflections with I > 2σ(I)
graphiteRint = 0.026
[var phi] and ω scansθmax = 34.7°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −13→13
Tmin = 0.945, Tmax = 0.975k = −19→19
15091 measured reflectionsl = −12→12

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0579P)2 + 0.0092P] where P = (Fo2 + 2Fc2)/3
3387 reflections(Δ/σ)max < 0.001
270 parametersΔρmax = 0.41 e Å3
2 restraintsΔρmin = −0.22 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1)K.
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 > 2sigma(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O11.03560 (11)0.14592 (7)1.07661 (12)0.01241 (15)
O21.29186 (11)0.47147 (8)1.22084 (12)0.01554 (17)
O30.81723 (11)0.48152 (7)0.83916 (11)0.01375 (16)
O40.58471 (11)0.32057 (7)0.97921 (12)0.01402 (16)
O50.41464 (11)0.06573 (8)0.55640 (12)0.01527 (17)
O60.94414 (10)0.14952 (7)0.66677 (12)0.01358 (16)
N11.16599 (12)0.30914 (8)1.13935 (13)0.01118 (16)
N21.05010 (13)0.47550 (7)1.03408 (14)0.01113 (16)
N30.50054 (11)0.19796 (8)0.76033 (12)0.01090 (16)
N40.67803 (12)0.11318 (8)0.60677 (13)0.01124 (16)
C11.03474 (13)0.24831 (9)1.05040 (14)0.00980 (17)
C21.17569 (14)0.42182 (9)1.13520 (15)0.01120 (18)
C30.92023 (13)0.42115 (9)0.93130 (15)0.01017 (17)
C40.91423 (13)0.30599 (9)0.93888 (15)0.00967 (17)
C50.77985 (13)0.24525 (9)0.83177 (14)0.00979 (18)
C60.62473 (13)0.25855 (9)0.86409 (14)0.01016 (17)
C70.52552 (13)0.12277 (9)0.63627 (15)0.01075 (18)
C80.80944 (13)0.17050 (9)0.70160 (15)0.01024 (17)
C91.29964 (15)0.25137 (11)1.24737 (16)0.0154 (2)
H9A1.39820.28371.22990.023*
H9B1.29720.17521.21420.023*
H9C1.29120.25731.36890.023*
C101.04993 (17)0.59583 (9)1.03645 (19)0.0170 (2)
H10A1.14710.62181.10730.025*
H10B0.96080.62161.08480.025*
H10C1.04180.62310.91890.025*
C110.34045 (15)0.20432 (11)0.80192 (18)0.0174 (2)
H11A0.26270.19520.69640.026*
H11B0.32610.27470.85300.026*
H11C0.32740.14720.88370.026*
C120.70481 (16)0.04107 (12)0.46407 (19)0.0201 (2)
H12A0.60550.00870.40920.030*
H12B0.7785−0.01590.51030.030*
H12C0.74800.08310.37890.030*
N50.08583 (12)0.04901 (9)0.41174 (14)0.01257 (17)
H1N50.061 (3)−0.020 (2)0.410 (3)0.027 (6)*
H2N50.067 (3)0.083 (2)0.315 (3)0.029 (5)*
H3N50.195 (3)0.0572 (17)0.456 (3)0.020 (5)*
H4N50.035 (3)0.0832 (18)0.486 (3)0.025 (5)*
N60.56158 (13)0.46002 (9)0.56578 (14)0.01434 (18)
H1N60.566 (3)0.4075 (16)0.488 (3)0.016 (4)*
H2N60.465 (3)0.4638 (17)0.604 (3)0.022 (5)*
H3N60.568 (3)0.5221 (19)0.520 (3)0.023 (5)*
H4N60.641 (3)0.4479 (18)0.654 (3)0.023 (5)*
O1W0.69194 (13)0.30906 (8)0.33669 (14)0.01932 (18)
H1W10.753 (3)0.364 (2)0.346 (3)0.026 (5)*
H2W10.667 (3)0.297 (2)0.236 (4)0.033 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0146 (4)0.0091 (3)0.0126 (3)0.0000 (3)0.0001 (3)0.0007 (3)
O20.0123 (4)0.0164 (4)0.0170 (4)−0.0048 (3)0.0002 (3)−0.0031 (3)
O30.0144 (4)0.0107 (3)0.0147 (4)0.0010 (3)−0.0010 (3)0.0005 (3)
O40.0141 (4)0.0137 (4)0.0147 (4)0.0001 (3)0.0039 (3)−0.0042 (3)
O50.0098 (3)0.0165 (4)0.0179 (4)−0.0020 (3)−0.0017 (3)−0.0043 (3)
O60.0096 (3)0.0153 (4)0.0158 (4)0.0003 (3)0.0024 (3)−0.0037 (3)
N10.0091 (4)0.0118 (4)0.0117 (4)−0.0009 (3)−0.0005 (3)−0.0001 (3)
N20.0107 (4)0.0087 (3)0.0133 (4)−0.0016 (3)0.0002 (3)−0.0012 (3)
N30.0081 (4)0.0126 (4)0.0119 (4)0.0000 (3)0.0016 (3)−0.0014 (3)
N40.0092 (4)0.0112 (4)0.0128 (4)−0.0003 (3)0.0009 (3)−0.0041 (3)
C10.0086 (4)0.0109 (4)0.0098 (4)−0.0006 (3)0.0014 (3)−0.0008 (3)
C20.0105 (4)0.0122 (4)0.0110 (4)−0.0027 (4)0.0025 (3)−0.0010 (3)
C30.0098 (4)0.0103 (4)0.0102 (4)−0.0009 (3)0.0015 (3)−0.0010 (3)
C40.0090 (4)0.0090 (4)0.0104 (4)−0.0004 (3)0.0001 (3)−0.0015 (3)
C50.0097 (4)0.0089 (4)0.0102 (4)−0.0004 (3)0.0002 (3)−0.0011 (3)
C60.0100 (4)0.0092 (4)0.0107 (4)−0.0006 (3)0.0004 (3)0.0001 (3)
C70.0096 (4)0.0095 (4)0.0124 (4)−0.0003 (3)0.0001 (3)−0.0002 (3)
C80.0101 (4)0.0090 (4)0.0109 (4)−0.0009 (3)0.0001 (3)−0.0003 (3)
C90.0112 (4)0.0172 (5)0.0160 (5)0.0002 (4)−0.0023 (4)0.0023 (4)
C100.0188 (5)0.0099 (4)0.0211 (5)−0.0024 (4)0.0004 (4)−0.0014 (4)
C110.0102 (5)0.0222 (6)0.0204 (5)−0.0007 (4)0.0044 (4)−0.0033 (4)
C120.0133 (5)0.0243 (6)0.0224 (6)−0.0025 (4)0.0027 (4)−0.0145 (5)
N50.0120 (4)0.0126 (4)0.0130 (4)−0.0014 (3)0.0018 (3)0.0006 (3)
N60.0141 (4)0.0137 (4)0.0147 (4)−0.0007 (3)0.0013 (3)0.0008 (3)
O1W0.0220 (5)0.0170 (4)0.0176 (4)−0.0044 (3)0.0001 (3)−0.0003 (3)

Geometric parameters (Å, °)

O1—C11.2611 (14)C9—H9A0.9600
O2—C21.2433 (14)C9—H9B0.9600
O3—C31.2611 (14)C9—H9C0.9600
O4—C61.2620 (14)C10—H10A0.9600
O5—C71.2427 (13)C10—H10B0.9600
O6—C81.2544 (14)C10—H10C0.9600
N1—C21.3733 (15)C11—H11A0.9600
N1—C11.4117 (14)C11—H11B0.9600
N1—C91.4642 (15)C11—H11C0.9600
N2—C21.3710 (15)C12—H12A0.9600
N2—C31.4052 (15)C12—H12B0.9600
N2—C101.4631 (14)C12—H12C0.9600
N3—C71.3713 (15)N5—H1N50.86 (2)
N3—C61.4139 (14)N5—H2N50.85 (3)
N3—C111.4623 (15)N5—H3N50.94 (2)
N4—C71.3672 (15)N5—H4N50.89 (2)
N4—C81.4072 (14)N6—H1N60.88 (2)
N4—C121.4616 (16)N6—H2N60.93 (2)
C1—C41.4033 (15)N6—H3N60.84 (2)
C3—C41.4028 (15)N6—H4N60.88 (2)
C4—C51.4830 (15)O1W—H1W10.84 (3)
C5—C61.4013 (15)O1W—H2W10.79 (3)
C5—C81.4143 (15)
C2—N1—C1123.86 (10)N1—C9—H9B109.5
C2—N1—C9116.61 (10)H9A—C9—H9B109.5
C1—N1—C9119.51 (10)N1—C9—H9C109.5
C2—N2—C3123.53 (9)H9A—C9—H9C109.5
C2—N2—C10118.11 (10)H9B—C9—H9C109.5
C3—N2—C10118.34 (10)N2—C10—H10A109.5
C7—N3—C6123.30 (9)N2—C10—H10B109.5
C7—N3—C11117.50 (10)H10A—C10—H10B109.5
C6—N3—C11118.70 (9)N2—C10—H10C109.5
C7—N4—C8124.21 (9)H10A—C10—H10C109.5
C7—N4—C12117.63 (10)H10B—C10—H10C109.5
C8—N4—C12118.14 (10)N3—C11—H11A109.5
O1—C1—C4125.05 (10)N3—C11—H11B109.5
O1—C1—N1117.25 (10)H11A—C11—H11B109.5
C4—C1—N1117.69 (9)N3—C11—H11C109.5
O2—C2—N2122.47 (10)H11A—C11—H11C109.5
O2—C2—N1121.16 (11)H11B—C11—H11C109.5
N2—C2—N1116.36 (10)N4—C12—H12A109.5
O3—C3—C4125.29 (10)N4—C12—H12B109.5
O3—C3—N2116.25 (10)H12A—C12—H12B109.5
C4—C3—N2118.46 (10)N4—C12—H12C109.5
C3—C4—C1119.76 (10)H12A—C12—H12C109.5
C3—C4—C5120.26 (9)H12B—C12—H12C109.5
C1—C4—C5119.97 (9)H1N5—N5—H2N5117 (2)
C6—C5—C8120.00 (9)H1N5—N5—H3N5109.6 (19)
C6—C5—C4120.09 (9)H2N5—N5—H3N5107 (2)
C8—C5—C4119.86 (10)H1N5—N5—H4N5108 (2)
O4—C6—C5125.63 (10)H2N5—N5—H4N5108 (2)
O4—C6—N3116.18 (10)H3N5—N5—H4N5107 (2)
C5—C6—N3118.19 (9)H1N6—N6—H2N6113.9 (19)
O5—C7—N4122.03 (11)H1N6—N6—H3N6110.3 (19)
O5—C7—N3121.25 (10)H2N6—N6—H3N6103 (2)
N4—C7—N3116.71 (10)H1N6—N6—H4N6106.3 (19)
O6—C8—N4117.44 (10)H2N6—N6—H4N6111 (2)
O6—C8—C5125.09 (10)H3N6—N6—H4N6112 (2)
N4—C8—C5117.44 (10)H1W1—O1W—H2W1106 (3)
N1—C9—H9A109.5
C2—N1—C1—O1−174.49 (10)C3—C4—C5—C8117.68 (12)
C9—N1—C1—O13.76 (15)C1—C4—C5—C8−63.31 (14)
C2—N1—C1—C45.98 (15)C8—C5—C6—O4178.22 (11)
C9—N1—C1—C4−175.76 (10)C4—C5—C6—O40.76 (17)
C3—N2—C2—O2177.67 (11)C8—C5—C6—N3−1.73 (15)
C10—N2—C2—O2−3.67 (17)C4—C5—C6—N3−179.19 (9)
C3—N2—C2—N1−3.18 (16)C7—N3—C6—O4−176.44 (10)
C10—N2—C2—N1175.47 (10)C11—N3—C6—O4−4.80 (15)
C1—N1—C2—O2177.56 (10)C7—N3—C6—C53.52 (15)
C9—N1—C2—O2−0.74 (16)C11—N3—C6—C5175.16 (10)
C1—N1—C2—N2−1.60 (16)C8—N4—C7—O5−175.66 (11)
C9—N1—C2—N2−179.90 (10)C12—N4—C7—O56.19 (17)
C2—N2—C3—O3−176.92 (10)C8—N4—C7—N33.66 (16)
C10—N2—C3—O34.43 (16)C12—N4—C7—N3−174.49 (11)
C2—N2—C3—C43.31 (17)C6—N3—C7—O5174.96 (10)
C10—N2—C3—C4−175.34 (10)C11—N3—C7—O53.22 (16)
O3—C3—C4—C1−178.39 (11)C6—N3—C7—N4−4.37 (15)
N2—C3—C4—C11.36 (16)C11—N3—C7—N4−176.11 (10)
O3—C3—C4—C50.63 (18)C7—N4—C8—O6176.38 (10)
N2—C3—C4—C5−179.62 (9)C12—N4—C8—O6−5.48 (16)
O1—C1—C4—C3174.85 (11)C7—N4—C8—C5−2.08 (16)
N1—C1—C4—C3−5.66 (15)C12—N4—C8—C5176.06 (11)
O1—C1—C4—C5−4.17 (17)C6—C5—C8—O6−177.28 (11)
N1—C1—C4—C5175.32 (9)C4—C5—C8—O60.18 (17)
C3—C4—C5—C6−64.86 (14)C6—C5—C8—N41.05 (15)
C1—C4—C5—C6114.15 (12)C4—C5—C8—N4178.51 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N5—H1N5···O1i0.87 (2)2.04 (2)2.7629 (14)141 (2)
N5—H1N5···O6i0.87 (2)2.52 (2)3.1697 (14)132.9 (19)
N5—H2N5···O1ii0.85 (2)1.97 (2)2.8116 (14)173 (2)
N5—H3N5···O50.94 (3)1.90 (3)2.8312 (14)176.1 (19)
N5—H4N5···O6iii0.89 (2)1.90 (2)2.7819 (14)173 (2)
N6—H1N6···O1W0.88 (2)2.10 (2)2.9126 (15)152 (2)
N6—H2N6···O2iv0.93 (3)2.03 (2)2.9074 (15)157.8 (19)
N6—H3N6···O4v0.84 (2)1.95 (2)2.7665 (14)164 (2)
N6—H4N6···O30.88 (2)1.92 (2)2.7597 (14)158 (2)
O1W—H1W1···O3v0.84 (3)1.96 (2)2.7602 (13)158 (2)
O1W—H2W1···O4vi0.78 (3)2.01 (3)2.7563 (14)161 (3)
C9—H9A···O1Wvii0.962.513.3658 (17)148
C10—H10C···Cg1v0.962.963.8822 (15)162

Symmetry codes: (i) x−1, −y, z−1/2; (ii) x−1, y, z−1; (iii) x−1, y, z; (iv) x−1, −y+1, z−1/2; (v) x, −y+1, z−1/2; (vi) x, y, z−1; (vii) x+1, y, z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2548).

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