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Acta Crystallogr Sect E Struct Rep Online. 2009 April 1; 65(Pt 4): o848–o849.
Published online 2009 March 25. doi:  10.1107/S1600536809010095
PMCID: PMC2968866

4,4′,6,6′-Tetra­methyl-2,2′-bipyrimidine hexa­hydrate

Abstract

In the title compound, C12H14N4·6H2O, the two pyrimidine rings make a dihedral angle of 5.285 (6)°. Inter­molecular O—H(...)O hydrogen bonds link the six water mol­ecules, generating edge-fused four-, five- or six-membered ring motifs and forming two-dimensional sheets. The sheets are stabilized by the formation of O—H(...)N hydrogen bonds between the water mol­ecules and the bipyrimidine mol­ecules, resulting in a three-dimensional network.

Related literature

For 2,2′-bipyrimidine and its derivatives, see: Ji et al. (2000 [triangle]); Baumann et al. (1998 [triangle]). For hydrogen-bonded water clusters, see: Buck & Huisken (2000 [triangle]); Lakshminarayanan et al. (2006 [triangle]). For water–water inter­actions in bulk water or ice, see: Zhang et al. (2005 [triangle]). For bond lengths and angles, see: Berg et al. (2002 [triangle]). For the preparation of the compound by the Ullmann coupling method, see: Vlad & Horvath (2002 [triangle]).

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Object name is e-65-0o848-scheme1.jpg

Experimental

Crystal data

  • C12H14N4·6H2O
  • M r = 322.37
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o848-efi1.jpg
  • a = 6.8622 (19) Å
  • b = 11.098 (3) Å
  • c = 11.750 (3) Å
  • α = 98.233 (3)°
  • β = 91.774 (4)°
  • γ = 102.599 (4)°
  • V = 862.4 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 296 K
  • 0.41 × 0.31 × 0.21 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.961, T max = 0.980
  • 6492 measured reflections
  • 3196 independent reflections
  • 2026 reflections with I > 2σ(I)
  • R int = 0.023

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.148
  • S = 1.04
  • 3196 reflections
  • 204 parameters
  • H-atom parameters constrained
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.15 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXS97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]) and DIAMOND (Brandenburg, 2006 [triangle]); 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/S1600536809010095/at2743sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809010095/at2743Isup2.hkl

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

Acknowledgments

We are grateful to the National Natural Science Foundation of China (grant No. 20872057) and the Natural Science Foundation of Henan Province (No. 082300420040) for financial support.

supplementary crystallographic information

Comment

2,2'-Bipyrimidine and its derivatives have been used as the ligands in inorganic and organometallic chemistry (Ji et al. 2000; Baumann et al. 1998). On the other hand, the investigations of hydrogen-bonded water clusters in compound have recently attracted a great deal of interest (Buck et al. 2000; Lakshminarayanan et al. 2006). These studies can provided clues to understand the nature of water-water interactions in bulk water or ice (Zhang et al. 2005). In view of the importance of these compound, we herein report the synthesis and crystal structure of the title compound.

The molecule of the title compound (Fig. 1.), is built up form one pyrimidine ring connected to the other pyrimidine ring through the 2 and 2' carbon atoms, in which the bond lengths and angles are within ranges as reported by Berg et al. (2002). In the crystal structure, the four substituent methyl groups lie in the corresponding pyrimidine ring plane, respectively. And, the dihedral angle between the two pyrimidine rings is 5.285 (6)°. It must be pointed out that the striking feature of the title compound is the interesting arrangement of the six water molecules, which connected each other by the formation of intermolecular O—H···O hydrogen bonds, generating the edge-fused four-, five-, or six-membered ring motifs, to form a two-dimensional sheet (Fig.2.). Interestingly, every water O atom in the sheet is tri-coordination, which unlike the water at the surface of ice or in liquid water shows four coordination. Furthermore, the sheets are anchored in four nitrogen atoms of the titlelte molecule by the formation of O—H···N hydrogen bonds, resulting in a three-dimensional network, in which these hydrogen bonding interactions, with O—H···O hydrogen bonds may be effective in the stabilization of the crystal packing. Detail hydrogen bonds are given in Table 1.

Experimental

The title compound was prepared according to the reported Ullmann coupling method (Vlad & Horvath, 2002). Under nitrogen-protected, 4,6-dimethyl-2-iodopyrimidine (351 mg, 1.5 mmol), absolute DMF (2.0 ml) and activated copper powder (508 mg, 8.0 mmol) were placed in a 25 ml flask. The reaction mixture was heated to 358 K with vigorous stirring. After 4 h, 127 mg (2 mmol) of activated copper powder was added to the mixture. After another 3.5 h, the temperature was increased to 398 K and the stirring was continued for 2 h. The suspension was then cooled to 273 K, carefully drowned into a solution of 1.4 g potassium cyanide in 6 ml of 25% aqueous solution of ammonia, and filtered. The solid residue on the filter was extracted with the same amount of cyanide solution and filtered again. The combined filtrates were treated with 58 mg of potassium cyanide and extracted with chloroform (5 times 20 ml). Washed with water and dried. Recrystallization of the crude product from ethyl acetate-petroleum ether gave 81 mg. The crystalline compound was luckily obtained by the reaction of the title compound with NdCl3 under the hydrothermal condition.

Refinement

All H atoms were positioned geometrically and treated as riding, with C—H bond lengths constrained to 0.93 Å (aromatic CH), 0.96 Å (methyl CH3), and 0.83 or 0.84 Å (OH), and with Uĩso(H) = 1.2Ueq(C) or 1.5Ueq(methylene C or OH).

Figures

Fig. 1.
View of the title molecular structure with atom numbering scheme and 30% probability displacement ellipsoids for non-hydrogen atoms.
Fig. 2.
View of the two-dimensional sheet constructed by the lattice water molecules (O—H···O hydrogen bonds are represented as dashed lines).

Crystal data

C12H14N4·6H2OZ = 2
Mr = 322.37F(000) = 348
Triclinic, P1Dx = 1.241 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.8622 (19) ÅCell parameters from 1270 reflections
b = 11.098 (3) Åθ = 1.0–1.0°
c = 11.750 (3) ŵ = 0.10 mm1
α = 98.233 (3)°T = 296 K
β = 91.774 (4)°Block, colourless
γ = 102.599 (4)°0.41 × 0.31 × 0.21 mm
V = 862.4 (4) Å3

Data collection

Bruker APEXII CCD area-detector diffractometer3196 independent reflections
Radiation source: fine-focus sealed tube2026 reflections with I > 2σ(I)
graphiteRint = 0.023
[var phi] and ω scansθmax = 25.5°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −8→8
Tmin = 0.961, Tmax = 0.980k = −13→13
6492 measured reflectionsl = −14→14

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.148w = 1/[σ2(Fo2) + (0.074P)2 + 0.0388P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3196 reflectionsΔρmax = 0.23 e Å3
204 parametersΔρmin = −0.15 e Å3
0 restraintsExtinction correction: SHELXS97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.045 (6)

Special details

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 takeninto account individually in the estimation of e.s.d.'s in distances, anglesand torsion angles; correlations between e.s.d.'s in cell parameters are onlyused 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 andgoodness of fit S are based on F2, conventional R-factors R are basedon F, with F set to zero for negative F2. The threshold expression ofF2 > σ(F2) is used only for calculating R-factors(gt) etc. and isnot relevant to the choice of reflections for refinement. R-factors basedon 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
O11.0078 (2)0.66049 (15)0.38126 (13)0.0642 (5)
H1W0.95760.63410.31420.096*
H2W0.91940.65010.42850.096*
O20.4638 (2)0.32153 (14)0.82784 (13)0.0576 (5)
H3W0.39780.24910.82840.086*
H4W0.55910.33790.87870.086*
O30.1279 (3)0.42962 (14)0.85957 (13)0.0620 (5)
H5W0.04320.39090.89850.093*
H6W0.22260.39520.84930.093*
O40.6255 (3)0.40256 (16)0.62491 (14)0.0672 (5)
H7W0.57770.37900.68460.101*
H8W0.73360.37880.61550.101*
O50.2031 (2)0.66114 (14)1.01180 (14)0.0624 (5)
H9W0.21190.72810.98690.094*
H10W0.18970.60130.95860.094*
O60.7043 (3)0.63916 (16)0.54052 (14)0.0705 (5)
H11W0.60240.64110.50150.106*
H12W0.68440.57440.57100.106*
N10.2840 (3)0.14305 (16)0.99505 (14)0.0417 (4)
N20.2855 (3)0.04691 (15)0.77127 (13)0.0417 (4)
N30.2336 (2)−0.15832 (15)0.82104 (14)0.0403 (4)
N40.2327 (2)−0.06158 (15)1.04606 (14)0.0407 (4)
C10.1870 (4)−0.1038 (2)1.24073 (18)0.0559 (6)
H1A0.0530−0.15351.22640.084*
H1B0.2033−0.05871.31780.084*
H1C0.2801−0.15721.23190.084*
C20.2256 (3)−0.0134 (2)1.15686 (17)0.0414 (5)
C30.2480 (3)0.1139 (2)1.18979 (17)0.0452 (5)
H30.24340.14711.26670.054*
C40.2775 (3)0.19090 (19)1.10592 (17)0.0432 (5)
C50.3011 (4)0.3293 (2)1.1331 (2)0.0632 (7)
H5A0.41900.37041.10020.095*
H5B0.31330.35431.21520.095*
H5C0.18610.35221.10150.095*
C60.2612 (3)0.01975 (18)0.97125 (16)0.0365 (5)
C70.2621 (3)−0.03399 (18)0.84670 (16)0.0363 (5)
C80.1946 (4)−0.3443 (2)0.6791 (2)0.0617 (7)
H8A0.3139−0.36910.70170.093*
H8B0.1661−0.36850.59750.093*
H8C0.0846−0.38450.71890.093*
C90.2245 (3)−0.20604 (19)0.70895 (17)0.0432 (5)
C100.2398 (3)−0.1290 (2)0.62551 (18)0.0496 (6)
H100.2286−0.16250.54770.060*
C110.2719 (3)−0.00161 (19)0.65939 (17)0.0449 (5)
C120.2935 (4)0.0891 (2)0.57525 (19)0.0644 (7)
H12A0.19770.14020.58870.097*
H12B0.27050.04420.49820.097*
H12C0.42620.14130.58490.097*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0689 (12)0.0708 (11)0.0513 (10)0.0119 (9)0.0050 (8)0.0098 (8)
O20.0637 (11)0.0499 (9)0.0589 (10)0.0082 (8)0.0062 (8)0.0138 (8)
O30.0686 (11)0.0632 (11)0.0583 (10)0.0187 (8)0.0111 (8)0.0151 (8)
O40.0691 (12)0.0825 (12)0.0556 (10)0.0191 (9)0.0074 (8)0.0251 (9)
O50.0743 (12)0.0495 (9)0.0617 (10)0.0089 (8)0.0045 (9)0.0101 (8)
O60.0698 (12)0.0794 (12)0.0626 (11)0.0096 (9)0.0030 (9)0.0231 (9)
N10.0440 (10)0.0440 (10)0.0355 (9)0.0073 (8)0.0036 (8)0.0043 (8)
N20.0505 (11)0.0413 (10)0.0332 (9)0.0100 (8)0.0055 (8)0.0052 (8)
N30.0430 (10)0.0412 (10)0.0365 (9)0.0090 (8)0.0047 (8)0.0057 (8)
N40.0407 (10)0.0472 (10)0.0349 (9)0.0105 (8)0.0049 (7)0.0076 (8)
C10.0706 (16)0.0596 (15)0.0415 (13)0.0177 (12)0.0136 (11)0.0141 (11)
C20.0357 (11)0.0537 (13)0.0351 (11)0.0096 (10)0.0038 (9)0.0082 (9)
C30.0448 (13)0.0571 (14)0.0328 (11)0.0124 (10)0.0058 (9)0.0023 (10)
C40.0422 (12)0.0469 (12)0.0387 (12)0.0091 (10)0.0017 (9)0.0021 (9)
C50.0879 (19)0.0528 (15)0.0461 (14)0.0161 (13)0.0047 (13)−0.0024 (11)
C60.0326 (11)0.0438 (12)0.0330 (11)0.0083 (9)0.0031 (8)0.0060 (9)
C70.0317 (10)0.0417 (11)0.0356 (11)0.0079 (9)0.0035 (8)0.0067 (9)
C80.0899 (19)0.0485 (14)0.0475 (14)0.0197 (13)0.0058 (13)0.0033 (11)
C90.0462 (13)0.0427 (12)0.0397 (12)0.0088 (9)0.0047 (9)0.0044 (9)
C100.0640 (15)0.0482 (13)0.0322 (11)0.0072 (11)0.0025 (10)0.0002 (10)
C110.0523 (13)0.0462 (13)0.0361 (11)0.0098 (10)0.0050 (10)0.0078 (9)
C120.103 (2)0.0525 (15)0.0378 (13)0.0139 (14)0.0069 (13)0.0121 (11)

Geometric parameters (Å, °)

O1—H1W0.8358C1—H1B0.9600
O1—H2W0.8355C1—H1C0.9600
O2—H3W0.8334C2—C31.383 (3)
O2—H4W0.8431C3—C41.386 (3)
O3—H5W0.8342C3—H30.9300
O3—H6W0.8269C4—C51.496 (3)
O4—H7W0.8351C5—H5A0.9600
O4—H8W0.8443C5—H5B0.9600
O5—H9W0.8278C5—H5C0.9600
O5—H10W0.8314C6—C71.500 (3)
O6—H11W0.8302C8—C91.492 (3)
O6—H12W0.8353C8—H8A0.9600
N1—C61.330 (2)C8—H8B0.9600
N1—C41.340 (3)C8—H8C0.9600
N2—C71.338 (2)C9—C101.383 (3)
N2—C111.340 (3)C10—C111.379 (3)
N3—C71.339 (2)C10—H100.9300
N3—C91.341 (3)C11—C121.498 (3)
N4—C61.337 (2)C12—H12A0.9600
N4—C21.341 (3)C12—H12B0.9600
C1—C21.493 (3)C12—H12C0.9600
C1—H1A0.9600
H1W—O1—H2W110.2H5A—C5—H5C109.5
H3W—O2—H4W109.0H5B—C5—H5C109.5
H5W—O3—H6W111.2N1—C6—N4126.97 (18)
H7W—O4—H8W108.4N1—C6—C7116.44 (17)
H9W—O5—H10W111.6N4—C6—C7116.57 (18)
H11W—O6—H12W109.9N3—C7—N2126.13 (18)
C6—N1—C4116.54 (17)N3—C7—C6117.13 (17)
C7—N2—C11116.80 (17)N2—C7—C6116.70 (17)
C7—N3—C9116.70 (17)C9—C8—H8A109.5
C6—N4—C2116.31 (18)C9—C8—H8B109.5
C2—C1—H1A109.5H8A—C8—H8B109.5
C2—C1—H1B109.5C9—C8—H8C109.5
H1A—C1—H1B109.5H8A—C8—H8C109.5
C2—C1—H1C109.5H8B—C8—H8C109.5
H1A—C1—H1C109.5N3—C9—C10120.62 (19)
H1B—C1—H1C109.5N3—C9—C8117.30 (18)
N4—C2—C3120.80 (18)C10—C9—C8122.07 (19)
N4—C2—C1116.81 (19)C11—C10—C9118.96 (19)
C3—C2—C1122.37 (19)C11—C10—H10120.5
C2—C3—C4118.69 (19)C9—C10—H10120.5
C2—C3—H3120.7N2—C11—C10120.71 (18)
C4—C3—H3120.7N2—C11—C12116.59 (19)
N1—C4—C3120.68 (19)C10—C11—C12122.71 (19)
N1—C4—C5116.81 (19)C11—C12—H12A109.5
C3—C4—C5122.50 (19)C11—C12—H12B109.5
C4—C5—H5A109.5H12A—C12—H12B109.5
C4—C5—H5B109.5C11—C12—H12C109.5
H5A—C5—H5B109.5H12A—C12—H12C109.5
C4—C5—H5C109.5H12B—C12—H12C109.5
C6—N4—C2—C3−0.3 (3)C11—N2—C7—N32.5 (3)
C6—N4—C2—C1178.04 (18)C11—N2—C7—C6−175.32 (18)
N4—C2—C3—C40.2 (3)N1—C6—C7—N3−178.13 (16)
C1—C2—C3—C4−178.1 (2)N4—C6—C7—N30.3 (3)
C6—N1—C4—C3−0.1 (3)N1—C6—C7—N2−0.1 (3)
C6—N1—C4—C5−179.45 (19)N4—C6—C7—N2178.33 (16)
C2—C3—C4—N10.1 (3)C7—N3—C9—C10−1.4 (3)
C2—C3—C4—C5179.3 (2)C7—N3—C9—C8179.46 (19)
C4—N1—C6—N40.0 (3)N3—C9—C10—C112.3 (3)
C4—N1—C6—C7178.16 (17)C8—C9—C10—C11−178.5 (2)
C2—N4—C6—N10.3 (3)C7—N2—C11—C10−1.4 (3)
C2—N4—C6—C7−177.94 (17)C7—N2—C11—C12178.63 (19)
C9—N3—C7—N2−1.1 (3)C9—C10—C11—N2−0.9 (3)
C9—N3—C7—C6176.71 (17)C9—C10—C11—C12179.1 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1W···O3i0.842.082.914 (2)172
O1—H2W···O60.842.002.837 (2)175
O2—H3W···N20.832.202.995 (2)158
O2—H3W···N10.832.493.083 (2)129
O2—H4W···O5ii0.842.042.872 (2)167
O3—H5W···O5iii0.832.042.847 (2)163
O3—H6W···O20.832.012.832 (2)177
O4—H7W···O20.842.012.841 (2)180
O4—H8W···O1iv0.841.922.755 (2)171
O5—H9W···N4v0.832.313.007 (2)142
O5—H9W···N3v0.832.463.196 (2)149
O5—H10W···O30.832.042.849 (2)166
O6—H11W···O4i0.832.052.851 (2)162
O6—H12W···O40.842.062.886 (2)173

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2743).

References

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Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography