


Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807053585/rz2169sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S1600536807053585/rz2169Isup2.hkl |
CCDC reference: 667478
The crystals of the title compound were obtained by cooling down to -18° a saturated solution of thymine in 50% hydrogen peroxide. The experimental data were measured at 120 K due to the instability of the compound at ambient conditions.
All hydrogen atoms were located in a difference Fourier map. The hydrogen peroxide H1 and H2 atoms were refined with the same Uiso and the H1—O1 and H2—O2 distances restrained to be approximately equal (SADI instruction in XL software). The water hydrogen atoms H3 and H4 were also refined with the same Uiso and the H3—O12 and H4—O12 distances restrained (SADI).
Hydrogen bonding plays the main role in forming crystals of peroxosolvates. It was supposed that it might be possible to design stable hydrogen peroxide carriers by maximizing the number of hydrogen bonds in the structure (Adams & Ramdas, 1978). Moreover, hydrogen peroxide complexes are of great importance for various biochemical processes (Rojkind et al., 2002). Previously, the structure of adenine hydrogen peroxide adduct was determined (Serra et al., 1992). Herein we report the structure of the title compound as part of our study of organic hydrogen peroxide solvates (Churakov et al., 2005, 2006).
In the structure of the title compound, thymine molecules exhibit the expected planar molecular geometry (Fig. 1). Centrosymmetrically related thymine molecules are linked together by N1—H11···O3 and N2—H21···O3 (Table 1) hydrogen bonds forming chains parallel to ac diagonal (Fig. 2).
The H2O2 molecule has a skew conformation with H—O—O—H torsion angle equal to 113 (4)°. The O—O bond length (1.453 (4) Å) is somewhat shorter than that observed in crystalline hydrogen peroxide (1.461 (3) Å; Savariault & Lehmann, 1980). The disordered peroxide and water molecules occupy the same positions in the crystal lattice. A similar disorder was observed in the structures of hydrogen peroxide water solvates of PPh4+ and AsPh4+ halides (Churakov et al., 2005). Hydrogen peroxide molecules are combined by strong O2—H2···O1 hydrogen bonds to give chains parallel to the c axis.
Both kinds of chains are organized in a three-dimensional network by peroxide–thymine O1—H1···O4 interactions (Fig. 4). Thus, the H2O2 molecule is involved in three hydrogen bonds with adjacent molecules, forming two donor and one acceptor interactions. The inclusion of the disordered water molecule does not break the packing motif while it forms three somewhat longer hydrogen bonds with the same neighbouring molecules.
For general background, see: Adams & Ramdas (1978); Churakov et al. (2005, 2006); Rojkind et al. (2002); Savariault & Lehmann (1980); Serra et al. (1992).
Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SHELXTL (Bruker, 2003); program(s) used to refine structure: SHELXTL (Bruker, 2003); molecular graphics: SHELXTL (Bruker, 2003); software used to prepare material for publication: SHELXTL (Bruker, 2003).
C5H6N2O2·0.55H2O2·0.45H2O | F(000) = 321.6 |
Mr = 152.93 | Dx = 1.542 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1539 reflections |
a = 6.5047 (16) Å | θ = 3.3–29.5° |
b = 19.194 (5) Å | µ = 0.13 mm−1 |
c = 5.6190 (13) Å | T = 120 K |
β = 110.078 (5)° | Prism, colourless |
V = 658.9 (3) Å3 | 0.20 × 0.20 × 0.10 mm |
Z = 4 |
Bruker SMART 1K diffractometer | 1733 independent reflections |
Radiation source: fine-focus sealed tube | 1174 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.038 |
ω scans | θmax = 29.0°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2003) | h = −7→8 |
Tmin = 0.974, Tmax = 0.987 | k = −25→23 |
4556 measured reflections | l = −6→7 |
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)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.108 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0537P)2] where P = (Fo2 + 2Fc2)/3 |
1733 reflections | (Δ/σ)max < 0.001 |
147 parameters | Δρmax = 0.23 e Å−3 |
3 restraints | Δρmin = −0.24 e Å−3 |
C5H6N2O2·0.55H2O2·0.45H2O | V = 658.9 (3) Å3 |
Mr = 152.93 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.5047 (16) Å | µ = 0.13 mm−1 |
b = 19.194 (5) Å | T = 120 K |
c = 5.6190 (13) Å | 0.20 × 0.20 × 0.10 mm |
β = 110.078 (5)° |
Bruker SMART 1K diffractometer | 1733 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2003) | 1174 reflections with I > 2σ(I) |
Tmin = 0.974, Tmax = 0.987 | Rint = 0.038 |
4556 measured reflections |
R[F2 > 2σ(F2)] = 0.045 | 3 restraints |
wR(F2) = 0.108 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.23 e Å−3 |
1733 reflections | Δρmin = −0.24 e Å−3 |
147 parameters |
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 taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used 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 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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
N1 | 0.5189 (2) | 0.43892 (7) | 0.7551 (3) | 0.0193 (3) | |
N2 | 0.1954 (2) | 0.43931 (7) | 0.4159 (2) | 0.0201 (3) | |
O3 | 0.22793 (17) | 0.50240 (5) | 0.77214 (19) | 0.0214 (3) | |
O4 | 0.81449 (18) | 0.37725 (6) | 0.7577 (2) | 0.0269 (3) | |
C1 | 0.3077 (2) | 0.46216 (7) | 0.6531 (3) | 0.0180 (3) | |
C2 | 0.2878 (3) | 0.39447 (8) | 0.2885 (3) | 0.0206 (3) | |
C3 | 0.4944 (2) | 0.37063 (7) | 0.3883 (3) | 0.0187 (3) | |
C4 | 0.6227 (2) | 0.39384 (7) | 0.6405 (3) | 0.0192 (3) | |
C5 | 0.5985 (3) | 0.32256 (9) | 0.2523 (3) | 0.0239 (4) | |
O1 | 0.0489 (5) | 0.26290 (15) | 0.7488 (6) | 0.0323 (7) | 0.55 |
O2 | 0.2145 (5) | 0.29347 (15) | 0.6611 (7) | 0.0320 (7) | 0.55 |
H1 | −0.040 (7) | 0.302 (2) | 0.740 (9) | 0.057 (11)* | 0.55 |
H2 | 0.183 (8) | 0.269 (2) | 0.503 (8) | 0.057 (11)* | 0.55 |
O12 | 0.1421 (8) | 0.2877 (2) | 0.7417 (7) | 0.0324 (8) | 0.45 |
H3 | 0.041 (10) | 0.320 (2) | 0.711 (10) | 0.049 (13)* | 0.45 |
H4 | 0.124 (11) | 0.269 (3) | 0.592 (10) | 0.049 (13)* | 0.45 |
H22 | 0.191 (3) | 0.3837 (9) | 0.119 (3) | 0.025 (5)* | |
H53 | 0.501 (3) | 0.3136 (9) | 0.082 (4) | 0.030 (5)* | |
H52 | 0.638 (3) | 0.2786 (10) | 0.342 (4) | 0.032 (5)* | |
H11 | 0.590 (3) | 0.4559 (10) | 0.893 (4) | 0.031 (5)* | |
H51 | 0.738 (3) | 0.3440 (10) | 0.241 (3) | 0.029 (5)* | |
H21 | 0.055 (4) | 0.4561 (11) | 0.337 (4) | 0.043 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0163 (6) | 0.0200 (6) | 0.0183 (7) | 0.0007 (5) | 0.0018 (5) | −0.0030 (5) |
N2 | 0.0142 (6) | 0.0223 (6) | 0.0207 (7) | 0.0020 (5) | 0.0020 (5) | −0.0018 (5) |
O3 | 0.0169 (6) | 0.0230 (6) | 0.0224 (6) | 0.0026 (4) | 0.0044 (5) | −0.0034 (4) |
O4 | 0.0182 (6) | 0.0316 (6) | 0.0263 (6) | 0.0081 (5) | 0.0016 (5) | −0.0019 (5) |
C1 | 0.0152 (7) | 0.0163 (7) | 0.0205 (8) | −0.0012 (5) | 0.0036 (6) | 0.0014 (6) |
C2 | 0.0204 (8) | 0.0218 (7) | 0.0190 (8) | −0.0010 (6) | 0.0059 (6) | −0.0007 (6) |
C3 | 0.0205 (8) | 0.0170 (7) | 0.0196 (8) | −0.0012 (6) | 0.0081 (6) | 0.0001 (6) |
C4 | 0.0188 (7) | 0.0171 (7) | 0.0223 (8) | 0.0018 (6) | 0.0079 (6) | 0.0034 (6) |
C5 | 0.0241 (8) | 0.0241 (8) | 0.0237 (9) | 0.0028 (7) | 0.0082 (7) | 0.0000 (7) |
O1 | 0.0287 (15) | 0.0302 (15) | 0.0441 (17) | 0.0045 (12) | 0.0201 (14) | 0.0113 (12) |
O2 | 0.0252 (15) | 0.0292 (14) | 0.0436 (19) | −0.0035 (11) | 0.0143 (14) | 0.0008 (12) |
O12 | 0.026 (2) | 0.037 (2) | 0.032 (2) | 0.0122 (18) | 0.0064 (18) | −0.0006 (17) |
N1—C1 | 1.3689 (19) | C3—C4 | 1.446 (2) |
N1—C4 | 1.385 (2) | C3—C5 | 1.500 (2) |
N1—H11 | 0.82 (2) | C5—H53 | 0.965 (19) |
N2—C1 | 1.3544 (19) | C5—H52 | 0.972 (19) |
N2—C2 | 1.382 (2) | C5—H51 | 1.016 (19) |
N2—H21 | 0.93 (2) | O1—O2 | 1.453 (4) |
O3—C1 | 1.2453 (18) | O1—H1 | 0.93 (4) |
O4—C4 | 1.2361 (18) | O2—H2 | 0.97 (4) |
C2—C3 | 1.346 (2) | O12—H3 | 0.87 (5) |
C2—H22 | 0.968 (18) | O12—H4 | 0.89 (5) |
C1—N1—C4 | 126.05 (14) | C4—C3—C5 | 118.65 (14) |
C1—N1—H11 | 115.0 (14) | O4—C4—N1 | 118.51 (14) |
C4—N1—H11 | 118.8 (14) | O4—C4—C3 | 125.46 (14) |
C1—N2—C2 | 121.90 (13) | N1—C4—C3 | 116.03 (13) |
C1—N2—H21 | 118.0 (13) | C3—C5—H53 | 111.0 (11) |
C2—N2—H21 | 120.0 (13) | C3—C5—H52 | 110.7 (11) |
O3—C1—N2 | 123.11 (13) | H53—C5—H52 | 109.1 (15) |
O3—C1—N1 | 121.37 (14) | C3—C5—H51 | 110.4 (10) |
N2—C1—N1 | 115.51 (14) | H53—C5—H51 | 107.8 (14) |
C3—C2—N2 | 123.03 (15) | H52—C5—H51 | 107.7 (16) |
C3—C2—H22 | 123.9 (10) | O2—O1—H1 | 100 (3) |
N2—C2—H22 | 113.0 (10) | O1—O2—H2 | 99 (2) |
C2—C3—C4 | 117.47 (14) | H3—O12—H4 | 105 (5) |
C2—C3—C5 | 123.88 (14) | ||
C2—N2—C1—O3 | −179.79 (14) | C1—N1—C4—O4 | −179.59 (14) |
C2—N2—C1—N1 | 1.2 (2) | C1—N1—C4—C3 | 1.0 (2) |
C4—N1—C1—O3 | 179.41 (14) | C2—C3—C4—O4 | −179.46 (15) |
C4—N1—C1—N2 | −1.5 (2) | C5—C3—C4—O4 | −0.2 (2) |
C1—N2—C2—C3 | −0.4 (2) | C2—C3—C4—N1 | −0.1 (2) |
N2—C2—C3—C4 | −0.1 (2) | C5—C3—C4—N1 | 179.10 (14) |
N2—C2—C3—C5 | −179.33 (14) | H1—O1—O2—H2 | −113 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O4i | 0.93 (4) | 1.75 (4) | 2.683 (3) | 173 (5) |
O12—H3···O4i | 0.87 (5) | 1.93 (5) | 2.764 (4) | 160 (5) |
O2—H2···O1ii | 0.97 (4) | 1.52 (4) | 2.446 (5) | 159 (4) |
O12—H4···O1ii | 0.89 (5) | 1.92 (5) | 2.798 (5) | 172 (6) |
N1—H11···O3iii | 0.82 (2) | 2.01 (2) | 2.8347 (18) | 178.1 (18) |
N2—H21···O3iv | 0.93 (2) | 1.90 (2) | 2.8204 (18) | 170.3 (18) |
Symmetry codes: (i) x−1, y, z; (ii) x, −y+1/2, z−1/2; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H6N2O2·0.55H2O2·0.45H2O |
Mr | 152.93 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 6.5047 (16), 19.194 (5), 5.6190 (13) |
β (°) | 110.078 (5) |
V (Å3) | 658.9 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.20 × 0.20 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART 1K |
Absorption correction | Multi-scan (SADABS; Bruker, 2003) |
Tmin, Tmax | 0.974, 0.987 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4556, 1733, 1174 |
Rint | 0.038 |
(sin θ/λ)max (Å−1) | 0.682 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.108, 1.02 |
No. of reflections | 1733 |
No. of parameters | 147 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.24 |
Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2003), SHELXTL (Bruker, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O4i | 0.93 (4) | 1.75 (4) | 2.683 (3) | 173 (5) |
O12—H3···O4i | 0.87 (5) | 1.93 (5) | 2.764 (4) | 160 (5) |
O2—H2···O1ii | 0.97 (4) | 1.52 (4) | 2.446 (5) | 159 (4) |
O12—H4···O1ii | 0.89 (5) | 1.92 (5) | 2.798 (5) | 172 (6) |
N1—H11···O3iii | 0.82 (2) | 2.01 (2) | 2.8347 (18) | 178.1 (18) |
N2—H21···O3iv | 0.93 (2) | 1.90 (2) | 2.8204 (18) | 170.3 (18) |
Symmetry codes: (i) x−1, y, z; (ii) x, −y+1/2, z−1/2; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+1. |
Hydrogen bonding plays the main role in forming crystals of peroxosolvates. It was supposed that it might be possible to design stable hydrogen peroxide carriers by maximizing the number of hydrogen bonds in the structure (Adams & Ramdas, 1978). Moreover, hydrogen peroxide complexes are of great importance for various biochemical processes (Rojkind et al., 2002). Previously, the structure of adenine hydrogen peroxide adduct was determined (Serra et al., 1992). Herein we report the structure of the title compound as part of our study of organic hydrogen peroxide solvates (Churakov et al., 2005, 2006).
In the structure of the title compound, thymine molecules exhibit the expected planar molecular geometry (Fig. 1). Centrosymmetrically related thymine molecules are linked together by N1—H11···O3 and N2—H21···O3 (Table 1) hydrogen bonds forming chains parallel to ac diagonal (Fig. 2).
The H2O2 molecule has a skew conformation with H—O—O—H torsion angle equal to 113 (4)°. The O—O bond length (1.453 (4) Å) is somewhat shorter than that observed in crystalline hydrogen peroxide (1.461 (3) Å; Savariault & Lehmann, 1980). The disordered peroxide and water molecules occupy the same positions in the crystal lattice. A similar disorder was observed in the structures of hydrogen peroxide water solvates of PPh4+ and AsPh4+ halides (Churakov et al., 2005). Hydrogen peroxide molecules are combined by strong O2—H2···O1 hydrogen bonds to give chains parallel to the c axis.
Both kinds of chains are organized in a three-dimensional network by peroxide–thymine O1—H1···O4 interactions (Fig. 4). Thus, the H2O2 molecule is involved in three hydrogen bonds with adjacent molecules, forming two donor and one acceptor interactions. The inclusion of the disordered water molecule does not break the packing motif while it forms three somewhat longer hydrogen bonds with the same neighbouring molecules.