Thymine hydrogen peroxide 0.55-solvate 0.45-hydrate

Churakov, A.V.; Howard, J.A.K.

doi:10.1107/S1600536807053585

Thymine hydrogen peroxide 0.55-solvate 0.45-hydrate

Thymine crystallizes from 50% hydrogen peroxide to give the title hydrogen peroxide water solvate, C₅H₆N₂O₂·0.55H₂O₂·0.45H₂O. The disordered peroxide and water molecules occupy the same positions. Thymine molecules are linked together by N—H

O hydrogen bonds forming chains parallel to the ac diagonal. Hydrogen peroxide molecules are combined by O—H

O hydrogen bonds to give chains parallel to the c axis. Both kinds of chains are organized in a three-dimensional hydrogen-bonded network.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807053585/rz2169sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807053585/rz2169Isup2.hkl Contains datablock I

CCDC reference: 667478

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Key indicators

Single-crystal X-ray study
T = 120 K
Mean (C-C) = 0.002 Å
Disorder in main residue
R factor = 0.045
wR factor = 0.108
Data-to-parameter ratio = 11.8

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No syntax errors found



Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT077_ALERT_4_C Unitcell contains non-integer number of atoms ..          ?
PLAT301_ALERT_3_C Main Residue  Disorder .........................      13.00 Perc.
PLAT432_ALERT_2_C Short Inter X...Y Contact  O2     ..  C2      ..       3.01 Ang.

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          3

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

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.

Related literature top

For general background, see: Adams & Ramdas (1978); Churakov et al. (2005, 2006); Rojkind et al. (2002); Savariault & Lehmann (1980); Serra et al. (1992).

Experimental top

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.

Structure description top

For general background, see: Adams & Ramdas (1978); Churakov et al. (2005, 2006); Rojkind et al. (2002); Savariault & Lehmann (1980); Serra et al. (1992).

Computing details top

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).

Figures top

	Fig. 1. The asymmetric unit of the title compound, showing the numbering scheme adopted. Displacement ellipsoids are shown at the 50% probability level.
	Fig. 2. The hydrogen bonded (dashed lines) chains of thymine molecules in the title compound parallel to the ac diagonal. H atoms not involved in hydrogen bonds are omitted. [Symmetry codes: (i) 1 - x, 1 - y, 2 - z; (ii) -x, 1 - y, 1 - z; (iii) 1 + x, y, 1 + z].
	Fig. 3. The hydrogen bonded (dashed lines) chains of H₂O₂ molecules in the title compound parallel to the c axis. [Symmetry codes: (i) x, 0.5 - y, -0.5 + z; (ii) x, 0.5 - y, 0.5 + z; (iii) x, y, -1 + z].
	Fig. 4. The three-dimensional hydrogen bonded network (dashed lines) in the title compound. H atoms not involved in hydrogen bonds are omitted.

Thymine hydrogen peroxide 0.55-solvate 0.45-hydrate top

Crystal data top

C₅H₆N₂O₂·0.55H₂O₂·0.45H₂O	F(000) = 321.6
M_r = 152.93	D_x = 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

Data collection top

Bruker SMART 1K diffractometer	1733 independent reflections
Radiation source: fine-focus sealed tube	1174 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.038
ω scans	θ_max = 29.0°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2003)	h = −7→8
T_min = 0.974, T_max = 0.987	k = −25→23
4556 measured reflections	l = −6→7

Refinement top

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(F_o²) + (0.0537P)²] where P = (F_o² + 2F_c²)/3
1733 reflections	(Δ/σ)_max < 0.001
147 parameters	Δρ_max = 0.23 e Å⁻³
3 restraints	Δρ_min = −0.24 e Å⁻³

Crystal data top

C₅H₆N₂O₂·0.55H₂O₂·0.45H₂O	V = 658.9 (3) Å³
M_r = 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)°

Data collection top

Bruker SMART 1K diffractometer	1733 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2003)	1174 reflections with I > 2σ(I)
T_min = 0.974, T_max = 0.987	R_int = 0.038
4556 measured reflections

Refinement top

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	Δρ_max = 0.23 e Å⁻³
1733 reflections	Δρ_min = −0.24 e Å⁻³
147 parameters

Special details top

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.

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

	x	y	z	U_iso*/U_eq	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)*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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···O3^iv	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
M_r	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)
T_min, T_max	0.974, 0.987
No. of measured, independent and observed [I > 2σ(I)] reflections	4556, 1733, 1174
R_int	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
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.24

Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2003), SHELXTL (Bruker, 2003).

Hydrogen-bond geometry (Å, º) top

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···O3^iv	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.

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