The first mol­ecular structure containing four hydro­peroxo groups: piperazine-2,3,5,6-tetrayl tetra­hydro­peroxide pyrazine disolvate dihydrate

Churakov, A.V.; Kuz'mina, L.G.; Prikhodchenko, P.V.; Howard, J.A.K.

doi:10.1107/S1600536806016485

organic compounds

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ISSN: 2056-9890

Volume 62| Part 6| June 2006| Pages o2265-o2267

https://doi.org/10.1107/S1600536806016485

The first molecular structure containing four hydroperoxo groups: piperazine-2,3,5,6-tetrayl tetrahydroperoxide pyrazine disolvate dihydrate

Andrei V. Churakov,^a ^* Lyudmila G. Kuz'mina,^a Petr V. Prikhodchenko ^a and Judith A. K. Howard ^b

^aN. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Science, 31 Leninskii prospect, Moscow 119991, Russian Federation, and ^bDepartment of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, England
^*Correspondence e-mail: churakov@igic.ras.ru

(Received 21 April 2006; accepted 4 May 2006; online 10 May 2006)

The reaction of pyrazine with hydrogen peroxide resulted in piperazine-2,3,5,6-tetrayl tetrahydroperoxide, crystallizing as its pyrazine disolvate dihydrate, C₄H₁₀N₂O₈·2C₄H₄N₂·2H₂O. In the crystal structure, the tetraperoxo molecules, which possess a crystallographically imposed centre of symmetry, are linked into a three-dimensional network by hydrogen-bonding interactions involving the pyrazine and water molecules.

Comment

Peroxo derivatives of organic compounds attract particular interest as environmentally friendly bleaching compounds and oxidation agents in organic synthesis (Marwah et al., 2004 ). As part of our study of organic hydrogen peroxide solvates (Churakov et al., 2004 , 2005 ), we tried to investigate the behaviour of small organic donor molecules, such as pyrazine or pyrimidine, in concentrated H₂O₂ solutions. The unexpected title compound, (I), was formed upon freezing of a pyrazine solution in 50% hydrogen peroxide. The nature of this process remains unclear. The centrosymmetric molecule of (I) (Fig. 1) contains four hydroperoxo substituents. The piperazine ring adopts a chair conformation and all hydroperoxo groups occupy axial positions. Atom N3 is slightly flattened, the sum of valence angles around it being 346.0°. The O—O bond lengths [1.470 (1) and 1.471 (1) Å] are somewhat longer than the mean value of 1.462 Å found for related compounds (85 entries, 106 fragments) in the Cambridge Structural Database (CSD, Version 5.27 of January 2006; Allen, 2002 ).

The hydroperoxo atom O3 acts as both donor (for symmetry-related) molecules and acceptor (for water molecules) of hydrogen bonds, forming layers perpendicular to the c axis (Fig. 2). Pyrazine molecules accept hydrogen bonds from the peroxo O4 and water O5 atoms, cross-linking the layers of the main molecules into a three-dimensional network (Fig. 3).

To date, the CSD contains structures of compounds with no more than two hydroperoxo groups. The title compound is the first example of a molecular structure containing four OOH substituents. To the best of our knowledge, (I) is one of the most rich in oxygen organic molecules.

Figure 1
The molecular structure of the tetraperoxo molecule of (I)

, showing 50% probability displacement ellipsoids [symmetry code: (i) 1 − y, 2 − x, 2 − z].

Figure 2
The hydrogen-bonded (dashed lines) layer in (I)

perpendicular to the c axis. H atoms not involved in hydrogen bonds have been omitted for clarity.

Figure 3
The crystal packing of (I)

, viewed approximately along the a axis. Hydrogen bonds are shown as dashed lines. H atoms not involved in hydrogen bonds have been omitted for clarity.

Experimental

Pyrazine (99%) and 50% hydrogen peroxide were purchased from Aldrich. Pyrazine (0.03 g) was dissolved in approximately 1 ml of 50% H₂O₂. This solution was stored in a freezer at 255 K. After six months, several tiny crystals were found on the wall of a sample bottle. The amount of crystalline material was not enough to investigate it with usual spectroscopic methods. In order to analyse the mother liquor by NMR, it was evaporated in vacuum and the residual oil was dissolved in D₂O. Unfortunately, the recorded ¹H and ¹³C spectra of this complex mixture were non-interpretable.

Crystal data

C₄H₁₀N₂O₈·2C₄H₄N₂·2H₂O
M_r = 410.36
Triclinic, $[P \overline 1]$
a = 6.1538 (6) Å
b = 7.3047 (8) Å
c = 10.3364 (12) Å
α = 97.729 (3)°
β = 95.974 (4)°
γ = 91.417 (3)°
V = 457.56 (9) Å³
Z = 1
D_x = 1.489 Mg m⁻³
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 120 (2) K
Needle, colourless
0.25 × 0.04 × 0.03 mm

Data collection

Bruker SMART 6K diffractometer
ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 1997 ) T_min = 0.968, T_max = 0.996
2645 measured reflections
2162 independent reflections
1710 reflections with I > 2σ(I)
R_int = 0.012
θ_max = 28.0°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.090
S = 0.99
2162 reflections
170 parameters
All H-atom parameters refined
w = 1/[σ²(F_o²) + (0.0248P)² + 0.2345P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H41⋯N1ⁱ	0.88 (2)	1.88 (2)	2.7573 (18)	176.2 (18)
O3—H31⋯O5ⁱⁱ	0.88 (2)	1.74 (2)	2.6068 (16)	168.2 (19)
N3—H32⋯O3ⁱⁱⁱ	0.83 (2)	2.17 (2)	2.9985 (16)	178.1 (17)
O5—H51⋯N2	0.88 (3)	1.97 (3)	2.8483 (19)	177 (2)
O5—H52⋯N3^iv	0.86 (3)	2.14 (3)	2.9648 (18)	160 (2)
Symmetry codes: (i) x-1, y, z; (ii) x, y+1, z+1; (iii) -x, -y+2, -z+2; (iv) x, y, z-1.

All H atoms were located in a difference Fourier map and refined isotropically.

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (Bruker, 2000 ); software used to prepare material for publication: SHELXTL-Plus.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536806016485/rz2031sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806016485/rz2031Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (Bruker, 2000); software used to prepare material for publication: SHELXTL-Plus.

piperazine-2,3,5,6-tetrayl tetrahydroperoxide pyrazine disolvate dihydrate top

Crystal data top

C₄H₁₀N₂O₈·2C₄H₄N₂·2H₂O	Z = 1
M_r = 410.36	F(000) = 216
Triclinic, P1	D_x = 1.489 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.1538 (6) Å	Cell parameters from 1131 reflections
b = 7.3047 (8) Å	θ = 2.8–30.5°
c = 10.3364 (12) Å	µ = 0.13 mm⁻¹
α = 97.729 (3)°	T = 120 K
β = 95.974 (4)°	Needle, colourless
γ = 91.417 (3)°	0.25 × 0.04 × 0.03 mm
V = 457.56 (9) Å³

Data collection top

Bruker SMART 6K diffractometer	2162 independent reflections
Radiation source: fine-focus sealed tube	1710 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.012
ω scans	θ_max = 28.0°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 1997)	h = −8→7
T_min = 0.968, T_max = 0.996	k = −9→9
2645 measured reflections	l = −13→11

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)] = 0.037	Hydrogen site location: difference Fourier map
wR(F²) = 0.090	All H-atom parameters refined
S = 0.99	w = 1/[σ²(F_o²) + (0.0248P)² + 0.2345P] where P = (F_o² + 2F_c²)/3
2162 reflections	(Δ/σ)_max < 0.001
170 parameters	Δρ_max = 0.31 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

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
N1	1.1231 (2)	0.79178 (18)	0.50775 (13)	0.0261 (3)
N2	0.7499 (2)	0.63944 (18)	0.35086 (14)	0.0290 (3)
C1	0.9426 (3)	0.7464 (2)	0.55999 (16)	0.0281 (3)
C2	0.7583 (3)	0.6716 (2)	0.48149 (18)	0.0299 (4)
C3	1.1158 (3)	0.7607 (2)	0.37735 (15)	0.0256 (3)
C4	0.9304 (3)	0.6850 (2)	0.29966 (16)	0.0272 (3)
N3	0.32175 (19)	0.87876 (16)	0.97556 (12)	0.0182 (3)
C5	0.3104 (2)	1.03857 (19)	1.07043 (14)	0.0176 (3)
C6	0.4605 (2)	0.88510 (19)	0.87366 (14)	0.0182 (3)
O1	0.36537 (16)	1.00211 (14)	0.78281 (10)	0.0218 (2)
O2	0.19076 (15)	1.17748 (13)	1.00797 (10)	0.0200 (2)
O3	0.11802 (16)	1.30694 (14)	1.11516 (11)	0.0228 (2)
O4	0.47963 (18)	0.96406 (16)	0.66468 (11)	0.0265 (3)
O5	0.4042 (2)	0.58225 (17)	0.14218 (13)	0.0325 (3)
H1	0.940 (3)	0.768 (3)	0.651 (2)	0.033 (5)*
H2	0.628 (3)	0.643 (3)	0.519 (2)	0.040 (5)*
H3	1.240 (3)	0.794 (2)	0.3417 (18)	0.027 (5)*
H4	0.929 (3)	0.668 (2)	0.2075 (19)	0.029 (5)*
H51	0.508 (4)	0.600 (4)	0.209 (3)	0.068 (8)*
H52	0.412 (4)	0.661 (4)	0.088 (3)	0.061 (7)*
H5	0.230 (3)	1.008 (2)	1.1425 (16)	0.017 (4)*
H6	0.469 (2)	0.764 (2)	0.8258 (15)	0.012 (4)*
H32	0.202 (3)	0.826 (3)	0.9490 (18)	0.026 (5)*
H31	0.211 (3)	1.400 (3)	1.1126 (19)	0.034 (5)*
H41	0.369 (3)	0.907 (3)	0.612 (2)	0.034*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0255 (7)	0.0265 (7)	0.0251 (7)	0.0008 (5)	−0.0012 (5)	0.0022 (5)
N2	0.0236 (7)	0.0254 (7)	0.0367 (8)	0.0001 (5)	−0.0034 (6)	0.0042 (6)
C1	0.0340 (9)	0.0272 (8)	0.0236 (8)	0.0036 (6)	0.0055 (6)	0.0028 (6)
C2	0.0250 (8)	0.0265 (8)	0.0399 (9)	0.0009 (6)	0.0086 (7)	0.0064 (7)
C3	0.0248 (8)	0.0268 (8)	0.0255 (8)	−0.0005 (6)	0.0023 (6)	0.0050 (6)
C4	0.0304 (8)	0.0271 (8)	0.0234 (8)	0.0025 (6)	−0.0017 (6)	0.0043 (6)
N3	0.0118 (5)	0.0184 (6)	0.0227 (6)	−0.0051 (4)	−0.0016 (4)	0.0009 (5)
C5	0.0131 (6)	0.0187 (6)	0.0204 (7)	−0.0018 (5)	−0.0004 (5)	0.0030 (5)
C6	0.0150 (6)	0.0171 (6)	0.0211 (7)	−0.0023 (5)	−0.0014 (5)	0.0008 (5)
O1	0.0198 (5)	0.0249 (5)	0.0203 (5)	0.0018 (4)	−0.0001 (4)	0.0034 (4)
O2	0.0163 (5)	0.0197 (5)	0.0228 (5)	0.0014 (4)	−0.0007 (4)	0.0007 (4)
O3	0.0166 (5)	0.0204 (5)	0.0303 (6)	−0.0018 (4)	0.0050 (4)	−0.0025 (4)
O4	0.0209 (5)	0.0369 (6)	0.0208 (5)	−0.0035 (5)	0.0015 (4)	0.0024 (4)
O5	0.0359 (7)	0.0268 (6)	0.0327 (7)	−0.0132 (5)	−0.0085 (5)	0.0082 (5)

Geometric parameters (Å, º) top

N1—C3	1.332 (2)	C5—O2	1.4502 (16)
N1—C1	1.338 (2)	C5—C6ⁱ	1.5286 (19)
N2—C4	1.333 (2)	C5—H5	0.984 (16)
N2—C2	1.334 (2)	C6—O1	1.4427 (17)
C1—C2	1.379 (2)	C6—C5ⁱ	1.5286 (19)
C1—H1	0.932 (19)	C6—H6	0.958 (16)
C2—H2	0.95 (2)	O1—O4	1.4695 (14)
C3—C4	1.382 (2)	O2—O3	1.4713 (14)
C3—H3	0.924 (18)	O3—H31	0.88 (2)
C4—H4	0.943 (19)	O4—H41	0.88 (2)
N3—C5	1.4281 (18)	O5—H51	0.88 (3)
N3—C6	1.4279 (18)	O5—H52	0.86 (3)
N3—H32	0.83 (2)

C3—N1—C1	116.91 (14)	N3—C5—O2	108.69 (11)
C4—N2—C2	116.13 (14)	N3—C5—C6ⁱ	110.81 (11)
N1—C1—C2	121.06 (15)	O2—C5—C6ⁱ	110.11 (11)
N1—C1—H1	119.6 (12)	N3—C5—H5	110.3 (10)
C2—C1—H1	119.4 (12)	O2—C5—H5	107.5 (9)
N2—C2—C1	122.40 (15)	C6ⁱ—C5—H5	109.3 (10)
N2—C2—H2	116.8 (13)	N3—C6—O1	108.62 (11)
C1—C2—H2	120.8 (13)	N3—C6—C5ⁱ	111.10 (12)
N1—C3—C4	121.54 (15)	O1—C6—C5ⁱ	109.50 (11)
N1—C3—H3	116.6 (12)	N3—C6—H6	110.2 (9)
C4—C3—H3	121.9 (12)	O1—C6—H6	107.5 (9)
N2—C4—C3	121.95 (15)	C5ⁱ—C6—H6	109.8 (9)
N2—C4—H4	118.5 (11)	C6—O1—O4	105.82 (9)
C3—C4—H4	119.5 (11)	C5—O2—O3	106.00 (9)
C5—N3—C6	119.31 (11)	O2—O3—H31	98.2 (12)
C5—N3—H32	113.8 (12)	O1—O4—H41	97.7 (12)
C6—N3—H32	112.9 (12)	H51—O5—H52	113 (2)

C3—N1—C1—C2	−0.2 (2)	C6—N3—C5—C6ⁱ	−49.07 (18)
C4—N2—C2—C1	−0.5 (2)	C5—N3—C6—O1	−71.31 (15)
N1—C1—C2—N2	0.5 (3)	C5—N3—C6—C5ⁱ	49.20 (18)
C1—N1—C3—C4	0.0 (2)	N3—C6—O1—O4	−165.20 (10)
C2—N2—C4—C3	0.2 (2)	C5ⁱ—C6—O1—O4	73.31 (12)
N1—C3—C4—N2	0.0 (2)	N3—C5—O2—O3	160.69 (10)
C6—N3—C5—O2	72.06 (15)	C6ⁱ—C5—O2—O3	−77.76 (12)

Symmetry code: (i) −x+1, −y+2, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O4—H41···N1ⁱⁱ	0.88 (2)	1.88 (2)	2.7573 (18)	176.2 (18)
O3—H31···O5ⁱⁱⁱ	0.88 (2)	1.74 (2)	2.6068 (16)	168.2 (19)
N3—H32···O3^iv	0.83 (2)	2.17 (2)	2.9985 (16)	178.1 (17)
O5—H51···N2	0.88 (3)	1.97 (3)	2.8483 (19)	177 (2)
O5—H52···N3^v	0.86 (3)	2.14 (3)	2.9648 (18)	160 (2)

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

Acknowledgements

AVC is grateful to the Russian Science Support Foundation.

References

Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Bruker (2000). SHELXTL-Plus. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Churakov, A. V., Prikhodchenko, P. V. & Howard, J. A. K. (2005). CrystEngComm, 7, 664–669. Web of Science CSD CrossRef CAS Google Scholar
Churakov, A. V., Prikhodchenko, P. V., Kuz'mina, L. G. & Howard, J. A. K. (2004). Chem. Listy, 98, s43–s44. Google Scholar
Marwah, P., Marwah, A. & Lardy, H. A. (2004). Green Chem. 6, 570–577. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (1997). SADABS, SHELXS97 and SHELXL97. University of Göttingen, Germany. Google Scholar

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