Bis(4,6-diamino­pyrimidin-2-yl) disulfide dimethyl sufoxide disolvate

Papastavrou, E.; Shakhatreh, S.; Akrivos, P.D.; Gdaniec, M.

doi:10.1107/S160053680802480X

organic compounds

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Volume 64| Part 9| September 2008| Page o1724

doi:10.1107/S160053680802480X

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Bis(4,6-diaminopyrimidin-2-yl) disulfide dimethyl sufoxide disolvate

Ephthymia Papastavrou,^a Saleh Shakhatreh,^b Pericles D. Akrivos ^a and Maria Gdaniec ^c ^*

^aDepartment of Chemistry, Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece, ^bAl Huson University College, Al Balqa' Applied University, Al-Huson, Jordan, and ^cFaculty of Chemistry, Adam Mickiewicz University, 60-780 Poznań, Poland
^*Correspondence e-mail: magdan@amu.edu.pl

(Received 31 July 2008; accepted 1 August 2008; online 9 August 2008)

The title compound, C₈H₁₀N₈S₂·2C₂H₆SO, was obtained unintentionally during an attempt to prepare a thiolate derivative of trimethyltin. The complete disulfide molecule is generated by twofold rotation symmetry and the C—S—S—C torsion angle around the S—S bond is −85.70 (10)°. The molecules are connected via N—H⋯N hydrogen bonds into strongly corrugated layers parallel to (001), generating an R₂²(8) motif. The solvent molecule, which exhibits minor disorder of its S atom [site occupancies = 0.9591 (18) and 0.0409 (18)], is linked to this layer via a pair of N—H⋯O interactions.

Related literature

For information on the preferred conformations of organic disulfides, see: Sączewski et al. (2006 ).

Experimental

Crystal data

C₈H₁₀N₈S₂·2C₂H₆OS
M_r = 438.62
Orthorhombic, P c c n
a = 11.2612 (4) Å
b = 11.9948 (5) Å
c = 15.0754 (6) Å
V = 2036.32 (14) Å³
Z = 4
Mo Kα radiation
μ = 0.49 mm⁻¹
T = 130 (2) K
0.40 × 0.10 × 0.10 mm

Data collection

Kuma KM-4-CCD κ geometry diffractometer
Absorption correction: none
17524 measured reflections
2240 independent reflections
1944 reflections with I > 2σ(I)
R_int = 0.035

Refinement

R[F² > 2σ(F²)] = 0.029
wR(F²) = 0.078
S = 1.04
2240 reflections
146 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N7—H7A⋯O1ⁱ	0.78 (2)	2.20 (2)	2.959 (2)	165 (2)
N7—H7B⋯N1ⁱⁱ	0.846 (19)	2.33 (2)	3.169 (2)	175.1 (16)
N8—H8A⋯O1ⁱⁱⁱ	0.84 (2)	2.09 (2)	2.9109 (19)	164.4 (18)
N8—H8B⋯N3^iv	0.81 (2)	2.33 (2)	3.088 (2)	156.8 (19)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y, z-{\script{1\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iv) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CrysAlis CCD (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, Oxfordshire, England.]$ ); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, Oxfordshire, England.]$ ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989 ) and Mercury (Macrae et al., 2006 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680802480X/hb2773sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053680802480X/hb2773Isup2.hkl

checkCIF report

Comment top

The title compound, (I), is shown in Fig. 1. In the crystal it adopts a chiral conformation of C₂ symmetry with the torsion angle around the S–S bond of -85.70 (10)°. The S–S bond length of 2.0249 (7) Å is typical of disulfides in a screw conformation (Sączewski et al., 2006). In turn the torsion angle of -8.23 (13)° around the C–S bond shows that the disulfide S atoms are situated close to the pyrimidine plane.

The component molecules of (I) are connected via weak N—H···N interactions generating R₂²(8) hydrogen-bond motif into strongly corrugated layer parallel to (001) (Fig. 2, Table 1). The solvent molecules, which exhibit minor disorder of their S atoms, join to this layer via a pair of N—H···O interactions and thus all N–H donors are involved in hydrogen bonding. Crystal packing in the title compound is shown in Fig. 3.

Related literature top

For information on the preferred conformations of organic disulfides, see: Sączewski et al. (2006).

Experimental top

1 mmol of 4,6-diaminopyrimidine-2-thiol was dissolved in 10 ml of DMSO at room temperature and was neutralized by the addition of 1 ml of 1 M solution of NaOH in methanol. Then, 5 ml of a methanolic solution containing 1 mmol of triorganotin chloride was added and the solution was stirred at room temperature for 1 h. Filtration removed minor solid byproducts and the solution was concentrated by rotary evaporation. After cooling and leaving the solution in the refrigerator for about one week, colourless prisms of (I) appeared.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2003); cell refinement: CrysAlis CCD (Oxford Diffraction, 2003); data reduction: CrysAlis RED (Oxford Diffraction, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. : The molecular structure of (I) with displacement ellipsoids shown at the 50% probability level. Bonds of the DMSO molecule in the minor orientation are shown as dashed lines. The unlabelled atoms of the disulfide molecule are generated by the symmetry operation (3/2-x, 1/2-y, z).
	Fig. 2. : The crystal structure of (I) viewed down the b axis. Hydrogen bonds are shown with dashed lines.
	Fig. 3. : Hydrogen-bonded two-dimesional assembly of molecules in (I), parallel to the (001) plane. Hydrogen bonds are shown with dashed lines.

Bis(4,6-diaminopyrimidin-2-yl) disulfide dimethyl sufoxide disolvate top

Crystal data top

C₈H₁₀N₈S₂·2C₂H₆OS	F(000) = 920
M_r = 438.62	D_x = 1.431 Mg m⁻³
Orthorhombic, Pccn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ab 2ac	Cell parameters from 8255 reflections
a = 11.2612 (4) Å	θ = 4–27°
b = 11.9948 (5) Å	µ = 0.49 mm⁻¹
c = 15.0754 (6) Å	T = 130 K
V = 2036.32 (14) Å³	Prism, colourless
Z = 4	0.40 × 0.10 × 0.10 mm

Data collection top

Kuma KM-4-CCD κ geometry diffractometer	1944 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.035
Graphite monochromator	θ_max = 27.1°, θ_min = 4.7°
ω scans	h = −14→14
17524 measured reflections	k = −15→15
2240 independent reflections	l = −19→12

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)] = 0.029	Hydrogen site location: difmap and geom
wR(F²) = 0.078	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0487P)²] where P = (F_o² + 2F_c²)/3
2240 reflections	(Δ/σ)_max < 0.001
146 parameters	Δρ_max = 0.23 e Å⁻³
0 restraints	Δρ_min = −0.31 e Å⁻³

Crystal data top

C₈H₁₀N₈S₂·2C₂H₆OS	V = 2036.32 (14) Å³
M_r = 438.62	Z = 4
Orthorhombic, Pccn	Mo Kα radiation
a = 11.2612 (4) Å	µ = 0.49 mm⁻¹
b = 11.9948 (5) Å	T = 130 K
c = 15.0754 (6) Å	0.40 × 0.10 × 0.10 mm

Data collection top

Kuma KM-4-CCD κ geometry diffractometer	1944 reflections with I > 2σ(I)
17524 measured reflections	R_int = 0.035
2240 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.029	0 restraints
wR(F²) = 0.078	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	Δρ_max = 0.23 e Å⁻³
2240 reflections	Δρ_min = −0.31 e Å⁻³
146 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. DMSO molecule is slightly disordered. In the minor orientation the DMSO C and O atoms superimpose with the C and O atoms of the major orientation. The S atom is split into two positions with occupancies 0.96 and 0.04.

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
S1	0.69207 (3)	0.18545 (3)	0.35324 (2)	0.01604 (12)
N1	0.57870 (10)	0.31222 (10)	0.22912 (8)	0.0152 (3)
C2	0.58248 (12)	0.21471 (12)	0.26959 (9)	0.0144 (3)
N3	0.51503 (10)	0.12462 (10)	0.25880 (8)	0.0170 (3)
C4	0.43156 (13)	0.13306 (12)	0.19373 (10)	0.0189 (3)
C5	0.42109 (13)	0.22991 (12)	0.14298 (10)	0.0198 (3)
H5A	0.3656	0.2345	0.0948	0.028 (5)*
C6	0.49402 (13)	0.31911 (12)	0.16390 (10)	0.0166 (3)
N7	0.36069 (14)	0.04423 (12)	0.18104 (11)	0.0279 (4)
H7A	0.3204 (18)	0.0445 (16)	0.1393 (13)	0.026 (5)*
H7B	0.3746 (16)	−0.0163 (16)	0.2079 (11)	0.024 (5)*
N8	0.48636 (13)	0.41723 (12)	0.11984 (10)	0.0221 (3)
H8A	0.4314 (19)	0.4234 (16)	0.0824 (13)	0.036 (6)*
H8B	0.5057 (18)	0.4735 (17)	0.1454 (14)	0.035 (6)*
S2	0.26010 (4)	0.05431 (4)	0.41883 (3)	0.02342 (15)	0.9591 (18)
O1	0.26997 (10)	0.08760 (10)	0.51429 (7)	0.0276 (3)
C9	0.21608 (17)	−0.08841 (15)	0.41993 (13)	0.0341 (4)
H9A	0.2808	−0.1338	0.4402	0.057 (7)*
H9B	0.1495	−0.0974	0.4591	0.047 (6)*
H9C	0.1939	−0.1109	0.3611	0.071 (8)*
C10	0.1254 (2)	0.1121 (2)	0.37893 (17)	0.0564 (7)
H10A	0.1327	0.1916	0.3738	0.071 (8)*
H10B	0.1072	0.0809	0.3219	0.104 (11)*
H10C	0.0628	0.0944	0.4199	0.056 (7)*
S2'	0.1601 (14)	0.0428 (13)	0.4582 (10)	0.056 (5)*	0.0409 (18)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01515 (19)	0.01586 (19)	0.0171 (2)	0.00024 (13)	−0.00058 (14)	0.00286 (14)
N1	0.0156 (6)	0.0131 (6)	0.0167 (7)	0.0008 (5)	−0.0011 (5)	−0.0004 (5)
C2	0.0139 (6)	0.0154 (7)	0.0138 (7)	0.0025 (5)	0.0023 (5)	−0.0012 (6)
N3	0.0172 (6)	0.0151 (6)	0.0185 (7)	−0.0009 (5)	−0.0007 (5)	−0.0001 (5)
C4	0.0186 (7)	0.0161 (7)	0.0221 (8)	0.0002 (6)	−0.0010 (6)	−0.0024 (6)
C5	0.0201 (7)	0.0168 (8)	0.0226 (8)	0.0006 (6)	−0.0058 (6)	−0.0014 (6)
C6	0.0179 (7)	0.0158 (7)	0.0162 (7)	0.0024 (5)	0.0010 (6)	−0.0013 (6)
N7	0.0306 (8)	0.0179 (7)	0.0353 (9)	−0.0077 (6)	−0.0162 (7)	0.0053 (7)
N8	0.0252 (7)	0.0164 (7)	0.0247 (8)	−0.0013 (6)	−0.0099 (6)	0.0019 (6)
S2	0.0229 (2)	0.0294 (3)	0.0179 (2)	0.00107 (17)	−0.00281 (17)	0.00052 (17)
O1	0.0298 (6)	0.0316 (7)	0.0215 (6)	0.0015 (5)	−0.0053 (5)	−0.0091 (5)
C9	0.0388 (10)	0.0317 (10)	0.0318 (11)	−0.0018 (8)	−0.0077 (8)	−0.0085 (8)
C10	0.0490 (14)	0.0504 (14)	0.0697 (17)	0.0079 (11)	−0.0347 (13)	0.0077 (13)

Geometric parameters (Å, º) top

S1—C2	1.7990 (15)	N7—H7B	0.846 (19)
S1—S1ⁱ	2.0249 (7)	N8—H8A	0.84 (2)
N1—C2	1.3198 (18)	N8—H8B	0.81 (2)
N1—C6	1.3722 (19)	S2—O1	1.4976 (11)
C2—N3	1.3309 (19)	S2—C10	1.773 (2)
N3—C4	1.3623 (19)	S2—C9	1.7822 (19)
C4—N7	1.345 (2)	C9—H9A	0.9600
C4—C5	1.396 (2)	C9—H9B	0.9601
C5—C6	1.385 (2)	C9—H9C	0.9601
C5—H5A	0.9601	C10—H10A	0.9601
C6—N8	1.354 (2)	C10—H10B	0.9601
N7—H7A	0.78 (2)	C10—H10C	0.9600

C2—S1—S1ⁱ	107.03 (5)	C6—N8—H8A	116.9 (13)
C2—N1—C6	114.02 (12)	C6—N8—H8B	118.4 (14)
N1—C2—N3	130.14 (13)	H8A—N8—H8B	116 (2)
N1—C2—S1	121.27 (11)	O1—S2—C10	106.58 (10)
N3—C2—S1	108.59 (10)	O1—S2—C9	105.54 (8)
C2—N3—C4	114.92 (12)	C10—S2—C9	98.08 (11)
N7—C4—N3	116.94 (14)	S2—C9—H9A	109.7
N7—C4—C5	122.08 (15)	S2—C9—H9B	109.3
N3—C4—C5	120.98 (13)	H9A—C9—H9B	109.5
C6—C5—C4	117.90 (14)	S2—C9—H9C	109.5
C6—C5—H5A	120.9	H9A—C9—H9C	109.5
C4—C5—H5A	121.2	H9B—C9—H9C	109.5
N8—C6—N1	116.62 (13)	S2—C10—H10A	110.0
N8—C6—C5	121.46 (14)	S2—C10—H10B	109.5
N1—C6—C5	121.91 (13)	H10A—C10—H10B	109.5
C4—N7—H7A	117.4 (15)	S2—C10—H10C	108.9
C4—N7—H7B	120.2 (12)	H10A—C10—H10C	109.5
H7A—N7—H7B	119.9 (19)	H10B—C10—H10C	109.5

C6—N1—C2—N3	−2.4 (2)	C2—N3—C4—C5	0.6 (2)
C6—N1—C2—S1	176.75 (10)	N7—C4—C5—C6	176.79 (15)
S1ⁱ—S1—C2—N1	−8.23 (13)	N3—C4—C5—C6	−3.3 (2)
S1ⁱ—S1—C2—N3	171.09 (8)	C2—N1—C6—N8	−179.77 (13)
N1—C2—N3—C4	2.5 (2)	C2—N1—C6—C5	−0.8 (2)
S1—C2—N3—C4	−176.76 (10)	C4—C5—C6—N8	−177.67 (14)
C2—N3—C4—N7	−179.45 (14)	C4—C5—C6—N1	3.4 (2)

Symmetry code: (i) −x+3/2, −y+1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N7—H7A···O1ⁱⁱ	0.78 (2)	2.20 (2)	2.959 (2)	165 (2)
N7—H7B···N1ⁱⁱⁱ	0.846 (19)	2.33 (2)	3.169 (2)	175.1 (16)
N8—H8A···O1^iv	0.84 (2)	2.09 (2)	2.9109 (19)	164.4 (18)
N8—H8B···N3^v	0.81 (2)	2.33 (2)	3.088 (2)	156.8 (19)

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

Experimental details

Crystal data
Chemical formula	C₈H₁₀N₈S₂·2C₂H₆OS
M_r	438.62
Crystal system, space group	Orthorhombic, Pccn
Temperature (K)	130
a, b, c (Å)	11.2612 (4), 11.9948 (5), 15.0754 (6)
V (Å³)	2036.32 (14)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.49
Crystal size (mm)	0.40 × 0.10 × 0.10

Data collection
Diffractometer	Kuma KM-4-CCD κ geometry diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	17524, 2240, 1944
R_int	0.035
(sin θ/λ)_max (Å⁻¹)	0.641

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.078, 1.04
No. of reflections	2240
No. of parameters	146
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.31

Computer programs: CrysAlis CCD (Oxford Diffraction, 2003), CrysAlis RED (Oxford Diffraction, 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), Stereochemical Workstation Operation Manual (Siemens, 1989) and Mercury (Macrae et al., 2006).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N7—H7A···O1ⁱ	0.78 (2)	2.20 (2)	2.959 (2)	165 (2)
N7—H7B···N1ⁱⁱ	0.846 (19)	2.33 (2)	3.169 (2)	175.1 (16)
N8—H8A···O1ⁱⁱⁱ	0.84 (2)	2.09 (2)	2.9109 (19)	164.4 (18)
N8—H8B···N3^iv	0.81 (2)	2.33 (2)	3.088 (2)	156.8 (19)

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

References

Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457. Web of Science CrossRef CAS IUCr Journals Google Scholar
Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, Oxfordshire, England. Google Scholar
Sączewski, J., Frontera, A., Gdaniec, M., Brzozowski, Z., Sączewski, F., Tabin, P., Quinoñero, D. & Deyà, P. M. (2006). Chem. Phys. Lett. 422, 234–239. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Siemens (1989). Stereochemical Workstation Operation Manual. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 64| Part 9| September 2008| Page o1724

doi:10.1107/S160053680802480X

Open

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