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The title compound, C11H17N2O3PS2, is a cyclic thio­phos­phoryl pyrimidine derivative exhibiting insecticidal properties. The crystal structure determination gives evidence for the presence of the thione isomer of the compound. The pyrimidine nucleus is planar and its substituents have small deviations from the least-squares plane. The dioxaphos­phorinane ring adopts a chair conformation. The lack of classical hydrogen bonds and the weak intermolecular interactions lead to a `loose' packing characterized by channels in the structure.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270102005218/av1105sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270102005218/av1105Isup2.hkl
Contains datablock I

CCDC reference: 187932

Comment top

The biological activity of organophosphorus compounds enables their utilization both as pesticides, and as sterilization agents in the food industry and medicine (Almasi, 1976; Safe & Hutzinger, 1976; Durand & Barcelo, 1991). Pyrimidine thiophosphoric esters are also known for their applications as performance insecticides (Authors1, 1966; Authors2, 1970; Wegler, 1981). In order to extend the activity domain of these insecticides, cyclic thiophosphorylic compounds have been synthesized. From among the 2-(O-2-substituted-6-methylpyrimidine-4-yl)-2-thiono-5,5-dimethyl- 1,3,2-dioxaphosphorinane derivatives obtained, the structure of the title compound, (I), was studied because of its insecticidal properties (Musat et al., 1990). From the two possible isomers of (I), i.e. the thionic P(S)—O– and thiolic P(O)—S– forms, the present structure determination gives evidence for the formation of the thionic isomer (Fig. 1). \sch

The dioxaphosphorinane ring in (I) adopts an almost perfect P1CC2 chair conformation (Saenger, 1984; Landolt-Bornstein, 1989), in which atoms P1 and C2 are displaced from the least-squares plane by 0.147 (1) and -0.276 (3) Å, respectively. The torsion angles of the dioxaphosphorinane ring are listed in Table 1. The O-pyrimidine substituent is in the axial position, and atom S1 is in the equatorial position of the dioxaphosphorinane ring.

The pyrimidine ring is planar, with a maximum deviation of 0.006 (3) Å for atom C5. Also, atom S2 is situated in the pyrimidyl plane, 0.004 (1) Å from the pyrimidyl least-squares plane, and the deviations of the methyl atoms C10 and C11, and of atom O3, from the pyrimidyl least-squares plane are less than 0.074 (2) Å. The torsion angle about the O3—C4 bond [P1—O3—C4—N1 139.23 (18)°] corresponds to an anti conformation and the orientation about the exocyclic S2—C7 bond [C11—S2—C7—N1 - 2.1 (2)°] is syn periplanar.

The dioxaphosphorinane units in (I) are bridged via a weak intermolecular C8—H82···O2 bond [C8—H82 0.96 Å, H82···O2 2.51 Å, C8···O2 3.429 (3) Å and C8—H82···O2 160.47°], forming zigzag chains running along the [101] direction. These chains are situated in layers approximately parallel to the crystallographic bc plane. The planar pyrimidine rings are packed in columns running along the b axis and form an angle of 36.20 (8)° with it. This packing (Fig. 2) leaves two types of channels in the structure along b, namely, empty channels and channels containing the phosphorylic S atoms. The two channel types alternate along both [101] and [101] directions, and are bordered via C—H···π intermolecular interactions between the dioxaphosphorinane atoms C3 and C9 and the pyrimidine nuclei (Table 2), and via short interactions between parallel pyrimidine rings [CgCg(2 - x, -y, -z) 3.4659 (15) Å; Cg is the ring centroid]. The `loose' packing of the molecules of (I) can be explained by the presence of exclusively weak intermolecular interactions.

Experimental top

Compound (I) was synthesized from the substitution of the Cl atom by reacting 2-chloro-2-thiono-5,5-dimethyl-1,3,2-dioxaphosphorinane with 2-S-methyl-6-methyl-4-hydroxypyrimidine in the presence of K2CO3 and dimethylformamide as solvent at 323 K. Analytical data, and IR, 1H NMR, 31P NMR, 13C NMR and mass spectra confirmed the formation of (I). Single crystals of (I) were obtained from a 1/1 mixture of ethanol and diethyl ether.

Refinement top

All H atoms were placed in geometric positions Is this revision correct? and refined as riding atoms, with C—H = 0.93–0.97 Å and Uiso(H) = 1.2Ueq(C). Are these the correct constraints?

Computing details top

Data collection: CAD-4-PC Software (Enraf-Nonius, 1992); cell refinement: local program; data reduction: Please provide missing details; program(s) used to solve structure: SIR97 (Altomare et al., 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Please provide missing details.

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of (I) showing the atom-labelling scheme and with 50% probability displacement ellipsoids. H atoms are drawn as as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A packing diagram for (I) viewed down the b axis. Note the two channel types formed along b.
5,5-Dimethyl-2-[6-methyl-2-(methylsulfanyl)pyrimidin-4-yloxy]- 1,3,2-dioxaphosphorinane-2-thione top
Crystal data top
C11H17N2O3PS2F(000) = 672
Mr = 320.36Dx = 1.354 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.5418 Å
Hall symbol: -P 2ybcCell parameters from 23 reflections
a = 9.900 (2) Åθ = 40.0–43.5°
b = 9.330 (2) ŵ = 4.09 mm1
c = 17.010 (3) ÅT = 293 K
β = 90.23 (2)°Prism, colourless
V = 1571.2 (5) Å30.30 × 0.30 × 0.25 mm
Z = 4
Data collection top
Enraf-Nonius CAD-4
diffractometer
Rint = 0.089
Radiation source: fine-focus sealed tubeθmax = 74.0°, θmin = 4.5°
Graphite monochromatorh = 1111
ω/2θ scansk = 312
3703 measured reflectionsl = 2110
3185 independent reflections2 standard reflections every 60 min
2626 reflections with I > 2σ(I) intensity decay: 6%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.059H-atom parameters constrained
wR(F2) = 0.154 w = 1/[σ2(Fo2) + (0.0947P)2 + 0.4685P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.005
3185 reflectionsΔρmax = 0.97 e Å3
177 parametersΔρmin = 0.48 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0099 (9)
Crystal data top
C11H17N2O3PS2V = 1571.2 (5) Å3
Mr = 320.36Z = 4
Monoclinic, P21/cCu Kα radiation
a = 9.900 (2) ŵ = 4.09 mm1
b = 9.330 (2) ÅT = 293 K
c = 17.010 (3) Å0.30 × 0.30 × 0.25 mm
β = 90.23 (2)°
Data collection top
Enraf-Nonius CAD-4
diffractometer
Rint = 0.089
3703 measured reflections2 standard reflections every 60 min
3185 independent reflections intensity decay: 6%
2626 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0590 restraints
wR(F2) = 0.154H-atom parameters constrained
S = 1.07Δρmax = 0.97 e Å3
3185 reflectionsΔρmin = 0.48 e Å3
177 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.

Least-square planes and deviations from them calculated using PLATON software [Spek, A. L. (1999). PLATON. January 1999 version. University of Utrecht, The Netherlands.]

PLANE NUMBER 1 - DIOXAPHOSPHORINANE RING =============== EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S 0.9490 (3) -0.1358 (11) -0.2846 (9) 5.016 (5)

ATOM DIST(A) P1 DEFINING 0.147 (1) O1 DEFINING -0.189 (2) C1 DEFINING 0.259 (3) C2 DEFINING -0.276 (3) C3 DEFINING 0.250 (3) O2 DEFINING -0.191 (2)

PLANE NUMBER 2 - PYRIMIDINE NUCLEUS ===============

EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S 0.6312 (8) -0.5903 (8) 0.5031 (8) 4.537 (8)

ATOM DIST(A) N1 DEFINING -0.002 (2) C4 DEFINING -0.002 (2) C5 DEFINING 0.006 (3) C6 DEFINING -0.005 (2) N2 DEFINING 0.000 (2) C7 DEFINING 0.004 (2) S2 NON-DEFINING -0.004 (1) O3 NON-DEFINING 0.074 (2) C10 NON-DEFINING 0.040 (3) C11 NON-DEFINING -0.059 (3)

#Table 1. H-bonding

#loop_ #_geom_hbond_atom_site_label_D #_geom_hbond_atom_site_label_H #_geom_hbond_atom_site_label_A #_geom_hbond_distance_DH #_geom_hbond_distance_HA #_geom_hbond_distance_DA #_geom_hbond_angle_DHA #_geom_hbond_site_symmetry_A #_geom_hbond_publ_flag # # Short contacts # ===== ======== # # D H A D—H H···A D···A D—H···A symm publ # - - - — —– —– ——- —- —- # C8 H82 O2 0.96 2.509 3.429 (3) 160 2_645 no

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
xyzUiso*/Ueq
S10.50695 (10)0.27240 (12)0.02876 (5)0.0789 (3)
S21.15227 (8)0.29194 (7)0.12452 (5)0.0601 (3)
P10.63259 (6)0.20343 (6)0.10651 (3)0.0426 (2)
O10.59314 (19)0.05838 (18)0.13681 (10)0.0499 (5)
O20.6484 (2)0.29258 (17)0.18254 (10)0.0525 (5)
O30.79901 (19)0.1961 (2)0.08193 (10)0.0506 (5)
N10.9551 (2)0.2350 (2)0.01586 (11)0.0413 (4)
N20.9768 (2)0.0878 (2)0.12732 (11)0.0443 (5)
C10.6699 (3)0.0057 (3)0.20605 (15)0.0514 (6)
H110.63560.08790.22060.062*
H120.76390.00570.19150.062*
C20.6620 (3)0.1019 (3)0.27525 (13)0.0439 (5)
C30.7234 (3)0.2374 (3)0.25065 (15)0.0519 (6)
H310.81720.22210.23680.062*
H320.72010.30620.29340.062*
C40.8506 (2)0.1555 (3)0.00940 (13)0.0405 (5)
C50.8019 (3)0.0422 (3)0.02909 (15)0.0467 (6)
H50.72870.01110.01120.056*
C60.8707 (2)0.0101 (3)0.09910 (14)0.0446 (5)
C71.0128 (2)0.1962 (2)0.08401 (13)0.0411 (5)
C80.5069 (3)0.1200 (3)0.30306 (17)0.0566 (7)
H810.50270.18710.34580.085*
H820.47240.02900.32000.085*
H830.45340.15490.25990.085*
C90.7536 (4)0.0437 (4)0.3418 (2)0.0765 (10)
H910.84440.03440.32290.115*
H920.72100.04830.35850.115*
H930.75220.10900.38540.115*
C100.8316 (3)0.1128 (4)0.1458 (2)0.0676 (8)
H1010.82860.08620.20040.101*
H1020.74390.14520.12970.101*
H1030.89620.18830.13850.101*
C111.1717 (4)0.4290 (3)0.0566 (2)0.0749 (10)
H1111.09920.49660.06260.112*
H1121.25630.47660.06530.112*
H1131.17030.38990.00440.112*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0765 (6)0.1059 (7)0.0545 (4)0.0255 (5)0.0013 (4)0.0224 (4)
S20.0704 (5)0.0480 (4)0.0623 (4)0.0066 (3)0.0303 (4)0.0028 (3)
P10.0525 (4)0.0401 (3)0.0352 (3)0.0003 (2)0.0082 (2)0.0018 (2)
O10.0707 (12)0.0371 (8)0.0420 (9)0.0136 (8)0.0056 (8)0.0069 (7)
O20.0845 (13)0.0286 (8)0.0445 (9)0.0027 (8)0.0128 (9)0.0006 (6)
O30.0556 (10)0.0607 (11)0.0356 (8)0.0061 (8)0.0103 (7)0.0027 (7)
N10.0487 (11)0.0373 (9)0.0380 (10)0.0036 (8)0.0064 (8)0.0028 (7)
N20.0496 (11)0.0435 (10)0.0399 (10)0.0053 (8)0.0018 (8)0.0001 (8)
C10.0703 (17)0.0319 (11)0.0519 (14)0.0010 (11)0.0079 (12)0.0001 (10)
C20.0549 (14)0.0396 (11)0.0371 (11)0.0041 (10)0.0012 (10)0.0025 (9)
C30.0669 (16)0.0429 (13)0.0459 (13)0.0167 (12)0.0012 (12)0.0056 (10)
C40.0442 (12)0.0432 (11)0.0340 (10)0.0054 (9)0.0017 (9)0.0048 (9)
C50.0492 (13)0.0478 (13)0.0432 (12)0.0039 (10)0.0034 (10)0.0045 (10)
C60.0478 (13)0.0449 (12)0.0410 (11)0.0027 (10)0.0049 (10)0.0004 (10)
C70.0480 (12)0.0363 (11)0.0391 (11)0.0070 (9)0.0034 (9)0.0051 (9)
C80.0670 (17)0.0551 (15)0.0479 (14)0.0059 (13)0.0168 (12)0.0008 (11)
C90.094 (2)0.077 (2)0.0583 (17)0.0038 (19)0.0166 (17)0.0156 (16)
C100.0710 (19)0.0692 (19)0.0625 (17)0.0128 (15)0.0033 (15)0.0192 (15)
C110.083 (2)0.0472 (15)0.095 (2)0.0125 (15)0.0310 (19)0.0128 (16)
Geometric parameters (Å, º) top
S1—P11.9227 (10)C3—H310.9700
S2—C111.734 (3)C3—H320.9700
S2—C71.785 (3)C4—C51.333 (4)
P1—O11.5004 (18)C5—C61.407 (3)
P1—O21.5452 (18)C5—H50.9300
P1—O31.7028 (19)C6—C101.447 (4)
O1—C11.483 (3)C8—H810.9600
O2—C31.467 (3)C8—H820.9600
O3—C41.390 (3)C8—H830.9600
N1—C71.344 (3)C9—H910.9600
N1—C41.344 (3)C9—H920.9600
N2—C71.300 (3)C9—H930.9600
N2—C61.365 (3)C10—H1010.9600
C1—C21.482 (3)C10—H1020.9600
C1—H110.9700C10—H1030.9600
C1—H120.9700C11—H1110.9600
C2—C31.465 (3)C11—H1120.9600
C2—C91.546 (4)C11—H1130.9600
C2—C81.617 (4)
C11—S2—C7101.30 (13)C4—C5—C6114.1 (2)
O1—P1—O2102.92 (9)C4—C5—H5122.9
O1—P1—O3107.56 (11)C6—C5—H5122.9
O2—P1—O397.58 (11)N2—C6—C5124.1 (2)
O1—P1—S1111.69 (9)N2—C6—C10115.6 (2)
O2—P1—S1117.31 (9)C5—C6—C10120.2 (2)
O3—P1—S1117.93 (7)N2—C7—N1125.6 (2)
C1—O1—P1116.01 (15)N2—C7—S2112.39 (17)
C3—O2—P1121.45 (16)N1—C7—S2122.02 (18)
C4—O3—P1126.04 (16)C2—C8—H81109.5
C7—N1—C4117.2 (2)C2—C8—H82109.5
C7—N2—C6115.0 (2)H81—C8—H82109.5
C2—C1—O1113.7 (2)C2—C8—H83109.5
C2—C1—H11108.8H81—C8—H83109.5
O1—C1—H11108.8H82—C8—H83109.5
C2—C1—H12108.8C2—C9—H91109.5
O1—C1—H12108.8C2—C9—H92109.5
H11—C1—H12107.7H91—C9—H92109.5
C3—C2—C1105.8 (2)C2—C9—H93109.5
C3—C2—C9105.6 (2)H91—C9—H93109.5
C1—C2—C9109.7 (2)H92—C9—H93109.5
C3—C2—C8112.9 (2)C6—C10—H101109.5
C1—C2—C8110.4 (2)C6—C10—H102109.5
C9—C2—C8112.2 (2)H101—C10—H102109.5
C2—C3—O2108.6 (2)C6—C10—H103109.5
C2—C3—H31110.0H101—C10—H103109.5
O2—C3—H31110.0H102—C10—H103109.5
C2—C3—H32110.0S2—C11—H111109.5
O2—C3—H32110.0S2—C11—H112109.5
H31—C3—H32108.3H111—C11—H112109.5
C5—C4—N1123.9 (2)S2—C11—H113109.5
C5—C4—O3121.2 (2)H111—C11—H113109.5
N1—C4—O3114.8 (2)H112—C11—H113109.5
P1—O1—C1—C258.1 (3)C2—C3—O2—P157.6 (3)
O1—C1—C2—C362.2 (3)C3—O2—P1—O146.5 (2)
C1—C2—C3—O258.7 (3)O2—P1—O1—C143.60 (19)

Experimental details

Crystal data
Chemical formulaC11H17N2O3PS2
Mr320.36
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)9.900 (2), 9.330 (2), 17.010 (3)
β (°) 90.23 (2)
V3)1571.2 (5)
Z4
Radiation typeCu Kα
µ (mm1)4.09
Crystal size (mm)0.30 × 0.30 × 0.25
Data collection
DiffractometerEnraf-Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
3703, 3185, 2626
Rint0.089
(sin θ/λ)max1)0.624
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.059, 0.154, 1.07
No. of reflections3185
No. of parameters177
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.97, 0.48

Computer programs: CAD-4-PC Software (Enraf-Nonius, 1992), local program, Please provide missing details, SIR97 (Altomare et al., 1997), SHELXL97 (Sheldrick, 1997).

Selected torsion angles (º) top
P1—O1—C1—C258.1 (3)C2—C3—O2—P157.6 (3)
O1—C1—C2—C362.2 (3)C3—O2—P1—O146.5 (2)
C1—C2—C3—O258.7 (3)O2—P1—O1—C143.60 (19)
Geometry of X-H···Cg(π-ring) interactions (Å, °) top
C3-H32···Cg2i3.231353.973 (3)
C9-H93···Cg2i3.121383.888 (4)
Symmetry code: (i) x, 1/2 - y, z - 1/2.
 

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