Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270102005218/av1105sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270102005218/av1105Isup2.hkl |
CCDC reference: 187932
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.
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?
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.
C11H17N2O3PS2 | F(000) = 672 |
Mr = 320.36 | Dx = 1.354 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.5418 Å |
Hall symbol: -P 2ybc | Cell parameters from 23 reflections |
a = 9.900 (2) Å | θ = 40.0–43.5° |
b = 9.330 (2) Å | µ = 4.09 mm−1 |
c = 17.010 (3) Å | T = 293 K |
β = 90.23 (2)° | Prism, colourless |
V = 1571.2 (5) Å3 | 0.30 × 0.30 × 0.25 mm |
Z = 4 |
Enraf-Nonius CAD-4 diffractometer | Rint = 0.089 |
Radiation source: fine-focus sealed tube | θmax = 74.0°, θmin = 4.5° |
Graphite monochromator | h = −11→11 |
ω/2θ scans | k = −3→12 |
3703 measured reflections | l = −21→10 |
3185 independent reflections | 2 standard reflections every 60 min |
2626 reflections with I > 2σ(I) | intensity decay: 6% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.059 | H-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 reflections | Δρmax = 0.97 e Å−3 |
177 parameters | Δρmin = −0.48 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0099 (9) |
C11H17N2O3PS2 | V = 1571.2 (5) Å3 |
Mr = 320.36 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 9.900 (2) Å | µ = 4.09 mm−1 |
b = 9.330 (2) Å | T = 293 K |
c = 17.010 (3) Å | 0.30 × 0.30 × 0.25 mm |
β = 90.23 (2)° |
Enraf-Nonius CAD-4 diffractometer | Rint = 0.089 |
3703 measured reflections | 2 standard reflections every 60 min |
3185 independent reflections | intensity decay: 6% |
2626 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.059 | 0 restraints |
wR(F2) = 0.154 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.97 e Å−3 |
3185 reflections | Δρmin = −0.48 e Å−3 |
177 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. 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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.50695 (10) | 0.27240 (12) | 0.02876 (5) | 0.0789 (3) | |
S2 | 1.15227 (8) | 0.29194 (7) | −0.12452 (5) | 0.0601 (3) | |
P1 | 0.63259 (6) | 0.20343 (6) | 0.10651 (3) | 0.0426 (2) | |
O1 | 0.59314 (19) | 0.05838 (18) | 0.13681 (10) | 0.0499 (5) | |
O2 | 0.6484 (2) | 0.29258 (17) | 0.18254 (10) | 0.0525 (5) | |
O3 | 0.79901 (19) | 0.1961 (2) | 0.08193 (10) | 0.0506 (5) | |
N1 | 0.9551 (2) | 0.2350 (2) | −0.01586 (11) | 0.0413 (4) | |
N2 | 0.9768 (2) | 0.0878 (2) | −0.12732 (11) | 0.0443 (5) | |
C1 | 0.6699 (3) | 0.0057 (3) | 0.20605 (15) | 0.0514 (6) | |
H11 | 0.6356 | −0.0879 | 0.2206 | 0.062* | |
H12 | 0.7639 | −0.0057 | 0.1915 | 0.062* | |
C2 | 0.6620 (3) | 0.1019 (3) | 0.27525 (13) | 0.0439 (5) | |
C3 | 0.7234 (3) | 0.2374 (3) | 0.25065 (15) | 0.0519 (6) | |
H31 | 0.8172 | 0.2221 | 0.2368 | 0.062* | |
H32 | 0.7201 | 0.3062 | 0.2934 | 0.062* | |
C4 | 0.8506 (2) | 0.1555 (3) | 0.00940 (13) | 0.0405 (5) | |
C5 | 0.8019 (3) | 0.0422 (3) | −0.02909 (15) | 0.0467 (6) | |
H5 | 0.7287 | −0.0111 | −0.0112 | 0.056* | |
C6 | 0.8707 (2) | 0.0101 (3) | −0.09910 (14) | 0.0446 (5) | |
C7 | 1.0128 (2) | 0.1962 (2) | −0.08401 (13) | 0.0411 (5) | |
C8 | 0.5069 (3) | 0.1200 (3) | 0.30306 (17) | 0.0566 (7) | |
H81 | 0.5027 | 0.1871 | 0.3458 | 0.085* | |
H82 | 0.4724 | 0.0290 | 0.3200 | 0.085* | |
H83 | 0.4534 | 0.1549 | 0.2599 | 0.085* | |
C9 | 0.7536 (4) | 0.0437 (4) | 0.3418 (2) | 0.0765 (10) | |
H91 | 0.8444 | 0.0344 | 0.3229 | 0.115* | |
H92 | 0.7210 | −0.0483 | 0.3585 | 0.115* | |
H93 | 0.7522 | 0.1090 | 0.3854 | 0.115* | |
C10 | 0.8316 (3) | −0.1128 (4) | −0.1458 (2) | 0.0676 (8) | |
H101 | 0.8286 | −0.0862 | −0.2004 | 0.101* | |
H102 | 0.7439 | −0.1452 | −0.1297 | 0.101* | |
H103 | 0.8962 | −0.1883 | −0.1385 | 0.101* | |
C11 | 1.1717 (4) | 0.4290 (3) | −0.0566 (2) | 0.0749 (10) | |
H111 | 1.0992 | 0.4966 | −0.0626 | 0.112* | |
H112 | 1.2563 | 0.4766 | −0.0653 | 0.112* | |
H113 | 1.1703 | 0.3899 | −0.0044 | 0.112* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0765 (6) | 0.1059 (7) | 0.0545 (4) | 0.0255 (5) | 0.0013 (4) | 0.0224 (4) |
S2 | 0.0704 (5) | 0.0480 (4) | 0.0623 (4) | −0.0066 (3) | 0.0303 (4) | −0.0028 (3) |
P1 | 0.0525 (4) | 0.0401 (3) | 0.0352 (3) | −0.0003 (2) | 0.0082 (2) | 0.0018 (2) |
O1 | 0.0707 (12) | 0.0371 (8) | 0.0420 (9) | −0.0136 (8) | 0.0056 (8) | −0.0069 (7) |
O2 | 0.0845 (13) | 0.0286 (8) | 0.0445 (9) | −0.0027 (8) | 0.0128 (9) | −0.0006 (6) |
O3 | 0.0556 (10) | 0.0607 (11) | 0.0356 (8) | −0.0061 (8) | 0.0103 (7) | −0.0027 (7) |
N1 | 0.0487 (11) | 0.0373 (9) | 0.0380 (10) | 0.0036 (8) | 0.0064 (8) | 0.0028 (7) |
N2 | 0.0496 (11) | 0.0435 (10) | 0.0399 (10) | 0.0053 (8) | 0.0018 (8) | 0.0001 (8) |
C1 | 0.0703 (17) | 0.0319 (11) | 0.0519 (14) | 0.0010 (11) | 0.0079 (12) | 0.0001 (10) |
C2 | 0.0549 (14) | 0.0396 (11) | 0.0371 (11) | −0.0041 (10) | 0.0012 (10) | 0.0025 (9) |
C3 | 0.0669 (16) | 0.0429 (13) | 0.0459 (13) | −0.0167 (12) | 0.0012 (12) | −0.0056 (10) |
C4 | 0.0442 (12) | 0.0432 (11) | 0.0340 (10) | 0.0054 (9) | 0.0017 (9) | 0.0048 (9) |
C5 | 0.0492 (13) | 0.0478 (13) | 0.0432 (12) | −0.0039 (10) | 0.0034 (10) | 0.0045 (10) |
C6 | 0.0478 (13) | 0.0449 (12) | 0.0410 (11) | 0.0027 (10) | −0.0049 (10) | −0.0004 (10) |
C7 | 0.0480 (12) | 0.0363 (11) | 0.0391 (11) | 0.0070 (9) | 0.0034 (9) | 0.0051 (9) |
C8 | 0.0670 (17) | 0.0551 (15) | 0.0479 (14) | −0.0059 (13) | 0.0168 (12) | 0.0008 (11) |
C9 | 0.094 (2) | 0.077 (2) | 0.0583 (17) | 0.0038 (19) | −0.0166 (17) | 0.0156 (16) |
C10 | 0.0710 (19) | 0.0692 (19) | 0.0625 (17) | −0.0128 (15) | −0.0033 (15) | −0.0192 (15) |
C11 | 0.083 (2) | 0.0472 (15) | 0.095 (2) | −0.0125 (15) | 0.0310 (19) | −0.0128 (16) |
S1—P1 | 1.9227 (10) | C3—H31 | 0.9700 |
S2—C11 | 1.734 (3) | C3—H32 | 0.9700 |
S2—C7 | 1.785 (3) | C4—C5 | 1.333 (4) |
P1—O1 | 1.5004 (18) | C5—C6 | 1.407 (3) |
P1—O2 | 1.5452 (18) | C5—H5 | 0.9300 |
P1—O3 | 1.7028 (19) | C6—C10 | 1.447 (4) |
O1—C1 | 1.483 (3) | C8—H81 | 0.9600 |
O2—C3 | 1.467 (3) | C8—H82 | 0.9600 |
O3—C4 | 1.390 (3) | C8—H83 | 0.9600 |
N1—C7 | 1.344 (3) | C9—H91 | 0.9600 |
N1—C4 | 1.344 (3) | C9—H92 | 0.9600 |
N2—C7 | 1.300 (3) | C9—H93 | 0.9600 |
N2—C6 | 1.365 (3) | C10—H101 | 0.9600 |
C1—C2 | 1.482 (3) | C10—H102 | 0.9600 |
C1—H11 | 0.9700 | C10—H103 | 0.9600 |
C1—H12 | 0.9700 | C11—H111 | 0.9600 |
C2—C3 | 1.465 (3) | C11—H112 | 0.9600 |
C2—C9 | 1.546 (4) | C11—H113 | 0.9600 |
C2—C8 | 1.617 (4) | ||
C11—S2—C7 | 101.30 (13) | C4—C5—C6 | 114.1 (2) |
O1—P1—O2 | 102.92 (9) | C4—C5—H5 | 122.9 |
O1—P1—O3 | 107.56 (11) | C6—C5—H5 | 122.9 |
O2—P1—O3 | 97.58 (11) | N2—C6—C5 | 124.1 (2) |
O1—P1—S1 | 111.69 (9) | N2—C6—C10 | 115.6 (2) |
O2—P1—S1 | 117.31 (9) | C5—C6—C10 | 120.2 (2) |
O3—P1—S1 | 117.93 (7) | N2—C7—N1 | 125.6 (2) |
C1—O1—P1 | 116.01 (15) | N2—C7—S2 | 112.39 (17) |
C3—O2—P1 | 121.45 (16) | N1—C7—S2 | 122.02 (18) |
C4—O3—P1 | 126.04 (16) | C2—C8—H81 | 109.5 |
C7—N1—C4 | 117.2 (2) | C2—C8—H82 | 109.5 |
C7—N2—C6 | 115.0 (2) | H81—C8—H82 | 109.5 |
C2—C1—O1 | 113.7 (2) | C2—C8—H83 | 109.5 |
C2—C1—H11 | 108.8 | H81—C8—H83 | 109.5 |
O1—C1—H11 | 108.8 | H82—C8—H83 | 109.5 |
C2—C1—H12 | 108.8 | C2—C9—H91 | 109.5 |
O1—C1—H12 | 108.8 | C2—C9—H92 | 109.5 |
H11—C1—H12 | 107.7 | H91—C9—H92 | 109.5 |
C3—C2—C1 | 105.8 (2) | C2—C9—H93 | 109.5 |
C3—C2—C9 | 105.6 (2) | H91—C9—H93 | 109.5 |
C1—C2—C9 | 109.7 (2) | H92—C9—H93 | 109.5 |
C3—C2—C8 | 112.9 (2) | C6—C10—H101 | 109.5 |
C1—C2—C8 | 110.4 (2) | C6—C10—H102 | 109.5 |
C9—C2—C8 | 112.2 (2) | H101—C10—H102 | 109.5 |
C2—C3—O2 | 108.6 (2) | C6—C10—H103 | 109.5 |
C2—C3—H31 | 110.0 | H101—C10—H103 | 109.5 |
O2—C3—H31 | 110.0 | H102—C10—H103 | 109.5 |
C2—C3—H32 | 110.0 | S2—C11—H111 | 109.5 |
O2—C3—H32 | 110.0 | S2—C11—H112 | 109.5 |
H31—C3—H32 | 108.3 | H111—C11—H112 | 109.5 |
C5—C4—N1 | 123.9 (2) | S2—C11—H113 | 109.5 |
C5—C4—O3 | 121.2 (2) | H111—C11—H113 | 109.5 |
N1—C4—O3 | 114.8 (2) | H112—C11—H113 | 109.5 |
P1—O1—C1—C2 | 58.1 (3) | C2—C3—O2—P1 | −57.6 (3) |
O1—C1—C2—C3 | −62.2 (3) | C3—O2—P1—O1 | 46.5 (2) |
C1—C2—C3—O2 | 58.7 (3) | O2—P1—O1—C1 | −43.60 (19) |
Experimental details
Crystal data | |
Chemical formula | C11H17N2O3PS2 |
Mr | 320.36 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 9.900 (2), 9.330 (2), 17.010 (3) |
β (°) | 90.23 (2) |
V (Å3) | 1571.2 (5) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 4.09 |
Crystal size (mm) | 0.30 × 0.30 × 0.25 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3703, 3185, 2626 |
Rint | 0.089 |
(sin θ/λ)max (Å−1) | 0.624 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.154, 1.07 |
No. of reflections | 3185 |
No. of parameters | 177 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
P1—O1—C1—C2 | 58.1 (3) | C2—C3—O2—P1 | −57.6 (3) |
O1—C1—C2—C3 | −62.2 (3) | C3—O2—P1—O1 | 46.5 (2) |
C1—C2—C3—O2 | 58.7 (3) | O2—P1—O1—C1 | −43.60 (19) |
C3-H32···Cg2i | 3.23 | 135 | 3.973 (3) |
C9-H93···Cg2i | 3.12 | 138 | 3.888 (4) |
Symmetry code: (i) x, 1/2 - y, z - 1/2. |
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 [Cg—Cg(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.