The title compound, C
9H
11N
4O
2S, consisting of a pyrimidine ring and a thiourea carboxylic acid methyl ester, possesses mirror symmetry and an intramolecular N—H
N hydrogen bond. In the crystal structure, N—H
S hydrogen bonds link symmetry-related molecules to form dimers, which in turn are linked by a C—H
O hydogen bond to form a two-dimensional planar structure.
Supporting information
CCDC reference: 266688
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.004 Å
- R factor = 0.039
- wR factor = 0.116
- Data-to-parameter ratio = 9.5
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ?
PLAT088_ALERT_3_C Poor Data / Parameter Ratio .................... 9.47
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ?
PLAT199_ALERT_1_C Check the Reported _cell_measurement_temperature 293 K
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C8
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 5
PLAT350_ALERT_3_C Short C-H Bond (0.96A) C1 - H1A ... 0.84 Ang.
PLAT350_ALERT_3_C Short C-H Bond (0.96A) C1 - H1A_a ... 0.84 Ang.
PLAT350_ALERT_3_C Short C-H Bond (0.96A) C5 - H5A ... 0.84 Ang.
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety C1
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety C5
PLAT390_ALERT_3_C Deviating Methyl C1 X-C-H Bond Angle ...... 116.20 Deg.
PLAT390_ALERT_3_C Deviating Methyl C1 X-C-H Bond Angle ...... 116.20 Deg.
PLAT391_ALERT_3_C Deviating Methyl C1 H-C-H Bond Angle ...... 100.00 Deg.
PLAT391_ALERT_3_C Deviating Methyl C1 H-C-H Bond Angle ...... 100.00 Deg.
PLAT391_ALERT_3_C Deviating Methyl C9 H-C-H Bond Angle ...... 101.00 Deg.
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
16 ALERT level C = Check and explain
0 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
10 ALERT type 3 Indicator that the structure quality may be low
3 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXTL.
Methyl
N-[4-(4,6-dimethylpyrimidin-2-ylamino)thiocarbonyl]carbamate
top
Crystal data top
C9H12N4O2S | F(000) = 504 |
Mr = 240.29 | Dx = 1.375 Mg m−3 |
Monoclinic, C2/m | Mo Kα radiation, λ = 0.71073 Å |
a = 17.537 (5) Å | Cell parameters from 1090 reflections |
b = 6.759 (2) Å | θ = 2.6–24.0° |
c = 11.148 (3) Å | µ = 0.27 mm−1 |
β = 118.557 (4)° | T = 293 K |
V = 1160.5 (6) Å3 | Block, colourless |
Z = 4 | 0.27 × 0.12 × 0.08 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1117 independent reflections |
Radiation source: fine-focus sealed tube | 873 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
φ and ω scans | θmax = 25.1°, θmin = 2.5° |
Absorption correction: multi-scan SADABS (Sheldrick, 1996) | h = −20→20 |
Tmin = 0.962, Tmax = 0.979 | k = −8→8 |
2964 measured reflections | l = −11→13 |
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)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.116 | Only H-atom coordinates refined |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0829P)2] where P = (Fo2 + 2Fc2)/3 |
1117 reflections | (Δ/σ)max < 0.001 |
118 parameters | Δρmax = 0.18 e Å−3 |
0 restraints | Δρmin = −0.21 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 | Uiso*/Ueq | |
S1 | 0.42358 (5) | 0.0000 | 0.28149 (7) | 0.0684 (3) | |
N1 | 0.36437 (14) | 0.0000 | 0.6602 (2) | 0.0537 (5) | |
N2 | 0.23026 (13) | 0.0000 | 0.4527 (2) | 0.0506 (5) | |
N3 | 0.36658 (15) | 0.0000 | 0.4587 (2) | 0.0529 (6) | |
N4 | 0.25798 (14) | 0.0000 | 0.2360 (2) | 0.0562 (6) | |
O1 | 0.24719 (18) | 0.0000 | 0.0222 (2) | 0.1142 (10) | |
O2 | 0.13102 (14) | 0.0000 | 0.05291 (19) | 0.0705 (6) | |
C1 | 0.3750 (3) | 0.0000 | 0.8824 (3) | 0.0769 (9) | |
C2 | 0.32075 (19) | 0.0000 | 0.7309 (3) | 0.0557 (6) | |
C3 | 0.23133 (19) | 0.0000 | 0.6655 (3) | 0.0593 (7) | |
C4 | 0.18634 (17) | 0.0000 | 0.5252 (3) | 0.0542 (6) | |
C5 | 0.0897 (2) | 0.0000 | 0.4438 (4) | 0.0730 (8) | |
C6 | 0.31628 (16) | 0.0000 | 0.5246 (2) | 0.0466 (6) | |
C7 | 0.34475 (17) | 0.0000 | 0.3232 (3) | 0.0499 (6) | |
C8 | 0.2158 (2) | 0.0000 | 0.0947 (3) | 0.0624 (7) | |
C9 | 0.0754 (3) | 0.0000 | −0.0931 (3) | 0.0882 (11) | |
H3 | 0.419 (3) | 0.0000 | 0.518 (4) | 0.080* | |
H4 | 0.223 (2) | 0.0000 | 0.273 (4) | 0.080* | |
H3A | 0.201 (2) | 0.0000 | 0.711 (4) | 0.080* | |
H1B | 0.343 (2) | 0.0000 | 0.928 (3) | 0.080* | |
H1A | 0.4056 (16) | 0.101 (3) | 0.917 (2) | 0.080* | |
H5A | 0.068 (3) | 0.0000 | 0.497 (3) | 0.080* | |
H5B | 0.0707 (14) | 0.116 (4) | 0.387 (2) | 0.080* | |
H9A | 0.018 (3) | 0.0000 | −0.103 (3) | 0.080* | |
H9B | 0.0895 (15) | 0.106 (3) | −0.132 (2) | 0.080* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0488 (5) | 0.1060 (6) | 0.0616 (5) | 0.000 | 0.0353 (4) | 0.000 |
N1 | 0.0417 (12) | 0.0686 (13) | 0.0538 (12) | 0.000 | 0.0251 (10) | 0.000 |
N2 | 0.0379 (12) | 0.0628 (13) | 0.0554 (12) | 0.000 | 0.0258 (10) | 0.000 |
N3 | 0.0341 (11) | 0.0750 (14) | 0.0530 (12) | 0.000 | 0.0236 (10) | 0.000 |
N4 | 0.0448 (13) | 0.0778 (15) | 0.0501 (13) | 0.000 | 0.0261 (11) | 0.000 |
O1 | 0.0714 (15) | 0.222 (3) | 0.0577 (14) | 0.000 | 0.0378 (12) | 0.000 |
O2 | 0.0507 (11) | 0.1025 (15) | 0.0506 (11) | 0.000 | 0.0180 (9) | 0.000 |
C1 | 0.066 (2) | 0.111 (3) | 0.0542 (18) | 0.000 | 0.0291 (17) | 0.000 |
C2 | 0.0570 (16) | 0.0634 (16) | 0.0554 (15) | 0.000 | 0.0339 (13) | 0.000 |
C3 | 0.0513 (16) | 0.0737 (17) | 0.0675 (18) | 0.000 | 0.0402 (14) | 0.000 |
C4 | 0.0405 (13) | 0.0614 (15) | 0.0668 (17) | 0.000 | 0.0306 (13) | 0.000 |
C5 | 0.0412 (16) | 0.096 (2) | 0.087 (2) | 0.000 | 0.0355 (16) | 0.000 |
C6 | 0.0387 (13) | 0.0541 (14) | 0.0512 (14) | 0.000 | 0.0248 (11) | 0.000 |
C7 | 0.0452 (15) | 0.0556 (14) | 0.0517 (14) | 0.000 | 0.0255 (12) | 0.000 |
C8 | 0.0521 (17) | 0.0798 (19) | 0.0561 (16) | 0.000 | 0.0265 (14) | 0.000 |
C9 | 0.071 (2) | 0.125 (3) | 0.0521 (18) | 0.000 | 0.0167 (17) | 0.000 |
Geometric parameters (Å, º) top
S1—C7 | 1.656 (3) | O2—C9 | 1.443 (4) |
N1—C6 | 1.333 (3) | C1—C2 | 1.490 (4) |
N1—C2 | 1.336 (3) | C1—H1B | 0.91 (3) |
N2—C6 | 1.327 (3) | C1—H1A | 0.84 (2) |
N2—C4 | 1.357 (3) | C2—C3 | 1.378 (4) |
N3—C7 | 1.370 (3) | C3—C4 | 1.375 (4) |
N3—C6 | 1.392 (3) | C3—H3A | 0.89 (3) |
N3—H3 | 0.84 (4) | C4—C5 | 1.492 (4) |
N4—C7 | 1.359 (3) | C5—H5A | 0.85 (3) |
N4—C8 | 1.383 (3) | C5—H5B | 0.96 (2) |
N4—H4 | 0.88 (4) | C9—H9A | 0.96 (4) |
O1—C8 | 1.176 (3) | C9—H9B | 0.93 (2) |
O2—C8 | 1.329 (4) | | |
| | | |
C6—N1—C2 | 116.0 (2) | N2—C4—C3 | 119.8 (2) |
C6—N2—C4 | 116.4 (2) | N2—C4—C5 | 116.2 (3) |
C7—N3—C6 | 132.0 (2) | C3—C4—C5 | 124.0 (3) |
C7—N3—H3 | 119 (2) | C4—C5—H5A | 110 (3) |
C6—N3—H3 | 109 (2) | C4—C5—H5B | 109.7 (13) |
C7—N4—C8 | 128.4 (2) | H5A—C5—H5B | 109.1 (18) |
C7—N4—H4 | 117 (2) | N2—C6—N1 | 127.2 (2) |
C8—N4—H4 | 115 (2) | N2—C6—N3 | 120.3 (2) |
C8—O2—C9 | 115.8 (3) | N1—C6—N3 | 112.4 (2) |
C2—C1—H1B | 114 (2) | N4—C7—N3 | 114.6 (2) |
C2—C1—H1A | 115.9 (17) | N4—C7—S1 | 126.81 (19) |
H1B—C1—H1A | 100 (2) | N3—C7—S1 | 118.6 (2) |
N1—C2—C3 | 121.0 (2) | O1—C8—O2 | 124.9 (3) |
N1—C2—C1 | 115.7 (3) | O1—C8—N4 | 127.7 (3) |
C3—C2—C1 | 123.2 (3) | O2—C8—N4 | 107.4 (2) |
C4—C3—C2 | 119.4 (2) | O2—C9—H9A | 104 (2) |
C4—C3—H3A | 118 (2) | O2—C9—H9B | 109.8 (15) |
C2—C3—H3A | 122 (2) | H9A—C9—H9B | 116.2 (19) |
| | | |
C6—N1—C2—C3 | 0.000 (1) | C2—N1—C6—N3 | 180.0 |
C6—N1—C2—C1 | 180.000 (1) | C7—N3—C6—N2 | 0.0 |
N1—C2—C3—C4 | 0.000 (1) | C7—N3—C6—N1 | 180.0 |
C1—C2—C3—C4 | 180.000 (1) | C8—N4—C7—N3 | 180.0 |
C6—N2—C4—C3 | 0.0 | C8—N4—C7—S1 | 0.0 |
C6—N2—C4—C5 | 180.0 | C6—N3—C7—N4 | 0.0 |
C2—C3—C4—N2 | 0.000 (1) | C6—N3—C7—S1 | 180.0 |
C2—C3—C4—C5 | 180.000 (1) | C9—O2—C8—O1 | 0.0 |
C4—N2—C6—N1 | 0.0 | C9—O2—C8—N4 | 180.0 |
C4—N2—C6—N3 | 180.0 | C7—N4—C8—O1 | 0.0 |
C2—N1—C6—N2 | 0.0 | C7—N4—C8—O2 | 180.0 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3···S1i | 0.84 (4) | 2.59 (4) | 3.426 (2) | 174 (3) |
N4—H4···N2 | 0.88 (4) | 1.95 (4) | 2.683 (3) | 140 (3) |
C1—H1B···O1ii | 0.91 (3) | 2.37 (4) | 3.284 (5) | 174 (3) |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, y, z+1. |