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The electron density and electronic energy densities in ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate have been studied from accurate X-ray diffraction measurements at 110 K and theoretical single-molecule and periodic crystal calculations. The Quantum Theory of Atoms in Molecules and Crystals (QTAMC) was applied to analyze the electron-density and electronic energy-density features to estimate their reproducibility in molecules and crystals. It was found that the local electron-density values at the bond critical points derived by different methods are in reasonable agreement, while the Laplacian of the electron density computed from wavefunctions, and electron densities derived from experimental or theoretical structure factors in terms of the Hansen-Coppens multipole model differ significantly. This disagreement results from insufficient flexibility of the multipole model to describe the longitudinal electron-density curvature in the case of shared atomic interactions. This deficiency runs through all the existing QTAMC bonding descriptors which contain the Laplacian term. The integrated atomic characteristics, however, suffer noticeably less from the aforementioned shortcoming. We conclude that the electron-density and electronic energy QTAMC characteristics derived from wavefunctions, especially the integrated quantities, are nowadays the most suitable candidates for analysis of the transferability of atoms and atomic groups in similar compounds.
Supporting information
CCDC reference: 618477
Data collection: CrystalClear,(2005); cell refinement: Otwinowski & Minor (1997); data reduction: Zhurov et al.,(2005); program(s) used to solve structure: Sheldrick (1997); program(s) used to refine structure: Koritsanszky et al., (2003); molecular graphics: Koritsanszky et al., (2003); software used to prepare material for publication: Koritsanszky et al., (2003).
Crystal data top
C9H14N2O2S | Z = 2 |
Mr = 214.28 | F(000) = 228 |
Triclinic, P1 | Dx = 1.358 Mg m−3 |
a = 7.2934 (2) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 7.8145 (2) Å | Cell parameters from 71444 reflections |
c = 10.2181 (3) Å | θ = 2.1–55.8° |
α = 87.055 (1)° | µ = 0.29 mm−1 |
β = 70.569 (1)° | T = 110 K |
γ = 72.898 (1)° | Rhombic, colorless |
V = 524.22 (3) Å3 | 0.36 × 0.24 × 0.16 mm |
Data collection top
Bruker diffractometer with a SMART 6000 CCD detector | Rint = 0.029 |
ω scans | θmax = 55.8°, θmin = 2.1° |
71444 measured reflections | h = 0→16 |
12501 independent reflections | k = −16→18 |
9412 reflections with I > 3σ | l = −22→23 |
Refinement top
Refinement on F2 | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.019 | w = 1/[s2(Fsqd)] |
wR(F2) = 0.022 | (Δ/σ)max = 0.020 |
S = 1.20 | Δρmax = 0.13 e Å−3 |
9412 reflections | Δρmin = −0.22 e Å−3 |
398 parameters | |
Crystal data top
C9H14N2O2S | γ = 72.898 (1)° |
Mr = 214.28 | V = 524.22 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.2934 (2) Å | Mo Kα radiation |
b = 7.8145 (2) Å | µ = 0.29 mm−1 |
c = 10.2181 (3) Å | T = 110 K |
α = 87.055 (1)° | 0.36 × 0.24 × 0.16 mm |
β = 70.569 (1)° | |
Data collection top
Bruker diffractometer with a SMART 6000 CCD detector | 9412 reflections with I > 3σ |
71444 measured reflections | Rint = 0.029 |
12501 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.019 | 398 parameters |
wR(F2) = 0.022 | All H-atom parameters refined |
S = 1.20 | Δρmax = 0.13 e Å−3 |
9412 reflections | Δρmin = −0.22 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S | 0.18730 (1) | 0.96544 (2) | 0.11564 (1) | 0.016 | |
O1 | 0.86080 (4) | 0.76666 (6) | 0.44893 (3) | 0.021 | |
O2 | 0.60553 (4) | 0.69576 (5) | 0.61292 (3) | 0.018 | |
N1 | 0.26671 (3) | 0.82174 (5) | 0.33850 (3) | 0.014 | |
N3 | 0.52655 (4) | 0.90635 (5) | 0.17878 (3) | 0.016 | |
C2 | 0.33887 (4) | 0.89339 (5) | 0.21355 (3) | 0.013 | |
C4 | 0.67488 (4) | 0.82071 (5) | 0.24809 (3) | 0.014 | |
C4' | 0.82546 (5) | 0.65044 (7) | 0.16374 (4) | 0.019 | |
C5 | 0.56472 (4) | 0.78479 (5) | 0.39624 (3) | 0.013 | |
C5' | 0.68923 (4) | 0.75005 (5) | 0.48707 (3) | 0.013 | |
C6 | 0.36891 (4) | 0.78006 (5) | 0.43451 (3) | 0.013 | |
C6' | 0.24022 (5) | 0.73565 (7) | 0.57232 (3) | 0.019 | |
C7 | 0.73244 (4) | 0.64908 (6) | 0.70039 (3) | 0.016 | |
C8 | 0.60562 (6) | 0.60082 (7) | 0.83881 (4) | 0.020 | |
H1 | 0.12339 | 0.81300 | 0.36711 | 0.021 (5) | |
H3 | 0.58135 | 0.96254 | 0.08855 | 0.029 (5) | |
H4 | 0.76430 | 0.91253 | 0.24388 | 0.022 (4) | |
H41' | 0.94100 | 0.59726 | 0.20830 | 0.038 (6) | |
H42' | 0.89434 | 0.68682 | 0.06209 | 0.023 (5) | |
H43' | 0.74845 | 0.55609 | 0.16028 | 0.022 (4) | |
H61' | 0.20632 | 0.83088 | 0.65339 | 0.058 (7) | |
H62' | 0.10438 | 0.71738 | 0.56776 | 0.063 (8) | |
H63' | 0.32515 | 0.61199 | 0.59844 | 0.046 (6) | |
H71 | 0.77831 | 0.76703 | 0.71180 | 0.027 (5) | |
H72 | 0.86353 | 0.53738 | 0.64578 | 0.023 (5) | |
H81 | 0.47685 | 0.71072 | 0.88634 | 0.038 (6) | |
H82 | 0.56521 | 0.48427 | 0.82788 | 0.034 (5) | |
H83 | 0.69243 | 0.56565 | 0.90617 | 0.040 (6) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S | 0.01146 (2) | 0.02336 (4) | 0.01337 (2) | −0.00552 (2) | −0.00531 (2) | 0.00517 (2) |
O1 | 0.01176 (6) | 0.03285 (15) | 0.01717 (8) | −0.01151 (7) | −0.00626 (6) | 0.00671 (9) |
O2 | 0.01218 (5) | 0.02717 (12) | 0.01323 (7) | −0.00882 (6) | −0.00564 (5) | 0.00576 (7) |
N1 | 0.01049 (5) | 0.02014 (10) | 0.01236 (7) | −0.00724 (6) | −0.00465 (5) | 0.00449 (7) |
N3 | 0.01038 (5) | 0.02167 (10) | 0.01477 (7) | −0.00641 (6) | −0.00452 (5) | 0.00735 (7) |
C2 | 0.01026 (6) | 0.01593 (9) | 0.01216 (7) | −0.00439 (6) | −0.00393 (5) | 0.00299 (7) |
C4 | 0.00963 (6) | 0.01910 (10) | 0.01305 (8) | −0.00569 (6) | −0.00376 (5) | 0.00387 (7) |
C4' | 0.01515 (8) | 0.02637 (15) | 0.01556 (10) | 0.00004 (9) | −0.00329 (7) | 0.00099 (10) |
C5 | 0.00923 (5) | 0.01713 (9) | 0.01211 (7) | −0.00532 (6) | −0.00377 (5) | 0.00285 (7) |
C5' | 0.00957 (5) | 0.01766 (10) | 0.01281 (7) | −0.00539 (6) | −0.00428 (5) | 0.00259 (7) |
C6 | 0.00936 (5) | 0.01724 (9) | 0.01135 (7) | −0.00541 (6) | −0.00340 (5) | 0.00262 (7) |
C6' | 0.01286 (7) | 0.03141 (17) | 0.01321 (8) | −0.01027 (9) | −0.00420 (6) | 0.00678 (10) |
C7 | 0.01325 (7) | 0.02095 (11) | 0.01313 (8) | −0.00509 (7) | −0.00550 (6) | 0.00181 (8) |
C8 | 0.01982 (10) | 0.02545 (15) | 0.01362 (9) | −0.00616 (10) | −0.00459 (8) | 0.00322 (10) |
Geometric parameters (Å, º) top
S—C2 | 1.6887 (3) | N3—C4 | 1.4679 (4) |
O1—C5' | 1.2249 (4) | C4—C5 | 1.5151 (4) |
O2—C5' | 1.3343 (4) | C4—C4' | 1.5323 (5) |
O2—C7 | 1.4514 (4) | C5—C6 | 1.3607 (4) |
N1—C2 | 1.3687 (4) | C5—C5' | 1.4661 (4) |
N1—C6 | 1.3910 (4) | C6—C6' | 1.4988 (4) |
N3—C2 | 1.3283 (4) | C7—C8 | 1.5094 (5) |
| | | |
C5'—O2—C7 | 116.36 (3) | C6—C5—C4 | 120.43 (3) |
C2—N1—C6 | 124.02 (2) | C5'—C5—C4 | 114.34 (3) |
C2—N3—C4 | 125.59 (3) | O1—C5'—O2 | 122.07 (3) |
N3—C2—N1 | 116.50 (3) | O1—C5'—C5 | 122.10 (3) |
N3—C2—S | 123.79 (3) | O2—C5'—C5 | 115.81 (3) |
N1—C2—S | 119.70 (2) | C5—C6—N1 | 119.00 (3) |
N3—C4—C5 | 109.78 (3) | C5—C6—C6' | 128.13 (3) |
N3—C4—C4' | 109.71 (3) | N1—C6—C6' | 112.87 (2) |
C5—C4—C4' | 112.73 (3) | O2—C7—C8 | 107.50 (3) |
C6—C5—C5' | 125.19 (3) | | |
Experimental details
Crystal data |
Chemical formula | C9H14N2O2S |
Mr | 214.28 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 110 |
a, b, c (Å) | 7.2934 (2), 7.8145 (2), 10.2181 (3) |
α, β, γ (°) | 87.055 (1), 70.569 (1), 72.898 (1) |
V (Å3) | 524.22 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.29 |
Crystal size (mm) | 0.36 × 0.24 × 0.16 |
|
Data collection |
Diffractometer | Bruker diffractometer with a SMART 6000 CCD detector |
Absorption correction | – |
No. of measured, independent and observed (I > 3σ) reflections | 71444, 12501, 9412 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 1.164 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.019, 0.022, 1.20 |
No. of reflections | 9412 |
No. of parameters | 398 |
No. of restraints | ? |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.13, −0.22 |
Selected geometric parameters (Å, º) topS—C2 | 1.6887 (3) | N3—C4 | 1.4679 (4) |
O1—C5' | 1.2249 (4) | C4—C5 | 1.5151 (4) |
O2—C5' | 1.3343 (4) | C4—C4' | 1.5323 (5) |
O2—C7 | 1.4514 (4) | C5—C6 | 1.3607 (4) |
N1—C2 | 1.3687 (4) | C5—C5' | 1.4661 (4) |
N1—C6 | 1.3910 (4) | C6—C6' | 1.4988 (4) |
N3—C2 | 1.3283 (4) | C7—C8 | 1.5094 (5) |
| | | |
C5'—O2—C7 | 116.36 (3) | C6—C5—C4 | 120.43 (3) |
C2—N1—C6 | 124.02 (2) | C5'—C5—C4 | 114.34 (3) |
C2—N3—C4 | 125.59 (3) | O1—C5'—O2 | 122.07 (3) |
N3—C2—N1 | 116.50 (3) | O1—C5'—C5 | 122.10 (3) |
N3—C2—S | 123.79 (3) | O2—C5'—C5 | 115.81 (3) |
N1—C2—S | 119.70 (2) | C5—C6—N1 | 119.00 (3) |
N3—C4—C5 | 109.78 (3) | C5—C6—C6' | 128.13 (3) |
N3—C4—C4' | 109.71 (3) | N1—C6—C6' | 112.87 (2) |
C5—C4—C4' | 112.73 (3) | O2—C7—C8 | 107.50 (3) |
C6—C5—C5' | 125.19 (3) | | |
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