Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768106016326/av5058sup1.cif
Contains datablock GUR2

fcf

Structure factor file (CIF format) https://doi.org/10.1107/S0108768106016326/av5058sup2.fcf
Contains datablock f

CCDC reference: 618477

Computing details top

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).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
[Figure 4]
(GUR2) top
Crystal data top
C9H14N2O2SZ = 2
Mr = 214.28F(000) = 228
Triclinic, P1Dx = 1.358 Mg m3
a = 7.2934 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.8145 (2) ÅCell parameters from 71444 reflections
c = 10.2181 (3) Åθ = 2.1–55.8°
α = 87.055 (1)°µ = 0.29 mm1
β = 70.569 (1)°T = 110 K
γ = 72.898 (1)°Rhombic, colorless
V = 524.22 (3) Å30.36 × 0.24 × 0.16 mm
Data collection top
Bruker
diffractometer with a SMART 6000 CCD detector
Rint = 0.029
ω scansθmax = 55.8°, θmin = 2.1°
71444 measured reflectionsh = 016
12501 independent reflectionsk = 1618
9412 reflections with I > 3σl = 2223
Refinement top
Refinement on F2All H-atom parameters refined
R[F2 > 2σ(F2)] = 0.019 w = 1/[s2(Fsqd)]
wR(F2) = 0.022(Δ/σ)max = 0.020
S = 1.20Δρmax = 0.13 e Å3
9412 reflectionsΔρmin = 0.22 e Å3
398 parameters
Crystal data top
C9H14N2O2Sγ = 72.898 (1)°
Mr = 214.28V = 524.22 (3) Å3
Triclinic, P1Z = 2
a = 7.2934 (2) ÅMo Kα radiation
b = 7.8145 (2) ŵ = 0.29 mm1
c = 10.2181 (3) ÅT = 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 reflectionsRint = 0.029
12501 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.019398 parameters
wR(F2) = 0.022All H-atom parameters refined
S = 1.20Δρmax = 0.13 e Å3
9412 reflectionsΔρmin = 0.22 e Å3
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S0.18730 (1)0.96544 (2)0.11564 (1)0.016
O10.86080 (4)0.76666 (6)0.44893 (3)0.021
O20.60553 (4)0.69576 (5)0.61292 (3)0.018
N10.26671 (3)0.82174 (5)0.33850 (3)0.014
N30.52655 (4)0.90635 (5)0.17878 (3)0.016
C20.33887 (4)0.89339 (5)0.21355 (3)0.013
C40.67488 (4)0.82071 (5)0.24809 (3)0.014
C4'0.82546 (5)0.65044 (7)0.16374 (4)0.019
C50.56472 (4)0.78479 (5)0.39624 (3)0.013
C5'0.68923 (4)0.75005 (5)0.48707 (3)0.013
C60.36891 (4)0.78006 (5)0.43451 (3)0.013
C6'0.24022 (5)0.73565 (7)0.57232 (3)0.019
C70.73244 (4)0.64908 (6)0.70039 (3)0.016
C80.60562 (6)0.60082 (7)0.83881 (4)0.020
H10.123390.813000.367110.021 (5)
H30.581350.962540.088550.029 (5)
H40.764300.912530.243880.022 (4)
H41'0.941000.597260.208300.038 (6)
H42'0.894340.686820.062090.023 (5)
H43'0.748450.556090.160280.022 (4)
H61'0.206320.830880.653390.058 (7)
H62'0.104380.717380.567760.063 (8)
H63'0.325150.611990.598440.046 (6)
H710.778310.767030.711800.027 (5)
H720.863530.537380.645780.023 (5)
H810.476850.710720.886340.038 (6)
H820.565210.484270.827880.034 (5)
H830.692430.565650.906170.040 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S0.01146 (2)0.02336 (4)0.01337 (2)0.00552 (2)0.00531 (2)0.00517 (2)
O10.01176 (6)0.03285 (15)0.01717 (8)0.01151 (7)0.00626 (6)0.00671 (9)
O20.01218 (5)0.02717 (12)0.01323 (7)0.00882 (6)0.00564 (5)0.00576 (7)
N10.01049 (5)0.02014 (10)0.01236 (7)0.00724 (6)0.00465 (5)0.00449 (7)
N30.01038 (5)0.02167 (10)0.01477 (7)0.00641 (6)0.00452 (5)0.00735 (7)
C20.01026 (6)0.01593 (9)0.01216 (7)0.00439 (6)0.00393 (5)0.00299 (7)
C40.00963 (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)
C50.00923 (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)
C60.00936 (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)
C70.01325 (7)0.02095 (11)0.01313 (8)0.00509 (7)0.00550 (6)0.00181 (8)
C80.01982 (10)0.02545 (15)0.01362 (9)0.00616 (10)0.00459 (8)0.00322 (10)
Geometric parameters (Å, º) top
S—C21.6887 (3)N3—C41.4679 (4)
O1—C5'1.2249 (4)C4—C51.5151 (4)
O2—C5'1.3343 (4)C4—C4'1.5323 (5)
O2—C71.4514 (4)C5—C61.3607 (4)
N1—C21.3687 (4)C5—C5'1.4661 (4)
N1—C61.3910 (4)C6—C6'1.4988 (4)
N3—C21.3283 (4)C7—C81.5094 (5)
C5'—O2—C7116.36 (3)C6—C5—C4120.43 (3)
C2—N1—C6124.02 (2)C5'—C5—C4114.34 (3)
C2—N3—C4125.59 (3)O1—C5'—O2122.07 (3)
N3—C2—N1116.50 (3)O1—C5'—C5122.10 (3)
N3—C2—S123.79 (3)O2—C5'—C5115.81 (3)
N1—C2—S119.70 (2)C5—C6—N1119.00 (3)
N3—C4—C5109.78 (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—C8107.50 (3)
C6—C5—C5'125.19 (3)

Experimental details

Crystal data
Chemical formulaC9H14N2O2S
Mr214.28
Crystal system, space groupTriclinic, 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)
V3)524.22 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.29
Crystal size (mm)0.36 × 0.24 × 0.16
Data collection
DiffractometerBruker
diffractometer with a SMART 6000 CCD detector
Absorption correction
No. of measured, independent and
observed (I > 3σ) reflections
71444, 12501, 9412
Rint0.029
(sin θ/λ)max1)1.164
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.019, 0.022, 1.20
No. of reflections9412
No. of parameters398
No. of restraints?
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.13, 0.22

Computer programs: CrystalClear,(2005), Otwinowski & Minor (1997), Zhurov et al.,(2005), Sheldrick (1997), Koritsanszky et al., (2003).

Selected geometric parameters (Å, º) top
S—C21.6887 (3)N3—C41.4679 (4)
O1—C5'1.2249 (4)C4—C51.5151 (4)
O2—C5'1.3343 (4)C4—C4'1.5323 (5)
O2—C71.4514 (4)C5—C61.3607 (4)
N1—C21.3687 (4)C5—C5'1.4661 (4)
N1—C61.3910 (4)C6—C6'1.4988 (4)
N3—C21.3283 (4)C7—C81.5094 (5)
C5'—O2—C7116.36 (3)C6—C5—C4120.43 (3)
C2—N1—C6124.02 (2)C5'—C5—C4114.34 (3)
C2—N3—C4125.59 (3)O1—C5'—O2122.07 (3)
N3—C2—N1116.50 (3)O1—C5'—C5122.10 (3)
N3—C2—S123.79 (3)O2—C5'—C5115.81 (3)
N1—C2—S119.70 (2)C5—C6—N1119.00 (3)
N3—C4—C5109.78 (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—C8107.50 (3)
C6—C5—C5'125.19 (3)
 

Subscribe to Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email support@iucr.org for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

Follow Acta Cryst. B
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds