Literature DB >> 21578771

5-Acetyl-4-(4-methoxy-phen-yl)-6-methyl-3,4-dihydro-pyrimidine-2(1H)-thione.

N Anuradha, A Thiruvalluvar, K Pandiarajan, S Chitra, R J Butcher.   

Abstract

In the title mol-ecule, C(14)H(16)N(2)O(2)S, the heterocyclic ring adopts an envelope conformation with the plane through the five coplanar atoms making a dihedral angle of 88.99 (4)° with the benzene ring, which adopts an axial orientation. The thionyl, acetyl and methyl groups all have equatorial orientations. Inter-molecular N-H⋯S, N-H⋯O, C-H⋯O and C-H⋯S hydrogen bonds are found in the crystal structure.

Entities:  

Year:  2009        PMID： 21578771      PMCID： PMC2972144          DOI： 10.1107/S160053680904639X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For related crystal structures and their chemical and biological applications, see: Anuradha et al. (2008 ▶, 2009 ▶); Chitra et al. (2009 ▶).

Experimental

Crystal data

C14H16N2O2S M = 276.36 Monoclinic, a = 12.0415 (2) Å b = 6.2219 (1) Å c = 18.0192 (3) Å β = 100.901 (1)° V = 1325.66 (4) Å3 Z = 4 Cu Kα radiation μ = 2.17 mm−1 T = 110 K 0.53 × 0.13 × 0.10 mm

Data collection

Oxford Diffraction Xcalibur Ruby Gemini diffractometer Absorption correction: multi-scan (CrysAlis Pro; Oxford Diffraction, 2009 ▶) T min = 0.418, T max = 1.000 5263 measured reflections 2616 independent reflections 2447 reflections with I > 2σ(I) R int = 0.020

Refinement

R[F 2 > 2σ(F 2)] = 0.039 wR(F 2) = 0.112 S = 1.09 2616 reflections 183 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.44 e Å−3 Δρmin = −0.28 e Å−3 Data collection: CrysAlis Pro (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis Pro; data reduction: CrysAlis Pro; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680904639X/wn2363sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053680904639X/wn2363Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C14H16N2O2SF(000) = 584
Mr = 276.36Dx = 1.385 Mg m−3
Monoclinic, P21/nMelting point: 469.5 K
Hall symbol: -P 2ynCu Kα radiation, λ = 1.54184 Å
a = 12.0415 (2) ÅCell parameters from 4545 reflections
b = 6.2219 (1) Åθ = 4.9–74.1°
c = 18.0192 (3) ŵ = 2.17 mm−1
β = 100.901 (1)°T = 110 K
V = 1325.66 (4) Å3Needle, colorless
Z = 40.53 × 0.13 × 0.10 mm
Oxford Diffraction Xcalibur Ruby Gemini diffractometer2616 independent reflections
Radiation source: fine-focus sealed tube2447 reflections with I > 2σ(I)
graphiteRint = 0.020
Detector resolution: 10.5081 pixels mm-1θmax = 74.1°, θmin = 4.9°
ω scansh = −12→15
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −7→7
Tmin = 0.418, Tmax = 1.000l = −21→22
5263 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.0764P)2 + 0.4468P] where P = (Fo2 + 2Fc2)/3
2616 reflections(Δ/σ)max = 0.001
183 parametersΔρmax = 0.44 e Å−3
0 restraintsΔρmin = −0.28 e Å−3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
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 > 2σ(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.
xyzUiso*/Ueq
S20.88945 (3)0.40406 (6)0.57843 (2)0.0167 (1)
O140.29443 (9)0.06284 (18)0.34383 (6)0.0192 (3)
O150.74168 (10)−0.43229 (18)0.35876 (6)0.0240 (3)
N10.90803 (10)0.2225 (2)0.44765 (7)0.0155 (3)
N30.80719 (10)0.0321 (2)0.52096 (7)0.0151 (3)
C20.86586 (11)0.2080 (2)0.51219 (8)0.0139 (4)
C40.75819 (12)−0.1161 (2)0.45957 (8)0.0140 (4)
C50.82669 (12)−0.1056 (2)0.39675 (8)0.0140 (4)
C60.89493 (12)0.0647 (2)0.39170 (8)0.0139 (4)
C140.26371 (13)0.2480 (3)0.29726 (9)0.0237 (4)
C150.80594 (12)−0.2907 (2)0.34489 (8)0.0158 (4)
C160.85846 (12)−0.3124 (2)0.27577 (8)0.0181 (4)
C410.63430 (12)−0.0628 (2)0.43028 (8)0.0148 (4)
C420.60296 (12)0.1390 (3)0.40073 (8)0.0162 (4)
C430.49062 (12)0.1883 (2)0.37094 (8)0.0169 (4)
C440.40836 (12)0.0309 (3)0.37140 (8)0.0159 (4)
C450.43784 (12)−0.1707 (3)0.40213 (8)0.0185 (4)
C460.55023 (12)−0.2172 (2)0.43155 (8)0.0172 (4)
C610.96218 (13)0.1116 (2)0.33106 (8)0.0178 (4)
H10.9539 (17)0.328 (3)0.4448 (11)0.022 (5)*
H30.7815 (18)0.021 (4)0.5615 (12)0.028 (5)*
H40.76299−0.265650.480250.0167*
H14A0.309230.252720.257590.0356*
H14B0.183370.239870.274040.0356*
H14C0.277500.378140.328270.0356*
H16A0.83989−0.453710.252700.0271*
H16B0.82891−0.199690.239370.0271*
H16C0.94075−0.297970.290240.0271*
H420.659400.245700.400830.0194*
H430.470360.326830.350650.0202*
H450.38117−0.276420.403000.0222*
H460.57023−0.354850.452710.0206*
H61A0.912140.106240.281420.0267*
H61B0.995950.255030.339160.0267*
H61C1.022180.004140.333140.0267*
U11U22U33U12U13U23
S20.0187 (2)0.0159 (2)0.0155 (2)−0.0015 (1)0.0030 (1)−0.0042 (1)
O140.0145 (5)0.0235 (6)0.0196 (5)−0.0007 (4)0.0030 (4)0.0031 (4)
O150.0333 (7)0.0176 (6)0.0225 (5)−0.0084 (4)0.0087 (5)−0.0039 (4)
N10.0175 (6)0.0134 (6)0.0161 (6)−0.0030 (5)0.0042 (5)−0.0007 (5)
N30.0162 (6)0.0175 (6)0.0118 (5)−0.0020 (5)0.0034 (5)−0.0011 (5)
C20.0127 (6)0.0139 (7)0.0140 (6)0.0025 (5)−0.0003 (5)−0.0006 (5)
C40.0164 (7)0.0112 (6)0.0139 (6)−0.0026 (5)0.0020 (5)−0.0002 (5)
C50.0152 (7)0.0135 (7)0.0128 (6)0.0016 (5)0.0014 (5)−0.0003 (5)
C60.0136 (7)0.0140 (7)0.0135 (6)0.0014 (5)0.0012 (5)0.0007 (5)
C140.0191 (7)0.0262 (8)0.0253 (8)0.0031 (6)0.0028 (6)0.0052 (7)
C150.0184 (7)0.0129 (7)0.0149 (6)0.0013 (5)−0.0002 (5)0.0003 (5)
C160.0222 (7)0.0162 (7)0.0154 (6)−0.0001 (5)0.0025 (5)−0.0029 (5)
C410.0168 (7)0.0167 (7)0.0110 (6)−0.0015 (5)0.0030 (5)−0.0012 (5)
C420.0173 (7)0.0166 (7)0.0151 (6)−0.0042 (5)0.0042 (5)0.0004 (6)
C430.0193 (7)0.0161 (7)0.0159 (6)0.0000 (5)0.0048 (5)0.0016 (5)
C440.0147 (7)0.0205 (7)0.0128 (6)−0.0008 (5)0.0032 (5)−0.0014 (5)
C450.0176 (7)0.0186 (8)0.0200 (7)−0.0056 (6)0.0051 (5)−0.0008 (6)
C460.0198 (7)0.0143 (7)0.0178 (7)−0.0021 (5)0.0046 (5)0.0001 (5)
C610.0204 (7)0.0170 (7)0.0172 (7)−0.0037 (5)0.0067 (6)−0.0014 (5)
S2—C21.6927 (14)C42—C431.392 (2)
O14—C141.432 (2)C43—C441.394 (2)
O14—C441.3822 (18)C44—C451.390 (3)
O15—C151.2290 (18)C45—C461.387 (2)
N1—C21.3571 (19)C4—H41.0000
N1—C61.3947 (18)C14—H14A0.9800
N3—C21.3282 (18)C14—H14B0.9800
N3—C41.4749 (18)C14—H14C0.9800
N1—H10.87 (2)C16—H16A0.9800
N3—H30.85 (2)C16—H16B0.9800
C4—C411.522 (2)C16—H16C0.9800
C4—C51.523 (2)C42—H420.9500
C5—C61.3544 (19)C43—H430.9500
C5—C151.4744 (19)C45—H450.9500
C6—C611.507 (2)C46—H460.9500
C15—C161.506 (2)C61—H61A0.9800
C41—C461.3989 (19)C61—H61B0.9800
C41—C421.388 (2)C61—H61C0.9800
S2···N1i3.4641 (13)C43···H14C2.8000
S2···C16ii3.6641 (15)C43···H14A2.7200
S2···H4iii2.9400C44···H3vi2.80 (2)
S2···H1i2.61 (2)C45···H3vi2.99 (2)
S2···H14Civ3.1600C61···H16B2.8400
S2···H16Cii2.9000C61···H16C2.6500
S2···H61Bi2.8000H1···H61B2.1100
S2···H61Cii3.0800H1···S2i2.61 (2)
O14···C14v3.181 (2)H3···O14vi2.15 (2)
O14···N3vi2.9849 (16)H3···C44vi2.80 (2)
O15···N1vii3.1588 (17)H3···C45vi2.99 (2)
O15···C42vii3.310 (2)H4···S2vii2.9400
O15···C463.1575 (18)H4···O152.3900
O15···C413.0411 (18)H4···H462.3500
O14···H3vi2.15 (2)H14A···C432.7200
O14···H14Av2.7900H14A···H432.3600
O15···H42.3900H14A···O14ix2.7900
O15···H42vii2.4200H14C···C432.8000
O15···H16Bviii2.4600H14C···H432.3000
O15···H61Aviii2.8500H14C···S2iv3.1600
N1···O15iii3.1588 (17)H16A···C15viii3.0700
N1···S2i3.4641 (13)H16A···C42viii3.0300
N3···O14vi2.9849 (16)H16A···H16Bviii2.5700
N3···H422.8600H16B···C612.8400
C2···C423.440 (2)H16B···H61A2.2200
C2···C6ii3.5055 (19)H16B···O15x2.4600
C6···C423.580 (2)H16B···C42viii2.9700
C6···C2ii3.5055 (19)H16B···H16Ax2.5700
C14···C14v3.532 (3)H16B···H42viii2.5800
C14···C14ix3.532 (3)H16C···C63.0200
C14···O14ix3.181 (2)H16C···C612.6500
C16···C43viii3.480 (2)H16C···H61A2.5400
C16···S2ii3.6641 (15)H16C···H61C2.1900
C16···C613.0069 (18)H16C···S2ii2.9000
C16···C42viii3.314 (2)H42···O15iii2.4200
C41···O153.0411 (18)H42···N32.8600
C42···C63.580 (2)H42···C22.8900
C42···O15iii3.310 (2)H42···C52.9800
C42···C16x3.314 (2)H42···C63.0800
C42···C23.440 (2)H42···H16Bx2.5800
C43···C16x3.480 (2)H43···C142.5400
C46···O153.1575 (18)H43···H14A2.3600
C61···C163.0069 (18)H43···H14C2.3000
C2···H422.8900H46···H42.3500
C5···H422.9800H61A···C153.1000
C6···H16C3.0200H61A···C162.6800
C6···H423.0800H61A···H16B2.2200
C14···H432.5400H61A···H16C2.5400
C15···H16Ax3.0700H61A···O15x2.8500
C15···H61A3.1000H61B···H12.1100
C16···H61C2.8400H61B···S2i2.8000
C16···H61A2.6800H61C···C162.8400
C42···H16Bx2.9700H61C···H16C2.1900
C42···H16Ax3.0300H61C···S2ii3.0800
C14—O14—C44117.07 (12)C41—C46—C45120.48 (13)
C2—N1—C6124.27 (12)N3—C4—H4108.00
C2—N3—C4124.91 (12)C5—C4—H4108.00
C2—N1—H1116.6 (13)C41—C4—H4108.00
C6—N1—H1118.5 (13)O14—C14—H14A109.00
C2—N3—H3117.3 (16)O14—C14—H14B109.00
C4—N3—H3115.8 (16)O14—C14—H14C109.00
S2—C2—N3122.14 (11)H14A—C14—H14B109.00
N1—C2—N3116.77 (12)H14A—C14—H14C109.00
S2—C2—N1121.08 (10)H14B—C14—H14C109.00
N3—C4—C5109.55 (11)C15—C16—H16A109.00
N3—C4—C41110.53 (11)C15—C16—H16B109.00
C5—C4—C41111.47 (12)C15—C16—H16C109.00
C4—C5—C15112.76 (11)H16A—C16—H16B109.00
C6—C5—C15126.92 (13)H16A—C16—H16C109.00
C4—C5—C6120.28 (12)H16B—C16—H16C109.00
N1—C6—C5119.29 (13)C41—C42—H42119.00
N1—C6—C61112.65 (11)C43—C42—H42119.00
C5—C6—C61128.06 (12)C42—C43—H43121.00
C5—C15—C16123.16 (12)C44—C43—H43121.00
O15—C15—C5117.96 (13)C44—C45—H45120.00
O15—C15—C16118.88 (12)C46—C45—H45120.00
C4—C41—C46120.64 (11)C41—C46—H46120.00
C42—C41—C46118.84 (13)C45—C46—H46120.00
C4—C41—C42120.51 (12)C6—C61—H61A109.00
C41—C42—C43121.41 (14)C6—C61—H61B109.00
C42—C43—C44118.86 (14)C6—C61—H61C109.00
O14—C44—C43123.70 (15)H61A—C61—H61B109.00
C43—C44—C45120.54 (14)H61A—C61—H61C109.00
O14—C44—C45115.74 (14)H61B—C61—H61C109.00
C44—C45—C46119.84 (14)
C14—O14—C44—C4314.8 (2)C4—C5—C6—N14.6 (2)
C14—O14—C44—C45−166.54 (13)C4—C5—C6—C61−175.22 (13)
C6—N1—C2—S2178.02 (11)C15—C5—C6—N1−177.58 (13)
C6—N1—C2—N3−1.0 (2)C15—C5—C6—C612.6 (2)
C2—N1—C6—C57.1 (2)C4—C5—C15—O15−2.64 (19)
C2—N1—C6—C61−173.10 (13)C4—C5—C15—C16176.60 (12)
C4—N3—C2—S2163.27 (11)C6—C5—C15—O15179.36 (14)
C4—N3—C2—N1−17.7 (2)C6—C5—C15—C16−1.4 (2)
C2—N3—C4—C526.71 (18)C4—C41—C42—C43177.44 (13)
C2—N3—C4—C41−96.51 (16)C46—C41—C42—C43−1.6 (2)
N3—C4—C5—C6−19.06 (18)C4—C41—C46—C45−177.50 (13)
N3—C4—C5—C15162.80 (11)C42—C41—C46—C451.5 (2)
C41—C4—C5—C6103.60 (15)C41—C42—C43—C440.3 (2)
C41—C4—C5—C15−74.54 (14)C42—C43—C44—O14179.52 (13)
N3—C4—C41—C4259.07 (17)C42—C43—C44—C451.0 (2)
N3—C4—C41—C46−121.95 (14)O14—C44—C45—C46−179.68 (13)
C5—C4—C41—C42−63.03 (16)C43—C44—C45—C46−1.0 (2)
C5—C4—C41—C46115.95 (14)C44—C45—C46—C41−0.2 (2)
D—H···AD—HH···AD···AD—H···A
N1—H1···S2i0.87 (2)2.61 (2)3.464 (1)169.3 (18)
N3—H3···O14vi0.85 (2)2.15 (2)2.985 (2)170 (2)
C16—H16B···O15x0.982.463.4377 (17)176
C42—H42···O15iii0.952.423.310 (2)156
C61—H61B···S2i0.982.803.7190 (14)157
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N1—H1⋯S2i 0.87 (2)2.61 (2)3.464 (1)169.3 (18)
N3—H3⋯O14ii 0.85 (2)2.15 (2)2.985 (2)170 (2)
C16—H16B⋯O15iii 0.982.463.4377 (17)176
C42—H42⋯O15iv 0.952.423.310 (2)156
C61—H61B⋯S2i 0.982.803.7190 (14)157

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

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1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  5-Acetyl-4-(4-chloro-phen-yl)-6-methyl-3,4-dihydro-pyrimidine-2(1H)-thione.

Authors:  N Anuradha; A Thiruvalluvar; K Pandiarajan; S Chitra; R J Butcher
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-02-21

3.  5-Acetyl-4-(2-chloro-phen-yl)-6-methyl-3,4-dihydro-pyrimidin-2(1H)-one.

Authors:  N Anuradha; A Thiruvalluvar; K Pandiarajan; S Chitra; R J Butcher
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-11-29

4.  5-Acetyl-4-(4-methoxy-phen-yl)-6-methyl-3,4-dihydro-pyrimidin-2(1H)-one.

Authors:  S Chitra; K Pandiarajan; N Anuradha; A Thiruvalluvar
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-12-06

5.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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1.  1-(6-Methyl-4-phenyl-2-sulfanyl-idene-1,2,3,4-tetrahydro-pyrimidin-5-yl)ethanone.

Authors:  N Anuradha; A Thiruvalluvar; S Chitra; K Pandiarajan; R J Butcher
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-08-11
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