Literature DB >> 21578798

5-Acetyl-4-(2-chloro-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(13)H(13)ClN(2)OS, the heterocyclic ring adopts a flattened boat conformation with the plane through the four coplanar atoms making a dihedral angle of 85.6 (1)° with the benzene ring, which adopts an axial orientation. The thionyl, acetyl and methyl groups all have equatorial orientations. Inter-molecular N-H⋯O, N-H⋯S and C-H⋯S hydrogen bonds are found in the crystal structure. A weak C-H⋯π inter-action involving the benzene ring also occurs.

Entities:  

Year:  2009        PMID： 21578798      PMCID： PMC2972027          DOI： 10.1107/S1600536809047187

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


Related literature

For chemical and biological applications of dihydro­pyrimidinones, see: Atwal et al. (1990 ▶); Kappe (1993 ▶, 2000 ▶); Kappe et al. (2000 ▶); Rovnyak et al. (1995 ▶); Sadanandam et al. (1992 ▶). For related crystal structures, see: Anuradha et al. (2008 ▶, 2009 ▶); Chitra et al. (2009 ▶).

Experimental

Crystal data

C13H13ClN2OS M = 280.77 Monoclinic, a = 7.2346 (12) Å b = 22.585 (3) Å c = 8.0941 (15) Å β = 106.177 (17)° V = 1270.2 (4) Å3 Z = 4 Cu Kα radiation μ = 4.11 mm−1 T = 110 K 0.45 × 0.43 × 0.12 mm

Data collection

Oxford Diffraction Xcalibur Ruby Gemini diffractometer Absorption correction: multi-scan (CrysAlis Pro; Oxford Diffraction, 2009 ▶) T min = 0.451, T max = 1.000 4641 measured reflections 2497 independent reflections 2246 reflections with I > 2σ(I) R int = 0.035

Refinement

R[F 2 > 2σ(F 2)] = 0.062 wR(F 2) = 0.184 S = 1.13 2497 reflections 173 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 1.19 e Å−3 Δρmin = −0.39 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/S1600536809047187/wn2366sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809047187/wn2366Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H13ClN2OSF(000) = 584
Mr = 280.77Dx = 1.468 Mg m−3
Monoclinic, P21/cMelting point: 484.5 K
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.54184 Å
a = 7.2346 (12) ÅCell parameters from 3483 reflections
b = 22.585 (3) Åθ = 5.7–73.8°
c = 8.0941 (15) ŵ = 4.11 mm−1
β = 106.177 (17)°T = 110 K
V = 1270.2 (4) Å3Triangular-plate, colourless
Z = 40.45 × 0.43 × 0.12 mm
Oxford Diffraction Xcalibur Ruby Gemini diffractometer2497 independent reflections
Radiation source: Enhance (Cu) X-ray Source2246 reflections with I > 2σ(I)
graphiteRint = 0.035
Detector resolution: 10.5081 pixels mm-1θmax = 74.1°, θmin = 6.0°
ω scansh = −8→8
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −27→16
Tmin = 0.451, Tmax = 1.000l = −9→8
4641 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)] = 0.062Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.184H atoms treated by a mixture of independent and constrained refinement
S = 1.13w = 1/[σ2(Fo2) + (0.1043P)2 + 2.5484P] where P = (Fo2 + 2Fc2)/3
2497 reflections(Δ/σ)max = 0.001
173 parametersΔρmax = 1.19 e Å−3
1 restraintΔρmin = −0.38 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
Cl20.66371 (12)0.18610 (4)0.75112 (12)0.0277 (3)
S20.80912 (11)0.01280 (4)0.64291 (10)0.0198 (3)
O150.1673 (3)0.10482 (11)1.0187 (3)0.0216 (7)
N10.7634 (4)0.06358 (13)0.9244 (3)0.0185 (8)
N30.4871 (4)0.05026 (12)0.7069 (3)0.0162 (8)
C20.6750 (5)0.04420 (15)0.7613 (4)0.0164 (9)
C40.3680 (4)0.08463 (14)0.7922 (4)0.0150 (8)
C50.4719 (5)0.09279 (14)0.9816 (4)0.0156 (9)
C60.6658 (5)0.08508 (15)1.0377 (4)0.0168 (9)
C150.3405 (5)0.10641 (14)1.0875 (4)0.0164 (9)
C160.4118 (5)0.12310 (17)1.2760 (4)0.0228 (10)
C410.2962 (5)0.14262 (14)0.6951 (4)0.0170 (9)
C420.4137 (5)0.18851 (15)0.6678 (4)0.0200 (10)
C430.3389 (6)0.23843 (16)0.5701 (5)0.0246 (10)
C440.1437 (6)0.24424 (16)0.5040 (5)0.0257 (11)
C450.0217 (5)0.20019 (17)0.5320 (5)0.0247 (10)
C460.0963 (5)0.15024 (15)0.6247 (4)0.0207 (10)
C610.7992 (5)0.09730 (19)1.2130 (4)0.0269 (10)
H10.882 (5)0.0629 (17)0.962 (5)0.012 (9)*
H30.422 (7)0.032 (2)0.611 (7)0.029 (11)*
H40.251210.060160.786650.0180*
H16A0.301670.131961.319970.0342*
H16B0.494800.158081.288720.0342*
H16C0.485170.090051.341080.0342*
H430.422790.268150.549710.0295*
H440.091680.278370.438900.0309*
H45−0.113640.204510.487130.0297*
H460.011110.120310.641560.0249*
H61A0.787060.138861.243300.0406*
H61B0.932140.089371.212230.0406*
H61C0.765440.071661.297900.0406*
U11U22U33U12U13U23
Cl20.0192 (5)0.0300 (5)0.0347 (5)−0.0063 (3)0.0090 (4)0.0031 (3)
S20.0184 (4)0.0252 (5)0.0188 (4)−0.0016 (3)0.0102 (3)−0.0050 (3)
O150.0169 (13)0.0327 (13)0.0173 (12)−0.0004 (9)0.0084 (9)0.0002 (9)
N10.0148 (14)0.0282 (15)0.0131 (13)−0.0005 (11)0.0051 (11)−0.0036 (10)
N30.0190 (14)0.0206 (13)0.0112 (12)−0.0020 (11)0.0077 (10)−0.0052 (10)
C20.0192 (16)0.0209 (15)0.0111 (14)−0.0027 (12)0.0074 (12)0.0005 (11)
C40.0131 (15)0.0205 (15)0.0132 (14)−0.0014 (12)0.0066 (12)−0.0016 (11)
C50.0178 (16)0.0187 (15)0.0111 (14)−0.0008 (12)0.0055 (12)−0.0017 (11)
C60.0159 (16)0.0241 (16)0.0106 (14)−0.0018 (12)0.0039 (12)−0.0006 (12)
C150.0187 (17)0.0182 (15)0.0150 (15)−0.0010 (12)0.0092 (13)0.0025 (11)
C160.0264 (18)0.0319 (18)0.0132 (16)−0.0021 (14)0.0107 (13)−0.0041 (13)
C410.0213 (16)0.0211 (16)0.0101 (14)−0.0030 (12)0.0069 (12)−0.0036 (12)
C420.0221 (17)0.0250 (17)0.0152 (16)−0.0026 (13)0.0091 (13)−0.0016 (12)
C430.035 (2)0.0221 (17)0.0201 (17)−0.0056 (14)0.0131 (15)−0.0015 (13)
C440.034 (2)0.0243 (17)0.0194 (18)0.0016 (15)0.0087 (15)0.0035 (13)
C450.0230 (18)0.0310 (18)0.0186 (17)0.0003 (14)0.0032 (13)−0.0010 (14)
C460.0294 (19)0.0229 (16)0.0120 (15)−0.0033 (13)0.0092 (13)−0.0019 (12)
C610.0188 (17)0.045 (2)0.0155 (17)0.0003 (15)0.0024 (13)−0.0052 (14)
Cl2—C421.746 (4)C41—C421.397 (5)
S2—C21.697 (4)C42—C431.397 (5)
O15—C151.222 (4)C43—C441.370 (6)
N1—C21.369 (4)C44—C451.390 (6)
N1—C61.392 (4)C45—C461.379 (5)
N3—C21.314 (5)C4—H41.0000
N3—C41.467 (4)C16—H16A0.9800
N1—H10.83 (4)C16—H16B0.9800
N3—H30.89 (5)C16—H16C0.9800
C4—C411.541 (4)C43—H430.9500
C4—C51.519 (4)C44—H440.9500
C5—C61.360 (5)C45—H450.9500
C5—C151.479 (5)C46—H460.9500
C6—C611.503 (5)C61—H61A0.9800
C15—C161.516 (4)C61—H61B0.9800
C41—C461.410 (5)C61—H61C0.9800
Cl2···N13.095 (3)C6···H16C3.0900
Cl2···N33.304 (3)C15···H43viii2.9300
Cl2···C23.206 (4)C16···H61A2.8200
Cl2···C53.360 (4)C16···H61C2.7700
Cl2···C63.251 (3)C16···H43viii3.0800
Cl2···C45i3.538 (4)C41···H16Av3.0600
Cl2···C46i3.644 (4)C42···H16Av2.9900
Cl2···H45i3.0400C43···H16Bx2.9600
Cl2···H44ii3.1500C45···H61Axi2.8400
S2···C16iii3.604 (4)C46···H44viii3.0200
S2···N3iv3.355 (3)C61···H16B2.8000
S2···H61Cv3.0300C61···H16C2.7500
S2···H46i2.8400H1···O15i2.20 (4)
S2···H3iv2.48 (5)H1···H61B2.0400
S2···H16Ciii3.1800H3···S2iv2.48 (5)
S2···H61Bvi3.0000H4···O152.3600
O15···N1vii2.957 (4)H4···H462.2600
O15···C413.134 (4)H16A···C41ix3.0600
O15···C463.252 (4)H16A···C42ix2.9900
O15···C44viii3.414 (4)H16B···C612.8000
O15···H42.3600H16B···H61A2.2900
O15···H61Bvii2.6400H16B···C43viii2.9600
O15···H1vii2.20 (4)H16B···H43viii2.5000
O15···H44viii2.7300H16C···C63.0900
N1···Cl23.095 (3)H16C···C612.7500
N1···O15i2.957 (4)H16C···H61C2.1900
N3···Cl23.304 (3)H16C···S2iii3.1800
N3···S2iv3.355 (3)H43···C15x2.9300
C2···Cl23.206 (4)H43···C16x3.0800
C5···Cl23.360 (4)H43···H16Bx2.5000
C6···Cl23.251 (3)H44···Cl2xiii3.1500
C15···C43viii3.507 (5)H44···O15x2.7300
C16···S2iii3.604 (4)H44···C46x3.0200
C16···C43viii3.514 (5)H45···Cl2vii3.0400
C16···C42ix3.495 (5)H45···H61Axi2.4100
C16···C613.042 (5)H46···S2vii2.8400
C41···O153.134 (4)H46···H42.2600
C42···C16v3.495 (5)H61A···C162.8200
C43···C15x3.507 (5)H61A···C45xii2.8400
C43···C16x3.514 (5)H61A···H16B2.2900
C44···O15x3.414 (4)H61A···H45xii2.4100
C45···C61xi3.513 (5)H61B···O15i2.6400
C45···Cl2vii3.538 (4)H61B···H12.0400
C46···Cl2vii3.644 (4)H61B···S2vi3.0000
C46···O153.252 (4)H61C···S2ix3.0300
C61···C163.042 (5)H61C···C162.7700
C61···C45xii3.513 (5)H61C···H16C2.1900
C2—N1—C6124.1 (3)C42—C43—C44119.5 (4)
C2—N3—C4125.9 (3)C43—C44—C45120.0 (3)
C2—N1—H1121 (3)C44—C45—C46120.3 (4)
C6—N1—H1115 (3)C41—C46—C45121.5 (3)
C2—N3—H3119 (3)N3—C4—H4107.00
C4—N3—H3115 (3)C5—C4—H4107.00
S2—C2—N3123.7 (2)C41—C4—H4107.00
N1—C2—N3116.9 (3)C15—C16—H16A109.00
S2—C2—N1119.4 (3)C15—C16—H16B109.00
N3—C4—C5110.4 (3)C15—C16—H16C109.00
N3—C4—C41111.6 (3)H16A—C16—H16B109.00
C5—C4—C41114.4 (3)H16A—C16—H16C110.00
C4—C5—C15113.1 (3)H16B—C16—H16C109.00
C6—C5—C15127.1 (3)C42—C43—H43120.00
C4—C5—C6119.7 (3)C44—C43—H43120.00
N1—C6—C5119.4 (3)C43—C44—H44120.00
N1—C6—C61112.1 (3)C45—C44—H44120.00
C5—C6—C61128.6 (3)C44—C45—H45120.00
C5—C15—C16122.8 (3)C46—C45—H45120.00
O15—C15—C5118.2 (3)C41—C46—H46119.00
O15—C15—C16119.0 (3)C45—C46—H46119.00
C4—C41—C46118.2 (3)C6—C61—H61A109.00
C42—C41—C46116.5 (3)C6—C61—H61B109.00
C4—C41—C42125.3 (3)C6—C61—H61C109.00
Cl2—C42—C41121.8 (3)H61A—C61—H61B109.00
Cl2—C42—C43116.1 (3)H61A—C61—H61C109.00
C41—C42—C43122.1 (3)H61B—C61—H61C109.00
C6—N1—C2—S2−174.1 (3)C15—C5—C6—N1170.2 (3)
C6—N1—C2—N34.6 (5)C15—C5—C6—C61−10.3 (6)
C2—N1—C6—C5−6.2 (5)C4—C5—C15—O156.0 (4)
C2—N1—C6—C61174.3 (3)C4—C5—C15—C16−173.0 (3)
C4—N3—C2—S2−170.3 (2)C6—C5—C15—O15−171.3 (3)
C4—N3—C2—N111.1 (5)C6—C5—C15—C169.7 (5)
C2—N3—C4—C5−22.0 (4)C4—C41—C42—Cl2−2.6 (5)
C2—N3—C4—C41106.5 (3)C4—C41—C42—C43176.3 (3)
N3—C4—C5—C618.9 (4)C46—C41—C42—Cl2178.6 (2)
N3—C4—C5—C15−158.6 (3)C46—C41—C42—C43−2.5 (5)
C41—C4—C5—C6−108.0 (4)C4—C41—C46—C45−178.1 (3)
C41—C4—C5—C1574.5 (4)C42—C41—C46—C450.8 (5)
N3—C4—C41—C42−61.9 (4)Cl2—C42—C43—C44−178.4 (3)
N3—C4—C41—C46117.0 (3)C41—C42—C43—C442.7 (5)
C5—C4—C41—C4264.4 (4)C42—C43—C44—C45−1.0 (6)
C5—C4—C41—C46−116.8 (3)C43—C44—C45—C46−0.7 (6)
C4—C5—C6—N1−6.9 (5)C44—C45—C46—C410.8 (5)
C4—C5—C6—C61172.5 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1···O15i0.83 (4)2.20 (4)2.957 (4)152 (4)
N3—H3···S2iv0.89 (5)2.48 (5)3.355 (3)170 (4)
C46—H46···S2vii0.952.843.761 (4)165
C16—H16A···Cg1ix0.982.863.660 (4)139
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N1—H1⋯O15i 0.83 (4)2.20 (4)2.957 (4)152 (4)
N3—H3⋯S2ii 0.89 (5)2.48 (5)3.355 (3)170 (4)
C46—H46⋯S2iii 0.952.843.761 (4)165
C16—H16A⋯Cg1iv 0.982.863.660 (4)139

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) . Cg1 is the centroid of the benzene ring.

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1.  A short history of SHELX.

Authors:  George M Sheldrick
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Authors:  C O Kappe
Journal:  Eur J Med Chem       Date:  2000-12       Impact factor: 6.514

3.  Dihydropyrimidine calcium channel blockers. 2. 3-substituted-4-aryl-1,4-dihydro-6-methyl-5-pyrimidinecarboxylic acid esters as potent mimics of dihydropyridines.

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4.  Calcium entry blockers and activators: conformational and structural determinants of dihydropyrimidine calcium channel modulators.

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Journal:  J Med Chem       Date:  1995-01-06       Impact factor: 7.446

5.  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

6.  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

7.  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

8.  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
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  1 in total

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