Literature DB >> 23634063

2-(4-Bromo-anilino)-6-(4-chloro-phen-yl)-5-meth-oxy-carbonyl-4-methyl-3,6-dihydro-pyrimidin-1-ium chloride.

K N Venugopala1, Susanta K Nayak, Bharti Odhav.   

Abstract

In the title molecular salt, C19H18BrClN3O2 (+)·Cl(-), the dihedral angles between the pyrimidine ring and the chlorobenzene and bromobenzene rings are 72.4 (2) and 45.5 (2)°, respectively. The dihedral angle between the chlorobenzene and bromobenzene rings is 27.5 (2)°. The conformation of the mol-ecule is stabilized by an intra-molecular C-H⋯O inter-action. In the crystal, the anion and cation are linked by an N-H⋯Cl hydrogen bond. Pairs of weak C-H⋯O and C-H⋯Cl hydrogen bonds form inversion dimers. Further N-H⋯Cl hydrogen bonds form R 2 (1)(6) motifs and link the dimers into chains along [101]. Br⋯Cl short contacts [3.482 (2) Å] inter-link the hydrogen-bonded chains along the b-axis direction.

Entities:  

Year:  2013        PMID： 23634063      PMCID： PMC3629576          DOI： 10.1107/S1600536813006296

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


Related literature

For a study of chloride salts of dihydro­pyrimidine derivatives and their anti-tubercular activity, see: Venugopala, Nayak, Pillay et al. (2012 ▶). For the crystal structures of dihydro­pyrimidine derivatives, see: Venugopala, Nayak & Odhav (2012 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C19H18BrClN3O2 +·Cl− M = 471.17 Monoclinic, a = 13.2691 (15) Å b = 11.0965 (12) Å c = 14.9545 (17) Å β = 114.181 (3)° V = 2008.7 (4) Å3 Z = 4 Mo Kα radiation μ = 2.33 mm−1 T = 100 K 0.08 × 0.05 × 0.03 mm

Data collection

Bruker Kappa DUO APEXII diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.835, T max = 0.933 10242 measured reflections 3919 independent reflections 2511 reflections with I > 2σ(I) R int = 0.067

Refinement

R[F 2 > 2σ(F 2)] = 0.044 wR(F 2) = 0.096 S = 0.95 3919 reflections 246 parameters H-atom parameters constrained Δρmax = 0.42 e Å−3 Δρmin = −0.40 e Å−3 Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶) and PARST (Nardelli, 1995 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813006296/pv2621sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813006296/pv2621Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813006296/pv2621Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H18BrClN3O2+·Cl−F(000) = 952
Mr = 471.17Dx = 1.558 Mg m−3
Monoclinic, P21/nMelting point: 500(2) K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 13.2691 (15) ÅCell parameters from 650 reflections
b = 11.0965 (12) Åθ = 1.7–27.9°
c = 14.9545 (17) ŵ = 2.33 mm−1
β = 114.181 (3)°T = 100 K
V = 2008.7 (4) Å3Block, colorless
Z = 40.08 × 0.05 × 0.03 mm
Bruker Kappa DUO APEXII diffractometer3919 independent reflections
Radiation source: fine-focus sealed tube2511 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.067
0.5° φ scans and ω scansθmax = 26.0°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −16→16
Tmin = 0.835, Tmax = 0.933k = −13→13
10242 measured reflectionsl = −18→16
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H-atom parameters constrained
S = 0.95w = 1/[σ2(Fo2) + (0.0403P)2] where P = (Fo2 + 2Fc2)/3
3919 reflections(Δ/σ)max < 0.001
246 parametersΔρmax = 0.42 e Å−3
0 restraintsΔρmin = −0.40 e Å−3
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 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
Br10.13690 (4)0.30575 (4)0.48412 (3)0.03906 (15)
Cl10.62679 (9)0.43238 (11)0.13181 (9)0.0497 (3)
Cl20.18134 (7)0.73567 (10)0.24229 (7)0.0366 (3)
O10.4928 (2)1.0157 (2)0.21182 (19)0.0336 (7)
O20.6208 (2)1.1174 (3)0.3359 (2)0.0391 (7)
N10.4274 (2)0.7807 (3)0.3884 (2)0.0220 (7)
H10.35800.75790.36780.026*
N20.5907 (2)0.8308 (3)0.5160 (2)0.0244 (7)
H20.64220.81090.57360.029*
N30.4682 (2)0.7087 (3)0.5462 (2)0.0236 (7)
H30.50750.72510.60850.028*
C10.4941 (4)1.1104 (4)0.1460 (3)0.0420 (11)
H1A0.57031.13630.16320.063*
H1B0.45031.17880.15150.063*
H1C0.46241.08010.07850.063*
C20.5598 (3)1.0312 (3)0.3065 (3)0.0266 (9)
C30.5487 (3)0.9312 (3)0.3668 (3)0.0213 (8)
C40.6119 (3)0.9232 (3)0.4638 (3)0.0239 (9)
C50.7060 (3)1.0023 (3)0.5265 (3)0.0320 (10)
H5A0.69811.08190.49610.048*
H5B0.77600.96600.53290.048*
H5C0.70561.01050.59160.048*
C60.4680 (3)0.8309 (3)0.3176 (3)0.0217 (8)
H60.40330.86740.26250.026*
C70.5126 (3)0.7297 (3)0.2746 (2)0.0232 (8)
C80.6080 (3)0.7427 (4)0.2584 (3)0.0282 (9)
H80.65040.81450.27910.034*
C90.6427 (3)0.6536 (4)0.2129 (3)0.0308 (9)
H90.70700.66430.20080.037*
C100.5819 (3)0.5490 (4)0.1855 (3)0.0308 (10)
C110.4875 (3)0.5316 (4)0.2014 (3)0.0305 (10)
H110.44750.45810.18330.037*
C120.4528 (3)0.6233 (4)0.2441 (3)0.0268 (9)
H120.38630.61370.25290.032*
C130.4936 (3)0.7697 (3)0.4817 (3)0.0202 (8)
C140.3842 (3)0.6193 (3)0.5253 (3)0.0230 (8)
C150.3303 (3)0.6112 (4)0.5866 (3)0.0284 (9)
H150.34410.66920.63700.034*
C160.2553 (3)0.5180 (4)0.5747 (3)0.0301 (9)
H160.21840.51120.61700.036*
C170.2358 (3)0.4357 (3)0.5001 (3)0.0277 (9)
C180.2874 (3)0.4450 (3)0.4374 (3)0.0246 (9)
H180.27110.38890.38530.029*
C190.3625 (3)0.5356 (3)0.4501 (3)0.0237 (8)
H190.39960.54120.40780.028*
U11U22U33U12U13U23
Br10.0491 (3)0.0302 (2)0.0386 (3)−0.0145 (2)0.0188 (2)−0.0051 (2)
Cl10.0502 (7)0.0405 (7)0.0635 (8)0.0083 (5)0.0285 (6)−0.0154 (6)
Cl20.0226 (5)0.0571 (7)0.0259 (5)−0.0006 (5)0.0058 (4)0.0065 (5)
O10.0401 (16)0.0293 (17)0.0292 (16)−0.0082 (13)0.0117 (13)0.0027 (12)
O20.0433 (17)0.0265 (16)0.0440 (18)−0.0114 (14)0.0144 (14)−0.0019 (14)
N10.0136 (14)0.0266 (19)0.0221 (17)−0.0004 (12)0.0036 (13)0.0000 (13)
N20.0169 (16)0.0249 (19)0.0239 (17)−0.0012 (13)0.0007 (13)0.0002 (13)
N30.0243 (16)0.0268 (19)0.0173 (16)−0.0040 (14)0.0060 (13)−0.0026 (14)
C10.052 (3)0.040 (3)0.038 (3)−0.009 (2)0.022 (2)0.007 (2)
C20.027 (2)0.023 (2)0.034 (2)−0.0016 (17)0.0166 (19)−0.0060 (18)
C30.0227 (19)0.017 (2)0.026 (2)−0.0006 (15)0.0112 (17)−0.0029 (16)
C40.022 (2)0.017 (2)0.032 (2)−0.0007 (15)0.0109 (18)−0.0044 (16)
C50.026 (2)0.024 (2)0.038 (2)−0.0018 (17)0.0033 (18)−0.0081 (19)
C60.0198 (18)0.023 (2)0.0206 (19)−0.0013 (15)0.0063 (16)0.0009 (15)
C70.026 (2)0.023 (2)0.0172 (19)0.0028 (16)0.0063 (16)0.0027 (15)
C80.024 (2)0.028 (2)0.031 (2)−0.0029 (17)0.0097 (17)−0.0013 (18)
C90.028 (2)0.032 (2)0.038 (2)0.0020 (18)0.0194 (19)−0.0010 (19)
C100.033 (2)0.025 (2)0.032 (2)0.0083 (18)0.0110 (19)−0.0031 (18)
C110.028 (2)0.026 (2)0.031 (2)−0.0031 (17)0.0042 (18)−0.0004 (18)
C120.024 (2)0.030 (2)0.025 (2)0.0034 (17)0.0092 (17)0.0019 (18)
C130.0185 (18)0.019 (2)0.025 (2)0.0029 (15)0.0107 (17)−0.0035 (16)
C140.025 (2)0.019 (2)0.021 (2)0.0047 (15)0.0052 (17)0.0040 (16)
C150.038 (2)0.024 (2)0.024 (2)−0.0020 (18)0.0140 (19)−0.0055 (17)
C160.037 (2)0.030 (2)0.029 (2)−0.0050 (18)0.0176 (19)−0.0007 (18)
C170.034 (2)0.018 (2)0.027 (2)−0.0033 (16)0.0074 (18)−0.0001 (17)
C180.030 (2)0.022 (2)0.021 (2)−0.0001 (16)0.0093 (17)−0.0026 (16)
C190.025 (2)0.022 (2)0.024 (2)0.0063 (16)0.0098 (17)0.0028 (17)
Br1—C171.898 (4)C5—H5C0.9800
Cl1—C101.751 (4)C6—C71.529 (5)
O1—C21.339 (4)C6—H61.0000
O1—C11.445 (5)C7—C81.390 (5)
O2—C21.214 (4)C7—C121.391 (5)
N1—C131.315 (4)C8—C91.382 (5)
N1—C61.479 (4)C8—H80.9500
N1—H10.8800C9—C101.377 (5)
N2—C131.357 (4)C9—H90.9500
N2—C41.386 (5)C10—C111.381 (5)
N2—H20.8800C11—C121.377 (5)
N3—C131.330 (4)C11—H110.9500
N3—C141.428 (4)C12—H120.9500
N3—H30.8800C14—C151.377 (5)
C1—H1A0.9800C14—C191.395 (5)
C1—H1B0.9800C15—C161.395 (5)
C1—H1C0.9800C15—H150.9500
C2—C31.475 (5)C16—C171.381 (5)
C3—C41.349 (5)C16—H160.9500
C3—C61.510 (5)C17—C181.373 (5)
C4—C51.500 (5)C18—C191.374 (5)
C5—H5A0.9800C18—H180.9500
C5—H5B0.9800C19—H190.9500
C2—O1—C1116.1 (3)C8—C7—C6122.3 (3)
C13—N1—C6120.9 (3)C12—C7—C6119.6 (3)
C13—N1—H1119.6C9—C8—C7121.5 (4)
C6—N1—H1119.6C9—C8—H8119.3
C13—N2—C4122.4 (3)C7—C8—H8119.3
C13—N2—H2118.8C10—C9—C8118.5 (4)
C4—N2—H2118.8C10—C9—H9120.7
C13—N3—C14127.0 (3)C8—C9—H9120.7
C13—N3—H3116.5C9—C10—C11121.9 (4)
C14—N3—H3116.5C9—C10—Cl1119.5 (3)
O1—C1—H1A109.5C11—C10—Cl1118.6 (3)
O1—C1—H1B109.5C12—C11—C10118.4 (4)
H1A—C1—H1B109.5C12—C11—H11120.8
O1—C1—H1C109.5C10—C11—H11120.8
H1A—C1—H1C109.5C11—C12—C7121.6 (4)
H1B—C1—H1C109.5C11—C12—H12119.2
O2—C2—O1122.6 (4)C7—C12—H12119.2
O2—C2—C3126.2 (4)N1—C13—N3124.0 (3)
O1—C2—C3111.1 (3)N1—C13—N2118.3 (3)
C4—C3—C2122.2 (3)N3—C13—N2117.6 (3)
C4—C3—C6118.7 (3)C15—C14—C19120.1 (3)
C2—C3—C6119.0 (3)C15—C14—N3118.2 (3)
C3—C4—N2118.3 (3)C19—C14—N3121.6 (3)
C3—C4—C5128.8 (4)C14—C15—C16120.1 (4)
N2—C4—C5112.9 (3)C14—C15—H15120.0
C4—C5—H5A109.5C16—C15—H15120.0
C4—C5—H5B109.5C17—C16—C15118.8 (4)
H5A—C5—H5B109.5C17—C16—H16120.6
C4—C5—H5C109.5C15—C16—H16120.6
H5A—C5—H5C109.5C18—C17—C16121.4 (4)
H5B—C5—H5C109.5C18—C17—Br1118.9 (3)
N1—C6—C3108.8 (3)C16—C17—Br1119.7 (3)
N1—C6—C7110.0 (3)C17—C18—C19119.8 (3)
C3—C6—C7115.3 (3)C17—C18—H18120.1
N1—C6—H6107.5C19—C18—H18120.1
C3—C6—H6107.5C18—C19—C14119.9 (3)
C7—C6—H6107.5C18—C19—H19120.1
C8—C7—C12118.0 (4)C14—C19—H19120.1
C1—O1—C2—O2−2.1 (5)C8—C9—C10—C110.6 (6)
C1—O1—C2—C3178.1 (3)C8—C9—C10—Cl1−177.6 (3)
O2—C2—C3—C4−3.4 (6)C9—C10—C11—C121.4 (6)
O1—C2—C3—C4176.4 (3)Cl1—C10—C11—C12179.7 (3)
O2—C2—C3—C6179.9 (4)C10—C11—C12—C7−2.6 (6)
O1—C2—C3—C6−0.3 (5)C8—C7—C12—C111.6 (5)
C2—C3—C4—N2175.7 (3)C6—C7—C12—C11177.4 (3)
C6—C3—C4—N2−7.6 (5)C6—N1—C13—N3−168.9 (3)
C2—C3—C4—C5−4.6 (6)C6—N1—C13—N215.6 (5)
C6—C3—C4—C5172.2 (3)C14—N3—C13—N118.7 (6)
C13—N2—C4—C3−18.5 (5)C14—N3—C13—N2−165.8 (3)
C13—N2—C4—C5161.7 (3)C4—N2—C13—N114.7 (5)
C13—N1—C6—C3−37.3 (4)C4—N2—C13—N3−161.0 (3)
C13—N1—C6—C789.8 (4)C13—N3—C14—C15−146.4 (4)
C4—C3—C6—N132.5 (4)C13—N3—C14—C1938.7 (5)
C2—C3—C6—N1−150.7 (3)C19—C14—C15—C161.2 (5)
C4—C3—C6—C7−91.6 (4)N3—C14—C15—C16−173.8 (3)
C2—C3—C6—C785.3 (4)C14—C15—C16—C17−0.7 (6)
N1—C6—C7—C8−139.6 (3)C15—C16—C17—C18−0.9 (6)
C3—C6—C7—C8−16.2 (5)C15—C16—C17—Br1178.5 (3)
N1—C6—C7—C1244.8 (4)C16—C17—C18—C191.9 (6)
C3—C6—C7—C12168.2 (3)Br1—C17—C18—C19−177.4 (3)
C12—C7—C8—C90.5 (5)C17—C18—C19—C14−1.4 (5)
C6—C7—C8—C9−175.2 (3)C15—C14—C19—C18−0.1 (5)
C7—C8—C9—C10−1.5 (6)N3—C14—C19—C18174.7 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl20.882.343.136 (3)151
N2—H2···Cl2i0.882.413.179 (3)146
N3—H3···Cl2i0.882.393.191 (3)151
C5—H5A···O20.982.222.897 (5)125
C15—H15···O2ii0.952.423.197 (5)139
C18—H18···Cl2iii0.952.813.702 (4)156
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N1—H1⋯Cl20.882.343.136 (3)151
N2—H2⋯Cl2i 0.882.413.179 (3)146
N3—H3⋯Cl2i 0.882.393.191 (3)151
C5—H5A⋯O20.982.222.897 (5)125
C15—H15⋯O2ii 0.952.423.197 (5)139
C18—H18⋯Cl2iii 0.952.813.702 (4)156

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

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

2.  Synthesis and antitubercular activity of 2-(substituted phenyl/benzyl-amino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chlorides.

Authors:  Venugopala K Narayanaswamy; Susanta K Nayak; Melendhran Pillay; Renuka Prasanna; Yacoob M Coovadia; Bharti Odhav
Journal:  Chem Biol Drug Des       Date:  2012-11-14       Impact factor: 2.817

3.  Methyl (E)-2-[(3-chloro-4-cyano-phenyl)-imino]-4-(4-chloro-phen-yl)-6-methyl-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

Authors:  K N Venugopala; Susanta K Nayak; Bharti Odhav
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-09-22

4.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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