Literature DB >> 22065507

2,4-Diamino-5-(4-chloro-phen-yl)-6-ethyl-pyrimidin-1-ium 2-propanamido-benzoate.

Sampath Natarajan1, Rita Mathews.   

Abstract

In the title salt, C(12)H(14)ClN(4) (+)·C(10)H(10)NO(3) (-), zwitterionic N-H⋯O inter-actions form an R(2) (2)(8) ring. The crystal structure is stabilized by N-H⋯O and N-H⋯N hydrogen bonds involving two different eight-membered rings. An N-H⋯O inter-action occurs between the pyrimidine ring (donor) and carboxyl-ate group (acceptor) while the other ring is formed by N-H⋯N inter-actions, which form a dimer between two symmetry-related salts. An intra-molecular N-H⋯O hydrogen bond forms a six-membered ring in the benzoate. Inter-molecular C-H⋯O inter-actions are also observed.

Entities:  

Year:  2011        PMID: 22065507      PMCID: PMC3201463          DOI: 10.1107/S1600536811035501

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


Related literature

For amino­pyrimidine carboxyl­ates, see: Chinnakali et al. (1999 ▶); Lynch & Jones (2004 ▶); Stanley et al. (2005 ▶). For amino­pyrimidine and benzoic acid adducts, see: Balasub­ram­ani et al. (2005 ▶, 2006 ▶); Thanigaimani et al. (2006 ▶, 2007 ▶). For hydrogen bonding in mol­ecular recognition and crystal engin­eering, see: Desiraju (1989 ▶). For puckering and asymmetry parameters, see: Cremer & Pople, (1975 ▶); Nardelli (1995 ▶).

Experimental

Crystal data

C12H14ClN4C10H10NO3 M = 441.91 Monoclinic, a = 22.144 (3) Å b = 9.4915 (14) Å c = 21.844 (3) Å β = 99.071 (3)° V = 4533.7 (12) Å3 Z = 8 Mo Kα radiation μ = 0.20 mm−1 T = 293 K 0.50 × 0.45 × 0.42 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer 17933 measured reflections 5077 independent reflections 2719 reflections with I > 2σ(I) R int = 0.039

Refinement

R[F 2 > 2σ(F 2)] = 0.088 wR(F 2) = 0.228 S = 1.06 5077 reflections 281 parameters H-atom parameters constrained Δρmax = 0.29 e Å−3 Δρmin = −0.24 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); 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 (Farrugia, 1997 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811035501/ff2025sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811035501/ff2025Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811035501/ff2025Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C12H14ClN4+·C10H10NO3F(000) = 1856
Mr = 441.91Dx = 1.295 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 22.144 (3) ÅCell parameters from 17933 reflections
b = 9.4915 (14) Åθ = 1.9–28.0°
c = 21.844 (3) ŵ = 0.20 mm1
β = 99.071 (3)°T = 293 K
V = 4533.7 (12) Å3Block, colorless
Z = 80.50 × 0.45 × 0.42 mm
Bruker SMART APEX CCD area-detector diffractometer2719 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.039
graphiteθmax = 28.0°, θmin = 1.9°
ω scansh = −28→29
17933 measured reflectionsk = −10→12
5077 independent reflectionsl = −28→28
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.088Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.228H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.1005P)2 + 1.940P] where P = (Fo2 + 2Fc2)/3
5077 reflections(Δ/σ)max = 0.002
281 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = −0.24 e Å3
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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
Cl10.62790 (7)−0.12826 (18)0.25493 (7)0.1465 (7)
O10.25218 (12)0.3854 (3)0.05381 (12)0.0926 (9)
O20.25430 (14)0.2607 (4)0.13892 (13)0.1067 (11)
O30.37717 (11)0.3960 (3)0.33389 (11)0.0809 (7)
N10.43891 (11)0.3633 (3)−0.01402 (11)0.0567 (7)
N20.34901 (13)0.3749 (3)−0.08192 (12)0.0708 (8)
H2A0.36260.4469−0.09940.085*
H2B0.31300.3430−0.09530.085*
N30.36043 (12)0.2008 (3)−0.00894 (12)0.0640 (7)
H30.32370.1738−0.02280.077*
N40.52835 (12)0.3481 (3)0.05255 (12)0.0654 (7)
H4A0.53990.42200.03480.078*
H4B0.55250.30930.08250.078*
N50.32811 (13)0.3417 (3)0.23743 (12)0.0763 (9)
H50.29900.29000.21880.092*
C20.38321 (14)0.3137 (3)−0.03469 (14)0.0567 (8)
C40.39373 (15)0.1283 (4)0.03825 (14)0.0620 (9)
C50.45211 (14)0.1711 (3)0.06071 (13)0.0562 (8)
C60.47322 (14)0.2937 (3)0.03366 (13)0.0544 (8)
C70.49398 (15)0.0933 (4)0.10941 (14)0.0590 (8)
C80.51370 (18)−0.0416 (4)0.09988 (16)0.0780 (10)
H80.4995−0.08730.06270.094*
C90.5542 (2)−0.1100 (4)0.1447 (2)0.0925 (13)
H90.5666−0.20140.13780.111*
C100.57609 (18)−0.0431 (5)0.19934 (18)0.0828 (11)
C110.55717 (17)0.0894 (5)0.21009 (16)0.0770 (11)
H110.57220.13410.24730.092*
C120.51563 (16)0.1586 (4)0.16609 (15)0.0676 (9)
H120.50210.24840.17420.081*
C130.36238 (19)0.0048 (4)0.06172 (18)0.0857 (12)
H13A0.3875−0.03020.09900.103*
H13B0.32380.03600.07290.103*
C140.3503 (3)−0.1118 (5)0.0168 (3)0.1222 (18)
H14A0.3300−0.18700.03480.183*
H14B0.3883−0.14550.00640.183*
H14C0.3247−0.0788−0.02000.183*
C150.33329 (14)0.4293 (4)0.13458 (15)0.0596 (8)
C160.36330 (15)0.5078 (4)0.09550 (16)0.0663 (9)
H160.34670.51320.05370.080*
C170.41712 (16)0.5788 (4)0.11626 (18)0.0754 (10)
H170.43640.63130.08910.090*
C180.44141 (17)0.5700 (4)0.17795 (19)0.0833 (11)
H180.47770.61690.19270.100*
C190.41304 (16)0.4932 (4)0.21807 (18)0.0774 (10)
H190.43030.48880.25970.093*
C200.35892 (15)0.4216 (4)0.19784 (15)0.0620 (8)
C210.27569 (16)0.3551 (4)0.10749 (16)0.0687 (9)
C220.33649 (17)0.3327 (4)0.29967 (16)0.0758 (10)
C230.2921 (2)0.2325 (7)0.3252 (2)0.1161 (17)
H23A0.25830.21260.29240.139*
H23B0.31310.14420.33630.139*
C240.2684 (5)0.2828 (11)0.3771 (4)0.247 (6)
H24A0.24120.21390.38980.371*
H24B0.24650.36890.36650.371*
H24C0.30140.29990.41040.371*
U11U22U33U12U13U23
Cl10.1356 (12)0.1739 (14)0.1179 (10)0.0501 (10)−0.0176 (8)0.0603 (10)
O10.0793 (17)0.122 (2)0.0646 (15)−0.0330 (16)−0.0247 (13)0.0108 (15)
O20.097 (2)0.132 (3)0.0758 (17)−0.0575 (19)−0.0334 (15)0.0152 (17)
O30.0685 (15)0.104 (2)0.0626 (14)0.0039 (14)−0.0119 (12)−0.0153 (14)
N10.0503 (14)0.0625 (16)0.0522 (14)−0.0062 (13)−0.0077 (11)0.0027 (12)
N20.0611 (16)0.0756 (19)0.0667 (17)−0.0151 (15)−0.0177 (14)0.0160 (15)
N30.0519 (15)0.0730 (19)0.0613 (16)−0.0176 (14)−0.0093 (12)0.0036 (14)
N40.0542 (15)0.0687 (18)0.0675 (17)−0.0089 (14)−0.0082 (13)0.0185 (14)
N50.0629 (17)0.100 (2)0.0574 (17)−0.0223 (17)−0.0183 (14)−0.0015 (16)
C20.0562 (19)0.0574 (19)0.0522 (17)−0.0120 (16)−0.0045 (15)−0.0012 (15)
C40.062 (2)0.067 (2)0.0534 (18)−0.0103 (17)−0.0020 (15)0.0032 (16)
C50.0576 (18)0.061 (2)0.0484 (16)−0.0032 (16)0.0024 (14)0.0017 (14)
C60.0513 (17)0.060 (2)0.0494 (17)−0.0062 (16)0.0014 (14)−0.0001 (14)
C70.0579 (18)0.065 (2)0.0528 (18)−0.0041 (16)0.0051 (15)0.0059 (15)
C80.098 (3)0.072 (3)0.061 (2)0.006 (2)0.005 (2)0.0003 (18)
C90.116 (4)0.078 (3)0.085 (3)0.033 (3)0.020 (3)0.019 (2)
C100.075 (2)0.104 (3)0.068 (2)0.014 (2)0.005 (2)0.026 (2)
C110.072 (2)0.099 (3)0.055 (2)−0.005 (2)−0.0049 (18)0.009 (2)
C120.069 (2)0.073 (2)0.058 (2)0.0008 (18)0.0028 (17)0.0016 (17)
C130.081 (3)0.089 (3)0.080 (2)−0.021 (2)−0.009 (2)0.016 (2)
C140.132 (4)0.085 (3)0.139 (4)−0.026 (3)−0.013 (4)0.007 (3)
C150.0490 (17)0.063 (2)0.0607 (19)0.0016 (16)−0.0089 (15)−0.0106 (16)
C160.061 (2)0.076 (2)0.0568 (18)−0.0003 (18)−0.0051 (16)−0.0004 (17)
C170.055 (2)0.084 (3)0.084 (3)−0.0058 (19)0.0027 (18)0.006 (2)
C180.061 (2)0.090 (3)0.091 (3)−0.017 (2)−0.013 (2)0.002 (2)
C190.065 (2)0.086 (3)0.071 (2)−0.012 (2)−0.0202 (18)0.000 (2)
C200.0519 (18)0.066 (2)0.0625 (19)−0.0002 (17)−0.0091 (15)−0.0040 (17)
C210.062 (2)0.078 (2)0.060 (2)−0.0134 (19)−0.0081 (17)−0.0059 (19)
C220.065 (2)0.095 (3)0.061 (2)0.008 (2)−0.0099 (18)−0.005 (2)
C230.100 (3)0.174 (5)0.073 (3)−0.012 (3)0.009 (2)0.015 (3)
C240.312 (13)0.252 (10)0.206 (9)−0.147 (10)0.126 (9)−0.044 (8)
Cl1—C101.734 (4)C10—C111.357 (6)
O1—C211.240 (4)C11—C121.387 (5)
O2—C211.265 (4)C11—H110.9300
O3—C221.232 (4)C12—H120.9300
N1—C21.331 (4)C13—C141.475 (6)
N1—C61.360 (4)C13—H13A0.9700
N2—C21.315 (4)C13—H13B0.9700
N2—H2A0.8600C14—H14A0.9600
N2—H2B0.8600C14—H14B0.9600
N3—C21.345 (4)C14—H14C0.9600
N3—C41.356 (4)C15—C161.380 (5)
N3—H30.8600C15—C201.410 (4)
N4—C61.330 (4)C15—C211.495 (5)
N4—H4A0.8600C16—C171.382 (5)
N4—H4B0.8600C16—H160.9300
N5—C221.346 (4)C17—C181.372 (5)
N5—C201.405 (4)C17—H170.9300
N5—H50.8600C18—C191.366 (5)
C4—C51.370 (4)C18—H180.9300
C4—C131.494 (5)C19—C201.388 (5)
C5—C61.417 (4)C19—H190.9300
C5—C71.492 (4)C22—C231.534 (6)
C7—C81.379 (5)C23—C241.406 (9)
C7—C121.400 (4)C23—H23A0.9700
C8—C91.381 (5)C23—H23B0.9700
C8—H80.9300C24—H24A0.9600
C9—C101.372 (6)C24—H24B0.9600
C9—H90.9300C24—H24C0.9600
C2—N1—C6117.6 (3)C14—C13—H13B108.8
C2—N2—H2A120.0C4—C13—H13B108.8
C2—N2—H2B120.0H13A—C13—H13B107.7
H2A—N2—H2B120.0C13—C14—H14A109.5
C2—N3—C4121.8 (3)C13—C14—H14B109.5
C2—N3—H3119.1H14A—C14—H14B109.5
C4—N3—H3119.1C13—C14—H14C109.5
C6—N4—H4A120.0H14A—C14—H14C109.5
C6—N4—H4B120.0H14B—C14—H14C109.5
H4A—N4—H4B120.0C16—C15—C20118.4 (3)
C22—N5—C20130.8 (3)C16—C15—C21118.3 (3)
C22—N5—H5114.6C20—C15—C21123.4 (3)
C20—N5—H5114.6C15—C16—C17122.3 (3)
N2—C2—N1119.9 (3)C15—C16—H16118.8
N2—C2—N3118.2 (3)C17—C16—H16118.8
N1—C2—N3121.9 (3)C18—C17—C16118.5 (4)
N3—C4—C5119.4 (3)C18—C17—H17120.8
N3—C4—C13115.6 (3)C16—C17—H17120.8
C5—C4—C13125.0 (3)C19—C18—C17120.9 (3)
C4—C5—C6116.6 (3)C19—C18—H18119.5
C4—C5—C7123.6 (3)C17—C18—H18119.5
C6—C5—C7119.7 (3)C18—C19—C20121.2 (3)
N4—C6—N1115.1 (3)C18—C19—H19119.4
N4—C6—C5122.4 (3)C20—C19—H19119.4
N1—C6—C5122.5 (3)C19—C20—N5123.1 (3)
C8—C7—C12118.2 (3)C19—C20—C15118.7 (3)
C8—C7—C5121.9 (3)N5—C20—C15118.1 (3)
C12—C7—C5119.9 (3)O1—C21—O2122.7 (3)
C7—C8—C9121.0 (4)O1—C21—C15118.0 (3)
C7—C8—H8119.5O2—C21—C15119.2 (3)
C9—C8—H8119.5O3—C22—N5123.6 (4)
C10—C9—C8120.0 (4)O3—C22—C23122.0 (3)
C10—C9—H9120.0N5—C22—C23114.4 (3)
C8—C9—H9120.0C24—C23—C22115.1 (6)
C11—C10—C9120.2 (4)C24—C23—H23A108.5
C11—C10—Cl1120.0 (3)C22—C23—H23A108.5
C9—C10—Cl1119.9 (4)C24—C23—H23B108.5
C10—C11—C12120.5 (4)C22—C23—H23B108.5
C10—C11—H11119.7H23A—C23—H23B107.5
C12—C11—H11119.7C23—C24—H24A109.5
C11—C12—C7120.0 (4)C23—C24—H24B109.5
C11—C12—H12120.0H24A—C24—H24B109.5
C7—C12—H12120.0C23—C24—H24C109.5
C14—C13—C4114.0 (4)H24A—C24—H24C109.5
C14—C13—H13A108.8H24B—C24—H24C109.5
C4—C13—H13A108.8
C6—N1—C2—N2−178.0 (3)C10—C11—C12—C7−1.6 (5)
C6—N1—C2—N31.5 (5)C8—C7—C12—C111.9 (5)
C4—N3—C2—N2177.3 (3)C5—C7—C12—C11−176.4 (3)
C4—N3—C2—N1−2.2 (5)N3—C4—C13—C1467.1 (5)
C2—N3—C4—C50.3 (5)C5—C4—C13—C14−112.8 (4)
C2—N3—C4—C13−179.6 (3)C20—C15—C16—C17−0.1 (5)
N3—C4—C5—C62.0 (5)C21—C15—C16—C17−179.3 (3)
C13—C4—C5—C6−178.1 (3)C15—C16—C17—C180.2 (6)
N3—C4—C5—C7−175.7 (3)C16—C17—C18—C19−0.2 (6)
C13—C4—C5—C74.2 (5)C17—C18—C19—C200.1 (6)
C2—N1—C6—N4−179.8 (3)C18—C19—C20—N5−179.8 (3)
C2—N1—C6—C51.0 (4)C18—C19—C20—C150.0 (6)
C4—C5—C6—N4178.1 (3)C22—N5—C20—C1910.9 (6)
C7—C5—C6—N4−4.1 (5)C22—N5—C20—C15−168.9 (4)
C4—C5—C6—N1−2.7 (5)C16—C15—C20—C190.0 (5)
C7—C5—C6—N1175.0 (3)C21—C15—C20—C19179.2 (3)
C4—C5—C7—C863.2 (5)C16—C15—C20—N5179.9 (3)
C6—C5—C7—C8−114.4 (4)C21—C15—C20—N5−1.0 (5)
C4—C5—C7—C12−118.5 (4)C16—C15—C21—O1−11.5 (5)
C6—C5—C7—C1263.9 (4)C20—C15—C21—O1169.3 (3)
C12—C7—C8—C9−0.7 (5)C16—C15—C21—O2165.7 (3)
C5—C7—C8—C9177.6 (3)C20—C15—C21—O2−13.5 (5)
C7—C8—C9—C10−0.9 (6)C20—N5—C22—O3−2.3 (6)
C8—C9—C10—C111.3 (6)C20—N5—C22—C23179.6 (4)
C8—C9—C10—Cl1−178.9 (3)O3—C22—C23—C2444.3 (8)
C9—C10—C11—C12−0.1 (6)N5—C22—C23—C24−137.5 (7)
Cl1—C10—C11—C12−179.8 (3)
D—H···AD—HH···AD···AD—H···A
N5—H5···O20.861.892.605 (4)140
N2—H2A···O3i0.862.152.977 (4)163
N4—H4A···N1ii0.862.162.988 (4)163
N3—H3···O1iii0.861.802.660 (4)178
C14—H14C···O1iii0.962.533.323 (6)140
N2—H2B···O2iii0.861.912.746 (4)164
N4—H4B···O3iv0.862.353.017 (3)134
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N5—H5⋯O20.861.892.605 (4)140
N2—H2A⋯O3i0.862.152.977 (4)163
N4—H4A⋯N1ii0.862.162.988 (4)163
N3—H3⋯O1iii0.861.802.660 (4)178
C14—H14C⋯O1iii0.962.533.323 (6)140
N2—H2B⋯O2iii0.861.912.746 (4)164
N4—H4B⋯O3iv0.862.353.017 (3)134

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

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