Literature DB >> 21201453

2-Amino-4,6-dimethyl-pyrimidinium 3,5-dinitro-benzoate dihydrate.

Annamalai Subashini, Packianathan Thomas Muthiah, Daniel E Lynch.   

Abstract

In the title compound, C(6)H(10)N(3) (+)·C(7)H(3)N(2)O(6) (-)·2H(2)O, the amino-pyrimidine mol-ecule is protonated at one of the pyrimidine N atoms. The carboxyl-ate group of the 3,5-dinitro-benzoate anion inter-acts with the protonated pyrimidine N atom and the 2-amino group through a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) motif. Two inversion-related pyrimidine rings are linked via a pair of N-H⋯N hydrogen bonds, also forming an R(2) (2)(8) ring motif.

Entities:  

Year:  2008        PMID： 21201453      PMCID： PMC2960285          DOI： 10.1107/S1600536808000524

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


Related literature

For related literature, see: Allen et al. (1998 ▶); Baker & Santi (1965 ▶); Baskar Raj et al. (2003 ▶); Desiraju (1989 ▶); Hunt et al. (1980 ▶); Lynch & Jones (2004 ▶); Panneerselvam et al. (2004 ▶); Prince et al. (1991 ▶); Stanley et al. (2005 ▶); Subashini et al. (2006 ▶).

Experimental

Crystal data

C6H10N3 +·C7H3N2O6 −·2H2O M = 371.32 Triclinic, a = 7.1465 (3) Å b = 11.0215 (5) Å c = 11.1531 (4) Å α = 99.473 (3)° β = 101.322 (3)° γ = 100.826 (2)° V = 827.33 (6) Å3 Z = 2 Mo Kα radiation μ = 0.13 mm−1 T = 120 K 0.44 × 0.36 × 0.23 mm

Data collection

Bruker–Nonius KappaCCD area-detector diffractometer Absorption correction: none 15739 measured reflections 3235 independent reflections 2283 reflections with I > 2σ(I) R int = 0.043

Refinement

R[F 2 > 2σ(F 2)] = 0.059 wR(F 2) = 0.171 S = 1.04 3235 reflections 238 parameters H-atom parameters constrained Δρmax = 0.50 e Å−3 Δρmin = −0.55 e Å−3 Data collection: COLLECT (Nonius, 1998 ▶); cell refinement: DENZO (Otwinowski & Minor, 1997 ▶) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2003 ▶); software used to prepare material for publication: PLATON. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808000524/rz2189sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808000524/rz2189Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H10N3+·C7H3N2O6–·2H2OZ = 2
Mr = 371.32F000 = 388
Triclinic, P1Dx = 1.491 Mg m−3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 7.1465 (3) ÅCell parameters from 2.5 reflections
b = 11.0215 (5) Åθ = 3.8–26.0º
c = 11.1531 (4) ŵ = 0.13 mm−1
α = 99.473 (3)ºT = 120 K
β = 101.322 (3)ºBlock, brown
γ = 100.826 (2)º0.44 × 0.36 × 0.23 mm
V = 827.33 (6) Å3
Bruker–Nonius KappaCCD area-detector diffractometer2283 reflections with I > 2σ(I)
Radiation source: Bruker–Nonius FR591 rotating anodeRint = 0.043
Monochromator: graphiteθmax = 26.0º
T = 120 Kθmin = 3.8º
φ and ω scansh = −8→8
Absorption correction: nonek = −13→13
15739 measured reflectionsl = −13→13
3235 independent reflections
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.059  w = 1/[σ2(Fo2) + (0.0801P)2 + 0.6543P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.171(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.50 e Å−3
3235 reflectionsΔρmin = −0.55 e Å−3
238 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001Fc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.026 (9)
Secondary atom site location: difference Fourier map
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'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 on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2> σ(F2) is used only for calculating -R-factor-obs 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
N10.2027 (3)0.33914 (19)0.72583 (18)0.0274 (6)
N20.1151 (3)0.35467 (18)0.51987 (17)0.0283 (6)
N30.0823 (3)0.51366 (18)0.67131 (17)0.0284 (6)
C20.1339 (3)0.4032 (2)0.6397 (2)0.0255 (7)
C40.1050 (4)0.5608 (2)0.7929 (2)0.0316 (7)
C50.1819 (4)0.4998 (2)0.8853 (2)0.0344 (8)
C60.2299 (4)0.3872 (2)0.8500 (2)0.0321 (8)
C70.0403 (4)0.6801 (3)0.8255 (2)0.0434 (9)
C80.3079 (4)0.3114 (3)0.9388 (2)0.0425 (9)
O10.2748 (3)0.11664 (16)0.66737 (15)0.0340 (5)
O20.1737 (3)0.11087 (15)0.46282 (15)0.0330 (5)
O30.2112 (3)−0.24607 (19)0.15879 (17)0.0491 (7)
O40.3323 (3)−0.39796 (18)0.21663 (17)0.0432 (6)
O50.5402 (3)−0.39570 (18)0.65403 (19)0.0467 (7)
O60.4999 (3)−0.2476 (2)0.79214 (18)0.0545 (8)
N40.2803 (3)−0.2987 (2)0.23984 (19)0.0335 (7)
N50.4871 (3)−0.2986 (2)0.6838 (2)0.0355 (7)
C90.2796 (3)−0.0654 (2)0.5226 (2)0.0258 (7)
C100.2515 (3)−0.1244 (2)0.3983 (2)0.0271 (7)
C110.3026 (3)−0.2394 (2)0.3714 (2)0.0275 (7)
C120.3787 (3)−0.3000 (2)0.4618 (2)0.0285 (7)
C130.4021 (3)−0.2388 (2)0.5846 (2)0.0284 (7)
C140.3543 (3)−0.1233 (2)0.6170 (2)0.0279 (7)
C150.2368 (3)0.0642 (2)0.5522 (2)0.0282 (7)
O1W0.0473 (17)0.0204 (5)0.1315 (8)0.279 (6)
O2W0.229 (3)−0.0073 (6)−0.0151 (9)0.474 (10)
H10.230000.265800.701300.0330*
H2A0.069600.394400.462300.0340*
H2B0.148300.282700.497900.0340*
H50.200500.536300.971300.0410*
H7A0.081100.737800.772500.0650*
H7B0.099900.719600.913500.0650*
H7C−0.102800.661400.811800.0650*
H8A0.207200.235500.933300.0640*
H8B0.343900.362101.024200.0640*
H8C0.423800.286600.917300.0640*
H100.19820−0.086500.332800.0320*
H120.41290−0.378700.441200.0340*
H140.37250−0.084600.702400.0330*
H1W0.085700.031200.211000.5000*
H2W0.086400.092800.113600.5000*
H3W0.27840−0.065300.017300.5000*
H4W0.313800.01390−0.062800.5000*
U11U22U33U12U13U23
N10.0299 (11)0.0296 (11)0.0237 (10)0.0107 (8)0.0048 (8)0.0057 (8)
N20.0387 (11)0.0276 (11)0.0201 (10)0.0132 (9)0.0051 (8)0.0048 (8)
N30.0335 (11)0.0288 (11)0.0224 (10)0.0102 (9)0.0049 (8)0.0023 (8)
C20.0258 (12)0.0260 (12)0.0247 (12)0.0069 (9)0.0044 (9)0.0057 (9)
C40.0340 (13)0.0349 (13)0.0242 (12)0.0086 (11)0.0057 (10)0.0019 (10)
C50.0377 (14)0.0418 (15)0.0210 (12)0.0098 (12)0.0052 (10)−0.0002 (11)
C60.0310 (13)0.0429 (15)0.0223 (12)0.0089 (11)0.0044 (10)0.0079 (11)
C70.0584 (18)0.0442 (16)0.0293 (14)0.0246 (14)0.0089 (13)−0.0008 (12)
C80.0509 (17)0.0532 (17)0.0275 (13)0.0204 (14)0.0061 (12)0.0137 (12)
O10.0443 (10)0.0293 (9)0.0276 (9)0.0117 (8)0.0058 (8)0.0034 (7)
O20.0418 (10)0.0282 (9)0.0306 (9)0.0130 (8)0.0058 (7)0.0081 (7)
O30.0682 (14)0.0540 (13)0.0280 (10)0.0282 (11)0.0047 (9)0.0079 (9)
O40.0543 (12)0.0393 (11)0.0371 (10)0.0195 (9)0.0120 (9)−0.0005 (8)
O50.0540 (12)0.0408 (11)0.0513 (12)0.0265 (10)0.0066 (9)0.0150 (9)
O60.0819 (16)0.0477 (12)0.0293 (11)0.0239 (11)−0.0054 (10)0.0069 (9)
N40.0348 (12)0.0362 (12)0.0286 (11)0.0105 (10)0.0052 (9)0.0038 (9)
N50.0394 (12)0.0330 (12)0.0334 (12)0.0108 (10)0.0018 (9)0.0098 (9)
C90.0220 (11)0.0244 (12)0.0295 (12)0.0042 (9)0.0043 (9)0.0045 (10)
C100.0237 (12)0.0293 (13)0.0274 (12)0.0055 (10)0.0019 (9)0.0093 (10)
C110.0253 (12)0.0314 (13)0.0245 (12)0.0063 (10)0.0050 (9)0.0034 (10)
C120.0261 (12)0.0261 (12)0.0333 (13)0.0078 (10)0.0060 (10)0.0049 (10)
C130.0245 (12)0.0291 (12)0.0317 (13)0.0068 (10)0.0020 (10)0.0110 (10)
C140.0257 (12)0.0301 (13)0.0260 (12)0.0039 (10)0.0047 (9)0.0048 (10)
C150.0259 (12)0.0271 (12)0.0318 (13)0.0065 (10)0.0072 (10)0.0057 (10)
O1W0.516 (15)0.093 (4)0.240 (8)0.075 (6)0.084 (9)0.065 (4)
O2W1.00 (3)0.072 (3)0.178 (6)−0.018 (11)−0.117 (16)0.013 (4)
O1—C151.272 (3)C4—C71.487 (4)
O2—C151.241 (3)C5—C61.366 (3)
O3—N41.226 (3)C6—C81.490 (4)
O4—N41.224 (3)C5—H50.9499
O5—N51.218 (3)C7—H7C0.9802
O6—N51.224 (3)C7—H7A0.9801
O1W—H1W0.8562C7—H7B0.9797
O1W—H2W0.8633C8—H8B0.9799
O2W—H4W0.9051C8—H8C0.9797
O2W—H3W0.8801C8—H8A0.9803
N1—C21.353 (3)C9—C141.389 (3)
N1—C61.360 (3)C9—C151.514 (3)
N2—C21.326 (3)C9—C101.389 (3)
N3—C21.349 (3)C10—C111.386 (3)
N3—C41.336 (3)C11—C121.379 (3)
N1—H10.8796C12—C131.386 (3)
N2—H2B0.8804C13—C141.389 (3)
N2—H2A0.8797C10—H100.9509
N4—C111.469 (3)C12—H120.9492
N5—C131.468 (3)C14—H140.9502
C4—C51.400 (3)
O1···N12.605 (3)C9···C10i3.461 (3)
O1···C83.349 (3)C9···O2iii3.224 (3)
O1···C11i3.211 (3)C9···C9i3.378 (3)
O1W···O2W2.30 (2)C10···C14i3.588 (3)
O1W···O1Wii2.817 (12)C10···C9i3.461 (3)
O1W···O2Wii2.10 (2)C10···C15i3.506 (3)
O2···N22.787 (3)C11···C2iii3.266 (3)
O2···C15iii3.151 (3)C11···O1i3.211 (3)
O2···C9iii3.224 (3)C11···C15i3.355 (3)
O2···C12i3.339 (3)C12···O2i3.339 (3)
O2···C13i3.275 (3)C12···C15i3.457 (3)
O2W···O1Wii2.10 (2)C12···C2iii3.518 (3)
O2W···O1W2.30 (2)C13···O2i3.275 (3)
O3···C6iii3.218 (4)C14···C10i3.588 (3)
O4···O5iv3.070 (3)C15···N13.395 (3)
O4···C4iii3.271 (3)C15···C10i3.506 (3)
O4···C6i3.340 (4)C15···C11i3.355 (3)
O4···N1i3.177 (3)C15···C12i3.457 (3)
O5···C2v3.264 (3)C15···C15iii3.305 (3)
O5···O4iv3.070 (3)C15···O2iii3.151 (3)
O6···C8vi3.290 (3)C4···H2Ax3.0334
O6···C7v3.340 (4)C7···H2Wx2.8424
O6···C4v3.194 (3)C7···H2Ax3.0813
O1···H11.7288C15···H12.5614
O1···H142.5138C15···H2B2.7328
O1W···H3Wii2.7574H1···H8C2.4826
O1W···H3W2.5016H1···O11.7288
O1W···H2Wii2.7104H1···O22.8247
O1W···H102.8265H1···C152.5614
O1W···H4Wii2.4802H1···H2B2.2763
O2···H12.8247H1W···H102.1720
O2···H2B1.9198H1W···O2W2.9005
O2···H102.4637H1W···O22.7096
O2···H1W2.7096H1W···O2Wii2.7495
O2W···H8Avii2.8539H2A···C4x3.0334
O2W···H1W2.9005H2A···C7x3.0813
O2W···H2Wii2.2504H2A···N3x2.1682
O2W···H2W2.1890H2B···O21.9198
O2W···H7Bviii2.9025H2B···H12.2763
O2W···H1Wii2.7495H2B···C152.7328
O3···H3W2.7683H2W···O1Wii2.7104
O3···H5viii2.8895H2W···C7x2.8424
O3···H7Bviii2.6367H2W···O2W2.1890
O3···H102.4242H2W···O2Wii2.2504
O4···H8Ci2.7564H3W···H7Bviii2.4431
O4···H5viii2.6416H3W···O1W2.5016
O4···H122.4213H3W···O1Wii2.7574
O5···H12iv2.6470H3W···O32.7683
O5···H122.4207H4W···O1Wii2.4802
O5···H7Cix2.6965H5···H8B2.4411
O6···H142.4304H5···H7B2.4096
O6···H8Bvi2.7417H5···O4xii2.6416
N1···O4i3.177 (3)H5···O3xii2.8895
N1···O12.605 (3)H7B···O2Wxii2.9025
N1···C153.395 (3)H7B···O3xii2.6367
N2···N3x3.041 (3)H7B···H52.4096
N2···O22.787 (3)H7B···H3Wxii2.4431
N3···N2x3.041 (3)H7C···O5xiii2.6965
N3···N5xi3.189 (3)H8A···O2Wxiv2.8539
N5···C4v3.417 (3)H8B···O6vi2.7417
N5···N3v3.189 (3)H8B···H52.4411
N3···H2Ax2.1682H8C···H12.4826
C2···C12iii3.518 (3)H8C···O4i2.7564
C2···C11iii3.266 (3)H10···O22.4637
C2···O5xi3.264 (3)H10···O32.4242
C4···N5xi3.417 (3)H10···O1W2.8265
C4···O6xi3.194 (3)H10···H1W2.1720
C4···O4iii3.271 (3)H12···O5iv2.6470
C6···O3iii3.218 (4)H12···O52.4207
C6···O4i3.340 (4)H12···O42.4213
C7···O6xi3.340 (4)H14···O62.4304
C8···O6vi3.290 (3)H14···O12.5138
C8···O13.349 (3)
H1W—O1W—H2W105.95H7B—C7—H7C109.53
H3W—O2W—H4W100.59C4—C7—H7B109.45
C2—N1—C6120.5 (2)C4—C7—H7A109.44
C2—N3—C4117.6 (2)H8B—C8—H8C109.45
C6—N1—H1119.74C6—C8—H8B109.50
C2—N1—H1119.71C6—C8—H8A109.44
H2A—N2—H2B119.98H8A—C8—H8C109.41
C2—N2—H2B119.99H8A—C8—H8B109.50
C2—N2—H2A120.02C6—C8—H8C109.53
O3—N4—C11118.3 (2)C10—C9—C15118.94 (19)
O4—N4—C11118.4 (2)C14—C9—C15121.27 (19)
O3—N4—O4123.3 (2)C10—C9—C14119.7 (2)
O6—N5—C13117.7 (2)C9—C10—C11118.9 (2)
O5—N5—C13118.5 (2)N4—C11—C12117.9 (2)
O5—N5—O6123.8 (2)N4—C11—C10118.59 (19)
N1—C2—N3122.4 (2)C10—C11—C12123.5 (2)
N1—C2—N2118.5 (2)C11—C12—C13115.8 (2)
N2—C2—N3119.0 (2)N5—C13—C14119.25 (19)
C5—C4—C7121.4 (2)C12—C13—C14123.1 (2)
N3—C4—C7116.7 (2)N5—C13—C12117.6 (2)
N3—C4—C5121.8 (2)C9—C14—C13118.9 (2)
C4—C5—C6119.1 (2)O1—C15—C9116.30 (19)
N1—C6—C5118.5 (2)O1—C15—O2126.1 (2)
C5—C6—C8124.3 (2)O2—C15—C9117.57 (19)
N1—C6—C8117.2 (2)C11—C10—H10120.58
C6—C5—H5120.51C9—C10—H10120.55
C4—C5—H5120.44C11—C12—H12122.06
H7A—C7—H7C109.42C13—C12—H12122.12
H7A—C7—H7B109.53C13—C14—H14120.45
C4—C7—H7C109.45C9—C14—H14120.62
C6—N1—C2—N2178.0 (2)C4—C5—C6—C8−178.4 (3)
C6—N1—C2—N3−2.6 (4)C4—C5—C6—N10.6 (4)
C2—N1—C6—C51.5 (4)C14—C9—C10—C11−1.2 (3)
C2—N1—C6—C8−179.4 (2)C15—C9—C10—C11175.9 (2)
C4—N3—C2—N11.3 (4)C10—C9—C14—C130.9 (3)
C4—N3—C2—N2−179.3 (2)C15—C9—C14—C13−176.1 (2)
C2—N3—C4—C50.9 (4)C10—C9—C15—O1−176.4 (2)
C2—N3—C4—C7−177.8 (2)C10—C9—C15—O21.6 (3)
O4—N4—C11—C12−0.9 (3)C14—C9—C15—O10.7 (3)
O3—N4—C11—C10−2.4 (3)C14—C9—C15—O2178.7 (2)
O4—N4—C11—C10177.4 (2)C9—C10—C11—N4−177.5 (2)
O3—N4—C11—C12179.4 (2)C9—C10—C11—C120.7 (3)
O5—N5—C13—C14−175.2 (2)N4—C11—C12—C13178.3 (2)
O5—N5—C13—C123.0 (3)C10—C11—C12—C130.1 (3)
O6—N5—C13—C12−176.9 (2)C11—C12—C13—N5−178.6 (2)
O6—N5—C13—C144.9 (3)C11—C12—C13—C14−0.4 (3)
N3—C4—C5—C6−1.9 (4)N5—C13—C14—C9178.0 (2)
C7—C4—C5—C6176.7 (3)C12—C13—C14—C9−0.1 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.881.732.605 (3)174
N2—H2A···N3x0.882.173.041 (3)172
N2—H2B···O20.881.922.787 (3)168
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N1—H1⋯O10.881.732.605 (3)174
N2—H2A⋯N3i0.882.173.041 (3)172
N2—H2B⋯O20.881.922.787 (3)168

Symmetry code: (i) .

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3.  Analogs of tetrahydrofolic acid XXIV. Further observations on the mode of pyrimidyl binding to dihydrofolic reductase and thymidylate synthetase by the 2-amino-5-(3-anilinopropyl)-6-methyl-4-pyrimidinol type of inhibitor.

Authors:  B R Baker; D V Santi
Journal:  J Pharm Sci       Date:  1965-09       Impact factor: 3.534

4.  Crystallographic and molecular-orbital studies on the geometry of antifolate drugs.

Authors:  W E Hunt; C H Schwalbe; K Bird; P D Mallinson
Journal:  Biochem J       Date:  1980-05-01       Impact factor: 3.857
  4 in total
  2 in total

1.  Design of co-crystals/salts of some Nitrogenous bases and some derivatives of thiophene carboxylic acids through a combination of hydrogen and halogen bonds.

Authors:  Samson Jegan Jennifer; Packianathan Thomas Muthiah
Journal:  Chem Cent J       Date:  2014-03-22       Impact factor: 4.215

2.  Crystal structure of 4-amino-5-chloro-2,6-di-methyl-pyrimidinium thio-phene-2,5-di-carboxyl-ate.

Authors:  Ammaiyappan Rajam; Packianathan Thomas Muthiah; Ray J Butcher; Matthias Zeller
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2016-06-24
  2 in total

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