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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2235
https://doi.org/10.1107/S1600536812028401

6-Amino-4-(3-iodo­anilino)-2-methyl­pyrimidin-1-ium chloride

Wafaa A. Zaghary,a Detlef Geffkenb and Seik Weng Ngc,d*

aDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia, bInstitut für Pharmazie, Bundesstrasse 45 20146, Hamburg, Germany, cDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, and dChemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203 Jeddah, Saudi Arabia
*Correspondence e-mail: seikweng@um.edu.my

(Received 19 June 2012; accepted 22 June 2012; online 27 June 2012)

In the cation of the title salt, C11H12IN4+·Cl−, the two aromatic rings are oriented to each other at 9.3 (2)°. In the crystal, the two independent Cl− anions lie on twofold rotation axes. N—H⋯Cl hydrogen bonds between the cations and anions generate a supra­molecular layer parallel to (010).

Related literature

For the synthesis of 6-amino-4-[(4-chloro­phen­yl)amino]-2-methyl­pyridimidine hydro­chloride, see: Craveri & Zoni (1958[Craveri, F. & Zoni, G. (1958). Bol. Sci. Fac. Chim. Ind. Bologna, 16, 126-131.]). For the synthesis of the reacta­nts, see: Dox (1941[Dox, A. W. (1941). Organic Syntheses, Collected Vol. 1, p. 5. New York: Wiley.]); Foldi et al. (1942[Foldi, Z., Fodor, G. V., Demjen, I., Szekere, H. & Halmos, I. (1942). Chem. Ber. 75, 755-763.]).

[Scheme 1]

Experimental

Crystal data

  • C11H12IN4+·Cl−

  • Mr = 362.60

  • Orthorhombic, P n n 2

  • a = 12.6323 (5) Å

  • b = 19.8608 (7) Å

  • c = 5.1267 (2) Å

  • V = 1286.23 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 2.68 mm−1

  • T = 100 K

  • 0.25 × 0.05 × 0.03 mm
Data collection

  • Agilent SuperNova Dual diffractometer with an Atlas detector

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]) Tmin = 0.554, Tmax = 0.924

  • 10009 measured reflections

  • 2981 independent reflections

  • 2833 reflections with I > 2σ(I)

  • Rint = 0.036
Refinement

  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.078

  • S = 1.07

  • 2981 reflections

  • 172 parameters

  • 5 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.51 e Å−3

  • Δρmin = −0.70 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1321 Friedel pairs

  • Flack parameter: −0.04 (3)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯Cl1 0.88 (4) 2.48 (4) 3.325 (4) 162 (4)
N3—H3⋯Cl2 0.88 (5) 2.23 (4) 3.096 (4) 168 (4)
N4—H4A⋯Cl2 0.89 (4) 2.66 (4) 3.462 (4) 150 (3)
N4—H4B⋯Cl1i 0.88 (2) 2.64 (3) 3.404 (4) 146 (4)
Symmetry code: (i) x, y, z+1.

Data collection: CrysAlis PRO (Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: X-SEED (Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812028401/xu5569sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812028401/xu5569Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812028401/xu5569Isup3.cml

checkCIF report


Comment top

The synthesis of 6-amino-4-[(3-iodophenyl)amino]-2-methylpyridimidine, which was synthesized with the intention of labeling it with 99mTc for a study of its biotransformation, requires a small amount of hydrochloric acid as catalyst. A mole of hydrochloric acid is incorporated into the final product, so that the compound is formally 6-amino-4-[(3-iodophenyl)amino]-2-methylpyrimidin-1-ium chloride (Scheme I).

Protonation occurs on the aromatic nitrogen atom that is para to the secondary amino substituent. The non-hydrogen atoms of the cation lie on an approximate plane (r.m.s. deviation 0.132 Å); the two aromatic rings were twisted by 9.3 (2) °. The secondary amino and the tertiary pyrimidinium N atoms each forms a hydrogen bonds to a chloride ion to generate a layer parallel to (0 1 0) (Table 1).

Related literature top

For the synthesis of 6-amino-4-[(4-chlorophenyl)amino]-2-methylpyridimidine hydrochloride, see: Craveri & Zoni (1958). For the synthesis of the reactants, see: Dox (1941); Foldi et al. (1942).

Experimental top

A mixture of 4-amino-2-methyl-6-chloropyrimidine (1.55 g, 0.01 mol) and 3-iodoaniline (2.19, 0.01 mol) in absolute ethanol (10 ml) and drop of hydrochloric acid was refluxed for 12 h; 4-amino-2-methyl-6-chloropyrimidine was synthesized from two other reactants (Dox, 1941; Foldi et al., 1942). The reaction mixture was cooled and poured onto ice water. The formed precipitate was filtered, washed with water and recrystallized from ethanol to give the title compound in 60% yield; m.p. 535–537 K. The synthesis duplicates that used for of 6-amino-4-[(4-chlorophenyl)amino]-2-methylpyridimidine, which also exists as a hydrochloride (Craveri & Zoni, 1958).

Refinement top

Carbon-bound H-atoms were placed in calculated positions [C–H 0.95 to 0.98 Å, Uiso(H) 1.2 to 1.5Ueq(C)] and were included in the refinement in the riding model approximation.

The amino H-atoms were located in a difference Fourier map, and were refined with a distance restraint of N–H 0.88±0.01 Å; their temperature factors were refined.

Structure description top

The synthesis of 6-amino-4-[(3-iodophenyl)amino]-2-methylpyridimidine, which was synthesized with the intention of labeling it with 99mTc for a study of its biotransformation, requires a small amount of hydrochloric acid as catalyst. A mole of hydrochloric acid is incorporated into the final product, so that the compound is formally 6-amino-4-[(3-iodophenyl)amino]-2-methylpyrimidin-1-ium chloride (Scheme I).

Protonation occurs on the aromatic nitrogen atom that is para to the secondary amino substituent. The non-hydrogen atoms of the cation lie on an approximate plane (r.m.s. deviation 0.132 Å); the two aromatic rings were twisted by 9.3 (2) °. The secondary amino and the tertiary pyrimidinium N atoms each forms a hydrogen bonds to a chloride ion to generate a layer parallel to (0 1 0) (Table 1).

For the synthesis of 6-amino-4-[(4-chlorophenyl)amino]-2-methylpyridimidine hydrochloride, see: Craveri & Zoni (1958). For the synthesis of the reactants, see: Dox (1941); Foldi et al. (1942).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of C11H12N4I+ Cl- at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.
6-Amino-4-(3-iodoanilino)-2-methylpyrimidin-1-ium chloride top
Crystal data top
C11H12IN4+·Cl−F(000) = 704
Mr = 362.60Dx = 1.872 Mg m−3
Orthorhombic, Pnn2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2 -2nCell parameters from 5603 reflections
a = 12.6323 (5) Åθ = 2.6–27.5°
b = 19.8608 (7) ŵ = 2.68 mm−1
c = 5.1267 (2) ÅT = 100 K
V = 1286.23 (8) Å3Prism, colorless
Z = 40.25 × 0.05 × 0.03 mm
Data collection top
Agilent SuperNova Dual
diffractometer with an Atlas detector		2981 independent reflections
Radiation source: SuperNova (Mo) X-ray Source2833 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.036
Detector resolution: 10.4041 pixels mm-1θmax = 27.6°, θmin = 2.6°
ω scanh = −16→11
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)		k = −25→25
Tmin = 0.554, Tmax = 0.924l = −6→6
10009 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.078 w = 1/[σ2(Fo2) + (0.0455P)2 + 0.098P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
2981 reflectionsΔρmax = 0.51 e Å−3
172 parametersΔρmin = −0.70 e Å−3
5 restraintsAbsolute structure: Flack (1983), 1321 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: −0.04 (3)
Crystal data top
C11H12IN4+·Cl−V = 1286.23 (8) Å3
Mr = 362.60Z = 4
Orthorhombic, Pnn2Mo Kα radiation
a = 12.6323 (5) ŵ = 2.68 mm−1
b = 19.8608 (7) ÅT = 100 K
c = 5.1267 (2) Å0.25 × 0.05 × 0.03 mm
Data collection top
Agilent SuperNova Dual
diffractometer with an Atlas detector		2981 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)		2833 reflections with I > 2σ(I)
Tmin = 0.554, Tmax = 0.924Rint = 0.036
10009 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.078Δρmax = 0.51 e Å−3
S = 1.07Δρmin = −0.70 e Å−3
2981 reflectionsAbsolute structure: Flack (1983), 1321 Friedel pairs
172 parametersAbsolute structure parameter: −0.04 (3)
5 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.859538 (17)0.859281 (10)0.49964 (10)0.01803 (9)
Cl10.50000.50000.7100 (3)0.0165 (3)
Cl21.00000.50001.8561 (3)0.0189 (3)
N10.6726 (3)0.62226 (17)0.8346 (7)0.0133 (7)
H10.616 (3)0.597 (2)0.815 (12)0.030 (15)*
N20.8301 (3)0.63625 (14)1.0653 (6)0.0115 (8)
N30.8681 (3)0.56332 (17)1.4102 (7)0.0127 (7)
H30.911 (4)0.551 (2)1.537 (8)0.032 (14)*
N40.7588 (3)0.47680 (17)1.5483 (7)0.0158 (8)
H4A0.809 (3)0.471 (2)1.667 (7)0.019 (12)*
H4B0.6921 (14)0.465 (2)1.559 (12)0.037 (16)*
C10.7485 (3)0.78043 (16)0.4921 (11)0.0132 (7)
C20.6725 (3)0.7825 (2)0.2979 (8)0.0153 (8)
H20.67240.81750.17160.018*
C30.5960 (3)0.7318 (2)0.2927 (8)0.0174 (9)
H3A0.54180.73280.16440.021*
C40.5988 (3)0.68030 (16)0.4730 (9)0.0138 (8)
H40.54640.64600.46680.017*
C50.6770 (3)0.67774 (17)0.6634 (8)0.0116 (7)
C60.7534 (3)0.72929 (18)0.6783 (9)0.0141 (8)
H60.80620.72920.81010.017*
C70.7378 (3)0.60225 (16)1.0287 (9)0.0116 (8)
C80.7081 (3)0.54705 (17)1.1824 (8)0.0126 (7)
H80.64380.52351.15150.015*
C90.7757 (3)0.52821 (18)1.3798 (8)0.0121 (8)
C100.8926 (3)0.61518 (19)1.2527 (8)0.0110 (7)
C110.9960 (4)0.64830 (19)1.3029 (9)0.0190 (9)
H11A0.99530.69381.22920.029*
H11B1.05280.62211.22120.029*
H11C1.00830.65091.49140.029*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.01513 (14)0.01341 (13)0.02556 (15)−0.00259 (7)−0.00545 (16)0.00610 (14)
Cl10.0112 (6)0.0149 (6)0.0234 (8)−0.0017 (5)0.0000.000
Cl20.0187 (7)0.0262 (7)0.0117 (7)0.0092 (5)0.0000.000
N10.0139 (17)0.0138 (14)0.0122 (16)−0.0050 (14)−0.0026 (14)0.0015 (14)
N20.0101 (16)0.0122 (14)0.012 (2)−0.0018 (11)−0.0021 (13)0.0017 (11)
N30.0130 (18)0.0130 (15)0.0121 (16)0.0006 (12)−0.0030 (13)0.0017 (13)
N40.0135 (16)0.0214 (15)0.012 (2)−0.0011 (12)−0.0009 (14)0.0067 (14)
C10.0133 (16)0.0117 (14)0.0146 (16)0.0003 (12)0.003 (2)0.002 (2)
C20.014 (2)0.0166 (18)0.015 (2)0.0006 (16)−0.0014 (17)0.0031 (16)
C30.016 (2)0.0180 (18)0.018 (2)0.0008 (16)−0.0055 (17)0.0016 (17)
C40.0132 (16)0.0123 (14)0.016 (2)0.0005 (12)0.000 (2)−0.0008 (18)
C50.0115 (18)0.0116 (16)0.0118 (18)0.0008 (14)0.0002 (16)0.0019 (16)
C60.0126 (19)0.0157 (17)0.0139 (17)0.0002 (14)−0.0026 (16)−0.0006 (16)
C70.0101 (16)0.0120 (14)0.013 (2)0.0001 (11)−0.0003 (17)−0.0014 (17)
C80.0117 (19)0.0122 (16)0.0139 (18)−0.0014 (14)−0.0001 (16)0.0026 (16)
C90.016 (2)0.0103 (15)0.0099 (18)−0.0011 (14)0.0015 (15)−0.0004 (14)
C100.0123 (19)0.0121 (18)0.0085 (17)0.0006 (15)0.0004 (15)0.0006 (15)
C110.016 (2)0.022 (2)0.020 (2)−0.0062 (16)−0.0060 (18)0.0083 (17)
Geometric parameters (Å, º) top
I1—C12.103 (3)C2—H20.9500
N1—C71.351 (5)C3—C41.380 (6)
N1—C51.410 (5)C3—H3A0.9500
N1—H10.88 (1)C4—C51.390 (6)
N2—C101.313 (5)C4—H40.9500
N2—C71.360 (5)C5—C61.409 (5)
N3—C101.345 (5)C6—H60.9500
N3—C91.369 (5)C7—C81.401 (5)
N3—H30.88 (1)C8—C91.375 (5)
N4—C91.354 (5)C8—H80.9500
N4—H4A0.88 (1)C10—C111.485 (6)
N4—H4B0.88 (1)C11—H11A0.9800
C1—C21.384 (6)C11—H11B0.9800
C1—C61.395 (6)C11—H11C0.9800
C2—C31.396 (6)
C7—N1—C5131.6 (3)C4—C5—N1116.0 (3)
C7—N1—H1114 (4)C6—C5—N1124.1 (4)
C5—N1—H1114 (4)C1—C6—C5117.5 (4)
C10—N2—C7117.3 (3)C1—C6—H6121.2
C10—N3—C9121.2 (3)C5—C6—H6121.2
C10—N3—H3122 (3)N1—C7—N2118.5 (3)
C9—N3—H3117 (3)N1—C7—C8118.8 (3)
C9—N4—H4A115 (3)N2—C7—C8122.7 (4)
C9—N4—H4B113 (4)C9—C8—C7117.4 (4)
H4A—N4—H4B128 (5)C9—C8—H8121.3
C2—C1—C6123.0 (3)C7—C8—H8121.3
C2—C1—I1117.0 (3)N4—C9—N3116.5 (3)
C6—C1—I1120.0 (3)N4—C9—C8125.2 (4)
C1—C2—C3118.2 (4)N3—C9—C8118.3 (4)
C1—C2—H2120.9N2—C10—N3123.0 (4)
C3—C2—H2120.9N2—C10—C11121.0 (4)
C4—C3—C2120.3 (4)N3—C10—C11116.0 (4)
C4—C3—H3A119.8C10—C11—H11A109.5
C2—C3—H3A119.8C10—C11—H11B109.5
C3—C4—C5121.1 (3)H11A—C11—H11B109.5
C3—C4—H4119.5C10—C11—H11C109.5
C5—C4—H4119.5H11A—C11—H11C109.5
C4—C5—C6119.9 (4)H11B—C11—H11C109.5
C6—C1—C2—C31.5 (7)C5—N1—C7—C8174.7 (4)
I1—C1—C2—C3−178.2 (3)C10—N2—C7—N1−179.0 (4)
C1—C2—C3—C4−1.8 (6)C10—N2—C7—C80.4 (6)
C2—C3—C4—C50.3 (7)N1—C7—C8—C9−179.5 (4)
C3—C4—C5—C61.6 (6)N2—C7—C8—C91.1 (6)
C3—C4—C5—N1−179.2 (4)C10—N3—C9—N4179.8 (4)
C7—N1—C5—C4175.8 (4)C10—N3—C9—C80.3 (6)
C7—N1—C5—C6−5.0 (7)C7—C8—C9—N4179.1 (4)
C2—C1—C6—C50.4 (7)C7—C8—C9—N3−1.4 (6)
I1—C1—C6—C5−179.9 (3)C7—N2—C10—N3−1.6 (6)
C4—C5—C6—C1−1.9 (6)C7—N2—C10—C11178.6 (4)
N1—C5—C6—C1179.0 (4)C9—N3—C10—N21.3 (6)
C5—N1—C7—N2−5.8 (6)C9—N3—C10—C11−178.9 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl10.88 (4)2.48 (4)3.325 (4)162 (4)
N3—H3···Cl20.88 (5)2.23 (4)3.096 (4)168 (4)
N4—H4A···Cl20.89 (4)2.66 (4)3.462 (4)150 (3)
N4—H4B···Cl1i0.88 (2)2.64 (3)3.404 (4)146 (4)
Symmetry code: (i) x, y, z+1.

Experimental details

Crystal data
Chemical formulaC11H12IN4+·Cl−
Mr362.60
Crystal system, space groupOrthorhombic, Pnn2
Temperature (K)100
a, b, c (Å)12.6323 (5), 19.8608 (7), 5.1267 (2)
V (Å3)1286.23 (8)
Z4
Radiation typeMo Kα
µ (mm−1)2.68
Crystal size (mm)0.25 × 0.05 × 0.03
Data collection
DiffractometerAgilent SuperNova Dual
diffractometer with an Atlas detector
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2012)
Tmin, Tmax0.554, 0.924
No. of measured, independent and
observed [I > 2σ(I)] reflections		10009, 2981, 2833
Rint0.036
(sin θ/λ)max (Å−1)0.651
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.078, 1.07
No. of reflections2981
No. of parameters172
No. of restraints5
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.51, −0.70
Absolute structureFlack (1983), 1321 Friedel pairs
Absolute structure parameter−0.04 (3)

Computer programs: CrysAlis PRO (Agilent, 2012), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl10.88 (4)2.48 (4)3.325 (4)162 (4)
N3—H3···Cl20.88 (5)2.23 (4)3.096 (4)168 (4)
N4—H4A···Cl20.89 (4)2.66 (4)3.462 (4)150 (3)
N4—H4B···Cl1i0.88 (2)2.64 (3)3.404 (4)146 (4)
Symmetry code: (i) x, y, z+1.
 

Acknowledgements

We thank the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University, and the Ministry of Higher Education of Malaysia (grant No. UM.C/HIR/MOHE/SC/12) for supporting this study.

References

First citationAgilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.  Google Scholar
 First citationBarbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.  CrossRef CAS Google Scholar
 First citationCraveri, F. & Zoni, G. (1958). Bol. Sci. Fac. Chim. Ind. Bologna, 16, 126–131.  CAS Google Scholar
 First citationDox, A. W. (1941). Organic Syntheses, Collected Vol. 1, p. 5. New York: Wiley.  Google Scholar
 First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationFoldi, Z., Fodor, G. V., Demjen, I., Szekere, H. & Halmos, I. (1942). Chem. Ber. 75, 755–763.  Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page o2235
https://doi.org/10.1107/S1600536812028401
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