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

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ISSN: 2056-9890

2-Amino-5-chloro­pyrimidin-1-ium hydrogen maleate

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bBiomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore 138673
*Correspondence e-mail: hkfun@usm.my

(Received 30 November 2011; accepted 30 November 2011; online 14 December 2011)

In the title salt, C4H5ClN3+·C4H3O4, the 2-amino-5-chloro­pyrimidinium cation is protonated at one of its pyrimidine N atoms. In the roughly planar (r.m.s. deviation = 0.026 Å) hydrogen malate anion, an intra­molecular O—H⋯O hydrogen bond generates an S(7) ring. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H⋯O hydrogen bonds, forming an R22(8) ring motif. The ion pairs are connected via further N—H⋯O hydrogen bonds and a short C—H⋯O inter­action, forming layers lying parallel to the bc plane.

Related literature

For background to pyrimidine compounds, see: Glidewell et al. (2003[Glidewell, C., Low, J. N., Melguizo, M. & Quesada, A. (2003). Acta Cryst. C59, o9-o13.]); Panneerselvam et al. (2004[Panneerselvam, P., Muthiah, P. T. & Francis, S. (2004). Acta Cryst. E60, o747-o749.]). For details of maleic acid, see: James & Williams (1974[James, M. N. G. & Williams, G. J. B. (1974). Acta Cryst. B30, 1249-1257.]); Bertolasi et al. (1980[Bertolasi, V., Borea, P. A., Gilli, G. & Sacerdoti, M. (1980). Acta Cryst. B36, 2287-2291.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C4H5ClN3+·C4H3O4

  • Mr = 245.62

  • Monoclinic, P 21 /c

  • a = 9.3974 (6) Å

  • b = 5.5167 (4) Å

  • c = 20.0654 (13) Å

  • β = 95.264 (1)°

  • V = 1035.86 (12) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.37 mm−1

  • T = 296 K

  • 0.42 × 0.36 × 0.13 mm

Data collection
  • Bruker APEXII DUO CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.860, Tmax = 0.954

  • 12808 measured reflections

  • 3443 independent reflections

  • 2745 reflections with I > 2σ(I)

  • Rint = 0.023

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.109

  • S = 1.04

  • 3443 reflections

  • 161 parameters

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

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.36 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1N2⋯O4i 0.881 (19) 1.810 (18) 2.6897 (14) 177.6 (19)
N3—H1N3⋯O1ii 0.860 (17) 2.592 (18) 3.0814 (16) 117.2 (14)
N3—H1N3⋯O2ii 0.860 (17) 2.128 (17) 2.9795 (16) 170.2 (16)
N3—H2N3⋯O3i 0.893 (18) 1.975 (18) 2.8629 (17) 172.8 (16)
O1—H1O3⋯O3 0.86 (3) 1.60 (3) 2.4514 (15) 179 (3)
C2—H2A⋯O2iii 0.93 2.39 3.3117 (17) 173
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x, y+1, z; (iii) [-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyrimidine compounds have attracted much attention for their biological activities and molecular structures. The crystal structures of some 2-amino-substituted pyrimidine compounds, such as 2-amino-4-methoxy 6-methylpyrimidine (Glidewell et al., 2003) and 2-amino-4,6-dimethyl pyrimidinium bromide (Panneerselvam et al., 2004) have previously been elucidated. A study of the structural chemistry of maleic acid and related substances arises from the fact that these systems possess short but highly strained hydrogen bonds (James & Williams, 1974). The crystal structures of maleic acid (James & Williams, 1974) and carbinoxamine maleate (Bertolasi et al., 1980) have been reported in the literature. We report here the molecular structure of a title compound (I), formed from the reaction of 2-amino-5-chloropyrimidine with maleic acid. It was prepared in order to extend our study on D—H···A hydrogen bonding in organic systems.

The asymmetric unit of the title compound is shown in Fig. 1. The 2-amino-5-chloropyridinium (N1,N2/C1–C4) cation is essentially planar, with a maximum deviation of 0.004 (1) Å for atom N1. In the 2-amino-5- chloropyrimidine molecule, a wide angle [C1—N2—C4 = 121.33 (10)°] is subtended at the protonated N2 atom. In the hydrogen malate anion, an intramolecular O—H···O hydrogen bond generates an S(7) (Bernstein et al., 1995) ring and results in a folded conformation.

In the crystal structure, (Fig. 2), the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H···O hydrogen bonds, forming an R22(8) ring motif. The ion pairs are further connected via N—H···O and C—H···O hydrogen bonds (Table 1), forming a layer parallel to the bc plane.

Related literature top

For background to pyrimidine compounds, see: Glidewell et al. (2003); Panneerselvam et al. (2004). For details of maleic acid, see: James & Williams (1974); Bertolasi et al. (1980). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Experimental top

A hot methanol solution (20 ml) of 2-amino-5-chloropyrimidine (32 mg, Aldrich) and maleic acid (29 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and colourless blocks of the title compound appeared after a few days.

Refinement top

Atoms H1N2, H1N3, H2N3 and H1O3 were located from a difference Fourier maps and refined freely [N–H = 0.858 (19)–0.89 (2) Å and O–H = 0.86 (3) Å]. The remaining H atoms were positioned geometrically [C–H = 0.93 Å] and were refined using a riding model, with Uiso(H) = 1.2 Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound, showing 50% probability displacement ellipsoids. Intramolecular hydrogen bonds shown by dashed lines.
[Figure 2] Fig. 2. The crystal packing of title compound (I).
2-Amino-5-chloropyrimidin-1-ium hydrogen maleate top
Crystal data top
C4H5ClN3+·C4H3O4F(000) = 504
Mr = 245.62Dx = 1.575 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4623 reflections
a = 9.3974 (6) Åθ = 2.8–31.4°
b = 5.5167 (4) ŵ = 0.37 mm1
c = 20.0654 (13) ÅT = 296 K
β = 95.264 (1)°Block, colourless
V = 1035.86 (12) Å30.42 × 0.36 × 0.13 mm
Z = 4
Data collection top
Bruker APEXII DUO CCD
diffractometer
3443 independent reflections
Radiation source: fine-focus sealed tube2745 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
ϕ and ω scansθmax = 31.7°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 1313
Tmin = 0.860, Tmax = 0.954k = 78
12808 measured reflectionsl = 2929
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.109H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0515P)2 + 0.2504P]
where P = (Fo2 + 2Fc2)/3
3443 reflections(Δ/σ)max = 0.001
161 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = 0.36 e Å3
Crystal data top
C4H5ClN3+·C4H3O4V = 1035.86 (12) Å3
Mr = 245.62Z = 4
Monoclinic, P21/cMo Kα radiation
a = 9.3974 (6) ŵ = 0.37 mm1
b = 5.5167 (4) ÅT = 296 K
c = 20.0654 (13) Å0.42 × 0.36 × 0.13 mm
β = 95.264 (1)°
Data collection top
Bruker APEXII DUO CCD
diffractometer
3443 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2745 reflections with I > 2σ(I)
Tmin = 0.860, Tmax = 0.954Rint = 0.023
12808 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.109H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.35 e Å3
3443 reflectionsΔρmin = 0.36 e Å3
161 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.07132 (4)0.34821 (8)0.119864 (19)0.05434 (13)
O10.34314 (14)0.1959 (2)0.47054 (5)0.0547 (3)
O20.20761 (12)0.3832 (2)0.39206 (5)0.0483 (3)
O30.44057 (12)0.28155 (19)0.58566 (5)0.0477 (3)
O40.43276 (11)0.5756 (2)0.65981 (4)0.0456 (2)
N10.14846 (11)0.8848 (2)0.24914 (5)0.0364 (2)
N20.32969 (11)0.59171 (19)0.27016 (5)0.0305 (2)
N30.32863 (14)0.9408 (2)0.33347 (6)0.0424 (3)
C10.26868 (12)0.8052 (2)0.28452 (5)0.0307 (2)
C20.09165 (13)0.7456 (3)0.20036 (6)0.0372 (3)
H2A0.00860.79770.17570.045*
C30.15083 (13)0.5224 (2)0.18395 (6)0.0343 (2)
C40.27274 (13)0.4492 (2)0.22009 (6)0.0335 (2)
H4A0.31600.30330.21040.040*
C50.26812 (14)0.3825 (2)0.44879 (6)0.0351 (3)
C60.25815 (15)0.6000 (2)0.49162 (6)0.0391 (3)
H6A0.20490.72650.47140.047*
C70.31273 (15)0.6453 (2)0.55439 (6)0.0387 (3)
H7A0.29210.79850.57030.046*
C80.40123 (13)0.4898 (2)0.60285 (5)0.0328 (2)
H1N20.4062 (19)0.537 (4)0.2941 (9)0.048 (5)*
H1N30.2848 (19)1.066 (3)0.3469 (9)0.047 (5)*
H2N30.402 (2)0.884 (3)0.3604 (9)0.051 (5)*
H1O30.376 (3)0.225 (5)0.5110 (14)0.093 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0550 (2)0.0562 (2)0.0486 (2)0.00891 (17)0.01285 (15)0.01739 (16)
O10.0821 (8)0.0392 (6)0.0379 (5)0.0180 (5)0.0202 (5)0.0097 (4)
O20.0577 (6)0.0494 (6)0.0343 (5)0.0033 (5)0.0154 (4)0.0049 (4)
O30.0627 (6)0.0412 (5)0.0358 (4)0.0183 (5)0.0148 (4)0.0045 (4)
O40.0498 (5)0.0551 (6)0.0298 (4)0.0150 (5)0.0085 (4)0.0093 (4)
N10.0357 (5)0.0351 (5)0.0367 (5)0.0036 (4)0.0055 (4)0.0018 (4)
N20.0331 (5)0.0313 (5)0.0261 (4)0.0025 (4)0.0023 (3)0.0008 (4)
N30.0491 (7)0.0373 (6)0.0376 (5)0.0081 (5)0.0136 (5)0.0095 (5)
C10.0338 (5)0.0305 (5)0.0272 (5)0.0001 (4)0.0009 (4)0.0010 (4)
C20.0319 (5)0.0412 (7)0.0369 (6)0.0007 (5)0.0065 (4)0.0009 (5)
C30.0354 (6)0.0361 (6)0.0306 (5)0.0068 (5)0.0023 (4)0.0029 (5)
C40.0387 (6)0.0310 (6)0.0306 (5)0.0009 (5)0.0018 (4)0.0018 (4)
C50.0399 (6)0.0342 (6)0.0298 (5)0.0010 (5)0.0045 (4)0.0006 (4)
C60.0492 (7)0.0335 (6)0.0326 (5)0.0106 (5)0.0070 (5)0.0002 (5)
C70.0495 (7)0.0335 (6)0.0316 (5)0.0110 (5)0.0039 (5)0.0031 (5)
C80.0330 (5)0.0381 (6)0.0265 (5)0.0040 (5)0.0012 (4)0.0004 (4)
Geometric parameters (Å, º) top
Cl1—C31.7201 (12)N3—H1N30.858 (19)
O1—C51.3005 (16)N3—H2N30.89 (2)
O1—H1O30.86 (3)C2—C31.4027 (19)
O2—C51.2248 (15)C2—H2A0.9300
O3—C81.2645 (16)C3—C41.3599 (17)
O4—C81.2475 (14)C4—H4A0.9300
N1—C21.3178 (17)C5—C61.4837 (18)
N1—C11.3512 (15)C6—C71.3393 (17)
N2—C41.3473 (15)C6—H6A0.9300
N2—C11.3527 (15)C7—C81.4916 (17)
N2—H1N20.880 (18)C7—H7A0.9300
N3—C11.3192 (16)
C5—O1—H1O3108.0 (18)C2—C3—Cl1120.76 (9)
C2—N1—C1117.60 (11)N2—C4—C3118.81 (11)
C4—N2—C1121.33 (10)N2—C4—H4A120.6
C4—N2—H1N2117.2 (12)C3—C4—H4A120.6
C1—N2—H1N2121.4 (12)O2—C5—O1120.36 (12)
C1—N3—H1N3120.2 (12)O2—C5—C6119.16 (12)
C1—N3—H2N3120.3 (12)O1—C5—C6120.46 (11)
H1N3—N3—H2N3117.3 (16)C7—C6—C5131.05 (12)
N3—C1—N1119.11 (11)C7—C6—H6A114.5
N3—C1—N2119.47 (11)C5—C6—H6A114.5
N1—C1—N2121.41 (10)C6—C7—C8130.40 (12)
N1—C2—C3122.92 (11)C6—C7—H7A114.8
N1—C2—H2A118.5C8—C7—H7A114.8
C3—C2—H2A118.5O4—C8—O3122.95 (11)
C4—C3—C2117.92 (11)O4—C8—C7116.77 (11)
C4—C3—Cl1121.32 (10)O3—C8—C7120.28 (10)
C2—N1—C1—N3179.67 (12)C2—C3—C4—N20.81 (18)
C2—N1—C1—N20.63 (18)Cl1—C3—C4—N2179.38 (9)
C4—N2—C1—N3179.27 (12)O2—C5—C6—C7179.72 (16)
C4—N2—C1—N10.23 (18)O1—C5—C6—C72.0 (2)
C1—N1—C2—C30.3 (2)C5—C6—C7—C80.8 (3)
N1—C2—C3—C40.4 (2)C6—C7—C8—O4177.01 (16)
N1—C2—C3—Cl1179.77 (10)C6—C7—C8—O32.8 (2)
C1—N2—C4—C30.52 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O4i0.881 (19)1.810 (18)2.6897 (14)177.6 (19)
N3—H1N3···O1ii0.860 (17)2.592 (18)3.0814 (16)117.2 (14)
N3—H1N3···O2ii0.860 (17)2.128 (17)2.9795 (16)170.2 (16)
N3—H2N3···O3i0.893 (18)1.975 (18)2.8629 (17)172.8 (16)
O1—H1O3···O30.86 (3)1.60 (3)2.4514 (15)179 (3)
C2—H2A···O2iii0.932.393.3117 (17)173
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z; (iii) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H5ClN3+·C4H3O4
Mr245.62
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)9.3974 (6), 5.5167 (4), 20.0654 (13)
β (°) 95.264 (1)
V3)1035.86 (12)
Z4
Radiation typeMo Kα
µ (mm1)0.37
Crystal size (mm)0.42 × 0.36 × 0.13
Data collection
DiffractometerBruker APEXII DUO CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.860, 0.954
No. of measured, independent and
observed [I > 2σ(I)] reflections
12808, 3443, 2745
Rint0.023
(sin θ/λ)max1)0.739
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.109, 1.04
No. of reflections3443
No. of parameters161
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.35, 0.36

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O4i0.881 (19)1.810 (18)2.6897 (14)177.6 (19)
N3—H1N3···O1ii0.860 (17)2.592 (18)3.0814 (16)117.2 (14)
N3—H1N3···O2ii0.860 (17)2.128 (17)2.9795 (16)170.2 (16)
N3—H2N3···O3i0.893 (18)1.975 (18)2.8629 (17)172.8 (16)
O1—H1O3···O30.86 (3)1.60 (3)2.4514 (15)179 (3)
C2—H2A···O2iii0.932.393.3117 (17)173
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z; (iii) x, y+1/2, z+1/2.
 

Footnotes

Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

HKF and MH thank the Malaysian Government and Universiti Sains Malaysia for the Research University grant No. 1001/PFIZIK/811160. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science
First citationBertolasi, V., Borea, P. A., Gilli, G. & Sacerdoti, M. (1980). Acta Cryst. B36, 2287–2291.  CSD CrossRef CAS IUCr Journals Web of Science
First citationBruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationGlidewell, C., Low, J. N., Melguizo, M. & Quesada, A. (2003). Acta Cryst. C59, o9–o13.  Web of Science CSD CrossRef CAS IUCr Journals
First citationJames, M. N. G. & Williams, G. J. B. (1974). Acta Cryst. B30, 1249–1257.  CSD CrossRef IUCr Journals Web of Science
First citationPanneerselvam, P., Muthiah, P. T. & Francis, S. (2004). Acta Cryst. E60, o747–o749.  Web of Science CSD CrossRef IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals

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