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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

4-Chloro-6-meth­­oxy­pyrimidin-2-amine–succinic acid (2/1)

aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my

(Received 30 October 2012; accepted 8 November 2012; online 14 November 2012)

The asymmetric unit of the title compound, 2C5H6ClN3O·C4H6O4, consists of one 4-chloro-6-meth­oxy­pyrimidin-2-amine mol­ecule and one half-mol­ecule of succinic acid which lies about an inversion centre. In the crystal, the acid and base mol­ecules are linked through N—H⋯O and O—H⋯N hydrogen bonds, forming a tape along [1-10] in which R22(8) and R42(8) hydrogen-bond motifs are observed. The tapes are further inter­linked through a pair of C—H⋯O hydrogen bonds into a sheet parallel to (11-2).

Related literature

For applications of pyrimidine derivatives, see: Condon et al. (1993[Condon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Protection Conference on Weeds, pp. 41-46. Alton, Hampshire, England: BCPC Publications.]); Maeno et al. (1990[Maeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415-422. Alton, Hampshire, England: BCPC Publications.]); Gilchrist (1997[Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261-276. Singapore: Addison Wesley Longman.]). For applications of succinic acid, see: Zeikus et al. (1999[Zeikus, J. G., Jain, M. K. & Elankovan, P. (1999). Appl. Microbiol. Biotechnol. 51, 545-552.]); Song & Lee (2006[Song, H. & Lee, S. Y. (2006). Enzyme Microb. Technol. 39, 352-361.]). 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.]). For bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • 2C5H6ClN3O·C4H6O4

  • Mr = 437.24

  • Triclinic, [P \overline 1]

  • a = 5.0094 (2) Å

  • b = 8.5459 (4) Å

  • c = 10.8736 (5) Å

  • α = 82.337 (1)°

  • β = 88.952 (1)°

  • γ = 86.904 (1)°

  • V = 460.64 (4) Å3

  • Z = 1

  • Mo Kα radiation

  • μ = 0.40 mm−1

  • T = 100 K

  • 0.60 × 0.22 × 0.14 mm

Data collection
  • Bruker SMART APEXII DUO CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.796, Tmax = 0.945

  • 7766 measured reflections

  • 1875 independent reflections

  • 1808 reflections with I > 2σ(I)

  • Rint = 0.016

Refinement
  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 0.069

  • S = 1.09

  • 1875 reflections

  • 140 parameters

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

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H1N3⋯O3 0.847 (17) 2.223 (17) 3.0055 (13) 153.7 (14)
N3—H2N3⋯O3i 0.844 (16) 2.095 (16) 2.9369 (13) 175.4 (15)
O2—H1O2⋯N2i 0.806 (16) 1.923 (16) 2.7266 (13) 174.6 (18)
C3—H3A⋯O1ii 0.95 2.45 3.3911 (14) 172
Symmetry codes: (i) -x, -y+1, -z; (ii) -x+2, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. 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 derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely-used anti-AIDS drug (Gilchrist, 1997). The dicarboxylic acid, succinic acid, is a precursor for many chemicals of industrial importance (Zeikus et al., 1999; Song & Lee, 2006). In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.

The asymmetric unit of the title compound consists of a 4-chloro-6-methoxypyrimidin-2-amine molecule and a half of the succinic acid molecule (Fig. 1). The acid molecule is lying about an inversion centre. The 4-chloro-6-methoxypyrimidin-2-amine molecule is approximately planar, with a maximum deviation of 0.037 (1) Å for atom O1. The bond lengths (Allen et al., 1987) and angle are normal.

In the crystal packing, the 4-chloro-6-methoxypyrimidin-2-amine molecules interact with the carboxylic group of the respective succinic acid molecules through N3—H2N3···O3i and O2—H1O2···N2i hydrogen bonds (symmetry code in Table 1), forming a hydrogen-bonded ring motif R22(8) (Bernstein et al., 1995). These motifs are centrosymmetrically paired via N3—H2N3···O3 hydrogen bonds, forming a complementary DADA array. These arrays are further interlinked with a neighboring array through a couple of C3—H3A···O1ii hydrogen bonds (symmetry code in Table 1) combine together to form a large ring motif, with graph-set notation R66(34). These ring motifs extend to give a sheet parallel to (112) plane as shown in Fig. 2.

Related literature top

For applications of pyrimidine derivatives, see: Condon et al. (1993); Maeno et al. (1990); Gilchrist (1997). For applications of succinic acid, see: Zeikus et al. (1999); Song & Lee (2006). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).

Experimental top

Hot methanol solutions (20 ml) of 4-chloro-6-methoxypyrimidin-2-amine (36 mg, Aldrich) and succinic 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 crystals of the title compound (I) appeared after a few days.

Refinement top

O- and N-bound H atoms were located in a difference Fourier map and refined freely [refined distances: N—H = 0.846 (17) and 0.842 (18) Å, O—H = 0.804 (19) Å]. The remaining hydrogen atoms were positioned geometrically (C—H= 0.95–0.99 Å) and were refined using a riding model, with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). A rotating group model was used for the methyl group. Three outliers were omitted (-4 5 3, -1 2 1 and 1 0 1) in the final refinement.

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 molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of the title compound. The H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.
4-Chloro-6-methoxypyrimidin-2-amine–succinic acid (2/1) top
Crystal data top
2C5H6ClN3O·C4H6O4Z = 1
Mr = 437.24F(000) = 226
Triclinic, P1Dx = 1.576 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.0094 (2) ÅCell parameters from 8335 reflections
b = 8.5459 (4) Åθ = 3.3–32.6°
c = 10.8736 (5) ŵ = 0.40 mm1
α = 82.337 (1)°T = 100 K
β = 88.952 (1)°Block, colourless
γ = 86.904 (1)°0.60 × 0.22 × 0.14 mm
V = 460.64 (4) Å3
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer
1875 independent reflections
Radiation source: fine-focus sealed tube1808 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ϕ and ω scansθmax = 26.5°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 66
Tmin = 0.796, Tmax = 0.945k = 1010
7766 measured reflectionsl = 1313
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)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.069H atoms treated by a mixture of independent and constrained refinement
S = 1.09 w = 1/[σ2(Fo2) + (0.0384P)2 + 0.1625P]
where P = (Fo2 + 2Fc2)/3
1875 reflections(Δ/σ)max < 0.001
140 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
2C5H6ClN3O·C4H6O4γ = 86.904 (1)°
Mr = 437.24V = 460.64 (4) Å3
Triclinic, P1Z = 1
a = 5.0094 (2) ÅMo Kα radiation
b = 8.5459 (4) ŵ = 0.40 mm1
c = 10.8736 (5) ÅT = 100 K
α = 82.337 (1)°0.60 × 0.22 × 0.14 mm
β = 88.952 (1)°
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer
1875 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
1808 reflections with I > 2σ(I)
Tmin = 0.796, Tmax = 0.945Rint = 0.016
7766 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0240 restraints
wR(F2) = 0.069H atoms treated by a mixture of independent and constrained refinement
S = 1.09Δρmax = 0.33 e Å3
1875 reflectionsΔρmin = 0.26 e Å3
140 parameters
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.42007 (6)0.86198 (3)0.41239 (3)0.02047 (11)
O10.94601 (17)0.35939 (10)0.35994 (8)0.01945 (19)
N10.59391 (18)0.43360 (11)0.22863 (9)0.0147 (2)
C30.7047 (2)0.59435 (13)0.38427 (10)0.0166 (2)
H3A0.81460.61300.45050.020*
N30.2475 (2)0.52018 (12)0.09782 (10)0.0179 (2)
C10.3960 (2)0.54346 (13)0.19395 (10)0.0140 (2)
N20.33618 (18)0.67556 (11)0.24763 (9)0.0140 (2)
C20.4949 (2)0.69401 (13)0.34172 (10)0.0144 (2)
C40.7434 (2)0.46134 (13)0.32110 (10)0.0151 (2)
C50.9799 (3)0.21688 (14)0.30162 (12)0.0227 (3)
H5A1.13720.15400.33590.034*
H5B1.00460.24510.21190.034*
H5C0.82080.15500.31750.034*
O20.04847 (16)0.09366 (10)0.17679 (8)0.01766 (19)
O30.18536 (16)0.23812 (9)0.03536 (8)0.01799 (19)
C70.4170 (2)0.01172 (13)0.05581 (10)0.0146 (2)
H7A0.53700.01790.12850.018*
H7B0.32870.11330.03810.018*
C60.2070 (2)0.12009 (13)0.08705 (10)0.0135 (2)
H1N30.286 (3)0.439 (2)0.0627 (15)0.022 (4)*
H2N30.123 (3)0.588 (2)0.0758 (15)0.026 (4)*
H1O20.059 (3)0.166 (2)0.1960 (16)0.029 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.02672 (17)0.01570 (16)0.02024 (16)0.00612 (11)0.00563 (11)0.00917 (11)
O10.0221 (4)0.0146 (4)0.0220 (4)0.0072 (3)0.0089 (3)0.0058 (3)
N10.0155 (4)0.0127 (4)0.0160 (5)0.0016 (4)0.0023 (4)0.0032 (4)
C30.0196 (5)0.0153 (5)0.0153 (5)0.0010 (4)0.0051 (4)0.0037 (4)
N30.0180 (5)0.0156 (5)0.0215 (5)0.0057 (4)0.0071 (4)0.0094 (4)
C10.0131 (5)0.0128 (5)0.0162 (5)0.0004 (4)0.0004 (4)0.0028 (4)
N20.0144 (4)0.0127 (4)0.0152 (4)0.0018 (3)0.0014 (4)0.0037 (3)
C20.0179 (5)0.0115 (5)0.0143 (5)0.0000 (4)0.0008 (4)0.0035 (4)
C40.0154 (5)0.0129 (5)0.0163 (5)0.0017 (4)0.0014 (4)0.0007 (4)
C50.0275 (6)0.0142 (5)0.0264 (6)0.0086 (5)0.0071 (5)0.0064 (5)
O20.0176 (4)0.0145 (4)0.0214 (4)0.0050 (3)0.0078 (3)0.0057 (3)
O30.0181 (4)0.0146 (4)0.0220 (4)0.0040 (3)0.0055 (3)0.0064 (3)
C70.0139 (5)0.0124 (5)0.0178 (5)0.0020 (4)0.0021 (4)0.0036 (4)
C60.0121 (5)0.0131 (5)0.0152 (5)0.0011 (4)0.0007 (4)0.0013 (4)
Geometric parameters (Å, º) top
Cl1—C21.7370 (11)N2—C21.3379 (15)
O1—C41.3379 (14)C5—H5A0.9800
O1—C51.4471 (14)C5—H5B0.9800
N1—C41.3184 (15)C5—H5C0.9800
N1—C11.3511 (14)O2—C61.3191 (13)
C3—C21.3637 (16)O2—H1O20.804 (19)
C3—C41.4075 (16)O3—C61.2175 (14)
C3—H3A0.9500C7—C61.5080 (15)
N3—C11.3363 (15)C7—C7i1.525 (2)
N3—H1N30.846 (17)C7—H7A0.9900
N3—H2N30.842 (18)C7—H7B0.9900
C1—N21.3556 (14)
C4—O1—C5117.22 (9)O1—C4—C3116.16 (10)
C4—N1—C1116.08 (9)O1—C5—H5A109.5
C2—C3—C4113.88 (10)O1—C5—H5B109.5
C2—C3—H3A123.1H5A—C5—H5B109.5
C4—C3—H3A123.1O1—C5—H5C109.5
C1—N3—H1N3117.9 (11)H5A—C5—H5C109.5
C1—N3—H2N3117.7 (11)H5B—C5—H5C109.5
H1N3—N3—H2N3124.4 (16)C6—O2—H1O2112.9 (12)
N3—C1—N1117.06 (10)C6—C7—C7i112.44 (11)
N3—C1—N2117.23 (10)C6—C7—H7A109.1
N1—C1—N2125.71 (10)C7i—C7—H7A109.1
C2—N2—C1114.50 (9)C6—C7—H7B109.1
N2—C2—C3125.78 (10)C7i—C7—H7B109.1
N2—C2—Cl1115.19 (8)H7A—C7—H7B107.8
C3—C2—Cl1119.02 (9)O3—C6—O2123.52 (10)
N1—C4—O1119.81 (10)O3—C6—C7123.89 (10)
N1—C4—C3124.03 (10)O2—C6—C7112.59 (9)
C4—N1—C1—N3177.94 (10)C1—N1—C4—O1179.08 (9)
C4—N1—C1—N21.63 (16)C1—N1—C4—C30.99 (16)
N3—C1—N2—C2178.75 (10)C5—O1—C4—N13.63 (15)
N1—C1—N2—C20.81 (16)C5—O1—C4—C3176.31 (10)
C1—N2—C2—C30.73 (16)C2—C3—C4—N10.32 (17)
C1—N2—C2—Cl1179.61 (7)C2—C3—C4—O1179.62 (9)
C4—C3—C2—N21.25 (17)C7i—C7—C6—O35.35 (17)
C4—C3—C2—Cl1179.10 (8)C7i—C7—C6—O2174.64 (11)
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H1N3···O30.847 (17)2.223 (17)3.0055 (13)153.7 (14)
N3—H2N3···O3ii0.844 (16)2.095 (16)2.9369 (13)175.4 (15)
O2—H1O2···N2ii0.806 (16)1.923 (16)2.7266 (13)174.6 (18)
C3—H3A···O1iii0.952.453.3911 (14)172
Symmetry codes: (ii) x, y+1, z; (iii) x+2, y+1, z+1.

Experimental details

Crystal data
Chemical formula2C5H6ClN3O·C4H6O4
Mr437.24
Crystal system, space groupTriclinic, P1
Temperature (K)100
a, b, c (Å)5.0094 (2), 8.5459 (4), 10.8736 (5)
α, β, γ (°)82.337 (1), 88.952 (1), 86.904 (1)
V3)460.64 (4)
Z1
Radiation typeMo Kα
µ (mm1)0.40
Crystal size (mm)0.60 × 0.22 × 0.14
Data collection
DiffractometerBruker SMART APEXII DUO CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.796, 0.945
No. of measured, independent and
observed [I > 2σ(I)] reflections
7766, 1875, 1808
Rint0.016
(sin θ/λ)max1)0.628
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.069, 1.09
No. of reflections1875
No. of parameters140
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.26

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
N3—H1N3···O30.847 (17)2.223 (17)3.0055 (13)153.7 (14)
N3—H2N3···O3i0.844 (16)2.095 (16)2.9369 (13)175.4 (15)
O2—H1O2···N2i0.806 (16)1.923 (16)2.7266 (13)174.6 (18)
C3—H3A···O1ii0.952.453.3911 (14)172
Symmetry codes: (i) x, y+1, z; (ii) x+2, y+1, z+1.
 

Footnotes

Thomson Reuters ResearcherID: A-5599-2009.

Acknowledgements

The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and Fundamental Research Grant Scheme (FRGS) No. 203/PFIZIK/6711171 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CrossRef Web of Science
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 citationBruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationCondon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Protection Conference on Weeds, pp. 41–46. Alton, Hampshire, England: BCPC Publications.
First citationCosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.  CrossRef CAS Web of Science IUCr Journals
First citationGilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman.
First citationMaeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415–422. Alton, Hampshire, England: BCPC Publications.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSong, H. & Lee, S. Y. (2006). Enzyme Microb. Technol. 39, 352–361.  Web of Science CrossRef CAS
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals
First citationZeikus, J. G., Jain, M. K. & Elankovan, P. (1999). Appl. Microbiol. Biotechnol. 51, 545–552.  Web of Science CrossRef CAS

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
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds