Literature DB >> 23476258

2,6-Diamino-4-chloro-pyrimidine-benzoic acid (1/1).

Kaliyaperumal Thanigaimani1, Nuridayanti Che Khalib, Suhana Arshad, Ibrahim Abdul Razak.   

Abstract

The benzoic acid mol-ecule of the title compound, C4H5ClN4·C7H6O2, is approximately planar, with a dihedral angle of 1.28 (9)° between the carb-oxy group and the benzene ring. In the crystal, two acid and two base mol-ecules are linked through N-H⋯O and O-H⋯N hydrogen bonds, forming a centrosymmetric 2 + 2 unit with R2(2)(8) and R4(2)(8) motifs. These units are further linked through a pair of N-H⋯N hydrogen bonds into a tape structure along [1-20]. The crystal structure also features weak π-π [centroid-centroid distance = 3.5984 (11) Å] and C-H⋯π inter-actions.

Entities:  

Year:  2012        PMID: 23476258      PMCID: PMC3589022          DOI: 10.1107/S160053681204768X

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


Related literature

For the biological activity of pyrimidine and amino­pyrimidine derivatives, see: Hunt et al. (1980 ▶); Baker & Santi (1965 ▶). For related structures, see: Schwalbe & Williams (1982 ▶); Hu et al. (2002 ▶); Chinnakali et al. (1999 ▶); Skovsgaard & Bond (2009 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C4H5ClN4·C7H6O2 M = 266.69 Monoclinic, a = 8.7817 (17) Å b = 5.7032 (12) Å c = 24.026 (4) Å β = 95.493 (4)° V = 1197.8 (4) Å3 Z = 4 Mo Kα radiation μ = 0.32 mm−1 T = 100 K 0.36 × 0.30 × 0.16 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.895, T max = 0.951 7539 measured reflections 2097 independent reflections 1891 reflections with I > 2σ(I) R int = 0.052

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.101 S = 1.09 2097 reflections 183 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.25 e Å−3 Δρmin = −0.24 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681204768X/is5218sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681204768X/is5218Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681204768X/is5218Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C4H5ClN4·C7H6O2F(000) = 552
Mr = 266.69Dx = 1.479 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5646 reflections
a = 8.7817 (17) Åθ = 3.0–30.0°
b = 5.7032 (12) ŵ = 0.32 mm1
c = 24.026 (4) ÅT = 100 K
β = 95.493 (4)°Block, colourless
V = 1197.8 (4) Å30.36 × 0.30 × 0.16 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer2097 independent reflections
Radiation source: fine-focus sealed tube1891 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.052
φ and ω scansθmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −10→10
Tmin = 0.895, Tmax = 0.951k = −6→6
7539 measured 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)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.101H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.0471P)2 + 0.4196P] where P = (Fo2 + 2Fc2)/3
2097 reflections(Δ/σ)max < 0.001
183 parametersΔρmax = 0.25 e Å3
1 restraintΔρmin = −0.24 e Å3
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.
xyzUiso*/Ueq
Cl1−0.05557 (4)0.64565 (9)0.367228 (16)0.03348 (18)
O10.43197 (13)0.5175 (2)0.61239 (5)0.0312 (3)
O20.52962 (16)0.1720 (2)0.59015 (5)0.0372 (3)
N10.07033 (15)0.7543 (3)0.46563 (5)0.0274 (4)
N20.27154 (14)0.5362 (3)0.51588 (5)0.0266 (4)
N30.16941 (19)0.8669 (3)0.55310 (6)0.0313 (4)
N40.37676 (16)0.2112 (3)0.47835 (7)0.0325 (4)
C10.07703 (17)0.5991 (3)0.42471 (7)0.0272 (4)
C20.17389 (17)0.4136 (4)0.42399 (7)0.0287 (4)
H2A0.17340.31080.39290.034*
C30.27541 (17)0.3846 (3)0.47284 (7)0.0272 (4)
C40.17144 (17)0.7163 (3)0.51057 (6)0.0265 (4)
C50.71603 (19)0.1587 (3)0.69200 (7)0.0264 (4)
H5A0.72200.03020.66720.032*
C60.80722 (19)0.1626 (3)0.74236 (7)0.0276 (4)
H6A0.87600.03720.75190.033*
C70.79790 (17)0.3497 (3)0.77877 (7)0.0251 (4)
H7A0.86080.35260.81320.030*
C80.69723 (17)0.5321 (3)0.76507 (7)0.0258 (4)
H8A0.69080.65940.79020.031*
C90.60544 (17)0.5293 (3)0.71455 (7)0.0241 (4)
H9A0.53610.65420.70520.029*
C100.61545 (17)0.3430 (3)0.67768 (6)0.0214 (4)
C110.52134 (18)0.3366 (3)0.62273 (7)0.0249 (4)
H2N30.233 (3)0.851 (4)0.5785 (10)0.039 (6)*
H2N40.432 (2)0.196 (4)0.5105 (10)0.045 (6)*
H1N40.388 (2)0.113 (4)0.4508 (9)0.033 (5)*
H1N30.109 (2)0.983 (4)0.5499 (9)0.037 (6)*
H1O10.386 (3)0.508 (7)0.5789 (7)0.113 (13)*
U11U22U33U12U13U23
Cl10.0286 (3)0.0508 (4)0.0183 (2)−0.00328 (18)−0.01233 (16)0.00310 (18)
O10.0260 (6)0.0437 (8)0.0220 (6)0.0042 (6)−0.0080 (5)0.0035 (6)
O20.0521 (8)0.0321 (8)0.0240 (6)−0.0019 (6)−0.0147 (6)−0.0010 (6)
N10.0230 (6)0.0382 (9)0.0190 (7)−0.0093 (6)−0.0076 (5)0.0077 (7)
N20.0203 (6)0.0395 (9)0.0183 (7)−0.0085 (6)−0.0059 (5)0.0068 (6)
N30.0318 (8)0.0370 (10)0.0217 (8)−0.0044 (7)−0.0144 (6)0.0040 (7)
N40.0262 (7)0.0503 (11)0.0195 (7)−0.0020 (7)−0.0058 (6)0.0009 (7)
C10.0202 (7)0.0439 (11)0.0159 (8)−0.0113 (7)−0.0071 (6)0.0080 (7)
C20.0218 (8)0.0457 (12)0.0177 (8)−0.0074 (8)−0.0032 (6)0.0029 (8)
C30.0178 (7)0.0447 (12)0.0181 (8)−0.0098 (7)−0.0029 (6)0.0071 (7)
C40.0214 (7)0.0387 (11)0.0178 (8)−0.0124 (7)−0.0062 (6)0.0083 (7)
C50.0325 (9)0.0257 (10)0.0201 (8)0.0009 (7)−0.0015 (7)−0.0003 (7)
C60.0283 (8)0.0292 (10)0.0244 (8)0.0070 (7)−0.0030 (7)0.0050 (7)
C70.0220 (8)0.0322 (10)0.0196 (8)−0.0019 (7)−0.0053 (6)0.0024 (7)
C80.0249 (8)0.0268 (10)0.0244 (8)−0.0006 (7)−0.0038 (6)−0.0034 (7)
C90.0199 (7)0.0248 (10)0.0267 (8)0.0005 (7)−0.0027 (6)0.0028 (7)
C100.0192 (7)0.0263 (9)0.0181 (8)−0.0046 (6)−0.0014 (6)0.0039 (6)
C110.0243 (8)0.0291 (10)0.0205 (8)−0.0063 (7)−0.0023 (6)0.0043 (7)
Cl1—C11.7395 (15)C2—C31.414 (2)
O1—C111.306 (2)C2—H2A0.9500
O1—H1O10.866 (10)C5—C61.386 (2)
O2—C111.229 (2)C5—C101.395 (2)
N1—C11.328 (2)C5—H5A0.9500
N1—C41.348 (2)C6—C71.387 (3)
N2—C41.350 (2)C6—H6A0.9500
N2—C31.351 (2)C7—C81.384 (2)
N3—C41.336 (2)C7—H7A0.9500
N3—H2N30.79 (2)C8—C91.392 (2)
N3—H1N30.85 (2)C8—H8A0.9500
N4—C31.328 (3)C9—C101.391 (2)
N4—H2N40.88 (2)C9—H9A0.9500
N4—H1N40.88 (2)C10—C111.490 (2)
C1—C21.358 (3)
C11—O1—H1O1110 (2)C6—C5—C10120.18 (16)
C1—N1—C4114.40 (16)C6—C5—H5A119.9
C4—N2—C3118.60 (14)C10—C5—H5A119.9
C4—N3—H2N3117.1 (16)C5—C6—C7119.92 (16)
C4—N3—H1N3119.2 (15)C5—C6—H6A120.0
H2N3—N3—H1N3123 (2)C7—C6—H6A120.0
C3—N4—H2N4118.1 (15)C8—C7—C6120.20 (15)
C3—N4—H1N4121.4 (13)C8—C7—H7A119.9
H2N4—N4—H1N4121 (2)C6—C7—H7A119.9
N1—C1—C2126.90 (15)C7—C8—C9120.15 (16)
N1—C1—Cl1114.35 (13)C7—C8—H8A119.9
C2—C1—Cl1118.76 (14)C9—C8—H8A119.9
C1—C2—C3115.25 (17)C10—C9—C8119.83 (15)
C1—C2—H2A122.4C10—C9—H9A120.1
C3—C2—H2A122.4C8—C9—H9A120.1
N4—C3—N2117.76 (15)C9—C10—C5119.71 (15)
N4—C3—C2122.23 (17)C9—C10—C11121.29 (15)
N2—C3—C2120.01 (17)C5—C10—C11118.99 (15)
N3—C4—N1116.94 (17)O2—C11—O1123.62 (15)
N3—C4—N2118.24 (15)O2—C11—C10121.44 (16)
N1—C4—N2124.81 (16)O1—C11—C10114.94 (15)
C4—N1—C1—C2−0.5 (2)C10—C5—C6—C70.3 (3)
C4—N1—C1—Cl1179.02 (11)C5—C6—C7—C80.3 (3)
N1—C1—C2—C31.1 (3)C6—C7—C8—C9−0.4 (2)
Cl1—C1—C2—C3−178.45 (11)C7—C8—C9—C10−0.2 (2)
C4—N2—C3—N4178.65 (15)C8—C9—C10—C50.9 (2)
C4—N2—C3—C2−1.2 (2)C8—C9—C10—C11−178.71 (14)
C1—C2—C3—N4179.98 (15)C6—C5—C10—C9−0.9 (2)
C1—C2—C3—N2−0.1 (2)C6—C5—C10—C11178.67 (15)
C1—N1—C4—N3−179.82 (14)C9—C10—C11—O2−179.79 (15)
C1—N1—C4—N2−1.0 (2)C5—C10—C11—O20.6 (2)
C3—N2—C4—N3−179.31 (15)C9—C10—C11—O10.5 (2)
C3—N2—C4—N11.9 (2)C5—C10—C11—O1−179.08 (14)
D—H···AD—HH···AD···AD—H···A
O1—H1O1···N20.87 (2)1.74 (2)2.5976 (18)168 (3)
N4—H2N4···O20.88 (2)2.03 (2)2.894 (2)171.2 (18)
N4—H1N4···O2i0.88 (2)2.07 (2)2.902 (2)158.2 (19)
N3—H1N3···N1ii0.85 (2)2.18 (2)3.020 (2)171 (2)
C9—H9A···Cg1iii0.952.993.6557 (19)128
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C5–C10 ring.

D—H⋯A D—HH⋯A DA D—H⋯A
O1—H1O1⋯N20.87 (2)1.74 (2)2.5976 (18)168 (3)
N4—H2N4⋯O20.88 (2)2.03 (2)2.894 (2)171.2 (18)
N4—H1N4⋯O2i 0.88 (2)2.07 (2)2.902 (2)158.2 (19)
N3—H1N3⋯N1ii 0.85 (2)2.18 (2)3.020 (2)171 (2)
C9—H9ACg1iii 0.952.993.6557 (19)128

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

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