Literature DB >> 21587607

4,6-Dimeth-oxy-pyrimidin-2-amine-2-(1H-indol-3-yl)acetic acid (1/1).

Samuel Ebenezer1, Packianathan Thomas Muthiah.   

Abstract

In the title co-crystal C(6)H(9)N(3)O(2)·C(10)H(9)NO(2), the 4,6-dimeth-oxy-pyrimidin-2-amine mol-ecule inter-acts with the carboxyl group of the 2-(1H-indol-3-yl)acetic acid mol-ecule through N-H⋯O and O-H⋯N hydrogen bonds, forming a cyclic hydrogen-bonded R(2) (2)(8) motif, which is further linked by an N-H⋯N hydrogen bond, forming a supra-molecular chain along the c axis. Neighboring chains are inter-linked via C-H⋯O hydrogen bonds, forming a supra-molecular ladder.

Entities:  

Year:  2010        PMID： 21587607      PMCID： PMC2983259          DOI： 10.1107/S1600536810037724

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


Related literature

For background to crystal engineering, see: Desiraju (1989 ▶). For the role of amino­pyrimidine–carboxyl­ate inter­actions in protein-nuleic acid recognition and protein-drug binding, see: Hunt et al. (1980 ▶); Baker & Santi (1965 ▶). 2-Amino­pyrimidine forms a wide variety of 1:1 adducts with mono and dicarb­oxy­lic acids (Etter & Adsmond, 1990 ▶) rather than individual self-assembly compounds (Scheinbeim & Schempp, 1976 ▶). The (8) motif is frequently observed when a carb­oxy­lic acid inter­acts with a 2-amino heterocyclic ring system, see: Lynch & Jones (2004 ▶). It is also one of the most commonly occuring motifs, see: Allen et al. (1998 ▶). For the biological activity of amino­pyrimidine derivatives and 2-(1H-indol-3-yl)acetic acid, see: Hunt et al. (1980 ▶); Arteca (1996 ▶). For related structures, see: Karle et al. (1964 ▶); Low et al. (2002 ▶). For related co-crystals of amino­pyrimidines, see: Thanigaimani et al. (2006 ▶, 2007 ▶, 2008 ▶). For stacking intera­ctions, see: Hunter (1994 ▶). For hydrogen-bond motifs, see:, see: Bernstein et al. (1995 ▶); Etter (1990 ▶).

Experimental

Crystal data

C10H9NO2·C6H9N3O2 M = 330.34 Triclinic, a = 7.4555 (1) Å b = 10.7197 (2) Å c = 11.2537 (2) Å α = 62.981 (1)° β = 85.863 (1)° γ = 85.584 (1)° V = 798.16 (2) Å3 Z = 2 Mo Kα radiation μ = 0.10 mm−1 T = 293 K 0.30 × 0.25 × 0.22 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.970, T max = 0.978 19719 measured reflections 5363 independent reflections 3979 reflections with I > 2σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.046 wR(F 2) = 0.137 S = 1.06 5363 reflections 220 parameters H-atom parameters constrained Δρmax = 0.23 e Å−3 Δρmin = −0.22 e Å−3 Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: PLATON. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810037724/bv2155sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810037724/bv2155Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C10H9NO2·C6H9N3O2Z = 2
Mr = 330.34F(000) = 348
Triclinic, P1Dx = 1.375 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.4555 (1) ÅCell parameters from 5363 reflections
b = 10.7197 (2) Åθ = 2.0–31.8°
c = 11.2537 (2) ŵ = 0.10 mm−1
α = 62.981 (1)°T = 293 K
β = 85.863 (1)°Prism, colourless
γ = 85.584 (1)°0.30 × 0.25 × 0.22 mm
V = 798.16 (2) Å3
Bruker SMART APEXII CCD area-detector diffractometer5363 independent reflections
Radiation source: fine-focus sealed tube3979 reflections with I > 2σ(I)
graphiteRint = 0.028
φ and ω scansθmax = 31.8°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −10→10
Tmin = 0.970, Tmax = 0.978k = −15→15
19719 measured reflectionsl = −16→16
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.137H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0654P)2 + 0.0927P] where P = (Fo2 + 2Fc2)/3
5363 reflections(Δ/σ)max < 0.001
220 parametersΔρmax = 0.23 e Å−3
0 restraintsΔρmin = −0.22 e Å−3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su'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
O30.47314 (13)0.61367 (8)0.19523 (8)0.0511 (3)
O40.41360 (15)0.83007 (9)0.17016 (9)0.0610 (3)
N40.33691 (16)0.67797 (12)−0.21918 (11)0.0549 (4)
C90.47507 (14)0.75081 (11)0.12695 (11)0.0401 (3)
C100.56115 (15)0.79980 (13)−0.01155 (11)0.0458 (3)
C110.44583 (15)0.77265 (11)−0.09994 (11)0.0409 (3)
C120.47745 (18)0.67593 (13)−0.14708 (13)0.0514 (4)
C130.20837 (16)0.77659 (11)−0.21974 (11)0.0429 (3)
C140.27307 (14)0.83893 (10)−0.14517 (10)0.0372 (3)
C150.16352 (16)0.94084 (11)−0.12571 (11)0.0438 (3)
C16−0.00356 (18)0.97665 (13)−0.17950 (13)0.0526 (4)
C17−0.06486 (18)0.91367 (14)−0.25289 (14)0.0567 (4)
C180.03945 (18)0.81345 (14)−0.27433 (13)0.0532 (4)
O10.05798 (14)0.34071 (10)0.80461 (9)0.0602 (3)
O20.34975 (14)0.31388 (9)0.43080 (9)0.0556 (3)
N10.29633 (12)0.51850 (9)0.43555 (8)0.0385 (2)
N20.24541 (15)0.73208 (10)0.43481 (10)0.0492 (3)
N30.15054 (12)0.54001 (10)0.62253 (9)0.0421 (3)
C20.23037 (13)0.59256 (10)0.49907 (10)0.0368 (3)
C40.13751 (15)0.40253 (12)0.68250 (11)0.0433 (3)
C50.20213 (16)0.31430 (11)0.62803 (11)0.0450 (3)
C60.28114 (14)0.37938 (11)0.50225 (11)0.0398 (3)
C7−0.0202 (2)0.42776 (17)0.86200 (15)0.0684 (5)
C80.3549 (2)0.16378 (14)0.49465 (17)0.0659 (5)
H30.416700.593000.266400.0770*
H40.330100.62570−0.258100.0660*
H10A0.579700.89940−0.050000.0550*
H10B0.677800.75120−0.006100.0550*
H120.580300.61690−0.132200.0620*
H150.203100.98350−0.077200.0530*
H16−0.077201.04400−0.166800.0630*
H17−0.178600.94000−0.288000.0680*
H18−0.001500.77200−0.323500.0640*
H2A0.295800.770200.356100.0590*
H2B0.204600.783300.472400.0590*
H50.192700.217600.673500.0540*
H7A0.073200.473500.879300.1030*
H7B−0.084200.371300.944200.1030*
H7C−0.102000.497000.801100.1030*
H8A0.420700.128500.574700.0990*
H8B0.413100.129800.435400.0990*
H8C0.234300.132400.516700.0990*
U11U22U33U12U13U23
O30.0697 (5)0.0377 (4)0.0429 (4)−0.0047 (4)0.0080 (4)−0.0168 (3)
O40.0885 (7)0.0381 (4)0.0480 (5)0.0014 (4)0.0132 (5)−0.0150 (4)
N40.0687 (7)0.0542 (6)0.0561 (6)0.0007 (5)0.0025 (5)−0.0387 (5)
C90.0420 (5)0.0379 (5)0.0382 (5)−0.0017 (4)−0.0039 (4)−0.0151 (4)
C100.0439 (5)0.0476 (6)0.0420 (6)−0.0072 (4)0.0042 (4)−0.0170 (5)
C110.0467 (5)0.0377 (5)0.0352 (5)−0.0028 (4)0.0065 (4)−0.0149 (4)
C120.0560 (6)0.0490 (6)0.0510 (7)0.0056 (5)0.0053 (5)−0.0265 (5)
C130.0552 (6)0.0392 (5)0.0349 (5)−0.0069 (4)0.0053 (4)−0.0175 (4)
C140.0473 (5)0.0311 (4)0.0300 (4)−0.0056 (4)0.0055 (4)−0.0115 (4)
C150.0564 (6)0.0341 (5)0.0398 (5)−0.0021 (4)0.0030 (4)−0.0165 (4)
C160.0553 (6)0.0429 (6)0.0527 (7)0.0058 (5)0.0020 (5)−0.0174 (5)
C170.0521 (6)0.0554 (7)0.0534 (7)−0.0018 (5)−0.0064 (5)−0.0161 (6)
C180.0626 (7)0.0539 (7)0.0441 (6)−0.0107 (6)−0.0034 (5)−0.0216 (5)
O10.0812 (6)0.0527 (5)0.0390 (4)−0.0194 (4)0.0135 (4)−0.0137 (4)
O20.0780 (6)0.0368 (4)0.0509 (5)−0.0012 (4)0.0043 (4)−0.0201 (4)
N10.0450 (4)0.0338 (4)0.0330 (4)−0.0032 (3)−0.0023 (3)−0.0117 (3)
N20.0683 (6)0.0343 (5)0.0418 (5)−0.0048 (4)0.0059 (4)−0.0152 (4)
N30.0480 (5)0.0405 (5)0.0349 (4)−0.0054 (4)−0.0001 (3)−0.0142 (4)
C20.0388 (5)0.0352 (5)0.0341 (5)−0.0026 (4)−0.0056 (4)−0.0129 (4)
C40.0469 (5)0.0443 (6)0.0335 (5)−0.0096 (4)−0.0026 (4)−0.0119 (4)
C50.0556 (6)0.0342 (5)0.0389 (5)−0.0082 (4)−0.0046 (4)−0.0098 (4)
C60.0454 (5)0.0348 (5)0.0378 (5)−0.0026 (4)−0.0065 (4)−0.0145 (4)
C70.0834 (10)0.0718 (9)0.0483 (7)−0.0218 (7)0.0227 (7)−0.0266 (7)
C80.0883 (10)0.0380 (6)0.0730 (9)−0.0021 (6)−0.0022 (8)−0.0268 (6)
O3—C91.3142 (15)C13—C181.3907 (18)
O4—C91.2048 (16)C14—C151.4009 (17)
O3—H30.8200C15—C161.3746 (18)
O1—C71.427 (2)C16—C171.398 (2)
O1—C41.3397 (14)C17—C181.377 (2)
O2—C61.3415 (16)C10—H10A0.9700
O2—C81.432 (2)C10—H10B0.9700
N4—C121.3637 (18)C12—H120.9300
N4—C131.3693 (18)C15—H150.9300
N4—H40.8600C16—H160.9300
N1—C21.3371 (15)C17—H170.9300
N1—C61.3405 (16)C18—H180.9300
N2—C21.3431 (16)C4—C51.3843 (18)
N3—C21.3502 (13)C5—C61.3723 (16)
N3—C41.3213 (17)C5—H50.9300
N2—H2B0.8600C7—H7A0.9600
N2—H2A0.8600C7—H7B0.9600
C9—C101.5103 (16)C7—H7C0.9600
C10—C111.4961 (17)C8—H8A0.9600
C11—C141.4311 (16)C8—H8B0.9600
C11—C121.362 (2)C8—H8C0.9600
C13—C141.4146 (17)
O2···C12i3.3132 (16)C5···H8C2.7400
O2···N4i3.1900 (15)C5···H8A2.7300
O3···N4i3.2341 (17)C6···H32.7900
O3···N12.6979 (12)C8···H52.5400
O3···C12i3.3749 (18)C9···H2A2.9000
O3···C4ii3.2606 (15)C12···H8Bi3.0400
O4···N22.8927 (14)C13···H7Bvii2.8900
O1···H10Bii2.8800C14···H7Bvii2.7500
O2···H32.7700C15···H5viii2.8100
O2···H4i2.8800C16···H5viii2.8100
O3···H4i2.6800H2A···C92.9000
O4···H2A2.0400H2A···O42.0400
O4···H10Aiii2.5900H3···N11.8800
O4···H16iv2.7500H3···C22.8700
N1···O32.6979 (12)H3···C62.7900
N2···O42.8927 (14)H3···O22.7700
N3···N4v3.2184 (17)H4···O3i2.6800
N4···O3i3.2341 (17)H4···C2vi3.0600
N4···N3vi3.2184 (17)H4···H7Avi2.5500
N4···O2i3.1900 (15)H4···N3vi2.4500
N1···H31.8800H4···O2i2.8800
N3···H18v2.9500H5···C15ix2.8100
N3···H7C2.5600H5···C16ix2.8100
N3···H4v2.4500H5···C82.5400
N3···H7A2.6700H5···H8A2.3400
N4···H7Avi2.8400H5···H8C2.3200
C2···C4vii3.5198 (15)H7A···N4v2.8400
C2···C5vii3.5089 (15)H7A···N32.6700
C4···C9ii3.5501 (16)H7A···H4v2.5500
C4···O3ii3.2606 (15)H7B···C13vii2.8900
C4···C2vii3.5198 (15)H7B···C14vii2.7500
C5···C2vii3.5089 (15)H7C···N32.5600
C5···C9ii3.5822 (16)H8A···H52.3400
C9···C153.5484 (16)H8A···C52.7300
C9···C4ii3.5501 (16)H8B···C12i3.0400
C9···C5ii3.5822 (16)H8C···H52.3200
C12···O3i3.3749 (18)H8C···C52.7400
C12···O2i3.3132 (16)H10A···O4iii2.5900
C15···C93.5484 (16)H10B···O1ii2.8800
C2···H32.8700H16···O4iv2.7500
C2···H4v3.0600H18···N3vi2.9500
C9—O3—H3109.00C11—C12—H12125.00
C4—O1—C7118.24 (12)N4—C12—H12125.00
C6—O2—C8117.57 (11)C16—C15—H15121.00
C12—N4—C13109.14 (12)C14—C15—H15121.00
C12—N4—H4125.00C17—C16—H16119.00
C13—N4—H4125.00C15—C16—H16119.00
C2—N1—C6116.09 (9)C18—C17—H17119.00
C2—N3—C4115.07 (11)C16—C17—H17119.00
C2—N2—H2B120.00C13—C18—H18121.00
C2—N2—H2A120.00C17—C18—H18121.00
H2A—N2—H2B120.00N1—C2—N2117.23 (9)
O3—C9—C10113.48 (11)N1—C2—N3126.02 (11)
O4—C9—C10123.11 (12)N2—C2—N3116.74 (11)
O3—C9—O4123.41 (11)N3—C4—C5124.42 (10)
C9—C10—C11111.17 (10)O1—C4—N3119.52 (12)
C12—C11—C14106.25 (11)O1—C4—C5116.06 (12)
C10—C11—C14126.02 (11)C4—C5—C6115.35 (11)
C10—C11—C12127.64 (11)O2—C6—N1111.97 (10)
N4—C12—C11110.41 (12)O2—C6—C5124.99 (12)
N4—C13—C14107.17 (10)N1—C6—C5123.04 (11)
C14—C13—C18122.00 (12)C4—C5—H5122.00
N4—C13—C18130.78 (13)C6—C5—H5122.00
C11—C14—C13107.03 (10)O1—C7—H7A109.00
C11—C14—C15133.95 (11)O1—C7—H7B109.00
C13—C14—C15118.96 (10)O1—C7—H7C109.00
C14—C15—C16118.84 (12)H7A—C7—H7B109.00
C15—C16—C17121.25 (13)H7A—C7—H7C109.00
C16—C17—C18121.46 (13)H7B—C7—H7C110.00
C13—C18—C17117.48 (13)O2—C8—H8A110.00
H10A—C10—H10B108.00O2—C8—H8B109.00
C11—C10—H10B109.00O2—C8—H8C109.00
C11—C10—H10A109.00H8A—C8—H8B109.00
C9—C10—H10A109.00H8A—C8—H8C109.00
C9—C10—H10B109.00H8B—C8—H8C109.00
C7—O1—C4—C5−176.42 (11)C10—C11—C12—N4176.92 (11)
C7—O1—C4—N33.89 (17)C10—C11—C14—C13−176.77 (11)
C8—O2—C6—N1175.18 (11)C10—C11—C14—C150.2 (2)
C8—O2—C6—C5−5.60 (17)C12—C11—C14—C13−0.14 (13)
C13—N4—C12—C11−0.47 (15)C12—C11—C14—C15176.84 (13)
C12—N4—C13—C140.36 (14)N4—C13—C14—C15−177.65 (10)
C12—N4—C13—C18−177.05 (13)C18—C13—C14—C11177.55 (11)
C6—N1—C2—N3−0.22 (15)N4—C13—C14—C11−0.13 (13)
C2—N1—C6—O2179.64 (9)C18—C13—C14—C150.03 (17)
C6—N1—C2—N2179.42 (10)N4—C13—C18—C17176.85 (13)
C2—N1—C6—C50.40 (16)C14—C13—C18—C17−0.23 (19)
C2—N3—C4—C51.29 (16)C13—C14—C15—C160.16 (16)
C4—N3—C2—N2179.77 (10)C11—C14—C15—C16−176.54 (12)
C2—N3—C4—O1−179.05 (10)C14—C15—C16—C17−0.16 (19)
C4—N3—C2—N1−0.59 (15)C15—C16—C17—C180.0 (2)
O4—C9—C10—C11−109.62 (14)C16—C17—C18—C130.2 (2)
O3—C9—C10—C1170.10 (13)O1—C4—C5—C6179.20 (10)
C9—C10—C11—C12−109.00 (14)N3—C4—C5—C6−1.13 (17)
C9—C10—C11—C1466.91 (16)C4—C5—C6—O2−178.92 (11)
C14—C11—C12—N40.37 (14)C4—C5—C6—N10.21 (17)
D—H···AD—HH···AD···AD—H···A
N2—H2A···O40.862.042.8927 (14)171
O3—H3···N10.821.882.6979 (12)172
N4—H4···N3vi0.862.453.2184 (17)149
C10—H10A···O4iii0.972.593.5491 (18)172
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N2—H2A⋯O40.862.042.8927 (14)171
O3—H3⋯N10.821.882.6979 (12)172
N4—H4⋯N3i0.862.453.2184 (17)149
C10—H10A⋯O4ii0.972.593.5491 (18)172

Symmetry codes: (i) ; (ii) .

  7 in total

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Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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3.  Geometry of the 2-aminoheterocyclic-carboxylic acid R2(2)(8) graph set: implications for crystal engineering.

Authors:  Daniel E Lynch; Glyn D Jones
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4.  Hydrogen-bonding patterns in the cocrystal 2-amino-4,6-dimethoxy-pyrimidine-anthranilic acid (1/1).

Authors:  Kaliyaperumal Thanigaimani; Packianathan Thomas Muthiah; Daniel E Lynch
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2007-12-06

5.  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

6.  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

7.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  7 in total
  4 in total

1.  4,4'-Bipyridine-cyclo-hexane-1,2,4,5-tetra-carb-oxy-lic acid (1/1).

Authors:  Jian-Qiang Liu
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-10-09

2.  2-Amino-4,6-dimeth-oxy-pyrimidin-1-ium p-toluene-sulfonate.

Authors:  Sundaramoorthy Gomathi; Packianathan Thomas Muthiah
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-17

3.  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

4.  2-Amino-4,6-di-methyl-pyrimidine-sorbic acid (1/1).

Authors:  Sundaramoorthy Gomathi; Packianathan Thomas Muthiah
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2013-07-10
  4 in total

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