Literature DB >> 21580290

2-Amino-4,6-dimethyl-pyrimidine-anthranilic acid (1/1).

Samuel Ebenezer1, Packianathan Thomas Muthiah.   

Abstract

In the title 1:1 adduct, C(6)H(9)N(3)·C(7)H(7)NO(2), the crystal structure is stabilized by hydrogen bonds involving two different R(2) (2)(8) motifs. One of them is formed by the inter-action of 2-amino-4,6-dimethyl-pyrimidine (AMPY) with the carboxyl group of anthranilic acid (AA) through N-H⋯O and O-H⋯N hydrogen bonds, whereas the other is formed through the inter-action of two centrosymmetrically related pyrimidines involving N-H⋯N hydrogen bonds. These two combined motifs form a heterotetra-mer. The heterotetra-mer sheets are stacked into three-dimensional network.

Entities:  

Year:  2010        PMID： 21580290      PMCID： PMC2983637          DOI： 10.1107/S1600536810003661

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


Related literature

For the importance the reaction of amino­pyrimidine derivatives and carboxylic acids in protein–nucleic acid recognition and drug binding, see: Hunt et al. (1980 ▶); Baker & Santi (1965 ▶). For pyrimidine–carboxylic acid inter­actions, see: Allen et al. (1999 ▶). For co-crystals of AMPY, see: Balasubramani et al. (2005 ▶, 2006 ▶); Devi & Muthiah (2007 ▶). For hydrogen-bonded synthons, see: Thakur & Desiraju (2008 ▶). For packing patterns in 2-amino-4,6-dimethyl­pyrimidine-salicylate, see: Muthiah et al. (2006 ▶). For typical geometric parameters in aromatic stacking, see: Hunter (1994 ▶).

Experimental

Crystal data

C6H9N3·C7H7NO2 M = 260.30 Triclinic, a = 7.1922 (2) Å b = 7.4269 (2) Å c = 13.0675 (3) Å α = 77.583 (1)° β = 78.990 (1)° γ = 82.473 (1)° V = 666.19 (3) Å3 Z = 2 Mo Kα radiation μ = 0.09 mm−1 T = 293 K 0.28 × 0.22 × 0.20 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.975, T max = 0.982 16171 measured reflections 4279 independent reflections 3021 reflections with I > 2σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.053 wR(F 2) = 0.174 S = 1.04 4279 reflections 182 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.27 e Å−3 Δρmin = −0.24 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/S1600536810003661/kp2248sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810003661/kp2248Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C6H9N3·C7H7NO2Z = 2
Mr = 260.30F(000) = 276
Triclinic, P1Dx = 1.298 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.1922 (2) ÅCell parameters from 4279 reflections
b = 7.4269 (2) Åθ = 1.6–31.3°
c = 13.0675 (3) ŵ = 0.09 mm−1
α = 77.583 (1)°T = 293 K
β = 78.990 (1)°Prism, brown
γ = 82.473 (1)°0.28 × 0.22 × 0.20 mm
V = 666.19 (3) Å3
Bruker SMART APEXII CCD area-detector diffractometer4279 independent reflections
Radiation source: fine-focus sealed tube3021 reflections with I > 2σ(I)
graphiteRint = 0.024
φ and ω scansθmax = 31.3°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −10→10
Tmin = 0.975, Tmax = 0.982k = −10→10
16171 measured reflectionsl = −19→19
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.053Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.174H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0991P)2 + 0.0554P] where P = (Fo2 + 2Fc2)/3
4279 reflections(Δ/σ)max < 0.001
182 parametersΔρmax = 0.27 e Å−3
0 restraintsΔρmin = −0.24 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 esds 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
N10.27302 (13)0.63647 (13)0.24381 (7)0.0389 (3)
N20.24994 (14)0.50645 (17)0.42161 (8)0.0546 (4)
N3−0.01789 (13)0.67010 (14)0.36590 (8)0.0438 (3)
C20.16646 (15)0.60562 (16)0.34206 (9)0.0398 (3)
C4−0.09918 (16)0.77159 (16)0.28620 (10)0.0428 (3)
C5−0.00014 (17)0.80839 (17)0.18345 (10)0.0465 (4)
C60.18851 (16)0.73870 (15)0.16483 (9)0.0406 (3)
C70.3091 (2)0.7734 (2)0.05754 (10)0.0551 (4)
C8−0.30286 (18)0.8452 (2)0.31434 (13)0.0589 (4)
O10.62794 (12)0.47921 (13)0.18713 (7)0.0520 (3)
O20.62400 (13)0.35172 (16)0.35704 (7)0.0646 (3)
N40.94272 (18)0.17934 (18)0.41965 (9)0.0555 (3)
C90.70902 (15)0.38005 (16)0.26562 (9)0.0402 (3)
C100.90843 (15)0.30730 (14)0.23577 (8)0.0364 (3)
C110.99344 (17)0.33560 (16)0.12857 (9)0.0438 (3)
C121.18091 (18)0.27621 (19)0.09731 (11)0.0517 (4)
C131.28729 (18)0.18659 (19)0.17468 (12)0.0536 (4)
C141.20848 (18)0.15583 (18)0.27979 (11)0.0503 (4)
C151.01624 (16)0.21446 (15)0.31397 (9)0.0408 (3)
H2A0.186500.485600.485100.0650*
H2B0.367200.463200.409400.0650*
H5−0.058900.878200.128300.0560*
H7A0.236400.851600.007800.0830*
H7B0.350800.657700.035000.0830*
H7C0.417800.833200.060700.0830*
H8A−0.360500.876500.251500.0710*
H8B−0.308200.953700.344000.0710*
H8C−0.370300.752500.365500.0710*
H10.518100.511000.209400.0780*
H4A0.820 (3)0.238 (3)0.4358 (16)0.088 (6)*
H4B1.032 (3)0.151 (3)0.4607 (16)0.093 (6)*
H110.921200.396100.077200.0530*
H121.235200.295700.025800.0620*
H131.414500.146800.154600.0640*
H141.283000.094900.329900.0600*
U11U22U33U12U13U23
N10.0312 (4)0.0465 (5)0.0358 (5)0.0002 (4)−0.0026 (3)−0.0059 (4)
N20.0341 (5)0.0840 (8)0.0344 (5)0.0112 (5)−0.0005 (4)−0.0018 (5)
N30.0305 (4)0.0512 (5)0.0450 (5)0.0019 (4)−0.0010 (4)−0.0073 (4)
C20.0306 (5)0.0491 (6)0.0368 (5)0.0006 (4)−0.0025 (4)−0.0073 (4)
C40.0325 (5)0.0406 (5)0.0537 (7)0.0012 (4)−0.0077 (5)−0.0084 (5)
C50.0404 (6)0.0455 (6)0.0501 (7)0.0025 (5)−0.0125 (5)−0.0016 (5)
C60.0387 (5)0.0410 (5)0.0403 (6)−0.0029 (4)−0.0069 (4)−0.0043 (4)
C70.0544 (7)0.0623 (8)0.0406 (6)−0.0004 (6)−0.0029 (5)0.0001 (5)
C80.0343 (6)0.0600 (8)0.0762 (9)0.0086 (5)−0.0082 (6)−0.0089 (7)
O10.0348 (4)0.0706 (6)0.0412 (5)0.0105 (4)−0.0062 (3)0.0000 (4)
O20.0427 (5)0.0916 (7)0.0414 (5)0.0189 (5)0.0008 (4)0.0043 (4)
N40.0513 (6)0.0679 (7)0.0395 (5)0.0100 (5)−0.0121 (5)0.0012 (5)
C90.0341 (5)0.0442 (6)0.0384 (5)0.0016 (4)−0.0052 (4)−0.0037 (4)
C100.0319 (5)0.0371 (5)0.0372 (5)0.0010 (4)−0.0053 (4)−0.0040 (4)
C110.0395 (6)0.0476 (6)0.0392 (6)0.0032 (5)−0.0053 (5)−0.0032 (4)
C120.0421 (6)0.0576 (7)0.0483 (7)0.0027 (5)0.0037 (5)−0.0094 (5)
C130.0353 (6)0.0558 (7)0.0657 (8)0.0078 (5)−0.0039 (5)−0.0142 (6)
C140.0400 (6)0.0522 (7)0.0571 (7)0.0081 (5)−0.0152 (5)−0.0082 (5)
C150.0392 (5)0.0387 (5)0.0428 (6)0.0024 (4)−0.0100 (4)−0.0054 (4)
O1—C91.3136 (15)C7—H7A0.9600
O2—C91.2214 (14)C7—H7C0.9600
O1—H10.8100C7—H7B0.9600
N1—C61.3390 (15)C8—H8C0.9600
N1—C21.3535 (14)C8—H8B0.9600
N2—C21.3330 (16)C8—H8A0.9600
N3—C41.3320 (16)C9—C101.4748 (16)
N3—C21.3507 (15)C10—C151.4073 (16)
N2—H2B0.8600C10—C111.4001 (15)
N2—H2A0.8600C11—C121.3750 (18)
N4—C151.3627 (16)C12—C131.387 (2)
N4—H4A0.94 (2)C13—C141.364 (2)
N4—H4B0.89 (2)C14—C151.4110 (18)
C4—C81.5003 (18)C11—H110.9300
C4—C51.3830 (18)C12—H120.9300
C5—C61.3828 (17)C13—H130.9300
C6—C71.4910 (17)C14—H140.9300
C5—H50.9300
O1···C73.3882 (17)C9···H2B2.8800
O1···N12.7014 (13)C11···H11viii2.9900
O2···N42.6571 (17)C12···H11viii3.0700
O2···N22.8303 (15)H1···C72.9500
O1···H112.4000H1···H2B2.6000
O2···H2B1.9800H1···C62.8100
O2···H4A1.91 (2)H1···N11.9000
N1···O12.7014 (13)H1···C22.8800
N2···N3i3.0745 (14)H2A···H4Aiii2.4800
N2···O22.8303 (15)H2A···N3i2.2600
N3···N2i3.0745 (14)H2A···C2i3.1000
N4···N4ii3.1409 (18)H2B···C92.8800
N4···O22.6571 (17)H2B···H12.6000
N1···H11.9000H2B···O21.9800
N2···H4Aiii2.87 (2)H4A···H2Aiii2.4800
N3···H2Ai2.2600H4A···O21.91 (2)
N3···H4Biii2.84 (2)H4A···C92.48 (2)
N4···H4Bii2.62 (2)H4A···N2iii2.87 (2)
C2···C15iv3.3428 (16)H4B···N4ii2.62 (2)
C2···C14iv3.5670 (18)H4B···H4Bii2.32 (3)
C4···C9iv3.4584 (17)H4B···N3iii2.84 (2)
C6···C13v3.5249 (18)H4B···H142.3000
C7···O13.3882 (17)H5···H7A2.4000
C9···C4vi3.4584 (17)H5···H8A2.4400
C13···C6vii3.5249 (18)H7A···H52.4000
C14···C2vi3.5670 (18)H8A···H52.4400
C15···C2vi3.3428 (16)H11···O12.4000
C2···H12.8800H11···C11viii2.9900
C2···H2Ai3.1000H11···C12viii3.0700
C6···H12.8100H11···H11viii2.4500
C7···H13viii3.0800H13···C7viii3.0800
C7···H12.9500H14···H4B2.3000
C9···H4A2.48 (2)
C9—O1—H1110.00C4—C8—H8B109.00
C2—N1—C6117.21 (10)C4—C8—H8C109.00
C2—N3—C4116.98 (10)H8A—C8—H8B109.00
C2—N2—H2A120.00C4—C8—H8A109.00
C2—N2—H2B120.00H8A—C8—H8C109.00
H2A—N2—H2B120.00H8B—C8—H8C109.00
H4A—N4—H4B127.5 (19)O2—C9—C10122.73 (11)
C15—N4—H4B112.9 (13)O1—C9—O2121.75 (11)
C15—N4—H4A113.4 (12)O1—C9—C10115.52 (10)
N1—C2—N3124.84 (10)C9—C10—C15120.80 (10)
N1—C2—N2117.74 (10)C11—C10—C15119.51 (10)
N2—C2—N3117.42 (10)C9—C10—C11119.66 (10)
N3—C4—C8116.34 (11)C10—C11—C12121.70 (11)
N3—C4—C5121.65 (11)C11—C12—C13118.63 (12)
C5—C4—C8122.01 (12)C12—C13—C14121.14 (13)
C4—C5—C6118.28 (11)C13—C14—C15121.38 (12)
N1—C6—C7116.38 (11)N4—C15—C14119.47 (11)
C5—C6—C7122.59 (11)C10—C15—C14117.64 (11)
N1—C6—C5121.03 (11)N4—C15—C10122.90 (11)
C6—C5—H5121.00C10—C11—H11119.00
C4—C5—H5121.00C12—C11—H11119.00
C6—C7—H7B109.00C11—C12—H12121.00
C6—C7—H7C109.00C13—C12—H12121.00
C6—C7—H7A109.00C12—C13—H13119.00
H7A—C7—H7B109.00C14—C13—H13119.00
H7A—C7—H7C109.00C13—C14—H14119.00
H7B—C7—H7C109.00C15—C14—H14119.00
C6—N1—C2—N2−178.98 (11)O2—C9—C10—C11176.12 (12)
C6—N1—C2—N30.06 (17)O2—C9—C10—C15−5.78 (18)
C2—N1—C6—C5−0.37 (17)C9—C10—C11—C12177.60 (12)
C2—N1—C6—C7179.13 (11)C15—C10—C11—C12−0.53 (18)
C4—N3—C2—N1−0.10 (18)C9—C10—C15—N42.90 (18)
C4—N3—C2—N2178.93 (11)C9—C10—C15—C14−177.28 (11)
C2—N3—C4—C50.47 (17)C11—C10—C15—N4−178.99 (12)
C2—N3—C4—C8−178.87 (11)C11—C10—C15—C140.83 (16)
N3—C4—C5—C6−0.78 (19)C10—C11—C12—C13−0.2 (2)
C8—C4—C5—C6178.53 (12)C11—C12—C13—C140.6 (2)
C4—C5—C6—N10.72 (18)C12—C13—C14—C15−0.3 (2)
C4—C5—C6—C7−178.75 (12)C13—C14—C15—N4179.37 (13)
O1—C9—C10—C11−4.29 (16)C13—C14—C15—C10−0.45 (19)
O1—C9—C10—C15173.81 (10)
D—H···AD—HH···AD···AD—H···A
O1—H1···N10.811.902.7014 (13)168
N2—H2A···N3i0.862.263.0745 (14)159
N2—H2B···O20.861.982.8303 (15)169
N4—H4A···O20.94 (2)1.91 (2)2.6571 (17)135.5 (17)
N4—H4B···N4ii0.89 (2)2.62 (2)3.1409 (18)118.7 (17)
C11—H11···O10.932.402.7353 (15)101
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
O1—H1⋯N10.811.902.7014 (13)168
N2—H2A⋯N3i0.862.263.0745 (14)159
N2—H2B⋯O20.861.982.8303 (15)169
N4—H4A⋯O20.94 (2)1.91 (2)2.6571 (17)135.5 (17)
N4—H4B⋯N4ii0.89 (2)2.62 (2)3.1409 (18)118.7 (17)

Symmetry codes: (i) ; (ii) .

  5 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Hydrogen-bonding and pi-pi interactions in 2-amino-4,6-dimethylpyrimidinium salicylate.

Authors:  Packianathan Thomas Muthiah; Kasthuri Balasubramani; Urszula Rychlewska; Agnieszka Plutecka
Journal:  Acta Crystallogr C       Date:  2006-09-12       Impact factor: 1.172

3.  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

4.  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

5.  Structure validation in chemical crystallography.

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

1.  6-Chloro-N(4),N(4)-dimethyl-pyrimidine-2,4-diamine.

Authors:  Yuan-Yuan Pang; Kai Yu; Bin Sun; Dian-Shun Guo
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-04-04

2.  2-Amino-4,6-dimethyl-pyrimidin-1-ium 2,3,5-triiodo-benzoate 2,3,5-triiodo-benzoic acid monosolvate.

Authors:  Sevaiyan Malathy; Packianathan Thomas Muthiah
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-11-09

3.  Crystal structure of 4-amino-5-chloro-2,6-di-methyl-pyrimidinium thio-phene-2,5-di-carboxyl-ate.

Authors:  Ammaiyappan Rajam; Packianathan Thomas Muthiah; Ray J Butcher; Matthias Zeller
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2016-06-24

4.  Pyrimethaminium 2-{[4-(tri-fluoro-meth-yl)phen-yl]sulfan-yl}benzoate dimethyl sulfoxide monosolvate.

Authors:  Thammarse S Yamuna; Manpreet Kaur; Jerry P Jasinski; H S Yathirajan
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-05-17
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.