organic compounds
Pyrimidin-2-amine–1-phenylcyclopentane-1-carboxylic acid (1/1)
aInstitute of Chemical and Engineering Sciences, A*STAR (Agency for Science, Technology and Research), 1 Pesek Road, Jurong Island, Singapore 627833, and bDepartment of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576
*Correspondence e-mail: he_guangwen@ices.a-star.edu.sg, reginald_tan@ices.a-star.edu.sg
In the 4H5N3·C12H14O2, the components are linked by N—H⋯O and O—H⋯N hydrogen bonds. Self-assembly of these dimeric units results in a four-component supramolecular unit featuring a homosynthon between two molecules of the pyrimidin-2-amine involving two N—H⋯O hydrogen bonds, and two heterosynthons between each one molecule of pyrimidin-2-amine and 1-phenylcyclopentane-1-carboxylic acid involving N—H⋯O and O—H⋯N hydrogen bonds.
of the title CRelated literature
For the structure of pyrimidin-2-amine, see: Scheinbeim & Schempp (1976) and for the structure of 1-phenylcyclopentane-1-carboxylic acid, see: Margulis (1975). For molecular co-crystals of pyrimidin-2-amine, see: Serafin & Wheeler (2007); Shan et al. (2002); Goswami et al. (1999a,b, 2000); Chinnakali et al. (1999); Lynch et al. (1997). For a salt of 2-aminopyridine and 1-phenyl-1-cyclopropanecarboxylic acid, see: He et al. (2010). For a recent screening study for and salt formation using pulse-gradient spin–echo nuclear magnetic resonance, see: He et al. (2009).
Experimental
Crystal data
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Refinement
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Data collection: CrystalClear (Rigaku, 2007); cell CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536811003667/ng5101sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811003667/ng5101Isup2.hkl
0.0957 g (1 mmol) of pyrimidin-2-amine (Alfa Aesar, 99%) and 0.1909 g (1 mmol) of 1-phenylcyclopentane-1-carboxylic acid (Alfa Aesar, 98%) and were dissolved into 7.6 ml of ethyl acetate (Fisher Scientific, HPLC). Solution was then filtered through a 0.22µm PTFE filter. Filtered solution was finally sealed with Parafilm and small holes were made to allow solvent to slowly evaporate. The block-shaped crystal (0.44 × 0.44 × 0.22 mm) suitable for single-crystal X-ray diffraction (Rigaku Saturn 70 CCD area detector with Mo Kα radiation = 0.71073 Å at 50 kV and 40 mA) was collected after one day. Fourier Transform Infrared (FT—IR) experiments were performed using Bio-Rad spectrometer (FTS3000MX) to confirm whether the resulting molecular complex is a cocrystal or a salt.
H atoms bonded to N and O atoms were located in a difference map and allowed to ride on their parent atoms in the
cycles.The O2—H6 bond distance which was found to be long in the normal cycles was fixed using DFIX command in SHELX. Other H atoms were positioned geometrically and refined using a riding model.Data collection: CrystalClear (Rigaku, 2007); cell
CrystalClear (Rigaku, 2007); data reduction: CrystalClear (Rigaku, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C4H5N3·C12H14O2 | F(000) = 608 |
Mr = 285.34 | Dx = 1.290 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 9.1461 (18) Å | Cell parameters from 4896 reflections |
b = 10.490 (2) Å | θ = 1.9–31.1° |
c = 15.474 (3) Å | µ = 0.09 mm−1 |
β = 98.14 (3)° | T = 110 K |
V = 1469.7 (5) Å3 | Block, colorless |
Z = 4 | 0.44 × 0.44 × 0.22 mm |
Rigaku Saturn 70 CCD area-detector diffractometer | 3641 independent reflections |
Radiation source: fine-focus sealed tube | 3516 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.036 |
ω scans | θmax = 28.3°, θmin = 2.4° |
Absorption correction: multi-scan (Blessing, 1995) | h = −12→12 |
Tmin = 0.963, Tmax = 0.981 | k = −13→13 |
20335 measured reflections | l = −20→20 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.068 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.178 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.21 | w = 1/[σ2(Fo2) + (0.0804P)2 + 0.5855P] where P = (Fo2 + 2Fc2)/3 |
3641 reflections | (Δ/σ)max < 0.001 |
202 parameters | Δρmax = 0.28 e Å−3 |
1 restraint | Δρmin = −0.27 e Å−3 |
C4H5N3·C12H14O2 | V = 1469.7 (5) Å3 |
Mr = 285.34 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.1461 (18) Å | µ = 0.09 mm−1 |
b = 10.490 (2) Å | T = 110 K |
c = 15.474 (3) Å | 0.44 × 0.44 × 0.22 mm |
β = 98.14 (3)° |
Rigaku Saturn 70 CCD area-detector diffractometer | 3641 independent reflections |
Absorption correction: multi-scan (Blessing, 1995) | 3516 reflections with I > 2σ(I) |
Tmin = 0.963, Tmax = 0.981 | Rint = 0.036 |
20335 measured reflections |
R[F2 > 2σ(F2)] = 0.068 | 1 restraint |
wR(F2) = 0.178 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.21 | Δρmax = 0.28 e Å−3 |
3641 reflections | Δρmin = −0.27 e Å−3 |
202 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O2 | 0.04632 (14) | 0.55094 (13) | 0.70052 (8) | 0.0344 (3) | |
O1 | 0.22224 (15) | 0.40633 (14) | 0.73866 (9) | 0.0397 (3) | |
C16 | 0.12059 (18) | 0.47154 (16) | 0.75641 (11) | 0.0281 (3) | |
C6 | −0.09084 (18) | 0.42117 (16) | 0.83708 (10) | 0.0273 (3) | |
C5 | 0.06701 (18) | 0.47220 (17) | 0.84621 (11) | 0.0289 (4) | |
C8 | −0.35533 (19) | 0.45531 (18) | 0.80273 (12) | 0.0337 (4) | |
H8 | −0.4356 | 0.5110 | 0.7842 | 0.040* | |
C12 | 0.17880 (19) | 0.3999 (2) | 0.91211 (12) | 0.0396 (4) | |
H12A | 0.2180 | 0.3247 | 0.8843 | 0.047* | |
H12B | 0.1319 | 0.3709 | 0.9625 | 0.047* | |
C7 | −0.21065 (18) | 0.50062 (17) | 0.81043 (11) | 0.0305 (4) | |
H7 | −0.1936 | 0.5873 | 0.7972 | 0.037* | |
C10 | −0.2643 (2) | 0.24866 (18) | 0.84809 (12) | 0.0362 (4) | |
H10 | −0.2821 | 0.1620 | 0.8610 | 0.043* | |
C11 | −0.1195 (2) | 0.29396 (17) | 0.85543 (12) | 0.0332 (4) | |
H11 | −0.0395 | 0.2376 | 0.8731 | 0.040* | |
C15 | 0.0807 (2) | 0.6105 (2) | 0.88196 (13) | 0.0380 (4) | |
H15A | 0.0410 | 0.6727 | 0.8365 | 0.046* | |
H15B | 0.0279 | 0.6204 | 0.9332 | 0.046* | |
C9 | −0.3820 (2) | 0.32934 (19) | 0.82208 (12) | 0.0354 (4) | |
H9 | −0.4805 | 0.2985 | 0.8175 | 0.042* | |
C13 | 0.3039 (2) | 0.4964 (3) | 0.94177 (14) | 0.0523 (6) | |
H13A | 0.3269 | 0.4975 | 1.0062 | 0.063* | |
H13B | 0.3945 | 0.4731 | 0.9172 | 0.063* | |
C14 | 0.2473 (2) | 0.6273 (2) | 0.90771 (16) | 0.0517 (6) | |
H14A | 0.2684 | 0.6930 | 0.9537 | 0.062* | |
H14B | 0.2944 | 0.6530 | 0.8566 | 0.062* | |
H6 | 0.082 (3) | 0.557 (3) | 0.6516 (13) | 0.066 (8)* | |
C2 | 0.24306 (19) | 0.66091 (17) | 0.39920 (12) | 0.0318 (4) | |
H2 | 0.2760 | 0.6860 | 0.3462 | 0.038* | |
N3 | 0.36606 (18) | 0.47957 (17) | 0.58582 (11) | 0.0391 (4) | |
N1 | 0.14713 (15) | 0.58831 (14) | 0.54997 (9) | 0.0299 (3) | |
N2 | 0.33123 (16) | 0.58740 (14) | 0.45437 (10) | 0.0314 (3) | |
C3 | 0.1056 (2) | 0.70251 (18) | 0.41554 (12) | 0.0345 (4) | |
H3 | 0.0445 | 0.7554 | 0.3757 | 0.041* | |
C4 | 0.06304 (19) | 0.66250 (18) | 0.49318 (12) | 0.0346 (4) | |
H4 | −0.0304 | 0.6890 | 0.5068 | 0.041* | |
H5 | 0.331 (3) | 0.447 (2) | 0.6325 (17) | 0.051 (7)* | |
C1 | 0.27973 (18) | 0.55295 (16) | 0.52886 (11) | 0.0285 (3) | |
H1 | 0.451 (3) | 0.454 (2) | 0.5716 (16) | 0.051 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O2 | 0.0317 (6) | 0.0434 (7) | 0.0300 (6) | 0.0106 (5) | 0.0113 (5) | 0.0085 (5) |
O1 | 0.0385 (7) | 0.0472 (8) | 0.0361 (7) | 0.0150 (6) | 0.0146 (6) | 0.0093 (6) |
C16 | 0.0247 (7) | 0.0303 (8) | 0.0297 (8) | −0.0005 (6) | 0.0056 (6) | 0.0009 (6) |
C6 | 0.0259 (7) | 0.0322 (8) | 0.0249 (8) | −0.0013 (6) | 0.0071 (6) | −0.0011 (6) |
C5 | 0.0226 (7) | 0.0380 (9) | 0.0268 (8) | −0.0023 (6) | 0.0055 (6) | −0.0003 (6) |
C8 | 0.0249 (8) | 0.0410 (9) | 0.0361 (9) | 0.0003 (7) | 0.0070 (7) | −0.0050 (7) |
C12 | 0.0264 (8) | 0.0626 (13) | 0.0297 (9) | 0.0001 (8) | 0.0039 (7) | 0.0093 (8) |
C7 | 0.0279 (8) | 0.0307 (8) | 0.0336 (9) | −0.0016 (6) | 0.0074 (6) | −0.0031 (7) |
C10 | 0.0408 (10) | 0.0329 (9) | 0.0364 (9) | −0.0097 (7) | 0.0102 (7) | −0.0021 (7) |
C11 | 0.0331 (9) | 0.0333 (9) | 0.0336 (9) | 0.0005 (7) | 0.0058 (7) | 0.0018 (7) |
C15 | 0.0305 (9) | 0.0449 (10) | 0.0402 (10) | −0.0110 (7) | 0.0106 (7) | −0.0113 (8) |
C9 | 0.0303 (8) | 0.0436 (10) | 0.0339 (9) | −0.0108 (7) | 0.0104 (7) | −0.0084 (7) |
C13 | 0.0274 (9) | 0.0954 (18) | 0.0335 (10) | −0.0092 (10) | 0.0018 (8) | −0.0042 (11) |
C14 | 0.0357 (10) | 0.0700 (15) | 0.0500 (12) | −0.0211 (10) | 0.0082 (9) | −0.0156 (11) |
C2 | 0.0328 (8) | 0.0344 (9) | 0.0292 (8) | 0.0018 (7) | 0.0077 (6) | 0.0018 (7) |
N3 | 0.0306 (8) | 0.0513 (10) | 0.0383 (9) | 0.0149 (7) | 0.0150 (7) | 0.0168 (7) |
N1 | 0.0238 (6) | 0.0371 (8) | 0.0294 (7) | 0.0027 (5) | 0.0065 (5) | 0.0024 (6) |
N2 | 0.0294 (7) | 0.0340 (7) | 0.0320 (8) | 0.0035 (6) | 0.0087 (6) | 0.0040 (6) |
C3 | 0.0304 (8) | 0.0403 (10) | 0.0326 (9) | 0.0052 (7) | 0.0045 (7) | 0.0057 (7) |
C4 | 0.0257 (8) | 0.0437 (10) | 0.0348 (9) | 0.0070 (7) | 0.0060 (6) | 0.0041 (7) |
C1 | 0.0256 (8) | 0.0291 (8) | 0.0316 (8) | 0.0016 (6) | 0.0066 (6) | 0.0010 (6) |
O2—C16 | 1.318 (2) | C15—H15A | 0.9900 |
O2—H6 | 0.869 (17) | C15—H15B | 0.9900 |
O1—C16 | 1.217 (2) | C9—H9 | 0.9500 |
C16—C5 | 1.537 (2) | C13—C14 | 1.535 (4) |
C6—C7 | 1.392 (2) | C13—H13A | 0.9900 |
C6—C11 | 1.397 (2) | C13—H13B | 0.9900 |
C6—C5 | 1.527 (2) | C14—H14A | 0.9900 |
C5—C12 | 1.538 (2) | C14—H14B | 0.9900 |
C5—C15 | 1.551 (3) | C2—N2 | 1.334 (2) |
C8—C9 | 1.384 (3) | C2—C3 | 1.387 (2) |
C8—C7 | 1.395 (2) | C2—H2 | 0.9500 |
C8—H8 | 0.9500 | N3—C1 | 1.340 (2) |
C12—C13 | 1.548 (3) | N3—H5 | 0.90 (3) |
C12—H12A | 0.9900 | N3—H1 | 0.88 (3) |
C12—H12B | 0.9900 | N1—C4 | 1.334 (2) |
C7—H7 | 0.9500 | N1—C1 | 1.352 (2) |
C10—C9 | 1.384 (3) | N2—C1 | 1.355 (2) |
C10—C11 | 1.397 (2) | C3—C4 | 1.380 (3) |
C10—H10 | 0.9500 | C3—H3 | 0.9500 |
C11—H11 | 0.9500 | C4—H4 | 0.9500 |
C15—C14 | 1.530 (3) | ||
C16—O2—H6 | 113.4 (19) | C5—C15—H15B | 111.1 |
O1—C16—O2 | 123.13 (16) | H15A—C15—H15B | 109.1 |
O1—C16—C5 | 123.93 (16) | C10—C9—C8 | 119.54 (16) |
O2—C16—C5 | 112.93 (14) | C10—C9—H9 | 120.2 |
C7—C6—C11 | 118.03 (15) | C8—C9—H9 | 120.2 |
C7—C6—C5 | 120.77 (15) | C14—C13—C12 | 106.50 (16) |
C11—C6—C5 | 121.20 (15) | C14—C13—H13A | 110.4 |
C6—C5—C16 | 109.44 (13) | C12—C13—H13A | 110.4 |
C6—C5—C12 | 114.81 (15) | C14—C13—H13B | 110.4 |
C16—C5—C12 | 109.27 (14) | C12—C13—H13B | 110.4 |
C6—C5—C15 | 112.84 (14) | H13A—C13—H13B | 108.6 |
C16—C5—C15 | 107.86 (14) | C15—C14—C13 | 105.13 (18) |
C12—C5—C15 | 102.24 (15) | C15—C14—H14A | 110.7 |
C9—C8—C7 | 120.06 (17) | C13—C14—H14A | 110.7 |
C9—C8—H8 | 120.0 | C15—C14—H14B | 110.7 |
C7—C8—H8 | 120.0 | C13—C14—H14B | 110.7 |
C5—C12—C13 | 105.58 (17) | H14A—C14—H14B | 108.8 |
C5—C12—H12A | 110.6 | N2—C2—C3 | 123.13 (16) |
C13—C12—H12A | 110.6 | N2—C2—H2 | 118.4 |
C5—C12—H12B | 110.6 | C3—C2—H2 | 118.4 |
C13—C12—H12B | 110.6 | C1—N3—H5 | 120.2 (16) |
H12A—C12—H12B | 108.8 | C1—N3—H1 | 118.2 (16) |
C6—C7—C8 | 121.24 (16) | H5—N3—H1 | 121 (2) |
C6—C7—H7 | 119.4 | C4—N1—C1 | 117.03 (15) |
C8—C7—H7 | 119.4 | C2—N2—C1 | 116.58 (15) |
C9—C10—C11 | 120.36 (17) | C4—C3—C2 | 115.97 (16) |
C9—C10—H10 | 119.8 | C4—C3—H3 | 122.0 |
C11—C10—H10 | 119.8 | C2—C3—H3 | 122.0 |
C10—C11—C6 | 120.76 (17) | N1—C4—C3 | 122.94 (16) |
C10—C11—H11 | 119.6 | N1—C4—H4 | 118.5 |
C6—C11—H11 | 119.6 | C3—C4—H4 | 118.5 |
C14—C15—C5 | 103.19 (17) | N3—C1—N1 | 117.64 (16) |
C14—C15—H15A | 111.1 | N3—C1—N2 | 118.00 (15) |
C5—C15—H15A | 111.1 | N1—C1—N2 | 124.36 (16) |
C14—C15—H15B | 111.1 |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H6···N1 | 0.87 (2) | 1.79 (2) | 2.653 (2) | 173 (3) |
N3—H5···O1 | 0.90 (3) | 2.08 (3) | 2.966 (2) | 168 (2) |
N3—H1···N2i | 0.88 (3) | 2.13 (3) | 3.006 (2) | 173 (2) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C4H5N3·C12H14O2 |
Mr | 285.34 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 110 |
a, b, c (Å) | 9.1461 (18), 10.490 (2), 15.474 (3) |
β (°) | 98.14 (3) |
V (Å3) | 1469.7 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.44 × 0.44 × 0.22 |
Data collection | |
Diffractometer | Rigaku Saturn 70 CCD area-detector diffractometer |
Absorption correction | Multi-scan (Blessing, 1995) |
Tmin, Tmax | 0.963, 0.981 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 20335, 3641, 3516 |
Rint | 0.036 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.068, 0.178, 1.21 |
No. of reflections | 3641 |
No. of parameters | 202 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.28, −0.27 |
Computer programs: CrystalClear (Rigaku, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H6···N1 | 0.869 (17) | 1.788 (18) | 2.653 (2) | 173 (3) |
N3—H5···O1 | 0.90 (3) | 2.08 (3) | 2.966 (2) | 168 (2) |
N3—H1···N2i | 0.88 (3) | 2.13 (3) | 3.006 (2) | 173 (2) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Acknowledgements
This work was supported by the Science and Engineering Research Council of A*STAR (Agency for Science, Technology and Research), Singapore.
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An analysis of the crystal structure of pyrimidin-2-amine reveals that it forms a homosynthon (I) involving two N–H···N hydrogen bonds (Scheinbeim and Schempp, 1976). However, when it is cocrystallized with the molecules possessing at least one carboxylic acid group in the structure, it forms a pyrimidin-2-amine–carboxylic acid supramolecular heterosynthon (II) (Fig. 1) involving two hydrogen bonds, namely N–H···O and O–H···N. These strong hydrogen bonds are preferred over potential alternative arrangements and play a significant role in structure-directing (Shan et al., 2002). We have chosen pyrimidin-2-amine and 1-phenylcyclopentane-1-carboxylic acid for cocrystallization experiment as an extension work to our previous study on screening for molecular cocrystals and salts (He et al., 2009).
The crystal structure of the title cocrystal contains one molecule of pyrimidin-2-amine and one molecule of 1-phenylcyclopentane-1-carboxylic acid in the crystallographic asymmetric unit (Fig. 2). The identity of the cocrystal was confirmed by Fourier Transform Infrared (FT—IR) spectrum which showed carboxylic acid O—H stretching band at 3167 cm-1 and carbonyl stretching band at 1685 cm-1 (Fig. 3). Two pyrimidin-2-amine molecules that are related by an inversion center form the synthon I involving N–H···O (N···O = 3.006 (2) Å) hydrogen bonds. Two 1-phenylcyclopentane-1-carboxylic acid molecules hydrogen bond to either side of the dimeric motif involving synthon II which is sustained by N–H···O (N···O = 2.966 (2) Å) and O–H···O (O···O = 2.653 (2) Å) hydrogen bonds and forms a four-component supramolecular unit (Fig. 4). These four-component supramolecular units self assemble in the crystal structure via several weak C–H···O interactions (Fig. 5).