The molecular structure of the title compound comprises an essentially planar pyrimidine ring from which the propynyl group is rotated by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N—H
O, N—H
N and C—H
O hydrogen-bonding and slipped π–π stacking interactions, leading to narrow channels extending parallel to the
c axis.
Supporting information
CCDC reference: 2308262
Key indicators
Structure: I
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.001 Å
- R factor = 0.040
- wR factor = 0.113
- Data-to-parameter ratio = 23.6
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density .... 2.32 Report
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L= 0.600 16 Report
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF .... 7 Note
Alert level G
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite 3 Note
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical ? Check
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records 1 Report
PLAT230_ALERT_2_G Hirshfeld Test Diff for C5 --C6 . 9.8 s.u.
PLAT860_ALERT_3_G Number of Least-Squares Restraints ............. 2 Note
PLAT899_ALERT_4_G SHELXL2018 is Deprecated and Succeeded by SHELXL 2019/3 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min). 4 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L= 0.600 7 Note
PLAT933_ALERT_2_G Number of HKL-OMIT Records in Embedded .res File 1 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density. 4 Info
PLAT992_ALERT_5_G Repd & Actual _reflns_number_gt Values Differ by 2 Check
0 ALERT level A = Most likely a serious problem - resolve or explain
0 ALERT level B = A potentially serious problem, consider carefully
3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
11 ALERT level G = General information/check it is not something unexpected
1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
5 ALERT type 2 Indicator that the structure model may be wrong or deficient
4 ALERT type 3 Indicator that the structure quality may be low
3 ALERT type 4 Improvement, methodology, query or suggestion
1 ALERT type 5 Informative message, check
4-Amino-1-(prop-2-yn-1-yl)pyrimidin-2(1
H)-one
top
Crystal data top
C7H7N3O | F(000) = 312 |
Mr = 149.16 | Dx = 1.465 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 5.3864 (6) Å | Cell parameters from 9914 reflections |
b = 18.013 (2) Å | θ = 4.0–33.2° |
c = 7.0112 (8) Å | µ = 0.10 mm−1 |
β = 96.288 (4)° | T = 150 K |
V = 676.18 (13) Å3 | Plate, colourless |
Z = 4 | 0.34 × 0.32 × 0.07 mm |
Data collection top
Bruker D8 QUEST PHOTON 3 diffractometer | 2554 independent reflections |
Radiation source: fine-focus sealed tube | 2251 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.035 |
Detector resolution: 7.3910 pixels mm-1 | θmax = 33.2°, θmin = 4.0° |
ω scans | h = −8→8 |
Absorption correction: numerical (SADABS; Krause et al., 2015) | k = −27→27 |
Tmin = 0.96, Tmax = 0.99 | l = −10→10 |
28024 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.040 | Hydrogen site location: mixed |
wR(F2) = 0.113 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0627P)2 + 0.1628P] where P = (Fo2 + 2Fc2)/3 |
2554 reflections | (Δ/σ)max < 0.001 |
108 parameters | Δρmax = 0.47 e Å−3 |
2 restraints | Δρmin = −0.20 e Å−3 |
Special details top
Experimental. The diffraction data were obtained from 8 sets of frames,
each of width 0.5° in ω, collected with scan parameters
determined by the "strategy" routine in APEX3. The scan
time was 5 sec/frame. |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds 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 > 2sigma(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. H-atoms attached to carbon
were placed in calculated positions (C—H = 0.95 - 1.00 Å) and were
included as riding contributions with isotropic displacement parameters
1.2 - 1.5 times those of the attached atoms. Those attached to nitrogen
were placed in locations derived from a difference map and refined with
a DFIX 0.91 0.01 instruction. One reflection affected by the beamstop was
omitted from the final refinement. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.66696 (11) | 0.40841 (3) | 0.85317 (8) | 0.01939 (14) | |
N1 | 0.39821 (12) | 0.36777 (4) | 0.60167 (9) | 0.01532 (14) | |
N2 | 0.75623 (12) | 0.43923 (3) | 0.55258 (9) | 0.01525 (14) | |
N3 | 0.83960 (13) | 0.46704 (4) | 0.24590 (10) | 0.01878 (15) | |
H3A | 0.805 (3) | 0.4626 (8) | 0.1187 (12) | 0.031 (3)* | |
H3B | 0.976 (2) | 0.4921 (7) | 0.296 (2) | 0.033 (3)* | |
C1 | 0.61327 (14) | 0.40625 (4) | 0.67606 (11) | 0.01469 (14) | |
C2 | 0.33252 (14) | 0.36368 (4) | 0.40859 (11) | 0.01677 (15) | |
H2 | 0.183831 | 0.338315 | 0.361154 | 0.020* | |
C3 | 0.47496 (14) | 0.39504 (4) | 0.28349 (11) | 0.01730 (15) | |
H3 | 0.431950 | 0.391252 | 0.148775 | 0.021* | |
C4 | 0.69319 (14) | 0.43416 (4) | 0.36256 (11) | 0.01446 (14) | |
C5 | 0.24325 (15) | 0.33434 (4) | 0.73922 (11) | 0.01883 (16) | |
H5A | 0.352977 | 0.308719 | 0.841101 | 0.023* | |
H5B | 0.153456 | 0.374207 | 0.800556 | 0.023* | |
C6 | 0.06137 (15) | 0.28125 (4) | 0.64860 (11) | 0.01895 (16) | |
C7 | −0.08594 (16) | 0.23629 (5) | 0.57853 (12) | 0.02220 (17) | |
H7 | −0.202500 | 0.200721 | 0.523077 | 0.027* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0215 (3) | 0.0237 (3) | 0.0123 (3) | −0.0033 (2) | −0.0012 (2) | −0.00096 (19) |
N1 | 0.0150 (3) | 0.0178 (3) | 0.0128 (3) | −0.0033 (2) | 0.0001 (2) | −0.0006 (2) |
N2 | 0.0154 (3) | 0.0169 (3) | 0.0130 (3) | −0.0025 (2) | −0.0001 (2) | −0.0009 (2) |
N3 | 0.0190 (3) | 0.0232 (3) | 0.0140 (3) | −0.0051 (2) | 0.0011 (2) | 0.0000 (2) |
C1 | 0.0142 (3) | 0.0153 (3) | 0.0140 (3) | −0.0008 (2) | −0.0008 (2) | −0.0015 (2) |
C2 | 0.0161 (3) | 0.0194 (3) | 0.0142 (3) | −0.0028 (2) | −0.0009 (2) | −0.0017 (2) |
C3 | 0.0177 (3) | 0.0207 (3) | 0.0130 (3) | −0.0034 (2) | −0.0008 (2) | −0.0023 (2) |
C4 | 0.0145 (3) | 0.0148 (3) | 0.0138 (3) | 0.0002 (2) | 0.0003 (2) | −0.0010 (2) |
C5 | 0.0195 (3) | 0.0218 (3) | 0.0151 (3) | −0.0051 (3) | 0.0014 (3) | 0.0004 (2) |
C6 | 0.0192 (3) | 0.0206 (3) | 0.0170 (3) | −0.0014 (3) | 0.0019 (3) | 0.0025 (3) |
C7 | 0.0227 (4) | 0.0240 (4) | 0.0195 (4) | −0.0044 (3) | 0.0007 (3) | 0.0015 (3) |
Geometric parameters (Å, º) top
O1—C1 | 1.2444 (9) | C2—C3 | 1.3507 (11) |
N1—C2 | 1.3632 (10) | C2—H2 | 0.9500 |
N1—C1 | 1.4007 (10) | C3—C4 | 1.4294 (10) |
N1—C5 | 1.4716 (10) | C3—H3 | 0.9500 |
N2—C4 | 1.3415 (10) | C5—C6 | 1.4635 (11) |
N2—C1 | 1.3570 (10) | C5—H5A | 0.9900 |
N3—C4 | 1.3353 (10) | C5—H5B | 0.9900 |
N3—H3A | 0.894 (8) | C6—C7 | 1.2005 (11) |
N3—H3B | 0.899 (9) | C7—H7 | 0.9500 |
| | | |
C2—N1—C1 | 120.71 (6) | C2—C3—H3 | 121.4 |
C2—N1—C5 | 121.63 (6) | C4—C3—H3 | 121.4 |
C1—N1—C5 | 117.63 (6) | N3—C4—N2 | 118.42 (7) |
C4—N2—C1 | 120.28 (6) | N3—C4—C3 | 119.79 (7) |
C4—N3—H3A | 120.0 (9) | N2—C4—C3 | 121.78 (7) |
C4—N3—H3B | 119.5 (10) | C6—C5—N1 | 112.56 (6) |
H3A—N3—H3B | 120.4 (13) | C6—C5—H5A | 109.1 |
O1—C1—N2 | 122.47 (7) | N1—C5—H5A | 109.1 |
O1—C1—N1 | 118.64 (7) | C6—C5—H5B | 109.1 |
N2—C1—N1 | 118.88 (6) | N1—C5—H5B | 109.1 |
C3—C2—N1 | 121.21 (7) | H5A—C5—H5B | 107.8 |
C3—C2—H2 | 119.4 | C7—C6—C5 | 178.11 (9) |
N1—C2—H2 | 119.4 | C6—C7—H7 | 180.0 |
C2—C3—C4 | 117.12 (7) | | |
| | | |
C4—N2—C1—O1 | 178.71 (7) | N1—C2—C3—C4 | −1.57 (11) |
C4—N2—C1—N1 | −0.74 (10) | C1—N2—C4—N3 | −179.62 (7) |
C2—N1—C1—O1 | −179.75 (7) | C1—N2—C4—C3 | 0.61 (11) |
C5—N1—C1—O1 | 2.17 (10) | C2—C3—C4—N3 | −179.22 (7) |
C2—N1—C1—N2 | −0.27 (11) | C2—C3—C4—N2 | 0.55 (11) |
C5—N1—C1—N2 | −178.35 (6) | C2—N1—C5—C6 | 15.87 (11) |
C1—N1—C2—C3 | 1.48 (12) | C1—N1—C5—C6 | −166.07 (7) |
C5—N1—C2—C3 | 179.48 (7) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O1i | 0.89 (1) | 2.16 (1) | 3.0002 (9) | 156 (1) |
N3—H3B···N2ii | 0.90 (1) | 2.10 (1) | 2.9854 (10) | 169 (1) |
C3—H3···O1i | 0.95 | 2.56 | 3.3036 (10) | 135 |
C7—H7···O1iii | 0.95 | 2.37 | 3.2559 (11) | 156 |
Symmetry codes: (i) x, y, z−1; (ii) −x+2, −y+1, −z+1; (iii) x−1, −y+1/2, z−1/2. |
Comparison of selected X-ray and DFT bond lengths and angles
(Å, °) topBonds/angles | X-ray | B3LYP/6-311G(d,p) |
O1—C1 | 1.2444 (9) | 1.2457 |
N1—C2 | 1.3632 (10) | 1.3645 |
N1—C5 | 1.4716 (10) | 1.4782 |
N2—C4 | 1.3415 (10) | 1.3423 |
N2—C1 | 1.3570 (10) | 1.3542 |
N3—C4 | 1.3353 (10) | 1.3392 |
C2—N1—C1 | 120.71 (6) | 120.82 |
O1—C1—N2 | 122.47 (7) | 122.17 |
O1—C1—N1 | 118.64 (7) | 118.54 |
N2—C1—N1 | 118.88 (6) | 118.53 |
Calculated energies and quantum-chemical parameters of (I) topTotal Energy, TE (eV) | -13800.94 |
EHOMO (eV) | -9.28 |
ELUMO (eV) | -2.64 |
Gap, ΔE (eV) | 6.64 |
Dipole moment, µ (Debye) | 7.47 |
Ionisation potential, I (eV) | 9.28 |
Electron affinity, A | 2.64 |
Electronegativity, χ | 3.20 |
Hardness, η | 5.96 |
Softness, σ | 0.15 |
Electrophilicity index, ω | 5.35 |