Download citation
Download citation
link to html
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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989023009933/wm5702sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2056989023009933/wm5702Isup2.hkl
Contains datablock I

cdx

Chemdraw file https://doi.org/10.1107/S2056989023009933/wm5702Isup3.cdx
Supplementary material

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989023009933/wm5702Isup4.cml
Supplementary material

CCDC reference: 2308262

Key indicators

Structure: I
  • Single-crystal X-ray study
  • T = 150 K
  • Mean [sigma](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

Computing details top

4-Amino-1-(prop-2-yn-1-yl)pyrimidin-2(1H)-one top
Crystal data top
C7H7N3OF(000) = 312
Mr = 149.16Dx = 1.465 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 5.3864 (6) ÅCell parameters from 9914 reflections
b = 18.013 (2) Åθ = 4.0–33.2°
c = 7.0112 (8) ŵ = 0.10 mm1
β = 96.288 (4)°T = 150 K
V = 676.18 (13) Å3Plate, colourless
Z = 40.34 × 0.32 × 0.07 mm
Data collection top
Bruker D8 QUEST PHOTON 3
diffractometer
2554 independent reflections
Radiation source: fine-focus sealed tube2251 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
Detector resolution: 7.3910 pixels mm-1θmax = 33.2°, θmin = 4.0°
ω scansh = 88
Absorption correction: numerical
(SADABS; Krause et al., 2015)
k = 2727
Tmin = 0.96, Tmax = 0.99l = 1010
28024 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: mixed
wR(F2) = 0.113H 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 parametersΔρmax = 0.47 e Å3
2 restraintsΔρmin = 0.20 e Å3
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
xyzUiso*/Ueq
O10.66696 (11)0.40841 (3)0.85317 (8)0.01939 (14)
N10.39821 (12)0.36777 (4)0.60167 (9)0.01532 (14)
N20.75623 (12)0.43923 (3)0.55258 (9)0.01525 (14)
N30.83960 (13)0.46704 (4)0.24590 (10)0.01878 (15)
H3A0.805 (3)0.4626 (8)0.1187 (12)0.031 (3)*
H3B0.976 (2)0.4921 (7)0.296 (2)0.033 (3)*
C10.61327 (14)0.40625 (4)0.67606 (11)0.01469 (14)
C20.33252 (14)0.36368 (4)0.40859 (11)0.01677 (15)
H20.1838310.3383150.3611540.020*
C30.47496 (14)0.39504 (4)0.28349 (11)0.01730 (15)
H30.4319500.3912520.1487750.021*
C40.69319 (14)0.43416 (4)0.36256 (11)0.01446 (14)
C50.24325 (15)0.33434 (4)0.73922 (11)0.01883 (16)
H5A0.3529770.3087190.8411010.023*
H5B0.1534560.3742070.8005560.023*
C60.06137 (15)0.28125 (4)0.64860 (11)0.01895 (16)
C70.08594 (16)0.23629 (5)0.57853 (12)0.02220 (17)
H70.2025000.2007210.5230770.027*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0215 (3)0.0237 (3)0.0123 (3)0.0033 (2)0.0012 (2)0.00096 (19)
N10.0150 (3)0.0178 (3)0.0128 (3)0.0033 (2)0.0001 (2)0.0006 (2)
N20.0154 (3)0.0169 (3)0.0130 (3)0.0025 (2)0.0001 (2)0.0009 (2)
N30.0190 (3)0.0232 (3)0.0140 (3)0.0051 (2)0.0011 (2)0.0000 (2)
C10.0142 (3)0.0153 (3)0.0140 (3)0.0008 (2)0.0008 (2)0.0015 (2)
C20.0161 (3)0.0194 (3)0.0142 (3)0.0028 (2)0.0009 (2)0.0017 (2)
C30.0177 (3)0.0207 (3)0.0130 (3)0.0034 (2)0.0008 (2)0.0023 (2)
C40.0145 (3)0.0148 (3)0.0138 (3)0.0002 (2)0.0003 (2)0.0010 (2)
C50.0195 (3)0.0218 (3)0.0151 (3)0.0051 (3)0.0014 (3)0.0004 (2)
C60.0192 (3)0.0206 (3)0.0170 (3)0.0014 (3)0.0019 (3)0.0025 (3)
C70.0227 (4)0.0240 (4)0.0195 (4)0.0044 (3)0.0007 (3)0.0015 (3)
Geometric parameters (Å, º) top
O1—C11.2444 (9)C2—C31.3507 (11)
N1—C21.3632 (10)C2—H20.9500
N1—C11.4007 (10)C3—C41.4294 (10)
N1—C51.4716 (10)C3—H30.9500
N2—C41.3415 (10)C5—C61.4635 (11)
N2—C11.3570 (10)C5—H5A0.9900
N3—C41.3353 (10)C5—H5B0.9900
N3—H3A0.894 (8)C6—C71.2005 (11)
N3—H3B0.899 (9)C7—H70.9500
C2—N1—C1120.71 (6)C2—C3—H3121.4
C2—N1—C5121.63 (6)C4—C3—H3121.4
C1—N1—C5117.63 (6)N3—C4—N2118.42 (7)
C4—N2—C1120.28 (6)N3—C4—C3119.79 (7)
C4—N3—H3A120.0 (9)N2—C4—C3121.78 (7)
C4—N3—H3B119.5 (10)C6—C5—N1112.56 (6)
H3A—N3—H3B120.4 (13)C6—C5—H5A109.1
O1—C1—N2122.47 (7)N1—C5—H5A109.1
O1—C1—N1118.64 (7)C6—C5—H5B109.1
N2—C1—N1118.88 (6)N1—C5—H5B109.1
C3—C2—N1121.21 (7)H5A—C5—H5B107.8
C3—C2—H2119.4C7—C6—C5178.11 (9)
N1—C2—H2119.4C6—C7—H7180.0
C2—C3—C4117.12 (7)
C4—N2—C1—O1178.71 (7)N1—C2—C3—C41.57 (11)
C4—N2—C1—N10.74 (10)C1—N2—C4—N3179.62 (7)
C2—N1—C1—O1179.75 (7)C1—N2—C4—C30.61 (11)
C5—N1—C1—O12.17 (10)C2—C3—C4—N3179.22 (7)
C2—N1—C1—N20.27 (11)C2—C3—C4—N20.55 (11)
C5—N1—C1—N2178.35 (6)C2—N1—C5—C615.87 (11)
C1—N1—C2—C31.48 (12)C1—N1—C5—C6166.07 (7)
C5—N1—C2—C3179.48 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O1i0.89 (1)2.16 (1)3.0002 (9)156 (1)
N3—H3B···N2ii0.90 (1)2.10 (1)2.9854 (10)169 (1)
C3—H3···O1i0.952.563.3036 (10)135
C7—H7···O1iii0.952.373.2559 (11)156
Symmetry codes: (i) x, y, z1; (ii) x+2, y+1, z+1; (iii) x1, y+1/2, z1/2.
Comparison of selected X-ray and DFT bond lengths and angles (Å, °) top
Bonds/anglesX-rayB3LYP/6-311G(d,p)
O1—C11.2444 (9)1.2457
N1—C21.3632 (10)1.3645
N1—C51.4716 (10)1.4782
N2—C41.3415 (10)1.3423
N2—C11.3570 (10)1.3542
N3—C41.3353 (10)1.3392
C2—N1—C1120.71 (6)120.82
O1—C1—N2122.47 (7)122.17
O1—C1—N1118.64 (7)118.54
N2—C1—N1118.88 (6)118.53
Calculated energies and quantum-chemical parameters of (I) top
Total 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, A2.64
Electronegativity, χ3.20
Hardness, η5.96
Softness, σ0.15
Electrophilicity index, ω5.35
 

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds