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Acta Crystallogr Sect E Struct Rep Online. 2008 October 1; 64(Pt 10): o1928.
Published online 2008 September 13. doi:  10.1107/S1600536808028900
PMCID: PMC2959440

2-(2-Chloro­pyrimidin-4-yl)-3,5,6,7,8,9-hexahydro-2H-1,2,4-triazolo[4,3-a]azepin-3-one

Abstract

In the title compound, C11H12ClN5O, the triazolone and pyrimidine rings are almost coplanar [dihedral angle = 2.98 (14)°]. The total puckering amplitude QT of the seven-membered lactam ring is 0.706 (3) Å.

Related literature

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993 [triangle]); as agrochemicals, see: Maeno et al. (1990 [triangle]); as anti­viral agents, see: Gilchrist (1997 [triangle]); as herbicides, see: Selby et al. (2002 [triangle]). For puckering paramteres, see: Cremer & Pople (1975 [triangle]).

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Object name is e-64-o1928-scheme1.jpg

Experimental

Crystal data

  • C11H12ClN5O
  • M r = 265.71
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1928-efi1.jpg
  • a = 8.6810 (16) Å
  • b = 14.718 (3) Å
  • c = 9.4251 (17) Å
  • β = 92.359 (3)°
  • V = 1203.2 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.31 mm−1
  • T = 294 (2) K
  • 0.24 × 0.16 × 0.10 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.926, T max = 0.969
  • 6734 measured reflections
  • 2461 independent reflections
  • 1291 reflections with I > 2σ(I)
  • R int = 0.047

Refinement

  • R[F 2 > 2σ(F 2)] = 0.045
  • wR(F 2) = 0.130
  • S = 1.01
  • 2461 reflections
  • 163 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: SMART (Bruker, 1999 [triangle]); cell refinement: SAINT (Bruker, 1999 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808028900/at2624sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808028900/at2624Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the Program for New Century Excellent Talents in Universities of Henan Province (grant No. 2005HANCET-17), the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Education Department, China (grant No. 2007150036).

supplementary crystallographic information

Comment

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as azidothymidine (AZT), which is the most widely used anti-AIDS drug (Gilchrist, 1997). Recently, a new series of highly active herbicides of substituted azolylpyrimidines were reported (Selby et al., 2002). In order to discover further biologically active pyrimidine compounds, the title compound, (I), was synthesized and its crystal structure determined (Fig. 1).

In the crystal structure of (I), the triazolone and pyrimidine rings are almost coplanar. The dihedral angle between them is 2.99 (18)°. The total puckering amplitude QT (Cremer & Pople, 1975) of the seven-membered lactam ring gives a quantitative evaluation of puckering being 0.706 (3) Å.

Experimental

The reaction of 6,7,8,9-tetrahydro-2H-[1,2,4]triazolo[4,3-a]azepin-3(5H)-one (0.184 g, 1.2 mmol) with 4-(3-chlorophenoxy)-2-chloropyrimidine (0.241 g, 1 mmol) in the precence of potassium carbonate (0.207 g, 1.5 mmol) was carried out in N,N-dimethylformamide (20 ml) at 343 K overnight. The reaction was cooled and partitioned between 20 ml dichloromethane and 20 ml water. The aqueous layer was extracted with dichloromethane. After removal of the solvent, colourless crystals were obtained by recrystallization from ethyl acetate solution by slow evaporation (yield 30%).

Refinement

All H atoms were placed in calculated positions, with C—H = 0.93 or 0.97 Å, and refined using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The asymmetric unit of (I), with displacement ellipsoids drawn at the 30% probability level.

Crystal data

C11H12ClN5OF(000) = 552
Mr = 265.71Dx = 1.467 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1409 reflections
a = 8.6810 (16) Åθ = 2.6–21.9°
b = 14.718 (3) ŵ = 0.31 mm1
c = 9.4251 (17) ÅT = 294 K
β = 92.359 (3)°Prism, colourless
V = 1203.2 (4) Å30.24 × 0.16 × 0.10 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer2461 independent reflections
Radiation source: fine-focus sealed tube1291 reflections with I > 2σ(I)
graphiteRint = 0.047
[var phi] and oω scansθmax = 26.4°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −10→8
Tmin = 0.926, Tmax = 0.969k = −18→17
6734 measured reflectionsl = −11→11

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H-atom parameters constrained
S = 1.01w = 1/[σ2(Fo2) + (0.0559P)2 + 0.1252P] where P = (Fo2 + 2Fc2)/3
2461 reflections(Δ/σ)max = 0.002
163 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = −0.23 e Å3

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Cl11.10477 (10)0.59079 (6)0.12418 (10)0.0753 (3)
O10.6140 (2)0.37929 (13)0.5659 (2)0.0643 (6)
N10.7797 (2)0.25640 (15)0.5395 (2)0.0446 (6)
N20.8353 (3)0.38014 (15)0.4293 (2)0.0462 (6)
N30.9482 (3)0.31650 (15)0.3968 (2)0.0505 (6)
N40.9548 (3)0.48516 (15)0.2886 (2)0.0488 (6)
N50.8656 (3)0.63806 (16)0.2619 (3)0.0603 (7)
C10.9097 (3)0.24464 (18)0.4640 (3)0.0463 (7)
C20.9975 (4)0.1581 (2)0.4627 (3)0.0600 (9)
H2A1.08480.16550.40280.072*
H2B0.93180.11110.42060.072*
C31.0563 (3)0.1263 (2)0.6091 (3)0.0580 (8)
H3A1.13560.08080.59740.070*
H3B1.10350.17750.65910.070*
C40.9327 (4)0.0867 (2)0.6996 (3)0.0596 (8)
H4A0.98240.06080.78440.072*
H4B0.88290.03730.64720.072*
C50.8092 (4)0.1522 (2)0.7447 (3)0.0582 (8)
H5A0.74640.12160.81270.070*
H5B0.85930.20290.79330.070*
C60.7045 (3)0.18922 (19)0.6280 (3)0.0517 (8)
H6A0.66760.13940.56840.062*
H6B0.61570.21710.66960.062*
C70.7269 (3)0.34300 (19)0.5188 (3)0.0456 (7)
C80.8418 (3)0.46838 (18)0.3766 (3)0.0431 (7)
C90.7356 (3)0.53480 (18)0.4117 (3)0.0492 (7)
H90.65620.52300.47230.059*
C100.7550 (4)0.6178 (2)0.3520 (3)0.0601 (9)
H100.68690.66370.37520.072*
C110.9571 (3)0.5687 (2)0.2385 (3)0.0502 (7)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0592 (6)0.0746 (6)0.0940 (7)−0.0024 (5)0.0242 (5)0.0263 (5)
O10.0519 (13)0.0689 (14)0.0746 (14)0.0205 (11)0.0324 (11)0.0145 (11)
N10.0400 (14)0.0512 (14)0.0438 (13)0.0063 (11)0.0147 (11)0.0071 (11)
N20.0433 (14)0.0459 (14)0.0508 (14)0.0082 (11)0.0167 (11)0.0065 (11)
N30.0451 (15)0.0494 (14)0.0587 (15)0.0120 (12)0.0224 (12)0.0085 (12)
N40.0409 (14)0.0527 (15)0.0535 (15)0.0011 (11)0.0097 (12)0.0097 (12)
N50.0670 (19)0.0487 (15)0.0658 (17)0.0016 (13)0.0091 (14)0.0049 (13)
C10.0444 (17)0.0501 (17)0.0456 (16)0.0077 (14)0.0171 (13)0.0042 (14)
C20.062 (2)0.0566 (18)0.064 (2)0.0175 (16)0.0283 (16)0.0089 (16)
C30.0465 (19)0.0531 (18)0.075 (2)0.0107 (15)0.0113 (16)0.0119 (16)
C40.058 (2)0.0604 (19)0.0612 (19)0.0065 (16)0.0093 (16)0.0161 (16)
C50.060 (2)0.067 (2)0.0485 (17)0.0048 (16)0.0130 (15)0.0141 (16)
C60.0426 (17)0.0586 (18)0.0551 (18)−0.0039 (15)0.0166 (14)0.0098 (15)
C70.0424 (17)0.0532 (17)0.0418 (16)0.0049 (14)0.0102 (13)0.0054 (14)
C80.0407 (16)0.0493 (17)0.0393 (16)−0.0002 (13)0.0015 (13)0.0012 (13)
C90.0495 (18)0.0514 (18)0.0472 (17)0.0023 (15)0.0100 (14)−0.0039 (14)
C100.070 (2)0.0496 (18)0.061 (2)0.0104 (17)0.0104 (18)−0.0016 (16)
C110.0445 (18)0.0543 (19)0.0520 (18)−0.0051 (15)0.0045 (14)0.0060 (15)

Geometric parameters (Å, °)

Cl1—C111.739 (3)C2—H2B0.9700
O1—C71.216 (3)C3—C41.514 (4)
N1—C71.366 (3)C3—H3A0.9700
N1—C11.370 (3)C3—H3B0.9700
N1—C61.465 (3)C4—C51.516 (4)
N2—C81.392 (3)C4—H4A0.9700
N2—N31.399 (3)C4—H4B0.9700
N2—C71.400 (3)C5—C61.500 (4)
N3—C11.284 (3)C5—H5A0.9700
N4—C111.318 (3)C5—H5B0.9700
N4—C81.333 (3)C6—H6A0.9700
N5—C111.317 (4)C6—H6B0.9700
N5—C101.341 (4)C8—C91.393 (4)
C1—C21.485 (4)C9—C101.358 (4)
C2—C31.525 (4)C9—H90.9300
C2—H2A0.9700C10—H100.9300
C7—N1—C1108.8 (2)H4A—C4—H4B107.4
C7—N1—C6123.8 (2)C6—C5—C4116.1 (2)
C1—N1—C6127.4 (2)C6—C5—H5A108.3
C8—N2—N3120.5 (2)C4—C5—H5A108.3
C8—N2—C7128.1 (2)C6—C5—H5B108.3
N3—N2—C7111.4 (2)C4—C5—H5B108.3
C1—N3—N2104.1 (2)H5A—C5—H5B107.4
C11—N4—C8114.7 (2)N1—C6—C5113.1 (2)
C11—N5—C10112.7 (2)N1—C6—H6A109.0
N3—C1—N1112.9 (2)C5—C6—H6A109.0
N3—C1—C2124.0 (2)N1—C6—H6B109.0
N1—C1—C2123.2 (2)C5—C6—H6B109.0
C1—C2—C3114.1 (2)H6A—C6—H6B107.8
C1—C2—H2A108.7O1—C7—N1128.9 (2)
C3—C2—H2A108.7O1—C7—N2128.3 (3)
C1—C2—H2B108.7N1—C7—N2102.8 (2)
C3—C2—H2B108.7N4—C8—N2115.9 (2)
H2A—C2—H2B107.6N4—C8—C9121.9 (3)
C4—C3—C2114.1 (3)N2—C8—C9122.2 (2)
C4—C3—H3A108.7C10—C9—C8116.0 (3)
C2—C3—H3A108.7C10—C9—H9122.0
C4—C3—H3B108.7C8—C9—H9122.0
C2—C3—H3B108.7N5—C10—C9124.5 (3)
H3A—C3—H3B107.6N5—C10—H10117.8
C3—C4—C5116.0 (3)C9—C10—H10117.8
C3—C4—H4A108.3N5—C11—N4130.2 (3)
C5—C4—H4A108.3N5—C11—Cl1115.1 (2)
C3—C4—H4B108.3N4—C11—Cl1114.7 (2)
C5—C4—H4B108.3
C8—N2—N3—C1178.5 (2)C6—N1—C7—N2179.7 (2)
C7—N2—N3—C1−0.2 (3)C8—N2—C7—O12.1 (5)
N2—N3—C1—N1−0.3 (3)N3—N2—C7—O1−179.3 (3)
N2—N3—C1—C2−179.5 (3)C8—N2—C7—N1−177.9 (3)
C7—N1—C1—N30.8 (3)N3—N2—C7—N10.7 (3)
C6—N1—C1—N3−179.7 (3)C11—N4—C8—N2179.0 (2)
C7—N1—C1—C2179.9 (3)C11—N4—C8—C90.0 (4)
C6—N1—C1—C2−0.6 (4)N3—N2—C8—N43.9 (4)
N3—C1—C2—C3120.7 (3)C7—N2—C8—N4−177.6 (2)
N1—C1—C2—C3−58.3 (4)N3—N2—C8—C9−177.1 (2)
C1—C2—C3—C475.0 (4)C7—N2—C8—C91.4 (4)
C2—C3—C4—C5−65.9 (4)N4—C8—C9—C10−0.6 (4)
C3—C4—C5—C666.4 (4)N2—C8—C9—C10−179.6 (3)
C7—N1—C6—C5−122.9 (3)C11—N5—C10—C9−1.2 (5)
C1—N1—C6—C557.7 (4)C8—C9—C10—N51.3 (5)
C4—C5—C6—N1−73.1 (4)C10—N5—C11—N40.4 (5)
C1—N1—C7—O1179.1 (3)C10—N5—C11—Cl1−179.2 (2)
C6—N1—C7—O1−0.4 (5)C8—N4—C11—N50.1 (5)
C1—N1—C7—N2−0.8 (3)C8—N4—C11—Cl1179.8 (2)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2624).

References

  • Bruker (1999). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Condon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Protection Conference on Weeds, pp. 41–46. Alton, Hampshire, England: BCPC Publications.
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
  • Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman.
  • Maeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415–422. Alton, Hampshire, England: BCPC Publications.
  • Selby, T. P., Drumm, J. E., Coats, R. A., Coppo, F. T., Gee, S. K., Hay, J. V., Pasteris, R. J. & Stevenson, T. M. (2002). ACS Symposium Series, Vol. 800, Synthesis and Chemistry of Agrochemicals VI, pp. 74–84. Washington DC: American Chemical Society.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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