1-Dichloro­acetyl-8a-methyl-1,2,3,4,6,7,8,8a-octa­hydro­pyrrolo­[1,2-a]pyrimidin-6-one

Gao, S.; Zhao, L.; Ye, F.; Fu, Y.; Xing, Z.

doi:10.1107/S1600536812024063

organic compounds

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ISSN: 2056-9890

Volume 68| Part 7| July 2012| Page o1982

https://doi.org/10.1107/S1600536812024063

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1-Dichloroacetyl-8a-methyl-1,2,3,4,6,7,8,8a-octahydropyrrolo[1,2-a]pyrimidin-6-one

Shuang Gao,^a Li-xia Zhao,^a Fei Ye,^a Ying Fu ^a ^* and Zhi-yong Xing ^a

^aCollege of Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
^*Correspondence e-mail: fuying@neau.edu.cn

(Received 26 April 2012; accepted 26 May 2012; online 2 June 2012)

In the title compound, C₁₀H₁₄Cl₂N₂O₂, the five-membered ring adopts an envelope conformation (with the methylene C atom closest to the C—N bridge as the flap), while the conformation of the six-membered ring is close to a twist-boat. In the crystal, molecules are linked by weak C—H⋯O hydrogen bonds, forming chains along the c-axis direction.

Related literature

For general background to 1,5-diazabicyclo compounds, see: Fuerst & Lamoureux (1992 ); Hutton & Bartlett (2007 ); Koptelov et al. (2011 ); Loriga et al. (2007 ); Moreland et al. (1993 ); Taylor et al. (2010 ). For details of the synthesis, see: Sun & Ye (2010 ); Rohr et al. (1984 ,1986 ). For applications of N-dichloroacetyl-1,5-diazabicyclo compounds, see: Lamoureux & Rusness (1992 ); Hatzios & Burgos (2004 ).

Experimental

Crystal data

C₁₀H₁₄Cl₂N₂O₂
M_r = 265.13
Orthorhombic, P b c a
a = 10.312 (2) Å
b = 14.997 (3) Å
c = 15.666 (3) Å
V = 2422.7 (8) Å³
Z = 8
Mo Kα radiation
μ = 0.52 mm⁻¹
T = 293 K
0.23 × 0.19 × 0.16 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.889, T_max = 0.922
22128 measured reflections
2770 independent reflections
2376 reflections with I > 2σ(I)
R_int = 0.038

Refinement

R[F² > 2σ(F²)] = 0.052
wR(F²) = 0.156
S = 1.11
2770 reflections
146 parameters
H-atom parameters constrained
Δρ_max = 0.74 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1⋯O2ⁱ	0.98	2.15	3.115 (2)	168
C3—H3B⋯O2ⁱ	0.97	2.55	3.502 (3)	169
Symmetry code: (i) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: RAPID-AUTO (Rigaku, 1999 ); cell refinement: RAPID-AUTO; data reduction: CrystalClear (Rigaku/MSC, 2002 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536812024063/yk2055sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812024063/yk2055Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812024063/yk2055Isup3.cml

checkCIF report

Comment top

Diazabicyclo derivatives are extremely important synthetic intermediates in the syntheses of compounds with potential high biological activity (Fuerst & Lamoureux, 1992; Loriga et al., 2007; Hutton & Bartlett, 2007; Taylor et al., 2010). N-dichloroacetyl-1,5-diazabicyclo compounds have been investigated for usage as herbicide safeners which protect crops from the injury by herbicides (Lamoureux & Rusness, 1992; Hatzios & Burgos, 2004). As a part of our ongoing investigation on the diazabicyclo derivatives we have determined the crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. In the crystal, molecules are linked by weak intermolecular C—H···O hydrogen bonds, forming chains along the c direction (Fig. 2).

Related literature top

For general background to 1,5-diazabicyclo compounds, see: Fuerst & Lamoureux (1992); Hutton & Bartlett (2007); Koptelov et al. (2011); Loriga et al. (2007); Moreland et al. (1993); Taylor et al. (2010). For details of the synthesis, see: Sun & Ye (2010); Rohr et al. (1984,1986). For applications of N-dichloroacetyl-1,5-diazabicyclo compounds, see: Lamoureux & Rusness (1992); Hatzios & Burgos (2004).

Experimental top

The title compound was prepared according to the literature procedure (Sun & Ye, 2010). The single crystal suitable for X-ray structural analysis was obtained by slow evaporation of a solution in the mixture of petroleum ether and ethyl acetate at room temperature.

Structure description top

For general background to 1,5-diazabicyclo compounds, see: Fuerst & Lamoureux (1992); Hutton & Bartlett (2007); Koptelov et al. (2011); Loriga et al. (2007); Moreland et al. (1993); Taylor et al. (2010). For details of the synthesis, see: Sun & Ye (2010); Rohr et al. (1984,1986). For applications of N-dichloroacetyl-1,5-diazabicyclo compounds, see: Lamoureux & Rusness (1992); Hatzios & Burgos (2004).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1999); cell refinement: RAPID-AUTO (Rigaku, 1999); data reduction: CrystalClear (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A partial packing view showing hydrogen bonds.

1-Dichloroacetyl-8a-methyl-1,2,3,4,6,7,8,8a- octahydropyrrolo[1,2-a]pyrimidin-6-one top

Crystal data top

C₁₀H₁₄Cl₂N₂O₂	F(000) = 1104
M_r = 265.13	D_x = 1.454 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 9134 reflections
a = 10.312 (2) Å	θ = 3.2–27.6°
b = 14.997 (3) Å	µ = 0.52 mm⁻¹
c = 15.666 (3) Å	T = 293 K
V = 2422.7 (8) Å³	Block, colourless
Z = 8	0.23 × 0.19 × 0.16 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2770 independent reflections
Radiation source: fine-focus sealed tube	2376 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.038
Detector resolution: 10 pixels mm^-1	θ_max = 27.5°, θ_min = 3.0°
ω scan	h = −13→11
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −19→19
T_min = 0.889, T_max = 0.922	l = −20→20
22128 measured reflections

Refinement top

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.156	H-atom parameters constrained
S = 1.11	w = 1/[σ²(F_o²) + (0.097P)² + 0.5072P] where P = (F_o² + 2F_c²)/3
2770 reflections	(Δ/σ)_max = 0.001
146 parameters	Δρ_max = 0.74 e Å⁻³
0 restraints	Δρ_min = −0.36 e Å⁻³

Crystal data top

C₁₀H₁₄Cl₂N₂O₂	V = 2422.7 (8) Å³
M_r = 265.13	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 10.312 (2) Å	µ = 0.52 mm⁻¹
b = 14.997 (3) Å	T = 293 K
c = 15.666 (3) Å	0.23 × 0.19 × 0.16 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2770 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	2376 reflections with I > 2σ(I)
T_min = 0.889, T_max = 0.922	R_int = 0.038
22128 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	0 restraints
wR(F²) = 0.156	H-atom parameters constrained
S = 1.11	Δρ_max = 0.74 e Å⁻³
2770 reflections	Δρ_min = −0.36 e Å⁻³
146 parameters

Special details top

Geometry. All s.u.'s (except the s.u.'s in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s 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.

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

	x	y	z	U_iso*/U_eq
C1	0.44507 (19)	0.93130 (12)	0.76600 (12)	0.0425 (4)
H1	0.4067	0.8855	0.7293	0.051*
C2	0.36708 (16)	0.93818 (10)	0.84965 (10)	0.0356 (3)
C3	0.3554 (3)	0.77230 (13)	0.84857 (16)	0.0717 (8)
H3A	0.4348	0.7471	0.8712	0.086*
H3B	0.3654	0.7784	0.7873	0.086*
C4	0.2472 (4)	0.71165 (18)	0.86658 (17)	0.0951 (11)
H4A	0.2620	0.6552	0.8380	0.114*
H4B	0.1675	0.7370	0.8444	0.114*
C5	0.2331 (3)	0.69585 (16)	0.96139 (15)	0.0778 (8)
H5A	0.1427	0.6854	0.9753	0.093*
H5B	0.2824	0.6435	0.9779	0.093*
C6	0.27314 (17)	0.86362 (11)	0.97259 (10)	0.0388 (4)
C7	0.1334 (2)	0.89612 (19)	0.96606 (15)	0.0643 (6)
H7A	0.0849	0.8564	0.9301	0.096*
H7B	0.1321	0.9550	0.9420	0.096*
H7C	0.0951	0.8974	1.0219	0.096*
C8	0.3550 (2)	0.91831 (13)	1.03659 (11)	0.0490 (5)
H8A	0.4403	0.9306	1.0133	0.059*
H8B	0.3128	0.9745	1.0497	0.059*
C9	0.3655 (2)	0.86100 (14)	1.11572 (12)	0.0512 (5)
H9A	0.4529	0.8626	1.1385	0.061*
H9B	0.3057	0.8813	1.1594	0.061*
C10	0.33128 (18)	0.76904 (13)	1.08684 (12)	0.0460 (4)
Cl1	0.60562 (5)	0.89949 (5)	0.79454 (4)	0.0661 (2)
Cl2	0.44643 (7)	1.03447 (4)	0.71183 (3)	0.0634 (2)
N1	0.33425 (15)	0.86043 (9)	0.88631 (9)	0.0376 (3)
N2	0.28063 (18)	0.77378 (10)	1.00813 (10)	0.0495 (4)
O1	0.34367 (15)	1.01088 (8)	0.88014 (9)	0.0493 (4)
O2	0.34379 (18)	0.69963 (12)	1.12676 (10)	0.0677 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0509 (10)	0.0420 (9)	0.0347 (8)	−0.0063 (7)	−0.0010 (7)	−0.0023 (7)
C2	0.0419 (8)	0.0325 (8)	0.0325 (8)	−0.0003 (6)	−0.0051 (6)	−0.0013 (6)
C3	0.133 (2)	0.0307 (9)	0.0519 (12)	−0.0056 (11)	0.0152 (13)	−0.0057 (8)
C4	0.177 (3)	0.0556 (14)	0.0523 (14)	−0.0532 (18)	−0.0047 (16)	−0.0051 (10)
C5	0.132 (2)	0.0500 (12)	0.0517 (13)	−0.0423 (14)	−0.0074 (13)	0.0063 (10)
C6	0.0463 (9)	0.0384 (8)	0.0318 (8)	−0.0040 (7)	−0.0051 (6)	0.0021 (6)
C7	0.0486 (11)	0.0909 (17)	0.0534 (12)	0.0083 (11)	0.0025 (9)	0.0066 (11)
C8	0.0672 (12)	0.0430 (9)	0.0367 (9)	−0.0096 (8)	−0.0075 (8)	−0.0038 (7)
C9	0.0591 (11)	0.0615 (12)	0.0330 (9)	−0.0038 (9)	−0.0070 (8)	−0.0004 (8)
C10	0.0472 (9)	0.0549 (11)	0.0359 (9)	0.0012 (8)	0.0030 (7)	0.0098 (8)
Cl1	0.0494 (3)	0.0859 (5)	0.0629 (4)	0.0085 (3)	0.0054 (2)	−0.0065 (3)
Cl2	0.0924 (5)	0.0559 (4)	0.0419 (3)	−0.0146 (3)	0.0005 (2)	0.0120 (2)
N1	0.0490 (8)	0.0311 (7)	0.0328 (7)	−0.0019 (5)	−0.0022 (6)	−0.0014 (5)
N2	0.0691 (10)	0.0393 (8)	0.0400 (8)	−0.0153 (7)	−0.0084 (7)	0.0076 (6)
O1	0.0724 (9)	0.0308 (6)	0.0448 (7)	0.0038 (6)	0.0064 (6)	−0.0010 (5)
O2	0.0858 (11)	0.0644 (10)	0.0528 (9)	0.0071 (8)	0.0007 (8)	0.0255 (7)

Geometric parameters (Å, º) top

C1—C2	1.541 (2)	C6—N2	1.460 (2)
C1—Cl2	1.7647 (19)	C6—N1	1.492 (2)
C1—Cl1	1.780 (2)	C6—C7	1.525 (3)
C1—H1	0.9800	C6—C8	1.546 (2)
C2—O1	1.214 (2)	C7—H7A	0.9600
C2—N1	1.343 (2)	C7—H7B	0.9600
C3—N1	1.464 (2)	C7—H7C	0.9600
C3—C4	1.467 (4)	C8—C9	1.512 (3)
C3—H3A	0.9700	C8—H8A	0.9700
C3—H3B	0.9700	C8—H8B	0.9700
C4—C5	1.511 (4)	C9—C10	1.494 (3)
C4—H4A	0.9700	C9—H9A	0.9700
C4—H4B	0.9700	C9—H9B	0.9700
C5—N2	1.464 (3)	C10—O2	1.221 (2)
C5—H5A	0.9700	C10—N2	1.341 (2)
C5—H5B	0.9700

C2—C1—Cl2	110.76 (12)	N2—C6—C8	102.31 (13)
C2—C1—Cl1	106.84 (12)	N1—C6—C8	111.95 (15)
Cl2—C1—Cl1	110.39 (10)	C7—C6—C8	112.96 (17)
C2—C1—H1	109.6	C6—C7—H7A	109.5
Cl2—C1—H1	109.6	C6—C7—H7B	109.5
Cl1—C1—H1	109.6	H7A—C7—H7B	109.5
O1—C2—N1	124.12 (16)	C6—C7—H7C	109.5
O1—C2—C1	119.90 (15)	H7A—C7—H7C	109.5
N1—C2—C1	115.91 (14)	H7B—C7—H7C	109.5
N1—C3—C4	111.7 (2)	C9—C8—C6	105.61 (15)
N1—C3—H3A	109.3	C9—C8—H8A	110.6
C4—C3—H3A	109.3	C6—C8—H8A	110.6
N1—C3—H3B	109.3	C9—C8—H8B	110.6
C4—C3—H3B	109.3	C6—C8—H8B	110.6
H3A—C3—H3B	107.9	H8A—C8—H8B	108.7
C3—C4—C5	111.1 (2)	C10—C9—C8	105.05 (15)
C3—C4—H4A	109.4	C10—C9—H9A	110.7
C5—C4—H4A	109.4	C8—C9—H9A	110.7
C3—C4—H4B	109.4	C10—C9—H9B	110.7
C5—C4—H4B	109.4	C8—C9—H9B	110.7
H4A—C4—H4B	108.0	H9A—C9—H9B	108.8
N2—C5—C4	109.54 (17)	O2—C10—N2	123.87 (19)
N2—C5—H5A	109.8	O2—C10—C9	127.37 (19)
C4—C5—H5A	109.8	N2—C10—C9	108.75 (15)
N2—C5—H5B	109.8	C2—N1—C3	125.00 (15)
C4—C5—H5B	109.8	C2—N1—C6	117.77 (13)
H5A—C5—H5B	108.2	C3—N1—C6	117.23 (14)
N2—C6—N1	107.07 (14)	C10—N2—C6	114.85 (15)
N2—C6—C7	111.75 (17)	C10—N2—C5	123.23 (16)
N1—C6—C7	110.41 (14)	C6—N2—C5	121.90 (16)

Cl2—C1—C2—O1	−17.6 (2)	N2—C6—N1—C2	−164.27 (15)
Cl1—C1—C2—O1	102.68 (17)	C7—C6—N1—C2	73.9 (2)
Cl2—C1—C2—N1	165.39 (13)	C8—C6—N1—C2	−52.9 (2)
Cl1—C1—C2—N1	−74.34 (16)	N2—C6—N1—C3	15.0 (2)
N1—C3—C4—C5	−62.4 (4)	C7—C6—N1—C3	−106.9 (2)
C3—C4—C5—N2	28.4 (4)	C8—C6—N1—C3	126.3 (2)
N2—C6—C8—C9	−17.3 (2)	O2—C10—N2—C6	179.24 (19)
N1—C6—C8—C9	−131.65 (17)	C9—C10—N2—C6	0.3 (2)
C7—C6—C8—C9	103.0 (2)	O2—C10—N2—C5	0.7 (3)
C6—C8—C9—C10	17.9 (2)	C9—C10—N2—C5	−178.2 (2)
C8—C9—C10—O2	169.3 (2)	N1—C6—N2—C10	128.79 (17)
C8—C9—C10—N2	−11.8 (2)	C7—C6—N2—C10	−110.2 (2)
O1—C2—N1—C3	176.6 (2)	C8—C6—N2—C10	10.9 (2)
C1—C2—N1—C3	−6.5 (3)	N1—C6—N2—C5	−52.6 (3)
O1—C2—N1—C6	−4.3 (3)	C7—C6—N2—C5	68.4 (3)
C1—C2—N1—C6	172.63 (14)	C8—C6—N2—C5	−170.5 (2)
C4—C3—N1—C2	−142.1 (2)	C4—C5—N2—C10	−151.3 (3)
C4—C3—N1—C6	38.8 (3)	C4—C5—N2—C6	30.2 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O2ⁱ	0.98	2.15	3.115 (2)	168
C3—H3B···O2ⁱ	0.97	2.55	3.502 (3)	169

Symmetry code: (i) x, −y+3/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₄Cl₂N₂O₂
M_r	265.13
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	10.312 (2), 14.997 (3), 15.666 (3)
V (Å³)	2422.7 (8)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.52
Crystal size (mm)	0.23 × 0.19 × 0.16

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.889, 0.922
No. of measured, independent and observed [I > 2σ(I)] reflections	22128, 2770, 2376
R_int	0.038
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.052, 0.156, 1.11
No. of reflections	2770
No. of parameters	146
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.74, −0.36

Computer programs: RAPID-AUTO (Rigaku, 1999), CrystalClear (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O2ⁱ	0.98	2.15	3.115 (2)	167.5
C3—H3B···O2ⁱ	0.97	2.55	3.502 (3)	168.7

Symmetry code: (i) x, −y+3/2, z−1/2.

Acknowledgements

We thank the National Natural Science Foundation of China (No. 31101473), the China Postdoctoral Science Foundation funded project (2011M500634), the Heilongjiang Province Foundation for Young Scholars (QC2009C44), the Research Science Foundation in Technology Innovation of Harbin (2010RFQYN108) and the Northeast Agricultural University Doctoral Foundation for generously supporting this study.

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Volume 68| Part 7| July 2012| Page o1982

https://doi.org/10.1107/S1600536812024063

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

1-Di­chloro­acetyl-8a-methyl-1,2,3,4,6,7,8,8a-octa­hydro­pyrrolo­[1,2-a]pyrimidin-6-one

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

1-Dichloroacetyl-8a-methyl-1,2,3,4,6,7,8,8a-octahydropyrrolo[1,2-a]pyrimidin-6-one