1 [4 (4 Methyl­pyrimidin 2 yl)piperazin 1 ylmeth­yl] 1H benzotriazole

organic papers

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16H19N7 doi:10.1107/S1600536805022208 Acta Cryst.(2005). E61, o2602–o2604

Acta Crystallographica Section E Structure Reports

Online

ISSN 1600-5368

1-[4-(4-Methylpyrimidin-2-yl)piperazin-1-yl-methyl]-1

H

-benzotriazole

Feng-Qi He, Bao-Lei Wang, Zheng-Ming Li* and

Hai-Bin Song

State Key Laboratory Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, People’s Republic of China

Correspondence e-mail: hefengqi@mail.nankai.edu.cn

Key indicators

Single-crystal X-ray study

T= 294 K

Mean(C–C) = 0.004 A˚

Rfactor = 0.048

wRfactor = 0.135

Data-to-parameter ratio = 14.9

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2005 International Union of Crystallography

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The title compound, C16H19N7, is a potent new herbicide.

X-ray analysis reveals that the piperazine ring adopts a chair conformation and weak C—H N hydrogen bonds link the molecules into a chain along theaaxis.

Comment

Based on the reported 1.65 A˚ high-resolution crystal structure of spinach KARI (ketol-acid reductoisomerase) complex (Biou et al., 1997), we obtained 279 molecules with low binding energy toward KARI from MDL/ACD three-dimen-sional database searching, using the program DOCK 4.0 (Wang et al., 2004). These potential structures provide infor-mation for further design of new targeted KARI herbicidal molecules. According to the structural information and bioactivity data of benzotriazole, one of the 279 molecules provided by MDL/ACD three-dimensional database searching, a series of benzotriazole derivatives has been designed and synthesized. The X-ray crystal structure deter-mination of the title compound, (I), was undertaken to investigate the relationship between structure and herbicidal activity.

The molecular structure of (I) is shown in Fig. 1. The X-ray analysis reveals that the piperazine ring is in a chair confor-mation. The C12—N5 distance of 1.370 (2) A˚ is shorter than the normal C—N single-bond distance of 1.47 A˚ (Carey, 2000), which shows that C12—N5 is conjugated with the pyrimidine ring. The molecules translated one unit cell along the a-axis direction are linked by weak C—H N hydrogen-bonding interactions to form a chain (Fig. 2 and Table 2).

Experimental

Compound (I) was prepared according to the reported procedure of Bachman & Heisey (1946), using benzotriazole (0.01 mol), 4-methyl-2-(piperazin-1-yl)pyrimidine (0.11 mol) (Xu et al., 1993), 40% formalin (0.012 mol) and methanol (15 ml) (2.47 g, 80% yield). Colourless single crystals suitable for X-ray diffraction analysis were obtained by recrystallization from ethanol.

Crystal data

C16H19N7

Mr= 309.38

Triclinic,P1

a= 6.5207 (17) A˚

b= 9.2488 (16) A˚

c= 13.429 (4) A˚

= 102.108 (8)

= 94.112 (7)

= 101.504 (8)

V= 770.5 (3) A˚3

Z= 2

Dx= 1.334 Mg m 3

MoKradiation Cell parameters from 1635

reflections

= 2.3–26.2

= 0.09 mm1

T= 294 (2) K Prism, colourless 0.260.240.20 mm

Data collection

Bruker SMART CCD area-detector diffractometer

’and!scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1996)

Tmin= 0.972,Tmax= 0.983

4365 measured reflections

3104 independent reflections 2102 reflections withI> 2(I)

Rint= 0.018

max= 26.5

h=8!8

k=11!11

l=16!7

Refinement

Refinement onF2

R[F2_{> 2(F}2_{)] = 0.048}

wR(F2_{) = 0.135}

S= 1.02 3104 reflections 209 parameters

H-atom parameters constrained

w= 1/[2_(F

o2) + (0.0614P)2

+ 0.1903P]

whereP= (Fo2+ 2Fc2)/3

(/)max= 0.001

max= 0.34 e A˚ 3

min=0.18 e A˚ 3

Table 1

Selected geometric parameters (A˚ ,_).

N1—N2 1.352 (2) N1—C1 1.360 (2) N1—C7 1.473 (2) N2—N3 1.298 (3) N3—C2 1.365 (3) N4—C7 1.430 (2) N4—C8 1.457 (2) N4—C11 1.457 (2)

N5—C12 1.370 (2) N5—C9 1.451 (2) N5—C10 1.452 (2) N6—C12 1.337 (2) N6—C13 1.352 (3) N7—C15 1.330 (3) N7—C12 1.336 (3) N4—C7—N1 115.55 (15)

N7—C12—N6 126.34 (19) N7—C12—N5 117.49 (17)

N6—C13—C16 115.8 (2) C14—C13—C16 123.0 (2)

Table 2

Hydrogen-bond geometry (A˚ ,_).

D—H A D—H H A D A D—H A

C6—H6 N3i

0.93 2.50 3.430 (3) 176 C9—H9A N7 0.97 2.34 2.746 (3) 105 C10—H10B N6 0.97 2.33 2.744 (3) 105

Symmetry code: (i)xþ1;y;z.

H atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H distances of 0.93 (aromatic), 0.97 (methylene) or 0.97 A˚ (methyl), and with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C).

Data collection:SMART(Bruker, 1998); cell refinement:SAINT (Bruker, 1999); data reduction:SAINT; program(s) used to solve structure:SHELXS97(Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1999); software used to prepare material for publication:SHELXTL.

This project was supported by the Major State Basic Research Development Program of China (973 Program) (grant No. 2003CB114406).

organic papers

Acta Cryst.(2005). E61, o2602–o2604 Heet al. _C

16H19N7

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Figure 1

The molecular structure of (I), showing displacement ellipsoids drawn at the 30% probability level.

Figure 2

References

Bachman, G. B. & Heisey, L. V. (1946).J. Am. Chem. Soc.68, 2496–2499. Biou, V., Dumas, R. & Cohen-Addad, C. (1997).EMBO J.16, 3405–3415. Bruker (1998).SMART. Bruker AXS Inc., Madison, Wisconsin, USA. Bruker (1999). SAINT and SHELXTL. Bruker AXS Inc., Madison,

Wisconsin, USA.

Carey, F. A. (2000).Organic Chemistry, 4th ed. p. 861. New York: McGraw– Hill.

Sheldrick, G. M. (1996).SADABS. University of Go¨ttingen, Germany. Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of

Go¨ttingen, Germany.

Wang, B.-L., Li, Z.-M. & Ma, Y., Wang, J.-G., Luo, X.-M. & Zuo, Z.-L. (2004).

Chin. J. Org. Chem.24, 973–976. (In Chinese.)

Xu, Y., Zhu, Z.-H. & Tong, Z.-J. (1993). Chin. J. Pharm. 24, 49–51. (In Chinese.)

organic papers

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supporting information

sup-1 Acta Cryst. (2005). E61, o2602–o2604

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Acta Cryst. (2005). E61, o2602–o2604 [https://doi.org/10.1107/S1600536805022208]

1-[4-(4-Methylpyrimidin-2-yl)piperazin-1-ylmethyl]-1

H

-benzotriazole

Feng-Qi He, Bao-Lei Wang, Zheng-Ming Li and Hai-Bin Song

1-[4-(4-Methylpyrimidin-2-yl)piperazin-1-ylmethyl]-1H-benzotriazole

Crystal data

C16H19N7 Mr = 309.38 Triclinic, P1 Hall symbol: -P 1

a = 6.5207 (17) Å

b = 9.2488 (16) Å

c = 13.429 (4) Å

α = 102.108 (8)°

β = 94.112 (7)°

γ = 101.504 (8)°

V = 770.5 (3) Å3

Z = 2

F(000) = 328

Dx = 1.334 Mg m−3

Mo Kα radiation, λ = 0.71073 Å Cell parameters from 1635 reflections

θ = 2.3–26.2°

µ = 0.09 mm−1 T = 294 K Prism, colourless 0.26 × 0.24 × 0.20 mm

Data collection

Bruker SMART CCD area-detector diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

φ and ω scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1996)

Tmin = 0.972, Tmax = 0.983

4365 measured reflections 3104 independent reflections 2102 reflections with I > 2σ(I)

Rint = 0.018

θmax = 26.5°, θmin = 2.3° h = −8→8

k = −11→11

l = −16→7

Refinement

Refinement on F2 Least-squares matrix: full

R[F2 _{> 2σ(F}2_{)] = 0.048} wR(F2_{) = 0.135} S = 1.02 3104 reflections 209 parameters 0 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H-atom parameters constrained

w = 1/[σ2_(F

o2) + (0.0614P)2 + 0.1903P] where P = (Fo2 + 2Fc2)/3

(Δ/σ)max = 0.001 Δρmax = 0.34 e Å−3 Δρmin = −0.18 e Å−3

Special details

supporting information

sup-2 Acta Cryst. (2005). E61, o2602–o2604

Refinement. Refinement of F2 _{against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F}2_, conventional R-factors R are based on F, with F set to zero for negative F2_{. The threshold expression of F}2 _{> σ(F}2_{) 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₎

x y z Uiso*/Ueq

N1 0.0256 (2) 0.16368 (18) 0.08980 (12) 0.0448 (4)

N2 −0.1810 (3) 0.1463 (2) 0.10249 (14) 0.0596 (5)

N3 −0.2741 (3) 0.2019 (2) 0.03535 (14) 0.0624 (5)

N4 0.2611 (2) 0.23005 (17) 0.25140 (11) 0.0396 (4)

N5 0.3795 (3) 0.51160 (17) 0.39374 (11) 0.0416 (4)

N6 0.4797 (3) 0.74315 (18) 0.35356 (12) 0.0488 (4)

N7 0.1601 (3) 0.6799 (2) 0.42649 (14) 0.0583 (5)

C1 0.0669 (3) 0.2329 (2) 0.01128 (13) 0.0409 (4)

C2 −0.1273 (3) 0.2571 (2) −0.02272 (14) 0.0465 (5)

C3 −0.1475 (4) 0.3256 (3) −0.10485 (16) 0.0598 (6)

H3 −0.2763 0.3430 −0.1280 0.072*

C4 0.0276 (4) 0.3657 (3) −0.14938 (18) 0.0676 (7)

H4 0.0191 0.4120 −0.2042 0.081*

C5 0.2217 (4) 0.3394 (3) −0.11507 (18) 0.0683 (7)

H5 0.3382 0.3682 −0.1483 0.082*

C6 0.2461 (3) 0.2730 (3) −0.03465 (16) 0.0544 (6)

H6 0.3754 0.2559 −0.0121 0.065*

C7 0.1670 (3) 0.1167 (2) 0.16130 (14) 0.0475 (5)

H7A 0.0879 0.0298 0.1823 0.057*

H7B 0.2787 0.0838 0.1247 0.057*

C8 0.1087 (3) 0.2894 (2) 0.31321 (14) 0.0426 (5)

H8A 0.0066 0.2060 0.3266 0.051*

H8B 0.0338 0.3461 0.2759 0.051*

C9 0.2186 (3) 0.3908 (2) 0.41291 (14) 0.0444 (5)

H9A 0.1170 0.4339 0.4520 0.053*

H9B 0.2829 0.3321 0.4529 0.053*

C10 0.5331 (3) 0.4520 (2) 0.33370 (14) 0.0440 (5)

H10A 0.6055 0.3946 0.3714 0.053*

H10B 0.6370 0.5350 0.3211 0.053*

C11 0.4240 (3) 0.3514 (2) 0.23333 (14) 0.0428 (5)

H11A 0.3610 0.4109 0.1934 0.051*

H11B 0.5260 0.3084 0.1946 0.051*

C12 0.3364 (3) 0.6498 (2) 0.39045 (13) 0.0424 (5)

C13 0.4403 (4) 0.8812 (2) 0.35349 (16) 0.0536 (5)

C14 0.2630 (4) 0.9204 (3) 0.38875 (19) 0.0661 (7)

H14 0.2360 1.0154 0.3885 0.079*

C15 0.1277 (4) 0.8168 (3) 0.42415 (19) 0.0696 (7)

H15 0.0064 0.8426 0.4480 0.084*

C16 0.5980 (4) 0.9835 (3) 0.3114 (2) 0.0813 (8)

supporting information

sup-3 Acta Cryst. (2005). E61, o2602–o2604

H16B 0.5962 1.0870 0.3415 0.122*

H16C 0.5645 0.9641 0.2384 0.122*

Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

N1 0.0422 (10) 0.0491 (10) 0.0396 (9) 0.0098 (7) 0.0015 (7) 0.0037 (7)

N2 0.0438 (11) 0.0734 (13) 0.0550 (11) 0.0049 (9) 0.0067 (8) 0.0078 (9)

N3 0.0420 (10) 0.0844 (14) 0.0569 (11) 0.0155 (10) 0.0020 (9) 0.0074 (10)

N4 0.0451 (9) 0.0355 (8) 0.0368 (8) 0.0081 (7) 0.0034 (7) 0.0062 (6)

N5 0.0502 (10) 0.0346 (8) 0.0389 (8) 0.0060 (7) 0.0082 (7) 0.0086 (7)

N6 0.0522 (10) 0.0437 (10) 0.0498 (9) 0.0036 (8) 0.0033 (8) 0.0163 (8)

N7 0.0666 (13) 0.0545 (11) 0.0616 (11) 0.0218 (10) 0.0229 (9) 0.0174 (9)

C1 0.0408 (11) 0.0429 (10) 0.0352 (9) 0.0118 (8) −0.0011 (8) 0.0002 (8)

C2 0.0396 (11) 0.0534 (12) 0.0410 (10) 0.0140 (9) −0.0019 (8) −0.0027 (9)

C3 0.0562 (14) 0.0708 (15) 0.0522 (12) 0.0268 (12) −0.0096 (11) 0.0070 (11) C4 0.0748 (17) 0.0808 (17) 0.0534 (13) 0.0237 (14) −0.0017 (12) 0.0260 (12)

C5 0.0585 (15) 0.0934 (19) 0.0591 (14) 0.0152 (13) 0.0109 (11) 0.0310 (13)

C6 0.0411 (12) 0.0763 (15) 0.0499 (12) 0.0193 (11) 0.0057 (9) 0.0172 (11)

C7 0.0584 (13) 0.0406 (11) 0.0415 (10) 0.0133 (10) 0.0002 (9) 0.0047 (8)

C8 0.0461 (11) 0.0390 (10) 0.0420 (10) 0.0050 (9) 0.0086 (8) 0.0111 (8)

C9 0.0550 (12) 0.0391 (10) 0.0396 (10) 0.0066 (9) 0.0145 (9) 0.0106 (8)

C10 0.0417 (11) 0.0439 (11) 0.0453 (10) 0.0065 (9) 0.0046 (8) 0.0109 (9)

C11 0.0447 (11) 0.0468 (11) 0.0395 (10) 0.0130 (9) 0.0107 (8) 0.0106 (8)

C12 0.0524 (12) 0.0406 (11) 0.0313 (9) 0.0044 (9) 0.0008 (8) 0.0085 (8)

C13 0.0617 (14) 0.0448 (12) 0.0513 (12) 0.0029 (10) −0.0011 (10) 0.0156 (10) C14 0.0810 (18) 0.0520 (14) 0.0736 (16) 0.0243 (13) 0.0162 (13) 0.0211 (12) C15 0.0791 (17) 0.0641 (16) 0.0769 (16) 0.0316 (14) 0.0271 (14) 0.0198 (13)

C16 0.0808 (19) 0.0605 (16) 0.110 (2) 0.0069 (14) 0.0187 (16) 0.0424 (16)

Geometric parameters (Å, º)

N1—N2 1.352 (2) C5—H5 0.93

N1—C1 1.360 (2) C6—H6 0.93

N1—C7 1.473 (2) C7—H7A 0.97

N2—N3 1.298 (3) C7—H7B 0.97

N3—C2 1.365 (3) C8—C9 1.501 (3)

N4—C7 1.430 (2) C8—H8A 0.97

N4—C8 1.457 (2) C8—H8B 0.97

N4—C11 1.457 (2) C9—H9A 0.97

N5—C12 1.370 (2) C9—H9B 0.97

N5—C9 1.451 (2) C10—C11 1.504 (3)

N5—C10 1.452 (2) C10—H10A 0.97

N6—C12 1.337 (2) C10—H10B 0.97

N6—C13 1.352 (3) C11—H11A 0.97

N7—C15 1.330 (3) C11—H11B 0.97

N7—C12 1.336 (3) C13—C14 1.366 (3)

supporting information

sup-4 Acta Cryst. (2005). E61, o2602–o2604

C1—C2 1.391 (3) C14—C15 1.356 (3)

C2—C3 1.393 (3) C14—H14 0.93

C3—C4 1.349 (3) C15—H15 0.93

C3—H3 0.93 C16—H16A 0.96

C4—C5 1.400 (3) C16—H16B 0.96

C4—H4 0.93 C16—H16C 0.96

C5—C6 1.364 (3)

N2—N1—C1 109.99 (16) N4—C8—H8B 109.6

N2—N1—C7 119.05 (16) C9—C8—H8B 109.6

C1—N1—C7 130.86 (16) H8A—C8—H8B 108.1

N3—N2—N1 109.01 (17) N5—C9—C8 110.09 (14)

N2—N3—C2 108.31 (17) N5—C9—H9A 109.6

C7—N4—C8 113.74 (15) C8—C9—H9A 109.6

C7—N4—C11 114.47 (15) N5—C9—H9B 109.6

C8—N4—C11 111.63 (14) C8—C9—H9B 109.6

C12—N5—C9 120.77 (16) H9A—C9—H9B 108.2

C12—N5—C10 121.44 (15) N5—C10—C11 109.74 (15)

C9—N5—C10 111.52 (15) N5—C10—H10A 109.7

C12—N6—C13 116.02 (18) C11—C10—H10A 109.7

C15—N7—C12 115.34 (19) N5—C10—H10B 109.7

N1—C1—C6 133.72 (18) C11—C10—H10B 109.7

N1—C1—C2 103.99 (17) H10A—C10—H10B 108.2

C6—C1—C2 122.27 (18) N4—C11—C10 110.20 (14)

N3—C2—C1 108.69 (18) N4—C11—H11A 109.6

N3—C2—C3 130.69 (19) C10—C11—H11A 109.6

C1—C2—C3 120.61 (19) N4—C11—H11B 109.6

C4—C3—C2 117.2 (2) C10—C11—H11B 109.6

C4—C3—H3 121.4 H11A—C11—H11B 108.1

C2—C3—H3 121.4 N7—C12—N6 126.34 (19)

C3—C4—C5 121.6 (2) N7—C12—N5 117.49 (17)

C3—C4—H4 119.2 N6—C12—N5 116.15 (18)

C5—C4—H4 119.2 N6—C13—C14 121.1 (2)

C6—C5—C4 122.4 (2) N6—C13—C16 115.8 (2)

C6—C5—H5 118.8 C14—C13—C16 123.0 (2)

C4—C5—H5 118.8 C15—C14—C13 118.0 (2)

C5—C6—C1 115.9 (2) C15—C14—H14 121.0

C5—C6—H6 122.1 C13—C14—H14 121.0

C1—C6—H6 122.1 N7—C15—C14 123.2 (2)

N4—C7—N1 115.55 (15) N7—C15—H15 118.4

N4—C7—H7A 108.4 C14—C15—H15 118.4

N1—C7—H7A 108.4 C13—C16—H16A 109.5

N4—C7—H7B 108.4 C13—C16—H16B 109.5

N1—C7—H7B 108.4 H16A—C16—H16B 109.5

H7A—C7—H7B 107.5 C13—C16—H16C 109.5

N4—C8—C9 110.24 (16) H16A—C16—H16C 109.5

N4—C8—H8A 109.6 H16B—C16—H16C 109.5

supporting information

sup-5 Acta Cryst. (2005). E61, o2602–o2604

C1—N1—N2—N3 −0.1 (2) C7—N4—C8—C9 172.07 (15)

C7—N1—N2—N3 176.62 (17) C11—N4—C8—C9 −56.53 (19)

N1—N2—N3—C2 −0.1 (2) C12—N5—C9—C8 94.3 (2)

N2—N1—C1—C6 −177.9 (2) C10—N5—C9—C8 −58.2 (2)

C7—N1—C1—C6 5.8 (4) N4—C8—C9—N5 56.3 (2)

N2—N1—C1—C2 0.3 (2) C12—N5—C10—C11 −94.0 (2)

C7—N1—C1—C2 −175.98 (18) C9—N5—C10—C11 58.37 (19)

N2—N3—C2—C1 0.2 (2) C7—N4—C11—C10 −172.10 (15)

N2—N3—C2—C3 179.1 (2) C8—N4—C11—C10 56.88 (19)

N1—C1—C2—N3 −0.3 (2) N5—C10—C11—N4 −56.9 (2)

C6—C1—C2—N3 178.17 (18) C15—N7—C12—N6 0.3 (3)

N1—C1—C2—C3 −179.27 (18) C15—N7—C12—N5 178.34 (19)

C6—C1—C2—C3 −0.8 (3) C13—N6—C12—N7 0.2 (3)

N3—C2—C3—C4 −178.3 (2) C13—N6—C12—N5 −177.93 (16)

C1—C2—C3—C4 0.4 (3) C9—N5—C12—N7 13.9 (3)

C2—C3—C4—C5 0.2 (4) C10—N5—C12—N7 163.73 (17)

C3—C4—C5—C6 −0.5 (4) C9—N5—C12—N6 −167.80 (15)

C4—C5—C6—C1 0.1 (4) C10—N5—C12—N6 −18.0 (3)

N1—C1—C6—C5 178.5 (2) C12—N6—C13—C14 −0.4 (3)

C2—C1—C6—C5 0.6 (3) C12—N6—C13—C16 −179.30 (19)

C8—N4—C7—N1 58.0 (2) N6—C13—C14—C15 0.2 (4)

C11—N4—C7—N1 −72.0 (2) C16—C13—C14—C15 179.0 (2)

N2—N1—C7—N4 −88.9 (2) C12—N7—C15—C14 −0.5 (4)

C1—N1—C7—N4 87.1 (2) C13—C14—C15—N7 0.3 (4)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A

C6—H6···N3i _{0.93 2.50 3.430 (3) 176}

C9—H9A···N7 0.97 2.34 2.746 (3) 105

C10—H10B···N6 0.97 2.33 2.744 (3) 105