Literature DB >> 23424445

N-(7-Dibromo-methyl-5-methyl-1,8-naphthyridin-2-yl)acetamide-pyrrolidine-2,5-dione (1/1).

Gao-Zhang Gou¹, Jun-Feng Kou, Qing-Di Zhou, Shao-Ming Chi.

Abstract

In the title co-crystal, C(12)H(11)Br(2)N(3)O·C(4)H(5)NO(2), the naphthyridine derivative and the pyrrolidine-2,5-dione mol-ecules have crystallographic mirror-plane symmetry with all non-H atoms, except the Br atom, located on the mirror plane. In the crystal, N-H⋯N, N-H⋯O and C-H⋯O hydrogen bonds link the mol-ecules into heterodimers. These dimers are further linked into a one-dimensional structure along [010] by weak C-Br⋯O inter-actions [Br⋯O = 3.028 (5) Å and C-Br⋯O = 158.52 (4)°].

Entities: Chemical Disease Species

Year: 2013 PMID： 23424445 PMCID： PMC3569222 DOI： 10.1107/S1600536812051112

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For coordination properties of 1,8-naphthyridine ligands, see: Gan et al. (2011 ▶); Chang et al. (2011 ▶); Das et al. (2012 ▶); Li et al. (2011 ▶). For similar structures, see: Li et al. (2011 ▶). For applications of similar compounds, see: Samadi et al. (2011 ▶); Li et al. (2012 ▶); Tanaka et al. (2012 ▶). For information on their synthesis, see: Henry & Hammond (1977 ▶); Wang et al. (2008 ▶).

Experimental

Crystal data

C12H11Br2N3O·C4H5NO2 M = 472.15 Monoclinic, a = 11.537 (2) Å b = 7.0093 (14) Å c = 11.632 (2) Å β = 106.57 (3)° V = 901.6 (3) Å3 Z = 2 Mo Kα radiation μ = 4.52 mm−1 T = 293 K 0.21 × 0.19 × 0.18 mm

Data collection

Rigaku R-AXIS RAPID diffractometer Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T min = 0.450, T max = 0.497 7056 measured reflections 1723 independent reflections 1220 reflections with I > 2σ(I) R int = 0.042

Refinement

R[F 2 > 2σ(F 2)] = 0.051 wR(F 2) = 0.164 S = 1.12 1723 reflections 148 parameters H-atom parameters constrained Δρmax = 0.72 e Å−3 Δρmin = −0.92 e Å−3 Data collection: PROCESS-AUTO (Rigaku, 1998 ▶); cell refinement: PROCESS-AUTO; data reduction: CrystalClear (Rigaku/MSC, 2006 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg,1999 ▶); software used to prepare material for publication: SHELXL97. Click here for additional data file. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812051112/gk2541sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812051112/gk2541Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812051112/gk2541Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₂H₁₁Br₂N₃O·C₄H₅NO₂	F(000) = 468
M_r = 472.15	D_x = 1.739 Mg m⁻³
Monoclinic, P2₁/m	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yb	Cell parameters from 25 reflections
a = 11.537 (2) Å	θ = 3.4–25.0°
b = 7.0093 (14) Å	µ = 4.52 mm⁻¹
c = 11.632 (2) Å	T = 293 K
β = 106.57 (3)°	Block, colourless
V = 901.6 (3) Å³	0.21 × 0.19 × 0.18 mm
Z = 2

Rigaku R-AXIS RAPID diffractometer	1723 independent reflections
Radiation source: fine-focus sealed tube	1220 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.042
ω scan	θ_max = 25.0°, θ_min = 3.4°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −13→13
T_min = 0.450, T_max = 0.497	k = −8→7
7056 measured reflections	l = −13→13

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)] = 0.051	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.164	H-atom parameters constrained
S = 1.12	w = 1/[σ²(F_o²) + (0.0757P)² + 1.6111P] where P = (F_o² + 2F_c²)/3
1723 reflections	(Δ/σ)_max < 0.001
148 parameters	Δρ_max = 0.72 e Å⁻³
0 restraints	Δρ_min = −0.92 e Å⁻³

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.

	x	y	z	U_iso*/U_eq
C1	0.5310 (7)	0.2500	0.7838 (6)	0.0437 (17)
C2	0.4522 (7)	0.2500	0.8575 (7)	0.0486 (18)
H2A	0.3689	0.2500	0.8226	0.058*
C3	0.4977 (7)	0.2500	0.9803 (6)	0.0452 (17)
C4	0.6257 (7)	0.2500	1.0284 (6)	0.0405 (16)
C5	0.6882 (7)	0.2500	1.1520 (6)	0.0482 (18)
H5A	0.6446	0.2500	1.2080	0.058*
C6	0.8109 (7)	0.2500	1.1903 (7)	0.053 (2)
H6A	0.8518	0.2500	1.2717	0.063*
C7	0.8749 (6)	0.2500	1.1028 (6)	0.0456 (18)
C8	0.6974 (7)	0.2500	0.9487 (6)	0.0415 (16)
C9	0.4859 (8)	0.2500	0.6506 (7)	0.058 (2)
H9A	0.5554	0.2500	0.6180	0.069*
C10	0.4146 (7)	0.2500	1.0597 (7)	0.0491 (18)
H10A	0.3319	0.2500	1.0112	0.074*
H10B	0.4298	0.1382	1.1094	0.074*
C11	1.0841 (7)	0.2500	1.2427 (7)	0.055 (2)
C12	1.2128 (7)	0.2500	1.2408 (8)	0.067 (2)
H12A	1.2652	0.2500	1.3214	0.101*
H12B	1.2279	0.1382	1.1997	0.101*
C13	0.0377 (8)	0.2500	0.8080 (8)	0.057 (2)
C14	0.0885 (8)	0.2500	0.7021 (8)	0.069 (2)
H14A	0.1368	0.1384	0.7023	0.082*
C15	−0.0232 (9)	0.2500	0.5948 (8)	0.080 (3)
H15A	−0.0251	0.1387	0.5463	0.095*
C16	−0.1280 (8)	0.2500	0.6435 (8)	0.056 (2)
N1	0.6503 (6)	0.2500	0.8271 (5)	0.0477 (15)
N2	0.8206 (6)	0.2500	0.9860 (5)	0.0461 (15)
N3	1.0008 (6)	0.2500	1.1320 (5)	0.0524 (16)
H3A	1.0303	0.2500	1.0719	0.063*
N4	−0.0857 (6)	0.2500	0.7663 (5)	0.0502 (16)
H4A	−0.1322	0.2500	0.8124	0.060*
O1	1.0553 (6)	0.2500	1.3339 (5)	0.093 (3)
O2	0.0955 (5)	0.2500	0.9136 (5)	0.0759 (19)
O3	−0.2342 (6)	0.2500	0.5882 (6)	0.081 (2)
Br1	0.38805 (7)	0.02689 (12)	0.59139 (6)	0.0801 (4)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.041 (4)	0.052 (4)	0.042 (4)	0.000	0.018 (3)	0.000
C2	0.043 (4)	0.060 (5)	0.045 (4)	0.000	0.018 (3)	0.000
C3	0.045 (4)	0.048 (4)	0.050 (4)	0.000	0.025 (4)	0.000
C4	0.044 (4)	0.044 (4)	0.039 (4)	0.000	0.020 (3)	0.000
C5	0.053 (5)	0.059 (5)	0.041 (4)	0.000	0.026 (3)	0.000
C6	0.046 (5)	0.079 (6)	0.036 (4)	0.000	0.016 (3)	0.000
C7	0.041 (4)	0.054 (4)	0.044 (4)	0.000	0.016 (3)	0.000
C8	0.046 (5)	0.046 (4)	0.035 (4)	0.000	0.018 (3)	0.000
C9	0.054 (5)	0.076 (6)	0.047 (4)	0.000	0.021 (4)	0.000
C10	0.041 (4)	0.062 (5)	0.051 (4)	0.000	0.024 (3)	0.000
C11	0.046 (5)	0.075 (6)	0.041 (4)	0.000	0.009 (4)	0.000
C12	0.042 (5)	0.102 (7)	0.057 (5)	0.000	0.012 (4)	0.000
C13	0.059 (6)	0.061 (5)	0.058 (5)	0.000	0.027 (4)	0.000
C14	0.059 (6)	0.083 (6)	0.074 (6)	0.000	0.034 (5)	0.000
C15	0.091 (8)	0.107 (8)	0.052 (5)	0.000	0.039 (5)	0.000
C16	0.054 (5)	0.061 (5)	0.054 (5)	0.000	0.017 (4)	0.000
N1	0.047 (4)	0.060 (4)	0.043 (3)	0.000	0.024 (3)	0.000
N2	0.042 (4)	0.062 (4)	0.039 (3)	0.000	0.020 (3)	0.000
N3	0.043 (4)	0.079 (5)	0.041 (3)	0.000	0.022 (3)	0.000
N4	0.042 (4)	0.070 (4)	0.042 (3)	0.000	0.017 (3)	0.000
O1	0.051 (4)	0.188 (8)	0.041 (3)	0.000	0.014 (3)	0.000
O2	0.054 (4)	0.114 (6)	0.057 (4)	0.000	0.012 (3)	0.000
O3	0.067 (5)	0.116 (6)	0.057 (4)	0.000	0.011 (3)	0.000
Br1	0.0936 (7)	0.0929 (6)	0.0563 (5)	−0.0237 (4)	0.0254 (4)	−0.0161 (3)

C1—N1	1.324 (9)	C9—H9A	0.9800
C1—C2	1.417 (10)	C10—H10A	0.9600
C1—C9	1.487 (10)	C10—H10B	0.9600
C2—C3	1.373 (10)	C11—O1	1.199 (10)
C2—H2A	0.9300	C11—N3	1.370 (10)
C3—C4	1.422 (10)	C11—C12	1.490 (11)
C3—C10	1.509 (9)	C12—H12A	0.9600
C4—C8	1.407 (10)	C12—H12B	0.9601
C4—C5	1.413 (10)	C13—O2	1.220 (10)
C5—C6	1.357 (11)	C13—N4	1.367 (10)
C5—H5A	0.9300	C13—C14	1.508 (12)
C6—C7	1.418 (10)	C14—C15	1.517 (13)
C6—H6A	0.9300	C14—H14A	0.9600
C7—N2	1.324 (9)	C15—C16	1.474 (13)
C7—N3	1.394 (9)	C15—H15A	0.9600
C8—N1	1.363 (9)	C16—O3	1.210 (10)
C8—N2	1.363 (9)	C16—N4	1.372 (10)
C9—Br1	1.936 (5)	N3—H3A	0.8600
C9—Br1ⁱ	1.936 (5)	N4—H4A	0.8600

N1—C1—C2	123.1 (7)	C3—C10—H10A	109.8
N1—C1—C9	114.4 (6)	C3—C10—H10B	109.3
C2—C1—C9	122.4 (7)	H10A—C10—H10B	109.5
C3—C2—C1	120.5 (7)	O1—C11—N3	122.3 (8)
C3—C2—H2A	119.7	O1—C11—C12	122.8 (7)
C1—C2—H2A	119.7	N3—C11—C12	114.9 (7)
C2—C3—C4	117.1 (6)	C11—C12—H12A	109.8
C2—C3—C10	121.0 (7)	C11—C12—H12B	109.3
C4—C3—C10	121.9 (7)	H12A—C12—H12B	109.5
C8—C4—C5	116.5 (7)	O2—C13—N4	124.9 (8)
C8—C4—C3	118.7 (6)	O2—C13—C14	126.5 (8)
C5—C4—C3	124.9 (6)	N4—C13—C14	108.6 (8)
C6—C5—C4	121.0 (7)	C13—C14—C15	103.6 (7)
C6—C5—H5A	119.5	C13—C14—H14A	111.0
C4—C5—H5A	119.5	C15—C14—H14A	111.0
C5—C6—C7	118.2 (7)	C16—C15—C14	106.4 (7)
C5—C6—H6A	120.9	C16—C15—H15A	110.0
C7—C6—H6A	120.9	C14—C15—H15A	110.8
N2—C7—N3	113.9 (6)	O3—C16—N4	124.0 (8)
N2—C7—C6	123.1 (7)	O3—C16—C15	127.8 (8)
N3—C7—C6	123.1 (7)	N4—C16—C15	108.2 (8)
N1—C8—N2	113.6 (6)	C1—N1—C8	117.3 (6)
N1—C8—C4	123.3 (7)	C7—N2—C8	118.1 (6)
N2—C8—C4	123.1 (6)	C11—N3—C7	129.2 (7)
C1—C9—Br1	111.5 (3)	C11—N3—H3A	115.4
C1—C9—Br1ⁱ	111.5 (3)	C7—N3—H3A	115.4
Br1—C9—Br1ⁱ	107.7 (4)	C16—N4—C13	113.2 (7)
C1—C9—H9A	108.7	C16—N4—H4A	123.4
Br1—C9—H9A	108.7	C13—N4—H4A	123.4
Br1ⁱ—C9—H9A	108.7

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6A···O1	0.93	2.25	2.838 (10)	121
C9—H9A···O3ⁱⁱ	0.98	2.55	3.507 (11)	166
N4—H4A···N1ⁱⁱⁱ	0.86	2.56	3.317 (9)	147
N4—H4A···N2ⁱⁱⁱ	0.86	2.24	3.045 (8)	157
N3—H3A···O2ⁱⁱ	0.86	2.18	3.038 (9)	177

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C6—H6A⋯O1	0.93	2.25	2.838 (10)	121
C9—H9A⋯O3ⁱ	0.98	2.55	3.507 (11)	166
N4—H4A⋯N1ⁱⁱ	0.86	2.56	3.317 (9)	147
N4—H4A⋯N2ⁱⁱ	0.86	2.24	3.045 (8)	157
N3—H3A⋯O2ⁱ	0.86	2.18	3.038 (9)	177

Symmetry codes: (i) ; (ii) .

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1. Crystal structure of N-(7-di-bromo-methyl-5-methyl-1,8-naphthyridin-2-yl)benzamide-pyrrolidine-2,5-dione (1/1).

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