Di­aqua­dibenz­imidazole­bis(5-fluoro-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-1-acetato)­nickel(II)

Hu, M.-L.; Wang, W.-D.

doi:10.1107/S1600536805012432

Diaquadibenzimidazolebis(5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-1-acetato)nickel(II)

In the title centrosymmetric compound, [Ni(C₆H₄FN₂O₄)₂(C₇H₆N₂)₂(H₂O)₂], each Ni^II ion is coordinated by two 5-fluorouracil-1-acetate (5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-1-acetate) anions via carboxylate O atoms, two water molecules and two benzimidazole ligands, forming a six-coordinate octahedral environment; the N—H

F, N—H

O and O—H

O hydrogen-bonding interactions link adjacent molecules into a three-dimensional network.

Read article Similar articles

Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805012432/ng6139sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536805012432/ng6139Isup2.hkl Contains datablock I

CCDC reference: 272050

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (C-C) = 0.003 Å
R factor = 0.029
wR factor = 0.074
Data-to-parameter ratio = 10.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT480_ALERT_4_C Long H...A H-Bond Reported H4     ..  F1      ..       2.56 Ang.

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); 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, 2002); software used to prepare material for publication: SHELXL97.

Diaquadibenzimidazolebis(5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine- 1-acetato)nickel(II) top

Crystal data top

[Ni(C₆H₄FN₂O₄)₂(C₇H₆N₂)₂(H₂O)₂]	Z = 1
M_r = 705.24	F(000) = 362
Triclinic, P1	D_x = 1.707 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.2955 (5) Å	Cell parameters from 3096 reflections
b = 8.3616 (6) Å	θ = 2.6–25.2°
c = 11.9300 (8) Å	µ = 0.80 mm⁻¹
α = 89.059 (1)°	T = 298 K
β = 88.827 (1)°	Block, green
γ = 70.549 (1)°	0.28 × 0.18 × 0.13 mm
V = 686.04 (8) Å³

Data collection top

Bruker APEX area-detector diffractometer	2444 independent reflections
Radiation source: fine-focus sealed tube	2296 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.015
φ and ω scans	θ_max = 25.3°, θ_min = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2002)	h = −8→8
T_min = 0.808, T_max = 0.904	k = −9→10
5024 measured reflections	l = −14→14

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)] = 0.029	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0386P)² + 0.2919P] where P = (F_o² + 2F_c²)/3
2444 reflections	(Δ/σ)_max = 0.001
227 parameters	Δρ_max = 0.22 e Å⁻³
4 restraints	Δρ_min = −0.31 e Å⁻³

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

	x	y	z	U_iso*/U_eq
Ni1	0.5000	0.5000	0.5000	0.02270 (12)
F1	0.1728 (2)	0.52798 (16)	0.91480 (11)	0.0556 (4)
O1	0.35226 (19)	0.33151 (18)	0.52543 (11)	0.0320 (3)
O2	0.10112 (19)	0.34327 (17)	0.41585 (11)	0.0305 (3)
O3	0.3301 (2)	−0.06870 (18)	0.71442 (13)	0.0433 (4)
O4	0.3838 (2)	0.22879 (18)	1.01925 (11)	0.0365 (3)
O5	0.2580 (2)	0.69772 (18)	0.56434 (12)	0.0324 (3)
N1	0.1901 (2)	0.2184 (2)	0.70605 (13)	0.0276 (3)
N2	0.3518 (2)	0.0839 (2)	0.86496 (13)	0.0290 (4)
N3	0.5996 (2)	0.43874 (19)	0.66166 (12)	0.0255 (3)
N4	0.6673 (3)	0.4857 (2)	0.83579 (14)	0.0335 (4)
C1	0.1973 (3)	0.3066 (2)	0.50327 (15)	0.0235 (4)
C2	0.1141 (3)	0.2176 (3)	0.59354 (16)	0.0339 (5)
H2A	−0.0260	0.2716	0.5966	0.041*
H2B	0.1405	0.1008	0.5715	0.041*
C3	0.2928 (3)	0.0690 (2)	0.75745 (16)	0.0283 (4)
C4	0.3219 (3)	0.2301 (2)	0.92354 (16)	0.0286 (4)
C5	0.2122 (3)	0.3781 (2)	0.86207 (17)	0.0331 (4)
C6	0.1508 (3)	0.3705 (3)	0.75905 (17)	0.0319 (4)
H6	0.0799	0.4701	0.7222	0.038*
C7	0.5998 (3)	0.5526 (3)	0.73565 (16)	0.0305 (4)
H7	0.5573	0.6684	0.7203	0.037*
C8	0.6739 (3)	0.2827 (2)	0.71783 (15)	0.0253 (4)
C9	0.7186 (3)	0.3121 (3)	0.82787 (16)	0.0298 (4)
C10	0.8030 (3)	0.1803 (3)	0.90278 (18)	0.0382 (5)
H10	0.8311	0.2007	0.9758	0.046*
C11	0.8425 (3)	0.0190 (3)	0.86409 (19)	0.0415 (5)
H11	0.9011	−0.0722	0.9117	0.050*
C12	0.7975 (3)	−0.0129 (3)	0.75464 (19)	0.0394 (5)
H12	0.8263	−0.1244	0.7315	0.047*
C13	0.7114 (3)	0.1178 (3)	0.68102 (17)	0.0312 (4)
H13	0.6794	0.0965	0.6090	0.037*
H5A	0.264 (3)	0.774 (2)	0.6074 (16)	0.037*
H4	0.674 (3)	0.545 (3)	0.8913 (14)	0.037*
H5B	0.152 (2)	0.681 (3)	0.5774 (19)	0.037*
H2	0.424 (2)	−0.0075 (17)	0.8947 (16)	0.027 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Ni1	0.02315 (19)	0.0288 (2)	0.01807 (18)	−0.01108 (14)	−0.00421 (12)	0.00075 (13)
F1	0.0849 (11)	0.0295 (7)	0.0440 (8)	−0.0071 (7)	−0.0106 (7)	−0.0084 (6)
O1	0.0300 (7)	0.0404 (8)	0.0318 (7)	−0.0198 (6)	−0.0079 (6)	0.0070 (6)
O2	0.0311 (7)	0.0389 (8)	0.0229 (7)	−0.0134 (6)	−0.0073 (6)	0.0032 (6)
O3	0.0517 (9)	0.0339 (8)	0.0413 (9)	−0.0089 (7)	−0.0152 (7)	−0.0089 (7)
O4	0.0491 (9)	0.0368 (8)	0.0227 (7)	−0.0126 (7)	−0.0093 (6)	−0.0005 (6)
O5	0.0263 (7)	0.0379 (8)	0.0337 (8)	−0.0112 (6)	−0.0029 (6)	−0.0093 (6)
N1	0.0294 (8)	0.0339 (9)	0.0211 (8)	−0.0124 (7)	−0.0059 (6)	0.0042 (7)
N2	0.0345 (9)	0.0254 (9)	0.0246 (8)	−0.0061 (7)	−0.0087 (7)	0.0024 (7)
N3	0.0268 (8)	0.0288 (8)	0.0216 (8)	−0.0099 (7)	−0.0050 (6)	0.0002 (6)
N4	0.0415 (10)	0.0365 (10)	0.0213 (8)	−0.0108 (8)	−0.0082 (7)	−0.0062 (7)
C1	0.0247 (9)	0.0212 (9)	0.0236 (9)	−0.0062 (7)	−0.0014 (7)	−0.0028 (7)
C2	0.0360 (11)	0.0498 (13)	0.0240 (10)	−0.0247 (10)	−0.0103 (8)	0.0073 (9)
C3	0.0265 (10)	0.0310 (10)	0.0275 (10)	−0.0095 (8)	−0.0035 (8)	−0.0007 (8)
C4	0.0299 (10)	0.0326 (10)	0.0241 (10)	−0.0113 (8)	−0.0013 (8)	−0.0008 (8)
C5	0.0419 (12)	0.0247 (10)	0.0300 (11)	−0.0076 (9)	−0.0006 (9)	−0.0028 (8)
C6	0.0330 (11)	0.0288 (10)	0.0309 (11)	−0.0064 (8)	−0.0037 (8)	0.0069 (8)
C7	0.0324 (10)	0.0300 (10)	0.0278 (10)	−0.0085 (8)	−0.0051 (8)	−0.0001 (8)
C8	0.0219 (9)	0.0300 (10)	0.0241 (9)	−0.0088 (8)	−0.0005 (7)	0.0012 (7)
C9	0.0278 (10)	0.0369 (11)	0.0245 (10)	−0.0103 (8)	−0.0035 (8)	0.0000 (8)
C10	0.0374 (12)	0.0479 (13)	0.0286 (11)	−0.0133 (10)	−0.0113 (9)	0.0090 (9)
C11	0.0376 (12)	0.0391 (12)	0.0452 (13)	−0.0092 (9)	−0.0094 (10)	0.0154 (10)
C12	0.0381 (12)	0.0300 (11)	0.0486 (13)	−0.0096 (9)	0.0007 (10)	0.0013 (9)
C13	0.0312 (10)	0.0351 (11)	0.0289 (10)	−0.0133 (9)	0.0011 (8)	−0.0025 (8)

Geometric parameters (Å, º) top

Ni1—O1ⁱ	2.0549 (13)	N4—C7	1.342 (3)
Ni1—O1	2.0549 (13)	N4—C9	1.378 (3)
Ni1—N3ⁱ	2.0705 (14)	N4—H4	0.845 (10)
Ni1—N3	2.0705 (14)	C1—C2	1.527 (3)
Ni1—O5ⁱ	2.1168 (14)	C2—H2A	0.9700
Ni1—O5	2.1168 (14)	C2—H2B	0.9700
F1—C5	1.352 (2)	C4—C5	1.430 (3)
O1—C1	1.250 (2)	C5—C6	1.326 (3)
O2—C1	1.245 (2)	C6—H6	0.9300
O3—C3	1.212 (2)	C7—H7	0.9300
O4—C4	1.235 (2)	C8—C13	1.390 (3)
O5—H5A	0.837 (10)	C8—C9	1.404 (3)
O5—H5B	0.840 (10)	C9—C10	1.389 (3)
N1—C3	1.367 (2)	C10—C11	1.368 (3)
N1—C6	1.370 (3)	C10—H10	0.9300
N1—C2	1.464 (2)	C11—C12	1.404 (3)
N2—C4	1.369 (2)	C11—H11	0.9300
N2—C3	1.382 (2)	C12—C13	1.376 (3)
N2—H2	0.847 (9)	C12—H12	0.9300
N3—C7	1.309 (2)	C13—H13	0.9300
N3—C8	1.400 (2)

O1ⁱ—Ni1—O1	180.0	N1—C2—H2B	108.5
O1ⁱ—Ni1—N3ⁱ	86.21 (6)	C1—C2—H2B	108.5
O1—Ni1—N3ⁱ	93.79 (6)	H2A—C2—H2B	107.5
O1ⁱ—Ni1—N3	93.79 (6)	O3—C3—N1	123.79 (18)
O1—Ni1—N3	86.21 (6)	O3—C3—N2	120.95 (18)
N3ⁱ—Ni1—N3	180.0	N1—C3—N2	115.25 (17)
O1ⁱ—Ni1—O5ⁱ	89.95 (6)	O4—C4—N2	121.96 (17)
O1—Ni1—O5ⁱ	90.05 (6)	O4—C4—C5	125.48 (18)
N3ⁱ—Ni1—O5ⁱ	89.48 (6)	N2—C4—C5	112.56 (16)
N3—Ni1—O5ⁱ	90.52 (6)	C6—C5—F1	121.22 (18)
O1ⁱ—Ni1—O5	90.05 (6)	C6—C5—C4	122.40 (18)
O1—Ni1—O5	89.95 (6)	F1—C5—C4	116.38 (17)
N3ⁱ—Ni1—O5	90.52 (6)	C5—C6—N1	121.07 (18)
N3—Ni1—O5	89.48 (6)	C5—C6—H6	119.5
O5ⁱ—Ni1—O5	180.0	N1—C6—H6	119.5
C1—O1—Ni1	142.61 (12)	N3—C7—N4	113.42 (18)
Ni1—O5—H5A	125.1 (16)	N3—C7—H7	123.3
Ni1—O5—H5B	120.3 (16)	N4—C7—H7	123.3
H5A—O5—H5B	108 (2)	C13—C8—N3	131.06 (17)
C3—N1—C6	121.33 (16)	C13—C8—C9	120.15 (18)
C3—N1—C2	120.06 (17)	N3—C8—C9	108.75 (16)
C6—N1—C2	118.58 (16)	N4—C9—C10	132.66 (19)
C4—N2—C3	127.37 (16)	N4—C9—C8	105.22 (16)
C4—N2—H2	117.0 (14)	C10—C9—C8	122.09 (19)
C3—N2—H2	115.3 (14)	C11—C10—C9	116.8 (2)
C7—N3—C8	105.09 (15)	C11—C10—H10	121.6
C7—N3—Ni1	123.14 (13)	C9—C10—H10	121.6
C8—N3—Ni1	131.75 (12)	C10—C11—C12	121.9 (2)
C7—N4—C9	107.50 (16)	C10—C11—H11	119.0
C7—N4—H4	123.3 (16)	C12—C11—H11	119.0
C9—N4—H4	129.2 (16)	C13—C12—C11	121.2 (2)
O2—C1—O1	128.51 (17)	C13—C12—H12	119.4
O2—C1—C2	114.79 (16)	C11—C12—H12	119.4
O1—C1—C2	116.69 (16)	C12—C13—C8	117.79 (19)
N1—C2—C1	115.01 (15)	C12—C13—H13	121.1
N1—C2—H2A	108.5	C8—C13—H13	121.1
C1—C2—H2A	108.5

N3ⁱ—Ni1—O1—C1	−35.8 (2)	N2—C4—C5—C6	−0.9 (3)
N3—Ni1—O1—C1	144.2 (2)	O4—C4—C5—F1	−0.6 (3)
O5ⁱ—Ni1—O1—C1	−125.3 (2)	N2—C4—C5—F1	178.80 (17)
O5—Ni1—O1—C1	54.7 (2)	F1—C5—C6—N1	−179.68 (18)
O1—Ni1—N3—C7	−133.59 (16)	C4—C5—C6—N1	0.0 (3)
O1ⁱ—Ni1—N3—C7	46.41 (16)	C3—N1—C6—C5	0.4 (3)
O5ⁱ—Ni1—N3—C7	136.40 (15)	C2—N1—C6—C5	178.39 (18)
O5—Ni1—N3—C7	−43.60 (15)	C8—N3—C7—N4	−0.1 (2)
O1—Ni1—N3—C8	45.11 (16)	Ni1—N3—C7—N4	178.89 (13)
O1ⁱ—Ni1—N3—C8	−134.89 (16)	C9—N4—C7—N3	0.7 (2)
O5ⁱ—Ni1—N3—C8	−44.90 (16)	C7—N3—C8—C13	−178.29 (19)
O5—Ni1—N3—C8	135.10 (16)	Ni1—N3—C8—C13	2.8 (3)
Ni1—O1—C1—O2	35.2 (3)	C7—N3—C8—C9	−0.5 (2)
Ni1—O1—C1—C2	−145.72 (17)	Ni1—N3—C8—C9	−179.37 (13)
C3—N1—C2—C1	−116.9 (2)	C7—N4—C9—C10	176.9 (2)
C6—N1—C2—C1	65.1 (2)	C7—N4—C9—C8	−0.9 (2)
O2—C1—C2—N1	−162.95 (17)	C13—C8—C9—N4	178.96 (17)
O1—C1—C2—N1	17.8 (3)	N3—C8—C9—N4	0.9 (2)
C6—N1—C3—O3	179.48 (19)	C13—C8—C9—C10	0.8 (3)
C2—N1—C3—O3	1.5 (3)	N3—C8—C9—C10	−177.23 (18)
C6—N1—C3—N2	0.2 (3)	N4—C9—C10—C11	−176.9 (2)
C2—N1—C3—N2	−177.81 (16)	C8—C9—C10—C11	0.6 (3)
C4—N2—C3—O3	179.40 (19)	C9—C10—C11—C12	−1.1 (3)
C4—N2—C3—N1	−1.3 (3)	C10—C11—C12—C13	0.2 (3)
C3—N2—C4—O4	−178.95 (19)	C11—C12—C13—C8	1.2 (3)
C3—N2—C4—C5	1.6 (3)	N3—C8—C13—C12	175.85 (19)
O4—C4—C5—C6	179.6 (2)	C9—C8—C13—C12	−1.7 (3)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O5—H5a···O3ⁱⁱ	0.84 (1)	2.03 (1)	2.852 (2)	170 (2)
N4—H4···O4ⁱⁱⁱ	0.85 (1)	2.10 (1)	2.889 (2)	155 (2)
N4—H4···F1ⁱⁱⁱ	0.85 (1)	2.56 (2)	3.204 (2)	134 (2)
O5—H5b···O2^iv	0.84 (1)	1.93 (1)	2.756 (2)	171 (2)
N2—H2···O4^v	0.85 (1)	2.17 (1)	3.016 (2)	175 (2)

Symmetry codes: (ii) x, y+1, z; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+1; (v) −x+1, −y, −z+2.

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

Di­aqua­dibenz­imidazole­bis(5-fluoro-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-1-acetato)­nickel(II)

Supporting information

Key indicators

checkCIF/PLATON results

Diaquadibenzimidazolebis(5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-1-acetato)nickel(II)