2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dinitrate

Dai, J.

doi:10.1107/S1600536809018558

organic compounds

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Volume 65| Part 6| June 2009| Page o1360

doi:10.1107/S1600536809018558

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2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dinitrate

Jing Dai ^a ^*

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: fudavid88@yahoo.com.cn

(Received 3 April 2009; accepted 16 May 2009; online 23 May 2009)

In the title compound, C₁₁H₁₅N₃²⁺·2NO₃⁻, one of the imidazole N atoms and the N atom of the pyrrolidine ring are protonated. The pyrrolidine ring adopts an envelope conformation, with the C atom carrying the benzoimidazolium substituent as the flap atom. In the crystal structure, cations and anions are linked through N—H⋯O hydrogen bonds, forming chains that run parallel to the c axis.

Related literature

For background to the applications of proline derivatives, see: Fu et al. (2007 ); Aminabhavi et al. (1986 ). For the structures of metal complexes with ligands similar to the title compound, see: Dai & Fu (2008a ,b ); Fu & Ye (2007 ).

Experimental

Crystal data

C₁₁H₁₅N₃²⁺·2NO₃⁻
M_r = 313.28
Monoclinic, C 2/c
a = 22.078 (2) Å
b = 11.154 (1) Å
c = 14.670 (1) Å
β = 127.18 (1)°
V = 2878.3 (4) Å³
Z = 8
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 298 K
0.35 × 0.30 × 0.15 mm

Data collection

Rigaku Mercury2 diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.959, T_max = 0.982
14543 measured reflections
3276 independent reflections
2195 reflections with I > 2σ(I)
R_int = 0.048

Refinement

R[F² > 2σ(F²)] = 0.059
wR(F²) = 0.144
S = 1.09
3276 reflections
199 parameters
H-atom parameters constrained
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯O4ⁱ	0.86	1.93	2.788 (2)	177
N3—H3A⋯O5ⁱ	0.86	2.50	3.020 (2)	120
N5—H5B⋯O1ⁱ	0.90	1.89	2.771 (2)	167
N5—H5B⋯O3ⁱ	0.90	2.64	3.149 (2)	117
N5—H5A⋯O5ⁱⁱ	0.90	1.90	2.768 (2)	162
N4—H4A⋯O1	0.86	2.04	2.850 (2)	157
N4—H4A⋯O2	0.86	2.42	3.121 (3)	139
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[x, -y+1, z-{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; 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: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018558/sj2610sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809018558/sj2610Isup2.hkl

checkCIF report

Comment top

Heterocyclic amine derivatives have found wide range of applications in material science and display ferroelectric, fluorescence and dielectric behaviors. There has also been an increased interest in the preparation of coordination compounds from these heterocyclic ligands (Aminabhavi et al., 1986; Dai & Fu, 2008a,b; Fu & Ye, 2007; Fu et al., 2007). We report here the crystal structure of the title compound, (I), 2-(pyrrolidinium-2-yl)-1H-benzo[d] imidazol-3-ium dinitrate.

In the title compound, (C₁₁H₁₅N₃)²⁺.2(NO₃)^-, the N4 atom of the imidazole and the N5 atom of pyrrolidine ring are protonated. The pyrrolidine ring adopts an envelope conformation with the C8 atom carrying the benzoimidazolium substituent as the flap atom. In the crystal structure, cations and anions are linked through N—H···O hydrogen bonds forming chains that run parallel to the c axis. (Fig. 2, Table 1).

Related literature top

For background to the applications of proline derivatives, see: Fu et al. (2007); Aminabhavi et al. (1986). For the structures of metal complexes with ligands similar to the title compound, see: Dai & Fu (2008a,b); Fu & Ye (2007).

Experimental top

The homochiral ligand S-2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole was synthesized by reaction of S-pyrrolidine-2-carboxylic acid and benzene-1,2-diamine according to the procedure described in the literature (Aminabhavi et al., 1986). S-2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole (3 mmol) was dissolved in distilled water (20 ml) and nitric acid (1 ml). The solution was evaporated in air affording colorless block-like crystals of (I) suitable for X-ray analysis.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. A view of the title compound with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. Partial packing view of the title compound showing the formation of a chain parallel to the c axis. All H atoms not involved in hydrogen bonding (dashed lines) were omitted for clarity.

2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dinitrate top

Crystal data top

C₁₁H₁₅N₃²⁺·2NO₃⁻	F(000) = 1312
M_r = 313.28	D_x = 1.446 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 3275 reflections
a = 22.078 (2) Å	θ = 3.2–27.5°
b = 11.154 (1) Å	µ = 0.12 mm⁻¹
c = 14.670 (1) Å	T = 298 K
β = 127.18 (1)°	Block, colourless
V = 2878.3 (4) Å³	0.35 × 0.30 × 0.15 mm
Z = 8

Data collection top

Rigaku Mercury2 diffractometer	3276 independent reflections
Radiation source: fine-focus sealed tube	2195 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.048
Detector resolution: 13.6612 pixels mm^-1	θ_max = 27.5°, θ_min = 3.2°
ω scans	h = −28→28
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −14→14
T_min = 0.959, T_max = 0.982	l = −18→19
14543 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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.144	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.0493P)² + 2.1933P] where P = (F_o² + 2F_c²)/3
3276 reflections	(Δ/σ)_max < 0.001
199 parameters	Δρ_max = 0.31 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₁₁H₁₅N₃²⁺·2NO₃⁻	V = 2878.3 (4) Å³
M_r = 313.28	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 22.078 (2) Å	µ = 0.12 mm⁻¹
b = 11.154 (1) Å	T = 298 K
c = 14.670 (1) Å	0.35 × 0.30 × 0.15 mm
β = 127.18 (1)°

Data collection top

Rigaku Mercury2 diffractometer	3276 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	2195 reflections with I > 2σ(I)
T_min = 0.959, T_max = 0.982	R_int = 0.048
14543 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.059	0 restraints
wR(F²) = 0.144	H-atom parameters constrained
S = 1.09	Δρ_max = 0.31 e Å⁻³
3276 reflections	Δρ_min = −0.19 e Å⁻³
199 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
N3	0.66938 (10)	0.39290 (15)	0.56483 (15)	0.0433 (4)
H3A	0.6966	0.3290	0.5937	0.052*
N4	0.63804 (11)	0.58040 (17)	0.53606 (17)	0.0513 (5)
H4A	0.6414	0.6572	0.5428	0.062*
N5	0.83307 (9)	0.45350 (16)	0.71441 (14)	0.0429 (4)
H5A	0.8163	0.4119	0.6506	0.052*
H5B	0.8425	0.4016	0.7686	0.052*
C1	0.57133 (13)	0.5163 (2)	0.4595 (2)	0.0500 (6)
C2	0.49697 (15)	0.5521 (3)	0.3784 (3)	0.0709 (8)
H2	0.4832	0.6325	0.3664	0.085*
C3	0.44437 (16)	0.4628 (3)	0.3162 (3)	0.0778 (9)
H3	0.3939	0.4834	0.2599	0.093*
C4	0.46486 (16)	0.3430 (3)	0.3353 (2)	0.0725 (8)
H4	0.4273	0.2856	0.2920	0.087*
C5	0.53812 (15)	0.3057 (2)	0.4155 (2)	0.0593 (7)
H5	0.5513	0.2250	0.4276	0.071*
C6	0.59181 (12)	0.3961 (2)	0.47789 (19)	0.0448 (5)
C7	0.69499 (12)	0.50468 (19)	0.59632 (18)	0.0418 (5)
C8	0.77457 (13)	0.54335 (19)	0.6904 (2)	0.0465 (6)
H8	0.7785	0.5530	0.7602	0.056*
C9	0.80026 (15)	0.6590 (2)	0.6698 (2)	0.0616 (7)
H9A	0.7799	0.7281	0.6831	0.074*
H9B	0.7852	0.6626	0.5926	0.074*
C10	0.88635 (15)	0.6521 (2)	0.7577 (2)	0.0617 (7)
H10A	0.9112	0.7044	0.7367	0.074*
H10B	0.9022	0.6745	0.8331	0.074*
C11	0.90467 (14)	0.5220 (2)	0.7552 (2)	0.0556 (6)
H11A	0.9471	0.4953	0.8308	0.067*
H11B	0.9174	0.5107	0.7030	0.067*
O1	0.64618 (11)	0.82051 (14)	0.60914 (14)	0.0612 (5)
O2	0.58007 (14)	0.83408 (18)	0.42662 (16)	0.0852 (7)
O3	0.59348 (11)	0.98868 (15)	0.52487 (15)	0.0672 (5)
N1	0.60605 (11)	0.88315 (18)	0.51830 (16)	0.0492 (5)
O4	0.74570 (10)	0.68205 (14)	0.85048 (13)	0.0533 (4)
O5	0.81397 (9)	0.66960 (14)	1.03479 (13)	0.0513 (4)
O6	0.74016 (11)	0.52300 (15)	0.93113 (17)	0.0698 (5)
N2	0.76639 (11)	0.62317 (16)	0.93912 (16)	0.0447 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N3	0.0448 (10)	0.0328 (9)	0.0462 (10)	0.0007 (8)	0.0243 (9)	−0.0039 (8)
N4	0.0516 (12)	0.0344 (10)	0.0625 (13)	0.0033 (9)	0.0316 (11)	−0.0006 (9)
N5	0.0440 (10)	0.0434 (10)	0.0335 (9)	−0.0035 (8)	0.0193 (8)	−0.0069 (8)
C1	0.0441 (13)	0.0517 (14)	0.0519 (14)	0.0021 (11)	0.0278 (12)	0.0013 (11)
C2	0.0538 (17)	0.0731 (19)	0.0754 (19)	0.0149 (14)	0.0336 (15)	0.0152 (15)
C3	0.0405 (15)	0.110 (3)	0.0671 (19)	0.0017 (17)	0.0243 (14)	0.0035 (18)
C4	0.0516 (17)	0.092 (2)	0.0664 (18)	−0.0206 (16)	0.0319 (15)	−0.0162 (17)
C5	0.0569 (16)	0.0599 (16)	0.0629 (16)	−0.0148 (13)	0.0371 (14)	−0.0149 (13)
C6	0.0439 (13)	0.0464 (13)	0.0459 (13)	−0.0027 (10)	0.0280 (11)	−0.0055 (10)
C7	0.0455 (13)	0.0349 (11)	0.0445 (12)	−0.0014 (9)	0.0270 (11)	−0.0066 (9)
C8	0.0518 (13)	0.0391 (12)	0.0487 (13)	−0.0036 (10)	0.0304 (12)	−0.0098 (10)
C9	0.0662 (17)	0.0392 (13)	0.0772 (18)	−0.0109 (12)	0.0421 (15)	−0.0112 (13)
C10	0.0657 (16)	0.0575 (16)	0.0641 (16)	−0.0226 (13)	0.0404 (14)	−0.0202 (13)
C11	0.0496 (14)	0.0642 (16)	0.0529 (14)	−0.0100 (12)	0.0310 (12)	−0.0077 (12)
O1	0.0807 (12)	0.0462 (10)	0.0502 (10)	0.0166 (9)	0.0361 (10)	0.0115 (8)
O2	0.1258 (19)	0.0759 (14)	0.0539 (12)	−0.0102 (13)	0.0543 (13)	−0.0108 (10)
O3	0.0808 (13)	0.0431 (10)	0.0649 (12)	0.0163 (9)	0.0373 (10)	0.0099 (8)
N1	0.0563 (12)	0.0456 (12)	0.0463 (11)	0.0003 (9)	0.0313 (10)	0.0037 (9)
O4	0.0766 (12)	0.0444 (9)	0.0399 (9)	0.0054 (8)	0.0357 (9)	0.0043 (7)
O5	0.0596 (10)	0.0485 (9)	0.0389 (9)	−0.0026 (8)	0.0261 (8)	0.0033 (7)
O6	0.0716 (12)	0.0441 (10)	0.0778 (13)	−0.0113 (9)	0.0367 (11)	0.0063 (9)
N2	0.0514 (11)	0.0372 (10)	0.0485 (11)	0.0065 (9)	0.0318 (10)	0.0053 (9)

Geometric parameters (Å, º) top

N3—C7	1.331 (3)	C5—H5	0.9300
N3—C6	1.386 (3)	C7—C8	1.499 (3)
N3—H3A	0.8600	C8—C9	1.511 (3)
N4—C7	1.316 (3)	C8—H8	0.9800
N4—C1	1.393 (3)	C9—C10	1.523 (4)
N4—H4A	0.8600	C9—H9A	0.9700
N5—C8	1.499 (3)	C9—H9B	0.9700
N5—C11	1.516 (3)	C10—C11	1.514 (4)
N5—H5A	0.9000	C10—H10A	0.9700
N5—H5B	0.9000	C10—H10B	0.9700
C1—C2	1.382 (4)	C11—H11A	0.9700
C1—C6	1.388 (3)	C11—H11B	0.9700
C2—C3	1.375 (4)	O1—N1	1.274 (2)
C2—H2	0.9300	O2—N1	1.227 (2)
C3—C4	1.384 (4)	O3—N1	1.226 (2)
C3—H3	0.9300	O4—N2	1.270 (2)
C4—C5	1.369 (4)	O5—N2	1.249 (2)
C4—H4	0.9300	O6—N2	1.231 (2)
C5—C6	1.396 (3)

C7—N3—C6	108.93 (18)	N3—C7—C8	127.21 (19)
C7—N3—H3A	125.5	N5—C8—C7	112.84 (17)
C6—N3—H3A	125.5	N5—C8—C9	104.12 (19)
C7—N4—C1	109.12 (19)	C7—C8—C9	115.8 (2)
C7—N4—H4A	125.4	N5—C8—H8	107.9
C1—N4—H4A	125.4	C7—C8—H8	107.9
C8—N5—C11	107.51 (17)	C9—C8—H8	107.9
C8—N5—H5A	110.2	C8—C9—C10	102.4 (2)
C11—N5—H5A	110.2	C8—C9—H9A	111.3
C8—N5—H5B	110.2	C10—C9—H9A	111.3
C11—N5—H5B	110.2	C8—C9—H9B	111.3
H5A—N5—H5B	108.5	C10—C9—H9B	111.3
C2—C1—C6	121.6 (2)	H9A—C9—H9B	109.2
C2—C1—N4	132.3 (2)	C11—C10—C9	104.05 (19)
C6—C1—N4	106.1 (2)	C11—C10—H10A	110.9
C3—C2—C1	116.8 (3)	C9—C10—H10A	110.9
C3—C2—H2	121.6	C11—C10—H10B	110.9
C1—C2—H2	121.6	C9—C10—H10B	110.9
C2—C3—C4	121.5 (3)	H10A—C10—H10B	109.0
C2—C3—H3	119.2	C10—C11—N5	105.2 (2)
C4—C3—H3	119.2	C10—C11—H11A	110.7
C5—C4—C3	122.7 (3)	N5—C11—H11A	110.7
C5—C4—H4	118.7	C10—C11—H11B	110.7
C3—C4—H4	118.7	N5—C11—H11B	110.7
C4—C5—C6	116.0 (3)	H11A—C11—H11B	108.8
C4—C5—H5	122.0	O3—N1—O2	122.4 (2)
C6—C5—H5	122.0	O3—N1—O1	119.45 (19)
N3—C6—C1	106.27 (19)	O2—N1—O1	118.1 (2)
N3—C6—C5	132.2 (2)	O6—N2—O5	120.74 (19)
C1—C6—C5	121.5 (2)	O6—N2—O4	120.96 (19)
N4—C7—N3	109.58 (19)	O5—N2—O4	118.29 (18)
N4—C7—C8	123.10 (19)

C7—N4—C1—C2	−180.0 (3)	C1—N4—C7—N3	−0.9 (3)
C7—N4—C1—C6	0.2 (3)	C1—N4—C7—C8	−177.2 (2)
C6—C1—C2—C3	−0.4 (4)	C6—N3—C7—N4	1.2 (3)
N4—C1—C2—C3	179.8 (3)	C6—N3—C7—C8	177.4 (2)
C1—C2—C3—C4	1.0 (4)	C11—N5—C8—C7	149.12 (19)
C2—C3—C4—C5	−0.9 (5)	C11—N5—C8—C9	22.8 (2)
C3—C4—C5—C6	0.1 (4)	N4—C7—C8—N5	−157.4 (2)
C7—N3—C6—C1	−1.0 (2)	N3—C7—C8—N5	26.9 (3)
C7—N3—C6—C5	−180.0 (2)	N4—C7—C8—C9	−37.6 (3)
C2—C1—C6—N3	−179.4 (2)	N3—C7—C8—C9	146.7 (2)
N4—C1—C6—N3	0.5 (2)	N5—C8—C9—C10	−38.4 (2)
C2—C1—C6—C5	−0.3 (4)	C7—C8—C9—C10	−162.8 (2)
N4—C1—C6—C5	179.6 (2)	C8—C9—C10—C11	39.8 (3)
C4—C5—C6—N3	179.2 (2)	C9—C10—C11—N5	−25.8 (3)
C4—C5—C6—C1	0.4 (4)	C8—N5—C11—C10	2.0 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···O4ⁱ	0.86	1.93	2.788 (2)	177
N3—H3A···O5ⁱ	0.86	2.50	3.020 (2)	120
N5—H5B···O1ⁱ	0.90	1.89	2.771 (2)	167
N5—H5B···O3ⁱ	0.90	2.64	3.149 (2)	117
N5—H5A···O5ⁱⁱ	0.90	1.90	2.768 (2)	162
N4—H4A···O1	0.86	2.04	2.850 (2)	157
N4—H4A···O2	0.86	2.42	3.121 (3)	139

Symmetry codes: (i) −x+3/2, y−1/2, −z+3/2; (ii) x, −y+1, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₁H₁₅N₃²⁺·2NO₃⁻
M_r	313.28
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	298
a, b, c (Å)	22.078 (2), 11.154 (1), 14.670 (1)
β (°)	127.18 (1)
V (Å³)	2878.3 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.12
Crystal size (mm)	0.35 × 0.30 × 0.15

Data collection
Diffractometer	Rigaku Mercury2 diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.959, 0.982
No. of measured, independent and observed [I > 2σ(I)] reflections	14543, 3276, 2195
R_int	0.048
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.059, 0.144, 1.09
No. of reflections	3276
No. of parameters	199
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.31, −0.19

Computer programs: CrystalClear (Rigaku, 2005), 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
N3—H3A···O4ⁱ	0.86	1.93	2.788 (2)	176.6
N3—H3A···O5ⁱ	0.86	2.50	3.020 (2)	119.9
N5—H5B···O1ⁱ	0.90	1.89	2.771 (2)	167.2
N5—H5B···O3ⁱ	0.90	2.64	3.149 (2)	117.1
N5—H5A···O5ⁱⁱ	0.90	1.90	2.768 (2)	161.6
N4—H4A···O1	0.86	2.04	2.850 (2)	157.1
N4—H4A···O2	0.86	2.42	3.121 (3)	139.3

Symmetry codes: (i) −x+3/2, y−1/2, −z+3/2; (ii) x, −y+1, z−1/2.

Acknowledgements

This work was supported by a start-up grant from Southeast University to Professor Ren-Gen Xiong.

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