Literature DB >> 21583211

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

Jing Dai1.   

Abstract

In the title compound, C(11)H(15)N(3) (2+)·2NO(3) (-), 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.

Entities:  

Year:  2009        PMID: 21583211      PMCID: PMC2969558          DOI: 10.1107/S1600536809018558

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


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

C11H15N3 2+·2NO3 − M = 313.28 Monoclinic, 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[F 2 > 2σ(F 2)] = 0.059 wR(F 2) = 0.144 S = 1.09 3276 reflections 199 parameters H-atom parameters constrained Δρmax = 0.31 e Å−3 Δρmin = −0.19 e Å−3 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. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018558/sj2610sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018558/sj2610Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C11H15N32+·2NO3F(000) = 1312
Mr = 313.28Dx = 1.446 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3275 reflections
a = 22.078 (2) Åθ = 3.2–27.5°
b = 11.154 (1) ŵ = 0.12 mm1
c = 14.670 (1) ÅT = 298 K
β = 127.18 (1)°Block, colourless
V = 2878.3 (4) Å30.35 × 0.30 × 0.15 mm
Z = 8
Rigaku Mercury2 diffractometer3276 independent reflections
Radiation source: fine-focus sealed tube2195 reflections with I > 2σ(I)
graphiteRint = 0.048
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.2°
ω scansh = −28→28
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −14→14
Tmin = 0.959, Tmax = 0.982l = −18→19
14543 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.144H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.0493P)2 + 2.1933P] where P = (Fo2 + 2Fc2)/3
3276 reflections(Δ/σ)max < 0.001
199 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = −0.19 e Å3
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.
xyzUiso*/Ueq
N30.66938 (10)0.39290 (15)0.56483 (15)0.0433 (4)
H3A0.69660.32900.59370.052*
N40.63804 (11)0.58040 (17)0.53606 (17)0.0513 (5)
H4A0.64140.65720.54280.062*
N50.83307 (9)0.45350 (16)0.71441 (14)0.0429 (4)
H5A0.81630.41190.65060.052*
H5B0.84250.40160.76860.052*
C10.57133 (13)0.5163 (2)0.4595 (2)0.0500 (6)
C20.49697 (15)0.5521 (3)0.3784 (3)0.0709 (8)
H20.48320.63250.36640.085*
C30.44437 (16)0.4628 (3)0.3162 (3)0.0778 (9)
H30.39390.48340.25990.093*
C40.46486 (16)0.3430 (3)0.3353 (2)0.0725 (8)
H40.42730.28560.29200.087*
C50.53812 (15)0.3057 (2)0.4155 (2)0.0593 (7)
H50.55130.22500.42760.071*
C60.59181 (12)0.3961 (2)0.47789 (19)0.0448 (5)
C70.69499 (12)0.50468 (19)0.59632 (18)0.0418 (5)
C80.77457 (13)0.54335 (19)0.6904 (2)0.0465 (6)
H80.77850.55300.76020.056*
C90.80026 (15)0.6590 (2)0.6698 (2)0.0616 (7)
H9A0.77990.72810.68310.074*
H9B0.78520.66260.59260.074*
C100.88635 (15)0.6521 (2)0.7577 (2)0.0617 (7)
H10A0.91120.70440.73670.074*
H10B0.90220.67450.83310.074*
C110.90467 (14)0.5220 (2)0.7552 (2)0.0556 (6)
H11A0.94710.49530.83080.067*
H11B0.91740.51070.70300.067*
O10.64618 (11)0.82051 (14)0.60914 (14)0.0612 (5)
O20.58007 (14)0.83408 (18)0.42662 (16)0.0852 (7)
O30.59348 (11)0.98868 (15)0.52487 (15)0.0672 (5)
N10.60605 (11)0.88315 (18)0.51830 (16)0.0492 (5)
O40.74570 (10)0.68205 (14)0.85048 (13)0.0533 (4)
O50.81397 (9)0.66960 (14)1.03479 (13)0.0513 (4)
O60.74016 (11)0.52300 (15)0.93113 (17)0.0698 (5)
N20.76639 (11)0.62317 (16)0.93912 (16)0.0447 (5)
U11U22U33U12U13U23
N30.0448 (10)0.0328 (9)0.0462 (10)0.0007 (8)0.0243 (9)−0.0039 (8)
N40.0516 (12)0.0344 (10)0.0625 (13)0.0033 (9)0.0316 (11)−0.0006 (9)
N50.0440 (10)0.0434 (10)0.0335 (9)−0.0035 (8)0.0193 (8)−0.0069 (8)
C10.0441 (13)0.0517 (14)0.0519 (14)0.0021 (11)0.0278 (12)0.0013 (11)
C20.0538 (17)0.0731 (19)0.0754 (19)0.0149 (14)0.0336 (15)0.0152 (15)
C30.0405 (15)0.110 (3)0.0671 (19)0.0017 (17)0.0243 (14)0.0035 (18)
C40.0516 (17)0.092 (2)0.0664 (18)−0.0206 (16)0.0319 (15)−0.0162 (17)
C50.0569 (16)0.0599 (16)0.0629 (16)−0.0148 (13)0.0371 (14)−0.0149 (13)
C60.0439 (13)0.0464 (13)0.0459 (13)−0.0027 (10)0.0280 (11)−0.0055 (10)
C70.0455 (13)0.0349 (11)0.0445 (12)−0.0014 (9)0.0270 (11)−0.0066 (9)
C80.0518 (13)0.0391 (12)0.0487 (13)−0.0036 (10)0.0304 (12)−0.0098 (10)
C90.0662 (17)0.0392 (13)0.0772 (18)−0.0109 (12)0.0421 (15)−0.0112 (13)
C100.0657 (16)0.0575 (16)0.0641 (16)−0.0226 (13)0.0404 (14)−0.0202 (13)
C110.0496 (14)0.0642 (16)0.0529 (14)−0.0100 (12)0.0310 (12)−0.0077 (12)
O10.0807 (12)0.0462 (10)0.0502 (10)0.0166 (9)0.0361 (10)0.0115 (8)
O20.1258 (19)0.0759 (14)0.0539 (12)−0.0102 (13)0.0543 (13)−0.0108 (10)
O30.0808 (13)0.0431 (10)0.0649 (12)0.0163 (9)0.0373 (10)0.0099 (8)
N10.0563 (12)0.0456 (12)0.0463 (11)0.0003 (9)0.0313 (10)0.0037 (9)
O40.0766 (12)0.0444 (9)0.0399 (9)0.0054 (8)0.0357 (9)0.0043 (7)
O50.0596 (10)0.0485 (9)0.0389 (9)−0.0026 (8)0.0261 (8)0.0033 (7)
O60.0716 (12)0.0441 (10)0.0778 (13)−0.0113 (9)0.0367 (11)0.0063 (9)
N20.0514 (11)0.0372 (10)0.0485 (11)0.0065 (9)0.0318 (10)0.0053 (9)
N3—C71.331 (3)C5—H50.9300
N3—C61.386 (3)C7—C81.499 (3)
N3—H3A0.8600C8—C91.511 (3)
N4—C71.316 (3)C8—H80.9800
N4—C11.393 (3)C9—C101.523 (4)
N4—H4A0.8600C9—H9A0.9700
N5—C81.499 (3)C9—H9B0.9700
N5—C111.516 (3)C10—C111.514 (4)
N5—H5A0.9000C10—H10A0.9700
N5—H5B0.9000C10—H10B0.9700
C1—C21.382 (4)C11—H11A0.9700
C1—C61.388 (3)C11—H11B0.9700
C2—C31.375 (4)O1—N11.274 (2)
C2—H20.9300O2—N11.227 (2)
C3—C41.384 (4)O3—N11.226 (2)
C3—H30.9300O4—N21.270 (2)
C4—C51.369 (4)O5—N21.249 (2)
C4—H40.9300O6—N21.231 (2)
C5—C61.396 (3)
C7—N3—C6108.93 (18)N3—C7—C8127.21 (19)
C7—N3—H3A125.5N5—C8—C7112.84 (17)
C6—N3—H3A125.5N5—C8—C9104.12 (19)
C7—N4—C1109.12 (19)C7—C8—C9115.8 (2)
C7—N4—H4A125.4N5—C8—H8107.9
C1—N4—H4A125.4C7—C8—H8107.9
C8—N5—C11107.51 (17)C9—C8—H8107.9
C8—N5—H5A110.2C8—C9—C10102.4 (2)
C11—N5—H5A110.2C8—C9—H9A111.3
C8—N5—H5B110.2C10—C9—H9A111.3
C11—N5—H5B110.2C8—C9—H9B111.3
H5A—N5—H5B108.5C10—C9—H9B111.3
C2—C1—C6121.6 (2)H9A—C9—H9B109.2
C2—C1—N4132.3 (2)C11—C10—C9104.05 (19)
C6—C1—N4106.1 (2)C11—C10—H10A110.9
C3—C2—C1116.8 (3)C9—C10—H10A110.9
C3—C2—H2121.6C11—C10—H10B110.9
C1—C2—H2121.6C9—C10—H10B110.9
C2—C3—C4121.5 (3)H10A—C10—H10B109.0
C2—C3—H3119.2C10—C11—N5105.2 (2)
C4—C3—H3119.2C10—C11—H11A110.7
C5—C4—C3122.7 (3)N5—C11—H11A110.7
C5—C4—H4118.7C10—C11—H11B110.7
C3—C4—H4118.7N5—C11—H11B110.7
C4—C5—C6116.0 (3)H11A—C11—H11B108.8
C4—C5—H5122.0O3—N1—O2122.4 (2)
C6—C5—H5122.0O3—N1—O1119.45 (19)
N3—C6—C1106.27 (19)O2—N1—O1118.1 (2)
N3—C6—C5132.2 (2)O6—N2—O5120.74 (19)
C1—C6—C5121.5 (2)O6—N2—O4120.96 (19)
N4—C7—N3109.58 (19)O5—N2—O4118.29 (18)
N4—C7—C8123.10 (19)
C7—N4—C1—C2−180.0 (3)C1—N4—C7—N3−0.9 (3)
C7—N4—C1—C60.2 (3)C1—N4—C7—C8−177.2 (2)
C6—C1—C2—C3−0.4 (4)C6—N3—C7—N41.2 (3)
N4—C1—C2—C3179.8 (3)C6—N3—C7—C8177.4 (2)
C1—C2—C3—C41.0 (4)C11—N5—C8—C7149.12 (19)
C2—C3—C4—C5−0.9 (5)C11—N5—C8—C922.8 (2)
C3—C4—C5—C60.1 (4)N4—C7—C8—N5−157.4 (2)
C7—N3—C6—C1−1.0 (2)N3—C7—C8—N526.9 (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—C9146.7 (2)
N4—C1—C6—N30.5 (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—C5179.6 (2)C8—C9—C10—C1139.8 (3)
C4—C5—C6—N3179.2 (2)C9—C10—C11—N5−25.8 (3)
C4—C5—C6—C10.4 (4)C8—N5—C11—C102.0 (2)
D—H···AD—HH···AD···AD—H···A
N3—H3A···O4i0.861.932.788 (2)177
N3—H3A···O5i0.862.503.020 (2)120
N5—H5B···O1i0.901.892.771 (2)167
N5—H5B···O3i0.902.643.149 (2)117
N5—H5A···O5ii0.901.902.768 (2)162
N4—H4A···O10.862.042.850 (2)157
N4—H4A···O20.862.423.121 (3)139
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N3—H3A⋯O4i0.861.932.788 (2)177
N3—H3A⋯O5i0.862.503.020 (2)120
N5—H5B⋯O1i0.901.892.771 (2)167
N5—H5B⋯O3i0.902.643.149 (2)117
N5—H5A⋯O5ii0.901.902.768 (2)162
N4—H4A⋯O10.862.042.850 (2)157
N4—H4A⋯O20.862.423.121 (3)139

Symmetry codes: (i) ; (ii) .

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