Literature DB >> 25309291

Crystal structure of 1H-imidazol-3-ium 2-(1,3-dioxoisoindolin-2-yl)acetate.

Shaaban K Mohamed1, Mehmet Akkurt2, Herman Potgieter3, Muizz Ali4.   

Abstract

The title salt, C3H5N2 (+)·C10H6NO4 (-), was obtained during a study of the co-crystallization of N'-[bis-(1H-imidazol-1-yl)methyl-ene]isonicotinohydrazide with (1,3-dioxoisoindolin-2-yl)acetic acid under aqueous conditions. The 1,3-dioxoisoindolinyl ring system of the anion is essentially planar [maximum deviation = 0.023 (2) Å]. In the crystal, cations and anions are linked via classical N-H⋯O hydrogen bonds and weak C-H⋯O hydrogen bonds, forming a three-dimensional network. Weak C-H⋯π inter-actions and π-π stacking inter-actions [centroid-centroid distances = 3.4728 (13) and 3.7339 (13) Å] also occur in the crystal.

Entities:  

Keywords:  1H-imidazol-3-ium salt; 2-(1,3-dioxoisoindolin-2-yl)acetate salt; co-crystallization; crystal structure; hydrogen bonding; pharmaceuticals; π–π stacking inter­actions

Year:  2014        PMID： 25309291      PMCID： PMC4186205          DOI： 10.1107/S1600536814017619

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


Related literature

For the use of co-crystals in drug design, see: Babu & Nangia (2011 ▶); Sekhon (2013 ▶); Frantz (2006 ▶); Pan et al. (2008 ▶); Vermeire et al. (2001 ▶).

Experimental

Crystal data

C3H5N2 +·C10H6NO4 − M = 273.25 Monoclinic, a = 9.8750 (7) Å b = 18.0543 (15) Å c = 7.0942 (5) Å β = 100.955 (7)° V = 1241.75 (16) Å3 Z = 4 Mo Kα radiation μ = 0.11 mm−1 T = 150 K 0.09 × 0.02 × 0.02 mm

Data collection

Agilent SuperNova, Single source at offset, Eos diffractometer Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013 ▶) T min = 0.859, T max = 1.000 4781 measured reflections 2756 independent reflections 1993 reflections with I > 2σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.053 wR(F 2) = 0.118 S = 1.06 2756 reflections 189 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.26 e Å−3 Δρmin = −0.26 e Å−3

Data collection: CrysAlis PRO (Agilent, 2013 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶) and PLATON (Spek, 2009 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814017619/xu5807sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814017619/xu5807Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S1600536814017619/xu5807Isup3.cml Click here for additional data file. . DOI: 10.1107/S1600536814017619/xu5807fig1.tif Perspective view of the title compound (I). Displacement ellipsoids are drawn at the 50% probability level. Click here for additional data file. a . DOI: 10.1107/S1600536814017619/xu5807fig2.tif Packing viewed down the a axis showing the inter­molecular inter­actions as dotted lines. CCDC reference: 1017262 Additional supporting information: crystallographic information; 3D view; checkCIF report
C3H5N2+·C10H6NO4−F(000) = 568
Mr = 273.25Dx = 1.462 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.7107 Å
Hall symbol: -P 2ybcCell parameters from 1373 reflections
a = 9.8750 (7) Åθ = 4.0–27.4°
b = 18.0543 (15) ŵ = 0.11 mm−1
c = 7.0942 (5) ÅT = 150 K
β = 100.955 (7)°Block, colourless
V = 1241.75 (16) Å30.09 × 0.02 × 0.02 mm
Z = 4
Agilent SuperNova, Single source at offset, Eos diffractometer2756 independent reflections
Radiation source: SuperNova (Mo) X-ray Source1993 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.028
Detector resolution: 8.0714 pixels mm-1θmax = 29.1°, θmin = 3.1°
ω scansh = −12→12
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2013)k = −9→23
Tmin = 0.859, Tmax = 1.000l = −9→5
4781 measured reflections
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.053H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.118w = 1/[σ2(Fo2) + (0.0327P)2 + 0.2765P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2756 reflectionsΔρmax = 0.26 e Å−3
189 parametersΔρmin = −0.26 e Å−3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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
O10.16235 (14)0.29586 (8)−0.05484 (19)0.0277 (5)
O20.54966 (15)0.42729 (9)0.1952 (2)0.0316 (5)
O30.24304 (16)0.45939 (9)0.33073 (19)0.0310 (5)
O40.14750 (14)0.54438 (8)0.11691 (18)0.0236 (5)
N10.33840 (16)0.37710 (10)0.0589 (2)0.0202 (5)
C10.5087 (2)0.29370 (12)0.1790 (3)0.0215 (6)
C20.6297 (2)0.25882 (14)0.2609 (3)0.0292 (7)
C30.6299 (2)0.18176 (14)0.2585 (3)0.0344 (8)
C40.5146 (3)0.14112 (14)0.1752 (3)0.0343 (8)
C50.3917 (2)0.17722 (12)0.0932 (3)0.0265 (7)
C60.3923 (2)0.25360 (12)0.0988 (3)0.0207 (6)
C70.2809 (2)0.30730 (12)0.0234 (3)0.0199 (6)
C80.4768 (2)0.37384 (13)0.1526 (3)0.0221 (6)
C90.2655 (2)0.44563 (12)0.0027 (3)0.0231 (7)
C100.2159 (2)0.48474 (12)0.1675 (3)0.0212 (6)
N20.90678 (17)0.40848 (10)0.2486 (2)0.0228 (6)
N30.91310 (17)0.40494 (10)0.5539 (2)0.0221 (6)
C110.8627 (2)0.44091 (13)0.3939 (3)0.0227 (6)
C120.9894 (2)0.34962 (12)0.3193 (3)0.0244 (7)
C130.9924 (2)0.34743 (12)0.5102 (3)0.0247 (7)
H20.709500.286200.316600.0350*
H30.711400.156100.315600.0410*
H40.519000.088600.173700.0410*
H50.311700.150300.036400.0320*
H9A0.184900.43490−0.099800.0280*
H9B0.327200.47940−0.051500.0280*
H2N0.885 (3)0.4263 (15)0.114 (4)0.061 (8)*
H3N0.894 (2)0.4211 (13)0.677 (3)0.040 (7)*
H110.804300.483100.384200.0270*
H121.035400.316800.247700.0290*
H131.040700.312500.598200.0300*
U11U22U33U12U13U23
O10.0257 (8)0.0262 (9)0.0296 (8)−0.0052 (7)0.0014 (6)−0.0001 (7)
O20.0293 (8)0.0287 (10)0.0353 (9)−0.0110 (7)0.0026 (6)0.0010 (7)
O30.0450 (10)0.0266 (10)0.0218 (8)0.0109 (8)0.0074 (7)0.0055 (7)
O40.0313 (8)0.0196 (9)0.0195 (7)0.0062 (7)0.0040 (6)0.0007 (6)
N10.0209 (8)0.0159 (10)0.0235 (9)0.0004 (7)0.0038 (7)−0.0011 (7)
C10.0241 (10)0.0227 (12)0.0191 (10)0.0015 (9)0.0080 (8)0.0019 (9)
C20.0248 (11)0.0383 (15)0.0259 (11)0.0047 (11)0.0083 (9)0.0046 (10)
C30.0383 (14)0.0365 (16)0.0308 (13)0.0171 (12)0.0130 (10)0.0083 (11)
C40.0523 (15)0.0262 (14)0.0280 (12)0.0147 (12)0.0168 (11)0.0067 (11)
C50.0395 (13)0.0205 (13)0.0209 (11)−0.0008 (10)0.0090 (9)−0.0030 (9)
C60.0270 (11)0.0205 (12)0.0164 (10)0.0007 (9)0.0091 (8)−0.0002 (9)
C70.0237 (10)0.0199 (12)0.0174 (10)−0.0018 (9)0.0069 (8)−0.0009 (9)
C80.0211 (10)0.0267 (13)0.0191 (10)−0.0018 (9)0.0057 (8)0.0015 (9)
C90.0257 (11)0.0199 (12)0.0233 (11)0.0017 (9)0.0039 (8)0.0016 (9)
C100.0217 (10)0.0206 (12)0.0206 (10)−0.0034 (9)0.0025 (8)0.0003 (9)
N20.0241 (9)0.0260 (11)0.0190 (9)0.0016 (8)0.0061 (7)0.0021 (8)
N30.0245 (9)0.0233 (11)0.0184 (9)0.0000 (8)0.0038 (7)0.0003 (8)
C110.0223 (10)0.0240 (12)0.0212 (11)0.0017 (9)0.0025 (8)0.0007 (9)
C120.0225 (10)0.0234 (13)0.0285 (12)0.0052 (9)0.0079 (8)0.0010 (10)
C130.0236 (11)0.0208 (13)0.0289 (12)0.0059 (9)0.0033 (9)0.0057 (9)
O1—C71.214 (2)C2—C31.391 (4)
O2—C81.207 (3)C3—C41.389 (3)
O3—C101.227 (3)C4—C51.403 (3)
O4—C101.285 (3)C5—C61.380 (3)
N1—C71.386 (3)C6—C71.488 (3)
N1—C81.403 (3)C9—C101.524 (3)
N1—C91.449 (3)C2—H20.9500
N2—C111.329 (3)C3—H30.9500
N2—C121.375 (3)C4—H40.9500
N3—C111.320 (3)C5—H50.9500
N3—C131.371 (3)C9—H9A0.9900
N2—H2N0.99 (3)C9—H9B0.9900
N3—H3N0.97 (2)C12—C131.350 (3)
C1—C81.485 (3)C11—H110.9500
C1—C21.378 (3)C12—H120.9500
C1—C61.386 (3)C13—H130.9500
C7—N1—C8112.13 (17)O3—C10—O4125.81 (19)
C7—N1—C9124.17 (16)O3—C10—C9120.46 (19)
C8—N1—C9123.69 (18)O4—C10—C9113.72 (17)
C11—N2—C12108.47 (16)C3—C2—H2121.00
C11—N3—C13108.44 (16)C1—C2—H2121.00
C12—N2—H2N127.4 (16)C2—C3—H3119.00
C11—N2—H2N124.1 (16)C4—C3—H3119.00
C13—N3—H3N130.3 (13)C3—C4—H4120.00
C11—N3—H3N121.2 (13)C5—C4—H4120.00
C2—C1—C8130.2 (2)C4—C5—H5122.00
C6—C1—C8108.52 (18)C6—C5—H5122.00
C2—C1—C6121.3 (2)C10—C9—H9A109.00
C1—C2—C3117.1 (2)N1—C9—H9B109.00
C2—C3—C4122.1 (2)H9A—C9—H9B108.00
C3—C4—C5120.4 (2)N1—C9—H9A109.00
C4—C5—C6117.0 (2)C10—C9—H9B109.00
C1—C6—C5122.19 (19)N2—C11—N3108.95 (19)
C1—C6—C7107.83 (18)N2—C12—C13106.68 (18)
C5—C6—C7129.97 (19)N3—C13—C12107.47 (18)
N1—C7—C6106.14 (17)N2—C11—H11126.00
O1—C7—N1124.34 (19)N3—C11—H11126.00
O1—C7—C6129.5 (2)N2—C12—H12127.00
N1—C8—C1105.36 (18)C13—C12—H12127.00
O2—C8—C1130.18 (19)N3—C13—H13126.00
O2—C8—N1124.5 (2)C12—C13—H13126.00
N1—C9—C10113.57 (17)
C9—N1—C7—C6178.15 (17)C2—C1—C6—C5−1.2 (3)
C7—N1—C8—O2178.4 (2)C6—C1—C2—C30.3 (3)
C9—N1—C8—O2−0.4 (3)C8—C1—C6—C7−1.6 (2)
C7—N1—C8—C1−0.3 (2)C8—C1—C6—C5177.06 (19)
C8—N1—C7—O1179.48 (19)C6—C1—C8—O2−177.4 (2)
C9—N1—C7—O1−1.7 (3)C6—C1—C8—N11.2 (2)
C8—N1—C7—C6−0.7 (2)C1—C2—C3—C40.9 (3)
C8—N1—C9—C10−79.5 (2)C2—C3—C4—C5−1.3 (3)
C9—N1—C8—C1−179.10 (17)C3—C4—C5—C60.4 (3)
C7—N1—C9—C10101.9 (2)C4—C5—C6—C7179.2 (2)
C12—N2—C11—N3−0.4 (2)C4—C5—C6—C10.8 (3)
C11—N2—C12—C130.5 (2)C1—C6—C7—O1−178.8 (2)
C13—N3—C11—N20.0 (2)C5—C6—C7—N1−177.1 (2)
C11—N3—C13—C120.3 (2)C1—C6—C7—N11.4 (2)
C2—C1—C8—O20.7 (4)C5—C6—C7—O12.7 (4)
C2—C1—C8—N1179.3 (2)N1—C9—C10—O4−177.97 (17)
C2—C1—C6—C7−179.89 (19)N1—C9—C10—O32.7 (3)
C8—C1—C2—C3−177.6 (2)N2—C12—C13—N3−0.5 (2)
D—H···AD—HH···AD···AD—H···A
N2—H2N···O4i0.99 (3)1.69 (3)2.6846 (19)178 (4)
N3—H3N···O3ii0.97 (2)2.54 (2)3.087 (2)115.4 (16)
N3—H3N···O4ii0.97 (2)1.71 (2)2.680 (2)175 (2)
C3—H3···O4iii0.952.453.321 (3)153
C5—H5···O3iv0.952.483.266 (3)141
C9—H9A···O10.992.552.891 (3)100
C9—H9B···O2i0.992.413.397 (3)172
C11—H11···O3ii0.952.402.987 (3)120
C13—H13···O1v0.952.543.352 (2)143
C2—H2···Cg40.952.873.805 (2)166
Table 1

Hydrogen-bond geometry (Å, °)

Cg4 is the centroid of the N2/N3/C11–C13 ring.

D—H⋯A D—HH⋯A D⋯A D—H⋯A
N2—H2N⋯O4i 0.99 (3)1.69 (3)2.6846 (19)178 (4)
N3—H3N⋯O4ii 0.97 (2)1.71 (2)2.680 (2)175 (2)
C3—H3⋯O4iii 0.952.453.321 (3)153
C5—H5⋯O3iv 0.952.483.266 (3)141
C9—H9B⋯O2i 0.992.413.397 (3)172
C11—H11⋯O3ii 0.952.402.987 (3)120
C13—H13⋯O1v 0.952.543.352 (2)143
C2—H2⋯Cg40.952.873.805 (2)166

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

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