Literature DB >> 26396888

Crystal structure of 2-amino-pyridinium 6-chloro-nicotinate.

N Jeeva Jasmine1, A Rajam1, P Thomas Muthiah1, N Stanley1, I Abdul Razak2, M Mustaqim Rosli2.   

Abstract

In the title salt, C5H7N(+)·C6H3ClNO(-), the 2-amino-pyri-din-ium cation inter-acts with the carboxyl-ate group of the 6-chloro-nicotinate anion through a pair of independent N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. In the crystal, these dimeric units are connected further via N-H⋯O hydrogen bonds, forming chains along [001]. In addition, weak C-H⋯N and C-H⋯O hydrogen bonds, together with weak π-π inter-actions, with centroid-centroid distances of 3.6560 (5) and 3.6295 (5) Å, connect the chains, forming a two-dimensional network parallel to (100).

Entities:  

Keywords:  2-amino­pyridinium; 6-chloro­nicotinate; 6-chloro­pyridine-3-carboxyl­ate; crystal structure; noncovalent inter­actions; π–π stacking inter­actions

Year:  2015        PMID： 26396888      PMCID： PMC4555436          DOI： 10.1107/S2056989015014796

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


Related literature

For a background to noncovalent inter­actions, see: García-Raso et al. (2009 ▸). For the applications of pyridine compounds, see: Schwid et al. (1997 ▸); Rajkumar et al. (2015 ▸). For related structures, see: Xie (2007 ▸); Jennifer & Mu­thiah (2014 ▸); Chao et al. (1975 ▸); Bis & Zaworotko (2005 ▸); Jebas & Balasubramanian (2006 ▸). For information on π–π stacking inter­actions, see: Hunter (1994 ▸). For hydrogen-bond graph-set motifs, see: Bernstein et al. (1995 ▸);

Experimental

Crystal data

C5H7N2 +·C6H3ClNO2 − M = 251.67 Monoclinic, a = 8.6844 (4) Å b = 10.8112 (5) Å c = 11.9235 (6) Å β = 95.2046 (9)° V = 1114.87 (9) Å3 Z = 4 Mo Kα radiation μ = 0.34 mm−1 T = 100 K 0.51 × 0.40 × 0.17 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T min = 0.993, T max = 0.994 15546 measured reflections 4073 independent reflections 3771 reflections with I > 2σ(I) R int = 0.019

Refinement

R[F 2 > 2σ(F 2)] = 0.031 wR(F 2) = 0.092 S = 1.07 4073 reflections 166 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.50 e Å−3 Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT (Bruker, 2009 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: PLATON (Spek, 2009 ▸) and Mercury (Macrae et al., 2008 ▸); software used to prepare material for publication: PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015014796/lh5778sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015014796/lh5778Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S2056989015014796/lh5778Isup3.cml Click here for additional data file. . DOI: 10.1107/S2056989015014796/lh5778fig1.tif The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids. Click here for additional data file. . DOI: 10.1107/S2056989015014796/lh5778fig2.tif Part of the crystal structure with hydrogen bonds shown as dashed lines. Hydrogen atoms not involved hydrogen bonding have been removed for clarity. CCDC reference: 1417413 Additional supporting information: crystallographic information; 3D view; checkCIF report
C5H7N2+·C6H3ClNO2−Z = 4
Mr = 251.67F(000) = 520
Monoclinic, P21/cDx = 1.499 Mg m−3
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 8.6844 (4) Åθ = 2.4–32.7°
b = 10.8112 (5) ŵ = 0.34 mm−1
c = 11.9235 (6) ÅT = 100 K
β = 95.2046 (9)°Plate, colourless
V = 1114.87 (9) Å30.51 × 0.40 × 0.17 mm
Bruker SMART APEXII DUO CCD area-detector diffractometer4073 independent reflections
Radiation source: fine-focus sealed tube3771 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
φ and ω scansθmax = 32.7°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→13
Tmin = 0.993, Tmax = 0.994k = −16→16
15546 measured reflectionsl = −18→18
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092H atoms treated by a mixture of independent and constrained refinement
S = 1.07 W = 1/[Σ2(FO2) + (0.0539P)2 + 0.2679P] where P = (FO2 + 2FC2)/3
4073 reflections(Δ/σ)max < 0.001
166 parametersΔρmax = 0.50 e Å−3
0 restraintsΔρmin = −0.22 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
N20.08234 (8)0.17345 (6)0.03387 (6)0.0142 (2)
N3−0.02920 (9)0.19691 (7)0.20096 (6)0.0184 (2)
C70.17904 (9)0.11677 (8)−0.03367 (7)0.0177 (2)
C80.26497 (11)0.01655 (9)0.00290 (8)0.0228 (2)
C90.25206 (11)−0.02551 (8)0.11385 (8)0.0238 (2)
C100.15609 (10)0.03247 (8)0.18212 (7)0.0197 (2)
C110.06759 (9)0.13562 (7)0.14076 (6)0.0146 (2)
Cl10.54962 (2)0.18137 (2)0.23646 (2)0.0203 (1)
O10.18876 (7)0.61122 (6)−0.08641 (5)0.0192 (2)
O20.07082 (7)0.63585 (6)0.07132 (5)0.0171 (2)
N10.33406 (8)0.35025 (7)0.22723 (6)0.0166 (2)
C10.43180 (9)0.29272 (7)0.16629 (7)0.0150 (2)
C20.44779 (9)0.31497 (8)0.05297 (7)0.0168 (2)
C30.35703 (9)0.40792 (8)0.00135 (6)0.0158 (2)
C40.25507 (8)0.47360 (7)0.06340 (6)0.0129 (2)
C50.24641 (9)0.43930 (7)0.17505 (6)0.0152 (2)
C60.16403 (8)0.58120 (7)0.01150 (6)0.0135 (2)
H1N20.0255 (18)0.2389 (16)0.0024 (14)0.038 (4)*
H2N3−0.0831 (18)0.2538 (16)0.1688 (13)0.032 (4)*
H1N3−0.0454 (17)0.1728 (14)0.2703 (13)0.031 (4)*
H7A0.186900.14750−0.107600.0210*
H8A0.33130−0.02370−0.044700.0270*
H9A0.31080−0.095000.141400.0290*
H10A0.148800.003800.256800.0240*
H2A0.517700.268600.012800.0200*
H3A0.364100.42690−0.075800.0190*
H5A0.174400.481200.216900.0180*
U11U22U33U12U13U23
N20.0166 (3)0.0150 (3)0.0112 (3)−0.0003 (2)0.0027 (2)0.0014 (2)
N30.0217 (3)0.0218 (3)0.0125 (3)0.0003 (3)0.0053 (2)0.0033 (2)
C70.0201 (3)0.0187 (3)0.0148 (3)−0.0004 (3)0.0040 (3)−0.0023 (3)
C80.0229 (4)0.0206 (4)0.0249 (4)0.0039 (3)0.0024 (3)−0.0044 (3)
C90.0256 (4)0.0174 (4)0.0274 (4)0.0034 (3)−0.0034 (3)0.0010 (3)
C100.0234 (3)0.0170 (3)0.0180 (3)−0.0014 (3)−0.0024 (3)0.0050 (3)
C110.0166 (3)0.0150 (3)0.0121 (3)−0.0037 (2)0.0007 (2)0.0017 (2)
Cl10.0195 (1)0.0189 (1)0.0224 (1)0.0050 (1)0.0020 (1)0.0033 (1)
O10.0249 (3)0.0212 (3)0.0123 (2)0.0042 (2)0.0063 (2)0.0025 (2)
O20.0212 (3)0.0187 (3)0.0119 (2)0.0056 (2)0.0047 (2)0.0000 (2)
N10.0196 (3)0.0161 (3)0.0145 (3)0.0028 (2)0.0036 (2)0.0008 (2)
C10.0144 (3)0.0138 (3)0.0167 (3)0.0005 (2)0.0016 (2)0.0004 (2)
C20.0164 (3)0.0175 (3)0.0173 (3)0.0017 (2)0.0060 (3)−0.0007 (2)
C30.0172 (3)0.0171 (3)0.0136 (3)0.0004 (3)0.0050 (2)−0.0005 (2)
C40.0140 (3)0.0130 (3)0.0119 (3)−0.0008 (2)0.0025 (2)−0.0007 (2)
C50.0182 (3)0.0150 (3)0.0129 (3)0.0021 (3)0.0043 (2)0.0000 (2)
C60.0151 (3)0.0142 (3)0.0112 (3)−0.0008 (2)0.0019 (2)−0.0008 (2)
Cl1—C11.7438 (8)C10—C111.4173 (12)
O1—C61.2489 (9)C7—H7A0.9500
O2—C61.2719 (9)C8—H8A0.9500
N2—C111.3556 (10)C9—H9A0.9500
N2—C71.3609 (11)C10—H10A0.9500
N3—C111.3305 (11)C1—C21.3917 (12)
N2—H1N20.923 (17)C2—C31.3863 (12)
N3—H2N30.844 (16)C3—C41.3980 (11)
N3—H1N30.890 (15)C4—C51.3905 (10)
N1—C51.3444 (11)C4—C61.5075 (10)
N1—C11.3218 (11)C2—H2A0.9500
C7—C81.3645 (13)C3—H3A0.9500
C8—C91.4129 (13)C5—H5A0.9500
C9—C101.3687 (13)
Cl1···C4i3.5893 (8)C6···N2v3.4200 (10)
Cl1···C5i3.2804 (8)C6···O2v3.2056 (10)
Cl1···C93.6238 (10)C7···C33.5149 (12)
Cl1···H8Aii3.1000C7···C23.2663 (12)
Cl1···H3Aiii3.1000C7···N1vii3.2808 (11)
Cl1···H9Aiv3.0200C9···Cl13.6238 (10)
O1···N3v2.7830 (10)C10···O1iii3.1574 (10)
O1···C2vi3.2450 (10)C11···C13.5787 (11)
O1···C10vii3.1574 (10)C11···N13.3719 (11)
O2···C6v3.2056 (10)C3···H3Avi3.0700
O2···C4v3.3415 (10)C5···H7Aiii2.8500
O2···N3viii2.8490 (9)C6···H1N3viii3.049 (15)
O2···N2v2.7000 (9)C6···H1N2v2.544 (17)
O1···H3A2.5000C6···H2N3v2.833 (16)
O1···H1N2v2.726 (16)H1N2···H2N32.28 (2)
O1···H10Avii2.2500H1N2···O1v2.726 (16)
O1···H2N3v1.942 (17)H1N2···O2v1.781 (17)
O2···H5A2.5200H1N2···C6v2.544 (17)
O2···H1N2v1.781 (17)H2N3···O1v1.942 (17)
O2···H1N3viii1.962 (15)H2N3···C6v2.833 (16)
N1···C113.3719 (11)H2N3···H1N22.28 (2)
N1···C7iii3.2808 (11)H1N3···C6ix3.049 (15)
N2···O2v2.7000 (9)H1N3···H10A2.5000
N2···C6v3.4200 (10)H1N3···O2ix1.962 (15)
N3···O1v2.7830 (10)H1N3···H5Aix2.3700
N3···O2ix2.8490 (9)H3A···O12.5000
N1···H7Aiii2.4400H3A···C3vi3.0700
N3···H5Aix2.8700H3A···Cl1vii3.1000
C1···C113.5787 (11)H5A···O22.5200
C2···C3vi3.5309 (12)H5A···N3viii2.8700
C2···C73.2663 (12)H5A···H1N3viii2.3700
C2···O1vi3.2450 (10)H5A···H7Aiii2.5100
C3···C3vi3.1853 (12)H7A···H5Avii2.5100
C3···C73.5149 (12)H7A···N1vii2.4400
C3···C2vi3.5309 (12)H7A···C5vii2.8500
C4···Cl1iv3.5893 (8)H8A···Cl1ii3.1000
C4···O2v3.3415 (10)H9A···Cl1i3.0200
C5···Cl1iv3.2804 (8)H10A···O1iii2.2500
C6···C6v3.3366 (10)H10A···H1N32.5000
C7—N2—C11122.45 (7)C9—C10—H10A120.00
C7—N2—H1N2116.2 (10)C11—C10—H10A120.00
C11—N2—H1N2121.4 (10)Cl1—C1—N1116.05 (6)
C11—N3—H2N3118.0 (11)Cl1—C1—C2118.64 (6)
C11—N3—H1N3121.1 (10)N1—C1—C2125.31 (7)
H2N3—N3—H1N3120.5 (14)C1—C2—C3116.97 (7)
C1—N1—C5116.58 (7)C2—C3—C4119.68 (7)
N2—C7—C8121.16 (8)C3—C4—C5117.59 (7)
C7—C8—C9117.85 (8)C3—C4—C6120.56 (6)
C8—C9—C10120.92 (8)C5—C4—C6121.80 (6)
C9—C10—C11119.58 (8)N1—C5—C4123.81 (7)
N3—C11—C10123.60 (7)O1—C6—O2125.14 (7)
N2—C11—N3118.37 (7)O1—C6—C4117.13 (6)
N2—C11—C10118.04 (7)O2—C6—C4117.71 (6)
N2—C7—H7A119.00C1—C2—H2A122.00
C8—C7—H7A119.00C3—C2—H2A121.00
C9—C8—H8A121.00C2—C3—H3A120.00
C7—C8—H8A121.00C4—C3—H3A120.00
C8—C9—H9A120.00N1—C5—H5A118.00
C10—C9—H9A120.00C4—C5—H5A118.00
C11—N2—C7—C81.11 (12)Cl1—C1—C2—C3−177.22 (6)
C7—N2—C11—N3179.67 (8)N1—C1—C2—C32.22 (13)
C7—N2—C11—C10−0.50 (11)C1—C2—C3—C4−0.29 (12)
C1—N1—C5—C4−0.78 (12)C2—C3—C4—C5−1.86 (11)
C5—N1—C1—Cl1177.76 (6)C2—C3—C4—C6175.44 (7)
C5—N1—C1—C2−1.69 (12)C3—C4—C5—N12.51 (12)
N2—C7—C8—C9−0.90 (13)C6—C4—C5—N1−174.75 (7)
C7—C8—C9—C100.14 (14)C3—C4—C6—O1−2.82 (11)
C8—C9—C10—C110.44 (13)C3—C4—C6—O2178.64 (7)
C9—C10—C11—N2−0.26 (12)C5—C4—C6—O1174.36 (7)
C9—C10—C11—N3179.55 (8)C5—C4—C6—O2−4.18 (11)
D—H···AD—HH···AD···AD—H···A
N2—H1N2···O2v0.923 (17)1.781 (17)2.7000 (9)173.5 (15)
N3—H2N3···O1v0.844 (16)1.942 (17)2.7830 (10)174.1 (15)
N3—H1N3···O2ix0.890 (15)1.962 (15)2.8490 (9)174.0 (13)
C7—H7A···N1vii0.952.443.2808 (11)147
C10—H10A···O1iii0.952.253.1574 (10)160
Table 1

Hydrogen-bond geometry (, )

DHA DHHA D A DHA
N2H1N2O2i 0.923(17)1.781(17)2.7000(9)173.5(15)
N3H2N3O1i 0.844(16)1.942(17)2.7830(10)174.1(15)
N3H1N3O2ii 0.890(15)1.962(15)2.8490(9)174.0(13)
C7H7AN1iii 0.952.443.2808(11)147
C10H10AO1iv 0.952.253.1574(10)160

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

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