Literature DB >> 21588612

2-Amino-5-bromo-pyridinium 6-oxo-1,6-dihydro-pyridine-2-carboxyl-ate monohydrate.

Madhukar Hemamalini1, Hoong-Kun Fun.   

Abstract

In the crystal structure of the title salt, C(5)H(6)BrN(2) (+)·C(6)H(4)NO(3) (-)·H(2)O, the protonated N atom and the 2-amino group of the cation are n class="Chemical">hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are further connected via O-H⋯O, N-H⋯O, N-H⋯Br and C-H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. The water mol-ecules self-assemble through O-H⋯O hydrogen bonds, forming one-dimensional supra-molecular chains along the a axis, with graph-set notation C(2) (2)(4).

Entities:  

Year:  2010        PMID: 21588612      PMCID: PMC3008071          DOI: 10.1107/S1600536810030916

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


Related literature

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 ▶); Katritzky et al. (1996 ▶). For details of 6-hy­droxy­picolinic acid, see: Sun et al. (2004 ▶); Soares-Santos et al. (2003 ▶). For a related structure, see: Sawada & Ohashi (1998 ▶). For details of n class="Chemical">hydrogen bonding, see: Jeffrey & Saenger (1991 ▶); Jeffrey (1997 ▶); Scheiner (1997 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C5H6BrN2n class="Chemical">C6H4NO3 −·H2O M = 330.15 Orthorhombic, a = 3.8616 (1) Å b = 15.8227 (2) Å c = 20.8961 (3) Å V = 1276.77 (4) Å3 Z = 4 Mo Kα radiation μ = 3.23 mm−1 T = 296 K 0.35 × 0.18 × 0.12 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.400, T max = 0.694 8884 measured reflections 3718 independent reflections 3105 reflections with I > 2σ(I) R int = 0.022

Refinement

R[F 2 > 2σ(F 2)] = 0.031 wR(F 2) = 0.097 S = 1.09 3718 reflections 172 parameters 3 restraints H-atom parameters constrained Δρmax = 0.37 e Å−3 Δρmin = −0.32 e Å−3 Absolute structure: Flack (1983 ▶), 1482 Friedel pairs Flack parameter: 0.011 (12) Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810030916/is2585sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810030916/is2585Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H6BrN2+·C6H4NO3·H2OF(000) = 664
Mr = 330.15Dx = 1.718 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 4297 reflections
a = 3.8616 (1) Åθ = 2.6–27.5°
b = 15.8227 (2) ŵ = 3.23 mm1
c = 20.8961 (3) ÅT = 296 K
V = 1276.77 (4) Å3Block, colourless
Z = 40.35 × 0.18 × 0.12 mm
Bruker SMART APEXII CCD area-detector diffractometer3718 independent reflections
Radiation source: fine-focus sealed tube3105 reflections with I > 2σ(I)
graphiteRint = 0.022
φ and ω scansθmax = 30.1°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −5→5
Tmin = 0.400, Tmax = 0.694k = −22→19
8884 measured reflectionsl = −20→29
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.031H-atom parameters constrained
wR(F2) = 0.097w = 1/[σ2(Fo2) + (0.036P)2 + 0.5546P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
3718 reflectionsΔρmax = 0.37 e Å3
172 parametersΔρmin = −0.32 e Å3
3 restraintsAbsolute structure: Flack (1983), 1482 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.011 (12)
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
Br10.68523 (9)0.02155 (2)0.832419 (15)0.04315 (11)
N10.9529 (7)0.01356 (17)1.02199 (12)0.0358 (5)
H1B1.0573−0.02211.04630.043*
N20.8795 (10)0.09857 (18)1.10959 (13)0.0490 (8)
H2A0.98000.06091.13270.059*
H2B0.80670.14461.12680.059*
C10.9123 (9)−0.00566 (19)0.95935 (15)0.0357 (7)
H1A0.9939−0.05700.94370.043*
C20.7526 (7)0.04972 (19)0.91899 (14)0.0347 (7)
C30.6342 (9)0.1270 (2)0.94344 (16)0.0408 (7)
H3A0.52710.16570.91640.049*
C40.6750 (10)0.14591 (18)1.00655 (15)0.0384 (7)
H4A0.59810.19741.02270.046*
C50.8371 (10)0.08579 (19)1.04763 (14)0.0363 (6)
O10.1449 (9)0.24380 (15)0.84486 (11)0.0517 (7)
O20.1646 (8)0.08864 (15)0.59255 (11)0.0525 (6)
O30.3456 (8)0.03807 (15)0.68650 (11)0.0529 (7)
N30.1458 (8)0.17784 (15)0.74829 (11)0.0337 (5)
H3B0.24650.13540.76600.040*
C60.0674 (9)0.24462 (19)0.78634 (16)0.0374 (7)
C7−0.0997 (9)0.3135 (2)0.75378 (17)0.0427 (8)
H7A−0.15830.36210.77640.051*
C8−0.1722 (11)0.3084 (2)0.69074 (17)0.0438 (7)
H8A−0.28410.35320.67080.053*
C9−0.0818 (10)0.2363 (2)0.65430 (15)0.0398 (7)
H9A−0.13210.23330.61080.048*
C100.0787 (9)0.1721 (2)0.68434 (14)0.0351 (7)
C110.2065 (10)0.09186 (19)0.65253 (14)0.0378 (7)
O1W0.5862 (19)0.3110 (3)0.51273 (19)0.133 (2)
H1W0.44510.34960.49060.159*
H2W0.71110.27780.48320.159*
U11U22U33U12U13U23
Br10.04628 (18)0.04800 (18)0.03519 (15)−0.00207 (15)−0.00408 (15)−0.00074 (15)
N10.0457 (14)0.0297 (12)0.0319 (11)0.0062 (12)−0.0001 (11)0.0035 (11)
N20.076 (2)0.0353 (13)0.0355 (13)0.0094 (15)−0.0032 (15)0.0006 (12)
C10.0412 (16)0.0307 (15)0.0353 (14)0.0010 (12)0.0025 (13)−0.0024 (12)
C20.0359 (19)0.0369 (14)0.0312 (13)−0.0034 (12)0.0007 (12)−0.0003 (12)
C30.0340 (18)0.0442 (17)0.0443 (16)0.0034 (14)−0.0016 (15)0.0061 (14)
C40.0444 (16)0.0276 (13)0.0432 (16)0.0049 (14)0.0015 (17)0.0124 (12)
C50.0387 (16)0.0338 (14)0.0365 (14)0.0010 (14)0.0007 (15)−0.0001 (12)
O10.0781 (19)0.0436 (13)0.0334 (11)−0.0015 (14)−0.0032 (13)−0.0099 (10)
O20.0727 (17)0.0530 (13)0.0318 (10)0.0202 (14)−0.0018 (13)−0.0070 (10)
O30.0790 (19)0.0410 (13)0.0388 (11)0.0190 (13)−0.0049 (13)−0.0051 (10)
N30.0465 (15)0.0257 (11)0.0288 (11)0.0039 (11)−0.0007 (12)0.0035 (9)
C60.0464 (18)0.0300 (15)0.0357 (15)−0.0040 (13)0.0034 (14)−0.0069 (13)
C70.044 (2)0.0346 (16)0.0492 (18)0.0092 (14)0.0090 (16)−0.0031 (14)
C80.0439 (18)0.0401 (16)0.0475 (17)0.0097 (17)0.0011 (17)0.0005 (14)
C90.0464 (18)0.0403 (17)0.0327 (15)0.0047 (14)0.0000 (13)0.0055 (13)
C100.0374 (16)0.0370 (15)0.0308 (14)0.0004 (13)0.0030 (12)−0.0009 (12)
C110.0475 (18)0.0330 (14)0.0329 (14)0.0045 (14)0.0000 (14)−0.0007 (11)
O1W0.216 (7)0.109 (3)0.074 (2)−0.002 (4)−0.033 (4)0.026 (2)
Br1—C21.881 (3)O2—C111.265 (4)
N1—C51.339 (4)O3—C111.231 (4)
N1—C11.353 (4)N3—C61.356 (4)
N1—H1B0.8600N3—C101.364 (4)
N2—C51.321 (4)N3—H3B0.8600
N2—H2A0.8600C6—C71.438 (5)
N2—H2B0.8600C7—C81.349 (5)
C1—C21.364 (4)C7—H7A0.9300
C1—H1A0.9300C8—C91.415 (5)
C2—C31.402 (5)C8—H8A0.9300
C3—C41.361 (5)C9—C101.345 (5)
C3—H3A0.9300C9—H9A0.9300
C4—C51.426 (4)C10—C111.516 (4)
C4—H4A0.9300O1W—H1W0.9404
O1—C61.259 (4)O1W—H2W0.9428
C5—N1—C1122.7 (3)C6—N3—H3B117.2
C5—N1—H1B118.6C10—N3—H3B117.2
C1—N1—H1B118.6O1—C6—N3120.5 (3)
C5—N2—H2A120.0O1—C6—C7125.0 (3)
C5—N2—H2B120.0N3—C6—C7114.4 (3)
H2A—N2—H2B120.0C8—C7—C6120.6 (3)
N1—C1—C2120.4 (3)C8—C7—H7A119.7
N1—C1—H1A119.8C6—C7—H7A119.7
C2—C1—H1A119.8C7—C8—C9121.5 (3)
C1—C2—C3118.9 (3)C7—C8—H8A119.2
C1—C2—Br1120.3 (2)C9—C8—H8A119.2
C3—C2—Br1120.8 (2)C10—C9—C8118.1 (3)
C4—C3—C2120.4 (3)C10—C9—H9A121.0
C4—C3—H3A119.8C8—C9—H9A121.0
C2—C3—H3A119.8C9—C10—N3119.7 (3)
C3—C4—C5119.2 (3)C9—C10—C11125.3 (3)
C3—C4—H4A120.4N3—C10—C11115.0 (3)
C5—C4—H4A120.4O3—C11—O2126.8 (3)
N2—C5—N1118.8 (3)O3—C11—C10117.9 (3)
N2—C5—C4122.9 (3)O2—C11—C10115.3 (3)
N1—C5—C4118.4 (3)H1W—O1W—H2W109.7
C6—N3—C10125.7 (3)
C5—N1—C1—C20.9 (5)O1—C6—C7—C8180.0 (4)
N1—C1—C2—C30.6 (5)N3—C6—C7—C81.1 (5)
N1—C1—C2—Br1−178.3 (2)C6—C7—C8—C9−1.1 (6)
C1—C2—C3—C4−0.7 (5)C7—C8—C9—C100.2 (6)
Br1—C2—C3—C4178.1 (3)C8—C9—C10—N30.7 (5)
C2—C3—C4—C5−0.5 (5)C8—C9—C10—C11−177.5 (3)
C1—N1—C5—N2178.2 (3)C6—N3—C10—C9−0.8 (5)
C1—N1—C5—C4−2.2 (5)C6—N3—C10—C11177.6 (3)
C3—C4—C5—N2−178.5 (4)C9—C10—C11—O3−179.1 (4)
C3—C4—C5—N11.9 (5)N3—C10—C11—O32.6 (5)
C10—N3—C6—O1−179.1 (4)C9—C10—C11—O22.6 (6)
C10—N3—C6—C7−0.1 (5)N3—C10—C11—O2−175.7 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1B···O2i0.861.792.640 (4)171.
O1W—H1W···O2ii0.942.172.730 (5)117.
N2—H2A···O3i0.862.042.896 (4)172.
N2—H2B···O1iii0.861.962.819 (4)173.
O1W—H2W···O1Wii0.942.022.782 (9)137.
N3—H3B···Br10.862.843.681 (3)168.
C3—H3A···O10.932.443.351 (4)167.
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1B⋯O2i0.861.792.640 (4)171
O1W—H1W⋯O2ii0.942.172.730 (5)117
N2—H2A⋯O3i0.862.042.896 (4)172
N2—H2B⋯O1iii0.861.962.819 (4)173
O1W—H2W⋯O1Wii0.942.022.782 (9)137
N3—H3B⋯Br10.862.843.681 (3)168
C3—H3A⋯O10.932.443.351 (4)167

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

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  2 in total
  2 in total

1.  2-Amino-5-chloro-pyridinium 6-oxo-1,6-dihydro-pyridine-2-carboxyl-ate 0.85-hydrate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-08-18

2.  Crystal structure and Hirshfeld surface analysis of 2-(4-bromo-phen-yl)-4-methyl-6-oxo-1-phenyl-1,6-di-hydro-pyridine-3-carbo-nitrile.

Authors:  Farid N Naghiyev; Victor N Khrustalev; Ekaterina V Dobrokhotova; Mehmet Akkurt; Ali N Khalilov; Ajaya Bhattarai; İbrahim G Mamedov
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2022-07-05
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.