Literature DB >> 22058823

4-Amino-pyridinium cis-2-carb-oxy-cyclo-hexane-1-carboxyl-ate.

Graham Smith1, Urs D Wermuth.   

Abstract

In the structure of the title molecular salt, C(5)H(7)N(2) (+)·C(8)H(11)O(4) (-), the cis monoanions associate through short O-H⋯O hydrogen bonds in the carb-oxy-lic acid groups [graph set C(7)], forming zigzag chains which extend along the c axis. These are inter-linked through pyridinium and amine N-H⋯O hydrogen bonds, giving a three-dimensional network structure.

Entities:  

Year:  2011        PMID: 22058823      PMCID: PMC3201255          DOI: 10.1107/S1600536811039547

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


Related literature

For the structure of racemic cis-cyclo­hexane-1,2-dicarb­oxy­lic acid, see: Benedetti et al. (1970 ▶). For the structure of the racemic ammonium and 2-amino­pyridinium salts of cis-2-carb­oxy­cyclo­hexane-1-carboxyl­ate, see: Smith & Wermuth (2011a ▶,b ▶). For graph-set analysis, see Etter et al. (1990 ▶).

Experimental

Crystal data

C5H7N2C8H11O4 M = 266.29 Orthorhombic, a = 12.1359 (3) Å b = 9.8351 (3) Å c = 11.1850 (3) Å V = 1335.02 (6) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 200 K 0.30 × 0.25 × 0.20 mm

Data collection

Oxford Diffraction Gemini-S CCD-detector diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010 ▶) T min = 0.948, T max = 0.990 9670 measured reflections 1709 independent reflections 1448 reflections with I > 2σ(I) R int = 0.029

Refinement

R[F 2 > 2σ(F 2)] = 0.028 wR(F 2) = 0.060 S = 0.99 1709 reflections 188 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.15 e Å−3 Δρmin = −0.16 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2010 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶) within WinGX (Farrugia, 1999 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811039547/fj2453sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811039547/fj2453Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811039547/fj2453Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H7N2+·C8H11O4F(000) = 568
Mr = 266.29Dx = 1.325 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 4840 reflections
a = 12.1359 (3) Åθ = 3.2–28.7°
b = 9.8351 (3) ŵ = 0.10 mm1
c = 11.1850 (3) ÅT = 200 K
V = 1335.02 (6) Å3Block, colourless
Z = 40.30 × 0.25 × 0.20 mm
Oxford Diffraction Gemini-S CCD-detector diffractometer1709 independent reflections
Radiation source: Enhance (Mo) X-ray source1448 reflections with I > 2σ(I)
graphiteRint = 0.029
Detector resolution: 16.077 pixels mm-1θmax = 28.8°, θmin = 3.2°
ω scansh = −16→15
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)k = −12→13
Tmin = 0.948, Tmax = 0.990l = −13→15
9670 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)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.060H atoms treated by a mixture of independent and constrained refinement
S = 0.99w = 1/[σ2(Fo2) + (0.0357P)2] where P = (Fo2 + 2Fc2)/3
1709 reflections(Δ/σ)max < 0.001
188 parametersΔρmax = 0.15 e Å3
1 restraintΔρmin = −0.16 e Å3
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 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
O11−0.08623 (9)0.42384 (12)0.16082 (11)0.0293 (4)
O120.08627 (8)0.38250 (12)0.21757 (10)0.0262 (3)
O210.01171 (10)0.40723 (12)0.51058 (12)0.0285 (3)
O220.17703 (9)0.30714 (12)0.50187 (12)0.0296 (3)
C1−0.06239 (12)0.25883 (16)0.31330 (14)0.0202 (4)
C20.02258 (13)0.20096 (16)0.40246 (15)0.0223 (5)
C30.10393 (14)0.10098 (18)0.34520 (18)0.0311 (5)
C40.04378 (15)−0.01169 (19)0.2767 (2)0.0410 (6)
C5−0.03704 (15)0.04676 (19)0.18597 (18)0.0340 (6)
C6−0.11879 (14)0.14099 (17)0.24603 (17)0.0272 (5)
C11−0.01574 (12)0.36284 (16)0.22481 (14)0.0200 (5)
C210.07930 (13)0.30994 (17)0.47466 (14)0.0222 (5)
N1A0.16603 (12)0.28917 (15)0.99803 (15)0.0301 (4)
N41A0.30073 (13)0.14997 (18)0.68510 (15)0.0320 (5)
C2A0.14635 (14)0.35553 (19)0.89470 (16)0.0306 (5)
C3A0.18908 (13)0.31222 (17)0.78984 (16)0.0285 (5)
C4A0.25659 (12)0.19462 (16)0.78670 (15)0.0236 (5)
C5A0.27516 (14)0.12848 (18)0.89698 (16)0.0289 (5)
C6A0.22940 (14)0.17671 (18)0.99826 (17)0.0309 (5)
H1−0.119400.305100.360200.0240*
H2−0.020100.147400.460100.0270*
H210.046 (2)0.473 (3)0.561 (3)0.069 (8)*
H31B0.152000.149900.290800.0370*
H32B0.149400.060500.407000.0370*
H41B0.09730−0.068000.235500.0490*
H42B0.00420−0.068800.332800.0490*
H51B0.003200.096400.125100.0410*
H52B−0.07640−0.026900.147200.0410*
H61B−0.163000.089100.302000.0330*
H62B−0.167900.178300.186000.0330*
H1A0.1408 (18)0.319 (2)1.0674 (19)0.038 (6)*
H2A0.102300.432900.895600.0370*
H3A0.174200.359600.719700.0340*
H5A0.319200.051200.899700.0350*
H6A0.241900.131301.069900.0370*
H41A0.3409 (18)0.078 (2)0.687 (2)0.047 (6)*
H42A0.2841 (16)0.193 (2)0.615 (2)0.038 (6)*
U11U22U33U12U13U23
O110.0297 (6)0.0270 (6)0.0312 (7)0.0010 (5)−0.0051 (5)0.0106 (6)
O120.0244 (6)0.0291 (6)0.0251 (6)−0.0047 (5)0.0004 (5)0.0028 (5)
O210.0321 (6)0.0263 (6)0.0272 (6)0.0042 (5)−0.0021 (6)−0.0066 (6)
O220.0304 (6)0.0316 (6)0.0269 (6)0.0036 (5)−0.0062 (5)−0.0019 (6)
C10.0205 (7)0.0188 (8)0.0212 (8)0.0009 (6)0.0009 (6)−0.0003 (7)
C20.0267 (8)0.0193 (8)0.0209 (8)−0.0009 (7)0.0007 (7)0.0046 (7)
C30.0325 (9)0.0253 (9)0.0354 (10)0.0084 (8)−0.0064 (8)−0.0016 (8)
C40.0439 (10)0.0247 (9)0.0543 (13)0.0080 (8)−0.0046 (10)−0.0118 (9)
C50.0387 (10)0.0270 (9)0.0363 (11)−0.0064 (8)−0.0040 (9)−0.0106 (8)
C60.0269 (8)0.0226 (8)0.0322 (10)−0.0068 (7)−0.0053 (7)0.0039 (8)
C110.0254 (8)0.0166 (8)0.0179 (8)−0.0006 (6)−0.0006 (6)−0.0031 (6)
C210.0287 (8)0.0222 (8)0.0157 (8)0.0017 (7)−0.0004 (6)0.0051 (7)
N1A0.0318 (7)0.0344 (8)0.0240 (8)0.0016 (6)0.0021 (7)−0.0067 (8)
N41A0.0366 (8)0.0293 (9)0.0302 (9)0.0098 (7)0.0024 (7)−0.0044 (7)
C2A0.0324 (9)0.0258 (9)0.0335 (10)0.0077 (8)0.0012 (8)−0.0007 (9)
C3A0.0334 (9)0.0241 (9)0.0281 (9)0.0057 (7)−0.0019 (8)0.0023 (8)
C4A0.0225 (7)0.0209 (8)0.0275 (9)−0.0010 (6)−0.0021 (7)−0.0032 (8)
C5A0.0305 (9)0.0233 (9)0.0329 (10)0.0054 (7)−0.0085 (8)−0.0012 (8)
C6A0.0334 (9)0.0328 (9)0.0264 (9)−0.0001 (8)−0.0080 (8)0.0013 (9)
O11—C111.2665 (19)C1—H10.9800
O12—C111.2556 (18)C2—H20.9800
O21—C211.323 (2)C3—H32B0.9700
O22—C211.2248 (19)C3—H31B0.9700
O21—H210.95 (3)C4—H42B0.9700
N1A—C6A1.347 (2)C4—H41B0.9700
N1A—C2A1.349 (2)C5—H51B0.9700
N41A—C4A1.331 (2)C5—H52B0.9700
N1A—H1A0.88 (2)C6—H61B0.9700
N41A—H41A0.86 (2)C6—H62B0.9700
N41A—H42A0.91 (2)C2A—C3A1.351 (2)
C1—C21.543 (2)C3A—C4A1.418 (2)
C1—C111.532 (2)C4A—C5A1.413 (2)
C1—C61.542 (2)C5A—C6A1.348 (3)
C2—C31.534 (2)C2A—H2A0.9300
C2—C211.508 (2)C3A—H3A0.9300
C3—C41.532 (3)C5A—H5A0.9300
C4—C51.524 (3)C6A—H6A0.9300
C5—C61.515 (3)
C21—O21—H21113.6 (15)C2—C3—H31B109.00
C2A—N1A—C6A120.01 (16)C2—C3—H32B109.00
C6A—N1A—H1A117.9 (13)C5—C4—H41B109.00
C2A—N1A—H1A122.0 (13)C5—C4—H42B109.00
H41A—N41A—H42A122 (2)C3—C4—H42B109.00
C4A—N41A—H41A118.6 (15)C3—C4—H41B109.00
C4A—N41A—H42A119.4 (13)H41B—C4—H42B108.00
C2—C1—C6109.55 (13)C6—C5—H51B109.00
C2—C1—C11114.64 (12)C4—C5—H52B109.00
C6—C1—C11110.53 (13)C6—C5—H52B109.00
C1—C2—C21112.88 (13)H51B—C5—H52B108.00
C1—C2—C3113.38 (14)C4—C5—H51B109.00
C3—C2—C21112.67 (13)C5—C6—H62B109.00
C2—C3—C4111.46 (14)H61B—C6—H62B108.00
C3—C4—C5111.52 (15)C1—C6—H61B109.00
C4—C5—C6110.92 (16)C1—C6—H62B109.00
C1—C6—C5112.68 (14)C5—C6—H61B109.00
O11—C11—C1115.58 (13)N1A—C2A—C3A121.56 (17)
O11—C11—O12123.82 (14)C2A—C3A—C4A120.03 (16)
O12—C11—C1120.59 (13)N41A—C4A—C3A121.53 (16)
O21—C21—C2113.18 (13)C3A—C4A—C5A116.50 (15)
O22—C21—C2123.99 (15)N41A—C4A—C5A121.97 (15)
O21—C21—O22122.77 (15)C4A—C5A—C6A120.41 (16)
C6—C1—H1107.00N1A—C6A—C5A121.50 (17)
C2—C1—H1107.00N1A—C2A—H2A119.00
C11—C1—H1107.00C3A—C2A—H2A119.00
C1—C2—H2106.00C2A—C3A—H3A120.00
C3—C2—H2106.00C4A—C3A—H3A120.00
C21—C2—H2106.00C4A—C5A—H5A120.00
C4—C3—H32B109.00C6A—C5A—H5A120.00
H31B—C3—H32B108.00N1A—C6A—H6A119.00
C4—C3—H31B109.00C5A—C6A—H6A119.00
C6A—N1A—C2A—C3A−0.2 (3)C3—C2—C21—O21171.15 (14)
C2A—N1A—C6A—C5A0.6 (3)C3—C2—C21—O22−11.6 (2)
C6—C1—C2—C351.98 (17)C1—C2—C21—O2141.13 (19)
C11—C1—C2—C2156.73 (18)C1—C2—C21—O22−141.58 (16)
C6—C1—C2—C21−178.36 (13)C2—C3—C4—C553.7 (2)
C11—C1—C2—C3−72.93 (17)C3—C4—C5—C6−56.2 (2)
C2—C1—C11—O11−171.66 (14)C4—C5—C6—C157.4 (2)
C2—C1—C11—O129.2 (2)N1A—C2A—C3A—C4A−0.2 (3)
C6—C1—C11—O1163.95 (18)C2A—C3A—C4A—N41A−179.40 (16)
C6—C1—C11—O12−115.22 (16)C2A—C3A—C4A—C5A0.0 (2)
C11—C1—C6—C572.82 (18)N41A—C4A—C5A—C6A179.81 (17)
C2—C1—C6—C5−54.43 (19)C3A—C4A—C5A—C6A0.4 (2)
C21—C2—C3—C4177.72 (15)C4A—C5A—C6A—N1A−0.7 (3)
C1—C2—C3—C4−52.5 (2)
D—H···AD—HH···AD···AD—H···A
N1A—H1A···O12i0.88 (2)1.91 (2)2.795 (2)180 (3)
N41A—H41A···O12ii0.86 (2)2.14 (2)2.989 (2)168 (2)
N41A—H42A···O220.91 (2)2.13 (2)2.974 (2)152.6 (18)
O21—H21···O11iii0.95 (3)1.59 (3)2.5302 (17)170 (3)
C2A—H2A···O21iii0.932.463.287 (2)149
C3A—H3A···O220.932.493.225 (2)136
C3A—H3A···O11iii0.932.473.222 (2)138
C6A—H6A···O11iv0.932.383.048 (2)128
C3—H31B···O120.972.563.123 (2)117
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1A—H1A⋯O12i0.88 (2)1.91 (2)2.795 (2)180 (3)
N41A—H41A⋯O12ii0.86 (2)2.14 (2)2.989 (2)168 (2)
N41A—H42A⋯O220.91 (2)2.13 (2)2.974 (2)152.6 (18)
O21—H21⋯O11iii0.95 (3)1.59 (3)2.5302 (17)170 (3)

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

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1.  A short history of SHELX.

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

2.  Graph-set analysis of hydrogen-bond patterns in organic crystals.

Authors:  M C Etter; J C MacDonald; J Bernstein
Journal:  Acta Crystallogr B       Date:  1990-04-01

3.  rac-Ammonium cis-2-carb-oxy-cyclo-hexane-1-carboxyl-ate.

Authors:  Graham Smith; Urs D Wermuth
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-12-18

4.  rac-2-Amino-pyridinium cis-2-carb-oxy-cyclo-hexane-1-carboxyl-ate.

Authors:  Graham Smith; Urs D Wermuth
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-07-02

5.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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1.  rac-4-Carbamoylpiperidinium cis-2-car-boxy-cyclo-hexane-1-carboxyl-ate.

Authors:  Graham Smith; Urs D Wermuth
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