Literature DB >> 22090951

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

Graham Smith1, Urs D Wermuth.   

Abstract

In the structure of the title compound, C(5)H(7)N(2) (+)·C(8)H(11)O(4) (-), the cis anions associate through head-to-tail carb-oxy-lic acid-carboxyl O-H⋯O hydrogen bonds [graph set C(7)], forming chains which extend along c and are inter-linked through the carboxyl groups, forming cyclic R(2) (2)(8) associations with the pyridinium and an amine H-atom donor of the cation. Further amine-carboxyl N-H⋯O inter-actions form enlarged centrosymmetric rings [graph set R(4) (4)(18)] and extensions down b, giving a three-dimensional structure.

Entities:  

Year:  2011        PMID： 22090951      PMCID： PMC3212294          DOI： 10.1107/S1600536811025256

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 racemic ammonium cis-2-carb­oxy­cyclo­hexane-1-carboxyl­ate, see: Smith & Wermuth (2011 ▶) and of brucinium (1R,2S-2-carb­oxy­cyclo­hexane-1-carboxyl­ate dihydrate, see: Smith et al. (2011 ▶). For the structure of the adduct of cis-cyclo­hexane-1,2-dicarb­oxy­lic acid with 4,4′-bipyridine, see: Bhogala et al. (2005 ▶). For graph-set analysis, see: Etter et al. (1990) ▶.

Experimental

Crystal data

C5H7N2 +·C8H11O4 − M = 266.29 Monoclinic, a = 12.4709 (5) Å b = 10.4191 (5) Å c = 10.6451 (5) Å β = 101.250 (4)° V = 1356.60 (11) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 200 K 0.35 × 0.32 × 0.20 mm

Data collection

Oxford Diffraction Gemini-S CCD-detector diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010 ▶) T min = 0.90, T max = 0.98 9200 measured reflections 2658 independent reflections 1947 reflections with I > 2σ(I) R int = 0.022

Refinement

R[F 2 > 2σ(F 2)] = 0.033 wR(F 2) = 0.081 S = 0.99 2658 reflections 188 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.16 e Å−3 Δρmin = −0.15 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/S1600536811025256/wn2440sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811025256/wn2440Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H7N2+·C8H11O4−F(000) = 568
Mr = 266.29Dx = 1.304 Mg m−3
Monoclinic, P21/cMelting point: 396 K
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 12.4709 (5) ÅCell parameters from 4347 reflections
b = 10.4191 (5) Åθ = 3.4–28.7°
c = 10.6451 (5) ŵ = 0.10 mm−1
β = 101.250 (4)°T = 200 K
V = 1356.60 (11) Å3Block, colourless
Z = 40.35 × 0.32 × 0.20 mm
Oxford Diffraction Gemini-S CCD-detector diffractometer2658 independent reflections
Radiation source: Enhance (Mo) X-ray source1947 reflections with I > 2σ(I)
graphiteRint = 0.022
Detector resolution: 16.077 pixels mm-1θmax = 26.0°, θmin = 3.4°
ω scansh = −15→15
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)k = −12→12
Tmin = 0.90, Tmax = 0.98l = −13→13
9200 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)] = 0.033Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.081H atoms treated by a mixture of independent and constrained refinement
S = 0.99w = 1/[σ2(Fo2) + (0.0472P)2] where P = (Fo2 + 2Fc2)/3
2658 reflections(Δ/σ)max = 0.001
188 parametersΔρmax = 0.16 e Å−3
0 restraintsΔρmin = −0.15 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 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
O110.29045 (7)0.58197 (9)0.65073 (8)0.0412 (3)
O120.34131 (6)0.57102 (9)0.86187 (8)0.0405 (3)
O210.18216 (7)0.77924 (9)0.96839 (9)0.0411 (3)
O220.23826 (8)0.62543 (10)1.11054 (8)0.0494 (3)
C10.14901 (9)0.59059 (12)0.77138 (11)0.0310 (4)
C20.12817 (9)0.56727 (12)0.90706 (12)0.0327 (4)
C30.14384 (10)0.42684 (13)0.94720 (14)0.0426 (4)
C40.07163 (11)0.34055 (14)0.85100 (16)0.0529 (5)
C50.09356 (11)0.36091 (14)0.71709 (16)0.0521 (5)
C60.07708 (10)0.50055 (13)0.67677 (13)0.0422 (4)
C110.26966 (10)0.57955 (11)0.76400 (12)0.0308 (4)
C210.19003 (9)0.65774 (13)1.00503 (12)0.0341 (4)
N1A0.49126 (9)0.62635 (11)0.62208 (11)0.0387 (4)
N21A0.55457 (11)0.50551 (13)0.80144 (12)0.0474 (5)
C2A0.57435 (10)0.56346 (12)0.69688 (13)0.0356 (4)
C3A0.67632 (10)0.56253 (13)0.65925 (13)0.0410 (4)
C4A0.68805 (11)0.62558 (14)0.55114 (14)0.0467 (5)
C5A0.60091 (12)0.69282 (14)0.47783 (14)0.0509 (5)
C6A0.50392 (12)0.69068 (14)0.51527 (14)0.0473 (5)
H10.126000.678600.747400.0370*
H20.050600.586000.903100.0390*
H210.2185 (15)0.8363 (19)1.0383 (18)0.089 (6)*
H310.219800.402900.953000.0510*
H320.125700.415501.031100.0510*
H410.085400.251500.875700.0640*
H42−0.004600.358900.851400.0640*
H510.044600.307300.657100.0630*
H520.168000.335500.715000.0630*
H610.000900.523500.671200.0510*
H620.094400.511300.592400.0510*
H1A0.4183 (12)0.6177 (14)0.6427 (14)0.055 (4)*
H3A0.735200.519100.708000.0490*
H4A0.755200.624000.525500.0560*
H5A0.609700.737900.405100.0610*
H6A0.444700.734000.467100.0570*
H21A0.4889 (14)0.5126 (15)0.8261 (15)0.060 (5)*
H22A0.6077 (13)0.4646 (15)0.8509 (15)0.054 (4)*
U11U22U33U12U13U23
O110.0347 (5)0.0558 (6)0.0334 (5)0.0086 (4)0.0076 (4)0.0050 (5)
O120.0271 (4)0.0577 (6)0.0347 (5)0.0022 (4)0.0011 (4)0.0019 (4)
O210.0456 (5)0.0376 (5)0.0356 (5)0.0017 (4)−0.0031 (4)−0.0025 (4)
O220.0553 (6)0.0572 (7)0.0314 (5)0.0134 (5)−0.0024 (4)0.0036 (5)
C10.0273 (6)0.0309 (7)0.0323 (7)0.0041 (5)−0.0002 (5)0.0005 (5)
C20.0222 (6)0.0373 (7)0.0380 (7)0.0045 (5)0.0044 (5)0.0027 (6)
C30.0362 (7)0.0406 (8)0.0515 (8)0.0003 (6)0.0101 (6)0.0107 (7)
C40.0414 (8)0.0384 (8)0.0781 (11)−0.0057 (7)0.0094 (7)0.0034 (8)
C50.0402 (8)0.0424 (9)0.0703 (10)−0.0070 (6)0.0023 (7)−0.0179 (8)
C60.0309 (6)0.0505 (9)0.0418 (8)−0.0017 (6)−0.0009 (6)−0.0083 (7)
C110.0307 (6)0.0280 (7)0.0327 (7)0.0026 (5)0.0034 (5)0.0007 (5)
C210.0262 (6)0.0429 (8)0.0332 (7)0.0082 (5)0.0061 (5)0.0022 (6)
N1A0.0327 (6)0.0385 (6)0.0435 (7)0.0042 (5)0.0040 (5)0.0024 (5)
N21A0.0344 (7)0.0615 (9)0.0462 (8)0.0105 (6)0.0073 (6)0.0133 (6)
C2A0.0319 (6)0.0336 (7)0.0392 (7)0.0008 (5)0.0018 (6)−0.0030 (6)
C3A0.0311 (7)0.0437 (8)0.0468 (8)0.0005 (6)0.0039 (6)−0.0004 (7)
C4A0.0391 (8)0.0464 (9)0.0558 (9)−0.0082 (6)0.0121 (7)−0.0023 (7)
C5A0.0539 (9)0.0479 (9)0.0511 (9)−0.0059 (7)0.0109 (7)0.0115 (7)
C6A0.0473 (8)0.0414 (8)0.0498 (9)0.0045 (7)0.0009 (7)0.0083 (7)
O11—C111.2821 (15)C1—H10.9800
O12—C111.2363 (15)C2—H20.9800
O21—C211.3226 (16)C3—H320.9700
O22—C211.2137 (15)C3—H310.9700
O21—H210.991 (19)C4—H420.9700
N1A—C6A1.3554 (19)C4—H410.9700
N1A—C2A1.3473 (17)C5—H510.9700
N21A—C2A1.3310 (19)C5—H520.9700
N1A—H1A0.981 (15)C6—H610.9700
N21A—H21A0.911 (18)C6—H620.9700
N21A—H22A0.873 (16)C2A—C3A1.4059 (18)
C1—C21.5359 (17)C3A—C4A1.358 (2)
C1—C111.5262 (17)C4A—C5A1.396 (2)
C1—C61.5319 (18)C5A—C6A1.346 (2)
C2—C31.5261 (19)C3A—H3A0.9300
C2—C211.5025 (18)C4A—H4A0.9300
C3—C41.519 (2)C5A—H5A0.9300
C4—C51.518 (2)C6A—H6A0.9300
C5—C61.520 (2)
O11···N1A2.6223 (15)C11···H21i2.520 (19)
O11···C21i3.2513 (16)C11···H522.8400
O11···O21i2.5806 (13)C11···H312.8800
O11···C4Aii3.0969 (17)C21···H42viii3.0200
O11···O22i3.1292 (14)C21···H22Aiv2.972 (16)
O12···C6Aiii3.4134 (17)H1···O212.5500
O12···C33.1653 (16)H1···C4v3.0000
O12···O223.2105 (12)H1···H42v2.5100
O12···N21A2.9361 (16)H1A···C112.489 (15)
O12···C212.7964 (15)H1A···O111.656 (15)
O21···C113.3436 (15)H1A···O122.734 (15)
O21···O11iii2.5806 (13)H1A···H21i2.57 (2)
O22···O123.2105 (12)H1A···H21A2.26 (2)
O22···C3Aiv3.1555 (16)H2···H612.5100
O22···O11iii3.1292 (14)H2···H32viii2.4300
O22···N21Aiv2.9103 (17)H2···H422.5000
O22···C2Aiv3.4158 (16)H3A···H22A2.4700
O11···H622.5100H3A···O22iv2.4200
O11···H4Aii2.8300H4A···H41vii2.4500
O11···H21A2.886 (17)H4A···O11ii2.8300
O11···H1A1.656 (15)H5A···C2Ai3.0000
O11···H21i1.595 (19)H5A···N21Ai2.9200
O12···H312.6200H6A···O12i2.5500
O12···H21A2.044 (17)H21···O11iii1.595 (19)
O12···H1A2.734 (15)H21···C1iii2.886 (19)
O12···H6Aiii2.5500H21···H1Aiii2.57 (2)
O21···H62iii2.8800H21···H62iii2.3700
O21···H12.5500H21···C6iii3.031 (19)
O21···H51v2.9000H21···C11iii2.520 (19)
O22···H322.6500H21A···C112.774 (18)
O22···H3Aiv2.4200H21A···O112.886 (17)
O22···H22Aiv2.105 (16)H21A···H1A2.26 (2)
O22···H312.8400H21A···O122.044 (17)
N1A···O112.6223 (15)H22A···H3A2.4700
N1A···C113.4331 (17)H22A···O22iv2.105 (16)
N21A···O122.9361 (16)H22A···C21iv2.972 (16)
N21A···O22iv2.9103 (17)H31···O122.6200
N21A···H5Aiii2.9200H31···O222.8400
C2A···C6Aii3.494 (2)H31···H522.5900
C2A···O22iv3.4158 (16)H31···C112.8800
C3···O123.1653 (16)H32···O222.6500
C3A···O22iv3.1555 (16)H32···H2viii2.4300
C4A···O11ii3.0969 (17)H41···H4Aix2.4500
C6A···O12i3.4134 (17)H41···C4Aix3.0700
C6A···C2Aii3.494 (2)H42···H22.5000
C11···N1A3.4331 (17)H42···H612.5800
C11···O213.3436 (15)H42···C21viii3.0200
C21···O122.7964 (15)H42···H1vi2.5100
C21···O11iii3.2513 (16)H51···O21vi2.9000
C1···H21i2.886 (19)H52···H312.5900
C2A···H5Aiii3.0000H52···C112.8400
C4···H1vi3.0000H61···H22.5100
C4A···H41vii3.0700H61···H422.5800
C6···H21i3.031 (19)H62···O21i2.8800
C11···H21A2.774 (18)H62···H21i2.3700
C11···H1A2.489 (15)H62···O112.5100
C21—O21—H21110.9 (11)C2—C3—H31110.00
C2A—N1A—C6A122.30 (12)C2—C3—H32110.00
C6A—N1A—H1A119.9 (9)C5—C4—H41109.00
C2A—N1A—H1A117.6 (9)C5—C4—H42109.00
H21A—N21A—H22A119.0 (14)C3—C4—H42109.00
C2A—N21A—H21A121.9 (10)C3—C4—H41109.00
C2A—N21A—H22A118.9 (11)H41—C4—H42108.00
C2—C1—C6109.67 (10)C6—C5—H51109.00
C2—C1—C11112.70 (10)C4—C5—H52109.00
C6—C1—C11112.13 (10)C6—C5—H52109.00
C1—C2—C21113.29 (10)H51—C5—H52108.00
C1—C2—C3112.27 (10)C4—C5—H51109.00
C3—C2—C21112.76 (11)C5—C6—H62109.00
C2—C3—C4110.61 (11)H61—C6—H62108.00
C3—C4—C5111.02 (12)C1—C6—H61109.00
C4—C5—C6111.09 (12)C1—C6—H62109.00
C1—C6—C5111.78 (11)C5—C6—H61109.00
O11—C11—C1115.42 (11)N1A—C2A—C3A117.98 (12)
O11—C11—O12123.26 (12)N21A—C2A—C3A124.10 (13)
O12—C11—C1121.31 (11)N1A—C2A—N21A117.92 (12)
O21—C21—C2113.41 (11)C2A—C3A—C4A119.42 (12)
O22—C21—C2124.26 (12)C3A—C4A—C5A121.05 (13)
O21—C21—O22122.23 (12)C4A—C5A—C6A118.21 (14)
C6—C1—H1107.00N1A—C6A—C5A121.01 (14)
C2—C1—H1107.00C2A—C3A—H3A120.00
C11—C1—H1107.00C4A—C3A—H3A120.00
C1—C2—H2106.00C3A—C4A—H4A119.00
C3—C2—H2106.00C5A—C4A—H4A119.00
C21—C2—H2106.00C4A—C5A—H5A121.00
C4—C3—H32110.00C6A—C5A—H5A121.00
H31—C3—H32108.00N1A—C6A—H6A120.00
C4—C3—H31110.00C5A—C6A—H6A119.00
C6A—N1A—C2A—N21A178.49 (13)C3—C2—C21—O21176.42 (10)
C6A—N1A—C2A—C3A−1.86 (19)C3—C2—C21—O22−7.23 (17)
C2A—N1A—C6A—C5A1.1 (2)C1—C2—C21—O2147.52 (14)
C6—C1—C2—C354.66 (13)C1—C2—C21—O22−136.14 (12)
C11—C1—C2—C2158.14 (14)C21—C2—C3—C4174.78 (11)
C6—C1—C2—C21−176.19 (10)C2—C3—C4—C556.17 (14)
C2—C1—C11—O11171.57 (10)C3—C4—C5—C6−56.90 (15)
C2—C1—C11—O12−9.55 (16)C4—C5—C6—C156.70 (14)
C11—C1—C2—C3−71.01 (13)N1A—C2A—C3A—C4A0.9 (2)
C6—C1—C11—O12−133.87 (12)N21A—C2A—C3A—C4A−179.53 (14)
C11—C1—C6—C571.16 (13)C2A—C3A—C4A—C5A0.9 (2)
C6—C1—C11—O1147.24 (14)C3A—C4A—C5A—C6A−1.8 (2)
C2—C1—C6—C5−54.84 (14)C4A—C5A—C6A—N1A0.8 (2)
C1—C2—C3—C4−55.80 (14)
D—H···AD—HH···AD···AD—H···A
N1A—H1A···O110.981 (15)1.656 (15)2.6223 (15)167.7 (14)
N21A—H21A···O120.911 (18)2.044 (17)2.9361 (16)166.3 (14)
N21A—H22A···O22iv0.873 (16)2.105 (16)2.9103 (17)153.1 (14)
O21—H21···O11iii0.991 (19)1.595 (19)2.5806 (13)172.9 (18)
C3A—H3A···O22iv0.932.423.1555 (16)136
C6A—H6A···O12i0.932.553.4134 (17)155
C6—H62···O110.972.512.8574 (16)101
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N1A—H1A⋯O110.981 (15)1.656 (15)2.6223 (15)167.7 (14)
N21A—H21A⋯O120.911 (18)2.044 (17)2.9361 (16)166.3 (14)
N21A—H22A⋯O22i0.873 (16)2.105 (16)2.9103 (17)153.1 (14)
O21—H21⋯O11ii0.991 (19)1.595 (19)2.5806 (13)172.9 (18)

Symmetry codes: (i) ; (ii) .

  4 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.  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.  Structure validation in chemical crystallography.

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

1.  rac-cis-Cyclo-hexane-1,2-dicarb-oxy-lic acid-isoquinoline (1/1).

Authors:  Graham Smith; Urs D Wermuth
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-08-06

2.  rac-4-Carbamoylpiperidinium cis-2-car-boxy-cyclo-hexane-1-carboxyl-ate.

Authors:  Graham Smith; Urs D Wermuth
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-02-10

3.  4-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:  2011-09-30
  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.